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Rahmati M, Chebli J, Kumar Banote R, Roselli S, Agholme L, Zetterberg H, Abramsson A. Fine-Tuning Amyloid Precursor Protein Expression through Nonsense-Mediated mRNA Decay. eNeuro 2024; 11:ENEURO.0034-24.2024. [PMID: 38789273 DOI: 10.1523/eneuro.0034-24.2024] [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: 01/24/2024] [Revised: 03/22/2024] [Accepted: 04/16/2024] [Indexed: 05/26/2024] Open
Abstract
Studies on genetic robustness recently revealed transcriptional adaptation (TA) as a mechanism by which an organism can compensate for genetic mutations through activation of homologous genes. Here, we discovered that genetic mutations, introducing a premature termination codon (PTC) in the amyloid precursor protein-b (appb) gene, activated TA of two other app family members, appa and amyloid precursor-like protein-2 (aplp2), in zebrafish. The observed transcriptional response of appa and aplp2 required degradation of mutant mRNA and did not depend on Appb protein level. Furthermore, TA between amyloid precursor protein (APP) family members was observed in human neuronal progenitor cells; however, compensation was only present during early neuronal differentiation and could not be detected in a more differentiated neuronal stage or adult zebrafish brain. Using knockdown and chemical inhibition, we showed that nonsense-mediated mRNA decay (NMD) is involved in degradation of mutant mRNA and that Upf1 and Upf2, key proteins in the NMD pathway, regulate the endogenous transcript levels of appa, appb, aplp1, and aplp2 In conclusion, our results suggest that the expression level of App family members is regulated by the NMD pathway and that mutations destabilizing app/APP mRNA can induce genetic compensation by other family members through TA in both zebrafish and human neuronal progenitors.
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Affiliation(s)
- Maryam Rahmati
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg 413 45, Sweden
| | - Jasmine Chebli
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg 413 45, Sweden
| | - Rakesh Kumar Banote
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg 413 45, Sweden
| | - Sandra Roselli
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg 413 45, Sweden
| | - Lotta Agholme
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg 413 45, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg 413 45, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London WC1N #BG, United Kingdom
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal 431 41, Sweden
- United Kingdom Dementia Research Institute, London W1T 7NF, United Kingdom
- Hong Kong Center for Neurodegenerative Diseases, 17 Science Park W Ave, Hong Kong, China
- Wisconsin Alzheimer's Disease Research Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53792
| | - Alexandra Abramsson
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy, University of Gothenburg, Gothenburg 413 45, Sweden
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2
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Borrelli C, Gurtner A, Arnold IC, Moor AE. Stress-free single-cell transcriptomic profiling and functional genomics of murine eosinophils. Nat Protoc 2024; 19:1679-1709. [PMID: 38504138 DOI: 10.1038/s41596-024-00967-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 12/20/2023] [Indexed: 03/21/2024]
Abstract
Eosinophils are a class of granulocytes with pleiotropic functions in homeostasis and various human diseases. Nevertheless, they are absent from conventional single-cell RNA sequencing atlases owing to technical difficulties preventing their transcriptomic interrogation. Consequently, eosinophil heterogeneity and the gene regulatory networks underpinning their diverse functions remain poorly understood. We have developed a stress-free protocol for single-cell RNA capture from murine tissue-resident eosinophils, which revealed distinct intestinal subsets and their roles in colitis. Here we describe in detail how to enrich eosinophils from multiple tissues of residence and how to capture high-quality single-cell transcriptomes by preventing transcript degradation. By combining magnetic eosinophil enrichment with microwell-based single-cell RNA capture (BD Rhapsody), our approach minimizes shear stress and processing time. Moreover, we report how to perform genome-wide CRISPR pooled genetic screening in ex vivo-conditioned bone marrow-derived eosinophils to functionally probe pathways required for their differentiation and intestinal maturation. These protocols can be performed by any researcher with basic skills in molecular biology and flow cytometry, and can be adapted to investigate other granulocytes, such as neutrophils and mast cells, thereby offering potential insights into their roles in both homeostasis and disease pathogenesis. Single-cell transcriptomics of eosinophils can be performed in 2-3 d, while functional genomics assays may require up to 1 month.
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Affiliation(s)
- Costanza Borrelli
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Alessandra Gurtner
- Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland
| | - Isabelle C Arnold
- Institute of Experimental Immunology, University of Zürich, Zürich, Switzerland.
| | - Andreas E Moor
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.
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Guo J, Zou Z, Dou X, Zhao X, Wang Y, Wei L, Pi Y, Wang Y, He C, Guo S. Zebrafish Mbd5 binds to RNA m5C and regulates histone deubiquitylation and gene expression in development metabolism and behavior. Nucleic Acids Res 2024; 52:4257-4275. [PMID: 38366571 PMCID: PMC11077058 DOI: 10.1093/nar/gkae093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 01/24/2024] [Accepted: 02/05/2024] [Indexed: 02/18/2024] Open
Abstract
Complex biological processes are regulated by both genetic and epigenetic programs. One class of epigenetic modifications is methylation. Evolutionarily conserved methyl-CpG-binding domain (MBD)-containing proteins are known as readers of DNA methylation. MBD5 is linked to multiple human diseases but its mechanism of action remains unclear. Here we report that the zebrafish Mbd5 does not bind to methylated DNA; but rather, it directly binds to 5-methylcytosine (m5C)-modified mRNAs and regulates embryonic development, erythrocyte differentiation, iron metabolism, and behavior. We further show that Mbd5 facilitates removal of the monoubiquitin mark at histone H2A-K119 through an interaction with the Polycomb repressive deubiquitinase (PR-DUB) complex in vivo. The direct target genes of Mbd5 are enriched with both RNA m5C and H2A-K119 ubiquitylation signals. Together, we propose that zebrafish MBD5 is an RNA m5C reader that potentially links RNA methylation to histone modification and in turn transcription regulation in vivo.
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Affiliation(s)
- Jianhua Guo
- State Key Laboratory of Genetic Engineering, National Demonstration Center for Experimental Biology Education, School of Life Sciences, Fudan University, Shanghai, China
| | - Zhongyu Zou
- Department of Chemistry and Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Xiaoyang Dou
- Department of Chemistry and Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Xiang Zhao
- Department of Bioengineering and Therapeutic Sciences, Programs in Human Genetics and Biological Sciences, University of California, San Francisco, CA 94143, USA
| | - Yimin Wang
- Department of Neurology, Children's Hospital of Fudan University, National Children's Medical Center, No. 399, Wanyuan Road, Minhang District, Shanghai, China
| | - Liqiang Wei
- State Key Laboratory of Genetic Engineering, National Demonstration Center for Experimental Biology Education, School of Life Sciences, Fudan University, Shanghai, China
- Department of Bioengineering and Therapeutic Sciences, Programs in Human Genetics and Biological Sciences, University of California, San Francisco, CA 94143, USA
| | - Yan Pi
- State Key Laboratory of Genetic Engineering, National Demonstration Center for Experimental Biology Education, School of Life Sciences, Fudan University, Shanghai, China
- Department of Bioengineering and Therapeutic Sciences, Programs in Human Genetics and Biological Sciences, University of California, San Francisco, CA 94143, USA
| | - Yi Wang
- Department of Neurology, Children's Hospital of Fudan University, National Children's Medical Center, No. 399, Wanyuan Road, Minhang District, Shanghai, China
| | - Chuan He
- Department of Chemistry and Howard Hughes Medical Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Su Guo
- Department of Bioengineering and Therapeutic Sciences, Programs in Human Genetics and Biological Sciences, University of California, San Francisco, CA 94143, USA
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4
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Li Y, Fang Z, Tan L, Wu Q, Liu Q, Wang Y, Weng Q, Chen Q. Gene redundancy and gene compensation of insulin-like peptides in the oocyte development of bean beetle. PLoS One 2024; 19:e0302992. [PMID: 38713664 DOI: 10.1371/journal.pone.0302992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 04/16/2024] [Indexed: 05/09/2024] Open
Abstract
Bean beetle (Callosobruchus maculatus) exhibits clear phenotypic plasticity depending on population density; However, the underlying molecular mechanism remains unknown. Compared to low-density individuals, high-density individuals showed a faster terminal oocyte maturity rate. Four insulin-like peptide (ILP) genes were identified in the bean beetle, which had higher expression levels in the head than in the thorax and abdomen. The population density could regulate the expression levels of CmILP1-3, CmILP2-3, and CmILP1 as well as CmILP3 in the head, thorax, and abdomen, respectively. RNA interference results showed that each CmILP could regulate terminal oocyte maturity rate, indicating that there was functional redundancy among CmILPs. Silencing each CmILP could lead to down-regulation of some other CmILPs, however, CmILP3 was up-regulated in the abdomen after silencing CmILP1 or CmILP2. Compared to single gene silencing, silencing CmILP3 with CmILP1 or CmILP2 at the same time led to more serious retardation in oocyte development, suggesting CmILP3 could be up-regulated to functionally compensate for the down-regulation of CmILP1 and CmILP2. In conclusion, population density-dependent plasticity in terminal oocyte maturity rate of bean beetle was regulated by CmILPs, which exhibited gene redundancy and gene compensation.
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Affiliation(s)
- Yongqin Li
- School of Life Sciences, Guizhou Normal University, Gui'an, Guizhou, China
| | - Zheng Fang
- School of Life Sciences, Guizhou Normal University, Gui'an, Guizhou, China
| | - Leitao Tan
- School of Life Sciences, Guizhou Normal University, Gui'an, Guizhou, China
| | - Qingshan Wu
- School of Life Sciences, Guizhou Normal University, Gui'an, Guizhou, China
| | - Qiuping Liu
- School of Life Sciences, Guizhou Normal University, Gui'an, Guizhou, China
| | - Yeying Wang
- School of Life Sciences, Guizhou Normal University, Gui'an, Guizhou, China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Gui'an, Guizhou, China
- Qiannan Normal University for Nationalities, Duyun, Guizhou, China
| | - Qianquan Chen
- School of Life Sciences, Guizhou Normal University, Gui'an, Guizhou, China
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5
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Pomreinke AP, Müller P. Zebrafish nampt-a mutants are viable despite perturbed primitive hematopoiesis. Hereditas 2024; 161:14. [PMID: 38685093 PMCID: PMC11057069 DOI: 10.1186/s41065-024-00318-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
BACKGROUND Nicotinamide phosphoribosyltransferase (Nampt) is required for recycling NAD+ in numerous cellular contexts. Morpholino-based knockdown of zebrafish nampt-a has been shown to cause abnormal development and defective hematopoiesis concomitant with decreased NAD+ levels. However, surprisingly, nampt-a mutant zebrafish were recently found to be viable, suggesting a discrepancy between the phenotypes in knockdown and knockout conditions. Here, we address this discrepancy by directly comparing loss-of-function approaches that result in identical defective transcripts in morphants and mutants. RESULTS Using CRISPR/Cas9-mediated mutagenesis, we generated nampt-a mutant lines that carry the same mis-spliced mRNA as nampt-a morphants. Despite reduced NAD+ levels and perturbed expression of specific blood markers, nampt-a mutants did not display obvious developmental defects and were found to be viable. In contrast, injection of nampt-a morpholinos into wild-type or mutant nampt-a embryos caused aberrant phenotypes. Moreover, nampt-a morpholinos caused additional reduction of blood-related markers in nampt-a mutants, suggesting that the defects observed in nampt-a morphants can be partially attributed to off-target effects of the morpholinos. CONCLUSIONS Our findings show that zebrafish nampt-a mutants are viable despite reduced NAD+ levels and a perturbed hematopoietic gene expression program, indicating strong robustness of primitive hematopoiesis during early embryogenesis.
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Affiliation(s)
- Autumn Penecilla Pomreinke
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany
- University of Hohenheim, Stuttgart, Germany
| | - Patrick Müller
- Friedrich Miescher Laboratory of the Max Planck Society, Tübingen, Germany.
- University of Konstanz, Konstanz, Germany.
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6
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Franks SN, Heon-Roberts R, Ryan BJ. CRISPRi: a way to integrate iPSC-derived neuronal models. Biochem Soc Trans 2024; 52:539-551. [PMID: 38526223 PMCID: PMC11088925 DOI: 10.1042/bst20230190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 02/28/2024] [Accepted: 03/13/2024] [Indexed: 03/26/2024]
Abstract
The genetic landscape of neurodegenerative diseases encompasses genes affecting multiple cellular pathways which exert effects in an array of neuronal and glial cell-types. Deconvolution of the roles of genes implicated in disease and the effects of disease-associated variants remains a vital step in the understanding of neurodegeneration and the development of therapeutics. Disease modelling using patient induced pluripotent stem cells (iPSCs) has enabled the generation of key cell-types associated with disease whilst maintaining the genomic variants that predispose to neurodegeneration. The use of CRISPR interference (CRISPRi), alongside other CRISPR-perturbations, allows the modelling of the effects of these disease-associated variants or identifying genes which modify disease phenotypes. This review summarises the current applications of CRISPRi in iPSC-derived neuronal models, such as fluorescence-activated cell sorting (FACS)-based screens, and discusses the future opportunities for disease modelling, identification of disease risk modifiers and target/drug discovery in neurodegeneration.
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Affiliation(s)
- Sarah N.J. Franks
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
| | - Rachel Heon-Roberts
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
| | - Brent J. Ryan
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3QU, UK
- Kavli Institute for Nanoscience Discovery, Dorothy Crowfoot Hodgkin Building, University of Oxford, Oxford OX1 3QU, UK
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7
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Wu Z, Wu D, Zhong Q, Zou X, Liu Z, Long H, Wei J, Li X, Dai F. The role of zyxin in signal transduction and its relationship with diseases. Front Mol Biosci 2024; 11:1371549. [PMID: 38712343 PMCID: PMC11070705 DOI: 10.3389/fmolb.2024.1371549] [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: 01/16/2024] [Accepted: 04/08/2024] [Indexed: 05/08/2024] Open
Abstract
This review highlighted the pivotal role of zyxin, an essential cell focal adhesions protein, in cellular biology and various diseases. Zyxin can orchestrate the restructuring and dynamic alterations of the cellular cytoskeleton, which is involved in cell proliferation, adhesion, motility, and gene transcription. Aberrant zyxin expression is closely correlated with tumor cell activity and cardiac function in both tumorigenesis and cardiovascular diseases. Moreover, in fibrotic and inflammatory conditions, zyxin can modulate cellular functions and inflammatory responses. Therefore, a comprehensive understanding of zyxin is crucial for deciphering signal transduction networks and disease pathogenesis. Investigating its role in diseases holds promise for novel avenues in early diagnosis and therapeutic strategies. Nevertheless, targeting zyxin as a therapeutic focal point presents challenges in terms of specificity, safety, drug delivery, and resistance. Nonetheless, in-depth studies on zyxin and the application of precision medicine could offer new possibilities for personalized treatment modalities.
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Affiliation(s)
- Zelan Wu
- Department of Cardiovascular Medicine, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Daiqin Wu
- Department of Cardiovascular Medicine, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Qin Zhong
- Clinical Research Center, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Xue Zou
- Clinical Research Center, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Zhongjing Liu
- Clinical Research Center, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Hehua Long
- School of Clinical Laboratory Science, Guizhou Medical University, Guiyang, China
| | - Jing Wei
- Department of Endocrinology, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Xia Li
- Guizhou Precision Medicine Institute, Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Fangjie Dai
- Department of Cardiovascular Medicine, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
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8
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Panina SB, Schweer JV, Zhang Q, Raina G, Hardtke HA, Kim S, Yang W, Siegel D, Zhang YJ. Targeting of REST with rationally-designed small molecule compounds exhibits synergetic therapeutic potential in human glioblastoma cells. BMC Biol 2024; 22:83. [PMID: 38609948 PMCID: PMC11015551 DOI: 10.1186/s12915-024-01879-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 04/04/2024] [Indexed: 04/14/2024] Open
Abstract
BACKGROUND Glioblastoma (GBM) is an aggressive brain cancer associated with poor prognosis, intrinsic heterogeneity, plasticity, and therapy resistance. In some GBMs, cell proliferation is fueled by a transcriptional regulator, repressor element-1 silencing transcription factor (REST). RESULTS Using CRISPR/Cas9, we identified GBM cell lines dependent on REST activity. We developed new small molecule inhibitory compounds targeting small C-terminal domain phosphatase 1 (SCP1) to reduce REST protein level and transcriptional activity in glioblastoma cells. Top leads of the series like GR-28 exhibit potent cytotoxicity, reduce REST protein level, and suppress its transcriptional activity. Upon the loss of REST protein, GBM cells can potentially compensate by rewiring fatty acid metabolism, enabling continued proliferation. Combining REST inhibition with the blockade of this compensatory adaptation using long-chain acyl-CoA synthetase inhibitor Triacsin C demonstrated substantial synergetic potential without inducing hepatotoxicity. CONCLUSIONS Our results highlight the efficacy and selectivity of targeting REST alone or in combination as a therapeutic strategy to combat high-REST GBM.
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Affiliation(s)
- Svetlana B Panina
- Department of Molecular Biosciences, The University of Texas at Austin, 2500 Speedway, Austin, TX, USA
| | - Joshua V Schweer
- Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego, 9500 Gilman Drive 0741, La Jolla, CA, USA
| | - Qian Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, 2500 Speedway, Austin, TX, USA
| | - Gaurav Raina
- Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego, 9500 Gilman Drive 0741, La Jolla, CA, USA
| | - Haley A Hardtke
- Department of Molecular Biosciences, The University of Texas at Austin, 2500 Speedway, Austin, TX, USA
| | - Seungjin Kim
- Department of Molecular Biosciences, The University of Texas at Austin, 2500 Speedway, Austin, TX, USA
| | - Wanjie Yang
- Department of Molecular Biosciences, The University of Texas at Austin, 2500 Speedway, Austin, TX, USA
| | - Dionicio Siegel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, The University of California San Diego, 9500 Gilman Drive 0741, La Jolla, CA, USA
| | - Y Jessie Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, 2500 Speedway, Austin, TX, USA.
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Liang S, Zhou Y, Chang Y, Li J, Zhang M, Gao P, Li Q, Yu H, Kawakami K, Ma J, Zhang R. A novel gene-trap line reveals the dynamic patterns and essential roles of cysteine and glycine-rich protein 3 in zebrafish heart development and regeneration. Cell Mol Life Sci 2024; 81:158. [PMID: 38556571 PMCID: PMC10982097 DOI: 10.1007/s00018-024-05189-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 02/13/2024] [Accepted: 02/28/2024] [Indexed: 04/02/2024]
Abstract
Mutations in cysteine and glycine-rich protein 3 (CSRP3)/muscle LIM protein (MLP), a key regulator of striated muscle function, have been linked to hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM) in patients. However, the roles of CSRP3 in heart development and regeneration are not completely understood. In this study, we characterized a novel zebrafish gene-trap line, gSAIzGFFM218A, which harbors an insertion in the csrp3 genomic locus, heterozygous fish served as a csrp3 expression reporter line and homozygous fish served as a csrp3 mutant line. We discovered that csrp3 is specifically expressed in larval ventricular cardiomyocytes (CMs) and that csrp3 deficiency leads to excessive trabeculation, a common feature of CSRP3-related HCM and DCM. We further revealed that csrp3 expression increased in response to different cardiac injuries and was regulated by several signaling pathways vital for heart regeneration. Csrp3 deficiency impeded zebrafish heart regeneration by impairing CM dedifferentiation, hindering sarcomere reassembly, and reducing CM proliferation while aggravating apoptosis. Csrp3 overexpression promoted CM proliferation after injury and ameliorated the impairment of ventricle regeneration caused by pharmacological inhibition of multiple signaling pathways. Our study highlights the critical role of Csrp3 in both zebrafish heart development and regeneration, and provides a valuable animal model for further functional exploration that will shed light on the molecular pathogenesis of CSRP3-related human cardiac diseases.
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Affiliation(s)
- Shuzhang Liang
- TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, 430071, China
- School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Yating Zhou
- Shanghai Key Laboratory of Regulatory Biology, Institute of Molecular Medicine, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yue Chang
- School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Jiayi Li
- TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, 430071, China
| | - Min Zhang
- Shanghai Pediatric Congenital Heart Disease Institute and Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, 200127, China
| | - Peng Gao
- TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, 430071, China
| | - Qi Li
- TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, 430071, China
| | - Hong Yu
- TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, 430071, China
- Institute of Myocardial Injury and Repair, Wuhan University, Wuhan, 430071, China
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China
| | - Koichi Kawakami
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Shizuoka, 411-8540, Japan
- Department of Genetics, Graduate University for Advanced Studies (SOKENDAI), Mishima, Shizuoka, 411-8540, Japan
| | - Jinmin Ma
- Medical Frontier Innovation Research Center, The First Hospital of Lanzhou University, The First Clinical Medical College of Lanzhou University, Lanzhou, 730000, China.
| | - Ruilin Zhang
- TaiKang Medical School (School of Basic Medical Sciences), Wuhan University, Wuhan, 430071, China.
- Institute of Myocardial Injury and Repair, Wuhan University, Wuhan, 430071, China.
- Hubei Provincial Key Laboratory of Developmentally Originated Disease, Wuhan, 430071, China.
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10
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Yang W, Liu X, He Z, Zhang Y, Tan X, Liu C. odd skipped-related 2 as a novel mark for labeling the proximal convoluted tubule within the zebrafish kidney. Heliyon 2024; 10:e27582. [PMID: 38496848 PMCID: PMC10944271 DOI: 10.1016/j.heliyon.2024.e27582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 12/15/2023] [Accepted: 03/03/2024] [Indexed: 03/19/2024] Open
Abstract
The proximal convoluted tubule (PCT) of the kidney is a crucial functional segment responsible for reabsorption, secretion, and the maintenance of electrolyte and water balance within the renal tubule. However, there is a lack of a well-defined endogenous transgenic line for studying PCT morphogenesis. By analyzing single-cell transcriptome data from the adult zebrafish kidney, we have identified the expression of odd-skipped-related 2 (osr2, which encodes an odd-skipped zinc-finger transcription factor) in the PCT. To gain insight into the role of osr2 in PCT morphogenesis, we have generated a transgenic zebrafish line Tg(osr2:EGFP), expressing enhanced green fluorescent protein (EGFP). The EGFP expression pattern closely mirrors that of endogenous Osr2, faithfully recapitulating its native expression profile. During kidney development, we can use EGFP to track PCT development, which is also preserved in adult zebrafish. Additionally, osr2:EGFP-labeled zebrafish PCT fragments displayed short lengths with infrequent overlap, rendering them conducive for nephrons counting. The generation of Tg(osr2:EGFP) transgenic line is accompanied by simultaneous disruption of osr2 activity. Importantly, our findings demonstrate that osr2 inactivation had no discernible impact on the development and regeneration of Tg(osr2:EGFP) zebrafish nephrons. Overall, the establishment of this transgenic zebrafish line offers a valuable tool for both genetic and chemical analysis of PCT.
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Affiliation(s)
- Wenmin Yang
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Chongqing Clinical Research Center of Kidney and Urology Diseases, Xinqiao Hospital, Army Medical University (Third Military Medical University), 400037, Chongqing, PR China
| | - Xiaoliang Liu
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Chongqing Clinical Research Center of Kidney and Urology Diseases, Xinqiao Hospital, Army Medical University (Third Military Medical University), 400037, Chongqing, PR China
| | - Zhongwei He
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Chongqing Clinical Research Center of Kidney and Urology Diseases, Xinqiao Hospital, Army Medical University (Third Military Medical University), 400037, Chongqing, PR China
| | - Yunfeng Zhang
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Chongqing Clinical Research Center of Kidney and Urology Diseases, Xinqiao Hospital, Army Medical University (Third Military Medical University), 400037, Chongqing, PR China
| | - Xiaoqin Tan
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Chongqing Clinical Research Center of Kidney and Urology Diseases, Xinqiao Hospital, Army Medical University (Third Military Medical University), 400037, Chongqing, PR China
| | - Chi Liu
- Department of Nephrology, The Key Laboratory for the Prevention and Treatment of Chronic Kidney Disease of Chongqing, Chongqing Clinical Research Center of Kidney and Urology Diseases, Xinqiao Hospital, Army Medical University (Third Military Medical University), 400037, Chongqing, PR China
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11
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Duan Q, Zheng H, Qin Y, Yan J, Wang J, Burgess SM, Fan C. Stat3 Has a Different Role in Axon Growth During Development Than It Does in Axon Regeneration After Injury. Mol Neurobiol 2024; 61:1753-1768. [PMID: 37775721 DOI: 10.1007/s12035-023-03644-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 09/07/2023] [Indexed: 10/01/2023]
Abstract
Signal transducer and activator of transcription 3 (STAT3) is essential for neural development and regeneration as a key transcription factor and mitochondrial activator. However, the mechanism of Stat3 in axon development and regeneration has not been fully understood. In this study, using zebrafish posterior lateral line (PLL) axons, we demonstrate that Stat3 plays distinct roles in PLL axon embryonic growth and regeneration. Our experiments indicate that stat3 is required for PLL axon extension. In stat3 mutant zebrafish, the PLL axon ends were stalled at the level of the cloaca, and expression of stat3 rescues the PLL axon growth in a cell-autonomous manner. Jak/Stat signaling inhibition did not affect PLL axon growth indicating Jak/Stat was dispensable for PLL axon growth. In addition, we found that Stat3 was co-localized with mitochondria in PLL axons and important for the mitochondrial membrane potential and ATPase activity. The PLL axon growth defect of stat3 mutants was mimicked and rescued by rotenone and DCHC treatment, respectively, which suggests that Stat3 regulates PLL axon growth through mitochondrial Stat3. By contrast, mutation of stat3 or Jak/Stat signaling inhibition retarded PLL axon regeneration. Meanwhile, we also found Schwann cell migration was also inhibited in stat3 mutants. Taken together, Stat3 is required for embryonic PLL axon growth by regulating the ATP synthesis efficiency of mitochondria, whereas Stat3 stimulates PLL axon regeneration by regulating Schwann cell migration via Jak/Stat signaling. Our findings show a new mechanism of Stat3 in axon growth and regeneration.
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Affiliation(s)
- Qinwen Duan
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Hongfei Zheng
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Yanjun Qin
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Jizhou Yan
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Jian Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China
| | - Shawn M Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, MD, USA
| | - Chunxin Fan
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China.
- International Research Center for Marine Biosciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, China.
- Marine Biomedical Science and Technology Innovation Platform of Lingang New Area, Shanghai, China.
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12
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Sun J, Ruiz Daniels R, Balic A, Andresen AMS, Bjørgen H, Dobie R, Henderson NC, Koppang EO, Martin SAM, Fosse JH, Taylor RS, Macqueen DJ. Cell atlas of the Atlantic salmon spleen reveals immune cell heterogeneity and cell-specific responses to bacterial infection. FISH & SHELLFISH IMMUNOLOGY 2024; 145:109358. [PMID: 38176627 DOI: 10.1016/j.fsi.2024.109358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/23/2023] [Accepted: 01/02/2024] [Indexed: 01/06/2024]
Abstract
The spleen is a conserved secondary lymphoid organ that emerged in parallel to adaptive immunity in early jawed vertebrates. Recent studies have applied single cell transcriptomics to reveal the cellular composition of spleen in several species, cataloguing diverse immune cell types and subpopulations. In this study, 51,119 spleen nuclei transcriptomes were comprehensively investigated in the commercially important teleost Atlantic salmon (Salmo salar L.), contrasting control animals with those challenged with the bacterial pathogen Aeromonas salmonicida. We identified clusters of nuclei representing the expected major cell types, namely T cells, B cells, natural killer-like cells, granulocytes, mononuclear phagocytes, endothelial cells, mesenchymal cells, erythrocytes and thrombocytes. We discovered heterogeneity within several immune lineages, providing evidence for resident macrophages and melanomacrophages, infiltrating monocytes, several candidate dendritic cell subpopulations, and B cells at distinct stages of differentiation, including plasma cells and an igt + subset. We provide evidence for twelve candidate T cell subsets, including cd4+ T helper and regulatory T cells, one cd8+ subset, three γδT subsets, and populations double negative for cd4 and cd8. The number of genes showing differential expression during the early stages of Aeromonas infection was highly variable across immune cell types, with the largest changes observed in macrophages and infiltrating monocytes, followed by resting mature B cells. Our analysis provides evidence for a local inflammatory response to infection alongside B cell maturation in the spleen, and upregulation of ccr9 genes in igt + B cells, T helper and cd8+ cells, and monocytes, consistent with the recruitment of immune cell populations to the gut to deal with Aeromonas infection. Overall, this study provides a new cell-resolved perspective of the immune actions of Atlantic salmon spleen, highlighting extensive heterogeneity hidden to bulk transcriptomics. We further provide a large catalogue of cell-specific marker genes that can be leveraged to further explore the function and structural organization of the salmonid immune system.
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Affiliation(s)
- Jianxuan Sun
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Rose Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Adam Balic
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK; Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | | | - Håvard Bjørgen
- Unit of Anatomy, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Ross Dobie
- Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK
| | - Neil C Henderson
- Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Erling Olaf Koppang
- Unit of Anatomy, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Samuel A M Martin
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | | | - Richard S Taylor
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Daniel J Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK.
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13
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Liu P, Yu S, Zheng W, Zhang Q, Qiao J, Li Z, Deng Z, Zhang H. Identification and functional verification of Y-chromosome-specific gene typo-gyf in Bactrocera dorsalis. INSECT SCIENCE 2024. [PMID: 38189161 DOI: 10.1111/1744-7917.13311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 01/09/2024]
Abstract
Genes on the Y chromosome play important roles in male sex determination and development. The identification of Y-chromosome-specific genes not only provides a theoretical basis for the study of male reproductive development, but also offers genetic control targets for agricultural pests. However, Y-chromosome genes are rarely characterized due to their high repeatability and high heterochromatinization, especially in the oriental fruit fly. In this study, 1 011 Y-chromosome-specific candidate sequences were screened from 2 to 4 h Bactrocera dorsalis embryo datasets with the chromosome quotient method, 6 of which were identified as Y-chromosome-specific sequences by polymerase chain reaction, including typo-gyf, a 19 126-bp DNA sequence containing a 575-amino acid open reading frame. Testicular deformation and a significant reduction in sperm number were observed after typo-gyf knockdown with RNA interference in embryos. After typo-gyf knockout with clustered regularly interspaced palindromic repeats (CRISPR) / CRISPR-associated protein 9 in the embryonic stage, the sex ratio of the emergent adults was unbalanced, with far more females than males. A genotype analysis of these females with the Y-chromosome gene MoY revealed no sex reversal. Typo-gyf knockout led to the death of XY individuals in the embryonic stage. We conclude that typo-gyf is an essential gene for male survival, and is also involved in testicular development and spermatogenesis. The identification of typo-gyf and its functional verification provide insight into the roles of Y-chromosome genes in male development.
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Affiliation(s)
- Peipei Liu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, China-Australia Joint Research Centre for Horticultural and Urban Pests, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shuning Yu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, China-Australia Joint Research Centre for Horticultural and Urban Pests, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wenping Zheng
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, China-Australia Joint Research Centre for Horticultural and Urban Pests, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Qiuyuan Zhang
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, China-Australia Joint Research Centre for Horticultural and Urban Pests, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Jiao Qiao
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, China-Australia Joint Research Centre for Horticultural and Urban Pests, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ziniu Li
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, China-Australia Joint Research Centre for Horticultural and Urban Pests, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zhurong Deng
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, China-Australia Joint Research Centre for Horticultural and Urban Pests, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hongyu Zhang
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, China-Australia Joint Research Centre for Horticultural and Urban Pests, Institute of Urban and Horticultural Entomology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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14
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Chiang DY, Verkerk AO, Victorio R, Shneyer BI, van der Vaart B, Jouni M, Narendran N, Kc A, Sampognaro JR, Vetrano-Olsen F, Oh JS, Buys E, de Jonge B, Shah DA, Kiviniemi T, Burridge PW, Bezzina CR, Akhmanova A, MacRae CA. The Role of MAPRE2 and Microtubules in Maintaining Normal Ventricular Conduction. Circ Res 2024; 134:46-59. [PMID: 38095085 DOI: 10.1161/circresaha.123.323231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 11/28/2023] [Indexed: 01/06/2024]
Abstract
BACKGROUND Brugada syndrome is associated with loss-of-function SCN5A variants, yet these account for only ≈20% of cases. A recent genome-wide association study identified a novel locus within MAPRE2, which encodes EB2 (microtubule end-binding protein 2), implicating microtubule involvement in Brugada syndrome. METHODS A mapre2 knockout zebrafish model was generated using CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/clustered regularly interspaced short palindromic repeat-associated protein 9) and validated by Western blot. Larval hearts at 5 days post-fertilization were isolated for voltage mapping and immunocytochemistry. Adult fish hearts were used for ECG, patch clamping, and immunocytochemistry. Morpholinos were injected into embryos at 1-cell stage for knockdown experiments. A transgenic zebrafish line with cdh2 tandem fluorescent timer was used to study adherens junctions. Microtubule plus-end tracking and patch clamping were performed in human induced pluripotent stem cell derived cardiomyocytes (iPSC-CMs) with MAPRE2 knockdown and knockout, respectively. RESULTS Voltage mapping of mapre2 knockout hearts showed a decrease in ventricular maximum upstroke velocity of the action potential and conduction velocity, suggesting loss of cardiac voltage-gated sodium channel function. ECG showed QRS prolongation in adult knockout fish, and patch clamping showed decreased sodium current density in knockout ventricular myocytes and arrhythmias in knockout iPSC-CMs. Confocal imaging showed disorganized adherens junctions and mislocalization of mature Ncad (N-cadherin) with mapre2 loss of function, associated with a decrease of detyrosinated tubulin. MAPRE2 knockdown in iPSC-CMs led to an increase in microtubule growth velocity and distance, indicating changes in microtubule dynamics. Finally, knockdown of ttl encoding tubulin tyrosine ligase in mapre2 knockout larvae rescued tubulin detyrosination and ventricular maximum upstroke velocity of the action potential. CONCLUSIONS Genetic ablation of mapre2 led to a decrease in voltage-gated sodium channel function, a hallmark of Brugada syndrome, associated with disruption of adherens junctions, decrease of detyrosinated tubulin as a marker of microtubule stability, and changes in microtubule dynamics. Restoration of the detyrosinated tubulin fraction with ttl knockdown led to rescue of voltage-gated sodium channel-related functional parameters in mapre2 knockout hearts. Taken together, our study implicates microtubule dynamics in the modulation of ventricular conduction.
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Affiliation(s)
- David Y Chiang
- Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (D.Y.C., R.V., N.N., A.K., J.R.S., F.V.-O., J.S.O., E.B., C.A.M.)
| | - Arie O Verkerk
- Department of Experimental Cardiology, Heart Center (A.O.V., C.R.B.), Academic Medical Center, Amsterdam UMC, the Netherlands
| | - Rachelle Victorio
- Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (D.Y.C., R.V., N.N., A.K., J.R.S., F.V.-O., J.S.O., E.B., C.A.M.)
| | - Boris I Shneyer
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, the Netherlands (B.I.S., B.v.d.V., A.A.)
| | - Babet van der Vaart
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, the Netherlands (B.I.S., B.v.d.V., A.A.)
| | - Mariam Jouni
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (M.J., D.A.S., P.W.B.)
| | - Nakul Narendran
- Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (D.Y.C., R.V., N.N., A.K., J.R.S., F.V.-O., J.S.O., E.B., C.A.M.)
| | - Ashmita Kc
- Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (D.Y.C., R.V., N.N., A.K., J.R.S., F.V.-O., J.S.O., E.B., C.A.M.)
| | - James R Sampognaro
- Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (D.Y.C., R.V., N.N., A.K., J.R.S., F.V.-O., J.S.O., E.B., C.A.M.)
| | - Franki Vetrano-Olsen
- Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (D.Y.C., R.V., N.N., A.K., J.R.S., F.V.-O., J.S.O., E.B., C.A.M.)
| | - John S Oh
- Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (D.Y.C., R.V., N.N., A.K., J.R.S., F.V.-O., J.S.O., E.B., C.A.M.)
| | - Eva Buys
- Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (D.Y.C., R.V., N.N., A.K., J.R.S., F.V.-O., J.S.O., E.B., C.A.M.)
| | - Berend de Jonge
- Department of Medical Biology (B.d.J.), Academic Medical Center, Amsterdam UMC, the Netherlands
| | - Disheet A Shah
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (M.J., D.A.S., P.W.B.)
| | - Tuomas Kiviniemi
- Heart Center, Turku University Hospital and University of Turku, Finland (T.K.)
| | - Paul W Burridge
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL (M.J., D.A.S., P.W.B.)
| | - Connie R Bezzina
- Department of Experimental Cardiology, Heart Center (A.O.V., C.R.B.), Academic Medical Center, Amsterdam UMC, the Netherlands
| | - Anna Akhmanova
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, the Netherlands (B.I.S., B.v.d.V., A.A.)
| | - Calum A MacRae
- Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (D.Y.C., R.V., N.N., A.K., J.R.S., F.V.-O., J.S.O., E.B., C.A.M.)
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15
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Lin X, Jiang JY, Hong DJ, Lin KJ, Li JJ, Chen YJ, Qiu YS, Wang Z, Liao YC, Yang K, Shi Y, Wang MW, Hsu SL, Hong S, Zeng YH, Chen XC, Wang N, Lee YC, Chen WJ. Biallelic COQ4 Variants in Hereditary Spastic Paraplegia: Clinical and Molecular Characterization. Mov Disord 2024; 39:152-163. [PMID: 38014483 DOI: 10.1002/mds.29664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 10/31/2023] [Accepted: 11/07/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Hereditary spastic paraplegias (HSP) are neurologic disorders characterized by progressive lower-extremity spasticity. Despite the identification of several HSP-related genes, many patients lack a genetic diagnosis. OBJECTIVES The aims were to confirm the pathogenic role of biallelic COQ4 mutations in HSP and elucidate the clinical, genetic, and functional molecular features of COQ4-associated HSP. METHODS Whole exome sequences of 310 index patients with HSP of unknown cause from three distinct populations were analyzed to identify potential HSP causal genes. Clinical data obtained from patients harboring candidate causal mutations were examined. Functional characterization of COQ4 variants was performed using bioinformatic tools, single-cell RNA sequencing, biochemical assays in cell lines, primary fibroblasts, induced pluripotent stem cell-derived pyramidal neurons, and zebrafish. RESULTS Compound heterozygous variants in COQ4, which cosegregated with HSP in pedigrees, were identified in 7 patients from six unrelated families. Patients from four of the six families presented with pure HSP, whereas probands of the other two families exhibited complicated HSP with epilepsy or with cerebellar ataxia. In patient-derived fibroblasts and COQ4 knockout complementation lines, stable expression of these missense variants exerted loss-of-function effects, including mitochondrial reactive oxygen species accumulation, decreased mitochondrial membrane potential, and lower ubiquinone biosynthesis. Whereas differentiated pyramidal neurons expressed high COQ4 levels, coq4 knockdown zebrafish displayed severe motor dysfunction, reflecting motor neuron dysregulation. CONCLUSIONS Our study confirms that loss-of-function, compound heterozygous, pathogenic COQ4 variants are causal for autosomal recessive pure and complicated HSP. Moreover, reduced COQ4 levels attributable to variants correspond with decreased ubiquinone biosynthesis, impaired mitochondrial function, and higher phenotypic disease severity. © 2023 International Parkinson and Movement Disorder Society.
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Affiliation(s)
- Xiang Lin
- Department of Neurology, Department of Rare Diseases, Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Jun-Yi Jiang
- Department of Neurology, Department of Rare Diseases, Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Dao-Jun Hong
- Department of Neurology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Kai-Jun Lin
- Department of Neurology, Department of Rare Diseases, Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Jin-Jing Li
- Department of Neurology, Department of Rare Diseases, Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Yi-Jun Chen
- Department of Neurology, Department of Rare Diseases, Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Yu-Sen Qiu
- Department of Neurology, Department of Rare Diseases, Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Zishuai Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yi-Chu Liao
- Department of Neurology, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Neurology, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Kang Yang
- Department of Neurology, Department of Rare Diseases, Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Yan Shi
- Department of Neurology, Department of Rare Diseases, Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Meng-Wen Wang
- Department of Neurology, Department of Rare Diseases, Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Shao-Lun Hsu
- Department of Neurology, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Neurology, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Shunyan Hong
- Department of Neurology, Department of Rare Diseases, Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Yi-Heng Zeng
- Department of Neurology, Department of Rare Diseases, Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Xiao-Chun Chen
- Fujian Key Laboratory of Molecular Neurology, Institute of Neuroscience, Fujian Medical University, Fuzhou, China
| | - Ning Wang
- Department of Neurology, Department of Rare Diseases, Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
| | - Yi-Chung Lee
- Department of Neurology, Taipei Veterans General Hospital, Taipei, Taiwan
- Department of Neurology, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Wan-Jin Chen
- Department of Neurology, Department of Rare Diseases, Institute of Neurology of First Affiliated Hospital, Institute of Neuroscience, and Fujian Key Laboratory of Molecular Neurology, Fujian Medical University, Fuzhou, China
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16
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Karimpour M, Totonchi M, Behmanesh M, Montazeri H. Pathway-driven analysis of synthetic lethal interactions in cancer using perturbation screens. Life Sci Alliance 2024; 7:e202302268. [PMID: 37863651 PMCID: PMC10589366 DOI: 10.26508/lsa.202302268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/10/2023] [Accepted: 10/10/2023] [Indexed: 10/22/2023] Open
Abstract
Synthetic lethality offers a promising approach for developing effective therapeutic interventions in cancer when direct targeting of driver genes is impractical. In this study, we comprehensively analyzed large-scale CRISPR, shRNA, and PRISM screens to identify potential synthetic lethal (SL) interactions in pan-cancer and 12 individual cancer types, using a new computational framework that leverages the biological function and signaling pathway information of key driver genes to mitigate the confounding effects of background genetic alterations in different cancer cell lines. This approach has successfully identified several putative SL interactions, including KRAS-MAP3K2 and APC-TCF7L2 in pan cancer, and CCND1-METTL1, TP53-FRS3, SMO-MDM2, and CCNE1-MTOR in liver, blood, skin, and gastric cancers, respectively. In addition, we proposed several FDA-approved cancer-targeted drugs for various cancer types through PRISM drug screens, such as cabazitaxel for VHL-mutated kidney cancer and alectinib for lung cancer with NRAS or KRAS mutations. Leveraging pathway information can enhance the concordance of shRNA and CRISPR screens and provide clinically relevant findings such as the potential efficacy of dasatinib, an inhibitor of SRC, for colorectal cancer patients with mutations in the WNT signaling pathway. These analyses revealed that taking signaling pathway information into account results in the identification of more promising SL interactions.
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Affiliation(s)
- Mina Karimpour
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mehdi Totonchi
- Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehrdad Behmanesh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hesam Montazeri
- https://ror.org/05vf56z40 Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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17
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Turan FB, Ercan ME, Firat-Karalar EN. A Chemically Inducible Organelle Rerouting Assay to Probe Primary Cilium Assembly, Maintenance, and Disassembly in Cultured Cells. Methods Mol Biol 2024; 2725:55-78. [PMID: 37856017 DOI: 10.1007/978-1-0716-3507-0_3] [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] [Indexed: 10/20/2023]
Abstract
The primary cilium is a conserved, microtubule-based organelle that protrudes from the surface of most vertebrate cells as well as sensory cells of many organisms. It transduces extracellular chemical and mechanical cues to regulate diverse cellular processes during development and physiology. Loss-of-function studies via RNA interference and CRISPR/Cas9-mediated gene knockouts have been the main tool for elucidating the functions of proteins, protein complexes, and organelles implicated in cilium biology. However, these methods are limited in studying acute spatiotemporal functions of proteins as well as the connection between their cellular positioning and functions. A powerful approach based on inducible recruitment of plus or minus end-directed molecular motors to the protein of interest enables fast and precise control of protein activity in time and in space. In this chapter, we present a chemically inducible heterodimerization method for functional perturbation of centriolar satellites, an emerging membrane-less organelle involved in cilium biogenesis and function. The method we present is based on rerouting of centriolar satellites to the cell center or the periphery in mammalian epithelial cells. We also describe how this method can be applied to study the temporal functions of centriolar satellites during primary cilium assembly, maintenance, and disassembly.
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Affiliation(s)
- F Basak Turan
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | - M Erdem Ercan
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey
| | - Elif Nur Firat-Karalar
- Department of Molecular Biology and Genetics, Koç University, Istanbul, Turkey.
- Koc University School of Medicine, Istanbul, Turkey.
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18
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Torraca V, White RJ, Sealy IM, Mazon-Moya M, Duggan G, Willis AR, Busch-Nentwich EM, Mostowy S. Transcriptional profiling of zebrafish identifies host factors controlling susceptibility to Shigella flexneri. Dis Model Mech 2024; 17:dmm050431. [PMID: 38131137 PMCID: PMC10846535 DOI: 10.1242/dmm.050431] [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: 08/08/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023] Open
Abstract
Shigella flexneri is a human-adapted pathovar of Escherichia coli that can invade the intestinal epithelium, causing inflammation and bacillary dysentery. Although an important human pathogen, the host response to S. flexneri has not been fully described. Zebrafish larvae represent a valuable model for studying human infections in vivo. Here, we use a Shigella-zebrafish infection model to generate mRNA expression profiles of host response to Shigella infection at the whole-animal level. Immune response-related processes dominate the signature of early Shigella infection (6 h post-infection). Consistent with its clearance from the host, the signature of late Shigella infection (24 h post-infection) is significantly changed, and only a small set of immune-related genes remain differentially expressed, including acod1 and gpr84. Using mutant lines generated by ENU, CRISPR mutagenesis and F0 crispants, we show that acod1- and gpr84-deficient larvae are more susceptible to Shigella infection. Together, these results highlight the power of zebrafish to model infection by bacterial pathogens and reveal the mRNA expression of the early (acutely infected) and late (clearing) host response to Shigella infection.
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Affiliation(s)
- Vincenzo Torraca
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK
- School of Life Sciences, University of Westminster, London W1W 6UW, UK
| | - Richard J. White
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge CB2 0AW, UK
- School of Biological and Behavioural Sciences, Faculty of Science and Engineering, Queen Mary University of London, London E1 4NS, UK
| | - Ian M. Sealy
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge CB2 0AW, UK
- School of Biological and Behavioural Sciences, Faculty of Science and Engineering, Queen Mary University of London, London E1 4NS, UK
| | - Maria Mazon-Moya
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Gina Duggan
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Alexandra R. Willis
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
| | - Elisabeth M. Busch-Nentwich
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge CB2 0AW, UK
- School of Biological and Behavioural Sciences, Faculty of Science and Engineering, Queen Mary University of London, London E1 4NS, UK
| | - Serge Mostowy
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
- Section of Microbiology, MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, UK
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19
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Shiraki T, Kawakami K. Generation of Transgenic Fish Harboring CRISPR/Cas9-Mediated Somatic Mutations Via a tRNA-Based Multiplex sgRNA Expression. Methods Mol Biol 2024; 2707:305-318. [PMID: 37668921 DOI: 10.1007/978-1-0716-3401-1_20] [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] [Indexed: 09/06/2023]
Abstract
The controlled expression of Cas9 and/or sgRNA in transgenic zebrafish made it possible to knock out a gene in a spatially and/or temporally controlled manner. This transgenic approach can be more useful if multiple sgRNAs are efficiently expressed since we can improve the biallelic frame-shift mutation rate and circumvent the functional redundancy of genes and genetic compensation. We developed the tRNA-based system to express multiple functional sgRNAs from a single transcript in zebrafish and found that it is applicable to the transgenic expression of multiple sgRNAs. In this chapter, we describe a procedure for the generation of plasmids containing multiple sgRNAs flanked by tRNAs and a method to induce multiple CRISPR/Cas9-mediated genome modifications in transgenic zebrafish.
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Affiliation(s)
- Tomoya Shiraki
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Shizuoka, Japan.
| | - Koichi Kawakami
- Laboratory of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Shizuoka, Japan
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20
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An X, Zhang S, Jiang Y, Liu X, Fang C, Wang J, Zhao L, Hou Q, Zhang J, Wan X. CRISPR/Cas9-based genome editing of 14 lipid metabolic genes reveals a sporopollenin metabolon ZmPKSB-ZmTKPR1-1/-2 required for pollen exine formation in maize. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:216-232. [PMID: 37792967 PMCID: PMC10754010 DOI: 10.1111/pbi.14181] [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: 06/14/2023] [Revised: 08/20/2023] [Accepted: 09/12/2023] [Indexed: 10/06/2023]
Abstract
Lipid biosynthesis and transport are essential for plant male reproduction. Compared with Arabidopsis and rice, relatively fewer maize lipid metabolic genic male-sterility (GMS) genes have been identified, and the sporopollenin metabolon in maize anther remains unknown. Here, we identified two maize GMS genes, ZmTKPR1-1 and ZmTKPR1-2, by CRISPR/Cas9 mutagenesis of 14 lipid metabolic genes with anther stage-specific expression patterns. Among them, tkpr1-1/-2 double mutants displayed complete male sterility with delayed tapetum degradation and abortive pollen. ZmTKPR1-1 and ZmTKPR1-2 encode tetraketide α-pyrone reductases and have catalytic activities in reducing tetraketide α-pyrone produced by ZmPKSB (polyketide synthase B). Several conserved catalytic sites (S128/130, Y164/166 and K168/170 in ZmTKPR1-1/-2) are essential for their enzymatic activities. Both ZmTKPR1-1 and ZmTKPR1-2 are directly activated by ZmMYB84, and their encoded proteins are localized in both the endoplasmic reticulum and nuclei. Based on protein structure prediction, molecular docking, site-directed mutagenesis and biochemical assays, the sporopollenin biosynthetic metabolon ZmPKSB-ZmTKPR1-1/-2 was identified to control pollen exine formation in maize anther. Although ZmTKPR1-1/-2 and ZmPKSB formed a protein complex, their mutants showed different, even opposite, defective phenotypes of anther cuticle and pollen exine. Our findings discover new maize GMS genes that can contribute to male-sterility line-assisted maize breeding and also provide new insights into the metabolon-regulated sporopollenin biosynthesis in maize anther.
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Affiliation(s)
- Xueli An
- Research Institute of Biology and AgricultureUniversity of Science and Technology BeijingBeijingChina
- Industry Research Institute of Biotechnology BreedingYili Normal UniversityYiningChina
- Zhongzhi International Institute of Agricultural BiosciencesBeijingChina
- Beijing Engineering Laboratory of Main Crop Bio‐Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. Ltd.BeijingChina
| | - Shaowei Zhang
- Research Institute of Biology and AgricultureUniversity of Science and Technology BeijingBeijingChina
- Zhongzhi International Institute of Agricultural BiosciencesBeijingChina
| | - Yilin Jiang
- Research Institute of Biology and AgricultureUniversity of Science and Technology BeijingBeijingChina
- Zhongzhi International Institute of Agricultural BiosciencesBeijingChina
| | - Xinze Liu
- Research Institute of Biology and AgricultureUniversity of Science and Technology BeijingBeijingChina
- Zhongzhi International Institute of Agricultural BiosciencesBeijingChina
| | - Chaowei Fang
- Research Institute of Biology and AgricultureUniversity of Science and Technology BeijingBeijingChina
- Zhongzhi International Institute of Agricultural BiosciencesBeijingChina
| | - Jing Wang
- Research Institute of Biology and AgricultureUniversity of Science and Technology BeijingBeijingChina
- Zhongzhi International Institute of Agricultural BiosciencesBeijingChina
| | - Lina Zhao
- Research Institute of Biology and AgricultureUniversity of Science and Technology BeijingBeijingChina
- Zhongzhi International Institute of Agricultural BiosciencesBeijingChina
| | - Quancan Hou
- Research Institute of Biology and AgricultureUniversity of Science and Technology BeijingBeijingChina
- Zhongzhi International Institute of Agricultural BiosciencesBeijingChina
| | - Juan Zhang
- Research Institute of Biology and AgricultureUniversity of Science and Technology BeijingBeijingChina
- Industry Research Institute of Biotechnology BreedingYili Normal UniversityYiningChina
- Zhongzhi International Institute of Agricultural BiosciencesBeijingChina
| | - Xiangyuan Wan
- Research Institute of Biology and AgricultureUniversity of Science and Technology BeijingBeijingChina
- Industry Research Institute of Biotechnology BreedingYili Normal UniversityYiningChina
- Zhongzhi International Institute of Agricultural BiosciencesBeijingChina
- Beijing Engineering Laboratory of Main Crop Bio‐Tech Breeding, Beijing International Science and Technology Cooperation Base of Bio‐Tech BreedingBeijing Solidwill Sci‐Tech Co. Ltd.BeijingChina
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21
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Morel G, Ernest S, Serey-Gaut M, Jonard L, Balogoun AR, Parodi M, Loundon N, Achard S, Marlin S. RIPOR2: A new gene of non-syndromic cochleovestibular dysfunction, discrepancy between human pathology and animal models. Clin Genet 2023; 104:669-673. [PMID: 37864412 DOI: 10.1111/cge.14436] [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: 07/26/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/22/2023]
Abstract
Cochleovestibular dysfunctions are rare conditions misrecognized. A homozygous pathogenic variation c.1561C > T (p.Arg521*) in RIPOR2 (RHO family interacting cell polarization regulator 2) has been identified by WES in Tunisian siblings suffering from congenital bilateral profound hearing and vestibular dysfunctions. In contrast to the vestibular areflexia observed in our patients, deaf Ripor2 KO mouse model and our zebrafish model have normal vestibular function.
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Affiliation(s)
- Godelieve Morel
- Centre de Référence «Surdités Génétiques», Fédération de Génétique; Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
- Service de Génétique Médicale, CHU Felix Guyon, France
| | - Sylvain Ernest
- Laboratory of Embryology and Genetics of Malformations, Imagine Institute, INSERM UMR 1163, Université de Paris, Paris, France
| | - Margaux Serey-Gaut
- Centre de Référence «Surdités Génétiques», Fédération de Génétique; Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
- Centre de Recherche en Audiologie (CREA), Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Laurence Jonard
- Centre de Référence «Surdités Génétiques», Fédération de Génétique; Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
- Centre de Recherche en Audiologie (CREA), Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Abeke Ralyath Balogoun
- Centre de Référence «Surdités Génétiques», Fédération de Génétique; Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
- Centre de Recherche en Audiologie (CREA), Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Marine Parodi
- Service d'ORL Pédiatrique et de Chirurgie Cervico-Faciale, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Natalie Loundon
- Centre de Référence «Surdités Génétiques», Fédération de Génétique; Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
- Centre de Recherche en Audiologie (CREA), Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
- Service d'ORL Pédiatrique et de Chirurgie Cervico-Faciale, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Sophie Achard
- Centre de Référence «Surdités Génétiques», Fédération de Génétique; Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
- Service d'ORL Pédiatrique et de Chirurgie Cervico-Faciale, Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Sandrine Marlin
- Centre de Référence «Surdités Génétiques», Fédération de Génétique; Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
- Laboratory of Embryology and Genetics of Malformations, Imagine Institute, INSERM UMR 1163, Université de Paris, Paris, France
- Centre de Recherche en Audiologie (CREA), Hôpital Necker-Enfants Malades, Assistance Publique Hôpitaux de Paris, Paris, France
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22
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Zhou L, Yang L, Feng Y, Chen S. Pooled screening with next-generation gene editing tools. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2023; 28:100479. [PMID: 38222973 PMCID: PMC10786633 DOI: 10.1016/j.cobme.2023.100479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
Pooled screening creates a pool of cells with genetic variants, allowing for the simultaneous examination for changes in behavior or function. By selectively inducing mutations or perturbing expression, it enables scientists to systematically investigate the function of genes or genetic elements. Emerging gene editing tools, such as CRISPR, coupled with advances in sequencing and computational capabilities, provide growing opportunities to understand biological processes in humans, animals, and plants as well as to identify potential targets for therapeutic interventions and agricultural research. In this review, we highlight the recent advances of pooled screens using next-generation gene editing tools along with relevant challenges and describe potential future directions of this technology.
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Affiliation(s)
- Liqun Zhou
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Immunobiology Program, Yale University, New Haven, CT, USA
| | - Luojia Yang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA
| | - Yanzhi Feng
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Immunobiology Program, Yale University, New Haven, CT, USA
| | - Sidi Chen
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
- System Biology Institute, Yale University, West Haven, CT, USA
- Center for Cancer Systems Biology, Yale University, West Haven, CT, USA
- Immunobiology Program, Yale University, New Haven, CT, USA
- Molecular Cell Biology, Genetics, and Development Program, Yale University, New Haven, CT, USA
- Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT, USA
- Stem Cell Center, Yale University School of Medicine, New Haven, CT, USA
- Center for Biomedical Data Science, Yale University School of Medicine, New Haven, CT, USA
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23
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Mellis IA, Bodkin N, Melzer ME, Goyal Y. Prevalence of and gene regulatory constraints on transcriptional adaptation in single cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.14.553318. [PMID: 37645989 PMCID: PMC10462021 DOI: 10.1101/2023.08.14.553318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Cells and tissues have a remarkable ability to adapt to genetic perturbations via a variety of molecular mechanisms. Nonsense-induced transcriptional compensation, a form of transcriptional adaptation, has recently emerged as one such mechanism, in which nonsense mutations in a gene can trigger upregulation of related genes, possibly conferring robustness at cellular and organismal levels. However, beyond a handful of developmental contexts and curated sets of genes, to date, no comprehensive genome-wide investigation of this behavior has been undertaken for mammalian cell types and contexts. Moreover, how the regulatory-level effects of inherently stochastic compensatory gene networks contribute to phenotypic penetrance in single cells remains unclear. Here we combine computational analysis of existing datasets with stochastic mathematical modeling and machine learning to uncover the widespread prevalence of transcriptional adaptation in mammalian systems and the diverse single-cell manifestations of minimal compensatory gene networks. Regulon gene expression analysis of a pooled single-cell genetic perturbation dataset recapitulates important model predictions. Our integrative approach uncovers several putative hits-genes demonstrating possible transcriptional adaptation-to follow up on experimentally, and provides a formal quantitative framework to test and refine models of transcriptional adaptation.
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Affiliation(s)
- Ian A. Mellis
- Department of Pathology and Cell Biology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Nicholas Bodkin
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Madeline E. Melzer
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yogesh Goyal
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Center for Synthetic Biology, Northwestern University, Chicago, IL, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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24
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Serres MP, Shaughnessy R, Escot S, Hammich H, Cuvelier F, Salles A, Rocancourt M, Verdon Q, Gaffuri AL, Sourigues Y, Malherbe G, Velikovsky L, Chardon F, Sassoon N, Tinevez JY, Callebaut I, Formstecher E, Houdusse A, David NB, Pylypenko O, Echard A. MiniBAR/GARRE1 is a dual Rac and Rab effector required for ciliogenesis. Dev Cell 2023; 58:2477-2494.e8. [PMID: 37875118 DOI: 10.1016/j.devcel.2023.09.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 07/07/2023] [Accepted: 09/29/2023] [Indexed: 10/26/2023]
Abstract
Cilia protrude from the cell surface and play critical roles in intracellular signaling, environmental sensing, and development. Reduced actin-dependent contractility and intracellular trafficking are both required for ciliogenesis, but little is known about how these processes are coordinated. Here, we identified a Rac1- and Rab35-binding protein with a truncated BAR (Bin/amphiphysin/Rvs) domain that we named MiniBAR (also known as KIAA0355/GARRE1), which plays a key role in ciliogenesis. MiniBAR colocalizes with Rac1 and Rab35 at the plasma membrane and on intracellular vesicles trafficking to the ciliary base and exhibits fast pulses at the ciliary membrane. MiniBAR depletion leads to short cilia, resulting from abnormal Rac-GTP/Rho-GTP levels and increased acto-myosin-II-dependent contractility together with defective trafficking of IFT88 and ARL13B into cilia. MiniBAR-depleted zebrafish embryos display dysfunctional short cilia and hallmarks of ciliopathies, including left-right asymmetry defects. Thus, MiniBAR is a dual Rac and Rab effector that controls both actin cytoskeleton and membrane trafficking for ciliogenesis.
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Affiliation(s)
- Murielle P Serres
- Institut Pasteur, Université de Paris, CNRS UMR3691, Membrane Traffic and Cell Division Laboratory, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Ronan Shaughnessy
- Institut Pasteur, Université de Paris, CNRS UMR3691, Membrane Traffic and Cell Division Laboratory, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Sophie Escot
- Laboratoire d'Optique et Biosciences (LOB), CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Hussein Hammich
- Institut Curie, PSL Research University, CNRS UMR144, Structural Motility, 26 rue d'Ulm, 75005 Paris, France
| | - Frédérique Cuvelier
- Institut Pasteur, Université de Paris, CNRS UMR3691, Membrane Traffic and Cell Division Laboratory, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Audrey Salles
- Institut Pasteur, Université de Paris, UTechS Photonic BioImaging (UTechS PBI), Centre de Recherche et de Ressources Technologiques C2RT, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Murielle Rocancourt
- Institut Pasteur, Université de Paris, CNRS UMR3691, Membrane Traffic and Cell Division Laboratory, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Quentin Verdon
- Institut Pasteur, Université de Paris, CNRS UMR3691, Membrane Traffic and Cell Division Laboratory, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Anne-Lise Gaffuri
- Institut Pasteur, Université de Paris, CNRS UMR3691, Membrane Traffic and Cell Division Laboratory, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Yannick Sourigues
- Institut Curie, PSL Research University, CNRS UMR144, Structural Motility, 26 rue d'Ulm, 75005 Paris, France
| | - Gilles Malherbe
- Institut Curie, PSL Research University, CNRS UMR144, Structural Motility, 26 rue d'Ulm, 75005 Paris, France
| | - Leonid Velikovsky
- Institut Curie, PSL Research University, CNRS UMR144, Structural Motility, 26 rue d'Ulm, 75005 Paris, France
| | - Florian Chardon
- Institut Curie, PSL Research University, CNRS UMR144, Structural Motility, 26 rue d'Ulm, 75005 Paris, France
| | - Nathalie Sassoon
- Institut Pasteur, Université de Paris, CNRS UMR3691, Membrane Traffic and Cell Division Laboratory, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Jean-Yves Tinevez
- Institut Pasteur, Université de Paris, Image Analysis Hub, 25-28 rue du Dr Roux, 75015 Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Etienne Formstecher
- Hybrigenics Services SAS, 1 rue Pierre Fontaine 91000 Evry, Courcouronnes, France
| | - Anne Houdusse
- Institut Curie, PSL Research University, CNRS UMR144, Structural Motility, 26 rue d'Ulm, 75005 Paris, France
| | - Nicolas B David
- Laboratoire d'Optique et Biosciences (LOB), CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91120 Palaiseau, France
| | - Olena Pylypenko
- Institut Curie, PSL Research University, CNRS UMR144, Structural Motility, 26 rue d'Ulm, 75005 Paris, France
| | - Arnaud Echard
- Institut Pasteur, Université de Paris, CNRS UMR3691, Membrane Traffic and Cell Division Laboratory, 25-28 rue du Dr Roux, 75015 Paris, France.
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25
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Belcher B, Vestal J, Lane S, Kell M, Smith L, Camarata T. The zebrafish paralog six2b is required for early proximal pronephros morphogenesis. Sci Rep 2023; 13:19699. [PMID: 37952044 PMCID: PMC10640633 DOI: 10.1038/s41598-023-47046-3] [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: 05/24/2023] [Accepted: 11/08/2023] [Indexed: 11/14/2023] Open
Abstract
The transcription factor Six2 plays a crucial role in maintaining self-renewing nephron progenitor cap mesenchyme (CM) during metanephric kidney development. In mouse and human, expression at single-cell resolution has detected Six2 in cells as they leave the CM pool and differentiate. The role Six2 may play in these cells as they differentiate remains unknown. Here, we took advantage of the zebrafish pronephric kidney which forms directly from intermediate mesoderm to test six2b function during pronephric tubule development and differentiation. Expression of six2b during early zebrafish development was consistent with a role in pronephros formation. Using morpholino knock-down and CRISPR/Cas9 mutagenesis, we show a functional role for six2b in the development of proximal elements of the pronephros. By 48 h post-fertilization, six2b morphants and mutants showed disrupted pronephric tubule morphogenesis. We observed a lower-than-expected frequency of phenotypes in six2b stable genetic mutants suggesting compensation. Supporting this, we detected increased expression of six2a in six2b stable mutant embryos. To further confirm six2b function, F0 crispant embryos were analyzed and displayed similar phenotypes as morphants and stable mutants. Together our data suggests a conserved role for Six2 during nephrogenesis and a role in the morphogenesis of the proximal tubule.
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Affiliation(s)
- Beau Belcher
- Biological Sciences, Arkansas State University, Jonesboro, USA
| | - Justin Vestal
- Biomedical Sciences, NYIT College of Osteopathic Medicine at Arkansas State University, Jonesboro, USA
| | - Samuel Lane
- Biological Sciences, Arkansas State University, Jonesboro, USA
| | - Margaret Kell
- Biomedical Sciences, NYIT College of Osteopathic Medicine at Arkansas State University, Jonesboro, USA
| | - Luke Smith
- Biological Sciences, Arkansas State University, Jonesboro, USA
| | - Troy Camarata
- Biomedical Sciences, NYIT College of Osteopathic Medicine at Arkansas State University, Jonesboro, USA.
- Biomedical Sciences, Baptist University College of Osteopathic Medicine, Baptist Health Sciences University, 1003 Monroe Ave, Memphis, TN, 38104, USA.
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26
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Zou J, Anai S, Ota S, Ishitani S, Oginuma M, Ishitani T. Determining zebrafish dorsal organizer size by a negative feedback loop between canonical/non-canonical Wnts and Tlr4/NFκB. Nat Commun 2023; 14:7194. [PMID: 37938219 PMCID: PMC10632484 DOI: 10.1038/s41467-023-42963-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Accepted: 10/26/2023] [Indexed: 11/09/2023] Open
Abstract
In vertebrate embryos, the canonical Wnt ligand primes the formation of dorsal organizers that govern dorsal-ventral patterns by secreting BMP antagonists. In contrast, in Drosophila embryos, Toll-like receptor (Tlr)-mediated NFκB activation initiates dorsal-ventral patterning, wherein Wnt-mediated negative feedback regulation of Tlr/NFκB generates a BMP antagonist-secreting signalling centre to control the dorsal-ventral pattern. Although both Wnt and BMP antagonist are conserved among species, the involvement of Tlr/NFκB and feedback regulation in vertebrate organizer formation remains unclear. By imaging and genetic modification, we reveal that a negative feedback loop between canonical and non-canonical Wnts and Tlr4/NFκB determines the size of zebrafish organizer, and that Tlr/NFκB and Wnts switch initial cue and feedback mediator roles between Drosophila and zebrafish. Here, we show that canonical Wnt signalling stimulates the expression of the non-canonical Wnt5b ligand, activating the Tlr4 receptor to stimulate NFκB-mediated transcription of the Wnt antagonist frzb, restricting Wnt-dependent dorsal organizer formation.
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Affiliation(s)
- Juqi Zou
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Satoshi Anai
- Yuuai Medical Center, Tomigusuku, Okinawa, 901-0224, Japan
| | - Satoshi Ota
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Komaba 4-6-1, Meguro-ku, Tokyo, 153-8904, Japan
| | - Shizuka Ishitani
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Masayuki Oginuma
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan
| | - Tohru Ishitani
- Department of Homeostatic Regulation, Division of Cellular and Molecular Biology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, 565-0871, Japan.
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, 565-0871, Japan.
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Elizalde MJ, Gorelick DA. Mechanistic toxicology in light of genetic compensation. Toxicol Sci 2023; 197:kfad113. [PMID: 37941503 PMCID: PMC10823772 DOI: 10.1093/toxsci/kfad113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2023] Open
Abstract
Mechanistic toxicology seeks to identify the molecular and cellular mechanisms by which toxicants exert their deleterious effects. One powerful approach is to generate mutations in genes that respond to a particular toxicant, and then test how such mutations change the effects of the toxicant. CRISPR is a rapid and versatile approach to generate mutations in cultured cells and in animal models. Many studies use CRISPR to generate short insertions or deletions in a target gene and then assume that the resulting mutation, such as a premature termination codon, causes a loss of functional protein. However, recent studies demonstrate that this assumption is flawed. Cells can compensate for short insertion and deletion mutations, leading toxicologists to draw erroneous conclusions from mutant studies. In this review, we will discuss mechanisms by which a mutation in one gene may be rescued by compensatory activity. We will discuss how CRISPR insertion and deletion mutations are susceptible to compensation by transcriptional adaptation, alternative splicing, and rescue by maternally derived gene products. We will review evidence that measuring levels of messenger RNA transcribed from a mutated gene is an unreliable indicator of the severity of the mutation. Finally, we provide guidelines for using CRISPR to generate mutations that avoid compensation.
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Affiliation(s)
- Mary Jane Elizalde
- Department of Molecular & Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, United States
| | - Daniel A Gorelick
- Department of Molecular & Cellular Biology, Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, United States
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28
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Agostini V, Tessier A, Djaziri N, Khonsari RH, Galliani E, Kurihara Y, Honda M, Kurihara H, Hidaka K, Tuncbilek G, Picard A, Konas E, Amiel J, Gordon CT. Biallelic truncating variants in VGLL2 cause syngnathia in humans. J Med Genet 2023; 60:1084-1091. [PMID: 37666660 DOI: 10.1136/jmg-2022-109059] [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: 11/16/2022] [Accepted: 04/24/2023] [Indexed: 09/06/2023]
Abstract
BACKGROUND Syngnathia is an ultrarare craniofacial malformation characterised by an inability to open the mouth due to congenital fusion of the upper and lower jaws. The genetic causes of isolated bony syngnathia are unknown. METHODS We used whole exome and Sanger sequencing and microsatellite analysis in six patients (from four families) presenting with syngnathia. We used CRISPR/Cas9 genome editing to generate vgll2a and vgll4l germline mutant zebrafish, and performed craniofacial cartilage analysis in homozygous mutants. RESULTS We identified homozygous truncating variants in vestigial-like family member 2 (VGLL2) in all six patients. Two alleles were identified: one in families of Turkish origin and the other in families of Moroccan origin, suggesting a founder effect for each. A shared haplotype was confirmed for the Turkish patients. The VGLL family of genes encode cofactors of TEAD transcriptional regulators. Vgll2 is regionally expressed in the pharyngeal arches of model vertebrate embryos, and morpholino-based knockdown of vgll2a in zebrafish has been reported to cause defects in development of pharyngeal arch cartilages. However, we did not observe craniofacial anomalies in vgll2a or vgll4l homozygous mutant zebrafish nor in fish with double knockout of vgll2a and vgll4l. In Vgll2 -/- mice, which are known to present a skeletal muscle phenotype, we did not identify defects of the craniofacial skeleton. CONCLUSION Our results suggest that although loss of VGLL2 leads to a striking jaw phenotype in humans, other vertebrates may have the capacity to compensate for its absence during craniofacial development.
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Affiliation(s)
- Valeria Agostini
- Laboratory of embryology and genetics of human malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine and Université Paris Cité, Paris, France
| | - Aude Tessier
- Laboratory of embryology and genetics of human malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine and Université Paris Cité, Paris, France
| | - Nabila Djaziri
- Laboratory of embryology and genetics of human malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine and Université Paris Cité, Paris, France
| | - Roman Hossein Khonsari
- Service de Chirurgie Maxillofaciale et Chirurgie Plastique, Centre de référence Fentes et Malformations Faciales (MAFACE), Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Cité, Paris, France
| | - Eva Galliani
- Service de Chirurgie Maxillofaciale et Chirurgie Plastique, Centre de référence Fentes et Malformations Faciales (MAFACE), Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Cité, Paris, France
| | - Yukiko Kurihara
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masahiko Honda
- Department of Biochemistry, Faculty of Medicine, Kindai University, Osaka-Sayama, Japan
| | - Hiroki Kurihara
- Department of Physiological Chemistry and Metabolism, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kyoko Hidaka
- Department of Bioscience and Genetics, National Cerebral and Cardiovascular Center Research Institute, Suita, Japan
| | | | - Arnaud Picard
- Service de Chirurgie Maxillofaciale et Chirurgie Plastique, Centre de référence Fentes et Malformations Faciales (MAFACE), Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris (AP-HP), Université Paris Cité, Paris, France
| | | | - Jeanne Amiel
- Laboratory of embryology and genetics of human malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine and Université Paris Cité, Paris, France
- Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Christopher T Gordon
- Laboratory of embryology and genetics of human malformations, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR 1163, Institut Imagine and Université Paris Cité, Paris, France
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Smith A, Auer D, Johnson M, Sanchez E, Ross H, Ward C, Chakravarti A, Kapoor A. Cardiac muscle-restricted partial loss of Nos1ap expression has limited but significant impact on electrocardiographic features. G3 (BETHESDA, MD.) 2023; 13:jkad208. [PMID: 37708408 PMCID: PMC10627271 DOI: 10.1093/g3journal/jkad208] [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: 08/16/2023] [Revised: 08/16/2023] [Accepted: 09/06/2023] [Indexed: 09/16/2023]
Abstract
Genome-wide association studies have identified sequence polymorphisms in a functional enhancer of the NOS1AP gene as the most common genetic regulator of QT interval and human cardiac NOS1AP gene expression in the general population. Functional studies based on in vitro overexpression in murine cardiomyocytes and ex vivo knockdown in zebrafish embryonic hearts, by us and others, have also demonstrated that NOS1AP expression levels can alter cellular electrophysiology. Here, to explore the role of NOS1AP in cardiac electrophysiology at an organismal level, we generated and characterized constitutive and heart muscle-restricted Nos1ap knockout mice to assess whether NOS1AP disruption alters the QT interval in vivo. Constitutive loss of Nos1ap led to genetic background-dependent variable lethality at or right before birth. Heart muscle-restricted Nos1ap knockout, generated using cardiac-specific alpha-myosin heavy chain promoter-driven tamoxifen-inducible Cre, resulted in tissue-level Nos1ap expression reduced by half. This partial loss of expression had no detectable effect on the QT interval or other electrocardiographic and echocardiographic parameters, except for a small but significant reduction in the QRS interval. Given that challenges associated with defining the end of the T wave on murine electrocardiogram can limit identification of subtle effects on the QT interval and that common noncoding NOS1AP variants are also associated with the QRS interval, our findings support the role of NOS1AP in regulation of the cardiac electrical cycle.
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Affiliation(s)
- Alexa Smith
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Dallas Auer
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Morgan Johnson
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ernesto Sanchez
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Holly Ross
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Christopher Ward
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Aravinda Chakravarti
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Center for Human Genetics and Genomics, New York University School of Medicine, New York, NY 10016, USA
| | - Ashish Kapoor
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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30
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Child JR, Hofler AC, Chen Q, Yang BH, Kristofich J, Zheng T, Hannigan MM, Elles AL, Reid DW, Nicchitta CV. Examining SRP pathway function in mRNA localization to the endoplasmic reticulum. RNA (NEW YORK, N.Y.) 2023; 29:1703-1724. [PMID: 37643813 PMCID: PMC10578483 DOI: 10.1261/rna.079643.123] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 07/17/2023] [Indexed: 08/31/2023]
Abstract
Signal recognition particle (SRP) pathway function in protein translocation across the endoplasmic reticulum (ER) is well established; its role in RNA localization to the ER remains, however, unclear. In current models, mRNAs undergo translation- and SRP-dependent trafficking to the ER, with ER localization mediated via interactions between SRP-bound translating ribosomes and the ER-resident SRP receptor (SR), a heterodimeric complex comprising SRA, the SRP-binding subunit, and SRB, an integral membrane ER protein. To study SRP pathway function in RNA localization, SR knockout (KO) mammalian cell lines were generated and the consequences of SR KO on steady-state and dynamic mRNA localization examined. CRISPR/Cas9-mediated SRPRB KO resulted in profound destabilization of SRA. Pairing siRNA silencing of SRPRA in SRPRB KO cells yielded viable SR KO cells. Steady-state mRNA compositions and ER-localization patterns in parental and SR KO cells were determined by cell fractionation and deep sequencing. Notably, steady-state cytosol and ER mRNA compositions and partitioning patterns were largely unaltered by loss of SR expression. To examine SRP pathway function in RNA localization dynamics, the subcellular trafficking itineraries of newly exported mRNAs were determined by 4-thiouridine (4SU) pulse-labeling/4SU-seq/cell fractionation. Newly exported mRNAs were distinguished by high ER enrichment, with ER localization being SR-independent. Intriguingly, under conditions of translation initiation inhibition, the ER was the default localization site for all newly exported mRNAs. These data demonstrate that mRNA localization to the ER can be uncoupled from the SRP pathway function and reopen questions regarding the mechanism of RNA localization to the ER.
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Affiliation(s)
- Jessica R Child
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Alex C Hofler
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Qiang Chen
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Brenda H Yang
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - JohnCarlo Kristofich
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Tianli Zheng
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Molly M Hannigan
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Andrew L Elles
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - David W Reid
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
| | - Christopher V Nicchitta
- Department of Cell Biology, Duke University School of Medicine, Durham, North Carolina 27710, USA
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina 27710, USA
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31
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Guna A, Page KR, Replogle JM, Esantsi TK, Wang ML, Weissman JS, Voorhees RM. A dual sgRNA library design to probe genetic modifiers using genome-wide CRISPRi screens. BMC Genomics 2023; 24:651. [PMID: 37904134 PMCID: PMC10614335 DOI: 10.1186/s12864-023-09754-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 10/19/2023] [Indexed: 11/01/2023] Open
Abstract
Mapping genetic interactions is essential for determining gene function and defining novel biological pathways. We report a simple to use CRISPR interference (CRISPRi) based platform, compatible with Fluorescence Activated Cell Sorting (FACS)-based reporter screens, to query epistatic relationships at scale. This is enabled by a flexible dual-sgRNA library design that allows for the simultaneous delivery and selection of a fixed sgRNA and a second randomized guide, comprised of a genome-wide library, with a single transduction. We use this approach to identify epistatic relationships for a defined biological pathway, showing both increased sensitivity and specificity than traditional growth screening approaches.
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Affiliation(s)
- Alina Guna
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave, Pasadena, CA, 91125, USA
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Katharine R Page
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave, Pasadena, CA, 91125, USA
| | - Joseph M Replogle
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA, 94158, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Theodore K Esantsi
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Maxine L Wang
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave, Pasadena, CA, 91125, USA
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, 02142, USA
| | - Rebecca M Voorhees
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave, Pasadena, CA, 91125, USA.
- Howard Hughes Medical Institute Freeman Hrabowski Scholar, California Institute of Technology, Pasadena, CA, 91125, USA.
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32
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Fassad MR, Rumman N, Junger K, Patel MP, Thompson J, Goggin P, Ueffing M, Beyer T, Boldt K, Lucas JS, Mitchison HM. Defective airway intraflagellar transport underlies a combined motile and primary ciliopathy syndrome caused by IFT74 mutations. Hum Mol Genet 2023; 32:3090-3104. [PMID: 37555648 PMCID: PMC10586200 DOI: 10.1093/hmg/ddad132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/01/2023] [Indexed: 08/10/2023] Open
Abstract
Ciliopathies are inherited disorders caused by defective cilia. Mutations affecting motile cilia usually cause the chronic muco-obstructive sinopulmonary disease primary ciliary dyskinesia (PCD) and are associated with laterality defects, while a broad spectrum of early developmental as well as degenerative syndromes arise from mutations affecting signalling of primary (non-motile) cilia. Cilia assembly and functioning requires intraflagellar transport (IFT) of cargos assisted by IFT-B and IFT-A adaptor complexes. Within IFT-B, the N-termini of partner proteins IFT74 and IFT81 govern tubulin transport to build the ciliary microtubular cytoskeleton. We detected a homozygous 3-kb intragenic IFT74 deletion removing the exon 2 initiation codon and 40 N-terminal amino acids in two affected siblings. Both had clinical features of PCD with bronchiectasis, but no laterality defects. They also had retinal dysplasia and abnormal bone growth, with a narrowed thorax and short ribs, shortened long bones and digits, and abnormal skull shape. This resembles short-rib thoracic dysplasia, a skeletal ciliopathy previously linked to IFT defects in primary cilia, not motile cilia. Ciliated nasal epithelial cells collected from affected individuals had reduced numbers of shortened motile cilia with disarranged microtubules, some misorientation of the basal feet, and disrupted cilia structural and IFT protein distributions. No full-length IFT74 was expressed, only truncated forms that were consistent with N-terminal deletion and inframe translation from downstream initiation codons. In affinity purification mass spectrometry, exon 2-deleted IFT74 initiated from the nearest inframe downstream methionine 41 still interacts as part of the IFT-B complex, but only with reduced interaction levels and not with all its usual IFT-B partners. We propose that this is a hypomorphic mutation with some residual protein function retained, which gives rise to a primary skeletal ciliopathy combined with defective motile cilia and PCD.
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Affiliation(s)
- Mahmoud R Fassad
- Genetics and Genomic Medicine Research and Teaching Department, University College London, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, United Kingdom
- Department of Human Genetics, Medical Research Institute, Alexandria University, 22 El-Guish Road, El-Shatby, Alexandria 21526, Egypt
| | - Nisreen Rumman
- Department of Pediatrics, Faculty of Medicine, Makassed Hospital and Al-Quds University, East Jerusalem 91220, Palestine
- Section of Pulmonary, Critical Care and Sleep Medicine, Department of Internal Medicine, Yale University School of Medicine, 300 Cedar St #441, New Haven, CT 06520, United States
| | - Katrin Junger
- Institute for Ophthalmic Research, Eberhard Karl University of Tübingen, Elfreide-Alhorn-Strasse 5-7, Tübingen 72076, Germany
| | - Mitali P Patel
- Genetics and Genomic Medicine Research and Teaching Department, University College London, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, United Kingdom
- MRC Prion Unit at UCL, Institute of Prion Diseases, University College London, 33 Cleveland Street, London W1W 7FF, United Kingdom
| | - James Thompson
- Primary Ciliary Dyskinesia Centre, NIHR Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, United Kingdom
- School of Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, University Road, Southampton SO17 1BJ, United Kingdom
- Biomedical Imaging Unit, University of Southampton Faculty of Medicine, University Road, Southampton SO17 1BJ, United Kingdom
| | - Patricia Goggin
- Primary Ciliary Dyskinesia Centre, NIHR Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, United Kingdom
- Biomedical Imaging Unit, University of Southampton Faculty of Medicine, University Road, Southampton SO17 1BJ, United Kingdom
| | - Marius Ueffing
- Institute for Ophthalmic Research, Eberhard Karl University of Tübingen, Elfreide-Alhorn-Strasse 5-7, Tübingen 72076, Germany
| | - Tina Beyer
- Institute for Ophthalmic Research, Eberhard Karl University of Tübingen, Elfreide-Alhorn-Strasse 5-7, Tübingen 72076, Germany
| | - Karsten Boldt
- Institute for Ophthalmic Research, Eberhard Karl University of Tübingen, Elfreide-Alhorn-Strasse 5-7, Tübingen 72076, Germany
| | - Jane S Lucas
- Primary Ciliary Dyskinesia Centre, NIHR Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, United Kingdom
- School of Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, University Road, Southampton SO17 1BJ, United Kingdom
| | - Hannah M Mitchison
- Genetics and Genomic Medicine Research and Teaching Department, University College London, UCL Great Ormond Street Institute of Child Health, 30 Guilford Street, London WC1N 1EH, United Kingdom
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33
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Lo HY, Long DR, Holmes EA, Penewit K, Hodgson T, Lewis JD, Waalkes A, Salipante SJ. Transposon sequencing identifies genes impacting Staphylococcus aureus invasion in a human macrophage model. Infect Immun 2023; 91:e0022823. [PMID: 37676013 PMCID: PMC10580828 DOI: 10.1128/iai.00228-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 07/13/2023] [Indexed: 09/08/2023] Open
Abstract
Staphylococcus aureus is a facultative intracellular pathogen in many host cell types, facilitating its persistence in chronic infections. The genes contributing to intracellular pathogenesis have not yet been fully enumerated. Here, we cataloged genes influencing S. aureus invasion and survival within human THP-1 derived macrophages using two laboratory strains (ATCC2913 and JE2). We developed an in vitro transposition method to produce highly saturated transposon mutant libraries in S. aureus and performed transposon insertion sequencing (Tn-Seq) to identify candidate genes with significantly altered abundance following macrophage invasion. While some significant genes were strain-specific, 108 were identified as common across both S. aureus strains, with most (n = 106) being required for optimal macrophage infection. We used CRISPR interference (CRISPRi) to functionally validate phenotypic contributions for a subset of genes. Of the 20 genes passing validation, seven had previously identified roles in S. aureus virulence, and 13 were newly implicated. Validated genes frequently evidenced strain-specific effects, yielding opposing phenotypes when knocked down in the alternative strain. Genomic analysis of de novo mutations occurring in groups (n = 237) of clonally related S. aureus isolates from the airways of chronically infected individuals with cystic fibrosis (CF) revealed significantly greater in vivo purifying selection in conditionally essential candidate genes than those not associated with macrophage invasion. This study implicates a core set of genes necessary to support macrophage invasion by S. aureus, highlights strain-specific differences in phenotypic effects of effector genes, and provides evidence for selection of candidate genes identified by Tn-Seq analyses during chronic airway infection in CF patients in vivo.
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Affiliation(s)
- Hsin-Yu Lo
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Dustin R. Long
- Division of Critical Care Medicine, Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, Washington, USA
| | - Elizbeth A. Holmes
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Kelsi Penewit
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Taylor Hodgson
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Janessa D. Lewis
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Adam Waalkes
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
| | - Stephen J. Salipante
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, USA
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34
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Wang R, Yang D, Tu C, Lei C, Ding S, Guo T, Wang L, Liu Y, Lu C, Yang B, Ouyang S, Gong K, Tan Z, Deng Y, Tan Y, Qing J, Luo H. Dynein axonemal heavy chain 10 deficiency causes primary ciliary dyskinesia in humans and mice. Front Med 2023; 17:957-971. [PMID: 37314648 DOI: 10.1007/s11684-023-0988-8] [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: 11/15/2022] [Accepted: 01/31/2023] [Indexed: 06/15/2023]
Abstract
Primary ciliary dyskinesia (PCD) is a congenital, motile ciliopathy with pleiotropic symptoms. Although nearly 50 causative genes have been identified, they only account for approximately 70% of definitive PCD cases. Dynein axonemal heavy chain 10 (DNAH10) encodes a subunit of the inner arm dynein heavy chain in motile cilia and sperm flagella. Based on the common axoneme structure of motile cilia and sperm flagella, DNAH10 variants are likely to cause PCD. Using exome sequencing, we identified a novel DNAH10 homozygous variant (c.589C > T, p.R197W) in a patient with PCD from a consanguineous family. The patient manifested sinusitis, bronchiectasis, situs inversus, and asthenoteratozoospermia. Immunostaining analysis showed the absence of DNAH10 and DNALI1 in the respiratory cilia, and transmission electron microscopy revealed strikingly disordered axoneme 9+2 architecture and inner dynein arm defects in the respiratory cilia and sperm flagella. Subsequently, animal models of Dnah10-knockin mice harboring missense variants and Dnah10-knockout mice recapitulated the phenotypes of PCD, including chronic respiratory infection, male infertility, and hydrocephalus. To the best of our knowledge, this study is the first to report DNAH10 deficiency related to PCD in human and mouse models, which suggests that DNAH10 recessive mutation is causative of PCD.
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Affiliation(s)
- Rongchun Wang
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital of Central South University, Changsha, 410011, China
- Research Unit of Respiratory Disease, Central South University, Changsha, 410011, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, 410011, China
| | - Danhui Yang
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital of Central South University, Changsha, 410011, China
- Research Unit of Respiratory Disease, Central South University, Changsha, 410011, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, 410011, China
| | - Chaofeng Tu
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, 410078, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410078, China
| | - Cheng Lei
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital of Central South University, Changsha, 410011, China
- Research Unit of Respiratory Disease, Central South University, Changsha, 410011, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, 410011, China
| | - Shuizi Ding
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital of Central South University, Changsha, 410011, China
- Research Unit of Respiratory Disease, Central South University, Changsha, 410011, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, 410011, China
| | - Ting Guo
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital of Central South University, Changsha, 410011, China
- Research Unit of Respiratory Disease, Central South University, Changsha, 410011, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, 410011, China
| | - Lin Wang
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital of Central South University, Changsha, 410011, China
- Research Unit of Respiratory Disease, Central South University, Changsha, 410011, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, 410011, China
| | - Ying Liu
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital of Central South University, Changsha, 410011, China
- Research Unit of Respiratory Disease, Central South University, Changsha, 410011, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, 410011, China
| | - Chenyang Lu
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital of Central South University, Changsha, 410011, China
- Research Unit of Respiratory Disease, Central South University, Changsha, 410011, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, 410011, China
| | - Binyi Yang
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital of Central South University, Changsha, 410011, China
- Research Unit of Respiratory Disease, Central South University, Changsha, 410011, China
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, 410011, China
| | - Shi Ouyang
- Zebrafish Genetics Laboratory, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Ke Gong
- Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Central South University, Changsha, 410011, China
| | - Zhiping Tan
- Clinical Center for Gene Diagnosis and Therapy, Department of Cardiovascular Surgery, The Second Xiangya Hospital of Central South University, Changsha, 410011, China
| | - Yun Deng
- Zebrafish Genetics Laboratory, College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yueqiu Tan
- Institute of Reproductive and Stem Cell Engineering, NHC Key Laboratory of Human Stem Cell and Reproductive Engineering, School of Basic Medical Science, Central South University, Changsha, 410078, China
- Clinical Research Center for Reproduction and Genetics in Hunan Province, Reproductive and Genetic Hospital of CITIC-Xiangya, Changsha, 410078, China
| | - Jie Qing
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital of Central South University, Changsha, 410011, China.
- Research Unit of Respiratory Disease, Central South University, Changsha, 410011, China.
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, 410011, China.
| | - Hong Luo
- Department of Pulmonary and Critical Care Medicine, The Second Xiangya Hospital of Central South University, Changsha, 410011, China.
- Research Unit of Respiratory Disease, Central South University, Changsha, 410011, China.
- Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, 410011, China.
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35
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Kashio S, Masuda S, Miura M. Involvement of neuronal tachykinin-like receptor at 86C in Drosophila disc repair via regulation of kynurenine metabolism. iScience 2023; 26:107553. [PMID: 37636053 PMCID: PMC10457576 DOI: 10.1016/j.isci.2023.107553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 05/15/2023] [Accepted: 08/03/2023] [Indexed: 08/29/2023] Open
Abstract
Neurons contribute to the regeneration of projected tissues; however, it remains unclear whether they are involved in the non-innervated tissue regeneration. Herein, we showed that a neuronal tachykinin-like receptor at 86C (TkR86C) is required for the repair of non-innervated wing discs in Drosophila. Using a genetic tissue repair system in Drosophila larvae, we performed genetic screening for G protein-coupled receptors to search for signal mediatory systems for remote tissue repair. An evolutionarily conserved neuroinflammatory receptor, TkR86C, was identified as the candidate receptor. Neuron-specific knockdown of TkR86C impaired disc repair without affecting normal development. We investigated the humoral metabolites of the kynurenine (Kyn) pathway regulated in the fat body because of their role as tissue repair-mediating factors. Neuronal knockdown of TkR86C hampered injury-dependent changes in the expression of vermillion in the fat body and humoral Kyn metabolites. Our data indicate the involvement of TkR86C neurons upstream of Kyn metabolism in non-autonomous tissue regeneration.
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Affiliation(s)
- Soshiro Kashio
- Department of Genetics, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shu Masuda
- Department of Genetics, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Masayuki Miura
- Department of Genetics, Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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36
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Qin M, Yu-Wai-Man C. Glaucoma: Novel antifibrotic therapeutics for the trabecular meshwork. Eur J Pharmacol 2023; 954:175882. [PMID: 37391006 PMCID: PMC10804937 DOI: 10.1016/j.ejphar.2023.175882] [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: 04/03/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/02/2023]
Abstract
Glaucoma is a chronic and progressive neurodegenerative disease characterized by the loss of retinal ganglion cells and visual field defects, and currently affects around 1% of the world's population. Elevated intraocular pressure (IOP) is the best-known modifiable risk factor and a key therapeutic target in hypertensive glaucoma. The trabecular meshwork (TM) is the main site of aqueous humor outflow resistance and therefore a critical regulator of IOP. Fibrosis, a reparative process characterized by the excessive deposition of extracellular matrix components and contractile myofibroblasts, can impair TM function and contribute to the pathogenesis of primary open-angle glaucoma (POAG) as well as the failure of minimally invasive glaucoma surgery (MIGS) devices. This paper provides a detailed overview of the current anti-fibrotic therapeutics targeting the TM in glaucoma, along with their anti-fibrotic mechanisms, efficacy as well as the current research progress from pre-clinical to clinical studies.
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Affiliation(s)
- Mengqi Qin
- King's College London, London, SE1 7EH, UK
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37
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Balmas E, Sozza F, Bottini S, Ratto ML, Savorè G, Becca S, Snijders KE, Bertero A. Manipulating and studying gene function in human pluripotent stem cell models. FEBS Lett 2023; 597:2250-2287. [PMID: 37519013 DOI: 10.1002/1873-3468.14709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/04/2023] [Accepted: 07/05/2023] [Indexed: 08/01/2023]
Abstract
Human pluripotent stem cells (hPSCs) are uniquely suited to study human development and disease and promise to revolutionize regenerative medicine. These applications rely on robust methods to manipulate gene function in hPSC models. This comprehensive review aims to both empower scientists approaching the field and update experienced stem cell biologists. We begin by highlighting challenges with manipulating gene expression in hPSCs and their differentiated derivatives, and relevant solutions (transfection, transduction, transposition, and genomic safe harbor editing). We then outline how to perform robust constitutive or inducible loss-, gain-, and change-of-function experiments in hPSCs models, both using historical methods (RNA interference, transgenesis, and homologous recombination) and modern programmable nucleases (particularly CRISPR/Cas9 and its derivatives, i.e., CRISPR interference, activation, base editing, and prime editing). We further describe extension of these approaches for arrayed or pooled functional studies, including emerging single-cell genomic methods, and the related design and analytical bioinformatic tools. Finally, we suggest some directions for future advancements in all of these areas. Mastering the combination of these transformative technologies will empower unprecedented advances in human biology and medicine.
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Affiliation(s)
- Elisa Balmas
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Federica Sozza
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Sveva Bottini
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Maria Luisa Ratto
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Giulia Savorè
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Silvia Becca
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Kirsten Esmee Snijders
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
| | - Alessandro Bertero
- Department of Molecular Biotechnology and Health Sciences, Molecular Biotechnology Center "Guido Tarone", University of Turin, Torino, Italy
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38
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Pathway to Independence - an interview with Thomas Juan. Development 2023; 150:dev202257. [PMID: 37650567 DOI: 10.1242/dev.202257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Thomas Juan, one of Development's Pathway to Independence Fellows, is a Postdoctoral Researcher in Didier Stainier's lab at the Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany. We caught up with Thomas over a video call to talk about his background, his research into mechanosensation and cardiovascular development in zebrafish and his plans to become an independent group leader.
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39
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Miguel Sanz C, Martinez Navarro M, Caballero Diaz D, Sanchez-Elexpuru G, Di Donato V. Toward the use of novel alternative methods in epilepsy modeling and drug discovery. Front Neurol 2023; 14:1213969. [PMID: 37719765 PMCID: PMC10501616 DOI: 10.3389/fneur.2023.1213969] [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: 05/04/2023] [Accepted: 08/14/2023] [Indexed: 09/19/2023] Open
Abstract
Epilepsy is a chronic brain disease and, considering the amount of people affected of all ages worldwide, one of the most common neurological disorders. Over 20 novel antiseizure medications (ASMs) have been released since 1993, yet despite substantial advancements in our understanding of the molecular mechanisms behind epileptogenesis, over one-third of patients continue to be resistant to available therapies. This is partially explained by the fact that the majority of existing medicines only address seizure suppression rather than underlying processes. Understanding the origin of this neurological illness requires conducting human neurological and genetic studies. However, the limitation of sample sizes, ethical concerns, and the requirement for appropriate controls (many patients have already had anti-epileptic medication exposure) in human clinical trials underscore the requirement for supplemental models. So far, mammalian models of epilepsy have helped to shed light on the underlying causes of the condition, but the high costs related to breeding of the animals, low throughput, and regulatory restrictions on their research limit their usefulness in drug screening. Here, we present an overview of the state of art in epilepsy modeling describing gold standard animal models used up to date and review the possible alternatives for this research field. Our focus will be mainly on ex vivo, in vitro, and in vivo larval zebrafish models contributing to the 3R in epilepsy modeling and drug screening. We provide a description of pharmacological and genetic methods currently available but also on the possibilities offered by the continued development in gene editing methodologies, especially CRISPR/Cas9-based, for high-throughput disease modeling and anti-epileptic drugs testing.
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40
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Maili L, Tandon B, Yuan Q, Menezes S, Chiu F, Hashmi SS, Letra A, Eisenhoffer GT, Hecht JT. Disruption of fos causes craniofacial anomalies in developing zebrafish. Front Cell Dev Biol 2023; 11:1141893. [PMID: 37664458 PMCID: PMC10469461 DOI: 10.3389/fcell.2023.1141893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 06/21/2023] [Indexed: 09/05/2023] Open
Abstract
Craniofacial development is a complex and tightly regulated process and disruptions can lead to structural birth defects, the most common being nonsyndromic cleft lip and palate (NSCLP). Previously, we identified FOS as a candidate regulator of NSCLP through family-based association studies, yet its specific contributions to oral and palatal formation are poorly understood. This study investigated the role of fos during zebrafish craniofacial development through genetic disruption and knockdown approaches. Fos was expressed in the periderm, olfactory epithelium and other cell populations in the head. Genetic perturbation of fos produced an abnormal craniofacial phenotype with a hypoplastic oral cavity that showed significant changes in midface dimensions by quantitative facial morphometric analysis. Loss and knockdown of fos caused increased cell apoptosis in the head, followed by a significant reduction in cranial neural crest cells (CNCCs) populating the upper and lower jaws. These changes resulted in abnormalities of cartilage, bone and pharyngeal teeth formation. Periderm cells surrounding the oral cavity showed altered morphology and a subset of cells in the upper and lower lip showed disrupted Wnt/β-catenin activation, consistent with modified inductive interactions between mesenchymal and epithelial cells. Taken together, these findings demonstrate that perturbation of fos has detrimental effects on oral epithelial and CNCC-derived tissues suggesting that it plays a critical role in zebrafish craniofacial development and a potential role in NSCLP.
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Affiliation(s)
- Lorena Maili
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, TX, United States
- Genetics and Epigenetics Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, United States
| | - Bhavna Tandon
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Qiuping Yuan
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Simone Menezes
- Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, TX, United States
| | - Frankie Chiu
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, TX, United States
| | - S. Shahrukh Hashmi
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, TX, United States
| | - Ariadne Letra
- Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, TX, United States
- Department of Diagnostic and Biomedical Sciences, University of Texas Health Science Center School of Dentistry at Houston, Houston, TX, United States
| | - George T. Eisenhoffer
- Genetics and Epigenetics Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, United States
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Jacqueline T. Hecht
- Department of Pediatrics, McGovern Medical School at the University of Texas Health Science Center at Houston, Houston, TX, United States
- Genetics and Epigenetics Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX, United States
- Center for Craniofacial Research, University of Texas Health Science Center School of Dentistry at Houston, Houston, TX, United States
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Guna A, Page KR, Replogle JM, Esantsi TK, Wang ML, Weissman JS, Voorhees RM. A dual sgRNA library design to probe genetic modifiers using genome-wide CRISPRi screens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.22.525086. [PMID: 36711738 PMCID: PMC9882262 DOI: 10.1101/2023.01.22.525086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Mapping genetic interactions is essential for determining gene function and defining novel biological pathways. We report a simple to use CRISPR interference (CRISPRi) based platform, compatible with Fluorescence Activated Cell Sorting (FACS)-based reporter screens, to query epistatic relationships at scale. This is enabled by a flexible dual-sgRNA library design that allows for the simultaneous delivery and selection of a fixed sgRNA and a second randomized guide, comprised of a genome-wide library, with a single transduction. We use this approach to identify epistatic relationships for a defined biological pathway, showing both increased sensitivity and specificity than traditional growth screening approaches.
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Affiliation(s)
- Alina Guna
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave., Pasadena, CA 91125, USA
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Katharine R Page
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave., Pasadena, CA 91125, USA
| | - Joseph M Replogle
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Medical Scientist Training Program, University of California, San Francisco, San Francisco, CA 94158, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Theodore K Esantsi
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Maxine L Wang
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave., Pasadena, CA 91125, USA
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Jonathan S Weissman
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA,02142, USA
| | - Rebecca M Voorhees
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Ave., Pasadena, CA 91125, USA
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42
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Jiang R, Zhou S, Da X, Yan P, Wang K, Xu J, Mo X. OsMKK6 Regulates Disease Resistance in Rice. Int J Mol Sci 2023; 24:12678. [PMID: 37628859 PMCID: PMC10454111 DOI: 10.3390/ijms241612678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/02/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Mitogen-activated protein kinase cascades play important roles in various biological programs in plants, including immune responses, but the underlying mechanisms remain elusive. Here, we identified the lesion mimic mutant rsr25 (rust spots rice 25) and determined that the mutant harbored a loss-of-function allele for OsMKK6 (MITOGEN-ACTIVATED KINASE KINASE 6). rsr25 developed reddish-brown spots on its leaves at the heading stage, as well as on husks. Compared to the wild type, the rsr25 mutant exhibited enhanced resistance to the fungal pathogen Magnaporthe oryzae (M. oryzae) and to the bacterial pathogen Xanthomonas oryzae pv. oryzae (Xoo). OsMKK6 interacted with OsMPK4 (MITOGEN-ACTIVATED KINASE 4) in vivo, and OsMKK6 phosphorylated OsMPK4 in vitro. The Osmpk4 mutant is also a lesion mimic mutant, with reddish-brown spots on its leaves and husks. Pathogen-related genes were significantly upregulated in Osmpk4, and this mutant exhibited enhanced resistance to M. oryzae compared to the wild type. Our results indicate that OsMKK6 and OsMPK4 form a cascade that regulates immune responses in rice.
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Affiliation(s)
| | | | | | | | | | | | - Xiaorong Mo
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou 310058, China; (R.J.); (S.Z.); (X.D.); (P.Y.); (K.W.); (J.X.)
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43
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Cigliola V, Shoffner A, Lee N, Ou J, Gonzalez TJ, Hoque J, Becker CJ, Han Y, Shen G, Faw TD, Abd-El-Barr MM, Varghese S, Asokan A, Poss KD. Spinal cord repair is modulated by the neurogenic factor Hb-egf under direction of a regeneration-associated enhancer. Nat Commun 2023; 14:4857. [PMID: 37567873 PMCID: PMC10421883 DOI: 10.1038/s41467-023-40486-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Unlike adult mammals, zebrafish regenerate spinal cord tissue and recover locomotor ability after a paralyzing injury. Here, we find that ependymal cells in zebrafish spinal cords produce the neurogenic factor Hb-egfa upon transection injury. Animals with hb-egfa mutations display defective swim capacity, axon crossing, and tissue bridging after spinal cord transection, associated with disrupted indicators of neuron production. Local recombinant human HB-EGF delivery alters ependymal cell cycling and tissue bridging, enhancing functional regeneration. Epigenetic profiling reveals a tissue regeneration enhancer element (TREE) linked to hb-egfa that directs gene expression in spinal cord injuries. Systemically delivered recombinant AAVs containing this zebrafish TREE target gene expression to crush injuries of neonatal, but not adult, murine spinal cords. Moreover, enhancer-based HB-EGF delivery by AAV administration improves axon densities after crush injury in neonatal cords. Our results identify Hb-egf as a neurogenic factor necessary for innate spinal cord regeneration and suggest strategies to improve spinal cord repair in mammals.
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Affiliation(s)
- Valentina Cigliola
- Duke Regeneration Center, Duke University, Durham, NC, USA
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
- Université Côte d'Azur, Inserm, CNRS, Institut de Biologie Valrose, Nice, France
| | - Adam Shoffner
- Duke Regeneration Center, Duke University, Durham, NC, USA
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
| | - Nutishia Lee
- Duke Regeneration Center, Duke University, Durham, NC, USA
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Jianhong Ou
- Duke Regeneration Center, Duke University, Durham, NC, USA
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Trevor J Gonzalez
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
| | - Jiaul Hoque
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Clayton J Becker
- Duke Regeneration Center, Duke University, Durham, NC, USA
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Yanchao Han
- Department of Cardiovascular Surgery of the First Affiliated Hospital and Institute for Cardiovascular Science, Soochow University, Suzhou, Jiangsu, China
| | - Grace Shen
- Duke Regeneration Center, Duke University, Durham, NC, USA
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA
| | - Timothy D Faw
- Duke Regeneration Center, Duke University, Durham, NC, USA
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
- Duke Institute for Brain Sciences, Duke University, Durham, NC, USA
| | | | - Shyni Varghese
- Department of Orthopedic Surgery, Duke University School of Medicine, Durham, NC, USA
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Aravind Asokan
- Duke Regeneration Center, Duke University, Durham, NC, USA
- Department of Surgery, Duke University Medical Center, Durham, NC, USA
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Kenneth D Poss
- Duke Regeneration Center, Duke University, Durham, NC, USA.
- Department of Cell Biology, Duke University Medical Center, Durham, NC, USA.
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Giardoglou P, Deloukas P, Dedoussis G, Beis D. Cfdp1 Is Essential for Cardiac Development and Function. Cells 2023; 12:1994. [PMID: 37566073 PMCID: PMC10417793 DOI: 10.3390/cells12151994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/25/2023] [Accepted: 08/01/2023] [Indexed: 08/12/2023] Open
Abstract
Cardiovascular diseases (CVDs) are the prevalent cause of mortality worldwide. A combination of environmental and genetic effectors modulates the risk of developing them. Thus, it is vital to identify candidate genes and elucidate their role in the manifestation of the disease. Large-scale human studies have revealed the implication of Craniofacial Development Protein 1 (CFDP1) in Coronary Artery Disease (CAD). CFDP1 belongs to the evolutionary conserved Bucentaur (BCNT) family, and to date, its function and mechanism of action in Cardiovascular Development are still unclear. We utilized zebrafish to investigate the role of cfdp1 in the developing heart due to the high genomic homology, similarity in heart physiology, and ease of experimental manipulations. We showed that cfdp1 was expressed during development, and we tested two morpholinos and generated a cfdp1 mutant line. The cfdp1-/- embryos developed arrhythmic hearts and exhibited defective cardiac performance, which led to a lethal phenotype. Findings from both knockdown and knockout experiments showed that abrogation of cfdp1 leads to downregulation of Wnt signaling in embryonic hearts during valve development but without affecting Notch activation in this process. The cfdp1 zebrafish mutant line provides a valuable tool for unveiling the novel mechanism of regulating cardiac physiology and function. cfdp1 is essential for cardiac development, a previously unreported phenotype most likely due to early lethality in mice. The detected phenotype of bradycardia and arrhythmias is an observation with potential clinical relevance for humans carrying heterozygous CFDP1 mutations and their risk of developing CAD.
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Affiliation(s)
- Panagiota Giardoglou
- Zebrafish Disease Model Laboratory, Center for Clinical, Experimental Surgery & Translational Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece;
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, 17676 Athens, Greece;
| | - Panos Deloukas
- Clinical Pharmacology, William Harvey Research Institute, Barts and The London Medical School, Queen Mary University of London, London E1 4NS, UK;
| | - George Dedoussis
- Department of Nutrition and Dietetics, School of Health Science and Education, Harokopio University of Athens, 17676 Athens, Greece;
| | - Dimitris Beis
- Zebrafish Disease Model Laboratory, Center for Clinical, Experimental Surgery & Translational Research, Biomedical Research Foundation, Academy of Athens, 11527 Athens, Greece;
- Laboratory of Biological Chemistry, Faculty of Medicine, School of Health Sciences, University of Ioannina, 45110 Ioannina, Greece
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45
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Zheng H, Huang W, Li X, Huang H, Yuan Q, Liu R, Di H, Liang S, Wang M, Li M, Huang Z, Tang Y, Zheng Y, Miao H, Ma J, Li H, Wang Q, Sun B, Zhang F. CRISPR/Cas9-mediated BoaAOP2s editing alters aliphatic glucosinolate side-chain metabolic flux and increases the glucoraphanin content in Chinese kale. Food Res Int 2023; 170:112995. [PMID: 37316021 DOI: 10.1016/j.foodres.2023.112995] [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: 01/16/2023] [Revised: 05/14/2023] [Accepted: 05/16/2023] [Indexed: 06/16/2023]
Abstract
Glucoraphanin (GRA) is an aliphatic glucosinolate (GSL), and its hydrolysis product has powerful anticancer activity. ALKENYL HYDROXALKYL PRODUCING 2 (AOP2) gene, encodes a 2-oxoglutarate-dependent dioxygenase, which can catalyze GRA to form gluconapin (GNA). However, GRA only present in trace amounts in Chinese kale. To increase the content of GRA in Chinese kale, three copies of BoaAOP2 were isolated and edited using CRISPR/Cas9 system. The content of GRA was 11.71- to 41.29-fold (0.082-0.289 μmol g-1 FW) higher in T1 generation of boaaop2 mutants than in wild-type plants, and this was accompanied by an increase in the GRA/GNA ratio and reductions in the content of GNA and total aliphatic GSLs. BoaAOP2.1 is an effective gene for the alkenylation of aliphatic GSLs in Chinese kale. Overall, targeted editing of CRISPR/Cas9-mediated BoaAOP2s altered aliphatic GSL side-chain metabolic flux and enhanced the GRA content in Chinese kale, suggesting that metabolic engineering of BoaAOP2s has huge potential in improving nutritional quality of Chinese kale.
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Affiliation(s)
- Hao Zheng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Wenli Huang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiangxiang Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Huanhuan Huang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiao Yuan
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Ruobin Liu
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Hongmei Di
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Sha Liang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Mengyu Wang
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Mengyao Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhi Huang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yi Tang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Yangxia Zheng
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Huiying Miao
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Jie Ma
- Bijie Institute of Agricultural Science, Bijie 551700, China
| | - Huanxiu Li
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China
| | - Qiaomei Wang
- Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture, Department of Horticulture, Zhejiang University, Hangzhou 310058, China
| | - Bo Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China.
| | - Fen Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu 611130, China.
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46
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Sun YH, Wu YL, Liao BY. Phenotypic heterogeneity in human genetic diseases: ultrasensitivity-mediated threshold effects as a unifying molecular mechanism. J Biomed Sci 2023; 30:58. [PMID: 37525275 PMCID: PMC10388531 DOI: 10.1186/s12929-023-00959-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Accepted: 07/26/2023] [Indexed: 08/02/2023] Open
Abstract
Phenotypic heterogeneity is very common in genetic systems and in human diseases and has important consequences for disease diagnosis and treatment. In addition to the many genetic and non-genetic (e.g., epigenetic, environmental) factors reported to account for part of the heterogeneity, we stress the importance of stochastic fluctuation and regulatory network topology in contributing to phenotypic heterogeneity. We argue that a threshold effect is a unifying principle to explain the phenomenon; that ultrasensitivity is the molecular mechanism for this threshold effect; and discuss the three conditions for phenotypic heterogeneity to occur. We suggest that threshold effects occur not only at the cellular level, but also at the organ level. We stress the importance of context-dependence and its relationship to pleiotropy and edgetic mutations. Based on this model, we provide practical strategies to study human genetic diseases. By understanding the network mechanism for ultrasensitivity and identifying the critical factor, we may manipulate the weak spot to gently nudge the system from an ultrasensitive state to a stable non-disease state. Our analysis provides a new insight into the prevention and treatment of genetic diseases.
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Affiliation(s)
- Y Henry Sun
- Institute of Molecular and Genomic Medicine, National Health Research Institute, Zhunan, Miaoli, Taiwan.
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.
| | - Yueh-Lin Wu
- Institute of Molecular and Genomic Medicine, National Health Research Institute, Zhunan, Miaoli, Taiwan
- Division of Nephrology, Department of Internal Medicine, Wei-Gong Memorial Hospital, Miaoli, Taiwan
- Division of Nephrology, Department of Internal Medicine, Taipei Medical University Hospital, Taipei, Taiwan
- TMU Research Center of Urology and Kidney, Taipei Medical University, Taipei, Taiwan
- Division of Nephrology, Department of Internal Medicine, Wan Fang Hospital, Taipei Medical University, Taipei City, Taiwan
| | - Ben-Yang Liao
- Institute of Population Health Sciences, National Health Research Institute, Zhunan, Miaoli, Taiwan
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47
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Landi E, Karabatas L, Rodríguez Gomez T, Salatino L, Scaglia P, Ramírez L, Keselman A, Braslavsky D, Sanguineti N, Pennisi P, Rey RA, Bergadá I, Jasper HG, Domené HM, Plazas PV, Domené S. An in vivo functional assay to characterize human STAT5B genetic variants during zebrafish development. Hum Mol Genet 2023; 32:2473-2484. [PMID: 37162340 DOI: 10.1093/hmg/ddad078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/19/2023] [Accepted: 05/07/2023] [Indexed: 05/11/2023] Open
Abstract
Growth hormone (GH) binding to GH receptor activates janus kinase 2 (JAK2)-signal transducer and activator of transcription 5b (STAT5b) pathway, which stimulates transcription of insulin-like growth factor-1 (IGF1), insulin-like growth factor binding protein 3 (IGFBP3) and insulin-like growth factor acid-labile subunit (IGFALS). Although STAT5B deficiency was established as an autosomal recessive disorder, heterozygous dominant-negative STAT5B variants have been reported in patients with less severe growth deficit and milder immune dysfunction. We developed an in vivo functional assay in zebrafish to characterize the pathogenicity of three human STAT5B variants (p.Ala630Pro, p.Gln474Arg and p.Lys632Asn). Overexpression of human wild-type (WT) STAT5B mRNA and its variants led to a significant reduction of body length together with developmental malformations in zebrafish embryos. Overexpression of p.Ala630Pro, p.Gln474Arg or p.Lys632Asn led to an increased number of embryos with pericardial edema, cyclopia and bent spine compared with WT STAT5B. Although co-injection of WT and p.Gln474Arg and WT and p.Lys632Asn STAT5B mRNA in zebrafish embryos partially or fully rescues the length and the developmental malformations in zebrafish embryos, co-injection of WT and p.Ala630Pro STAT5B mRNA leads to a greater number of embryos with developmental malformations and a reduction in body length of these embryos. These results suggest that these variants could interfere with endogenous stat5.1 signaling through different mechanisms. In situ hybridization of zebrafish embryos overexpressing p.Gln474Arg and p.Lys632Asn STAT5B mRNA shows a reduction in igf1 expression. In conclusion, our study reveals the pathogenicity of the STAT5B variants studied.
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Affiliation(s)
- Estefanía Landi
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET-FEI-División de Endocrinología, Hospital de Niños Ricardo Gutiérrez Buenos Aires C1425EFD, Argentina
| | - Liliana Karabatas
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET-FEI-División de Endocrinología, Hospital de Niños Ricardo Gutiérrez Buenos Aires C1425EFD, Argentina
| | - Tomás Rodríguez Gomez
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET-FEI-División de Endocrinología, Hospital de Niños Ricardo Gutiérrez Buenos Aires C1425EFD, Argentina
| | - Lucía Salatino
- Instituto de Farmacología, Facultad de Medicina, Universidad de Buenos Aires (UBA), Paraguay 2155, C1121ABG, Buenos Aires, Argentina
| | - Paula Scaglia
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET-FEI-División de Endocrinología, Hospital de Niños Ricardo Gutiérrez Buenos Aires C1425EFD, Argentina
| | - Laura Ramírez
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET-FEI-División de Endocrinología, Hospital de Niños Ricardo Gutiérrez Buenos Aires C1425EFD, Argentina
| | - Ana Keselman
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET-FEI-División de Endocrinología, Hospital de Niños Ricardo Gutiérrez Buenos Aires C1425EFD, Argentina
| | - Débora Braslavsky
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET-FEI-División de Endocrinología, Hospital de Niños Ricardo Gutiérrez Buenos Aires C1425EFD, Argentina
| | - Nora Sanguineti
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET-FEI-División de Endocrinología, Hospital de Niños Ricardo Gutiérrez Buenos Aires C1425EFD, Argentina
| | - Patricia Pennisi
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET-FEI-División de Endocrinología, Hospital de Niños Ricardo Gutiérrez Buenos Aires C1425EFD, Argentina
| | - Rodolfo A Rey
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET-FEI-División de Endocrinología, Hospital de Niños Ricardo Gutiérrez Buenos Aires C1425EFD, Argentina
| | - Ignacio Bergadá
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET-FEI-División de Endocrinología, Hospital de Niños Ricardo Gutiérrez Buenos Aires C1425EFD, Argentina
| | - Héctor G Jasper
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET-FEI-División de Endocrinología, Hospital de Niños Ricardo Gutiérrez Buenos Aires C1425EFD, Argentina
| | - Horacio M Domené
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET-FEI-División de Endocrinología, Hospital de Niños Ricardo Gutiérrez Buenos Aires C1425EFD, Argentina
| | - Paola V Plazas
- Instituto de Farmacología, Facultad de Medicina, Universidad de Buenos Aires (UBA), Paraguay 2155, C1121ABG, Buenos Aires, Argentina
| | - Sabina Domené
- Centro de Investigaciones Endocrinológicas "Dr. César Bergadá" (CEDIE), CONICET-FEI-División de Endocrinología, Hospital de Niños Ricardo Gutiérrez Buenos Aires C1425EFD, Argentina
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48
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Fu XD, Mobley WC. Therapeutic Potential of PTB Inhibition Through Converting Glial Cells to Neurons in the Brain. Annu Rev Neurosci 2023; 46:145-165. [PMID: 37428606 DOI: 10.1146/annurev-neuro-083022-113120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Cell replacement therapy represents a promising approach for treating neurodegenerative diseases. Contrary to the common addition strategy to generate new neurons from glia by overexpressing a lineage-specific transcription factor(s), a recent study introduced a subtraction strategy by depleting a single RNA-binding protein, Ptbp1, to convert astroglia to neurons not only in vitro but also in the brain. Given its simplicity, multiple groups have attempted to validate and extend this attractive approach but have met with difficulty in lineage tracing newly induced neurons from mature astrocytes, raising the possibility of neuronal leakage as an alternative explanation for apparent astrocyte-to-neuron conversion. This review focuses on the debate over this critical issue. Importantly, multiple lines of evidence suggest that Ptbp1 depletion can convert a selective subpopulation of glial cells into neurons and, via this and other mechanisms, reverse deficits in a Parkinson's disease model, emphasizing the importance of future efforts in exploring this therapeutic strategy.
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Affiliation(s)
- Xiang-Dong Fu
- Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China;
| | - William C Mobley
- Department of Neuroscience, University of California, San Diego, La Jolla, California, USA;
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49
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Pal DS, Banerjee T, Lin Y, de Trogoff F, Borleis J, Iglesias PA, Devreotes PN. Actuation of single downstream nodes in growth factor network steers immune cell migration. Dev Cell 2023; 58:1170-1188.e7. [PMID: 37220748 PMCID: PMC10524337 DOI: 10.1016/j.devcel.2023.04.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 03/14/2023] [Accepted: 04/27/2023] [Indexed: 05/25/2023]
Abstract
Ras signaling is typically associated with cell growth, but not direct regulation of motility or polarity. By optogenetically targeting different nodes in the Ras/PI3K/Akt network in differentiated human HL-60 neutrophils, we abruptly altered protrusive activity, bypassing the chemoattractant receptor/G-protein network. First, global recruitment of active KRas4B/HRas isoforms or a RasGEF, RasGRP4, immediately increased spreading and random motility. Second, activating Ras at the cell rear generated new protrusions, reversed pre-existing polarity, and steered sustained migration in neutrophils or murine RAW 264.7 macrophages. Third, recruiting a RasGAP, RASAL3, to cell fronts extinguished protrusions and changed migration direction. Remarkably, persistent RASAL3 recruitment at stable fronts abrogated directed migration in three different chemoattractant gradients. Fourth, local recruitment of the Ras-mTORC2 effector, Akt, in neutrophils or Dictyostelium amoebae generated new protrusions and rearranged pre-existing polarity. Overall, these optogenetic effects were mTORC2-dependent but relatively independent of PI3K. Thus, receptor-independent, local activations of classical growth-control pathways directly control actin assembly, cell shape, and migration modes.
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Affiliation(s)
- Dhiman Sankar Pal
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
| | - Tatsat Banerjee
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Yiyan Lin
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Félix de Trogoff
- Department of Mechanical Engineering, STI School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Department of Electrical and Computer Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jane Borleis
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Pablo A Iglesias
- Department of Electrical and Computer Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Peter N Devreotes
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD, USA.
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50
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Pal DS, Lin Y, Zhan H, Banerjee T, Kuhn J, Providence S, Devreotes PN. Optogenetic modulation of guanine nucleotide exchange factors of Ras superfamily proteins directly controls cell shape and movement. Front Cell Dev Biol 2023; 11:1195806. [PMID: 37492221 PMCID: PMC10363612 DOI: 10.3389/fcell.2023.1195806] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/27/2023] [Indexed: 07/27/2023] Open
Abstract
In this article, we provide detailed protocols on using optogenetic dimerizers to acutely perturb activities of guanine nucleotide exchange factors (GEFs) specific to Ras, Rac or Rho small GTPases of the migratory networks in various mammalian and amoeba cell lines. These GEFs are crucial components of signal transduction networks which link upstream G-protein coupled receptors to downstream cytoskeletal components and help cells migrate through their dynamic microenvironment. Conventional approaches to perturb and examine these signaling and cytoskeletal networks, such as gene knockout or overexpression, are protracted which allows networks to readjust through gene expression changes. Moreover, these tools lack spatial resolution to probe the effects of local network activations. To overcome these challenges, blue light-inducible cryptochrome- and LOV domain-based dimerization systems have been recently developed to control signaling or cytoskeletal events in a spatiotemporally precise manner. We illustrate that, within minutes of global membrane recruitment of full-length GEFs or their catalytic domains only, widespread increases or decreases in F-actin rich protrusions and cell size occur, depending on the particular node in the networks targeted. Additionally, we demonstrate localized GEF recruitment as a robust assay system to study local network activation-driven changes in polarity and directed migration. Altogether, these optical tools confirmed GEFs of Ras superfamily GTPases as regulators of cell shape, actin dynamics, and polarity. Furthermore, this optogenetic toolbox may be exploited in perturbing complex signaling interactions in varied physiological contexts including mammalian embryogenesis.
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Affiliation(s)
- Dhiman Sankar Pal
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Yiyan Lin
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
- Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Huiwang Zhan
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Tatsat Banerjee
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, United States
| | - Jonathan Kuhn
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
| | - Stephenie Providence
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
- Ingenuity Research Program, Baltimore Polytechnic Institute, Baltimore, MD, United States
| | - Peter N. Devreotes
- Department of Cell Biology and Center for Cell Dynamics, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
- Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore, MD, United States
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