116 research outputs found

    The Genetic Dissection of Isolated Congenital Asplenia in Humans

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    L asplĂ©nie ou l absence de la rate peut ĂȘtre congĂ©nitale, c est- Ă  -dire absente dĂšs la naissance, ou bien acquise, par exemple lors d une opĂ©ration aprĂšs un accident. L asplĂ©nie congĂ©nitale est le plus souvent associĂ©e Ă  d autres problĂšmes dĂ©veloppementaux. En particulier l asplĂ©nie congĂ©nitale est associĂ©e Ă  des problĂšmes de dĂ©veloppement du cƓur, dans le cadre des syndromes d hĂ©tĂ©rotaxie. Ces syndromes d hĂ©tĂ©rotaxie sont caractĂ©risĂ©s par des problĂšmes de latĂ©ralitĂ© droite-gauche. Ainsi une personne ayant deux parties droites n aura pas de rate. A contrario, l asplĂ©nie congĂ©nitale isolĂ©e est caractĂ©risĂ©e par l absence de rate et aucune autre malformation. L asplĂ©nie congĂ©nitale isolĂ©e est une maladie trĂšs rare. Nous avons estimĂ© la frĂ©quence de la maladie Ă  un cas pour un million de naissances. C est aussi une maladie extrĂȘmement mortelle. La grande majoritĂ© des patients ayant une asplĂ©nie congĂ©nitale isolĂ©e souffrent d infections bactĂ©riennes sĂ©vĂšres lors de l enfance et la moitie des cas reportĂ©s sont dĂ©cĂ©dĂ©s dus Ă  une infection bactĂ©rienne, le plus souvent du Ă  une infection par Streptococcus pneumoniae. MalgrĂ© la sĂ©vĂ©ritĂ© de cette maladie, celle-ci reste trĂšs peu connue et trĂšs peu Ă©tudiĂ©e. Ainsi le diagnostique est souvent trop tardif. Parmi les quelques dizaines de cas dĂ©crits dans la littĂ©rature, la moitiĂ© sont des cas familiaux avec plusieurs membres de la mĂȘme famille affectĂ©e. Le mode de transmission semble ĂȘtre autosomique dominant dans la majoritĂ© des cas. En outre aucune preuve n existe concernant un facteur environnemental pour cette maladie. Enfin des travaux rĂ©cents ont montrĂ©s que l absence de pancrĂ©as chez l homme Ă©tait une maladie gĂ©nĂ©tique, et due Ă  des mutations dans le gĂšne GATA6 chez la moitiĂ© des patients. L objectif de cette thĂšse est donc de dĂ©terminer l origine gĂ©nĂ©tique de l asplĂ©nie congĂ©nitale isolĂ©e chez l homme. J ai fait l hypothĂšse que l asplĂ©nie congĂ©nitale isolĂ©e chez l homme est due Ă  des mutations mendĂ©liennes dans un gĂšne important pour le dĂ©veloppement de la rate. Afin de tester notre hypothĂšse nous avons recrutĂ© des patients Ă  travers des collaborations avec des mĂ©decins Ă©trangers ainsi qu un partenariat avec toutes les unitĂ©s pĂ©diatriques de France. Nous avons finalement pu recruter 37 patients appartenant Ă  24 familles diffĂ©rentes. La littĂ©rature sur le dĂ©veloppement de la rate chez la souris et encore plus sur l homme Ă©tant minimale, il Ă©tait difficile d identifier de bons gĂšnes candidats pour ĂȘtre responsables de l asplĂ©nie. Nous avons donc optĂ© pour une stratĂ©gie portant sur le gĂ©nome entier, sans biais lier a la littĂ©rature. La stratĂ©gie Ă©tait d utiliser le sĂ©quençage de l exome de tous les patients. Le sĂ©quençage de l exome est en fait le sĂ©quençage de tous les exons du gĂ©nome, ou au moins 90% des exons du gĂ©nome. La technique du sĂ©quençage de l exome est arrivĂ©e Ă  la fin de l annĂ©e 2009 et nous avons Ă©tĂ© un des premiers laboratoires Ă  l utiliser. Il fallait donc que nous l essayons en premier sur un cas facile afin de vĂ©rifier que cette technique fonctionnait. Nous avons donc fait une Ă©tude prĂ©liminaire sur un cas facile . Par cas facile, il faut comprendre un cas oĂč la probabilitĂ© que ce soit une mutation mendĂ©lienne dans un gĂšne qui soit responsable de la maladie soit la plus forte possible, et oĂč le nombre de gĂšnes Ă  regarder soit le plus faible possible. Un cas facile est donc le cas d une famille avec de nombreux patients, et de surcroit une famille consanguine. Dans le cas d une famille consanguine la probabilitĂ© que ce soit une mutation rĂ©cessive qui soit responsable de la maladie gĂ©nĂ©tique est trĂšs importante. On peut alors se restreindre Ă  analyser les rĂ©gions du gĂ©nome ou toutes les variations sont homozygotes. Nous avions une famille dans ce cas. Il y avait 4 patients dans cette famille souffrant d infections bactĂ©riennes sĂ©vĂšres dues Ă  une asplenie fonctionnelle, ainsi que d infections viralesIsolated congenital asplenia (ICA) is a rare primary immunodeficiency, first described in 1956, thattypically manifests in childhood with sudden, life-threatening, invasive bacterial disease. Patients withICA do not display any other overt developmental anomalies. The genetic etiology of ICA has remainedelusive. I hypothesized that ICA results from single-gene inborn errors of spleen development. I aimedto decipher the molecular genetic basis of ICA by pursuing a genome-wide approach, based on thesequencing of the whole-exome and the detection of copy number variations in all patients of ourcohort. I found that heterozygous mutations in RPSA, ribosomal protein SA, were present in more thanhalf of ICA patients (19/33). I then showed that haploinsufficiency of RPSA led to ICA in one kindredat least. RPSA is a protein involved in pre-rRNA processing and is an integral part of the ribosome. Thechallenge is, now, to understand the pathogenesis of the disease. How does a mutation in a ubiquitousand highly expressed gene lead to a spleen specific phenotype? This discovery will set the basis for abroader understanding of the development of the spleen in humans and the function of a ribosomalprotein. This discovery will also be beneficial to the families of patients with ICA, guiding geneticcounseling. It will lead to prevention of infections in newborns with mutations in RPSA. Finally themethod we used to analyze the exomes of the ICA cohort will be useful to discover the genetic etiologyof other genetic diseases.PARIS5-Bibliotheque electronique (751069902) / SudocSudocFranceF

    A Mild Form of SLC29A3 Disorder: A Frameshift Deletion Leads to the Paradoxical Translation of an Otherwise Noncoding mRNA Splice Variant

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    We investigated two siblings with granulomatous histiocytosis prominent in the nasal area, mimicking rhinoscleroma and Rosai-Dorfman syndrome. Genome-wide linkage analysis and whole-exome sequencing identified a homozygous frameshift deletion in SLC29A3, which encodes human equilibrative nucleoside transporter-3 (hENT3). Germline mutations in SLC29A3 have been reported in rare patients with a wide range of overlapping clinical features and inherited disorders including H syndrome, pigmented hypertrichosis with insulin-dependent diabetes, and Faisalabad histiocytosis. With the exception of insulin-dependent diabetes and mild finger and toe contractures in one sibling, the two patients with nasal granulomatous histiocytosis studied here displayed none of the many SLC29A3-associated phenotypes. This mild clinical phenotype probably results from a remarkable genetic mechanism. The SLC29A3 frameshift deletion prevents the expression of the normally coding transcripts. It instead leads to the translation, expression, and function of an otherwise noncoding, out-of-frame mRNA splice variant lacking exon 3 that is eliminated by nonsense-mediated mRNA decay (NMD) in healthy individuals. The mutated isoform differs from the wild-type hENT3 by the modification of 20 residues in exon 2 and the removal of another 28 amino acids in exon 3, which include the second transmembrane domain. As a result, this new isoform displays some functional activity. This mechanism probably accounts for the narrow and mild clinical phenotype of the patients. This study highlights the ‘rescue’ role played by a normally noncoding mRNA splice variant of SLC29A3, uncovering a new mechanism by which frameshift mutations can be hypomorphic

    Using symptom-based case predictions to identify host genetic factors that contribute to COVID-19 susceptibility

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    Epidemiological and genetic studies on COVID-19 are currently hindered by inconsistent and limited testing policies to confirm SARS-CoV-2 infection. Recently, it was shown that it is possible to predict COVID-19 cases using cross-sectional self-reported disease-related symptoms. Here, we demonstrate that this COVID-19 prediction model has reasonable and consistent performance across multiple independent cohorts and that our attempt to improve upon this model did not result in improved predictions. Using the existing COVID-19 prediction model, we then conducted a GWAS on the predicted phenotype using a total of 1,865 predicted cases and 29,174 controls. While we did not find any common, large-effect variants that reached genome-wide significance, we do observe suggestive genetic associations at two SNPs (rs11844522, p = 1.9x10-7; rs5798227, p = 2.2x10-7). Explorative analyses furthermore suggest that genetic variants associated with other viral infectious diseases do not overlap with COVID-19 susceptibility and that severity of COVID-19 may have a different genetic architecture compared to COVID-19 susceptibility. This study represents a first effort that uses a symptom-based predicted phenotype as a proxy for COVID-19 in our pursuit of understanding the genetic susceptibility of the disease. We conclude that the inclusion of symptom-based predicted cases could be a useful strategy in a scenario of limited testing, either during the current COVID-19 pandemic or any future viral outbreak

    Gain-of-function human STAT1 mutations impair IL-17 immunity and underlie chronic mucocutaneous candidiasis

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    Chronic mucocutaneous candidiasis disease (CMCD) may be caused by autosomal dominant (AD) IL-17F deficiency or autosomal recessive (AR) IL-17RA deficiency. Here, using whole-exome sequencing, we identified heterozygous germline mutations in STAT1 in 47 patients from 20 kindreds with AD CMCD. Previously described heterozygous STAT1 mutant alleles are loss-of-function and cause AD predisposition to mycobacterial disease caused by impaired STAT1-dependent cellular responses to IFN-Îł. Other loss-of-function STAT1 alleles cause AR predisposition to intracellular bacterial and viral diseases, caused by impaired STAT1-dependent responses to IFN-α/ÎČ, IFN-Îł, IFN-λ, and IL-27. In contrast, the 12 AD CMCD-inducing STAT1 mutant alleles described here are gain-of-function and increase STAT1-dependent cellular responses to these cytokines, and to cytokines that predominantly activate STAT3, such as IL-6 and IL-21. All of these mutations affect the coiled-coil domain and impair the nuclear dephosphorylation of activated STAT1, accounting for their gain-of-function and dominance. Stronger cellular responses to the STAT1-dependent IL-17 inhibitors IFN-α/ÎČ, IFN-Îł, and IL-27, and stronger STAT1 activation in response to the STAT3-dependent IL-17 inducers IL-6 and IL-21, hinder the development of T cells producing IL-17A, IL-17F, and IL-22. Gain-of-function STAT1 alleles therefore cause AD CMCD by impairing IL-17 immunity

    Blacklisting variants common in private cohorts but not in public databases optimizes human exome analysis

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    Computational analyses of human patient exomes aim to filter out as many nonpathogenic genetic variants (NPVs) as possible, without removing the true disease-causing mutations. This involves comparing the patient's exome with public databases to remove reported variants inconsistent with disease prevalence, mode of inheritance, or clinical penetrance. However, variants frequent in a given exome cohort, but absent or rare in public databases, have also been reported and treated as NPVs, without rigorous exploration. We report the generation of a blacklist of variants frequent within an in-house cohort of 3,104 exomes. This blacklist did not remove known pathogenic mutations from the exomes of 129 patients and decreased the number of NPVs remaining in the 3,104 individual exomes by a median of 62%. We validated this approach by testing three other independent cohorts of 400, 902, and 3,869 exomes. The blacklist generated from any given cohort removed a substantial proportion of NPVs (11-65%). We analyzed the blacklisted variants computationally and experimentally. Most of the blacklisted variants corresponded to false signals generated by incomplete reference genome assembly, location in low-complexity regions, bioinformatic misprocessing, or limitations inherent to cohort-specific private alleles (e.g., due to sequencing kits, and genetic ancestries). Finally, we provide our precalculated blacklists, together with ReFiNE, a program for generating customized blacklists from any medium-sized or large in-house cohort of exome (or other next-generation sequencing) data via a user-friendly public web server. This work demonstrates the power of extracting variant blacklists from private databases as a specific in-house but broadly applicable tool for optimizing exome analysis

    IL-12RÎČ1 Deficiency in Two of Fifty Children with Severe Tuberculosis from Iran, Morocco, and Turkey

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    BACKGROUND AND OBJECTIVES: In the last decade, autosomal recessive IL-12RÎČ1 deficiency has been diagnosed in four children with severe tuberculosis from three unrelated families from Morocco, Spain, and Turkey, providing proof-of-principle that tuberculosis in otherwise healthy children may result from single-gene inborn errors of immunity. We aimed to estimate the fraction of children developing severe tuberculosis due to IL-12RÎČ1 deficiency in areas endemic for tuberculosis and where parental consanguinity is common. METHODS AND PRINCIPAL FINDINGS: We searched for IL12RB1 mutations in a series of 50 children from Iran, Morocco, and Turkey. All children had established severe pulmonary and/or disseminated tuberculosis requiring hospitalization and were otherwise normally resistant to weakly virulent BCG vaccines and environmental mycobacteria. In one child from Iran and another from Morocco, homozygosity for loss-of-function IL12RB1 alleles was documented, resulting in complete IL-12RÎČ1 deficiency. Despite the small sample studied, our findings suggest that IL-12RÎČ1 deficiency is not a very rare cause of pediatric tuberculosis in these countries, where it should be considered in selected children with severe disease. SIGNIFICANCE: This finding may have important medical implications, as recombinant IFN-Îł is an effective treatment for mycobacterial infections in IL-12RÎČ1-deficient patients. It also provides additional support for the view that severe tuberculosis in childhood may result from a collection of single-gene inborn errors of immunity

    Autoantibodies against type I IFNs in patients with critical influenza pneumonia

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    In an international cohort of 279 patients with hypoxemic influenza pneumonia, we identified 13 patients (4.6%) with autoantibodies neutralizing IFN-alpha and/or -omega, which were previously reported to underlie 15% cases of life-threatening COVID-19 pneumonia and one third of severe adverse reactions to live-attenuated yellow fever vaccine. Autoantibodies neutralizing type I interferons (IFNs) can underlie critical COVID-19 pneumonia and yellow fever vaccine disease. We report here on 13 patients harboring autoantibodies neutralizing IFN-alpha 2 alone (five patients) or with IFN-omega (eight patients) from a cohort of 279 patients (4.7%) aged 6-73 yr with critical influenza pneumonia. Nine and four patients had antibodies neutralizing high and low concentrations, respectively, of IFN-alpha 2, and six and two patients had antibodies neutralizing high and low concentrations, respectively, of IFN-omega. The patients' autoantibodies increased influenza A virus replication in both A549 cells and reconstituted human airway epithelia. The prevalence of these antibodies was significantly higher than that in the general population for patients 70 yr of age (3.1 vs. 4.4%, P = 0.68). The risk of critical influenza was highest in patients with antibodies neutralizing high concentrations of both IFN-alpha 2 and IFN-omega (OR = 11.7, P = 1.3 x 10(-5)), especially those <70 yr old (OR = 139.9, P = 3.1 x 10(-10)). We also identified 10 patients in additional influenza patient cohorts. Autoantibodies neutralizing type I IFNs account for similar to 5% of cases of life-threatening influenza pneumonia in patients <70 yr old

    Vaccine breakthrough hypoxemic COVID-19 pneumonia in patients with auto-Abs neutralizing type I IFNs

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    Life-threatening `breakthrough' cases of critical COVID-19 are attributed to poor or waning antibody response to the SARS- CoV-2 vaccine in individuals already at risk. Pre-existing autoantibodies (auto-Abs) neutralizing type I IFNs underlie at least 15% of critical COVID-19 pneumonia cases in unvaccinated individuals; however, their contribution to hypoxemic breakthrough cases in vaccinated people remains unknown. Here, we studied a cohort of 48 individuals ( age 20-86 years) who received 2 doses of an mRNA vaccine and developed a breakthrough infection with hypoxemic COVID-19 pneumonia 2 weeks to 4 months later. Antibody levels to the vaccine, neutralization of the virus, and auto- Abs to type I IFNs were measured in the plasma. Forty-two individuals had no known deficiency of B cell immunity and a normal antibody response to the vaccine. Among them, ten (24%) had auto-Abs neutralizing type I IFNs (aged 43-86 years). Eight of these ten patients had auto-Abs neutralizing both IFN-a2 and IFN-., while two neutralized IFN-omega only. No patient neutralized IFN-ss. Seven neutralized 10 ng/mL of type I IFNs, and three 100 pg/mL only. Seven patients neutralized SARS-CoV-2 D614G and the Delta variant (B.1.617.2) efficiently, while one patient neutralized Delta slightly less efficiently. Two of the three patients neutralizing only 100 pg/mL of type I IFNs neutralized both D61G and Delta less efficiently. Despite two mRNA vaccine inoculations and the presence of circulating antibodies capable of neutralizing SARS-CoV-2, auto-Abs neutralizing type I IFNs may underlie a significant proportion of hypoxemic COVID-19 pneumonia cases, highlighting the importance of this particularly vulnerable population

    Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative

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