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The use of multigene panel testing for patients with a predisposition to Hereditary Breast and Ovarian Cancer syndrome (HBOC) is increasing as the identification of mutations is useful for diagnosis and disease management. Here, we conducted a retrospective analysis of BRCA1/2 and non-BRCA gene sequencing in 4630 French HBOC suspected patients. Patients were investigated using a germline cancer panel including the 13 genes defined by The French Genetic and Cancer Group (GGC)—Unicancer. In the patients analyzed, 528 pathogenic and likely pathogenic variants (P/LP) were identified, including BRCA1 (n = 203, 38%), BRCA2 (n = 198, 37%), PALB2 (n = 46, 9%), RAD51C (n = 36, 7%), TP53 (n = 16, 3%), and RAD51D (n = 13, 2%). In addition, 35 novel (P/LP) variants, according to our knowledge, were identified, and double mutations in two distinct genes were found in five patients. Interestingly, retesting a subset of BRCA1/2-negative individuals with an expanded panel produced clinically relevant results in 5% of cases. Additionally, combining in silico (splicing impact prediction tools) and in vitro analyses (RT-PCR and Sanger sequencing) highlighted the deleterious impact of four candidate variants on splicing and translation. Our results present an overview of pathogenic variations of HBOC genes in the southeast of France, emphasizing the clinical relevance of cDNA analysis and the importance of retesting BRCA-negative individuals with an expanded panel.

International audience; BackgroundThe present article is an English-language version of the French National Diagnostic and Care Protocol, a pragmatic tool to optimize and harmonize the diagnosis, care pathway, management and follow-up of lymphangioleiomyomatosis in France.MethodsPractical recommendations were developed in accordance with the method for developing a National Diagnosis and Care Protocol for rare diseases of the Haute Autorité de Santé and following international guidelines and literature on lymphangioleiomyomatosis. It was developed by a multidisciplinary group, with the help of patient representatives and of RespiFIL, the rare disease network on respiratory diseases.ResultsLymphangioleiomyomatosis is a rare lung disease characterised by a proliferation of smooth muscle cells that leads to the formation of multiple lung cysts. It occurs sporadically or as part of a genetic disease called tuberous sclerosis complex (TSC). The document addresses multiple aspects of the disease, to guide the clinicians regarding when to suspect a diagnosis of lymphangioleiomyomatosis, what to do in case of recurrent pneumothorax or angiomyolipomas, what investigations are needed to make the diagnosis of lymphangioleiomyomatosis, what the diagnostic criteria are for lymphangioleiomyomatosis, what the principles of management are, and how follow-up can be organised. Recommendations are made regarding the use of pharmaceutical specialties and treatment other than medications.ConclusionThese recommendations are intended to guide the diagnosis and practical management of pulmonary lymphangioleiomyomatosis.

Purpose: Diagnostic screening of the BRCA1/2 genes in breast cancer families is mostly done on genomic DNA. For families with a very strong family history and no mutation identified in the coding sequences or the exon–intron boundaries, BRCA1/2 transcripts' analysis is an efficient approach to uncover gene inversion and pre-mRNA splicing defaults missed by conventional DNA-based protocols.Experimental Design: We analyzed RNA from patients of negative BRCA families by reverse transcriptase PCR and identified an insertion in one family that we characterized by sequencing and by using a minigene splicing assay. More than 2,000 additional BRCA1/2 negative families were subsequently screened for this mutation using a dedicated PCR approach.Results: Nine families were found to harbor a BRCA2 mutant transcript containing a 95-nucleotide cryptic exon between exons 12 and 13. This cryptic exon results from a new mutation located deep into intron 12, c.6937+594T > G, which reinforces the strength of a preexisting 5′ splice site, turning it into a perfect consensus sequence. It is systematically included in transcripts produced by the mutant allele in cells from mutation carriers or produced by a mutant splicing reporter minigene. The inclusion of the cryptic exon was prevented when we cotransfected the minigene with antisense oligonucleotides complementary to the 3′ or mutated 5′ splice sites.Conclusion: This first deep intronic BRCA mutation emphasizes the importance of analyzing RNA to provide comprehensive BRCA1/2 diagnostic tests and opens the possibility of using antisense therapy in the future as an alternative strategy for cancer prevention. Clin Cancer Res; 18(18); 4903–9. ©2012 AACR.

PDF file, 764K, BRCA2 exon 12 to exon 13 gene, transcript and protein sequences (Supp Fig 1); Enhancer motifs contained within the cryptic exon and the constitutive surrounding exons (Supp Fig 2); Conservation of the cryptic exon across species (Supp Fig 3); Primers used for BRCA1 and BRCA2 routine mRNA analyses (Supp Table 1).

CCR Translation for This Article from BRCA2 Deep Intronic Mutation Causing Activation of a Cryptic Exon: Opening toward a New Preventive Therapeutic Strategy

International audience; Sarcoidosis is a multisystem disease characterized by the development and accumulation of granulomas, the hallmark of an inflammatory process induced by environmental and/or infectious and or genetic factors. This auto-inflammatory disease mainly affects the lungs, the gateway to environmental aggressions and viral infections. We have shown previously that genetic predisposition to sarcoidosis occurring in familial cases is related to a large spectrum of pathogenic variants with, however, a clustering around mTOR (mammalian Target Of Rapamycin)-related pathways and autophagy regulation. The context of the COVID-19 pandemic led us to evaluate whether such genetic defects may increase the risk of a severe course of SARS-CoV2 infection in patients with sarcoidosis. We extended a whole exome screening to 13 families predisposed to sarcoidosis and crossed the genes sharing mutations with the list of genes involved in the SARS-CoV2 host-pathogen protein-protein interactome. A similar analysis protocol was applied to a series of 100 healthy individuals. Using ENRICH.R, a comprehensive gene set enrichment web server, we identified the functional pathways represented in the set of genes carrying deleterious mutations and confirmed the overrepresentation of autophagy- and mitophagy-related functions in familial cases of sarcoidosis. The same protocol was applied to the set of genes common to sarcoidosis and the SARS-CoV2-host interactome and found a significant enrichment of genes related to mitochondrial factors involved in autophagy, mitophagy, and RIG-I-like (Retinoic Acid Inducible Gene 1) Receptor antiviral response signaling. From these results, we discuss the hypothesis according to which sarcoidosis is a model for studying genetic abnormalities associated with host response to viral infections as a consequence of defects in autophagy and mitophagy processes.

International audience; Paediatric sarcoidosis is an extremely rare disease characterized by a granulomatous inflammation. The estimated incidence is 0.6–1.02/100,000 children, but in the absence of international registers, the disease is probably under-reported. Its pathophysiologic basis is not clearly understood but the current hypothesis is a combination of a genetic predisposition and an environmental exposure that could be either organic or mineral. Contrary to adult forms of the disease, general symptoms are often at the forefront at diagnosis. In its most frequent form, paediatric sarcoidosis is a multi-organ disorder affecting preferentially the lungs, the lymphatic system and the liver, but all organs can be affected. This review aims to provide an overview of current knowledge on sarcoidosis in children, providing a summary of the data available from cohort studies on the presentation, the management and the evolution of the disease in this specific population.

Sarcoidosis is a multi-system disease of unknown etiology characterized by the formation of granulomas in various organs. It affects people of all ethnic backgrounds and occurs at any time of life but is more frequent in African Americans and Scandinavians and in adults between 30 and 50 years of age. Sarcoidosis can affect any organ with a frequency varying according to ethnicity, sex and age. Intrathoracic involvement occurs in 90% of patients with symmetrical bilateral hilar adenopathy and/or diffuse lung micronodules, mainly along the lymphatic structures which are the most affected system. Among extrapulmonary manifestations, skin lesions, uveitis, liver or splenic involvement, peripheral and abdominal lymphadenopathy and peripheral arthritis are the most frequent with a prevalence of 25–50%. Finally, cardiac and neurological manifestations which can be the initial manifestation of sarcoidosis, as can be bilateral parotitis, nasosinusal or laryngeal signs, hypercalcemia and renal dysfunction, affect less than 10% of patients. The diagnosis is not standardized but is based on three major criteria: a compatible clinical and/or radiological presentation, the histological evidence of non-necrotizing granulomatous inflammation in one or more tissues and the exclusion of alternative causes of granulomatous disease. Certain clinical features are considered to be highly specific of the disease (e.g., Löfgren’s syndrome, lupus pernio, Heerfordt’s syndrome) and do not require histological confirmation. New diagnostic guidelines were recently published. Specific clinical criteria have been developed for the diagnosis of cardiac, neurological and ocular sarcoidosis. This article focuses on the clinical presentation and the common differentials that need to be considered when appropriate.

Multiple endocrine neoplasia type 1 (MEN1) is a rare syndrome characterized by the co-occurrence of primary hyperparathyroidism, duodenopancreatic neuroendocrine tumours (NETs) and/or pituitary adenomas. MEN1 can predispose patients to other endocrine and non-endocrine tumours, such as cutaneous tumours, central nervous system tumours and breast cancer. Endocrine tumours in patients with MEN1 differ from sporadic tumours in that they have a younger age at onset, present as multiple tumours in the same organ and have a different clinical course. Therefore, patients with overt MEN1 and those who carry a MEN1 mutation should be offered tailored biochemical and imaging screening to detect tumours and evaluate their progression over time. Fortunately, over the past 10 years, knowledge about the clinical phenotype of these tumours has markedly progressed, thanks to the implementation of national registries, particularly in France and the Netherlands. This Review provides an update on the clinical management of MEN1-related tumours. Epidemiology, the clinical picture, diagnostic work-up and the main lines of treatment for MEN1-related tumours are summarized. Controversial therapeutic aspects and issues that still need to be addressed are also discussed. Moreover, special attention is given to MEN1 manifestations in children and adolescents.

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and mainly affects the lungs. Sarcoidosis is an autoinflammatory disease characterized by the diffusion of granulomas in the lungs and other organs. Here, we discuss how the two diseases might involve some common mechanistic cellular pathways around the regulation of autophagy.

Introduction La sarcoidose est une granulomatose systemique d’etiologie indeterminee [1] . De nombreux cas et des series d’infections opportunistes (IO) chez des patients atteints de sarcoidose sont rapportes dans la litterature medicale [2] , [3] . Sont generalement exclues les aspergilloses cavitaires et les tuberculoses, associees respectivement a la fibrose et a des elements demographiques communs. Les agents opportunistes rapportes sont varies (Cryptococcus neoformans, JC virus, mycobacteries atypiques, Nocardia spp.) mais actuellement aucun facteur de risque d’infection opportuniste n’est decrit au cours de la sarcoidose. Patients et methodes Nous avons effectue un recueil de la litterature medicale via le moteur de recherche Medline et realise un appel a observations via le groupe sarcoidose francophone a la recherche d’associations « infection opportuniste » et « sarcoidose ». Les caracteristiques cliniques des IO ont ete comparees a une population temoin constituee de patients porteurs d’une sarcoidose sans IO issus d’une cohorte de notre service. Resultats La revue de la litterature a permis de recenser 164 cas d’infections qualifiees d’opportunistes chez des patients porteurs d’une sarcoidose. Parmi ces 164 infections, 83 etaient des cryptococcoses (51 %) et 39 etaient des leuco-encephalopathies multifocales progressives (LEMP) (24 %). Notre appel a observations a permis de recenser 50 IO chez 49 patients, incluant : 24 cryptococcoses (49 %), 12 LEMP (24 %), 7 pneumocystoses (14 %) et 7 autres infections (14 %) dont 3 mycobacterioses atypiques, 2 nocardioses et 2 infections a cytomegalovirus. Ces 49 patients avec IO ont ete compares a 135 controles porteurs d’une sarcoidose sans IO. Dans le groupe infection opportuniste, le compte lymphocytaire moyen etait de 1000/mm3 (100-2680/mm3) et 14 patients ne presentaient pas de lymphopenie (29 %). Les facteurs de risques identifies en analyse univariee etaient : le sexe masculin (OR = 4,76; IC95 % [2,12 ; 10,00]), la presence d’adenopathies peripheriques (OR = 3,45 ; [1,49 ; 8,04]), d’une hepatomegalie (OR = 8,10 ; [1,91 ; 40,41]) ou d’une splenomegalie (OR = 9,00, [1,80 ; 58,86]), la presence d’une atteinte pulmonaire de stade ≥2 (OR = 6,66 ; [2,80 ; 17,74]), d’une atteinte neurologique centrale (OR = 8,73 ; [1,98 ; 53,52]) ou d’une insuffisance renale (OR = 5,65 ; [1,33 ; 25,24]), la corticotherapie (OR = 10,26 ; [4,15 ; 29,22]) et l’utilisation du cyclophosphamide (OR = 9,42 ; [1,61 ; 98,92]) ou d’un anti-TNFα (OR = 7,68 ; [1,21 ; 83,62]). En analyse multivariee (ajustement sur l’âge et le sexe), les facteurs de risque identifies etaient l’utilisation de corticoides (OR = 10,60 ; [4,31 ; 29,57]) ou d’un anti-TNFα (OR = 13,47 ; [2,05 ; 129,43]), la presence d’une hepatomegalie (OR = 9,91 ; [2,23 ; 55,85]), une atteinte pulmonaire de stade 2 ou superieur (OR = 5,65 ; [2,34 ; 15,36]) et l’insuffisance renale (OR = 11,76 ; [2,32 ; 68,35]). La lymphopenie Conclusion Les facteurs de risque d’IO dans notre etude sont associes a la gravite de la sarcoidose et/ou a sa diffusion systemique. Il existe un facteur confondant lie a l’utilisation des immunosuppresseurs chez des patients avec une sarcoidose plus severe. Dans notre serie, 6 % des patients ont developpe une infection opportuniste sans aucun facteur de risque, suggerant neanmoins une immunosuppression propre a la sarcoidose dans ces cas.

Introduction: Sarcoidosis is a systemic granulomatous disease of unknown etiology mostly affecting lungs and lymph nodes. Previous whole-exome sequencing (WES) studies have shown that autophagy and especially Ras-related C3 botulinum toxin substrate 1 (RAC1) and mammalian target of rapamycin (mTOR) pathways were possibly implicated in sarcoidosis (Pacheco et al. Trends Immunol 2020 Accepted manuscript). Aims: The SARCFAM (familial sarcoidosis) cohort gathered families aggregating sarcoidosis cases. We hypothesized that relevant genes variants in patients with sarcoidosis and uveitis phenotype were also related to autophagy. Methods: A WES study was performed on 20 patients in 6 families out of the SARCFAM cohort compared with 10 internal controls among siblings. 2 genomic subtractions were performed to compare uveitis and sarcoidosis phenotype to sarcoidosis without uveitis phenotype and to healthy controls. Results: 4 of the 20 patients presented uveitis phenotype. In 3 different families, 38, 142 and 104 variants concerning autophagy were found and respectively 12, 40 and 34 were associated with the uveitis clinical phenotype. Most relevant genes were NOD2, UNC93B, NLRP14, UBQLNL and those related to Toll-like receptors (TLR5). All genes were shown to be related to autophagy/mTOR/RAC1 pathways. NLRP14/NOD2 polymorphisms were respectively found to be related to Behcet uveitis and Blau syndrome. These proteins are targets for various environmental antigens (viruses, mycobacteria) suggesting imbrication of genetic predisposition and environmental triggers. Conclusion: Autophagy could be a major key point in the pathophysiology of sarcoidosis and mTOR may represent an interesting target to treat sarcoidosis.

Sarcoidosis is a multisystem disease of unknown etiology characterized by multiple granuloma formation. The role of autophagy, mammalian target of rapamycin (mTOR) and Ras-related C3 botulinum toxin substrate 1 (RAC1) abnormalities was recently reported in the course of sarcoidosis (Pacheco et al. Trends Immunol 2020 Accepted). RAC1 is one of the main targets of azathioprine (AZA), an immunosuppressive drug used in corticosteroid (CS) refractory sarcoidosis. A woman presenting severe, histologically proved sarcoidosis involving lung, liver and spleen was treated during one year with AZA after receiving CS for 6 months. A whole exome sequencing (WES) study of this patient was performed. Relevant homozygous mutations were found in 8 genes : ARFGAP1, NCOR2, CRIPAK, CGAS, CERK, RCAN3, IPH3, MEOX2. All those genes were found to be involved in autophagic processes. ARFGAP1 seemed to be the most interesting one since its role in sarcoidosis was previously highlighted in proteomic studies (Haggmark et al. Am J Respir Crit Care Med 2015 5;574-583). The C terminal domain of ARFGAP1 was shown to interact and inhibit RAC1 in vitro. ARFGAP1 is also an inhibitor of ARF1 (ADP-ribosylation factor 1), a small GTPase located in the Golgi apparatus implicated in autophagy through mTOR activation and autophagosome formation. We would hypothesize that ARFGAP1 mutated isoforms have lost their inhibitory function with a consequence of hyperactivation of RAC1 thus leading to autophagy inhibition. Autophagy disruption seems to be an interesting element of pathophysiology in sarcoidosis, previously evoked in WES studies and through the efficacy of autophagy modulating drug during sarcoidosis.

Introduction and Aims: Sarcoidosis is a multifactorial disease characterized by the formation and diffusion of granuloma in lungs and many other organs. Genetic and environmental factors have been involved in etiology of the disease. The existence of familial forms suggests that genetic predisposition plays a significant role and we recently identified a series of deleterious mutations in genes related to regulation of autophagy, around the Rac1 and mTor related pathways. Our aim was to replicate the genetic screening in a series of patients of the French GSF cohort in order to identify genetic markers putatively correlated with severe forms of sarcoidosis. Methods: A panel of 88 genes identified from previous familial exome analysis was applied to a series of 100 patients classified in : SEV-1: advanced pulmonary disease, SEV-2: extrapulmonary lesions and CTRL: 9benign9 and/or resolving disease. Results: A significant clustering of mutations in genes direcly related to autophagy (e.g. ATG), mTOR signaling pathways (e.g. DDIT4/L, BRSK2, Annexins) and Rac1 regulation (e.g. EPHA, KALRN, STEF, DOCK) occurs in SEV-1 and SEV-2 groups compared to CTRL suggesting that specific defects in these pathways may be related to progressive and/or multisystemic sarcoidosis. Perspectives: Identification of genetic biomarkers linked to severe forms of sarcoidosis is a challenge for the early management of patients and optimal therapeutic adaptation. Our study allows the definition of a first set of genes which could be implemented by further functional analysis and international cooperative studies.

Sarcoidosis is an enigmatic multisystem disease characterized by the development and accumulation of granulomas: a compact collection of macrophages that have differentiated into epithelioid cells and which are associated with T helper (Th)1 and Th17 cells. Although no single causative factor has been shown to underlie sarcoidosis in humans, its etiology has been related to microbial, environmental, and genetic factors. We examine how these factors play a role in sarcoidosis pathogenesis. Specifically, we propose that dysfunction of mTOR, Rac1, and autophagy-related pathways not only hampers pathogen or nonorganic particle clearance but also participates in T cell and macrophage dysfunction, driving granuloma formation. This concept opens new avenues for potentially treating sarcoidosis and may serve as a blueprint for other granulomatous disorders.

Background Sarcoidosis (OMIM 181000) is a multi-systemic granulomatous disorder of unknown origin. Despite multiple genome-wide association (GWAS) studies, no major pathogenic pathways have been identified to date. To find out relevant sarcoidosis predisposing genes, we searched for de novo and recessive mutations in 3 young probands with sarcoidosis and their healthy parents using a whole-exome sequencing (WES) methodology. Methods From the SARCFAM project based on a national network collecting familial cases of sarcoidosis, we selected three families (trios) in which a child, despite healthy parents, develop the disease before age 15 yr. Each trio was genotyped by WES (Illumina HiSEQ 2500) and we selected the gene variants segregating as 1) new mutations only occurring in affected children and 2) as recessive traits transmitted from each parents. The identified coding variants were compared between the three families. Allelic frequencies and in silico functional results were analyzed using ExAC, SIFT and Polyphenv2 databases. The clinical and genetic studies were registered by the ClinicalTrials.gov - Protocol Registration and Results System (PRS) (https://clinicaltrials.gov) receipt under the reference NCT02829853 and has been approved by the ethical committee (CPP LYON SUD EST – 2 – REF IRB 00009118 – September 21, 2016). Results We identified 37 genes sharing coding variants occurring either as recessive mutations in at least 2 trios or de novo mutations in one of the three affected children. The genes were classified according to their potential roles in immunity related pathways: 9 to autophagy and intracellular trafficking, 6 to G-proteins regulation, 4 to T-cell activation, 4 to cell cycle and immune synapse, 2 to innate immunity. Ten of the 37 genes were studied in a bibliographic way to evaluate the functional link with sarcoidosis. Conclusions Whole exome analysis of case-parent trios is useful for the identification of genes predisposing to complex genetic diseases as sarcoidosis. Our data identified 37 genes that could be putatively linked to a pediatric form of sarcoidosis in three trios. Our in-depth focus on 10 of these 37 genes may suggest that the formation of the characteristic lesion in sarcoidosis, granuloma, results from combined deficits in autophagy and intracellular trafficking (ex: Sec16A, AP5B1 and RREB1), G-proteins regulation (ex: OBSCN, CTTND2 and DNAH11), T-cell activation (ex: IDO2, IGSF3), mitosis and/or immune synapse (ex: SPICE1 and KNL1). The significance of these findings needs to be confirmed by functional tests on selected gene variants. Electronic supplementary material The online version of this article (10.1186/s12920-018-0338-x) contains supplementary material, which is available to authorized users.

Summary Lynch syndrome is due to germline mutations in mismatch repair genes: MLH1, MSH2, MSH6 and PMS2. It is characterized by an increased risk of various cancers including colorectal and endometrial cancers. Early diagnosis of these patients allows for appropriate surveillance and improves survival rates. Differentiating between patients who should undergo genetic testing and those for whom it is not necessary is difficult despite various established criteria (Amsterdam and Bethesda). Often, health professionals meet in multidisciplinary committees (MDC) to discuss patient cases regarding Lynch syndrome. In this study, we evaluated if the prediction model PREMM 1,2,6 could be used to enhance MDC decision-making and whether it should be included in our own routine practice and in those of other French teams. Using the prediction model in our cohort would have avoided 12% of the analyses recommended by our MDC. Furthermore, all patients with a mutation in one of the MMR genes would have been detected. In addition, according to the model, we should have provided 20% more genetic testing, which suggests that the decision-making criteria used by the professionals in our MDC, was too restrictive. These results suggest that PREMM 1,2,6 should be used in current practice to validate the decisions of the MDC before genetic testing is performed in complex cases. The model should be added as a major quality criterion for genetic testing, along with somatic tests, as previously reported in the literature.

Context Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant disease caused by mutations in the MEN1 gene characterized by a broad spectrum of clinical manifestations, of which the most frequent are primary hyperparathyroidism, pituitary adenomas, and neuroendocrine tumors. Objective The aim of this work was to facilitate interpretation of variants and improve the genetic counseling and medical care of families of patients with MEN1. Design, Setting, and Patients The TENGEN network (Oncogenetics Network of Neuroendocrine Tumors) has interpreted and collected all allelic variants and clinical characteristics of the MEN1-positive patients identified through genetic testing performed in the French population from 1997 to 2015. Patients and their variants were registered in the locus-specific UMD-MEN1 database (www.umd.be/MEN1/). Main Outcomes Variant classification, age-related penetrance, and odds ratios. Results A total of 370 distinct variants reported in 1676 patients, including 181 unpublished variants, have been registered. This database analysis revealed a low frequency (6.6%) of benign or likely benign missense variants in MEN1. Eight families (1.9%) had members with familial isolated hyperparathyroidism and harbored the same mutations as that found in families with authentic MEN1. An association existed between large rearrangements and an earlier onset of the disease, whereas no difference was observed between truncating and nontruncating variants. Conclusion The UMD-MEN1 database provides an exhaustive overview of the MEN1 variants present in the French population. For each variant, a classification is publicly available. Clinical data collections allow the determination of genotype-phenotype correlation and age-related penetrance of lesions in the cohort.

International audience; In 2015, the ACMG-AMP guidelines provided a general procedure for the objective and reproducible classification of genomic variants. While the benefits of this framework are of major importance, its adaptation for locus-specific use is needed. Multiple Endocrine Neoplasia type 1 (MEN1) occurs due to inactivating mutations in the tumour suppressor gene MEN1, including 20% of missense variants. The classification of these variants may be extremely challenging. Here, we compared the interpretation of the 122 MEN1 missense variants, identified in the French population over the past 15 years by the TENGEN network (French oncogenetics network of neuroendocrine tumors) versus by using the ACMG-AMP guidelines, and analyzed the causes of discordance. A total of 59.8% of missense variants were termed as (likely)-pathogenic variants by TENGEN versus only 28.7% using ACMG-AMP guidelines. Actually, 53.4% (39/73) of TENGEN (likely)-pathogenic variants were declassified in variant of uncertain significance (VUS) by using ACMG-AMP guidelines, thereby affecting the clinical management of patients and their families. Twenty of these ACMG-AMP VUS were found in patients with a clinically authentic MEN1 disease. Here, TENGEN proposes adjustments to the ACMG-AMP framework for the interpretation of MEN1 missense variants. These propositions merge both the classification systems, and are particularly interesting, as MEN1 is included in the ACMG secondary findings list for reporting in clinical genomic sequencing.

Sarcoidosis is a multifactorial disease induced by environmental and genetic factors. Whole exome sequencing in 5 familial cases of the disease suggest that genetic defects in Rac1 and mTor functional hubs may be relevant to sarcoidosis pathogenesis. http://bit.ly/2xooHx3

BackgroundUveitis is a frequent and early feature of sarcoidosis. As BTNL2 (butyrophilin-like 2) gene polymorphism was found linked with the susceptibility to sarcoidosis, we investigated whether a specific genotype of BTNL2 gene G16071A (or rs2076530) single-nucleotide polymorphism (SNP) would be associated with the risk of sarcoid uveitis in all patient subgroups.MethodsThe study compared the genotype frequencies of SNP G16071A of 135 patients with sarcoid uveitis (Sa+Uv+) with those of 196 patients with sarcoidosis without uveitis (Sa+Uv−), 81 patients with uveitis without sarcoidosis (Sa−Uv+), and 271 controls with no sarcoidosis nor uveitis (Sa−Uv−). Three hypothetical subgroups of patients with sarcoid uveitis (Sa+Uv+ cases) were considered: (1) subgroup I: patients aged 45 years; and (3) subgroup III: all other patients.ResultsA statistically significant difference in genotype frequencies was found between the groups Sa+Uv− and Sa−Uv− (p=3.2×10−6) and between the groups Sa+Uv+ and Sa+Uv− (p=7.1×10−3). There was no difference between the three subgroups of Sa+Uv+ patients. There was a statistically significant difference in genotype frequencies between Sa+Uv− and Sa+Uv+ subgroup II (p=0.005) but no difference between Sa+Uv− and Sa+Uv+ subgroup I.ConclusionNo association was found between G16071A and the susceptibility to sarcoid uveitis. BTNL2 gene G16071A SNP seems to be a predisposing factor for sarcoidosis except in Caucasian postmenopausal women with sarcoid uveitis in whom the GG genotype prevails. These and future results will help in understanding differences between particular subgroups of patients with sarcoid uveitis.

Nanoparticles are increasingly suspected as a strong etiologic factor of granuloma formation.The aim of our study was to compare lung inflammatory response and histology changes following exposure of mice to two widely used nanoparticles: carbon nanotubes (MWCNT) and cadmium-based nanoparticles (QDOT705) in an attempt to better our understanding of granulomatous inflammation.Various groups of mice were included: control mice and mice that were intranasally instilled with QDOT or MWCNT. At defined time points post-challenge, bronchoalveolar lavages (BALs) and lung tissues were collected to study inflammatory and histologic changes.Analyses of lung BAL fluids and tissues of nanoparticles-challenged mice in comparison to controls found: (1) increased cellularity in BALs, (2) increase of total protein concentration, LDH activity and proteolytic activity in BALs; (3) patchy granulomas, (4) macrophages, CD3 ± T, Treg and B cell infiltration in granulomatous areas; and (5) altered regulation of key inflammatory mediators and receptors. Importantly, these changes were nanoparticle type-dependent.Our work enhances understanding of nanoparticles-induced lung inflammatory and histological changes that result in granuloma formation. We provide compelling evidence that not only exposure to nanoparticles leads to granulomatous lung inflammation, but the severity of this latter is nanostructure type-dependent. Of importance, while nanotechnology has the potential to revolutionize various fields including medicine, nanoparticles form the potential for an entirely new lung health risk that it is necessary to take seriously into consideration by setting up and/or reinforcing adequate safety measures.

Introduction La sarcoidose est une maladie granulomateuse qui affecte principalement les poumons et dont le determinisme multifactoriel associe des facteurs environnementaux et genetiques. Nous avons publie en 2018 une analyse complete d’exome de cas pediatriques suggerant des anomalies dans l’autophagie, le cycle cellulaire et les processus de reponse immunitaire innee. Notre etude actuelle se focalise sur les formes familiales a presentation autosomique dominante et penetrance forte, afin de mettre en evidence des mutations deleteres agissant comme des triggers puissants de la predisposition. Methodes Nous avons sequence un total de 22 sujets, dont 14 malades et 8 controles internes sains, appartenant a 5 familles predisposees a la sarcoidose. Le protocole de sequencage est base sur la methodologie d’enrichissement en solution Agilent (SureSelect, Agilent) (Human Clinical Research Exome, Agilent), suivie d’un sequencage massif parallele sur Illumina HiSEQ 4000. La selection des variants geniques est basee sur la faible frequence allelique (MAF Resultats La selection des genes a permis d’identifier une serie de 192 genes dont 52 (27 %) semblent etre concentres autour de centres fonctionnels de Rac1 Rho GTPase et le hub du complexe mTor ( Fig. 1 ). Ces resultats ont ete confirmes par des methodes d’enrichissement de reseaux fonctionnels tel ConsensusPathDB. Un nombre significatif de mutations deleteres a egalement ete observe dans des genes codant pour des facteurs intrinseques de l’autophagie et du transport vesiculaire. Une analyse retrospective de 196 patients versus temoins suggere une concentration de mutations dans les genes regulateurs de Rac1 dans 4 % des cas, chez des patients presentant des formes severes, chroniques, multisystemiques et/ou evolutives de la maladie. Conclusion Notre travail suggere que la predisposition genetique a la sarcoidose pourrait etre liee a un effet combine de mutations deleteres de genes impliques dans la regulation de l’autophagie et des hubs fonctionnels Rac1 et mTor, ouvrant la voie a un depistage precoce des formes les plus evolutives.

International audience; Infantile spasms syndrome (ISs) is characterized by clinical spasms with ictal electrodecrement, usually occurring before the age of 1 year and frequently associated with cognitive impairment. Etiology is widely heterogeneous, the cause remaining elusive in 40% of patients. We searched for de novo mutations in 10 probands with ISs and their parents using whole-exome sequencing (WES). Patients had neither consanguinity nor family history of epilepsy. Common causes of ISs were excluded by brain magnetic resonance imaging (MRI), metabolic screening, array-comparative genomic hybridization (CGH) and testing for mutations in CDKL5, STXBP1, and for ARX duplications. We found a probably pathogenic mutation in four patients. Missense mutations in SCN2A (p.Leu1342Pro) and KCNQ2 (p.Ala306Thr) were found in two patients with no history of epilepsy before the onset of ISs. The p.Asn107Ser missense mutation of ALG13 had been previously reported in four females with ISs. The fourth mutation was an in-frame deletion (p.Phe110del) in NR2F1, a gene whose mutations cause intellectual disability, epilepsy, and optic atrophy. In addition, we found a possibly pathogenic variant in KIF3C that encodes a kinesin expressed during neural development. Our results confirm that WES improves significantly the diagnosis yield in patients with sporadic ISs.

Methyl-CpG-binding protein 2 (MECP2) deleterious variants, which are responsible for Rett syndrome in girls, are involved in a wide spectrum of developmental disabilities in males. A neuropsychiatric phenotype without intellectual disability is uncommon in patients with MECP2 deleterious variants. We report on two dizygotic twins with an MECP2-related psychiatric disorder without intellectual disability. Neuropsychological and psychiatric phenotype assessments were performed, and a genetic analysis was carried out. Both patients fulfilled the Pervasive Developmental Disorder criteria on Autism Diagnostic Observation Schedule and Asperger syndrome criteria on Diagnostic and Statistical Manual of Mental Disorders, 4th ed. (DSM-IV). One patient developed early-onset schizophrenia (DSM-IV criteria) with two acute psychotic episodes, the latest one following corticosteroids and sodium valproate intake, with major hyperammonemia. A novel MECP2 gene transversion c.491 G>T [p.(Ser164Ile)] was found in both twins. Pathogenicity of this variant was considered on the basis of strong clinical and molecular data. The underlying molecular basis of neuropsychiatric disorders may have important consequences on genetic counseling and therapeutic strategies.

Mutations of the CDKL5 gene cause early epileptic encephalopathy. Patients manifest refractory epilepsy, beginning before the age of 3 months, which is associated with severe psychomotor delay and features that overlap with Rett syndrome. We report here a patient with mosaicism for CDKL5 exonic deletion, with the presence of two mutant alleles. The affected 4-year-old girl presented with infantile spasms, beginning at the age of 9 months, but subsequent progression of the disease was consistent with the classical CDKL5-related phenotype. A deletion of exons 17 and 18 was suspected on the basis of Multiplex Ligation Probe Amplification analysis, but unexpected results for cDNA analysis, which showed the presence of an abnormal transcript with the deletion of exon 18 only, led us to suspect that two distinct events might have occurred. We used custom array-CGH to determine the size and breakpoints of these deletions. Exon 18 was deleted from one of the abnormal alleles, and exon 17 was deleted from the other. A Fork Stalling and Template Switching (FoSTeS) mechanism was proposed to explain the two events, given the presence of regions of microhomology at the breakpoints. We propose here an original involvement of the FoSTeS mechanism to explain the co-occurrence of these two events in the CDKL5 gene in a single patient. This patient highlights the difficulties involved in the detection of such abnormalities, particularly when they occur in a mosaic state and involve two distinct mutational events in a single gene.

Mutations in the KCNQ2 and KCNQ3 genes encoding for Kv 7.2 (KCNQ2; Q2) and Kv 7.3 (KCNQ3; Q3) voltage-dependent K(+) channel subunits, respectively, cause neonatal epilepsies with wide phenotypic heterogeneity. In addition to benign familial neonatal epilepsy (BFNE), KCNQ2 mutations have been recently found in families with one or more family members with a severe outcome, including drug-resistant seizures with psychomotor retardation, electroencephalogram (EEG) suppression-burst pattern (Ohtahara syndrome), and distinct neuroradiological features, a condition that was named "KCNQ2 encephalopathy." In the present article, we describe clinical, genetic, and functional data from 17 patients/families whose electroclinical presentation was consistent with the diagnosis of BFNE. Sixteen different heterozygous mutations were found in KCNQ2, including 10 substitutions, three insertions/deletions and three large deletions. One substitution was found in KCNQ3. Most of these mutations were novel, except for four KCNQ2 substitutions that were shown to be recurrent. Electrophysiological studies in mammalian cells revealed that homomeric or heteromeric KCNQ2 and/or KCNQ3 channels carrying mutant subunits with newly found substitutions displayed reduced current densities. In addition, we describe, for the first time, that some mutations impair channel regulation by syntaxin-1A, highlighting a novel pathogenetic mechanism for KCNQ2-related epilepsies.

Introduction La sarcoidose reste une maladie d’etiologie meconnue. Les approches explicatives sont actuellement environnementales et/ou genetiques. Les hypotheses fonctionnelles et biochimiques ont aborde les voies de signalisation : NFkB, STAT1, Galphai, RIP2, IRAK et plus recemment mTOR. L’etude nationale SARCFAM [1] a permis de collecter plus de 150 familles presentant une predisposition a la maladie. Methodes Au sein de cette cohorte, six familles reunissant au moins deux ou trois sujets malades et un ou deux temoins sains ont pu beneficier d’une etude en WES. Le sequencage a ete realise sur Illumina HiSEQ2500 en cooperation avec INTEGRAGEN et les donnees sources ont ete analysees par un pipeline informatique developpe au sein de l’equipe suivant les recommandations du Broad Institute ( https://www.broadinstitute.org/gatk/guide/best-practices ). Tous les cas et temoins ont ete sequences deux fois dans des protocoles independants et seuls les resultats reproductibles ont ete retenus. Une selection de variants geniques a ete confirmee par sequencage SANGER. Resultats Les resultats montrent : (a) que cette maladie presente une tres forte heterogeneite genetique, (b) que des variations genotypiques entre patients d’une meme famille sont susceptibles d’expliquer une expressivite variable de la maladie, (c) qu’il existe une forte concentration de mutations dans la sphere immunologique, (d) que ces mutations interessent les voies de signalisation et de regulation de l’autophagie autour des voies Rac1 et mTOR, (e) qu’il existe une concentration par famille de variants pathogenes in silico dans ces voies fonctionnelles, 3 a 8 pour Rac1, 2 a 6 pour mTOR et l’autophagie, suggerant une complementation des effets pathogenes a l’origine de la predisposition. Conclusion Ces observations conduisent a des hypotheses seduisantes sur un dysfonctionnement du processus d’autophagie rendant les malades plus vulnerables a divers facteurs de l’environnement. Elles permettent d’envisager des etudes fonctionnelles et des analyses genetiques sur une grande cohorte.

CD4+ T lymphocytes play a major role in the pathophysiology of sarcoidosis. Many studies have investigated the immunological and genetic abnormalities in this disease. There are few studies concerning the metabolic pathways. Essentially they concern the pathways: STAT1, MAPK38, NF-κB, Galphai, cAMP and cGMP PDE and PEMT1. Using studies in the literature and results of our own work concerning some metabolic aspects of T lymphocytes in sarcoidosis, we present a revue of the various hypotheses, which involve dysfunction of cAMP signaling pathways, such as RAS/RAF/MEK/ERK in T lymphocytes, leading to a disorder of immunity.

Multiple endocrine neoplasia type 1 (MEN1) is an autosomal dominant familial cancer syndrome characterized by parathyroid, pancreatic, and anterior pituitary tumors. The MEN1 locus has been previously localized to chromosome 11q13, and a 2-Mb gene-rich region flanked by D11S1883 and D11S449 has been defined. We have pursued studies to facilitate identification of the MEN1 gene by narrowing this critical region to a 900-kb interval between the VRF and D11S1783 loci through meiotic mapping. This was achieved by investigating 17 cosmids for microsatellite polymorphisms, which defined two novel polymorphisms at the VRF and A0138 loci, and utilizing these to characterize recombinants in MEN1 families. In addition, we have established a 1200-kb sequence-ready contig consisting of 26 cosmids, eight BACs, and eight PACS that encompass this region. The precise locations for 19 genes and three ESTs within this contig have been determined, and three gene clusters consisting of a centromeric group (VRF, FKBP2, PNG, and PLCB3), a middle group (PYGM, ZFM1, SCG1, SCG2 (which proved to be the MEN1 gene), and PPP2R5B), and a telomeric group (H4B, ANG3, ANG2, ANG1, FON, FAU, NOF, NON, and D11S2196E) were observed. These results represent a valuable transcriptional map of chromosome 11q13 that will help in the search for disease genes in this region.

BackgroundMEN1, which is secondary to the mutation of the MEN1 gene, is a rare autosomal-dominant disease that predisposes mutation carriers to endocrine tumors. Most studies demonstrated the absence of direct genotype-phenotype correlations. The existence of a higher risk of death in the Groupe d'étude des Tumeurs Endocrines-cohort associated with a mutation in the JunD interacting domain suggests heterogeneity across families in disease expressivity. This study aims to assess the existence of modifying genetic factors by estimating the intrafamilial correlations and heritability of the six main tumor types in MEN1.MethodsThe study included 797 patients from 265 kindred and studied seven phenotypic criteria: parathyroid and pancreatic neuroendocrine tumors (NETs) and pituitary, adrenal, bronchial, and thymic (thNET) tumors and the presence of metastasis. Intrafamilial correlations and heritability estimates were calculated from family tree data using specific validated statistical analysis software.ResultsIntrafamilial correlations were significant and decreased along parental degrees distance for pituitary, adrenal and thNETs. The heritability of these three tumor types was consistently strong and significant with 64% (s.e.m.=0.13; Ps.e.m.=0.21; Ps.e.m.=0.41; P=0.006) for thNETs.ConclusionThe present study shows the existence of modifying genetic factors for thymus, adrenal, and pituitary MEN1 tumor types. The identification of at-risk subgroups of individuals within cohorts is the first step toward personalization of care. Next generation sequencing on this subset of tumors will help identify the molecular basis of MEN1 variable genetic expressivity.

The Birt-Hogg-Dube (BHD) syndrome is associated with cutaneous disorders including fibrofolliculomas and trichodiscomas, and also lung pneumatocysts and kidney tumours. The BHD syndrome occurs as a consequence of an autosomal dominantly inherited genodermatosis, linked to multiple germline mutations in the 14 exons of the BHD gene, mapped on 17p11.2 and encoding for folliculin (FLCN). The size and number of lung pneumatocysts are extremely variable and the cysts are surrounded by normal pulmonary tissue. In the absence of smoking lung function is usually unimpaired. The lung cysts are frequently complicated by the development of recurrent pneumothoraces. Treatment of pneumothorax in patients with the BHD syndrome is similar to the approach taken for patients with spontaneous pneumothorax. Lung cysts in the BHD syndrome are a rare cause of cystic pulmonary lesions. However, they must be systematically evaluated since kidney tumours occur in one third of patients. We report a case of classical BHD syndrome with specific cutaneous involvement, recurrent pneumothoraces complicating lung cysts, an exon 12 germline mutation on BHD gene and a familial history suggesting other related cases. This observation allows us to update this orphan disease, to consider BHD in the differential diagnosis of lung cysts and, above all, to highlight the high frequency and the prognostic significance of associated kidney tumours.