The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases

The SIB Swiss Institute of Bioinformatics (www.isb-sib.ch) provides world-class bioinformatics databases, software tools, services and training to the international life science community in academia and industry. These solutions allow life scientists to turn the exponentially growing amount of data into knowledge. Here, we provide an overview of SIB's resources and competence areas, with a strong focus on curated databases and SIB's most popular and widely used resources. In particular, SIB's Bioinformatics resource portal ExPASy features over 150 resources, including UniProtKB/Swiss-Prot, ENZYME, PROSITE, neXtProt, STRING, UniCarbKB, SugarBindDB, SwissRegulon, EPD, arrayMap, Bgee, SWISS-MODEL Repository, OMA, OrthoDB and other databases, which are briefly described in this article

Caractérisation de variations responsables de troubles du neurodéveloppement dans les gènes PTBP1 et PTBP2

Heterogeneous nuclear ribonucleoproteins (hnRNPs) polypyrimidine tract-binding protein 1 and 2 (PTBP1 and PTBP2) are splicing regulators, shuttling between nucleus and cytoplasm thanks to the action of partially overlapping nuclear localization and export signals (NLS and NES respectively). These two paralog proteins share similar RNA binding properties although they exhibit different expression levels and kinetics, post-translational modifications and cofactor interactions across tissues and cell types, thus regulating RNA metabolism in a cell- specific manner. Despite their fundamental role as alternative splicing factors implicated in cell growth, neuronal cell differentiation, and immune cells activation, little is known about their involvement in human disease.Here, we identified 25 individuals with de novo or inherited pathogenic start-loss or missense variants affecting either NLS or NLS/NES functions in PTBP1 (n=23) or PTBP2 (n=2), associated with osteochondrodysplasia and autism spectrum disorder with attention deficit hyperactivity disorder respectively. Intellectual functioning was variable across the whole cohort ranging from normal to moderately delayed. Epilepsy was reported in 3 out of 25 individuals. Using a combination of molecular genetics and transcriptomics approaches in patient-derivedfibroblasts and independent cellular and in vivo models, we demonstrated that pathogenic 86variants cause partial cytoplasmic retention and accumulation of PTBP1 and PTBP2 in processing bodies eventually causing alteration of mRNA stability without perturbing nuclear splicing. Overall, our data demonstrate that heterozygous pathogenic variants in PTBP1 and PTBP2 affecting their nucleocytoplasmic distribution are associated with developmental defects with or without intellectual disability.Les ribonucléoprotéines nucléaires hétérogènes (hnRNP) polypyrimidine tract-binding protein 1 et 2 (PTBP1 et PTBP2) sont des régulateurs de l'épissage, se déplaçant entre le noyau et le cytoplasme grâce à l'action de signaux de localisation nucléaire et d'exportation (NLS et NES respectivement) qui se chevauchent partiellement. Ces deux protéines paralogues partagent des propriétés de liaison à l'ARN similaires, bien qu'elles présentent des niveaux et des cinétiques d'expression, des modifications post-traductionnelles et des interactions de cofacteurs différents selon les tissus et les types de cellules, régulant ainsi le métabolisme de l'ARN de manière spécifique. Malgré leur rôle fondamental en tant que facteurs d'épissage alternatif impliqués dans la croissance cellulaire, la différenciation des cellules neuronales et l'activation des cellules immunitaires, on sait peu de choses sur leur implication dans les maladies humaines.Ici, nous avons identifié 25 individus avec des variants de novo ou héréditaires pathogènes, touchant le codon d’initiation ou faux-sens affectant soit les locus NLS ou NLS/NES dans PTBP1 (n=23) ou PTBP2 (n=2), associés respectivement à l'ostéochondrodysplasie et au trouble du spectre autistique avec déficit d'attention et hyperactivité. Le fonctionnement intellectuel était variable dans l'ensemble de la cohorte, allant de normal à modérément retardé. L'épilepsie a été signalée chez 3 des 25 individus. En utilisant une combinaison d'approches de génétique moléculaire et de transcriptomique dans des fibroblastes dérivés de patients et dans des modèles cellulaires et in vivo indépendants, nous avons démontré que les variants pathogènes provoquent une rétention cytoplasmique partielle et une accumulation de PTBP1 et PTBP2 dans les corps de traitement (p-bodies), ce qui entraîne une altération de la stabilité du transcriptome, sans perturber l'épissage nucléaire. Globalement, nos données démontrent que les variants pathogènes hétérozygotes de PTBP1 et PTBP2 affectant leur distribution nucléocytoplasmique sont associés à des défauts de développement avec ou sans déficience intellectuelle

Stepwise use of genomics and transcriptomics technologies increases diagnostic yield in Mendelian disorders

International audiencePurpose: Multi-omics offer worthwhile and increasingly accessible technologies to diagnostic laboratories seeking potential second-tier strategies to help patients with unresolved rare diseases, especially patients clinically diagnosed with a rare OMIM (Online Mendelian Inheritance in Man) disease. However, no consensus exists regarding the optimal diagnostic care pathway to adopt after negative results with standard approaches. Methods: In 15 unsolved individuals clinically diagnosed with recognizable OMIM diseases but with negative or inconclusive first-line genetic results, we explored the utility of a multi-step approach using several novel omics technologies to establish a molecular diagnosis. Inclusion criteria included a clinical autosomal recessive disease diagnosis and single heterozygous pathogenic variant in the gene of interest identified by first-line analysis (60%–9/15) or a clinical diagnosis of an X-linked recessive or autosomal dominant disease with no causative variant identified (40%–6/15). We performed a multi-step analysis involving short-read genome sequencing (srGS) and complementary approaches such as mRNA sequencing (mRNA-seq), long-read genome sequencing (lrG), or optical genome mapping (oGM) selected according to the outcome of the GS analysis. Results: SrGS alone or in combination with additional genomic and/or transcriptomic technologies allowed us to resolve 87% of individuals by identifying single nucleotide variants/indels missed by first-line targeted tests, identifying variants affecting transcription, or structural variants sometimes requiring lrGS or oGM for their characterization. Conclusion: Hypothesis-driven implementation of combined omics technologies is particularly effective in identifying molecular etiologies. In this study, we detail our experience of the implementation of genomics and transcriptomics technologies in a pilot cohort of previously investigated patients with a typical clinical diagnosis without molecular etiology

Bi-allelic loss-of-function variants in TMEM147 cause moderate to profound intellectual disability with facial dysmorphism and pseudo-Pelger-Huët anomaly

International audienceThe transmembrane protein TMEM147 has a dual function: first at the nuclear envelope, where it anchors lamin B receptor (LBR) to the inner membrane, and second at the endoplasmic reticulum (ER), where it facilitates the translation of nascent polypeptides within the ribosome-bound TMCO1 translocon complex. Through international data sharing, we identified 23 individuals from 15 unrelated families with bi-allelic TMEM147 loss-of-function variants, including splice-site, nonsense, frameshift, and missense variants. These affected children displayed congruent clinical features including coarse facies, developmental delay, intellectual disability, and behavioral problems. In silico structural analyses predicted disruptive consequences of the identified amino acid substitutions on translocon complex assembly and/or function, and in vitro analyses documented accelerated protein degradation via the autophagy-lysosomal-mediated pathway. Furthermore, TMEM147-deficient cells showed CKAP4 (CLIMP-63) and RTN4 (NOGO) upregulation with a concomitant reorientation of the ER, which was also witnessed in primary fibroblast cell culture. LBR mislocalization and nuclear segmentation was observed in primary fibroblast cells. Abnormal nuclear segmentation and chromatin compaction were also observed in approximately 20% of neutrophils, indicating the presence of a pseudo-Pelger-Huët anomaly. Finally, co-expression analysis revealed significant correlation with neurodevelopmental genes in the brain, further supporting a role of TMEM147 in neurodevelopment. Our findings provide clinical, genetic, and functional evidence that bi-allelic loss-of-function variants in TMEM147 cause syndromic intellectual disability due to ER-translocon and nuclear organization dysfunction