1
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Arana ÁJ, Sánchez L. Knockout, Knockdown, and the Schrödinger Paradox: Genetic Immunity to Phenotypic Recapitulation in Zebrafish. Genes (Basel) 2024; 15:1164. [PMID: 39336755 PMCID: PMC11431394 DOI: 10.3390/genes15091164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 08/27/2024] [Accepted: 08/30/2024] [Indexed: 09/30/2024] Open
Abstract
Previous research has highlighted significant phenotypic discrepancies between knockout and knockdown approaches in zebrafish, raising concerns about the reliability of these methods. However, our study suggests that these differences are not as pronounced as was once believed. By carefully examining the roles of maternal and zygotic gene contributions, we demonstrate that these factors significantly influence phenotypic outcomes, often accounting for the observed discrepancies. Our findings emphasize that morpholinos, despite their potential off-target effects, can be effective tools when used with rigorous controls. We introduce the concept of graded maternal contribution, which explains how the uneven distribution of maternal mRNA and proteins during gametogenesis impacts phenotypic variability. Our research categorizes genes into three types-susceptible, immune, and "Schrödinger" (conditional)-based on their phenotypic expression and interaction with genetic compensation mechanisms. This distinction provides new insights into the paradoxical outcomes observed in genetic studies. Ultimately, our work underscores the importance of considering both maternal and zygotic contributions, alongside rigorous experimental controls, to accurately interpret gene function and the mechanisms underlying disease. This study advocates for the continued use of morpholinos in conjunction with advanced genetic tools like CRISPR/Cas9, stressing the need for a meticulous experimental design to optimize the utility of zebrafish in genetic research and therapeutic development.
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2
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Sun F, Xiao M, Ji D, Zheng F, Shi T. Deciphering potential causative factors for undiagnosed Waardenburg syndrome through multi-data integration. Orphanet J Rare Dis 2024; 19:226. [PMID: 38844942 PMCID: PMC11155130 DOI: 10.1186/s13023-024-03220-y] [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: 03/17/2023] [Accepted: 05/19/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND Waardenburg syndrome (WS) is a rare genetic disorder mainly characterized by hearing loss and pigmentary abnormalities. Currently, seven causative genes have been identified for WS, but clinical genetic testing results show that 38.9% of WS patients remain molecularly unexplained. In this study, we performed multi-data integration analysis through protein-protein interaction and phenotype-similarity to comprehensively decipher the potential causative factors of undiagnosed WS. In addition, we explored the association between genotypes and phenotypes in WS with the manually collected 443 cases from published literature. RESULTS We predicted two possible WS pathogenic genes (KIT, CHD7) through multi-data integration analysis, which were further supported by gene expression profiles in single cells and phenotypes in gene knockout mouse. We also predicted twenty, seven, and five potential WS pathogenic variations in gene PAX3, MITF, and SOX10, respectively. Genotype-phenotype association analysis showed that white forelock and telecanthus were dominantly present in patients with PAX3 variants; skin freckles and premature graying of hair were more frequently observed in cases with MITF variants; while aganglionic megacolon and constipation occurred more often in those with SOX10 variants. Patients with variations of PAX3 and MITF were more likely to have synophrys and broad nasal root. Iris pigmentary abnormality was more common in patients with variations of PAX3 and SOX10. Moreover, we found that patients with variants of SOX10 had a higher risk of suffering from auditory system diseases and nervous system diseases, which were closely associated with the high expression abundance of SOX10 in ear tissues and brain tissues. CONCLUSIONS Our study provides new insights into the potential causative factors of WS and an alternative way to explore clinically undiagnosed cases, which will promote clinical diagnosis and genetic counseling. However, the two potential disease-causing genes (KIT, CHD7) and 32 potential pathogenic variants (PAX3: 20, MITF: 7, SOX10: 5) predicted by multi-data integration in this study are all computational predictions and need to be further verified through experiments in follow-up research.
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Affiliation(s)
- Fengying Sun
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China
| | - Minmin Xiao
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China
| | - Dong Ji
- Department of Otolaryngology, Head and Neck Surgery, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China
| | - Feng Zheng
- Wuhu Hospital and Health Science Center, East China Normal University, Shanghai, 200241, China
| | - Tieliu Shi
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
- Center for Bioinformatics and Computational Biology, the Institute of Biomedical Sciences and the School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Beijing Advanced Innovation Center, for Big Data-Based Precision Medicine, Beihang University & Capital Medical University, Beijing, 100083, China.
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3
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Yang D, Jian Z, Tang C, Chen Z, Zhou Z, Zheng L, Peng X. Zebrafish Congenital Heart Disease Models: Opportunities and Challenges. Int J Mol Sci 2024; 25:5943. [PMID: 38892128 PMCID: PMC11172925 DOI: 10.3390/ijms25115943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/18/2024] [Accepted: 05/23/2024] [Indexed: 06/21/2024] Open
Abstract
Congenital heart defects (CHDs) are common human birth defects. Genetic mutations potentially cause the exhibition of various pathological phenotypes associated with CHDs, occurring alone or as part of certain syndromes. Zebrafish, a model organism with a strong molecular conservation similar to humans, is commonly used in studies on cardiovascular diseases owing to its advantageous features, such as a similarity to human electrophysiology, transparent embryos and larvae for observation, and suitability for forward and reverse genetics technology, to create various economical and easily controlled zebrafish CHD models. In this review, we outline the pros and cons of zebrafish CHD models created by genetic mutations associated with single defects and syndromes and the underlying pathogenic mechanism of CHDs discovered in these models. The challenges of zebrafish CHD models generated through gene editing are also discussed, since the cardiac phenotypes resulting from a single-candidate pathological gene mutation in zebrafish might not mirror the corresponding human phenotypes. The comprehensive review of these zebrafish CHD models will facilitate the understanding of the pathogenic mechanisms of CHDs and offer new opportunities for their treatments and intervention strategies.
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4
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Breuer M, Rummler M, Singh J, Maher S, Zaouter C, Jamadagni P, Pilon N, Willie BM, Patten SA. CHD7 regulates craniofacial cartilage development via controlling HTR2B expression. J Bone Miner Res 2024; 39:498-512. [PMID: 38477756 PMCID: PMC11262153 DOI: 10.1093/jbmr/zjae024] [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: 04/19/2023] [Revised: 12/19/2023] [Accepted: 01/17/2024] [Indexed: 03/14/2024]
Abstract
Mutations in the Chromodomain helicase DNA-binding protein 7 - coding gene (CHD7) cause CHARGE syndrome (CS). Although craniofacial and skeletal abnormalities are major features of CS patients, the role of CHD7 in bone and cartilage development remain largely unexplored. Here, using a zebrafish (Danio rerio) CS model, we show that chd7-/- larvae display abnormal craniofacial cartilage development and spinal deformities. The craniofacial and spine defects are accompanied by a marked reduction of bone mineralization. At the molecular level, we show that these phenotypes are associated with significant reduction in the expression levels of osteoblast differentiation markers. Additionally, we detected a marked depletion of collagen 2α1 in the cartilage of craniofacial regions and vertebrae, along with significantly reduced number of chondrocytes. Chondrogenesis defects are at least in part due to downregulation of htr2b, which we found to be also dysregulated in human cells derived from an individual with CHD7 mutation-positive CS. Overall, this study thus unveils an essential role for CHD7 in cartilage and bone development, with potential clinical relevance for the craniofacial defects associated with CS.
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Affiliation(s)
- Maximilian Breuer
- Institut National de la Recherche Scientifique (INRS) – Centre Armand Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada
| | - Maximilian Rummler
- Research Centre, Shriners Hospital for Children-Canada, Department of Biological and Biomedical Engineering, Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal H4A 0A9, Canada
| | - Jaskaran Singh
- Institut National de la Recherche Scientifique (INRS) – Centre Armand Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada
| | - Sabrina Maher
- Institut National de la Recherche Scientifique (INRS) – Centre Armand Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada
- Research Centre, Shriners Hospital for Children-Canada, Department of Biological and Biomedical Engineering, Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal H4A 0A9, Canada
- Département de Neurosciences, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Charlotte Zaouter
- Institut National de la Recherche Scientifique (INRS) – Centre Armand Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada
| | - Priyanka Jamadagni
- Institut National de la Recherche Scientifique (INRS) – Centre Armand Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada
| | - Nicolas Pilon
- Molecular Genetics of Development Laboratory, Départment des Sciences Biologiques, Université du Québec à Montréal (UQAM), Montréal, QC H3C 3P8, Canada
- Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois (CERMO-FC), Université du Québec à Montréal (UQAM), Montréal, QC H3C 3P8, Canada
| | - Bettina M Willie
- Research Centre, Shriners Hospital for Children-Canada, Department of Biological and Biomedical Engineering, Faculty of Dental Medicine and Oral Health Sciences, McGill University, Montreal H4A 0A9, Canada
| | - Shunmoogum A Patten
- Institut National de la Recherche Scientifique (INRS) – Centre Armand Frappier Santé Biotechnologie, Laval, QC H7V 1B7, Canada
- Département de Neurosciences, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Centre d'Excellence en Recherche sur les Maladies Orphelines - Fondation Courtois (CERMO-FC), Université du Québec à Montréal (UQAM), Montréal, QC H3C 3P8, Canada
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5
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Uribe RA. Genetic regulation of enteric nervous system development in zebrafish. Biochem Soc Trans 2024; 52:177-190. [PMID: 38174765 PMCID: PMC10903509 DOI: 10.1042/bst20230343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/13/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024]
Abstract
The enteric nervous system (ENS) is a complex series of interconnected neurons and glia that reside within and along the entire length of the gastrointestinal tract. ENS functions are vital to gut homeostasis and digestion, including local control of peristalsis, water balance, and intestinal cell barrier function. How the ENS develops during embryological development is a topic of great concern, as defects in ENS development can result in various diseases, the most common being Hirschsprung disease, in which variable regions of the infant gut lack ENS, with the distal colon most affected. Deciphering how the ENS forms from its progenitor cells, enteric neural crest cells, is an active area of research across various animal models. The vertebrate animal model, zebrafish, has been increasingly leveraged to understand early ENS formation, and over the past 20 years has contributed to our knowledge of the genetic regulation that underlies enteric development. In this review, I summarize our knowledge regarding the genetic regulation of zebrafish enteric neuronal development, and based on the most current literature, present a gene regulatory network inferred to underlie its construction. I also provide perspectives on areas for future zebrafish ENS research.
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Affiliation(s)
- Rosa A. Uribe
- Biosciences Department, Rice University, Houston, TX 77005, U.S.A
- Laboratory of Neural Crest and Enteric Nervous System Development, Rice University, Houston, TX 77005, U.S.A
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Cintrón-Rivera LG, Burns N, Patel R, Plavicki JS. Exposure to the aryl hydrocarbon receptor agonist dioxin disrupts formation of the muscle, nerves, and vasculature in the developing jaw. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 337:122499. [PMID: 37660771 DOI: 10.1016/j.envpol.2023.122499] [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: 06/23/2023] [Revised: 08/14/2023] [Accepted: 08/31/2023] [Indexed: 09/05/2023]
Abstract
Human exposure to environmental pollutants can disrupt embryonic development and impact juvenile and adult health outcomes by adversely affecting cell and organ function. Notwithstanding, environmental contamination continues to increase due to industrial development, insufficient regulations, and the mobilization of pollutants as a result of extreme weather events. Dioxins are a class of structurally related persistent organic pollutants that are highly toxic, carcinogenic, and teratogenic. 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is the most potent dioxin compound and has been shown to induce toxic effects in developing organisms by activating the aryl hydrocarbon receptor (AHR), a ligand activated transcription factor targeted by multiple persistent organic pollutants. Contaminant-induced AHR activation results in malformations of the craniofacial cartilages and neurocranium; however, the mechanisms mediating these phenotypes are not well understood. In this study, we utilized the optically transparent zebrafish model to elucidate novel cellular targets and potential transcriptional targets underlying TCDD-induced craniofacial malformations. To this end, we exposed zebrafish embryos at 4 h post fertilization to TCDD and employed a mixed-methods approach utilizing immunohistochemistry staining, transgenic reporter lines, fixed and in vivo confocal imaging, and timelapse microscopy to determine the targets mediating TCDD-induced craniofacial phenotypes. Our data indicate that embryonic TCDD exposure reduced jaw and pharyngeal arch Sox10+ chondrocytes and Tcf21+ pharyngeal mesoderm progenitors. Exposure to TCDD correspondingly led to a reduction in collagen type II deposition in Sox10+ domains. Embryonic TCDD exposure impaired development of tissues derived from or guided by Tcf21+ progenitors, namely: nerves, muscle, and vasculature. Specifically, TCDD exposure disrupted development of the hyoid and mandibular arch muscles, decreased neural innervation of the jaw, resulted in compression of cranial nerves V and VII, and led to jaw vasculature malformations. Collectively, these findings reveal novel structural targets and potential transcriptional targets of TCDD-induced toxicity, showcasing how contaminant exposures lead to congenital craniofacial malformations.
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Affiliation(s)
- Layra G Cintrón-Rivera
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship St, Providence, RI, 02903, USA
| | - Nicole Burns
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship St, Providence, RI, 02903, USA
| | - Ratna Patel
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship St, Providence, RI, 02903, USA
| | - Jessica S Plavicki
- Department of Pathology and Laboratory Medicine, Brown University, 70 Ship St, Providence, RI, 02903, USA.
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7
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Zhang L, Zhou J. Zebrafish: A smart tool for heart disease research. JOURNAL OF FISH BIOLOGY 2023. [PMID: 37824489 DOI: 10.1111/jfb.15585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 09/07/2023] [Accepted: 10/09/2023] [Indexed: 10/14/2023]
Abstract
The increasing prevalence of heart disease poses a significant threat to human survival and safety. However, the current treatments available for heart disease are quite limited. Therefore, it is of great importance to utilize suitable animal models that can accurately simulate the physiological characteristics of heart disease. This would help improve our understanding of this disease and aid in the development of new treatment methods and drugs. Zebrafish hearts not only exhibit similarities to mammalian hearts, but they also share ~70% of homologous genes with humans. Utilizing zebrafish as an alternative to costly and time-consuming mammalian models offers numerous advantages. Zebrafish models can be easily established and maintained, and compound screening and genetic methods allow for the creation of various economical and easily controlled zebrafish and zebrafish embryonic heart disease models in a short period of time. Consequently, zebrafish have become a powerful tool for exploring the pathological mechanisms of heart disease and identifying new effective genes. In this review, we summarize recent studies on different zebrafish models of heart disease. We also describe the techniques and protocols used to develop zebrafish models of myocardial infarction, heart failure, and congenital heart disease, including surgical procedures, forward and reverse genetics, as well as drug and combination screening. This review aims to promote the utilization of zebrafish models in investigating diverse pathological mechanisms of heart disease, enhancing our knowledge and comprehension of heart disease, and offering novel insights and objectives for exploring the prevention and treatment of heart disease.
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Affiliation(s)
- Lantian Zhang
- Education Branch, Chongqing Publishing Group, Chongqing, China
| | - Jinrun Zhou
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Qingdao, China
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8
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Shi L, Wang Z, Li Y, Song Z, Yin W, Hu B. Deletion of the chd7 Hinders Oligodendrocyte Progenitor Cell Development and Myelination in Zebrafish. Int J Mol Sci 2023; 24:13535. [PMID: 37686337 PMCID: PMC10488005 DOI: 10.3390/ijms241713535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
CHD7, an encoding ATP-dependent chromodomain helicase DNA-binding protein 7, has been identified as the causative gene involved in CHARGE syndrome (Coloboma of the eye, Heart defects, Atresia choanae, Retardation of growth and/or development, Genital abnormalities and Ear abnormalities). Although studies in rodent models have expanded our understanding of CHD7, its role in oligodendrocyte (OL) differentiation and myelination in zebrafish is still unclear. In this study, we generated a chd7-knockout strain with CRISPR/Cas9 in zebrafish. We observed that knockout (KO) of chd7 intensely impeded the oligodendrocyte progenitor cells' (OPCs) migration and myelin formation due to massive expression of chd7 in oilg2+ cells, which might provoke upregulation of the MAPK signal pathway. Thus, our study demonstrates that chd7 is critical to oligodendrocyte migration and myelination during early development in zebrafish and describes a mechanism potentially associated with CHARGE syndrome.
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Affiliation(s)
- Lingyu Shi
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; (L.S.)
| | - Zongyi Wang
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; (L.S.)
| | - Yujiao Li
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; (L.S.)
| | - Zheng Song
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; (L.S.)
| | - Wu Yin
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
| | - Bing Hu
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China; (L.S.)
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230001, China
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9
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Lone BA, Siraj F, Sharma I, Verma S, Karna SKL, Ahmad F, Nagar P, Sachidanandan C, Pokharel YR. Non-POU Domain-Containing Octomer-Binding (NONO) protein expression and stability promotes the tumorigenicity and activation of Akt/MAPK/β-catenin pathways in human breast cancer cells. Cell Commun Signal 2023; 21:157. [PMID: 37370134 PMCID: PMC10294335 DOI: 10.1186/s12964-023-01179-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Breast cancer is one of the most common cancers with a high mortality rate, underscoring the need to identify new therapeutic targets. Here we report that non-POU domain-containing octamer-binding (NONO) protein is overexpressed in breast cancer and validated the interaction of the WW domain of PIN1 with c-terminal threonine-proline (thr-pro) motifs of NONO. The interaction of NONO with PIN1 increases the stability of NONO by inhibiting its proteasomal degradation, and this identifies PIN1 as a positive regulator of NONO in promoting breast tumor development. Functionally, silencing of NONO inhibits the growth, survival, migration, invasion, epithelial to mesenchymal transition (EMT), and stemness of breast cancer cells in vitro. A human metastatic breast cancer cell xenograft was established in transparent zebrafish (Danio rerio) embryos to study the metastatic inability of NONO-silenced breast cancer cells in vivo. Mechanistically, NONO depletion promotes the expression of the PDL1 cell-surface protein in breast cancer cells. The identification of novel interactions of NONO with c-Jun and β-catenin proteins and activation of the Akt/MAPK/β-catenin signaling suggests that NONO is a novel regulator of Akt/MAPK/β-catenin signaling pathways. Taken together, our results indicated an essential role of NONO in the tumorigenicity of breast cancer and could be a potential target for anti-cancerous drugs. Video Abstract.
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Affiliation(s)
- Bilal Ahmad Lone
- Cancer Biology Laboratory, Faculty of Life Science and Biotechnology, South Asian University, Rajpur Road, Maidangarhi, New Delhi, 110068, India
| | - Fouzia Siraj
- National Institute of Pathology, Safdarjung Hospital Campus, Room No.610, 6th Floor, Ansari Nagar, New Delhi, 110029, India
| | - Ira Sharma
- National Institute of Pathology, Safdarjung Hospital Campus, Room No.610, 6th Floor, Ansari Nagar, New Delhi, 110029, India
| | - Shweta Verma
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Gaziabad, 201002, India
| | - Shibendra Kumar Lal Karna
- Cancer Biology Laboratory, Faculty of Life Science and Biotechnology, South Asian University, Rajpur Road, Maidangarhi, New Delhi, 110068, India
| | - Faiz Ahmad
- Cancer Biology Laboratory, Faculty of Life Science and Biotechnology, South Asian University, Rajpur Road, Maidangarhi, New Delhi, 110068, India
| | - Preeti Nagar
- Cancer Biology Laboratory, Faculty of Life Science and Biotechnology, South Asian University, Rajpur Road, Maidangarhi, New Delhi, 110068, India
| | - Chetana Sachidanandan
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, 110025, India
- Academy of Scientific and Innovative Research (AcSIR), Gaziabad, 201002, India
| | - Yuba Raj Pokharel
- Cancer Biology Laboratory, Faculty of Life Science and Biotechnology, South Asian University, Rajpur Road, Maidangarhi, New Delhi, 110068, India.
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10
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Hodorovich DR, Lindsley PM, Berry AA, Burton DF, Marsden KC. Morphological and sensorimotor phenotypes in a zebrafish CHARGE syndrome model are domain-dependent. GENES, BRAIN, AND BEHAVIOR 2023; 22:e12839. [PMID: 36717082 PMCID: PMC10242184 DOI: 10.1111/gbb.12839] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 12/22/2022] [Accepted: 01/20/2023] [Indexed: 02/01/2023]
Abstract
CHARGE syndrome is a heterogeneous disorder characterized by a spectrum of defects affecting multiple tissues and behavioral difficulties such as autism, attention-deficit/hyperactivity disorder, obsessive-compulsive disorder, anxiety, and sensory deficits. Most CHARGE cases arise from de novo, loss-of-function mutations in chromodomain-helicase-DNA-binding-protein-7 (CHD7). CHD7 is required for processes such as neuronal differentiation and neural crest cell migration, but how CHD7 affects neural circuit function to regulate behavior is unclear. To investigate the pathophysiology of behavioral symptoms in CHARGE, we established a mutant chd7 zebrafish line that recapitulates multiple CHARGE phenotypes including ear, cardiac, and craniofacial defects. Using a panel of behavioral assays, we found that chd7 mutants have specific auditory and visual behavior deficits that are independent of defects in sensory structures. Mauthner cell-dependent short-latency acoustic startle responses are normal in chd7 mutants, while Mauthner-independent long-latency responses are reduced. Responses to sudden decreases in light are also reduced in mutants, while responses to sudden increases in light are normal, suggesting that the retinal OFF pathway may be affected. Furthermore, by analyzing multiple chd7 alleles we observed that the penetrance of morphological and behavioral phenotypes is influenced by genetic background but that it also depends on the mutation location, with a chromodomain mutation causing the highest penetrance. This pattern is consistent with analysis of a CHARGE patient dataset in which symptom penetrance was highest in subjects with mutations in the CHD7 chromodomains. These results provide new insight into the heterogeneity of CHARGE and will inform future work to define CHD7-dependent neurobehavioral mechanisms.
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Affiliation(s)
- Dana R. Hodorovich
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Patrick M. Lindsley
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA
- University of Virginia School of Medicine, University of VirginiaCharlottesvilleVAUSA
| | - Austen A. Berry
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA
- BiogenDurhamNCUSA
| | - Derek F. Burton
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA
- Washington UniversitySt. LouisMOUSA
| | - Kurt C. Marsden
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA
- Washington UniversitySt. LouisMOUSA
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11
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MacLean JE, Wertman JN, Prykhozhij SV, Chedrawe E, Langley S, Steele SL, Ban K, Blake K, Berman JN. phox2ba: The Potential Genetic Link behind the Overlap in the Symptomatology between CHARGE and Central Congenital Hypoventilation Syndromes. Genes (Basel) 2023; 14:genes14051086. [PMID: 37239446 DOI: 10.3390/genes14051086] [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: 10/12/2022] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
CHARGE syndrome typically results from mutations in the gene encoding chromodomain helicase DNA-binding protein 7 (CHD7). CHD7 is involved in regulating neural crest development, which gives rise to tissues of the skull/face and the autonomic nervous system (ANS). Individuals with CHARGE syndrome are frequently born with anomalies requiring multiple surgeries and often experience adverse events post-anesthesia, including oxygen desaturations, decreased respiratory rates, and heart rate abnormalities. Central congenital hypoventilation syndrome (CCHS) affects ANS components that regulate breathing. Its hallmark feature is hypoventilation during sleep, clinically resembling observations in anesthetized CHARGE patients. Loss of PHOX2B (paired-like homeobox 2b) underlies CCHS. Employing a chd7-null zebrafish model, we investigated physiologic responses to anesthesia and compared these to loss of phox2b. Heart rates were lower in chd7 mutants compared to the wild-type. Exposure to tricaine, a zebrafish anesthetic/muscle relaxant, revealed that chd7 mutants took longer to become anesthetized, with higher respiratory rates during recovery. chd7 mutant larvae demonstrated unique phox2ba expression patterns. The knockdown of phox2ba reduced larval heart rates similar to chd7 mutants. chd7 mutant fish are a valuable preclinical model to investigate anesthesia in CHARGE syndrome and reveal a novel functional link between CHARGE syndrome and CCHS.
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Affiliation(s)
- Jessica E MacLean
- Department of Pediatrics, Dalhousie University, Halifax, NS B3K 6R8, Canada
| | - Jaime N Wertman
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Sergey V Prykhozhij
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Emily Chedrawe
- Department of Pediatrics, Dalhousie University, Halifax, NS B3K 6R8, Canada
| | - Stewart Langley
- Department of Pediatrics, Dalhousie University, Halifax, NS B3K 6R8, Canada
| | - Shelby L Steele
- Department of Pediatrics, Dalhousie University, Halifax, NS B3K 6R8, Canada
| | - Kevin Ban
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Kim Blake
- Department of Pediatrics, Dalhousie University, Halifax, NS B3K 6R8, Canada
| | - Jason N Berman
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
- Departments of Pediatrics and Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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12
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Bmp5 Mutation Alters mRNA Expression During External Ear Development. J Craniofac Surg 2023; 34:790-796. [PMID: 36166492 DOI: 10.1097/scs.0000000000009025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 08/12/2022] [Indexed: 11/27/2022] Open
Abstract
To understand changes in gene regulation and mRNA expression in external ear development, we used a bone morphogenetic protein 5 (BMP5) short-ear mouse model. External ear tissues at E15.5 and E17.5 were collected, and mRNA expression profiles were analyzed. Upregulated and downregulated mRNA expression was identified using find_circ and CIRI2 software. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed using the differentially expressed mRNAs. Alterations in related signal pathways were identified from the upregulated and downregulated mRNA transcripts. The results showed a correlation between the mRNA expression during external ear development in BMP5 short-ear mice, including key regulatory mRNA changes after point mutations of the Bmp5 gene. This study provides evidence for the mechanism underlying mRNA regulation during external ear development. Changes in mRNA expression profiles also provide clues for future studies regarding the regulatory mechanisms underlying external ear development.
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13
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Singh MK, Yadav R, Bhaskar AK, Sengupta S, Sachidanandan C. A diet-independent zebrafish model for NAFLD recapitulates patient lipid profiles and offers a system for small molecule screening. Biochim Biophys Acta Mol Cell Biol Lipids 2023; 1868:159246. [PMID: 36202338 DOI: 10.1016/j.bbalip.2022.159246] [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: 04/20/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 02/25/2023]
Abstract
Non-alcoholic Fatty Liver Disease (NAFLD) or pathological hepatic lipid overload, is considered to affect obese individuals. However, NAFLD in lean individuals is prevalent, especially in South Asian population. The pathophysiology of lean NAFLD is not well understood and most animal models of NAFLD use the high-fat diet paradigm. To bridge this gap, we have developed a diet-independent model of NAFLD in zebrafish. We have previously shown that chronic systemic inflammation causes metabolic changes in the liver leading to hepatic fat accumulation in an IL6 overexpressing (IL6-OE) zebrafish model. In the present study, we compared the hepatic lipid composition of adult IL6-OE zebrafish to the controls and found an accumulation of saturated triacylglycerols and a reduction in the unsaturated triacylglycerol species reminiscent of NAFLD patients. Zebrafish is an ideal system for chemical genetic screens. We tested whether the hepatic lipid accumulation in the IL6-OE is responsive to chemical treatment. We found that PPAR-gamma agonist Rosiglitazone, known to reduce lipid overload in the high-fat diet models of NAFLD, could ameliorate the fatty liver phenotype of the IL6-OE fish. Rosiglitazone treatment reduced the accumulation of saturated lipids and showed a concomitant increase in unsaturated TAG species in our inflammation-induced NAFLD model. Our observations suggest that the IL6-OE model can be effective for small molecule screening to identify compounds that can reverse hepatic lipid accumulation, especially relevant to lean NAFLD.
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Affiliation(s)
- Manoj K Singh
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), South Campus, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| | - Rohit Yadav
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), South Campus, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Akash Kumar Bhaskar
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), South Campus, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shantanu Sengupta
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), South Campus, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Chetana Sachidanandan
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), South Campus, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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14
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Diagnostic potential of the amniotic fluid cells transcriptome in deciphering mendelian disease: a proof-of-concept. NPJ Genom Med 2022; 7:74. [PMID: 36577754 PMCID: PMC9797484 DOI: 10.1038/s41525-022-00347-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 12/07/2022] [Indexed: 12/29/2022] Open
Abstract
RNA sequencing (RNA-seq) is emerging in genetic diagnoses as it provides functional support for the interpretation of variants of uncertain significance. However, the use of amniotic fluid (AF) cells for RNA-seq has not yet been explored. Here, we examined the expression of clinically relevant genes in AF cells (n = 48) compared with whole blood and fibroblasts. The number of well-expressed genes in AF cells was comparable to that in fibroblasts and much higher than that in blood across different disease categories. We found AF cells RNA-seq feasible and beneficial in prenatal diagnosis (n = 4) as transcriptomic data elucidated the molecular consequence leading to the pathogenicity upgrade of variants in CHD7 and COL1A2 and revising the in silico prediction of a variant in MYRF. AF cells RNA-seq could become a reasonable choice for postnatal patients with advantages over fibroblasts and blood as it prevents invasive procedures.
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15
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Sun Y, Kumar SR, Wong CED, Tian Z, Bai H, Crump JG, Bajpai R, Lien CL. Craniofacial and cardiac defects in chd7 zebrafish mutants mimic CHARGE syndrome. Front Cell Dev Biol 2022; 10:1030587. [PMID: 36568983 PMCID: PMC9768498 DOI: 10.3389/fcell.2022.1030587] [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: 08/29/2022] [Accepted: 11/03/2022] [Indexed: 12/12/2022] Open
Abstract
Congenital heart defects occur in almost 80% of patients with CHARGE syndrome, a sporadically occurring disease causing craniofacial and other abnormalities due to mutations in the CHD7 gene. Animal models have been generated to mimic CHARGE syndrome; however, heart defects are not extensively described in zebrafish disease models of CHARGE using morpholino injections or genetic mutants. Here, we describe the co-occurrence of craniofacial abnormalities and heart defects in zebrafish chd7 mutants. These mutant phenotypes are enhanced in the maternal zygotic mutant background. In the chd7 mutant fish, we found shortened craniofacial cartilages and extra cartilage formation. Furthermore, the length of the ventral aorta is altered in chd7 mutants. Many CHARGE patients have aortic arch anomalies. It should be noted that the aberrant branching of the first branchial arch artery is observed for the first time in chd7 fish mutants. To understand the cellular mechanism of CHARGE syndrome, neural crest cells (NCCs), that contribute to craniofacial and cardiovascular tissues, are examined using sox10:Cre lineage tracing. In contrast to its function in cranial NCCs, we found that the cardiac NCC-derived mural cells along the ventral aorta and aortic arch arteries are not affected in chd7 mutant fish. The chd7 fish mutants we generated recapitulate some of the craniofacial and cardiovascular phenotypes found in CHARGE patients and can be used to further determine the roles of CHD7.
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Affiliation(s)
- Yuhan Sun
- Saban Research Institute and Heart Institute, Children’s Hospital Los Angeles, Los Angeles, CA, United States,Center for Craniofacial Molecular Biology, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, United States
| | - S. Ram Kumar
- Saban Research Institute and Heart Institute, Children’s Hospital Los Angeles, Los Angeles, CA, United States,Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Chee Ern David Wong
- Saban Research Institute and Heart Institute, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Zhiyu Tian
- Saban Research Institute and Heart Institute, Children’s Hospital Los Angeles, Los Angeles, CA, United States
| | - Haipeng Bai
- Saban Research Institute and Heart Institute, Children’s Hospital Los Angeles, Los Angeles, CA, United States,State Key Laboratory of Chemical Oncogenomics, Key Laboratory of Chemical Genomics, Peking University Shenzhen Graduate School, Shenzhen, China
| | - J. Gage Crump
- Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Ruchi Bajpai
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry, University of Southern California, Los Angeles, CA, United States,Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Ching Ling Lien
- Saban Research Institute and Heart Institute, Children’s Hospital Los Angeles, Los Angeles, CA, United States,Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States,Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States,*Correspondence: Ching Ling Lien,
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16
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Jofré DM, Hoffman DK, Cervino AS, Hahn GM, Grundy M, Yun S, Amrit FRG, Stolz DB, Godoy LF, Salvatore E, Rossi FA, Ghazi A, Cirio MC, Yanowitz JL, Hochbaum D. The CHARGE syndrome ortholog CHD-7 regulates TGF-β pathways in Caenorhabditis elegans. Proc Natl Acad Sci U S A 2022; 119:e2109508119. [PMID: 35394881 PMCID: PMC9169646 DOI: 10.1073/pnas.2109508119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 02/24/2022] [Indexed: 11/18/2022] Open
Abstract
CHARGE syndrome is a complex developmental disorder caused by mutations in the chromodomain helicase DNA-binding protein-7 (CHD7) and characterized by retarded growth and malformations in the heart and nervous system. Despite the public health relevance of this disorder, relevant cellular pathways and targets of CHD7 that relate to disease pathology are still poorly understood. Here we report that chd-7, the nematode ortholog of Chd7, is required for dauer morphogenesis, lifespan determination, stress response, and body size determination. Consistent with our discoveries, we found chd-7 to be allelic to scd-3, a previously identified dauer suppressor from the DAF-7/ tumor growth factor-β (TGF-β) pathway. Epistatic analysis places CHD-7 at the level of the DAF-3/DAF-5 complex, but we found that CHD-7 also directly impacts the expression of multiple components of this pathway. Transcriptomic analysis revealed that chd-7 mutants fail to repress daf-9 for execution of the dauer program. In addition, CHD-7 regulates the DBL-1/BMP pathway components and shares roles in male tail development and cuticle synthesis. To explore a potential conserved function for chd-7 in vertebrates, we used Xenopus laevis embryos, an established model to study craniofacial development. Morpholino-mediated knockdown of Chd7 led to a reduction in col2a1 messenger RNA (mRNA) levels, a collagen whose expression depends on TGF-β signaling. Both embryonic lethality and craniofacial defects in Chd7-depleted tadpoles were partially rescued by overexpression of col2a1 mRNA. We suggest that Chd7 has conserved roles in regulation of the TGF-β signaling pathway and pathogenic Chd7 could lead to a defective extracellular matrix deposition.
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Affiliation(s)
- Diego M. Jofré
- Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1053 Buenos Aires, Argentina
| | | | - Ailen S. Cervino
- Instituto de Fisiología, Biología Molecular y Neurociencias, Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1053 Buenos Aires, Argentina
| | - Gabriella M. Hahn
- Interdisciplinary Biomedical Graduate Program, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | | | - Sijung Yun
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20814
| | - Francis R. G. Amrit
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - Donna B. Stolz
- Center for Biologic Imaging, University of Pittsburgh Medical School, Pittsburgh, PA 15213
| | - Luciana F. Godoy
- Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1053 Buenos Aires, Argentina
| | - Esteban Salvatore
- Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1053 Buenos Aires, Argentina
| | - Fabiana A. Rossi
- Instituto de Investigaciones en Medicina Traslacional, Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Universidad Austral, B1630 Pilar, Argentina
| | - Arjumand Ghazi
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
- Department of Cell Biology & Physiology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15213
| | - M. Cecilia Cirio
- Instituto de Fisiología, Biología Molecular y Neurociencias, Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1053 Buenos Aires, Argentina
| | - Judith L. Yanowitz
- Magee-Womens Research Institute, Pittsburgh, PA 15213
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of Pittsburgh, Pittsburgh, PA 15213
- Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA 15213
| | - Daniel Hochbaum
- Departamento de Biodiversidad y Biología Experimental, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, C1053 Buenos Aires, Argentina
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17
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Wang B, Chen T, Wang A, Fang J, Wang J, Yao W, Wu Y. Anisodamine affects the pigmentation, mineral density, craniofacial area, and eye development in zebrafish embryos. J Appl Toxicol 2021; 42:1067-1077. [PMID: 34967033 DOI: 10.1002/jat.4278] [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: 11/05/2021] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 11/11/2022]
Abstract
Anisodamine is one of the major components of the tropine alkaloid family and is widely used in the treatment of pain, motion sickness, pupil dilatation, and detoxification of organophosphorus poisoning. As a muscarinic receptor antagonist, the low toxicity and moderate drug effect of anisodamine often result in high doses for clinical use, making it important to fully investigate its toxicity. In this study, zebrafish embryos were exposed to 1.3-, 2.6-, and 5.2-mM anisodamine for 7 days to study the toxic effects of drug exposure on pigmentation, mineral density, craniofacial area, and eye development. The results showed that exposure to anisodamine at 1.3 mM resulted in cranial malformations and abnormal pigmentation in zebrafish embryos; 2.6- and 5.2-mM anisodamine resulted in significant eye development defects and reduced bone density in zebrafish embryos. The associated toxicities were correlated with functional development of neural crest cells through gene expression (col1a2, ddb1, dicer1, mab21l1, mab21l2, sox10, tyrp1b, and mitfa) in the dose of 5.2-mM exposed group. In conclusion, this study provides new evidence of the developmental toxicity of high doses of anisodamine in aqueous solutions to organisms and provides a warning for the safe use of this drug.
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Affiliation(s)
- Binjie Wang
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province, The Department of Criminal Science and Technology, Zhejiang Police College, Hangzhou, Zhejiang, People's Republic of China
| | - Tianyi Chen
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province, The Department of Criminal Science and Technology, Zhejiang Police College, Hangzhou, Zhejiang, People's Republic of China
| | - Anli Wang
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province, The Department of Criminal Science and Technology, Zhejiang Police College, Hangzhou, Zhejiang, People's Republic of China.,National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing; Fuli Institute of Food Science, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, Zhejiang, People's Republic of China
| | - Jiakai Fang
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province, The Department of Criminal Science and Technology, Zhejiang Police College, Hangzhou, Zhejiang, People's Republic of China.,Thermo Fisher Scientific China Co Ltd, Hangzhou, Zhejiang, People's Republic of China
| | - Jiye Wang
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province, The Department of Criminal Science and Technology, Zhejiang Police College, Hangzhou, Zhejiang, People's Republic of China
| | - Weixuan Yao
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province, The Department of Criminal Science and Technology, Zhejiang Police College, Hangzhou, Zhejiang, People's Republic of China
| | - Yuanzhao Wu
- Key Laboratory of Drug Prevention and Control Technology of Zhejiang Province, The Department of Criminal Science and Technology, Zhejiang Police College, Hangzhou, Zhejiang, People's Republic of China
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18
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Lettieri A, Oleari R, Paganoni AJJ, Gervasini C, Massa V, Fantin A, Cariboni A. Semaphorin Regulation by the Chromatin Remodeler CHD7: An Emerging Genetic Interaction Shaping Neural Cells and Neural Crest in Development and Cancer. Front Cell Dev Biol 2021; 9:638674. [PMID: 33869187 PMCID: PMC8047133 DOI: 10.3389/fcell.2021.638674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/24/2021] [Indexed: 12/16/2022] Open
Abstract
CHD7 is a chromatin remodeler protein that controls gene expression via the formation of multi-protein complexes with specific transcription factors. During development, CHD7 controls several differentiation programs, mainly by acting on neural progenitors and neural crest (NC) cells. Thus, its roles range from the central nervous system to the peripheral nervous system and the organs colonized by NC cells, including the heart. Accordingly, mutated CHD7 is linked to CHARGE syndrome, which is characterized by several neuronal dysfunctions and by malformations of NC-derived/populated organs. Altered CHD7 has also been associated with different neoplastic transformations. Interestingly, recent evidence revealed that semaphorins, a class of molecules involved in developmental and pathological processes similar to those controlled by CHD7, are regulated by CHD7 in a context-specific manner. In this article, we will review the recent insights that support the existence of genetic interactions between these pathways, both during developmental processes and cancer progression.
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Affiliation(s)
- Antonella Lettieri
- CRC Aldo Ravelli for Neurotechnology and Experimental Brain Therapeutics, Università degli Studi di Milano, Milan, Italy.,Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Roberto Oleari
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Alyssa J J Paganoni
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
| | - Cristina Gervasini
- CRC Aldo Ravelli for Neurotechnology and Experimental Brain Therapeutics, Università degli Studi di Milano, Milan, Italy.,Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Valentina Massa
- CRC Aldo Ravelli for Neurotechnology and Experimental Brain Therapeutics, Università degli Studi di Milano, Milan, Italy.,Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Alessandro Fantin
- Department of Biosciences, Università degli Studi di Milano, Milan, Italy
| | - Anna Cariboni
- Department of Pharmacological and Biomolecular Sciences, Università degli Studi di Milano, Milan, Italy
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19
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Singh MK, Jayarajan R, Varshney S, Upadrasta S, Singh A, Yadav R, Scaria V, Sengupta S, Shanmugam D, Shalimar, Sivasubbu S, Gandotra S, Sachidanandan C. Chronic systemic exposure to IL6 leads to deregulation of glycolysis and fat accumulation in the zebrafish liver. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:158905. [PMID: 33582286 DOI: 10.1016/j.bbalip.2021.158905] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 01/21/2021] [Accepted: 02/09/2021] [Indexed: 02/08/2023]
Abstract
Inflammation is a constant in Non-Alcoholic Fatty Liver Disease (NAFLD), although their relationship is unclear. In a transgenic zebrafish system with chronic systemic overexpression of human IL6 (IL6-OE) we show that inflammation can cause intra-hepatic accumulation of triglycerides. Transcriptomics and proteomics analysis of the IL6-OE liver revealed a deregulation of glycolysis/gluconeogenesis pathway, especially a striking down regulation of the glycolytic enzyme aldolase b. Metabolomics analysis by mass spectrometry showed accumulation of hexose monophosphates and their derivatives, which can act as precursors for triglyceride synthesis. Our results suggest that IL6-driven repression of glycolysis/gluconeogenesis, specifically aldolase b, may be a novel mechanism for fatty liver. This mechanism may be relevant for NAFLD in lean individuals, an emerging class of NAFLD prevalent more in Asian Indian populations.
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Affiliation(s)
- Manoj K Singh
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rijith Jayarajan
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Swati Varshney
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sindhuri Upadrasta
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-National Chemical Laboratory, Pune, India
| | - Archana Singh
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rajni Yadav
- All India Institute of Medical Sciences, New Delhi, India
| | - Vinod Scaria
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shantanu Sengupta
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Dhanasekaran Shanmugam
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India; CSIR-National Chemical Laboratory, Pune, India
| | - Shalimar
- All India Institute of Medical Sciences, New Delhi, India
| | - Sridhar Sivasubbu
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sheetal Gandotra
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Chetana Sachidanandan
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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20
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CHD7 regulates cardiovascular development through ATP-dependent and -independent activities. Proc Natl Acad Sci U S A 2020; 117:28847-28858. [PMID: 33127760 DOI: 10.1073/pnas.2005222117] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
CHD7 encodes an ATP-dependent chromatin remodeling factor. Mutation of this gene causes multiple developmental disorders, including CHARGE (Coloboma of the eye, Heart defects, Atresia of the choanae, Retardation of growth/development, Genital abnormalities, and Ear anomalies) syndrome, in which conotruncal anomalies are the most prevalent form of heart defects. How CHD7 regulates conotruncal development remains unclear. In this study, we establish that deletion of Chd7 in neural crest cells (NCCs) causes severe conotruncal defects and perinatal lethality, thus providing mouse genetic evidence demonstrating that CHD7 cell-autonomously regulates cardiac NCC development, thereby clarifying a long-standing controversy in the literature. Using transcriptomic analyses, we show that CHD7 fine-tunes the expression of a gene network that is critical for cardiac NCC development. To gain further molecular insights into gene regulation by CHD7, we performed a protein-protein interaction screen by incubating recombinant CHD7 on a protein array. We find that CHD7 directly interacts with several developmental disorder-mutated proteins including WDR5, a core component of H3K4 methyltransferase complexes. This direct interaction suggested that CHD7 may recruit histone-modifying enzymes to target loci independently of its remodeling functions. We therefore generated a mouse model that harbors an ATPase-deficient allele and demonstrates that mutant CHD7 retains the ability to recruit H3K4 methyltransferase activity to its targets. Thus, our data uncover that CHD7 regulates cardiovascular development through ATP-dependent and -independent activities, shedding light on the etiology of CHD7-related congenital disorders. Importantly, our data also imply that patients carrying a premature stop codon versus missense mutations will likely display different molecular alterations; these patients might therefore require personalized therapeutic interventions.
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21
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Sinagoga KL, Larimer-Picciani AM, George SM, Spencer SA, Lister JA, Gross JM. Mitf-family transcription factor function is required within cranial neural crest cells to promote choroid fissure closure. Development 2020; 147:dev187047. [PMID: 32541011 PMCID: PMC7375471 DOI: 10.1242/dev.187047] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 05/29/2020] [Indexed: 12/13/2022]
Abstract
A crucial step in eye development is the closure of the choroid fissure (CF), a transient structure in the ventral optic cup through which vasculature enters the eye and ganglion cell axons exit. Although many factors have been identified that function during CF closure, the molecular and cellular mechanisms mediating this process remain poorly understood. Failure of CF closure results in colobomas. Recently, MITF was shown to be mutated in a subset of individuals with colobomas, but how MITF functions during CF closure is unknown. To address this issue, zebrafish with mutations in mitfa and tfec, two members of the Mitf family of transcription factors, were analyzed and their functions during CF closure determined. mitfa;tfec mutants possess severe colobomas and our data demonstrate that Mitf activity is required within cranial neural crest cells (cNCCs) during CF closure. In the absence of Mitf function, cNCC migration and localization in the optic cup are perturbed. These data shed light on the cellular mechanisms underlying colobomas in individuals with MITF mutations and identify a novel role for Mitf function in cNCCs during CF closure.
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Affiliation(s)
- Katie L Sinagoga
- Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, The University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Alessandra M Larimer-Picciani
- Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, The University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Stephanie M George
- Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, The University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
| | - Samantha A Spencer
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - James A Lister
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA
| | - Jeffrey M Gross
- Departments of Ophthalmology and Developmental Biology, Louis J. Fox Center for Vision Restoration, The University of Pittsburgh School of Medicine, Pittsburgh, PA 15213, USA
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22
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Schwenty-Lara J, Nehl D, Borchers A. The histone methyltransferase KMT2D, mutated in Kabuki syndrome patients, is required for neural crest cell formation and migration. Hum Mol Genet 2020; 29:305-319. [PMID: 31813957 PMCID: PMC7003132 DOI: 10.1093/hmg/ddz284] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 12/30/2022] Open
Abstract
Kabuki syndrome is an autosomal dominant developmental disorder with high similarities to CHARGE syndrome. It is characterized by a typical facial gestalt in combination with short stature, intellectual disability, skeletal findings and additional features like cardiac and urogenital malformations, cleft palate, hearing loss and ophthalmological anomalies. The major cause of Kabuki syndrome are mutations in KMT2D, a gene encoding a histone H3 lysine 4 (H3K4) methyltransferase belonging to the group of chromatin modifiers. Here we provide evidence that Kabuki syndrome is a neurocrestopathy, by showing that Kmt2d loss-of-function inhibits specific steps of neural crest (NC) development. Using the Xenopus model system, we find that Kmt2d loss-of-function recapitulates major features of Kabuki syndrome including severe craniofacial malformations. A detailed marker analysis revealed defects in NC formation as well as migration. Transplantation experiments confirm that Kmt2d function is required in NC cells. Furthermore, analyzing in vivo and in vitro NC migration behavior demonstrates that Kmt2d is necessary for cell dispersion but not protrusion formation of migrating NC cells. Importantly, Kmt2d knockdown correlates with a decrease in H3K4 monomethylation and H3K27 acetylation supporting a role of Kmt2d in the transcriptional activation of target genes. Consistently, using a candidate approach, we find that Kmt2d loss-of-function inhibits Xenopus Sema3F expression, and overexpression of Sema3F can partially rescue Kmt2d loss-of-function defects. Taken together, our data reveal novel functions of Kmt2d in multiple steps of NC development and support the hypothesis that major features of Kabuki syndrome are caused by defects in NC development.
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Affiliation(s)
- Janina Schwenty-Lara
- Department of Biology, Molecular Embryology, Philipps-Universität Marburg, Marburg 35043, Germany
| | - Denise Nehl
- Department of Biology, Molecular Embryology, Philipps-Universität Marburg, Marburg 35043, Germany
| | - Annette Borchers
- Department of Biology, Molecular Embryology, Philipps-Universität Marburg, Marburg 35043, Germany
- DFG Research Training Group, Membrane Plasticity in Tissue Development and Remodeling, GRK 2213, Philipps-Universität Marburg, Marburg 35043, Germany
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23
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Meisner JK, Martin DM. Congenital heart defects in CHARGE: The molecular role of CHD7 and effects on cardiac phenotype and clinical outcomes. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 184:81-89. [PMID: 31833191 DOI: 10.1002/ajmg.c.31761] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 12/02/2019] [Indexed: 02/06/2023]
Abstract
CHARGE syndrome is characterized by a pattern of congenital anomalies (Coloboma of the eye, Heart defects, Atresia of the choanae, Retardation of growth, Genital abnormalities, and Ear abnormalities). De novo mutations of chromodomain helicase DNA binding protein 7 (CHD7) are the primary cause of CHARGE syndrome. The clinical phenotype is highly variable including a wide spectrum of congenital heart defects. Here, we review the range of congenital heart defects and the molecular effects of CHD7 on cardiovascular development that lead to an over-representation of atrioventricular septal, conotruncal, and aortic arch defects in CHARGE syndrome. Further, we review the overlap of cardiovascular and noncardiovascular comorbidities present in CHARGE and their impact on the peri-operative morbidity and mortality in individuals with CHARGE syndrome.
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Affiliation(s)
- Joshua K Meisner
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan
| | - Donna M Martin
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan.,Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
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24
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Asad Z, Sachidanandan C. Chemical screens in a zebrafish model of CHARGE syndrome identifies small molecules that ameliorate disease-like phenotypes in embryo. Eur J Med Genet 2019; 63:103661. [PMID: 31051269 DOI: 10.1016/j.ejmg.2019.04.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 04/09/2019] [Accepted: 04/28/2019] [Indexed: 01/03/2023]
Abstract
CHARGE syndrome is an autosomal dominant congenital disorder caused primarily by mutations in the CHD7 gene. Using a small molecule screen in a zebrafish model of CHARGE syndrome, we identified 4 compounds that rescue embryos from disease-like phenotypes. Our screen yielded DAPT, a Notch signaling inhibitor that could ameliorate the craniofacial, cranial neuronal and myelination defects in chd7 morphant zebrafish embryos. We discovered that Procainamide, an inhibitor of DNA methyltransferase 1, was able to recover the pattern of expression of isl2a, a cranial neuronal marker while also reducing the effect on craniofacial cartilage and myelination. M344, an inhibitor of Histone deacetylases had a strong recovery effect on craniofacial cartilage defects and could also modestly revert the myelination defects in zebrafish embryos. CHIC-35, a SIRT1 inhibitor partially restored the expression of isl2a in cranial neurons while causing a partial reversion of myelination and craniofacial cartilage defects. Our results suggest that a modular approach to phenotypic rescue in multi-organ syndromes might be a more successful approach to treat these disorders. Our findings also open up the possibility of using these compounds for other disorders with shared phenotypes.
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Affiliation(s)
- Zainab Asad
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, 110025, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, India
| | - Chetana Sachidanandan
- CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, 110025, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi, India.
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25
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Kurosaka H. Choanal atresia and stenosis: Development and diseases of the nasal cavity. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2018; 8:e336. [PMID: 30320458 DOI: 10.1002/wdev.336] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 09/10/2018] [Accepted: 09/19/2018] [Indexed: 12/16/2022]
Abstract
Proper craniofacial development in vertebrates depends on growth and fusion of the facial processes during embryogenesis. Failure of any step in this process could lead to craniofacial anomalies such as facial clefting, which has been well studied with regard to its molecular etiology and cellular pathogenesis. Nasal cavity invagination is also a critical event in proper craniofacial development, and is required for the formation of a functional nasal cavity and airway. The nasal cavity must connect the nasopharynx with the primitive choanae to complete an airway from the nostril to the nasopharynx. In contrast to orofacial clefts, defects in nasal cavity and airway formation, such as choanal atresia (CA), in which the connection between the nasal airway and nasopharynx is physically blocked, have largely been understudied. This is also true for a narrowed connection between the nasal cavity and the nasopharynx, which is known as choanal stenosis (CS). CA occurs in approximately 1 in 5,000 live births, and can present in isolation but typically arises as part of a syndrome. Despite the fact that CA and CS usually require immediate intervention, and substantially affect the quality of life of affected individuals, the etiology and pathogenesis of CA and CS have remained elusive. In this review I focus on the process of nasal cavity development with respect to forming a functional airway and discuss the cellular behavior and molecular networks governing this process. Additionally, the etiology of human CA is discussed using examples of disorders which involve CA or CS. This article is categorized under: Signaling Pathways > Cell Fate Signaling Comparative Development and Evolution > Model Systems Birth Defects > Craniofacial and Nervous System Anomalies.
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Affiliation(s)
- Hiroshi Kurosaka
- Department of Orthodontics and Dentofacial Orthopedics, Graduate School of Dentistry, Osaka University, Osaka, Japan
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26
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Pla P, Monsoro-Burq AH. The neural border: Induction, specification and maturation of the territory that generates neural crest cells. Dev Biol 2018; 444 Suppl 1:S36-S46. [PMID: 29852131 DOI: 10.1016/j.ydbio.2018.05.018] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Revised: 05/23/2018] [Accepted: 05/23/2018] [Indexed: 11/17/2022]
Abstract
The neural crest is induced at the edge between the neural plate and the nonneural ectoderm, in an area called the neural (plate) border, during gastrulation and neurulation. In recent years, many studies have explored how this domain is patterned, and how the neural crest is induced within this territory, that also participates to the prospective dorsal neural tube, the dorsalmost nonneural ectoderm, as well as placode derivatives in the anterior area. This review highlights the tissue interactions, the cell-cell signaling and the molecular mechanisms involved in this dynamic spatiotemporal patterning, resulting in the induction of the premigratory neural crest. Collectively, these studies allow building a complex neural border and early neural crest gene regulatory network, mostly composed by transcriptional regulations but also, more recently, including novel signaling interactions.
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Affiliation(s)
- Patrick Pla
- Univ. Paris Sud, Université Paris Saclay, CNRS UMR 3347, INSERM U1021, Centre Universitaire, 15, rue Georges Clémenceau, F-91405 Orsay, France; Institut Curie Research Division, PSL Research University, CNRS UMR 3347, INSERM U1021, F-91405 Orsay, France
| | - Anne H Monsoro-Burq
- Univ. Paris Sud, Université Paris Saclay, CNRS UMR 3347, INSERM U1021, Centre Universitaire, 15, rue Georges Clémenceau, F-91405 Orsay, France; Institut Curie Research Division, PSL Research University, CNRS UMR 3347, INSERM U1021, F-91405 Orsay, France; Institut Universitaire de France, F-75005, Paris.
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27
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Cloney K, Steele SL, Stoyek MR, Croll RP, Smith FM, Prykhozhij SV, Brown MM, Midgen C, Blake K, Berman JN. Etiology and functional validation of gastrointestinal motility dysfunction in a zebrafish model of CHARGE syndrome. FEBS J 2018; 285:2125-2140. [PMID: 29660852 DOI: 10.1111/febs.14473] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 03/17/2018] [Accepted: 04/09/2018] [Indexed: 12/21/2022]
Abstract
CHARGE syndrome is linked to autosomal-dominant mutations in the CHD7 gene and results in a number of physiological and structural abnormalities, including heart defects, hearing and vision loss, and gastrointestinal (GI) problems. Of these challenges, GI problems have a profound impact throughout an individual's life, resulting in increased morbidity and mortality. A homolog of CHD7 has been identified in the zebrafish, the loss of which recapitulates many of the features of the human disease. Using a morpholino chd7 knockdown model complemented by a chd7 null mutant zebrafish line, we examined GI structure, innervation, and motility in larval zebrafish. Loss of chd7 resulted in physically smaller GI tracts with normal epithelial and muscular histology, but decreased and disorganized vagal projections, particularly in the foregut. chd7 morphant larvae had significantly less ability to empty their GI tract of gavaged fluorescent beads, and this condition was only minimally improved by the prokinetic agents, domperidone and erythromycin, in keeping with mixed responses to these agents in patients with CHARGE syndrome. The conserved genetics and transparency of the zebrafish have provided new insights into the consequences of chd7 gene dysfunction on the GI system and cranial nerve patterning. These findings highlight the opportunity of the zebrafish to serve as a preclinical model for studying compounds that may improve GI motility in individuals with CHARGE syndrome.
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Affiliation(s)
- Kellie Cloney
- Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - Shelby L Steele
- Department of Pediatrics, Dalhousie University, Halifax, Canada
| | - Matthew R Stoyek
- Department of Physiology and Biophysics, Dalhousie University, Halifax, Canada
| | - Roger P Croll
- Department of Physiology and Biophysics, Dalhousie University, Halifax, Canada
| | - Frank M Smith
- Department of Medical Neuroscience, Dalhousie University, Halifax, Canada
| | | | - Mary M Brown
- Departments of Pediatrics and Obstetrics and Gynaecology, Dalhousie University, Halifax, Canada
| | - Craig Midgen
- Department of Pathology, Dalhousie University, Halifax, Canada
| | - Kim Blake
- Faculty of Medicine, Dalhousie University, Halifax, Canada.,Department of Pediatrics, Dalhousie University, Halifax, Canada
| | - Jason N Berman
- Department of Pediatrics, Dalhousie University, Halifax, Canada.,Department of Pathology, Dalhousie University, Halifax, Canada.,Department of Microbiology and Immunology, Dalhousie University, Halifax, Canada
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28
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Babu A, Kamaraj M, Basu M, Mukherjee D, Kapoor S, Ranjan S, Swamy MM, Kaypee S, Scaria V, Kundu TK, Sachidanandan C. Chemical and genetic rescue of an ep300 knockdown model for Rubinstein Taybi Syndrome in zebrafish. Biochim Biophys Acta Mol Basis Dis 2018; 1864:1203-1215. [PMID: 29409755 DOI: 10.1016/j.bbadis.2018.01.029] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/08/2018] [Accepted: 01/27/2018] [Indexed: 10/18/2022]
Abstract
EP300 is a member of the EP300/CBP family of lysine acetyltransferases (KATs) with multiple roles in development and physiology. Loss of EP300/CBP activity in humans causes a very rare congenital disorder called Rubinstein Taybi Syndrome (RSTS). The zebrafish genome has two co-orthologs of lysine acetyltransferase EP300 (KAT3B) in zebrafish viz. ep300a and ep300b. Chemical inhibition of Ep300 with C646, a competitive inhibitor and morpholino-based genetic knockdown of ep300a and ep300b cause defects in embryonic development reminiscent of the human RSTS syndrome. Remarkably, overexpression of Ep300a KAT domain results in near complete rescue of the jaw development defects, a characteristic feature of RSTS in human suggesting the dispensability of the protein-interaction and DNA-binding domains for at least some developmental roles of Ep300. We also perform a chemical screen and identify two inhibitors of deacetylases, CHIC35 and HDACi III, that can partially rescue the RSTS-like phenotypes. Thus, modeling rare human genetic disorders in zebrafish allows for functional understanding of the genes involved and can also yield small molecule candidates towards therapeutic goals.
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Affiliation(s)
- Aswini Babu
- CSIR-Institute of Genomics & Integrative Biology, South Campus, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi 110025, India
| | - Mageshi Kamaraj
- CSIR-Institute of Genomics & Integrative Biology, South Campus, New Delhi 110025, India
| | - Moumita Basu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru 560064, India
| | - Debanjan Mukherjee
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru 560064, India
| | - Shruti Kapoor
- CSIR-Institute of Genomics & Integrative Biology, South Campus, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi 110025, India
| | - Shashi Ranjan
- CSIR-Institute of Genomics & Integrative Biology, South Campus, New Delhi 110025, India
| | - Mahadeva M Swamy
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru 560064, India
| | - Stephanie Kaypee
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru 560064, India
| | - Vinod Scaria
- CSIR-Institute of Genomics & Integrative Biology, South Campus, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi 110025, India
| | - Tapas K Kundu
- Transcription and Disease Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bengaluru 560064, India.
| | - Chetana Sachidanandan
- CSIR-Institute of Genomics & Integrative Biology, South Campus, New Delhi 110025, India; Academy of Scientific and Innovative Research (AcSIR), New Delhi 110025, India.
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29
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Dysregulation of cotranscriptional alternative splicing underlies CHARGE syndrome. Proc Natl Acad Sci U S A 2018; 115:E620-E629. [PMID: 29311329 DOI: 10.1073/pnas.1715378115] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
CHARGE syndrome-which stands for coloboma of the eye, heart defects, atresia of choanae, retardation of growth/development, genital abnormalities, and ear anomalies-is a severe developmental disorder with wide phenotypic variability, caused mainly by mutations in CHD7 (chromodomain helicase DNA-binding protein 7), known to encode a chromatin remodeler. The genetic lesions responsible for CHD7 mutation-negative cases are unknown, at least in part because the pathogenic mechanisms underlying CHARGE syndrome remain poorly defined. Here, we report the characterization of a mouse model for CHD7 mutation-negative cases of CHARGE syndrome generated by insertional mutagenesis of Fam172a (family with sequence similarity 172, member A). We show that Fam172a plays a key role in the regulation of cotranscriptional alternative splicing, notably by interacting with Ago2 (Argonaute-2) and Chd7. Validation studies in a human cohort allow us to propose that dysregulation of cotranscriptional alternative splicing is a unifying pathogenic mechanism for both CHD7 mutation-positive and CHD7 mutation-negative cases. We also present evidence that such splicing defects can be corrected in vitro by acute rapamycin treatment.
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30
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Okuno H, Renault Mihara F, Ohta S, Fukuda K, Kurosawa K, Akamatsu W, Sanosaka T, Kohyama J, Hayashi K, Nakajima K, Takahashi T, Wysocka J, Kosaki K, Okano H. CHARGE syndrome modeling using patient-iPSCs reveals defective migration of neural crest cells harboring CHD7 mutations. eLife 2017; 6. [PMID: 29179815 PMCID: PMC5705211 DOI: 10.7554/elife.21114] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 10/22/2017] [Indexed: 12/11/2022] Open
Abstract
CHARGE syndrome is caused by heterozygous mutations in the chromatin remodeler, CHD7, and is characterized by a set of malformations that, on clinical grounds, were historically postulated to arise from defects in neural crest formation during embryogenesis. To better delineate neural crest defects in CHARGE syndrome, we generated induced pluripotent stem cells (iPSCs) from two patients with typical syndrome manifestations, and characterized neural crest cells differentiated in vitro from these iPSCs (iPSC-NCCs). We found that expression of genes associated with cell migration was altered in CHARGE iPSC-NCCs compared to control iPSC-NCCs. Consistently, CHARGE iPSC-NCCs showed defective delamination, migration and motility in vitro, and their transplantation in ovo revealed overall defective migratory activity in the chick embryo. These results support the historical inference that CHARGE syndrome patients exhibit defects in neural crest migration, and provide the first successful application of patient-derived iPSCs in modeling craniofacial disorders. CHARGE syndrome is a disease in which organs including the heart, eyes and ears may not develop properly. The cells that form the tissues affected by CHARGE syndrome develop in embryos from precursor cells called neural crest cells. Individuals with CHARGE syndrome also have mutations in a gene called CHD7. However, it is difficult to examine how CHD7 mutations affect neural crest cells in embryos. In recent years, cell reprogramming techniques have made it possible to create induced pluripotent stem cells (iPSCs) from the specialized somatic cells found in the human body. These iPSCs can be developed into many different cell types, including neural crest cells. Okuno et al. created iPSCs from the skin cells of people with CHARGE syndrome, developed these cells into neural crest cells, and compared them with neural crest cells that were developed from the skin cells of people without CHARGE syndrome. The neural crest cells developed from people with CHARGE syndrome showed multiple abnormalities. For example, they were not able to move around correctly. This is an important observation because neural crest cells must move through tissues to form the various organs affected by CHARGE syndrome. Okuno et al. also observed changes in the activity of many genes other than CHD7 in the neural crest cells developed from CHARGE patients. Further research is now needed to find out which genes are the most important for restoring the normal activity of neural crest cells.
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Affiliation(s)
- Hironobu Okuno
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | | | - Shigeki Ohta
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Kimiko Fukuda
- Department of Biological Science, Tokyo Metropolitan University, Tokyo, Japan
| | - Kenji Kurosawa
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Wado Akamatsu
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan.,Center for Genomic and Regenerative Medicine, Juntendo University School of Medicine, Tokyo, Japan
| | - Tsukasa Sanosaka
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Jun Kohyama
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Kanehiro Hayashi
- Department of Anatomy, Keio University School of Medicine, Tokyo, Japan
| | - Kazunori Nakajima
- Department of Anatomy, Keio University School of Medicine, Tokyo, Japan
| | - Takao Takahashi
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Joanna Wysocka
- Department of Developmental Biology, Stanford University School of Medicine, Stanford, United States.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, United States.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States.,Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, United States
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
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31
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van Ravenswaaij-Arts C, Martin DM. New insights and advances in CHARGE syndrome: Diagnosis, etiologies, treatments, and research discoveries. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2017; 175:397-406. [PMID: 29171162 DOI: 10.1002/ajmg.c.31592] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 10/02/2017] [Accepted: 10/04/2017] [Indexed: 01/17/2023]
Abstract
CHARGE syndrome is a multiple congenital anomaly condition caused, in a majority of individuals, by loss of function pathogenic variants in the gene CHD7. In this special issue of the American Journal of Medical Genetics part C, authors of eleven manuscripts describe specific organ system features of CHARGE syndrome, with a focus on recent developments in diagnosis, etiologies, and treatments. Since 2004, when CHD7 was identified as the major causative gene in CHARGE, several animal models (mice, zebrafish, flies, and frog) and cell-based systems have been developed to explore the underlying pathophysiology of this condition. In this article, we summarize those advances, highlight opportunities for new discoveries, and encourage readers to explore specific organ systems in more detail in each individual article. We hope the excitement around innovative research and development in CHARGE syndrome will encourage others to join this effort, and will stimulate other investigators and professionals to engage with individuals diagnosed as having CHARGE syndrome, their families, and their care providers.
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Affiliation(s)
- Conny van Ravenswaaij-Arts
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, Netherlands
| | - Donna M Martin
- Departments of Human Genetics, The University of Michigan Medical School, Ann Arbor, Michigan.,Departments of Pediatrics, The University of Michigan Medical School, Ann Arbor, Michigan
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32
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Pauli S, Bajpai R, Borchers A. CHARGEd with neural crest defects. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2017; 175:478-486. [PMID: 29082625 DOI: 10.1002/ajmg.c.31584] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 08/23/2017] [Accepted: 08/31/2017] [Indexed: 12/15/2022]
Abstract
Neural crest cells are highly migratory pluripotent cells that give rise to diverse derivatives including cartilage, bone, smooth muscle, pigment, and endocrine cells as well as neurons and glia. Abnormalities in neural crest-derived tissues contribute to the etiology of CHARGE syndrome, a complex malformation disorder that encompasses clinical symptoms like coloboma, heart defects, atresia of the choanae, retarded growth and development, genital hypoplasia, ear anomalies, and deafness. Mutations in the chromodomain helicase DNA-binding protein 7 (CHD7) gene are causative of CHARGE syndrome and loss-of-function data in different model systems have firmly established a role of CHD7 in neural crest development. Here, we will summarize our current understanding of the function of CHD7 in neural crest development and discuss possible links of CHARGE syndrome to other developmental disorders.
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Affiliation(s)
- Silke Pauli
- Institute of Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Ruchi Bajpai
- Center for Craniofacial Molecular Biology, Ostrow School of Dentistry and Department of Biochemistry and Molecular Biology, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Annette Borchers
- Department of Biology, Molecular Embryology, Philipps-University Marburg, Marburg, Germany
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33
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Sarasamma S, Varikkodan MM, Liang ST, Lin YC, Wang WP, Hsiao CD. Zebrafish: A Premier Vertebrate Model for Biomedical Research in Indian Scenario. Zebrafish 2017; 14:589-605. [PMID: 29023224 DOI: 10.1089/zeb.2017.1447] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The zebrafish (Danio rerio) is a versatile model organism that has been used in biomedical research for several decades to study a wide range of biological phenomena. There are many technical advantages of using zebrafish over other vertebrate models. They are readily available, hardy, easy, and inexpensive to maintain in the laboratory, have a short life cycle, and have excellent fecundity. Due to its optical clarity and reproducible capabilities, it has become one of the predominant models of human genetic diseases. Zebrafish research has made rapid strides in the United States and Europe, but in India the field is at an early stage and many researchers still remain unaware of the full research potential of this tiny fish. The zebrafish model system was introduced into India in the early 2000s. Up to now, more than 200 scientific referred articles have been published by Indian researchers. This review gives an overview of the current state of knowledge for zebrafish research in India, with the aim of promoting wider utilization of zebrafish for high level biological studies.
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Affiliation(s)
- Sreeja Sarasamma
- 1 Department of Chemistry, Chung Yuan Christian University , Chung-Li, Taiwan .,2 Department of Bioscience Technology, Chung Yuan Christian University , Chung-Li, Taiwan .,3 Department of Chemical Biology, Rajiv Gandhi Centre for Biotechnology , Thiruvananthapuram, Kerala, India
| | - Muhammed Muhsin Varikkodan
- 1 Department of Chemistry, Chung Yuan Christian University , Chung-Li, Taiwan .,2 Department of Bioscience Technology, Chung Yuan Christian University , Chung-Li, Taiwan .,4 Department of Biotechnology and Genetic Engineering, Bharathidasan University , Tiruchirapalli, India
| | - Sung-Tzu Liang
- 1 Department of Chemistry, Chung Yuan Christian University , Chung-Li, Taiwan
| | - Yen-Chang Lin
- 5 Graduate Institute of Biotechnology, Chinese Culture University , Taipei, Taiwan
| | - Wen-Pin Wang
- 6 Institute of Medical Sciences, Tzu-Chi University , Hualien, Taiwan .,7 Department of Molecular Biology and Human Genetics, Tzu-Chi University , Hualien, Taiwan
| | - Chung-Der Hsiao
- 1 Department of Chemistry, Chung Yuan Christian University , Chung-Li, Taiwan .,8 Center for Biomedical Technology, Chung Yuan Christian University , Chung-Li, Taiwan .,9 Center for Nanotechnology, Chung Yuan Christian University , Chung-Li, Taiwan
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