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DeGroat W, Inoue F, Ashuach T, Yosef N, Ahituv N, Kreimer A. Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation. Genome Biol 2024; 25:221. [PMID: 39143563 PMCID: PMC11323586 DOI: 10.1186/s13059-024-03365-w] [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: 11/17/2023] [Accepted: 08/01/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND Increasing evidence suggests that a substantial proportion of disease-associated mutations occur in enhancers, regions of non-coding DNA essential to gene regulation. Understanding the structures and mechanisms of the regulatory programs this variation affects can shed light on the apparatuses of human diseases. RESULTS We collect epigenetic and gene expression datasets from seven early time points during neural differentiation. Focusing on this model system, we construct networks of enhancer-promoter interactions, each at an individual stage of neural induction. These networks serve as the base for a rich series of analyses, through which we demonstrate their temporal dynamics and enrichment for various disease-associated variants. We apply the Girvan-Newman clustering algorithm to these networks to reveal biologically relevant substructures of regulation. Additionally, we demonstrate methods to validate predicted enhancer-promoter interactions using transcription factor overexpression and massively parallel reporter assays. CONCLUSIONS Our findings suggest a generalizable framework for exploring gene regulatory programs and their dynamics across developmental processes; this includes a comprehensive approach to studying the effects of disease-associated variation on transcriptional networks. The techniques applied to our networks have been published alongside our findings as a computational tool, E-P-INAnalyzer. Our procedure can be utilized across different cellular contexts and disorders.
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Affiliation(s)
- William DeGroat
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, 679 Hoes Lane West, Piscataway, NJ, 08854, USA
| | - Fumitaka Inoue
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Tal Ashuach
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, 387 Soda Hall, Berkeley, CA, 94720, USA
| | - Nir Yosef
- Department of Systems Immunology, Weizmann Institute of Science, 234 Herzl Street, Rehovot, 7610001, Israel
- Chan-Zuckerberg Biohub, 499 Illinois St, San Francisco, CA, 94158, USA
- Department of Systems Immunology, Ragon Institute of MGH, MIT, and Harvard Institute of Science, 400 Technology Square, Cambridge, MA, 02139, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, 513 Parnassus Ave, San Francisco, CA, 94143, USA
- Institute for Human Genetics, University of California, 513 Parnassus Ave, San Francisco, CA, 94143, USA
| | - Anat Kreimer
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, 679 Hoes Lane West, Piscataway, NJ, 08854, USA.
- Department of Biochemistry and Molecular Biology, Rutgers, The State University of New Jersey, 604 Allison Road, Piscataway, NJ, 08854, USA.
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Yun S, Noh M, Yu J, Kim HJ, Hui CC, Lee H, Son JE. Unlocking biological mechanisms with integrative functional genomics approaches. Mol Cells 2024; 47:100092. [PMID: 39019219 PMCID: PMC11345568 DOI: 10.1016/j.mocell.2024.100092] [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: 06/08/2024] [Revised: 07/01/2024] [Accepted: 07/08/2024] [Indexed: 07/19/2024] Open
Abstract
Reverse genetics offers precise functional insights into genes through the targeted manipulation of gene expression followed by phenotypic assessment. While these approaches have proven effective in model organisms such as Saccharomyces cerevisiae, large-scale genetic manipulations in human cells were historically unfeasible due to methodological limitations. However, recent advancements in functional genomics, particularly clustered regularly interspaced short palindromic repeats (CRISPR)-based screening technologies and next-generation sequencing platforms, have enabled pooled screening technologies that allow massively parallel, unbiased assessments of biological phenomena in human cells. This review provides a comprehensive overview of cutting-edge functional genomic screening technologies applicable to human cells, ranging from short hairpin RNA screens to modern CRISPR screens. Additionally, we explore the integration of CRISPR platforms with single-cell approaches to monitor gene expression, chromatin accessibility, epigenetic regulation, and chromatin architecture following genetic perturbations at the omics level. By offering an in-depth understanding of these genomic screening methods, this review aims to provide insights into more targeted and effective strategies for genomic research and personalized medicine.
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Affiliation(s)
- Sehee Yun
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Minsoo Noh
- Department of Life Sciences, Korea University, Seoul 02841, Korea; Department of Internal Medicine and Laboratory of Genomics and Translational Medicine, Gachon University College of Medicine, Incheon 21565, Korea
| | - Jivin Yu
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Hyeon-Jai Kim
- Department of Life Sciences, Korea University, Seoul 02841, Korea
| | - Chi-Chung Hui
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Hunsang Lee
- Department of Life Sciences, Korea University, Seoul 02841, Korea.
| | - Joe Eun Son
- School of Food Science and Biotechnology, Kyungpook National University, Daegu 41566, Korea.
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Catela C, Assimacopoulos S, Chen Y, Tsioras K, Feng W, Kratsios P. The Iroquois ( Iro/Irx) homeobox genes are conserved Hox targets involved in motor neuron development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.30.596714. [PMID: 38853975 PMCID: PMC11160718 DOI: 10.1101/2024.05.30.596714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The Iroquois (Iro/Irx) homeobox genes encode transcription factors with fundamental roles in animal development. Despite their link to various congenital conditions in humans, our understanding of Iro/Irx gene expression, function, and regulation remains incomplete. Here, we conducted a systematic expression analysis of all six mouse Irx genes in the embryonic spinal cord. We found five Irx genes (Irx1, Irx2, Irx3, Irx5, and Irx6) to be confined mostly to ventral spinal domains, offering new molecular markers for specific groups of post-mitotic motor neurons (MNs). Further, we engineered Irx2, Irx5, and Irx6 mouse mutants and uncovered essential but distinct roles for Irx2 and Irx6 in MN development. Last, we found that the highly conserved regulators of MN development across species, the HOX proteins, directly control Irx gene expression both in mouse and C. elegans MNs, critically expanding the repertoire of HOX target genes in the developing nervous system. Altogether, our study provides important insights into Iro/Irx expression and function in the developing spinal cord, and uncovers an ancient gene regulatory relationship between HOX and Iro/Irx genes.
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Affiliation(s)
- Catarina Catela
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Stavroula Assimacopoulos
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Yihan Chen
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Konstantinos Tsioras
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Weidong Feng
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
| | - Paschalis Kratsios
- Department of Neurobiology, University of Chicago, Chicago, IL, USA
- Neuroscience Institute, University of Chicago, Chicago, IL, USA
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Son JE. Genetics, pharmacotherapy, and dietary interventions in childhood obesity. JOURNAL OF PHARMACY & PHARMACEUTICAL SCIENCES : A PUBLICATION OF THE CANADIAN SOCIETY FOR PHARMACEUTICAL SCIENCES, SOCIETE CANADIENNE DES SCIENCES PHARMACEUTIQUES 2024; 27:12861. [PMID: 38863827 PMCID: PMC11165095 DOI: 10.3389/jpps.2024.12861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 05/16/2024] [Indexed: 06/13/2024]
Abstract
Childhood obesity has emerged as a major global health issue, contributing to the increased prevalence of chronic conditions and adversely affecting the quality of life and future prospects of affected individuals, thereby presenting a substantial societal challenge. This complex condition, influenced by the interplay of genetic predispositions and environmental factors, is characterized by excessive energy intake due to uncontrolled appetite regulation and a Westernized diet. Managing obesity in childhood requires specific considerations compared with adulthood, given the vulnerability of the critical juvenile-adolescent period to toxicity and developmental defects. Consequently, common treatment options for adult obesity may not directly apply to younger populations. Therefore, research on childhood obesity has focused on genetic defects in regulating energy intake, alongside pharmacotherapy and dietary interventions as management approaches, with an emphasis on safety concerns. This review aims to summarize canonical knowledge and recent findings on genetic factors contributing to childhood obesity. Additionally, it assesses the efficacy and safety of existing pharmacotherapies and dietary interventions and suggests future research directions. By providing a comprehensive understanding of the complex dynamics of childhood obesity, this review aims to offer insights into more targeted and effective strategies for addressing this condition, including personalized healthcare solutions.
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Affiliation(s)
- Joe Eun Son
- School of Food Science and Biotechnology, Research Institute of Tailored Food Technology, Kyungpook National University, Daegu, Republic of Korea
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DeGroat W, Inoue F, Ashuach T, Yosef N, Ahituv N, Kreimer A. Comprehensive network modeling approaches unravel dynamic enhancer-promoter interactions across neural differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595375. [PMID: 38826254 PMCID: PMC11142193 DOI: 10.1101/2024.05.22.595375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Background Increasing evidence suggests that a substantial proportion of disease-associated mutations occur in enhancers, regions of non-coding DNA essential to gene regulation. Understanding the structures and mechanisms of regulatory programs this variation affects can shed light on the apparatuses of human diseases. Results We collected epigenetic and gene expression datasets from seven early time points during neural differentiation. Focusing on this model system, we constructed networks of enhancer-promoter interactions, each at an individual stage of neural induction. These networks served as the base for a rich series of analyses, through which we demonstrated their temporal dynamics and enrichment for various disease-associated variants. We applied the Girvan-Newman clustering algorithm to these networks to reveal biologically relevant substructures of regulation. Additionally, we demonstrated methods to validate predicted enhancer-promoter interactions using transcription factor overexpression and massively parallel reporter assays. Conclusions Our findings suggest a generalizable framework for exploring gene regulatory programs and their dynamics across developmental processes. This includes a comprehensive approach to studying the effects of disease-associated variation on transcriptional networks. The techniques applied to our networks have been published alongside our findings as a computational tool, E-P-INAnalyzer. Our procedure can be utilized across different cellular contexts and disorders.
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Affiliation(s)
- William DeGroat
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, 679 Hoes Lane West, Piscataway, NJ 08854, UAS
| | - Fumitaka Inoue
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
| | - Tal Ashuach
- Department of Electrical Engineering and Computer Sciences and Center for Computational Biology, University of California, Berkeley, 387 Soda Hall, Berkeley, CA 94720, USA
| | - Nir Yosef
- Department of Systems Immunology, Weizmann Institute of Science, 234 Herzl Street, Rehovot 7610001, Israel
- Chan-Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA
- Department of Systems Immunology, Ragon Institute of MGH, MIT, and Harvard Institute of Science, 400 Technology Square, Cambridge, MA 02139, USA
| | - Nadav Ahituv
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, 513 Parnassus Ave, CA 94143, USA
- Institute for Human Genetics, University of California, San Francisco, 513 Parnassus Ave, CA 94143, USA
| | - Anat Kreimer
- Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, 679 Hoes Lane West, Piscataway, NJ 08854, UAS
- Department of Biochemistry and Molecular Biology, Rutgers, The State University of New Jersey, 604 Allison Road, Piscataway, NJ 08854, USA
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Liu S, Song S, Wang S, Cai T, Qin L, Wang X, Zhu G, Wang H, Yang W, Fang C, Wei Y, Zhou F, Yu Y, Lin S, Peng S, Li L. Hypothalamic FTO promotes high-fat diet-induced leptin resistance in mice through increasing CX3CL1 expression. J Nutr Biochem 2024; 123:109512. [PMID: 37907171 DOI: 10.1016/j.jnutbio.2023.109512] [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: 06/26/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/02/2023]
Abstract
Long-term consumption of a high-fat diet (HFD) disrupts energy homeostasis and leads to weight gain. The fat mass and obesity-associated (FTO) gene has been consistently identified to be associated with HFD-induced obesity. The hypothalamus is crucial for regulating energy balance, and HFD-induced hypothalamic leptin resistance contributes to obesity. FTO, an N6-methyladenosine (m6A) RNA methylation regulator, may be a key mediator of leptin resistance. However, the exact mechanisms remain unclear. Therefore, the present study aims to investigate the association between FTO and leptin resistance. After HFD or standard diet (SD) feeding in male mice for 22 weeks, m6A-sequencing and western blotting assays were used to identify target genes and assess protein level, and molecular interaction changes. CRISPR/Cas9 gene knockout system was employed to investigate the potential function of FTO in leptin resistance and obesity. Our data showed that chemokine (C-X3-C motif) ligand 1 (CX3CL1) was a direct downstream target of FTO-mediated m6A modification. Furthermore, upregulation of FTO/CX3CL1 and suppressor of cytokine signaling 3 (SOCS3) in the hypothalamus impaired leptin-signal transducer and activator of transcription 3 signaling, resulting in leptin resistance and obesity. Compared to wild-type (WT) mice, FTO deficiency in leptin receptor-expressing neurons of the hypothalamus significantly inhibited the upregulation of CX3CL1 and SOCS3, and partially ameliorating leptin resistance under HFD conditions. Our findings reveal that FTO involved in the hypothalamic leptin resistance and provides novel insight into the function of FTO in the contribution to hypothalamic leptin resistance and obesity.
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Affiliation(s)
- Shujing Liu
- Key Laboratory of Sports Technique, Tactics and Physical Function of General Administration of Sport of China, Scientific Research Center, Guangzhou Sport University, Guangzhou 510500, P.R. China
| | - Shiyu Song
- Key Laboratory of Sports Technique, Tactics and Physical Function of General Administration of Sport of China, Scientific Research Center, Guangzhou Sport University, Guangzhou 510500, P.R. China
| | - Shuan Wang
- Key Laboratory of Sports Technique, Tactics and Physical Function of General Administration of Sport of China, Scientific Research Center, Guangzhou Sport University, Guangzhou 510500, P.R. China
| | - Tonghui Cai
- The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, P.R. China
| | - Lian Qin
- Key Laboratory of Sports Technique, Tactics and Physical Function of General Administration of Sport of China, Scientific Research Center, Guangzhou Sport University, Guangzhou 510500, P.R. China
| | - Xinzhuang Wang
- Key Laboratory of Sports Technique, Tactics and Physical Function of General Administration of Sport of China, Scientific Research Center, Guangzhou Sport University, Guangzhou 510500, P.R. China
| | - Guangming Zhu
- Key Laboratory of Sports Technique, Tactics and Physical Function of General Administration of Sport of China, Scientific Research Center, Guangzhou Sport University, Guangzhou 510500, P.R. China
| | - Haibo Wang
- Key Laboratory of Sports Technique, Tactics and Physical Function of General Administration of Sport of China, Scientific Research Center, Guangzhou Sport University, Guangzhou 510500, P.R. China
| | - Wenqi Yang
- Key Laboratory of Sports Technique, Tactics and Physical Function of General Administration of Sport of China, Scientific Research Center, Guangzhou Sport University, Guangzhou 510500, P.R. China
| | - Chunlu Fang
- Key Laboratory of Sports Technique, Tactics and Physical Function of General Administration of Sport of China, Scientific Research Center, Guangzhou Sport University, Guangzhou 510500, P.R. China
| | - Yuan Wei
- Key Laboratory of Sports Technique, Tactics and Physical Function of General Administration of Sport of China, Scientific Research Center, Guangzhou Sport University, Guangzhou 510500, P.R. China
| | - Fu Zhou
- Key Laboratory of Sports Technique, Tactics and Physical Function of General Administration of Sport of China, Scientific Research Center, Guangzhou Sport University, Guangzhou 510500, P.R. China
| | - Yang Yu
- Key Laboratory of Sports Technique, Tactics and Physical Function of General Administration of Sport of China, Scientific Research Center, Guangzhou Sport University, Guangzhou 510500, P.R. China; School of Sport and Health Sciences, Guangzhou Sport University, Guangzhou 510500, China
| | - Shaozhang Lin
- The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, P.R. China.
| | - Shuang Peng
- Key Laboratory of Sports Technique, Tactics and Physical Function of General Administration of Sport of China, Scientific Research Center, Guangzhou Sport University, Guangzhou 510500, P.R. China; School of Sport and Health Sciences, Guangzhou Sport University, Guangzhou 510500, China.
| | - Liangming Li
- Key Laboratory of Sports Technique, Tactics and Physical Function of General Administration of Sport of China, Scientific Research Center, Guangzhou Sport University, Guangzhou 510500, P.R. China; School of Sport and Health Sciences, Guangzhou Sport University, Guangzhou 510500, China.
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Boyd RJ, McClymont SA, Barrientos NB, Hook PW, Law WD, Rose RJ, Waite EL, Rathinavelu J, Avramopoulos D, McCallion AS. Evaluating the mouse neural precursor line, SN4741, as a suitable proxy for midbrain dopaminergic neurons. BMC Genomics 2023; 24:306. [PMID: 37286935 PMCID: PMC10245633 DOI: 10.1186/s12864-023-09398-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: 01/27/2023] [Accepted: 05/23/2023] [Indexed: 06/09/2023] Open
Abstract
To overcome the ethical and technical limitations of in vivo human disease models, the broader scientific community frequently employs model organism-derived cell lines to investigate disease mechanisms, pathways, and therapeutic strategies. Despite the widespread use of certain in vitro models, many still lack contemporary genomic analysis supporting their use as a proxy for the affected human cells and tissues. Consequently, it is imperative to determine how accurately and effectively any proposed biological surrogate may reflect the biological processes it is assumed to model. One such cellular surrogate of human disease is the established mouse neural precursor cell line, SN4741, which has been used to elucidate mechanisms of neurotoxicity in Parkinson disease for over 25 years. Here, we are using a combination of classic and contemporary genomic techniques - karyotyping, RT-qPCR, single cell RNA-seq, bulk RNA-seq, and ATAC-seq - to characterize the transcriptional landscape, chromatin landscape, and genomic architecture of this cell line, and evaluate its suitability as a proxy for midbrain dopaminergic neurons in the study of Parkinson disease. We find that SN4741 cells possess an unstable triploidy and consistently exhibits low expression of dopaminergic neuron markers across assays, even when the cell line is shifted to the non-permissive temperature that drives differentiation. The transcriptional signatures of SN4741 cells suggest that they are maintained in an undifferentiated state at the permissive temperature and differentiate into immature neurons at the non-permissive temperature; however, they may not be dopaminergic neuron precursors, as previously suggested. Additionally, the chromatin landscapes of SN4741 cells, in both the differentiated and undifferentiated states, are not concordant with the open chromatin profiles of ex vivo, mouse E15.5 forebrain- or midbrain-derived dopaminergic neurons. Overall, our data suggest that SN4741 cells may reflect early aspects of neuronal differentiation but are likely not a suitable proxy for dopaminergic neurons as previously thought. The implications of this study extend broadly, illuminating the need for robust biological and genomic rationale underpinning the use of in vitro models of molecular processes.
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Affiliation(s)
- Rachel J. Boyd
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Sarah A. McClymont
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Nelson B. Barrientos
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Paul W. Hook
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - William D. Law
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Rebecca J. Rose
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Eric L. Waite
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Jay Rathinavelu
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Dimitrios Avramopoulos
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Andrew S. McCallion
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287 USA
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Boyd RJ, McClymont SA, Barrientos NB, Hook PW, Law WD, Rose RJ, Waite EL, Rathinavelu J, Avramopoulos D, McCallion AS. Evaluating the mouse neural precursor line, SN4741, as a suitable proxy for midbrain dopaminergic neurons. RESEARCH SQUARE 2023:rs.3.rs-2520557. [PMID: 36824793 PMCID: PMC9949168 DOI: 10.21203/rs.3.rs-2520557/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
To overcome the ethical and technical limitations of in vivo human disease models, the broader scientific community frequently employs model organism-derived cell lines to investigate of disease mechanisms, pathways, and therapeutic strategies. Despite the widespread use of certain in vitro models, many still lack contemporary genomic analysis supporting their use as a proxy for the affected human cells and tissues. Consequently, it is imperative to determine how accurately and effectively any proposed biological surrogate may reflect the biological processes it is assumed to model. One such cellular surrogate of human disease is the established mouse neural precursor cell line, SN4741, which has been used to elucidate mechanisms of neurotoxicity in Parkinson disease for over 25 years. Here, we are using a combination of classic and contemporary genomic techniques - karyotyping, RT-qPCR, single cell RNA-seq, bulk RNA-seq, and ATAC-seq - to characterize the transcriptional landscape, chromatin landscape, and genomic architecture of this cell line, and evaluate its suitability as a proxy for midbrain dopaminergic neurons in the study of Parkinson disease. We find that SN4741 cells possess an unstable triploidy and consistently exhibits low expression of dopaminergic neuron markers across assays, even when the cell line is shifted to the non-permissive temperature that drives differentiation. The transcriptional signatures of SN4741 cells suggest that they are maintained in an undifferentiated state at the permissive temperature and differentiate into immature neurons at the non-permissive temperature; however, they may not be dopaminergic neuron precursors, as previously suggested. Additionally, the chromatin landscapes of SN4741 cells, in both the differentiated and undifferentiated states, are not concordant with the open chromatin profiles of ex vivo , mouse E15.5 forebrain- or midbrain-derived dopaminergic neurons. Overall, our data suggest that SN4741 cells may reflect early aspects of neuronal differentiation but are likely not a suitable a proxy for dopaminergic neurons as previously thought. The implications of this study extend broadly, illuminating the need for robust biological and genomic rationale underpinning the use of in vitro models of molecular processes.
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Muraro EN, Sbardelotto BM, Guareschi ZM, de Almeida W, Souza Dos Santos A, Grassiolli S, Centenaro LA. Vitamin D supplementation combined with aerobic physical exercise restores the cell density in hypothalamic nuclei of rats exposed to monosodium glutamate. Clin Nutr ESPEN 2022; 52:20-27. [PMID: 36513455 DOI: 10.1016/j.clnesp.2022.09.009] [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: 02/07/2022] [Revised: 08/29/2022] [Accepted: 09/07/2022] [Indexed: 01/28/2023]
Abstract
BACKGROUND & AIMS In view of the increase in the prevalence of obesity and metabolic syndrome in childhood and adolescence, this study proposed the early and combined use of treatments to restore brain areas related to satiety. The vitamin D supplementation, aerobic exercise and the combination of these interventions on the structure of arcuate (ARC) and ventromedial (VMH) nuclei of hypothalamus were investigated in monosodium glutamate (MSG)-treated rats. METHODS Wistar rats were separated into five groups: Control group (CT); Obese group injected with MSG (OB); Obese group supplemented with vitamin D (OBvd); Obese group submitted to forced swimming training (OBexe) and Obese group treated with vitamin D supplementation and forced swimming training (OBvd + exe). RESULTS In the OB group, the visceral fat weight was significantly higher, there was a reduction in the number of glial cells in the ARC nucleus and also in the number of neurons in the ARC and VMH nuclei. Aerobic exercise was able to reduce the visceral fat weight in the OBexe group. The combination of treatments used in the OBvd + exe group reversed the loss of neurons and glial cells produced by MSG in the ARC nucleus. All treated groups exhibited a higher number of neurons in VMH nucleus, but an increase in the glial cells were observed only in the OBexe and OBvd + exe groups. CONCLUSIONS The effectiveness of obesity treatment can be favored through the early and combined use of vitamin D supplementation and aerobic exercise, since these therapies are able to restore brain nuclei involved in the control of food intake.
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Affiliation(s)
- Eduardo Natan Muraro
- Laboratório de Morfologia Experimental, Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná, Rua Universitária, 1619, Cascavel, Paraná, CEP: 85819-110, Brazil.
| | - Bruno Marques Sbardelotto
- Laboratório de Morfologia Experimental, Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná, Rua Universitária, 1619, Cascavel, Paraná, CEP: 85819-110, Brazil.
| | - Zoé Maria Guareschi
- Laboratório de Fisiologia Endócrina e Metabólica, Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná, Rua Universitária, 1619, Cascavel, Paraná, CEP: 85819-110, Brazil.
| | - Wellington de Almeida
- Laboratório de Morfologia Experimental, Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná, Rua Universitária, 1619, Cascavel, Paraná, CEP: 85819-110, Brazil.
| | - Adriana Souza Dos Santos
- Laboratório de Morfologia Experimental, Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná, Rua Universitária, 1619, Cascavel, Paraná, CEP: 85819-110, Brazil.
| | - Sabrina Grassiolli
- Laboratório de Fisiologia Endócrina e Metabólica, Centro de Ciências Biológicas e da Saúde, Universidade Estadual do Oeste do Paraná, Rua Universitária, 1619, Cascavel, Paraná, CEP: 85819-110, Brazil.
| | - Lígia Aline Centenaro
- Laboratório de Morfologia Experimental, Centro de Ciências Médicas e Farmacêuticas, Universidade Estadual do Oeste do Paraná, Rua Universitária, 1619, Cascavel, Paraná, CEP: 85819-110, Brazil.
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Cabrera Zapata LE, Cambiasso MJ, Arevalo MA. Epigenetic modifier Kdm6a/Utx controls the specification of hypothalamic neuronal subtypes in a sex-dependent manner. Front Cell Dev Biol 2022; 10:937875. [PMID: 36268511 PMCID: PMC9577230 DOI: 10.3389/fcell.2022.937875] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 09/07/2022] [Indexed: 11/23/2022] Open
Abstract
Kdm6a is an X-chromosome-linked H3K27me2/3 demethylase that promotes chromatin accessibility and gene transcription and is critical for tissue/cell-specific differentiation. Previous results showed higher Kdm6a levels in XX than in XY hypothalamic neurons and a female-specific requirement for Kdm6a in mediating increased axogenesis before brain masculinization. Here, we explored the sex-specific role of Kdm6a in the specification of neuronal subtypes in the developing hypothalamus. Hypothalamic neuronal cultures were established from sex-segregated E14 mouse embryos and transfected with siRNAs to knockdown Kdm6a expression (Kdm6a-KD). We evaluated the effect of Kdm6a-KD on Ngn3 expression, a bHLH transcription factor regulating neuronal sub-specification in hypothalamus. Kdm6a-KD decreased Ngn3 expression in females but not in males, abolishing basal sex differences. Then, we analyzed Kdm6a-KD effect on Ascl1, Pomc, Npy, Sf1, Gad1, and Th expression by RT-qPCR. While Kdm6a-KD downregulated Ascl1 in both sexes equally, we found sex-specific effects for Pomc, Npy, and Th. Pomc and Th expressed higher in female than in male neurons, and Kdm6a-KD reduced their levels only in females, while Npy expressed higher in male than in female neurons, and Kdm6a-KD upregulated its expression only in females. Identical results were found by immunofluorescence for Pomc and Npy neuropeptides. Finally, using ChIP-qPCR, we found higher H3K27me3 levels at Ngn3, Pomc, and Npy promoters in male neurons, in line with Kdm6a higher expression and demethylase activity in females. At all three promoters, Kdm6a-KD induced an enrichment of H3K27me3 only in females. These results indicate that Kdm6a plays a sex-specific role in controlling the expression of transcription factors and neuropeptides critical for the differentiation of hypothalamic neuronal populations regulating food intake and energy homeostasis.
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Affiliation(s)
| | - María Julia Cambiasso
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC-CONICET, Universidad Nacional de Córdoba, Córdoba, Argentina
- Facultad de Odontología, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Maria Angeles Arevalo
- Instituto Cajal (IC), CSIC, Madrid, Spain
- Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), Instituto de Salud Carlos III, Madrid, Spain
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Nampoothiri S, Nogueiras R, Schwaninger M, Prevot V. Glial cells as integrators of peripheral and central signals in the regulation of energy homeostasis. Nat Metab 2022; 4:813-825. [PMID: 35879459 PMCID: PMC7613794 DOI: 10.1038/s42255-022-00610-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 06/15/2022] [Indexed: 01/03/2023]
Abstract
Communication between the periphery and the brain is key for maintaining energy homeostasis. To do so, peripheral signals from the circulation reach the brain via the circumventricular organs (CVOs), which are characterized by fenestrated vessels lacking the protective blood-brain barrier (BBB). Glial cells, by virtue of their plasticity and their ideal location at the interface of blood vessels and neurons, participate in the integration and transmission of peripheral information to neuronal networks in the brain for the neuroendocrine control of whole-body metabolism. Metabolic diseases, such as obesity and type 2 diabetes, can disrupt the brain-to-periphery communication mediated by glial cells, highlighting the relevance of these cell types in the pathophysiology of such complications. An improved understanding of how glial cells integrate and respond to metabolic and humoral signals has become a priority for the discovery of promising therapeutic strategies to treat metabolic disorders. This Review highlights the role of glial cells in the exchange of metabolic signals between the periphery and the brain that are relevant for the regulation of whole-body energy homeostasis.
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Affiliation(s)
- Sreekala Nampoothiri
- Univ. Lille, Inserm, CHU Lille, Laboratory of Development and Plasticity of the Neuroendocrine Brain, Lille Neuroscience & Cognition, UMR-S1172, EGID, DISTALZ, Lille, France
| | - Ruben Nogueiras
- Universidade de Santiago de Compostela-Instituto de Investigation Sanitaria, Santiago de Compostela, Spain
- CIBER Fisiopatologia de la Obesidad y Nutrition, Santiago de Compostela, Spain
| | - Markus Schwaninger
- Institute for Experimental and Clinical Pharmacology and Toxicology, University of Lübeck, Lübeck, Germany
| | - Vincent Prevot
- Univ. Lille, Inserm, CHU Lille, Laboratory of Development and Plasticity of the Neuroendocrine Brain, Lille Neuroscience & Cognition, UMR-S1172, EGID, DISTALZ, Lille, France.
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