Projects

Please find further information on our subprojects here.

Subproject 1: Coordination unit of the consortium

In order to ensure the achievement of the overall goals of CHROMATIN-Net and given the large number of centres involved, a dedicated management structure is required. The man-agement coordinates the complementary and cooperative aspects of the work program and controls the achievement of milestones. A central database for the storage of harmonized patients’ phenotype data will be established and maintained which also allows progress mon-itoring based on data submission. Regular project leader meetings ensure discussion of sci-entific progress of the network and support joint data analysis. Regular clinical meetings will allow to establish genotype-phenotype correlation and to define diagnostic criteria. Additional regular conference calls allow further fine tuning. Public relations issues will be addressed by creating and maintaining a webpage in German and English language. In addition, a newsletter aiming especially at affected families and patient support groups will be produced.

Project leader: Prof. Dr. med. André Reis, Universität Erlangen-Nürnberg

Subproject 2: Dissecting the molecular mechanisms of cognitive disorders with mutations in the SWI/SNF complex

Patients with mutations in subunits of the SWI/SNF-complex exhibit a broad and overlapping spectrum of clinical manifestations. We want to investigate if mutations in the SWI/SNF com-plex are associated with changes at the DNA, chromatin and transcription levels giving in-sights into the molecular basis for clinical variability and allow discovery of interventional tar-gets. We will objectively evaluate phenotypes for harmonized genotype-phenotype correlation within the entire project. Transcriptional profiling of patients’ cells including induced pluripotent cells will yield insights into pathways affected. Changes will be characterised in detail and linked to genomic and epigenetic changes determined in other subprojects on materials from the same patients. These will be related to the phenotypic expression. Patients with overlapping phenotypic presentation but without known mutation(s) in the complex shall be investigated for mutations in other genes encoding proteins involved in chromatin dynamics. We expect new insights into genotypes, phenotypes and molecular alterations of SWI/SNF related disorders, which will improve genetic counselling and establish a basis for therapeutic approaches.

Project leader: Prof. Dr. med. André Reis, Universität Erlangen-Nürnberg

Subproject 3: Intellectual disability (ID) and syndromic entities associated with mutations in the SWI/SNF complex

Coffin-Siris and Nicolaides-Baraitser syndromes and unspecific intellectual disability are caused by mutations in genes encoding components of the SWI/SNF complex. The number of patients is limited and therefore genotype-phenotype correlation is preliminary. Subproject 3 intends to recruit additional patients, to harmonize phenotyping, to develop a scoring system to objectively categorize patients and phenotype severity, and to apply computerbased analysis of facial traits. Targeted resequencing will be performed to identify mutations in genes known to be associated with these phenotypes and to test the hypothesis if the extreme phenotypic variation of ARID1B mutation carriers is caused by diverging somatic mosaicism in different tissues. SNP genotyping and haplotyping will be performed in patients with ARID1B mutations to evaluate parent-of-origin effects on the phenotype. To identify new genes involved in these phenotypes whole genome sequencing will be performed and functional studies done depending on the newly identified genes and their products. These data will improve clinical and molecular knowledge of SWI/SNF associated and newly defined disorders, will lead to better genetic and clinical counselling and will establish the basis for therapeutic approaches.

Project leader: Prof. Dr. med. Dagmar Wieczorek, Heinrich-Heine-Universität Düsseldorf

Subproject 4: The nucleosome landscape of Coffin-Siris and Nicolaides-Baraitser syndrome patients with mutations in the SWI/SNF complex

Mutations in components of the switch/sucrose nonfermenting (SWI/SNF) chromatin-remodeling complex have been identified in patients with rare intellectual disability disorders, such as Coffin-Siris Syndrome (CSS) and Nicolaides-Baraitser Syndrome (NBRS). The phe-notypic overlay of these syndromes has been attributed to their common molecular etiology, but the molecular consequences of mutations in this chromatin-remodeling complex have yet to be investigated. In this subproject, we set out to characterize the impact of mutations in SWI/SNF-complex members on the epigenetic architecture in a disease-relevant tissue utiliz-ing NOMe-Seq (nucleosome occupancy and methylome sequencing), determine their influ-ence on gene expression and increase the understanding of the molecular etiology and pathophysiological mechanisms of the CSS/NBRS syndromes.

Project leader: Dr. med. Nuria Brämswig, Prof. Dr. Bernhard Horsthemke, Universität Duisburg-Essen

Subproject 5: Functional and phenotypical interaction of cohesin with SWI/SNF-associated disease

Cornelia de Lange Syndrome (CdLS) is a clinically and genetically heterogeneous congenital anomaly syndrome. Interestingly, all five CdLS genes identified encode components of the chromatin-associated cohesin complex. While typical CdLS is caused by mutations in NIPBL, patients with mutations in the other four genes SMC1A, SMC3, HDAC8 and RAD21, usually show milder phenotype or less typical facial features. The latter patients often show clinical features overlapping with patients mutated in other chromatin-associated proteins such as the SWI/SNF complex. In the focus of this subproject are molecular investigations to illuminate the functional interaction of cohesin with other chromatin-associated complexes. Proteomic approaches will be used to investigate a direct interaction on protein level and functional analysis in patient cells will be conducted to examine the relevance on physiological level. In a parallel approach selected candidate genes will be analysed by high-throughput sequencing in large cohorts of patients with CdLS-overlapping phenotypes. By this, we will identify novel genetic causes of chromatin-related phenotypes and get new insights into the physiological defects caused by these mutations. The results obtained will help to correlate genotype-phenotype relationships and serve as a basis to improve the diagnosis and prognosis of the patients and future therapies.

Project leader: Prof. Dr. rer. nat. Frank J. Kaiser, Prof. Dr. med. Gabriele Gillessen-Kaesbach, Universität zu Lübeck

Subproject 6: Whole Genome Sequencing and Analysis

As the community moves from exome to genome sequencing, there is a massive opportunity to improve our understanding of the morbid human genome by identifying a larger range of variation than ever before possible, including clinically relevant variants in non-coding sequences. We propose to establish a common genome sequencing and analysis platform for the subprojects which is embedded into similar efforts in other projects. An already established sequencing core laboratory provides the prerequisite for a competitive sequencing program accompanying disease gene identification projects for Mendelian disorders. Optimized data security, professional handling of consent issues and the provision of an ad-vanced analytical pipeline are further assets of this proposal. The platform will also improve the concerted collection of genetic and phenotypic metadata and their submission to international databases.

Project leader: PD Dr. med. Tim M Strom, Helmholtz Zentrum München

Subproject 7: Establishing human disease specific cortical neurons

This subproject will perform in vitro disease modeling using human cortical neurons from patient-derived hiPSCs or transdifferentiation from human primary cultures. The goal is to provide the other projects with material for neural lineage specific analysis of pathways which are involved in chromatin remodeling in intellectual disability. Patients will be asked for either plucked hair or the use of fibroblasts (e.g. generated for diagnostic reasons). We will generate primary cultures from these tissues, perform genetic and viral quality controls and store this biomaterial. The primary cultures will be reprogrammed to hiPSC using a retroviral approach and the pluripotency and genetic stability of the hiPSC will be validated. HiPSCs will be differentiated into NPC and neuronal cultures according to published protocols. In addition we will establish the generation of neuronal cultures via transdifferentiation. Frozen neural progenitor cells (NPCs), life cultures or NPCs or neurons, or DNA, RNA or protein derived from these cells will be transferred to the other subprojects.

Project leader: Prof. Dr. med. Beate Winner, Friedrich-Alexander-Universität Erlangen-Nürnberg