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Hernandez RA, Hearn JI, Bhoopalan V, Hamzeh AR, Kwong K, Diamand K, Davies A, Li FJ, Padmanabhan H, Milne R, Ballard F, Spensberger D, Gardiner EE, Miraghazadeh B, Enders A, Cook MC. L-plastin associated syndrome of immune deficiency and hematologic cytopenia. J Allergy Clin Immunol 2024; 154:767-777. [PMID: 38710235 DOI: 10.1016/j.jaci.2024.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 04/01/2024] [Accepted: 05/01/2024] [Indexed: 05/08/2024]
Abstract
BACKGROUND LCP1 encodes L-plastin, an actin-bundling protein primarily expressed in hematopoietic cells. In mouse and fish models, LCP1 deficiency has been shown to result in hematologic and immune defects. OBJECTIVE This study aimed to determine the nature of a human inborn error of immunity resulting from a novel genetic variant of LCP1. METHODS We performed genetic, protein, and cellular analysis of PBMCs from a kindred with apparent autosomal dominant immune deficiency. We identified a candidate causal mutation in LCP1, which we evaluated by engineering the orthologous mutation in mice and Jurkat cells. RESULTS A splice-site variant in LCP1 segregated with lymphopenia, neutropenia, and thrombocytopenia. The splicing defect resulted in at least 2 aberrant transcripts, producing an in-frame deletion of 24 nucleotides, and a frameshift deletion of exon 8. Cellular analysis of the kindred revealed a proportionate reduction of T and B cells and a mild expansion of transitional B cells. Similarly, mice carrying the orthologous genetic variant exhibited the same in-frame aberrant transcript, reduced expression Lcp1 and gene dose-dependent leukopenia, mild thrombocytopenia, and lymphopenia, with a significant reduction of T-cell populations. Functional analysis revealed that LCP1c740-1G>A confers a defect in platelet development and function with aberrant spreading on collagen. Immunologic analysis revealed defective actin organization in T cells, reduced migration of PBMCs from patients, splenocytes from mutant mice, and a mutant Jurkat cell line in response to CXCL12; impaired germinal center B-cell expansion after immunization; and reduced cytokinesis during T cell proliferation. CONCLUSIONS We describe a unique human hematopoietic defect affecting neutrophils, lymphocytes, and platelets arising from partial LCP1 deficiency.
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Affiliation(s)
- Raquel A Hernandez
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - James I Hearn
- Division of Genome Sciences and Cancer, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Vijay Bhoopalan
- Division of Genome Sciences and Cancer, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | | | - Kristy Kwong
- Australian Phenomics Facility and John Curtin School of Medical Research, Australian National University, Canberra, Australia; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Koula Diamand
- Australian Phenomics Facility and John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Ainsley Davies
- Australian Phenomics Facility and John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Fei-Ju Li
- Australian Phenomics Facility and John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Harish Padmanabhan
- Australian Phenomics Facility and John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Rachel Milne
- Australian Phenomics Facility and John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Fiona Ballard
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Dominik Spensberger
- Australian Phenomics Facility and John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Elizabeth E Gardiner
- Division of Genome Sciences and Cancer, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Bahar Miraghazadeh
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Anselm Enders
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Matthew C Cook
- Division of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, Australia; Canberra Clinical Genomics, Canberra, Australia; Cambridge Institute of Therapeutic Immunology and Infectious Disease, Department of Medicine, University of Cambridge, Cambridge, United Kingdom.
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2
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Gillman R, Field MA, Schmitz U, Karamatic R, Hebbard L. Identifying cancer driver genes in individual tumours. Comput Struct Biotechnol J 2023; 21:5028-5038. [PMID: 37867967 PMCID: PMC10589724 DOI: 10.1016/j.csbj.2023.10.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/10/2023] [Accepted: 10/11/2023] [Indexed: 10/24/2023] Open
Abstract
Cancer is a heterogeneous disease with a strong genetic component making it suitable for precision medicine approaches aimed at identifying the underlying molecular drivers within a tumour. Large scale population-level cancer sequencing consortia have identified many actionable mutations common across both cancer types and sub-types, resulting in an increasing number of successful precision medicine programs. Nonetheless, such approaches fail to consider the effects of mutations unique to an individual patient and may miss rare driver mutations, necessitating personalised approaches to driver-gene prioritisation. One approach is to quantify the functional importance of individual mutations in a single tumour based on how they affect the expression of genes in a gene interaction network (GIN). These GIN-based approaches can be broadly divided into those that utilise an existing reference GIN and those that construct de novo patient-specific GINs. These single-tumour approaches have several limitations that likely influence their results, such as use of reference cohort data, network choice, and approaches to mathematical approximation, and more research is required to evaluate the in vitro and in vivo applicability of their predictions. This review examines the current state of the art methods that identify driver genes in single tumours with a focus on GIN-based driver prioritisation.
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Affiliation(s)
- Rhys Gillman
- Department of Biomedical Sciences and Molecular and Cell Biology, College of Public Health, Medical, and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, Queensland, Australia
| | - Matt A. Field
- Department of Biomedical Sciences and Molecular and Cell Biology, College of Public Health, Medical, and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, Queensland, Australia
- Immunogenomics Lab, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
- Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia
| | - Ulf Schmitz
- Department of Biomedical Sciences and Molecular and Cell Biology, College of Public Health, Medical, and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, Queensland, Australia
| | - Rozemary Karamatic
- Gastroenterology and Hepatology, Townsville University Hospital, PO Box 670, Townsville, Queensland 4810, Australia
- College of Medicine and Dentistry, Division of Tropical Health and Medicine, James Cook University, Townsville, Queensland, Australia
| | - Lionel Hebbard
- Department of Biomedical Sciences and Molecular and Cell Biology, College of Public Health, Medical, and Veterinary Sciences, James Cook University, Townsville, Queensland, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, Queensland, Australia
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, Sydney, New South Wales, Australia
- Australian Institute for Tropical Health and Medicine, Townsville, Queensland, Australia
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3
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A multimorphic mutation in IRF4 causes human autosomal dominant combined immunodeficiency. Sci Immunol 2023; 8:eade7953. [PMID: 36662884 PMCID: PMC10825898 DOI: 10.1126/sciimmunol.ade7953] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 12/22/2022] [Indexed: 01/22/2023]
Abstract
Interferon regulatory factor 4 (IRF4) is a transcription factor (TF) and key regulator of immune cell development and function. We report a recurrent heterozygous mutation in IRF4, p.T95R, causing an autosomal dominant combined immunodeficiency (CID) in seven patients from six unrelated families. The patients exhibited profound susceptibility to opportunistic infections, notably Pneumocystis jirovecii, and presented with agammaglobulinemia. Patients' B cells showed impaired maturation, decreased immunoglobulin isotype switching, and defective plasma cell differentiation, whereas their T cells contained reduced TH17 and TFH populations and exhibited decreased cytokine production. A knock-in mouse model of heterozygous T95R showed a severe defect in antibody production both at the steady state and after immunization with different types of antigens, consistent with the CID observed in these patients. The IRF4T95R variant maps to the TF's DNA binding domain, alters its canonical DNA binding specificities, and results in a simultaneous multimorphic combination of loss, gain, and new functions for IRF4. IRF4T95R behaved as a gain-of-function hypermorph by binding to DNA with higher affinity than IRF4WT. Despite this increased affinity for DNA, the transcriptional activity on IRF4 canonical genes was reduced, showcasing a hypomorphic activity of IRF4T95R. Simultaneously, IRF4T95R functions as a neomorph by binding to noncanonical DNA sites to alter the gene expression profile, including the transcription of genes exclusively induced by IRF4T95R but not by IRF4WT. This previously undescribed multimorphic IRF4 pathophysiology disrupts normal lymphocyte biology, causing human disease.
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4
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Lázaro-Guevara JM, Flores-Robles BJ, Garrido-Lopez KM, McKeown RJ, Flores-Morán AE, Labrador-Sánchez E, Pinillos-Aransay V, Trasahedo EA, López-Martín JA, Soberanis LSR, Melgar MY, Téllez-Arreola JL, Thébault SC. Identification of RP1 as the genetic cause of retinitis pigmentosa in a multi-generational pedigree using Extremely Low-Coverage Whole Genome Sequencing (XLC-WGS). Gene X 2023; 851:146956. [DOI: 10.1016/j.gene.2022.146956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 09/25/2022] [Accepted: 10/03/2022] [Indexed: 11/04/2022] Open
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5
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Field MA. Bioinformatic Challenges Detecting Genetic Variation in Precision Medicine Programs. Front Med (Lausanne) 2022; 9:806696. [PMID: 35463004 PMCID: PMC9024231 DOI: 10.3389/fmed.2022.806696] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 03/21/2022] [Indexed: 11/13/2022] Open
Abstract
Precision medicine programs to identify clinically relevant genetic variation have been revolutionized by access to increasingly affordable high-throughput sequencing technologies. A decade of continual drops in per-base sequencing costs means it is now feasible to sequence an individual patient genome and interrogate all classes of genetic variation for < $1,000 USD. However, while advances in these technologies have greatly simplified the ability to obtain patient sequence information, the timely analysis and interpretation of variant information remains a challenge for the rollout of large-scale precision medicine programs. This review will examine the challenges and potential solutions that exist in identifying predictive genetic biomarkers and pharmacogenetic variants in a patient and discuss the larger bioinformatic challenges likely to emerge in the future. It will examine how both software and hardware development are aiming to overcome issues in short read mapping, variant detection and variant interpretation. It will discuss the current state of the art for genetic disease and the remaining challenges to overcome for complex disease. Success across all types of disease will require novel statistical models and software in order to ensure precision medicine programs realize their full potential now and into the future.
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Affiliation(s)
- Matt A. Field
- Centre for Tropical Bioinformatics and Molecular Biology, College of Public Health, Medical and Veterinary Science, James Cook University, Cairns, QLD, Australia
- Immunogenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
- Menzies School of Health Research, Charles Darwin University, Darwin, NT, Australia
- *Correspondence: Matt A. Field
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6
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Zinngrebe J, Moepps B, Monecke T, Gierschik P, Schlichtig F, Barth TFE, Strauß G, Boldrin E, Posovszky C, Schulz A, Beringer O, Rieser E, Jacobsen E, Lorenz MR, Schwarz K, Pannicke U, Walczak H, Niessing D, Schuetz C, Fischer‐Posovszky P, Debatin K. Compound heterozygous variants in OTULIN are associated with fulminant atypical late-onset ORAS. EMBO Mol Med 2022; 14:e14901. [PMID: 35170849 PMCID: PMC8899767 DOI: 10.15252/emmm.202114901] [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: 07/26/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 01/11/2023] Open
Abstract
Autoinflammatory diseases are a heterogenous group of disorders defined by fever and systemic inflammation suggesting involvement of genes regulating innate immune responses. Patients with homozygous loss-of-function variants in the OTU-deubiquitinase OTULIN suffer from neonatal-onset OTULIN-related autoinflammatory syndrome (ORAS) characterized by fever, panniculitis, diarrhea, and arthritis. Here, we describe an atypical form of ORAS with distinct clinical manifestation of the disease caused by two new compound heterozygous variants (c.258G>A (p.M86I)/c.500G>C (p.W167S)) in the OTULIN gene in a 7-year-old affected by a life-threatening autoinflammatory episode with sterile abscess formation. On the molecular level, we find binding of OTULIN to linear ubiquitin to be compromised by both variants; however, protein stability and catalytic activity is most affected by OTULIN variant p.W167S. These molecular changes together lead to increased levels of linear ubiquitin linkages in patient-derived cells triggering the disease. Our data indicate that the spectrum of ORAS patients is more diverse than previously thought and, thus, supposedly asymptomatic individuals might also be affected. Based on our results, we propose to subdivide the ORAS into classical and atypical entities.
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Affiliation(s)
- Julia Zinngrebe
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | - Barbara Moepps
- Institute of Pharmacology and ToxicologyUlm UniversityUlmGermany
| | - Thomas Monecke
- Institute of Pharmaceutical BiotechnologyUlm UniversityUlmGermany
| | - Peter Gierschik
- Institute of Pharmacology and ToxicologyUlm UniversityUlmGermany
| | - Ferdinand Schlichtig
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | | | - Gudrun Strauß
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | - Elena Boldrin
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | - Carsten Posovszky
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | - Ansgar Schulz
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | - Ortraud Beringer
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | - Eva Rieser
- Institute of Biochemistry I & CECAD Research CenterUniversity of CologneCologneGermany
| | - Eva‐Maria Jacobsen
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
| | | | - Klaus Schwarz
- Institute for Transfusion MedicineUlm UniversityUlmGermany
- Institute for Clinical Transfusion Medicine and Immunogenetics UlmGerman Red Cross Blood Service Baden‐Wuerttemberg – HessenUlmGermany
| | | | - Henning Walczak
- Institute of Biochemistry I & CECAD Research CenterUniversity of CologneCologneGermany
- UCL Cancer InstituteLondonUK
| | - Dierk Niessing
- Institute of Pharmaceutical BiotechnologyUlm UniversityUlmGermany
| | | | | | - Klaus‐Michael Debatin
- Department of Pediatrics and Adolescent MedicineUlm University Medical CenterUlmGermany
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7
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Jiang SH, Mercan S, Papa I, Moldovan M, Walters GD, Koina M, Fadia M, Stanley M, Lea-Henry T, Cook A, Ellyard J, McMorran B, Sundaram M, Thomson R, Canete PF, Hoy W, Hutton H, Srivastava M, McKeon K, de la Rúa Figueroa I, Cervera R, Faria R, D’Alfonso S, Gatto M, Athanasopoulos V, Field M, Mathews J, Cho E, Andrews TD, Kitching AR, Cook MC, Riquelme MA, Bahlo M, Vinuesa CG. Deletions in VANGL1 are a risk factor for antibody-mediated kidney disease. Cell Rep Med 2021; 2:100475. [PMID: 35028616 PMCID: PMC8714939 DOI: 10.1016/j.xcrm.2021.100475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/11/2021] [Accepted: 11/23/2021] [Indexed: 12/11/2022]
Abstract
We identify an intronic deletion in VANGL1 that predisposes to renal injury in high risk populations through a kidney-intrinsic process. Half of all SLE patients develop nephritis, yet the predisposing mechanisms to kidney damage remain poorly understood. There is limited evidence of genetic contribution to specific organ involvement in SLE.1,2 We identify a large deletion in intron 7 of Van Gogh Like 1 (VANGL1), which associates with nephritis in SLE patients. The same deletion occurs at increased frequency in an indigenous population (Tiwi Islanders) with 10-fold higher rates of kidney disease compared with non-indigenous populations. Vangl1 hemizygosity in mice results in spontaneous IgA and IgG deposition within the glomerular mesangium in the absence of autoimmune nephritis. Serum transfer into B cell-deficient Vangl1+/- mice results in mesangial IgG deposition indicating that Ig deposits occur in a kidney-intrinsic fashion in the absence of Vangl1. These results suggest that Vangl1 acts in the kidney to prevent Ig deposits and its deficiency may trigger nephritis in individuals with SLE.
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Affiliation(s)
- Simon H. Jiang
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Canberra, Australian National University, Canberra 2601, Australia
- Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Australian National University, Canberra 2601, Australia
- Department of Renal Medicine, The Canberra Hospital, Canberra 2605, Australia
| | - Sevcan Mercan
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Canberra, Australian National University, Canberra 2601, Australia
- Department of Bioengineering, Kafkas University, Kars 36100, Turkey
| | - Ilenia Papa
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Canberra, Australian National University, Canberra 2601, Australia
| | - Max Moldovan
- Centre for Population Health Research, University of South Australia, South Australian Health and Medical Research Institute (SAHMRI), Adelaide 5001, Australia
- Australian Institute of Health Innovation, Macquarie University, Sydney 2109, Australia
| | - Giles D. Walters
- Department of Renal Medicine, The Canberra Hospital, Canberra 2605, Australia
| | - Mark Koina
- Department of Pathology, The Canberra Hospital, Canberra 2605, Australia
| | - Mitali Fadia
- Department of Pathology, The Canberra Hospital, Canberra 2605, Australia
| | - Maurice Stanley
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Canberra, Australian National University, Canberra 2601, Australia
| | - Tom Lea-Henry
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Canberra, Australian National University, Canberra 2601, Australia
| | - Amelia Cook
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Canberra, Australian National University, Canberra 2601, Australia
| | - Julia Ellyard
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Canberra, Australian National University, Canberra 2601, Australia
- Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Australian National University, Canberra 2601, Australia
| | - Brendan McMorran
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Canberra, Australian National University, Canberra 2601, Australia
| | - Madhivanan Sundaram
- Department of Renal Medicine, Royal Darwin Hospital, Northern Territory 0811, Australia
| | - Russell Thomson
- Centre for Research in Mathematics and Data Science, School of Computer, Data and Mathematical Sciences, Western Sydney University, Parramatta 2150, NSW, Australia
| | - Pablo F. Canete
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Canberra, Australian National University, Canberra 2601, Australia
- Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Australian National University, Canberra 2601, Australia
| | - Wendy Hoy
- Centre for Chronic Disease, Faculty of Health, The University of Queensland, Brisbane 4029, QLD, Australia
| | - Holly Hutton
- Centre for Inflammatory Diseases, Monash University, Melbourne 3168, VIC, Australia
| | - Monika Srivastava
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Canberra, Australian National University, Canberra 2601, Australia
| | - Kathryn McKeon
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Canberra, Australian National University, Canberra 2601, Australia
- Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Australian National University, Canberra 2601, Australia
| | | | - Ricard Cervera
- Department of Autoimmune Diseases, Hospital Clinic, Barcelona 08036, Spain
| | - Raquel Faria
- Unidade de Imunologia Clinica, Centro Hospitalar Unisersitario do Porto, Porto 4099-001, Portugal
| | | | - Mariele Gatto
- Department of Rheumatology, University of Padova, Italy
| | - Vicki Athanasopoulos
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Canberra, Australian National University, Canberra 2601, Australia
- Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Australian National University, Canberra 2601, Australia
| | - Matthew Field
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns 4870, QLD, Australia
| | - John Mathews
- School of Population and Global Health, University of Melbourne, Melbourne 3053, Australia
| | - Eun Cho
- Genome Informatics Laboratory, John Curtin School of Medical Research, Australian National University, Canberra 2601, Australia
| | - Thomas D. Andrews
- Genome Informatics Laboratory, John Curtin School of Medical Research, Australian National University, Canberra 2601, Australia
| | - A. Richard Kitching
- Centre for Inflammatory Diseases, Monash University, Melbourne 3168, VIC, Australia
- Departments Nephrology and Paediatric Nephrology. Monash Health, Melbourne 3168, Australia
| | - Matthew C. Cook
- Department of Immunology, The Canberra Hospital, Canberra 2605, Australia
| | - Marta Alarcon Riquelme
- Department of Medical Genomics, GENYO. Centre for Genomics and Oncological Research: Pfizer/University of Granada/Andalusian Regional Government, Granada, 18016, Spain
| | - Melanie Bahlo
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville 3010 VIC, Australia
| | - Carola G. Vinuesa
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Canberra, Australian National University, Canberra 2601, Australia
- Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Australian National University, Canberra 2601, Australia
- China Australia Centre for Personalised Immunology, Renji Hospital Shanghai, JiaoTong University Shanghai 200001, China
- Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK
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8
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Durward-Akhurst SA, Schaefer RJ, Grantham B, Carey WK, Mickelson JR, McCue ME. Genetic Variation and the Distribution of Variant Types in the Horse. Front Genet 2021; 12:758366. [PMID: 34925451 PMCID: PMC8676274 DOI: 10.3389/fgene.2021.758366] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/10/2021] [Indexed: 11/13/2022] Open
Abstract
Genetic variation is a key contributor to health and disease. Understanding the link between an individual's genotype and the corresponding phenotype is a major goal of medical genetics. Whole genome sequencing (WGS) within and across populations enables highly efficient variant discovery and elucidation of the molecular nature of virtually all genetic variation. Here, we report the largest catalog of genetic variation for the horse, a species of importance as a model for human athletic and performance related traits, using WGS of 534 horses. We show the extent of agreement between two commonly used variant callers. In data from ten target breeds that represent major breed clusters in the domestic horse, we demonstrate the distribution of variants, their allele frequencies across breeds, and identify variants that are unique to a single breed. We investigate variants with no homozygotes that may be potential embryonic lethal variants, as well as variants present in all individuals that likely represent regions of the genome with errors, poor annotation or where the reference genome carries a variant. Finally, we show regions of the genome that have higher or lower levels of genetic variation compared to the genome average. This catalog can be used for variant prioritization for important equine diseases and traits, and to provide key information about regions of the genome where the assembly and/or annotation need to be improved.
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Affiliation(s)
- S. A. Durward-Akhurst
- Department of Veterinary Population Medicine, University of Minnesota, Minneapolis, MN, United States
| | - R. J. Schaefer
- Department of Veterinary Population Medicine, University of Minnesota, Minneapolis, MN, United States
| | - B. Grantham
- Interval Bio LLC, Mountain View, CA, United States
| | - W. K. Carey
- Interval Bio LLC, Mountain View, CA, United States
| | - J. R. Mickelson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Minneapolis, MN, United States
| | - M. E. McCue
- Department of Veterinary Population Medicine, University of Minnesota, Minneapolis, MN, United States
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9
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McConnell H, Andrews TD, Field MA. Efficacy of computational predictions of the functional effect of idiosyncratic pharmacogenetic variants. PeerJ 2021; 9:e11774. [PMID: 34316407 PMCID: PMC8286708 DOI: 10.7717/peerj.11774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 06/23/2021] [Indexed: 01/04/2023] Open
Abstract
Background Pharmacogenetic variation is important to drug responses through diverse and complex mechanisms. Predictions of the functional impact of missense pharmacogenetic variants primarily rely on the degree of sequence conservation between species as a primary discriminator. However, idiosyncratic or off-target drug-variant interactions sometimes involve effects that are peripheral or accessory to the central systems in which a gene functions. Given the importance of sequence conservation to functional prediction tools-these idiosyncratic pharmacogenetic variants may violate the assumptions of predictive software commonly used to infer their effect. Methods Here we exhaustively assess the effectiveness of eleven missense mutation functional inference tools on all known pharmacogenetic missense variants contained in the Pharmacogenomics Knowledgebase (PharmGKB) repository. We categorize PharmGKB entries into sub-classes to catalog likely off-target interactions, such that we may compare predictions across different variant annotations. Results As previously demonstrated, functional inference tools perform variably across the complete set of PharmGKB variants, with large numbers of variants incorrectly classified as 'benign'. However, we find substantial differences amongst PharmGKB variant sub-classes, particularly in variants known to cause off-target, type B adverse drug reactions, that are largely unrelated to the main pharmacological action of the drug. Specifically, variants associated with off-target effects (hence referred to as off-target variants) were most often incorrectly classified as 'benign'. These results highlight the importance of understanding the underlying mechanism of pharmacogenetic variants and how variants associated with off-target effects will ultimately require new predictive algorithms. Conclusion In this work we demonstrate that functional inference tools perform poorly on pharmacogenetic variants, particularly on subsets enriched for variants causing off-target, type B adverse drug reactions. We describe how to identify variants associated with off-target effects within PharmGKB in order to generate a training set of variants that is needed to develop new algorithms specifically for this class of variant. Development of such tools will lead to more accurate functional predictions and pave the way for the increased wide-spread adoption of pharmacogenetics in clinical practice.
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Affiliation(s)
- Hannah McConnell
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - T Daniel Andrews
- John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Matt A Field
- Australian Institute of Tropical Health and Medicine, Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Smithfield, Australia.,Immunogenomics Lab, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
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10
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Raspin K, FitzGerald LM, Marthick JR, Field MA, Malley RC, Banks A, Donovan S, Thomson RJ, Foley GR, Stanford JL, Dickinson JL. A rare variant in EZH2 is associated with prostate cancer risk. Int J Cancer 2021; 149:1089-1099. [PMID: 33821477 DOI: 10.1002/ijc.33584] [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: 09/12/2020] [Revised: 02/26/2021] [Accepted: 03/09/2021] [Indexed: 11/11/2022]
Abstract
Prostate cancer (PrCa) is highly heritable, and although rare variants contribute significantly to PrCa risk, few have been identified to date. Herein, whole-genome sequencing was performed in a large PrCa family featuring multiple affected relatives spanning several generations. A rare, predicted splice site EZH2 variant, rs78589034 (G > A), was identified as segregating with disease in all but two individuals in the family, one of whom was affected with lymphoma and bowel cancer and a female relative. This variant was significantly associated with disease risk in combined familial and sporadic PrCa datasets (n = 1551; odds ratio [OR] = 3.55, P = 1.20 × 10-5 ). Transcriptome analysis was performed on prostate tumour needle biopsies available for two rare variant carriers and two wild-type cases. Although no allele-dependent differences were detected in EZH2 transcripts, a distinct differential gene expression signature was observed when comparing prostate tissue from the rare variant carriers with the wild-type samples. The gene expression signature comprised known downstream targets of EZH2 and included the top-ranked genes, DUSP1, FOS, JUNB and EGR1, which were subsequently validated by qPCR. These data provide evidence that rs78589034 is associated with increased PrCa risk in Tasmanian men and further, that this variant may be associated with perturbed EZH2 function in prostate tissue. Disrupted EZH2 function is a driver of tumourigenesis in several cancers, including prostate, and is of significant interest as a therapeutic target.
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Affiliation(s)
- Kelsie Raspin
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Liesel M FitzGerald
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - James R Marthick
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Matt A Field
- Australian Institute of Tropical Health and Medicine and Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, Queensland, Australia.,John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Roslyn C Malley
- Hobart Pathology, Hobart, Tasmania, Australia.,Tasmanian School of Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - Annette Banks
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | | | - Russell J Thomson
- Centre for Research in Mathematics and Data Science, Western Sydney University, Sydney, New South Wales, Australia
| | - Georgea R Foley
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Janet L Stanford
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Joanne L Dickinson
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
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11
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Edwards RJ, Field MA, Ferguson JM, Dudchenko O, Keilwagen J, Rosen BD, Johnson GS, Rice ES, Hillier LD, Hammond JM, Towarnicki SG, Omer A, Khan R, Skvortsova K, Bogdanovic O, Zammit RA, Aiden EL, Warren WC, Ballard JWO. Chromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome. BMC Genomics 2021; 22:188. [PMID: 33726677 PMCID: PMC7962210 DOI: 10.1186/s12864-021-07493-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/28/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Basenjis are considered an ancient dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness. RESULTS Here, we report two high quality de novo Basenji genome assemblies: a female, China (CanFam_Bas), and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three dog breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). CanFam_Bas is superior to CanFam3.1 in terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. By aligning short read data from 58 representative dog breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection. CONCLUSIONS The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific dog breeds. However, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach. Collectively this work highlights the importance the choice of reference genome makes in all variation studies.
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Affiliation(s)
- Richard J. Edwards
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052 Australia
| | - Matt A. Field
- Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD 4878 Australia
- John Curtin School of Medical Research, Australian National University, Canberra, ACT 2600 Australia
| | - James M. Ferguson
- Kinghorn Center for Clinical Genomics, Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010 Australia
| | - Olga Dudchenko
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Department of Computer Science, Rice University, Houston, TX USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX USA
| | - Jens Keilwagen
- Julius Kühn-Institut, Erwin-Baur-Str, 27 06484 Quedlinburg, Germany
| | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA, Beltsville, MD 20705 USA
| | - Gary S. Johnson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211 USA
| | - Edward S. Rice
- Department of Surgery, University of Missouri, Columbia, MO 65211 USA
| | | | - Jillian M. Hammond
- Kinghorn Center for Clinical Genomics, Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010 Australia
| | - Samuel G. Towarnicki
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052 Australia
| | - Arina Omer
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Department of Computer Science, Rice University, Houston, TX USA
| | - Ruqayya Khan
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Department of Computer Science, Rice University, Houston, TX USA
| | - Ksenia Skvortsova
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010 Australia
- St Vincent’s Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW 2010 Australia
| | - Ozren Bogdanovic
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052 Australia
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Victoria Street, Darlinghurst, NSW 2010 Australia
| | - Robert A. Zammit
- Vineyard Veterinary Hospital, 703 Windsor Rd, Vineyard, NSW 2765 Australia
| | - Erez Lieberman Aiden
- The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX USA
- Department of Computer Science, Rice University, Houston, TX USA
- Center for Theoretical and Biological Physics, Rice University, Houston, TX USA
- Faculty of Science, UWA School of Agriculture and Environment, University of Western Australia, Perth, WA 6009 Australia
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China
| | - Wesley C. Warren
- Department of Animal Sciences, University of Missouri, Columbia, MO 65211 Australia
| | - J. William O. Ballard
- Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Victoria 3086 Australia
- School of Biosciences, University of Melbourne, Parkville, Victoria 3052 Australia
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12
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Detecting Causal Variants in Mendelian Disorders Using Whole-Genome Sequencing. Methods Mol Biol 2021; 2243:1-25. [PMID: 33606250 DOI: 10.1007/978-1-0716-1103-6_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] [Indexed: 02/23/2023]
Abstract
Increasingly affordable sequencing technologies are revolutionizing the field of genomic medicine. It is now feasible to interrogate all major classes of variation in an individual across the entire genome for less than $1000 USD. While the generation of patient sequence information using these technologies has become routine, the analysis and interpretation of this data remains the greatest obstacle to widespread clinical implementation. This chapter summarizes the steps to identify, annotate, and prioritize variant information required for clinical report generation. We discuss methods to detect each variant class and describe strategies to increase the likelihood of detecting causal variant(s) in Mendelian disease. Lastly, we describe a sample workflow for synthesizing large amount of genetic information into concise clinical reports.
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13
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Field MA. Detecting pathogenic variants in autoimmune diseases using high-throughput sequencing. Immunol Cell Biol 2020; 99:146-156. [PMID: 32623783 PMCID: PMC7891608 DOI: 10.1111/imcb.12372] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/22/2020] [Accepted: 07/02/2020] [Indexed: 12/12/2022]
Abstract
Sequencing the first human genome in 2003 took 15 years and cost $2.7 billion. Advances in sequencing technologies have since decreased costs to the point where it is now feasible to resequence a whole human genome for $1000 in a single day. These advances have allowed the generation of huge volumes of high‐quality human sequence data used to construct increasingly large catalogs of both population‐level and disease‐causing variation. The existence of such databases, coupled with a high‐quality human reference genome, means we are able to interrogate and annotate all types of genetic variation and identify pathogenic variants for many diseases. Increasingly, sequencing‐based approaches are being used to elucidate the underlying genetic cause of autoimmune diseases, a group of roughly 80 polygenic diseases characterized by abnormal immune responses where healthy tissue is attacked. Although sequence data generation has become routine and affordable, significant challenges remain with no gold‐standard methodology to identify pathogenic variants currently available. This review examines the latest methodologies used to identify pathogenic variants in autoimmune diseases and considers available sequencing options and subsequent bioinformatic methodologies and strategies. The development of reliable and robust sequencing and analytic workflows to detect pathogenic variants is critical to realize the potential of precision medicine programs where patient variant information is used to inform clinical practice.
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Affiliation(s)
- Matt A Field
- Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia.,John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
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14
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Howson LJ, Awad W, von Borstel A, Lim HJ, McWilliam HEG, Sandoval-Romero ML, Majumdar S, Hamzeh AR, Andrews TD, McDermott DH, Murphy PM, Le Nours J, Mak JYW, Liu L, Fairlie DP, McCluskey J, Villadangos JA, Cook MC, Turner SJ, Davey MS, Ojaimi S, Rossjohn J. Absence of mucosal-associated invariant T cells in a person with a homozygous point mutation in MR1. Sci Immunol 2020; 5:5/49/eabc9492. [PMID: 32709702 DOI: 10.1126/sciimmunol.abc9492] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 06/11/2020] [Indexed: 12/12/2022]
Abstract
The role unconventional T cells play in protective immunity in humans is unclear. Mucosal-associated invariant T (MAIT) cells are an unconventional T cell subset restricted to the antigen-presenting molecule MR1. Here, we report the discovery of a patient homozygous for a rare Arg31His (R9H in the mature protein) mutation in MR1 who has a history of difficult-to-treat viral and bacterial infections. MR1R9H was unable to present the potent microbially derived MAIT cell stimulatory ligand. The MR1R9H crystal structure revealed that the stimulatory ligand cannot bind due to the mutation lying within, and causing structural perturbation to, the ligand-binding domain of MR1. While MR1R9H could bind and be up-regulated by a MAIT cell inhibitory ligand, the patient lacked circulating MAIT cells. This shows the importance of the stimulatory ligand for MAIT cell selection in humans. The patient had an expanded γδ T cell population, indicating a compensatory interplay between these unconventional T cell subsets.
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Affiliation(s)
- Lauren J Howson
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.
| | - Wael Awad
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Anouk von Borstel
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Hui Jing Lim
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Hamish E G McWilliam
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Maria L Sandoval-Romero
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Shamik Majumdar
- Molecular Signaling Section, Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Abdul Rezzak Hamzeh
- Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory, Australia.,Department of Immunology, Canberra Hospital, Canberra, Australian Capital Territory, Australia
| | - Thomas D Andrews
- Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory, Australia.,Department of Immunology, Canberra Hospital, Canberra, Australian Capital Territory, Australia
| | - David H McDermott
- Molecular Signaling Section, Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Philip M Murphy
- Molecular Signaling Section, Laboratory of Molecular Immunology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Jérôme Le Nours
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia
| | - Jeffrey Y W Mak
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of Queensland, Brisbane, Queensland, Australia
| | - Ligong Liu
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of Queensland, Brisbane, Queensland, Australia
| | - David P Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.,ARC Centre of Excellence in Advanced Molecular Imaging, University of Queensland, Brisbane, Queensland, Australia
| | - James McCluskey
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia
| | - Jose A Villadangos
- Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia.,Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Matthew C Cook
- Centre for Personalised Immunology, John Curtin School of Medical Research, Australian National University, Acton, Australian Capital Territory, Australia.,Department of Immunology, Canberra Hospital, Canberra, Australian Capital Territory, Australia
| | - Stephen J Turner
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Martin S Davey
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Samar Ojaimi
- Department of Infectious Diseases, Monash Health, Clayton, Victoria, Australia.,Centre for Inflammatory Diseases, Monash University, Clayton, Victoria, Australia.,Department of Allergy and Immunology, Monash Health, Clayton, Victoria, Australia
| | - Jamie Rossjohn
- Infection and Immunity Program and Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia. .,Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria, Australia.,Institute of Infection and Immunity, Cardiff University School of Medicine, Heath Park, Cardiff, UK
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15
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Loughland JR, Woodberry T, Field M, Andrew DW, SheelaNair A, Dooley NL, Piera KA, Amante FH, Kenangalem E, Price RN, Engwerda CR, Anstey NM, McCarthy JS, Boyle MJ, Minigo G. Transcriptional profiling and immunophenotyping show sustained activation of blood monocytes in subpatent Plasmodium falciparum infection. Clin Transl Immunology 2020; 9:e1144. [PMID: 32566226 PMCID: PMC7302943 DOI: 10.1002/cti2.1144] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/17/2020] [Accepted: 05/18/2020] [Indexed: 01/13/2023] Open
Abstract
OBJECTIVES Malaria, caused by Plasmodium infection, remains a major global health problem. Monocytes are integral to the immune response, yet their transcriptional and functional responses in primary Plasmodium falciparum infection and in clinical malaria are poorly understood. METHODS The transcriptional and functional profiles of monocytes were examined in controlled human malaria infection with P. falciparum blood stages and in children and adults with acute malaria. Monocyte gene expression and functional phenotypes were examined by RNA sequencing and flow cytometry at peak infection and compared to pre-infection or at convalescence in acute malaria. RESULTS In subpatent primary infection, the monocyte transcriptional profile was dominated by an interferon (IFN) molecular signature. Pathways enriched included type I IFN signalling, innate immune response and cytokine-mediated signalling. Monocytes increased TNF and IL-12 production upon in vitro toll-like receptor stimulation and increased IL-10 production upon in vitro parasite restimulation. Longitudinal phenotypic analyses revealed sustained significant changes in the composition of monocytes following infection, with increased CD14+CD16- and decreased CD14-CD16+ subsets. In acute malaria, monocyte CD64/FcγRI expression was significantly increased in children and adults, while HLA-DR remained stable. Although children and adults showed a similar pattern of differentially expressed genes, the number and magnitude of gene expression change were greater in children. CONCLUSIONS Monocyte activation during subpatent malaria is driven by an IFN molecular signature with robust activation of genes enriched in pathogen detection, phagocytosis, antimicrobial activity and antigen presentation. The greater magnitude of transcriptional changes in children with acute malaria suggests monocyte phenotypes may change with age or exposure.
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Affiliation(s)
- Jessica R Loughland
- QIMR Berghofer Medical Research InstituteBrisbaneQLDAustralia,Menzies School of Health ResearchDarwinNTAustralia
| | - Tonia Woodberry
- Menzies School of Health ResearchDarwinNTAustralia,Charles Darwin UniversityDarwinNTAustralia,Present address:
The University of NewcastleCallaghanNSWAustralia
| | - Matt Field
- Australian Institute of Tropical Health and Medicine and Centre for Tropical Bioinformatics and Molecular BiologyJames Cook UniversityCairnsQLDAustralia,John Curtin School of Medical ResearchAustralian National UniversityCanberraACTAustralia
| | - Dean W Andrew
- QIMR Berghofer Medical Research InstituteBrisbaneQLDAustralia
| | - Arya SheelaNair
- QIMR Berghofer Medical Research InstituteBrisbaneQLDAustralia
| | | | - Kim A Piera
- Menzies School of Health ResearchDarwinNTAustralia,Charles Darwin UniversityDarwinNTAustralia
| | - Fiona H Amante
- QIMR Berghofer Medical Research InstituteBrisbaneQLDAustralia
| | - Enny Kenangalem
- Timika Malaria Research ProgramPapuan Health and Community Development FoundationTimikaIndonesia,District Health AuthorityTimikaIndonesia
| | - Ric N Price
- Menzies School of Health ResearchDarwinNTAustralia,Charles Darwin UniversityDarwinNTAustralia,Centre for Tropical Medicine and Global HealthNuffield Department of Clinical MedicineUniversity of OxfordOxfordUK,Mahidol‐Oxford Tropical Medicine Research UnitFaculty of Tropical MedicineMahidol UniversityBangkokThailand
| | | | - Nicholas M Anstey
- Menzies School of Health ResearchDarwinNTAustralia,Charles Darwin UniversityDarwinNTAustralia
| | | | - Michelle J Boyle
- QIMR Berghofer Medical Research InstituteBrisbaneQLDAustralia,Menzies School of Health ResearchDarwinNTAustralia
| | - Gabriela Minigo
- Menzies School of Health ResearchDarwinNTAustralia,Charles Darwin UniversityDarwinNTAustralia,College of Health and Human SciencesCharles Darwin UniversityDarwinNTAustralia
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16
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Łyszkiewicz M, Ziętara N, Frey L, Pannicke U, Stern M, Liu Y, Fan Y, Puchałka J, Hollizeck S, Somekh I, Rohlfs M, Yilmaz T, Ünal E, Karakukcu M, Patiroğlu T, Kellerer C, Karasu E, Sykora KW, Lev A, Simon A, Somech R, Roesler J, Hoenig M, Keppler OT, Schwarz K, Klein C. Human FCHO1 deficiency reveals role for clathrin-mediated endocytosis in development and function of T cells. Nat Commun 2020; 11:1031. [PMID: 32098969 PMCID: PMC7042371 DOI: 10.1038/s41467-020-14809-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 01/23/2020] [Indexed: 01/05/2023] Open
Abstract
Clathrin-mediated endocytosis (CME) is critical for internalisation of molecules across cell membranes. The FCH domain only 1 (FCHO1) protein is key molecule involved in the early stages of CME formation. The consequences of mutations in FCHO1 in humans were unknown. We identify ten unrelated patients with variable T and B cell lymphopenia, who are homozygous for six distinct mutations in FCHO1. We demonstrate that these mutations either lead to mislocalisation of the protein or prevent its interaction with binding partners. Live-cell imaging of cells expressing mutant variants of FCHO1 provide evidence of impaired formation of clathrin coated pits (CCP). Patient T cells are unresponsive to T cell receptor (TCR) triggering. Internalisation of the TCR receptor is severely perturbed in FCHO1-deficient Jurkat T cells but can be rescued by expression of wild-type FCHO1. Thus, we discovered a previously unrecognised critical role of FCHO1 and CME during T-cell development and function in humans.
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Affiliation(s)
- Marcin Łyszkiewicz
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU, Munich, Germany.
- Institute for Immunology, Biomedical Center Munich, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Munich, Germany.
| | - Natalia Ziętara
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU, Munich, Germany
- Institute for Immunology, Biomedical Center Munich, Ludwig-Maximilians-Universität München, Planegg-Martinsried, 82152, Munich, Germany
| | - Laura Frey
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU, Munich, Germany
| | - Ulrich Pannicke
- Institute for Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Marcel Stern
- Max von Pettenkofer Institute, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
| | - Yanshan Liu
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU, Munich, Germany
| | - Yanxin Fan
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU, Munich, Germany
| | - Jacek Puchałka
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU, Munich, Germany
| | - Sebastian Hollizeck
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU, Munich, Germany
| | - Ido Somekh
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU, Munich, Germany
| | - Meino Rohlfs
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU, Munich, Germany
| | - Tuğba Yilmaz
- Department of Pediatrics, Division of Pediatric Hematology & Oncology, Erciyes University, Kayseri, Turkey
| | - Ekrem Ünal
- Department of Pediatrics, Division of Pediatric Hematology & Oncology, Erciyes University, Kayseri, Turkey
| | - Musa Karakukcu
- Department of Pediatrics, Division of Pediatric Hematology & Oncology, Erciyes University, Kayseri, Turkey
| | - Türkan Patiroğlu
- Department of Pediatrics, Division of Pediatric Hematology & Oncology, Erciyes University, Kayseri, Turkey
- Department of Pediatrics, Division of Pediatric Immunology, Erciyes University, Kayseri, Turkey
| | | | - Ebru Karasu
- Institute for Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Karl-Walter Sykora
- Department of Pediatric Hematology/Oncology, Hannover Medical School, Hannover, Germany
| | - Atar Lev
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer and Sackler Faculty of Medicine Tel Aviv University, Tel Aviv, Israel
| | - Amos Simon
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer and Sackler Faculty of Medicine Tel Aviv University, Tel Aviv, Israel
| | - Raz Somech
- Pediatric Department A and the Immunology Service, Jeffrey Modell Foundation Center, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer and Sackler Faculty of Medicine Tel Aviv University, Tel Aviv, Israel
| | - Joachim Roesler
- Department of Pediatrics, Carl Gustav Carus Technical University Dresden, Dresden, Germany
| | - Manfred Hoenig
- Department of Pediatrics, University Medical Centre Ulm, Ulm, Germany
| | - Oliver T Keppler
- Max von Pettenkofer Institute, Virology, National Reference Center for Retroviruses, Faculty of Medicine, LMU München, Munich, Germany
- German Center for Infection Research (DZIF), Partner Site Munich, Munich, Germany
| | - Klaus Schwarz
- Institute for Transfusion Medicine, University of Ulm, Ulm, Germany
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Wuerttemberg, Hessen, Germany
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU, Munich, Germany.
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17
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Singh M, Jackson KJL, Wang JJ, Schofield P, Field MA, Koppstein D, Peters TJ, Burnett DL, Rizzetto S, Nevoltris D, Masle-Farquhar E, Faulks ML, Russell A, Gokal D, Hanioka A, Horikawa K, Colella AD, Chataway TK, Blackburn J, Mercer TR, Langley DB, Goodall DM, Jefferis R, Gangadharan Komala M, Kelleher AD, Suan D, Rischmueller M, Christ D, Brink R, Luciani F, Gordon TP, Goodnow CC, Reed JH. Lymphoma Driver Mutations in the Pathogenic Evolution of an Iconic Human Autoantibody. Cell 2020; 180:878-894.e19. [PMID: 32059783 DOI: 10.1016/j.cell.2020.01.029] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 11/11/2019] [Accepted: 01/22/2020] [Indexed: 12/26/2022]
Abstract
Pathogenic autoantibodies arise in many autoimmune diseases, but it is not understood how the cells making them evade immune checkpoints. Here, single-cell multi-omics analysis demonstrates a shared mechanism with lymphoid malignancy in the formation of public rheumatoid factor autoantibodies responsible for mixed cryoglobulinemic vasculitis. By combining single-cell DNA and RNA sequencing with serum antibody peptide sequencing and antibody synthesis, rare circulating B lymphocytes making pathogenic autoantibodies were found to comprise clonal trees accumulating mutations. Lymphoma driver mutations in genes regulating B cell proliferation and V(D)J mutation (CARD11, TNFAIP3, CCND3, ID3, BTG2, and KLHL6) were present in rogue B cells producing the pathogenic autoantibody. Antibody V(D)J mutations conferred pathogenicity by causing the antigen-bound autoantibodies to undergo phase transition to insoluble aggregates at lower temperatures. These results reveal a pre-neoplastic stage in human lymphomagenesis and a cascade of somatic mutations leading to an iconic pathogenic autoantibody.
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Affiliation(s)
- Mandeep Singh
- The Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | | | - Jing J Wang
- Department of Immunology, Flinders University and SA Pathology, Bedford Park, SA 5042, Australia
| | - Peter Schofield
- The Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Matt A Field
- Australian Institute of Tropical Health and Medicine and Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Smithfield, QLD 4878, Australia; The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - David Koppstein
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Timothy J Peters
- The Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Deborah L Burnett
- The Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Simone Rizzetto
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Damien Nevoltris
- The Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Etienne Masle-Farquhar
- The Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Megan L Faulks
- The Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Amanda Russell
- The Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Divya Gokal
- The Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Asami Hanioka
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia; Tokyo Medical and Dental University, Tokyo 113-851, Japan
| | - Keisuke Horikawa
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia
| | - Alexander D Colella
- Department of Immunology, Flinders University and SA Pathology, Bedford Park, SA 5042, Australia; Flinders Proteomics Facility, Flinders University, Bedford Park, SA 5042, Australia
| | - Timothy K Chataway
- Flinders Proteomics Facility, Flinders University, Bedford Park, SA 5042, Australia
| | - James Blackburn
- The Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Tim R Mercer
- The Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2052, Australia; Altius Institute for Biomedical Sciences, Seattle, WA 98121, USA
| | - David B Langley
- The Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - D Margaret Goodall
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Roy Jefferis
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | | | - Anthony D Kelleher
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Dan Suan
- The Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; Westmead Clinical School, The University of Sydney, Westmead, NSW 2145, Australia
| | - Maureen Rischmueller
- Rheumatology Department, The Queen Elizabeth Hospital and Discipline of Medicine, University of Adelaide, Woodville South, SA 5011, Australia
| | - Daniel Christ
- The Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Robert Brink
- The Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Fabio Luciani
- Kirby Institute for Infection and Immunity, UNSW Sydney, Sydney, NSW 2052, Australia; School of Medical Sciences and Cellular Genomics Futures Institute, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Tom P Gordon
- Department of Immunology, Flinders University and SA Pathology, Bedford Park, SA 5042, Australia
| | - Christopher C Goodnow
- The Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; School of Medical Sciences and Cellular Genomics Futures Institute, UNSW Sydney, Sydney, NSW 2052, Australia.
| | - Joanne H Reed
- The Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; St. Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW 2052, Australia.
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18
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AMLVaran: a software approach to implement variant analysis of targeted NGS sequencing data in an oncological care setting. BMC Med Genomics 2020; 13:17. [PMID: 32019565 PMCID: PMC7001226 DOI: 10.1186/s12920-020-0668-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 01/21/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Next-Generation Sequencing (NGS) enables large-scale and cost-effective sequencing of genetic samples in order to detect genetic variants. After successful use in research-oriented projects, NGS is now entering clinical practice. Consequently, variant analysis is increasingly important to facilitate a better understanding of disease entities and prognoses. Furthermore, variant calling allows to adapt and optimize specific treatments of individual patients, and thus is an integral part of personalized medicine.However, the analysis of NGS data typically requires a number of complex bioinformatics processing steps. A flexible and reliable software that combines the variant analysis process with a simple, user-friendly interface is therefore highly desirable, but still lacking. RESULTS With AMLVaran (AML Variant Analyzer), we present a web-based software, that covers the complete variant analysis workflow of targeted NGS samples. The software provides a generic pipeline that allows free choice of variant calling tools and a flexible language (SSDL) for filtering variant lists. AMLVaran's interactive website presents comprehensive annotation data and includes curated information on relevant hotspot regions and driver mutations. A concise clinical report with rule-based diagnostic recommendations is generated.An AMLVaran configuration with eight variant calling tools and a complex scoring scheme, based on the somatic variant calling pipeline appreci8, was used to analyze three datasets from AML and MDS studies with 402 samples in total. Maximum sensitivity and positive predictive values were 1.0 and 0.96, respectively. The tool's usability was found to be satisfactory by medical professionals. CONCLUSION Coverage analysis, reproducible variant filtering and software usability are important for clinical assessment of variants. AMLVaran performs reliable NGS variant analyses and generates reports fulfilling the requirements of a clinical setting. Due to its generic design, the software can easily be adapted for use with different targeted panels for other tumor entities, or even for whole-exome data. AMLVaran has been deployed to a public web server and is distributed with Docker scripts for local use.
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19
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Field MA, Burgio G, Chuah A, Al Shekaili J, Hassan B, Al Sukaiti N, Foote SJ, Cook MC, Andrews TD. Recurrent miscalling of missense variation from short-read genome sequence data. BMC Genomics 2019; 20:546. [PMID: 31307400 PMCID: PMC6631443 DOI: 10.1186/s12864-019-5863-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Short-read resequencing of genomes produces abundant information of the genetic variation of individuals. Due to their numerous nature, these variants are rarely exhaustively validated. Furthermore, low levels of undetected variant miscalling will have a systematic and disproportionate impact on the interpretation of individual genome sequence information, especially should these also be carried through into in reference databases of genomic variation. RESULTS We find that sequence variation from short-read sequence data is subject to recurrent-yet-intermittent miscalling that occurs in a sequence intrinsic manner and is very sensitive to sequence read length. The miscalls arise from difficulties aligning short reads to redundant genomic regions, where the rate of sequencing error approaches the sequence diversity between redundant regions. We find the resultant miscalled variants to be sensitive to small sequence variations between genomes, and thereby are often intrinsic to an individual, pedigree, strain or human ethnic group. In human exome sequences, we identify 2-300 recurrent false positive variants per individual, almost all of which are present in public databases of human genomic variation. From the exomes of non-reference strains of inbred mice, we identify 3-5000 recurrent false positive variants per mouse - the number of which increasing with greater distance between an individual mouse strain and the reference C57BL6 mouse genome. We show that recurrently miscalled variants may be reproduced for a given genome from repeated simulation rounds of read resampling, realignment and recalling. As such, it is possible to identify more than two-thirds of false positive variation from only ten rounds of simulation. CONCLUSION Identification and removal of recurrent false positive variants from specific individual variant sets will improve overall data quality. Variant miscalls arising are highly sequence intrinsic and are often specific to an individual, pedigree or ethnicity. Further, read length is a strong determinant of whether given false variants will be called for any given genome - which has profound significance for cohort studies that pool datasets collected and sequenced at different points in time.
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Affiliation(s)
- Matthew A Field
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
- Australian Institute of Tropical Health and Medicine, Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, Queensland, Australia
| | - Gaetan Burgio
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Aaron Chuah
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Jalila Al Shekaili
- Department of Microbiology and Immunology, Sultan Qaboos University Hospital, Seeb, Oman
| | - Batool Hassan
- Department of Medicine, Sultan Qaboos University Hospital, Muscat, Oman
| | - Nashat Al Sukaiti
- Department of Paediatrics, Allergy, and Clinical Immunology Unit, Royal Hospital, Muscat, Oman
| | - Simon J Foote
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Matthew C Cook
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
- Department of Immunology, Canberra Hospital, Canberra, Australian Capital Territory, Australia
| | - T Daniel Andrews
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia.
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20
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Gao P, Zhang R, Li J. Comprehensive elaboration of database resources utilized in next-generation sequencing-based tumor somatic mutation detection. Biochim Biophys Acta Rev Cancer 2019; 1872:122-137. [PMID: 31265877 DOI: 10.1016/j.bbcan.2019.06.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/16/2019] [Accepted: 06/26/2019] [Indexed: 12/20/2022]
Abstract
The rapid evolution of next-generation sequencing (NGS)-based tumor genomic profile detection and the emergence of molecularly targeted therapies have enabled precision oncology. In NGS-based analysis, various types of databases have been developed to perform different functions. However, many problems still exist when using these public databases. Therefore, it is important to better understand the characteristics and limitations of each database and have them complement each other to provide useful clinical evidence for NGS testing. In this review, we elaborate on the important role of databases and their concrete applications in NGS-based somatic mutation detection. We introduce the typically used databases for sequence alignment, variant filtration, and variant interpretation, and compare the differences between the databases with similar functions. Subsequently, we determine the limitations of each database and provide the corresponding solutions. Furthermore, we present an overview diagram to clearly illustrate the database used in the entire NGS-based somatic mutation detection pipeline.
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Affiliation(s)
- Peng Gao
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China.
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, National Center of Gerontology, Beijing, People's Republic of China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, People's Republic of China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, People's Republic of China.
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21
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Anuar ND, Kurscheid S, Field M, Zhang L, Rebar E, Gregory P, Buchou T, Bowles J, Koopman P, Tremethick DJ, Soboleva TA. Gene editing of the multi-copy H2A.B gene and its importance for fertility. Genome Biol 2019; 20:23. [PMID: 30704500 PMCID: PMC6357441 DOI: 10.1186/s13059-019-1633-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 01/16/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Altering the biochemical makeup of chromatin by the incorporation of histone variants during development represents a key mechanism in regulating gene expression. The histone variant H2A.B, H2A.B.3 in mice, appeared late in evolution and is most highly expressed in the testis. In the mouse, it is encoded by three different genes. H2A.B expression is spatially and temporally regulated during spermatogenesis being most highly expressed in the haploid round spermatid stage. Active genes gain H2A.B where it directly interacts with polymerase II and RNA processing factors within splicing speckles. However, the importance of H2A.B for gene expression and fertility are unknown. RESULTS Here, we report the first mouse knockout of this histone variant and its effects on fertility, nuclear organization, and gene expression. In view of the controversy related to the generation of off-target mutations by gene editing approaches, we test the specificity of TALENs by disrupting the H2A.B multi-copy gene family using only one pair of TALENs. We show that TALENs do display a high level of specificity since no off-target mutations are detected by bioinformatics analyses of exome sequences obtained from three consecutive generations of knockout mice and by Sanger DNA sequencing. Male H2A.B.3 knockout mice are subfertile and display an increase in the proportion of abnormal sperm and clogged seminiferous tubules. Significantly, a loss of proper RNA Pol II targeting to distinct transcription-splicing territories and changes to pre-mRNA splicing are observed. CONCLUSION We have produced the first H2A.B knockout mouse using the TALEN approach.
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Affiliation(s)
- Nur Diana Anuar
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia
| | - Sebastian Kurscheid
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Matt Field
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia.,Present Address: James Cook University, PO Box 6811, Cairns, QLD, 4870, Australia.,Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Lei Zhang
- Sangamo Therapeutics, 501 Canal Blvd, Richmond, CA, 94804, USA
| | - Edward Rebar
- Sangamo Therapeutics, 501 Canal Blvd, Richmond, CA, 94804, USA
| | - Philip Gregory
- Sangamo Therapeutics, 501 Canal Blvd, Richmond, CA, 94804, USA.,Present Address: bluebird bio, 60 Binney St, Cambridge, MA, 02142, USA
| | - Thierry Buchou
- CNRS UMR 5309, Inserm U1209, Universite' Grenoble Alpes, Institute for Advanced Biosciences, 38700, Grenoble, France
| | - Josephine Bowles
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Peter Koopman
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - David J Tremethick
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia.
| | - Tatiana A Soboleva
- The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, 2601, Australia.
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22
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Cardinez C, Miraghazadeh B, Tanita K, da Silva E, Hoshino A, Okada S, Chand R, Asano T, Tsumura M, Yoshida K, Ohnishi H, Kato Z, Yamazaki M, Okuno Y, Miyano S, Kojima S, Ogawa S, Andrews TD, Field MA, Burgio G, Morio T, Vinuesa CG, Kanegane H, Cook MC. Gain-of-function IKBKB mutation causes human combined immune deficiency. J Exp Med 2018; 215:2715-2724. [PMID: 30337470 PMCID: PMC6219745 DOI: 10.1084/jem.20180639] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 06/27/2018] [Accepted: 09/24/2018] [Indexed: 12/16/2022] Open
Abstract
Genetic mutations account for many devastating early onset immune deficiencies. In contrast, less severe and later onset immune diseases, including in patients with no prior family history, remain poorly understood. Whole exome sequencing in two cohorts of such patients identified a novel heterozygous de novo IKBKB missense mutation (c.607G>A) in two separate kindreds in whom probands presented with immune dysregulation, combined T and B cell deficiency, inflammation, and epithelial defects. IKBKB encodes IKK2, which activates NF-κB signaling. IKK2V203I results in enhanced NF-κB signaling, as well as T and B cell functional defects. IKK2V203 is a highly conserved residue, and to prove causation, we generated an accurate mouse model by introducing the precise orthologous codon change in Ikbkb using CRISPR/Cas9. Mice and humans carrying this missense mutation exhibit remarkably similar cellular and biochemical phenotypes. Accurate mouse models engineered by CRISPR/Cas9 can help characterize novel syndromes arising from de novo germline mutations and yield insight into pathogenesis.
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Affiliation(s)
- Chelisa Cardinez
- Centre for Personalised Immunology, Australian National University, Canberra, Australia.,Department of Immunology Canberra Hospital, Canberra, Australia.,Department of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Bahar Miraghazadeh
- Centre for Personalised Immunology, Australian National University, Canberra, Australia.,Department of Immunology Canberra Hospital, Canberra, Australia.,Department of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Kay Tanita
- Department of Child Health and Development, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | | | - Akihiro Hoshino
- Department of Child Health and Development, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Satoshi Okada
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Rochna Chand
- Centre for Personalised Immunology, Australian National University, Canberra, Australia.,Department of Immunology Canberra Hospital, Canberra, Australia.,Department of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Takaki Asano
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Miyuki Tsumura
- Department of Pediatrics, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hidenori Ohnishi
- Department of Pediatrics, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Zenichiro Kato
- Department of Pediatrics, Gifu University Graduate School of Medicine, Gifu, Japan.,Structural Medicine, United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | | | - Yusuke Okuno
- Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan.,Laboratory of Sequence Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Seiji Kojima
- Department of Pediatrics, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - T Daniel Andrews
- Centre for Personalised Immunology, Australian National University, Canberra, Australia.,Department of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Matthew A Field
- Centre for Personalised Immunology, Australian National University, Canberra, Australia.,Department of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, Australia.,Australian Institute for Tropical Health and Medicine, James Cook University, Cairns, Australia
| | - Gaetan Burgio
- Department of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Tomohiro Morio
- Department of Child Health and Development, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Carola G Vinuesa
- Centre for Personalised Immunology, Australian National University, Canberra, Australia.,Department of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, Australia
| | - Hirokazu Kanegane
- Department of Child Health and Development, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Matthew C Cook
- Centre for Personalised Immunology, Australian National University, Canberra, Australia .,Department of Immunology Canberra Hospital, Canberra, Australia.,Department of Immunology and Infectious Diseases, John Curtin School of Medical Research, Australian National University, Canberra, Australia
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23
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Gonçalves S, Patat J, Guida MC, Lachaussée N, Arrondel C, Helmstädter M, Boyer O, Gribouval O, Gubler MC, Mollet G, Rio M, Charbit M, Bole-Feysot C, Nitschke P, Huber TB, Wheeler PG, Haynes D, Juusola J, Billette de Villemeur T, Nava C, Afenjar A, Keren B, Bodmer R, Antignac C, Simons M. A homozygous KAT2B variant modulates the clinical phenotype of ADD3 deficiency in humans and flies. PLoS Genet 2018; 14:e1007386. [PMID: 29768408 PMCID: PMC5973622 DOI: 10.1371/journal.pgen.1007386] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 05/29/2018] [Accepted: 04/30/2018] [Indexed: 12/25/2022] Open
Abstract
Recent evidence suggests that the presence of more than one pathogenic mutation in a single patient is more common than previously anticipated. One of the challenges hereby is to dissect the contribution of each gene mutation, for which animal models such as Drosophila can provide a valuable aid. Here, we identified three families with mutations in ADD3, encoding for adducin-γ, with intellectual disability, microcephaly, cataracts and skeletal defects. In one of the families with additional cardiomyopathy and steroid-resistant nephrotic syndrome (SRNS), we found a homozygous variant in KAT2B, encoding the lysine acetyltransferase 2B, with impact on KAT2B protein levels in patient fibroblasts, suggesting that this second mutation might contribute to the increased disease spectrum. In order to define the contribution of ADD3 and KAT2B mutations for the patient phenotype, we performed functional experiments in the Drosophila model. We found that both mutations were unable to fully rescue the viability of the respective null mutants of the Drosophila homologs, hts and Gcn5, suggesting that they are indeed pathogenic in flies. While the KAT2B/Gcn5 mutation additionally showed a significantly reduced ability to rescue morphological and functional defects of cardiomyocytes and nephrocytes (podocyte-like cells), this was not the case for the ADD3 mutant rescue. Yet, the simultaneous knockdown of KAT2B and ADD3 synergistically impaired kidney and heart function in flies as well as the adhesion and migration capacity of cultured human podocytes, indicating that mutations in both genes may be required for the full clinical manifestation. Altogether, our studies describe the expansion of the phenotypic spectrum in ADD3 deficiency associated with a homozygous likely pathogenic KAT2B variant and thereby identify KAT2B as a susceptibility gene for kidney and heart disease in ADD3-associated disorders.
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Affiliation(s)
- Sara Gonçalves
- Laboratory of Hereditary Kidney Diseases, Institut National de la Santé et de la Recherche Médicale (Inserm) UMR1163, Imagine Institute, Paris, France
- Laboratory of Epithelial Biology and Disease, Institut National de la Santé et de la Recherche Médicale (Inserm) UMR1163, Imagine Institute, Paris, France
- Université Paris Descartes—Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Julie Patat
- Laboratory of Hereditary Kidney Diseases, Institut National de la Santé et de la Recherche Médicale (Inserm) UMR1163, Imagine Institute, Paris, France
- Université Paris Descartes—Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Maria Clara Guida
- Development, Aging and Regeneration Program, Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, United States of America
| | - Noelle Lachaussée
- Laboratory of Hereditary Kidney Diseases, Institut National de la Santé et de la Recherche Médicale (Inserm) UMR1163, Imagine Institute, Paris, France
- Université Paris Descartes—Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Christelle Arrondel
- Laboratory of Hereditary Kidney Diseases, Institut National de la Santé et de la Recherche Médicale (Inserm) UMR1163, Imagine Institute, Paris, France
- Université Paris Descartes—Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Martin Helmstädter
- Department of Medicine IV, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Olivia Boyer
- Laboratory of Hereditary Kidney Diseases, Institut National de la Santé et de la Recherche Médicale (Inserm) UMR1163, Imagine Institute, Paris, France
- Université Paris Descartes—Sorbonne Paris Cité, Imagine Institute, Paris, France
- Department of Pediatric Nephrology, Centre de Référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte (MARHEA), Hôpital Necker-Enfants Malades, Assistance Publique—Hôpitaux de Paris (AP-HP), Paris, France
| | - Olivier Gribouval
- Laboratory of Hereditary Kidney Diseases, Institut National de la Santé et de la Recherche Médicale (Inserm) UMR1163, Imagine Institute, Paris, France
- Université Paris Descartes—Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Marie-Claire Gubler
- Laboratory of Hereditary Kidney Diseases, Institut National de la Santé et de la Recherche Médicale (Inserm) UMR1163, Imagine Institute, Paris, France
- Université Paris Descartes—Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Geraldine Mollet
- Laboratory of Hereditary Kidney Diseases, Institut National de la Santé et de la Recherche Médicale (Inserm) UMR1163, Imagine Institute, Paris, France
- Université Paris Descartes—Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Marlène Rio
- Department of Genetics, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
| | - Marina Charbit
- Department of Pediatric Nephrology, Centre de Référence des Maladies Rénales Héréditaires de l'Enfant et de l'Adulte (MARHEA), Hôpital Necker-Enfants Malades, Assistance Publique—Hôpitaux de Paris (AP-HP), Paris, France
| | | | - Patrick Nitschke
- Université Paris Descartes—Sorbonne Paris Cité, Imagine Institute, Paris, France
| | - Tobias B. Huber
- Department of Medicine IV, Medical Center–University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- BIOSS Center for Biological Signalling Studies and Center for Systems Biology (ZBSA), Albert-Ludwigs-University, Freiburg, Germany
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Patricia G. Wheeler
- Division of Genetics, Arnold Palmer Hospital for Children, Orlando Health, Orlando, FL, United States of America
| | - Devon Haynes
- Division of Genetics, Arnold Palmer Hospital for Children, Orlando Health, Orlando, FL, United States of America
| | - Jane Juusola
- GeneDx, Inc, Gaithersburg, MD, United States of America
| | - Thierry Billette de Villemeur
- Sorbonne Université, UPMC, GRC ConCer-LD and AP-HP, Hôpital Trousseau, Service de Neuropédiatrie—Pathologie du développement, Paris, France
- Centre de référence des déficits intellectuels de causes rares, Inserm U 1141, Paris, France
| | - Caroline Nava
- Sorbonne Universités, UPMC Univ Paris 06, Inserm U1127, CNRS UMR 7225, Institut du Cerveau et de la Moèlle Épinière (ICM), Paris, France
- AP-HP, GH Pitié-Salpêtrière, Department of Genetics, Unit of Developmental Genomics, Paris, France
| | - Alexandra Afenjar
- AP-HP, Hôpital Trousseau, Centre de référence des malformations et maladies congénitales du cervelet, Département de génétique et embryologie médicale, Paris, France
| | - Boris Keren
- AP-HP, GH Pitié-Salpêtrière, Department of Genetics, Unit of Developmental Genomics, Paris, France
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, United States of America
| | - Corinne Antignac
- Laboratory of Hereditary Kidney Diseases, Institut National de la Santé et de la Recherche Médicale (Inserm) UMR1163, Imagine Institute, Paris, France
- Université Paris Descartes—Sorbonne Paris Cité, Imagine Institute, Paris, France
- Department of Genetics, Hôpital Necker-Enfants Malades, AP-HP, Paris, France
- * E-mail: (CA); (MS)
| | - Matias Simons
- Laboratory of Epithelial Biology and Disease, Institut National de la Santé et de la Recherche Médicale (Inserm) UMR1163, Imagine Institute, Paris, France
- Université Paris Descartes—Sorbonne Paris Cité, Imagine Institute, Paris, France
- * E-mail: (CA); (MS)
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24
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Impact of the G84E variant on HOXB13 gene and protein expression in formalin-fixed, paraffin-embedded prostate tumours. Sci Rep 2017; 7:17778. [PMID: 29259341 PMCID: PMC5736598 DOI: 10.1038/s41598-017-18217-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 12/05/2017] [Indexed: 01/01/2023] Open
Abstract
The HOXB13 G84E variant is associated with risk of prostate cancer (PCa), however the role this variant plays in PCa development is unknown. This study examined 751 cases, 450 relatives and 355 controls to determine the contribution of this variant to PCa risk in Tasmania and investigated HOXB13 gene and protein expression in tumours from nine G84E heterozygote variant and 13 wild-type carriers. Quantitative PCR and immunohistochemistry showed that HOXB13 gene and protein expression did not differ between tumour samples from variant and wild-type carriers. Allele-specific transcription revealed that two of seven G84E carriers transcribed both the variant and wild-type allele, while five carriers transcribed the wild-type allele. Methylation of surrounding CpG sites was lower in the variant compared to the wild-type allele, however overall methylation across the region was very low. Notably, tumour characteristics were less aggressive in the two variant carriers that transcribed the variant allele compared to the five that did not. This study has shown that HOXB13 expression does not differ between tumour tissue of G84E variant carriers and non-carriers. Intriguingly, the G84E variant allele was rarely transcribed in carriers, suggesting that HOXB13 expression may be driven by the wild-type allele in the majority of carriers.
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25
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Loughland JR, Minigo G, Sarovich DS, Field M, Tipping PE, Montes de Oca M, Piera KA, Amante FH, Barber BE, Grigg MJ, William T, Good MF, Doolan DL, Engwerda CR, Anstey NM, McCarthy JS, Woodberry T. Plasmacytoid dendritic cells appear inactive during sub-microscopic Plasmodium falciparum blood-stage infection, yet retain their ability to respond to TLR stimulation. Sci Rep 2017; 7:2596. [PMID: 28572564 PMCID: PMC5453946 DOI: 10.1038/s41598-017-02096-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/05/2017] [Indexed: 12/13/2022] Open
Abstract
Plasmacytoid dendritic cells (pDC) are activators of innate and adaptive immune responses that express HLA-DR, toll-like receptor (TLR) 7, TLR9 and produce type I interferons. The role of human pDC in malaria remains poorly characterised. pDC activation and cytokine production were assessed in 59 malaria-naive volunteers during experimental infection with 150 or 1,800 P. falciparum-parasitized red blood cells. Using RNA sequencing, longitudinal changes in pDC gene expression were examined in five adults before and at peak-infection. pDC responsiveness to TLR7 and TLR9 stimulation was assessed in-vitro. Circulating pDC remained transcriptionally stable with gene expression altered for 8 genes (FDR < 0.07). There was no upregulation of co-stimulatory molecules CD86, CD80, CD40, and reduced surface expression of HLA-DR and CD123 (IL-3R-α). pDC loss from the circulation was associated with active caspase-3, suggesting pDC apoptosis during primary infection. pDC remained responsive to TLR stimulation, producing IFN-α and upregulating HLA-DR, CD86, CD123 at peak-infection. In clinical malaria, pDC retained HLA-DR but reduced CD123 expression compared to convalescence. These data demonstrate pDC retain function during a first blood-stage P. falciparum exposure despite sub-microscopic parasitaemia downregulating HLA-DR. The lack of evident pDC activation in both early infection and malaria suggests little response of circulating pDC to infection.
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Affiliation(s)
- Jessica R Loughland
- Menzies School of Health Research, Darwin, Australia and Charles Darwin University, Darwin, Australia.
| | - Gabriela Minigo
- Menzies School of Health Research, Darwin, Australia and Charles Darwin University, Darwin, Australia
| | - Derek S Sarovich
- Menzies School of Health Research, Darwin, Australia and Charles Darwin University, Darwin, Australia.,Centre for Animal Health Innovation, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - Matt Field
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia
| | - Peta E Tipping
- Menzies School of Health Research, Darwin, Australia and Charles Darwin University, Darwin, Australia.,Royal Darwin Hospital, Darwin, Australia
| | | | - Kim A Piera
- Menzies School of Health Research, Darwin, Australia and Charles Darwin University, Darwin, Australia
| | - Fiona H Amante
- QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Bridget E Barber
- Menzies School of Health Research, Darwin, Australia and Charles Darwin University, Darwin, Australia.,Infectious Diseases Unit, Queen Elizabeth Hospital, Kota Kinabalu, Sabah, Malaysia
| | - Matthew J Grigg
- Menzies School of Health Research, Darwin, Australia and Charles Darwin University, Darwin, Australia.,Infectious Diseases Unit, Queen Elizabeth Hospital, Kota Kinabalu, Sabah, Malaysia
| | - Timothy William
- Infectious Diseases Unit, Queen Elizabeth Hospital, Kota Kinabalu, Sabah, Malaysia.,Sabah Department of Health, Kota Kinabalu, Sabah, Malaysia
| | | | - Denise L Doolan
- Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia.,QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - Nicholas M Anstey
- Menzies School of Health Research, Darwin, Australia and Charles Darwin University, Darwin, Australia.,Royal Darwin Hospital, Darwin, Australia
| | | | - Tonia Woodberry
- Menzies School of Health Research, Darwin, Australia and Charles Darwin University, Darwin, Australia
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26
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Ho CC, Tai SM, Lee ECN, Mak TSH, Liu TKT, Tang VWL, Poon WT. Rapid Identification of Pathogenic Variants in Two Cases of Charcot-Marie-Tooth Disease by Gene-Panel Sequencing. Int J Mol Sci 2017; 18:ijms18040770. [PMID: 28379183 PMCID: PMC5412354 DOI: 10.3390/ijms18040770] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 03/28/2017] [Accepted: 03/31/2017] [Indexed: 12/14/2022] Open
Abstract
Charcot-Marie-Tooth disease (CMT) is a common inherited peripheral neuropathy affecting up to 1 in 1214 of the general population with more than 60 nuclear genes implicated in its pathogenesis. Traditional molecular diagnostic pathways based on relative prevalence and clinical phenotyping are limited by long turnaround time, population-specific prevalence of causative variants and inability to assess multiple co-existing variants. In this study, a CMT gene panel comprising 27 genes was used to uncover the pathogenic mutations in two index patients. The first patient is a 15-year-old boy, born of consanguineous parents, who has had frequent trips and falls since infancy, and was later found to have inverted champagne bottle appearance of bilateral legs and foot drop. His elder sister is similarly affected. The second patient is a 37-year-old woman referred for pre-pregnancy genetic diagnosis. During early adulthood, she developed progressive lower limb weakness, difficulties in tip-toe walking and thinning of calf muscles. Both patients are clinically compatible with CMT, have undergone multiple genetic testings and have not previously received a definitive genetic diagnosis. Patients 1 and 2 were found to have pathogenic homozygous HSPB1:NM_001540:c.250G>A (p.G84R) variant and heterozygous GDAP1:NM_018972:c.358C>T (p.R120W) variant, respectively. Advantages and limitations of the current approach are discussed.
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Affiliation(s)
- Chi-Chun Ho
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong, China.
| | - Shuk-Mui Tai
- Department of Paediatrics & Adolescent Medicine, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong, China.
| | - Edmond Chi-Nam Lee
- Department of Medicine, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong, China.
| | - Timothy Shin-Heng Mak
- Centre for Genomic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China.
| | - Timothy Kam-Tim Liu
- Department of Paediatrics & Adolescent Medicine, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong, China.
| | - Victor Wai-Lun Tang
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong, China.
| | - Wing-Tat Poon
- Department of Clinical Pathology, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong, China.
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27
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Evaluating the Calling Performance of a Rare Disease NGS Panel for Single Nucleotide and Copy Number Variants. Mol Diagn Ther 2017; 21:303-313. [DOI: 10.1007/s40291-017-0268-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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28
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Levano S, Gonzalez A, Singer M, Demougin P, Rüffert H, Urwyler A, Girard T. Resequencing array for gene variant detection in malignant hyperthermia and butyrylcholinestherase deficiency. Neuromuscul Disord 2017; 27:492-499. [PMID: 28259615 DOI: 10.1016/j.nmd.2017.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Revised: 12/20/2016] [Accepted: 02/15/2017] [Indexed: 11/30/2022]
Abstract
Malignant hyperthermia (MH) and butyrylcholinestherase (BCHE) deficiency are two relevant pharmacogenetic disorders in anesthetic practice linked with sequence variants, the former in the RyR1 and CACNA1S genes, the latter in the BCHE gene. Genotyping for known pathogenic variants in these genes is useful to help identify susceptible individuals, and others may exist but remain unknown, because full-length sequence of these genes is, in general, not investigated. To facilitate this task, we developed a resequencing DNA array, the perioperative patient safety (POPS) array, to be able to screen the entire coding sequences of the RyR1, CACNA1S and BCHE genes. MH-susceptible individuals (n = 121) identified with the in vitro contracture test, the standard diagnostic tool for MH susceptibility, were genotyped with the arrays. Compared with capillary sequencing, call rates with the arrays could achieve 100% at maximal sensitivity, although to reduce false positive rates, sensitivity was adjusted to 0.85, 0.87 and 0.66 for RyR1, CACNA1S and BCHE respectively, with overall base call specificity exceeding 99%. Detection of 29 predetermined RyR1 variants in 44 individuals was successful in 97% of the cases, among them all 16 variants of established diagnostic value. In a trial application of the arrays, 21 MH-susceptible subjects with no known RyR1 or CACNA1S variants were screened, resulting in the discovery of new variants, all confirmed by capillary sequencing. In conclusion, arrays offer an efficient high-throughput alternative for diagnostic genotyping of candidate genes affecting MH susceptibility, BCHE deficiency and other neuromuscular disorders, simultaneously enabling a comprehensive search for rare variants in these genes.
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Affiliation(s)
- Soledad Levano
- Department of Biomedicine, University Hospital Basel, Switzerland; Department Anesthesiology, University Hospital Basel, Switzerland
| | - Asensio Gonzalez
- Department of Biomedicine, University Hospital Basel, Switzerland; Department Anesthesiology, University Hospital Basel, Switzerland.
| | - Martine Singer
- Department of Biomedicine, University Hospital Basel, Switzerland; Department Anesthesiology, University Hospital Basel, Switzerland
| | - Philippe Demougin
- Biozentrum, Life Sciences Training Facility, University of Basel, Switzerland
| | - Henrik Rüffert
- University of Leipzig, Helios Kliniken Leipziger Land Leipzig, Germany
| | - Albert Urwyler
- Department of Biomedicine, University Hospital Basel, Switzerland; Department Anesthesiology, University Hospital Basel, Switzerland
| | - Thierry Girard
- Department of Biomedicine, University Hospital Basel, Switzerland; Department Anesthesiology, University Hospital Basel, Switzerland
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29
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Lovric S, Goncalves S, Gee HY, Oskouian B, Srinivas H, Choi WI, Shril S, Ashraf S, Tan W, Rao J, Airik M, Schapiro D, Braun DA, Sadowski CE, Widmeier E, Jobst-Schwan T, Schmidt JM, Girik V, Capitani G, Suh JH, Lachaussée N, Arrondel C, Patat J, Gribouval O, Furlano M, Boyer O, Schmitt A, Vuiblet V, Hashmi S, Wilcken R, Bernier FP, Innes AM, Parboosingh JS, Lamont RE, Midgley JP, Wright N, Majewski J, Zenker M, Schaefer F, Kuss N, Greil J, Giese T, Schwarz K, Catheline V, Schanze D, Franke I, Sznajer Y, Truant AS, Adams B, Désir J, Biemann R, Pei Y, Ars E, Lloberas N, Madrid A, Dharnidharka VR, Connolly AM, Willing MC, Cooper MA, Lifton RP, Simons M, Riezman H, Antignac C, Saba JD, Hildebrandt F. Mutations in sphingosine-1-phosphate lyase cause nephrosis with ichthyosis and adrenal insufficiency. J Clin Invest 2017; 127:912-928. [PMID: 28165339 DOI: 10.1172/jci89626] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 12/12/2016] [Indexed: 12/24/2022] Open
Abstract
Steroid-resistant nephrotic syndrome (SRNS) causes 15% of chronic kidney disease cases. A mutation in 1 of over 40 monogenic genes can be detected in approximately 30% of individuals with SRNS whose symptoms manifest before 25 years of age. However, in many patients, the genetic etiology remains unknown. Here, we have performed whole exome sequencing to identify recessive causes of SRNS. In 7 families with SRNS and facultative ichthyosis, adrenal insufficiency, immunodeficiency, and neurological defects, we identified 9 different recessive mutations in SGPL1, which encodes sphingosine-1-phosphate (S1P) lyase. All mutations resulted in reduced or absent SGPL1 protein and/or enzyme activity. Overexpression of cDNA representing SGPL1 mutations resulted in subcellular mislocalization of SGPL1. Furthermore, expression of WT human SGPL1 rescued growth of SGPL1-deficient dpl1Δ yeast strains, whereas expression of disease-associated variants did not. Immunofluorescence revealed SGPL1 expression in mouse podocytes and mesangial cells. Knockdown of Sgpl1 in rat mesangial cells inhibited cell migration, which was partially rescued by VPC23109, an S1P receptor antagonist. In Drosophila, Sply mutants, which lack SGPL1, displayed a phenotype reminiscent of nephrotic syndrome in nephrocytes. WT Sply, but not the disease-associated variants, rescued this phenotype. Together, these results indicate that SGPL1 mutations cause a syndromic form of SRNS.
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30
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Suitability of Different Mapping Algorithms for Genome-Wide Polymorphism Scans with Pool-Seq Data. G3-GENES GENOMES GENETICS 2016; 6:3507-3515. [PMID: 27613752 PMCID: PMC5100849 DOI: 10.1534/g3.116.034488] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The cost-effectiveness of sequencing pools of individuals (Pool-Seq) provides the basis for the popularity and widespread use of this method for many research questions, ranging from unraveling the genetic basis of complex traits, to the clonal evolution of cancer cells. Because the accuracy of Pool-Seq could be affected by many potential sources of error, several studies have determined, for example, the influence of sequencing technology, the library preparation protocol, and mapping parameters. Nevertheless, the impact of the mapping tools has not yet been evaluated. Using simulated and real Pool-Seq data, we demonstrate a substantial impact of the mapping tools, leading to characteristic false positives in genome-wide scans. The problem of false positives was particularly pronounced when data with different read lengths and insert sizes were compared. Out of 14 evaluated algorithms novoalign, bwa mem and clc4 are most suitable for mapping Pool-Seq data. Nevertheless, no single algorithm is sufficient for avoiding all false positives. We show that the intersection of the results of two mapping algorithms provides a simple, yet effective, strategy to eliminate false positives. We propose that the implementation of a consistent Pool-Seq bioinformatics pipeline, building on the recommendations of this study, can substantially increase the reliability of Pool-Seq results, in particular when libraries generated with different protocols are being compared.
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31
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Andrews TD, Jeelall Y, Talaulikar D, Goodnow CC, Field MA. DeepSNVMiner: a sequence analysis tool to detect emergent, rare mutations in subsets of cell populations. PeerJ 2016; 4:e2074. [PMID: 27257550 PMCID: PMC4888318 DOI: 10.7717/peerj.2074] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 05/03/2016] [Indexed: 01/13/2023] Open
Abstract
Background. Massively parallel sequencing technology is being used to sequence highly diverse populations of DNA such as that derived from heterogeneous cell mixtures containing both wild-type and disease-related states. At the core of such molecule tagging techniques is the tagging and identification of sequence reads derived from individual input DNA molecules, which must be first computationally disambiguated to generate read groups sharing common sequence tags, with each read group representing a single input DNA molecule. This disambiguation typically generates huge numbers of reads groups, each of which requires additional variant detection analysis steps to be run specific to each read group, thus representing a significant computational challenge. While sequencing technologies for producing these data are approaching maturity, the lack of available computational tools for analysing such heterogeneous sequence data represents an obstacle to the widespread adoption of this technology. Results. Using synthetic data we successfully detect unique variants at dilution levels of 1 in a 1,000,000 molecules, and find DeeepSNVMiner obtains significantly lower false positive and false negative rates compared to popular variant callers GATK, SAMTools, FreeBayes and LoFreq, particularly as the variant concentration levels decrease. In a dilution series with genomic DNA from two cells lines, we find DeepSNVMiner identifies a known somatic variant when present at concentrations of only 1 in 1,000 molecules in the input material, the lowest concentration amongst all variant callers tested. Conclusions. Here we present DeepSNVMiner; a tool to disambiguate tagged sequence groups and robustly identify sequence variants specific to subsets of starting DNA molecules that may indicate the presence of a disease. DeepSNVMiner is an automated workflow of custom sequence analysis utilities and open source tools able to differentiate somatic DNA variants from artefactual sequence variants that likely arose during DNA amplification. The workflow remains flexible such that it may be customised to variants of the data production protocol used, and supports reproducible analysis through detailed logging and reporting of results. DeepSNVMiner is available for academic non-commercial research purposes at https://github.com/mattmattmattmatt/DeepSNVMiner.
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Affiliation(s)
- T Daniel Andrews
- Department of Immunology, John Curtin School of Medical Research, Australian National University, Canberra ACT, Australia; National Computational Infrastructure, Canberra ACT, Australia
| | - Yogesh Jeelall
- Department of Immunology, John Curtin School of Medical Research, Australian National University, Canberra ACT, Australia; School of Medicine and Pharmacology, University of Western Australia, Harry Perkins Institute, Perth, Australia
| | - Dipti Talaulikar
- Department of Immunology, John Curtin School of Medical Research, Australian National University, Canberra ACT, Australia; Haematology Translational Research Unit, Haematology Unit, ACT Pathology, Canberra ACT, Australia; ANU Medical School, Australian National University, Canberra ACT, Australia
| | - Christopher C Goodnow
- Department of Immunology, John Curtin School of Medical Research, Australian National University, Canberra ACT, Australia; Immunology Division, Garvan Institute of Medical Research, Sydney NSW, Australia; St Vincent's Clinical School, University of New South Wales, Darlinghurst NSW, Australia
| | - Matthew A Field
- Department of Immunology, John Curtin School of Medical Research, Australian National University , Canberra ACT , Australia
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32
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Luo W, Ren Z, Gao S, Jin H, Zhang G, Zhou L, Zheng S. Clinical correlation of calpain-1 and glypican-3 expression with gallbladder carcinoma. Oncol Lett 2016; 11:1345-1352. [PMID: 26893741 PMCID: PMC4734278 DOI: 10.3892/ol.2016.4079] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Accepted: 11/27/2015] [Indexed: 11/30/2022] Open
Abstract
Gallbladder carcinoma (GBC) possesses a poor prognosis, which is primarily attributed to the lack of early and timely surgical intervention. Calpain-1 and glypican-3 have been implicated in the progression of various types of cancer. The present study aimed to detect the expression of calpain-1 and glypican-3 in GBC, and analyzed whether the expression levels of these proteins correlated with any clinicopathological variables. A total of 100 patients with GBC and 30 patients with cholecystitis who accepted surgical treatment were enrolled in the present study. Pathological and clinical data were obtained from all patients. The expression of calpain-1 and glypican-3 was detected in paraffin-embedded tissues by immunohistochemistry. Calpain-1 expression was manually assessed with an immunohistochemical H-score with a slight modification. Glypican-3 expression was assessed as negative and positive. The correlations between protein expression and clinicopathological characteristics, and the associations between the proteins were analyzed. All patients exhibited positive expression of calpain-1. Notably, the high expression rate of calpain-1 was significantly increased in patients with GBC, compared with patients with cholecystitis (32.0 vs. 6.7%; χ2=7.668; P=0.006), suggesting that calpain-1 expression may be associated with progression from cholecystitis to GBC. In addition, the positive rate of glypican-3 expression was 53.0% in patients with GBC and 63.3% in patients with cholecystitis, with no significant difference (χ2=0.997; P=0.318). Furthermore, the expression of calpain-1 and glypican-3 had no significant correlation with gender, age, degree of tumor differentiation and tumor-node-metastasis classification in patients with GBC. Notably, the expression of calpain-1 and glypican-3 displayed a significant positive correlation in patients with GBC (r=0.517; P<0.01), but a significantly negative correlation (r=-0.856; P<0.01) in patients with cholecystitis. In conclusion, calpain-1 expression may be associated with progression from cholecystitis to GBC. Combined detection of calpain-1 and glypican-3 may be beneficial for prognosis assessment of GBC.
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Affiliation(s)
- Weiqing Luo
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China; Department of General Surgery, The People's Hospital of Deqing County, Huzhou, Zhejiang 313200, P.R. China
| | - Zhigang Ren
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Sheng Gao
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Hailong Jin
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Geer Zhang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Lin Zhou
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Shusen Zheng
- Key Laboratory of Combined Multi-Organ Transplantation, Ministry of Public Health, Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
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