C9orf72-mediated features transcriptomic signatures and translational studies for frontotemporal dementia and related disorders

PROJECT SUMMARY/ABSTRACT We seek to perform in-depth characterization studies to unravel the clinico-pathological variability associated with frontotemporal dementia (FTD) and related neurodegenerative diseases caused by an expanded repeat in the C9orf72-SMCR8 complex subunit (C9orf72). To this end, we will examine a range of neuroanatomical regions (e.g., frontal cortex, temporal cortex, motor cortex, spinal cord, and cerebellum) and span the full spectrum from frontotemporal lobar degeneration (FTLD) – a neuropathological diagnosis of FTD – to amyotrophic lateral sclerosis (ALS). For each region, we will assess features of C9orf72-linked diseases, such as levels of C9orf72 transcripts, RNA foci, and dipeptide repeat proteins (Aim 1). Moreover, we will use an innovative targeted long-read sequencing technology to measure the size, purity, and methylation status of the expanded repeat. Additionally, we will perform whole-tissue RNA sequencing to detect overall changes in a complex context, basically taking a snapshot (Aim 2). This data will be accompanied by single-nuclei transcriptomic data to acquire gene expression levels while deciphering the cellular diversity encountered in the central nervous system. Since splicing defects have been reported in C9orf72-related diseases, we will combine short- and long-read sequencing strategies. The inclusion of long-read sequencing data creates the opportunity to obtain the full-length transcriptome with highly accurate splice junctions, even for large transcripts. These combined approaches, therefore, will enable us to capture the entire landscape of transcriptomic changes. Top hits identified through our in-depth transcriptomic studies will be further investigated in our extensive collection of clinical and pathological specimens and tested as potential biomarkers. Taken together, our detailed examinations will uncover crucial region- and disease-specific similarities and/or differences, thus laying the foundation for improved understanding of the heterogeneity associated with the FTLD-ALS spectrum and the identification of disease modifiers, translatable biomarkers, and therapeutic targets.