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Cerdà P, Castillo SD, Aguilera C, Iriarte A, Rocamora JL, Larrinaga AM, Viñals F, Graupera M, Riera-Mestre A. New genetic drivers in hemorrhagic hereditary telangiectasia. Eur J Intern Med 2024; 119:99-108. [PMID: 37689549 DOI: 10.1016/j.ejim.2023.08.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/11/2023]
Abstract
BACKGROUND Hereditary hemorrhagic telangiectasia (HHT) is a rare vascular disease inherited in an autosomal dominant manner. Disease-causing variants in endoglin (ENG) and activin A receptor type II-like 1 (ACVRL1) genes are detected in around 90% of the patients; also 2% of patients harbor pathogenic variants at SMAD4 and GDF2. Importantly, the genetic cause of 8% of patients with clinical HHT remains unknown. Here, we present new putative genetic drivers of HHT. METHODS To identify new HHT genetic drivers, we performed exome sequencing of 19 HHT patients and relatives with unknown HHT genetic etiology. We applied a multistep filtration strategy to catalog deleterious variants and prioritize gene candidates based on their known relevance in endothelial cell biology. Additionally, we performed in vitro validation of one of the identified variants. RESULTS We identified variants in the INHA, HIF1A, JAK2, DNM2, POSTN, ANGPTL4, FOXO1 and SMAD6 genes as putative drivers in HHT. We have identified the SMAD6 p.(Glu407Lys) variant in one of the families; this is a loss-of-function variant leading to the activation of the BMP/TGFβ signaling in endothelial cells. CONCLUSIONS Variants in these genes should be considered for genetic testing in patients with HHT phenotype and negative for ACVRL1/ENG mutations.
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Affiliation(s)
- Pau Cerdà
- HHT Unit, Hospital Universitari de Bellvitge, L'Hospitalet de Llobregat, Spain; Internal Medicine Department, Hospital Universitari de Bellvitge, L'Hospitalet de Llobregat, Spain; Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Sandra D Castillo
- Endothelial Pathobiology and Microenvironment Group, Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | - Cinthia Aguilera
- HHT Unit, Hospital Universitari de Bellvitge, L'Hospitalet de Llobregat, Spain; Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; Genetics Laboratory, Laboratori Clínic Territorial Metropolitana Sud, Hospital Universitari de Bellvitge, L'Hospitalet de Llobregat, Spain
| | - Adriana Iriarte
- HHT Unit, Hospital Universitari de Bellvitge, L'Hospitalet de Llobregat, Spain; Internal Medicine Department, Hospital Universitari de Bellvitge, L'Hospitalet de Llobregat, Spain; Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - José Luis Rocamora
- HHT Unit, Hospital Universitari de Bellvitge, L'Hospitalet de Llobregat, Spain; Molecular Signaling Group, Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Institut d'Investigacio Biomedica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Ane M Larrinaga
- Endothelial Pathobiology and Microenvironment Group, Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | - Francesc Viñals
- Molecular Signaling Group, Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Institut d'Investigacio Biomedica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; Department of Physiological Sciences, Faculty of Medicine and Health Sciences, Universitat de Barcelona (UB), L'Hospitalet de Llobregat, Spain; Program Against Cancer Therapeutic Resistance (ProCURE), Institut Catala d'Oncologia (ICO), L'Hospitalet de Llobregat, Spain
| | - Mariona Graupera
- Endothelial Pathobiology and Microenvironment Group, Josep Carreras Leukaemia Research Institute, Badalona, Spain; CIBERONC, Instituto de Salud Carlos III, Madrid, Spain; ICREA, Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Antoni Riera-Mestre
- HHT Unit, Hospital Universitari de Bellvitge, L'Hospitalet de Llobregat, Spain; Internal Medicine Department, Hospital Universitari de Bellvitge, L'Hospitalet de Llobregat, Spain; Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain; Department of Clinical Sciences, Faculty of Medicine and Health Sciences, Universitat de Barcelona (UB), L'Hospitalet de Llobregat, Spain.
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Versbraegen N, Gravel B, Nachtegael C, Renaux A, Verkinderen E, Nowé A, Lenaerts T, Papadimitriou S. Faster and more accurate pathogenic combination predictions with VarCoPP2.0. BMC Bioinformatics 2023; 24:179. [PMID: 37127601 PMCID: PMC10152795 DOI: 10.1186/s12859-023-05291-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/14/2023] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND The prediction of potentially pathogenic variant combinations in patients remains a key task in the field of medical genetics for the understanding and detection of oligogenic/multilocus diseases. Models tailored towards such cases can help shorten the gap of missing diagnoses and can aid researchers in dealing with the high complexity of the derived data. The predictor VarCoPP (Variant Combinations Pathogenicity Predictor) that was published in 2019 and identified potentially pathogenic variant combinations in gene pairs (bilocus variant combinations), was the first important step in this direction. Despite its usefulness and applicability, several issues still remained that hindered a better performance, such as its False Positive (FP) rate, the quality of its training set and its complex architecture. RESULTS We present VarCoPP2.0: the successor of VarCoPP that is a simplified, faster and more accurate predictive model identifying potentially pathogenic bilocus variant combinations. Results from cross-validation and on independent data sets reveal that VarCoPP2.0 has improved in terms of both sensitivity (95% in cross-validation and 98% during testing) and specificity (5% FP rate). At the same time, its running time shows a significant 150-fold decrease due to the selection of a simpler Balanced Random Forest model. Its positive training set now consists of variant combinations that are more confidently linked with evidence of pathogenicity, based on the confidence scores present in OLIDA, the Oligogenic Diseases Database ( https://olida.ibsquare.be ). The improvement of its performance is also attributed to a more careful selection of up-to-date features identified via an original wrapper method. We show that the combination of different variant and gene pair features together is important for predictions, highlighting the usefulness of integrating biological information at different levels. CONCLUSIONS Through its improved performance and faster execution time, VarCoPP2.0 enables a more accurate analysis of larger data sets linked to oligogenic diseases. Users can access the ORVAL platform ( https://orval.ibsquare.be ) to apply VarCoPP2.0 on their data.
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Affiliation(s)
- Nassim Versbraegen
- Machine Learning Group, Université Libre de Bruxelles, 1050, Brussels, Belgium.
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050, Brussels, Belgium.
| | - Barbara Gravel
- Machine Learning Group, Université Libre de Bruxelles, 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050, Brussels, Belgium
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, 1050, Brussels, Belgium
| | - Charlotte Nachtegael
- Machine Learning Group, Université Libre de Bruxelles, 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050, Brussels, Belgium
| | - Alexandre Renaux
- Machine Learning Group, Université Libre de Bruxelles, 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050, Brussels, Belgium
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, 1050, Brussels, Belgium
| | - Emma Verkinderen
- Machine Learning Group, Université Libre de Bruxelles, 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050, Brussels, Belgium
| | - Ann Nowé
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050, Brussels, Belgium
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, 1050, Brussels, Belgium
| | - Tom Lenaerts
- Machine Learning Group, Université Libre de Bruxelles, 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050, Brussels, Belgium
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, 1050, Brussels, Belgium
| | - Sofia Papadimitriou
- Machine Learning Group, Université Libre de Bruxelles, 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050, Brussels, Belgium
- Artificial Intelligence Laboratory, Vrije Universiteit Brussel, 1050, Brussels, Belgium
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3
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Zhu M, Tang M, Du Y. Identification of TAC1 Associated with Alzheimer's Disease Using a Robust Rank Aggregation Approach. J Alzheimers Dis 2023; 91:1339-1349. [PMID: 36617784 DOI: 10.3233/jad-220950] [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: 01/07/2023]
Abstract
BACKGROUND Alzheimer's disease (AD) brings heavy burden to society and family. There is an urgent need to find effective methods for disease diagnosis and treatment. The robust rank aggregation (RRA) approach that could aggregate the resulting gene lists has been widely utilized in genomic data analysis. OBJECTIVE To identify hub genes using RRA approach in AD. METHODS Seven microarray datasets in frontal cortex from GEO database were used to identify differential expressed genes (DEGs) in AD patients using RRA approach. STRING was performed to explore the protein-to-protein interaction (PPI). Gene Ontology enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses were utilized for enrichment analysis. Human Gene Connectome and Gene Set Enrichment Analysis were used for functional annotation. Finally, the expression levels of hub genes were validated in the cortex of 5xFAD mice by quantitative real-time polymerase chain reaction. RESULTS After RRA analysis, 473 DEGs (216 upregulated and 257 downregulated) were identified in AD samples. PPI showed that DEGs had a total of 416 nodes and 2750 edges. These genes were divided into 17 clusters, each of which contains at least three genes. After functional annotation and enrichment analysis, TAC1 is identified as the hub gene and may be related to synaptic function and inflammation. In addition, Tac1 was found downregulated in cortices of 5xFAD mice. CONCLUSION In the current study, TAC1 is identified as a key gene in the frontal cortex of AD, providing insight into the possible pathogenesis and potential therapeutic targets for this disease.
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Affiliation(s)
- Min Zhu
- Department of Neurology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, People's Republic of China.,Department of Neurology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, People's Republic of China
| | - Minglu Tang
- Department of Neurology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, People's Republic of China.,Department of Neurology (Cognitive sleep ward), Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, People's Republic of China
| | - Yifeng Du
- Department of Neurology, Shandong Provincial Hospital, Shandong University, Jinan, Shandong, People's Republic of China.,Department of Neurology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, People's Republic of China
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Sheikh F, Alajlan H, Albanyan M, Alruwaili H, Alawami F, Sumayli S, Al Gazlan S, Abu Awwad S, Al-Dhekri H, Al-Saud B, Arnaout R, Alrayes H, Sayes N, Al-Hamed MH, Al-Mousa H, AlShareef S, Alazami AM. Phenotypic and Genotypic Characterization of Hereditary Angioedema in Saudi Arabia. J Clin Immunol 2023; 43:479-484. [PMID: 36348183 DOI: 10.1007/s10875-022-01399-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 10/27/2022] [Indexed: 11/09/2022]
Abstract
Hereditary angioedema (HAE) is a potentially life-threatening autosomal dominant disorder affecting roughly 1:50,000 individuals. It is commonly characterized by swelling of the larynx, gastrointestinal tract, extremities, and skin. There is growing genetic heterogeneity associated with this disease but more than 95% of mutations are found in SERPING1, the gene which encodes complement 1 inhibitor (C1-INH). HAE cohorts from several populations have been published but no large scale study has been reported from the Arab world to date. Here we document the clinical and genetic findings of HAE patients from a single Saudi institution, which is a major referral center at the national level. A total of 51 patients across 17 unrelated families were recruited including two large multi-generational families, of which one contained an in-frame exonic deletion that was resolved through MLPA. Two cases were negative for all the genes we tested (including F12, PLG, ANGPT1, MYOF, KNG1, and HS3ST6). The predominant HAE subtype in our cohort was type I, at 76%. We were able to uncover a mutation in 49 patients (96%). No type III (normal C1-INH) patients were encountered in the clinic, suggesting that this subtype does not play a major role in HAE pathogenesis in Saudi Arabia. Additionally, the existence of four patients with consistently normal complement 4 (C4) levels alongside abnormal C1-INH profiles highlights the utility of dual screening for both proteins in suspected patients.
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Affiliation(s)
- Farrukh Sheikh
- Department of Medicine, Allergy and Immunology Section, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Huda Alajlan
- Translational Genomics Department, Centre for Genomic Medicine, King Faisal Specialist Hospital & Research Centre, MBC 3, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Maram Albanyan
- Department of Medicine, Allergy and Immunology Section, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Hibah Alruwaili
- Translational Genomics Department, Centre for Genomic Medicine, King Faisal Specialist Hospital & Research Centre, MBC 3, P.O. Box 3354, Riyadh, 11211, Saudi Arabia
| | - Fatimah Alawami
- Department of Medicine, Allergy and Immunology Section, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Safia Sumayli
- Department of Medicine, Allergy and Immunology Section, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Sulaiman Al Gazlan
- Department of Medicine, Allergy and Immunology Section, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Sawsan Abu Awwad
- Department of Pediatrics, Allergy and Immunology Section, Faisal Specialist Hospital and Research Centre, Riyadh, King, Saudi Arabia
| | - Hasan Al-Dhekri
- Department of Pediatrics, Allergy and Immunology Section, Faisal Specialist Hospital and Research Centre, Riyadh, King, Saudi Arabia
| | - Bandar Al-Saud
- Department of Pediatrics, Allergy and Immunology Section, Faisal Specialist Hospital and Research Centre, Riyadh, King, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Rand Arnaout
- Department of Medicine, Allergy and Immunology Section, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Hassan Alrayes
- Department of Medicine, Allergy and Immunology Section, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Najla Sayes
- Department of Medicine, King Faisal Specialist Hospital and Research Centre, Jeddah, Saudi Arabia
| | - Mohamed H Al-Hamed
- Clinical Genomics Department, Centre for Genomic Medicine, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Hamoud Al-Mousa
- Department of Pediatrics, Allergy and Immunology Section, Faisal Specialist Hospital and Research Centre, Riyadh, King, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia
| | - Saad AlShareef
- Department of Medicine, Allergy and Immunology Section, King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Anas M Alazami
- Translational Genomics Department, Centre for Genomic Medicine, King Faisal Specialist Hospital & Research Centre, MBC 3, P.O. Box 3354, Riyadh, 11211, Saudi Arabia.
- Saudi Human Genome Program, King Abdulaziz City for Science and Technology, Riyadh, Saudi Arabia.
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Varzari A, Deyneko IV, Bruun GH, Dembic M, Hofmann W, Cebotari VM, Ginda SS, Andresen BS, Illig T. Candidate genes and sequence variants for susceptibility to mycobacterial infection identified by whole-exome sequencing. Front Genet 2022; 13:969895. [PMID: 36338958 PMCID: PMC9632272 DOI: 10.3389/fgene.2022.969895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 10/04/2022] [Indexed: 11/13/2022] Open
Abstract
Inborn errors of immunity are known to influence susceptibility to mycobacterial infections. The aim of this study was to characterize the genetic profile of nine patients with mycobacterial infections (eight with BCGitis and one with disseminated tuberculosis) from the Republic of Moldova using whole-exome sequencing. In total, 12 variants in eight genes known to be associated with Mendelian Susceptibility to Mycobacterial Disease (MSMD) were detected in six out of nine patients examined. In particular, a novel splice site mutation c.373–2A>C in STAT1 gene was found and functionally confirmed in a patient with disseminated tuberculosis. Trio analysis was possible for seven out of nine patients, and resulted in 23 candidate variants in 15 novel genes. Four of these genes - GBP2, HEATR3, PPP1R9B and KDM6A were further prioritized, considering their elevated expression in immune-related tissues. Compound heterozygosity was found in GBP2 in a single patient, comprising a maternally inherited missense variant c.412G>A/p.(Ala138Thr) predicted to be deleterious and a paternally inherited intronic mutation c.1149+14T>C. Functional studies demonstrated that the intronic mutation affects splicing and the level of transcript. Finally, we analyzed pathogenicity of variant combinations in gene pairs and identified five patients with putative oligogenic inheritance. In summary, our study expands the spectrum of genetic variation contributing to susceptibility to mycobacterial infections in children and provides insight into the complex/oligogenic disease-causing mode.
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Affiliation(s)
- Alexander Varzari
- Laboratory of Human Genetics, Chiril Draganiuc Institute of Phthisiopneumology, Kishinev, Moldova
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
- *Correspondence: Alexander Varzari,
| | - Igor V. Deyneko
- Laboratory of Functional Genomics, Timiryazev Institute of Plant Physiology Russian Academy of Sciences, Moscow, Russia
| | - Gitte Hoffmann Bruun
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
- The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Maja Dembic
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
- The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Department of Mathematics and Computer Science, University of Southern Denmark, Odense, Denmark
| | - Winfried Hofmann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Victor M. Cebotari
- Municipal Hospital of Phthisiopneumology, Department of Pediatrics, Kishinev, Moldova
| | - Sergei S. Ginda
- Laboratory of Immunology and Allergology, Chiril Draganiuc Institute of Phthisiopneumology, Kishinev, Moldova
| | - Brage S. Andresen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
- The Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Thomas Illig
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
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Yuan Y, Zhang L, Long Q, Jiang H, Li M. An accurate prediction model of digenic interaction for estimating pathogenic gene pairs of human diseases. Comput Struct Biotechnol J 2022; 20:3639-3652. [PMID: 35891796 PMCID: PMC9289819 DOI: 10.1016/j.csbj.2022.07.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 07/04/2022] [Accepted: 07/04/2022] [Indexed: 12/04/2022] Open
Abstract
Numerous pathogenic interactions are yet to be revealed efficiently due to dimension burden. Existing methods are underpowered and inaccurate to estimate pathogenic interactions. We developed an accurate bioinformatic method to predict digenic interaction effects based on gene-level features. The new method created a valuable resource of genome-wide pathogenic digenic interactions. We found that known causal genes in Mendelian and Oligogenic diseases may be enriched with interactive effects for the first time.
Increasing evidence shows that genetic interaction across the entire genome may explain a non-trivial fraction of genetic diseases. Digenic interaction is the simplest manifestation of genetic interaction among genes. However, systematic exploration of digenic interactive effects on the whole genome is often discouraged by the high dimension burden. Thus, numerous digenic interactions are yet to be identified for many diseases. Here, we propose a Digenic Interaction Effect Predictor (DIEP), an accurate machine-learning approach to identify the genome-wide pathogenic coding gene pairs with digenic interaction effects. This approach achieved high accuracy and sensitivity in independent testing datasets, outperforming another gene-level digenic predictor (DiGePred). DIEP was also able to discriminate digenic interaction effect from bi-locus effects dual molecular diagnosis (pseudo-digenic). Using DIEP, we provided a valuable resource of genome-wide digenic interactions and demonstrated the enrichment of the digenic interaction effect in Mendelian and Oligogenic diseases. Therefore, DIEP will play a useful role in facilitating the genomic mapping of interactive causal genes for human diseases.
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Affiliation(s)
- Yangyang Yuan
- Program in Bioinformatics, Zhongshan School of Medicine and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
- Center for Precision Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Center for Disease Genome Research, Sun Yat-sen University, Guangzhou 510080, China
| | - Liubin Zhang
- Program in Bioinformatics, Zhongshan School of Medicine and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
- Center for Precision Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Center for Disease Genome Research, Sun Yat-sen University, Guangzhou 510080, China
| | - Qihan Long
- Program in Bioinformatics, Zhongshan School of Medicine and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
- Center for Precision Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Center for Disease Genome Research, Sun Yat-sen University, Guangzhou 510080, China
| | - Hui Jiang
- Program in Bioinformatics, Zhongshan School of Medicine and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
- Center for Precision Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Center for Disease Genome Research, Sun Yat-sen University, Guangzhou 510080, China
| | - Miaoxin Li
- Program in Bioinformatics, Zhongshan School of Medicine and The Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
- Center for Precision Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Center for Disease Genome Research, Sun Yat-sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Disease Control (SYSU), Ministry of Education, Guangzhou 510080, China
- Guangdong Provincial Key Laboratory of Biomedical Imaging and Guangdong Provincial Engineering Research Center of Molecular Imaging, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
- Corresponding author at: Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.
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Novel brown adipose tissue candidate genes predicted by the human gene connectome. Sci Rep 2022; 12:7614. [PMID: 35534514 PMCID: PMC9085833 DOI: 10.1038/s41598-022-11317-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/06/2022] [Indexed: 11/08/2022] Open
Abstract
Brown adipose tissue (BAT) is a promising therapeutic target against obesity. Therefore, research on the genetic architecture of BAT could be key for the development of successful therapies against this complex phenotype. Hypothesis-driven candidate gene association studies are useful for studying genetic determinants of complex traits, but they are dependent upon the previous knowledge to select candidate genes. Here, we predicted 107 novel-BAT candidate genes in silico using the uncoupling protein one (UCP1) as the hallmark of BAT activity. We first identified the top 1% of human genes predicted by the human gene connectome to be biologically closest to the UCP1, estimating 167 additional pathway genes (BAT connectome). We validated this prediction by showing that 60 genes already associated with BAT were included in the connectome and they were biologically closer to each other than expected by chance (p < 2.2 × 10-16). The rest of genes (107) are potential candidates for BAT, being also closer to known BAT genes and more expressed in BAT biopsies than expected by chance (p < 2.2 × 10-16; p = 4.39 × 10-02). The resulting new list of predicted human BAT genes should be useful for the discovery of novel BAT genes and metabolic pathways.
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8
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Hamanaka K, Miyake N, Mizuguchi T, Miyatake S, Uchiyama Y, Tsuchida N, Sekiguchi F, Mitsuhashi S, Tsurusaki Y, Nakashima M, Saitsu H, Yamada K, Sakamoto M, Fukuda H, Ohori S, Saida K, Itai T, Azuma Y, Koshimizu E, Fujita A, Erturk B, Hiraki Y, Ch'ng GS, Kato M, Okamoto N, Takata A, Matsumoto N. Large-scale discovery of novel neurodevelopmental disorder-related genes through a unified analysis of single-nucleotide and copy number variants. Genome Med 2022; 14:40. [PMID: 35468861 PMCID: PMC9040275 DOI: 10.1186/s13073-022-01042-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 03/25/2022] [Indexed: 12/12/2022] Open
Abstract
Background Previous large-scale studies of de novo variants identified a number of genes associated with neurodevelopmental disorders (NDDs); however, it was also predicted that many NDD-associated genes await discovery. Such genes can be discovered by integrating copy number variants (CNVs), which have not been fully considered in previous studies, and increasing the sample size. Methods We first constructed a model estimating the rates of de novo CNVs per gene from several factors such as gene length and number of exons. Second, we compiled a comprehensive list of de novo single-nucleotide variants (SNVs) in 41,165 individuals and de novo CNVs in 3675 individuals with NDDs by aggregating our own and publicly available datasets, including denovo-db and the Deciphering Developmental Disorders study data. Third, summing up the de novo CNV rates that we estimated and SNV rates previously established, gene-based enrichment of de novo deleterious SNVs and CNVs were assessed in the 41,165 cases. Significantly enriched genes were further prioritized according to their similarity to known NDD genes using a deep learning model that considers functional characteristics (e.g., gene ontology and expression patterns). Results We identified a total of 380 genes achieving statistical significance (5% false discovery rate), including 31 genes affected by de novo CNVs. Of the 380 genes, 52 have not previously been reported as NDD genes, and the data of de novo CNVs contributed to the significance of three genes (GLTSCR1, MARK2, and UBR3). Among the 52 genes, we reasonably excluded 18 genes [a number almost identical to the theoretically expected false positives (i.e., 380 × 0.05 = 19)] given their constraints against deleterious variants and extracted 34 “plausible” candidate genes. Their validity as NDD genes was consistently supported by their similarity in function and gene expression patterns to known NDD genes. Quantifying the overall similarity using deep learning, we identified 11 high-confidence (> 90% true-positive probabilities) candidate genes: HDAC2, SUPT16H, HECTD4, CHD5, XPO1, GSK3B, NLGN2, ADGRB1, CTR9, BRD3, and MARK2. Conclusions We identified dozens of new candidates for NDD genes. Both the methods and the resources developed here will contribute to the further identification of novel NDD-associated genes. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01042-w.
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Affiliation(s)
- Kohei Hamanaka
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
| | - Noriko Miyake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Takeshi Mizuguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satoko Miyatake
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Clinical Genetics Department, Yokohama City University Hospital, Yokohama, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Japan
| | - Futoshi Sekiguchi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Satomi Mitsuhashi
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yoshinori Tsurusaki
- Faculty of Nutritional Science, Sagami Women's University, Sagamihara, Japan
| | - Mitsuko Nakashima
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hirotomo Saitsu
- Department of Biochemistry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kohei Yamada
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Masamune Sakamoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Hiromi Fukuda
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Sachiko Ohori
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ken Saida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Toshiyuki Itai
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Yoshiteru Azuma
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.,Department of Pediatrics, Aichi Medical University, Nagakute, Japan
| | - Eriko Koshimizu
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Atsushi Fujita
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Biray Erturk
- Department of Medical Genetics, Ege University Faculty of Medicine, Izmir, Turkey.,Current affiliation: Department of Medical Genetics, Prof. Dr. Cemil Tascioglu City Hospital, Istanbul, Turkey
| | - Yoko Hiraki
- Hiroshima Municipal Center for Child Health and Development, Hiroshima, Japan
| | | | - Mitsuhiro Kato
- Department of Pediatrics, Showa University School of Medicine, Tokyo, Japan
| | - Nobuhiko Okamoto
- Department of Medical Genetics, Osaka Women's and Children's Hospital, Izumi, Japan
| | - Atsushi Takata
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan. .,Laboratory for Molecular Pathology of Psychiatric Disorders, RIKEN Center for Brain Science, Wako, Japan.
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
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9
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Buphamalai P, Kokotovic T, Nagy V, Menche J. Network analysis reveals rare disease signatures across multiple levels of biological organization. Nat Commun 2021; 12:6306. [PMID: 34753928 PMCID: PMC8578255 DOI: 10.1038/s41467-021-26674-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 10/19/2021] [Indexed: 01/26/2023] Open
Abstract
Rare genetic diseases are typically caused by a single gene defect. Despite this clear causal relationship between genotype and phenotype, identifying the pathobiological mechanisms at various levels of biological organization remains a practical and conceptual challenge. Here, we introduce a network approach for evaluating the impact of rare gene defects across biological scales. We construct a multiplex network consisting of over 20 million gene relationships that are organized into 46 network layers spanning six major biological scales between genotype and phenotype. A comprehensive analysis of 3,771 rare diseases reveals distinct phenotypic modules within individual layers. These modules can be exploited to mechanistically dissect the impact of gene defects and accurately predict rare disease gene candidates. Our results show that the disease module formalism can be applied to rare diseases and generalized beyond physical interaction networks. These findings open up new venues to apply network-based tools for cross-scale data integration.
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Affiliation(s)
- Pisanu Buphamalai
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna BioCenter 5, 1030, Vienna, Austria
| | - Tomislav Kokotovic
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
- Department of Neurology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Vanja Nagy
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
- Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria
- Department of Neurology, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| | - Jörg Menche
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14, AKH BT 25.3, 1090, Vienna, Austria.
- Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Campus Vienna BioCenter 5, 1030, Vienna, Austria.
- Faculty of Mathematics, University of Vienna, Oskar-Morgenstern-Platz 1, 1090, Vienna, Austria.
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10
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Cananzi M, Wohler E, Marzollo A, Colavito D, You J, Jing H, Bresolin S, Gaio P, Martin R, Mescoli C, Bade S, Posey JE, Dalle Carbonare M, Tung W, Jhangiani SN, Bosa L, Zhang Y, Filho JS, Gabelli M, Kellermayer R, Kader HA, Oliva-Hemker M, Perilongo G, Lupski JR, Biffi A, Valle D, Leon A, de Macena Sobreira NL, Su HC, Guerrerio AL. IFIH1 loss-of-function variants contribute to very early-onset inflammatory bowel disease. Hum Genet 2021; 140:1299-1312. [PMID: 34185153 PMCID: PMC8423350 DOI: 10.1007/s00439-021-02300-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/07/2021] [Indexed: 02/06/2023]
Abstract
Genetic defects of innate immunity impairing intestinal bacterial sensing are linked to the development of Inflammatory Bowel Disease (IBD). Although much evidence supports a role of the intestinal virome in gut homeostasis, most studies focus on intestinal viral composition rather than on host intestinal viral sensitivity. To demonstrate the association between the development of Very Early Onset IBD (VEOIBD) and variants in the IFIH1 gene which encodes MDA5, a key cytosolic sensor for viral nucleic acids. Whole exome sequencing (WES) was performed in two independent cohorts of children with VEOIBD enrolled in Italy (n = 18) and USA (n = 24). Luciferase reporter assays were employed to assess MDA5 activity. An enrichment analysis was performed on IFIH1 comparing 42 VEOIBD probands with 1527 unrelated individuals without gastrointestinal or immunological issues. We identified rare, likely loss-of-function (LoF), IFIH1 variants in eight patients with VEOIBD from a combined cohort of 42 children. One subject, carrying a homozygous truncating variant resulting in complete LoF, experienced neonatal-onset, pan-gastrointestinal, IBD-like enteropathy plus multiple infectious episodes. The remaining seven subjects, affected by VEOIBD without immunodeficiency, were carriers of one LoF variant in IFIH1. Among these, two patients also carried a second hypomorphic variant, with partial function apparent when MDA5 was weakly stimulated. Furthermore, IFIH1 variants were significantly enriched in children with VEOIBD as compared to controls (p = 0.007). Complete and partial MDA5 deficiency is associated with VEOIBD with variable penetrance and expressivity, suggesting a role for impaired intestinal viral sensing in IBD pathogenesis.
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Affiliation(s)
- Mara Cananzi
- Unit of Pediatric Gastroenterology, Digestive Endoscopy, Hepatology and Care of the Child with Liver Transplantation, Department of Women's and Children's Health, University Hospital of Padova, Padova, Italy.
| | - Elizabeth Wohler
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Antonio Marzollo
- Pediatric Hematology, Oncology and Stem Cell Transplant Division, Department of Women's and Children's Health, University Hospital of Padova, Padova, Italy
- Istituto di Ricerca Pediatrica, Fondazione Città della Speranza, Padova, Italy
| | - Davide Colavito
- Research & Innovation (R&I Genetics) Srl, C.so Stati Uniti 4, Padova, Italy
| | - Jing You
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Huie Jing
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Silvia Bresolin
- Pediatric Hematology, Oncology and Stem Cell Transplant Division, Department of Women's and Children's Health, University Hospital of Padova, Padova, Italy
- Istituto di Ricerca Pediatrica, Fondazione Città della Speranza, Padova, Italy
| | - Paola Gaio
- Unit of Pediatric Gastroenterology, Digestive Endoscopy, Hepatology and Care of the Child with Liver Transplantation, Department of Women's and Children's Health, University Hospital of Padova, Padova, Italy
| | - Renan Martin
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Claudia Mescoli
- Surgical Pathology and Cytopathology Unit, Department of Medicine (DIMED), University Hospital of Padova, Padova, Italy
| | - Sangeeta Bade
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jennifer E Posey
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Wesley Tung
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Shalini N Jhangiani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Luca Bosa
- Unit of Pediatric Gastroenterology, Digestive Endoscopy, Hepatology and Care of the Child with Liver Transplantation, Department of Women's and Children's Health, University Hospital of Padova, Padova, Italy
| | - Yu Zhang
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Joselito Sobreira Filho
- Division of Genetics, Department of Morphology and Genetics, Universidade Federal de Sao Paulo, Sao Paulo, Brazil
| | - Maria Gabelli
- Pediatric Hematology, Oncology and Stem Cell Transplant Division, Department of Women's and Children's Health, University Hospital of Padova, Padova, Italy
| | - Richard Kellermayer
- Section of Pediatric Gastroenterology, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Howard A Kader
- Department of Pediatrics, Division of Pediatric Gastroenterology & Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Maria Oliva-Hemker
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Giorgio Perilongo
- Unit of Pediatric Gastroenterology, Digestive Endoscopy, Hepatology and Care of the Child with Liver Transplantation, Department of Women's and Children's Health, University Hospital of Padova, Padova, Italy
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Texas Children's Hospital, Houston, Texas, USA
| | - Alessandra Biffi
- Pediatric Hematology, Oncology and Stem Cell Transplant Division, Department of Women's and Children's Health, University Hospital of Padova, Padova, Italy
| | - David Valle
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Alberta Leon
- Research & Innovation (R&I Genetics) Srl, C.so Stati Uniti 4, Padova, Italy
| | | | - Helen C Su
- Human Immunological Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Anthony L Guerrerio
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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11
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Khan HA, Butte MJ. Expanding the potential genes of inborn errors of immunity through protein interactions. BMC Genomics 2021; 22:618. [PMID: 34391382 PMCID: PMC8364696 DOI: 10.1186/s12864-021-07909-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 07/22/2021] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Inborn errors of immunity (IEI) are a group of genetic disorders that impair the immune system, with over 400 genes described so far, and hundreds more to be discovered. To facilitate the search for new genes, we need a way to prioritize among all the genes in the genome those most likely to play an important role in immunity. RESULTS Here we identify a new list of genes by linking known IEI genes to new ones by using open-source databases of protein-protein interactions, post-translational modifications, and transcriptional regulation. We analyze this new set of 2,530 IEI-related genes for their tolerance of genetic variation and by their expression levels in various immune cell types. CONCLUSIONS By merging genes derived from protein interactions of known IEI genes with transcriptional data, we offer a new list of candidate genes that may play a role in as-yet undiscovered IEIs.
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Affiliation(s)
- Humza A Khan
- Division of Immunology, Allergy, and Rheumatology, Department of Pediatrics, University of California Los Angeles, 10833 Le Conte Ave, MDCC Building, Room 12-430, Los Angeles, CA, 90095, USA
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, 10833 Le Conte Ave, MDCC Building, Room 12-430, Los Angeles, CA, 90095, USA
| | - Manish J Butte
- Division of Immunology, Allergy, and Rheumatology, Department of Pediatrics, University of California Los Angeles, 10833 Le Conte Ave, MDCC Building, Room 12-430, Los Angeles, CA, 90095, USA.
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, 10833 Le Conte Ave, MDCC Building, Room 12-430, Los Angeles, CA, 90095, USA.
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12
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Lea-Henry TN, Chuah A, Stanley M, Athanasopoulos V, Starkey MR, Christiadi D, Kitching AR, Cook MC, Andrews TD, Vinuesa CG, Walters GD, Jiang SH. Increased burden of rare variants in genes of the endosomal Toll-like receptor pathway in patients with systemic lupus erythematosus. Lupus 2021; 30:1756-1763. [PMID: 34266320 DOI: 10.1177/09612033211033979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
OBJECTIVE To compare the frequency of rare variants in genes of the pathophysiologically relevant endosomal Toll-like receptor (eTLR) pathway and any quantifiable differences in variant rarity, predicted deleteriousness, or molecular proximity in patients with systemic lupus erythematosus (SLE) and healthy controls. PATIENTS AND METHODS 65 genes associated with the eTLR pathway were identified by literature search and pathway analysis. Using next generation sequencing techniques, these were compared in two randomised cohorts of patients with SLE (n = 114 and n = 113) with 197 healthy controls. Genetically determined ethnicity was used to normalise minor allele frequencies (MAF) for the identified genetic variants and these were then compared by their frequency: rare (MAF < 0.005), uncommon (MAF 0.005-0.02), and common (MAF >0.02). This was compared to the results for 65 randomly selected genes. RESULTS Patients with SLE are more likely to carry a rare nonsynonymous variant affecting proteins within the eTLR pathway than healthy controls. Furthermore, individuals with SLE are more likely to have multiple rare variants in this pathway. There were no differences in rarity, Combined Annotation Dependent Depletion (CADD) score, or molecular proximity for rare eTLR pathway variants. CONCLUSIONS Rare non-synonymous variants are enriched in patients with SLE in the eTLR pathway. This supports the hypothesis that SLE arises from several rare variants of relatively large effect rather than many common variants of small effect.
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Affiliation(s)
- Tom N Lea-Henry
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Aaron Chuah
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Maurice Stanley
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia.,Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Canberra, ACT, Australia
| | - Vicki Athanasopoulos
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia.,Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Canberra, ACT, Australia.,China Australia Centre for Personalised Immunology, Shanghai Renji Hospital, Jiao Tong University Shanghai, Huangpu Qu, China
| | - Malcolm R Starkey
- Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Daniel Christiadi
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia.,Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Canberra, ACT, Australia
| | - A Richard Kitching
- Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Canberra, ACT, Australia.,Centre for Inflammatory Diseases, 439191Monash University Department of Medicine, Monash University Department of Medicine, Clayton, VIC, Australia.,Department of Nephrology, Monash Health, Clayton, VIC, Australia.,Department of Paediatric Nephrology. Monash Health, Clayton, VIC, Australia
| | - Matthew C Cook
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia.,Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Canberra, ACT, Australia.,China Australia Centre for Personalised Immunology, Shanghai Renji Hospital, Jiao Tong University Shanghai, Huangpu Qu, China
| | - Thomas D Andrews
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia
| | - Carola G Vinuesa
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia.,Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Canberra, ACT, Australia.,China Australia Centre for Personalised Immunology, Shanghai Renji Hospital, Jiao Tong University Shanghai, Huangpu Qu, China
| | - Giles D Walters
- Department of Renal Medicine, 34381Canberra Hospital, The Canberra Hospital, Garran, ACT, Australia
| | - Simon H Jiang
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia.,Centre for Personalised Immunology, NHMRC Centre for Research Excellence, Canberra, ACT, Australia.,China Australia Centre for Personalised Immunology, Shanghai Renji Hospital, Jiao Tong University Shanghai, Huangpu Qu, China.,Department of Renal Medicine, 34381Canberra Hospital, The Canberra Hospital, Garran, ACT, Australia
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13
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Pirch S, Müller F, Iofinova E, Pazmandi J, Hütter CVR, Chiettini M, Sin C, Boztug K, Podkosova I, Kaufmann H, Menche J. The VRNetzer platform enables interactive network analysis in Virtual Reality. Nat Commun 2021; 12:2432. [PMID: 33893283 PMCID: PMC8065164 DOI: 10.1038/s41467-021-22570-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 03/09/2021] [Indexed: 12/17/2022] Open
Abstract
Networks provide a powerful representation of interacting components within complex systems, making them ideal for visually and analytically exploring big data. However, the size and complexity of many networks render static visualizations on typically-sized paper or screens impractical, resulting in proverbial ‘hairballs’. Here, we introduce a Virtual Reality (VR) platform that overcomes these limitations by facilitating the thorough visual, and interactive, exploration of large networks. Our platform allows maximal customization and extendibility, through the import of custom code for data analysis, integration of external databases, and design of arbitrary user interface elements, among other features. As a proof of concept, we show how our platform can be used to interactively explore genome-scale molecular networks to identify genes associated with rare diseases and understand how they might contribute to disease development. Our platform represents a general purpose, VR-based data exploration platform for large and diverse data types by providing an interface that facilitates the interaction between human intuition and state-of-the-art analysis methods. Data-rich networks can be difficult to interpret beyond a certain size. Here, the authors introduce a platform that uses virtual reality to allow the visual exploration of large networks, while interfacing with data repositories and other analytical methods to improve the interpretation of big data.
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Affiliation(s)
- Sebastian Pirch
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Felix Müller
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Eugenia Iofinova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Julia Pazmandi
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria.,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria
| | - Christiane V R Hütter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Martin Chiettini
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Celine Sin
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | - Kaan Boztug
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.,Ludwig Boltzmann Institute for Rare and Undiagnosed Diseases, Vienna, Austria.,St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria.,St. Anna Children's Hospital, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria.,Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Iana Podkosova
- Institute of Visual Computing and Human-Centered Technology, TU Wien, Vienna, Austria
| | - Hannes Kaufmann
- Institute of Visual Computing and Human-Centered Technology, TU Wien, Vienna, Austria
| | - Jörg Menche
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria. .,Department of Structural and Computational Biology, Max Perutz Labs, University of Vienna, Vienna, Austria. .,Faculty of Mathematics, University of Vienna, Vienna, Austria.
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14
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Lee K, Abraham RS. Next-generation sequencing for inborn errors of immunity. Hum Immunol 2021; 82:871-882. [PMID: 33715910 DOI: 10.1016/j.humimm.2021.02.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/19/2021] [Accepted: 02/23/2021] [Indexed: 12/27/2022]
Abstract
Inborn errors of immunity (IEIs) include several hundred gene defects affecting various components of the immune system. As with other constitutional disorders, next-generation sequencing (NGS) is a powerful tool for the diagnosis of these diseases. While NGS can provide molecular confirmation of disease in a patient with a suspected or classic phenotype, it can also identify new molecular defects of the immune system, expand gene-disease phenotypes, clarify mechanism of disease, pattern of inheritance or identify new gene-disease associations. Multiple clinical specialties are involved in the diagnosis and management of patients with IEI, and most have no formal genetic training or expertise. To effectively utilize NGS tools and data in clinical practice, it is relevant and pragmatic to obtain a modicum of knowledge about genetic terminology, the variety of platforms and tools available for high-throughput genomic analysis, the interpretation and implementation of such data in clinical practice. There is considerable variability not only in the technologies and analytical tools used for NGS but in the bioinformatics approach to variant identification and interpretation. The ability to provide a molecular basis for disease has the potential to alter therapeutic management and longer-term treatment of the disease, including developing personalized approaches with molecularly targeted therapies. This review is intended for the clinical specialist or diagnostic immunologist who works in the area of inborn errors of immunity, and provides an overview of the need for genetic testing in these patients (the "why" aspect), the various technologies and analytical approaches, bioinformatics tools, resources, and challenges (the "how" aspect), and the clinical evidence for identifying which patients might be best served by such testing (the "when" aspect).
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Affiliation(s)
- Kristy Lee
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, The Ohio State University College of Medicine, Columbus, OH, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Roshini S Abraham
- Diagnostic Immunology Laboratory, Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, The Ohio State University College of Medicine, Columbus, OH, USA; Department of Pathology, The Ohio State University College of Medicine, Columbus, OH, USA.
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15
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Yang R, Mele F, Worley L, Langlais D, Rosain J, Benhsaien I, Elarabi H, Croft CA, Doisne JM, Zhang P, Weisshaar M, Jarrossay D, Latorre D, Shen Y, Han J, Ogishi M, Gruber C, Markle J, Al Ali F, Rahman M, Khan T, Seeleuthner Y, Kerner G, Husquin LT, Maclsaac JL, Jeljeli M, Errami A, Ailal F, Kobor MS, Oleaga-Quintas C, Roynard M, Bourgey M, El Baghdadi J, Boisson-Dupuis S, Puel A, Batteux F, Rozenberg F, Marr N, Pan-Hammarström Q, Bogunovic D, Quintana-Murci L, Carroll T, Ma CS, Abel L, Bousfiha A, Di Santo JP, Glimcher LH, Gros P, Tangye SG, Sallusto F, Bustamante J, Casanova JL. Human T-bet Governs Innate and Innate-like Adaptive IFN-γ Immunity against Mycobacteria. Cell 2020; 183:1826-1847.e31. [PMID: 33296702 PMCID: PMC7770098 DOI: 10.1016/j.cell.2020.10.046] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 06/25/2020] [Accepted: 10/26/2020] [Indexed: 12/17/2022]
Abstract
Inborn errors of human interferon gamma (IFN-γ) immunity underlie mycobacterial disease. We report a patient with mycobacterial disease due to inherited deficiency of the transcription factor T-bet. The patient has extremely low counts of circulating Mycobacterium-reactive natural killer (NK), invariant NKT (iNKT), mucosal-associated invariant T (MAIT), and Vδ2+ γδ T lymphocytes, and of Mycobacterium-non reactive classic TH1 lymphocytes, with the residual populations of these cells also producing abnormally small amounts of IFN-γ. Other lymphocyte subsets develop normally but produce low levels of IFN-γ, with the exception of CD8+ αβ T and non-classic CD4+ αβ TH1∗ lymphocytes, which produce IFN-γ normally in response to mycobacterial antigens. Human T-bet deficiency thus underlies mycobacterial disease by preventing the development of innate (NK) and innate-like adaptive lymphocytes (iNKT, MAIT, and Vδ2+ γδ T cells) and IFN-γ production by them, with mycobacterium-specific, IFN-γ-producing, purely adaptive CD8+ αβ T, and CD4+ αβ TH1∗ cells unable to compensate for this deficit.
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Affiliation(s)
- Rui Yang
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA.
| | - Federico Mele
- Center of Medical Immunology, Institute for Research in Biomedicine, Faculty of Biomedical Sciences, University of Italian Switzerland (USI), 6500 Bellinzona, Switzerland
| | - Lisa Worley
- Garvan Institute of Medical Research, Darlinghurst 2010, NSW, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Darlinghurst 2010, NSW, Australia
| | - David Langlais
- Department of Human Genetics, Department of Microbiology and Immunology, McGill University, Montreal, QC H3A 0G1, Canada; McGill University Genome Center, McGill Research Centre on Complex Traits, Montreal, QC H3A 0G1, Canada
| | - Jérémie Rosain
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Ibithal Benhsaien
- Laboratory of Clinical Immunology, Inflammation and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, 20460 Casablanca, Morocco; Clinical Immunology Unit, Department of Pediatric Infectious Diseases, Children's Hospital, CHU Averroes, 20460 Casablanca, Morocco
| | - Houda Elarabi
- Pediatrics Department, Hassan II Hospital, 80030 Dakhla, Morocco
| | - Carys A Croft
- Innate Immunity Unit, Institut Pasteur, 75724 Paris, France; INSERM U1223, 75015 Paris, France; University of Paris, 75006 Paris, France
| | - Jean-Marc Doisne
- Innate Immunity Unit, Institut Pasteur, 75724 Paris, France; INSERM U1223, 75015 Paris, France
| | - Peng Zhang
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Marc Weisshaar
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - David Jarrossay
- Center of Medical Immunology, Institute for Research in Biomedicine, Faculty of Biomedical Sciences, University of Italian Switzerland (USI), 6500 Bellinzona, Switzerland
| | - Daniela Latorre
- Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - Yichao Shen
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Jing Han
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Masato Ogishi
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Conor Gruber
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Janet Markle
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA
| | - Fatima Al Ali
- Research Branch, Sidra Medicine, Doha, PO 26999, Qatar
| | | | - Taushif Khan
- Research Branch, Sidra Medicine, Doha, PO 26999, Qatar
| | - Yoann Seeleuthner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Gaspard Kerner
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Lucas T Husquin
- Human Evolutionary Genetics Unit, CNRS UMR2000, Institut Pasteur, 75015 Paris, France
| | - Julia L Maclsaac
- BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Mohamed Jeljeli
- University of Paris, 75006 Paris, France; Immunology Laboratory, Cochin Hospital, AH-HP, 75014 Paris, France
| | - Abderrahmane Errami
- Laboratory of Clinical Immunology, Inflammation and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, 20460 Casablanca, Morocco
| | - Fatima Ailal
- Laboratory of Clinical Immunology, Inflammation and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, 20460 Casablanca, Morocco; Clinical Immunology Unit, Department of Pediatric Infectious Diseases, Children's Hospital, CHU Averroes, 20460 Casablanca, Morocco
| | - Michael S Kobor
- BC Children's Hospital Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Carmen Oleaga-Quintas
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Manon Roynard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Mathieu Bourgey
- McGill University Genome Center, McGill Research Centre on Complex Traits, Montreal, QC H3A 0G1, Canada; Canadian Centre for Computational Genomics, Montreal, QC H3A 0G1, Canada
| | | | - Stéphanie Boisson-Dupuis
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Anne Puel
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Fréderic Batteux
- University of Paris, 75006 Paris, France; Immunology Laboratory, Cochin Hospital, AH-HP, 75014 Paris, France
| | - Flore Rozenberg
- University of Paris, 75006 Paris, France; Virology Laboratory, Cochin Hospital, AH-HP, 75014 Paris, France
| | - Nico Marr
- Research Branch, Sidra Medicine, Doha, PO 26999, Qatar; College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, PO 34110, Qatar
| | - Qiang Pan-Hammarström
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Dusan Bogunovic
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, CNRS UMR2000, Institut Pasteur, 75015 Paris, France; Chair of Human Genomics and Evolution, Collège de France, 75005 Paris, France
| | - Thomas Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Cindy S Ma
- Garvan Institute of Medical Research, Darlinghurst 2010, NSW, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Darlinghurst 2010, NSW, Australia
| | - Laurent Abel
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France
| | - Aziz Bousfiha
- Laboratory of Clinical Immunology, Inflammation and Allergy, Faculty of Medicine and Pharmacy of Casablanca, King Hassan II University, 20460 Casablanca, Morocco; Clinical Immunology Unit, Department of Pediatric Infectious Diseases, Children's Hospital, CHU Averroes, 20460 Casablanca, Morocco
| | - James P Di Santo
- Innate Immunity Unit, Institut Pasteur, 75724 Paris, France; INSERM U1223, 75015 Paris, France
| | - Laurie H Glimcher
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Philippe Gros
- McGill University Genome Center, McGill Research Centre on Complex Traits, Montreal, QC H3A 0G1, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Stuart G Tangye
- Garvan Institute of Medical Research, Darlinghurst 2010, NSW, Australia; St Vincent's Clinical School, Faculty of Medicine, UNSW Sydney, Darlinghurst 2010, NSW, Australia
| | - Federica Sallusto
- Center of Medical Immunology, Institute for Research in Biomedicine, Faculty of Biomedical Sciences, University of Italian Switzerland (USI), 6500 Bellinzona, Switzerland; Institute of Microbiology, ETH Zurich, 8093 Zurich, Switzerland
| | - Jacinta Bustamante
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France; Study Center for Primary Immunodeficiencies, Necker Children Hospital, AP-HP, 75015 Paris, France
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY 10065, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM UMR 1163, Necker Hospital for Sick Children, 75015 Paris, France; University of Paris, Imagine Institute, 75015 Paris, France; Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, AP-HP, 75015 Paris, France; Howard Hughes Medical Institute, New York, NY, USA.
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16
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Li J, Ritelli M, Ma CS, Rao G, Habib T, Corvilain E, Bougarn S, Cypowyj S, Grodecká L, Lévy R, Béziat V, Shang L, Payne K, Avery DT, Migaud M, Boucherit S, Boughorbel S, Guennoun A, Chrabieh M, Rapaport F, Bigio B, Itan Y, Boisson B, Cormier-Daire V, Syx D, Malfait F, Zoppi N, Abel L, Freiberger T, Dietz HC, Marr N, Tangye SG, Colombi M, Casanova JL, Puel A. Chronic mucocutaneous candidiasis and connective tissue disorder in humans with impaired JNK1-dependent responses to IL-17A/F and TGF-β. Sci Immunol 2020; 4:4/41/eaax7965. [PMID: 31784499 DOI: 10.1126/sciimmunol.aax7965] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 11/01/2019] [Indexed: 12/12/2022]
Abstract
Genetic etiologies of chronic mucocutaneous candidiasis (CMC) disrupt human IL-17A/F-dependent immunity at mucosal surfaces, whereas those of connective tissue disorders (CTDs) often impair the TGF-β-dependent homeostasis of connective tissues. The signaling pathways involved are incompletely understood. We report a three-generation family with an autosomal dominant (AD) combination of CMC and a previously undescribed form of CTD that clinically overlaps with Ehlers-Danlos syndrome (EDS). The patients are heterozygous for a private splice-site variant of MAPK8, the gene encoding c-Jun N-terminal kinase 1 (JNK1), a component of the MAPK signaling pathway. This variant is loss-of-expression and loss-of-function in the patients' fibroblasts, which display AD JNK1 deficiency by haploinsufficiency. These cells have impaired, but not abolished, responses to IL-17A and IL-17F. Moreover, the development of the patients' TH17 cells was impaired ex vivo and in vitro, probably due to the involvement of JNK1 in the TGF-β-responsive pathway and further accounting for the patients' CMC. Consistently, the patients' fibroblasts displayed impaired JNK1- and c-Jun/ATF-2-dependent induction of key extracellular matrix (ECM) components and regulators, but not of EDS-causing gene products, in response to TGF-β. Furthermore, they displayed a transcriptional pattern in response to TGF-β different from that of fibroblasts from patients with Loeys-Dietz syndrome caused by mutations of TGFBR2 or SMAD3, further accounting for the patients' complex and unusual CTD phenotype. This experiment of nature indicates that the integrity of the human JNK1-dependent MAPK signaling pathway is essential for IL-17A- and IL-17F-dependent mucocutaneous immunity to Candida and for the TGF-β-dependent homeostasis of connective tissues.
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Affiliation(s)
- Juan Li
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Marco Ritelli
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Cindy S Ma
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Geetha Rao
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | | | - Emilie Corvilain
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France.,University of Paris, Imagine Institute, 75015 Paris, France
| | | | - Sophie Cypowyj
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Lucie Grodecká
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno 65691, Czech Republic
| | - Romain Lévy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France.,University of Paris, Imagine Institute, 75015 Paris, France
| | - Vivien Béziat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France.,University of Paris, Imagine Institute, 75015 Paris, France
| | - Lei Shang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Kathryn Payne
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Danielle T Avery
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Mélanie Migaud
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France.,University of Paris, Imagine Institute, 75015 Paris, France
| | - Soraya Boucherit
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France.,University of Paris, Imagine Institute, 75015 Paris, France
| | | | | | - Maya Chrabieh
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France.,University of Paris, Imagine Institute, 75015 Paris, France
| | - Franck Rapaport
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Benedetta Bigio
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA
| | - Yuval Itan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA.,The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France.,University of Paris, Imagine Institute, 75015 Paris, France
| | - Valérie Cormier-Daire
- University of Paris, Imagine Institute, 75015 Paris, France.,Department of Medical Genetics, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France
| | - Delfien Syx
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Fransiska Malfait
- Center for Medical Genetics, Ghent University Hospital, 9000 Ghent, Belgium
| | - Nicoletta Zoppi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA.,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France.,University of Paris, Imagine Institute, 75015 Paris, France
| | - Tomáš Freiberger
- Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation, Brno 65691, Czech Republic.,Faculty of Medicine and Central European Institute of Technology, Masaryk University, Brno 62500, Czech Republic
| | - Harry C Dietz
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.,Howard Hughes Medical Institute, Baltimore, MD 21205, USA
| | - Nico Marr
- Sidra Medicine, P.O. Box 26999, Doha, Qatar.,College of Health and Life Sciences, Hamad Bin Khalifa University, P.O. Box 34110, Doha, Qatar
| | - Stuart G Tangye
- Immunology Division, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia.,St. Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, New South Wales 2010, Australia
| | - Marina Colombi
- Division of Biology and Genetics, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA. .,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France.,University of Paris, Imagine Institute, 75015 Paris, France.,Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, 75015 Paris, France.,Howard Hughes Medical Institute, New York, NY 10065, USA
| | - Anne Puel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065, USA. .,Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, 75015 Paris, France.,University of Paris, Imagine Institute, 75015 Paris, France
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17
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Renaux A, Papadimitriou S, Versbraegen N, Nachtegael C, Boutry S, Nowé A, Smits G, Lenaerts T. ORVAL: a novel platform for the prediction and exploration of disease-causing oligogenic variant combinations. Nucleic Acids Res 2020; 47:W93-W98. [PMID: 31147699 PMCID: PMC6602484 DOI: 10.1093/nar/gkz437] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 05/01/2019] [Accepted: 05/09/2019] [Indexed: 12/16/2022] Open
Abstract
A tremendous amount of DNA sequencing data is being produced around the world with the ambition to capture in more detail the mechanisms underlying human diseases. While numerous bioinformatics tools exist that allow the discovery of causal variants in Mendelian diseases, little to no support is provided to do the same for variant combinations, an essential task for the discovery of the causes of oligogenic diseases. ORVAL (the Oligogenic Resource for Variant AnaLysis), which is presented here, provides an answer to this problem by focusing on generating networks of candidate pathogenic variant combinations in gene pairs, as opposed to isolated variants in unique genes. This online platform integrates innovative machine learning methods for combinatorial variant pathogenicity prediction with visualization techniques, offering several interactive and exploratory tools, such as pathogenic gene and protein interaction networks, a ranking of pathogenic gene pairs, as well as visual mappings of the cellular location and pathway information. ORVAL is the first web-based exploration platform dedicated to identifying networks of candidate pathogenic variant combinations with the sole ambition to help in uncovering oligogenic causes for patients that cannot rely on the classical disease analysis tools. ORVAL is available at https://orval.ibsquare.be.
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Affiliation(s)
- Alexandre Renaux
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Machine Learning Group, Université Libre de Bruxelles, 1050 Brussels, Belgium.,Artificial Intelligence lab, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Sofia Papadimitriou
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Machine Learning Group, Université Libre de Bruxelles, 1050 Brussels, Belgium.,Artificial Intelligence lab, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Nassim Versbraegen
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Machine Learning Group, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Charlotte Nachtegael
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Machine Learning Group, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - Simon Boutry
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Laboratory of Human Molecular Genetics, de Duve Institute, UCLouvain, 1200 Brussels, Belgium
| | - Ann Nowé
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Artificial Intelligence lab, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Guillaume Smits
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Hôpital Universitaire des Enfants Reine Fabiola, 1020 Brussels, Belgium.,Center of Human Genetics, Hôpital Erasme, 1070 Brussels, Belgium
| | - Tom Lenaerts
- Interuniversity Institute of Bioinformatics in Brussels, Université Libre de Bruxelles-Vrije Universiteit Brussel, 1050 Brussels, Belgium.,Machine Learning Group, Université Libre de Bruxelles, 1050 Brussels, Belgium.,Artificial Intelligence lab, Vrije Universiteit Brussel, 1050 Brussels, Belgium
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18
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Sevim Bayrak C, Itan Y. Identifying disease-causing mutations in genomes of single patients by computational approaches. Hum Genet 2020; 139:769-776. [PMID: 32405658 DOI: 10.1007/s00439-020-02179-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/05/2020] [Indexed: 12/11/2022]
Abstract
Over the last decade next generation sequencing (NGS) has been extensively used to identify new pathogenic mutations and genes causing rare genetic diseases. The efficient analyses of NGS data is not trivial and requires a technically and biologically rigorous pipeline that addresses data quality control, accurate variant filtration to minimize false positives and false negatives, and prioritization of the remaining genes based on disease genomics and physiological knowledge. This review provides a pipeline including all these steps, describes popular software for each step of the analysis, and proposes a general framework for the identification of causal mutations and genes in individual patients of rare genetic diseases.
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Affiliation(s)
- Cigdem Sevim Bayrak
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, US.
| | - Yuval Itan
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, US.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, US
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19
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Sevim Bayrak C, Zhang P, Tristani-Firouzi M, Gelb BD, Itan Y. De novo variants in exomes of congenital heart disease patients identify risk genes and pathways. Genome Med 2020; 12:9. [PMID: 31941532 PMCID: PMC6961332 DOI: 10.1186/s13073-019-0709-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 12/26/2019] [Indexed: 12/14/2022] Open
Abstract
Background Congenital heart disease (CHD) affects ~ 1% of live births and is the most common birth defect. Although the genetic contribution to the CHD has been long suspected, it has only been well established recently. De novo variants are estimated to contribute to approximately 8% of sporadic CHD. Methods CHD is genetically heterogeneous, making pathway enrichment analysis an effective approach to explore and statistically validate CHD-associated genes. In this study, we performed novel gene and pathway enrichment analyses of high-impact de novo variants in the recently published whole-exome sequencing (WES) data generated from a cohort of CHD 2645 parent-offspring trios to identify new CHD-causing candidate genes and mutations. We performed rigorous variant- and gene-level filtrations to identify potentially damaging variants, followed by enrichment analyses and gene prioritization. Results Our analyses revealed 23 novel genes that are likely to cause CHD, including HSP90AA1, ROCK2, IQGAP1, and CHD4, and sharing biological functions, pathways, molecular interactions, and properties with known CHD-causing genes. Conclusions Ultimately, these findings suggest novel genes that are likely to be contributing to CHD pathogenesis.
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Affiliation(s)
- Cigdem Sevim Bayrak
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Peng Zhang
- St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, USA
| | - Martin Tristani-Firouzi
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, UT, USA
| | - Bruce D Gelb
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yuval Itan
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA. .,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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20
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Chinn IK, Chan AY, Chen K, Chou J, Dorsey MJ, Hajjar J, Jongco AM, Keller MD, Kobrynski LJ, Kumanovics A, Lawrence MG, Leiding JW, Lugar PL, Orange JS, Patel K, Platt CD, Puck JM, Raje N, Romberg N, Slack MA, Sullivan KE, Tarrant TK, Torgerson TR, Walter JE. Diagnostic interpretation of genetic studies in patients with primary immunodeficiency diseases: A working group report of the Primary Immunodeficiency Diseases Committee of the American Academy of Allergy, Asthma & Immunology. J Allergy Clin Immunol 2019; 145:46-69. [PMID: 31568798 DOI: 10.1016/j.jaci.2019.09.009] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 09/02/2019] [Accepted: 09/20/2019] [Indexed: 12/19/2022]
Abstract
Genetic testing has become an integral component of the diagnostic evaluation of patients with suspected primary immunodeficiency diseases. Results of genetic testing can have a profound effect on clinical management decisions. Therefore clinical providers must demonstrate proficiency in interpreting genetic data. Because of the need for increased knowledge regarding this practice, the American Academy of Allergy, Asthma & Immunology Primary Immunodeficiency Diseases Committee established a work group that reviewed and summarized information concerning appropriate methods, tools, and resources for evaluating variants identified by genetic testing. Strengths and limitations of tests frequently ordered by clinicians were examined. Summary statements and tables were then developed to guide the interpretation process. Finally, the need for research and collaboration was emphasized. Greater understanding of these important concepts will improve the diagnosis and management of patients with suspected primary immunodeficiency diseases.
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Affiliation(s)
- Ivan K Chinn
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Section of Immunology, Allergy, and Rheumatology, Texas Children's Hospital, Houston, Tex.
| | - Alice Y Chan
- Department of Pediatrics, Division of Allergy, Immunology, and Bone Marrow Transplantation, University of California at San Francisco, San Francisco, Calif
| | - Karin Chen
- Division of Allergy and Immunology, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, Utah
| | - Janet Chou
- Department of Pediatrics, Harvard Medical School, Boston, Mass; Division of Allergy and Immunology, Boston Children's Hospital, Boston, Mass
| | - Morna J Dorsey
- Department of Pediatrics, Division of Allergy, Immunology, and Bone Marrow Transplantation, University of California at San Francisco, San Francisco, Calif
| | - Joud Hajjar
- Department of Pediatrics, Baylor College of Medicine, Houston, Tex; Section of Immunology, Allergy, and Rheumatology, Texas Children's Hospital, Houston, Tex
| | - Artemio M Jongco
- Departments of Medicine and Pediatrics, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Great Neck, NY; Center for Health Innovations and Outcomes Research, Feinstein Institute for Medical Research, Great Neck, NY; Division of Allergy & Immunology, Cohen Children's Medical Center of New York, Great Neck, NY
| | - Michael D Keller
- Department of Allergy and Immunology, Children's National Hospital, Washington, DC
| | - Lisa J Kobrynski
- Department of Pediatrics, Division of Allergy and Immunology, Emory University School of Medicine, Atlanta, Ga
| | - Attila Kumanovics
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minn
| | - Monica G Lawrence
- Department of Medicine, Division of Asthma, Allergy and Immunology, University of Virginia Health System, Charlottesville, Va
| | - Jennifer W Leiding
- Departments of Pediatrics and Medicine, University of South Florida, St Petersburg, Fla; Division of Pediatric Allergy/Immunology, Johns Hopkins-All Children's Hospital, St Petersburg, Fla; Cancer and Blood Disorders Institute, Johns Hopkins-All Children's Hospital, St Petersburg, Fla
| | - Patricia L Lugar
- Department of Medicine, Division of Pulmonary, Allergy, and Critical Care Medicine, Duke University Medical Center, Durham, NC
| | - Jordan S Orange
- Department of Pediatrics, Columbia University College of Physicians and Surgeons, New York, NY; New York Presbyterian Morgan Stanley Children's Hospital, New York, NY
| | - Kiran Patel
- Department of Pediatrics, Division of Allergy and Immunology, Emory University School of Medicine, Atlanta, Ga
| | - Craig D Platt
- Department of Pediatrics, Harvard Medical School, Boston, Mass; Division of Allergy and Immunology, Boston Children's Hospital, Boston, Mass
| | - Jennifer M Puck
- Department of Pediatrics, Division of Allergy, Immunology, and Bone Marrow Transplantation, University of California at San Francisco, San Francisco, Calif
| | - Nikita Raje
- Department of Pediatrics, University of Missouri-Kansas City, Kansas City, Mo; Division of Allergy/Asthma/Immunology, Children's Mercy Hospital, Kansas City, Mo
| | - Neil Romberg
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pa; Division of Allergy/Immunology, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Maria A Slack
- Department of Medicine, Division of Allergy, Immunology, and Rheumatology, University of Rochester Medical Center, Rochester, NY; Department of Pediatrics, Division of Pediatric Allergy and Immunology, University of Rochester Medical Center, Rochester, NY
| | - Kathleen E Sullivan
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pa; Division of Allergy/Immunology, Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Teresa K Tarrant
- Department of Medicine, Division of Rheumatology and Immunology, Duke University Medical Center, Durham, NC
| | - Troy R Torgerson
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Wash; Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, Wash
| | - Jolan E Walter
- Departments of Pediatrics and Medicine, University of South Florida, St Petersburg, Fla; Division of Pediatric Allergy/Immunology, Johns Hopkins-All Children's Hospital, St Petersburg, Fla; Division of Pediatric Allergy Immunology, Massachusetts General Hospital, Boston, Mass
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21
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Using game theory and decision decomposition to effectively discern and characterise bi-locus diseases. Artif Intell Med 2019; 99:101690. [PMID: 31606112 DOI: 10.1016/j.artmed.2019.06.006] [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: 09/11/2018] [Revised: 06/21/2019] [Accepted: 06/30/2019] [Indexed: 01/08/2023]
Abstract
In order to gain insight into oligogenic disorders, understanding those involving bi-locus variant combinations appears to be key. In prior work, we showed that features at multiple biological scales can already be used to discriminate among two types, i.e. disorders involving true digenic and modifier combinations. The current study expands this machine learning work towards dual molecular diagnosis cases, providing a classifier able to effectively distinguish between these three types. To reach this goal and gain an in-depth understanding of the decision process, game theory and tree decomposition techniques are applied to random forest predictors to investigate the relevance of feature combinations in the prediction. A machine learning model with high discrimination capabilities was developed, effectively differentiating the three classes in a biologically meaningful manner. Combining prediction interpretation and statistical analysis, we propose a biologically meaningful characterization of each class relying on specific feature strengths. Figuring out how biological characteristics shift samples towards one of three classes provides clinically relevant insight into the underlying biological processes as well as the disease itself.
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22
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Abstract
Directly assessing the pathogenicity of variant combinations in multiple genes was until now difficult. Nonetheless, this type of assessment can provide important benefits in identifying the genetic causes of rare diseases. The work presented in this paper aims to resolve this problem by presenting a machine-learning method able to predict the pathogenicity of variant combinations in gene pairs, based on pathogenic data. We demonstrate the high accuracy of this method and its effective capacity to identify novel instances. The method’s decision-making process is also made explicit, a contribution that is useful for clinical interpretation. This pioneering work will lead to toolboxes for geneticists and clinicians that can aid them in counselling their patients more effectively. Notwithstanding important advances in the context of single-variant pathogenicity identification, novel breakthroughs in discerning the origins of many rare diseases require methods able to identify more complex genetic models. We present here the Variant Combinations Pathogenicity Predictor (VarCoPP), a machine-learning approach that identifies pathogenic variant combinations in gene pairs (called digenic or bilocus variant combinations). We show that the results produced by this method are highly accurate and precise, an efficacy that is endorsed when validating the method on recently published independent disease-causing data. Confidence labels of 95% and 99% are identified, representing the probability of a bilocus combination being a true pathogenic result, providing geneticists with rational markers to evaluate the most relevant pathogenic combinations and limit the search space and time. Finally, the VarCoPP has been designed to act as an interpretable method that can provide explanations on why a bilocus combination is predicted as pathogenic and which biological information is important for that prediction. This work provides an important step toward the genetic understanding of rare diseases, paving the way to clinical knowledge and improved patient care.
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23
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Requena D, Maffucci P, Bigio B, Shang L, Abhyankar A, Boisson B, Stenson PD, Cooper DN, Cunningham-Rundles C, Casanova JL, Abel L, Itan Y. CDG: An Online Server for Detecting Biologically Closest Disease-Causing Genes and its Application to Primary Immunodeficiency. Front Immunol 2018; 9:1340. [PMID: 29997612 PMCID: PMC6030251 DOI: 10.3389/fimmu.2018.01340] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 05/29/2018] [Indexed: 11/17/2022] Open
Abstract
High-throughput genomic technologies yield about 20,000 variants in the protein-coding exome of each individual. A commonly used approach to select candidate disease-causing variants is to test whether the associated gene has been previously reported to be disease-causing. In the absence of known disease-causing genes, it can be challenging to associate candidate genes with specific genetic diseases. To facilitate the discovery of novel gene-disease associations, we determined the putative biologically closest known genes and their associated diseases for 13,005 human genes not currently reported to be disease-associated. We used these data to construct the closest disease-causing genes (CDG) server, which can be used to infer the closest genes with an associated disease for a user-defined list of genes or diseases. We demonstrate the utility of the CDG server in five immunodeficiency patient exomes across different diseases and modes of inheritance, where CDG dramatically reduced the number of candidate genes to be evaluated. This resource will be a considerable asset for ascertaining the potential relevance of genetic variants found in patient exomes to specific diseases of interest. The CDG database and online server are freely available to non-commercial users at: http://lab.rockefeller.edu/casanova/CDG.
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Affiliation(s)
- David Requena
- St. Giles Laboratory of Human Genetics of Infectious Diseases (Rockefeller Branch), The Rockefeller University, New York, NY, United States
| | - Patrick Maffucci
- St. Giles Laboratory of Human Genetics of Infectious Diseases (Rockefeller Branch), The Rockefeller University, New York, NY, United States.,Graduate School, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Medicine, Division of Clinical Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Benedetta Bigio
- St. Giles Laboratory of Human Genetics of Infectious Diseases (Rockefeller Branch), The Rockefeller University, New York, NY, United States
| | - Lei Shang
- St. Giles Laboratory of Human Genetics of Infectious Diseases (Rockefeller Branch), The Rockefeller University, New York, NY, United States
| | | | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases (Rockefeller Branch), The Rockefeller University, New York, NY, United States.,Laboratory of Human Genetics of Infectious Diseases (Necker Branch), INSERM U1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Peter D Stenson
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Charlotte Cunningham-Rundles
- Graduate School, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Medicine, Division of Clinical Immunology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases (Rockefeller Branch), The Rockefeller University, New York, NY, United States.,Laboratory of Human Genetics of Infectious Diseases (Necker Branch), INSERM U1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France.,Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom.,Howard Hughes Medical Institute, New York, NY, United States.,Pediatric Immunology-Hematology Unit, Necker Hospital for Sick Children, Paris, France
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases (Rockefeller Branch), The Rockefeller University, New York, NY, United States.,Laboratory of Human Genetics of Infectious Diseases (Necker Branch), INSERM U1163, Paris, France.,Paris Descartes University, Imagine Institute, Paris, France
| | - Yuval Itan
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States.,Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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24
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de Valles-Ibáñez G, Esteve-Solé A, Piquer M, González-Navarro EA, Hernandez-Rodriguez J, Laayouni H, González-Roca E, Plaza-Martin AM, Deyà-Martínez Á, Martín-Nalda A, Martínez-Gallo M, García-Prat M, Del Pino-Molina L, Cuscó I, Codina-Solà M, Batlle-Masó L, Solís-Moruno M, Marquès-Bonet T, Bosch E, López-Granados E, Aróstegui JI, Soler-Palacín P, Colobran R, Yagüe J, Alsina L, Juan M, Casals F. Evaluating the Genetics of Common Variable Immunodeficiency: Monogenetic Model and Beyond. Front Immunol 2018; 9:636. [PMID: 29867916 PMCID: PMC5960686 DOI: 10.3389/fimmu.2018.00636] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/14/2018] [Indexed: 12/16/2022] Open
Abstract
Common variable immunodeficiency (CVID) is the most frequent symptomatic primary immunodeficiency characterized by recurrent infections, hypogammaglobulinemia and poor response to vaccines. Its diagnosis is made based on clinical and immunological criteria, after exclusion of other diseases that can cause similar phenotypes. Currently, less than 20% of cases of CVID have a known underlying genetic cause. We have analyzed whole-exome sequencing and copy number variants data of 36 children and adolescents diagnosed with CVID and healthy relatives to estimate the proportion of monogenic cases. We have replicated an association of CVID to p.C104R in TNFRSF13B and reported the second case of homozygous patient to date. Our results also identify five causative genetic variants in LRBA, CTLA4, NFKB1, and PIK3R1, as well as other very likely causative variants in PRKCD, MAPK8, or DOCK8 among others. We experimentally validate the effect of the LRBA stop-gain mutation which abolishes protein production and downregulates the expression of CTLA4, and of the frameshift indel in CTLA4 producing expression downregulation of the protein. Our results indicate a monogenic origin of at least 15–24% of the CVID cases included in the study. The proportion of monogenic patients seems to be lower in CVID than in other PID that have also been analyzed by whole exome or targeted gene panels sequencing. Regardless of the exact proportion of CVID monogenic cases, other genetic models have to be considered for CVID. We propose that because of its prevalence and other features as intermediate penetrancies and phenotypic variation within families, CVID could fit with other more complex genetic scenarios. In particular, in this work, we explore the possibility of CVID being originated by an oligogenic model with the presence of heterozygous mutations in interacting proteins or by the accumulation of detrimental variants in particular immunological pathways, as well as perform association tests to detect association with rare genetic functional variation in the CVID cohort compared to healthy controls.
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Affiliation(s)
- Guillem de Valles-Ibáñez
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Ana Esteve-Solé
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain.,Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - Mònica Piquer
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain.,Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - E Azucena González-Navarro
- Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain.,Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Jessica Hernandez-Rodriguez
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Hafid Laayouni
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.,Bioinformatics Studies, ESCI-UPF, Barcelona, Spain
| | - Eva González-Roca
- Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain.,Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Ana María Plaza-Martin
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain.,Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - Ángela Deyà-Martínez
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain.,Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - Andrea Martín-Nalda
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Mónica Martínez-Gallo
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain.,Immunology Division, Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marina García-Prat
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Lucía Del Pino-Molina
- Clinical Immunology Department, University Hospital La Paz and Physiopathology of Lymphocytes in Immunodeficiencies Group, IdiPAZ Institute for Health Research, Madrid, Spain
| | - Ivón Cuscó
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBER-ER), Madrid, Spain
| | - Marta Codina-Solà
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBER-ER), Madrid, Spain
| | - Laura Batlle-Masó
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.,Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Manuel Solís-Moruno
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.,Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Tomàs Marquès-Bonet
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Elena Bosch
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Eduardo López-Granados
- Clinical Immunology Department, University Hospital La Paz and Physiopathology of Lymphocytes in Immunodeficiencies Group, IdiPAZ Institute for Health Research, Madrid, Spain
| | - Juan Ignacio Aróstegui
- Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain.,Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Pere Soler-Palacín
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Institut de Recerca (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain
| | - Roger Colobran
- Jeffrey Modell Diagnostic and Research Center for Primary Immunodeficiencies, Barcelona, Spain.,Immunology Division, Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron (HUVH), Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,Department of Cell Biology, Physiology and Immunology, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jordi Yagüe
- Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain.,Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Laia Alsina
- Allergy and Clinical Immunology Department, Hospital Sant Joan de Déu, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Barcelona, Spain.,Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain
| | - Manel Juan
- Functional Unit of Clinical Immunology Hospital Sant Joan de Déu-Hospital Clinic, Barcelona, Spain.,Servei d'Immunologia, Centre de Diagnòstic Biomèdic, Hospital Clinic-IDIBAPS, Barcelona, Spain
| | - Ferran Casals
- Servei de Genòmica, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
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25
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Whole exome sequencing in inborn errors of immunity: use the power but mind the limits. Curr Opin Allergy Clin Immunol 2017; 17:421-430. [DOI: 10.1097/aci.0000000000000398] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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26
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Xu M, Zhang D, Luo R, Wu Y, Zhou H, Kong L, Bi R, Yao Y. A systematic integrated analysis of brain expression profiles reveals
YAP1
and other prioritized hub genes as important upstream regulators in Alzheimer's disease. Alzheimers Dement 2017; 14:215-229. [DOI: 10.1016/j.jalz.2017.08.012] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 08/06/2017] [Accepted: 08/07/2017] [Indexed: 01/28/2023]
Affiliation(s)
- Min Xu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of Zoology Kunming Yunnan China
- Kunming College of Life Science University of Chinese Academy of Sciences Kunming Yunnan China
| | - Deng‐Feng Zhang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of Zoology Kunming Yunnan China
| | - Rongcan Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of Zoology Kunming Yunnan China
- Kunming College of Life Science University of Chinese Academy of Sciences Kunming Yunnan China
| | - Yong Wu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of Zoology Kunming Yunnan China
- Kunming College of Life Science University of Chinese Academy of Sciences Kunming Yunnan China
| | - Hejiang Zhou
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of Zoology Kunming Yunnan China
| | - Li‐Li Kong
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of Zoology Kunming Yunnan China
- Institute of Health Science Anhui University Hefei Anhui China
| | - Rui Bi
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of Zoology Kunming Yunnan China
| | - Yong‐Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan Province Kunming Institute of Zoology Kunming Yunnan China
- Kunming College of Life Science University of Chinese Academy of Sciences Kunming Yunnan China
- CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences Shanghai China
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27
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Mossman K, Nebesio N, Vidal SM. Discovery of Variants Underlying Host Susceptibility to Virus Infection Using Whole-Exome Sequencing. Methods Mol Biol 2017; 1656:209-227. [PMID: 28808973 PMCID: PMC7120756 DOI: 10.1007/978-1-4939-7237-1_14] [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] [Indexed: 12/02/2022]
Abstract
The clinical course of any viral infection greatly differs in individuals. This variation results from various viral, host, and environmental factors. The identification of host genetic factors influencing inter-individual variation in susceptibility to several pathogenic viruses has tremendously increased our understanding of the mechanisms and pathways required for immunity. Next-generation sequencing of whole exomes represents a powerful tool in biomedical research. In this chapter, we briefly introduce whole-exome sequencing in the context of genetic approaches to identify host susceptibility genes to viral infections. We then describe general aspects of the workflow for whole-exome sequence analysis together with the tools and online resources that can be used to identify and annotate variant calls, and then prioritize them for their potential association to phenotypes of interest.
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Affiliation(s)
- Karen Mossman
- grid.25073.330000 0004 1936 8227Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON Canada
| | - Nestor Nebesio
- Department of Human Genetics, McGill University, Montreal, QC, Canada.,McGill University Research Center on Complex Traits, Montreal, QC, Canada.,Department of Medicine, McGill University, Montreal, QC, Canada
| | - Silvia M Vidal
- Department of Human Genetics, McGill University, Montreal, QC, Canada. .,McGill University Research Center on Complex Traits, Montreal, QC, Canada. .,Department of Medicine, McGill University, Montreal, QC, Canada.
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28
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Vélez JI, Lopera F, Patel HR, Johar AS, Cai Y, Rivera D, Tobón C, Villegas A, Sepulveda-Falla D, Lehmann SG, Easteal S, Mastronardi CA, Arcos-Burgos M. Mutations modifying sporadic Alzheimer's disease age of onset. Am J Med Genet B Neuropsychiatr Genet 2016; 171:1116-1130. [PMID: 27573710 DOI: 10.1002/ajmg.b.32493] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 08/15/2016] [Indexed: 11/10/2022]
Abstract
The identification of mutations modifying the age of onset (AOO) in Alzheimer's disease (AD) is crucial for understanding the natural history of AD and, therefore, for early interventions. Patients with sporadic AD (sAD) from a genetic isolate in the extremes of the AOO distribution were whole-exome genotyped. Single- and multi-locus linear mixed-effects models were used to identify functional variants modifying AOO. A posteriori enrichment and bioinformatic analyses were applied to evaluate the non-random clustering of the associate variants to physiopathological pathways involved in AD. We identified more than 20 pathogenic, genome-wide statistically significant mutations of major modifier effect on the AOO. These variants are harbored in genes implicated in neuron apoptosis, neurogenesis, inflammatory processes linked to AD, oligodendrocyte differentiation, and memory processes. This set of new genes harboring these mutations could be of importance for prediction, follow-up and eventually as therapeutical targets of AD. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Jorge I Vélez
- Genomics and Predictive Medicine Group, Department of Genome Sciences, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia.,Neuroscience Research Group, University of Antioquia, Medellín, Colombia
| | - Francisco Lopera
- Neuroscience Research Group, University of Antioquia, Medellín, Colombia
| | - Hardip R Patel
- Genomics and Predictive Medicine Group, Department of Genome Sciences, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Angad S Johar
- Genomics and Predictive Medicine Group, Department of Genome Sciences, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Yeping Cai
- Genomics and Predictive Medicine Group, Department of Genome Sciences, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Dora Rivera
- Neuroscience Research Group, University of Antioquia, Medellín, Colombia
| | - Carlos Tobón
- Neuroscience Research Group, University of Antioquia, Medellín, Colombia
| | - Andrés Villegas
- Neuroscience Research Group, University of Antioquia, Medellín, Colombia
| | - Diego Sepulveda-Falla
- Neuroscience Research Group, University of Antioquia, Medellín, Colombia.,Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Shaun G Lehmann
- Genome Diversity and Health Group, Department of Genome Sciences, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Simon Easteal
- Genome Diversity and Health Group, Department of Genome Sciences, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Claudio A Mastronardi
- Genomics and Predictive Medicine Group, Department of Genome Sciences, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Mauricio Arcos-Burgos
- Genomics and Predictive Medicine Group, Department of Genome Sciences, John Curtin School of Medical Research, The Australian National University, Canberra, Australian Capital Territory, Australia.,Neuroscience Research Group, University of Antioquia, Medellín, Colombia
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Capturing the biology of disease severity in a PSC-based model of familial dysautonomia. Nat Med 2016; 22:1421-1427. [PMID: 27841875 DOI: 10.1038/nm.4220] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Accepted: 09/30/2016] [Indexed: 02/08/2023]
Abstract
Familial dysautonomia (FD) is a debilitating disorder that affects derivatives of the neural crest (NC). For unknown reasons, people with FD show marked differences in disease severity despite carrying an identical, homozygous point mutation in IKBKAP, encoding IκB kinase complex-associated protein. Here we present disease-related phenotypes in human pluripotent stem cells (PSCs) that capture FD severity. Cells from individuals with severe but not mild disease show impaired specification of NC derivatives, including autonomic and sensory neurons. In contrast, cells from individuals with severe and mild FD show defects in peripheral neuron survival, indicating that neurodegeneration is the main culprit for cases of mild FD. Although genetic repair of the FD-associated mutation reversed early developmental NC defects, sensory neuron specification was not restored, indicating that other factors may contribute to disease severity. Whole-exome sequencing identified candidate modifier genes for individuals with severe FD. Our study demonstrates that PSC-based modeling is sensitive in recapitulating disease severity, which presents an important step toward personalized medicine.
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Meyts I, Bosch B, Bolze A, Boisson B, Itan Y, Belkadi A, Pedergnana V, Moens L, Picard C, Cobat A, Bossuyt X, Abel L, Casanova JL. Exome and genome sequencing for inborn errors of immunity. J Allergy Clin Immunol 2016; 138:957-969. [PMID: 27720020 PMCID: PMC5074686 DOI: 10.1016/j.jaci.2016.08.003] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 08/22/2016] [Accepted: 08/23/2016] [Indexed: 01/03/2023]
Abstract
The advent of next-generation sequencing (NGS) in 2010 has transformed medicine, particularly the growing field of inborn errors of immunity. NGS has facilitated the discovery of novel disease-causing genes and the genetic diagnosis of patients with monogenic inborn errors of immunity. Whole-exome sequencing (WES) is presently the most cost-effective approach for research and diagnostics, although whole-genome sequencing offers several advantages. The scientific or diagnostic challenge consists in selecting 1 or 2 candidate variants among thousands of NGS calls. Variant- and gene-level computational methods, as well as immunologic hypotheses, can help narrow down this genome-wide search. The key to success is a well-informed genetic hypothesis on 3 key aspects: mode of inheritance, clinical penetrance, and genetic heterogeneity of the condition. This determines the search strategy and selection criteria for candidate alleles. Subsequent functional validation of the disease-causing effect of the candidate variant is critical. Even the most up-to-date dry lab cannot clinch this validation without a seasoned wet lab. The multifariousness of variations entails an experimental rigor even greater than traditional Sanger sequencing-based approaches in order not to assign a condition to an irrelevant variant. Finding the needle in the haystack takes patience, prudence, and discernment.
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Affiliation(s)
- Isabelle Meyts
- Department of Immunology and Microbiology, Childhood Immunology, Department of Pediatrics, University Hospitals Leuven and KU Leuven, Leuven, Belgium.
| | - Barbara Bosch
- Department of Pediatrics, University Hospitals Leuven and KU Leuven, Leuven, Belgium; St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Alexandre Bolze
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Helix, San Carlos, Calif
| | - Bertrand Boisson
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Yuval Itan
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY
| | - Aziz Belkadi
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Vincent Pedergnana
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Leen Moens
- Laboratory Medicine, Experimental Laboratory Immunology, Department of Laboratory Medicine, University Hospitals Leuven and KU Leuven, Leuven, Belgium
| | - Capucine Picard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France; Paris Descartes University-Sorbonne Paris Cité, Paris, France; Study Center for Immunodeficiency, Necker-Enfants Malades Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
| | - Aurélie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Xavier Bossuyt
- Laboratory Medicine, Experimental Laboratory Immunology, Department of Laboratory Medicine, University Hospitals Leuven and KU Leuven, Leuven, Belgium
| | - Laurent Abel
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
| | - Jean-Laurent Casanova
- St Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, Rockefeller University, New York, NY; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France; Paris Descartes University, Imagine Institute, Paris, France; Howard Hughes Medical Institute, New York, NY; Pediatric Hematology and Immunology Unit, Assistance Publique-Hôpitaux de Paris, Necker Hospital for Sick Children, Paris, France
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Abstract
BACKGROUND Inborn errors of interferon-gamma (IFN-γ)-mediated immunity underlie disseminated disease caused by Mycobacterium bovis Bacillus Calmette-Guérin (BCG) live vaccines. We hypothesized that some patients with osteitis after BCG vaccination may have an impaired IFN-γ immunity. Our aim was to investigate interleukin (IL)-12 and IFN-γ ex vivo production stimulated with BCG and BCG + IFN-γ or BCG + IL-12, respectively, in BCG osteitis survivors. METHODS Fresh blood samples were collected from 132 former BCG osteitis Finnish patients now aged 21-49 years, and IL-12 and IFN-γ were measured in cell cultures with and without stimulation with BCG and with BCG + IFN-γ or BCG + IL-12, respectively. As a pilot study, known disease-causing genes controlling IFN-γ immunity (IFNGR1, IFNGR2, STAT1, IL12B, IL12RB1, ISG15, IRF8, NEMO and CYBB) were investigated in 20 selected patients by whole exome sequencing. RESULTS By the limit of <5th percentile, ex vivo IL-12 concentration and increase in concentration was low in 5 and ex vivo IFN-γ concentration and increase in concentration was low in 6 patients (including 2 samples with both IL-12 and IFN-γ findings). By the limit of <10th percentile, an additional 6 and 4 patients were, respectively, detected (including 2 samples with both findings). With 2 exceptions, low concentrations and low increases in concentrations picked-up the same cases. Mutations in known disease-causing IFN-γ-related genes were not found in any of these patients. CONCLUSION These findings call for searching of mutations in new genes governing IFN-γ-dependent immunity to live BCG vaccine.
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Itan Y. Evolutionary Genomics. Evol Bioinform Online 2016; 11:53-5. [PMID: 27127402 PMCID: PMC4841156 DOI: 10.4137/ebo.s39729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
This supplement is intended to focus on evolutionary genomics. Evolutionary Bioinformatics aims to provide researchers working in this complex, quickly developing field with online, open access to highly relevant scholarly articles by leading international researchers. In a field where the literature is ever-expanding, researchers increasingly need access to up-to-date, high quality scholarly articles on areas of specific contemporary interest. This supplement aims to address this by presenting high-quality articles that allow readers to distinguish the signal from the noise. The editor in chief hopes that through this effort, practitioners and researchers will be aided in finding answers to some of the most complex and pressing issues of our time.
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Affiliation(s)
- Yuval Itan
- Human Genetics of Infectious Diseases, The Rockefeller University, New York, NY, USA
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The human gene damage index as a gene-level approach to prioritizing exome variants. Proc Natl Acad Sci U S A 2015; 112:13615-20. [PMID: 26483451 DOI: 10.1073/pnas.1518646112] [Citation(s) in RCA: 172] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The protein-coding exome of a patient with a monogenic disease contains about 20,000 variants, only one or two of which are disease causing. We found that 58% of rare variants in the protein-coding exome of the general population are located in only 2% of the genes. Prompted by this observation, we aimed to develop a gene-level approach for predicting whether a given human protein-coding gene is likely to harbor disease-causing mutations. To this end, we derived the gene damage index (GDI): a genome-wide, gene-level metric of the mutational damage that has accumulated in the general population. We found that the GDI was correlated with selective evolutionary pressure, protein complexity, coding sequence length, and the number of paralogs. We compared GDI with the leading gene-level approaches, genic intolerance, and de novo excess, and demonstrated that GDI performed best for the detection of false positives (i.e., removing exome variants in genes irrelevant to disease), whereas genic intolerance and de novo excess performed better for the detection of true positives (i.e., assessing de novo mutations in genes likely to be disease causing). The GDI server, data, and software are freely available to noncommercial users from lab.rockefeller.edu/casanova/GDI.
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Kreins AY, Ciancanelli MJ, Okada S, Kong XF, Ramírez-Alejo N, Kilic SS, El Baghdadi J, Nonoyama S, Mahdaviani SA, Ailal F, Bousfiha A, Mansouri D, Nievas E, Ma CS, Rao G, Bernasconi A, Sun Kuehn H, Niemela J, Stoddard J, Deveau P, Cobat A, El Azbaoui S, Sabri A, Lim CK, Sundin M, Avery DT, Halwani R, Grant AV, Boisson B, Bogunovic D, Itan Y, Moncada-Velez M, Martinez-Barricarte R, Migaud M, Deswarte C, Alsina L, Kotlarz D, Klein C, Muller-Fleckenstein I, Fleckenstein B, Cormier-Daire V, Rose-John S, Picard C, Hammarstrom L, Puel A, Al-Muhsen S, Abel L, Chaussabel D, Rosenzweig SD, Minegishi Y, Tangye SG, Bustamante J, Casanova JL, Boisson-Dupuis S. Human TYK2 deficiency: Mycobacterial and viral infections without hyper-IgE syndrome. ACTA ACUST UNITED AC 2015; 212:1641-62. [PMID: 26304966 PMCID: PMC4577846 DOI: 10.1084/jem.20140280] [Citation(s) in RCA: 255] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 08/04/2015] [Indexed: 12/30/2022]
Abstract
Kreins et al. report the identification and immunological characterization of a group of TYK2-deficient patients. Autosomal recessive, complete TYK2 deficiency was previously described in a patient (P1) with intracellular bacterial and viral infections and features of hyper-IgE syndrome (HIES), including atopic dermatitis, high serum IgE levels, and staphylococcal abscesses. We identified seven other TYK2-deficient patients from five families and four different ethnic groups. These patients were homozygous for one of five null mutations, different from that seen in P1. They displayed mycobacterial and/or viral infections, but no HIES. All eight TYK2-deficient patients displayed impaired but not abolished cellular responses to (a) IL-12 and IFN-α/β, accounting for mycobacterial and viral infections, respectively; (b) IL-23, with normal proportions of circulating IL-17+ T cells, accounting for their apparent lack of mucocutaneous candidiasis; and (c) IL-10, with no overt clinical consequences, including a lack of inflammatory bowel disease. Cellular responses to IL-21, IL-27, IFN-γ, IL-28/29 (IFN-λ), and leukemia inhibitory factor (LIF) were normal. The leukocytes and fibroblasts of all seven newly identified TYK2-deficient patients, unlike those of P1, responded normally to IL-6, possibly accounting for the lack of HIES in these patients. The expression of exogenous wild-type TYK2 or the silencing of endogenous TYK2 did not rescue IL-6 hyporesponsiveness, suggesting that this phenotype was not a consequence of the TYK2 genotype. The core clinical phenotype of TYK2 deficiency is mycobacterial and/or viral infections, caused by impaired responses to IL-12 and IFN-α/β. Moreover, impaired IL-6 responses and HIES do not appear to be intrinsic features of TYK2 deficiency in humans.
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Affiliation(s)
- Alexandra Y Kreins
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065 Weill Cornell Graduate School of Medical Sciences, New York, NY 10065
| | - Michael J Ciancanelli
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
| | - Satoshi Okada
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
| | - Xiao-Fei Kong
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
| | - Noé Ramírez-Alejo
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
| | - Sara Sebnem Kilic
- Department of Pediatric Immunology, Uludağ University Faculty of Medicine, 16059 Görükle, Bursa, Turkey
| | - Jamila El Baghdadi
- Genetics Unit, Military Hospital Mohamed V, Hay Riad, 10100 Rabat, Morocco
| | - Shigeaki Nonoyama
- Department of Pediatrics, National Defense Medical College, Tokorozawa, Saitama 359-0042, Japan
| | - Seyed Alireza Mahdaviani
- Pediatric Respiratory Diseases Research Center; and Department of Clinical Immunology and Infectious Diseases, Masih Daneshvari Hospital; National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, 141556153 Tehran, Iran
| | - Fatima Ailal
- Clinical Immunology Unit, Department of Pediatrics, King Hassan II University, CHU Ibn Rochd, 20000 Casablanca, Morocco
| | - Aziz Bousfiha
- Clinical Immunology Unit, Department of Pediatrics, King Hassan II University, CHU Ibn Rochd, 20000 Casablanca, Morocco
| | - Davood Mansouri
- Pediatric Respiratory Diseases Research Center; and Department of Clinical Immunology and Infectious Diseases, Masih Daneshvari Hospital; National Research Institute of Tuberculosis and Lung Diseases, Shahid Beheshti University of Medical Sciences, 141556153 Tehran, Iran
| | - Elma Nievas
- Immunology Unit, Pediatric Hospital A. Fleming-OSEP, Mendoza 5500, Argentina
| | - Cindy S Ma
- Immunology Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia St. Vincent's Clinical School, University of New South Wales, Darlinghurst, New South Wales 2010, Australia
| | - Geetha Rao
- Immunology Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Andrea Bernasconi
- Immunology and Rheumatology Service, Garrahan Hospital, Buenos Aires 1408, Argentina
| | - Hye Sun Kuehn
- Department of Laboratory Medicine, Clinical Center; and Primary Immunodeficiency Clinic, National Institute of Allergy and Infectious Diseases; National Institutes of Health, Bethesda, MD 20892
| | - Julie Niemela
- Department of Laboratory Medicine, Clinical Center; and Primary Immunodeficiency Clinic, National Institute of Allergy and Infectious Diseases; National Institutes of Health, Bethesda, MD 20892
| | - Jennifer Stoddard
- Department of Laboratory Medicine, Clinical Center; and Primary Immunodeficiency Clinic, National Institute of Allergy and Infectious Diseases; National Institutes of Health, Bethesda, MD 20892
| | - Paul Deveau
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Enfants Malades Hospital, 75015 Paris, France University Paris Descartes, Imagine Institute, 75006 Paris, France
| | - Aurelie Cobat
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Enfants Malades Hospital, 75015 Paris, France University Paris Descartes, Imagine Institute, 75006 Paris, France
| | - Safa El Azbaoui
- Genetics Unit, Military Hospital Mohamed V, Hay Riad, 10100 Rabat, Morocco Faculty of Science-Kenitra, Ibn Tofaïl University, 14000 Kenitra, Morocco
| | - Ayoub Sabri
- Genetics Unit, Military Hospital Mohamed V, Hay Riad, 10100 Rabat, Morocco Faculty of Science-Kenitra, Ibn Tofaïl University, 14000 Kenitra, Morocco
| | - Che Kang Lim
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, 141 52 Stockholm, Sweden Department of Clinical Research, Singapore General Hospital, Singapore 169856
| | - Mikael Sundin
- Pediatric Hematology/Immunology, Astrid Lindgrens Children's Hospital and Karolinska Institutet, 141 86 Stockholm, Sweden
| | - Danielle T Avery
- Immunology Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia
| | - Rabih Halwani
- Asthma Research Chair and Prince Naif Center for Immunology Research, Department of Pediatrics, College of Medicine, King Saud University, Riyadh 12372, Saudi Arabia
| | - Audrey V Grant
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Enfants Malades Hospital, 75015 Paris, France University Paris Descartes, Imagine Institute, 75006 Paris, France
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
| | - Dusan Bogunovic
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
| | - Yuval Itan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
| | - Marcela Moncada-Velez
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065 Group of Primary Immunodeficiencies, Institute of Biology, University of Antioquia UdeA, 1226 Medellín, Colombia
| | - Ruben Martinez-Barricarte
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
| | - Melanie Migaud
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Enfants Malades Hospital, 75015 Paris, France University Paris Descartes, Imagine Institute, 75006 Paris, France
| | - Caroline Deswarte
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Enfants Malades Hospital, 75015 Paris, France University Paris Descartes, Imagine Institute, 75006 Paris, France
| | - Laia Alsina
- Baylor Institute for Immunology Research and Baylor Research Institute, Dallas, TX 75204 Baylor Institute for Immunology Research and Baylor Research Institute, Dallas, TX 75204 Allergy and Clinical Immunology Department, Hospital Sant Joan de Deu, Barcelona University, 08950 Barcelona, Spain
| | - Daniel Kotlarz
- Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig Maximilians University, D-80337 Munich, Germany
| | - Christoph Klein
- Department of Pediatrics, Dr. von Hauner Children's Hospital, Ludwig Maximilians University, D-80337 Munich, Germany
| | - Ingrid Muller-Fleckenstein
- Institute of Clinical and Molecular Virology, University of Erlangen-Nuremberg, D-91054 Erlangen, Germany
| | - Bernhard Fleckenstein
- Institute of Clinical and Molecular Virology, University of Erlangen-Nuremberg, D-91054 Erlangen, Germany
| | - Valerie Cormier-Daire
- Department of Genetics, INSERM U1163, University Paris Descartes-Sorbonne Paris Cite, Imagine Institute, Necker Enfants Malades Hospital, 75015 Paris, France
| | - Stefan Rose-John
- Institute of Biochemistry, University of Kiel, D-24098 Kiel, Germany
| | - Capucine Picard
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065 Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Enfants Malades Hospital, 75015 Paris, France University Paris Descartes, Imagine Institute, 75006 Paris, France Center for the Study of Primary Immunodeficiencies, Assistance Publique-Hôpitaux de Paris, Necker Enfants Malades Hospital, 75015 Paris, France
| | - Lennart Hammarstrom
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, 141 52 Stockholm, Sweden
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Enfants Malades Hospital, 75015 Paris, France University Paris Descartes, Imagine Institute, 75006 Paris, France
| | - Saleh Al-Muhsen
- Asthma Research Chair and Prince Naif Center for Immunology Research, Department of Pediatrics, College of Medicine, King Saud University, Riyadh 12372, Saudi Arabia
| | - Laurent Abel
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065 Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Enfants Malades Hospital, 75015 Paris, France University Paris Descartes, Imagine Institute, 75006 Paris, France
| | - Damien Chaussabel
- Systems Biology Department, Sidra Medical and Research Center, Doha, Qatar
| | - Sergio D Rosenzweig
- Department of Laboratory Medicine, Clinical Center; and Primary Immunodeficiency Clinic, National Institute of Allergy and Infectious Diseases; National Institutes of Health, Bethesda, MD 20892 Department of Laboratory Medicine, Clinical Center; and Primary Immunodeficiency Clinic, National Institute of Allergy and Infectious Diseases; National Institutes of Health, Bethesda, MD 20892
| | - Yoshiyuki Minegishi
- Department of Immune Regulation, Graduate School, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Stuart G Tangye
- Immunology Program, Garvan Institute of Medical Research, Darlinghurst, New South Wales 2010, Australia St. Vincent's Clinical School, University of New South Wales, Darlinghurst, New South Wales 2010, Australia
| | - Jacinta Bustamante
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Enfants Malades Hospital, 75015 Paris, France University Paris Descartes, Imagine Institute, 75006 Paris, France Center for the Study of Primary Immunodeficiencies, Assistance Publique-Hôpitaux de Paris, Necker Enfants Malades Hospital, 75015 Paris, France
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065 Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Enfants Malades Hospital, 75015 Paris, France University Paris Descartes, Imagine Institute, 75006 Paris, France Pediatric Immunology and Hematology Unit, Necker Enfants Malades Hospital, 75015 Paris, France Howard Hughes Medical Institute, New York, NY 10065
| | - Stéphanie Boisson-Dupuis
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065 Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Enfants Malades Hospital, 75015 Paris, France University Paris Descartes, Imagine Institute, 75006 Paris, France
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Johar AS, Mastronardi C, Rojas-Villarraga A, Patel HR, Chuah A, Peng K, Higgins A, Milburn P, Palmer S, Silva-Lara MF, Velez JI, Andrews D, Field M, Huttley G, Goodnow C, Anaya JM, Arcos-Burgos M. Novel and rare functional genomic variants in multiple autoimmune syndrome and Sjögren's syndrome. J Transl Med 2015; 13:173. [PMID: 26031516 PMCID: PMC4450850 DOI: 10.1186/s12967-015-0525-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/08/2015] [Indexed: 12/16/2022] Open
Abstract
Background Multiple autoimmune syndrome (MAS), an extreme phenotype of autoimmune disorders, is a very well suited trait to tackle genomic variants of these conditions. Whole exome sequencing (WES) is a widely used strategy for detection of protein coding and splicing variants associated with inherited diseases. Methods The DNA of eight patients affected by MAS [all of whom presenting with Sjögren’s syndrome (SS)], four patients affected by SS alone and 38 unaffected individuals, were subject to WES. Filters to identify novel and rare functional (pathogenic–deleterious) homozygous and/or compound heterozygous variants in these patients and controls were applied. Bioinformatics tools such as the Human gene connectome as well as pathway and network analysis were applied to test overrepresentation of genes harbouring these variants in critical pathways and networks involved in autoimmunity. Results Eleven novel and rare functional variants were identified in cases but not in controls, harboured in: MACF1, KIAA0754, DUSP12, ICA1, CELA1, LRP1/STAT6, GRIN3B, ANKLE1, TMEM161A, and FKRP. These were subsequently subject to network analysis and their functional relatedness to genes already associated with autoimmunity was evaluated. Notably, the LRP1/STAT6 novel mutation was homozygous in one MAS affected patient and heterozygous in another. LRP1/STAT6 disclosed the strongest plausibility for autoimmunity. LRP1/STAT6 are involved in extracellular and intracellular anti-inflammatory pathways that play key roles in maintaining the homeostasis of the immune system. Further; networks, pathways, and interaction analyses showed that LRP1 is functionally related to the HLA-B and IL10 genes and it has a substantial impact within immunological pathways and/or reaction to bacterial and other foreign proteins (phagocytosis, regulation of phospholipase A2 activity, negative regulation of apoptosis and response to lipopolysaccharides). Further, ICA1 and STAT6 were also closely related to AIRE and IRF5, two very well known autoimmunity genes. Conclusions Novel and rare exonic mutations that may account for autoimmunity were identified. Among those, the LRP1/STAT6 novel mutation has the strongest case for being categorised as potentially causative of MAS given the presence of intriguing patterns of functional interaction with other major genes shaping autoimmunity. Electronic supplementary material The online version of this article (doi:10.1186/s12967-015-0525-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Angad S Johar
- Genomics and Predictive Medicine, Genome Biology Department, John Curtin School of Medical Research, ANU College of Medicine, Biology and Environment, The Australian National University, Canberra, ACT, Australia.
| | - Claudio Mastronardi
- Genomics and Predictive Medicine, Genome Biology Department, John Curtin School of Medical Research, ANU College of Medicine, Biology and Environment, The Australian National University, Canberra, ACT, Australia.
| | - Adriana Rojas-Villarraga
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia.
| | - Hardip R Patel
- Genome Discovery Unit, Genome Biology Department, John Curtin School of Medical Research, ANU College of Medicine, Biology and Environment, The Australian National University, Canberra, ACT, Australia.
| | - Aaron Chuah
- Genome Discovery Unit, Genome Biology Department, John Curtin School of Medical Research, ANU College of Medicine, Biology and Environment, The Australian National University, Canberra, ACT, Australia.
| | - Kaiman Peng
- Biomolecular Resource Facility, John Curtin School of Medical Research, ANU College of Medicine, Biology and Environment, The Australian National University, Canberra, ACT, Australia.
| | - Angela Higgins
- Biomolecular Resource Facility, John Curtin School of Medical Research, ANU College of Medicine, Biology and Environment, The Australian National University, Canberra, ACT, Australia.
| | - Peter Milburn
- Biomolecular Resource Facility, John Curtin School of Medical Research, ANU College of Medicine, Biology and Environment, The Australian National University, Canberra, ACT, Australia.
| | - Stephanie Palmer
- Biomolecular Resource Facility, John Curtin School of Medical Research, ANU College of Medicine, Biology and Environment, The Australian National University, Canberra, ACT, Australia.
| | - Maria Fernanda Silva-Lara
- Genomics and Predictive Medicine, Genome Biology Department, John Curtin School of Medical Research, ANU College of Medicine, Biology and Environment, The Australian National University, Canberra, ACT, Australia.
| | - Jorge I Velez
- Genomics and Predictive Medicine, Genome Biology Department, John Curtin School of Medical Research, ANU College of Medicine, Biology and Environment, The Australian National University, Canberra, ACT, Australia.
| | - Dan Andrews
- Immunogenomics and Bioinformatics Group, Immunology Department, John Curtin School of Medical Research, ANU College of Medicine, Biology and Environment, The Australian National University, Canberra, ACT, Australia.
| | - Matthew Field
- Immunogenomics and Bioinformatics Group, Immunology Department, John Curtin School of Medical Research, ANU College of Medicine, Biology and Environment, The Australian National University, Canberra, ACT, Australia.
| | - Gavin Huttley
- Biomolecular Resource Facility, John Curtin School of Medical Research, ANU College of Medicine, Biology and Environment, The Australian National University, Canberra, ACT, Australia.
| | - Chris Goodnow
- Immunogenomics and Bioinformatics Group, Immunology Department, John Curtin School of Medical Research, ANU College of Medicine, Biology and Environment, The Australian National University, Canberra, ACT, Australia.
| | - Juan-Manuel Anaya
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogota, Colombia.
| | - Mauricio Arcos-Burgos
- Genomics and Predictive Medicine, Genome Biology Department, John Curtin School of Medical Research, ANU College of Medicine, Biology and Environment, The Australian National University, Canberra, ACT, Australia.
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Ling Y, Cypowyj S, Aytekin C, Galicchio M, Camcioglu Y, Nepesov S, Ikinciogullari A, Dogu F, Belkadi A, Levy R, Migaud M, Boisson B, Bolze A, Itan Y, Goudin N, Cottineau J, Picard C, Abel L, Bustamante J, Casanova JL, Puel A. Inherited IL-17RC deficiency in patients with chronic mucocutaneous candidiasis. ACTA ACUST UNITED AC 2015; 212:619-31. [PMID: 25918342 PMCID: PMC4419340 DOI: 10.1084/jem.20141065] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 04/08/2015] [Indexed: 11/26/2022]
Abstract
Autosomal-recessive IL-17RA, IL-17RC, and ACT1 deficiencies and autosomal-dominant IL-17F deficiency in humans underlie susceptibility to chronic mucocutaneous candidiasis. Chronic mucocutaneous candidiasis (CMC) is characterized by recurrent or persistent infections of the skin, nail, oral, and genital mucosae with Candida species, mainly C. albicans. Autosomal-recessive (AR) IL-17RA and ACT1 deficiencies and autosomal-dominant IL-17F deficiency, each reported in a single kindred, underlie CMC in otherwise healthy patients. We report three patients from unrelated kindreds, aged 8, 12, and 37 yr with isolated CMC, who display AR IL-17RC deficiency. The patients are homozygous for different nonsense alleles that prevent the expression of IL-17RC on the cell surface. The defect is complete, abolishing cellular responses to IL-17A and IL-17F homo- and heterodimers. However, in contrast to what is observed for the IL-17RA– and ACT1-deficient patients tested, the response to IL-17E (IL-25) is maintained in these IL-17RC–deficient patients. These experiments of nature indicate that human IL-17RC is essential for mucocutaneous immunity to C. albicans but is otherwise largely redundant.
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Affiliation(s)
- Yun Ling
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, French Institute of Health and Medical Research (INSERM) U1163, 75015 Paris, France Imagine Institute, Paris Descartes University, 75015 Paris, France
| | - Sophie Cypowyj
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
| | - Caner Aytekin
- Department of Pediatric Immunology, Dr. Sami Ulus Maternity and Children's Health and Diseases Training and Research Hospital, 06080 Ankara, Turkey
| | - Miguel Galicchio
- Victor J. Vilela Children's Hospital, Rosario, 2000 Santa Fe, Argentina
| | - Yildiz Camcioglu
- Division of Infectious Diseases, Clinical Immunology, and Allergy, Department of Pediatrics, Cerrahpaşa Medical Faculty, Istanbul University, 34452 Istanbul, Turkey
| | - Serdar Nepesov
- Division of Infectious Diseases, Clinical Immunology, and Allergy, Department of Pediatrics, Cerrahpaşa Medical Faculty, Istanbul University, 34452 Istanbul, Turkey
| | - Aydan Ikinciogullari
- Department of Pediatric Immunology and Allergy, Ankara University School of Medicine, 06100 Ankara, Turkey
| | - Figen Dogu
- Department of Pediatric Immunology and Allergy, Ankara University School of Medicine, 06100 Ankara, Turkey
| | - Aziz Belkadi
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, French Institute of Health and Medical Research (INSERM) U1163, 75015 Paris, France Imagine Institute, Paris Descartes University, 75015 Paris, France
| | - Romain Levy
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, French Institute of Health and Medical Research (INSERM) U1163, 75015 Paris, France Imagine Institute, Paris Descartes University, 75015 Paris, France
| | - Mélanie Migaud
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, French Institute of Health and Medical Research (INSERM) U1163, 75015 Paris, France Imagine Institute, Paris Descartes University, 75015 Paris, France
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
| | - Alexandre Bolze
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
| | - Yuval Itan
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
| | - Nicolas Goudin
- Imagine Institute, Paris Descartes University, 75015 Paris, France UMS24, Cell Imaging Platform, Federative Structure of Research (SFR), Pediatric Hematology-Immunology Unit, and Center for the Study of Primary Immunodeficiencies, Necker Hospital for Sick Children, 75015 Paris, France
| | - Julien Cottineau
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, French Institute of Health and Medical Research (INSERM) U1163, 75015 Paris, France Imagine Institute, Paris Descartes University, 75015 Paris, France
| | - Capucine Picard
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, French Institute of Health and Medical Research (INSERM) U1163, 75015 Paris, France Imagine Institute, Paris Descartes University, 75015 Paris, France St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065 UMS24, Cell Imaging Platform, Federative Structure of Research (SFR), Pediatric Hematology-Immunology Unit, and Center for the Study of Primary Immunodeficiencies, Necker Hospital for Sick Children, 75015 Paris, France
| | - Laurent Abel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, French Institute of Health and Medical Research (INSERM) U1163, 75015 Paris, France Imagine Institute, Paris Descartes University, 75015 Paris, France St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
| | - Jacinta Bustamante
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, French Institute of Health and Medical Research (INSERM) U1163, 75015 Paris, France Imagine Institute, Paris Descartes University, 75015 Paris, France St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065 UMS24, Cell Imaging Platform, Federative Structure of Research (SFR), Pediatric Hematology-Immunology Unit, and Center for the Study of Primary Immunodeficiencies, Necker Hospital for Sick Children, 75015 Paris, France
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, French Institute of Health and Medical Research (INSERM) U1163, 75015 Paris, France Imagine Institute, Paris Descartes University, 75015 Paris, France St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065 UMS24, Cell Imaging Platform, Federative Structure of Research (SFR), Pediatric Hematology-Immunology Unit, and Center for the Study of Primary Immunodeficiencies, Necker Hospital for Sick Children, 75015 Paris, France Howard Hughes Medical Institute, New York, NY 10065
| | - Anne Puel
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, French Institute of Health and Medical Research (INSERM) U1163, 75015 Paris, France Imagine Institute, Paris Descartes University, 75015 Paris, France St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065
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37
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Itan Y, Casanova JL. Novel primary immunodeficiency candidate genes predicted by the human gene connectome. Front Immunol 2015; 6:142. [PMID: 25883595 PMCID: PMC4381650 DOI: 10.3389/fimmu.2015.00142] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/15/2015] [Indexed: 01/06/2023] Open
Abstract
Germline genetic mutations underlie various primary immunodeficiency (PID) diseases. Patients with rare PID diseases (like most non-PID patients and healthy individuals) carry, on average, 20,000 rare and common coding variants detected by high-throughput sequencing. It is thus a major challenge to select only a few candidate disease-causing variants for experimental testing. One of the tools commonly used in the pipeline for estimating a potential PID-candidate gene is to test whether the specific gene is included in the list of genes that were already experimentally validated as PID-causing in previous studies. However, this approach is limited because it cannot detect the PID-causing mutation(s) in the many PID patients carrying causal mutations of as yet unidentified PID-causing genes. In this study, we expanded in silico the list of potential PID-causing candidate genes from 229 to 3,110. We first identified the top 1% of human genes predicted by the human genes connectome to be biologically close to the 229 known PID genes. We then further narrowed down the list of genes by retaining only the most biologically relevant genes, with functionally enriched gene ontology biological categories similar to those for the known PID genes. We validated this prediction by showing that 17 of the 21 novel PID genes published since the last IUIS classification fall into this group of 3,110 genes (p < 10−7). The resulting new extended list of 3,110 predicted PID genes should be useful for the discovery of novel PID genes in patients.
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Affiliation(s)
- Yuval Itan
- Rockefeller Branch, St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University , New York, NY , USA
| | - Jean-Laurent Casanova
- Rockefeller Branch, St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller University , New York, NY , USA ; Necker Branch, Laboratory of Human Genetics of Infectious Diseases, INSERM U1163 , Paris , France ; Imagine Institute, University Paris Descartes , Paris , France ; Howard Hughes Medical Institute , New York, NY , USA ; Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children , Paris , France
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