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Article ; Online: Clinical implications of host genetic variation and susceptibility to severe or critical COVID-19.

van der Made, Caspar I / Netea, Mihai G / van der Veerdonk, Frank L / Hoischen, Alexander

2022 Volume 14, Issue 1, Page(s) 96

Abstract: Since the start of the coronavirus disease 2019 (COVID-19) pandemic, important insights have been gained into virus biology and the host factors that modulate the human immune response against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). ...

Abstract	Since the start of the coronavirus disease 2019 (COVID-19) pandemic, important insights have been gained into virus biology and the host factors that modulate the human immune response against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 displays a highly variable clinical picture that ranges from asymptomatic disease to lethal pneumonia. Apart from well-established general risk factors such as advanced age, male sex and chronic comorbidities, differences in host genetics have been shown to influence the individual predisposition to develop severe manifestations of COVID-19. These differences range from common susceptibility loci to rare genetic variants with strongly predisposing effects, or proven pathogenic variants that lead to known or novel inborn errors of immunity (IEI), which constitute a growing group of heterogeneous Mendelian disorders with increased susceptibility to infectious disease, auto-inflammation, auto-immunity, allergy or malignancies. The current genetic findings point towards a convergence of common and rare genetic variants that impact the interferon signalling pathways in patients with severe or critical COVID-19. Monogenic risk factors that impact IFN-I signalling have an expected prevalence between 1 and 5% in young, previously healthy individuals (<60 years of age) with critical COVID-19. The identification of these IEI such as X-linked TLR7 deficiency indicates a possibility for targeted genetic screening and personalized clinical management. This review aims to provide an overview of our current understanding of the host genetic factors that predispose to severe manifestations of COVID-19 and focuses on rare variants in IFN-I signalling genes and their potential clinical implications.
MeSH term(s)	Antiviral Agents ; COVID-19/genetics ; Genetic Variation ; Humans ; Male ; Pandemics ; SARS-CoV-2
Chemical Substances	Antiviral Agents
Language	English
Publishing date	2022-08-19
Publishing country	England
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	2484394-5
ISSN	1756-994X ; 1756-994X
ISSN (online)	1756-994X
ISSN	1756-994X
DOI	10.1186/s13073-022-01100-3
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Article ; Online: Chronische anemie en onverklaarde ontsteking.

van Daele, Paul L A / van der Made, Caspar I / Leavis, Helen L / Hak, A E Liesbeth / Potjewijd, Judith / Rutgers, Abraham Bram

Nederlands tijdschrift voor geneeskunde

2023 Volume 167

Abstract: Background: VEXAS-syndrome is an X-linked acquired multisystemic autoinflammatory disease caused by a somatic mutation in UBA1.: Case description: In this manuscript we describe a 79-year-old male suffering from skin lesions, macrocytic anemia and ... ...

Title translation	Chronic anemia and unexplained inflammation: think of VEXAS syndrome.
Abstract	Background: VEXAS-syndrome is an X-linked acquired multisystemic autoinflammatory disease caused by a somatic mutation in UBA1. Case description: In this manuscript we describe a 79-year-old male suffering from skin lesions, macrocytic anemia and lab results showing inflammation in which, based on finding a mutation in UBA1, VEXAS was diagnosed. He was treated with a combination of high dose corticosteroids and anti-IL-6 with good response. Conclusion: In middle aged males presenting with multisystemic inflammation without evidence of infection a diagnosis of VEXAS should be considered, especially if there is evidence of a macrocytic anemia. Early testing for UBA1 mutations helps in making the diagnosis. Despite treatment with intensive immunosuppression mortality remains high.
MeSH term(s)	Male ; Middle Aged ; Humans ; Aged ; Anemia/diagnosis ; Anemia/etiology ; Anemia, Macrocytic ; Inflammation ; Mutation
Language	Dutch
Publishing date	2023-04-19
Publishing country	Netherlands
Document type	Case Reports ; English Abstract ; Journal Article
ZDB-ID	82073-8
ISSN	1876-8784 ; 0028-2162
ISSN (online)	1876-8784
ISSN	0028-2162
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Article ; Online: Next-Generation Sequencing in the Field of Primary Immunodeficiencies: Current Yield, Challenges, and Future Perspectives.

Vorsteveld, Emil E / Hoischen, Alexander / van der Made, Caspar I

Clinical reviews in allergy & immunology

2021 Volume 61, Issue 2, Page(s) 212–225

Abstract: Primary immunodeficiencies comprise a group of inborn errors of immunity that display significant clinical and genetic heterogeneity. Next-generation sequencing techniques and predominantly whole exome sequencing have revolutionized the understanding of ... ...

Abstract	Primary immunodeficiencies comprise a group of inborn errors of immunity that display significant clinical and genetic heterogeneity. Next-generation sequencing techniques and predominantly whole exome sequencing have revolutionized the understanding of the genetic and molecular basis of genetic diseases, thereby also leading to a sharp increase in the discovery of new genes associated with primary immunodeficiencies. In this review, we discuss the current diagnostic yield of this generic diagnostic approach by evaluating the studies that have employed next-generation sequencing techniques in cohorts of patients with primary immunodeficiencies. The average diagnostic yield for primary immunodeficiencies is determined to be 29% (range 10-79%) and 38% specifically for whole-exome sequencing (range 15-70%). The significant variation between studies is mainly the result of differences in clinical characteristics of the studied cohorts but is also influenced by varying sequencing approaches and (in silico) gene panel selection. We further discuss other factors contributing to the relatively low yield, including the inherent limitations of whole-exome sequencing, challenges in the interpretation of novel candidate genetic variants, and promises of exploring the non-coding part of the genome. We propose strategies to improve the diagnostic yield leading the way towards expanded personalized treatment in PIDs.
MeSH term(s)	Animals ; Genetic Heterogeneity ; High-Throughput Nucleotide Sequencing/trends ; Humans ; Primary Immunodeficiency Diseases/genetics
Language	English
Publishing date	2021-03-05
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	1239045-8
ISSN	1559-0267 ; 1080-0549
ISSN (online)	1559-0267
ISSN	1080-0549
DOI	10.1007/s12016-021-08838-5
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Article ; Online: OTULIN Haploinsufficiency-Related Fasciitis and Skin Necrosis Treated by TNF Inhibition.

Arts, Rob J W / van der Linden, Tristan J / van der Made, Caspar I / Hendriks, Marianne M C / van der Heijden, Wouter A / de Mast, Quirijn / Schuurs-Hoeijmakers, Janneke H M / Simons, Annet / Spaan, András N / Mulders-Manders, Catharina M / van de Veerdonk, Frank L

Journal of clinical immunology

2023 Volume 44, Issue 1, Page(s) 10

Abstract: Here, we describe an adult female with severe fasciitis and skin necrosis who carried a private, predicted deleterious missense mutation in OTULIN in heterozygosity. OTULIN is a cellular regulator of deubiquitination that has been shown to play a key ... ...

Abstract	Here, we describe an adult female with severe fasciitis and skin necrosis who carried a private, predicted deleterious missense mutation in OTULIN in heterozygosity. OTULIN is a cellular regulator of deubiquitination that has been shown to play a key role in intrinsic immunity against staphylococcal α-toxin. The patient was treated with broad-spectrum antibiotics, and multiple surgical explorations were conducted without clinical response. Since autoinflammation was the predominant clinical feature, TNF inhibition was started with a good clinical response. We show that excessive inflammation in OTULIN haploinsufficiency can be effectively treated by TNF inhibition.
MeSH term(s)	Female ; Humans ; Fasciitis ; Haploinsufficiency ; Inflammation/genetics ; Necrosis ; Ubiquitination
Language	English
Publishing date	2023-12-22
Publishing country	Netherlands
Document type	Case Reports ; Journal Article
ZDB-ID	779361-3
ISSN	1573-2592 ; 0271-9142
ISSN (online)	1573-2592
ISSN	0271-9142
DOI	10.1007/s10875-023-01630-4
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Article ; Online: SUsPECT: a pipeline for variant effect prediction based on custom long-read transcriptomes for improved clinical variant annotation.

Salz, Renee / Saraiva-Agostinho, Nuno / Vorsteveld, Emil / van der Made, Caspar I / Kersten, Simone / Stemerdink, Merel / Allen, Jamie / Volders, Pieter-Jan / Hunt, Sarah E / Hoischen, Alexander / 't Hoen, Peter A C

BMC genomics

2023 Volume 24, Issue 1, Page(s) 305

Abstract: Our incomplete knowledge of the human transcriptome impairs the detection of disease-causing variants, in particular if they affect transcripts only expressed under certain conditions. These transcripts are often lacking from reference transcript sets, ... ...

Abstract	Our incomplete knowledge of the human transcriptome impairs the detection of disease-causing variants, in particular if they affect transcripts only expressed under certain conditions. These transcripts are often lacking from reference transcript sets, such as Ensembl/GENCODE and RefSeq, and could be relevant for establishing genetic diagnoses. We present SUsPECT (Solving Unsolved Patient Exomes/gEnomes using Custom Transcriptomes), a pipeline based on the Ensembl Variant Effect Predictor (VEP) to predict variant impact on custom transcript sets, such as those generated by long-read RNA-sequencing, for downstream prioritization. Our pipeline predicts the functional consequence and likely deleteriousness scores for missense variants in the context of novel open reading frames predicted from any transcriptome. We demonstrate the utility of SUsPECT by uncovering potential mutational mechanisms of pathogenic variants in ClinVar that are not predicted to be pathogenic using the reference transcript annotation. In further support of SUsPECT's utility, we identified an enrichment of immune-related variants predicted to have a more severe molecular consequence when annotating with a newly generated transcriptome from stimulated immune cells instead of the reference transcriptome. Our pipeline outputs crucial information for further prioritization of potentially disease-causing variants for any disease and will become increasingly useful as more long-read RNA sequencing datasets become available.
MeSH term(s)	Humans ; Transcriptome ; Molecular Sequence Annotation ; Software ; Sequence Analysis, RNA/methods ; Exome ; High-Throughput Nucleotide Sequencing
Language	English
Publishing date	2023-06-06
Publishing country	England
Document type	Journal Article
ZDB-ID	2041499-7
ISSN	1471-2164 ; 1471-2164
ISSN (online)	1471-2164
ISSN	1471-2164
DOI	10.1186/s12864-023-09391-5
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Article ; Online: Primary immunodeficiencies in cytosolic pattern-recognition receptor pathways: Toward host-directed treatment strategies.

van der Made, Caspar I / Hoischen, Alexander / Netea, Mihai G / van de Veerdonk, Frank L

Immunological reviews

2020 Volume 297, Issue 1, Page(s) 247–272

Abstract: In the last decade, the paradigm of primary immunodeficiencies (PIDs) as rare recessive familial diseases that lead to broad, severe, and early-onset immunological defects has shifted toward collectively more common, but sporadic autosomal dominantly ... ...

Abstract	In the last decade, the paradigm of primary immunodeficiencies (PIDs) as rare recessive familial diseases that lead to broad, severe, and early-onset immunological defects has shifted toward collectively more common, but sporadic autosomal dominantly inherited isolated defects in the immune response. Patients with PIDs constitute a formidable area of research to study the genetics and the molecular mechanisms of complex immunological pathways. A significant subset of PIDs affect the innate immune response, which is a crucial initial host defense mechanism equipped with pattern-recognition receptors. These receptors recognize pathogen- and damage-associated molecular patterns in both the extracellular and intracellular space. In this review, we will focus on primary immunodeficiencies caused by genetic defects in cytosolic pattern-recognition receptor pathways. We discuss these PIDs organized according to their mutational mechanisms and consequences for the innate host response. The advanced understanding of these pathways obtained by the study of PIDs creates the opportunity for the development of new host-directed treatment strategies.
MeSH term(s)	Cytosol ; Humans ; Immunity, Innate ; Immunologic Deficiency Syndromes/genetics ; Immunologic Deficiency Syndromes/therapy ; Mutation ; Primary Immunodeficiency Diseases ; Receptors, Pattern Recognition
Chemical Substances	Receptors, Pattern Recognition
Language	English
Publishing date	2020-07-08
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	391796-4
ISSN	1600-065X ; 0105-2896
ISSN (online)	1600-065X
ISSN	0105-2896
DOI	10.1111/imr.12898
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Article ; Online: Genetic Predisposition to Neurological Complications in Patients with COVID-19.

Sahajpal, Nikhil Shri / Hastie, Alex R / Schieck, Maximilian / Mondal, Ashis K / Felde, Marc / van der Made, Caspar I / Chou, Janet S / Randolph, Adrienne G / Illig, Thomas / Zody, Michael C / Brownstein, Catherine A / Beggs, Alan H / Hoischen, Alexander / Chaubey, Alka / Kolhe, Ravindra

Biomolecules

2023 Volume 13, Issue 1

Abstract: Several studies have identified rare and common genetic variants associated with severe COVID-19, but no study has reported genetic determinants as predisposition factors for neurological complications. In this report, we identified rare/unique ... ...

Abstract	Several studies have identified rare and common genetic variants associated with severe COVID-19, but no study has reported genetic determinants as predisposition factors for neurological complications. In this report, we identified rare/unique structural variants (SVs) implicated in neurological functions in two individuals with neurological manifestations of COVID-19. This report highlights the possible genetic link to the neurological symptoms with COVID-19 and calls for a collective effort to study these cohorts for a possible genetic linkage.
MeSH term(s)	Humans ; COVID-19/complications ; COVID-19/genetics ; Genetic Predisposition to Disease ; Nervous System Diseases/genetics ; Genotype
Language	English
Publishing date	2023-01-09
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2701262-1
ISSN	2218-273X ; 2218-273X
ISSN (online)	2218-273X
ISSN	2218-273X
DOI	10.3390/biom13010133
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Article ; Online: Dexamethasone attenuates interferon-related cytokine hyperresponsiveness in COVID-19 patients.

Engel, Job J / van der Made, Caspar I / Keur, Nick / Setiabudiawan, Todia / Röring, Rutger J / Damoraki, Georgia / Dijkstra, Helga / Lemmers, Heidi / Ioannou, Sofia / Poulakou, Garyfallia / van der Meer, Jos W M / Giamarellos-Bourboulis, Evangelos J / Kumar, Vinod / van de Veerdonk, Frank L / Netea, Mihai G / Ziogas, Athanasios

Frontiers in immunology

2023 Volume 14, Page(s) 1233318

Abstract: Background: Dexamethasone improves the survival of COVID-19 patients in need of supplemental oxygen therapy. Although its broad immunosuppressive effects are well-described, the immunological mechanisms modulated by dexamethasone in patients ... ...

Abstract	Background: Dexamethasone improves the survival of COVID-19 patients in need of supplemental oxygen therapy. Although its broad immunosuppressive effects are well-described, the immunological mechanisms modulated by dexamethasone in patients hospitalized with COVID-19 remain to be elucidated. Objective: We combined functional immunological assays and an omics-based approach to investigate the Methods: Hospitalized COVID-19 patients eligible for dexamethasone therapy were recruited from the general care ward between February and July, 2021. Whole blood transcriptomic and targeted plasma proteomic analyses were performed before and after starting dexamethasone treatment. PBMCs were isolated from healthy individuals and COVID-19 patients and stimulated with inactivated SARS-CoV-2 Results: Dexamethasone efficiently inhibited SARS-CoV-2-induced Conclusion: We describe the anti-inflammatory impact of dexamethasone on the pathways contributing to cytokine hyperresponsiveness observed in severe manifestations of COVID-19, including type I/II IFN signaling. Dexamethasone could have adverse effects in COVID-19 patients with mild symptoms by inhibiting IFN responses in early stages of the disease, whereas it exhibits beneficial effects in patients with severe clinical phenotypes by efficiently diminishing cytokine hyperresponsiveness.
MeSH term(s)	Humans ; Cytokines ; Leukocytes, Mononuclear ; Ligands ; Proteomics ; COVID-19 ; SARS-CoV-2 ; COVID-19 Drug Treatment ; Interferon Type I ; Tumor Necrosis Factor-alpha ; Dexamethasone/pharmacology ; Dexamethasone/therapeutic use
Chemical Substances	Cytokines ; Ligands ; Interferon Type I ; Tumor Necrosis Factor-alpha ; Dexamethasone (7S5I7G3JQL)
Language	English
Publishing date	2023-08-08
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2606827-8
ISSN	1664-3224 ; 1664-3224
ISSN (online)	1664-3224
ISSN	1664-3224
DOI	10.3389/fimmu.2023.1233318
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Article ; Online: Effect of exogenous IL-37 on immune cells from a patient carrying a potential IL37 loss-of-function variant: A case study.

Teufel, Lisa U / van der Made, Caspar I / Klück, Viola / Simons, Annet / Hoischen, Alexander / Vernimmen, Vivian / Joosten, Leo A B / Arts, Rob J W

Cytokine

2022 Volume 162, Page(s) 156102

Abstract: Introduction: Chronic inflammatory or autoimmune diseases are commonly treated with immunosuppressive medication such as NSAIDs, corticosteroids, or antibodies against specific cytokines (TNF, IL-1 IL-17, IL-23, etc.) or signalling cascades (e.g. JAK- ... ...

Abstract	Introduction: Chronic inflammatory or autoimmune diseases are commonly treated with immunosuppressive medication such as NSAIDs, corticosteroids, or antibodies against specific cytokines (TNF, IL-1 IL-17, IL-23, etc.) or signalling cascades (e.g. JAK-STAT inhibitors). Using sequencing data to locate genetic mutations in relevant genes allows the identification of alternative targets in a patient-tailored therapy setting. Interleukin (IL)-37 is an anti-inflammatory cytokine with broad effects on innate and adaptive immune cell function. Dysfunctional IL-37 expression or signalling is linked to various autoinflammatory disorders. The administration of recombinant IL-37 to hyperinflammatory patients that are non-responsive to standard treatment bears the potential to alleviate symptoms. Methods: In this case study, the (hyper)responsiveness of immune cell subsets was investigated in a single patient with a seronegative autoimmune disorder who carries a heterozygous stop-gain variant in IL37 (IL37 Chr2(GRCh37):g.113670640G > A NM_014439.3:c.51G > A p.(Trp17)). As the patient has been non-responsive to blockage of TNF or IL-1 by Etanercept or Anakinra, respectively, additional in-vitro experiments were set out to elucidate whether treatment with recombinant IL-37 could normalise observed immune cell functions. Findings:* Characterisation of immune cell function showed no elevated overall production of acute-phase pro-inflammatory cytokines by patient PBMCs and neutrophils at baseline or upon stimulation. T-cell responses were elevated, as was the metabolic activity and IL-1Ra production of PBMCs at baseline. The identified stop-gain variant in IL37 does not result in the absence of the protein in circulation. In line with this, treatment with recombinant IL-37 did overall not dampen immune responses with the exception of the complete suppression of IL-17. Conclusion: The heterozygous stop-gain variant in IL37 (IL37 NM_014439.3:c.51G > A p.(Trp17*)) is not of functional relevance as we observed no clear pro-inflammatory phenotype in immune cells of a patient carrying this variant.
MeSH term(s)	Humans ; Interleukin-1/metabolism ; Interleukin-17/genetics ; Cytokines/genetics ; Inflammation ; Gene Expression
Chemical Substances	Interleukin-1 ; Interleukin-17 ; Cytokines ; IL37 protein, human
Language	English
Publishing date	2022-12-05
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1018055-2
ISSN	1096-0023 ; 1043-4666
ISSN (online)	1096-0023
ISSN	1043-4666
DOI	10.1016/j.cyto.2022.156102
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Article ; Online: "Deficiency in ELF4, X-Linked": a Monogenic Disease Entity Resembling Behçet's Syndrome and Inflammatory Bowel Disease.

Olyha, Sam J / O'Connor, Shannon K / Kribis, Marat / Bucklin, Molly L / Uthaya Kumar, Dinesh Babu / Tyler, Paul M / Alam, Faiad / Jones, Kate M / Sheikha, Hassan / Konnikova, Liza / Lakhani, Saquib A / Montgomery, Ruth R / Catanzaro, Jason / Du, Hongqiang / DiGiacomo, Daniel V / Rothermel, Holly / Moran, Christopher J / Fiedler, Karoline / Warner, Neil /

Hoppenreijs, Esther P A H / van der Made, Caspar I / Hoischen, Alexander / Olbrich, Peter / Neth, Olaf / Rodríguez-Martínez, Alejandro / Lucena Soto, José Manuel / van Rossum, Annemarie M C / Dalm, Virgil A S H / Muise, Aleixo M / Lucas, Carrie L

Journal of clinical immunology

2024 Volume 44, Issue 2, Page(s) 44

Abstract: Defining monogenic drivers of autoinflammatory syndromes elucidates mechanisms of disease in patients with these inborn errors of immunity and can facilitate targeted therapeutic interventions. Here, we describe a cohort of patients with a Behçet's- and ... ...

Abstract	Defining monogenic drivers of autoinflammatory syndromes elucidates mechanisms of disease in patients with these inborn errors of immunity and can facilitate targeted therapeutic interventions. Here, we describe a cohort of patients with a Behçet's- and inflammatory bowel disease (IBD)-like disorder termed "deficiency in ELF4, X-linked" (DEX) affecting males with loss-of-function variants in the ELF4 transcription factor gene located on the X chromosome. An international cohort of fourteen DEX patients was assessed to identify unifying clinical manifestations and diagnostic criteria as well as collate findings informing therapeutic responses. DEX patients exhibit a heterogeneous clinical phenotype including weight loss, oral and gastrointestinal aphthous ulcers, fevers, skin inflammation, gastrointestinal symptoms, arthritis, arthralgia, and myalgia, with findings of increased inflammatory markers, anemia, neutrophilic leukocytosis, thrombocytosis, intermittently low natural killer and class-switched memory B cells, and increased inflammatory cytokines in the serum. Patients have been predominantly treated with anti-inflammatory agents, with the majority of DEX patients treated with biologics targeting TNFα.
MeSH term(s)	Male ; Humans ; Behcet Syndrome/diagnosis ; Behcet Syndrome/genetics ; Inflammatory Bowel Diseases/diagnosis ; Inflammatory Bowel Diseases/genetics ; Arthralgia ; Arthritis ; Biological Products ; DNA-Binding Proteins ; Transcription Factors/genetics
Chemical Substances	Biological Products ; ELF4 protein, human ; DNA-Binding Proteins ; Transcription Factors
Language	English
Publishing date	2024-01-17
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	779361-3
ISSN	1573-2592 ; 0271-9142
ISSN (online)	1573-2592
ISSN	0271-9142
DOI	10.1007/s10875-023-01610-8
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