1
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Pasternak Y, Vong L, Merico D, Abrego Fuentes L, Scott O, Sham M, Fraser M, Watts-Dickens A, Willett Pachul J, Kim VH, Marshall CR, Scherer S, Roifman CM. Utilization of next-generation sequencing to define the role of heterozygous FOXN1 variants in immunodeficiency. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. GLOBAL 2024; 3:100267. [PMID: 38800615 PMCID: PMC11127205 DOI: 10.1016/j.jacig.2024.100267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/26/2024] [Accepted: 02/03/2024] [Indexed: 05/29/2024]
Abstract
Background Forkhead box protein N1 (FOXN1) transcription factor plays an essential role in the development of thymic epithelial cells, required for T-cell differentiation, maturation, and function. Biallelic pathogenic variants in FOXN1 cause severe combined immunodeficiency (SCID). More recently, heterozygous variants in FOXN1, identified by restricted gene panels, were also implicated with causing a less severe and variable immunodeficiency. Objective We undertook longitudinal follow-up and advanced genetic investigations, including whole exome sequencing and whole genome sequencing, of newborns with a heterozygous variant in FOXN1. Methods Five patients (3 female, 2 male) have been followed since they were first detected with low T-cell receptor excision circles during newborn screening for SCID. Patients underwent immune evaluation as well as genetic testing, including a primary immunodeficiency panel, whole exome sequencing, and whole genome sequencing in some cases. Results Median follow-up time was 6.5 years. Initial investigations revealed low CD3+ T lymphocytes in all patients. One patient presented with extremely low lymphocyte counts and depressed phytohemagglutinin responses leading to a tentative diagnosis of SCID. Over a period of 2 years, CD3+ T-cell counts rose, although in some patients it remained borderline low. One of 5 children continues to experience recurrent upper respiratory infections and asthma episodes. The remaining are asymptomatic except for eczema in 2 of 5 cases. Lymphocyte proliferation responses to phytohemagglutinin were initially low in 3 patients but normalized by age 10 months. In 3 of 5 cases, T lymphocyte counts remain low/borderline low. Conclusion In cases of monoallelic FOXN1 variants, using whole exome sequencing and whole genome sequencing to rule out possible other significant pathogenic variants allowed us to proceed with confidence in a conservative manner, even in extreme cases consistent with newborn screen-positive early presentation of SCID.
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Affiliation(s)
- Yehonatan Pasternak
- Division of Immunology and Allergy, Department of Paediatrics, The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada
| | - Linda Vong
- Division of Immunology and Allergy, Department of Paediatrics, The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada
- Canadian Centre for Primary Immunodeficiency and the Jeffrey Modell Research Laboratory for the Diagnosis of Primary Immunodeficiency, The Hospital for Sick Children and Research Institute, Toronto, Ontario, Canada
| | - Daniele Merico
- Vevo Therapeutics, San Francisco, Calif
- The Centre for Applied Genomics (TCAG), Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Laura Abrego Fuentes
- Division of Immunology and Allergy, Department of Paediatrics, The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada
| | - Ori Scott
- Division of Immunology and Allergy, Department of Paediatrics, The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada
| | - Marina Sham
- Division of Immunology and Allergy, Department of Paediatrics, The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada
| | - Meghan Fraser
- Newborn Screening Program, Department of Clinical and Metabolic Genetics, The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada
| | - Abby Watts-Dickens
- Newborn Screening Program, Department of Clinical and Metabolic Genetics, The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics and the McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada
| | - Jessica Willett Pachul
- Division of Immunology and Allergy, Department of Paediatrics, The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada
| | - Vy H.D. Kim
- Division of Immunology and Allergy, Department of Paediatrics, The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada
| | - Christian R. Marshall
- Division of Genome Diagnostics, Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Stephen Scherer
- The Centre for Applied Genomics (TCAG), Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics and the McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada
| | - Chaim M. Roifman
- Division of Immunology and Allergy, Department of Paediatrics, The Hospital for Sick Children and the University of Toronto, Toronto, Ontario, Canada
- Canadian Centre for Primary Immunodeficiency and the Jeffrey Modell Research Laboratory for the Diagnosis of Primary Immunodeficiency, The Hospital for Sick Children and Research Institute, Toronto, Ontario, Canada
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2
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Grosz BR, Parmar JM, Ellis M, Bryen S, Simons C, Reis ALM, Stevanovski I, Deveson IW, Nicholson G, Laing N, Wallis M, Ravenscroft G, Kumar KR, Vucic S, Kennerson ML. A deep intronic variant in MME causes autosomal recessive Charcot-Marie-Tooth neuropathy through aberrant splicing. J Peripher Nerv Syst 2024; 29:262-274. [PMID: 38860315 DOI: 10.1111/jns.12637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 05/26/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024]
Abstract
BACKGROUND Loss-of-function variants in MME (membrane metalloendopeptidase) are a known cause of recessive Charcot-Marie-Tooth Neuropathy (CMT). A deep intronic variant, MME c.1188+428A>G (NM_000902.5), was identified through whole genome sequencing (WGS) of two Australian families with recessive inheritance of axonal CMT using the seqr platform. MME c.1188+428A>G was detected in a homozygous state in Family 1, and in a compound heterozygous state with a known pathogenic MME variant (c.467del; p.Pro156Leufs*14) in Family 2. AIMS We aimed to determine the pathogenicity of the MME c.1188+428A>G variant through segregation and splicing analysis. METHODS The splicing impact of the deep intronic MME variant c.1188+428A>G was assessed using an in vitro exon-trapping assay. RESULTS The exon-trapping assay demonstrated that the MME c.1188+428A>G variant created a novel splice donor site resulting in the inclusion of an 83 bp pseudoexon between MME exons 12 and 13. The incorporation of the pseudoexon into MME transcript is predicted to lead to a coding frameshift and premature termination codon (PTC) in MME exon 14 (p.Ala397ProfsTer47). This PTC is likely to result in nonsense mediated decay (NMD) of MME transcript leading to a pathogenic loss-of-function. INTERPRETATION To our knowledge, this is the first report of a pathogenic deep intronic MME variant causing CMT. This is of significance as deep intronic variants are missed using whole exome sequencing screening methods. Individuals with CMT should be reassessed for deep intronic variants, with splicing impacts being considered in relation to the potential pathogenicity of variants.
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Affiliation(s)
- Bianca R Grosz
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, New South Wales, Australia
- The University of Sydney, Camperdown, New South Wales, Australia
| | - Jevin M Parmar
- Rare Disease Genetics and Functional Genomics Research Group, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
- Centre for Medical Research, Faculty of Health and Medical Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Melina Ellis
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, New South Wales, Australia
- The University of Sydney, Camperdown, New South Wales, Australia
| | - Samantha Bryen
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Cas Simons
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, New South Wales, Australia
- Centre for Population Genomics, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Andre L M Reis
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, New South Wales, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Igor Stevanovski
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, New South Wales, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Ira W Deveson
- Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, New South Wales, Australia
- Genomics and Inherited Disease Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- Faculty of Medicine, University of New South Wales, Sydney, New South Wales, Australia
| | - Garth Nicholson
- The University of Sydney, Camperdown, New South Wales, Australia
- Molecular Medicine Laboratory and Neurology Department, Concord Repatriation General Hospital, Concord, New South Wales, Australia
| | - Nigel Laing
- Rare Disease Genetics and Functional Genomics Research Group, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Mathew Wallis
- Tasmanian Clinical Genetics Service, Tasmanian Health Service, Hobart, Australia
- School of Medicine and Menzies Institute for Medical Research, University of Tasmania, Hobart, Australia
| | - Gianina Ravenscroft
- Rare Disease Genetics and Functional Genomics Research Group, Harry Perkins Institute of Medical Research, QEII Medical Centre, Nedlands, Western Australia, Australia
| | - Kishore R Kumar
- The University of Sydney, Camperdown, New South Wales, Australia
- Molecular Medicine Laboratory and Neurology Department, Concord Repatriation General Hospital, Concord, New South Wales, Australia
- Translational Neurogenomics Group, Genomic and Inherited Disease Program, The Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- St Vincent's Healthcare Campus, Faculty of Medicine, UNSW Sydney, Darlinghurst, New South Wales, Australia
| | - Steve Vucic
- The University of Sydney, Camperdown, New South Wales, Australia
- Brain and Nerve Research Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Marina L Kennerson
- Northcott Neuroscience Laboratory, ANZAC Research Institute, Sydney, New South Wales, Australia
- The University of Sydney, Camperdown, New South Wales, Australia
- Molecular Medicine Laboratory and Neurology Department, Concord Repatriation General Hospital, Concord, New South Wales, Australia
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3
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Toskov V, Kaiser-Labusch P, Lee-Kirsch MA, Ehl S, Wegehaupt O. Variable Syndromic Immunodeficiency in Patients with Biallelic PRIM1 Mutations. J Clin Immunol 2024; 44:129. [PMID: 38773012 PMCID: PMC11108906 DOI: 10.1007/s10875-024-01733-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 05/08/2024] [Indexed: 05/23/2024]
Abstract
Mutations in genes of the DNA polymerase complex have been linked to impaired immunological function next to distinct syndromic features. Biallelic mutations in PRIM1 are associated with a primordial dwarfism syndrome with variable hypogammaglobulinemia. The disease is mostly lethal in infancy due to pulmonary infections as well as hepatic cirrhosis. We studied 3 novel patients with PRIM1-deficiency with a focus on immunological consequences. All three shared dysmorphic features including a prominent forehead, triangular face and bilateral cryptorchidism. P1 carried the novel homozygous PRIM1 splice variant c.103+2T>G, allowing residual protein expression and associated with a mild clinical phenotype. P2 and P3 carried the known homozygous variant c.638+36C>G and died in infancy. Paradoxically, B cell lymphopenia was most pronounced in P1. No other significant lymphocyte abnormalities were detected. Interestingly, all 3 patients showed variable, but intermittently excessive Type I interferon signatures. In summary, the B-cell deficiency in PRIM1-deficiency is markedly variable and the severity of syndromic manifestations is not predictive of the immunological phenotype. We highlight a potential contribution of pathological type I interferon activation to disease pathogenesis which warrants further investigations.
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Affiliation(s)
- Vasil Toskov
- Clinic of Pediatric Hematology, Oncology and Stem Cell Transplantation, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Petra Kaiser-Labusch
- Prof. Hess Children's Hospital, Klinikum Bremen-Mitte, Gesundheit Nord gGmbH, Bremen, Germany
| | - Min Ae Lee-Kirsch
- Department of Pediatrics, Medizinische Fakultät Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Stephan Ehl
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, Breisacher Str. 115, 79106, Freiburg, Germany.
| | - Oliver Wegehaupt
- Clinic of Pediatric Hematology, Oncology and Stem Cell Transplantation, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
- Institute for Immunodeficiency, Center for Chronic Immunodeficiency (CCI), Medical Center, Faculty of Medicine, University of Freiburg, Breisacher Str. 115, 79106, Freiburg, Germany.
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4
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Yin Z, Kilkenny ML, Ker DS, Pellegrini L. CryoEM insights into RNA primer synthesis by the human primosome. FEBS J 2024; 291:1813-1829. [PMID: 38335062 DOI: 10.1111/febs.17082] [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: 09/21/2023] [Revised: 11/24/2023] [Accepted: 01/26/2024] [Indexed: 02/12/2024]
Abstract
Eukaryotic DNA replication depends on the primosome - a complex of DNA polymerase alpha (Pol α) and primase - to initiate DNA synthesis by polymerisation of an RNA-DNA primer. Primer synthesis requires the tight coordination of primase and polymerase activities. Recent cryo-electron microscopy (cryoEM) analyses have elucidated the extensive conformational transitions required for RNA primer handover between primase and Pol α and primer elongation by Pol α. Because of the intrinsic flexibility of the primosome, however, structural information about the initiation of RNA primer synthesis is still lacking. Here, we capture cryoEM snapshots of the priming reaction to reveal the conformational trajectory of the human primosome that brings DNA primase subunits 1 and 2 (PRIM1 and PRIM2, respectively) together, poised for RNA synthesis. Furthermore, we provide experimental evidence for the continuous association of primase subunit PRIM2 with the RNA primer during primer synthesis, and for how both initiation and termination of RNA primer polymerisation are licenced by specific rearrangements of DNA polymerase alpha catalytic subunit (POLA1), the polymerase subunit of Pol α. Our findings fill a critical gap in our understanding of the conformational changes that underpin the synthesis of the RNA primer by the primosome. Together with existing evidence, they provide a complete description of the structural dynamics of the human primosome during DNA replication initiation.
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Affiliation(s)
- Zhan Yin
- Department of Biochemistry, University of Cambridge, UK
| | | | - De-Sheng Ker
- Department of Biochemistry, University of Cambridge, UK
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5
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Baranovskiy AG, Morstadt LM, Babayeva ND, Tahirov TH. Human primosome requires replication protein A when copying DNA with inverted repeats. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.11.584335. [PMID: 38559116 PMCID: PMC10979909 DOI: 10.1101/2024.03.11.584335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The human primosome, a four-subunit complex of primase and DNA polymerase alpha (Polα), initiates DNA synthesis on both chromosome strands by generating chimeric RNA-DNA primers for loading DNA polymerases delta and epsilon (Polε). Replication protein A (RPA) tightly binds to single-stranded DNA strands, protecting them from nucleolytic digestion and unauthorized transactions. We report here that RPA plays a critical role for the human primosome during DNA synthesis across inverted repeats prone to hairpin formation. On other alternatively structured DNA forming a G-quadruplex, RPA provides no assistance for primosome. A stimulatory effect of RPA on DNA synthesis across hairpins was also observed for the catalytic domain of Polα but not of Polε. The important factors for an efficient hairpin bypass by primosome are the high affinity of RPA to DNA based on four DNA-binding domains and the interaction of the winged-helix-turn-helix domain of RPA with Polα. Binding studies indicate that this interaction stabilizes the RPA/Polα complex on the primed template. This work provides insight into a cooperative action of RPA and primosome on DNA, which is critical for DNA synthesis across inverted repeats.
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6
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Sun J, Ruiz Daniels R, Balic A, Andresen AMS, Bjørgen H, Dobie R, Henderson NC, Koppang EO, Martin SAM, Fosse JH, Taylor RS, Macqueen DJ. Cell atlas of the Atlantic salmon spleen reveals immune cell heterogeneity and cell-specific responses to bacterial infection. FISH & SHELLFISH IMMUNOLOGY 2024; 145:109358. [PMID: 38176627 DOI: 10.1016/j.fsi.2024.109358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/23/2023] [Accepted: 01/02/2024] [Indexed: 01/06/2024]
Abstract
The spleen is a conserved secondary lymphoid organ that emerged in parallel to adaptive immunity in early jawed vertebrates. Recent studies have applied single cell transcriptomics to reveal the cellular composition of spleen in several species, cataloguing diverse immune cell types and subpopulations. In this study, 51,119 spleen nuclei transcriptomes were comprehensively investigated in the commercially important teleost Atlantic salmon (Salmo salar L.), contrasting control animals with those challenged with the bacterial pathogen Aeromonas salmonicida. We identified clusters of nuclei representing the expected major cell types, namely T cells, B cells, natural killer-like cells, granulocytes, mononuclear phagocytes, endothelial cells, mesenchymal cells, erythrocytes and thrombocytes. We discovered heterogeneity within several immune lineages, providing evidence for resident macrophages and melanomacrophages, infiltrating monocytes, several candidate dendritic cell subpopulations, and B cells at distinct stages of differentiation, including plasma cells and an igt + subset. We provide evidence for twelve candidate T cell subsets, including cd4+ T helper and regulatory T cells, one cd8+ subset, three γδT subsets, and populations double negative for cd4 and cd8. The number of genes showing differential expression during the early stages of Aeromonas infection was highly variable across immune cell types, with the largest changes observed in macrophages and infiltrating monocytes, followed by resting mature B cells. Our analysis provides evidence for a local inflammatory response to infection alongside B cell maturation in the spleen, and upregulation of ccr9 genes in igt + B cells, T helper and cd8+ cells, and monocytes, consistent with the recruitment of immune cell populations to the gut to deal with Aeromonas infection. Overall, this study provides a new cell-resolved perspective of the immune actions of Atlantic salmon spleen, highlighting extensive heterogeneity hidden to bulk transcriptomics. We further provide a large catalogue of cell-specific marker genes that can be leveraged to further explore the function and structural organization of the salmonid immune system.
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Affiliation(s)
- Jianxuan Sun
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Rose Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Adam Balic
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK; Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | | | - Håvard Bjørgen
- Unit of Anatomy, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Ross Dobie
- Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK
| | - Neil C Henderson
- Centre for Inflammation Research, The Queen's Medical Research Institute, Edinburgh BioQuarter, University of Edinburgh, Edinburgh, UK; MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Erling Olaf Koppang
- Unit of Anatomy, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Ås, Norway
| | - Samuel A M Martin
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | | | - Richard S Taylor
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - Daniel J Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK.
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7
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Li MWY, Burnett L, Dai P, Avery DT, Noori T, Voskoboinik I, Shah PR, Tatian A, Tangye SG, Gray PE, Ma CS. Filaggrin-Associated Atopic Skin, Eye, Airways, and Gut Disease, Modifying the Presentation of X-Linked Reticular Pigmentary Disorder (XLPDR). J Clin Immunol 2024; 44:38. [PMID: 38165470 DOI: 10.1007/s10875-023-01637-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 12/02/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND X-linked reticular pigmentary disorder (XLPDR) is a rare condition characterized by skin hyperpigmentation, ectodermal features, multiorgan inflammation, and recurrent infections. All probands identified to date share the same intronic hemizygous POLA1 hypomorphic variant (NM_001330360.2(POLA1):c.1393-354A > G) on the X chromosome. Previous studies have supported excessive type 1 interferon (IFN) inflammation and natural killer (NK) cell dysfunction in disease pathogenesis. Common null polymorphisms in filaggrin (FLG) gene underlie ichthyosis vulgaris and atopic predisposition. CASE A 9-year-old boy born to non-consanguineous parents developed eczema with reticular skin hyperpigmentation in early infancy. He suffered recurrent chest infections with chronic cough, clubbing, and asthma, moderate allergic rhinoconjunctivitis with keratitis, multiple food allergies, and vomiting with growth failure. Imaging demonstrated bronchiectasis, while gastroscopy identified chronic eosinophilic gastroduodenitis. Interestingly, growth failure and bronchiectasis improved over time without specific treatment. METHODS Whole-genome sequencing (WGS) using Illumina short-read sequencing was followed by both manual and orthogonal automated bioinformatic analyses for single-nucleotide variants, small insertions/deletions (indels), and larger copy number variations. NK cell cytotoxic function was assessed using 51Cr release and degranulation assays. The presence of an interferon signature was investigated using a panel of six interferon-stimulated genes (ISGs) by QPCR. RESULTS WGS identified a de novo hemizygous intronic variant in POLA1 (NM_001330360.2(POLA1):c.1393-354A > G) giving a diagnosis of XLPDR, as well as a heterozygous nonsense FLG variant (NM_002016.2(FLG):c.441del, NP_0020.1:p.(Arg151Glyfs*43)). Compared to healthy controls, the IFN signature was elevated although the degree moderated over time with the improvement in his chest disease. NK cell functional studies showed normal cytotoxicity and degranulation. CONCLUSION This patient had multiple atopic manifestations affecting eye, skin, chest, and gut, complicating the presentation of XLPDR. This highlights that common FLG polymorphisms should always be considered when assessing genotype-phenotype correlations of other genetic variation in patients with atopic symptoms. Additionally, while the patient exhibited an enhanced IFN signature, he does not have an NK cell defect, suggesting this may not be a constant feature of XLPDR.
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Affiliation(s)
- Margaret W Y Li
- Department of Allergy and Immunology, Sydney Children's Hospital, Sydney, Australia.
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia.
| | - Leslie Burnett
- Garvan Institute of Medical Research, Sydney, Australia
- Clinical Immunogenomics Research Consortium Australasia (CIRCA), Sydney, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, St Vincent's Healthcare Clinical Campus, UNSW Sydney, Sydney, Australia
| | - Pei Dai
- Garvan Institute of Medical Research, Sydney, Australia
- Clinical Immunogenomics Research Consortium Australasia (CIRCA), Sydney, Australia
| | | | | | | | - Parth R Shah
- Department of Ophthalmology, Sydney Children's Hospital, Sydney, Australia
| | - Artiene Tatian
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
- Department of Dermatology, Sydney Children's Hospital, Sydney, Australia
| | - Stuart G Tangye
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
- Clinical Immunogenomics Research Consortium Australasia (CIRCA), Sydney, Australia
| | - Paul E Gray
- Department of Allergy and Immunology, Sydney Children's Hospital, Sydney, Australia.
- Clinical Immunogenomics Research Consortium Australasia (CIRCA), Sydney, Australia.
- School of Medicine, Western Sydney University, Sydney, Australia.
| | - Cindy S Ma
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Sydney, Australia
- Garvan Institute of Medical Research, Sydney, Australia
- Clinical Immunogenomics Research Consortium Australasia (CIRCA), Sydney, Australia
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8
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Li XY, Ma DL. X-Linked Reticulate Pigmentary Disorder. JAMA Dermatol 2023; 159:1383-1384. [PMID: 37851432 DOI: 10.1001/jamadermatol.2023.2980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
This case report describes a child with generalized reticulate hyperpigmentation and recurrent pneumonia, hypohidrosis, photophobia, and diarrhea.
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Affiliation(s)
- Xing-Yu Li
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, State Key Laboratory of Complex Severe and Rare Diseases, National Clinical Research Center for Dermatologic and Immunologic Diseases, Beijing, China
| | - Dong-Lai Ma
- Department of Dermatology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, State Key Laboratory of Complex Severe and Rare Diseases, National Clinical Research Center for Dermatologic and Immunologic Diseases, Beijing, China
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9
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Jin J, Li K, Du Y, Gao F, Wang Z, Li W. Multi-omics study identifies that PICK1 deficiency causes male infertility by inhibiting vesicle trafficking in Sertoli cells. Reprod Biol Endocrinol 2023; 21:114. [PMID: 38001535 PMCID: PMC10675906 DOI: 10.1186/s12958-023-01163-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 11/18/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND Infertility affects approximately 10-15% of reproductive-age men worldwide, and genetic causes play a role in one-third of cases. As a Bin-Amphiphysin-Rvs (BAR) domain protein, protein interacting with C-kinase 1 (PICK1) deficiency could lead to impairment of acrosome maturation. However, its effects on auxiliary germ cells such as Sertoli cells are unknown. PURPOSE The present work was aimed to use multi-omics analysis to research the effects of PICK1 deficiency on Sertoli cells and to identify effective biomarkers to distinguish fertile males from infertile males caused by PICK1 deficiency. METHODS Whole-exome sequencing (WES) was performed on 20 infertility patients with oligozoospermia to identify pathogenic PICK1 mutations. Multi-omics analysis of a PICK1 knockout (KO) mouse model was utilized to identify pathogenic mechanism. Animal and cell function experiments of Sertoli cell-specific PICK1 KO mouse were performed to verify the functional impairment of Sertoli cells. RESULTS Two loss-of-function deletion mutations c.358delA and c.364delA in PICK1 resulting in transcription loss of BAR functional domain were identified in infertility patients with a specific decrease in serum inhibin B, indicating functional impairment of Sertoli cells. Multi-omics analysis of PICK1 KO mouse illustrated that targeted genes of differentially expressed microRNAs and mRNAs are significantly enriched in the negative regulatory role in the vesicle trafficking pathway, while metabolomics analysis showed that the metabolism of amino acids, lipids, cofactors, vitamins, and endocrine factors changed. The phenotype of PICK1 KO mouse showed a reduction in testis volume, a decreased number of mature spermatozoa and impaired secretory function of Sertoli cells. In vitro experiments confirmed that the expression of growth factors secreted by Sertoli cells in PICK1 conditional KO mouse such as Bone morphogenetic protein 4 (BMP4) and Fibroblast growth factor 2 (FGF2) were decreased. CONCLUSIONS Our study attributed male infertility caused by PICK1 deficiency to impaired vesicle-related secretory function of Sertoli cells and identified a variety of significant candidate biomarkers for male infertility induced by PICK1 deficiency.
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Affiliation(s)
- Jing Jin
- Laboratory Medicine Center, Zhejiang Center for Clinical Laboratories, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310000, Zhejiang, China
| | - Kaiqiang Li
- Laboratory Medicine Center, Allergy Center, Department of Transfusion Medicine, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310000, Zhejiang, China
| | - Yaoqiang Du
- Laboratory Medicine Center, Allergy Center, Department of Transfusion Medicine, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310000, Zhejiang, China
| | - Fang Gao
- Center for Reproductive Medicine, Department of Reproductive Endocrinology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310000, Zhejiang, China
| | - Zhen Wang
- Laboratory Medicine Center, Allergy Center, Department of Transfusion Medicine, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310000, Zhejiang, China.
| | - Weixing Li
- Laboratory Medicine Center, Zhejiang Center for Clinical Laboratories, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, 310000, Zhejiang, China.
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10
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Wang CS. Type I Interferonopathies: A Clinical Review. Rheum Dis Clin North Am 2023; 49:741-756. [PMID: 37821193 DOI: 10.1016/j.rdc.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
This review will discuss when clinicians should consider evaluating for Type I interferonopathies, review clinical phenotypes and molecular defects of Type I interferonopathies, and discuss current treatments.
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Affiliation(s)
- Christine S Wang
- Department of Pediatric Rheumatology, C.S. Mott Children's Hospital, University of Michigan, 1500 East Medical Center Drive SPC 5718, Ann Arbor, MI 48109, USA.
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11
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Sun P, Gu L, Yu Q, Luan F. Pathogenic Genes for Congenital Microtia: A Bioinformatics Analysis. J Craniofac Surg 2023; 34:2560-2562. [PMID: 37643078 DOI: 10.1097/scs.0000000000009620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 06/20/2023] [Indexed: 08/31/2023] Open
Abstract
OBJECTIVE The purpose of this study is to accurately find the pathogenic genes of congenital microtia, so as to lay a theoretical foundation for genetic screening, diagnosis, and gene therapy of congenital microtia in the further stage. METHODS In this study, the authors used public data from the Mouse Genome Informatics database. The authors used the String database ( https://string-db.org/ ) to construct the Protein-Protein Interaction network. Then Gene Ontology classification and Kyoto Encyclopedia of Genes and Genomes pathway analysis were performed for the pathogenic genes. RESULTS The authors searched the Mouse Genome Informatics database and found 84 pathogenic genes of congenital microtia. The Protein-Protein Interaction network for pathogenic genes was constructed, which contained 81 nodes and 148 lines with MCM5, CDT1, POLA1, CDC45, CDC6, EFTUD2, ORC1, ORC4, ORC6, and TCOF1 . The authors conducted a Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis on pathogenic genes, and the results showed that pathogenic genes were involved in O-mannan biosynthesis, cell cycle, RNA polymerase, and other signaling pathways. CONCLUSIONS The authors' results indicated that the occurrence of congenital microtia is attributed to a variety of genes. Furthermore, the interactions of pathogenic genes were further elucidated by using a bioinformatics approach. This study will help to reveal the pathogenesis of congenital microtia and lay the foundation for accurate diagnosis and treatment of congenital microtia in the future.
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Affiliation(s)
- Pengfei Sun
- Department of Plastic Surgery, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing
| | - Luosha Gu
- Department of Plastic Surgery, Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing
| | - Qian Yu
- Department of Dermatologic Surgery, Shandong Provincial Hospital for Skin Disease & Shandong Provincial Institute of Dermatology and Venereology, Shandong First Medial University & Shandong Academy of Medical Sciences, Shandong
| | - Fang Luan
- Department of Plastic Surgery, Zibo Central Hospital, Shandong, China
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12
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Gao S, Zhang L, Wang H. Characterizing the key genes of COVID-19 that regulate tumor immune microenvironment and prognosis in hepatocellular carcinoma. Funct Integr Genomics 2023; 23:262. [PMID: 37540264 DOI: 10.1007/s10142-023-01184-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/05/2023]
Abstract
Hepatocellular carcinoma (HCC), a highly heterogeneous malignant tumor associated with a poor prognosis, is a common cause of cancer-related deaths worldwide, with a limited survival benefit for patients despite ongoing therapeutic breakthroughs. Coronavirus disease 2019 (COVID-19), a severe infectious disease caused by severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), is a global pandemic and a serious threat to human health. The increased susceptibility to SARS-CoV-2 infection and a poor prognosis in patients with cancer necessitate the exploration of the potential link between the two. No studies have investigated the relationship of COVID-19 genes with the prognosis and tumor development in patients with HCC. We screened prognosis-related COVID-19 genes in HCC, performed molecular typing, developed a stable and reliable COVID-19 genes signature for predicting survival, characterized the immune microenvironment in HCC patients, and explored new molecular therapeutic targets. Datasets of HCC patients, including RNA sequencing data and clinical information, were obtained from The Cancer Genome Atlas (TCGA), International Cancer Genome Consortium (ICGC), and Gene Expression Omnibus (GEO) databases. Prognosis-related COVID-19 genes were identified by univariate Cox analysis. Molecular typing of HCC was performed using the consensus non-negative matrix factorization method (cNMF), followed by the analysis of survival, tumor microenvironment, and pathway enrichment for each subtype. Prognostic signatures were constructed using LASSO-Cox regression models, and receiver operating characteristic (ROC) curves were used to validate the predictive performance of the signature. The same approach was used for the test and external validation sets. Seven software packages were applied to determine the abundance of immune infiltration in HCC patients and investigate its relationship with the risk scores. Gene set enrichment analysis (GSEA) was used to explore the potential mechanisms by which the COVID-19 genes affect hepatocarcinogenesis and prognosis. Three types of machine learning methods were combined to identify the most critical genes in the signature and localize their expression at the single cell level. We identified 53 prognosis-related COVID-19 genes and classified HCC into two molecular subtypes (C1, C2) by using the NMF method. The prognosis of C2 was significantly better than that of C1, and the two subtypes differed remarkably in terms of the tumor immune microenvironment and biological functions. The 17 COVID-19 genes were screened using the LASSO regression method to develop a 17 COVID-19 genes signature, which demonstrated a good predictive performance for 1-, 2- and 3-year OS of patients with HCC. The risk score as an independent prognostic factor for HCC has better predictive accuracy than traditional clinical variables. Patients in the TCGA cohort were categorized by risk score into the high- and low-risk groups, with the high-risk group mainly enriched in the immune modulation-related pathways and the low-risk group mainly enriched in the metabolism-related pathways, suggesting that the COVID-19 genes may affect disease progression and prognosis by regulating the tumor immune microenvironment and metabolism in HCC. NOL10 was identified as the most critical gene in the signature and hypothesized to be a potential therapeutic target for HCC. Objectively, the COVID-19 genes signature developed in this study, as an independent prognostic factor in HCC patients, is closely associated with the prognosis and tumor immune microenvironment of HCC patients and indicates that they may regulate the development of HCC in multiple ways, providing us with new perspectives for understanding the molecular mechanisms of HCC and finding effective therapeutic targets.
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Affiliation(s)
- Shuang Gao
- Division of Life Sciences and Medicine, Ward 4 of the Department of Oncology, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Lei Zhang
- Department of Oncology Surgery, The Second Affiliated Hospital of Bengbu Medical University, Bengbu, 233080, Anhui, China
| | - Huiyan Wang
- Division of Life Sciences and Medicine, Department of Laboratory Diagnostics, the First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China.
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13
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Willemsen M, Barber JS, Nieuwenhove EV, Staels F, Gerbaux M, Neumann J, Prezzemolo T, Pasciuto E, Lagou V, Boeckx N, Filtjens J, De Visscher A, Matthys P, Schrijvers R, Tousseyn T, O'Driscoll M, Bucciol G, Schlenner S, Meyts I, Humblet-Baron S, Liston A. Homozygous DBF4 mutation as a cause of severe congenital neutropenia. J Allergy Clin Immunol 2023; 152:266-277. [PMID: 36841265 DOI: 10.1016/j.jaci.2023.02.016] [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: 09/08/2022] [Revised: 01/23/2023] [Accepted: 02/16/2023] [Indexed: 02/26/2023]
Abstract
BACKGROUND Severe congenital neutropenia presents with recurrent infections early in life as a result of arrested granulopoiesis. Multiple genetic defects are known to block granulocyte differentiation; however, a genetic cause remains unknown in approximately 40% of cases. OBJECTIVE We aimed to characterize a patient with severe congenital neutropenia and syndromic features without a genetic diagnosis. METHODS Whole exome sequencing results were validated using flow cytometry, Western blotting, coimmunoprecipitation, quantitative PCR, cell cycle and proliferation analysis of lymphocytes and fibroblasts and granulocytic differentiation of primary CD34+ and HL-60 cells. RESULTS We identified a homozygous missense mutation in DBF4 in a patient with mild extra-uterine growth retardation, facial dysmorphism and severe congenital neutropenia. DBF4 is the regulatory subunit of the CDC7 kinase, together known as DBF4-dependent kinase (DDK), the complex essential for DNA replication initiation. The DBF4 variant demonstrated impaired ability to bind CDC7, resulting in decreased DDK-mediated phosphorylation, defective S-phase entry and progression and impaired differentiation of granulocytes associated with activation of the p53-p21 pathway. The introduction of wild-type DBF4 into patient CD34+ cells rescued the promyelocyte differentiation arrest. CONCLUSION Hypomorphic DBF4 mutation causes autosomal-recessive severe congenital neutropenia with syndromic features.
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Affiliation(s)
- Mathijs Willemsen
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - John S Barber
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Erika Van Nieuwenhove
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium; Department of Pediatrics, University Hospitals Leuven, Leuven, Belgium
| | - Frederik Staels
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; Department of Microbiology, Immunology, and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
| | - Margaux Gerbaux
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; Pediatric Department, Academic Children Hospital Queen Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Julika Neumann
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Teresa Prezzemolo
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Emanuela Pasciuto
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Vasiliki Lagou
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Nancy Boeckx
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Jessica Filtjens
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Immunobiology, Rega Institute for Medical Research, KU Leuven, Leuve, Belgium
| | - Amber De Visscher
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Immunobiology, Rega Institute for Medical Research, KU Leuven, Leuve, Belgium
| | - Patrick Matthys
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Immunobiology, Rega Institute for Medical Research, KU Leuven, Leuve, Belgium
| | - Rik Schrijvers
- Department of Microbiology, Immunology, and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
| | - Thomas Tousseyn
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | - Mark O'Driscoll
- Human DNA Damage Response Disorders Group, Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
| | - Giorgia Bucciol
- Department of Microbiology, Immunology, and Transplantation, Laboratory for Inborn Errors of Immunity, KU Leuven, Leuven, Belgium; Department of Pediatrics, Division of Primary Immunodeficiencies, University Hospitals Leuven, Leuven
| | - Susan Schlenner
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium
| | - Isabelle Meyts
- Department of Microbiology, Immunology, and Transplantation, Laboratory for Inborn Errors of Immunity, KU Leuven, Leuven, Belgium; Department of Pediatrics, Division of Primary Immunodeficiencies, University Hospitals Leuven, Leuven.
| | - Stephanie Humblet-Baron
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium.
| | - Adrian Liston
- Department of Microbiology, Immunology, and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium; Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom.
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14
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Guilz NC, Ahn YO, Seo S, Mace EM. Unwinding the Role of the CMG Helicase in Inborn Errors of Immunity. J Clin Immunol 2023; 43:847-861. [PMID: 36809597 PMCID: PMC10789183 DOI: 10.1007/s10875-023-01437-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/20/2023] [Indexed: 02/23/2023]
Abstract
Inborn errors of immunity (IEI) are a collection of diseases resulting from genetic causes that impact the immune system through multiple mechanisms. Natural killer cell deficiency (NKD) is one such IEI where natural killer (NK) cells are the main immune lineage affected. Though rare, the deficiency of several genes has been described as underlying causes of NKD, including MCM4, GINS1, MCM10 , and GINS4 , all of which are involved in the eukaryotic CMG helicase. The CMG helicase is made up of C DC45 – M CM – G INS and accessory proteins including MCM10. The CMG helicase plays a critical role in DNA replication by unwinding the double helix and enabling access of polymerases to single-stranded DNA, and thus helicase proteins are active in any proliferating cell. Replication stress, DNA damage, and cell cycle arrest are among the cellular phenotypes attributed to loss of function variants in CMG helicase proteins. Despite the ubiquitous function of the CMG helicase, NK cells have an apparent susceptibility to the deficiency of helicase proteins. This review will examine the role of the CMG helicase in inborn errors of immunity through the lens of NKD and further discuss why natural killer cells can be so strongly affected by helicase deficiency.
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Affiliation(s)
- Nicole C Guilz
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center, 630 W 168th St., New York, NY, 10032, USA
| | - Yong-Oon Ahn
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center, 630 W 168th St., New York, NY, 10032, USA
| | - Seungmae Seo
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center, 630 W 168th St., New York, NY, 10032, USA
| | - Emily M Mace
- Vagelos College of Physicians and Surgeons, Department of Pediatrics, Columbia University Irving Medical Center, 630 W 168th St., New York, NY, 10032, USA.
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15
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Lin MH, Chou PC, Lee IC, Yang SF, Yu HS, Yu S. Inherited Reticulate Pigmentary Disorders. Genes (Basel) 2023; 14:1300. [PMID: 37372478 DOI: 10.3390/genes14061300] [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: 05/10/2023] [Revised: 06/12/2023] [Accepted: 06/18/2023] [Indexed: 06/29/2023] Open
Abstract
Reticulate pigmentary disorders (RPDs) are a group of inherited and acquired skin conditions characterized by hyperpigmented and/or hypopigmented macules. Inherited RPDs include dyschromatosis symmetrica hereditaria (DSH), dyschromatosis universalis hereditaria (DUH), reticulate acropigmentation of Kitamura (RAK), Dowling-Degos disease (DDD), dyskeratosis congenita (DKC), Naegeli-Franceschetti-Jadassohn syndrome (NFJS), dermatopathia pigmentosa reticularis (DPR), and X-linked reticulate pigmentary disorder. Although reticulate pattern of pigmentation is a common characteristic of this spectrum of disorders, the distribution of pigmentation varies among these disorders, and there may be clinical manifestations beyond pigmentation. DSH, DUH, and RAK are mostly reported in East Asian ethnicities. DDD is more common in Caucasians, although it is also reported in Asian countries. Other RPDs show no racial predilection. This article reviews the clinical, histological, and genetic variations of inherited RPDs.
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Affiliation(s)
- Min-Huei Lin
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Pei-Chen Chou
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - I-Chen Lee
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Syuan-Fei Yang
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Hsin-Su Yu
- Department of Dermatology, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Sebastian Yu
- Department of Dermatology, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Dermatology, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Neuroscience Research Center, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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16
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Yamaguchi M, Cotterill S. Association of Mutations in Replicative DNA Polymerase Genes with Human Disease: Possible Application of Drosophila Models for Studies. Int J Mol Sci 2023; 24:ijms24098078. [PMID: 37175782 PMCID: PMC10178534 DOI: 10.3390/ijms24098078] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Replicative DNA polymerases, such as DNA polymerase α-primase, δ and ε, are multi-subunit complexes that are responsible for the bulk of nuclear DNA replication during the S phase. Over the last decade, extensive genome-wide association studies and expression profiling studies of the replicative DNA polymerase genes in human patients have revealed a link between the replicative DNA polymerase genes and various human diseases and disorders including cancer, intellectual disability, microcephalic primordial dwarfism and immunodeficiency. These studies suggest the importance of dissecting the mechanisms involved in the functioning of replicative DNA polymerases in understanding and treating a range of human diseases. Previous studies in Drosophila have established this organism as a useful model to understand a variety of human diseases. Here, we review the studies on Drosophila that explored the link between DNA polymerases and human disease. First, we summarize the recent studies linking replicative DNA polymerases to various human diseases and disorders. We then review studies on replicative DNA polymerases in Drosophila. Finally, we suggest the possible use of Drosophila models to study human diseases and disorders associated with replicative DNA polymerases.
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Affiliation(s)
| | - Sue Cotterill
- Molecular and Clinical Sciences Research Institute, St George's University of London, London SW17 0RE, UK
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17
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He Q, Baranovskiy AG, Morstadt LM, Lisova AE, Babayeva ND, Lusk BL, Lim CJ, Tahirov TH. Structures of human primosome elongation complexes. Nat Struct Mol Biol 2023; 30:579-583. [PMID: 37069376 PMCID: PMC10268227 DOI: 10.1038/s41594-023-00971-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 03/20/2023] [Indexed: 04/19/2023]
Abstract
The synthesis of RNA-DNA primer by primosome requires coordination between primase and DNA polymerase α subunits, which is accompanied by unknown architectural rearrangements of multiple domains. Using cryogenic electron microscopy, we solved a 3.6 Å human primosome structure caught at an early stage of RNA primer elongation with deoxynucleotides. The structure confirms a long-standing role of primase large subunit and reveals new insights into how primosome is limited to synthesizing short RNA-DNA primers.
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Affiliation(s)
- Qixiang He
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Andrey G Baranovskiy
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Lucia M Morstadt
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Alisa E Lisova
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Nigar D Babayeva
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Benjamin L Lusk
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ci Ji Lim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Tahir H Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA.
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18
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Yilmaz Demirdag Y, Gupta S. Infections in DNA Repair Defects. Pathogens 2023; 12:pathogens12030440. [PMID: 36986362 PMCID: PMC10054915 DOI: 10.3390/pathogens12030440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
DNA repair defects are heterogenous conditions characterized by a wide spectrum of clinical phenotypes. The common presentations of DNA repair defects include increased risk of cancer, accelerated aging, and defects in the development of various organs and systems. The immune system can be affected in a subset of these disorders leading to susceptibility to infections and autoimmunity. Infections in DNA repair defects may occur due to primary defects in T, B, or NK cells and other factors such as anatomic defects, neurologic disorders, or during chemotherapy. Consequently, the characteristics of the infections may vary from mild upper respiratory tract infections to severe, opportunistic, and even fatal infections with bacteria, viruses, or fungi. Here, infections in 15 rare and sporadic DNA repair defects that are associated with immunodeficiencies are discussed. Because of the rarity of some of these conditions, limited information is available regarding infectious complications.
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19
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Willemsen M, Staels F, Gerbaux M, Neumann J, Schrijvers R, Meyts I, Humblet-Baron S, Liston A. DNA replication-associated inborn errors of immunity. J Allergy Clin Immunol 2023; 151:345-360. [PMID: 36395985 DOI: 10.1016/j.jaci.2022.11.003] [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: 09/13/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022]
Abstract
Inborn errors of immunity are a heterogeneous group of monogenic immunologic disorders caused by mutations in genes with critical roles in the development, maintenance, or function of the immune system. The genetic basis is frequently a mutation in a gene with restricted expression and/or function in immune cells, leading to an immune disorder. Several classes of inborn errors of immunity, however, result from mutation in genes that are ubiquitously expressed. Despite the genes participating in cellular processes conserved between cell types, immune cells are disproportionally affected, leading to inborn errors of immunity. Mutations in DNA replication, DNA repair, or DNA damage response factors can result in monogenic human disease, some of which are classified as inborn errors of immunity. Genetic defects in the DNA repair machinery are a well-known cause of T-B-NK+ severe combined immunodeficiency. An emerging class of inborn errors of immunity is those caused by mutations in DNA replication factors. Considerable heterogeneity exists within the DNA replication-associated inborn errors of immunity, with diverse immunologic defects and clinical manifestations observed. These differences are suggestive for differential sensitivity of certain leukocyte subsets to deficiencies in specific DNA replication factors. Here, we provide an overview of DNA replication-associated inborn errors of immunity and discuss the emerging mechanistic insights that can explain the observed immunologic heterogeneity.
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Affiliation(s)
- Mathijs Willemsen
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium.
| | - Frederik Staels
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium
| | - Margaux Gerbaux
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; Pediatric Department, Academic Children Hospital Queen Fabiola, Université Libre de Bruxelles, Brussels, Belgium
| | - Julika Neumann
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium
| | - Rik Schrijvers
- Department of Microbiology, Immunology and Transplantation, Allergy and Clinical Immunology Research Group, KU Leuven, Leuven, Belgium; Department of General Internal Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Isabelle Meyts
- Department of Microbiology, Immunology and Transplantation, Laboratory for Inborn Errors of Immunity, KU Leuven, Leuven, Belgium; Department of Pediatrics, Division of Primary Immunodeficiencies, University Hospitals Leuven, Leuven, Belgium; ERN-RITA Core Center Member, Leuven, Belgium
| | - Stephanie Humblet-Baron
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium.
| | - Adrian Liston
- Department of Microbiology, Immunology and Transplantation, Laboratory of Adaptive Immunity, KU Leuven, Leuven, Belgium; VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium; Immunology Program, The Babraham Institute, Babraham Research Campus, Cambridge.
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20
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Lisova AE, Baranovskiy AG, Morstadt LM, Babayeva ND, Tahirov T. Human DNA polymerase α has a strong mutagenic potential at the initial steps of DNA synthesis. Nucleic Acids Res 2022; 50:12266-12273. [PMID: 36454017 PMCID: PMC9757036 DOI: 10.1093/nar/gkac1101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/16/2022] [Accepted: 11/10/2022] [Indexed: 12/05/2022] Open
Abstract
DNA polymerase α (Polα) is essential for DNA replication initiation and makes a notable contribution to genome mutagenesis. The activity and fidelity of Polα during the early steps of DNA replication have not been well studied. Here we show that at the beginning of DNA synthesis, when extending the RNA primer received from primase, Polα is more mutagenic than during the later DNA elongation steps. Kinetic and binding studies revealed substantially higher activity and affinity to the template:primer when Polα interacts with ribonucleotides of a chimeric RNA-DNA primer. Polα activity greatly varies during first six steps of DNA synthesis, and the bias in the rates of correct and incorrect dNTP incorporation leads to impaired fidelity, especially upon the second step of RNA primer extension. Furthermore, increased activity and stability of Polα/template:primer complexes containing RNA-DNA primers result in higher efficiency of mismatch extension.
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Affiliation(s)
| | | | - Lucia M Morstadt
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Nigar D Babayeva
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Tahir H Tahirov
- To whom correspondence should be addressed. Tel: +1 402 559 7608; Fax: +1 402 559 3739;
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21
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Ma S, Damfo S, Lou J, Pinotsis N, Bowler MW, Haider S, Kozielski F. Two Ligand-Binding Sites on SARS-CoV-2 Non-Structural Protein 1 Revealed by Fragment-Based X-ray Screening. Int J Mol Sci 2022; 23:ijms232012448. [PMID: 36293303 PMCID: PMC9604401 DOI: 10.3390/ijms232012448] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
The regular reappearance of coronavirus (CoV) outbreaks over the past 20 years has caused significant health consequences and financial burdens worldwide. The most recent and still ongoing novel CoV pandemic, caused by Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) has brought a range of devastating consequences. Due to the exceptionally fast development of vaccines, the mortality rate of the virus has been curbed to a significant extent. However, the limitations of vaccination efficiency and applicability, coupled with the still high infection rate, emphasise the urgent need for discovering safe and effective antivirals against SARS-CoV-2 by suppressing its replication or attenuating its virulence. Non-structural protein 1 (nsp1), a unique viral and conserved leader protein, is a crucial virulence factor for causing host mRNA degradation, suppressing interferon (IFN) expression and host antiviral signalling pathways. In view of the essential role of nsp1 in the CoV life cycle, it is regarded as an exploitable target for antiviral drug discovery. Here, we report a variety of fragment hits against the N-terminal domain of SARS-CoV-2 nsp1 identified by fragment-based screening via X-ray crystallography. We also determined the structure of nsp1 at atomic resolution (0.99 Å). Binding affinities of hits against nsp1 and potential stabilisation were determined by orthogonal biophysical assays such as microscale thermophoresis and thermal shift assays. We identified two ligand-binding sites on nsp1, one deep and one shallow pocket, which are not conserved between the three medically relevant SARS, SARS-CoV-2 and MERS coronaviruses. Our study provides an excellent starting point for the development of more potent nsp1-targeting inhibitors and functional studies on SARS-CoV-2 nsp1.
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Affiliation(s)
- Shumeng Ma
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Shymaa Damfo
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Jiaqi Lou
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Nikos Pinotsis
- Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK
| | | | - Shozeb Haider
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
- UCL Centre for Advanced Research Computing, University College London, London WC1H 9RN, UK
| | - Frank Kozielski
- School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
- Correspondence:
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22
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Begemann A, Oneda B, Baumer A, Guldimann M, Tutschek B, Rauch A. A Xp22.11-p21.3 microdeletion in a three-generation family supports male lethality of POLA1 nullisomy resulting in reduced fertility of female carriers. Eur J Med Genet 2022; 65:104628. [PMID: 36182037 DOI: 10.1016/j.ejmg.2022.104628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/19/2022] [Accepted: 09/25/2022] [Indexed: 11/03/2022]
Abstract
POLA1 encodes a subunit of the DNA polymerase alpha, a key enzyme for the initiation of DNA synthesis. In males, hemizygous hypomorphic variants in POLA1 have been identified as the cause of X-linked pigmentary reticulate disorder (XLPDR) and a novel X-linked neurodevelopmental disorder termed Van Esch-O'Driscoll syndrome (VEODS), while female carriers have been reported to be healthy. Nullisomy for POLA1 was speculated to be lethal due to its crucial function, while the effect of loss of one allele in females remained unknown. Here, we report on a three-generation family harboring a deletion of POLA1 in females showing subfertility as the only phenotype. Our findings show that heterozygous deletions or truncating variants in females with skewed X inactivation do not cause VEODS and support the hypothesis of very early embryonic lethality in males with POLA1 nullisomy.
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Affiliation(s)
- Anaïs Begemann
- University of Zurich, Institute of Medical Genetics, Schlieren, Zurich, Switzerland
| | - Beatrice Oneda
- University of Zurich, Institute of Medical Genetics, Schlieren, Zurich, Switzerland
| | - Alessandra Baumer
- University of Zurich, Institute of Medical Genetics, Schlieren, Zurich, Switzerland
| | - Marina Guldimann
- University of Zurich, Institute of Medical Genetics, Schlieren, Zurich, Switzerland
| | - Boris Tutschek
- Prenatal Zürich, Zurich, Switzerland; Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
| | - Anita Rauch
- University of Zurich, Institute of Medical Genetics, Schlieren, Zurich, Switzerland; University Children's Hospital Zurich, University of Zurich, Zurich, Switzerland.
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23
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Starokadomskyy P. Editorial: Pattern-recognition receptors: Genetics, immunity, pathology. Front Cell Infect Microbiol 2022; 12:991898. [PMID: 36204646 PMCID: PMC9531015 DOI: 10.3389/fcimb.2022.991898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 08/26/2022] [Indexed: 11/24/2022] Open
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24
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Sriram N, Mukherjee S, Sah MK. Gene expression profiling and protein-protein interaction analysis reveals the dynamic role of MCM7 in Alzheimer's disorder and breast cancer. 3 Biotech 2022; 12:146. [PMID: 35698583 DOI: 10.1007/s13205-022-03207-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/14/2022] [Indexed: 11/01/2022] Open
Abstract
The interrelation of cancer and Alzheimer's disorder (AD)-associated molecular mechanisms, reported last decade, paved the path for drug discoveries. In this direction, while chemotherapy is well established for breast cancer (BC), the detection and targeted therapy for AD is not advanced due to a lack of recognized peripheral biomarkers. The present study aimed to find diagnostic and prognostic molecular signature markers common to both BC and AD for possible drug targeting and repurposing. For these disorders, two corresponding microarray datasets (GSE42568, GSE33000) were used for identifying the differentially expressed genes (DEGs), resulting in recognition of CD209 and MCM7 as the two common players. While the CD209 gene was upregulated in both disorders and has been studied vastly, the MCM7 gene showed a strikingly reverse pattern of expression level, downregulated in the case of BC while upregulated in the case of AD. Thus, the MCM7 gene was further analyzed for expression, predictions, and validations of its structure and protein-protein interaction (PPI) for the possible development of new treatment methods for AD. The study concluded with indicative drug repurposing studies to check the effect of existing clinically approved drugs for BC for rectifying the expression levels of the mutated MCM7 gene in AD. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03207-1.
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Affiliation(s)
- Navneeth Sriram
- Department of Biotechnology, Dr. B. R. Ambedkar National Institute of Technology, Jalandhar, Punjab 144011 India
| | - Sunny Mukherjee
- Department of Biotechnology, Dr. B. R. Ambedkar National Institute of Technology, Jalandhar, Punjab 144011 India
| | - Mahesh Kumar Sah
- Department of Biotechnology, Dr. B. R. Ambedkar National Institute of Technology, Jalandhar, Punjab 144011 India
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25
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Baranovskiy AG, Lisova AE, Morstadt LM, Babayeva ND, Tahirov TH. Insight into RNA-DNA primer length counting by human primosome. Nucleic Acids Res 2022; 50:6264-6270. [PMID: 35689638 PMCID: PMC9226528 DOI: 10.1093/nar/gkac492] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/19/2022] [Accepted: 06/08/2022] [Indexed: 11/15/2022] Open
Abstract
The human primosome, a four-subunit complex of primase and DNA polymerase alpha (Polα), synthesizes chimeric RNA–DNA primers of a limited length for DNA polymerases delta and epsilon to initiate DNA replication on both chromosome strands. Despite recent structural insights into the action of its two catalytic centers, the mechanism of DNA synthesis termination is still unclear. Here we report results of functional and structural studies revealing how the human primosome counts RNA–DNA primer length and timely terminates DNA elongation. Using a single-turnover primer extension assay, we defined two factors that determine a mature primer length (∼35-mer): (i) a tight interaction of the C-terminal domain of the DNA primase large subunit (p58C) with the primer 5′-end, and (ii) flexible tethering of p58C and the DNA polymerase alpha catalytic core domain (p180core) to the primosome platform domain by extended linkers. The obtained data allow us to conclude that p58C is a key regulator of all steps of RNA–DNA primer synthesis. The above-described findings provide a notable insight into the mechanism of DNA synthesis termination by a eukaryotic primosome, an important process for ensuring successful primer handover to replication DNA polymerases and for maintaining genome integrity.
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Affiliation(s)
- Andrey G Baranovskiy
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center. University of Nebraska Medical Center, Omaha, NE, USA
| | - Alisa E Lisova
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center. University of Nebraska Medical Center, Omaha, NE, USA
| | - Lucia M Morstadt
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center. University of Nebraska Medical Center, Omaha, NE, USA
| | - Nigar D Babayeva
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center. University of Nebraska Medical Center, Omaha, NE, USA
| | - Tahir H Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center. University of Nebraska Medical Center, Omaha, NE, USA
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26
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Borror MB, Girotti M, Kar A, Cain MK, Gao X, MacKay VL, Herron B, Bhaskaran S, Becerra S, Novy N, Ventura N, Johnson TE, Kennedy BK, Rea SL. Inhibition of ATR Reverses a Mitochondrial Respiratory Insufficiency. Cells 2022; 11:1731. [PMID: 35681427 PMCID: PMC9179431 DOI: 10.3390/cells11111731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/15/2022] [Accepted: 05/21/2022] [Indexed: 02/04/2023] Open
Abstract
Diseases that affect the mitochondrial electron transport chain (ETC) often manifest as threshold effect disorders, meaning patients only become symptomatic once a certain level of ETC dysfunction is reached. Cells can invoke mechanisms to circumvent reaching their critical ETC threshold, but it is an ongoing challenge to identify such processes. In the nematode Caenorhabditis elegans, severe reduction of mitochondrial ETC activity shortens life, but mild reduction actually extends it, providing an opportunity to identify threshold circumvention mechanisms. Here, we show that removal of ATL-1, but not ATM-1, worm orthologs of ATR and ATM, respectively, key nuclear DNA damage checkpoint proteins in human cells, unexpectedly lessens the severity of ETC dysfunction. Multiple genetic and biochemical tests show no evidence for increased mutation or DNA breakage in animals exposed to ETC disruption. Reduced ETC function instead alters nucleotide ratios within both the ribo- and deoxyribo-nucleotide pools, and causes stalling of RNA polymerase, which is also known to activate ATR. Unexpectedly, atl-1 mutants confronted with mitochondrial ETC disruption maintain normal levels of oxygen consumption, and have an increased abundance of translating ribosomes. This suggests checkpoint signaling by ATL-1 normally dampens cytoplasmic translation. Taken together, our data suggest a model whereby ETC insufficiency in C. elegans results in nucleotide imbalances leading to the stalling of RNA polymerase, activation of ATL-1, dampening of global translation, and magnification of ETC dysfunction. The loss of ATL-1 effectively reverses the severity of ETC disruption so that animals become phenotypically closer to wild type.
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Affiliation(s)
- Megan B. Borror
- The Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; (M.B.B.); (M.G.); (A.K.); (M.K.C.); (S.B.); (S.B.)
- Department of Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Milena Girotti
- The Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; (M.B.B.); (M.G.); (A.K.); (M.K.C.); (S.B.); (S.B.)
- Department of Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Adwitiya Kar
- The Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; (M.B.B.); (M.G.); (A.K.); (M.K.C.); (S.B.); (S.B.)
- Department of Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Meghan K. Cain
- The Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; (M.B.B.); (M.G.); (A.K.); (M.K.C.); (S.B.); (S.B.)
- Department of Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Xiaoli Gao
- Department of Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA;
| | - Vivian L. MacKay
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; (V.L.M.); (B.K.K.)
| | - Brent Herron
- Institute for Behavioral Genetics, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO 80309, USA; (B.H.); (T.E.J.)
| | - Shylesh Bhaskaran
- The Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; (M.B.B.); (M.G.); (A.K.); (M.K.C.); (S.B.); (S.B.)
- Department of Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Sandra Becerra
- The Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; (M.B.B.); (M.G.); (A.K.); (M.K.C.); (S.B.); (S.B.)
- Department of Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Nathan Novy
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA;
| | - Natascia Ventura
- IUF—Leibniz Research Institute for Environmental Medicine, 103045 Düsseldorf, Germany;
- Institute for Clinical Chemistry and Laboratory Diagnostic, Medical Faculty of the Heinrich Heine University, 103045 Düsseldorf, Germany
| | - Thomas E. Johnson
- Institute for Behavioral Genetics, Department of Integrative Physiology, University of Colorado Boulder, Boulder, CO 80309, USA; (B.H.); (T.E.J.)
| | - Brian K. Kennedy
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA; (V.L.M.); (B.K.K.)
- Buck Institute for Research on Aging, Novato, CA 94945, USA
- Departments of Biochemistry and Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117542, Singapore
| | - Shane L. Rea
- The Barshop Institute for Longevity and Aging Studies, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; (M.B.B.); (M.G.); (A.K.); (M.K.C.); (S.B.); (S.B.)
- Department of Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA;
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27
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Baranovskiy AG, Babayeva ND, Lisova AE, Morstadt LM, Tahirov TH. Structural and functional insight into mismatch extension by human DNA polymerase α. Proc Natl Acad Sci U S A 2022; 119:e2111744119. [PMID: 35467978 PMCID: PMC9169922 DOI: 10.1073/pnas.2111744119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 03/08/2022] [Indexed: 12/11/2022] Open
Abstract
Human DNA polymerase α (Polα) does not possess proofreading ability and plays an important role in genome replication and mutagenesis. Polα extends the RNA primers generated by primase and provides a springboard for loading other replication factors. Here we provide the structural and functional analysis of the human Polα interaction with a mismatched template:primer. The structure of the human Polα catalytic domain in the complex with an incoming deoxycytidine triphosphate (dCTP) and the template:primer containing a T-C mismatch at the growing primer terminus was solved at a 2.9 Å resolution. It revealed the absence of significant distortions in the active site and in the conformation of the substrates, except the primer 3′-end. The T-C mismatch acquired a planar geometry where both nucleotides moved toward each other by 0.4 Å and 0.7 Å, respectively, and made one hydrogen bond. The binding studies conducted at a physiological salt concentration revealed that Polα has a low affinity to DNA and is not able to discriminate against a mispaired template:primer in the absence of deoxynucleotide triphosphate (dNTP). Strikingly, in the presence of cognate dNTP, Polα showed a more than 10-fold higher selectivity for a correct duplex versus a mismatched one. According to pre-steady-state kinetic studies, human Polα extends the T-C mismatch with a 249-fold lower efficiency due to reduction of the polymerization rate constant by 38-fold and reduced affinity to the incoming nucleotide by 6.6-fold. Thus, a mismatch at the postinsertion site affects all factors important for primer extension: affinity to both substrates and the rate of DNA polymerization.
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Affiliation(s)
- Andrey G. Baranovskiy
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198
| | - Nigar D. Babayeva
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198
| | - Alisa E. Lisova
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198
| | - Lucia M. Morstadt
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198
| | - Tahir H. Tahirov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198
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28
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Nambu R, Warner N, Mulder DJ, Kotlarz D, McGovern DPB, Cho J, Klein C, Snapper SB, Griffiths AM, Iwama I, Muise AM. A Systematic Review of Monogenic Inflammatory Bowel Disease. Clin Gastroenterol Hepatol 2022; 20:e653-e663. [PMID: 33746097 PMCID: PMC8448782 DOI: 10.1016/j.cgh.2021.03.021] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/11/2021] [Accepted: 03/12/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Advances in genomic technologies have led to increasing reports of monogenic inflammatory bowel disease (IBD). Here, we systematically review the literature to determine the clinical features, genetic profile, and previously used treatment strategies in monogenic IBD. METHODS A systematic review of MEDLINE articles published between January 2000 and December 2020 was conducted. A total of 750 individual monogenic IBD cases were identified from 303 eligible articles. RESULTS The most frequently reported monogenic IBD genes were IL10RA/B, XIAP, CYBB, LRBA, and TTC7A. In total, 63.4% of patients developed IBD before 6 years of age, 17.4% developed IBD between ages 10 and 17.9 years, and 10.9% developed IBD after age 18. There was a substantial difference between these age groups and the underlying monogenic disorders. Only 31.7% had any history of extraintestinal comorbidity (EIC) before IBD onset, but 76.0% developed at least 1 EIC during their clinical course. The most common EICs were atypical infection (44.7%), dermatologic abnormality (38.4%), and autoimmunity (21.9%). Bowel surgery, biologic therapy, and hematopoietic stem cell transplantation were performed in 27.1%, 32.9%, and 23.1% of patients, respectively. CONCLUSIONS Monogenic IBD cases, although rare, have varied extraintestinal comorbidities and limited treatment options including surgery and transplant. Early identification and improved understanding of the characteristics of the genes and underlying disease processes in monogenic IBD is important for effective management.
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Affiliation(s)
- Ryusuke Nambu
- SickKids Inflammatory Bowel Disease Centre, the Hospital for Sick Children, Toronto, Canada,Cell Biology Program, Research Institute, the Hospital for Sick Children, Toronto, Canada,Division of Gastroenterology and Hepatology, Saitama Children’s Medical Center, Japan
| | - Neil Warner
- SickKids Inflammatory Bowel Disease Centre, the Hospital for Sick Children, Toronto, Canada,Cell Biology Program, Research Institute, the Hospital for Sick Children, Toronto, Canada
| | - Daniel J Mulder
- SickKids Inflammatory Bowel Disease Centre, the Hospital for Sick Children, Toronto, Canada,Cell Biology Program, Research Institute, the Hospital for Sick Children, Toronto, Canada
| | - Daniel Kotlarz
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Dermot PB McGovern
- F. Widjaja Foundation Inflammatory Bowel Disease Center and Immunobiology Research Institute at Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Judy Cho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, Hess Center for Science and Medicine, NY, USA
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children’s Hospital, University Hospital, LMU Munich, Munich, Germany
| | - Scott B Snapper
- Division of Gastroenterology, Hepatology and Nutrition, Boston Children’s Hospital, Harvard Medical School; Division of Gastroenterology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Anne M Griffiths
- SickKids Inflammatory Bowel Disease Centre, the Hospital for Sick Children, Toronto, Canada,Department of Pediatrics, Institute of Medical Science and Biochemistry, University of Toronto, the Hospital for Sick Children, Toronto, Canada
| | - Itaru Iwama
- Division of Gastroenterology and Hepatology, Saitama Children’s Medical Center, Japan
| | - Aleixo M Muise
- SickKids Inflammatory Bowel Disease Centre, Hospital for Sick Children, Toronto, Canada; Cell Biology Program, Research Institute, Hospital for Sick Children, Toronto, Canada; Department of Pediatrics, Institute of Medical Science and Biochemistry, University of Toronto, Hospital for Sick Children, Toronto, Canada.
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29
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Further Delineation of Duplications of ARX Locus Detected in Male Patients with Varying Degrees of Intellectual Disability. Int J Mol Sci 2022; 23:ijms23063084. [PMID: 35328505 PMCID: PMC8955779 DOI: 10.3390/ijms23063084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 11/20/2022] Open
Abstract
The X-linked gene encoding aristaless-related homeobox (ARX) is a bi-functional transcription factor capable of activating or repressing gene transcription, whose mutations have been found in a wide spectrum of neurodevelopmental disorders (NDDs); these include cortical malformations, paediatric epilepsy, intellectual disability (ID) and autism. In addition to point mutations, duplications of the ARX locus have been detected in male patients with ID. These rearrangements include telencephalon ultraconserved enhancers, whose structural alterations can interfere with the control of ARX expression in the developing brain. Here, we review the structural features of 15 gain copy-number variants (CNVs) of the ARX locus found in patients presenting wide-ranging phenotypic variations including ID, speech delay, hypotonia and psychiatric abnormalities. We also report on a further novel Xp21.3 duplication detected in a male patient with moderate ID and carrying a fully duplicated copy of the ARX locus and the ultraconserved enhancers. As consequences of this rearrangement, the patient-derived lymphoblastoid cell line shows abnormal activity of the ARX-KDM5C-SYN1 regulatory axis. Moreover, the three-dimensional (3D) structure of the Arx locus, both in mouse embryonic stem cells and cortical neurons, provides new insight for the functional consequences of ARX duplications. Finally, by comparing the clinical features of the 16 CNVs affecting the ARX locus, we conclude that—depending on the involvement of tissue-specific enhancers—the ARX duplications are ID-associated risk CNVs with variable expressivity and penetrance.
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30
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Lin B, Goldbach-Mansky R. Pathogenic insights from genetic causes of autoinflammatory inflammasomopathies and interferonopathies. J Allergy Clin Immunol 2022; 149:819-832. [PMID: 34893352 PMCID: PMC8901451 DOI: 10.1016/j.jaci.2021.10.027] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/31/2021] [Accepted: 10/06/2021] [Indexed: 12/22/2022]
Abstract
A number of systemic autoinflammatory diseases arise from gain-of-function mutations in genes encoding IL-1-activating inflammasomes or cytoplasmic nucleic acid sensors including the receptor and sensor STING and result in increased IL-1 and type I interferon production, respectively. Blocking these pathways in human diseases has provided proof-of-concept, confirming the prominent roles of these cytokines in disease pathogenesis. Recent insights into the multilayered regulation of these sensor pathways and insights into their role in amplifying the disease pathogenesis of monogenic and complex genetic diseases spurred new drug development targeting the sensors. This review provides insights into the pathogenesis and genetic causes of these "prototypic" diseases caused by gain-of function mutations in IL-1-activating inflammasomes (inflammasomopathies) and in interferon-activating pathways (interferonopathies) including STING-associated vasculopathy with onset in infancy, Aicardi-Goutieres syndrome, and proteasome-associated autoinflammatory syndromes that link activation of the viral sensors STING, "self" nucleic acid metabolism, and the ubiquitin-proteasome system to "type I interferon production" and human diseases. Clinical responses and biomarker changes to Janus kinase inhibitors confirm a role of interferons, and a growing number of diseases with "interferon signatures" unveil extensive cross-talk between major inflammatory pathways. Understanding these interactions promises new tools in tackling the significant clinical challenges in treating patients with these conditions.
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Affiliation(s)
- Bin Lin
- Translational Autoinflammatory Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
| | - Raphaela Goldbach-Mansky
- Translational Autoinflammatory Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md.
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Iron–sulfur clusters as inhibitors and catalysts of viral replication. Nat Chem 2022; 14:253-266. [DOI: 10.1038/s41557-021-00882-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/15/2021] [Indexed: 12/11/2022]
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Kilkenny ML, Veale CE, Guppy A, Hardwick SW, Chirgadze DY, Rzechorzek NJ, Maman JD, Pellegrini L. Structural basis for the interaction of SARS-CoV-2 virulence factor nsp1 with DNA polymerase α-primase. Protein Sci 2022; 31:333-344. [PMID: 34719824 PMCID: PMC8661717 DOI: 10.1002/pro.4220] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/28/2021] [Accepted: 10/28/2021] [Indexed: 11/21/2022]
Abstract
The molecular mechanisms that drive the infection by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-the causative agent of coronavirus disease 2019 (COVID-19)-are under intense current scrutiny to understand how the virus operates and to uncover ways in which the disease can be prevented or alleviated. Recent proteomic screens of the interactions between viral and host proteins have identified the human proteins targeted by SARS-CoV-2. The DNA polymerase α (Pol α)-primase complex or primosome-responsible for initiating DNA synthesis during genomic duplication-was identified as a target of nonstructural protein 1 (nsp1), a major virulence factor in the SARS-CoV-2 infection. Here, we validate the published reports of the interaction of nsp1 with the primosome by demonstrating direct binding with purified recombinant components and providing a biochemical characterization of their interaction. Furthermore, we provide a structural basis for the interaction by elucidating the cryo-electron microscopy structure of nsp1 bound to the primosome. Our findings provide biochemical evidence for the reported targeting of Pol α by the virulence factor nsp1 and suggest that SARS-CoV-2 interferes with Pol α's putative role in the immune response during the viral infection.
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Affiliation(s)
| | | | - Amir Guppy
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1GAUK
| | | | | | - Neil J. Rzechorzek
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1GAUK
- Present address:
The Francis Crick InstituteLondonNW1 1ATUK
| | - Joseph D. Maman
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1GAUK
| | - Luca Pellegrini
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1GAUK
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Hsu AP, Holland SM. Host genetics of innate immune system in infection. Curr Opin Immunol 2022; 74:140-149. [DOI: 10.1016/j.coi.2021.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/21/2021] [Accepted: 11/09/2021] [Indexed: 02/06/2023]
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Wang SS, Zeng X, Wang YL, Dongzhi Z, Zhao YF, Chen YZ. Chinese Medicine Meets Conventional Medicine in Targeting COVID-19 Pathophysiology, Complications and Comorbidities. Chin J Integr Med 2022; 28:627-635. [PMID: 35583580 PMCID: PMC9116066 DOI: 10.1007/s11655-022-3573-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2021] [Indexed: 01/09/2023]
Abstract
OBJECTIVE To investigate how the National Health Commission of China (NHCC)-recommended Chinese medicines (CMs) modulate the major maladjustments of coronavirus disease 2019 (COVID-19), particularly the clinically observed complications and comorbidities. METHODS By focusing on the potent targets in common with the conventional medicines, we investigated the mechanisms of 11 NHCC-recommended CMs in the modulation of the major COVID-19 pathophysiology (hyperinflammations, viral replication), complications (pain, headache) and comorbidities (hypertension, obesity, diabetes). The constituent herbs of these CMs and their chemical ingredients were from the Traditional Chinese Medicine Information Database. The experimentally-determined targets and the activity values of the chemical ingredients of these CMs were from the Natural Product Activity and Species Source Database. The approved and clinical trial drugs against these targets were searched from the Therapeutic Target Database and DrugBank Database. Pathways of the targets was obtained from Kyoto Encyclopedia of Genes and Genomes and additional literature search. RESULTS Overall, 9 CMs modulated 6 targets discovered by the COVID-19 target discovery studies, 8 and 11 CMs modulated 8 and 6 targets of the approved or clinical trial drugs for the treatment of the major COVID-19 complications and comorbidities, respectively. CONCLUSION The coordinated actions of each NHCC-recommended CM against a few targets of the major COVID-19 pathophysiology, complications and comorbidities, partly have common mechanisms with the conventional medicines.
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Affiliation(s)
- Shan-shan Wang
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang Province, 315211 China
| | - Xian Zeng
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, Fudan University School of Pharmacy, Shanghai, 201203 China
| | - Ya-li Wang
- Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, Singapore, 117543 Singapore
| | | | - Yu-fen Zhao
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang Province, 315211 China ,Department of Chemical Biology, College of Chemistry and Chemical Engineering, and The Key Laboratory for Chemical Biology of Fujian Province, Xiamen University, Xiamen, Fujian Province, 361005 China ,Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing, 102206 China
| | - Yu-zong Chen
- Qian Xuesen Collaborative Research Center of Astrochemistry and Space Life Sciences, Institute of Drug Discovery Technology, Ningbo University, Ningbo, Zhejiang Province, 315211 China ,Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, Singapore, 117543 Singapore
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Facioli FL, da Silva AN, Dos Santos ED, de Camargo J, Warpechowski MB, da Oliveira Cruz J, Lof LM, Zanella R. From Mendel laws to whole genetic association study to decipher the swine mulefoot phenotype. Res Vet Sci 2021; 143:58-65. [PMID: 34974356 DOI: 10.1016/j.rvsc.2021.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/24/2021] [Accepted: 12/16/2021] [Indexed: 11/28/2022]
Abstract
The swine mulefoot (SM) is a rare condition characterized by a non-cloven hoof due to the partial or total fusion of the phalanges. No comprehensive study has been conducted to identify associated markers with this phenotype until now. We aimed to characterize the association between SNP and the mulefoot phenotype using a Genome-Wide Association Study (GWAS). An experimental population was produced using a half-sib mating where the male had the mulefoot phenotype and the females (n = 6) had cloven hoofs. The cross resulted in 27 (47%) animals with the mulefoot characteristic and 30 (53%) normal animals, indicating the possible dominant gene action. Animals were further genotyped using the Illumina PorcineSNP50k BeadChip, and SNPs were tested for associations. Twenty-nine SNPs located on the SSC15, SSC4, and SSCX were associated with the mulefoot phenotype (p-value <5 × 10-5). Six markers were found in the intronic regions of VWC2L, CATIP, PDK3, PCYT1B, and POLA1 genes. The marker rs81277626, on SSC15:116,886,110 bp, is located in the Von Willebrand Factor C Domain (VWC2L), a possible functional candidate gene. The VWC2L is part of a biological process involved with the bone morphogenetic protein (BMP) signaling pathway, previously associated with syndactyly in other species. In conclusion, the identified markers suggest the involvement of the VWC2L gene in the SM phenotype in this population.
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Affiliation(s)
- Fernanda Luiza Facioli
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil
| | - Arthur Nery da Silva
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil
| | - Ezequiel Davi Dos Santos
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil
| | - Janine de Camargo
- Programa de Pós Graduação em Bioexperimentação, Faculdade de Agronomia e Medicina Veterinária,Universidade de Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil
| | - Marson Bruck Warpechowski
- Departamento de Zootecnia, Setor de Ciências Agrárias, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Juliano da Oliveira Cruz
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil
| | - Lucas Mallmann Lof
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil
| | - Ricardo Zanella
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil; Programa de Pós Graduação em Bioexperimentação, Faculdade de Agronomia e Medicina Veterinária,Universidade de Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil.
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Systemic Autoinflammatory Diseases: A Growing Family of Disorders of Overlapping Immune Dysfunction. Rheum Dis Clin North Am 2021; 48:371-395. [PMID: 34798958 DOI: 10.1016/j.rdc.2021.07.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Systemic autoinflammatory diseases (SAIDs) are characterized by unprovoked exaggerated inflammation on a continuum from benign recurrent oral ulceration to life-threatening strokes or amyloidosis, with renal failure as a potential sequela. The ability to discriminate these diagnoses rests on the genetic and mechanistic defect of each disorder, considering potential overlapping autoinflammation, autoimmunity, and immune deficiency. A comprehensive and strategic genetic investigation influences management as well as the consequential expected prognoses in these subsets of rare diseases. The ever-expanding therapeutic armamentarium reflects international collaborations, which will hasten genetic discovery and consensus-driven treatment.
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Dallavalle S, Musso L, Cincinelli R, Darwiche N, Gervasoni S, Vistoli G, Guglielmi MB, La Porta I, Pizzulo M, Modica E, Prosperi F, Signorino G, Colelli F, Cardile F, Fucci A, D'Andrea EL, Riccio A, Pisano C. Antitumor activity of novel POLA1-HDAC11 dual inhibitors. Eur J Med Chem 2021; 228:113971. [PMID: 34772529 DOI: 10.1016/j.ejmech.2021.113971] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 10/29/2021] [Accepted: 10/31/2021] [Indexed: 12/27/2022]
Abstract
Hybrid molecules targeting simultaneously DNA polymerase α (POLA1) and histone deacetylases (HDACs) were designed and synthesized to exploit a potential synergy of action. Among a library of screened molecules, MIR002 and GEM144 showed antiproliferative activity at nanomolar concentrations on a panel of human solid and haematological cancer cell lines. In vitro functional assays confirmed that these molecules inhibited POLA1 primer extension activity, as well as HDAC11. Molecular docking studies also supported these findings. Mechanistically, MIR002 and GEM144 induced acetylation of p53, activation of p21, G1/S cell cycle arrest, and apoptosis. Oral administration of these inhibitors confirmed their antitumor activity in in vivo models. In human non-small cancer cell (H460) xenografted in nude mice MIR002 at 50 mg/kg, Bid (qd × 5 × 3w) inhibited tumor growth (TGI = 61%). More interestingly, in POLA1 inhibitor resistant cells (H460-R9A), the in vivo combination of MIR002 with cisplatin showed an additive antitumor effect with complete disappearance of tumor masses in two animals at the end of the treatment. Moreover, in two human orthotopic malignant pleural mesothelioma xenografts (MM473 and MM487), oral treatments with MIR002 and GEM144 confirmed their significant antitumor activity (TGI = 72-77%). Consistently with recent results that have shown an inverse correlation between POLA1 expression and type I interferon levels, MIR002 significantly upregulated interferon-α in immunocompetent mice.
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Affiliation(s)
- Sabrina Dallavalle
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy.
| | - Loana Musso
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
| | - Raffaella Cincinelli
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
| | - Nadine Darwiche
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut, Lebanon
| | - Silvia Gervasoni
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, via Mangiagalli 25, Milano, 20133, Italy
| | - Giulio Vistoli
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, via Mangiagalli 25, Milano, 20133, Italy
| | - Mario B Guglielmi
- Biogem, Institute of Molecular Biology and Genetics, Via Camporeale, 83031 Ariano Irpino(AV), Italy
| | - Ilaria La Porta
- Biogem, Institute of Molecular Biology and Genetics, Via Camporeale, 83031 Ariano Irpino(AV), Italy
| | - Maddalena Pizzulo
- Biogem, Institute of Molecular Biology and Genetics, Via Camporeale, 83031 Ariano Irpino(AV), Italy
| | - Elisa Modica
- Biogem, Institute of Molecular Biology and Genetics, Via Camporeale, 83031 Ariano Irpino(AV), Italy
| | - Federica Prosperi
- Biogem, Institute of Molecular Biology and Genetics, Via Camporeale, 83031 Ariano Irpino(AV), Italy
| | - Giacomo Signorino
- Biogem, Institute of Molecular Biology and Genetics, Via Camporeale, 83031 Ariano Irpino(AV), Italy
| | - Fabiana Colelli
- Biogem, Institute of Molecular Biology and Genetics, Via Camporeale, 83031 Ariano Irpino(AV), Italy
| | - Francesco Cardile
- Biogem, Institute of Molecular Biology and Genetics, Via Camporeale, 83031 Ariano Irpino(AV), Italy
| | - Alessandra Fucci
- Biogem, Institute of Molecular Biology and Genetics, Via Camporeale, 83031 Ariano Irpino(AV), Italy
| | - Egildo Luca D'Andrea
- Biogem, Institute of Molecular Biology and Genetics, Via Camporeale, 83031 Ariano Irpino(AV), Italy
| | - Assunta Riccio
- Biogem, Institute of Molecular Biology and Genetics, Via Camporeale, 83031 Ariano Irpino(AV), Italy
| | - Claudio Pisano
- Biogem, Institute of Molecular Biology and Genetics, Via Camporeale, 83031 Ariano Irpino(AV), Italy.
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Chen X, Wang L, Hong L, Su Z, Zhong X, Zhou H, Zhang X, Wu J, Shao L. Identification of Aging-Related Genes Associated With Clinical and Prognostic Features of Hepatocellular Carcinoma. Front Genet 2021; 12:661988. [PMID: 34262594 PMCID: PMC8274591 DOI: 10.3389/fgene.2021.661988] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/04/2021] [Indexed: 01/04/2023] Open
Abstract
Background: Aging is a well-studied concept, but no studies have comprehensively analyzed the association between aging-related genes (AGs) and hepatocellular carcinoma (HCC) prognosis. Methods: Gene candidates were selected from differentially expressed genes and prognostic genes in The Cancer Genome Atlas (TCGA) database. A gene risk score for overall survival prediction was established using the least absolute shrinkage and selection operator (LASSO) regression analysis, and this was validated using data from the International Cancer Genome Consortium (ICGC) database. Functional analysis was conducted using gene ontology enrichment, Kyoto Encyclopedia of Genes and Genomes analysis, gene set enrichment analysis, and immune microenvironment and tumor stemness analyses. Results: Initially, 72 AGs from the TCGA database were screened as differentially expressed between normal and tumor tissues and as genes associated with HCC prognosis. Then, seven AGs (POLA1, CDK1, SOCS2, HDAC1, MAPT, RAE1, and EEF1E1) were identified using the LASSO regression analysis. The seven AGs were used to develop a risk score in the training set, and the risk was validated to have a significant prognostic value in the ICGC set (p < 0.05). Patients with high risk scores had lower tumor differentiation, higher stage, and worse prognosis (all p < 0.05). Multivariate Cox regression analyses also confirmed that the risk score was an independent prognostic factor for HCC in both the TCGA and ICGC sets (all p < 0.05). Further analysis showed that a high risk score was correlated with the downregulation of metabolism and tumor immunity. Conclusion: The risk score predicts HCC prognosis and could thus be used as a biomarker not only for predicting HCC prognosis but also for deciding on treatment.
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Affiliation(s)
- Xingte Chen
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Lei Wang
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Liang Hong
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Zhixiong Su
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Xiaohong Zhong
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Han Zhou
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Xueqing Zhang
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Junxin Wu
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Lingdong Shao
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
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A patient with POLA1 splice variant expands the yet evolving phenotype of Van Esch O'Driscoll syndrome. Eur J Med Genet 2021; 64:104261. [PMID: 34119699 DOI: 10.1016/j.ejmg.2021.104261] [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: 02/07/2021] [Revised: 05/24/2021] [Accepted: 06/08/2021] [Indexed: 11/23/2022]
Abstract
Van Esch-O'Driscoll syndrome (VEODS) is a rare cause of syndromic X-linked intellectual disability characterised by short stature, microcephaly, variable degree of intellectual disability, and hypogonadotropic hypogonadism. To date, heterozygous hypomorphic variants in the gene encoding the DNA Polymerase α subunit, POLA1, have been observed in nine patients from five unrelated families with VEODS. We report a three-year-old child with VEODS having borderline intellectual disability due to a novel splice site variant causing exon 6 skipping and reduced POLA1 expression.
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Putscher E, Hecker M, Fitzner B, Lorenz P, Zettl UK. Principles and Practical Considerations for the Analysis of Disease-Associated Alternative Splicing Events Using the Gateway Cloning-Based Minigene Vectors pDESTsplice and pSpliceExpress. Int J Mol Sci 2021; 22:5154. [PMID: 34068052 PMCID: PMC8152502 DOI: 10.3390/ijms22105154] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/11/2021] [Accepted: 05/12/2021] [Indexed: 12/23/2022] Open
Abstract
Splicing is an important RNA processing step. Genetic variations can alter the splicing process and thereby contribute to the development of various diseases. Alterations of the splicing pattern can be examined by gene expression analyses, by computational tools for predicting the effects of genetic variants on splicing, and by splicing reporter minigene assays for studying alternative splicing events under defined conditions. The minigene assay is based on transient transfection of cells with a vector containing a genomic region of interest cloned between two constitutive exons. Cloning can be accomplished by the use of restriction enzymes or by site-specific recombination using Gateway cloning. The vectors pDESTsplice and pSpliceExpress represent two minigene systems based on Gateway cloning, which are available through the Addgene plasmid repository. In this review, we describe the features of these two splicing reporter minigene systems. Moreover, we provide an overview of studies in which determinants of alternative splicing were investigated by using pDESTsplice or pSpliceExpress. The studies were reviewed with regard to the investigated splicing regulatory events and the experimental strategy to construct and perform a splicing reporter minigene assay. We further elaborate on how analyses on the regulation of RNA splicing offer promising prospects for gaining important insights into disease mechanisms.
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Affiliation(s)
- Elena Putscher
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Street 20, 18147 Rostock, Germany; (E.P.); (B.F.); (U.K.Z.)
| | - Michael Hecker
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Street 20, 18147 Rostock, Germany; (E.P.); (B.F.); (U.K.Z.)
| | - Brit Fitzner
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Street 20, 18147 Rostock, Germany; (E.P.); (B.F.); (U.K.Z.)
| | - Peter Lorenz
- Rostock University Medical Center, Institute of Immunology, Schillingallee 70, 18057 Rostock, Germany;
| | - Uwe Klaus Zettl
- Division of Neuroimmunology, Department of Neurology, Rostock University Medical Center, Gehlsheimer Street 20, 18147 Rostock, Germany; (E.P.); (B.F.); (U.K.Z.)
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41
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Spotlight on the Replisome: Aetiology of DNA Replication-Associated Genetic Diseases. Trends Genet 2021; 37:317-336. [DOI: 10.1016/j.tig.2020.09.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/07/2020] [Accepted: 09/09/2020] [Indexed: 12/26/2022]
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42
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Mizuno T, Hirabayashi K, Miyazawa S, Kobayashi Y, Shoji K, Kobayashi M, Hanaoka F, Imamoto N, Torigoe H. The intrinsically disordered N-terminal region of mouse DNA polymerase alpha mediates its interaction with POT1a/b at telomeres. Genes Cells 2021; 26:360-380. [PMID: 33711210 DOI: 10.1111/gtc.12845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 01/12/2023]
Abstract
Mouse telomerase and the DNA polymerase alpha-primase complex elongate the leading and lagging strands of telomeres, respectively. To elucidate the molecular mechanism of lagging strand synthesis, we investigated the interaction between DNA polymerase alpha and two paralogs of the mouse POT1 telomere-binding protein (POT1a and POT1b). Yeast two-hybrid analysis and a glutathione S-transferase pull-down assay indicated that the C-terminal region of POT1a/b binds to the intrinsically disordered N-terminal region of p180, the catalytic subunit of mouse DNA polymerase alpha. Subcellular distribution analyses showed that although POT1a, POT1b, and TPP1 were localized to the cytoplasm, POT1a-TPP1 and POT1b-TPP1 coexpressed with TIN2 localized to the nucleus in a TIN2 dose-dependent manner. Coimmunoprecipitation and cell cycle synchronization experiments indicated that POT1b-TPP1-TIN2 was more strongly associated with p180 than POT1a-TPP1-TIN2, and this complex accumulated during the S phase. Fluorescence in situ hybridization and proximity ligation assays showed that POT1a and POT1b interacted with p180 and TIN2 on telomeric chromatin. Based on the present study and a previous study, we propose a model in which POT1a/b-TPP1-TIN2 translocates into the nucleus in a TIN2 dose-dependent manner to target the telomere, where POT1a/b interacts with DNA polymerase alpha for recruitment at the telomere for lagging strand synthesis.
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Affiliation(s)
| | - Kei Hirabayashi
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, Tokyo, Japan
| | - Sae Miyazawa
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, Tokyo, Japan
| | - Yurika Kobayashi
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, Tokyo, Japan
| | - Kenta Shoji
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, Tokyo, Japan
| | - Masakazu Kobayashi
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, Tokyo, Japan
| | | | - Naoko Imamoto
- Cellular Dynamics Laboratory, CPR, RIKEN, Wako, Japan
| | - Hidetaka Torigoe
- Department of Applied Chemistry, Faculty of Science, Tokyo University of Science, Tokyo, Japan
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King JR, Notarangelo LD, Hammarström L. An appraisal of the Wilson & Jungner criteria in the context of genomic-based newborn screening for inborn errors of immunity. J Allergy Clin Immunol 2021; 147:428-438. [PMID: 33551024 PMCID: PMC8344044 DOI: 10.1016/j.jaci.2020.12.633] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 11/25/2022]
Abstract
Wilson and Jungner's recommendations for population-based screening have been used to guide decisions regarding candidate disease inclusion in newborn screening programs for the past 50 years. The advent of genomic-based technologies, including next-generation sequencing and its potential application to newborn screening, along with a changing landscape in terms of modern clinical practice and ethical, social, and legal considerations has led to a call for review of these criteria. Inborn errors of immunity (IEI) are a heterogeneous group of more than 450 genetically determined disorders of immunity, which are associated with significant morbidity and mortality, particularly where diagnosis and treatment are delayed. We argue that in addition to screening for severe combined immunodeficiency disease, which has already been initiated in several countries, other clinically significant IEI should be screened for at birth. Because of disease heterogeneity and identifiable genetic targets, a next-generation sequencing-based screening approach would be most suitable. A combination of worldwide experience and technological advances has improved our ability to diagnose and effectively treat patients with IEI. Considering IEI in the context of updated recommendations for population-based screening supports their potential inclusion as disease targets in newborn screening programs.
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Affiliation(s)
- Jovanka R King
- Department of Clinical Immunology, Karolinska University Hospital Huddinge, Stockholm, Sweden; Department of Immunopathology, SA Pathology, Women's and Children's Hospital Campus, Adelaide, Australia; Robinson Research Institute and Discipline of Paediatrics, School of Medicine, University of Adelaide, Adelaide, Australia
| | - Luigi D Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Md
| | - Lennart Hammarström
- Department of Clinical Immunology, Karolinska University Hospital Huddinge, Stockholm, Sweden.
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44
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Moghaddas F. Monogenic autoinflammatory disorders: beyond the periodic fever. Intern Med J 2021; 50:151-164. [PMID: 31260149 DOI: 10.1111/imj.14414] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 04/29/2019] [Accepted: 06/16/2019] [Indexed: 12/27/2022]
Abstract
The past two decades have seen an exponential increase in the number of monogenic autoinflammatory disorders described, coinciding with improved genetic sequencing techniques. This group of disorders has evolved to be heterogeneous and certainly more complex than the original four 'periodic fever syndromes' caused by innate immune over-activation. This review aims to provide an update on the classic periodic fever syndromes as well as introducing the broadening spectrum of clinical features seen in more recently described conditions.
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Affiliation(s)
- Fiona Moghaddas
- Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, Victoria, Australia.,Department of Immunology and Allergy, The Royal Melbourne Hospital, Melbourne, Victoria, Australia
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45
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Schmit M, Bielinsky AK. Congenital Diseases of DNA Replication: Clinical Phenotypes and Molecular Mechanisms. Int J Mol Sci 2021; 22:E911. [PMID: 33477564 PMCID: PMC7831139 DOI: 10.3390/ijms22020911] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 01/13/2021] [Accepted: 01/14/2021] [Indexed: 12/19/2022] Open
Abstract
Deoxyribonucleic acid (DNA) replication can be divided into three major steps: initiation, elongation and termination. Each time a human cell divides, these steps must be reiteratively carried out. Disruption of DNA replication can lead to genomic instability, with the accumulation of point mutations or larger chromosomal anomalies such as rearrangements. While cancer is the most common class of disease associated with genomic instability, several congenital diseases with dysfunctional DNA replication give rise to similar DNA alterations. In this review, we discuss all congenital diseases that arise from pathogenic variants in essential replication genes across the spectrum of aberrant replisome assembly, origin activation and DNA synthesis. For each of these conditions, we describe their clinical phenotypes as well as molecular studies aimed at determining the functional mechanisms of disease, including the assessment of genomic stability. By comparing and contrasting these diseases, we hope to illuminate how the disruption of DNA replication at distinct steps affects human health in a surprisingly cell-type-specific manner.
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Affiliation(s)
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA;
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46
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Starokadomskyy P, Escala Perez-Reyes A, Burstein E. Immune Dysfunction in Mendelian Disorders of POLA1 Deficiency. J Clin Immunol 2021; 41:285-293. [PMID: 33392852 DOI: 10.1007/s10875-020-00953-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 12/22/2020] [Indexed: 02/07/2023]
Abstract
POLA1 encodes the catalytic unit of DNA polymerase α, which together with the Primase complex launches the DNA replication process. While complete deficiency of this essential gene is presumed to be lethal, at least two conditions due to partial POLA1 deficiency have been described. The first genetic syndrome to be mapped to POLA1 was X-linked reticulate pigmentary disorder (XLPDR, MIM #301220), a rare syndrome characterized by skin hyperpigmentation, sterile multiorgan inflammation, recurrent infections, and distinct facial features. XLPDR has been shown to be accompanied by profound activation of type I interferon signaling, but unlike other interferonopathies, it is not associated with autoantibodies or classical autoimmunity. Rather, it is accompanied by marked Natural Killer (NK) cell dysfunction, which may explain the recurrent infections seen in this syndrome. To date, all XLPDR cases are caused by the same recurrent intronic mutation, which results in gene missplicing. Several hypomorphic mutations in POLA1, distinct from the XLPDR intronic mutation, have been recently reported and these mutations associate with a separate condition, van Esch-O'Driscoll syndrome (VEODS, MIM #301030). This condition results in growth retardation, microcephaly, hypogonadism, and in some cases, overlapping immunological features to those seen in XLPDR. This review summarizes our current understanding of the clinical manifestations of POLA1 gene mutations with an emphasis on its immunological consequences, as well as recent advances in understanding of its pathophysiologic basis and potential therapeutic options.
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Affiliation(s)
- Petro Starokadomskyy
- Department of Internal Medicine, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75235, USA.
| | - Andrea Escala Perez-Reyes
- Department of Internal Medicine, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75235, USA
| | - Ezra Burstein
- Department of Internal Medicine, UT Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX, 75235, USA. .,Department of Molecular Biology, UT Southwestern Medical Center, 5323 Harry Hines blvd, Dallas, TX, 75390-9151, USA.
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47
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d'Angelo DM, Di Filippo P, Breda L, Chiarelli F. Type I Interferonopathies in Children: An Overview. Front Pediatr 2021; 9:631329. [PMID: 33869112 PMCID: PMC8044321 DOI: 10.3389/fped.2021.631329] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/05/2021] [Indexed: 01/01/2023] Open
Abstract
Notable advances in gene sequencing methods in recent years have permitted enormous progress in the phenotypic and genotypic characterization of autoinflammatory syndromes. Interferonopathies are a recent group of inherited autoinflammatory diseases, characterized by a dysregulation of the interferon pathway, leading to constitutive upregulation of its activation mechanisms or downregulation of negative regulatory systems. They are clinically heterogeneous, but some peculiar clinical features may lead to suspicion: a familial "idiopathic" juvenile arthritis resistant to conventional treatments, an early necrotizing vasculitis, a non-infectious interstitial lung disease, and a panniculitis associated or not with a lipodystrophy may represent the "interferon alarm bells." The awareness of this group of diseases represents a challenge for pediatricians because, despite being rare, a differential diagnosis with the most common childhood rheumatological and immunological disorders is mandatory. Furthermore, the characterization of interferonopathy molecular pathogenetic mechanisms is allowing important steps forward in other immune dysregulation diseases, such as systemic lupus erythematosus and inflammatory myositis, implementing the opportunity of a more effective target therapy.
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Affiliation(s)
| | | | - Luciana Breda
- Department of Pediatrics, University of Chieti, Chieti, Italy
| | - Francesco Chiarelli
- Department of Pediatrics, University of Chieti, Chieti, Italy.,Center of Excellence on Aging, University of Chieti, Chieti, Italy
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48
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Cazzato S, Omenetti A, Ravaglia C, Poletti V. Lung involvement in monogenic interferonopathies. Eur Respir Rev 2020; 29:29/158/200001. [PMID: 33328278 PMCID: PMC9489100 DOI: 10.1183/16000617.0001-2020] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 05/27/2020] [Indexed: 12/29/2022] Open
Abstract
Monogenic type I interferonopathies are inherited heterogeneous disorders characterised by early onset of systemic and organ specific inflammation, associated with constitutive activation of type I interferons (IFNs). In the last few years, several clinical reports identified the lung as one of the key target organs of IFN-mediated inflammation. The major pulmonary patterns described comprise children's interstitial lung diseases (including diffuse alveolar haemorrhages) and pulmonary arterial hypertension but diagnosis may be challenging. Respiratory symptoms may be either mild or absent at disease onset and variably associated with systemic or organ specific inflammation. In addition, associated extrapulmonary clinical features may precede lung function impairment by years, and patients may display severe/endstage lung involvement, although this may be clinically hidden during the long-term disease course. Conversely, a few cases of atypical severe lung involvement at onset have been reported without clinically manifested extrapulmonary signs. Hence, a multidisciplinary approach involving pulmonologists, paediatricians and rheumatologists should always be considered when a monogenic interferonopathy is suspected. Pulmonologists should also be aware of the main pattern of presentation to allow prompt diagnosis and a targeted therapeutic strategy. In this regard, promising therapeutic strategies rely on Janus kinase-1/2 (JAK-1/2) inhibitors blocking the type I IFN-mediated intracellular cascade. Progressive severe lung impairment may occur clinically hidden during monogenic interferonopathies. Pulmonologists should be aware of the main patterns of presentation in order to allow prompt diagnosis and initiate targeted therapeutic strategy.https://bit.ly/2UeAeLn
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Affiliation(s)
- Salvatore Cazzato
- Pediatric Unit, Dept of Mother and Child Health, Salesi Children's Hospital, Ancona, Italy.,Joint first authors
| | - Alessia Omenetti
- Pediatric Unit, Dept of Mother and Child Health, Salesi Children's Hospital, Ancona, Italy.,Joint first authors
| | - Claudia Ravaglia
- Dept of Diseases of the Thorax, Ospedale GB Morgagni, Forlì, Italy
| | - Venerino Poletti
- Dept of Diseases of the Thorax, Ospedale GB Morgagni, Forlì, Italy.,Dept of Respiratory Diseases & Allergy, Aarhus University Hospital, Aarhus, Denmark
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49
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Chen Q, Suzuki K, Sifuentes-Dominguez L, Miyata N, Song J, Lopez A, Starokadomskyy P, Gopal P, Dozmorov I, Tan S, Ge B, Burstein E. Paneth cell-derived growth factors support tumorigenesis in the small intestine. Life Sci Alliance 2020; 4:4/3/e202000934. [PMID: 33372038 PMCID: PMC7772774 DOI: 10.26508/lsa.202000934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 12/17/2022] Open
Abstract
Paneth cells, known for their production of antimicrobial peptides and growth factors in the gut epithelium, are found to play a key role in intestinal tumor formation through secretion of Wnt3. Paneth cells (PCs) are small intestinal epithelial cells that secrete antimicrobial peptides and growth factors, such as Wnt ligands. Intriguingly, the context in which PC-derived Wnt secretion is relevant in vivo remains unknown as intestinal epithelial ablation of Wnt does not affect homeostatic proliferation or restitution after irradiation injury. Considering the importance of growth factors in tumor development, we explored here the role of PCs in intestinal carcinogenesis using a genetic model of PC depletion through conditional expression of diphtheria toxin-α subunit. PC depletion in ApcMin mice impaired adenoma development in the small intestine and led to decreased Wnt3 expression in small bowel adenomas. To determine if PC-derived Wnt3 was required for adenoma development, we examined tumor formation after PC-specific ablation of Wnt3. We found that this was sufficient to decrease small intestinal adenoma formation; moreover, organoids derived from these tumors displayed slower growth capacity. Overall, we report that PC-derived Wnt3 is required to sustain early tumorigenesis in the small bowel and identify a clear role for PC-derived Wnt production in intestinal pathology.
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Affiliation(s)
- Qing Chen
- Department of General Surgery, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, TX, USA
| | - Kohei Suzuki
- Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, TX, USA
| | - Luis Sifuentes-Dominguez
- Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, TX, USA.,Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Naoteru Miyata
- Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, TX, USA
| | - Jie Song
- Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, TX, USA
| | - Adam Lopez
- Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, TX, USA
| | - Petro Starokadomskyy
- Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, TX, USA
| | - Purva Gopal
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Igor Dozmorov
- Department of Immunology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Shuai Tan
- Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, TX, USA
| | - Bujun Ge
- Department of General Surgery, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ezra Burstein
- Department of Internal Medicine, University of Texas (UT) Southwestern Medical Center, Dallas, TX, USA .,Department of Molecular Biology, UT Southwestern Medical Center, Dallas, TX, USA
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50
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Cui L, Xue H, Wen Z, Lu Z, Liu Y, Zhang Y. Prognostic roles of metabolic reprogramming-associated genes in patients with hepatocellular carcinoma. Aging (Albany NY) 2020; 12:22199-22219. [PMID: 33188160 PMCID: PMC7695384 DOI: 10.18632/aging.104122] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 08/08/2020] [Indexed: 02/07/2023]
Abstract
Metabolic reprogramming for adaptation to the tumor microenvironment is recognized as a hallmark of cancer. Although many altered metabolic genes have been reported to be associated with tumor pathological processes, systematic analysis of metabolic genes implicated in hepatocellular carcinoma prognosis remains rare. The aim of this study was to identify key metabolic genes related to hepatocellular carcinoma, and to explore their clinical significance. We downloaded mRNA expression profiles and clinical hepatocellular carcinoma data from The Cancer Genome Atlas database to explore the prognostic roles of metabolic genes. Five prognosis-associated metabolic genes, including POLA1, UCK2, ACYP1, ENTPD2, and TXNRD1, were screened via univariate Cox regression analysis and a LASSO Cox regression model, which divided patients into high- and low-risk groups. Furthermore, gene set enrichment analysis revealed that significantly-enriched gene ontology terms and pathways involving high-risk patients were focused on regulation of nucleic and fatty acid metabolism. Taken together, our study identified five metabolic genes related to survival, which can be used to predict the prognosis of patients with hepatocellular carcinoma. These genes may play essential roles in metabolic microenvironment regulation, and represent potentially important candidate targets in metabolic therapy.
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Affiliation(s)
- Lijuan Cui
- Department of Pharmacology, School of Basic Medicine, Shanxi Medical University, Taiyuan 030001, China
| | - Huan Xue
- Department of Pharmacology, School of Basic Medicine, Shanxi Medical University, Taiyuan 030001, China
| | - Zhitong Wen
- Department of Pharmacology, School of Basic Medicine, Shanxi Medical University, Taiyuan 030001, China
| | - Zhihong Lu
- Department of Pharmacology, School of Basic Medicine, Shanxi Medical University, Taiyuan 030001, China
| | - Yunfeng Liu
- Department of Endocrinology, The First Affiliated Hospital of Shanxi Medical University, Taiyuan 030001, China
| | - Yi Zhang
- Department of Pharmacology, School of Basic Medicine, Shanxi Medical University, Taiyuan 030001, China
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