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Mariaselvam CM, Seth G, Kavadichanda C, Boukouaci W, Wu CL, Costes B, Thabah MM, Krishnamoorthy R, Leboyer M, Negi VS, Tamouza R. Low C4A copy numbers and higher HERV gene insertion contributes to increased risk of SLE, with absence of association with disease phenotype and disease activity. Immunol Res 2024:10.1007/s12026-024-09475-8. [PMID: 38594415 DOI: 10.1007/s12026-024-09475-8] [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: 01/18/2024] [Accepted: 03/23/2024] [Indexed: 04/11/2024]
Abstract
Low copy numbers (CNs) of C4 genes are associated with systemic autoimmune disorders and affects autoantibody diversity and disease subgroups. The primary objective of this study was to characterize diversity of complement (C4) and C4-Human Endogenous Retrovirus (HERV) gene copy numbers in SLE. We also sought to assess the association of C4 and C4-HERV CNs with serum complement levels, autoantibodies, disease phenotypes and activity. Finally, we checked the association of C4 and HERV CNs with specific HLA alleles. Genomic DNA from 70 SLE and 90 healthy controls of south Indian Tamil origin were included. Demographic, clinical and serological data was collected in a predetermined proforma. CNs of C4A and C4B genes and the frequency of insertion of 6.4kb HERV within C4 gene (C4AL, C4BL) was determined using droplet digital polymerase chain reaction (ddPCR). A four digit high resolution HLA genotyping was done using next generation sequencing. In our cohort, the total C4 gene copies ranged from 2 to 6. Compared to controls, presence of two or less copies of C4A gene was associated with SLE risk (p = 0.005; OR = 2.79; 95% CI = 1.29-6.22). Higher frequency of HERV insertion in C4A than in C4B increases such risk (p = 0.000; OR = 12.67; 95% CI = 2.80-115.3). AL-AL-AL-BS genotype was significantly higher in controls than SLE (9%vs1%, p = 0.04; OR = 0.15, 95% CI = 0.00-0.16). Distribution of HLA alleles was not different in SLE compared to controls as well as in SLE subjects with ≤ 2 copies and > 2 copies of C4A, but HLA allele distribution was diverse in subjects with C4B ≤ 2 copies and > 2 copies. Finally, there was no correlation between the C4 and the C4-HERV diversity and complement levels, autoantibodies, disease phenotypes and activity. In conclusion, our data show that, low C4A copy number and higher insertion of HERV-K in C4A increases the risk for SLE. C4 and C4-HERV CNs did not correlate with serum complements, autoantibodies, disease phenotypes and activity in SLE. Further validation in a larger homogenous SLE cohort is needed.
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Affiliation(s)
- Christina Mary Mariaselvam
- Department of Clinical Immunology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry, 605 006, India.
- AP-HP, DMU IMPACT, FHU ADAPT, Fondation FondaMental, IMRB, Translational Neuropsychiatry, INSERM UMR 955, Univ Paris Est Créteil, Créteil, F-94010, France.
| | - Gaurav Seth
- Department of Clinical Immunology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry, 605 006, India
| | - Chengappa Kavadichanda
- Department of Clinical Immunology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry, 605 006, India
| | - Wahid Boukouaci
- AP-HP, DMU IMPACT, FHU ADAPT, Fondation FondaMental, IMRB, Translational Neuropsychiatry, INSERM UMR 955, Univ Paris Est Créteil, Créteil, F-94010, France
| | - Ching-Lien Wu
- AP-HP, DMU IMPACT, FHU ADAPT, Fondation FondaMental, IMRB, Translational Neuropsychiatry, INSERM UMR 955, Univ Paris Est Créteil, Créteil, F-94010, France
| | - Bruno Costes
- IMRB, INSERM U955, Univ Paris Est Créteil, Créteil, F-94010, France
| | - Molly Mary Thabah
- Department of Clinical Immunology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry, 605 006, India
| | - Rajagopal Krishnamoorthy
- AP-HP, DMU IMPACT, FHU ADAPT, Fondation FondaMental, IMRB, Translational Neuropsychiatry, INSERM UMR 955, Univ Paris Est Créteil, Créteil, F-94010, France
| | - Marion Leboyer
- AP-HP, DMU IMPACT, FHU ADAPT, Fondation FondaMental, IMRB, Translational Neuropsychiatry, INSERM UMR 955, Univ Paris Est Créteil, Créteil, F-94010, France
| | - Vir Singh Negi
- Department of Clinical Immunology, Jawaharlal Institute of Postgraduate Medical Education and Research (JIPMER), Puducherry, 605 006, India
| | - Ryad Tamouza
- AP-HP, DMU IMPACT, FHU ADAPT, Fondation FondaMental, IMRB, Translational Neuropsychiatry, INSERM UMR 955, Univ Paris Est Créteil, Créteil, F-94010, France
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Zhang WN, Zhu H, Ma ZW, Yu J, Yang Y, Lu XB, Lv YF, Wang XD. Subcutaneous adipose tissue alteration in aging process associated with thyroid hormone signaling. BMC Med Genomics 2023; 16:202. [PMID: 37626392 PMCID: PMC10463827 DOI: 10.1186/s12920-023-01641-5] [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: 05/09/2023] [Accepted: 08/22/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Functional changes in subcutaneous adipose tissue (SAT) occur earlier in the aging process and play an important role in the occurrence and development of age-related metabolic diseases. The mechanism of this phenomenon is still unclear, and the change in adipose tissue with age is poorly understood. METHODS We used transcriptome sequencing (RNA seq) to screen differentially expressed genes at the mRNA level, and analyzed the functional characteristics of the differential genes through GO and KEGG analysis in human SAT of all ages. In order to clarify the specific mechanism of the functional change, we analyzed the chromatin accessibility in the promoter region in the same SAT used in the RNA seq by the assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) and obtained the functional genes in SAT changed with age. To verify these changes, we enlarged our sample content of human SAT. The primary mice adipocytes were extracted and stimulated by thyroid hormone of different concentration to construct an animal model, and the expression of the genes were determined through real-time Polymerase Chain Reaction(RT-PCR). The oxygen consumption test and immunofluorescence staining were used to determine the mitochondrial function of SAT. RESULTS RNA-seq showed characteristic gene expression of young and old human SAT, in which 331 genes were up-regulated and 349 genes were down-regulated. ATAC-seq, RNA-seq, combined with the mouse prediction model, determined the functional changed characteristics of seven genes. All these genes expressed differently in SAT of different ages, in which, NCF1, NLRP3, DUOX1 showed positive correlation with age; The expression of IFI30, P2RX1, P2RX6, PRODH, however, decreased with age. And all these genes showed dose dependent alternations under treatment of triiodothyroxine in mice SAT. The oxygen consumption rate revealed significant changes of the mitochondrial function and ROS accumulation in human SAT of different ages. CONCLUSION In elderly individuals, the function, in addition to distribution, of SAT undergoes significant changes, primarily in mitochondria, which may be due to insensitivity to thyroid hormone signaling. These results identified seven novel genes regulated by thyroid hormone, exhibiting significant changes in SAT of different age, and are probably related to the dysfunction of the aged SAT due to the mitochondrial damage and ROS accumulation.
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Affiliation(s)
- Wen-Na Zhang
- Division of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Hao Zhu
- Division of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Zhen-Wu Ma
- Division of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Jing Yu
- Division of Geriatric Endocrinology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Yun Yang
- Division of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Xuan-Bei Lu
- Division of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China
| | - Yi-Fan Lv
- Division of Geriatric Endocrinology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
| | - Xiao-Dong Wang
- Division of Endocrinology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China.
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Ambrosini C, Destefanis E, Kheir E, Broso F, Alessandrini F, Longhi S, Battisti N, Pesce I, Dassi E, Petris G, Cereseto A, Quattrone A. Translational enhancement by base editing of the Kozak sequence rescues haploinsufficiency. Nucleic Acids Res 2022; 50:10756-10771. [PMID: 36165847 PMCID: PMC9561285 DOI: 10.1093/nar/gkac799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 09/01/2022] [Accepted: 09/22/2022] [Indexed: 11/28/2022] Open
Abstract
A variety of single-gene human diseases are caused by haploinsufficiency, a genetic condition by which mutational inactivation of one allele leads to reduced protein levels and functional impairment. Translational enhancement of the spare allele could exert a therapeutic effect. Here we developed BOOST, a novel gene-editing approach to rescue haploinsufficiency loci by the change of specific single nucleotides in the Kozak sequence, which controls translation by regulating start codon recognition. We evaluated for translational strength 230 Kozak sequences of annotated human haploinsufficient genes and 4621 derived variants, which can be installed by base editing, by a high-throughput reporter assay. Of these variants, 149 increased the translation of 47 Kozak sequences, demonstrating that a substantial proportion of haploinsufficient genes are controlled by suboptimal Kozak sequences. Validation of 18 variants for 8 genes produced an average enhancement in an expression window compatible with the rescue of the genetic imbalance. Base editing of the NCF1 gene, whose monoallelic loss causes chronic granulomatous disease, resulted in the desired increase of NCF1 (p47phox) protein levels in a relevant cell model. We propose BOOST as a fine-tuned approach to modulate translation, applicable to the correction of dozens of haploinsufficient monogenic disorders independently of the causing mutation.
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Affiliation(s)
- Chiara Ambrosini
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Eliana Destefanis
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Eyemen Kheir
- Laboratory of Molecular Virology, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Francesca Broso
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Federica Alessandrini
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Sara Longhi
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Nicolò Battisti
- Laboratory of Translational Genomics, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Isabella Pesce
- Cell Analysis and Separation Core Facility, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Erik Dassi
- Laboratory of RNA Regulatory Networks, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
| | - Gianluca Petris
- Medical Research Council Laboratory of Molecular Biology (MRC LMB), Cambridge CB2 0QH, UK
| | - Anna Cereseto
- Laboratory of Molecular Virology, Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Trento 38123, Italy
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Yuan YH, Liu J, You YG, Chen XH, Yuan LC, Wen Y, Li HY, Zhang Y. Transcriptomic Analysis of Mycobacterium leprae-Stimulated Response in Peripheral Blood Mononuclear Cells Reveal Potential Biomarkers for Early Diagnosis of Leprosy. Front Cell Infect Microbiol 2022; 11:714396. [PMID: 34993156 PMCID: PMC8724050 DOI: 10.3389/fcimb.2021.714396] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/18/2021] [Indexed: 11/16/2022] Open
Abstract
We aimed to identify an unique host transcriptional signature in peripheral blood mononuclear cells (PBMCs) in response to Mycobacterium leprae antigens to distinguish between patients with leprosy and non-leprosy controls for early diagnosis of the disease. Sixteen individuals were enrolled in the discovery cohort [eight patients with leprosy, comprising four multibacillary (MB) and four paucibacillary (PB); and eight non-leprosy controls, comprising four healthy house contacts (HHCs) and four endemic controls (ECs)]. The differences in the transcriptome response of PBMCs to M. leprae sonicate antigen were evaluated between leprosy patients and non-leprosy controls, and 12 differentially expressed genes (CCL2/MCP-1, IL-8, JAKM, ATP, ND1, SERP, FLJ10489, LINC00659, LOC34487, LOC101928143, MIR22, and NCF1C) were identified. The accuracy of the 12 differentially expressed genes was further validated for the diagnosis of leprosy using real-time quantitative PCR in 82 individuals (13 MB, 10 PB, 37 HHCs, and 22 ECs) in the validation cohort. We found that a 5 gene signature set IL-8, CCL2/MCP-1, SERP, LINC00659 and FLJ10489 had a suitable performance in discriminating leprosy from ECs. In addition, elevated expression of IL-8, CCL2/MCP-1, SERP and LINC00659 was associated with MB diagnosis compared with ECs, whereas increased expression of IL-8, CCL2/MCP-1, SERP and FLJ10489 was found to be useful biomarkers for PB diagnosis from ECs. Moreover, we found decreased expression of NCF1C among leprosy patients could distinguish leprosy from HHCs, whereas higher expression of CCL2 among MB than PB could distinguish different leprosy patients. In conclusion, among the 12 candidate host genes identified, a three gene signature IL-8, CCL2/MCP-1, and SERP showed the best performance in distinguishing leprosy patients from healthy controls. These findings may have implications for developing a rapid blood-based test for early diagnosis of leprosy.
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Affiliation(s)
- You-Hua Yuan
- Department of Clinical Microbiology, Henan Provincial People's Hospital, People's Hospital of Zhengzhou University and People's Hospital of Henan University, Zhengzhou, China
| | - Jian Liu
- Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Research on Prevention and Treatment of Tropical Diseases, Capital Medical University, Beijing, China
| | - Yuan-Gang You
- Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Research on Prevention and Treatment of Tropical Diseases, Capital Medical University, Beijing, China
| | - Xiao-Hua Chen
- Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Research on Prevention and Treatment of Tropical Diseases, Capital Medical University, Beijing, China
| | - Lian-Chao Yuan
- Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Research on Prevention and Treatment of Tropical Diseases, Capital Medical University, Beijing, China
| | - Yan Wen
- Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Research on Prevention and Treatment of Tropical Diseases, Capital Medical University, Beijing, China
| | - Huan Ying Li
- Beijing Tropical Medicine Research Institute, Beijing Friendship Hospital, Capital Medical University, Beijing, China.,Beijing Key Laboratory for Research on Prevention and Treatment of Tropical Diseases, Capital Medical University, Beijing, China
| | - Ying Zhang
- State Key Laboratory for the Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Bakry O, Shoeib M, Soliman S, Kamal L. Neutrophil Cytosolic Factor-1 Genotyping in Acne Vulgaris. Skin Pharmacol Physiol 2021; 34:51-56. [PMID: 33596590 DOI: 10.1159/000513053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 11/13/2020] [Indexed: 11/19/2022]
Abstract
Acne vulgaris (AV) is a very common inflammatory dermatosis. It has a complex pathogenesis in which oxidative stress plays an important role. Neutrophil cytosolic factor (NCF)-1 gene encodes for NCF1 protein which shares in reactive oxygen species (ROS) production. Copy number variation (CNV) is a type of genetic variance in which gene copies are duplicated or deleted. The current work aimed to detect the association between NCF1 CNV and NCF-1 genotypes and AV to explore their possible role in increased disease risk or influencing its clinical presentation. Twenty-five cases with AV and 25 age- and gender-matched healthy volunteers were selected. NCF1 CNV and genotypes were determined using quantitative real-time polymerase chain reaction. NCF1 copy number was significantly increased in patients compared to the control group (p = 0.02). Higher copy number increased the risk of occurrence of AV by about 4-fold. The NCF1 genotype was more prevalent in patients (72%) compared to NCF1B (24%) and NCF1C (4%) variants, while NCF1B and NCF1C variants (68%) were more prevalent in the control group. The NCF1B genotype decreased the risk of occurrence of AV by 0.2-fold. NCF1 was significantly associated with cases more than controls (p = 0.005). It increased the risk of occurrence of acne by 5.4-fold. There was significant association between NCF1 copy number and disease duration where higher number was associated with long disease duration (p = 0.03). Higher copy number was also associated with the NCF1 genotype (p = 0.01). This study suggests that increased copy number of NCF1 gene may be a predisposing factor for AV development. However, the presence of NCF1B and NCF1C variants lowers ROS production and subsequently decreases the risk of development of AV.
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Affiliation(s)
- Ola Bakry
- Department of Dermatology, Andrology and STDs, Faculty of Medicine, Menoufiya University, Shibeen El Koom, Egypt,
| | - Mohamed Shoeib
- Department of Dermatology, Andrology and STDs, Faculty of Medicine, Menoufiya University, Shibeen El Koom, Egypt
| | - Shimaa Soliman
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Menoufiya University, Shibeen El Koom, Egypt.,Medical Biochemistry Unit, Department of Pathology, College of Medicine, Qassim University, Buraydah, Saudi Arabia
| | - Lamiaa Kamal
- Department of Dermatology, Andrology and STDs, Faculty of Medicine, Menoufiya University, Shibeen El Koom, Egypt
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Klatt D, Cheng E, Hoffmann D, Santilli G, Thrasher AJ, Brendel C, Schambach A. Differential Transgene Silencing of Myeloid-Specific Promoters in the AAVS1 Safe Harbor Locus of Induced Pluripotent Stem Cell-Derived Myeloid Cells. Hum Gene Ther 2020; 31:199-210. [PMID: 31773990 DOI: 10.1089/hum.2019.194] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Targeted integration into a genomic safe harbor, such as the AAVS1 locus on chromosome 19, promises predictable transgene expression and reduces the risk of insertional mutagenesis in the host genome. The application of gamma-retroviral long terminal repeat (LTR)-driven vectors, which semirandomly integrate into the genome, has previously caused severe adverse events in some clinical studies due to transactivation of neighboring proto-oncogenes. Consequently, the site-specific integration of a therapeutic transgene into a genomic safe harbor locus would allow stable genetic correction with a reduced risk of insertional mutagenesis. However, recent studies revealed that transgene silencing, especially in case of weaker cell type-specific promoters, can occur in the AAVS1 locus of human pluripotent stem cells (PSCs) and can impede transgene expression during differentiation. In this study, we aimed to correct p47phox deficiency, which is the second most common cause of chronic granulomatous disease, by insertion of a therapeutic p47phox transgene into the AAVS1 locus of human induced PSCs (iPSCs) using CRISPR-Cas9. We analyzed transgene expression and functional correction from three different myeloid-specific promoters (miR223, CatG/cFes, and myeloid-related protein 8 [MRP8]). Upon myeloid differentiation of corrected iPSC clones, we observed that the miR223 and CatG/cFes promoters achieved therapeutically relevant levels of p47phox expression and nicotinamide adenine dinucleotide phosphate oxidase activity, whereas the MRP8 promoter was less efficient. Analysis of the different promoters revealed high CpG methylation of the MRP8 promoter in differentiated cells, which correlated with the transgene expression data. In summary, we identified the miR223 and CatG/cFes promoters as cell type-specific promoters that allow stable transgene expression in the AAVS1 locus of iPSC-derived myeloid cells. Our findings further indicate that promoter silencing can occur in the AAVS1 safe harbor locus in differentiated hematopoietic cells and that a comparison of different promoters is necessary to achieve optimal transgene expression for therapeutic application of iPSC-derived cells.
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Affiliation(s)
- Denise Klatt
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Germany
| | - Erica Cheng
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Germany
| | - Dirk Hoffmann
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Germany
| | - Giorgia Santilli
- Infection, Immunity and Inflammation Program, Molecular and Cellular Immunology Section, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | - Adrian J Thrasher
- Infection, Immunity and Inflammation Program, Molecular and Cellular Immunology Section, UCL Great Ormond Street Institute of Child Health, University College London, London, United Kingdom.,Great Ormond Street Hospital NHS Foundation Trust, London, United Kingdom
| | - Christian Brendel
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,REBIRTH Cluster of Excellence, Hannover Medical School, Hannover, Germany.,Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
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7
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Urbonaviciute V, Luo H, Sjöwall C, Bengtsson A, Holmdahl R. Low Production of Reactive Oxygen Species Drives Systemic Lupus Erythematosus. Trends Mol Med 2019; 25:826-835. [DOI: 10.1016/j.molmed.2019.06.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/04/2019] [Accepted: 06/05/2019] [Indexed: 12/12/2022]
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8
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Kuhns DB, Hsu AP, Sun D, Lau K, Fink D, Griffith P, Huang DW, Priel DAL, Mendez L, Kreuzburg S, Zerbe CS, De Ravin SS, Malech HL, Holland SM, Wu X, Gallin JI. NCF1 (p47 phox)-deficient chronic granulomatous disease: comprehensive genetic and flow cytometric analysis. Blood Adv 2019; 3:136-147. [PMID: 30651282 PMCID: PMC6341190 DOI: 10.1182/bloodadvances.2018023184] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 12/02/2018] [Indexed: 11/20/2022] Open
Abstract
Mutations in NCF1 (p47phox) cause autosomal recessive chronic granulomatous disease (CGD) with abnormal dihydrorhodamine (DHR) assay and absent p47phox protein. Genetic identification of NCF1 mutations is complicated by adjacent highly conserved (>98%) pseudogenes (NCF1B and NCF1C). NCF1 has GTGT at the start of exon 2, whereas the pseudogenes each delete 1 GT (ΔGT). In p47phox CGD, the most common mutation is ΔGT in NCF1 (c.75_76delGT; p.Tyr26fsX26). Sequence homology between NCF1 and its pseudogenes precludes reliable use of standard Sanger sequencing for NCF1 mutations and for confirming carrier status. We first established by flow cytometry that neutrophils from p47phox CGD patients had negligible p47phox expression, whereas those from p47phox CGD carriers had ∼60% of normal p47phox expression, independent of the specific mutation in NCF1 We developed a droplet digital polymerase chain reaction (ddPCR) with 2 distinct probes, recognizing either the wild-type GTGT sequence or the ΔGT sequence. A second ddPCR established copy number by comparison with the single-copy telomerase reverse transcriptase gene, TERT We showed that 84% of p47phox CGD patients were homozygous for ΔGT NCF1 The ddPCR assay also enabled determination of carrier status of relatives. Furthermore, only 79.2% of normal volunteers had 2 copies of GTGT per 6 total (NCF1/NCF1B/NCF1C) copies, designated 2/6; 14.7% had 3/6, and 1.6% had 4/6 GTGT copies. In summary, flow cytometry for p47phox expression quickly identifies patients and carriers of p47phox CGD, and genomic ddPCR identifies patients and carriers of ΔGT NCF1, the most common mutation in p47phox CGD.
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Affiliation(s)
- Douglas B Kuhns
- Neutrophil Monitoring Laboratory, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Amy P Hsu
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - David Sun
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; and
| | - Karen Lau
- Neutrophil Monitoring Laboratory, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Danielle Fink
- Neutrophil Monitoring Laboratory, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Paul Griffith
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; and
| | - Da Wei Huang
- Lymphoid Malignances Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Debra A Long Priel
- Neutrophil Monitoring Laboratory, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Laura Mendez
- Neutrophil Monitoring Laboratory, Applied/Developmental Research Directorate, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Samantha Kreuzburg
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Christa S Zerbe
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Suk See De Ravin
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Harry L Malech
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Steven M Holland
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Xiaolin Wu
- Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD; and
| | - John I Gallin
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
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Abe H, Aoya D, Takeuchi HA, Inoue-Murayama M. Gene expression patterns of chicken neuregulin 3 in association with copy number variation and frameshift deletion. BMC Genet 2017; 18:69. [PMID: 28732471 PMCID: PMC5521077 DOI: 10.1186/s12863-017-0537-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 07/11/2017] [Indexed: 01/21/2023] Open
Abstract
Background Neuregulin 3 (NRG3) plays a key role in central nervous system development and is a strong candidate for human mental disorders. Thus, genetic variation in NRG3 may have some impact on a variety of phenotypes in non-mammalian vertebrates. Recently, genome-wide screening for short insertions and deletions in chicken (Gallus gallus) genomes has provided useful information about structural variation in functionally important genes. NRG3 is one such gene that has a putative frameshift deletion in exon 2, resulting in premature termination of translation. Our aims were to characterize the structure of chicken NRG3 and to compare expression patterns between NRG3 isoforms. Results Depending on the presence or absence of the 2-bp deletion in chicken NRG3, 3 breeds (red junglefowl [RJF], Boris Brown [BB], and Hinai-jidori [HJ]) were genotyped using flanking primers. In the commercial breeds (BB and HJ), approximately 45% of individuals had at least one exon 2 allele with the 2-bp deletion, whereas there was no deletion allele in RJF. The lack of a homozygous mutant indicated the existence of duplicated NRG3 segments in the chicken genome. Indeed, highly conserved elements consisting of exon 1, intron 1, exon 2, and part of intron 2 were found in the reference RJF genome, and quantitative PCR detected copy number variation (CNV) between breeds as well as between individuals. The copy number of conserved elements was significantly higher in chicks harboring the 2-bp deletion in exon 2. We identified 7 novel transcript variants using total mRNA isolated from the amygdala. Novel isoforms were found to lack the exon 2 cassette, which probably harbored the premature termination codon. The relative transcription levels of the newly identified isoforms were almost the same between chick groups with and without the 2-bp deletion, while chicks with the deletion showed significant suppression of the expression of previously reported isoforms. Conclusions A putative frameshift deletion and CNV in chicken NRG3 are structural mutations that occurred before the establishment of commercial chicken lines. Our results further suggest that the putative frameshift deletion in exon 2 may potentially affect the expression level of particular isoforms of chicken NRG3. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0537-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hideaki Abe
- Wildlife Research Center, Kyoto University, 2-24 Tanaka-Sekiden-cho, Sakyo, Kyoto, 606-8203, Japan.
| | - Daiki Aoya
- Akita Prefectural Livestock Experiment Station, 13-3 Kaisonumayachi, Jinguji, Daisen, Akita, 019-1701, Japan
| | - Hiro-Aki Takeuchi
- Department of Biological Science, Shizuoka University, 836 Ohya, Suruga, Shizuoka, 422-8529, Japan
| | - Miho Inoue-Murayama
- Wildlife Research Center, Kyoto University, 2-24 Tanaka-Sekiden-cho, Sakyo, Kyoto, 606-8203, Japan.,Wildlife Genome Collaborative Research Group, National Institute for Environmental Studies, 16-2 Onogawa, Tsukuba, Ibaraki, 305-8506, Japan
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10
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Olsson LM, Johansson ÅC, Gullstrand B, Jönsen A, Saevarsdottir S, Rönnblom L, Leonard D, Wetterö J, Sjöwall C, Svenungsson E, Gunnarsson I, Bengtsson AA, Holmdahl R. A single nucleotide polymorphism in theNCF1gene leading to reduced oxidative burst is associated with systemic lupus erythematosus. Ann Rheum Dis 2017; 76:1607-1613. [DOI: 10.1136/annrheumdis-2017-211287] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/30/2017] [Accepted: 05/05/2017] [Indexed: 01/02/2023]
Abstract
ObjectivesNcf1polymorphisms leading to low production of reactive oxygen species (ROS) are strongly associated with autoimmune diseases in animal models. The humanNCF1gene is very complex with both functional and non-functional gene copies and genotyping requires assays specific for functionalNCF1genes. We aimed at investigating association and function of the missense single nucleotide polymorphism (SNP), rs201802880 (here denoted NCF1-339) inNCF1with systemic lupus erythematosus (SLE).MethodsWe genotyped the NCF1-339 SNP in 973 Swedish patients with SLE and 1301 controls, using nested PCR and pyrosequencing. ROS production and gene expression of type 1 interferon-regulated genes were measured in isolated cells from subjects with different NCF1-339 genotypes.ResultsWe found an increased frequency of the NCF1-339 T allele in patients with SLE, 11% compared with 4% in controls, OR 3.0, 95% CI 2.4 to 3.9, p=7.0×10−20. The NCF1-339 T allele reduced extracellular ROS production in neutrophils (p=0.004) and led to an increase expression of type 1 interferon-regulated genes. In addition, the NCF1-339 T allele was associated with a younger age at diagnosis of SLE; mean age 30.3 compared with 35.9, p=2.0×1−6.ConclusionsThese results clearly demonstrate that a genetically controlled reduced production of ROS increases the risk of developing SLE and confirm the hypothesis that ROS regulate chronic autoimmune inflammatory diseases.
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11
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Merling RK, Kuhns DB, Sweeney CL, Wu X, Burkett S, Chu J, Lee J, Koontz S, Di Pasquale G, Afione SA, Chiorini JA, Kang EM, Choi U, De Ravin SS, Malech HL. Gene-edited pseudogene resurrection corrects p47 phox-deficient chronic granulomatous disease. Blood Adv 2017; 1:270-278. [PMID: 29296942 PMCID: PMC5727772 DOI: 10.1182/bloodadvances.2016001214] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/21/2016] [Indexed: 01/18/2023] Open
Abstract
Pseudogenes are duplicated genes with mutations rendering them nonfunctional. For single-gene disorders with homologous pseudogenes, the pseudogene might be a target for genetic correction. Autosomal-recessive p47phox-deficient chronic granulomatous disease (p47-CGD) is a life-threatening immune deficiency caused by mutations in NCF1, a gene with 2 pseudogenes, NCF1B and NCF1C. The most common NCF1 mutation, a GT deletion (ΔGT) at the start of exon 2 (>90% of alleles), is constitutive to NCF1B and NCF1C. NCF1 ΔGT results in premature termination, undetectable protein expression, and defective production of antimicrobial superoxide in neutrophils. We examined strategies for p47-CGD gene correction using engineered zinc-finger nucleases targeting the exon 2 ΔGT in induced pluripotent stem cells or CD34+ hematopoietic stem cells derived from p47-CGD patients. Correction of ΔGT in NCF1 pseudogenes restores oxidase function in p47-CGD, providing the first demonstration that targeted restoration of pseudogene function can correct a monogenic disorder.
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Affiliation(s)
- Randall K Merling
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Douglas B Kuhns
- Neutrophil Monitoring Laboratory, Applied/Developmental Research Directorate, and
| | - Colin L Sweeney
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Xiaolin Wu
- Genomics Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Sandra Burkett
- Molecular Cytogenetics Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD; and
| | - Jessica Chu
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Janet Lee
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Sherry Koontz
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Giovanni Di Pasquale
- Adeno-Associated Virus Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD
| | - Sandra A Afione
- Adeno-Associated Virus Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD
| | - John A Chiorini
- Adeno-Associated Virus Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD
| | - Elizabeth M Kang
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Uimook Choi
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Suk See De Ravin
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Harry L Malech
- Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
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12
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O'Neill S, Brault J, Stasia MJ, Knaus UG. Genetic disorders coupled to ROS deficiency. Redox Biol 2015; 6:135-156. [PMID: 26210446 PMCID: PMC4550764 DOI: 10.1016/j.redox.2015.07.009] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 07/15/2015] [Accepted: 07/16/2015] [Indexed: 12/24/2022] Open
Abstract
Maintaining the redox balance between generation and elimination of reactive oxygen species (ROS) is critical for health. Disturbances such as continuously elevated ROS levels will result in oxidative stress and development of disease, but likewise, insufficient ROS production will be detrimental to health. Reduced or even complete loss of ROS generation originates mainly from inactivating variants in genes encoding for NADPH oxidase complexes. In particular, deficiency in phagocyte Nox2 oxidase function due to genetic variants (CYBB, CYBA, NCF1, NCF2, NCF4) has been recognized as a direct cause of chronic granulomatous disease (CGD), an inherited immune disorder. More recently, additional diseases have been linked to functionally altered variants in genes encoding for other NADPH oxidases, such as for DUOX2/DUOXA2 in congenital hypothyroidism, or for the Nox2 complex, NOX1 and DUOX2 as risk factors for inflammatory bowel disease. A comprehensive overview of novel developments in terms of Nox/Duox-deficiency disorders is presented, combined with insights gained from structure-function studies that will aid in predicting functional defects of clinical variants.
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Affiliation(s)
- Sharon O'Neill
- Conway Institute, University College Dublin, Dublin, Ireland
| | - Julie Brault
- Université Grenoble Alpes, TIMC-IMAG Pôle Biologie, CHU de Grenoble, Grenoble, France; CGD Diagnosis and Research Centre, Pôle Biologie, CHU de Grenoble, Grenoble, France
| | - Marie-Jose Stasia
- Université Grenoble Alpes, TIMC-IMAG Pôle Biologie, CHU de Grenoble, Grenoble, France; CGD Diagnosis and Research Centre, Pôle Biologie, CHU de Grenoble, Grenoble, France
| | - Ulla G Knaus
- Conway Institute, University College Dublin, Dublin, Ireland.
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13
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Xu W, Ma L, Li W, Brunson TA, Tian X, Richards J, Li Q, Bythwood T, Yuan Z, Song Q. Functional pseudogenes inhibit the superoxide production. PRECISION MEDICINE 2015; 1:e745. [PMID: 26086043 PMCID: PMC4467915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We recently discovered a dynamic copy number variation on the NCF1 (neutrophil cytosolic factor 1) pseudogenes in human populations. In this study, we investigated whether these pseudogenes are functional or junk as described before. We sequenced the RNAs transcribed from the genome of this locus, and discovered over 10 splicing isoforms from the NCF1 pseudogenes. We cloned 4 splicing isoforms into expression vectors and introduced them into human vascular endothelial cells by transient transfection. We then used two chemical approaches to measure the superoxide production in the cells with and without these pseudogene overexpression. Our data showed that three pseudogene splicing products remarkably reduced the superoxide production after the GFP (Green fluorescent protein) normalization. We used an anti-HA (Hemagglutinin A) tag antibody to stain the cells and confirmed that the proteins transcribed from the NCF1 pseudogene were exclusively localized in the cytoplasm in the perinuclear area in the transient transfection assays. We further examined the tissue distribution of these splicing isoforms of NCF1 pseudogenes in human tissues by quantitative real-time PCR analysis. Our data showed that although these splicing variants are ubiquitously expressed in non-immune tissues in human, they seem to be under a tight control of transcription regulation and show a non-random distribution pattern across tissues. This study challenges the concept that pseudogenes in human genome are only junks without biological functions. Moreover, it suggests that those pseudogenes in human genome may serve as a natural resource for novel drug discovery.
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Affiliation(s)
- Wei Xu
- Department of Cardiovascular Medicine, Key Laboratory of Molecular Cardiology, Cardiovascular Research Center, and Key Laboratory of Environment and Genes Related to Diseases, First Affiliated Hospital of Medical School, Xi’an Jiaotong University, Xi’an, 710061, Shaanxi, China
- Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, Georgia 30310, USA
| | - Li Ma
- Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, Georgia 30310, USA
- 4DGENOME Inc, Atlanta,Georgia 30092, GA
| | - Wenzhi Li
- Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, Georgia 30310, USA
| | - Tiffany A. Brunson
- Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, Georgia 30310, USA
| | - Xiaohua Tian
- Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, Georgia 30310, USA
| | - Jendai Richards
- Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, Georgia 30310, USA
| | - Qiling Li
- Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, Georgia 30310, USA
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, 710061, Shaanxi, China
| | - Tameka Bythwood
- Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, Georgia 30310, USA
| | - Zuyi Yuan
- Department of Cardiovascular Medicine, Key Laboratory of Molecular Cardiology, Cardiovascular Research Center, and Key Laboratory of Environment and Genes Related to Diseases, First Affiliated Hospital of Medical School, Xi’an Jiaotong University, Xi’an, 710061, Shaanxi, China
| | - Qing Song
- Department of Cardiovascular Medicine, Key Laboratory of Molecular Cardiology, Cardiovascular Research Center, and Key Laboratory of Environment and Genes Related to Diseases, First Affiliated Hospital of Medical School, Xi’an Jiaotong University, Xi’an, 710061, Shaanxi, China
- Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, Georgia 30310, USA
- Department of Medicine, Morehouse School of Medicine, Atlanta, Georgia 30310, USA
- Department of Obstetrics and Gynecology, First Affiliated Hospital, Xi’an Jiaotong University, Xi’an, 710061, Shaanxi, China
- 4DGENOME Inc, Atlanta,Georgia 30092, GA
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14
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Zhang Z, Wang X, Li R, Ju Z, Qi C, Zhang Y, Guo F, Luo G, Li Q, Wang C, Zhong J, Xu Y, Huang J. Genetic mutations potentially cause two novel NCF1 splice variants up-regulated in the mammary gland, blood and neutrophil of cows infected by Escherichia coli. Microbiol Res 2015; 174:24-32. [PMID: 25946326 DOI: 10.1016/j.micres.2015.03.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 03/07/2015] [Accepted: 03/09/2015] [Indexed: 11/18/2022]
Abstract
Neutrophil cytosolic factor 1 (NCF1) plays a crucial role in host defense against microbial pathogens. In this study, we investigated the potential alternative splicing patterns, expression and splice-relevant single nucleotide polymorphisms (SNPs) of the bovine NCF1 gene to increase insights into its potential role against bovine mastitis caused by Escherichia coli infection. Using RT-PCR and clone sequencing methods, we found two novel splice variants designed as NCF1-TV1 (retained intron 6) and NCF1-TV2 (retained part of intron 8), respectively, encoding two putative truncated proteins (239AA and 283AA). Two splice variants were drastically up-regulated in the mastitis-infected cows' mammary tissues, blood and neutrophils compared with these of healthy cows using real-time RT-PCR. Genomic sequencing analysis identified four novel SNPs g.10112 G>A, g.10766 T>C, SNPs g.12085 G>A and g.12430 T>C at the ends of intron 6 and intron 8 of NCF1. ESE motif predicted that the SNP (g.10766 T>C) might affect the binding with splicing-related factors and subsequently caused the production of aberrant splice variant NCF1-TV1, which is one of the potential reasons that the functional SNP was associated with increased milk somatic cell score in cow. Our results would help in better understanding the NCF1 gene function in the process against pathogen infection, and the effect of splicing-related SNP on the production of aberrant splice variant and careful functional characterization in dairy cattle.
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Affiliation(s)
- Zijing Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Xiuge Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1)
| | - Rongling Li
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1)
| | - Zhihua Ju
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1)
| | - Chao Qi
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1)
| | - Yan Zhang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1)
| | - Fang Guo
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Guojing Luo
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China
| | - Qiuling Li
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1)
| | - Changfa Wang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1)
| | - Jifeng Zhong
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1)
| | - Yinxue Xu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, People's Republic of China.
| | - Jinming Huang
- Dairy Cattle Research Center, Shandong Academy of Agricultural Sciences, No. 159 North of Industry Road, Jinan, Shandong 250131, People's Republic of China(1).
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15
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Different unequal cross-over events between NCF1 and its pseudogenes in autosomal p47(phox)-deficient chronic granulomatous disease. Biochim Biophys Acta Mol Basis Dis 2013; 1832:1662-72. [PMID: 23688784 DOI: 10.1016/j.bbadis.2013.05.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 04/05/2013] [Accepted: 05/02/2013] [Indexed: 11/20/2022]
Abstract
Chronic granulomatous disease (CGD) is a rare congenital disorder in which phagocytes cannot generate superoxide (O2(-)) and other microbicidal oxidants due to mutations in one of the five components of the O2(-)-generating NADPH oxidase complex. The most common autosomal subtype of CGD is caused by mutations in NCF1, encoding the NADPH subunit p47(phox). Usually, these mutations are the result of unequal exchange of chromatid between NCF1 and one of its two pseudogenes. We have now investigated in detail the breakpoints within or between these (pseudo) NCF1 genes in 43 families with p47(phox)-deficient CGD by means of multiplex ligase-dependent probe amplification (MLPA). In 24 families the patients totally lacked NCF1 sequences, indicating that in these families the cross-over points are located between NCF1 and its pseudogenes. Six other families were compound heterozygous for a total NCF1 deletion and another mutation in NCF1 on the other allele. In 8 families, the patients lacked NCF1 exons 1-4 but had retained NCF1 exons 6-10, indicating that a cross-over point is located within NCF1 between exons 4 and 6. Similarly, in 4 families a cross-over point was located within NCF1 between exons 2 and 4. Similar cross-overs, in heterozygous form, were observed in family members of the patients. Several patients were compound heterozygous for total and partial NCF1 deletions. Thus, at least three different cross-over points exist within the NCF1 gene cluster, indicating that autosomal p47(phox)-deficient CGD is genetically heterogeneous but can be dissected in detail by MLPA.
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16
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Diabetes, renal and cardiovascular disease in p47 phox-/- chronic granulomatous disease. J Clin Immunol 2013; 33:725-30. [PMID: 23386289 DOI: 10.1007/s10875-013-9871-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 01/16/2013] [Indexed: 01/08/2023]
Abstract
Chronic granulomatous disease is a rare immunodeficiency due to defects in the phagocyte NADPH oxidase. The X-linked form (gp91 (phox) deficiency) accounts for about 70 % of cases; autosomal recessive p47 (phox) deficiency accounts for about 25 % of cases. We identified a 10 % incidence of diabetes in p47 (phox) deficient CGD, but none in X-linked CGD. Renal and cardiovascular diseases were also higher in p47 (phox) deficiency. p47 (phox) deficient CGD has non-infectious morbidities distinct from those in X-linked CGD.
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17
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Rueda OM, Rueda C, Diaz-Uriarte R. A Bayesian HMM with random effects and an unknown number of states for DNA copy number analysis. J STAT COMPUT SIM 2013. [DOI: 10.1080/00949655.2011.609818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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18
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Kringen MK, Stormo C, Grimholt RM, Berg JP, Piehler AP. Copy number variations of the ATP-binding cassette transporter ABCC6 gene and its pseudogenes. BMC Res Notes 2012; 5:425. [PMID: 22873774 PMCID: PMC3434077 DOI: 10.1186/1756-0500-5-425] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 08/01/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The ATP-binding cassette transporter ABCC6 gene is located on chromosome 16 between its two pseudogenes (ABCC6P1 and ABCC6P2). Previously, we have shown that ABCC6P1 is transcribed and affects ABCC6 at the transcriptional level. In this study we aimed to determine copy number variations of ABCC6, ABCC6P1 and ABCC6P2 in different populations. Moreover, we sought to study the transcription pattern of ABCC6 and ABCC6 pseudogenes in 39 different human tissues. FINDINGS Genomic DNA from healthy individuals from five populations, Chinese (n = 24), Middle East (n = 20), Mexicans (n = 24), Caucasians (n = 50) and Africans (n = 24), were examined for copy number variations of ABCC6 and its pseudogenes by pyrosequencing and quantitative PCR. Copy number variation of ABCC6 was very rare (2/142; 1.4%). However, one or three copies of ABCC6P1 were relatively common (3% and 8%, respectively). Only one person had a single copy of ABCC6P2 while none had three copies. In Chinese, deletions or duplications of ABCC6P1 were more frequent than in any other population (9/24; 37.5%). The transcription pattern of ABCC6P2 was highly similar to ABCC6 and ABCC6P1, with highest transcription in liver and kidney. Interestingly, the total transcription level of pseudogenes, ABCC6P1 + ABCC6P2, was higher than ABCC6 in most tissues, including liver and kidney. CONCLUSIONS Copy number variations of the ABCC6 pseudogenes are quite common, especially in populations of Chinese ancestry. The expression pattern of ABCC6P2 in 39 human tissues was highly similar to that of ABCC6 and ABCC6P1 suggesting similar regulatory mechanisms for ABCC6 and its pseudogenes.
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Affiliation(s)
- Marianne K Kringen
- Department of Pharmacology, Oslo University Hospital, Ullevål, Oslo, Norway.
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19
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Clinical, Functional and Genetic Analysis of Twenty-Four Patients with Chronic Granulomatous Disease – Identification of Eight Novel Mutations in CYBB and NCF2 Genes. J Clin Immunol 2012; 32:942-58. [DOI: 10.1007/s10875-012-9698-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Accepted: 04/10/2012] [Indexed: 01/05/2023]
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20
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Olsson LM, Nerstedt A, Lindqvist AK, Johansson SCM, Medstrand P, Olofsson P, Holmdahl R. Copy number variation of the gene NCF1 is associated with rheumatoid arthritis. Antioxid Redox Signal 2012; 16:71-8. [PMID: 21728841 DOI: 10.1089/ars.2011.4013] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
AIMS The aim of this study was to investigate genetic variants in the gene neutrophil cytosolic factor 1 (NCF1) for association with rheumatoid arthritis (RA). In rodent models, a single-nucleotide polymorphism (SNP) in Ncf1 has been shown to be a major locus regulating severity of arthritis. Ncf1 encodes one of five subunits of the NADPH oxidase complex. In humans the genomic structure of NCF1 is complex, excluding it from genome-wide association screens and complicating genetic analysis. In addition to copy number variation of NCF1, there are also two nonfunctional pseudogenes, nearly identical in sequence to NCF1. We have characterized copy number variation and SNPs in NCF1, and investigated these variants for association with RA. RESULTS We find that RA patients are less likely to have an increased copy number of NCF1, 7.6%, compared with 11.6% in controls; p=0.037. We also show that the T-allele of NCF1-339 (rs13447) is expressed in NCF1 and significantly reduces reactive oxygen species production. INNOVATION This is the first finding of genetic association of NCF1 with RA. The detailed characterization of genetic variants in NCF1 also helps elucidate the complexity of the NCF1 gene. CONCLUSION These data suggest that an increased copy number of NCF1 can be protective against developing RA and add support to previous findings of a role of NCF1 and the phagocyte NADPH oxidase complex in RA pathogenesis.
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Affiliation(s)
- Lina M Olsson
- Medical Inflammation Research, Department of Experimental Medical Science, Lund University, Sweden
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21
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Hultqvist M, Sareila O, Vilhardt F, Norin U, Olsson LM, Olofsson P, Hellman U, Holmdahl R. Positioning of a polymorphic quantitative trait nucleotide in the Ncf1 gene controlling oxidative burst response and arthritis severity in rats. Antioxid Redox Signal 2011; 14:2373-83. [PMID: 21275845 DOI: 10.1089/ars.2010.3440] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The Ncf1 gene, encoding the P47(PHOX) protein that regulates production of reactive oxygen species (ROS) by the phagocyte NADPH oxidase (NOX2) complex, is associated with autoimmunity and arthritis severity in rats. We have now identified that the single-nucleotide polymorphism (SNP) resulting in an M153T amino acid substitution mediates arthritis resistance and thus explains the molecular polymorphism underlying the earlier identified Ncf1 gene effect. We identified the SNP in position 153 to regulate ROS production using COS(PHOX) cells transfected with mutated Ncf1. To determine the role of this SNP for control of arthritis, we used the Wistar strain, identified to carry only the postulated arthritis resistant SNP in position 153. When this Ncf1 allele was backcrossed to the arthritis susceptible DA strain, both granulocyte ROS production and arthritis resistance were restored. Position 153 is located in the hinge region between the PX and SH3 domains of P47(PHOX). Mutational analysis of this position revealed a need for an -OH group in the side chain but we found no evidence for phosphorylation. The polymorphism did not affect assembly of the P47(PHOX)/P67(PHOX) complex in the cytosol or membrane localization, but is likely to operate downstream of assembly, affecting activity of the membrane NOX2 complex.
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Affiliation(s)
- Malin Hultqvist
- Medical Inflammation Research, C12 BMC, Lund University, Lund, Sweden
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Gottlieb B, Chalifour LE, Schweitzer M. A response to: BAK1 gene variation and abdominal aortic aneurysms-results may have been prematurely overrated. Questions of sequence fidelity, intraorganismal genetic heterogeneity, the nature of pseudogenes, and RNA editing. Hum Mutat 2010. [PMCID: PMC2992693 DOI: 10.1002/humu.21323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Bruce Gottlieb
- Lady Davis Institute for Medical Research, Jewish General HospitalMontréal, Québec, Canada
- Department of Human Genetics, McGill UniversityMontréal, Québec, Canada
- * Correspondence to: Bruce Gottlieb, Lady Davis Institute for Medical Research, Jewish General Hospital, 3755 Côte Ste. Catherine Road, Montréal, Québec, Canada, H3T 2E1. E-mail:
| | - Lorraine E Chalifour
- Lady Davis Institute for Medical Research, Jewish General HospitalMontréal, Québec, Canada
- Division of Experimental Medicine, Department of Medicine, McGill UniversityMontréal, Québec, Canada
| | - Morris Schweitzer
- Lady Davis Institute for Medical Research, Jewish General HospitalMontréal, Québec, Canada
- Department of Endocrinology, Jewish General HospitalMontréal, Québec, Canada
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