Evaluation of DNA Methylation Episignatures for Diagnosis and Phenotype Correlations in 42 Mendelian Neurodevelopmental Disorders.

Genetic syndromes frequently present with overlapping clinical features and inconclusive or ambiguous genetic findings which can confound accurate diagnosis and clinical management. An expanding number of genetic syndromes have been shown to have unique genomic DNA methylation patterns (called episignatures ). Peripheral blood episignatures can be used for diagnostic testing as well as for the interpretation of ambiguous genetic test results. We present here an approach to episignature mapping in 42 genetic syndromes, which has allowed the identification of 34 robust disease-specific episignatures. We examine emerging patterns of overlap, as well as similarities and hierarchical relationships across these episignatures, to highlight their key features as they are related to genetic heterogeneity, dosage effect, unaffected carrier status, and incomplete penetrance. We demonstrate the necessity of multiclass modeling for accurate genetic variant classification and show how disease classification using a single episignature at a time can sometimes lead to classification errors in closely related episignatures. We demonstrate the utility of this tool in resolving ambiguous clinical cases and identification of previously undiagnosed cases through mass screening of a large cohort of subjects with developmental delays and congenital anomalies. This study more than doubles the number of published syndromes with DNA methylation episignatures and, most significantly, opens new avenues for accurate diagnosis and clinical assessment in individuals affected by these disorders

Clinical spectrum of MTOR-related hypomelanosis of Ito with neurodevelopmental abnormalities.

PURPOSE: Hypomelanosis of Ito (HI) is a skin marker of somatic mosaicism. Mosaic MTOR pathogenic variants have been reported in HI with brain overgrowth. We sought to delineate further the pigmentary skin phenotype and clinical spectrum of neurodevelopmental manifestations of MTOR-related HI. METHODS: From two cohorts totaling 71 patients with pigmentary mosaicism, we identified 14 patients with Blaschko-linear and one with flag-like pigmentation abnormalities, psychomotor impairment or seizures, and a postzygotic MTOR variant in skin. Patient records, including brain magnetic resonance image (MRI) were reviewed. Immunostaining (n = 3) for melanocyte markers and ultrastructural studies (n = 2) were performed on skin biopsies. RESULTS: MTOR variants were present in skin, but absent from blood in half of cases. In a patient (p.[Glu2419Lys] variant), phosphorylation of p70S6K was constitutively increased. In hypopigmented skin of two patients, we found a decrease in stage 4 melanosomes in melanocytes and keratinocytes. Most patients (80%) had macrocephaly or (hemi)megalencephaly on MRI. CONCLUSION: MTOR-related HI is a recognizable neurocutaneous phenotype of patterned dyspigmentation, epilepsy, intellectual deficiency, and brain overgrowth, and a distinct subtype of hypomelanosis related to somatic mosaicism. Hypopigmentation may be due to a defect in melanogenesis, through mTORC1 activation, similar to hypochromic patches in tuberous sclerosis complex

Outcomes from elective colorectal cancer surgery during the SARS-CoV-2 pandemic

This study aimed to describe the change in surgical practice and the impact of SARS-CoV-2 on mortality after surgical resection of colorectal cancer during the initial phases of the SARS-CoV-2 pandemic

Multiancestry analysis of the HLA locus in Alzheimer's and Parkinson's diseases uncovers a shared adaptive immune response mediated by HLA-DRB1*04 subtypes

11 páginas, 4 figuras, 2 tablas. Datasets en su material suplementario. This article contains supporting information online at https://www.pnas.org/lookup/suppl/doi:10.1073/pnas.2302720120/-/DCSupplemental.Across multiancestry groups, we analyzed Human Leukocyte Antigen (HLA) associations in over 176,000 individuals with Parkinson's disease (PD) and Alzheimer's disease (AD) versus controls. We demonstrate that the two diseases share the same protective association at the HLA locus. HLA-specific fine-mapping showed that hierarchical protective effects of HLA-DRB1*04 subtypes best accounted for the association, strongest with HLA-DRB1*04:04 and HLA-DRB1*04:07, and intermediary with HLA-DRB1*04:01 and HLA-DRB1*04:03. The same signal was associated with decreased neurofibrillary tangles in postmortem brains and was associated with reduced tau levels in cerebrospinal fluid and to a lower extent with increased Aβ42. Protective HLA-DRB1*04 subtypes strongly bound the aggregation-prone tau PHF6 sequence, however only when acetylated at a lysine (K311), a common posttranslational modification central to tau aggregation. An HLA-DRB1*04-mediated adaptive immune response decreases PD and AD risks, potentially by acting against tau, offering the possibility of therapeutic avenues.This work was supported by the Michael J. Fox Foundation grant MJFF-020161 (E.M., Z.G.-O.), NIH and National Institute of Aging grants AG060747 (M.D.G.), AG066206 (Z.H.), AG066515 (Z.H., M.D.G.), the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie (grant agreement No. 890650, Y.L.G.), the Alzheimer’s Association (AARF-20-683984, M.E.B.), and the Iqbal Farrukh and Asad Jamal Fund, a grant from the EU Joint Programme—Neurodegenerative Disease Research (European Alzheimer DNA BioBank, EADB; JPND), the Japan Agency for Medical Research and Development JP21dk0207045 (T.I.), JP21dk020704 (K.O., S.N.), JP21km040550 (K.O.), the Einstein Center for Neurosciences in Berlin (S.M.Y.), the Swedish Research Council (#2018-02532, H.Z.), the European Research Council (#681712, H.Z.), and the Swedish State Support for Clinical Research (#ALFGBG-720931, H.Z.). Inserm UMR1167 is also funded by the Inserm, Institut Pasteur de Lille, Lille Métropole Communauté Urbaine, and the French government’s LABEX DISTALZ program (development of innovative strategies for a transdisciplinary approach to AD). Additional funders of individual investigators and institutions who contributed to data collection and genotyping are provided in SI Appendix.Peer reviewe

Multiancestry analysis of the HLA locus in Alzheimer’s and Parkinson’s diseases uncovers a shared adaptive immune response mediated by HLA-DRB1*04 subtypes

Across multiancestry groups, we analyzed Human Leukocyte Antigen (HLA) associations in over 176,000 individuals with Parkinson’s disease (PD) and Alzheimer’s disease (AD) versus controls. We demonstrate that the two diseases share the same protective association at the HLA locus. HLA-specific fine-mapping showed that hierarchical protective effects of HLA-DRB1*04 subtypes best accounted for the association, strongest with HLA-DRB1*04:04 and HLA-DRB1*04:07, and intermediary with HLA-DRB1*04:01 and HLA-DRB1*04:03. The same signal was associated with decreased neurofibrillary tangles in postmortem brains and was associated with reduced tau levels in cerebrospinal fluid and to a lower extent with increased Aβ42. Protective HLA-DRB1*04 subtypes strongly bound the aggregation-prone tau PHF6 sequence, however only when acetylated at a lysine (K311), a common posttranslational modification central to tau aggregation. An HLA-DRB1*04-mediated adaptive immune response decreases PD and AD risks, potentially by acting against tau, offering the possibility of therapeutic avenues

ANTICIPATE-CHUGA : dépistage précoce des maladies chroniques du foie : impact de la mise en place d’un parcours de soins systématisé pour l’identification des patients avec fibrose significative au CHUGA

Chronic liver disease (CLD) is a major and growing public health issue worldwide. Fibrosis is the only determinant of liver-related mortality. Unfortunately, CLD is most often discovered at a later stage associated with reduced survival. Early diagnosis of advanced hepatic fibrosis is therefore critical to improve the overall prognosis of CLD. Assessment of liver fibrosis is recommended in patients with risk factors for hepatic fatty liver : excessive alcohol consumption, metabolic syndrome, obesity and diabetes. The screening strategy relies on non-invasive tests, starting with the FIB-4 blood test. In the Grenoble Alpes University Hospital (CHUGA), we evaluated the implementation of a care pathway to screen for advanced liver fibrosis based on the systematic calculation of FIB-4 in departments with a high prevalence of metabolic risk factors for chronic liver disease. The FIB-4 result was implemented in the final laboratory reports if the FIB-4 was ≥ 2.67 in patients aged < 70 years, along with an incentive to request a second-line fibrosis test (Fibroscan®). The main objective of the study was to assess the ability to detect patients with significant liver fibrosis among patients managed in CHUGA departments with a high prevalence of metabolic risk factors for chronic liver disease, using a sequential strategy based on systematic calculation of FIB-4 and second line fibrosis testing (Fibroscan®). From November 16th 2020 to November 16th 2022, 6,327 FIB-4 were calculated, corresponding to 4,019 patients and 2,963 patients aged between 18 and 70 years.135 out of 2,963 FIB-4 tests were ≥ 2.67 (4.6%). Patients with obvious causes of false-positive FIB-4 were excluded (known liver disease, thrombocytopenia of non-hepatic origin, progressive cancer and acute resolving cytolysis); 4 patients with polycystic liver disease and one patient with short-term life-threatening disease were also excluded. In total, of the 135 patients, 47 were eligible for Fibroscan®, i.e. 34.8%. Of these 47 patients eligible for Fibroscan®, 35 (74.4%) had at least one risk factor for metabolic steatopathy, including obesity, metabolic syndrome, diabetes, sleep apnoea syndrome and excessive alcohol consumption; and 24/35 had at least 2 associated risk factors. Only 7 (14.9%) Fibroscan® requests were made at the initiative of the referent physician who prescribed the biological tests used to calculate the FIB-4. The other requests were made after an alert issued by the liver specialists involved in the care pathway. 40 patients actually had Fibroscan® (7 lost to follow-up before Fibroscan®), including 15 patients with significant fibrosis. 8 of the 15 patients were finally assessed by a liver specialist (7 lost to follow-up after Fibroscan®). In each of these 8 patients, cirrhosis was confirmed. Our pilot care pathway allowed for the identification of patients with significant and asymptomatic liver fibrosis who are eligible for specialized care. However, efforts need to be made to improve the care pathway. Awareness needs to be raised among practitioners working in the targeted departments to properly identify patients at risk eligible to the sequential fibrosis screening strategy, so all patients with FIB-4 ≥ 2,67are referred to the second-line test followed by a specialist assessment if needed.Les maladies chroniques du foie (MCF) représentent un problème de santé publique majeur et croissant dans le monde. La fibrose est l’unique déterminant de la mortalité liée au foie. Malheureusement les MCF sont découvertes le plus souvent à un stade tardif associé à une réduction de survie. Aussi, le diagnostic précoce de la fibrose hépatique avancée est un prérequis indispensable à l’amélioration du pronostic des MCF. L’évaluation de la fibrose hépatique est recommandée chez les patients présentant des facteurs de risque de stéatopathie hépatique : consommation excessive d’alcool, syndrome métabolique, obésité et diabète. La stratégie de dépistage s’appuie sur les tests non-invasifs, avec en première ligne le test sanguin FIB-4. Au CHU Grenoble Alpes (CHUGA), nous avons évalué la mise en place d’un parcours de soin pour dépister la fibrose hépatique avancée basé sur le calcul systématique du FIB-4 dans les services à forte prévalence de facteurs de risque métabolique de MCF. Le résultat du FIB-4 a été implémenté dans les résultats finaux du laboratoire si le FIB-4 était ≥2,67 chez les patients âgés de <70 ans, assorti d’une incitation à réaliser un test de fibrose de seconde ligne (Fibroscan®). L’objectif principal de l’étude était d’évaluer la capacité à dépister les patients avec fibrose hépatique significative parmi les patients pris en charge dans les services du CHUGA à forte prévalence de facteurs de risque métabolique de MCF grâce à cette stratégie séquentielle. Du 16 novembre 2020 au 16 novembre 2022, 6 327 FIB-4 ont été calculés, correspondant à 4 019 patients et à 2 963 patients âgés entre 18 et 70 ans. 135 FIB-4 sur 2 963 étaient ≥2,67 (4,6%). Les patients (N=88) avec cause évidente de faux-positif ont été exclus (hépatopathie connue, thrombopénie d’origine non hépatique, cancer évolutif et cytolyse aigue résolutive); de même que 4 patients atteints de polykystose hépatique et un patient avec pronostic vital engagé à court terme. Au final, 47 patients (34,8%) étaient éligibles au Fibroscan®. Parmi ces 47 patients, 35 patients (74,4%) présentaient au moins un facteur de risque de stéatopathie métabolique parmi : obésité, syndrome métabolique, diabète, syndrome d’apnée du sommeil, consommation excessive d’alcool, et 24/35 présentaient au moins 2 facteurs de risque associés. Seulement 7/47 Fibroscan® (14,9%) étaient à l’initiative du médecin prescripteur du bilan biologique ayant permis le calcul du FIB-4. Les autres demandes ayant été réalisées après alerte par les hépatologues impliqués dans le parcours de soins. 40/47 patients éligibles ont effectivement eu un Fibroscan®, parmi lesquels ont été identifiés 15 patients avec fibrose significative. Seulement 8 patients sur 15 ont bénéficié d’une consultation spécialisée d’hépatologie (7 perdus de vue après Fibroscan®). Le diagnostic de cirrhose a été retenu chez chacun de ces 8 patients. Notre parcours de soin mis en place au CHUGA permet de dépister efficacement des patients porteurs d’une fibrose hépatique significative asymptomatique éligibles à une prise en charge spécialisée en hépatologie. Cependant, des efforts doivent être faits pour améliorer le parcours de soin. Les praticiens exerçant dans les services ciblés doivent être mieux sensibilisés au repérage des patients à risque et à la stratégie séquentielle de dépistage de la fibrose afin que tous les patients avec FIB-4 élevé soient adressés au test de seconde ligne, puis, le cas échéant, à la consultation spécialisée

FrzS acts as a polar beacon to recruit SgmX , a central activator of type IV pili during Myxococcus xanthus motility

International audienceIn rod-shaped bacteria, type IV pili (Tfp) promote twitching motility by assembling and retracting at the cell pole. In Myxococcus xanthus, a bacterium that moves in highly coordinated cell groups, Tfp are activated by a polar activator protein, SgmX. However, while it is known that the Ras-like protein MglA is required for unipolar targeting, how SgmX accesses the cell pole to activate Tfp is unknown. Here, we demonstrate that a polar beacon protein, FrzS, recruits SgmX at the cell pole. We identified two main functional domains, including a Tfp-activating domain and a polarbinding domain. Within the latter, we show that the direct binding of MglA-GTP unveils a hidden motif that binds directly to the FrzS N-terminal response regulator (CheY). Structural analyses reveal that this binding occurs through a novel binding interface for response regulator domains. In conclusion, the findings unveil the protein interaction network leading to the spatial activation of Tfp at the cell pole. This tripartite system is at the root of complex collective behaviours in this predatory bacterium

A molecular switch controls assembly of bacterial focal adhesions

Cell motility universally relies on spatial regulation of focal adhesion complexes (FAs) connecting the substrate to cellular motors. In bacterial FAs, the Adventurous gliding motility machinery (Agl-Glt) assembles at the leading cell pole following a Mutual gliding-motility protein (MglA)-guanosine 5'-triphosphate (GTP) gradient along the cell axis. Here, we show that GltJ, a machinery membrane protein, contains cytosolic motifs binding MglA-GTP and AglZ and recruiting the MreB cytoskeleton to initiate movement toward the lagging cell pole. In addition, MglA-GTP binding triggers a conformational shift in an adjacent GltJ zinc-finger domain, facilitating MglB recruitment near the lagging pole. This prompts GTP hydrolysis by MglA, leading to complex disassembly. The GltJ switch thus serves as a sensor for the MglA-GTP gradient, controlling FA activity spatially

Plasma ALS and Gal-3BP differentiate early from advanced liver fibrosis in MASLD patients

International audienceBackground: Metabolic dysfunction-associated steatotic liver disease (MASLD) is estimated to affect 30% of the world’s population, and its prevalence is increasing in line with obesity. Liver fibrosis is closely related to mortality, making it the most important clinical parameter for MASLD. It is currently assessed by liver biopsy – an invasive procedure that has some limitations. There is thus an urgent need for a reliable non-invasive means to diagnose earlier MASLD stages. Methods: A discovery study was performed on 158 plasma samples from histologically-characterised MASLD patients using mass spectrometry (MS)-based quantitative proteomics. Differentially abundant proteins were selected for verification by ELISA in the same cohort. They were subsequently validated in an independent MASLD cohort ( n = 200). Results: From the 72 proteins differentially abundant between patients with early (F0-2) and advanced fibrosis (F3-4), we selected Insulin-like growth factor-binding protein complex acid labile subunit (ALS) and Galectin-3-binding protein (Gal-3BP) for further study. In our validation cohort, AUROCs with 95% CIs of 0.744 [0.673 – 0.816] and 0.735 [0.661 – 0.81] were obtained for ALS and Gal-3BP, respectively. Combining ALS and Gal-3BP improved the assessment of advanced liver fibrosis, giving an AUROC of 0.796 [0.731. 0.862]. The {ALS; Gal-3BP} model surpassed classic fibrosis panels in predicting advanced liver fibrosis. Conclusions: Further investigations with complementary cohorts will be needed to confirm the usefulness of ALS and Gal-3BP individually and in combination with other biomarkers for diagnosis of liver fibrosis. With the availability of ELISA assays, these findings could be rapidly clinically translated, providing direct benefits for patients