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1. Associations between HLA class II alleles and IgE sensitization to allergens in the Qatar Biobank cohort

Author

Taushif Khan, PhD, Isabella Marie Ledoux, BMLS, Ferdousey Aziz, MSc, Fatima Al Ali, MSc, Evonne Chin-Smith, PhD, Manar Ata, MSc, Mohammed Yousuf Karim, MD, and Nico Marr, PhD

Subjects
Allergens, association study, IgE sensitization, Qatar Biobank, Immunologic diseases. Allergy, RC581-607
Abstract

Background: Allergic disorders are the consequence of IgE sensitization to allergens. Population studies have shown that certain human leukocyte antigen (HLA) alleles are associated with increased or decreased risk of developing allergy. Objective: We aimed to characterize the relationship between HLA class II allelic diversity and IgE sensitization in an understudied Arab population. Methods: We explored associations between IgE sensitization to 7 allergen mixes and mesquite (comprising 41 food or aeroallergens) and 45 common classical HLA class II alleles in a well-defined cohort of 797 individuals representing the general adult population of Qatari nationals and long-term residents. To do so, we performed HLA calling from whole genome sequencing data at 2-field resolution using 2 independent algorithms. We then applied 3 different regression models to assess either each allergen mix independently, in the context of IgE sensitization to other allergens tested, or polysensitization. Results: More than half (n = 447) of the study participants showed IgE sensitization to at least 1 allergen, most of them (n = 400) to aeroallergens (Phadiatop). We identified statistically significant negative and positive associations with 24 HLA class II alleles. These have been reported to confer risk or protection from variety of diseases; however, only a few have previously been associated with allergy in other populations. Conclusions: Our study reveals several new risk and protective genetic markers for allergen-specific IgE sensitization. This is a first and essential step toward a better understanding of the origins of allergic diseases in this understudied population.

Published
2023
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2. Organizing training workshops on gene literature retrieval, profiling, and visualization for early career researchers [version 2; peer review: 2 approved]

Author

Alexandra K Marr, Davide Bedognetti, Basirudeen Syed Ahamed Kabeer, Fatima Al Ali, Nico Marr, Jessica Roelands, Mathieu Garand, Zohreh Tatari-Calderone, Mohammed Toufiq, Darawan Rinchai, Damien Chaussabel, and Mohamed Alfaki

Subjects
Literature profiling, Science education, Concept extraction, Data visualization, eng, Medicine, Science
Abstract

Early-career researchers must acquire the skills necessary to effectively search and extract information from biomedical literature. This ability is for instance crucial for evaluating the novelty of experimental results, and assessing potential publishing opportunities. Given the rapidly growing volume of publications in the field of biomedical research, new systematic approaches need to be devised and adopted for the retrieval and curation of literature relevant to a specific theme. In this context, we present a hands-on training curriculum aimed at retrieval, profiling, and visualization of literature associated with a given topic. The curriculum was implemented in a workshop in January 2021. Here we provide supporting material and step-by-step implementation guidelines with the ISG15 gene literature serving as an illustrative use case. Workshop participants can learn several skills, including: 1) building and troubleshoot PubMed queries in order to retrieve the literature associated with a gene of interest; 2) identifying key concepts relevant to given themes (such as cell types, diseases, and biological processes); 3) measuring the prevalence of these concepts in the gene literature; 4) extracting key information from relevant articles, and 5) developing a background section or summary on the basis of this information. Finally, trainees can learn to consolidate the structured information captured through this process for presentation via an interactive web application.

Published
2023
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3. Human leukocyte antigen class II gene diversity tunes antibody repertoires to common pathogens

Author

Taushif Khan, Mahbuba Rahman, Ikhlak Ahmed, Fatima Al Ali, Puthen Veettil Jithesh, and Nico Marr

Subjects
human antibody repertoires, microbial infection, phage immunoprecipitation sequencing, human leukocyte antigen, major histocompatibility complex, polymorphisms, Immunologic diseases. Allergy, RC581-607
Abstract

Allelic diversity of human leukocyte antigen (HLA) class II genes may help maintain humoral immunity against infectious diseases. In this study, we investigated germline genetic variation in classical HLA class II genes and employed a systematic, unbiased approach to explore the relative contribution of this genetic variation in the antibody repertoire to various common pathogens. We leveraged a well-defined cohort of 800 adults representing the general Arab population in which genetic material is shared because of the high frequency of consanguineous unions. By applying a high-throughput method for large-scale antibody profiling to this well-defined cohort, we were able to dissect the overall effect of zygosity for classical HLA class II genes, as well as the effects associated with specific HLA class II alleles, haplotypes and genotypes, on the antimicrobial antibody repertoire breadth and antibody specificity with unprecedented resolution. Our population genetic studies revealed that zygosity of the classical HLA class II genes is a strong predictor of antibody responses to common human pathogens, suggesting that classical HLA class II gene heterozygosity confers a selective advantage. Moreover, we demonstrated that multiple HLA class II alleles can have additive effects on the antibody repertoire to common pathogens. We also identified associations of HLA-DRB1 genotypes with specific antigens. Our findings suggest that HLA class II gene polymorphisms confer specific humoral immunity against common pathogens, which may have contributed to the genetic diversity of HLA class II loci during hominine evolution.

Published
2022
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4. Virome-wide serological profiling reveals association of herpesviruses with obesity

Author

Mohammad Rubayet Hasan, Mahbuba Rahman, Taushif Khan, Amira Saeed, Sathyavathi Sundararaju, Annaliza Flores, Phillip Hawken, Arun Rawat, Naser Elkum, Khalid Hussain, Rusung Tan, Patrick Tang, and Nico Marr

Subjects
Medicine, Science
Abstract

Abstract The relationship between viral infection and obesity has been known for several decades but epidemiological data is limited to only a few viral pathogens. The association between obesity and a wide range of viruses was assessed using VirScan, a pan-viral serological profiling tool. Serum specimens from 457 Qatari adults (lean = 184; obese = 273) and 231 Qatari children (lean = 111; obese = 120) were analyzed by VirScan. Associations with obesity were determined by odds ratio (OR) and Fisher’s test (p values), and by multivariate regression analysis to adjust for age and gender. Although there was no association of viral infections with obesity in the pediatric population, a nominal association of obesity with seropositivity to members of the Herpesviridae family is observed for the adult population (OR = 1.5–3.3; p

Published
2021
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5. Dromedary camels as a natural source of neutralizing nanobodies against SARS-CoV-2

Author

Lotfi Chouchane, Jean-Charles Grivel, Elmoubasher Abu Baker Abd Farag, Igor Pavlovski, Selma Maacha, Abbirami Sathappan, Hamad Eid Al-Romaihi, Sirin W.J. Abuaqel, Manar Mahmoud Ahmad Ata, Aouatef Ismail Chouchane, Sami Remadi, Najeeb Halabi, Arash Rafii, Mohammed H. Al-Thani, Nico Marr, Murugan Subramanian, and Jingxuan Shan

Subjects
COVID-19, Medicine
Abstract

The development of prophylactic and therapeutic agents for coronavirus disease 2019 (COVID-19) is a current global health priority. Here, we investigated the presence of cross-neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in dromedary camels that were Middle East respiratory syndrome coronavirus (MERS-CoV) seropositive but MERS-CoV free. The tested 229 dromedaries had anti–MERS-CoV camel antibodies with variable cross-reactivity patterns against SARS-CoV-2 proteins, including the S trimer and M, N, and E proteins. Using SARS-CoV-2 competitive immunofluorescence immunoassays and pseudovirus neutralization assays, we found medium-to-high titers of cross-neutralizing antibodies against SARS-CoV-2 in these animals. Through linear B cell epitope mapping using phage immunoprecipitation sequencing and a SARS-CoV-2 peptide/proteome microarray, we identified a large repertoire of Betacoronavirus cross-reactive antibody specificities in these dromedaries and demonstrated that the SARS-CoV-2–specific VHH antibody repertoire is qualitatively diverse. This analysis revealed not only several SARS-CoV-2 epitopes that are highly immunogenic in humans, including a neutralizing epitope, but also epitopes exclusively targeted by camel antibodies. The identified SARS-CoV-2 cross-neutralizing camel antibodies are not proposed as a potential treatment for COVID-19. Rather, their presence in nonimmunized camels supports the development of SARS-CoV-2 hyperimmune camels, which could be a prominent source of therapeutic agents for the prevention and treatment of COVID-19.

Published
2021
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6. Distinct antibody repertoires against endemic human coronaviruses in children and adults

Author

Taushif Khan, Mahbuba Rahman, Fatima Al Ali, Susie S. Y. Huang, Manar Ata, Qian Zhang, Paul Bastard, Zhiyong Liu, Emmanuelle Jouanguy, Vivien Béziat, Aurélie Cobat, Gheyath K. Nasrallah, Hadi M. Yassine, Maria K. Smatti, Amira Saeed, Isabelle Vandernoot, Jean-Christophe Goffard, Guillaume Smits, Isabelle Migeotte, Filomeen Haerynck, Isabelle Meyts, Laurent Abel, Jean-Laurent Casanova, Mohammad R. Hasan, and Nico Marr

Subjects
Immunology, Infectious disease, Medicine
Abstract

Four endemic human coronaviruses (HCoVs) are commonly associated with acute respiratory infection in humans. B cell responses to these “common cold” viruses remain incompletely understood. Here we report a comprehensive analysis of CoV-specific antibody repertoires in 231 children and 1168 adults using phage immunoprecipitation sequencing. Seroprevalence of antibodies against endemic HCoVs ranged between approximately 4% and 27% depending on the species and cohort. We identified at least 136 novel linear B cell epitopes. Antibody repertoires against endemic HCoVs were qualitatively different between children and adults in that anti-HCoV IgG specificities more frequently found among children targeted functionally important and structurally conserved regions of the spike, nucleocapsid, and matrix proteins. Moreover, antibody specificities targeting the highly conserved fusion peptide region and S2′ cleavage site of the spike protein were broadly cross-reactive with peptides of epidemic human and nonhuman coronaviruses. In contrast, an acidic tandem repeat in the N-terminal region of the Nsp3 subdomain of the HCoV-HKU1 polyprotein was the predominant target of antibody responses in adult donors. Our findings shed light on the dominant species-specific and pan-CoV target sites of human antibody responses to coronavirus infection, thereby providing important insights for the development of prophylactic or therapeutic monoclonal antibodies and vaccine design.

Published
2021
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7. A curated transcriptome dataset collection to investigate inborn errors of immunity [version 2; peer review: 2 approved]

Author

Salim Bougarn, Sabri Boughorbel, Damien Chaussabel, and Nico Marr

Subjects
Medicine, Science
Abstract

Primary immunodeficiencies (PIDs) are a heterogeneous group of inherited disorders, frequently caused by loss-of-function and less commonly by gain-of-function mutations, which can result in susceptibility to a broad or a very narrow range of infections but also in inflammatory, allergic or malignant diseases. Owing to the wide range in clinical manifestations and variability in penetrance and expressivity, there is an urgent need to better understand the underlying molecular, cellular and immunological phenotypes in PID patients in order to improve clinical diagnosis and management. Here we have compiled a manually curated collection of public transcriptome datasets mainly obtained from human whole blood, peripheral blood mononuclear cells (PBMCs) or fibroblasts of patients with PIDs and of control subjects for subsequent meta-analysis, query and interpretation. A total of eighteen (18) datasets derived from studies of PID patients were identified and retrieved from the NCBI Gene Expression Omnibus (GEO) database and loaded in GXB, a custom web application designed for interactive query and visualization of integrated large-scale data. The dataset collection includes samples from well characterized PID patients that were stimulated ex vivo under a variety of conditions to assess the molecular consequences of the underlying, naturally occurring gene defects on a genome-wide scale. Multiple sample groupings and rank lists were generated to facilitate comparisons of the transcriptional responses between different PID patients and control subjects. The GXB tool enables browsing of a single transcript across studies, thereby providing new perspectives on the role of a given molecule across biological systems and PID patients. This dataset collection is available at http://pid.gxbsidra.org/dm3/geneBrowser/list.

Published
2019
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8. A curated transcriptome dataset collection to investigate the blood transcriptional response to viral respiratory tract infection and vaccination. [version 1; peer review: 2 approved]

Author

Salim Bougarn, Sabri Boughorbel, Damien Chaussabel, and Nico Marr

Subjects
Medicine, Science
Abstract

The human immune defense mechanisms and factors associated with good versus poor health outcomes following viral respiratory tract infections (VRTI), as well as correlates of protection following vaccination against respiratory viruses, remain incompletely understood. To shed further light into these mechanisms, a number of systems-scale studies have been conducted to measure transcriptional changes in blood leukocytes of either naturally or experimentally infected individuals, or in individual’s post-vaccination. Here we are making available a public repository, for research investigators for interpretation, a collection of transcriptome datasets obtained from human whole blood and peripheral blood mononuclear cells (PBMC) to investigate the transcriptional responses following viral respiratory tract infection or vaccination against respiratory viruses. In total, Thirty one31 datasets, associated to viral respiratory tract infections and their related vaccination studies, were identified and retrieved from the NCBI Gene Expression Omnibus (GEO) and loaded in a custom web application designed for interactive query and visualization of integrated large-scale data. Quality control checks, using relevant biological markers, were performed. Multiple sample groupings and rank lists were created to facilitate dataset query and interpretation. Via this interface, users can generate web links to customized graphical views, which may be subsequently inserted into manuscripts to report novel findings. The GXB tool enables browsing of a single gene across projects, providing new perspectives on the role of a given molecule across biological systems in the diagnostic and prognostic following VRTI but also in identifying new correlates of protection. This dataset collection is available at: http://vri1.gxbsidra.org/dm3/geneBrowser/list.

Published
2019
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9. IRF4 haploinsufficiency in a family with Whipple’s disease

Author

Antoine Guérin, Gaspard Kerner, Nico Marr, Janet G Markle, Florence Fenollar, Natalie Wong, Sabri Boughorbel, Danielle T Avery, Cindy S Ma, Salim Bougarn, Matthieu Bouaziz, Vivien Béziat, Erika Della Mina, Carmen Oleaga-Quintas, Tomi Lazarov, Lisa Worley, Tina Nguyen, Etienne Patin, Caroline Deswarte, Rubén Martinez-Barricarte, Soraya Boucherit, Xavier Ayral, Sophie Edouard, Stéphanie Boisson-Dupuis, Vimel Rattina, Benedetta Bigio, Guillaume Vogt, Frédéric Geissmann, Lluis Quintana-Murci, Damien Chaussabel, Stuart G Tangye, Didier Raoult, Laurent Abel, Jacinta Bustamante, and Jean-Laurent Casanova

Subjects
Whipple's disease, primary immunodeficiency, IRF4, haploinsufficiency, Medicine, Science, Biology (General), QH301-705.5
Abstract

Most humans are exposed to Tropheryma whipplei (Tw). Whipple’s disease (WD) strikes only a small minority of individuals infected with Tw (

Published
2018
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10. Respiratory syncytial virus-neutralizing serum antibody titers in infants following palivizumab prophylaxis with an abbreviated dosing regimen.

Author

Jennifer Claydon, Amitava Sur, Allison Callejas, Mihoko Ladd, Eddie Kwan, Richard Taylor, Stuart E Turvey, Alfonso Solimano, Pascal M Lavoie, and Nico Marr

Subjects
Medicine, Science
Abstract

Monthly injections of palivizumab during the respiratory syncytial virus (RSV) season in at-risk infants reduces RSV-associated hospitalizations. However, the additive effect of naturally acquired immunity remains unclear. The objective of this study was to assess total neutralizing serum antibodies (NAb) against RSV in at-risk infants who had received an abbreviated course of palivizumab prophylaxis.Serum samples were collected from infants enrolled in the RSV Immunoprophylaxis Program in British Columbia, Canada over 2 consecutive RSV seasons (2013 to 2015). Infants in this program had received an abbreviated course of palivizumab in accordance with the provincial guidelines. Data were compared to adults and infants less than 12 months of age who did not receive palivizumab. Anti-RSV NAb titers were measured using an RSV microneutralization assay.Infants who received palivizumab had anti-RSV NAb titers at the end of the RSV season that persisted beyond what is expected from the pharmacokinetics of palivizumab alone. Moreover, 54% of the control infants who did not receive palivizumab and all tested adults had protective anti-RSV NAb titers.Based on our observations, we hypothesize that naturally acquired NAb provide additive protection, which may significantly reduce the need for additional doses of palivizumab in infants at risk of severe RSV infections.

Published
2017
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11. A curated transcriptome dataset collection to investigate the functional programming of human hematopoietic cells in early life [version 1; referees: 2 approved]

Author

Mahbuba Rahman, Sabri Boughorbel, Scott Presnell, Charlie Quinn, Chiara Cugno, Damien Chaussabel, and Nico Marr

Subjects
Bioinformatics, Data Sharing, Genomics, Medicine, Science
Abstract

Compendia of large-scale datasets made available in public repositories provide an opportunity to identify and fill gaps in biomedical knowledge. But first, these data need to be made readily accessible to research investigators for interpretation. Here we make available a collection of transcriptome datasets to investigate the functional programming of human hematopoietic cells in early life. Thirty two datasets were retrieved from the NCBI Gene Expression Omnibus (GEO) and loaded in a custom web application called the Gene Expression Browser (GXB), which was designed for interactive query and visualization of integrated large-scale data. Quality control checks were performed. Multiple sample groupings and gene rank lists were created allowing users to reveal age-related differences in transcriptome profiles, changes in the gene expression of neonatal hematopoietic cells to a variety of immune stimulators and modulators, as well as during cell differentiation. Available demographic, clinical, and cell phenotypic information can be overlaid with the gene expression data and used to sort samples. Web links to customized graphical views can be generated and subsequently inserted in manuscripts to report novel findings. GXB also enables browsing of a single gene across projects, thereby providing new perspectives on age- and developmental stage-specific expression of a given gene across the human hematopoietic system. This dataset collection is available at: http://developmentalimmunology.gxbsidra.org/dm3/geneBrowser/list.

Published
2016
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12. Assessment of genetic associations between common single nucleotide polymorphisms in RIG-I-like receptor and IL-4 signaling genes and severe respiratory syncytial virus infection in children: a candidate gene case-control study.

Author

Nico Marr, Aaron F Hirschfeld, Angie Lam, Shirley Wang, Pascal M Lavoie, and Stuart E Turvey

Subjects
Medicine, Science
Abstract

The majority of cases of severe pediatric respiratory syncytial virus (RSV) infection occur in otherwise healthy infants who have no identifiable risk factors, suggesting that additional subclinical factors, such as population genetic variation, influence the course of RSV infection. The objective of this study was to test if common single nucleotide polymorphisms (SNPs) in genes encoding for immune signalling components of the RIG-I-like receptor (RLR) and IL-4-signalling pathways affect the outcome of RSV infection in early life. We genotyped 8 SNPs using allele-specific probes combined with real-time PCR. Each of the SNPs tested had previously been established to have a functional impact on immune responsiveness and two of the SNPs in the IL4 and IL4R genes had previously been associated with severe RSV bronchiolitis. Association with susceptibility to severe RSV infection was tested by statistically comparing genotype and allele frequencies in infants and young children hospitalized with severe RSV bronchiolitis (n = 140) with two control groups-children who tested positive for RSV but did not require hospitalization (n = 100), and a general population control group (n = 285). Our study was designed with sufficient power (>80%) to detect clinically-relevant associations with effect sizes ≥1.5. However, we detected no statistically significant differences in allele and genotype frequencies of the investigated SNPs between the inpatient and control groups. To conclude, we could not replicate the previously reported association with SNPs in the IL4 and IL4R genes in our independent cohort, nor did we find that common SNPs in genes encoding for RLRs and the downstream adapter MAVS were associated with susceptibility to severe RSV infections. Despite the existing evidence demonstrating a functional immunological impact of these SNPs, our data suggest that the biological effect of each individual SNP is unlikely to affect clinical outcomes of RSV infection.

Published
2014
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13. Bordetella pertussis autotransporter Vag8 binds human C1 esterase inhibitor and confers serum resistance.

Author

Nico Marr, Nita R Shah, Rose Lee, Emma J Kim, and Rachel C Fernandez

Subjects
Medicine, Science
Abstract

Bordetella pertussis employs numerous strategies to evade the immune system, including the ability to resist killing via complement. Previously we have shown that B. pertussis binds a complement regulatory protein, C1 esterase inhibitor (C1inh) to its surface in a Bvg-regulated manner (i.e. during its virulence phase), but the B. pertussis factor was not identified. Here we set out to identify the B. pertussis C1inh-binding factor. Using a serum overlay assay, we found that this factor migrates at approximately 100 kDa on an SDS-PAGE gel. To identify this factor, we isolated proteins of approximately 100 kDa from wild type strain BP338 and from BP347, an isogenic Bvg mutant that does not bind C1inh. Using mass spectrometry and bioinformatics, we identified the autotransporter protein Vag8 as the putative C1inh binding protein. To prove that Vag8 binds C1inh, vag8 was disrupted in two different B. pertussis strains, namely BP338 and 18-323, and the mutants were tested for their ability to bind C1inh in a surface-binding assay. Neither mutant strain was capable of binding C1inh, whereas a complemented strain successfully bound C1inh. In addition, the passenger domain of Vag8 was expressed and purified as a histidine-tagged fusion protein and tested for C1inh-binding in an ELISA assay. Whereas the purified Vag8 passenger bound C1inh, the passenger domain of BrkA (a related autotransporter protein) failed to do so. Finally, serum assays were conducted to compare wild type and vag8 mutants. We determined that vag8 mutants from both strains were more susceptible to killing compared to their isogenic wild type counterparts. In conclusion, we have discovered a novel role for the previously uncharacterized protein Vag8 in the immune evasion of B. pertussis. Vag8 binds C1inh to the surface of the bacterium and confers serum resistance.

Published
2011
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14. Organizing training workshops on gene literature retrieval, profiling, and visualization for early career researchers [version 2; peer review: 2 approved]

Author

Fatima Al Ali, Alexandra K Marr, Zohreh Tatari-Calderone, Mohamed Alfaki, Mohammed Toufiq, Jessica Roelands, Basirudeen Syed Ahamed Kabeer, Davide Bedognetti, Nico Marr, Mathieu Garand, Darawan Rinchai, and Damien Chaussabel

Subjects
Method Article, Articles, Literature profiling, Science education, Concept extraction, Data visualization
Abstract

Early-career researchers must acquire the skills necessary to effectively search and extract information from biomedical literature. This ability is for instance crucial for evaluating the novelty of experimental results, and assessing potential publishing opportunities. Given the rapidly growing volume of publications in the field of biomedical research, new systematic approaches need to be devised and adopted for the retrieval and curation of literature relevant to a specific theme. In this context, we present a hands-on training curriculum aimed at retrieval, profiling, and visualization of literature associated with a given topic. The curriculum was implemented in a workshop in January 2021. Here we provide supporting material and step-by-step implementation guidelines with the ISG15 gene literature serving as an illustrative use case. Workshop participants can learn several skills, including: 1) building and troubleshoot PubMed queries in order to retrieve the literature associated with a gene of interest; 2) identifying key concepts relevant to given themes (such as cell types, diseases, and biological processes); 3) measuring the prevalence of these concepts in the gene literature; 4) extracting key information from relevant articles, and 5) developing a background section or summary on the basis of this information. Finally, trainees can learn to consolidate the structured information captured through this process for presentation via an interactive web application.

Published
2023
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15. Organizing gene literature retrieval, profiling, and visualization training workshops for early career researchers [version 1; peer review: 1 approved, 1 not approved]

Author

Fatima Al Ali, Alexandra K Marr, Zohreh Tatari-Calderone, Mohamed Alfaki, Mohammed Toufiq, Jessica Roelands, Basirudeen Syed Ahamed Kabeer, Davide Bedognetti, Nico Marr, Mathieu Garand, Darawan Rinchai, and Damien Chaussabel

Subjects
Method Article, Articles, Literature profiling, Science education, Concept extraction, Data visualization
Abstract

Developing the skills needed to effectively search and extract information from biomedical literature is essential for early-career researchers. It is, for instance, on this basis that the novelty of experimental results, and therefore publishing opportunities, can be evaluated. Given the unprecedented volume of publications in the field of biomedical research, new systematic approaches need to be devised and adopted for the retrieval and curation of literature relevant to a specific theme. Here we describe a hands-on training curriculum aimed at retrieval, profiling, and visualization of literature associated with a given topic. This curriculum was implemented in a workshop in January 2021. We provide supporting material and step-by-step implementation guidelines with the ISG15 gene literature serving as an illustrative use case. Through participation in such a workshop, trainees can learn: 1) to build and troubleshoot PubMed queries in order to retrieve the literature associated with a gene of interest; 2) to identify key concepts relevant to given themes (such as cell types, diseases, and biological processes); 3) to measure the prevalence of these concepts in the gene literature; 4) to extract key information from relevant articles, and 5) to develop a background section or summary on the basis of this information. Finally, trainees can learn to consolidate the structured information captured through this process for presentation via an interactive web application.

Published
2021
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16. A curated transcriptome dataset collection to investigate inborn errors of immunity [version 1; peer review: 2 approved with reservations]

Author

Salim Bougarn, Sabri Boughorbel, Damien Chaussabel, and Nico Marr

Subjects
Data Note, Articles, Transcriptomics, microarray, primary immunodeficiency disorders, inborn errors of immunity.
Abstract

Primary immunodeficiencies (PIDs) are a heterogeneous group of inherited disorders, frequently caused by loss-of-function and less commonly by gain-of-function mutations, which can result in susceptibility to a broad or a very narrow range of infections but also in inflammatory, allergic or malignant diseases. Owing to the wide range in clinical manifestations and variability in penetrance and expressivity, there is an urgent need to better understand the underlying molecular, cellular and immunological phenotypes in PID patients in order to improve clinical diagnosis and management. Here we have compiled a manually curated collection of public transcriptome datasets mainly obtained from human whole blood, peripheral blood mononuclear cells (PBMCs) or fibroblasts of patients with PIDs and of control subjects for subsequent meta-analysis, query and interpretation. A total of nineteen (19) datasets derived from studies of PID patients were identified and retrieved from the NCBI Gene Expression Omnibus (GEO) database and loaded in GXB, a custom web application designed for interactive query and visualization of integrated large-scale data. The dataset collection includes samples from well characterized PID patients that were stimulated ex vivo under a variety of conditions to assess the molecular consequences of the underlying, naturally occurring gene defects on a genome-wide scale. Multiple sample groupings and rank lists were generated to facilitate comparisons of the transcriptional responses between different PID patients and control subjects. The GXB tool enables browsing of a single transcript across studies, thereby providing new perspectives on the role of a given molecule across biological systems and PID patients. This dataset collection is available at http://pid.gxbsidra.org/dm3/geneBrowser/list.

Published
2019
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17. Encephalitis and poor neuronal death–mediated control of herpes simplex virus in human inherited RIPK3 deficiency

Author

Zhiyong Liu, Eduardo J. Garcia Reino, Oliver Harschnitz, Hongyan Guo, Yi-Hao Chan, Noopur V. Khobrekar, Mary L. Hasek, Kerry Dobbs, Darawan Rinchai, Marie Materna, Daniela Matuozzo, Danyel Lee, Paul Bastard, Jie Chen, Yoon Seung Lee, Seong K. Kim, Shuxiang Zhao, Param Amin, Lazaro Lorenzo, Yoann Seeleuthner, Remi Chevalier, Laure Mazzola, Claire Gay, Jean-Louis Stephan, Baptiste Milisavljevic, Soraya Boucherit, Flore Rozenberg, Rebeca Perez de Diego, Richard D. Dix, Nico Marr, Vivien Béziat, Aurelie Cobat, Mélodie Aubart, Laurent Abel, Stephane Chabrier, Gregory A. Smith, Luigi D. Notarangelo, Edward S. Mocarski, Lorenz Studer, Jean-Laurent Casanova, and Shen-Ying Zhang

Subjects
Immunology, General Medicine
Abstract

Inborn errors of TLR3-dependent type I IFN immunity in cortical neurons underlie forebrain herpes simplex virus-1 (HSV-1) encephalitis (HSE) due to uncontrolled viral growth and subsequent cell death. We report an otherwise healthy patient with HSE who was compound heterozygous for nonsense (R422*) and frameshift (P493fs9*) RIPK3 variants. Receptor-interacting protein kinase 3 (RIPK3) is a ubiquitous cytoplasmic kinase regulating cell death outcomes, including apoptosis and necroptosis. In vitro, the R422* and P493fs9* RIPK3 proteins impaired cellular apoptosis and necroptosis upon TLR3, TLR4, or TNFR1 stimulation and ZBP1/DAI-mediated necroptotic cell death after HSV-1 infection. The patient’s fibroblasts displayed no detectable RIPK3 expression. After TNFR1 or TLR3 stimulation, the patient’s cells did not undergo apoptosis or necroptosis. After HSV-1 infection, the cells supported excessive viral growth despite normal induction of antiviral IFN-β and IFN-stimulated genes (ISGs). This phenotype was, nevertheless, rescued by application of exogenous type I IFN. The patient’s human pluripotent stem cell (hPSC)–derived cortical neurons displayed impaired cell death and enhanced viral growth after HSV-1 infection, as did isogenic RIPK3-knockout hPSC-derived cortical neurons. Inherited RIPK3 deficiency therefore confers a predisposition to HSE by impairing the cell death–dependent control of HSV-1 in cortical neurons but not their production of or response to type I IFNs.

Published
2023

18. Human IL-23 is essential for IFN-γ–dependent immunity to mycobacteria

Author

Quentin Philippot, Masato Ogishi, Jonathan Bohlen, Julia Puchan, Andrés Augusto Arias, Tina Nguyen, Marta Martin-Fernandez, Clement Conil, Darawan Rinchai, Mana Momenilandi, Seyed Alireza Mahdaviani, Mohammad Keramatipour, Jérémie Rosain, Rui Yang, Taushif Khan, Anna-Lena Neehus, Marie Materna, Ji Eun Han, Jessica Peel, Federico Mele, Marc Weisshaar, Sandra Jovic, Paul Bastard, Romain Lévy, Tom Le Voyer, Peng Zhang, Majistor Raj Luxman Maglorius Renkilaraj, Carlos A. Arango-Franco, Simon Pelham, Yoann Seeleuthner, Mathieu Pochon, Manar Mahmoud Ahmad Ata, Fatima Al Ali, Mélanie Migaud, Camille Soudée, Tatiana Kochetkov, Anne Molitor, Raphael Carapito, Seiamak Bahram, Bertrand Boisson, Claire Fieschi, Davood Mansouri, Nico Marr, Satoshi Okada, Mohammad Shahrooei, Nima Parvaneh, Zahra Chavoshzadeh, Aurélie Cobat, Dusan Bogunovic, Laurent Abel, Stuart G. Tangye, Cindy S. Ma, Vivien Béziat, Federica Sallusto, Stéphanie Boisson-Dupuis, Jacinta Bustamante, Jean-Laurent Casanova, and Anne Puel

Subjects
Immunology, General Medicine
Abstract

Patients with autosomal recessive (AR) IL-12p40 or IL-12Rβ1 deficiency display Mendelian susceptibility to mycobacterial disease (MSMD) due to impaired IFN-γ production and, less commonly, chronic mucocutaneous candidiasis (CMC) due to impaired IL-17A/F production. We report six patients from four kindreds with AR IL-23R deficiency. These patients are homozygous for one of four different loss-of-function IL23R variants. All six patients have a history of MSMD, but only two suffered from CMC. We show that IL-23 induces IL-17A only in MAIT cells, possibly contributing to the incomplete penetrance of CMC in patients unresponsive to IL-23. By contrast, IL-23 is required for both baseline and Mycobacterium -inducible IFN-γ immunity in both Vδ2 + γδ T and MAIT cells, probably contributing to the higher penetrance of MSMD in these patients. Human IL-23 appears to contribute to IL-17A/F–dependent immunity to Candida in a single lymphocyte subset but is required for IFN-γ–dependent immunity to Mycobacterium in at least two lymphocyte subsets.

Published
2023

19. Human IRF1 governs macrophagic IFN-γ immunity to mycobacteria

Author

Jérémie Rosain, Anna-Lena Neehus, Jérémy Manry, Rui Yang, Jérémie Le Pen, Wassim Daher, Zhiyong Liu, Yi-Hao Chan, Natalia Tahuil, Özden Türel, Mathieu Bourgey, Masato Ogishi, Jean-Marc Doisne, Helena M. Izquierdo, Takayoshi Shirasaki, Tom Le Voyer, Antoine Guérin, Paul Bastard, Marcela Moncada-Vélez, Ji Eun Han, Taushif Khan, Franck Rapaport, Seon-Hui Hong, Andrew Cheung, Kathrin Haake, Barbara C. Mindt, Laura Pérez, Quentin Philippot, Danyel Lee, Peng Zhang, Darawan Rinchai, Fatima Al Ali, Manar Mahmoud Ahmad Ata, Mahbuba Rahman, Jessica N. Peel, Søren Heissel, Henrik Molina, Yasemin Kendir-Demirkol, Rasheed Bailey, Shuxiang Zhao, Jonathan Bohlen, Mathieu Mancini, Yoann Seeleuthner, Marie Roelens, Lazaro Lorenzo, Camille Soudée, María Elvira Josefina Paz, María Laura González, Mohamed Jeljeli, Jean Soulier, Serge Romana, Anne-Sophie L’Honneur, Marie Materna, Rubén Martínez-Barricarte, Mathieu Pochon, Carmen Oleaga-Quintas, Alexandre Michev, Mélanie Migaud, Romain Lévy, Marie-Alexandra Alyanakian, Flore Rozenberg, Carys A. Croft, Guillaume Vogt, Jean-François Emile, Laurent Kremer, Cindy S. Ma, Jörg H. Fritz, Stanley M. Lemon, András N. Spaan, Nicolas Manel, Laurent Abel, Margaret R. MacDonald, Stéphanie Boisson-Dupuis, Nico Marr, Stuart G. Tangye, James P. Di Santo, Qian Zhang, Shen-Ying Zhang, Charles M. Rice, Vivien Béziat, Nico Lachmann, David Langlais, Jean-Laurent Casanova, Philippe Gros, Jacinta Bustamante, Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Hannover Medical School [Hannover] (MHH), St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller University [New York], Institut de Recherche en Infectiologie de Montpellier (IRIM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Yong Loo Lin School of Medicine [Singapore], Hospital del Niño Jesus, San Miguel de Tucumán, Bezmiâlem Vakıf Üniversitesi, McGill University = Université McGill [Montréal, Canada], Immunité Innée - Innate Immunity, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Institut Curie [Paris], University of North Carolina System (UNC), Garvan Institute of medical research, The University of Sydney, CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Universidad de Antioquia = University of Antioquia [Medellín, Colombia], East China Normal University [Shangaï] (ECNU), Sidra Medicine [Doha, Qatar], 'Juan Pedro Garrahan' National Hospital of Pediatrics, Buenos Aires, Institut Necker Enfants-Malades (INEM - UM 111 (UMR 8253 / U1151)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Hôpital Cochin [AP-HP], Hopital Saint-Louis [AP-HP] (AP-HP), Vanderbilt University Medical Center [Nashville], Vanderbilt University [Nashville], Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP), Hôpital Ambroise Paré [AP-HP], Université de Montpellier (UM), Howard Hughes Medical Institute (HHMI), The Laboratory of Human Genetics of Infectious Diseases is supported in part by grants from Inserm, Paris Cité University, the St. Giles Foundation, The Rockefeller University, the Center for Clinical and Translational Science (UL1TR001866), the National Center for Research Resources and the National Center for Advancing Sciences, the National Institutes of Health (NIH), (R01AI095983, R01AI088364, R01AI163029, and U19AI162568), the National Institute of Allergy and Infectious Diseases, the French National Research Agency (ANR) under the 'Investments for the future' program (ANR-10-IAHU-01), the Integrative Biology of Emerging Infectious Diseases Laboratory of Excellence (ANR-10-LABX-62-IBEID), the French Foundation for Medical Research (FRM) (EQU201903007798), the ANRS Nord-Sud (ANRS-COV05), ANRS (ECTZ170784-ANRS0073), GENVIR (ANR-20-CE93-003), GENMSMD (ANR-16-CE17-0005-01), AABIFNCOV (ANR-20-CO11-0001), GenMIS-C (ANR-21-COVR-0039), SUNLIVE (ANR-19-CE15-0012-01), MAFMACRO (ANR-22-CE92-0008) grants, Ecos-NORD (ECOS N°C19S01), the Fisher Center for Alzheimer's Research Foundation, the Meyer Foundation, the JPB Foundation, the European Union’s Horizon 2020 research and innovation program (824110, EASI-Genomics), the Square Foundation, Grandir–Fonds de solidarité pour l’Enfance, the Fondation du Souffle, the SCOR Corporate Foundation for Science, the French Ministry of Higher Education, Research, and Innovation (MESRI-COVID-19), and REACTing-INSERM. The Laboratory of Virology and Infectious Disease was supported in part by the NIH (R01AI091707-10 to C.M.R.). J.L.P. was supported by the Francois Wallace Monahan Postdoctoral Fellowship at The Rockefeller University and the European Molecular Biology Organization Long-Term Fellowship (ALTF 380-2018). N. Marr was supported by Sidra Medicine and the Qatar National Research Fund (NPRP9-251-3-045). The Yale Center for Mendelian Genomics (UM1HG006504) was funded by the National Human Genome Research Institute, the Yale GSP Coordinating Center (U24 HG008956), and the Yale High-Performance Computing Center (S10OD018521). This research was partly supported by Calcul Québec, Compute Canada Canadian Institutes of Health Research (CIHR) Project Grant to D. Langlais. (#168959) and a CIHR Foundation Grant (to P.G.). D. Langlais was also supported by an FRQS Chercheur-Boursier Junior 1 Award and the Calgary Foundation for Innovation John R. Evans Leaders Fund. P.G. is supported by a Distinguished James McGill Professorship award from McGill University. S.M.L is supported by the NIH: R01-AI103083 and R01-AI150095. J.R. was supported by poste d’accueil Inserm'. J.R., P.B., and T.L.V were supported by the MD-PhD program of the Imagine Institute by the Bettencourt Schueller Foundation. N.L received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (852178 grant), German Research Foundation,(DFG) under Germany’s Excellence Strategy—EXC 2155—project number 390874280 and REBIRTH 'Förderung aus Mitteln des Niedersächsischen Vorab'. A.-L.N. was supported by the international PhD program of the Imagine Institute, by the Bettencourt Schueller Foundation and the fin de thèse FRM program (FDT202204015102). R.Y. was supported by the Sackler Center for Biomedicine and Nutrition, the Shapiro-Silverberg Fund for the Advancement of Translational Research at the Center for Clinical and Translational Science of the Rockefeller University, and the Research Grant Program from the Immune Deficiency Foundation. D. Lee. was supported by FRMfellowship (FDM202006011282). C.S.M was supported by an Early-Mid Career Research Fellowship from the Department of Health of the New South Wales Government of Australia. S.G.T was supported by an NHMRC Leadership 3 Investigator Grant (1176665) and NHMRC grant (1113904). M.O. was supported by the David Rockefeller Graduate Program, the Funai Foundation for Information Technology, the Honjo International Scholarship Foundation, and the New York Hideyo Noguchi Memorial Society. This work was supported by grants from ANRS (ECTZ118797), Sidaction (20-2-AEQ-12822-2), and FRM (EQU202103012774) to N. Manel, and H.I. was supported by fellowships from Institut Curie, Seneca Foundation (20941/PD/18), and ANRS (ECTZ171453). A.N.S. was supported in part by the European Union’s Horizon 2020 research and innovation program (789645 Marie Sklodowska-Curie grant). Y.-H.C. is supported by an A∗STAR International Fellowship. J. Bohlen is an EMBO postdoctoral fellow. We thank the NIH Tetramer Core Facility (NTCF) for providing the 5-OP-RU-loaded MR1 tetramer, which was developed jointly with Dr. James McCluskey, Dr. Jamie Rossjohn, and Dr. David Fairlie., ANR-10-IAHU-0001,Imagine,Institut Hospitalo-Universitaire Imagine(2010), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-16-CE17-0005,GENMSMD,Dissection génétique de la Susceptibilité Mendélienne aux infections mycobactériennes chez l'homme(2016), ANR-20-CO11-0001,AABIFNCOV,Bases génétiques et immunologiques des auto-anticorps contre les interférons de type I prédisposant aux formes sévères de COVID-19.(2020), ANR-21-COVR-0039,GenMIS-C,Recherche des Déficits immunitaires innées monogéniques prédisposant au syndrome inflammatoire multisystémique chez l'enfant.(2021), ANR-19-CE15-0012,SUNLIVE,Variabilité structurale et fonctionnelle des lipides complexes chez les mycobactéries : de l'assemblage de la paroi à la physiopathologie et virulence(2019), ANR-22-CE92-0008,MAFMACRO,Genetic predisposition and the role of myeloid cells in the susceptibility to mycobacterial infection(2022), European Project: 824110,H2020-INFRAIA-2018-1,EASI-Genomics(2019), and TÜREL, ÖZDEN

Subjects
inborn errors of immunity, Temel Bilimler, [SDV]Life Sciences [q-bio], interferon-stimulated gene, Life Sciences, Molecular Biology and Genetics, Genel Biyokimya, Genetik ve Moleküler Biyoloji, IRF1, General Biochemistry, Genetics and Molecular Biology, Mycobacterium, macrophages, interferon-γ, Yaşam Bilimleri, viruses, Cytogenetic, Natural Sciences, Moleküler Biyoloji ve Genetik, Sitogenetik
Abstract

Inborn errors of human IFN-γ-dependent macrophagic immunity underlie mycobacterial diseases, whereas inborn errors of IFN-α/β-dependent intrinsic immunity underlie viral diseases. Both types of IFNs induce the transcription factor IRF1. We describe unrelated children with inherited complete IRF1 deficiency and early-onset, multiple, life-threatening diseases caused by weakly virulent mycobacteria and related intramacrophagic pathogens. These children have no history of severe viral disease, despite exposure to many viruses, including SARS-CoV-2, which is life-threatening in individuals with impaired IFN-α/β immunity. In leukocytes or fibroblasts stimulated in vitro, IRF1-dependent responses to IFN-γ are, both quantitatively and qualitatively, much stronger than those to IFN-α/β. Moreover, IRF1-deficient mononuclear phagocytes do not control mycobacteria and related pathogens normally when stimulated with IFN-γ. By contrast, IFN-α/β-dependent intrinsic immunity to nine viruses, including SARS-CoV-2, is almost normal in IRF1-deficient fibroblasts. Human IRF1 is essential for IFN-γ-dependent macrophagic immunity to mycobacteria, but largely redundant for IFN-α/β-dependent antiviral immunity.

Published
2023

20. Inherited human ITK deficiency impairs IFN-γ immunity and underlies tuberculosis

Author

Masato Ogishi, Rui Yang, Rémy Rodriguez, Dominic P. Golec, Emmanuel Martin, Quentin Philippot, Jonathan Bohlen, Simon J. Pelham, Andrés Augusto Arias, Taushif Khan, Manar Ata, Fatima Al Ali, Flore Rozenberg, Xiao-Fei Kong, Maya Chrabieh, Candice Laine, Wei-Te Lei, Ji Eun Han, Yoann Seeleuthner, Zenia Kaul, Emmanuelle Jouanguy, Vivien Béziat, Leila Youssefian, Hassan Vahidnezhad, V. Koneti Rao, Bénédicte Neven, Claire Fieschi, Davood Mansouri, Mohammad Shahrooei, Sevgi Pekcan, Gulsum Alkan, Melike Emiroğlu, Hüseyin Tokgöz, Jouni Uitto, Fabian Hauck, Jacinta Bustamante, Laurent Abel, Sevgi Keles, Nima Parvaneh, Nico Marr, Pamela L. Schwartzberg, Sylvain Latour, Jean-Laurent Casanova, and Stéphanie Boisson-Dupuis

Subjects
Mice, Interferon-gamma, T-Lymphocyte Subsets, Receptors, Antigen, T-Cell, alpha-beta, Immunology, Animals, Humans, Tuberculosis, Immunology and Allergy, Receptors, Antigen, T-Cell, gamma-delta, Thymus Gland
Abstract

Inborn errors of IFN-γ immunity can underlie tuberculosis (TB). We report three patients from two kindreds without EBV viremia or disease but with severe TB and inherited complete ITK deficiency, a condition associated with severe EBV disease that renders immunological studies challenging. They have CD4+ αβ T lymphocytopenia with a concomitant expansion of CD4−CD8− double-negative (DN) αβ and Vδ2− γδ T lymphocytes, both displaying a unique CD38+CD45RA+T-bet+EOMES− phenotype. Itk-deficient mice recapitulated an expansion of the γδ T and DN αβ T lymphocyte populations in the thymus and spleen, respectively. Moreover, the patients’ T lymphocytes secrete small amounts of IFN-γ in response to TCR crosslinking, mitogens, or forced synapse formation with autologous B lymphocytes. Finally, the patients’ total lymphocytes secrete small amounts of IFN-γ, and CD4+, CD8+, DN αβ T, Vδ2+ γδ T, and MAIT cells display impaired IFN-γ production in response to BCG. Inherited ITK deficiency undermines the development and function of various IFN-γ–producing T cell subsets, thereby underlying TB.

Published
2022

21. Detection of Antinuclear Antibodies Targeting Intracellular Signal Transduction, Metabolism, Apoptotic Processes and Cell Death in Critical COVID-19 Patients

Author

Gheyath K, Nasarallah, Aisha D, Fakhroo, Taushif, Khan, Farhan S, Cyprian, Fatima, Al Ali, Manar M A, Ata, Sara, Taleb, Hadeel T, Zedan, Duaa W, Al-Sadeq, Fathima H, Amanullah, Ali A, Hssain, Ali H, Eid, Laith J, Abu-Raddad, Abdullatif, Al-Khal, Asmaa A, Al Thani, Nico, Marr, and Hadi M, Yassine

Subjects
Coronavirus, Infectious Diseases, ICU, COVID-19, Autoimmunity, Hematology, ANA
Abstract

Background and Objectives: The heterogeneity of the coronavirus disease of 2019 (COVID-19) lies within its diverse symptoms and severity, ranging from mild to lethal. Acute respiratory distress syndrome (ARDS) is a leading cause of mortality in COVID-19 patients, characterized by a hyper cytokine storm. Autoimmunity is proposed to occur as a result of COVID-19, given the high similarity of the immune responses observed in COVID-19 and autoimmune diseases. Here, we investigate the level of autoimmune antibodies in COVID-19 patients with different severities. Results: Initial screening for antinuclear antibodies (ANA) IgG using ELISA revealed that 1.58% (2/126) and 4% (5/126) of intensive care unit (ICU) COVID-19 cases expressed strong and moderate ANA levels, respectively. An additional sample was positive with immunofluorescence assays (IFA) screening. However, all the non-ICU cases (n=273) were ANA negative using both assays. Samples positive for ANA were further confirmed with large-scale autoantibody screening by phage immunoprecipitation-sequencing (PhIP-Seq). The majority of the ANA-positive samples showed "speckled" ANA pattern by microscopy and revealed autoantibody specificities that targeted proteins involved in intracellular signal transduction, metabolism, apoptotic processes, and cell death by PhIP-Seq; further denoting reactivity to nuclear and cytoplasmic antigens. Conclusion: Our results further support the notion of routine screening for autoimmune responses in COVID-19 patients, which might help improve disease prognosis and patient management. Further, results provide compelling evidence that ANA-positive individuals should be excluded from being donors for convalescent plasma therapy in the context of COVID-19. This study was supported by funds from QNRF, grant # NPRP11S-1212-170092.

Published
2022

22. Interferons and Resistance Mechanisms in Tumors and Pathogen-Driven Diseases—Focus on the Major Histocompatibility Complex (MHC) Antigen Processing Pathway

Author

Chiara Massa, Yuan Wang, Nico Marr, and Barbara Seliger

Subjects
Inorganic Chemistry, Organic Chemistry, General Medicine, Physical and Theoretical Chemistry, Molecular Biology, Spectroscopy, Catalysis, Computer Science Applications
Abstract

Interferons (IFNs), divided into type I, type II, and type III IFNs represent proteins that are secreted from cells in response to various stimuli and provide important information for understanding the evolution, structure, and function of the immune system, as well as the signaling pathways of other cytokines and their receptors. They exert comparable, but also distinct physiologic and pathophysiologic activities accompanied by pleiotropic effects, such as the modulation of host responses against bacterial and viral infections, tumor surveillance, innate and adaptive immune responses. IFNs were the first cytokines used for the treatment of tumor patients including hairy leukemia, renal cell carcinoma, and melanoma. However, tumor cells often develop a transient or permanent resistance to IFNs, which has been linked to the escape of tumor cells and unresponsiveness to immunotherapies. In addition, loss-of-function mutations in IFN signaling components have been associated with susceptibility to infectious diseases, such as COVID-19 and mycobacterial infections. In this review, we summarize general features of the three IFN families and their function, the expression and activity of the different IFN signal transduction pathways, and their role in tumor immune evasion and pathogen clearance, with links to alterations in the major histocompatibility complex (MHC) class I and II antigen processing machinery (APM). In addition, we discuss insights regarding the clinical applications of IFNs alone or in combination with other therapeutic options including immunotherapies as well as strategies reversing the deficient IFN signaling. Therefore, this review provides an overview on the function and clinical relevance of the different IFN family members, with a specific focus on the MHC pathways in cancers and infections and their contribution to immune escape of tumors.

Published
2023

23. Inherited IFNAR1 Deficiency in a Child with Both Critical COVID-19 Pneumonia and Multisystem Inflammatory Syndrome

Author

Hassan Abolhassani, Nils Landegren, Paul Bastard, Marie Materna, Mohammadreza Modaresi, Likun Du, Maribel Aranda-Guillén, Fabian Sardh, Fanglei Zuo, Peng Zhang, Harold Marcotte, Nico Marr, Taushif Khan, Manar Ata, Fatima Al-Ali, Remi Pescarmona, Alexandre Belot, Vivien Béziat, Qian Zhang, Jean-Laurent Casanova, Olle Kämpe, Shen-Ying Zhang, Lennart Hammarström, Qiang Pan-Hammarström, Department of Biosciences and Nutrition [Karolinska Insitutet, Sueden] (BioNut), Karolinska Institutet [Stockholm], Iran University of Medical Sciences [Tehran, Iran] (IUMS), Uppsala University, Department of medicine [Stockholm], Karolinska Institutet [Stockholm]-Karolinska University Hospital [Stockholm], St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller University [New York], Human genetics of infectious diseases : Mendelian predisposition (Equipe Inserm U1163), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Children’s Medical Center [Tehran, Liban], Tehran University of Medical Sciences (TUMS), Karolinska Institute, Sidra Medicine [Doha, Qatar], Hamad Bin Khalifa University (HBKU), Centre International de Recherche en Infectiologie (CIRI), École normale supérieure de Lyon (ENS de Lyon)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Université Jean Monnet - Saint-Étienne (UJM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Service d'immunologie [Centre Hospitalier Lyon Sud - HCL], Centre Hospitalier Lyon Sud [CHU - HCL] (CHLS), Hospices Civils de Lyon (HCL)-Hospices Civils de Lyon (HCL), Hôpital Femme Mère Enfant [CHU - HCL] (HFME), Hospices Civils de Lyon (HCL), Howard Hughes Medical Institute [New York] (HHMI), Howard Hughes Medical Institute (HHMI)-New York University School of Medicine, NYU System (NYU)-NYU System (NYU)-Rockefeller University [New York]-Columbia University Irving Medical Center (CUIMC), Karolinska University Hospital [Stockholm], Open access funding provided by Karolinska Institute. This work was supported by The European Union’s Horizon 2020 research and innovation program (ATAC, 101003650), the Center for Innovative Medicine at Karolinska Institutet, the Swedish Research Council, the Knut and Alice Wallenberg Foundation (KAW). The Laboratory of Human Genetics of Infectious Diseases is supported by the Howard Hughes Medical Institute, the Rockefeller University, the St. Giles Foundation, the National Institutes of Health (NIH) (R01AI088364 and R01AI163029), the National Center for Advancing Translational Sciences (NCATS), NIH Clinical and Translational Science Award (CTSA) program (UL1TR001866), a Fast Grant from Emergent Ventures, Mercatus Center at George Mason University, the Fisher Center for Alzheimer’s Research Foundation, the Meyer Foundation, the JPB Foundation, the French National Research Agency (ANR) under the 'Investments for the Future' program (ANR-10-IAHU-01), ANR grants (ANR-14-CE14-0008–01, ANR-18-CE15-0020–02, ANR-20-CE93-003, ANR-20-CO11-000,1 and ANR-21-COVR-0039), the Integrative Biology of Emerging Infectious Diseases Laboratory of Excellence (ANR-10-LABX-62-IBEID), the French Foundation for Medical Research (FRM) (EQU201903007798), the FRM and ANR GENCOVID project (ANR-20-COVI-0003), ANRS Nord-Sud (ANRS-COV05), the European Union’s Horizon 2020 research and innovation program under grant agreement no. 824110 (EASI-Genomics), the Square Foundation, Grandir-Fonds de solidarité pour l’enfance, the SCOR Corporate Foundation for Science, Fondation du Souffle, Institut National de la Santé et de la Recherche Médicale (INSERM), REACTing-INSERM, and the University of Paris. PB was supported by the French Foundation for Medical Research (FRM, EA20170638020). PB was supported by the MD-PhD program of the Imagine Institute (with the support of the Fondation Bettencourt-Schueller). NM received funding from Sidra Medicine (SDR400048) and the Qatar National Research Fund (NPRP9-251–3-045)., ANR-10-IAHU-0001,Imagine,Institut Hospitalo-Universitaire Imagine(2010), ANR-14-CE14-0008,IEIHSEER,L'encéphalite Herpétique de l'enfant résulte de déficits héréditaires d'immunité contre l'HSV-1: une exception ou une règle?(2014), ANR-18-CE15-0020,SEAe-HostFactors,Facteurs de susceptibilité de l'hôte à l'encéphalite pédiatrique en Asie du Sud Est(2018), ANR-20-CE93-0003,GENVIR,Analyse multi-omique de l'immunité anti-virale: de l'identification des circuits biologiques pertinents à la découverte de défauts monogéniques héréditaires de l'immunité chez les patients avec infections virales sévères(2020), ANR-20-CO11-0001,AABIFNCOV,Bases génétiques et immunologiques des auto-anticorps contre les interférons de type I prédisposant aux formes sévères de COVID-19.(2020), ANR-21-COVR-0039,GenMIS-C,Recherche des Déficits immunitaires innées monogéniques prédisposant au syndrome inflammatoire multisystémique chez l'enfant.(2021), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-20-COVI-0003,GENCOVID,Identification des défauts monogéniques de l'immunité responsables des formes sévères de COVID-19 chez les patients précédemment en bonne santé(2020), European Project: 824110,H2020-INFRAIA-2018-1,EASI-Genomics(2019), Université Paris Cité, Equipe HAL, Instituts Hospitalo-Universitaires - Institut Hospitalo-Universitaire Imagine - - Imagine2010 - ANR-10-IAHU-0001 - IAHU - VALID, Appel à projets générique - L'encéphalite Herpétique de l'enfant résulte de déficits héréditaires d'immunité contre l'HSV-1: une exception ou une règle? - - IEIHSEER2014 - ANR-14-CE14-0008 - Appel à projets générique - VALID, APPEL À PROJETS GÉNÉRIQUE 2018 - Facteurs de susceptibilité de l'hôte à l'encéphalite pédiatrique en Asie du Sud Est - - SEAe-HostFactors2018 - ANR-18-CE15-0020 - AAPG2018 - VALID, Analyse multi-omique de l'immunité anti-virale: de l'identification des circuits biologiques pertinents à la découverte de défauts monogéniques héréditaires de l'immunité chez les patients avec infections virales sévères - - GENVIR2020 - ANR-20-CE93-0003 - AAPG2020 - VALID, Bases génétiques et immunologiques des auto-anticorps contre les interférons de type I prédisposant aux formes sévères de COVID-19. - - AABIFNCOV2020 - ANR-20-CO11-0001 - COVID-19 - VALID, Recherche des Déficits immunitaires innées monogéniques prédisposant au syndrome inflammatoire multisystémique chez l'enfant. - - GenMIS-C2021 - ANR-21-COVR-0039 - COVID-19 - VALID, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, Identification des défauts monogéniques de l'immunité responsables des formes sévères de COVID-19 chez les patients précédemment en bonne santé - - GENCOVID2020 - ANR-20-COVI-0003 - COVID-19 - VALID, European Advanced infraStructure for Innovative Genomics - EASI-Genomics - - H2020-INFRAIA-2018-12019-02-01 - 2023-07-31 - 824110 - VALID, Centre International de Recherche en Infectiologie - UMR (CIRI), École normale supérieure - Lyon (ENS Lyon)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
inborn errors of immunity (IEI), multisystem inflammatory syndrome in children (MIS-C), [SDV.IMM] Life Sciences [q-bio]/Immunology, SARS-CoV-2, primary immunodeficiency (PID), Immunology, Immunology in the medical area, COVID-19, Receptor, Interferon alpha-beta, Systemic Inflammatory Response Syndrome, Child, Preschool, Immunologi inom det medicinska området, Interferon Type I, critical pneumonia, Immunology and Allergy, Cytokines, Humans, [SDV.IMM]Life Sciences [q-bio]/Immunology, Original Article, Autoantibodies, IFNAR1
Abstract

Background Inborn errors of immunity (IEI) and autoantibodies to type I interferons (IFNs) underlie critical COVID-19 pneumonia in at least 15% of the patients, while the causes of multisystem inflammatory syndrome in children (MIS-C) remain elusive. Objectives To detect causal genetic variants in very rare cases with concomitant critical COVID-19 pneumonia and MIS-C. Methods Whole exome sequencing was performed, and the impact of candidate gene variants was investigated. Plasma levels of cytokines, specific antibodies against the virus, and autoantibodies against type I IFNs were also measured. Results We report a 3-year-old child who died on day 56 of SARS-CoV-2 infection with an unusual clinical presentation, combining both critical COVID-19 pneumonia and MIS-C. We identified a large, homozygous loss-of-function deletion in IFNAR1, underlying autosomal recessive IFNAR1 deficiency. Conclusions Our findings confirm that impaired type I IFN immunity can underlie critical COVID-19 pneumonia, while suggesting that it can also unexpectedly underlie concomitant MIS-C. Our report further raises the possibility that inherited or acquired dysregulation of type I IFN immunity might contribute to MIS-C in other patients.

Published
2022

24. Inherited human IFN-γ deficiency underlies mycobacterial disease

Author

Jérémie Rosain, Bernhard Fleckenstein, Chih-Yu Chi, Cheng-Lung Ku, Nico Marr, Rui Yang, Jacinta Bustamante, Flore Rozenberg, Carmen Oleaga-Quintas, Vivien Béziat, Yoann Seeleuthner, Rubén Martínez-Barricarte, Franck Rapaport, Jing-Ya Ding, Michel J. Massaad, Stéphanie Boisson-Dupuis, Raif S. Geha, Fatima Al Ali, Antoine Guérin, Laurent Abel, Taushif Khan, Gaspard Kerner, Waleed Al-Herz, Mahbuba Rahman, Jean-Laurent Casanova, Caroline Deswarte, Manon Roynard, Diane S. T. Garcia, Ahmad Al-Khabaz, and Valentine Jeanne-Julien

Subjects
0301 basic medicine, medicine.medical_treatment, Biology, Frameshift mutation, Interferon-gamma, 03 medical and health sciences, symbols.namesake, Negative selection, 0302 clinical medicine, Immunity, medicine, Humans, Gene, Loss function, Receptors, Interferon, Sequence Deletion, Genetics, Mycobacterium Infections, Base Sequence, Homozygote, Genetic Diseases, Inborn, General Medicine, Mycobacterium bovis, Phenotype, 030104 developmental biology, Cytokine, 030220 oncology & carcinogenesis, Mendelian inheritance, symbols, Female, Research Article
Abstract

Mendelian susceptibility to mycobacterial disease (MSMD) is characterized by a selective predisposition to clinical disease caused by the Bacille Calmette-Guérin (BCG) vaccine and environmental mycobacteria. The known genetic etiologies of MSMD are inborn errors of IFN-γ immunity due to mutations of 15 genes controlling the production of or response to IFN-γ. Since the first MSMD-causing mutations were reported in 1996, biallelic mutations in the genes encoding IFN-γ receptor 1 (IFN-γR1) and IFN-γR2 have been reported in many patients of diverse ancestries. Surprisingly, mutations of the gene encoding the IFN-γ cytokine itself have not been reported, raising the remote possibility that there might be other agonists of the IFN-γ receptor. We describe 2 Lebanese cousins with MSMD, living in Kuwait, who are both homozygous for a small deletion within the IFNG gene (c.354_357del), causing a frameshift that generates a premature stop codon (p.T119Ifs4*). The mutant allele is loss of expression and loss of function. We also show that the patients’ herpesvirus Saimiri–immortalized T lymphocytes did not produce IFN-γ, a phenotype that can be rescued by retrotransduction with WT IFNG cDNA. The blood T and NK lymphocytes from these patients also failed to produce and secrete detectable amounts of IFN-γ. Finally, we show that human IFNG has evolved under stronger negative selection than IFNGR1 or IFNGR2, suggesting that it is less tolerant to heterozygous deleterious mutations than IFNGR1 or IFNGR2. This may account for the rarity of patients with autosomal-recessive, complete IFN-γ deficiency relative to patients with complete IFN-γR1 and IFN-γR2 deficiencies.

Published
2020

25. Fatal Cytomegalovirus Infection in an Adult with Inherited NOS2 Deficiency

Author

Fatima Al Ali, Laurent Abel, Jean-François Emile, Davood Mansouri, Mahbuba Rahman, Franck Rapaport, Stéphanie Boisson-Dupuis, Nicholas Hernandez, Taushif Khan, Anna-Lena Neehus, David Hum, Benedetta Bigio, Vivien Béziat, Nico Marr, Jean-Laurent Casanova, Scott Drutman, Jacinta Bustamante, Emmanuelle Jouanguy, Majid Marjani, Robert Fisch, Ruslana Bryk, Nahal Mansouri, Serkan Belkaya, Lazaro Lorenzo-Diaz, Carl Nathan, and Seyed Alireza Mahdaviani

Subjects
Male, Genotype, Congenital cytomegalovirus infection, Nitric Oxide Synthase Type II, Severe disease, macromolecular substances, 030204 cardiovascular system & hematology, Nitric Oxide, Article, 03 medical and health sciences, Fatal Outcome, 0302 clinical medicine, Loss of Function Mutation, parasitic diseases, Exome Sequencing, medicine, Humans, 030212 general & internal medicine, Frameshift Mutation, business.industry, Homozygote, fungi, food and beverages, virus diseases, General Medicine, Middle Aged, medicine.disease, Pedigree, Multiple infections, Cytomegalovirus infection, Cytomegalovirus Infections, Immunology, Female, business
Abstract

BACKGROUND: Cytomegalovirus (CMV) can cause severe disease in children and adults with a variety of inherited or acquired T-cell immunodeficiencies, who are prone to multiple infections. It can also rarely cause disease in otherwise healthy persons. The pathogenesis of idiopathic CMV disease is unknown. Inbred mice that lack the gene encoding nitric oxide synthase 2 (Nos2) are susceptible to the related murine CMV infection. METHODS: We studied a previously healthy 51-year-old man from Iran who after acute CMV infection had an onset of progressive CMV disease that led to his death 29 months later. We hypothesized that the patient may have had a novel type of inborn error of immunity. Thus, we performed whole-exome sequencing and tested candidate mutant alleles experimentally. RESULTS: We found a homozygous frameshift mutation in NOS2 encoding a truncated NOS2 protein that did not produce nitric oxide, which determined that the patient had autosomal recessive NOS2 deficiency. Moreover, all NOS2 variants that we found in homozygosity in public databases encoded functional proteins, as did all other variants with an allele frequency greater than 0.001. CONCLUSIONS: These findings suggest that inherited NOS2 deficiency was clinically silent in this patient until lethal infection with CMV. Moreover, NOS2 appeared to be redundant for control of other pathogens in this patient. (Funded by the National Center for Advancing Translational Sciences and others.)

Published
2020

26. Respiratory viral infections in otherwise healthy humans with inherited IRF7 deficiency

Author

Tessa Mollie, Campbell, Zhiyong, Liu, Qian, Zhang, Marcela, Moncada-Velez, Laura E, Covill, Peng, Zhang, Ilad, Alavi Darazam, Paul, Bastard, Lucy, Bizien, Giorgia, Bucciol, Sara, Lind Enoksson, Emmanuelle, Jouanguy, Şemsi Nur, Karabela, Taushif, Khan, Yasemin, Kendir-Demirkol, Andres Augusto, Arias, Davood, Mansouri, Per, Marits, Nico, Marr, Isabelle, Migeotte, Leen, Moens, Tayfun, Ozcelik, Isabelle, Pellier, Anton, Sendel, Sevtap, Şenoğlu, Mohammad, Shahrooei, C I Edvard, Smith, Isabelle, Vandernoot, Karen, Willekens, Kadriye, Kart Yaşar, Peter, Bergman, Laurent, Abel, Aurélie, Cobat, Jean-Laurent, Casanova, Isabelle, Meyts, and UCL - SSS/IREC/PNEU - Pôle de Pneumologie, ORL et Dermatologie

Subjects
Adult, SARS-CoV-2, Virus Diseases, viruses, Influenza, Human, Viruses, COVID-19, Humans
Abstract

Autosomal recessive IRF7 deficiency was previously reported in three patients with single critical influenza or COVID-19 pneumonia episodes. The patients' fibroblasts and plasmacytoid dendritic cells produced no detectable type I and III IFNs, except IFN-β. Having discovered four new patients, we describe the genetic, immunological, and clinical features of seven IRF7-deficient patients from six families and five ancestries. Five were homozygous and two were compound heterozygous for IRF7 variants. Patients typically had one episode of pulmonary viral disease. Age at onset was surprisingly broad, from 6 mo to 50 yr (mean age 29 yr). The respiratory viruses implicated included SARS-CoV-2, influenza virus, respiratory syncytial virus, and adenovirus. Serological analyses indicated previous infections with many common viruses. Cellular analyses revealed strong antiviral immunity and expanded populations of influenza- and SARS-CoV-2-specific memory CD4+ and CD8+ T cells. IRF7-deficient individuals are prone to viral infections of the respiratory tract but are otherwise healthy, potentially due to residual IFN-β and compensatory adaptive immunity. ispartof: JOURNAL OF EXPERIMENTAL MEDICINE vol:219 issue:7 ispartof: location:United States status: published

Published
2022

27. Impaired IL-23-dependent induction of IFN-gamma underlies mycobacterial disease in patients with inherited TYK2 deficiency

Author

Masato Ogishi, Andrés Augusto Arias, Rui Yang, Ji Eun Han, Peng Zhang, Darawan Rinchai, Joshua Halpern, Jeanette Mulwa, Narelle Keating, Maya Chrabieh, Candice Lainé, Yoann Seeleuthner, Noé Ramírez-Alejo, Nioosha Nekooie-Marnany, Andrea Guennoun, Ingrid Muller-Fleckenstein, Bernhard Fleckenstein, Sara S. Kilic, Yoshiyuki Minegishi, Stephan Ehl, Petra Kaiser-Labusch, Yasemin Kendir-Demirkol, Flore Rozenberg, Abderrahmane Errami, Shen-Ying Zhang, Qian Zhang, Jonathan Bohlen, Quentin Philippot, Anne Puel, Emmanuelle Jouanguy, Zahra Pourmoghaddas, Shahrzad Bakhtiar, Andre M. Willasch, Gerd Horneff, Genevieve Llanora, Lynette P. Shek, Louis Y.A. Chai, Sen Hee Tay, Hamid H. Rahimi, Seyed Alireza Mahdaviani, Serdar Nepesov, Aziz A. Bousfiha, Emine Hafize Erdeniz, Adem Karbuz, Nico Marr, Carmen Navarrete, Mehdi Adeli, Lennart Hammarstrom, Hassan Abolhassani, Nima Parvaneh, Saleh Al Muhsen, Mohammed F. Alosaimi, Fahad Alsohime, Maryam Nourizadeh, Mostafa Moin, Rand Arnaout, Saad Alshareef, Jamila El-Baghdadi, Ferah Genel, Roya Sherkat, Ayça Kiykim, Esra Yücel, Sevgi Keles, Jacinta Bustamante, Laurent Abel, Jean-Laurent Casanova, and Stéphanie Boisson-Dupuis

Subjects
TYK2 Kinase, Interferon-gamma, Human Cells, Immunology, Immunology and Allergy, Humans, Immunodeficiency, TYK2, Interleukin-23, Job Syndrome
Abstract

Human cells homozygous for rare loss-of-expression (LOE) TYK2 alleles have impaired, but not abolished, cellular responses to IFN-alpha/beta (underlying viral diseases in the patients) and to IL-12 and IL-23 (underlying mycobacterial diseases). Cells homozygous for the common P1104A TYK2 allele have selectively impaired responses to IL-23 (underlying isolated mycobacterial disease). We report three new forms of TYK2 deficiency in six patients from five families homozygous for rare TYK2 alleles (R864C, G996R, G634E, or G1010D) or compound heterozygous for P1104A and a rare allele (A928V). All these missense alleles encode detectable proteins. The R864C and G1010D alleles are hypomorphic and loss-of-function (LOF), respectively, across signaling pathways. By contrast, hypomorphic G996R, G634E, and A928V mutations selectively impair responses to IL-23, like P1104A. Impairment of the IL-23-dependent induction of IFN-gamma is the only mechanism of mycobacterial disease common to patients with complete TYK2 deficiency with or without TYK2 expression, partial TYK2 deficiency across signaling pathways, or rare or common partial TYK2 deficiency specific for IL-23 signaling. ANRS Nord-Sud ; CIBSS ; CODI ; Comité para el Desarrollo de la Investigación ; Fulbright Future Scholarship

Published
2022

28. Detection of antinuclear antibodies targeting intracellular signal transduction, metabolism, apoptotic processes and cell death in critical COVID-19 patients

Author

Fatma Ali, Hadi M. Yassine, Gheyath K. Nasrallah, Aisha Fakhroo, and Nico Marr

Subjects
Programmed cell death, Anti-nuclear antibody, Coronavirus disease 2019 (COVID-19), coronavirus, COVID-19, Autoimmunity, Metabolism, Biology, medicine.disease_cause, ANA, Cell biology, Intracellular signal transduction, Apoptosis, ICU, medicine, Coronavirus
Abstract

Background: The heterogeneity of COVID-19 lies within its diverse symptoms and severity, ranging from mild to lethal. Acute respiratory distress syndrome (ARDS) has been shown to be the leading cause of mortality in COVID-19 patients, characterized by a hyper cytokine storm. Autoimmunity is proposed to occur as a result of COVID-19, given the high similarity of the immune responses observed in COVID-19 and autoimmune diseases. Results: Here, we investigate the level of autoimmune antibodies in COVID-19 patients with different severities. Initial screening for antinuclear antibodies (ANA) IgG revealed that 1.6% (2/126) and 4% (5/126) of ICU COVID-19 cases developed strong and moderate ANA levels, respectively. However, all the non-ICU cases (n = 273) were ANA negative. The high ANA level was confirmed by immunofluorescence (IFA) and large-scale autoantibody screening by phage immunoprecipitation-sequencing (PhIP-Seq). Indeed, the majority of the samples showed "speckled" ANA pattern by microscopy, and we demonstrate that samples of ICU patients with strong and moderate ANA levels contain autoantibody specificities that predominantly targeted proteins involved in intracellular signal transduction, metabolism, apoptotic processes, and cell death; further denoting reactivity to nuclear and cytoplasmic antigens. Conclusion:Our results further support the notion of routine screening for autoimmune responses in COVID-19 patients, which might help improve disease prognosis and patient management. Further, results provide compelling evidence that ANA-positive individuals should be excluded from being donors for convalescent plasma therapy in the context of Covid-19.

Published
2021

29. Inherited human c-Rel deficiency disrupts myeloid and lymphoid immunity to multiple infectious agents

Author

Rui Yang, Rubén Martínez-Barricarte, Janet Markle, Franck Rapaport, Stuart G. Tangye, Mathieu Bourgey, David Langlais, Anne Puel, Aziz Belkadi, Masato Ogishi, Simon J. Pelham, Jean-Laurent Casanova, Bertrand Boisson, Cindy S. Ma, Vivien Béziat, Eman Abou Moussa, Jérémie Rosain, Laurent Abel, Tomi Lazarov, Serkan Belkaya, Fatima Ailal, Ibtihal Benhsaien, Coralie Briand, Alessandro Plebani, Romain Lévy, Frederic Geissmann, Caroline Deswarte, Andrea Guennoun, Luis R. Saraiva, Tanwir Habib, Mehdi Emam, Vassilios Lougaris, Philippe Gros, Yu Jerry Zhou, Ahmed Aziz Bousfiha, Geetha Rao, Kathryn Payne, Sylvain Breton, Ai Ing Lim, Kang Liu, Kunihiko Moriya, Danielle T. Avery, Bénédicte Neven, Nico Marr, Jacinta Bustamante, Mélanie Migaud, and James P. Di Santo

Subjects
Myeloid, Primary Immunodeficiency Diseases, Naive B cell, Adaptive Immunity, Biology, Lymphocyte Activation, Consanguinity, Immunity, medicine, Humans, Protein Isoforms, Myeloid Cells, Lymphocytes, Child, B cell, CD86, Host Microbial Interactions, Homozygote, Hematopoietic Stem Cell Transplantation, General Medicine, Acquired immune system, Immunity, Innate, Proto-Oncogene Proteins c-rel, medicine.anatomical_structure, Mutation, Immunology, Female, Genes, rel, REL, CD8, Research Article
Abstract

We studied a child with severe viral, bacterial, fungal, and parasitic diseases, who was homozygous for a loss-of-function mutation of REL, encoding c-Rel, which is selectively expressed in lymphoid and myeloid cells. The patient had low frequencies of NK, effector memory cells reexpressing CD45RA (Temra) CD8(+) T cells, memory CD4(+) T cells, including Th1 and Th1*, Tregs, and memory B cells, whereas the counts and proportions of other leukocyte subsets were normal. Functional deficits of myeloid cells included the abolition of IL-12 and IL-23 production by conventional DC1s (cDC1s) and monocytes, but not cDC2s. c-Rel was also required for induction of CD86 expression on, and thus antigen-presenting cell function of, cDCs. Functional deficits of lymphoid cells included reduced IL-2 production by naive T cells, correlating with low proliferation and survival rates and poor production of Th1, Th2, and Th17 cytokines by memory CD4(+) T cells. In naive CD4(+) T cells, c-Rel is dispensable for early IL2 induction but contributes to later phases of IL2 expression. The patient’s naive B cells displayed impaired MYC and BCL2L1 induction, compromising B cell survival and proliferation and preventing their differentiation into Ig-secreting plasmablasts. Inherited c-Rel deficiency disrupts the development and function of multiple myeloid and lymphoid cells, compromising innate and adaptive immunity to multiple infectious agents.

Published
2021

30. Human STAT3 variants underlie autosomal dominant hyper-IgE syndrome by negative dominance

Author

Capucine Picard, Joëlle Khourieh, Jane Peake, Antoine Guérin, Bertrand Boisson, Aziz Bousfiha, Jamila El Baghdadi, David Hum, Takaki Asano, Jean-Laurent Casanova, Andrew Williams, Simon J. Pelham, Stéphanie Boisson-Dupuis, Peng Zhang, Maya Chrabieh, Luke Droney, Wei-Te Lei, Ilham Fadil, Ji Eun Han, András N Spaan, Qian Zhang, Nevin Hatipoğlu, Franck Rapaport, Anne Puel, Tanwir Habib, Nico Marr, Fatih Celmeli, Vivien Béziat, Joseph Mackie, Biman Saikia, Stuart G. Tangye, Laurent Abel, Tayfun Ozcelik, Juan Li, Sudhir Gupta, Luckshman Ganeshanandan, and Özçelik, Tayfun

Subjects
Male, Infectious disease and host defense, Dominant negative, Innate immunity and inflammation, 0302 clinical medicine, Immunology and Allergy, 10. No inequality, STAT3, Child, Frameshift Mutation, Dominance (genetics), Genes, Dominant, Translation reinitiation, Genetics, 0303 health sciences, education.field_of_study, Middle Aged, 3. Good health, Pedigree, Codon, Nonsense, 030220 oncology & carcinogenesis, Child, Preschool, Autosomal dominant hyper-IgE syndrome, Female, Haploinsufficiency, Job Syndrome, Gene isoform, Adult, STAT3 Transcription Factor, Adolescent, Immunology, Population, Innate Immunity and Inflammation, Biology, Article, Infectious Disease and Host Defense, Evolution, Molecular, 03 medical and health sciences, Immunodeficiency, Humans, Family, RNA, Messenger, education, Alleles, 030304 developmental biology, Human disease genetics, Infant, Newborn, Infant, Alternative Splicing, Genetics, Population, HEK293 Cells, Protein Biosynthesis, Mutation, biology.protein, Human Disease Genetics
Abstract

Most patients with autosomal dominant hyper-IgE syndrome (AD-HIES) are heterozygous for rare STAT3 variants. The mechanism of dominance was recently questioned. The authors show that both in-frame and out-of-frame STAT3 variants underlie AD-HIES by negative dominance and not haploinsufficiency., Most patients with autosomal dominant hyper-IgE syndrome (AD-HIES) carry rare heterozygous STAT3 variants. Only six of the 135 in-frame variants reported have been experimentally shown to be dominant negative (DN), and it has been recently suggested that eight out-of-frame variants operate by haploinsufficiency. We experimentally tested these 143 variants, 7 novel out-of-frame variants found in HIES patients, and other STAT3 variants from the general population. Strikingly, all 15 out-of-frame variants were DN via their encoded (1) truncated proteins, (2) neoproteins generated from a translation reinitiation codon, and (3) isoforms from alternative transcripts or a combination thereof. Moreover, 128 of the 135 in-frame variants (95%) were also DN. The patients carrying the seven non-DN STAT3 in-frame variants have not been studied for other genetic etiologies. Finally, none of the variants from the general population tested, including an out-of-frame variant, were DN. Overall, our findings show that heterozygous STAT3 variants, whether in or out of frame, underlie AD-HIES through negative dominance rather than haploinsufficiency., Graphical Abstract

Published
2021

31. A deep intronic splice mutation of STAT3 underlies hyper IgE syndrome by negative dominance

Author

Henrik Molina, Vivien Béziat, Alain Lefevre-Utile, Marie-Olivia Chandesris, Danielle T. Avery, Maya Chrabieh, Stéphanie Boisson-Dupuis, Anne Puel, Tanwir Habib, Françoise Sarrot-Reynauld, Aziz Belkadi, Hanan Alwaseem, Geetha Rao, Agathe Senechal, Stuart G. Tangye, Qian Zhang, Olivier Lortholary, Bertrand Boisson, Joëlle Khourieh, Xiao-Fei Kong, Capucine Picard, Virginie Grandin, Nico Marr, Jean-Laurent Casanova, and Laurent Abel

Subjects
Adult, Male, STAT3 Transcription Factor, Heterozygote, T-Lymphocytes, Mutant, Biology, Exon, Loss of Function Mutation, Complementary DNA, Humans, Coding region, splice, Allele, Alleles, Dominance (genetics), Genetics, B-Lymphocytes, Multidisciplinary, Intron, Exons, Middle Aged, DNA-Binding Proteins, PNAS Plus, Gene Expression Regulation, Child, Preschool, Female, RNA Splice Sites, Job Syndrome
Abstract

Heterozygous in-frame mutations in coding regions of human STAT3 underlie the only known autosomal dominant form of hyper IgE syndrome (AD HIES). About 5% of familial cases remain unexplained. The mutant proteins are loss-of-function and dominant-negative when tested following overproduction in recipient cells. However, the production of mutant proteins has not been detected and quantified in the cells of heterozygous patients. We report a deep intronic heterozygous STAT3 mutation, c.1282-89C>T, in 7 relatives with AD HIES. This mutation creates a new exon in the STAT3 complementary DNA, which, when overexpressed, generates a mutant STAT3 protein (D427ins17) that is loss-of-function and dominant-negative in terms of tyrosine phosphorylation, DNA binding, and transcriptional activity. In immortalized B cells from these patients, the D427ins17 protein was 2 kDa larger and 4-fold less abundant than wild-type STAT3, on mass spectrometry. The patients’ primary B and T lymphocytes responded poorly to STAT3-dependent cytokines. These findings are reminiscent of the impaired responses of leukocytes from other patients with AD HIES due to typical STAT3 coding mutations, providing further evidence for the dominance of the mutant intronic allele. These findings highlight the importance of sequencing STAT3 introns in patients with HIES without candidate variants in coding regions and essential splice sites. They also show that AD HIES-causing STAT3 mutant alleles can be dominant-negative even if the encoded protein is produced in significantly smaller amounts than wild-type STAT3.

Published
2019

32. Inherited IFNAR1 deficiency in otherwise healthy patients with adverse reaction to measles and yellow fever live vaccines

Author

Stephen J. Seligman, Serkan Belkaya, Ruben Pholien, Ismail Reisli, Johan Neyts, Yoann Seeleuthner, Leen Moens, Afshin Shirkani, Scott Drutman, Charles M. Rice, Lazaro Lorenzo-Diaz, Isabelle Meyts, Margaret R. MacDonald, Emersom Ciclini Mesquita, Dick Zijlmans, Denise Cristina de Souza Matos, Nicholas Hernandez, Sheila Maria Barbosa de Lima, Maria de Lourdes de Sousa Maia, Alain Lefevre-Utile, Dirk Jochmans, Paul J. Hertzog, Tamiris Azamor da Costa Barros, Marilda M. Siqueira, Esra Hazar Sayar, Hans Heinrich Hoffmann, Xavier Bossuyt, Nico Marr, Qian Zhang, Patrícia Mouta Nunes de Oliveira, Laura Pöyhönen, Emmanuelle Jouanguy, Giorgia Bucciol, Andrea Jurado, Shen-Ying Zhang, Aurélie Cobat, Robbert Boudewijns, Hassan Rokni-Zadeh, Jérémie Le Pen, Ekaterini Goudouris, Rik Gijsbers, Ian Tietjen, Chibuzo U Enemchukwu, Reinaldo de Menezes Martins, Laurent Abel, Majid Changi-Ashtiani, Jean-Laurent Casanova, Mohammad Shahrooei, Mana Momenilandi, and Akira Homma

Subjects
Male, 0301 basic medicine, Adolescent, Measles-Mumps-Rubella Vaccine, Measles Vaccine, Immunology, Inheritance Patterns, Yellow fever vaccine, Receptor, Interferon alpha-beta, Rubella, Measles, Article, 03 medical and health sciences, 0302 clinical medicine, Immunity, medicine, Humans, Immunology and Allergy, Child, Research Articles, Alleles, business.industry, Yellow Fever Vaccine, Yellow fever, Infant, medicine.disease, Virology, Pedigree, 3. Good health, Vaccination, 030104 developmental biology, Interferon Type I, Mutation, Female, Mutant Proteins, Measles vaccine, business, Signal Transduction, 030215 immunology, medicine.drug
Abstract

We describe two unrelated patients with inherited IFNAR1 deficiency who suffered from life-threatening infections following measles or yellow fever virus vaccination and were otherwise healthy., Vaccination against measles, mumps, and rubella (MMR) and yellow fever (YF) with live attenuated viruses can rarely cause life-threatening disease. Severe illness by MMR vaccines can be caused by inborn errors of type I and/or III interferon (IFN) immunity (mutations in IFNAR2, STAT1, or STAT2). Adverse reactions to the YF vaccine have remained unexplained. We report two otherwise healthy patients, a 9-yr-old boy in Iran with severe measles vaccine disease at 1 yr and a 14-yr-old girl in Brazil with viscerotropic disease caused by the YF vaccine at 12 yr. The Iranian patient is homozygous and the Brazilian patient compound heterozygous for loss-of-function IFNAR1 variations. Patient-derived fibroblasts are susceptible to viruses, including the YF and measles virus vaccine strains, in the absence or presence of exogenous type I IFN. The patients’ fibroblast phenotypes are rescued with WT IFNAR1. Autosomal recessive, complete IFNAR1 deficiency can result in life-threatening complications of vaccination with live attenuated measles and YF viruses in previously healthy individuals.

Published
2019

33. Soluble TNF-R1, VEGF and other cytokines as markers of disease activity in systemic lupus erythematosus and lupus nephritis

Author

A Mortimer, Nico Marr, Mohammed Yousuf Karim, M El Anbari, S Anwar, and Z Adhya

Subjects
Adult, Male, Vascular Endothelial Growth Factor A, 0301 basic medicine, VEGF receptors, Lupus nephritis, Sensitivity and Specificity, Severity of Illness Index, Disease activity, 03 medical and health sciences, 0302 clinical medicine, Rheumatology, London, medicine, Humans, Lupus Erythematosus, Systemic, Chemokine CCL5, Chemokine CCL2, Chemokine CCL3, 030203 arthritis & rheumatology, Systemic lupus erythematosus, biology, business.industry, Middle Aged, medicine.disease, Lupus Nephritis, Chemokine CXCL10, Cross-Sectional Studies, Logistic Models, 030104 developmental biology, Receptors, Tumor Necrosis Factor, Type I, Immunology, Disease Progression, biology.protein, Female, business, Nephritis, Biomarkers, Glomerular Filtration Rate
Abstract

Background Current non-invasive methods of assessing disease activity in systemic lupus erythematosus (SLE) are of limited sensitivity and specificity. Testing includes acute phase markers, autoantibodies and complement levels. Although measurements of dsDNA antibodies and complement C3/C4 levels are routine, they remain of limited value. Improved blood and urine markers may help in early detection of flare, distinction between flare and chronic damage, and monitoring response to therapy. Methods A total of 87 patients with SLE were tested for the following cytokines in serum and urine: monocyte chemoattractant protein 1 (MCP-1), regulated upon activation, normal T cell expressed and secreted (RANTES), soluble tumour necrosis factor receptor 1 (sTNF-R1), interferon-inducible protein 10 (IP-10), monocyte inhibitory protein 1α (MIP-1α) and vascular endothelial growth factor (VEGF). Patients attending the Lupus Unit at St Thomas’ Hospital, London, UK were divided into active lupus nephritis (LN), inactive LN and non-renal SLE groups based on their renal pathology and SLE disease activity index (SLEDAI). Cytokine testing was performed using the FIDIS multiplex bead assay. Results The mean level of serum sTNF-R1 was higher in the active LN group compared with both inactive LN and non-renal SLE groups ( p Conclusion These results indicate that for active LN, sTNF-R1 could be a useful serum cytokine marker, with potential for VEGF in the urine. This study has confirmed the ability of the multiplex bead technique to detect cytokines in a good analytical range, including very low and high levels, in both serum and urine. Combining serum and urine markers provided additional sensitivity in distinguishing active from inactive LN.

Published
2019

34. A comparative study of the complete lipopolysaccharide structures and biosynthesis loci of Bordetella avium, B. hinzii, and B. trematum

Author

Martine Caroff, Alexey Novikov, Nico Marr, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Endotoxines, Structures et Réponses de l'hôte (ESHR), Département Microbiologie (Dpt Microbio), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)

Subjects
Lipopolysaccharides, 0301 basic medicine, chain linkage region, Bordetella, Virulence Factors, Bordetella avium, [SDV]Life Sciences [q-bio], B. trematum, Virulence, Context (language use), Biochemistry, Microbiology, Lipid A, 03 medical and health sciences, antigen, Endotoxin, bronchiseptica, Humans, takamatsuzuka tumulus, desorption mass-spectrometry, Gene, Pathogen, B. hinzii, Molecular Structure, 030102 biochemistry & molecular biology, biology, pertussis, sp nov, core, Genomics, General Medicine, parapertussis, biology.organism_classification, 3. Good health, 030104 developmental biology, Genetic Loci, o-specific polysaccharide, Lipopolysaccharide MALDI MS, Host adaptation
Abstract

International audience; A dozen species of human and animal pathogens have been described to date in the Bordetella genus, with the majority being respiratory tract pathogens. Bordetella avium lipopolysaccharides have been shown to be important virulence factors for this bird pathogen. B. hinzii is closely related to the B. avium species, but has also been isolated from humans. B. trematum is associated to ear and blood infections in humans. Its lipid A structure, the biological active moiety of LPS, was found to be closely related to those of B. avium and B. hinzii. It is important to unveil the subtle structural modifications orchestrated during the LPS biosynthetic pathway to better understand host adaptation. The present data are also important in the context of deciphering the virulence pathways of this important genus containing the major pathogens B. pertussis and B. parapertussis, responsible for whooping cough. We recently reported the isolated lipid A structures of the three presented species, following the previously identified O-chain structures. In the present study, we provide details on the free and O-chain-linked core oligosaccharides which were required to characterize the complete LPS structures. Data are presented here in relation to relevant biosynthesis genes. The present characterization of the three species is well illustrated by Matrix Assisted Laser Desorption Mass Spectrometry experiments, and data were obtained mainly on native LPS molecules for the first time. (C) 2018 Elsevier B.V. and Societe Francaise de Biochimie et Biologie Moleculaire (SFBBM). All rights reserved.

Published
2019

35. Detection of antinuclear antibodies targeting intracellular signal transduction, metabolism, apoptotic processes and cell death in critical COVID-19 patients

Author

Aisha D. Fakhroo, Gheyath K. Nasarallah, Taushif Khan, Farhan S. Cyprian, Fatima Al Ali, Manar M.A. Ata, Sara Taleb, Ali A. Hssain, Ali H. Eid, Laith J. Abu-Raddad, Abdullatif Al-Khal, Asmaa A. Al Thani, Nico Marr, and Hadi M. Yassine

Abstract

Background The heterogeneity of COVID-19 lies within its diverse symptoms and severity, ranging from mild to lethal. Acute respiratory distress syndrome (ARDS) has been shown to be the leading cause of mortality in COVID-19 patients, characterized by a hyper cytokine storm. Autoimmunity is proposed to occur as a result of COVID-19, given the high similarity of the immune responses observed in COVID-19 and autoimmune diseases. Results Here, we investigate the level of autoimmune antibodies in COVID-19 patients with different severities. Initial screening for antinuclear antibodies (ANA) IgG revealed that 1.6% (2/126) and 4% (5/126) of ICU COVID-19 cases developed strong and moderate ANA levels, respectively. However, all the non-ICU cases (n = 273) were ANA negative. The high ANA level was confirmed by immunofluorescence (IFA) and large-scale autoantibody screening by phage immunoprecipitation-sequencing (PhIP-Seq). Indeed, the majority of the samples showed "speckled" ANA pattern by microscopy, and we demonstrate that samples of ICU patients with strong and moderate ANA levels contain autoantibody specificities that predominantly targeted proteins involved in intracellular signal transduction, metabolism, apoptotic processes, and cell death; further denoting reactivity to nuclear and cytoplasmic antigens. Conclusion Our results further support the notion of routine screening for autoimmune responses in COVID-19 patients, which might help improve disease prognosis and patient management. Further, results provide compelling evidence that ANA-positive individuals should be excluded from being donors for convalescent plasma therapy in the context of Covid-19.

Published
2021

36. STK4 deficiency underlies impaired interferon signaling and T cell immunity

Author

Khalid A. Fakhro, Fatima Al Ali, Mehdi Adeli, Salim Bougarn, Alya Al-Shakaki, Amel Hassan, Debra O. Prosser, Eman Al Maslamani, Rafah Mackeh, Donald R. Love, Amal Al-Naimi, Taushif Khan, Manar Ata, Mohammed Yousuf Karim, Ronald G. Crystal, Bernice Lo, Waleed Aamer, Nico Marr, Khawla Al-Darwish, Ibrahim A. Janahi, Qian Zhang, Amjad Tuffaha, Mahbuba Rahman, Tanwir Habib, Amal Robay, Mohammad Janahi, Andrea Guennoun, and Evonne Chin-Smith

Subjects
Text mining, business.industry, Interferon, Immunology, medicine, T cell immunity, Biology, business, medicine.drug
Abstract

Purpose. Human serine/threonine kinase 4 (STK4) deficiency is a rare, autosomal recessive genetic disorder leading to combined immunodeficiency. The extent to which STK4 deficiency impairs immune signaling and host defenses is unclear. We assessed the functional consequences of a novel, homozygous nonsense STK4 mutation (NM_006282.2:c.871C>T, p.Arg291*) found in a pediatric patient by comparing the patient’s innate and adaptive cell-mediated and humoral immune responses with those of three heterozygous relatives and unrelated controls.Methods. The genetic etiology was identified by whole genome sequencing and confirmed by Sanger sequencing. STK4 gene and protein expression was measured by quantitative RT-PCR and immunoblotting, respectively. Cellular abnormalities were assessed by high-throughput RT-RCR, RNA-Seq, ELISA and polychromatic flow cytometry. Finally, antibody responses were delinated by ELISA and phage immunoprecipitation-sequencing.Results. The affected patient exhibited partial loss of STK4 expression and complete loss of STK4 function. The patient suffered from recurrent viral and bacterial infections, most notably persistent Epstein-Barr virus viremia and pulmonary tuberculosis. Cellular and molecular analyses revealed abnormalities to the fractions of T-cell subsets, plasmacytoid dendritic cells, and NK cells. The transcriptional responses of the patient’s whole blood and PBMC samples were reminiscent of dysregulated interferon signaling, impaired T immunity and increased T-cell apoptosis. Nonetheless, the patient had detectable vaccine-specific antibodies and IgG responses to various pathogens, consistent with a normal CD19 + B-cell fraction, albeit with a distinctive antibody repertoire, largely driven by herpesvirus antigens.Conclusion. Patients with STK4 deficiency can exhibit broad impairment of immune function extending beyond lymphoid cells.

Published
2021

37. Detection of autoimmune antibodies in severe but not in moderate or asymptomatic COVID-19 patients

Author

Fatima Al Ali, Asmaa A. Al Thani, Hadi M. Yassine, Aisha D. Fakhro, Ali Ait Hssain, Manar Ata, Farhan S. Cyprian, Taushif Khan, Ali H. Eid, Gheyath K. Nasrallah, Laith J. Abu-Raddad, Abdullatif Al-Khal, Nico Marr, and Sara Taleb

Subjects
biology, Anti-nuclear antibody, business.industry, Autoantibody, Context (language use), medicine.disease_cause, medicine.disease, Autoimmunity, Intracellular signal transduction, Antigen, Immunology, biology.protein, medicine, Antibody, business, Cytokine storm
Abstract

The heterogeneity of COVID-19 lies within its diverse symptoms and severity, ranging from mild to lethal. Acute respiratory distress syndrome (ARDS) has been shown to be the leading cause of mortality in COVID-19 patients, characterized by a hyper cytokine storm. Autoimmunity is proposed to occur as a result of COVID-19, given the high similarity of the immune responses observed in COVID-19 and autoimmune diseases. Here, we investigate the level of autoimmune antibodies in COVID-19 patients with different severities. Initial screening for antinuclear antibodies (ANA) IgG revealed that 1.6% (2/126) and 4% (5/126) of ICU COVID-19 cases developed strong and moderate ANA levels, respectively. However, all the non-ICU cases (n=273) were ANA negative. The high ANA level was confirmed by immunofluorescence (IFA) and large-scale autoantibody screening by phage immunoprecipitation-sequencing (PhIP-Seq). Indeed, the majority of the samples showed “speckled” ANA pattern by microscopy, and we demonstrate that samples of ICU patients with strong and moderate ANA levels contain autoantibody specificities that predominantly targeted proteins involved in intracellular signal transduction, metabolism, apoptotic processes, and cell death; further denoting reactivity to nuclear and cytoplasmic antigens. In conclusion, our results further support the notion of routine screening for autoimmune responses in COVID-19 patients, which might help improve disease prognosis and patient management. Further, results provide compelling evidence that ANA-positive individuals should be excluded from being donors for convalescent plasma therapy in the context of Covid-19.

Published
2021

38. Human leukocyte antigen class II gene diversity tunes antibody repertoires to common pathogens

Author

Ishfaq Ahmed, F. Al Ali, Puthen V. Jithesh, Mahbubur Rahman, Nico Marr, and Taushif Khan

Subjects
Adult, Genetics, Immunology, Genes, MHC Class II, Haplotype, Adaptive Immunity, Biology, Antibodies, Loss of heterozygosity, Gene Frequency, Haplotypes, Antibody Repertoire, Antigen, HLA Antigens, Genotype, Humoral immunity, biology.protein, Immunology and Allergy, Humans, Allele, Antibody, Alleles
Abstract

Allelic diversity of human leukocyte antigen (HLA) class II genes may help maintain humoral immunity against infectious diseases. In this study, we investigated germline genetic variation in classical HLA class II genes and employed a systematic, unbiased approach to explore the relative contribution of this genetic variation in the antibody repertoire to various common pathogens. We leveraged a well-defined cohort of 800 adults representing the general Arab population in which genetic material is shared because of the high frequency of consanguineous unions. By applying a high-throughput method for large-scale antibody profiling to this well-defined cohort, we were able to dissect the overall effect of zygosity for classical HLA class II genes, as well as the effects associated with specific HLA class II alleles, haplotypes and genotypes, on the antimicrobial antibody repertoire breadth and antibody specificity with unprecedented resolution. Our population genetic studies revealed that zygosity of the classical HLA class II genes is a strong predictor of antibody responses to common human pathogens, suggesting that classical HLA class II gene heterozygosity confers a selective advantage. Moreover, we demonstrated that multiple HLA class II alleles can have additive effects on the antibody repertoire to common pathogens. We also identified associations of HLA-DRB1 genotypes with specific antigens. Our findings suggest that HLA class II gene polymorphisms confer specific humoral immunity against common pathogens, which may have contributed to the genetic diversity of HLA class II loci during hominine evolution.

Published
2021

39. Herpes simplex encephalitis in a patient with a distinctive form of inherited IFNAR1 deficiency

Author

Jeremy Manry, Eduardo J. Garcia Reino, Taushif Khan, Romain Lévy, Mary Hasek, Jérémie Rosain, Yoann Seeleuthner, Isabelle Meyts, Lazaro Lorenzo, Laurent Abel, Zhi Li, Omar AbuZaitun, Shai Shrot, Paul Bastard, Jean-Laurent Casanova, Bertrand Boisson, Emmanuelle Jouangy, Flore Rozenberg, Nicholas Hernandez, Raz Somech, Benedetta Bigio, Shen-Ying Zhang, Mélodie Aubart, Vivien Béziat, Nico Marr, Jie Chen, Rik Gijsbers, Peng Zhang, Jacinta Bustamante, Qian Zhang, Yoon-Seung Lee, Sandra Pellegrini, Aurélie Cobat, Soraya Boucherit, Human genetics of infectious diseases : Mendelian predisposition (Equipe Inserm U1163), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller University [New York], Human genetics of infectious diseases: Complex predisposition (Equipe Inserm U1163), Sidra Medicine [Doha, Qatar], Service d'immuno-hématologie pédiatrique [CHU Necker], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Chaim Sheba Medical Center, Kfar Saba and Sackler School of Medicine, Service de neurochirurgie pédiatrique [CHU Necker], Faculté de Médecine et Médecine Dentaire [UCLouvain], Université Catholique de Louvain = Catholic University of Louvain (UCL), Signalisation des Cytokines - Cytokine Signaling, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de Virologie [CHU Cochin], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Hôpital Cochin [AP-HP], Hamad Bin Khalifa University (HBKU), Precision Immunology Institute [New-York] (PrIISM), Icahn School of Medicine at Mount Sinai [New York] (MSSM), CHU Necker - Enfants Malades [AP-HP], Howard Hughes Medical Institute [New York] (HHMI), Howard Hughes Medical Institute (HHMI)-New York University School of Medicine, NYU System (NYU)-NYU System (NYU)-Rockefeller University [New York]-Columbia University Irving Medical Center (CUIMC), This work was conducted in the two branches of the Laboratory of Human Genetics of Infectious Diseases, and was funded in part by the National Center for Advancing Translational Sciences (NCATS), National Institutes of Health (NIH), Clinical and Translational Science Award (CTSA) program, grant UL1TR001866, NIH grants R01AI088364, R01NS072381 and R21AI151663, the National Vaccine Program Office of the US Department of Health and Human Services grant VSRNV000006, grants from the Integrative Biology of Emerging Infectious Diseases Laboratory of Excellence (ANR-10-LABX-62-IBEID) and the French National Research Agency (ANR) under the 'Investments for the future' program (ANR-10-IAHU-01), the ANR grants IEIHSEER (ANR-14-CE14-0008-01), SEAeHostFactors (ANR-18-CE15-0020-02), and CNSVIRGEN (ANR-19-CE15-0009-01), the French Foundation for Medical Research (FRM) (EQU201903007798), the Rockefeller University, Institut National de la Santé et de la Recherche Médicale (INSERM), Paris Descartes University, and the St. Giles Foundation. PB was supported by the French Foundation for Medical Research (FRM, EA20170638020) and the MD-PhD program of the Imagine Institute (with the support of the Fondation Bettencourt-Schueller). JR was supported by the Inserm PhD program ('poste d’accueil Inserm'). JM was supported by ANR grants BURULIGEN (ANR-12-BSV3-0013-01) and MYCOPARADOX (ANR-16-CE12-0023)., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-10-IAHU-0001,Imagine,Institut Hospitalo-Universitaire Imagine(2010), ANR-14-CE14-0008,IEIHSEER,L'encéphalite Herpétique de l'enfant résulte de déficits héréditaires d'immunité contre l'HSV-1: une exception ou une règle?(2014), ANR-18-CE15-0020,SEAe-HostFactors,Facteurs de susceptibilité de l'hôte à l'encéphalite pédiatrique en Asie du Sud Est(2018), and ANR-19-CE15-0009,CNSVIRGEN,Déficits immunitaires innés dans les infections sévères du tronc cérébral(2019)

Subjects
Male, 0301 basic medicine, Untranslated region, Adolescent, [SDV]Life Sciences [q-bio], Immunology, Herpesvirus 1, Human, Receptor, Interferon alpha-beta, Biology, medicine.disease_cause, Rubella, 03 medical and health sciences, Exon, 0302 clinical medicine, Immunity, medicine, Humans, MESH: Receptor, Interferon alpha-beta, MESH: Interferons, Innate immunity, MESH: Adolescent, Infectious disease, MESH: Humans, MESH: Encephalitis, Herpes Simplex, MESH: Child, Preschool, General Medicine, medicine.disease, Virology, MESH: Male, MESH: Herpesvirus 1, Human, HEK293 Cells, 030104 developmental biology, Herpes simplex virus, Tyrosine kinase 2, Child, Preschool, 030220 oncology & carcinogenesis, MESH: HEK293 Cells, Cytokines, Encephalitis, Herpes Simplex, Interferons, Viral disease, Encephalitis, Research Article, Genetic diseases
Abstract

International audience; Inborn errors of TLR3-dependent IFN-α/β– and IFN-λ–mediated immunity in the CNS can underlie herpes simplex virus 1 (HSV-1) encephalitis (HSE). The respective contributions of IFN-α/β and IFN-λ are unknown. We report a child homozygous for a genomic deletion of the entire coding sequence and part of the 3′-UTR of the last exon of IFNAR1, who died of HSE at the age of 2 years. An older cousin died following vaccination against measles, mumps, and rubella at 12 months of age, and another 17-year-old cousin homozygous for the same variant has had other, less severe, viral illnesses. The encoded IFNAR1 protein is expressed on the cell surface but is truncated and cannot interact with the tyrosine kinase TYK2. The patient’s fibroblasts and EBV-B cells did not respond to IFN-α2b or IFN-β, in terms of STAT1, STAT2, and STAT3 phosphorylation or the genome-wide induction of IFN-stimulated genes. The patient’s fibroblasts were susceptible to viruses, including HSV-1, even in the presence of exogenous IFN-α2b or IFN-β. HSE is therefore a consequence of inherited complete IFNAR1 deficiency. This viral disease occurred in natural conditions, unlike those previously reported in other patients with IFNAR1 or IFNAR2 deficiency. This experiment of nature indicates that IFN-α/β are essential for anti–HSV-1 immunity in the CNS

Published
2021

40. Human T-bet Governs Innate and Innate-like Adaptive IFN-γ Immunity against Mycobacteria

Author

Laurent Abel, Laurie H. Glimcher, Lluis Quintana-Murci, Nico Marr, Fatima Al Ali, Jean Marc Doisne, David Langlais, Jacinta Bustamante, Marc Weisshaar, Jing Han, Jamila El Baghdadi, Frédéric Batteux, Manon Roynard, Yichao Shen, Mathieu Bourgey, Flore Rozenberg, Federica Sallusto, Peng Zhang, David Jarrossay, Carmen Oleaga-Quintas, Jean-Laurent Casanova, Daniela Latorre, Gaspard Kerner, Mahbuba Rahman, Houda Elarabi, Federico Mele, Yoann Seeleuthner, James P. Di Santo, Stuart G. Tangye, Michael S. Kobor, Janet Markle, Dusan Bogunovic, Stéphanie Boisson-Dupuis, Julia L. Maclsaac, Lucas T. Husquin, Lisa Worley, Conor Gruber, Cindy S. Ma, Jérémie Rosain, Taushif Khan, Thomas L. Carroll, Mohamed Jeljeli, Abderrahmane Errami, Anne Puel, Qiang Pan-Hammarström, Philippe Gros, Ibithal Benhsaien, Aziz Bousfiha, Fatima Ailal, Carys A. Croft, Rui Yang, Masato Ogishi, Rockefeller University [New York], Università della Svizzera italiana = University of Italian Switzerland (USI), Garvan Institute of medical research, McGill University = Université McGill [Montréal, Canada], Laboratory of Human Genetics of Infectious Diseases (Necker Branch - INSERM U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Université Hassan II [Casablanca] (UH2MC), Immunité Innée - Innate Immunity, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Paris Cité (UPCité), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Icahn School of Medicine at Mount Sinai [New York] (MSSM), We thank the patients and families, members of the laboratory, Cecilia Lindestam Arlehamn and Alessandro Sette, NIH Tetramer Core Facility (NTCF), James McCluskey, Jamie Rossjohn, and David Fairlie, the Genomics and the Flow Cytometry Resource Center of Rockefeller University, National Center for Advancing Translational Sciences of the National Institutes of Health (UL1TR001866 to Rockefeller University), Steven Elledge, National Institute of Allergy and Infectious Diseases (R37AI095983 to J.L.C. and U19AI118626 to F.S.), Sackler Center for Biomedicine and Nutrition at the Center for Clinical and Translational Science (CCTS), Shapiro-Silverberg Fund for the Advancement of Translational Research at CCTS, Rockefeller University (to R.Y.), Research Grant Program of the Immune Deficiency Foundation (to R.Y.), Integrative Biology of Emerging Infectious Diseases Laboratory of Excellence (ANR-10-LABX-62-IBEID), French National Research Agency under the 'Investments for the future' program (ANR-10-IAHU-01), ANR-GENMSMD (ANR-16-CE17-0005-01 to J.B.), ANR-LTh-MSMD-CMCD (ANR-18-CE93-0008-01 to A.P and F.S.), Fonds de Recherche en Santé Respiratoire (SRC2017 to J.B.), French Foundation for Medical Research (FRM) (EQU201903007798), the SCOR Corporate Foundation for Science, ECOS Nord (C19S01-63407 to J.B.), Swiss National Science Foundation (310030L_182728 to F.S.), French Foundation for Medical Research (FRM) (EQU201903007798), Helmut Horten Foundation, Canadian Center for Computational Genomics (C3G), Genomics Technology Platform (GTP), and Genome Canada. J. R. was supported by INSERM Poste d’accueil and and Imagine Institute, T.K. by Qatar National Research Fund (PPM1-1220-150017). S.G.T. by Program grant (1113904), Principal Research Fellowship (1042925), and Leadership 3 Investigator grant (1176665) from the National Health and Medical Research Council of Australia, C.S.M. by an Early/Mid-Career Development Research Fellowship, Ministry of Health, NSW Government, R.Y. by Stony Wold-Herbert Fund., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-10-IAHU-0001,Imagine,Institut Hospitalo-Universitaire Imagine(2010), ANR-16-CE17-0005,GENMSMD,Dissection génétique de la Susceptibilité Mendélienne aux infections mycobactériennes chez l'homme(2016), ANR-18-CE93-0008,LTh-MSMD-CMCD,Différenciation des lymphocytes T-helper (Th) dans les défauts génétiques de l'immunité contre Mycobacterium et/ou Candida species.(2018), Garvan Institute of Medical Research [Darlinghurst, Australia], Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), and Université de Paris (UP)

Subjects
Male, inborn errors of immunity, [SDV]Life Sciences [q-bio], Mendelian susceptibility to mycobacterial disease, MESH: Amino Acid Sequence, Adaptive Immunity, MESH: Base Sequence, Epigenesis, Genetic, mycobacterium, MESH: INDEL Mutation, 0302 clinical medicine, MESH: DNA Methylation, INDEL Mutation, Loss of Function Mutation, Interferon gamma, MESH: Epigenesis, Genetic, MESH: CpG Islands, IFN-γ, Immunodeficiency, 0303 health sciences, biology, MESH: Dendritic Cells, Homozygote, T-Lymphocytes, Helper-Inducer, MESH: Infant, Chromatin, Pedigree, 3. Good health, Killer Cells, Natural, Child, Preschool, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, MESH: Immunity, Innate, medicine.drug, MESH: Homozygote, MESH: Killer Cells, Natural, MESH: Pedigree, MESH: T-Box Domain Proteins, MESH: Interferon-gamma, T-bet, Article, General Biochemistry, Genetics and Molecular Biology, MESH: Chromatin, Interferon-gamma, 03 medical and health sciences, Immunity, medicine, MESH: Mycobacterium, Humans, Cell Lineage, Amino Acid Sequence, MESH: Mycobacterium Infections, MESH: T-Lymphocytes, Helper-Inducer, Transcription factor, 030304 developmental biology, Mycobacterium Infections, MESH: Humans, Base Sequence, MESH: Transcriptome, MESH: Child, Preschool, Infant, MESH: Loss of Function Mutation, Dendritic Cells, DNA Methylation, Mycobacterial disease, MESH: Cell Lineage, medicine.disease, biology.organism_classification, Immunity, Innate, MESH: Male, innate-like adaptive lymphocyte, Mycobacterial antigen, Immunology, CpG Islands, innate lymphocyte, T-Box Domain Proteins, Transcriptome, immunodeficiency, MESH: Female, 030217 neurology & neurosurgery, CD8, MESH: Adaptive Immunity, Mycobacterium
Abstract

International audience; 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.

Published
2020

41. Inherited PD-1 deficiency underlies tuberculosis and autoimmunity in a child

Author

Phillip Wong, Peng Zhang, Geetha Rao, Gaspard Kerner, Bertrand Boisson, Figen Dogu, Matthew Adamow, Taushif Khan, Ilhan Tezcan, Simon J. Pelham, Samuel C. Williams, Cindy S. Ma, Caner Aytekin, Deniz Cagdas, Mahbuba Rahman, Tasuku Honjo, Masato Ogishi, Jean-François Emile, Franck Rapaport, Jérémie Rosain, Conor Gruber, Leena Kainulainen, Nico Marr, Garrett Allington, Ferda O. Hosnut, Scott Drutman, Jedd D. Wolchok, David Langlais, Yuka Nakajima, Matthew D. Hellmann, Laurent Abel, Mathieu Bourgey, Aydan Ikinciogullari, Philippe Gros, Jacinta Bustamante, Wei-Te Lei, Stuart G. Tangye, Jean-Laurent Casanova, Flore Rozenberg, Richard P. Lifton, Fatima Al Ali, Michael S. Glickman, Maya Chrabieh, Stéphanie Boisson-Dupuis, Luigi D. Notarangelo, V. Koneti Rao, Ottavia M. Delmonte, Margaret K. Callahan, Vivien Béziat, Silvia Vilarinho, Dusan Bogunovic, András N Spaan, Tomonori Yaguchi, Kenji Chamoto, and Rui Yang

Subjects
0301 basic medicine, CD4-Positive T-Lymphocytes, Male, STAT3 Transcription Factor, Tuberculosis, Programmed Cell Death 1 Receptor, Hepatosplenomegaly, Autoimmunity, CD8-Positive T-Lymphocytes, medicine.disease_cause, Interleukin-23, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, 0302 clinical medicine, Immune system, Immunity, RAR-related orphan receptor gamma, Interferon, Neoplasms, Medicine, Humans, Child, Immune Checkpoint Inhibitors, Intraepithelial Lymphocytes, business.industry, Interleukin-6, Interleukin, General Medicine, Mycobacterium tuberculosis, Nuclear Receptor Subfamily 1, Group F, Member 3, medicine.disease, CD56 Antigen, 030104 developmental biology, 030220 oncology & carcinogenesis, Immunology, Immunotherapy, medicine.symptom, business, medicine.drug
Abstract

The pathophysiology of adverse events following programmed cell death protein 1 (PD-1) blockade, including tuberculosis (TB) and autoimmunity, remains poorly characterized. We studied a patient with inherited PD-1 deficiency and TB who died of pulmonary autoimmunity. The patient’s leukocytes did not express PD-1 or respond to PD-1-mediated suppression. The patient’s lymphocytes produced only small amounts of interferon (IFN)-γ upon mycobacterial stimuli, similarly to patients with inborn errors of IFN-γ production who are vulnerable to TB. This phenotype resulted from a combined depletion of Vδ2+ γδ T, mucosal-associated invariant T and CD56bright natural killer lymphocytes and dysfunction of other T lymphocyte subsets. Moreover, the patient displayed hepatosplenomegaly and an expansion of total, activated and RORγT+ CD4−CD8− double-negative αβ T cells, similar to patients with STAT3 gain-of-function mutations who display lymphoproliferative autoimmunity. This phenotype resulted from excessive amounts of STAT3-activating cytokines interleukin (IL)-6 and IL-23 produced by activated T lymphocytes and monocytes, and the STAT3-dependent expression of RORγT by activated T lymphocytes. Our work highlights the indispensable role of human PD-1 in governing both antimycobacterial immunity and self-tolerance, while identifying potentially actionable molecular targets for the diagnostic and therapeutic management of TB and autoimmunity in patients on PD-1 blockade. Dysregulated immune features in a patient with a homozygous loss-of-function mutation in PDCD1 suggest that IL-6, IL-23, STAT3 and RORγT might be potential targets for treatment of PD-1 blockade-induced autoimmunity.

Published
2020

42. Virome-wide serological profiling reveals association of herpesviruses with obesity

Author

Naser Elkum, Patrick Tang, Amira Saeed, Philip Hawken, Mahbuba Rahman, Annaliza Flores, Nico Marr, Sathyavathi Sundaraju, Mohammad Rubayet Hasan, Khalid Hussain, Rusung Tan, Taushif Khan, and Arun Rawat

Subjects
Adult, Male, medicine.medical_specialty, Science, Endocrine System, Article, Serology, symbols.namesake, Metabolic Diseases, Virology, Epidemiology, medicine, Humans, Human virome, Obesity, Herpesviridae, Fisher's exact test, Virome, business.industry, Endocrine system and metabolic diseases, Odds ratio, Middle Aged, Medical microbiology, medicine.disease, Bonferroni correction, Viral infection, Immunology, Multiple comparisons problem, symbols, Medicine, Female, business
Abstract

The relationship between viral infection and obesity has been known for several decades but epidemiological data related to obesity is limited to only a few viral pathogens. To identify associations between viral infections and obesity, a high-throughput virome-wide serological profiling tool, VirScan, was used to measure antibody responses to a wide range of viruses. Serum specimens from 457 Qatari adults (lean=184;obese=273) and 231 Qatari children (lean=111;obese=120) were assessed by VirScan. Pediatric specimens were simultaneously tested by conventional serology for several herpesviruses to validate VirScan results. Viral association with obesity was determined by calculation of odds ratio (OR) and p-values from Fisher test, and by multivariate regression analysis to adjust for age and gender, with Bonferroni correction for multiple testing. Comprehensive serological profiling of Qatari adult population with VirScan revealed positive and negative associations (pp-values for multiple comparisons, only herpes simplex virus 1 (HSV-1) and Rhinovirus A were positively (OR=3.3; 95%CI 2.15-4.99; p=2.787E-08) and negatively (OR=0.4; 95%CI 0.26-0.65; p=1.175E-03) associated with obesity. At the peptide level, higher prevalence of antibodies against several peptide epitopes of HSV-1/2 was positively (OR=2.35-3.82; p≤3.981E-05) associated with obesity. No such associations were seen at the species or peptide levels in the pediatric population. By multivariate regression analysis, HSV-1 was independently associated with obesity irrespective of age and gender. These findings are in agreement with limited data on the adipogenic properties of HSV-1 observed in vitro.ImportanceThe state of Qatar has one of the highest rates of obesity and associated morbidities in the world. Although obesity is predominantly caused by the intake of high calorie diet and reduced physical activities, other factors including infections with certain viruses have been reported. Among these viruses, human adenoviruses were widely studied but epidemiological data for other viruses in relation to human obesity are limited. Here, we studied the association of obesity in Qatari adults and children with a wide range of viral pathogens using VirScan, a virome-wide serological profiling tool. Our results indicate significant association HSV-1 with obesity in the adult population only. Furthermore, we have identified a set of HSV peptides as candidate obesogenic factors for future studies.

Published
2020

43. Human T-bet governs innate and innate-like adaptive IFN-γ immunity against mycobacteria

Author

Qiang Pan-Hammarström, Mathieu Bourgey, Conor Gruber, Fatima Al Ali, Lluis Quintana-Murci, Federico Mele, James P. Di Santo, Jean-Marc Doisne, Carmen Oleaga-Quintas, Flore Rozenberg, Carys A. Croft, Taushif Khan, Aziz Bousfiha, Daniela Latorre, Fatima Ailal, Houda Elarabi, Cindy S. Ma, Yoann Seeleuthner, Jing Han, Lucas T. Husquin, Stéphanie Boisson-Dupuis, David Jarrossay, Thomas L. Carroll, Janet Markle, Jean-Laurent Casanova, Anne Puel, Peng Zhang, David Langlais, Mohamed Jeljeli, Dusan Bogunovic, Jérémie Rosain, Laurent Abel, Gaspard Kerner, Lisa Worley, Laurie H. Glimcher, Michael S. Kobor, Nico Marr, Rui Yang, Frédéric Batteux, Julia L. Maclsaac, Yichao Shen, Stuart G. Tangye, Jacinta Bustamante, Marc Weisshaar, Federica Sallusto, Mahbuba Rahman, Manon Roynard, Philippe Gros, Ibithal Benhsaien, and Jamila El Baghdadi

Subjects
Immunity, DNA methylation, Immunology, Stimulation, Biology, Mycobacterial disease, Gene, Transcription factor, Lymphocyte subsets, Chromatin
Abstract

SummaryInborn errors of human IFN-γ immunity underlie mycobacterial disease. We report a patient with mycobacterial disease due to an inherited deficiency of the transcription factor T-bet. This deficiency abolishes the expression of T-bet target genes, including IFNG, by altering chromatin accessibility and DNA methylation in CD4+ T cells. The patient has profoundly diminished counts of mycobacterial-reactive circulating NK, invariant NKT (iNKT), mucosal-associated invariant T (MAIT), and Vδ2+ γδ T lymphocytes, and of non-mycobacterial-reactive classic TH1 lymphocytes, the remainders of which also produce abnormally low amounts of IFN-γ. Other IFN-γ-producing lymphocyte subsets however develop normally, but with low levels of IFN-γ production, with exception of Vδ2− γδ T lymphocytes, which produce normal amounts of IFN-γ in response to non-mycobacterial stimulation, and non-classic TH1 (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, and IFN-γ production by, innate (NK) and innate-like adaptive lymphocytes (iNKT, MAIT, and Vδ2+ γδ T cells), with mycobacterial-specific, IFN-γ-producing, purely adaptive αβ TH1* cells unable to compensate for this deficit.

Published
2020

44. Distinct antibody repertoires against endemic human coronaviruses in children and adults

Author

Amira Saeed, Isabelle Meyts, Isabelle Vandernoot, Gheyath K. Nasrallah, Vivien Béziat, Maria K. Smatti, Jean-Laurent Casanova, Emmanuelle Jouanguy, Zhiyong Liu, Qian Zhang, Mahbuba Rahman, Nico Marr, Laurent Abel, Guillaume Smits, Fatima Al Ali, Hadi M. Yassine, Susie S.Y. Huang, Mohammad Rubayet Hasan, Paul Bastard, Isabelle Migeotte, Taushif Khan, Manar Ata, Aurélie Cobat, Jean-Christophe Goffard, and Filomeen Haerynck

Subjects
0301 basic medicine, Male, Endemic Diseases, viruses, Common Cold, Antibodies, Viral, medicine.disease_cause, 0302 clinical medicine, Antibody Specificity, Seroepidemiologic Studies, Medicine and Health Sciences, Child, Antigens, Viral, Coronavirus, Infectious disease, virus diseases, Respiratory infection, General Medicine, OC43, Sciences bio-médicales et agricoles, Middle Aged, medicine.anatomical_structure, INFECTIONS, 030220 oncology & carcinogenesis, Child, Preschool, Epitopes, B-Lymphocyte, Medicine, VIRUS, Female, HKU1, Antibody, Coronavirus Infections, Research Article, Adult, Immunoprecipitation, medicine.drug_class, T cell, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), Immunology, Immunoglobulins, Cross Reactions, Biology, Monoclonal antibody, SEQUENCE, Virus, 03 medical and health sciences, Viral Proteins, Immune system, Tandem repeat, Protein Domains, medicine, Humans, Seroprevalence, 229E, B cell, Retrospective Studies, SARS, IDENTIFICATION, Virology, COV NUCLEOCAPSID PROTEIN, 030104 developmental biology, NL63, biology.protein
Abstract

Four endemic human coronaviruses (HCoVs) are commonly associated with acute respiratory infection in humans. B cell responses to these "common cold" viruses remain incompletely understood. Here we report a comprehensive analysis of CoV-specific antibody repertoires in 231 children and 1168 adults using phage-immunoprecipitation sequencing. Seroprevalence of antibodies to endemic HCoVs ranged between ~4 and 27% depending on the species and cohort. We identified at least 136 novel linear B cell epitopes. Antibody repertoires against endemic HCoVs were qualitatively different between children and adults in that anti-HCoV IgG specificities more frequently found among children targeted functionally important and structurally conserved regions of the spike, nucleocapsid and matrix proteins. Moreover, antibody specificities targeting the highly conserved fusion peptide region and S2' cleavage site of the spike protein were broadly cross-reactive with peptides of epidemic human and non-human coronaviruses. In contrast, an acidic tandem repeat in the N-terminal region of the Nsp3 subdomain of the HCoV-HKU1 polyprotein was the predominant target of antibody responses in adult donors. Our findings shed light on the dominant species-specific and pan-CoV target sites of human antibody responses to coronavirus infection, thereby providing important insights for the development of prophylactic or therapeutic monoclonal antibodies and vaccine design., info:eu-repo/semantics/published

Published
2020

45. Chronic mucocutaneous candidiasis and connective tissue disorder in humans with impaired JNK1-dependent responses to IL-17A/F and TGF-β

Author

Marco Ritelli, Harry C. Dietz, Danielle T. Avery, Bertrand Boisson, Soraya Boucherit, Lucie Grodecká, Stuart G. Tangye, Romain Lévy, Kathryn Payne, Tomáš Freiberger, Sophie Cypowyj, Juan Li, Valérie Cormier-Daire, Nicoletta Zoppi, Laurent Abel, Geetha Rao, Vivien Béziat, Andrea Guennoun, Benedetta Bigio, Maya Chrabieh, Salim Bougarn, Marina Colombi, Lei Shang, Emilie Corvilain, Yuval Itan, Anne Puel, Franck Rapaport, Nico Marr, Fransiska Malfait, Delfien Syx, Mélanie Migaud, Tanwir Habib, Sabri Boughorbel, Jean-Laurent Casanova, and Cindy S. Ma

Subjects
Male, 0301 basic medicine, Connective Tissue Disorder, MAPK8, Immunology, Mucocutaneous zone, Connective tissue, Extracellular matrix, 03 medical and health sciences, 0302 clinical medicine, Transforming Growth Factor beta, medicine, Humans, Mitogen-Activated Protein Kinase 8, Chronic mucocutaneous candidiasis, Connective Tissue Diseases, Alleles, Cells, Cultured, business.industry, Candidiasis, Chronic Mucocutaneous, Interleukin-17, General Medicine, medicine.disease, 030104 developmental biology, medicine.anatomical_structure, 030220 oncology & carcinogenesis, Mutation, Cancer research, Female, Signal transduction, Haploinsufficiency, business
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.

Published
2019

46. A curated transcriptome dataset collection to investigate the blood transcriptional response to viral respiratory tract infection and vaccination

Author

Damien Chaussabel, Salim Bougarn, Sabri Boughorbel, and Nico Marr

Subjects
0301 basic medicine, Immune defense, Bioinformatics, Viral respiratory infection, PBMC, Computational biology, Biology, Health outcomes, Data Note, Peripheral blood mononuclear cell, General Biochemistry, Genetics and Molecular Biology, Transcriptome, 03 medical and health sciences, 0302 clinical medicine, Viral Respiratory Tract Infection, Databases, Genetic, Humans, Influenza viruses, 030212 general & internal medicine, General Pharmacology, Toxicology and Pharmaceutics, Transcriptomics, Respiratory Tract Infections, Whole Blood, General Immunology and Microbiology, Respiratory tract infections, Vaccination, General Medicine, Articles, 030104 developmental biology, Blood, Respiratory syncytial viruses (RSV), Rhinoviruses, Viruses, Leukocytes, Mononuclear, Transcriptional response, Software
Abstract

The human immune defense mechanisms and factors associated with good versus poor health outcomes following viral respiratory tract infections (VRTI), as well as correlates of protection following vaccination against respiratory viruses, remain incompletely understood. To shed further light into these mechanisms, a number of systems-scale studies have been conducted to measure transcriptional changes in blood leukocytes of either naturally or experimentally infected individuals, or in individual’s post-vaccination. Here we are making available a public repository, for research investigators for interpretation, a collection of transcriptome datasets obtained from human whole blood and peripheral blood mononuclear cells (PBMC) to investigate the transcriptional responses following viral respiratory tract infection or vaccination against respiratory viruses. In total, Thirty one31 datasets, associated to viral respiratory tract infections and their related vaccination studies, were identified and retrieved from the NCBI Gene Expression Omnibus (GEO) and loaded in a custom web application designed for interactive query and visualization of integrated large-scale data. Quality control checks, using relevant biological markers, were performed. Multiple sample groupings and rank lists were created to facilitate dataset query and interpretation. Via this interface, users can generate web links to customized graphical views, which may be subsequently inserted into manuscripts to report novel findings. The GXB tool enables browsing of a single gene across projects, providing new perspectives on the role of a given molecule across biological systems in the diagnostic and prognostic following VRTI but also in identifying new correlates of protection. This dataset collection is available at: http://vri1.gxbsidra.org/dm3/geneBrowser/list.

Published
2019

47. Tuberculosis and impaired IL-23–dependent IFN-γ immunity in humans homozygous for a common TYK2 missense variant

Author

Durga Sivanesan, Cindy S. Ma, Zafer Caliskaner, Katia Abarca, Jaime Inostroza, Hicham Souhi, Nicholas Hernandez, Stephen W. Michnick, Alix Checchi, Tayfun Ozcelik, Ahmed Abid, Rubén Martínez-Barricarte, Noé Ramírez-Alejo, Adil Zegmout, Esra Hazar Sayar, Nico Marr, Ismail Reisli, Lluis Quintana-Murci, Jamila El-Baghdadi, Bernhard Fleckenstein, Hassan Abolhassani, Jacinta Bustamante, Ingrid Müller-Fleckenstein, Ismail Abderahmani Rhorfi, Antonio Condino-Neto, Jose Antonio Tavares de Albuquerque, Rodrigo Naves, Dimitry N. Krementsov, Beatriz Tavares Costa-Carvalho, Sandra Pellegrini, Aurélie Cobat, Robert Fisch, Michael J. Ciancanelli, Gaspard Kerner, Lorena Orozco, Geetha Rao, Jeanette Mulwa, Hans D. Ochs, Stuart G. Tangye, Fabienne Jabot-Hanin, Patricia García, Frederic Geissmann, Stéphanie Boisson-Dupuis, Humberto García-Ortiz, Zhi Li, Tomi Lazarov, Bertrand Boisson, Hicham Naji Amrani, María Elvira Balcells, Caroline Deswarte, Andrea Guennoun, Alexis Strickler, Carolyn C. Jackson, Sevgi Pekcan, Janet Markle, Joshua Halpern, Jean-Laurent Casanova, Cory Teuscher, Che Kang Lim, Anne Puel, Yuval Itan, Lennart Hammarström, Matthieu Bouaziz, Etienne Patin, Laurent Abel, Qian Zhang, Kathryn Payne, St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller University [New York], Human genetics of infectious diseases : Mendelian predisposition (Equipe Inserm U1163), Imagine - Institut des maladies génétiques (IMAGINE - U1163), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Signalisation des Cytokines - Cytokine Signaling, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Bioinformatique, Biostatistique et Biologie Intégrative (C3BI), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Génétique Evolutive Humaine - Human Evolutionary Genetics, Garvan Institute of Medical Research [Darlinghurst, Australia], Laboratory for the Modeling of Biological and Socio-technical Systems [Boston] (MoBS), Northeastern University [Boston], Memorial Sloane Kettering Cancer Center [New York], Laboratory of Genetic Medicine & Immunology, Weill Cornell Medicine [Qatar], Bases de données et traitement des langues naturelles (BDTLN), Laboratoire d'Informatique Fondamentale et Appliquée de Tours (LIFAT), Université de Tours-Institut National des Sciences Appliquées - Centre Val de Loire (INSA CVL), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut National des Sciences Appliquées - Centre Val de Loire (INSA CVL), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Institute of Virology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany, Sidra Medicine [Doha, Qatar], Tehran University of Medical Sciences (TUMS), Infectious Diseases Department, School of Medicine, Pontificia Universidad Católica de Chile (UC), Institute of Biomedical Sciences - Department of Immunology [Sao Paulo], University of São Paulo (USP), Hosp Puerto Montt, University of Washington [Seattle], Selcuk University, CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Garvan Institute for Medical Research, Génétique Humaine des Maladies Infectieuses (Inserm U980), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service d'immuno-hématologie pédiatrique [CHU Necker], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Necker - Enfants Malades [AP-HP], The Laboratory of Human Genetics of Infectious Diseases was supported, in part, by grants from the French National Agency for Research (ANR) under the 'Investissement d’avenir' program (grant no. ANR-10-IAHU-01), the TBPATHGEN project (grant no. ANR-14-CE14-0007-01), the GENMSMD project (grant no. ANR-16-CE17-0005-01), the Integrative Biology of Emerging Infectious Diseases Laboratory of Excellence (grant no. ANR-10-LABX-62-IBEID), the European Research Council (ERC, grant no. ERC-2010-AdG-268777), the SCOR Corporate Foundation for Science, the St. Giles Foundation, the National Center for Research Resources and the National Center for Advancing Sciences (NCATS), NIH (grant no. UL1TR001866), the National Institute of Allergy and Infectious Diseases (NIAID) (grant nos. 5R01AI089970, 5R37AI095983, 5U01AI088685, and 5U19AI111143), and The Rockefeller University. Work at the Cytokine Signaling Unit was supported, in part, by a grant from Fondation de la Recherche Médicale to S. Pellegrini (grant no. DEQ20170336741). J.B. was supported by Support of Clinical Research (grant no. SRC2017). C.S.M. and S.G.T. were supported by fellowships and grants from the National Health and Medical Research Council of Australia and the Office of Health and Medical Research of the Government of New South Wales (Australia). M.E.B. was supported by Fondo Nacional de Desarrollo Científico y Tecnológico (FONDECYT, grant no. 1171570) A.C.-N. was supported by Fundação de Amparo a Pesquisa do Estado e de São Paulo (Fapesp) and Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq). N.R.-A. was supported by fellowships from Consejo Nacional de Ciencia y Tecnología (CONACYT, grant no. 264011) and the Stony Wold-Herbert Fund. Z.L. was supported by the CNRS. J. Markle was supported by the Charles H. Revson Senior Fellowship in Biomedical Sciences and NIAID grant K99AI27932. C.C.J. was the Damon Runyon-Richard Lumsden Foundation Physician Scientist supported by the Damon Runyon Cancer Research Foundation (PST-03-15). H.D.O. was supported by the Jeffrey Modell Foundation. N.H. was supported by a Medical Scientist Training Program grant from the National Institute of General Medical Sciences of the NIH under award no. T32GM007739 to the Weill Cornell/Rockefeller/Sloan-Kettering Tri-Institutional MD-PhD Program. The content of this study is the sole responsibility of the authors and does not necessarily represent the official views of the NIH. The Yale Center for Mendelian Genomics (UM1HG006504) is funded by the National Human Genome Research Institute. Funds were also provided by the National Heart, Lung, and Blood Institute. The GSP Coordinating Center (U24 HG008956) contributed to cross-program scientific initiatives and provided logistical and general study coordination., ANR-10-IAHU-0001,Imagine,Institut Hospitalo-Universitaire Imagine(2010), ANR-14-CE14-0007,TBPATHGEN,Dissection de la pathogenèse de la tuberculose par l'identification de défauts monogéniques de l'immunité dans les formes pédiatriques sévères de la maladie(2014), ANR-16-CE17-0005,GENMSMD,Dissection génétique de la Susceptibilité Mendélienne aux infections mycobactériennes chez l'homme(2016), ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), European Project: 268777,EC:FP7:ERC,ERC-2010-AdG_20100317,GENTB(2011), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Garvan Institute of medical research, Université de Tours (UT)-Institut National des Sciences Appliquées - Centre Val de Loire (INSA CVL), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université de Tours (UT)-Institut National des Sciences Appliquées - Centre Val de Loire (INSA CVL), Universidade de São Paulo = University of São Paulo (USP), Özçelik, Tayfun, Li, Zhi, Instituts Hospitalo-Universitaires - Institut Hospitalo-Universitaire Imagine - - Imagine2010 - ANR-10-IAHU-0001 - IAHU - VALID, Appel à projets générique - Dissection de la pathogenèse de la tuberculose par l'identification de défauts monogéniques de l'immunité dans les formes pédiatriques sévères de la maladie - - TBPATHGEN2014 - ANR-14-CE14-0007 - Appel à projets générique - VALID, Dissection génétique de la Susceptibilité Mendélienne aux infections mycobactériennes chez l'homme - - GENMSMD2016 - ANR-16-CE17-0005 - AAPG2016 - VALID, Integrative Biology of Emerging Infectious Diseases - - IBEID2010 - ANR-10-LABX-0062 - LABX - VALID, Human Genetics of Tuberculosis - GENTB - - EC:FP7:ERC2011-06-01 - 2016-05-31 - 268777 - VALID, and Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Pasteur [Paris]

Subjects
0301 basic medicine, Tuberculosis, [SDV.IMM] Life Sciences [q-bio]/Immunology, medicine.medical_treatment, Immunology, [SDV.GEN] Life Sciences [q-bio]/Genetics, Biology, medicine.disease_cause, 03 medical and health sciences, 0302 clinical medicine, Immunity, medicine, Missense mutation, Allele, Receptor, Mutation, [SDV.GEN]Life Sciences [q-bio]/Genetics, General Medicine, medicine.disease, 3. Good health, 030104 developmental biology, Cytokine, Tyrosine kinase 2, [SDV.IMM]Life Sciences [q-bio]/Immunology, IMUNOGENÉTICA, 030215 immunology
Abstract

International audience; Inherited IL-12Rβ1 and TYK2 deficiencies impair both IL-12- and IL-23-dependent IFN-γ immunity and are rare monogenic causes of tuberculosis, each found in less than 1/600,000 individuals. We show that homozygosity for the common TYK2 P1104A allele, which is found in about 1/600 Europeans and between 1/1000 and 1/10,000 individuals in regions other than East Asia, is more frequent in a cohort of patients with tuberculosis from endemic areas than in ethnicity-adjusted controls (P = 8.37 × 10-8; odds ratio, 89.31; 95% CI, 14.7 to 1725). Moreover, the frequency of P1104A in Europeans has decreased, from about 9% to 4.2%, over the past 4000 years, consistent with purging of this variant by endemic tuberculosis. Surprisingly, we also show that TYK2 P1104A impairs cellular responses to IL-23, but not to IFN-α, IL-10, or even IL-12, which, like IL-23, induces IFN-γ via activation of TYK2 and JAK2. Moreover, TYK2 P1104A is properly docked on cytokine receptors and can be phosphorylated by the proximal JAK, but lacks catalytic activity. Last, we show that the catalytic activity of TYK2 is essential for IL-23, but not IL-12, responses in cells expressing wild-type JAK2. In contrast, the catalytic activity of JAK2 is redundant for both IL-12 and IL-23 responses, because the catalytically inactive P1057A JAK2, which is also docked and phosphorylated, rescues signaling in cells expressing wild-type TYK2. In conclusion, homozygosity for the catalytically inactive P1104A missense variant of TYK2 selectively disrupts the induction of IFN-γ by IL-23 and is a common monogenic etiology of tuberculosis.

Published
2018

48. The abundance of Nudix hydrolase 16 transcripts is elevated in human sepsis: perspectives gained during a hands-on reductionist investigation workshop

Author

Kabeer Bsa, Davide Bedognetti, Wouter Hendrickx, Jessica Roelands, Damien Chaussabel, Mathieu Garand, Mohamed Alfaki, Nico Marr, Mohammed Toufiq, Sabri Boughorbel, and Darawan Rinchai

Subjects
Transcriptome, Sepsis, Inosine Diphosphate, Candidate gene, medicine, RNA, Inflammation, Computational biology, Biology, medicine.symptom, medicine.disease, Nudix hydrolase, In vitro
Abstract

A hands-on training workshop was devised with omics data used as source material to emulate reductionist investigation approaches. NUDT16, a member of the Nudix hydrolase family was selected as a candidate gene on the basis of: 1) it being upregulated in neutrophils exposed in vitro to serum of patients with sepsis, AND 2) the absence of overlap between the NUDT16 and sepsis, inflammation or neutrophil literature. We next sought to corroborate the initial finding in five public transcriptome sepsis datasets in which NUDT16 transcript levels were measured. In each of these dataset NUDT16 transcript abundance was found to be significantly increased in septic patients in vivo in comparison to uninfected controls. Next, biological concepts were extracted from the NUDT16 literature. The main concepts to emerge from profiling this literature were RNA decapping, inosine triphosphate, and inosine diphosphate. Through these concepts, indirect links could be established between NUDT16 and the sepsis/inflammation/neutrophil literature. A potential role for NUDT16 could, in turn, be inferred in the degradation of mRNAs in activated neutrophils. Follow on experiments that would be necessary in order to further explore such inference are discussed.

Published
2018

49. Organizing gene literature retrieval, profiling, and visualization training workshops for early career researchers

Author

Damien Chaussabel, Basirudeen Syed Ahamed Kabeer, Fatima Al Ali, Jessica Roelands, Mathieu Garand, Alexandra K Marr, Darawan Rinchai, Davide Bedognetti, Zohreh Tatari-Calderone, Nico Marr, Mohammed Toufiq, and Mohamed Alfaki

Subjects
General Immunology and Microbiology, business.industry, Computer science, General Medicine, Data science, Science education, General Biochemistry, Genetics and Molecular Biology, Visualization, Data visualization, Key (cryptography), Web application, Profiling (information science), Early career, General Pharmacology, Toxicology and Pharmaceutics, business, Curriculum
Abstract

Developing the skills needed to effectively search and extract information from biomedical literature is essential for early-career researchers. It is, for instance, on this basis that the novelty of experimental results, and therefore publishing opportunities, can be evaluated. Given the unprecedented volume of publications in the field of biomedical research, new systematic approaches need to be devised and adopted for the retrieval and curation of literature relevant to a specific theme. Here we describe a hands-on training curriculum aimed at retrieval, profiling, and visualization of literature associated with a given topic. This curriculum was implemented in a workshop in January 2021. We provide supporting material and step-by-step implementation guidelines with the ISG15 gene literature serving as an illustrative use case. Through participation in such a workshop, trainees can learn: 1) to build and troubleshoot PubMed queries in order to retrieve the literature associated with a gene of interest; 2) to identify key concepts relevant to given themes (such as cell types, diseases, and biological processes); 3) to measure the prevalence of these concepts in the gene literature; 4) to extract key information from relevant articles, and 5) to develop a background section or summary on the basis of this information. Finally, trainees can learn to consolidate the structured information captured through this process for presentation via an interactive web application.

Published
2021

50. A recessive form of hyper-IgE syndrome by disruption of ZNF341-dependent STAT3 transcription and activity

Author

Warren J. Leonard, Nima Rezaei, Kathryn Payne, Isabelle Meyts, Laurent Abel, Cindy S. Ma, Marianne Leruez-Ville, Janet Chou, Alain Hovnanian, Jian-Xin Lin, Simon J. Pelham, Danielle T. Avery, Matthieu Bouaziz, Bethany Pillay, Tanwir Habib, Anne Puel, Sevgi Keles, Juan Li, Isabelle Pellier, Jamel El-Benna, Bernhard Fleckenstein, Ahmet Ozen, Vivien Béziat, Ingrid Müller-Fleckenstein, Damien Chaussabel, Samaneh Zoghi, Yi Wang, Paul Gray, Matthias Titeux, Yoann Zerbib, Talal A. Chatila, Marie-Alexandra Alyanakian, Capucine Picard, Orli Wargon, Ayper Somer, Marie-Olivia Chandesris, Thibaut Leclercq, Ibtihal Benhsaien, Aziz Belkadi, Jean-Laurent Casanova, Romain Lévy, Peng Li, Geetha Rao, Ai Ing Lim, James P. Di Santo, Nico Marr, Sylvie Fraitag, Frédégonde About, Elissa K. Deenick, Bertrand Boisson, Jacinta Bustamante, Mélanie Migaud, Bodo Grimbacher, Aziz Bousfiha, Fatima Ailal, Safa Baris, Antoine Guérin, Stuart G. Tangye, Romain Guery, Ning Du, Vimel Rattina, Imagine - Institut des maladies génétiques (IMAGINE - U1163), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Rockefeller University [New York], National Institutes of Health [Bethesda] (NIH), Garvan Institute of Medical Research [Darlinghurst, Australia], University of New South Wales [Sydney] (UNSW), CHU Ibn Rochd [Casablanca], Université Hassan II [Casablanca] (UH2MC), Service d'Immuno-Hémato-Oncologie Pédiatrique, Centre Hospitalier Universitaire d'Angers (CHU Angers), PRES Université Nantes Angers Le Mans (UNAM)-PRES Université Nantes Angers Le Mans (UNAM), Shahid Beheshti University of Medical Sciences [Tehran] (SBUMS), Shahid Beheshti University, Universal Scientific Education and Research Network (USERN), Marmara University [Kadıköy - İstanbul], Necmettin Erbakan University [Konya, Turquie], Immunité Innée, Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Harvard Medical School [Boston] (HMS), Boston Children's Hospital, Centre d'infectiologie Necker-Pasteur [CHU Necker], CHU Necker - Enfants Malades [AP-HP], Sidra Medicine, Centre de recherche sur l'Inflammation (CRI (UMR_S_1149 / ERL_8252 / U1149)), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7), Freiburg University Medical Center, Sydney children's hospital, Centre de Référence Déficits Immunitaires Héréditaires (CEREDIH), Assistance publique - Hôpitaux de Paris (AP-HP) (APHP)-CHU Necker - Enfants Malades [AP-HP], Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Genetic skin diseases : from disease mechanism to therapies (Equipe Inserm U1163), Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Service de pathologie [CHU Necker], Service d'immuno-hématologie pédiatrique [CHU Necker], Laboratoire de Virologie [CHU Necker], Université Paris Descartes - Paris 5 (UPD5), Centre d'étude des Déficits Immunitaires, University Hospitals Leuven [Leuven], Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Istanbul University, Research Center for Immunodeficiencies [Tehran, Iran], Tehran University of Medical Sciences (TUMS), University of New South Wales [Canberra Campus] (UNSW), Howard Hughes Medical Institute [New York], New York University School of Medicine, NYU System (NYU)-NYU System (NYU)-Rockefeller University [New York]-Columbia University Irving Medical Center (CUIMC), This work was supported by grants from INSERM, Paris Descartes University, Laboratoire d’Excellence Integrative Biology of Emerging Infectious Diseases (ANR-10-LABX-62-IBEID), the Jeffrey Modell Foundation Translational Research Program, the French National Research Agency (ANR, grant nos. GENCMCD-ANR-11-BSV3–005-01, HGDIFD-ANR-14-CE15-0006-01, NKIR-ANR-13-PDOC-0025-01, and EURO-CMC-ANR-14-RARE-0005-02), and grants awarded under the 'Investissement d’avenir' program (grant no. ANR-10-IAHU-01), the National Institute of Allergy and Infectious Diseases of the NIH (grant nos. U01AI109697 and R01AI127564), the Rockefeller University, the Howard Hughes Medical Institute, the St. Giles Foundation, the Institut Pasteur, and FP7, under grant agreements 305578 (PathCO) and 317057 (HOMIN). We thank the Centre de Recherche Translationnelle (Institut Pasteur) for technical assistance. V.B. is supported by the ANR (grant no. NKIR-ANR-13-PDOC-0025-01). R.L. is supported by the INSERM Ph.D. program (Poste d’Accueil INSERM), a Fulbright grant (Franco-American commission), and a Philippe Foundation scholarship. Y.Z. received the 'médaille d’or du Centre Hospitalier Universitaire d’Amiens.' Y.W. is supported by the French National Agency for Research on AIDS and Viral Hepatitis (ANRS, grant no. 13318). F. About holds a fellowship from Fondation pour la Recherche Médicale (FRM, grant no. FDM20140630671). A.G. is supported by an IFNGPHOX grant (no. ANR13-ISV3-0001-01) from ANR. B.G. was funded by BMBF (German Federal Ministry of Education and Research) grants 01E01303 and 01ZX1306F. I.M. is supported by a klinische onderzoeks-en opleidingsraad (clinical research council) grant from UZ Leuven, a klinisch onderzoeksfonds (clinical research fund) grant from KU Leuven, and an International Mobility Grant from Fonds voor Wetenschappelijk Onderzoek (fund for scientific research) Vlaanderen. C.S.M., E.K.D., and S.G.T. are supported by grants and fellowships from the National Health and Medical Research Council of Australia. C.S.M., P.G., E.K.D., and S.G.T. are members of CIRCA (Clinical Immunogenomics Research Consortia Australia), which is funded by the Office of Health and Medical Research of the NSW Government, the Jeffrey Modell Foundation, and the John Cook Brown Foundation. A.I.L. is a scholar of the Pasteur-Paris University International Ph.D. program and is supported by a Ph.D. International Training Network grant from the European Union’s Seventh Framework Program under grant agreement no. 317057 (HOMIN). T.A.C. was supported by a grant from the National Institute of Allergy and Infectious Diseases of the NIH (5R01AI065617). S.K. was supported by a grant from the Scientific and Technological Research Council of Turkey (1059B191300622). J.-X.L., P.L., N.D., and W.J.L. were supported by the Division of Intramural Research, National Heart, Lung, and Blood Institute, NIH. A.P. was supported by an AP-HP interface contract., We thank the patients and their families for participating in this study. We thank J. E. Darnell and C. Mertens for advice and for providing reagents. We thank the members of the laboratory, especially F. Jabot-Hanin and V. Pedergnana, for their valuable input on linkage analysis, L. Amar, Y. Nemirovskaya, D. Papandrea, E. Anderson, M. Woollett, C. Desvallées, C. Patissier, and M. Corrias for administrative assistance, E. Jouanguy and Y. Itan for helpful discussions, S. Boucherit for clinical data collection, S. Jacques and the Cochin genomics platform for microarray experiments, and N. Goudin and R. Desveaux of the Necker Institute Imaging Facility., Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Garvan Institute of medical research, Immunité Innée - Innate Immunity, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut Pasteur [Paris] (IP)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Sidra Medicine [Doha, Qatar], Université Paris Diderot - Paris 7 (UPD7)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Universitäts Klinikum Freiburg = University Medical Center Freiburg (Uniklinik), Sydney Children's hospital, Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Descartes - Paris 5 (UPD5)-Institut National de la Santé et de la Recherche Médicale (INSERM), Howard Hughes Medical Institute [New York] (HHMI), Howard Hughes Medical Institute (HHMI)-New York University School of Medicine, Institut Pasteur [Paris]-CHU Necker - Enfants Malades [AP-HP], Beziat, Vivien, Li, Juan, Lin, Jian-Xin, Ma, Cindy S., Li, Peng, Bousfiha, Aziz, Pellier, Isabelle, Zoghi, Samaneh, Baris, Safa, Keles, Sevgi, Gray, Paul, Du, Ning, Wang, Yi, Zerbib, Yoann, Levy, Romain, Leclercq, Thibaut, About, Fredegonde, Lim, Ai Ing, Rao, Geetha, Payne, Kathryn, Pelham, Simon J., Avery, Danielle T., Deenick, Elissa K., Pillay, Bethany, Chou, Janet, Guery, Romain, Belkadi, Aziz, Guerin, Antoine, Migaud, Melanie, Rattina, Vimel, Ailal, Fatima, Benhsaien, Ibtihal, Bouaziz, Matthieu, Habib, Tanwir, Chaussabel, Damien, Marr, Nico, El-Benna, Jamel, Grimbacher, Bodo, Wargon, Orli, Bustamante, Jacinta, Boisson, Bertrand, Mueller-Fleckenstein, Ingrid, Fleckenstein, Bernhard, Chandesris, Marie-Olivia, Titeux, Matthias, Fraitag, Sylvie, Alyanakian, Marie-Alexandra, Leruez-Ville, Marianne, Picard, Capucine, Meyts, Isabelle, Di Santo, James P., Hovnanian, Alain, Somer, Ayper, Ozen, Ahmet, Rezaei, Nima, Chatila, Talal A., Abel, Laurent, Leonard, Warren J., Tangye, Stuart G., Puel, Anne, and Casanova, Jean-Laurent

Subjects
0301 basic medicine, INBORN-ERRORS, Immunoglobulin E, MESH: STAT3 Transcription Factor/immunology, Loss of heterozygosity, PRECISION MEDICINE, Transcription (biology), OF-FUNCTION MUTATIONS, STAT3, MESH: Transcription Factors/metabolism, CELL-DIFFERENTIATION, MESH: Th2 Cells/metabolism, MESH: Immunoglobulin E/immunology, MESH: Middle Aged, MESH: Gene Expression Regulation/immunology, Cell Differentiation, General Medicine, MESH: RNA, Messenger/metabolism, MESH: Immunoglobulin E/blood, MESH: Zinc Fingers/genetics, READ ALIGNMENT, MESH: Transcription, Genetic/immunology, MESH: Cell Nucleus/metabolism, MESH: Young Adult, [SDV.IMM]Life Sciences [q-bio]/Immunology, SIGNAL TRANSDUCER, Job Syndrome, MESH: Homozygote, STAT3 Transcription Factor, Cell type, MESH: Lymphocyte Count, MESH: Pedigree, MESH: STAT3 Transcription Factor/genetics, Immunology, Biology, Article, MESH: Job Syndrome/immunology, MESH: Genes, Recessive/genetics, DIFFERENTIAL EXPRESSION, MESH: Genes, Recessive/immunology, MESH: Job Syndrome/blood, MESH: Transcription Factors/genetics, 03 medical and health sciences, MESH: Whole Exome Sequencing, MESH: Exons/genetics, Humans, Transcription factor, Gene, MESH: Adolescent, MESH: Consanguinity, MESH: Humans, CLINICAL-FEATURES, MESH: Th17 Cells/metabolism, MESH: Th17 Cells/immunology, MESH: Cytokines/immunology, MESH: Adult, MESH: Loss of Function Mutation, MESH: Job Syndrome/genetics, MESH: Cell Differentiation/genetics, Molecular biology, MESH: Male, MESH: Th2 Cells/immunology, IL-21 RECEPTOR, 030104 developmental biology, Gene Expression Regulation, MESH: STAT3 Transcription Factor/metabolism, MESH: Promoter Regions, Genetic/genetics, MESH: Cell Differentiation/immunology, T-CELLS, STAT protein, biology.protein, Th17 Cells, MESH: Transcription Factors/immunology, MESH: Cytokines/metabolism, MESH: Female
Abstract

Comment in :Who regulates whom: ZNF341 is an additional player in the STAT3/TH17 song. [Sci Immunol. 2018]; International audience; Heterozygosity for human signal transducer and activator of transcription 3 (STAT3) dominant-negative (DN) mutations underlies an autosomal dominant form of hyper-immunoglobulin E syndrome (HIES). We describe patients with an autosomal recessive form of HIES due to loss-of-function mutations of a previously uncharacterized gene, ZNF341 ZNF341 is a transcription factor that resides in the nucleus, where it binds a specific DNA motif present in various genes, including the STAT3 promoter. The patients' cells have low basal levels of STAT3 mRNA and protein. The autoinduction of STAT3 production, activation, and function by STAT3-activating cytokines is strongly impaired. Like patients with STAT3 DN mutations, ZNF341-deficient patients lack T helper 17 (TH17) cells, have an excess of TH2 cells, and have low memory B cells due to the tight dependence of STAT3 activity on ZNF341 in lymphocytes. Their milder extra-hematopoietic manifestations and stronger inflammatory responses reflect the lower ZNF341 dependence of STAT3 activity in other cell types. Human ZNF341 is essential for the STAT3 transcription-dependent autoinduction and sustained activity of STAT3.

Published
2018

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