Research Wouter De Coster

Abstract

Neurodegenerative diseases are a growing burden to patients, our society, and the healthcare system, yet therapeutic breakthroughs remain limited despite intense research. We investigate the genetic factors of frontotemporal dementia to identify critical factors involved early in the disease's process, as half of the patients are without a genetic diagnosis and without targets for (precision) therapy. Here I propose to tackle this issue from two angles, focusing on 1) tandem repeat length variation and expansions and 2) somatic variants in the brain. There is evidence of the involvement of both types of variants, but systematic assessments are necessary to determine their contribution to FTD. A crucial part of this project concerns the development of software for genome-wide characterization of tandem repeat variation and a database for population-scale repeat lengths. This research has only recently become possible, as novel sequencing technologies are now well-established for population-scale projects. I will investigate both causal and risk-associated roles for tandem repeat expansions using short and long-read sequencing cohorts. In addition, I will follow up on somatic single-nucleotide variants using long-read single-nuclei transcriptomics and identify somatic structural variants using deep genome sequencing from sorted neurons. Finally, target capture of cell-free DNA in plasma and CSF will be explored as a biomarker for the early detection of neurodegeneration.

Researcher(s)

• Promoter: Rademakers Rosa
• Fellow: De Coster Wouter

Research team(s)

• VIB CMN - Applied and Translational Neurogenomics

Project type(s)

• Research Project

Abstract

Frontotemporal lobar degeneration with TDP-43 inclusions (FTLD-TDP) is a heterogeneous neurodegenerative disorder. Patients present with severe disturbances in personality, behavior or language and die within a few years. Identification of two major FTLD-TDP genes (progranulin (GRN) and C9orf72) provided important insight into possible disease mechanisms and led to recently started clinical trials in genetic FTLD-TDP subtypes. However, for patients without known mutations, mechanisms of disease remain poorly understood with no hope for treatment. We hypothesize that a subgroup of FTLD-TDP patients without known mutations (FTLD-TDP type A) share common disease mechanisms with GRN mutation carriers and could benefit from the treatments that are in development. Here, we will use long-read whole-genome DNA sequencing, able to capture genomic and epigenomic alterations, to identify hitherto undiscovered disease-associated mutations in FTLD-TDP type A patients (WP1). Long-read cDNA sequencing and single-nuclei transcriptomics will be performed to correlate expression changes with possible disease-contributing variants and to provide additional insight into FTLD-TDP type A disease pathways (WP2). Finally, we will assess the value of translation products from differentially expressed genes or FTLD-TDP type A specific transcripts as fluid biomarkers (WP3). These studies will improve the biological understanding, diagnosis and potential for future treatment of FTLD-TDP type A patients.

Researcher(s)

• Promoter: Rademakers Rosa
• Co-promoter: De Coster Wouter

Research team(s)

• VIB CMN - Applied and Translational Neurogenomics

Project type(s)

• Research Project

Abstract

Frontotemporal lobar degeneration (FTLD) is an umbrella term that groups several different neurodegenerative diseases characterized by the predominant destruction of the frontal and temporal lobes of the brain. In this proposal we focus our efforts on a relatively rare subgroup of FTLD patients which have an unusual clinical phenotype and a uniform pathology characterized by FTLD with neuronal inclusions composed of the fused in sarcoma (FUS) protein (FTLD-FUS). More than a decade after its initial description no progress has been made towards understanding the etiology of this subgroup of patients, thus severely hampering translational research efforts. To fill this void, we established the international consortium on FTLD-FUS. Through the systematic collection of brain tissue samples and associated clinicopathological data from the majority of reported FTLD-FUS patients we will for the first time be in a position to decipher its molecular underpinnings. Based on its unique clinical and pathological features, we hypothesize that FTLD-FUS is caused by genomic or epigenomic mutations in one or a limited number of disease genes. The overall objective of this proposal is to identify these genetic and/or epigenetic factors through the study of our unique, highly characterized, cohort of FTLD-FUS patient samples and state-of the art methodologies able to capture a broad range of possible genomic and epigenomic alterations. This will include NanoNOMeseq to identify phased methylation and chromatin accessibility as well as genetic changes such as structural variations from a single assay. Deep transcriptomic profiling at the single cell level and bulk analyses of full-length transcripts using long-read sequencing technologies in brain tissues of FTLD-FUS patients and controls will further be generated to correlate expression changes with possible disease-contributing variants and to provide much needed insights into the FTLD-FUS associated disease pathways. The identification of disease causing or disease modifying factors for FTLD-FUS will be crucial for elucidating the pathogenetic mechanisms underlying this subgroup of FTLD patients and ultimately for the development of curative therapies.

Researcher(s)

• Promoter: Rademakers Rosa
• Co-promoter: De Coster Wouter
• Fellow: Alidadiani Sara

Research team(s)

• VIB CMN - Applied and Translational Neurogenomics

Project type(s)

• Research Project

Abstract

Heterozygous pathogenic variants in KCNQ2 with either a Dominant-negative (DN) or more rarely Gain of Function effect, are the most common cause of neonatal developmental and epileptic encephalopathy, named KCNQ2-Encephalopthy (KCNQ2-E). KCNQ2-E is characterized by difficult to treat neonatal seizures and severe developmental delay. The KCNQ2 encoded Kv7.2 subunit is part of a potassium channel that plays a key role in regulating the resting membrane potential of neurons, to control neuronal excitability. Although a role for Kv7.2 in neurodevelopment is increasingly accepted in the field, there are still many knowledge gaps to be addressed. Very recently, we highlighted eevidence for KCNQ2 expression in Human Induced Pluripotent Stem Cells (hiPSCs) and neural progenitor cells (NPCs), suggesting a role for Kv7.2 in earlier stages of neurodevelopment than anticipated. Based on publicly available short-read RNA sequencing datasets from iPSC-derived neuronal cultures, we furthermore hypothesize that different KCNQ2 transcripts are expressed during the course of neuronal development, which regulate Kv7.2 channel current densities. Although these available RNA sequencing datasets are of high value, it is very challenging to identify the exact transcripts that are expressed, due to the complex nature of the transcriptome, consisting of variable lengths and alternatively spliced transcripts for most genes, including KCNQ2. To overcome these limitations, in this project we will perform long-read RNA sequencing of hiPSC-derived neuronal cultures during development, using in-house Oxford Nanopore technology. By generating the full-length transcriptome profile of hiPSCs, including two control lines and two lines with recurrent DN KCNQ2-E variants, we will be able to unravel the differential expression pattern of KCNQ2 transcripts during the course of neurodevelopment, as well as the effect of DN KCNQ2-E variants on gene and transcript expression levels. Based on this information, we will identify key pathways involved in the neurodevelopmental aspect of KCNQ2-E, opening possibilities for future projects. Finally, by profiling the full transcriptome rather than targeted RNA sequencing, the generated full-length transcriptome dataset will be of use to study expression and splicing profiles of many other genes of interest by multiple groups within the department and broader scientific community.

Researcher(s)

• Promoter: De Coster Wouter

Research team(s)

• VIB CMN - Applied and Translational Neurogenomics

Project type(s)

• Research Project

Abstract

Structural variation accounts for the majority of the nucleotide diversity between humans, yet is systematically underrepresented using current technologies. We can identify about 25000 structural variants per genome with long-read nanopore sequencing, which we will perform in a discovery cohort of 200 control individuals and patients with frontotemporal dementia or Alzheimer's disease. I will optimize structural variant calling and the detection of expanded repeats and single nucleotide variants in highly repetitive sequences. By careful selection of this discovery cohort, we will be able to identify rare and more frequent structural variants explaining association signals from existing cohort studies or underlying disease in small families. In the next phase, the identified variants from longread sequencing will be genotyped in existing data from short-read genome sequencing of 20000 individuals with neurodegenerative brain diseases and healthy controls using recently developed graph genome methods. With association tests on the identified structural variants, I will be able to identify variants with a role in neurodegenerative diseases. Finally, as nanopore sequencing also identifies modified nucleotides I will quantify methylcytosine, per parental haplotypes. I will integrate this with existing data from RNA and protein expression studies and the identified variants, enabling a better functional understanding and identification of cis-regulatory variants.

Researcher(s)

• Promoter: Rademakers Rosa
• Fellow: De Coster Wouter

Research team(s)

• VIB CMN - Applied and Translational Neurogenomics

Project type(s)

• Research Project

Abstract

This project represents a research agreement between the UA and on the onther hand IWT. UA provides IWT research results mentioned in the title of the project under the conditions as stipulated in this contract.

Researcher(s)

• Promoter: Van Broeckhoven Christine
• Co-promoter: Theuns Jessie
• Fellow: De Coster Wouter

Research team(s)

Project type(s)

• Research Project