Multiplexed Quantification of the Protein Poly-ADP-Ribosylation Landscape in C9ORF72-ALS/FTD

Project Summary PARP1 is a nuclear protein that is critically involved in cell stress responses. Its main enzymatic function is to catalyze a protein posttranslational modification (PTM) known as Poly-ADP-ribosylation (PARylation). In response to genotoxic stress, PARP1 binds to nicked DNA and is rapidly activated, resulting in the synthesis of a large number of PARylated proteins and initiation of the DNA damage repair (DDR) mechanisms. Recent evidence suggests that PARylation serves as a death signal in neurons. Importantly, genetic deletion or pharmacological inhibition of PARP1 offers profound protection against brain dysfunction in the animal models of many dementias, including Alzheimer’s disease, Parkinson’s disease, amyotrophic lateral sclerosis/ALS and frontotemporal dementia/FTD. C9orf72 repeat expansion is the most common genetic cause of both amyotrophic lateral sclerosis and frontotemporal dementia. PARP1 is a common disease modifier of C9orf72-ALS/FTD, the inhibition of which (by pharmacological and genetic approaches) ameliorates neurodegeneration in various models of C9orf72-ALS/FTD. Furthermore, recent studies have shown that increased PARylation is a common pathological feature of ALS/FTD regardless of the underlying genetic causes. Despite these findings, the PARylation landscape in C9orf72-ALS/FTD is poorly defined, and the underlying mechanism by which deregulated PARylation contributes to C9orf72-ALS/FTD is elusive. To address this, we will leverage our published work and the extensive experience of my lab. PARylation is a notorious PTM for mass spectrometrists, because of its labile and heterogenous nature. We recently were able to overcome these challenges, and develop a large-scale mass spectrometric approach towards comprehensive characterization of the Asp- and Glu-PARylated proteome. Furthermore, we have elucidated the site-specific function of the PARylation events on many important signaling proteins. Based on these results, we will develop a “bar-coding” system for the multiplexed PARylation proteomic analyses. Using this approach, we will define, in a global, quantitative and site-specific manner, the PARylation landscape in C9orf72-ALS/FTD (Aim 1). Then we will generate the global protein expression profiles of C9orf72-ALS/FTD induced pluripotent stem-cell-derived neurons (iPSNs), and identify the cell-specific PARylation events that are driven by cell-specific expression patterns vs. cell-specific regulatory mechanisms (Aim 2). Finally, we will deploy bioinformatic tools to identify the potentially functionally important PARylated proteins. These high priority hits will be subject to biochemical and cell biology assays to understand their roles in C9orf72-ALS/FTD. We will also design and generate a web portal for the dissemination of the quantitative proteomic results (Aim 3). The information garnered from these studies will provide a fundamental understanding of the role of PARylation in C9orf72-ALS/FTD, paving the way for targeting this pathway for the treatment of C9orf72-ALS/FTD, and more broadly, the other related dementias.