Elucidating FTLD-FUS through international collaboration and long-read sequencing approaches. 01/10/2021 - 30/09/2025

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.

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  • Research Project

Comprehensive characterization of structural variation andnucleotide modifications in neurodegeneration through longread sequencing and data integration. 01/10/2020 - 30/09/2023

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.

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  • Research Project

Full-length transcriptome profiling of KCNQ2-Encephalopthy during development using iPSC-derived neurons. 01/04/2021 - 31/03/2022

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.

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  • Research Project

Deciphering the molecular landscape of Early Onset Parkinson Disease using an integrated approach of exome and transcriptome sequencing. 01/01/2015 - 31/12/2018

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.

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Project type(s)

  • Research Project