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Article ; Online: DNA replication-associated inborn errors of immunity.

Willemsen, Mathijs / Staels, Frederik / Gerbaux, Margaux / Neumann, Julika / Schrijvers, Rik / Meyts, Isabelle / Humblet-Baron, Stephanie / Liston, Adrian

The Journal of allergy and clinical immunology

2022 Volume 151, Issue 2, Page(s) 345–360

Abstract: Inborn errors of immunity are a heterogeneous group of monogenic immunologic disorders caused by mutations in genes with critical roles in the development, maintenance, or function of the immune system. The genetic basis is frequently a mutation in a ... ...

Abstract	Inborn errors of immunity are a heterogeneous group of monogenic immunologic disorders caused by mutations in genes with critical roles in the development, maintenance, or function of the immune system. The genetic basis is frequently a mutation in a gene with restricted expression and/or function in immune cells, leading to an immune disorder. Several classes of inborn errors of immunity, however, result from mutation in genes that are ubiquitously expressed. Despite the genes participating in cellular processes conserved between cell types, immune cells are disproportionally affected, leading to inborn errors of immunity. Mutations in DNA replication, DNA repair, or DNA damage response factors can result in monogenic human disease, some of which are classified as inborn errors of immunity. Genetic defects in the DNA repair machinery are a well-known cause of T
MeSH term(s)	Humans ; Immune System Diseases ; Leukocytes ; DNA Damage ; Mutation ; Genetic Diseases, Inborn
Language	English
Publishing date	2022-11-15
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	121011-7
ISSN	1097-6825 ; 1085-8725 ; 0091-6749
ISSN (online)	1097-6825 ; 1085-8725
ISSN	0091-6749
DOI	10.1016/j.jaci.2022.11.003
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Article ; Online: Missense mutations in inositol 1,4,5-trisphosphate receptor type 3 result in leaky Ca

Terry, Lara E / Arige, Vikas / Neumann, Julika / Wahl, Amanda M / Knebel, Taylor R / Chaffer, James W / Malik, Sundeep / Liston, Adrian / Humblet-Baron, Stephanie / Bultynck, Geert / Yule, David I

iScience

2022 Volume 25, Issue 12, Page(s) 105523

Abstract: Mutations in all subtypes of the inositol 1,4,5-trisphosphate receptor ... ...

Abstract	Mutations in all subtypes of the inositol 1,4,5-trisphosphate receptor Ca
Language	English
Publishing date	2022-11-07
Publishing country	United States
Document type	Journal Article
ISSN	2589-0042
ISSN (online)	2589-0042
DOI	10.1016/j.isci.2022.105523
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Article ; Online: A cross entropy test allows quantitative statistical comparison of t-SNE and UMAP representations.

Roca, Carlos P / Burton, Oliver T / Neumann, Julika / Tareen, Samar / Whyte, Carly E / Gergelits, Vaclav / Veiga, Rafael V / Humblet-Baron, Stéphanie / Liston, Adrian

Cell reports methods

2023 Volume 3, Issue 1, Page(s) 100390

Abstract: The advent of high-dimensional single-cell data has necessitated the development of dimensionality-reduction tools. t-Distributed stochastic neighbor embedding (t-SNE) and uniform manifold approximation and projection (UMAP) are the two most frequently ... ...

Abstract	The advent of high-dimensional single-cell data has necessitated the development of dimensionality-reduction tools. t-Distributed stochastic neighbor embedding (t-SNE) and uniform manifold approximation and projection (UMAP) are the two most frequently used approaches, allowing clear visualization of complex single-cell datasets. Despite the need for quantitative comparison, t-SNE and UMAP have largely remained visualization tools due to the lack of robust statistical approaches. Here, we have derived a statistical test for evaluating the difference between dimensionality-reduced datasets using the Kolmogorov-Smirnov test on the distributions of cross entropy of single cells within each dataset. As the approach uses the inter-relationship of single cells for comparison, the resulting statistic is robust and capable of identifying true biological variation. Further, the test provides a valid distance between single-cell datasets, allowing the organization of multiple samples into a dendrogram for quantitative comparison of complex datasets. These results demonstrate the largely untapped potential of dimensionality-reduction tools for biomedical data analysis beyond visualization.
MeSH term(s)	Algorithms ; Entropy ; Principal Component Analysis ; Correlation of Data
Language	English
Publishing date	2023-01-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2667-2375
ISSN (online)	2667-2375
DOI	10.1016/j.crmeth.2022.100390
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Article ; Online: CTLA4-Ig Effectively Controls Clinical Deterioration and Immune Condition in a Murine Model of Foxp3 Deficiency.

Gerbaux, Margaux / Roos, Evelyne / Willemsen, Mathijs / Staels, Frederik / Neumann, Julika / Bücken, Leoni / Haughton, Jeason / Yshii, Lidia / Dooley, James / Schlenner, Susan / Humblet-Baron, Stephanie / Liston, Adrian

Journal of clinical immunology

2023 Volume 43, Issue 6, Page(s) 1393–1402

Abstract: Purpose: FOXP3 deficiency results in severe multisystem autoimmunity in both mice and humans, driven by the absence of functional regulatory T cells. Patients typically present with early and severe autoimmune polyendocrinopathy, dermatitis, and severe ... ...

Abstract	Purpose: FOXP3 deficiency results in severe multisystem autoimmunity in both mice and humans, driven by the absence of functional regulatory T cells. Patients typically present with early and severe autoimmune polyendocrinopathy, dermatitis, and severe inflammation of the gut, leading to villous atrophy and ultimately malabsorption, wasting, and failure to thrive. In the absence of successful treatment, FOXP3-deficient patients usually die within the first 2 years of life. Hematopoietic stem cell transplantation provides a curative option but first requires adequate control over the inflammatory condition. Due to the rarity of the condition, no clinical trials have been conducted, with widely unstandardized therapeutic approaches. We sought to compare the efficacy of lead therapeutic candidates rapamycin, anti-CD4 antibody, and CTLA4-Ig in controlling the physiological and immunological manifestations of Foxp3 deficiency in mice. Method: We generated Foxp3-deficient mice and an appropriate clinical scoring system to enable direct comparison of lead therapeutic candidates rapamycin, nondepleting anti-CD4 antibody, and CTLA4-Ig. Results: We found distinct immunosuppressive profiles induced by each treatment, leading to unique protective combinations over distinct clinical manifestations. CTLA4-Ig provided superior breadth of protective outcomes, including highly efficient protection during the transplantation process. Conclusion: These results highlight the mechanistic diversity of pathogenic pathways initiated by regulatory T cell loss and suggest CTLA4-Ig as a potentially superior therapeutic option for FOXP3-deficient patients.
MeSH term(s)	Animals ; Humans ; Mice ; Abatacept/therapeutic use ; Clinical Deterioration ; CTLA-4 Antigen ; Disease Models, Animal ; Forkhead Transcription Factors/genetics ; Immune System Diseases/therapy ; Sirolimus/pharmacology ; Sirolimus/therapeutic use ; T-Lymphocytes, Regulatory
Chemical Substances	Abatacept (7D0YB67S97) ; CTLA-4 Antigen ; CTLA4 protein, human ; Forkhead Transcription Factors ; Foxp3 protein, mouse ; Sirolimus (W36ZG6FT64)
Language	English
Publishing date	2023-05-08
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	779361-3
ISSN	1573-2592 ; 0271-9142
ISSN (online)	1573-2592
ISSN	0271-9142
DOI	10.1007/s10875-023-01462-2
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Article ; Online: Author Correction: Disrupted Ca

Cellular & molecular immunology

2022

Language	English
Publishing date	2022-12-06
Publishing country	China
Document type	Published Erratum
ZDB-ID	2435097-7
ISSN	2042-0226 ; 1672-7681
ISSN (online)	2042-0226
ISSN	1672-7681
DOI	10.1038/s41423-022-00960-4
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Article ; Online: A Novel Homozygous Stop Mutation in IL23R Causes Mendelian Susceptibility to Mycobacterial Disease.

Staels, Frederik / Lorenzetti, Flaminia / De Keukeleere, Kerstin / Willemsen, Mathijs / Gerbaux, Margaux / Neumann, Julika / Tousseyn, Thomas / Pasciuto, Emanuela / De Munter, Paul / Bossuyt, Xavier / Gijsbers, Rik / Liston, Adrian / Humblet-Baron, Stephanie / Schrijvers, Rik

Journal of clinical immunology

2022 Volume 42, Issue 8, Page(s) 1638–1652

Abstract: Purpose: Mendelian susceptibility to mycobacterial disease (MSMD) is caused by inborn errors of IFN-γ immunity. The most frequent genetic defects are found in IL12 or a subunit of its receptor. IL23R deficiency in MSMD has only been reported once, in ... ...

Abstract	Purpose: Mendelian susceptibility to mycobacterial disease (MSMD) is caused by inborn errors of IFN-γ immunity. The most frequent genetic defects are found in IL12 or a subunit of its receptor. IL23R deficiency in MSMD has only been reported once, in two pediatric patients from the same kindred with isolated disseminated Bacille Calmette-Guérin disease. We evaluated the impact of a homozygous stop mutation in IL23R (R381X), identified by whole exome sequencing, in an adult patient with disseminated non-tuberculous mycobacterial disease. Methods: We performed functional validation of the R381X mutation by evaluating IL23R expression and IL-23 signaling (STAT3 phosphorylation, IFN-γ production) in primary cells (PBMCs, EBV-B cells) and cell lines (HeLa) with or without back-complementation of wild-type IL23R. Results: We report on a 48-year-old male with disseminated non-tuberculous mycobacterial disease. We identified and characterized a homozygous loss-of-function stop mutation underlying IL23R deficiency, resulting in near absent expression of membrane bound IL23R. IL23R deficiency was characterized by impaired IL-23-mediated IFN-γ secretion in CD4 Conclusion: We demonstrate that impaired IL-23 immunity caused by a homozygous R381X mutation in IL23R underlies MSMD, corroborating earlier findings with a homozygous p.C115Y IL23R mutation. Our report further supports a model of redundant contribution of IL-23- to IL-17-mediated anti-fungal immunity.1.
MeSH term(s)	Male ; Adult ; Humans ; Child ; Middle Aged ; Interleukin-17/genetics ; Nuclear Receptor Subfamily 1, Group F, Member 3/genetics ; Mycobacterium Infections/etiology ; Mycobacterium Infections, Nontuberculous/genetics ; Mycobacterium Infections, Nontuberculous/complications ; Mutation/genetics ; Interleukin-23 ; Genetic Predisposition to Disease ; Receptors, Interleukin/genetics
Chemical Substances	Interleukin-17 ; Nuclear Receptor Subfamily 1, Group F, Member 3 ; Interleukin-23 ; IL23R protein, human ; Receptors, Interleukin
Language	English
Publishing date	2022-07-13
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/s10875-022-01320-7
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Article ; Online: Homozygous DBF4 mutation as a cause of severe congenital neutropenia.

The Journal of allergy and clinical immunology

2023 Volume 152, Issue 1, Page(s) 266–277

Abstract: Background: Severe congenital neutropenia presents with recurrent infections early in life as a result of arrested granulopoiesis. Multiple genetic defects are known to block granulocyte differentiation; however, a genetic cause remains unknown in ... ...

Abstract	Background: Severe congenital neutropenia presents with recurrent infections early in life as a result of arrested granulopoiesis. Multiple genetic defects are known to block granulocyte differentiation; however, a genetic cause remains unknown in approximately 40% of cases. Objective: We aimed to characterize a patient with severe congenital neutropenia and syndromic features without a genetic diagnosis. Methods: Whole exome sequencing results were validated using flow cytometry, Western blotting, coimmunoprecipitation, quantitative PCR, cell cycle and proliferation analysis of lymphocytes and fibroblasts and granulocytic differentiation of primary CD34 Results: We identified a homozygous missense mutation in DBF4 in a patient with mild extra-uterine growth retardation, facial dysmorphism and severe congenital neutropenia. DBF4 is the regulatory subunit of the CDC7 kinase, together known as DBF4-dependent kinase (DDK), the complex essential for DNA replication initiation. The DBF4 variant demonstrated impaired ability to bind CDC7, resulting in decreased DDK-mediated phosphorylation, defective S-phase entry and progression and impaired differentiation of granulocytes associated with activation of the p53-p21 pathway. The introduction of wild-type DBF4 into patient CD34 Conclusion: Hypomorphic DBF4 mutation causes autosomal-recessive severe congenital neutropenia with syndromic features.
MeSH term(s)	Humans ; Cell Cycle Proteins/genetics ; Protein Serine-Threonine Kinases/genetics ; Saccharomyces cerevisiae Proteins/genetics ; Saccharomyces cerevisiae Proteins/metabolism ; Mutation ; Phosphorylation
Chemical Substances	Cell Cycle Proteins ; Protein Serine-Threonine Kinases (EC 2.7.11.1) ; Saccharomyces cerevisiae Proteins ; CDC7 protein, human (EC 2.7.1.-) ; DBF4 protein, human
Language	English
Publishing date	2023-02-24
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	121011-7
ISSN	1097-6825 ; 1085-8725 ; 0091-6749
ISSN (online)	1097-6825 ; 1085-8725
ISSN	0091-6749
DOI	10.1016/j.jaci.2023.02.016
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Article ; Online: Disrupted Ca

Cellular & molecular immunology

2022 Volume 20, Issue 1, Page(s) 11–25

Abstract: Calcium signaling is essential for lymphocyte activation, with genetic disruptions of store-operated calcium ( ... ...

Abstract	Calcium signaling is essential for lymphocyte activation, with genetic disruptions of store-operated calcium (Ca
MeSH term(s)	Animals ; Humans ; Mice ; Calcium/metabolism ; Calcium Signaling/genetics ; Calcium Signaling/immunology ; Homeostasis ; Inositol 1,4,5-Trisphosphate Receptors/genetics ; Inositol 1,4,5-Trisphosphate Receptors/immunology ; Inositol 1,4,5-Trisphosphate Receptors/metabolism ; Protein Isoforms/metabolism ; Immune System Diseases/metabolism
Chemical Substances	Calcium (SY7Q814VUP) ; Inositol 1,4,5-Trisphosphate Receptors ; ITPR3 protein, human ; Protein Isoforms
Language	English
Publishing date	2022-10-27
Publishing country	China
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2435097-7
ISSN	2042-0226 ; 1672-7681
ISSN (online)	2042-0226
ISSN	1672-7681
DOI	10.1038/s41423-022-00928-4
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Article ; Online: Systems vaccinology identifies clinical and immunological correlates of SARS-CoV-2 vaccine response in solid-organ transplant recipients

Gemander, Nicolas / Neumann, Julika / Veiga, Rafael / Etienne, Isabelle / Prezzemolo, Teresa / Kemlin, Delphine / Pannus, Pieter / Depickère, Stéphanie / Olislagers, Véronique / Vu Duc, Inès / Waegemans, Alexandra / Gerbaux, Margaux / Bücken, Leoni / Dahma, Hafid / Martin, Charlotte / Dauby, Nicolas / Goossens, Maria E / Desombere, Isabelle / Roca, Carlos P /

Willemsen, Mathijs / Goriely, Stanislas / Le Moine, Alain / Marchant, Arnaud / Liston, Adrian / Humblet-Baron, Stephanie

medRxiv

Abstract: Solid organ transplant (SOT) recipients are at enhanced risk of adverse outcomes following infectious challenges due to immunosuppressive treatment and additional comorbidities. Unfortunately, SOT recipients are also poor responders to the key medical ... ...

Abstract	Solid organ transplant (SOT) recipients are at enhanced risk of adverse outcomes following infectious challenges due to immunosuppressive treatment and additional comorbidities. Unfortunately, SOT recipients are also poor responders to the key medical intervention to preventing infection: vaccines. Here we performed a systems vaccinology study on a cohort of 59 kidney transplant recipients and 31 lung transplant recipients who received the mRNA Pfizer-BioNTech COVID-19 vaccine. Analyzing the immunological status of the patients prior to vaccination, we were able to identify multiple immunological associates of relatively improved vaccine responses following two or three doses of mRNA-based SARS-CoV-2 vaccine. These immunological associates predicted, with 95.0% and 93.3% accuracy, vaccine response after the second and third dose, respectively. Comparison of the immunological associates with vaccine response in SOT recipients revealed two distinct immune configurations: a non-classical configuration, distinct from the immune state of healthy subjects, associated with responses to two doses of mRNA vaccine and that could be mediated partly by the presence of double negative B cell subsets which are more prominently represented in responsive SOT recipients, and a -normalized- configuration, closer to the immune state of healthy subjects, associated with potent antibody responses to three doses of mRNA vaccine. These results suggest that immunosuppression in SOT recipients can result in distinct immune states associated with different trade-offs in vaccine responsiveness. Immune phenotyping of SOT recipients for immune constellation may be an effective approach for identifying patients most at risk of poor vaccine responses and susceptibility to vaccine-preventable diseases.
Keywords	covid19
Language	English
Publishing date	2024-04-06
Publisher	Cold Spring Harbor Laboratory Press
Document type	Article ; Online
DOI	10.1101/2024.04.05.24305357
Database	COVID19

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Article ; Online: Non-apoptotic FAS signaling controls mTOR activation and extrafollicular maturation in human B cells.

Staniek, Julian / Kalina, Tomas / Andrieux, Geoffroy / Boerries, Melanie / Janowska, Iga / Fuentes, Manuel / Díez, Paula / Bakardjieva, Marina / Stancikova, Jitka / Raabe, Jan / Neumann, Julika / Schwenk, Sabine / Arpesella, Leonardo / Stuchly, Jan / Benes, Vladimir / García Valiente, Rodrigo / Fernández García, Jonatan / Carsetti, Rita / Piano Mortari, Eva /

Catala, Albert / de la Calle, Oscar / Sogkas, Georgios / Neven, Bénédicte / Rieux-Laucat, Frédéric / Magerus, Aude / Neth, Olaf / Olbrich, Peter / Voll, Reinhard E / Alsina, Laia / Allende, Luis M / Gonzalez-Granado, Luis I / Böhler, Chiara / Thiel, Jens / Venhoff, Nils / Lorenzetti, Raquel / Warnatz, Klaus / Unger, Susanne / Seidl, Maximilian / Mielenz, Dirk / Schneider, Pascal / Ehl, Stephan / Rensing-Ehl, Anne / Smulski, Cristian Roberto / Rizzi, Marta

Science immunology

2024 Volume 9, Issue 91, Page(s) eadj5948

Abstract: Defective FAS (CD95/Apo-1/TNFRSF6) signaling causes autoimmune lymphoproliferative syndrome (ALPS). Hypergammaglobulinemia is a common feature in ALPS ... ...

Abstract	Defective FAS (CD95/Apo-1/TNFRSF6) signaling causes autoimmune lymphoproliferative syndrome (ALPS). Hypergammaglobulinemia is a common feature in ALPS with
MeSH term(s)	Humans ; Apoptosis/genetics ; Germinal Center ; Hypergammaglobulinemia ; Lymphoproliferative Disorders/genetics ; TOR Serine-Threonine Kinases
Chemical Substances	TOR Serine-Threonine Kinases (EC 2.7.11.1) ; FAS protein, human ; MTOR protein, human (EC 2.7.1.1)
Language	English
Publishing date	2024-01-12
Publishing country	United States
Document type	Journal Article
ISSN	2470-9468
ISSN (online)	2470-9468
DOI	10.1126/sciimmunol.adj5948
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