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Tritto V, Bettinaglio P, Mangano E, Cesaretti C, Marasca F, Castronovo C, Bordoni R, Battaglia C, Saletti V, Ranzani V, Bodega B, Eoli M, Natacci F, Riva P. Genetic/epigenetic effects in NF1 microdeletion syndrome: beyond the haploinsufficiency, looking at the contribution of not deleted genes. Hum Genet 2024; 143:775-795. [PMID: 38874808 PMCID: PMC11186880 DOI: 10.1007/s00439-024-02683-0] [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: 03/15/2024] [Accepted: 06/03/2024] [Indexed: 06/15/2024]
Abstract
NF1 microdeletion syndrome, accounting for 5-11% of NF1 patients, is caused by a deletion in the NF1 region and it is generally characterized by a severe phenotype. Although 70% of NF1 microdeletion patients presents the same 1.4 Mb type-I deletion, some patients may show additional clinical features. Therefore, the contribution of several pathogenic mechanisms, besides haploinsufficiency of some genes within the deletion interval, is expected and needs to be defined. We investigated an altered expression of deletion flanking genes by qPCR in patients with type-1 NF1 deletion, compared to healthy donors, possibly contributing to the clinical traits of NF1 microdeletion syndrome. In addition, the 1.4-Mb deletion leads to changes in the 3D chromatin structure in the 17q11.2 region. Specifically, this deletion alters DNA-DNA interactions in the regions flanking the breakpoints, as demonstrated by our 4C-seq analysis. This alteration likely causes position effect on the expression of deletion flanking genes.Interestingly, 4C-seq analysis revealed that in microdeletion patients, an interaction was established between the RHOT1 promoter and the SLC6A4 gene, which showed increased expression. We performed NGS on putative modifier genes, and identified two "likely pathogenic" rare variants in RAS pathway, possibly contributing to incidental phenotypic features.This study provides new insights into understanding the pathogenesis of NF1 microdeletion syndrome and suggests a novel pathomechanism that contributes to the expression phenotype in addition to haploinsufficiency of genes located within the deletion.This is a pivotal approach that can be applied to unravel microdeletion syndromes, improving precision medicine, prognosis and patients' follow-up.
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Affiliation(s)
- Viviana Tritto
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, Segrate, Milan, Italy
| | - Paola Bettinaglio
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, Segrate, Milan, Italy
| | - Eleonora Mangano
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Segrate (Milan), Italy
| | - Claudia Cesaretti
- Medical Genetics Unit, Woman-Child-Newborn Department, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milan, Italy
| | - Federica Marasca
- Genome Biology Unit, Istituto Nazionale di Genetica Molecolare (INGM) "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Chiara Castronovo
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Segrate (Milan), Italy
| | - Roberta Bordoni
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Segrate (Milan), Italy
| | - Cristina Battaglia
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, Segrate, Milan, Italy
- Institute for Biomedical Technologies (ITB), National Research Council (CNR), Segrate (Milan), Italy
| | - Veronica Saletti
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Valeria Ranzani
- Genome Biology Unit, Istituto Nazionale di Genetica Molecolare (INGM) "Romeo ed Enrica Invernizzi", Milan, Italy
| | - Beatrice Bodega
- Genome Biology Unit, Istituto Nazionale di Genetica Molecolare (INGM) "Romeo ed Enrica Invernizzi", Milan, Italy
- Department of Biosciences (DBS), University of Milan, Milan, Italy
| | - Marica Eoli
- Molecular Neuroncology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Federica Natacci
- Medical Genetics Unit, Woman-Child-Newborn Department, Fondazione IRCCS Ca' Granda-Ospedale Maggiore Policlinico, Milan, Italy.
| | - Paola Riva
- Department of Medical Biotechnology and Translational Medicine (BIOMETRA), University of Milan, Segrate, Milan, Italy.
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2
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Wu X, Pan X, Zhou Y, Pan J, Kang J, Yu JJJ, Cao Y, Quan C, Gong L, Li Y. Identification of key genes for atherosclerosis in different arterial beds. Sci Rep 2024; 14:6543. [PMID: 38503760 PMCID: PMC10951242 DOI: 10.1038/s41598-024-55575-8] [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: 01/16/2024] [Accepted: 02/25/2024] [Indexed: 03/21/2024] Open
Abstract
Atherosclerosis (AS) is the pathologic basis of various cardiovascular and cerebrovascular events, with a high degree of heterogeneity among different arterial beds. However, mechanistic differences between arterial beds remain unexplored. The aim of this study was to explore key genes and potential mechanistic differences between AS in different arterial beds through bioinformatics analysis. Carotid atherosclerosis (CAS), femoral atherosclerosis (FAS), infrapopliteal atherosclerosis (IPAS), abdominal aortic atherosclerosis (AAS), and AS-specific differentially expressed genes (DEGs) were screened from the GSE100927 and GSE57691 datasets. Immune infiltration analysis was used to identify AS immune cell infiltration differences. Unsupervised cluster analysis of AS samples from different regions based on macrophage polarization gene expression profiles. Weighted gene co-expression network analysis (WGCNA) was performed to identify the most relevant module genes with AS. Hub genes were then screened by LASSO regression, SVM-REF, and single-gene differential analysis, and a nomogram was constructed to predict the risk of AS development. The results showed that differential expression analysis identified 5, 4, 121, and 62 CAS, FAS, IPAS, AAS-specific DEGs, and 42 AS-common DEGs, respectively. Immune infiltration analysis demonstrated that the degree of macrophage and mast cell enrichment differed significantly in different regions of AS. The CAS, FAS, IPAS, and AAS could be distinguished into two different biologically functional and stable molecular clusters based on macrophage polarization gene expression profiles, especially for cardiomyopathy and glycolipid metabolic processes. Hub genes for 6 AS (ADAP2, CSF3R, FABP5, ITGAX, MYOC, and SPP1), 4 IPAS (CLECL1, DIO2, F2RL2, and GUCY1A2), and 3 AAS (RPL21, RPL26, and RPL10A) were obtained based on module gene, gender stratification, machine learning algorithms, and single-gene difference analysis, respectively, and these genes were effective in differentiating between different regions of AS. This study demonstrates that there are similarities and heterogeneities in the pathogenesis of AS between different arterial beds.
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Affiliation(s)
- Xize Wu
- Nantong Hospital of Traditional Chinese Medicine, Nantong Hospital Affiliated to Nanjing University of Chinese Medicine, No. 41 Jianshe Road, Chongchuan District, Nantong, 226000, Jiangsu, China
- Liaoning University of Traditional Chinese Medicine, Shenyang, 110847, Liaoning, China
| | - Xue Pan
- Liaoning University of Traditional Chinese Medicine, Shenyang, 110847, Liaoning, China
- Dazhou Vocational College of Chinese Medicine, Dazhou, 635000, Sichuan, China
| | - Yi Zhou
- Liaoning University of Traditional Chinese Medicine, Shenyang, 110847, Liaoning, China
| | - Jiaxiang Pan
- The Affiliated Hospital of Liaoning University of Traditional Chinese Medicine, No. 33, Beiling Street, Huanggu District, Shenyang, 110032, Liaoning, China
| | - Jian Kang
- Liaoning University of Traditional Chinese Medicine, Shenyang, 110847, Liaoning, China
| | - J J Jiajia Yu
- Liaoning University of Traditional Chinese Medicine, Shenyang, 110847, Liaoning, China
| | - Yingyue Cao
- Liaoning University of Traditional Chinese Medicine, Shenyang, 110847, Liaoning, China
| | - Chao Quan
- Nantong Hospital of Traditional Chinese Medicine, Nantong Hospital Affiliated to Nanjing University of Chinese Medicine, No. 41 Jianshe Road, Chongchuan District, Nantong, 226000, Jiangsu, China.
| | - Lihong Gong
- Liaoning University of Traditional Chinese Medicine, Shenyang, 110847, Liaoning, China.
- The Affiliated Hospital of Liaoning University of Traditional Chinese Medicine, No. 33, Beiling Street, Huanggu District, Shenyang, 110032, Liaoning, China.
- Liaoning Provincial Key Laboratory of TCM Geriatric Cardio-Cerebrovascular Diseases, Shenyang, 110847, Liaoning, China.
| | - Yue Li
- The Affiliated Hospital of Liaoning University of Traditional Chinese Medicine, No. 33, Beiling Street, Huanggu District, Shenyang, 110032, Liaoning, China.
- Liaoning Provincial Key Laboratory of TCM Geriatric Cardio-Cerebrovascular Diseases, Shenyang, 110847, Liaoning, China.
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3
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Pacot L, Girish M, Knight S, Spurlock G, Varghese V, Ye M, Thomas N, Pasmant E, Upadhyaya M. Correlation between large rearrangements and patient phenotypes in NF1 deletion syndrome: an update and review. BMC Med Genomics 2024; 17:73. [PMID: 38448973 PMCID: PMC10919053 DOI: 10.1186/s12920-024-01843-5] [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: 10/30/2023] [Accepted: 03/01/2024] [Indexed: 03/08/2024] Open
Abstract
About 5-10% of neurofibromatosis type 1 (NF1) patients exhibit large genomic germline deletions that remove the NF1 gene and its flanking regions. The most frequent NF1 large deletion is 1.4 Mb, resulting from homologous recombination between two low copy repeats. This "type-1" deletion is associated with a severe clinical phenotype in NF1 patients, with several phenotypic manifestations including learning disability, a much earlier development of cutaneous neurofibromas, an increased tumour risk, and cardiovascular malformations. NF1 adjacent co-deleted genes could act as modifier loci for the specific clinical manifestations observed in deleted NF1 patients. Furthermore, other genetic modifiers (such as CNVs) not located at the NF1 locus could also modulate the phenotype observed in patients with large deletions. In this study, we analysed 22 NF1 deletion patients by genome-wide array-CGH with the aim (1) to correlate deletion length to observed phenotypic features and their severity in NF1 deletion syndrome, and (2) to identify whether the deletion phenotype could also be modulated by copy number variations elsewhere in the genome. We then review the role of co-deleted genes in the 1.4 Mb interval of type-1 deletions, and their possible implication in the main clinical features observed in this high-risk group of NF1 patients.
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Affiliation(s)
- Laurence Pacot
- Fédération de Génétique et Médecine Génomique, Hôpital Cochin, DMU BioPhyGen, AP-HP, Centre-Université Paris Cité, Paris, France
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris Cité, CARPEM, Paris, France
| | - Milind Girish
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Samantha Knight
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | | | - Vinod Varghese
- All Wales Medical Genomics Service, Cardiff, Great Britain
| | - Manuela Ye
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris Cité, CARPEM, Paris, France
| | - Nick Thomas
- School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Eric Pasmant
- Fédération de Génétique et Médecine Génomique, Hôpital Cochin, DMU BioPhyGen, AP-HP, Centre-Université Paris Cité, Paris, France.
- Institut Cochin, Inserm U1016, CNRS UMR8104, Université Paris Cité, CARPEM, Paris, France.
| | - Meena Upadhyaya
- Division of Cancer and Genetics, Institute of Medical Genetics, Cardiff University, Heath Park, CF14 4XN, Cardiff, UK
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Zhang L, Zhou J. Zebrafish: A smart tool for heart disease research. JOURNAL OF FISH BIOLOGY 2023. [PMID: 37824489 DOI: 10.1111/jfb.15585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 09/07/2023] [Accepted: 10/09/2023] [Indexed: 10/14/2023]
Abstract
The increasing prevalence of heart disease poses a significant threat to human survival and safety. However, the current treatments available for heart disease are quite limited. Therefore, it is of great importance to utilize suitable animal models that can accurately simulate the physiological characteristics of heart disease. This would help improve our understanding of this disease and aid in the development of new treatment methods and drugs. Zebrafish hearts not only exhibit similarities to mammalian hearts, but they also share ~70% of homologous genes with humans. Utilizing zebrafish as an alternative to costly and time-consuming mammalian models offers numerous advantages. Zebrafish models can be easily established and maintained, and compound screening and genetic methods allow for the creation of various economical and easily controlled zebrafish and zebrafish embryonic heart disease models in a short period of time. Consequently, zebrafish have become a powerful tool for exploring the pathological mechanisms of heart disease and identifying new effective genes. In this review, we summarize recent studies on different zebrafish models of heart disease. We also describe the techniques and protocols used to develop zebrafish models of myocardial infarction, heart failure, and congenital heart disease, including surgical procedures, forward and reverse genetics, as well as drug and combination screening. This review aims to promote the utilization of zebrafish models in investigating diverse pathological mechanisms of heart disease, enhancing our knowledge and comprehension of heart disease, and offering novel insights and objectives for exploring the prevention and treatment of heart disease.
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Affiliation(s)
- Lantian Zhang
- Education Branch, Chongqing Publishing Group, Chongqing, China
| | - Jinrun Zhou
- Shandong Provincial Key Laboratory of Animal Cells and Developmental Biology, School of Life Science, Shandong University, Qingdao, China
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5
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Wang D, Wen X, Xu LL, Chen QX, Yan TX, Xiao HT, Xu XW. Nf1 in heart development: a potential causative gene for congenital heart disease: a narrative review. Physiol Genomics 2023; 55:415-426. [PMID: 37519249 DOI: 10.1152/physiolgenomics.00024.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/26/2023] [Accepted: 07/08/2023] [Indexed: 08/01/2023] Open
Abstract
Congenital heart disease is the most frequent congenital disorder, affecting a significant number of live births. Gaining insights into its genetic etiology could lead to a deeper understanding of this condition. Although the Nf1 gene has been identified as a potential causative gene, its role in congenital heart disease has not been thoroughly clarified. We searched and summarized evidence from cohort-based and experimental studies on the issue of Nf1 and heart development in congenital heart diseases from various databases. Available evidence demonstrates a correlation between Nf1 and congenital heart diseases, mainly pulmonary valvar stenosis. The mechanism underlying this correlation may involve dysregulation of epithelial-mesenchymal transition (EMT). The Nf1 gene affects the EMT process via multiple pathways, including directly regulating the expression of EMT-related transcription factors and indirectly regulating the EMT process by regulating the MAPK pathway. This narrative review provides a comprehensive account of the Nf1 involvement in heart development and congenital cardiovascular diseases in terms of epidemiology and potential mechanisms. RAS signaling may contribute to congenital heart disease independently or in cooperation with other signaling pathways. Efficient management of both NF1 and cardiovascular disease patients would benefit from further research into these issues.
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Affiliation(s)
- Dun Wang
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, People's Republic of China
| | - Xue Wen
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, People's Republic of China
| | - Li-Li Xu
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, People's Republic of China
| | - Qing-Xing Chen
- Department of Cardiology, Zhongshan Hospital, Fudan University, Shanghai Institute of Cardiovascular Diseases, Shanghai, People's Republic of China
| | - Tian-Xing Yan
- Central Laboratory, National Clinical Research Center for Oral Diseases, Peking University School and Hospital of Stomatology, Beijing, People's Republic of China
| | - Hai-Tao Xiao
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, People's Republic of China
| | - Xue-Wen Xu
- Department of Burn and Plastic Surgery, West China Hospital of Sichuan University, Chengdu, People's Republic of China
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6
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Hilal N, Chen Z, Chen MH, Choudhury S. RASopathies and cardiac manifestations. Front Cardiovasc Med 2023; 10:1176828. [PMID: 37529712 PMCID: PMC10387527 DOI: 10.3389/fcvm.2023.1176828] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/20/2023] [Indexed: 08/03/2023] Open
Abstract
As binary switches, RAS proteins switch to an ON/OFF state during signaling and are on a leash under normal conditions. However, in RAS-related diseases such as cancer and RASopathies, mutations in the genes that regulate RAS signaling or the RAS itself permanently activate the RAS protein. The structural basis of this switch is well understood; however, the exact mechanisms by which RAS proteins are regulated are less clear. RAS/MAPK syndromes are multisystem developmental disorders caused by germline mutations in genes associated with the RAS/mitogen-activated protein kinase pathway, impacting 1 in 1,000-2,500 children. These include a variety of disorders such as Noonan syndrome (NS) and NS-related disorders (NSRD), such as cardio facio cutaneous (CFC) syndrome, Costello syndrome (CS), and NS with multiple lentigines (NSML, also known as LEOPARD syndrome). A frequent manifestation of cardiomyopathy (CM) and hypertrophic cardiomyopathy associated with RASopathies suggest that RASopathies could be a potential causative factor for CM. However, the current supporting evidence is sporadic and unclear. RASopathy-patients also display a broad spectrum of congenital heart disease (CHD). More than 15 genes encode components of the RAS/MAPK signaling pathway that are essential for the cell cycle and play regulatory roles in proliferation, differentiation, growth, and metabolism. These genes are linked to the molecular genetic pathogenesis of these syndromes. However, genetic heterogeneity for a given syndrome on the one hand and alleles for multiple syndromes on the other make classification difficult in diagnosing RAS/MAPK-related diseases. Although there is some genetic homogeneity in most RASopathies, several RASopathies are allelic diseases. This allelism points to the role of critical signaling nodes and sheds light on the overlap between these related syndromes. Even though considerable progress has been made in understanding the pathophysiology of RASopathy with the identification of causal mutations and the functional analysis of their pathophysiological consequences, there are still unidentified causal genes for many patients diagnosed with RASopathies.
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Affiliation(s)
- Nazia Hilal
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Broad Institute of Harvard and MIT, Cambridge, MA, United States
| | - Zi Chen
- Harvard Medical School, Boston, MA, United States
- Department of Surgery, Brigham, and Women’s Hospital, Boston, MA, United States
| | - Ming Hui Chen
- Harvard Medical School, Boston, MA, United States
- Department of Cardiology, Boston Children’s Hospital, Boston, MA, United States
| | - Sangita Choudhury
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital, Boston, MA, United States
- Harvard Medical School, Boston, MA, United States
- Broad Institute of Harvard and MIT, Cambridge, MA, United States
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7
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Small GTPases and Their Regulators: A Leading Road toward Blood Vessel Development in Zebrafish. Int J Mol Sci 2022; 23:ijms23094991. [PMID: 35563380 PMCID: PMC9099977 DOI: 10.3390/ijms23094991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 12/26/2022] Open
Abstract
Members of the Ras superfamily have been found to perform several functions leading to the development of eukaryotes. These small GTPases are divided into five major subfamilies, and their regulators can “turn on” and “turn off” signals. Recent studies have shown that this superfamily of proteins has various roles in the process of vascular development, such as vasculogenesis and angiogenesis. Here, we discuss the role of these subfamilies in the development of the vascular system in zebrafish.
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8
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Ho SK, Luk HM, Ng SY, Yu KP, Cheng SS, Ng PP, Mok MT, Hau EW, Lo IF. Old and new perspectives on Neurofibromatosis type 1: Clinical and molecular characterization of 832 patients from a single centre over 16 years. Eur J Med Genet 2022; 65:104474. [PMID: 35240321 DOI: 10.1016/j.ejmg.2022.104474] [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: 09/29/2021] [Revised: 01/17/2022] [Accepted: 02/25/2022] [Indexed: 11/03/2022]
Abstract
Neurofibromatosis type 1 (NF1; OMIM #162200) is the commonest multi-systemic neurocutaneous tumour-predisposition disorder. It has an age-related complete penetrance but a highly variable inter- and intra-familial expressivity. This article summarizes the clinical features and molecular characteristics of 832 clinically or molecularly confirmed NF1 patients from 697 unrelated families recruited from a single centre in Hong Kong diagnosed during the 16 years period from Jan 2005 to Jan 2021. In this study, we have estimated the incidences of clinical features, reported on the molecular findings and explored new genotype-phenotype correlations.
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Affiliation(s)
- Stephanie Kl Ho
- Clinical Genetic Service, Department of Health, Hong Kong SAR, China
| | - Ho-Ming Luk
- Clinical Genetic Service, Department of Health, Hong Kong SAR, China
| | - Samuel Yl Ng
- Clinical Genetic Service, Department of Health, Hong Kong SAR, China
| | - Kris Pt Yu
- Clinical Genetic Service, Department of Health, Hong Kong SAR, China
| | - Shirley Sw Cheng
- Clinical Genetic Service, Department of Health, Hong Kong SAR, China
| | - Phoebe Py Ng
- Clinical Genetic Service, Department of Health, Hong Kong SAR, China
| | - Myth Ts Mok
- Clinical Genetic Service, Department of Health, Hong Kong SAR, China
| | - Edgar Wl Hau
- Clinical Genetic Service, Department of Health, Hong Kong SAR, China
| | - Ivan Fm Lo
- Clinical Genetic Service, Department of Health, Hong Kong SAR, China.
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9
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Wang W, Wei CJ, Cui XW, Li YH, Gu YH, Gu B, Li QF, Wang ZC. Impacts of NF1 Gene Mutations and Genetic Modifiers in Neurofibromatosis Type 1. Front Neurol 2021; 12:704639. [PMID: 34566848 PMCID: PMC8455870 DOI: 10.3389/fneur.2021.704639] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 07/15/2021] [Indexed: 12/26/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) is a tumor predisposition genetic disorder that directly affects more than 1 in 3,000 individuals worldwide. It results from mutations of the NF1 gene and shows almost complete penetrance. NF1 patients show high phenotypic variabilities, including cafe-au-lait macules, freckling, or other neoplastic or non-neoplastic features. Understanding the underlying mechanisms of the diversities of clinical symptoms might contribute to the development of personalized healthcare for NF1 patients. Currently, studies have shown that the different types of mutations in the NF1 gene might correlate with this phenomenon. In addition, genetic modifiers are responsible for the different clinical features. In this review, we summarize different genetic mutations of the NF1 gene and related genetic modifiers. More importantly, we focus on the genotype–phenotype correlation. This review suggests a novel aspect to explain the underlying mechanisms of phenotypic heterogeneity of NF1 and provides suggestions for possible novel therapeutic targets to prevent or delay the onset and development of different manifestations of NF1.
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Affiliation(s)
- Wei Wang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Cheng-Jiang Wei
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xi-Wei Cui
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yue-Hua Li
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yi-Hui Gu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bin Gu
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qing-Feng Li
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhi-Chao Wang
- Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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10
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Chen X, Li W. Isoflucypram cardiovascular toxicity in zebrafish (Danio rerio). THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 787:147529. [PMID: 33991914 DOI: 10.1016/j.scitotenv.2021.147529] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/28/2021] [Accepted: 05/01/2021] [Indexed: 06/12/2023]
Abstract
Isoflucypram belongs to the new generation of succinate dehydrogenase inhibitor (SDHI) fungicides that are commonly used in crop fungal disease control. Evidence indicates that isoflucypram poses a potential risk to aquatic organisms. However, the effects of isoflucypram during early embryogenesis are not fully understood. In the present study, zebrafish embryos were exposed to 0.025, 0.25, or 2.5 μM isoflucypram for three days. Isoflucypram caused severe developmental abnormalities (yolk sac edema, pericardial edema, and blood clotting clustering), hatching delay, and decreased heart rates in zebrafish. The expression levels of cardiac-specific genes (nkx2.5, myh7, myl7, and myh6) and erythropoiesis-related genes (gata1a, hbbe1, hbbe2, and alas2) were disrupted after isoflucypram exposure. Furthermore, enrichment analysis indicated that most of the differentially expressed genes (DEGs) were enriched in heart development or hemopoiesis processes. Overall, these findings suggest that exposure to isoflucypram is associated with developmental and cardiovascular toxicity in zebrafish.
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Affiliation(s)
- Xin Chen
- Engineering Research Center of Molecular Medicine of Ministry of Education, Key Laboratory of Fujian Molecular Medicine, Key Laboratory of Xiamen Marine and Gene Drugs, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, School of Biomedical Sciences, Huaqiao University, Xiamen 361021, PR China
| | - Wenhua Li
- Engineering Research Center of Molecular Medicine of Ministry of Education, Key Laboratory of Fujian Molecular Medicine, Key Laboratory of Xiamen Marine and Gene Drugs, Key Laboratory of Precision Medicine and Molecular Diagnosis of Fujian Universities, School of Biomedical Sciences, Huaqiao University, Xiamen 361021, PR China.
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11
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Wegscheid ML, Anastasaki C, Hartigan KA, Cobb OM, Papke JB, Traber JN, Morris SM, Gutmann DH. Patient-derived iPSC-cerebral organoid modeling of the 17q11.2 microdeletion syndrome establishes CRLF3 as a critical regulator of neurogenesis. Cell Rep 2021; 36:109315. [PMID: 34233200 PMCID: PMC8278229 DOI: 10.1016/j.celrep.2021.109315] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 04/21/2021] [Accepted: 06/04/2021] [Indexed: 12/22/2022] Open
Abstract
Neurodevelopmental disorders are often caused by chromosomal microdeletions comprising numerous contiguous genes. A subset of neurofibromatosis type 1 (NF1) patients with severe developmental delays and intellectual disability harbors such a microdeletion event on chromosome 17q11.2, involving the NF1 gene and flanking regions (NF1 total gene deletion [NF1-TGD]). Using patient-derived human induced pluripotent stem cell (hiPSC)-forebrain cerebral organoids (hCOs), we identify both neural stem cell (NSC) proliferation and neuronal maturation abnormalities in NF1-TGD hCOs. While increased NSC proliferation results from decreased NF1/RAS regulation, the neuronal differentiation, survival, and maturation defects are caused by reduced cytokine receptor-like factor 3 (CRLF3) expression and impaired RhoA signaling. Furthermore, we demonstrate a higher autistic trait burden in NF1 patients harboring a deleterious germline mutation in the CRLF3 gene (c.1166T>C, p.Leu389Pro). Collectively, these findings identify a causative gene within the NF1-TGD locus responsible for hCO neuronal abnormalities and autism in children with NF1.
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Affiliation(s)
- Michelle L Wegscheid
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Corina Anastasaki
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kelly A Hartigan
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Olivia M Cobb
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jason B Papke
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jennifer N Traber
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Stephanie M Morris
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David H Gutmann
- Department of Neurology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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12
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Büki G, Zsigmond A, Czakó M, Szalai R, Antal G, Farkas V, Fekete G, Nagy D, Széll M, Tihanyi M, Melegh B, Hadzsiev K, Bene J. Genotype-Phenotype Associations in Patients With Type-1, Type-2, and Atypical NF1 Microdeletions. Front Genet 2021; 12:673025. [PMID: 34168676 PMCID: PMC8217751 DOI: 10.3389/fgene.2021.673025] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/12/2021] [Indexed: 11/23/2022] Open
Abstract
Neurofibromatosis type 1 is a tumor predisposition syndrome inherited in autosomal dominant manner. Besides the intragenic loss-of-function mutations in NF1 gene, large deletions encompassing the NF1 gene and its flanking regions are responsible for the development of the variable clinical phenotype. These large deletions titled as NF1 microdeletions lead to a more severe clinical phenotype than those observed in patients with intragenic NF1 mutations. Around 5-10% of the cases harbor large deletion and four major types of NF1 microdeletions (type 1, 2, 3 and atypical) have been identified so far. They are distinguishable in term of their size and the location of the breakpoints, by the frequency of somatic mosaicism with normal cells not harboring the deletion and by the number of the affected genes within the deleted region. In our study genotype-phenotype analyses have been performed in 17 mostly pediatric patients with NF1 microdeletion syndrome identified by multiplex ligation-dependent probe amplification after systematic sequencing of the NF1 gene. Confirmation and classification of the NF1 large deletions were performed using array comparative genomic hybridization, where it was feasible. In our patient cohort 70% of the patients possess type-1 deletion, one patient harbors type-2 deletion and 23% of our cases have atypical NF1 deletion. All the atypical deletions identified in this study proved to be novel. One patient with atypical deletion displayed mosaicism. In our study NF1 microdeletion patients presented dysmorphic facial features, macrocephaly, large hands and feet, delayed cognitive development and/or learning difficulties, speech difficulties, overgrowth more often than patients with intragenic NF1 mutations. Moreover, neurobehavior problems, macrocephaly and overgrowth were less frequent in atypical cases compared to type-1 deletion. Proper diagnosis is challenging in certain patients since several clinical manifestations show age-dependency. Large tumor load exhibited more frequently in this type of disorder, therefore better understanding of genotype-phenotype correlations and progress of the disease is essential for individuals suffering from neurofibromatosis to improve the quality of their life. Our study presented additional clinical data related to NF1 microdeletion patients especially for pediatric cases and it contributes to the better understanding of this type of disorder.
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Affiliation(s)
- Gergely Büki
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Anna Zsigmond
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, Pécs, Hungary
| | - Márta Czakó
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Renáta Szalai
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Gréta Antal
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, Pécs, Hungary
| | - Viktor Farkas
- 1st Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - György Fekete
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Dóra Nagy
- Department of Medical Genetics, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Márta Széll
- Department of Medical Genetics, Faculty of Medicine, University of Szeged, Szeged, Hungary
| | - Marianna Tihanyi
- Genetic Laboratory, Szent Rafael Hospital of Zala County, Zalaegerszeg, Hungary
| | - Béla Melegh
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary.,Full member of the European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) - Project ID No. 739547, Pécs, Hungary
| | - Kinga Hadzsiev
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary
| | - Judit Bene
- Department of Medical Genetics, Clinical Center, Medical School, University of Pécs, Pécs, Hungary.,Szentágothai Research Centre, University of Pécs, Pécs, Hungary.,Full member of the European Reference Network on Genetic Tumour Risk Syndromes (ERN GENTURIS) - Project ID No. 739547, Pécs, Hungary
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13
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Osmak G, Baulina N, Koshkin P, Favorova O. Collapsing the list of myocardial infarction-related differentially expressed genes into a diagnostic signature. J Transl Med 2020; 18:231. [PMID: 32517814 PMCID: PMC7285786 DOI: 10.1186/s12967-020-02400-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/03/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Myocardial infarction (MI) is one of the most severe manifestations of coronary artery disease (CAD) and the leading cause of death from non-infectious diseases worldwide. It is known that the central component of CAD pathogenesis is a chronic vascular inflammation. However, the mechanisms underlying the changes that occur in T, B and NK lymphocytes, monocytes and other immune cells during CAD and MI are still poorly understood. One of those pathogenic mechanisms might be the dysregulation of intracellular signaling pathways in the immune cells. METHODS In the present study we performed a transcriptome profiling in peripheral blood mononuclear cells of MI patients and controls. The machine learning algorithm was then used to search for MI-associated signatures, that could reflect the dysregulation of intracellular signaling pathways. RESULTS The genes ADAP2, KLRC1, MIR21, PDGFD and CD14 were identified as the most important signatures for the classification model with L1-norm penalty function. The classifier output quality was equal to 0.911 by Receiver Operating Characteristic metric on test data. These results were validated on two independent open GEO datasets. Identified MI-associated signatures can be further assisted in MI diagnosis and/or prognosis. CONCLUSIONS Thus, our study presents a pipeline for collapsing the list of differential expressed genes, identified by high-throughput techniques, in order to define disease-associated diagnostic signatures.
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Affiliation(s)
- German Osmak
- National Medical Research Center for Cardiology, Moscow, 121552, Russia.
| | - Natalia Baulina
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia
| | - Philipp Koshkin
- National Medical Research Center for Cardiology, Moscow, 121552, Russia
| | - Olga Favorova
- Pirogov Russian National Research Medical University, Moscow, 117997, Russia
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14
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Serra G, Antona V, Corsello G, Zara F, Piro E, Falsaperla R. NF1 microdeletion syndrome: case report of two new patients. Ital J Pediatr 2019; 45:138. [PMID: 31703719 PMCID: PMC6839219 DOI: 10.1186/s13052-019-0718-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Accepted: 09/16/2019] [Indexed: 01/24/2023] Open
Abstract
Background 17q11.2 microdeletions, which include the neurofibromatosis type 1 (NF1) gene region, are responsible for the NF1 microdeletion syndrome, observed in 4.2% of all NF1 patients. Large deletions of the NF1 gene and its flanking regions are associated with a more severe NF1 phenotype than the NF1 general population. Case presentation We hereby describe the clinical and molecular features of two girls (aged 2 and 4 years, respectively), with non-mosaic atypical deletions. Patient 1 showed fifteen café-au-lait spots and axillary freckling, as well as a Lisch nodule in the left eye, strabismus, high-arched palate, malocclusion, severe kyphoscoliosis, bilateral calcaneovalgus foot, mild generalized hypotonia, hyperactivity and deficits of speech-related abilities. NF1 genomic rearrangements through multiplex ligation-dependent probe amplification (MLPA) detected an heterozygous deletion of the whole NF1 gene. Array comparative genomic hybridization (a-CGH) analysis defined a 17q11.2 deletion of about 1 Mb (breakpoints at positions 29,124,299 and 30,151,654), which involved different genes (partially CRLF3, ATAD5, TEFM, ADAP2, RNF135, OMG, EVI2B, EVI2A, RAB11FIP4), including NF1. Patient 2 showed growth and developmental delay, supravalvular pulmonary stenosis, twenty-five café-au-lait spots, axillary freckling, craniofacial dysmorphic features, short neck with pterygium, limb abnormalities and foci of neural dysplasia on brain magnetic resonance imaging (MRI). MLPA detected an heterozygous deletion of NF1, which was detailed by a-CGH indicating the positions 29,124,299 and 30,326,958 as its breakpoints, and which included aside from the genes deleted in Patient 1 also COPRS, UTP6 and partially SUZ12. Fluorescent in situ hybridization (FISH) analysis of the parents documented a de novo origin of the deletions in both cases. Conclusions The present report will likely provide further insights and a better characterization of NF1 microdeletion syndrome.
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Affiliation(s)
- Gregorio Serra
- Department of Sciences for Health Promotion and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Vincenzo Antona
- Department of Sciences for Health Promotion and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Giovanni Corsello
- Department of Sciences for Health Promotion and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy
| | - Federico Zara
- Laboratory of Neurogenetics and Neuroscience, Institute G. Gaslini, Genoa, Italy
| | - Ettore Piro
- Department of Sciences for Health Promotion and Mother and Child Care "G. D'Alessandro", University of Palermo, Palermo, Italy.
| | - Raffaele Falsaperla
- Unit of Pediatrics and Pediatric Emergency, University Hospital "Policlinico-Vittorio Emanuele", Catania, Italy
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15
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Brussa Reis L, Turchetto-Zolet AC, Fonini M, Ashton-Prolla P, Rosset C. The Role of Co-Deleted Genes in Neurofibromatosis Type 1 Microdeletions: An Evolutive Approach. Genes (Basel) 2019; 10:E839. [PMID: 31652930 PMCID: PMC6896060 DOI: 10.3390/genes10110839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/11/2019] [Accepted: 09/16/2019] [Indexed: 12/16/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) is a cancer predisposition syndrome that results from dominant loss-of-function mutations mainly in the NF1 gene. Large rearrangements are present in 5-10% of affected patients, generally encompass NF1 neighboring genes, and are correlated with a more severe NF1 phenotype. Evident genotype-phenotype correlations and the importance of the co-deleted genes are difficult to establish. In our study we employed an evolutionary approach to provide further insights into the understanding of the fundamental function of genes that are co-deleted in subjects with NF1 microdeletions. Our goal was to access the ortholog and paralog relationship of these genes in primates and verify if purifying or positive selection are acting on these genes. Fourteen genes were analyzed in twelve mammalian species. Of these, four and ten genes showed positive selection and purifying selection, respectively. The protein, RNF135, showed three sites under positive selection at the RING finger domain, which may have been selected to increase efficiency in ubiquitination routes in primates. The phylogenetic analysis suggests distinct evolutionary constraint between the analyzed genes. With these analyses, we hope to help clarify the correlation of the co-deletion of these genes and the more severe phenotype of NF1.
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Affiliation(s)
- Larissa Brussa Reis
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul 90035-903, Brazil.
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, UFRGS, Porto Alegre, Rio Grande do Sul 91501-970, Brazil.
| | - Andreia Carina Turchetto-Zolet
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, UFRGS, Porto Alegre, Rio Grande do Sul 91501-970, Brazil.
| | - Maievi Fonini
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul 90035-903, Brazil.
| | - Patricia Ashton-Prolla
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul 90035-903, Brazil.
- Programa de Pós-Graduação em Genética e Biologia Molecular, Departamento de Genética, UFRGS, Porto Alegre, Rio Grande do Sul 91501-970, Brazil.
- Serviço de Genética Médica do Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre, Rio Grande do Sul 90035-903, Brazil.
| | - Clévia Rosset
- Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Rio Grande do Sul 90035-903, Brazil.
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16
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Watanabe R, Nakanishi Y, Nijoukubo D, Teraoka H, Ogasawara H, Mori K. Usefulness of zebrafish in evaluating drug-induced teratogenicity in cardiovascular system. Drug Chem Toxicol 2018; 42:649-656. [PMID: 30025483 DOI: 10.1080/01480545.2018.1485686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
To confirm the usefulness of zebrafish for evaluating the teratogenic potential of drug candidates, the effect of O-ethylhydroxylamine hydrochloride (OHY), which induces mutagenesis by methylation, was evaluated in teratogenicity studies in rats and zebrafish. In the rat teratogenicity study, OHY-induced cardiovascular malformations such as increased abnormal vascular structures and ventricular septal defects. In the teratogenicity study using zebrafish-injected microspheres and green fluorescent protein-expressing Tg zebrafish (flk1:EGFP), OHY exposure was associated with the loss or malformation of the mandibular arch, opercular artery, and fourth branchial arch. These results suggested that OHY-induced external malformations in zebrafish eleutheroembryos adequately reflect OHY's teratogenicity in rat fetuses. Moreover, the zebrafish teratogenicity study incorporating vascular morphological examinations, including those of blood vessels in the heart, head and trunk, is an easy and reliable screening method to detect potential drug-induced teratogenicity and phenotypic characteristics.
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Affiliation(s)
- Ryo Watanabe
- Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd, Edogawa-ku, Tokyo, Japan.,Drug Discovery Technology Function, Asubio Pharma Co., Ltd, Chuo-ku Kobe, Japan
| | - Yuki Nakanishi
- Drug Discovery Technology Function, Asubio Pharma Co., Ltd, Chuo-ku Kobe, Japan
| | - Daisuke Nijoukubo
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan
| | - Hiroki Teraoka
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Hokkaido, Japan
| | - Hiroyuki Ogasawara
- Drug Discovery Technology Function, Asubio Pharma Co., Ltd, Chuo-ku Kobe, Japan
| | - Kazuhiko Mori
- Medicinal Safety Research Laboratories, Daiichi Sankyo Co., Ltd, Edogawa-ku, Tokyo, Japan
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17
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Razaghi B, Steele SL, Prykhozhij SV, Stoyek MR, Hill JA, Cooper MD, McDonald L, Lin W, Daugaard M, Crapoulet N, Chacko S, Lewis SM, Scott IC, Sorensen PHB, Berman JN. hace1 Influences zebrafish cardiac development via ROS-dependent mechanisms. Dev Dyn 2017; 247:289-303. [PMID: 29024245 DOI: 10.1002/dvdy.24600] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 08/23/2017] [Accepted: 09/15/2017] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND In this study, we reveal a previously undescribed role of the HACE1 (HECT domain and Ankyrin repeat Containing E3 ubiquitin-protein ligase 1) tumor suppressor protein in normal vertebrate heart development using the zebrafish (Danio rerio) model. We examined the link between the cardiac phenotypes associated with hace1 loss of function to the expression of the Rho small family GTPase, rac1, which is a known target of HACE1 and promotes ROS production via its interaction with NADPH oxidase holoenzymes. RESULTS We demonstrate that loss of hace1 in zebrafish via morpholino knockdown results in cardiac deformities, specifically a looping defect, where the heart is either tubular or "inverted". Whole-mount in situ hybridization of cardiac markers shows distinct abnormalities in ventricular morphology and atrioventricular valve formation in the hearts of these morphants, as well as increased expression of rac1. Importantly, this phenotype appears to be directly related to Nox enzyme-dependent ROS production, as both genetic inhibition by nox1 and nox2 morpholinos or pharmacologic rescue using ROS scavenging agents restores normal cardiac structure. CONCLUSIONS Our study demonstrates that HACE1 is critical in the normal development and proper function of the vertebrate heart via a ROS-dependent mechanism. Developmental Dynamics 247:289-303, 2018. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Babak Razaghi
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Shelby L Steele
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Sergey V Prykhozhij
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Matthew R Stoyek
- Department of Physiology & Biophysics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Jessica A Hill
- Department of Marine Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Matthew D Cooper
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Lindsay McDonald
- Department of Emergency Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - William Lin
- Undergraduate Program, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Mads Daugaard
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.,Vancouver Prostate Centre, Vancouver, British Columbia, Canada
| | | | - Simi Chacko
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada
| | - Stephen M Lewis
- Atlantic Cancer Research Institute, Moncton, New Brunswick, Canada
| | - Ian C Scott
- Department of Molecular Genetics, Hospital for Sick Children and University of Toronto, Toronto, Ontario, Canada
| | - Poul H B Sorensen
- Department of Molecular Oncology, British Columbia Cancer Research Centre, Vancouver, British Columbia, Canada.,Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jason N Berman
- Department of Pediatrics, Dalhousie University, Halifax, Nova Scotia, Canada.,IWK Health Centre, Halifax, Nova Scotia, Canada
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18
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Identification of an atypical microdeletion generating the RNF135-SUZ12 chimeric gene and causing a position effect in an NF1 patient with overgrowth. Hum Genet 2017; 136:1329-1339. [DOI: 10.1007/s00439-017-1832-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/26/2017] [Indexed: 02/02/2023]
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19
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Bist P, Kim SSY, Pulloor NK, McCaffrey K, Nair SK, Liu Y, Lin R, Krishnan MN. ArfGAP Domain-Containing Protein 2 (ADAP2) Integrates Upstream and Downstream Modules of RIG-I Signaling and Facilitates Type I Interferon Production. Mol Cell Biol 2017; 37:e00537-16. [PMID: 27956705 PMCID: PMC5335504 DOI: 10.1128/mcb.00537-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 10/28/2016] [Accepted: 12/06/2016] [Indexed: 01/15/2023] Open
Abstract
Transcription of type I interferon genes during RNA virus infection requires signal communication between several pattern recognition receptor (PRR)-adaptor complexes located at distinct subcellular membranous compartments and a central cytoplasmic TBK1-interferon regulatory factor 3 (IRF3) kinase-transcription factor module. However, how the cell integrates signal transduction through spatially distinct modules of antiviral signaling pathways is less defined. RIG-I is a major cytosolic PRR involved in the control of several RNA viruses. Here we identify ArfGAP domain-containing protein 2 (ADAP2) as a key novel scaffolding protein that integrates different modules of the RIG-I pathway, located at distinct subcellular locations, and mediates cellular antiviral type I interferon production. ADAP2 served to bridge the mitochondrial membrane-bound upstream RIG-I adaptor MAVS and the downstream cytosolic complex of NEMO (regulatory subunit of TBK1), TBK1, and IRF3, leading to IRF3 phosphorylation. Furthermore, independently, ADAP2 also functioned as a major orchestrator of the interaction of TBK1 with NEMO and IRF3. Mutational and in vitro cell-free reconstituted RIG-I signaling assay-based analyses identified that the ArfGAP domain of ADAP2 mediates the interferon response. TRAF3 acted as a trigger for ADAP2 to recruit RIG-I pathway component proteins into a single macromolecular complex. This study provides important novel insights into the assembly and integration of different modules of antiviral signaling cascades.
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Affiliation(s)
- Pradeep Bist
- Program on Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Susana Soo-Yeon Kim
- Program on Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Niyas Kudukil Pulloor
- Program on Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Kathleen McCaffrey
- Program on Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Sajith Kumar Nair
- Program on Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore, Singapore
| | - Yiliu Liu
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
| | - Rongtuan Lin
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
| | - Manoj N Krishnan
- Program on Emerging Infectious Diseases, Duke-NUS Graduate Medical School, Singapore, Singapore
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20
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Emerging genotype-phenotype relationships in patients with large NF1 deletions. Hum Genet 2017; 136:349-376. [PMID: 28213670 PMCID: PMC5370280 DOI: 10.1007/s00439-017-1766-y] [Citation(s) in RCA: 141] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 02/08/2017] [Indexed: 02/07/2023]
Abstract
The most frequent recurring mutations in neurofibromatosis type 1
(NF1) are large deletions encompassing the NF1
gene and its flanking regions (NF1
microdeletions). The majority of these deletions encompass 1.4-Mb and are associated
with the loss of 14 protein-coding genes and four microRNA genes. Patients with
germline type-1 NF1 microdeletions frequently
exhibit dysmorphic facial features, overgrowth/tall-for-age stature, significant
delay in cognitive development, large hands and feet, hyperflexibility of joints and
muscular hypotonia. Such patients also display significantly more cardiovascular
anomalies as compared with patients without large deletions and often exhibit
increased numbers of subcutaneous, plexiform and spinal neurofibromas as compared
with the general NF1 population. Further, an extremely high burden of internal
neurofibromas, characterised by >3000 ml tumour volume, is encountered
significantly, more frequently, in non-mosaic NF1
microdeletion patients than in NF1 patients lacking such deletions. NF1 microdeletion patients also have an increased risk of
malignant peripheral nerve sheath tumours (MPNSTs); their lifetime MPNST risk is
16–26%, rather higher than that of NF1 patients with intragenic NF1 mutations (8–13%). NF1 microdeletion patients, therefore, represent a high-risk group for
the development of MPNSTs, tumours which are very aggressive and difficult to treat.
Co-deletion of the SUZ12 gene in addition to
NF1 further increases the MPNST risk in
NF1 microdeletion patients. Here, we summarise
current knowledge about genotype–phenotype relationships in NF1 microdeletion patients and discuss the potential role of the genes
located within the NF1 microdeletion interval
whose haploinsufficiency may contribute to the more severe clinical
phenotype.
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21
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Regulators and Effectors of Arf GTPases in Neutrophils. J Immunol Res 2015; 2015:235170. [PMID: 26609537 PMCID: PMC4644846 DOI: 10.1155/2015/235170] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 09/30/2015] [Indexed: 12/22/2022] Open
Abstract
Polymorphonuclear neutrophils (PMNs) are key innate immune cells that represent the first line of defence against infection. They are the first leukocytes to migrate from the blood to injured or infected sites. This process involves molecular mechanisms that coordinate cell polarization, delivery of receptors, and activation of integrins at the leading edge of migrating PMNs. These phagocytes actively engulf microorganisms or form neutrophil extracellular traps (NETs) to trap and kill pathogens with bactericidal compounds. Association of the NADPH oxidase complex at the phagosomal membrane for production of reactive oxygen species (ROS) and delivery of proteolytic enzymes into the phagosome initiate pathogen killing and removal. G protein-dependent signalling pathways tightly control PMN functions. In this review, we will focus on the small monomeric GTPases of the Arf family and their guanine exchange factors (GEFs) and GTPase activating proteins (GAPs) as components of signalling cascades regulating PMN responses. GEFs and GAPs are multidomain proteins that control cellular events in time and space through interaction with other proteins and lipids inside the cells. The number of Arf GAPs identified in PMNs is expanding, and dissecting their functions will provide important insights into the role of these proteins in PMN physiology.
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22
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Stoll C, Dott B, Alembik Y, Roth MP. Associated noncardiac congenital anomalies among cases with congenital heart defects. Eur J Med Genet 2015; 58:75-85. [DOI: 10.1016/j.ejmg.2014.12.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Accepted: 12/03/2014] [Indexed: 12/15/2022]
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