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Freigeh GE, Michniacki TF. NF-κB and Related Autoimmune and Autoinflammatory Diseases. Rheum Dis Clin North Am 2023; 49:805-823. [PMID: 37821197 DOI: 10.1016/j.rdc.2023.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
The NF-κB pathway is a cardinal signaling pathway that has been implicated in the development of a diverse range of clinical diseases. Numerous cellular processes converge on this pathway, which results in cell proliferation and survival. Defects in this pathway and in its upstream regulators have been described as causing immunodeficiency. However, there is a growing body of literature connecting autoimmune and autoinflammatory conditions to NF-κB pathway dysfunction. This review serves as a current appraisal of the literature of these disorders.
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Affiliation(s)
- George E Freigeh
- Division of Allergy and Clinical Immunology, Department of Internal Medicine, University of Michigan, Lobby H Suite 2100, 24 Frank Lloyd Wright Drive, Ann Arbor, MI 48105, USA.
| | - Thomas F Michniacki
- Division of Hematology and Oncology, Department of Pediatrics, University of Michigan, 1522 Simpson Road East, Ann Arbor, MI 48109, USA
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2
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Dixon CL, Wu A, Fairn GD. Multifaceted roles and regulation of nucleotide-binding oligomerization domain containing proteins. Front Immunol 2023; 14:1242659. [PMID: 37869013 PMCID: PMC10585062 DOI: 10.3389/fimmu.2023.1242659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/19/2023] [Indexed: 10/24/2023] Open
Abstract
Nucleotide-binding oligomerization domain-containing proteins, NOD1 and NOD2, are cytosolic receptors that recognize dipeptides and tripeptides derived from the bacterial cell wall component peptidoglycan (PGN). During the past two decades, studies have revealed several roles for NODs beyond detecting PGN fragments, including activation of an innate immune anti-viral response, NOD-mediated autophagy, and ER stress induced inflammation. Recent studies have also clarified the dynamic regulation of NODs at cellular membranes to generate specific and balanced immune responses. This review will describe how NOD1 and NOD2 detect microbes and cellular stress and detail the molecular mechanisms that regulate activation and signaling while highlighting new evidence and the impact on inflammatory disease pathogenesis.
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Affiliation(s)
| | - Amy Wu
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Gregory D. Fairn
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada
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3
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Nasser KK, Shinawi T. Genotype-protein phenotype characterization of NOD2 and IL23R missense variants associated with inflammatory bowel disease: A paradigm from molecular modelling, dynamics, and docking simulations. Front Med (Lausanne) 2023; 9:1090120. [PMID: 36703890 PMCID: PMC9871552 DOI: 10.3389/fmed.2022.1090120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/21/2022] [Indexed: 01/12/2023] Open
Abstract
Inflammatory bowel disease (IBD) is a gastrointestinal disease with an underlying contribution of genetic, microbial, environment, immunity factors. The coding region risk markers identified by IBD genome wide association studies have not been well characterized at protein phenotype level. Therefore, this study is conducted to characterize the role of NOD2 (Arg675Trp and Gly908Arg) and IL23R (Gly149Arg and Arg381Gln) missense variants on the structural and functional features of corresponding proteins. Thus, we used different variant pathogenicity assays, molecular modelling, secondary structure, stability, molecular dynamics, and molecular docking analysis methods. Our findings suggest that SIFT, Polyphen, GREP++, PhyloP, SiPhy and REVEL methods are very sensitive in determining pathogenicity of NOD2 and IL23R missense variants. We have also noticed that all the tested missense variants could potentially alter secondary (α-helices, β-strands, and coils) and tertiary (residue level deviations) structural features. Moreover, our molecular dynamics (MD) simulation findings have simulated that NOD2 (Arg675Trp and Gly908Arg) and IL23R (Gly149Arg and Arg381Gln) variants creates rigid local structures comprising the protein flexibility and conformations. These predictions are corroborated by molecular docking results, where we noticed that NOD2 and IL23R missense variants induce molecular interaction deformities with RIPK2 and JAK2 ligand molecules, respectively. These functional alterations could potentially alter the signal transduction pathway cascade involved in inflammation and autoimmunity. Drug library searches and findings from docking studies have identified the inhibitory effects of Tacrolimus and Celecoxib drugs on NOD2 and IL23R variant forms, underlining their potential to contribute to personalized medicine for IBD. The present study supports the utilization of computational methods as primary filters (pre-in vitro and in vivo) in studying the disease potential mutations in the context of genptype-protein phenotype characteristics.
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Affiliation(s)
- Khalidah Khalid Nasser
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia,Princess Al-Jawhara Al-Brahim Center of Excellence in Research of Hereditary Disorders, King Abdulaziz University, Jeddah, Saudi Arabia,Centre for Artificial Intelligence in Precision Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Thoraia Shinawi
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia,*Correspondence: Thoraia Shinawi,
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4
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Ashton JJ, Seaby EG, Beattie RM, Ennis S. NOD2 in Crohn's disease- unfinished business. J Crohns Colitis 2022; 17:450-458. [PMID: 36006803 PMCID: PMC10069614 DOI: 10.1093/ecco-jcc/jjac124] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Indexed: 01/01/2023]
Abstract
Studies of Crohn's disease consistently implicate NOD2 as the most important gene in disease pathogenesis since first being identified in 2001. Since this point, genome-wide association, next-generation sequencing, and functional analyses have all confirmed a key role for NOD2, but despite this, NOD2 also has significant unresolved complexity. More recent studies have reinvigorated an early hypothesis that NOD2 may be a single-gene cause of disease, and the distinct ileal stricturing phenotype seen with NOD2-related disease presents an opportunity for personalised diagnosis, disease prediction and targeted therapy. The genomics of NOD2 has much that remains unknown, including the role of rare variation, phasing of variants across the haplotype block and the role of variation in the NOD2-regulatory regions. Here, we discuss the evidence and the unmet needs of NOD2-research, based on recently published evidence, and suggest methods that may meet these requirements.
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Affiliation(s)
- James J Ashton
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK.,Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, UK
| | - Eleanor G Seaby
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
| | - R Mark Beattie
- Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, UK
| | - Sarah Ennis
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
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5
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Azab B, Rabab’h O, Aburizeg D, Mohammad H, Dardas Z, Mustafa L, Khasawneh RA, Awad H, Hatmal MM, Altamimi E. Potential Composite Digenic Contribution of NPC1 and NOD2 Leading to Atypical Lethal Niemann-Pick Type C with Initial Crohn’s Disease-like Presentation: Genotype-Phenotype Correlation Study. Genes (Basel) 2022; 13:genes13060973. [PMID: 35741735 PMCID: PMC9223108 DOI: 10.3390/genes13060973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/31/2022] [Accepted: 05/25/2022] [Indexed: 11/29/2022] Open
Abstract
Niemann–Pick disease type C (NPC) is an autosomal recessive neurovisceral disease characterized by progressive neurodegeneration with variable involvement of multisystemic abnormalities. Crohn’s disease (CD) is an inflammatory bowel disease (IBD) with a multifactorial etiology influenced by variants in NOD2. Here, we investigated a patient with plausible multisystemic overlapping manifestations of both NPC and CD. Her initial hospitalization was due to a prolonged fever and non-bloody diarrhea. A few months later, she presented with recurrent skin tags and anal fissures. Later, her neurological and pulmonary systems progressively deteriorated, leading to her death at the age of three and a half years. Differential diagnosis of her disease encompassed a battery of clinical testing and genetic investigations. The patient’s clinical diagnosis was inconclusive. Specifically, the histopathological findings were directed towards an IBD disease. Nevertheless, the diagnosis of IBD was not consistent with the patient’s subsequent neurological and pulmonary deterioration. Consequently, we utilized a genetic analysis approach to guide the diagnosis of this vague condition. Our phenotype–genotype association attempts led to the identification of candidate disease-causing variants in both NOD2 and NPC1. In this study, we propose a potential composite digenic impact of these two genes as the underlying molecular etiology. This work lays the foundation for future functional and mechanistic studies to unravel the digenic role of NOD2 and NPC1.
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Affiliation(s)
- Bilal Azab
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY 10032, USA
- Department of Pathology and Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan; (D.A.); (H.M.); (L.M.); (H.A.)
- Correspondence: (B.A.); (E.A.)
| | - Omar Rabab’h
- Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA 52242, USA;
| | - Dunia Aburizeg
- Department of Pathology and Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan; (D.A.); (H.M.); (L.M.); (H.A.)
| | - Hashim Mohammad
- Department of Pathology and Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan; (D.A.); (H.M.); (L.M.); (H.A.)
| | - Zain Dardas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA;
| | - Lina Mustafa
- Department of Pathology and Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan; (D.A.); (H.M.); (L.M.); (H.A.)
| | - Ruba A. Khasawneh
- Department of Diagnostic Radiology and Nuclear Medicine, Faculty of Medicine King Abdullah University Hospital, Jordan University of Science and Technology, Irbid 22110, Jordan;
| | - Heyam Awad
- Department of Pathology and Microbiology and Forensic Medicine, School of Medicine, The University of Jordan, Amman 11942, Jordan; (D.A.); (H.M.); (L.M.); (H.A.)
| | - Ma’mon M. Hatmal
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, The Hashemite University, Zarqa 13133, Jordan;
| | - Eyad Altamimi
- Pediatric Department, Faculty of Medicine, Jordan University of Science and Technology, Irbid 22110, Jordan
- Correspondence: (B.A.); (E.A.)
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6
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Inborn Errors in the LRR Domain of Nod2 and Their Potential Consequences on the Function of the Receptor. Cells 2021; 10:cells10082031. [PMID: 34440800 PMCID: PMC8392326 DOI: 10.3390/cells10082031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/24/2022] Open
Abstract
The innate immune system plays a critical role in the early detection of pathogens, primarily by relying on pattern-recognition receptor (PRR) signaling molecules. Nucleotide-binding oligomerization domain 2 (NOD2) is a cytoplasmic receptor that recognizes invading molecules and danger signals inside the cells. Recent studies highlight the importance of NOD2′s function in maintaining the homeostasis of human body microbiota and innate immune responses, including induction of proinflammatory cytokines, regulation of autophagy, modulation of endoplasmic reticulum (ER) stress, etc. In addition, there is extensive cross-talk between NOD2 and the Toll-like receptors that are so important in the induction and tuning of adaptive immunity. Polymorphisms of NOD2′s encoding gene are associated with several pathological conditions, highlighting NOD2′s functional importance. In this study, we summarize NOD2′s role in cellular signaling pathways and take a look at the possible consequences of common NOD2 polymorphisms on the structure and function of this receptor.
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7
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Saternus R, Schwingel J, Müller CSL, Vogt T, Reichrath J. Ancient friends, revisited: Systematic review and case report of pyoderma gangrenosum-associated autoinflammatory syndromes. J Transl Autoimmun 2020; 3:100071. [PMID: 33305249 PMCID: PMC7718158 DOI: 10.1016/j.jtauto.2020.100071] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 12/29/2022] Open
Abstract
In the last decade, new scientific findings significantly improved our understanding of the molecular pathogenesis of autoinflammation and have resulted in the identification and definition of several pyoderma gangrenosum-associated autoinflammatory syndromes (PGAAIS) as new and distinct clinical entities. These different clinical entities include PAPA (pyogenic arthritis, pyoderma gangrenosum and acne conglobata), PASH (pyoderma gangrenosum, acne and suppurative hidradenitis), PAPASH (pyoderma gangrenosum, acne, suppurative hidradenitis and pyogenic arthritis), PsAPASH (pyoderma gangrenosum, acne, suppurative hidradenitis and psoriatic arthritis), PASS (pyoderma gangrenosum, acne conglobata, suppurative hidradenitis, and axial spondyloarthritis) and PAC (pyoderma gangrenosum, acne and ulcerative colitis), which can be distinguished by their clinical presentation and the presence or absence of mutations in several genes, such as the genes encoding proline-serine-threonine phosphatase-interacting protein 1 (PSTPIP1), nicastrin (NCSTN), Mediterranean fever (MEFV) and nucleotide-binding oligomerization domain-containing protein (NOD). In this systematic review, we summarize the present knowledge of this rapidly developing hot topic and provide a guide to enable the easy diagnosis of these syndromes in everyday clinical practice. Moreover, we report a rare case of PASS syndrome demonstrating successful treatment with adalimumab and another case of a previously unreported combination of symptoms, including psoriatic arthritis, pyoderma gangrenosum, suppurative hidradenitis and Crohn’s disease (newly coined PsAPSC), as examples. Because of the identification of similar genetic and pathogenic mechanisms of PGAAIS, we think the wide variety of seemingly different syndromes may represent distinct phenotypes of one disease. New scientific findings improved the understanding of the molecular pathogenesis of autoinflammation. There is a similar genetic background and clinical findings of PGAAIS. Because of the similar genetic and pathogenic mechanisms of PGAAIS may represent distinct phenotypes of one disease. We present a 4-sep guide to enable the easy diagnosis of theses disease in clinical practice.
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Affiliation(s)
- Roman Saternus
- Department of Dermatology, The Saarland University Hospital, 66421, Homburg, Germany
| | - Jérôme Schwingel
- Department of Internal Medicine, Caritasklinikum Saarbrücken St. Theresia, 66113, Saarbrücken, Germany
| | - Cornelia S L Müller
- Department of Dermatology, The Saarland University Hospital, 66421, Homburg, Germany
| | - Thomas Vogt
- Department of Dermatology, The Saarland University Hospital, 66421, Homburg, Germany
| | - Jörg Reichrath
- Department of Dermatology, The Saarland University Hospital, 66421, Homburg, Germany
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8
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Trindade BC, Chen GY. NOD1 and NOD2 in inflammatory and infectious diseases. Immunol Rev 2020; 297:139-161. [PMID: 32677123 DOI: 10.1111/imr.12902] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 12/12/2022]
Abstract
It has been long recognized that NOD1 and NOD2 are critical players in the host immune response, primarily by their sensing bacterial peptidoglycan-conserved motifs. Significant advances have been made from efforts that characterize their upstream activators, assembly of signaling complexes, and activation of downstream signaling pathways. Disruption in NOD1 and NOD2 signaling has also been associated with impaired host defense and resistance to the development of inflammatory diseases. In this review, we will describe how NOD1 and NOD2 sense microbes and cellular stress to regulate host responses that can affect disease pathogenesis and outcomes.
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Affiliation(s)
- Bruno C Trindade
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Grace Y Chen
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
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9
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Lega S, Pin A, Arrigo S, Cifaldi C, Girardelli M, Bianco AM, Malamisura M, Angelino G, Faraci S, Rea F, Romeo EF, Aloi M, Romano C, Barabino A, Martelossi S, Tommasini A, Di Matteo G, Cancrini C, De Angelis P, Finocchi A, Bramuzzo M. Diagnostic Approach to Monogenic Inflammatory Bowel Disease in Clinical Practice: A Ten-Year Multicentric Experience. Inflamm Bowel Dis 2020; 26:720-727. [PMID: 31375816 DOI: 10.1093/ibd/izz178] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND AND AIMS Multiple monogenic disorders present as very early onset inflammatory bowel disease (VEO-IBD) or as IBD with severe and atypical features. Establishing a genetic diagnosis may change patients' management and prognosis. In this study, we describe the diagnostic approach to suspected monogenic IBD in a real clinical setting, discussing genetic and phenotypic findings and therapeutic implications of molecular diagnosis. METHODS Information of patients with VEO-IBD and early onset IBD with severe/atypical phenotypes (EO-IBD s/a) managed between 2008-2017 who underwent a genetic workup were collected. RESULTS Ninety-three patients were included, and 12 (13%) reached a genetic diagnosis. Candidate sequencing (CS) was performed in 47 patients (50%), and next generation sequencing (NGS) was performed in 84 patients (90%). Candidate sequencing had a good diagnostic performance only when guided by clinical features specific for known monogenic diseases, whereas NGS helped finding new causative genetic variants and would have anticipated one monogenic diagnosis (XIAP) and consequent bone marrow transplant (BMT). Patients with monogenic IBD more frequently were male (92% vs 54%; P = 0.02), had extraintestinal findings (100% vs 34%; P < 0.001), and had disease onset ≤1 month of life (25% vs 1%; P = 0.006). Genetic diagnosis impacted patient management in 11 patients (92%), 7 of whom underwent BMT. CONCLUSION A genetic diagnosis can be established in a significant proportion of suspected monogenic IBD and has an impact on patients' management. Candidate sequencing may be deployed when clinical findings orientate toward a specific diagnosis. Next generation sequencing should be preferred in patients with nonspecific phenotypes.
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Affiliation(s)
- Sara Lega
- University of Trieste, Department of Medicine, Surgery and Health Sciences, Trieste, Italy
| | - Alessia Pin
- University of Trieste, Department of Medicine, Surgery and Health Sciences, Trieste, Italy
| | - Serena Arrigo
- Pediatric Gastroenterology and Endoscopy Unit, Institute Giannina Gaslini, Genoa, Italy
| | - Cristina Cifaldi
- Department of Pediatrics, Children's Hospital Bambino Gesù, Rome, Italy
| | - Martina Girardelli
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Anna Monica Bianco
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Monica Malamisura
- Digestive Diseases Unit, Children's Hospital Bambino Gesù, Rome, Italy
| | - Giulia Angelino
- Digestive Diseases Unit, Children's Hospital Bambino Gesù, Rome, Italy
| | - Simona Faraci
- Digestive Diseases Unit, Children's Hospital Bambino Gesù, Rome, Italy
| | - Francesca Rea
- Digestive Diseases Unit, Children's Hospital Bambino Gesù, Rome, Italy
| | | | - Marina Aloi
- Pediatric Gastroenterology And Liver Unit, Sapienza University of Rome, Rome, Italy
| | - Claudio Romano
- Pediatric Gastroenterology and Cystic Fibrosis Unit, University of Messina, Messina, Italy
| | - Arrigo Barabino
- Pediatric Gastroenterology and Endoscopy Unit, Institute Giannina Gaslini, Genoa, Italy
| | - Stefano Martelossi
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | - Alberto Tommasini
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
| | | | - Caterina Cancrini
- Department of Pediatrics, Children's Hospital Bambino Gesù, Rome, Italy
| | - Paola De Angelis
- Digestive Diseases Unit, Children's Hospital Bambino Gesù, Rome, Italy
| | - Andrea Finocchi
- Department of Pediatrics, Children's Hospital Bambino Gesù, Rome, Italy
| | - Matteo Bramuzzo
- Institute for Maternal and Child Health, IRCCS Burlo Garofolo, Trieste, Italy
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10
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Ashton JJ, Mossotto E, Stafford IS, Haggarty R, Coelho TA, Batra A, Afzal NA, Mort M, Bunyan D, Beattie RM, Ennis S. Genetic Sequencing of Pediatric Patients Identifies Mutations in Monogenic Inflammatory Bowel Disease Genes that Translate to Distinct Clinical Phenotypes. Clin Transl Gastroenterol 2020; 11:e00129. [PMID: 32463623 PMCID: PMC7145023 DOI: 10.14309/ctg.0000000000000129] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/03/2020] [Indexed: 12/19/2022] Open
Abstract
OBJECTIVES Monogenic inflammatory bowel disease (IBD) comprises rare Mendelian causes of gut inflammation, often presenting in infants with severe and atypical disease. This study aimed to identify clinically relevant variants within 68 monogenic IBD genes in an unselected pediatric IBD cohort. METHODS Whole exome sequencing was performed on patients with pediatric-onset disease. Variants fulfilling the American College of Medical Genetics criteria as "pathogenic" or "likely pathogenic" were assessed against phenotype at diagnosis and follow-up. Individual patient variants were assessed and processed to generate a per-gene, per-individual, deleteriousness score. RESULTS Four hundred one patients were included, and the median age of disease-onset was 11.92 years. In total, 11.5% of patients harbored a monogenic variant. TRIM22-related disease was implicated in 5 patients. A pathogenic mutation in the Wiskott-Aldrich syndrome (WAS) gene was confirmed in 2 male children with severe pancolonic inflammation and primary sclerosing cholangitis. In total, 7.3% of patients with Crohn's disease had apparent autosomal recessive, monogenic NOD2-related disease. Compared with non-NOD2 Crohn's disease, these patients had a marked stricturing phenotype (odds ratio 11.52, significant after correction for disease location) and had undergone significantly more intestinal resections (odds ratio 10.75). Variants in ADA, FERMT1, and LRBA did not meet the criteria for monogenic disease in any patients; however, case-control analysis of mutation burden significantly implicated these genes in disease etiology. DISCUSSION Routine whole exome sequencing in pediatric patients with IBD results in a precise molecular diagnosis for a subset of patients with IBD, providing the opportunity to personalize therapy. NOD2 status informs risk of stricturing disease requiring surgery, allowing clinicians to direct prognosis and intervention.
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Affiliation(s)
- James J. Ashton
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK;
- Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, UK;
| | - Enrico Mossotto
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK;
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK;
| | - Imogen S. Stafford
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK;
| | - Rachel Haggarty
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton, UK;
| | - Tracy A.F. Coelho
- Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, UK;
| | - Akshay Batra
- Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, UK;
| | - Nadeem A. Afzal
- Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, UK;
| | - Matthew Mort
- Human Genetic Mutation Database, Cardiff University, Cardiff, UK
| | - David Bunyan
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, UK.
| | - Robert Mark Beattie
- Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, UK;
| | - Sarah Ennis
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK;
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11
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Papa R, Picco P, Gattorno M. The expanding pathways of autoinflammation: a lesson from the first 100 genes related to autoinflammatory manifestations. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 120:1-44. [PMID: 32085880 DOI: 10.1016/bs.apcsb.2019.11.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
AutoInflammatory Diseases (AIDs) are a group of innate immune system disorders characterized by sterile inflammation without evidence of pathogenic autoantibodies or auto-reactive T lymphocytes. An expanding spectrum of genes and molecular pathways are associated with AIDs. Inflammasomopathies are secondary to dysregulation of multi-protein complexes, called inflammasomes, leading to an excessive maturation and secretion of IL1β and IL18. Patients present with persistent or recurrent systemic inflammation, abdominal and chest pain, skin rashes and are sensible to IL1 inhibitors. Unfolded proteins response causes a small number of AIDs that we propose to call immuno-proteinopathies, characterized by recurrent fevers and deep tissues inflammation. Other inflammatory conditions can occur in case of abnormalities of actin polymerization and the term of immuno-actinopathies is proposed. Generalized pustular psoriasis is a marker of autoinflammation mainly affecting the keratinocytes. Specific treatment targeting the p40 subunit of IL12 and IL23 or IL-17 are usually effective. Granulomatous inflammation characterizes AIDs related to NOD2 signaling defects. Defects in the ubiquitin-proteasome system cause a group of relopathies and some interferonopathies related to defect of the proteasome function (CANDLE syndrome). Gain of function of proteins regulating the production of type I interferons lead to severe inflammatory conditions, called interferonopathies. The JAK/STAT inhibitors are usually effective in these latter conditions. In conclusions, the identification of the main intracellular pathways involved in rare monogenic AIDs allows not only the proper classification of different conditions, but also highlight a pivotal role of possible novel therapeutic targets for the future.
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Affiliation(s)
- Riccardo Papa
- Autoinflammatory Diseases and Immunodeficiencies Centre, IRCCS Istituto Giannina Gaslini, Genova, GE, Italy
| | - Paolo Picco
- Autoinflammatory Diseases and Immunodeficiencies Centre, IRCCS Istituto Giannina Gaslini, Genova, GE, Italy
| | - Marco Gattorno
- Autoinflammatory Diseases and Immunodeficiencies Centre, IRCCS Istituto Giannina Gaslini, Genova, GE, Italy
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12
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Mossotto E, Ashton JJ, O'Gorman L, Pengelly RJ, Beattie RM, MacArthur BD, Ennis S. GenePy - a score for estimating gene pathogenicity in individuals using next-generation sequencing data. BMC Bioinformatics 2019; 20:254. [PMID: 31096927 PMCID: PMC6524327 DOI: 10.1186/s12859-019-2877-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 05/06/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Next-generation sequencing is revolutionising diagnosis and treatment of rare diseases, however its application to understanding common disease aetiology is limited. Rare disease applications binarily attribute genetic change(s) at a single locus to a specific phenotype. In common diseases, where multiple genetic variants within and across genes contribute to disease, binary modelling cannot capture the burden of pathogenicity harboured by an individual across a given gene/pathway. We present GenePy, a novel gene-level scoring system for integration and analysis of next-generation sequencing data on a per-individual basis that transforms NGS data interpretation from variant-level to gene-level. This simple and flexible scoring system is intuitive and amenable to integration for machine learning, network and topological approaches, facilitating the investigation of complex phenotypes. RESULTS Whole-exome sequencing data from 508 individuals were used to generate GenePy scores. For each variant a score is calculated incorporating: i) population allele frequency estimates; ii) individual zygosity, determined through standard variant calling pipelines and; iii) any user defined deleteriousness metric to inform on functional impact. GenePy then combines scores generated for all variants observed into a single gene score for each individual. We generated a matrix of ~ 14,000 GenePy scores for all individuals for each of sixteen popular deleteriousness metrics. All per-gene scores are corrected for gene length. The majority of genes generate GenePy scores < 0.01 although individuals harbouring multiple rare highly deleterious mutations can accumulate extremely high GenePy scores. In the absence of a comparator metric, we examine GenePy performance in discriminating genes known to be associated with three common, complex diseases. A Mann-Whitney U test conducted on GenePy scores for this positive control gene in cases versus controls demonstrates markedly more significant results (p = 1.37 × 10- 4) compared to the most commonly applied association tool that combines common and rare variation (p = 0.003). CONCLUSIONS Per-gene per-individual GenePy scores are intuitive when assessing genetic variation in individual patients or comparing scores between groups. GenePy outperforms the currently accepted best practice tools for combining common and rare variation. GenePy scores are suitable for downstream data integration with transcriptomic and proteomic data that also report at the gene level.
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Affiliation(s)
- E Mossotto
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK.
- Institute for Life Sciences, University of Southampton, Southampton, UK.
| | - J J Ashton
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
- Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, UK
| | - L O'Gorman
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
| | - R J Pengelly
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
- Institute for Life Sciences, University of Southampton, Southampton, UK
| | - R M Beattie
- Department of Paediatric Gastroenterology, Southampton Children's Hospital, Southampton, UK
| | - B D MacArthur
- Institute for Life Sciences, University of Southampton, Southampton, UK
| | - S Ennis
- Department of Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
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Dovrolis N, Filidou E, Kolios G. Systems biology in inflammatory bowel diseases: on the way to precision medicine. Ann Gastroenterol 2019; 32:233-246. [PMID: 31040620 PMCID: PMC6479645 DOI: 10.20524/aog.2019.0373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 02/25/2019] [Indexed: 02/07/2023] Open
Abstract
Inflammatory bowel diseases (IBD) are chronic and recurrent inflammatory disorders of the gastrointestinal tract. The elucidation of their etiopathology requires complex and multiple approaches. Systems biology has come to fulfill this need in approaching the pathogenetic mechanisms of IBD and its etiopathology, in a comprehensive way, by combining data from different scientific sources. In combination with bioinformatics and network medicine, it uses principles from computer science, mathematics, physics, chemistry, biology, medicine and computational tools to achieve its purposes. Systems biology utilizes scientific sources that provide data from omics studies (e.g., genomics, transcriptomics, etc.) and clinical observations, whose combined analysis leads to network formation and ultimately to a more integrative image of disease etiopathogenesis. In this review, we analyze the current literature on the methods and the tools utilized by systems biology in order to cover an innovative and exciting field: IBD-omics.
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Affiliation(s)
- Nikolas Dovrolis
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - Eirini Filidou
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
| | - George Kolios
- Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Alexandroupolis, Greece
- Correspondence to: Prof. George Kolios, MD PhD, Laboratory of Pharmacology, Faculty of Medicine, Democritus University of Thrace, Dragana, Alexandroupolis, 68100, Greece, e-mail:
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