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1. Whole-Transcriptome Sequencing–Based Profiling of the Cutaneous Virome in Patients with Secondary Immunodeficiency

Author: Leila Youssefian, Amir Hossein Saeidian, Zahra Saffarian, Mona Ariamanesh, Fahimeh Abdollahimajd, Sara Molkara, Mohammad Shahidi-Dadras, Reem Diab, Fatemeh Vahidnezhad, Sirous Zeinali, Vivien Béziat, Emmanuelle Jouanguy, Jean-Laurent Casanova, Jouni Uitto, and Hassan Vahidnezhad
Subjects: Cutaneous virome, Human papillomavirus, Immunodeficiency, RNA-Seq, Whole-transcriptome sequencing, Dermatology, RL1-803
Abstract: Most viral infections can be self-limited, with no requirement for medical intervention. However, the same viruses can cause severe diseases in patients with compromised immunity due to single-gene diseases, acquired immune deficiency syndrome, or hematologic malignancies or those receiving immunosuppressive drugs. Occasionally, these immunocompromised patients harbor >1 infectious agent, requiring several concomitant diagnostic tests. We have developed, to our knowledge, a previously unreported whole-transcriptome sequencing–based pipeline that allows virome profiling, quantitation, and expression pattern analysis of 926 distinct viruses by sequencing of RNA isolated from a single lesional skin biopsy. This pipeline can also explore host genetics if there is a Mendelian predisposition to infection. We applied this pipeline to 6 Iranian patients with viral-induced skin lesions associated with immune deficiency secondary to HIV, human T-lymphotropic virus 1, chronic lymphocytic leukemia, and post transplant immunosuppression. In 5 cases, definitive human papillomavirus infections were identified, some caused by multiple viral types. In addition to human papillomavirus, coinfection with other viruses (Merkle cell polyomavirus, cytomegalovirus, and human herpesvirus 4) was detected in some lesions. In 1 case, whole-transcriptome sequencing validated the clinical diagnosis of adult T-cell leukemia/lymphoma in a patient with an initial diagnosis of mycosis fungoides/Sézary syndrome. These findings attest to the power of whole-transcriptome sequencing in profiling the cutaneous virome in the context of compromised immunity.
Published: 2024
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2. Case Report of Two Independent Moroccan Families with Syndromic Epidermodysplasia Verruciformis and STK4 Deficiency

Author: Assiya El Kettani, Hind Ouair, Farida Marnissi, Jalila El Bakkouri, Rémi Chevalier, Lazaro Lorenzo, Halima Kholaiq, Vivien Béziat, Emmanuelle Jouanguy, Jean-Laurent Casanova, and Ahmed Aziz Bousfiha
Subjects: epidermodysplasia verruciformis, human papillomavirus, STK4 deficiency, CD4+ T cells, Microbiology, QR1-502
Abstract: Epidermodysplasia verruciformis (EV) is a rare genodermatosis caused by β-human papillomaviruses (HPV) in immunodeficient patients. EV is characterized by flat warts and pityriasis-like lesions and might be isolated or syndromic, associated with some other infectious manifestations. We report here three patients from two independent families, with syndromic EV for both of them. By whole exome sequencing, we found that the patients carry new homozygous variants in STK4, both leading to a premature stop codon. STK4 deficiency causes a combined immunodeficiency characterized by a broad infectious susceptibility to bacteria, viruses, and fungi. Auto-immune manifestations were also reported. Deep immunophenotyping revealed multiple cytopenia in the three affected patients, in particular deep CD4+ T cells deficiency. We report here the fourth and the fifth cases of the syndromic EV due to STK4 deficiency.
Published: 2024
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3. Human inherited complete STAT2 deficiency underlies inflammatory viral diseases

Author: Giorgia Bucciol, Leen Moens, Masato Ogishi, Darawan Rinchai, Daniela Matuozzo, Mana Momenilandi, Nacim Kerrouche, Catherine M. Cale, Elsa R. Treffeisen, Mohammad Al Salamah, Bandar K. Al-Saud, Alain Lachaux, Remi Duclaux-Loras, Marie Meignien, Aziz Bousfiha, Ibtihal Benhsaien, Anna Shcherbina, Anna Roppelt, COVID Human Genetic Effort, Florian Gothe, Nadhira Houhou-Fidouh, Scott J. Hackett, Lisa M. Bartnikas, Michelle C. Maciag, Mohammed F. Alosaimi, Janet Chou, Reem W. Mohammed, Bishara J. Freij, Emmanuelle Jouanguy, Shen-Ying Zhang, Stephanie Boisson-Dupuis, Vivien Béziat, Qian Zhang, Christopher J.A. Duncan, Sophie Hambleton, Jean-Laurent Casanova, and Isabelle Meyts
Subjects: Immunology, Medicine
Abstract: STAT2 is a transcription factor activated by type I and III IFNs. We report 23 patients with loss-of-function variants causing autosomal recessive (AR) complete STAT2 deficiency. Both cells transfected with mutant STAT2 alleles and the patients’ cells displayed impaired expression of IFN-stimulated genes and impaired control of in vitro viral infections. Clinical manifestations from early childhood onward included severe adverse reaction to live attenuated viral vaccines (LAV) and severe viral infections, particularly critical influenza pneumonia, critical COVID-19 pneumonia, and herpes simplex virus type 1 (HSV-1) encephalitis. The patients displayed various types of hyperinflammation, often triggered by viral infection or after LAV administration, which probably attested to unresolved viral infection in the absence of STAT2-dependent types I and III IFN immunity. Transcriptomic analysis revealed that circulating monocytes, neutrophils, and CD8+ memory T cells contributed to this inflammation. Several patients died from viral infection or heart failure during a febrile illness with no identified etiology. Notably, the highest mortality occurred during early childhood. These findings show that AR complete STAT2 deficiency underlay severe viral diseases and substantially impacts survival.
Published: 2023
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4. Whole transcriptome–based skin virome profiling in typical epidermodysplasia verruciformis reveals α-, β-, and γ-HPV infections

Author: Amir Hossein Saeidian, Leila Youssefian, Mahtab Naji, Hamidreza Mahmoudi, Samantha M. Barnada, Charles Huang, Karim Naghipoor, Amir Hozhabrpour, Jason S. Park, Flavia Manzo Margiotta, Fatemeh Vahidnezhad, Zahra Saffarian, Kambiz Kamyab-Hesari, Mohammad Tolouei, Niloofar Faraji, Seyyede Zeinab Azimi, Ghazal Namdari, Parvin Mansouri, Jean-Laurent Casanova, Vivien Béziat, Emmanuelle Jouanguy, Jouni Uitto, and Hassan Vahidnezhad
Subjects: Dermatology, Genetics, Medicine
Abstract: HPVs are DNA viruses include approximately 450 types that are classified into 5 genera (α-, β-, γ-, μ-, and ν-HPV). The γ- and β-HPVs are present in low copy numbers in healthy individuals; however, in patients with an inborn error of immunity, certain species of β-HPVs can cause epidermodysplasia verruciformis (EV), manifesting as recalcitrant cutaneous warts and skin cancer. EV presents as either typical or atypical. Manifestations of typical EV are limited to the skin and are caused by abnormal keratinocyte-intrinsic immunity to β-HPVs due to pathogenic sequence variants in TMC6, TMC8, or CIB1. We applied a transcriptome-based computational pipeline, VirPy, to RNA extracted from normal-appearing skin and wart samples of patients with typical EV to explore the viral and human genetic determinants. In 26 patients, 9 distinct biallelic mutations were detected in TMC6, TMC8, and CIB1, 7 of which are previously unreported to our knowledge. Additionally, 20 different HPV species, including 3 α-HPVs, 16 β-HPVs, and 1 γ-HPV, were detected, 8 of which are reported here for the first time to our knowledge in patients with EV (β-HPV-37, -47, -80, -151, and -159; α-HPV-2 and -57; and γ-HPV-128). This study expands the TMC6, TMC8, and CIB1 sequence variant spectrum and implicates new HPV subtypes in the pathogenesis of typical EV.
Published: 2023
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5. Whole-transcriptome sequencing–based concomitant detection of viral and human genetic determinants of cutaneous lesions

Author: Amir Hossein Saeidian, Leila Youssefian, Charles Y. Huang, Fahimeh Palizban, Mahtab Naji, Zahra Saffarian, Hamidreza Mahmoudi, Azadeh Goodarzi, Soheila Sotoudeh, Fatemeh Vahidnezhad, Maliheh Amani, Narjes Tavakoli, Ali Ajami, Samaneh Mozafarpoor, Mehrdad Teimoorian, Saeed Dorgaleleh, Sima Shokri, Mohammad Shenagari, Nima Abedi, Sirous Zeinali, Paolo Fortina, Vivien Béziat, Emmanuelle Jouanguy, Jean-Laurent Casanova, Jouni Uitto, and Hassan Vahidnezhad
Subjects: Genetics, Infectious disease, Medicine
Abstract: Severe viral infections of the skin can occur in patients with inborn errors of immunity (IEI). We report an all-in-one whole-transcriptome sequencing–based method by RNA-Seq on a single skin biopsy for concomitantly identifying the cutaneous virome and the underlying IEI. Skin biopsies were obtained from healthy and lesional skin from patients with cutaneous infections suspected to be of viral origin. RNA-Seq was utilized as the first-tier strategy for unbiased human genome-wide rare variant detection. Reads unaligned to the human genome were utilized for the exploration of 926 viruses in a viral genome catalog. In 9 families studied, the patients carried pathogenic variants in 6 human IEI genes, including IL2RG, WAS, CIB1, STK4, GATA2, and DOCK8. Gene expression profiling also confirmed pathogenicity of the human variants and permitted genome-wide homozygosity mapping, which assisted in identification of candidate genes in consanguineous families. This automated, online, all-in-one computational pipeline, called VirPy, enables simultaneous detection of the viral triggers and the human genetic variants underlying skin lesions in patients with suspected IEI and viral dermatosis.
Published: 2022
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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. HPV-Related Skin Phenotypes in Patients with Inborn Errors of Immunity

Author: Assiya El Kettani, Fatima Ailal, Jalila El Bakkouri, Khalid Zerouali, Vivien Béziat, Emmanuelle Jouanguy, Jean-Laurent Casanova, and Ahmed Aziz Bousfiha
Subjects: HPV, skin, inborn errors of immunity, Medicine
Abstract: Patients with inborn errors of immunity (IEI) are prone to develop infections, either due to a broad spectrum of pathogens or to only one microbe. Since skin is a major barrier tissue, cutaneous infections are among the most prevalent in patients with IEI due to high exposures to many microbes. In the general population, human papillomaviruses (HPVs) cause asymptomatic or self-healing infections, but, in patients with IEI, unusual clinical expression of HPV infection is observed ranging from epidermodysplasia verruciformis (EV) (a rare disease due to β-HPVs) to profuse, persistent, and recalcitrant warts (due to α-, γ-, and μ-HPVs) or even tree man syndrome (due to HPV2). Mutations in EVER1, EVER2, and CIB1 are associated with EV phenotype; GATA2, CXCR4, and DOCK8 mutations are typically associated with extensive HPV infections, but there are several other IEI that are less frequently associated with severe HPV lesions. In this review, we describe clinical, immunological, and genetic patterns of IEI related to severe HPV cutaneous infections and propose an algorithm for diagnosis of IEI with severe warts associated, or not, with lymphopenia.
Published: 2022
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8. Diagnostics of rare disorders: whole-exome sequencing deciphering locus heterogeneity in telomere biology disorders

Author: Luca Trotta, Anna Norberg, Mervi Taskinen, Vivien Béziat, Sofie Degerman, Ulla Wartiovaara-Kautto, Hannamari Välimaa, Kirsi Jahnukainen, Jean-Laurent Casanova, Mikko Seppänen, Janna Saarela, Minna Koskenvuo, and Timi Martelius
Subjects: Telomere biology disorders,Telomeropathies, Next-generation sequencing, Whole-exome sequencing, Dyskeratosis congenita, DKC1, TERT, RTEL1, Medicine
Abstract: Abstract Background The telomere biology disorders (TBDs) include a range of multisystem diseases characterized by mucocutaneous symptoms and bone marrow failure. In dyskeratosis congenita (DKC), the clinical features of TBDs stem from the depletion of crucial stem cell populations in highly proliferative tissues, resulting from abnormal telomerase function. Due to the wide spectrum of clinical presentations and lack of a conclusive laboratory test it may be challenging to reach a clinical diagnosis, especially if patients lack the pathognomonic clinical features of TBDs. Methods Clinical sequencing was performed on a cohort of patients presenting with variable immune phenotypes lacking molecular diagnoses. Hypothesis-free whole-exome sequencing (WES) was selected in the absence of compelling diagnostic hints in patients with variable immunological and haematological conditions. Results In four patients belonging to three families, we have detected five novel variants in known TBD-causing genes (DKC1, TERT and RTEL1). In addition to the molecular findings, they all presented shortened blood cell telomeres. These findings are consistent with the displayed TBD phenotypes, addressing towards the molecular diagnosis and subsequent clinical follow-up of the patients. Conclusions Our results strongly support the utility of WES-based approaches for routine genetic diagnostics of TBD patients with heterogeneous or atypical clinical presentation who otherwise might remain undiagnosed.
Published: 2018
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9. Critical Role of CD2 Co-stimulation in Adaptive Natural Killer Cell Responses Revealed in NKG2C-Deficient Humans

Author: Lisa L. Liu, Johannes Landskron, Eivind H. Ask, Monika Enqvist, Ebba Sohlberg, James A. Traherne, Quirin Hammer, Jodie P. Goodridge, Stella Larsson, Jyothi Jayaraman, Vincent Y.S. Oei, Marie Schaffer, Kjetil Taskén, Hans-Gustaf Ljunggren, Chiara Romagnani, John Trowsdale, Karl-Johan Malmberg, and Vivien Béziat
Subjects: Biology (General), QH301-705.5
Abstract: Infection by human cytomegalovirus (HCMV) leads to NKG2C-driven expansion of adaptive natural killer (NK) cells, contributing to host defense. However, approximately 4% of all humans carry a homozygous deletion of the gene that encodes NKG2C (NKG2C−/−). Assessment of NK cell repertoires in 60 NKG2C−/− donors revealed a broad range of NK cell populations displaying characteristic footprints of adaptive NK cells, including a terminally differentiated phenotype, functional reprogramming, and epigenetic remodeling of the interferon (IFN)-γ promoter. We found that both NKG2C− and NKG2C+ adaptive NK cells expressed high levels of CD2, which synergistically enhanced ERK and S6RP phosphorylation following CD16 ligation. Notably, CD2 co-stimulation was critical for the ability of adaptive NK cells to respond to antibody-coated target cells. These results reveal an unexpected redundancy in the human NK cell response to HCMV and suggest that CD2 provides “signal 2” in antibody-driven adaptive NK cell responses.
Published: 2016
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10. 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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11. Specificity and dynamics of effector and memory CD8 T cell responses in human tick-borne encephalitis virus infection.

Author: Kim Blom, Monika Braun, Jolita Pakalniene, Laura Dailidyte, Vivien Béziat, Margit H Lampen, Jonas Klingström, Nina Lagerqvist, Torbjörn Kjerstadius, Jakob Michaëlsson, Lars Lindquist, Hans-Gustaf Ljunggren, Johan K Sandberg, Aukse Mickiene, and Sara Gredmark-Russ
Subjects: Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5
Abstract: Tick-borne encephalitis virus (TBEV) is transferred to humans by ticks. The virus causes tick-borne encephalitis (TBE) with symptoms such as meningitis and meningoencephalitis. About one third of the patients suffer from long-lasting sequelae after clearance of the infection. Studies of the immune response during TBEV-infection are essential to the understanding of host responses to TBEV-infection and for the development of therapeutics. Here, we studied in detail the primary CD8 T cell response to TBEV in patients with acute TBE. Peripheral blood CD8 T cells mounted a considerable response to TBEV-infection as assessed by Ki67 and CD38 co-expression. These activated cells showed a CD45RA-CCR7-CD127- phenotype at day 7 after hospitalization, phenotypically defining them as effector cells. An immunodominant HLA-A2-restricted TBEV epitope was identified and utilized to study the characteristics and temporal dynamics of the antigen-specific response. The functional profile of TBEV-specific CD8 T cells was dominated by variants of mono-functional cells as the effector response matured. Antigen-specific CD8 T cells predominantly displayed a distinct Eomes+Ki67+T-bet+ effector phenotype at the peak of the response, which transitioned to an Eomes-Ki67-T-bet+ phenotype as the infection resolved and memory was established. These transcription factors thus characterize and discriminate stages of the antigen-specific T cell response during acute TBEV-infection. Altogether, CD8 T cells responded strongly to acute TBEV infection and passed through an effector phase, prior to gradual differentiation into memory cells with distinct transcription factor expression-patterns throughout the different phases.
Published: 2015
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12. Unconventional repertoire profile is imprinted during acute chikungunya infection for natural killer cells polarization toward cytotoxicity.

Author: Caroline Petitdemange, Pierre Becquart, Nadia Wauquier, Vivien Béziat, Patrice Debré, Eric M Leroy, and Vincent Vieillard
Subjects: Immunologic diseases. Allergy, RC581-607, Biology (General), QH301-705.5
Abstract: Chikungunya virus (CHIKV) is a worldwide emerging pathogen. In humans it causes a syndrome characterized by high fever, polyarthritis, and in some cases lethal encephalitis. Growing evidence indicates that the innate immune response plays a role in controlling CHIKV infection. We show here that CHIKV induces major but transient modifications in NK-cell phenotype and function soon after the onset of acute infection. We report a transient clonal expansion of NK cells that coexpress CD94/NKG2C and inhibitory receptors for HLA-C1 alleles and are correlated with the viral load. Functional tests reveal cytolytic capacity driven by NK cells in the absence of exogenous signals and severely impaired IFN-γ production. Collectively these data provide insight into the role of this unique subset of NK cells in controlling CHIKV infection by subset-specific expansion in response to acute infection, followed by a contraction phase after viral clearance.
Published: 2011
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13. NK cell terminal differentiation: correlated stepwise decrease of NKG2A and acquisition of KIRs.

Author: Vivien Béziat, Benjamin Descours, Christophe Parizot, Patrice Debré, and Vincent Vieillard
Subjects: Medicine, Science
Abstract: BACKGROUND: Terminal differentiation of NK cells is crucial in maintaining broad responsiveness to pathogens and discriminating normal cells from cells in distress. Although it is well established that KIRs, in conjunction with NKG2A, play a major role in the NK cell education that determines whether cells will end up competent or hyporesponsive, the events underlying the differentiation are still debated. METHODOLOGY/PRINCIPAL FINDINGS: A combination of complementary approaches to assess the kinetics of the appearance of each subset during development allowed us to obtain new insights into these terminal stages of differentiation, characterising their gene expression profiles at a pan-genomic level, their distinct surface receptor patterns and their prototypic effector functions. The present study supports the hypothesis that CD56dim cells derive from the CD56bright subset and suggests that NK cell responsiveness is determined by persistent inhibitory signals received during their education. We report here the inverse correlation of NKG2A expression with KIR expression and explore whether this correlation bestows functional competence on NK cells. We show that CD56dimNKG2A-KIR+ cells display the most differentiated phenotype associated to their unique ability to respond against HLA-E+ target cells. Importantly, after IL-12+IL-18 stimulation, reacquisition of NKG2A strongly correlates with IFN-gamma production in CD56dimNKG2A- NK cells. CONCLUSIONS/SIGNIFICANCE: Together, these findings call for the reclassification of mature human NK cells into distinct subsets and support a new model, in which the NK cell differentiation and functional fate are based on a stepwise decrease of NKG2A and acquisition of KIRs.
Published: 2010
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14. 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
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15. Supplementary Figures 1-5 from Ex Vivo Expanded Adaptive NK Cells Effectively Kill Primary Acute Lymphoblastic Leukemia Cells

Author: Karl-Johan Malmberg, Dan Grandér, Mats Heyman, Stefan Söderhäll, Eva Hellström-Lindberg, Sören Lehmann, Marie Schaffer, Aline Pfefferle, Vincent Y.S. Oei, Vivien Béziat, and Lisa L. Liu
Abstract: Supplementary Figure 1. Expansion of adaptive NK cells from C1/C2 donors depends on original imprint. Supplemental Figure 2. Selective expansion of NKG2C NKG2A- NK cells depends on stimulation with HLA-E expressing feeder cells. Supplementary Figure 3. Expression of granzymes and perforin before and after in vitro expansion of adaptive NK cells. Supplementary Figure 4. Adaptive NK cells recognize MDS and AML blasts. Supplementary Figure 5. Sorting of adaptive NK cells for functional studies.
Published: 2023
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16. Data from Ex Vivo Expanded Adaptive NK Cells Effectively Kill Primary Acute Lymphoblastic Leukemia Cells

Author: Karl-Johan Malmberg, Dan Grandér, Mats Heyman, Stefan Söderhäll, Eva Hellström-Lindberg, Sören Lehmann, Marie Schaffer, Aline Pfefferle, Vincent Y.S. Oei, Vivien Béziat, and Lisa L. Liu
Abstract: Manipulation of human natural killer (NK) cell repertoires promises more effective strategies for NK cell–based cancer immunotherapy. A subset of highly differentiated NK cells, termed adaptive NK cells, expands naturally in vivo in response to human cytomegalovirus (HCMV) infection, carries unique repertoires of inhibitory killer cell immunoglobulin-like receptors (KIR), and displays strong cytotoxicity against tumor cells. Here, we established a robust and scalable protocol for ex vivo generation and expansion of adaptive NK cells for cell therapy against pediatric acute lymphoblastic leukemia (ALL). Culture of polyclonal NK cells together with feeder cells expressing HLA-E, the ligand for the activating NKG2C receptor, led to selective expansion of adaptive NK cells with enhanced alloreactivity against HLA-mismatched targets. The ex vivo expanded adaptive NK cells gradually obtained a more differentiated phenotype and were specific and highly efficient killers of allogeneic pediatric T- and precursor B-cell acute lymphoblastic leukemia (ALL) blasts, previously shown to be refractory to killing by autologous NK cells and the NK-cell line NK92 currently in clinical testing. Selective expansion of NK cells that express one single inhibitory KIR for self-HLA class I would allow exploitation of the full potential of NK-cell alloreactivity in cancer immunotherapy. In summary, our data suggest that adaptive NK cells may hold utility for therapy of refractory ALL, either as a bridge to transplant or for patients that lack stem cell donors. Cancer Immunol Res; 5(8); 654–65. ©2017 AACR.
Published: 2023
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17. 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
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18. 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
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19. Impaired thymic AIRE expression underlies autoantibodies against type I IFNs in humans with inborn errors of the alternative NF-kB pathway

Author: Tom Le Voyer, Adrian Gervais, Jérémie Rosain, Audrey Parent, Axel Cederholm, Darawan Rinchai, Lucy Bizien, Gonca Hancioglu, Quentin Philippot, Mame Sokhna Gueye, Majistor Raj Luxman, Maglorius Renkilaraj, Masato Ogishi, Camille Soudée, Mélanie Migaud, Flore Rozenberg, Mana Momenilandi, Quentin Riller, Luisa Imberti, Ottavia Delmonte, Gabriele Müller, Bärbel Keller, Julio Orrego, William Alexander Gallego, Tamar Rubin, Melike Emiroglu, Nima Parvaneh, Daniel Eriksson, Maribel Aranda-Guillen, David I Berrios, Linda Vong, Connie H Katelaris, Peter Mustillo, Johannes Rädler, Jonathan Bohlen, Jale Bengi Celik, Camila Astudillo, Sarah Winter, Audrey Guichard, Vivien Béziat, Jacinta Bustamante, Qiang Pan-Hammarström, Yu Zhang, Lindsey B Rosen, Steve M Holland, Heather Kenney, Kaan Boztuğ, Nizar Mahlaoui, Sylvain Latour, Roshini Abraham, Vassilios Lougaris, Fabian Hauck, Anna Sediva, Faranaz Atschekzei, M Cecilia Poli, Mary A Slatter, Boaz Palterer, Michael D Keller, Alberto Pinzon-Charry, Anna Sullivan, Luke Droney, Daniel Suan, Nathalie Aladjidi, Miguel Hie, Estibaliz Lazaro, Jose Franco, Sevgi Keles, Marion Malphette, Marlene Pasquet, Maria Elena Maccari, Andrea Meinhardt, Aydan Ikinciogullari, Mohammad Shahrooei, Fatih Celmeli, Patrick Frosk, Christopher C Goodnow, Paul E Gray, Alexandre Belot, Hye Sun Kuehn, Sergio D Rosenzweig, Francesco Licciardi, Amélie Servettaz, Vincent Barlogis, Guillaume Le Guenno, Vera-Maria Herrmann, Taco Kuijpers, Grégoire Ducoux, Françoise Sarrot-Reynauld, Catharina Schuetz, Charlotte Cunningham-Rundles, Frédéric Rieux-Laucat, Stuart G Tangye, Cristina Sobacchi, Rainer Doffinger, Klaus Warnatz, Bodo Grimbacher, Claire Fieschi, Laureline Berteloot, Vanessa Bryant, Sophie Trouillet Assant, Luigi D Notarangelo, Helen Su, Benedicte Neven, Laurent Abel, Qian Zhang, Bertrand Boisson, Aurélie Cobat, Emmanuelle Jouanguy, Olle Kampe, Paul Bastard, Chaim Roifman, Nils Landegren, Mark S Anderson, Jean-Laurent Casanova, and Anne Puel
Abstract: Patients with inborn errors of the alternative NF-κB pathway have low thymic AIRE expression, leading to the development of auto-Abs neutralizing type I IFNs, and severe viral diseases.
Published: 2023
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20. Genetic Disorders of Interferons-, Interleukin-17, Interleukin-18, and Nuclear Factor-κB-Mediated Immunity

Author: Jacinta Bustamante, Shen-Ying Zhang, Bertrand Boisson, Vivien Béziat, Qian Zhang, Emmanuelle Jouanguy, Stéphanie Boisson-Dupuis, Anne Puel, and Jean-Laurent Casanova
Published: 2023
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21. Human germline heterozygous gain-of-function STAT6 variants cause severe allergic disease

Author: Mehul Sharma, Daniel Leung, Mana Momenilandi, Lauren C.W. Jones, Lucia Pacillo, Alyssa E. James, Jill R. Murrell, Selket Delafontaine, Jesmeen Maimaris, Maryam Vaseghi-Shanjani, Kate L. Del Bel, Henry Y. Lu, Gilbert T. Chua, Silvia Di Cesare, Oriol Fornes, Zhongyi Liu, Gigliola Di Matteo, Maggie P. Fu, Donato Amodio, Issan Yee San Tam, Gavin Shueng Wai Chan, Ashish A. Sharma, Joshua Dalmann, Robin van der Lee, Géraldine Blanchard-Rohner, Susan Lin, Quentin Philippot, Phillip A. Richmond, Jessica J. Lee, Allison Matthews, Michael Seear, Alexandra K. Turvey, Rachael L. Philips, Terri F. Brown-Whitehorn, Christopher J. Gray, Kosuke Izumi, James R. Treat, Kathleen H. Wood, Justin Lack, Asya Khleborodova, Julie E. Niemela, Xingtian Yang, Rui Liang, Lin Kui, Christina Sze Man Wong, Grace Wing Kit Poon, Alexander Hoischen, Caspar I. van der Made, Jing Yang, Koon Wing Chan, Jaime Sou Da Rosa Duque, Pamela Pui Wah Lee, Marco Hok Kung Ho, Brian Hon Yin Chung, Huong Thi Minh Le, Wanling Yang, Pejman Rohani, Ali Fouladvand, Hassan Rokni-Zadeh, Majid Changi-Ashtiani, Mohammad Miryounesi, Anne Puel, Mohammad Shahrooei, Andrea Finocchi, Paolo Rossi, Beatrice Rivalta, Cristina Cifaldi, Antonio Novelli, Chiara Passarelli, Stefania Arasi, Dominique Bullens, Kate Sauer, Tania Claeys, Catherine M. Biggs, Emma C. Morris, Sergio D. Rosenzweig, John J. O’Shea, Wyeth W. Wasserman, H. Melanie Bedford, Clara D.M. van Karnebeek, Paolo Palma, Siobhan O. Burns, Isabelle Meyts, Jean-Laurent Casanova, Jonathan J. Lyons, Nima Parvaneh, Anh Thi Van Nguyen, Caterina Cancrini, Jennifer Heimall, Hanan Ahmed, Margaret L. McKinnon, Yu Lung Lau, Vivien Béziat, and Stuart E. Turvey
Subjects: All institutes and research themes of the Radboud University Medical Center, Gain of Function Mutation, Immunology, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Humans, Immunology and Allergy, Metabolic Disorders Radboud Institute for Molecular Life Sciences [Radboudumc 6], Immunoglobulin E, STAT6 Transcription Factor, Asthma, Food Hypersensitivity
Abstract: STAT6 (signal transducer and activator of transcription 6) is a transcription factor that plays a central role in the pathophysiology of allergic inflammation. We have identified 16 patients from 10 families spanning three continents with a profound phenotype of early-life onset allergic immune dysregulation, widespread treatment-resistant atopic dermatitis, hypereosinophilia with esosinophilic gastrointestinal disease, asthma, elevated serum IgE, IgE-mediated food allergies, and anaphylaxis. The cases were either sporadic (seven kindreds) or followed an autosomal dominant inheritance pattern (three kindreds). All patients carried monoallelic rare variants in STAT6 and functional studies established their gain-of-function (GOF) phenotype with sustained STAT6 phosphorylation, increased STAT6 target gene expression, and TH2 skewing. Precision treatment with the anti-IL-4Rα antibody, dupilumab, was highly effective improving both clinical manifestations and immunological biomarkers. This study identifies heterozygous GOF variants in STAT6 as a novel autosomal dominant allergic disorder. We anticipate that our discovery of multiple kindreds with germline STAT6 GOF variants will facilitate the recognition of more affected individuals and the full definition of this new primary atopic disorder. ispartof: J Exp Med vol:220 issue:5 pages:e20221755- ispartof: location:United States status: published
Published: 2023

22. 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
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23. Human inborn errors of immunity to oncogenic viruses

Author: Vivien Béziat and Emmanuelle Jouanguy
Subjects: viruses, Hepatitis C virus, Immunology, Merkel cell polyomavirus, Autoimmunity, medicine.disease_cause, Article, Broad spectrum, Species Specificity, Immunity, medicine, Humans, Immunology and Allergy, Genetic Predisposition to Disease, Hepatitis B virus, biology, business.industry, Genetic Variation, virus diseases, biology.organism_classification, Phenotype, Virology, Epstein–Barr virus, Tumor Virus Infections, Host-Pathogen Interactions, Mutation, Oncogenic Viruses, business, Biomarkers, Oncovirus
Abstract: Oncoviruses are viruses that can cause tumors. Seven viruses are currently recognized as oncogenic in humans: Epstein Barr virus (EBV), Kaposi sarcoma-associated herpesvirus (KSHV, also known as HHV8), human papillomaviruses (HPVs), hepatitis B virus (HBV), hepatitis C virus (HCV), human T-lymphotropic virus-1 (HTLV-1), and Merkel cell polyomavirus (MCPyV). The clinical phenotypes resulting from infection with these oncoviruses range from asymptomatic infection to invasive cancers. Patients with inborn errors of immunity (IEI) are prone to the development of infectious diseases caused by a narrow or broad spectrum of pathogens, including oncoviruses in some cases. Studies of patients with IEI have deepened our understanding of the non-redundant mechanisms underlying the control of EBV, HHV8 and HPV infections. The human genetic factors conferring predisposition to oncogenic HBV, HCV, HTLV-1 and MCPyV manifestations remain elusive. We briefly review here what is currently known about the IEI conferring predisposition to severe infection with oncoviruses.
Published: 2021
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24. Inherited human ZNF341 deficiency

Author: Vivien Béziat, Claire Fieschi, Mana Momenilandi, Mélanie Migaud, Brahim Belaid, Reda Djidjik, and Anne Puel
Subjects: Immunology, Immunology and Allergy
Published: 2023
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25. A loss-of-function IFNAR1 allele in Polynesia underlies severe viral diseases in homozygotes

Author: Paul Bastard, Kuang-Chih Hsiao, Qian Zhang, Jeremy Choin, Emma Best, Jie Chen, Adrian Gervais, Lucy Bizien, Marie Materna, Christine Harmant, Maguelonne Roux, Nicola L. Hawley, Daniel E. Weeks, Stephen T. McGarvey, Karla Sandoval, Carmina Barberena-Jonas, Consuelo D. Quinto-Cortés, Erika Hagelberg, Alexander J. Mentzer, Kathryn Robson, Boubacar Coulibaly, Yoann Seeleuthner, Benedetta Bigio, Zhi Li, Gilles Uzé, Sandra Pellegrini, Lazaro Lorenzo, Zineb Sbihi, Sylvain Latour, Marianne Besnard, Tiphaine Adam de Beaumais, Evelyne Jacqz Aigrain, Vivien Béziat, Ranjan Deka, Litara Esera Tulifau, Satupa‘itea Viali, Muagututi‘a Sefuiva Reupena, Take Naseri, Peter McNaughton, Vanessa Sarkozy, Jane Peake, Annaliesse Blincoe, Sarah Primhak, Simon Stables, Kate Gibson, See-Tarn Woon, Kylie Marie Drake, Adrian V.S. Hill, Cheng-Yee Chan, Richard King, Rohan Ameratunga, Iotefa Teiti, Maite Aubry, Van-Mai Cao-Lormeau, Stuart G. Tangye, Shen-Ying Zhang, Emmanuelle Jouanguy, Paul Gray, Laurent Abel, Andrés Moreno-Estrada, Ryan L. Minster, Lluis Quintana-Murci, Andrew C. Wood, Jean-Laurent Casanova, Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Rockefeller University [New York], Human genetics of infectious diseases: Complex predisposition (Equipe Inserm 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), Département de Pédiatrie et maladies infectieuses [CHU Necker], CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Howard Hughes Medical Institute (HHMI), University of Auckland [Auckland], Génétique Evolutive Humaine - Human Evolutionary Genetics, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Collège de France - Chaire Génomique humaine et évolution, Collège de France (CdF (institution)), University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE), Langebio (CINVESTAV), University of New South Wales [Sydney] (UNSW), Sydney Children's hospital, Garvan Institute of medical research, UNSW Faculty of Medicine [Sydney], Institut Louis Malardé [Papeete] (ILM), Institut de Recherche pour le Développement (IRD), Auckland City Hospital, Canterbury Health Laboratories, University of Oxford, University of Queensland [Brisbane], Brown University, Ministry of Health [Samoa], Tupua Tamasese Meaole Hospital (TTM), University of Cincinnati (UC), Hopital Saint-Louis [AP-HP] (AP-HP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Université Paris Cité (UPCité), Institut Gustave Roussy (IGR), Centre Hospitalier de Polynésie Française, Signalisation des Cytokines - Cytokine Signaling, Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), Cellules Souches, Plasticité Cellulaire, Médecine Régénératrice et Immunothérapies (IRMB), Centre Hospitalier Régional Universitaire [Montpellier] (CHRU Montpellier)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Montpellier (UM), University of Oslo (UiO), National Laboratory of Genomics for Biodiversity (LANGEBIO), Centro de Investigacion y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV), Yale University [New Haven], Hub Bioinformatique et Biostatistique - Bioinformatics and Biostatistics HUB, Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité), Human genetics of infectious diseases : Mendelian predisposition (Equipe Inserm U1163), Shanghai Jiaotong University, Murdoch Children's Research Institute (MCRI), The laboratory of V.-M. Cao-Lormeau is supported by MATAEA grant no. 03557/MED/REC_29/05/2019 (Délégation à la recherche de la Polynésie française). The Laboratory of Human Evolutionary Genetics is supported by Institut Pasteur, Collège de France, the Centre national de la recherche scientifique, Fondation Allianz-Institut de France, the French Government’s Investissement d’Avenir program, Laboratoires d’Excellence 'Integrative Biology of Emerging Infectious Diseases' (ANR-10-LABX-62-IBEID) and 'Milieu Intérieur' (ANR-10-LABX-69-01), Fondation de France (grant no. 00106080), and Fondation pour la Recherche Médicale (Equipe FRM DEQ20180339214). 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, the NIH Clinical and Translational Science Award program (UL1 TR001866), a Fast Grant from Emergent Ventures, Mercatus Center at George Mason University, the Yale Center for Mendelian Genomics, and the Genome Sequencing Program Coordinating Center funded by the National Human Genome Research Institute (UM1HG006504 and U24HG008956), the Yale High-Performance Computing Center (S10OD018521), the Fisher Center for Alzheimer’s Research Foundation, the Meyer Foundation, 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 FRM and ANR GENCOVID project, the ANRS-COV05, ANR GENVIR (ANR-20-CE93-003), and ANR AABIFNCOV (ANR-20-CO11-0001) projects, the European Union’s Horizon 2020 research and innovation program under grant agreement 824110 (EASI-genomics), the Square Foundation, Grandir - Fonds de solidarité pour l’enfance, the Fondation du Souffle, the SCOR Corporate Foundation for Science, INSERM, the French Ministry of Higher Education, Research, and Innovation (MESRI-COVID-19), and the University of Paris. P. Bastard was supported by the FRM (EA20170638020) and by the MD-PhD program of the Imagine Institute (with the support of Fondation Bettencourt-Schueller). The National Laboratory of Genomics for Biodiversity (LANGEBIO-CINVESTAV) in Mexico is supported by Consejo Nacional de Ciencia y Technologia (grant number FONCICYT/50/2016), The Newton Fund through the Medical Research Council (grant number MR/N028937/1), and the International Center for Genetic Engineering and Biotechnology grant number CRP/MEX20-01, awarded to A. Moreno-Estrada. S.G. Tangye is supported by a Leadership 3 Investigator Grant awarded by the National Health and Medical Research Council of Australia (1176665) and the Jeffrey Modell Foundation. Clinical Immunogenomics Research Consortium Australasia investigators (K.-C. Hsiao, P. McNaughton, A. Blincoe, J. Peake, S.G. Tangye, and P. Gray) are supported by the John Brown Cook Foundation. This work was supported by the National Institutes of Health grants R01-HL093093 (S.T. McGarvey) and R01-HL133040 (R.L. Minster). Molecular data for the Trans-Omics in Precision Medicine (TOPMed) program were provided by the National Heart, Lung, and Blood Institute (NHLBI). Genome sequencing for the Soifua Manuia study, labeled 'NHLBI TOPMed: Genome-wide Association Study of Adiposity in Samoans' (phs000972.v4.p1) in the dbGaP, was performed at the Northwest Genomics Center (HHSN268201100037C) and the New York Genome Center (HHSN268201500016C). Core support, including centralized genomic read mapping and genotype calling, along with variant quality metrics and filtering, was provided by the TOPMed Informatics Research Center (3R01-HL117626-02S1, contract HHSN268201800002I). Core support, including phenotype harmonization, data management, sample-identity QC, and general program coordination, was also provided by the TOPMed Data Coordinating Center (R01-HL120393, U01-HL120393, contract HHSN268201800001I). We gratefully acknowledge the studies and participants who provided biological samples and data for TOPMed. This research was funded in whole or in part by the French National Research Agency (ANR)., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-10-LABX-0069,MILIEU INTERIEUR,GENETIC & ENVIRONMENTAL CONTROL OF IMMUNE PHENOTYPE VARIANCE: ESTABLISHING A PATH TOWARDS PERSONALIZED MEDICINE(2010), ANR-10-IAHU-0001,Imagine,Institut Hospitalo-Universitaire Imagine(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), 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), European Project: 824110,H2020-INFRAIA-2018-1,EASI-Genomics(2019), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPC), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPC), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPC), Institut Pasteur [Paris]-Université Paris Cité (UPC), University of Oxford [Oxford], Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPC), Institute for Regenerative Medicine and Biotherapy [Montpellier], Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre Hospitalier Universitaire de Montpellier (CHU Montpellier ), Université Paris Cité (UPC), Garvan Institute of Medical Research [Sydney, Australia], and Chaire Génomique humaine et évolution
Subjects: [SDV.GEN]Life Sciences [q-bio]/Genetics, Infectious disease and host defense, Homozygote, Immunology, Innate immunity and inflammation, Receptor, Interferon alpha-beta, Polynesia, Virus Diseases, [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases, Humans, Immunology and Allergy, Immunodeficiency, Child, Alleles, Human disease genetics
Abstract: International audience; Globally, autosomal recessive IFNAR1 deficiency is a rare inborn error of immunity underlying susceptibility to live attenuated vaccine and wild-type viruses. We report seven children from five unrelated kindreds of western Polynesian ancestry who suffered from severe viral diseases. All the patients are homozygous for the same nonsense IFNAR1 variant (p.Glu386*). This allele encodes a truncated protein that is absent from the cell surface and is loss-of-function. The fibroblasts of the patients do not respond to type I IFNs (IFN-α2, IFN-ω, or IFN-β). Remarkably, this IFNAR1 variant has a minor allele frequency >1% in Samoa and is also observed in the Cook, Society, Marquesas, and Austral islands, as well as Fiji, whereas it is extremely rare or absent in the other populations tested, including those of the Pacific region. Inherited IFNAR1 deficiency should be considered in individuals of Polynesian ancestry with severe viral illnesses.
Published: 2022
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26. 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
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27. 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
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28. Delayed Diagnosis of Chronic Necrotizing Granulomatous Skin Lesions due to TAP2 Deficiency

Author: Ilad Alavi Darazam, Atousa Hakamifard, Mana Momenilandi, Marie Materna, Farid Javandoust Gharehbagh, Mohammad Shahrooei, Nasrin Alipour Olyaei, Farahnaz Bidari Zerehpoosh, Antoine Fayand, Firouze Hatami, Legha Lotfollahi, Nahal Mansouri, Jean-Laurent Casanova, Vivien Béziat, and Davood Mansouri
Subjects: Immunology, Immunology and Allergy
Abstract: Major histocompatibility complex class I (MHC-I) deficiency, also known as bare lymphocyte syndrome type 1 (BLS-1), is a rare autosomal recessively inherited immunodeficiency disorder with remarkable clinical and biological heterogeneity. Transporter associated with antigen processing (TAP) is a member of the ATP-binding cassette superfamily of transporters and consists of two subunits, TAP1 or TAP2. Any defect resulting from a mutation or deletion of these two subunits may adversely affect the peptide translocation in the endoplasmic reticulum, which is an important process for properly assembling MHC-I molecules. To date, only 12 TAP2-deficient patients were reported in the literature. Herein, we described two Iranian cases with 2 and 3 decades of delayed diagnosis of chronic necrotizing granulomatous skin lesions due to TAP2 deficiency without pulmonary involvement. Segregation analysis in family members identified 3 additional homozygous asymptomatic carriers. In both asymptomatic and symptomatic carriers, HLA-I expression was only 4-15% of the one observed in healthy controls. We performed the first deep immunophenotyping in TAP2-deficient patients. While total CD8 T cell counts were normal as previously reported, the patients showed strongly impaired naïve CD8 T cell counts. Mucosal-associated invariant T (MAIT) cells and invariant natural killer T (iNKT) cell counts were increased.
Published: 2022

29. Recalcitrant Cutaneous Warts in a Family with Inherited ICOS Deficiency

Author: Leila Youssefian, Amir Hossein Saeidian, Ali Reza Tavasoli, Elnaz Kalamati, Karim Naghipoor, Amir Hozhabrpour, Mehrnaz Mesdaghi, Zahra Saffarian, Hamidreza Mahmoudi, Mohammad Nabavi, Sima Shokri, Sirous Zeinali, Vivien Béziat, Jean-Laurent Casanova, Emmanuelle Jouanguy, Jouni Uitto, and Hassan Vahidnezhad
Subjects: Adult, Inducible T-Cell Co-Stimulator Protein, Male, Papillomavirus Infections, Exome Sequencing, Humans, Cell Biology, Dermatology, Warts, Molecular Biology, Biochemistry, Papillomaviridae, Skin
Abstract: Recalcitrant warts, caused by human papillomaviruses (HPVs), can be a cutaneous manifestation of inborn error of immunity. This study investigated the clinical manifestations, immunodeficiency, single-gene susceptibility, and HPV repertoire in a consanguineous family with severe sinopulmonary infections and recalcitrant warts. Clinical and immunologic evaluations, including FACS and lymphocyte transformation test, provided evidence for immunodeficiency. Combined whole-exome sequencing and genome-wide homozygosity mapping were utilized to disclose candidate sequence variants. Whole-transcriptome sequencing was used to concomitantly investigate the HPV genotypes and the consequences of detected sequence variants in the host. The proband, a male aged 41 years, was found to be homozygous for the c.6delG, p.Lys2Asnfs∗17 variant in ICOS, encoding the inducible T-cell costimulator. This variant was located inside the 5 megabase of runs of homozygosity on 2q33.2. RNA sequencing confirmed the deleteriousness of the ICOS variant in three skin biopsies revealing significant downregulation of ICOS and its ligand, ICOSLG. Reads unaligned to the human genome were applied to 926 different viruses, and α-HPV57, β-HPV107, β-HPV14, and β-HPV17 were detected. Collectively, we describe a previously unrecognized inborn error of T-cell immunity to HPVs, indicating that autosomal recessive ICOS deficiency can underlie recalcitrant warts, emphasizing the immunologic underpinnings of recalcitrant warts at the nexus of human and viral genomic variation.
Published: 2021

30. Recalcitrant Warts, Epidermodysplasia Verruciformis, and the Tree-Man Syndrome: Phenotypic Spectrum of Cutaneous HPV Infections at the Intersection of Genetic Variability of Viral and Human Genomes

Author: Jouni Uitto, Leila Youssefian, Vivien Béziat, Jean-Laurent Casanova, Zahra Saffarian, Emmanuelle Jouanguy, Amir Hossein Saeidian, and Hassan Vahidnezhad
Subjects: Dermatology, Biology, Biochemistry, Article, Immunity, medicine, Humans, Genetic variability, Molecular Biology, Gene, Papillomaviridae, Common warts, Genome, Human, Papillomavirus Infections, Genetic disorder, virus diseases, Cell Biology, Epidermodysplasia verruciformis, Syndrome, medicine.disease, Virology, Phenotype, DNA, Viral, Epidermodysplasia Verruciformis, Human genome, Warts
Abstract: Human papilloma virus (HPV) infections can cause common warts, which usually resolve spontaneously or become recalcitrant, resistant to multiple treatments. In rare cases, they transform into cutaneous giant horns resulting in the tree-man syndrome (TMS). Defective β-HPVs can cause flat warts in epidermodysplasia verruciformis (EV), a genetic disorder. In typical EV, limited to the skin, the mutated genes are critical for keratinocyte-intrinsic immunity, while atypical, syndromic EV involves genes controlling T-cells. Inborn errors of immunity due to mutations in distinct genes underlying recalcitrant warts and the α-HPV2-driven TMS have been identified, all disrupting T-cell immunity. Collectively, these observations attest to the wide phenotypic spectrum of cutaneous infections caused by different HPV types, at the intersection of the genetic diversity of the viral and human genomes.
Published: 2021

31. The 'Editors' Take to RAG: Promise of CRISPR/Cas9/rAAV6-Based Gene Therapy for RAG2 Deficiency

Author: Isabelle Meyts and Vivien Béziat
Subjects: medicine.medical_specialty, Medical microbiology, business.industry, RAG2, Genetic enhancement, Immunology, MEDLINE, Immunology and Allergy, Medicine, CRISPR, business, Bioinformatics
Published: 2021
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32. Biochemically deleterious human NFKB1 variants underlie an autosomal dominant form of common variable immunodeficiency

Author: Peng Zhang, Katharina Thoma, Bingnan Lyu, Gulbu Uzel, Juan Li, Boualem Hammadi, András N Spaan, Jamila El Baghdadi, Alexandra F. Freeman, Charlotte Cunningham-Rundles, Yu Zhang, Jean-Laurent Casanova, Claire Fieschi, Franck Rapaport, Jérémie Rosain, Vivien Béziat, Simon J. Pelham, Wei-Te Lei, Anne Puel, Maya Chrabieh, Helen C. Su, V. Koneti Rao, David Hum, Stéphanie Boisson-Dupuis, Jacinta Bustamante, Mélanie Migaud, Anne-Sophie Korganow, Qian Zhang, Aurélie Cobat, Steven M. Holland, Laurent Abel, Vishukumar Aimanianda, Bertrand Boisson, Manfred Fliegauf, Benedetta Bigio, Bodo Grimbacher, Yoann Seeleuthner, Takaki Asano, Carol J Saunders, Shen-Ying Zhang, and Emmanuelle Jouanguy
Subjects: Transcriptional Activation, P50, Immunology, Mutant, Population, Haploinsufficiency, Biology, Cell Line, 03 medical and health sciences, 0302 clinical medicine, Chlorocebus aethiops, medicine, Animals, Humans, Immunology and Allergy, education, Loss function, 030304 developmental biology, Dominance (genetics), Genetics, 0303 health sciences, education.field_of_study, Common variable immunodeficiency, HEK 293 cells, NF-kappa B, NF-kappa B p50 Subunit, medicine.disease, Common Variable Immunodeficiency, HEK293 Cells, Phenotype, COS Cells, 030215 immunology
Abstract: Autosomal dominant (AD) NFKB1 deficiency is thought to be the most common genetic etiology of common variable immunodeficiency (CVID). However, the causal link between NFKB1 variants and CVID has not been demonstrated experimentally and genetically, as there has been insufficient biochemical characterization and enrichment analysis. We show that the cotransfection of NFKB1-deficient HEK293T cells (lacking both p105 and its cleaved form p50) with a κB reporter, NFKB1/p105, and a homodimerization-defective RELA/p65 mutant results in p50:p65 heterodimer–dependent and p65:p65 homodimer–independent transcriptional activation. We found that 59 of the 90 variants in patients with CVID or related conditions were loss of function or hypomorphic. By contrast, 258 of 260 variants in the general population or patients with unrelated conditions were neutral. None of the deleterious variants displayed negative dominance. The enrichment in deleterious NFKB1 variants of patients with CVID was selective and highly significant (P = 2.78 × 10−15). NFKB1 variants disrupting NFKB1/p50 transcriptional activity thus underlie AD CVID by haploinsufficiency, whereas neutral variants in this assay should not be considered causal.
Published: 2021
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33. 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
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34. 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
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35. 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
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36. Autoantibodies neutralizing type I IFNs are present in

Author: Paul, Bastard, Adrian, Gervais, Tom, Le Voyer, Jérémie, Rosain, Quentin, Philippot, Jérémy, Manry, Eleftherios, Michailidis, Hans-Heinrich, Hoffmann, Shohei, Eto, Marina, Garcia-Prat, Lucy, Bizien, Alba, Parra-Martínez, Rui, Yang, Liis, Haljasmägi, Mélanie, Migaud, Karita, Särekannu, Julia, Maslovskaja, Nicolas, de Prost, Yacine, Tandjaoui-Lambiotte, Charles-Edouard, Luyt, Blanca, Amador-Borrero, Alexandre, Gaudet, Julien, Poissy, Pascal, Morel, Pascale, Richard, Fabrice, Cognasse, Jesus, Troya, Sophie, Trouillet-Assant, Alexandre, Belot, Kahina, Saker, Pierre, Garçon, Jacques G, Rivière, Jean-Christophe, Lagier, Stéphanie, Gentile, Lindsey B, Rosen, Elana, Shaw, Tomohiro, Morio, Junko, Tanaka, David, Dalmau, Pierre-Louis, Tharaux, Damien, Sene, Alain, Stepanian, Bruno, Megarbane, Vasiliki, Triantafyllia, Arnaud, Fekkar, James R, Heath, José Luis, Franco, Juan-Manuel, Anaya, Jordi, Solé-Violán, Luisa, Imberti, Andrea, Biondi, Paolo, Bonfanti, Riccardo, Castagnoli, Ottavia M, Delmonte, Yu, Zhang, Andrew L, Snow, Steven M, Holland, Catherine, Biggs, Marcela, Moncada-Vélez, Andrés Augusto, Arias, Lazaro, Lorenzo, Soraya, Boucherit, Boubacar, Coulibaly, Dany, Anglicheau, Anna M, Planas, Filomeen, Haerynck, Sotirija, Duvlis, Robert L, Nussbaum, Tayfun, Ozcelik, Sevgi, Keles, Ahmed A, Bousfiha, Jalila, El Bakkouri, Carolina, Ramirez-Santana, Stéphane, Paul, Qiang, Pan-Hammarström, Lennart, Hammarström, Annabelle, Dupont, Alina, Kurolap, Christine N, Metz, Alessandro, Aiuti, Giorgio, Casari, Vito, Lampasona, Fabio, Ciceri, Lucila A, Barreiros, Elena, Dominguez-Garrido, Mateus, Vidigal, Mayana, Zatz, Diederik, van de Beek, Sabina, Sahanic, Ivan, Tancevski, Yurii, Stepanovskyy, Oksana, Boyarchuk, Yoko, Nukui, Miyuki, Tsumura, Loreto, Vidaur, Stuart G, Tangye, Sonia, Burrel, Darragh, Duffy, Lluis, Quintana-Murci, Adam, Klocperk, Nelli Y, Kann, Anna, Shcherbina, Yu-Lung, Lau, Daniel, Leung, Matthieu, Coulongeat, Julien, Marlet, Rutger, Koning, Luis Felipe, Reyes, Angélique, Chauvineau-Grenier, Fabienne, Venet, Guillaume, Monneret, Michel C, Nussenzweig, Romain, Arrestier, Idris, Boudhabhay, Hagit, Baris-Feldman, David, Hagin, Joost, Wauters, Isabelle, Meyts, Adam H, Dyer, Sean P, Kennelly, Nollaig M, Bourke, Rabih, Halwani, Narjes Saheb, Sharif-Askari, Karim, Dorgham, Jérome, Sallette, Souad Mehlal, Sedkaoui, Suzan, AlKhater, Raúl, Rigo-Bonnin, Francisco, Morandeira, Lucie, Roussel, Donald C, Vinh, Sisse Rye, Ostrowski, Antonio, Condino-Neto, Carolina, Prando, Anastasiia, Bonradenko, András N, Spaan, Laurent, Gilardin, Jacques, Fellay, Stanislas, Lyonnet, Kaya, Bilguvar, Richard P, Lifton, Shrikant, Mane, Mark S, Anderson, Bertrand, Boisson, Vivien, Béziat, Shen-Ying, Zhang, Evangelos, Vandreakos, Olivier, Hermine, Aurora, Pujol, Pärt, Peterson, Trine H, Mogensen, Lee, Rowen, James, Mond, Stéphanie, Debette, Xavier, de Lamballerie, Xavier, Duval, France, Mentré, Marie, Zins, Pere, Soler-Palacin, Roger, Colobran, Guy, Gorochov, Xavier, Solanich, Sophie, Susen, Javier, Martinez-Picado, Didier, Raoult, Marc, Vasse, Peter K, Gregersen, Lorenzo, Piemonti, Carlos, Rodríguez-Gallego, Luigi D, Notarangelo, Helen C, Su, Kai, Kisand, Satoshi, Okada, Anne, Puel, Emmanuelle, Jouanguy, Charles M, Rice, Pierre, Tiberghien, Qian, Zhang, Aurélie, Cobat, Laurent, Abel, and Hind, Hamzeh-Cognasse
Subjects: Adult, Aged, 80 and over, Adolescent, Critical Illness, Infant, Newborn, COVID-19, Infant, Interferon-alpha, Middle Aged, Antibodies, Neutralizing, Young Adult, Case-Control Studies, Child, Preschool, Immunoglobulin G, Interferon Type I, Humans, Child, Aged, Autoantibodies
Abstract: Circulating autoantibodies (auto-Abs) neutralizing high concentrations (10 ng/mL, in plasma diluted 1 to 10) of IFN-α and/or -ω are found in about 10% of patients with critical COVID-19 pneumonia, but not in subjects with asymptomatic infections. We detect auto-Abs neutralizing 100-fold lower, more physiological, concentrations of IFN-α and/or -ω (100 pg/mL, in 1/10 dilutions of plasma) in 13.6% of 3,595 patients with critical COVID-19, including 21% of 374 patients80 years, and 6.5% of 522 patients with severe COVID-19. These antibodies are also detected in 18% of the 1,124 deceased patients (aged 20 days-99 years; mean: 70 years). Moreover, another 1.3% of patients with critical COVID-19 and 0.9% of the deceased patients have auto-Abs neutralizing high concentrations of IFN-β. We also show, in a sample of 34,159 uninfected subjects from the general population, that auto-Abs neutralizing high concentrations of IFN-α and/or -ω are present in 0.18% of individuals between 18 and 69 years, 1.1% between 70 and 79 years, and 3.4%80 years. Moreover, the proportion of subjects carrying auto-Abs neutralizing lower concentrations is greater in a subsample of 10,778 uninfected individuals: 1% of individuals70 years, 2.3% between 70 and 80 years, and 6.3%80 years. By contrast, auto-Abs neutralizing IFN-β do not become more frequent with age. Auto-Abs neutralizing type I IFNs predate SARS-CoV-2 infection and sharply increase in prevalence after the age of 70 years. They account for about 20% of both critical COVID-19 cases in the over-80s, and total fatal COVID-19 cases.
Published: 2021

37. Human genetic and immunological dissection of papillomavirus-driven diseases: new insights into their pathogenesis

Author: Vivien Béziat, Jean-Laurent Casanova, and Emmanuelle Jouanguy
Subjects: Keratinocytes, Skin Neoplasms, T-Lymphocytes, Population, Biology, Article, Immune system, Uterine cancer, Virology, medicine, Animals, Humans, education, Papillomaviridae, Common warts, education.field_of_study, Papillomavirus Infections, HPV infection, virus diseases, Epidermodysplasia verruciformis, Acquired immune system, medicine.disease, female genital diseases and pregnancy complications, Human genetics, Immunology, Epidermodysplasia Verruciformis, Uterine Neoplasms, Carcinoma, Squamous Cell, Female
Abstract: Human papillomaviruses (HPVs) are responsible for cutaneous and mucosal lesions. Persistent HPV infection remains a leading cause of uterine cancer in women, but also of cutaneous squamous cell carcinoma in patients with epidermodysplasia verruciformis (EV), and of rare and devastating benign tumors, such as 'tree-man' syndrome. HPV infections are usually asymptomatic or benign in the general population. Severe manifestations in otherwise healthy subjects can attest to inherited immunodeficiencies. The human genetic dissection of these cases has identified critical components of the immune response to HPVs, including the non-redundant roles of keratinocyte-intrinsic immunity in controlling β-HPVs, and of T cell-dependent adaptive immunity for controlling all HPV types. A key role of the CD28 T-cell costimulation pathway in controlling common warts due to HPVs was recently discovered. This review summarizes the state of the art in the human genetics of HPV infection, focusing on two key affected cell types: keratinocytes and T cells.
Published: 2021

38. 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

39. Traitement par rétinoïdes oraux des maladies à papillomavirus humain : étude de 6 cas en vie réelle

Author: Martine Bagot, Hélène Péré, David Veyer, Sébastien Fouéré, Vivien Béziat, and F. Herms
Subjects: Ocean Engineering, Safety, Risk, Reliability and Quality
Published: 2021
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40. The 'Editors' Take to RAG: Promise of CRISPR/Cas9/rAAV6-Based Gene Therapy for RAG2 Deficiency

Author: Vivien, Béziat and Isabelle, Meyts
Subjects: DNA-Binding Proteins, Humans, Nuclear Proteins, chemical and pharmacologic phenomena, Genetic Therapy, CRISPR-Cas Systems, Article
Abstract: Severe combined immune deficiency (SCID) caused by RAG1 or RAG2 deficiency is a genetically-determined immune deficiency characterized by the virtual absence of T and B lymphocytes. Unless treated with hematopoietic stem cell transplantation (HSCT), patients with RAG deficiency succumb to severe infections early in life. However, HSCT carries the risk of graft-versus-host disease. Moreover, a high rate of graft failure and poor immune reconstitution have been reported after unconditioned HSCT. Expression of the RAG genes is tightly regulated, and preclinical attempts of gene therapy with heterologous promoters have led to controversial results. Using patient-derived induced pluripotent stem cells (iPSCs) and an in vitro artificial thymic organoid system as a model, here we demonstrate that gene editing rescues the progressive T-cell differentiation potential of RAG2 deficient cells to normal levels, with generation of a diversified T cell repertoire. These results suggest that targeted gene editing may represent a novel therapeutic option for correction of this immunodeficiency.
Published: 2021

41. Netherton syndrome subtypes share IL-17/IL-36 signature with distinct IFN-α and allergic responses

Author: Claire, Barbieux, Mathilde, Bonnet des Claustres, Matthias, Fahrner, Evgeniya, Petrova, Lam C, Tsoi, Olivier, Gouin, Florent, Leturcq, Pascale, Nicaise-Roland, Christine, Bole, Vivien, Béziat, Emmanuelle, Bourrat, Oliver, Schilling, Johann E, Gudjonsson, and Alain, Hovnanian
Subjects: Netherton Syndrome, Interleukin-17, Hypersensitivity, Proteinase Inhibitory Proteins, Secretory, Humans, Interferon-alpha, Serine Peptidase Inhibitor Kazal-Type 5, Epidermis, Skin Diseases, Skin
Abstract: Netherton syndrome (NS) is a rare recessive skin disorder caused by loss-of-function mutations in SPINK5 encoding the protease inhibitor LEKTI (lymphoepithelial Kazal-type-related inhibitor). NS patients experience severe skin barrier defects, display inflammatory skin lesions, and have superficial scaling with atopic manifestations. They present with typical ichthyosis linearis circumflexa (NS-ILC) or scaly erythroderma (NS-SE).We used a combination of several molecular profiling methods to comprehensively characterize the skin, immune cells, and allergic phenotypes of NS-ILC and NS-SE patients.We studied a cohort of 13 patients comprising 9 NS-ILC and 4 NS-SE.Integrated multiomics revealed abnormal epidermal proliferation and differentiation and IL-17/IL-36 signatures in lesion skin and in blood in both NS endotypes. Although the molecular profiles of NS-ILC and NS-SE lesion skin were very similar, nonlesion skin of each disease subtype displayed distinctive molecular features. Nonlesion and lesion NS-SE epidermis showed activation of the type I IFN signaling pathway, while lesion NS-ILC skin differed from nonlesion NS-ILC skin by increased complement activation and neutrophil infiltration. Serum cytokine profiling and immunophenotyping of circulating lymphocytes showed a TThis study confirms IL-17/IL-36 as the predominant signaling axes in both NS endotypes and unveils molecular features distinguishing NS-ILC and NS-SE. These results identify new therapeutic targets and could pave the way for precision medicine of NS.
Published: 2021

42. Negative selection on human genes underlying inborn errors depends on disease outcome and both the mode and mechanism of inheritance

Author: Lluis Quintana-Murci, Etienne Patin, Jean-Laurent Casanova, Laurent Abel, Anne Puel, Jérémie Rosain, Shen-Ying Zhang, Vivien Béziat, Joseph G. Gleeson, Anne Gregor, Emmanuelle Jouanguy, Franck Rapaport, Stéphanie Boisson-Dupuis, Qian Zhang, Bertrand Boisson, Jacinta Bustamante, St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller University [New York], Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), Friedrich-Alexander Universität Erlangen-Nürnberg (FAU), Center for the Study of Primary Immunodeficiencies [Paris], Université Paris Descartes - Paris 5 (UPD5)-CHU Necker - Enfants Malades [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Howard Hughes Medical Institute [La Jolla, CA, USA], Rady Children’s Institute of Genomic Medicine [La Jolla, CA, USA], University of California, Laboratory for Pediatric Brain Disease, Génétique Evolutive Humaine - Human Evolutionary Genetics, Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Collège de France (CdF (institution)), Howard Hughes Medical Institute [New York] (HHMI), Howard Hughes Medical Institute (HHMI)-Rockefeller University [New York]-Columbia University Irving Medical Center (CUIMC)-New York University School of Medicine, NYU System (NYU)-NYU System (NYU), This work was supported in part by the Rockefeller University, the St. Giles Foundation, Institut National de la Santé et de la Recherche Médicale, Paris Descartes University, the National Center for Research Resources and the National Center for Advancing Sciences, NIH Clinical and Translational Science Award program (Grant UL1TR001866), the Integrative Biology of Emerging Infectious Diseases Laboratory of Excellence (Grant ANR-10-LABX-62-IBEID), and the French National Research Agency (ANR) (Grants ANR-10-IAHU-01, ANR-15-CE17-0014). The laboratory of L.Q.-M. and E.P. is supported by the Institut Pasteur, the Collège de France, the Investissement d’Avenir program, Laboratoires d’Excellence 'Milieu Intérieur' (Grant ANR-10-LABX-69-01), Fondation pour la Recherche Médicale (Grant FRM DEQ20180339214), Fondation Allianz–Institut de France, and Fondation de France., ANR-10-LABX-0062,IBEID,Integrative Biology of Emerging Infectious Diseases(2010), ANR-10-IAHU-0001,Imagine,Institut Hospitalo-Universitaire Imagine(2010), ANR-15-CE17-0014,ProgLegio,Biomarqueurs bactériens et humains d'intérêt pronostic pour les légionelloses sévères(2015), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Paris Cité (UPCité), University of California (UC), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Collège de France - Chaire Génomique humaine et évolution, 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), and Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Candidate gene, Population, Genes, Recessive, Biology, 03 medical and health sciences, Negative selection, 0302 clinical medicine, Humans, Selection, Genetic, education, Selection (genetic algorithm), Loss function, Genes, Dominant, 030304 developmental biology, Genetics, 0303 health sciences, education.field_of_study, Multidisciplinary, Mechanism (biology), Immunity, Inheritance (genetic algorithm), Genetic Variation, Biological Sciences, Penetrance, 3. Good health, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, Metabolism, Inborn Errors, 030217 neurology & neurosurgery
Abstract: International audience; Genetic variants underlying life-threatening diseases, being unlikely to be transmitted to the next generation, are gradually and selectively eliminated from the population through negative selection. We study the determinants of this evolutionary process in human genes underlying monogenic diseases by comparing various negative selection scores and an integrative approach, CoNeS, at 366 loci underlying inborn errors of immunity (IEI). We find that genes underlying autosomal dominant (AD) or X-linked IEI have stronger negative selection scores than those underlying autosomal recessive (AR) IEI, whose scores are not different from those of genes not known to be disease causing. Nevertheless, genes underlying AR IEI that are lethal before reproductive maturity with complete penetrance have stronger negative selection scores than other genes underlying AR IEI. We also show that genes underlying AD IEI by loss of function have stronger negative selection scores than genes underlying AD IEI by gain of function, while genes underlying AD IEI by haploinsufficiency are under stronger negative selection than other genes underlying AD IEI. These results are replicated in 1,140 genes underlying inborn errors of neurodevelopment. Finally, we propose a supervised classifier, SCoNeS, which predicts better than state-of-the-art approaches whether a gene is more likely to underlie an AD or AR disease. The clinical outcomes of monogenic inborn errors, together with their mode and mechanisms of inheritance, determine the levels of negative selection at their corresponding loci. Integrating scores of negative selection may facilitate the prioritization of candidate genes and variants in patients suspected to carry an inborn error.
Published: 2021
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43. 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
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44. Auto-antibodies to type I IFNs can underlie adverse reactions to yellow fever live attenuated vaccine

Author: Yoann Seeleuthner, Marie Materna, Aurélie Cobat, Luigi D. Notarangelo, Quentin Philippot, Hans-Heinrich Hoffmann, Tom Le Voyer, Adrian Gervais, Rui Yang, Flore Rozenberg, Marwa Chbihi, Charles M. Rice, Ralph Huits, Steven M. Holland, Johannes Schäfer, Jean-Laurent Casanova, Tamiris Azamor, Ana Paula Dinis Ano Bom, Lindsey B. Rosen, Lazaro Lorenzo, Lucia V Erazo, Jérémie Rosain, Maya Chrabieh, Qian Zhang, Patrícia Mouta Nunes de Oliveira, Shen-Ying Zhang, Joseph D. Miller, Eleftherios Michailidis, Günther Slesak, Maria de Lourdes de Sousa Maia, Deborah Araújo da Conceição, Laurent Abel, Rafi Ahmed, Vivien Béziat, Margaret R. MacDonald, Lucy Bizien, Bali Pulendran, Paul Bastard, Emmanuelle Jouanguy, Akira Homma, Ekaterini Goudouris, Stephen J. Seligman, Anne Puel, Helen C. Su, and Mohamed Jeljeli
Subjects: 0301 basic medicine, Adult, Male, Adolescent, Immunology, Innate Immunity and Inflammation, Yellow fever vaccine, Receptor, Interferon alpha-beta, Vaccines, Attenuated, Virus, Autoimmune Diseases, 03 medical and health sciences, 0302 clinical medicine, medicine, Immunology and Allergy, Humans, Immunodeficiency, Adverse effect, Aged, Autoantibodies, Attenuated vaccine, biology, business.industry, SARS-CoV-2, Yellow fever, Yellow Fever Vaccine, Genetic Diseases, Inborn, Brief Definitive Report, COVID-19, Interferon-alpha, Middle Aged, medicine.disease, Antibodies, Neutralizing, Vaccination, Pneumonia, 030104 developmental biology, HEK293 Cells, 030220 oncology & carcinogenesis, biology.protein, Female, Antibody, Yellow fever virus, business, Human Disease Genetics, medicine.drug
Abstract: Yellow fever virus live attenuated vaccine can rarely cause life-threatening disease. Inherited IFNAR1 deficiency was previously reported in one patient. Here, we report a patient with inherited IFNAR2 deficiency and three other patients with neutralizing auto-antibodies against type I IFNs., Yellow fever virus (YFV) live attenuated vaccine can, in rare cases, cause life-threatening disease, typically in patients with no previous history of severe viral illness. Autosomal recessive (AR) complete IFNAR1 deficiency was reported in one 12-yr-old patient. Here, we studied seven other previously healthy patients aged 13 to 80 yr with unexplained life-threatening YFV vaccine–associated disease. One 13-yr-old patient had AR complete IFNAR2 deficiency. Three other patients vaccinated at the ages of 47, 57, and 64 yr had high titers of circulating auto-Abs against at least 14 of the 17 individual type I IFNs. These antibodies were recently shown to underlie at least 10% of cases of life-threatening COVID-19 pneumonia. The auto-Abs were neutralizing in vitro, blocking the protective effect of IFN-α2 against YFV vaccine strains. AR IFNAR1 or IFNAR2 deficiency and neutralizing auto-Abs against type I IFNs thus accounted for more than half the cases of life-threatening YFV vaccine-associated disease studied here. Previously healthy subjects could be tested for both predispositions before anti-YFV vaccination.
Published: 2020

45. 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

46. 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
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47. Dominant-negative mutations in human IL6ST underlie hyper-IgE syndrome

Author: Vivien, Béziat, Simon J, Tavernier, Yin-Huai, Chen, Cindy S, Ma, Marie, Materna, Arian, Laurence, Jens, Staal, Dominik, Aschenbrenner, Lisa, Roels, Lisa, Worley, Kathleen, Claes, Lisa, Gartner, Lisa A, Kohn, Marieke, De Bruyne, Klaus, Schmitz-Abe, Louis-Marie, Charbonnier, Sevgi, Keles, Justine, Nammour, Natasha, Vladikine, Majistor Raj Luxman, Maglorius Renkilaraj, Yoann, Seeleuthner, Mélanie, Migaud, Jérémie, Rosain, Mohamed, Jeljeli, Bertrand, Boisson, Eva, Van Braeckel, Jill A, Rosenfeld, Hongzheng, Dai, Lindsay C, Burrage, David R, Murdock, Bart N, Lambrecht, Véronique, Avettand-Fenoel, Tiphanie P, Vogel, Charles R, Esther, Sule, Haskologlu, Figen, Dogu, Peter, Ciznar, David, Boutboul, Marie, Ouachée-Chardin, Jean, Amourette, Marie-Noëlle, Lebras, Clément, Gauvain, Colas, Tcherakian, Aydan, Ikinciogullari, Rudi, Beyaert, Laurent, Abel, Joshua D, Milner, Bodo, Grimbacher, Louis-Jean, Couderc, Manish J, Butte, Alexandra F, Freeman, Émilie, Catherinot, Claire, Fieschi, Talal A, Chatila, Stuart G, Tangye, Holm H, Uhlig, Filomeen, Haerynck, Jean-Laurent, Casanova, Anne, Puel, St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller University [New York], Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP), 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), Ghent University Hospital, VIB-UGent Center for Inflammation Research [Gand, Belgique] (IRC), VIB [Belgium], Center for Medical Genetics [Ghent], John Radcliffe Hospital [Oxford University Hospital], University of Oxford [Oxford], Garvan Institute of Medical Research [Darlinghurst, Australia], St. Vincent’s Clinical School, Faculty of Medicine, University of New South Wales [Sydney] (UNSW), University of California, Boston Children's Hospital, Harvard Medical School [Boston] (HMS), Necmettin Erbakan University [Konya, Turquie], Hôpital Cochin [AP-HP], Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP), Baylor College of Medicine (BCM), Baylor University, Laboratoire de Virologie [CHU Necker], CHU Necker - Enfants Malades [AP-HP], University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC), Ankara University School of Medicine [Turkey], Comenius University in Bratislava, Service d'Immunopathologie [Hôpital Saint-Louis, Paris], Hopital Saint-Louis [AP-HP] (AP-HP), Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Assistance publique - Hôpitaux de Paris (AP-HP) (AP-HP)-Université de Paris (UP), Unité d'Hémato-Immunologie pédiatrique [Hôpital Robert Debré, Paris], Service d'Immuno-hématologie pédiatrique [Hôpital Robert Debré, Paris], Hôpital Robert Debré-Hôpital Robert Debré, Groupe Hospitalier Artois-Ternois Centre Hospitalier d’Arras, Service de pneumologie [Hôpital Foch], Hôpital Foch [Suresnes], National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Columbia University Irving Medical Center (CUIMC), Center for Chronic Immunodeficiency (CCI), University Medical Center Freiburg, Freiburg, Germany, Centre for Integrative Biological Signaling Studies [Freiburg, Germany], University of Freiburg [Freiburg], Hanover Medical School, Laboratoire de recherche sur les mécanismes moléculaires et pharmacologiques de l’obstruction bronchique (LOBIP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ), Université de Versailles Saint-Quentin-en-Yvelines - UFR Sciences de la santé Simone Veil (UVSQ Santé), Department of Pediatrics, Keck School of Medicine, University of Southern California, Los Angeles, Institut de Recherche Saint-Louis - Hématologie Immunologie Oncologie (Département de recherche de l’UFR de médecine, ex- Institut Universitaire Hématologie-IUH) (IRSL), Université de Paris (UP), St. Vincent’s Clinical School [Sydney, Australia], UNSW Faculty of Medicine [Sydney], and University of New South Wales [Sydney] (UNSW)-University of New South Wales [Sydney] (UNSW)
Subjects: Male, Adolescent, Models, Biological, Young Adult, Th2 Cells, Loss of Function Mutation, Cytokine Receptor gp130, Humans, Immunodeficiency, Child, Alleles, Cells, Cultured, Genes, Dominant, Human disease genetics, Cell Membrane, Correction, Fibroblasts, Middle Aged, Pedigree, Up-Regulation, Kinetics, C-Reactive Protein, Genetics, Population, HEK293 Cells, Phenotype, Mutation, Cytokines, [SDV.IMM]Life Sciences [q-bio]/Immunology, Female, Job Syndrome
Abstract: International audience; Autosomal dominant hyper-IgE syndrome (AD-HIES) is typically caused by dominant-negative (DN) STAT3 mutations. Patients suffer from cold staphylococcal lesions and mucocutaneous candidiasis, severe allergy, and skeletal abnormalities. We report 12 patients from 8 unrelated kindreds with AD-HIES due to DN IL6ST mutations. We identified seven different truncating mutations, one of which was recurrent. The mutant alleles encode GP130 receptors bearing the transmembrane domain but lacking both the recycling motif and all four STAT3-recruiting tyrosine residues. Upon overexpression, the mutant proteins accumulate at the cell surface and are loss of function and DN for cellular responses to IL-6, IL-11, LIF, and OSM. Moreover, the patients’ heterozygous leukocytes and fibroblasts respond poorly to IL-6 and IL-11. Consistently, patients with STAT3 and IL6ST mutations display infectious and allergic manifestations of IL-6R deficiency, and some of the skeletal abnormalities of IL-11R deficiency. DN STAT3 and IL6ST mutations thus appear to underlie clinical phenocopies through impairment of the IL-6 and IL-11 response pathways.
Published: 2020
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48. Improving the diagnostic efficiency of primary immunodeficiencies with targeted next-generation sequencing

Author: Brigitte Bader-Meunier, Thibault Comont, Felipe Suarez, Alain Fischer, Vincent Barlogis, David Boutboul, Claire Fieschi, Guillaume Vogt, Marlène Pasquet, Frédéric Rieux-Laucat, Jérémie Rosain, Marine Gil, Lionel Galicier, Etienne Merlin, Cécile Fourrage, Christine Bole, Nicholas Renaud, Wadih Abou Chahla, Capucine Picard, Sylvain Hanein, Stéphane Blanche, Patrick Nitschké, Despina Moshous, Benedicte Neven, Isabelle André, Virginie Grandin, Alexandre Alcaïs, Sylvain Latour, Jean-Pierre de Villartay, Chantal Lagresle-Peyrou, Jean-Sebastien Diana, Eric Oksenhendler, Marion Malphettes, Samuel Chevalier, Elisabeth Hulier-Ammar, Olivier Hermine, Mathieu Fusaro, Jacinta Bustamante, Nathalie Lambert, Vivien Béziat, Geneviève de Saint Basile, Nizar Mahlaoui, Martin Castelle, Sven Kracker, Alain Lefevre-Utile, Imagine - Institut des maladies génétiques (IHU) (Imagine - U1163), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Paris (UP)
Subjects: 0301 basic medicine, Adult, Male, Adolescent, Primary Immunodeficiency Diseases, health care facilities, manpower, and services, [SDV]Life Sciences [q-bio], Immunology, education, MEDLINE, Immunoglobulins, Bioinformatics, DNA sequencing, 03 medical and health sciences, Young Adult, 0302 clinical medicine, Immunology and Allergy, Medicine, Guanine Nucleotide Exchange Factors, Humans, Child, health care economics and organizations, Aged, Primary (chemistry), business.industry, Infant, Newborn, High-Throughput Nucleotide Sequencing, Infant, Middle Aged, medicine.disease, 3. Good health, I-kappa B Kinase, 030104 developmental biology, Child, Preschool, Cohort, Mutation, Etiology, Primary immunodeficiency, Female, business, 030215 immunology
Abstract: This study aims to validate a targeted next-generation sequencing panel of 300 genes to diagnose a cohort of 129 patients with primary immunodeficiency with no prior molecular etiology.
Published: 2020
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49. Human genetic dissection of papillomavirus-driven diseases: New insight into their pathogenesis

Author: Vivien Béziat
Subjects: Biology, Asymptomatic, Article, Pathogenesis, 03 medical and health sciences, Immunity, Genetics, medicine, Humans, Genetic Predisposition to Disease, Skin Diseases, Infectious, Papillomaviridae, Genetics (clinical), Tropism, 030304 developmental biology, 0303 health sciences, 030305 genetics & heredity, Papillomavirus Infections, virus diseases, Epidermodysplasia verruciformis, medicine.disease, Molecular medicine, Human genetics, Tumor Virus Infections, Immunology, Recurrent Respiratory Papillomatosis, medicine.symptom
Abstract: Human papillomaviruses (HPVs) infect mucosal or cutaneous stratified epithelia. There are five genera and more than 200 types of HPV, each with a specific tropism and virulence. HPV infections are typically asymptomatic or result in benign tumors, which may be disseminated or persistent in rare cases, but a few oncogenic HPVs can cause cancers. This review deals with the human genetic and immunological basis of interindividual clinical variability in the course of HPV infections of the skin and mucosae. Typical epidermodysplasia verruciformis (EV) is characterized by β-HPV-driven flat wart-like and pityriasis-like cutaneous lesions and non-melanoma skin cancers in patients with inborn errors of EVER1-EVER2-CIB1-dependent skin-intrinsic immunity. Atypical EV is associated with other infectious diseases in patients with inborn errors of T cells. Severe cutaneous or anogenital warts, including anogenital cancers, are also driven by certain α-, γ-, μ or ν-HPVs in patients with inborn errors of T lymphocytes and antigen-presenting cells. The genetic basis of HPV diseases at other mucosal sites, such as oral multifocal epithelial hyperplasia or juvenile recurrent respiratory papillomatosis (JRRP), remains poorly understood. The human genetic dissection of HPV-driven lesions will clarify the molecular and cellular basis of protective immunity to HPVs, and should lead to novel diagnostic, preventive, and curative approaches in patients.
Published: 2020

50. Negative selection on human genes causing severe inborn errors depends on disease outcome and both the mode and mechanism of inheritance

Author: Bertrand Boisson, Lluis Quintana-Murci, Jacinta Bustamante, Anne Gregor, Emmanuelle Jouanguy, Stéphanie Boisson-Dupuis, Anne Puel, Franck Rapaport, Jérémie Rosain, Vivien Béziat, Joseph G. Gleeson, Shen-Ying Zhang, Qian Zhang, Jean-Laurent Casanova, Etienne Patin, and Laurent Abel
Subjects: Genetics, 0303 health sciences, education.field_of_study, Candidate gene, Mechanism (biology), Population, Inheritance (genetic algorithm), Biology, Penetrance, 03 medical and health sciences, Negative selection, 0302 clinical medicine, education, Haploinsufficiency, 030217 neurology & neurosurgery, Selection (genetic algorithm), 030304 developmental biology
Abstract: BackgroundGenetic variants underlying severe diseases are less likely to be transmitted to the next generation, and are thus gradually and selectively eliminated from the population through negative selection. Here, we study the determinants of this evolutionary process in genes underlying severe diseases in humans.ResultsWe propose a novel approach, CoNeS, integrating known negative selection scores through principal component projection. We compare evidence for negative selection at 319 genes underlying inborn errors of immunity (IEI), which are life-threatening monogenic disorders. We find that genes underlying autosomal dominant (AD) or X-linked IEI are under stronger negative selection than those underlying autosomal recessive (AR) IEI, which are under no stronger selection than genes not known to be disease-causing. However, we find that genes with mutations causing AR IEI that are lethal before reproductive maturity and that display complete penetrance are under stronger negative selection than other genes underlying AR IEI. We also find that genes underlying AD IEI by haploinsufficiency are under stronger negative selection than other genes underlying AD IEI. Finally, we replicate these results in a study of 1,140 genes causing inborn errors of neurodevelopment.ConclusionsThese findings collectively show that the clinical outcomes of inborn errors, together with the mode and mechanism of inheritance of these errors, determine the strength of negative selection acting on severe disease-causing genes. These findings suggest that estimating the intensity of negative selection with CoNeS may facilitate the selection of candidate genes in patients suspected to carry an inborn error.
Published: 2020
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