Evangelos Kiskinis - US grants

Amyotrophic lateral sclerosis (ALS) is a progressive and untreatable neurodegenerative disease that is characterized by the selective death of upper and lower motor neurons (MNs). The overwhelming majority of the disease is sporadic in nature. However a relatively small (<12%) but highly informative fraction of patients suffer from familial forms of disease, which have enabled the identification of causative genetic variants that underlie their condition. Such genetic studies have demonstrated that ALS can be caused by mutations in genes that encode proteins involved in diverse set of cellular functions ranging from RNA processing, vesicle transport, cytoskeletal regulation, mitochondrial function, and protein quality control pathways. Nevertheless, ALS patients are uniformly characterized by a common pattern of progressive motor neurodegeneration. This raises the possibility that different disease initiating events could coalesce in one or more common molecular pathways. How the mutation of genes with dissimilar functions converge on MN degeneration has been and continues to be an outstanding question. Although all ALS patients exhibit neuropathological protein aggregates, the overall contribution of protein homeostasis in causing ALS has remained unclear. If we could identify a convergent mechanism, it may provide an opportunity to develop a broadly applicable therapeutic intervention strategy. In our preliminary studies, we conducted global analysis of protein degradation dynamics in mutant SOD1 and isogenic controls MNs derived from iPSC lines. Interestingly, we identified a number of proteins that are degraded at a slower rate in SOD1 MNs. Unexpectedly, this small panel of candidates included proteins whose genetic mutations cause ALS. In the proposed research we will use patient-derived neurons coupled with mass spectrometry analysis to determine the protein substrates, as well as the nature of the perturbation that arise as a result of mutations in the two most prevalent ALS genes: SOD1 and C9orf72. First, we will determine which proteins have reduced protein degradation dynamics. Second, we will determine which proteins have altered synthesis rates. Third, we will determine the overall degree of proteome-wide remodeling. Each of these approaches has strategic advantages over traditional work-flows and will allow us to determine not only which proteins have altered levels in ALS MNs but also the mechanism responsible for their perturbation. Taken together, our proposed aims will shed light into the cellular mechanisms compromised by changes in the proteostasis network in patient neurons and will likely uncover broadly relevant therapeutic targets for ALS.

ABSTRACT The most common genetic cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) is a hexanucleotide (G4C2)n repeat expansion (HRE) in the first intron of the C9orf72 (C9) gene. RNA and dipeptide repeats (DPRs) that are transcribed and translated from the C9-HRE respectively, have been shown to be neurotoxic. In a series of genetic screens in the fly and yeast, several groups recently showed that both RNA repeats and DPRs impair nucleocytoplasmic transport. However, the identities of the RNA and protein substrates affected by this defect in mutant C9 motor neurons (MNs), the specific downstream effects of these changes, and their contribution towards neurotoxicity remain unknown. What also remains elusive is the broader relevance of this mechanism for sporadic ALS, although cytoplasmic accumulation of nuclear proteins such as TDP43 is a neuropathological hallmark in almost all ALS and FTD patients. In our own preliminary work we have conducted large-scale sub-cellular proteomic analysis in a C9-HRE cellular model and have identified and validated a number of mislocalized candidate proteins including PRMT1. In the present study we will use patient-derived neurons, patient CNS tissue, and in vivo Drosophila models to test the hypothesis that ALS/FTD-related neurotoxicity is caused by a disruption the nucleus/cytoplasmic (N/C) distribution of specific classes of mRNAs and proteins. In Aim 1, we will use patient-specific iPSC-derived MNs and employ molecular and precise biochemical subcellular fractionation coupled to RNA-Seq and MS-based quantitative proteomics. We will use multiple C9 and control iPSCs, as well as an isogenic control iPSC line, in which we have corrected the HRE though CRISPR/Cas9 gene editing. Identifying the mRNAs and proteins that are miss- compartmentalized in patient MNs is an essential first step towards elucidating the link between defective nucleocytoplasmic transport and neurotoxicity. In Aim 2, we will use cellular models, patient tissue and in vivo Drosophila models of C9-HRE toxicity to systematically validate these molecular perturbations and assess their contribution towards ALS/FTD-related neurodegeneration. In Aim 3, we will determine how cytoplasmic accumulation of PRMT1, an essential arginine methyltransferase, impacts MN function and survival. Taken together, our proposed aims will shed light into the cellular mechanisms that are compromised by abnormal nucleocytoplasmic mRNA/protein distribution in patients and will likely uncover therapeutic targets for C9 and potentially sporadic ALS/FTD.

Amyotrophic lateral sclerosis (ALS) is a devastating neurological disease that is characterized by a progressive inability to stimulate and control muscle movement. The clinical manifestation of the disease is mediated by the selective dysfunction and degeneration of upper and lower motor neurons that connect the central nervous system (CNS) to the musculature. The overwhelming majority of ALS is sporadic in nature, while 10-12% of patients suffer from familial forms of disease, which have enabled the identification of causative genetic variants. Such genetic studies have demonstrated that ALS can be caused by mutations in genes that encode proteins involved in diverse cellular functions ranging from RNA processing, vesicle transport, cytoskeletal homeostasis, mitochondrial function and the processing of unfolded proteins. A series of recent genetic studies have highlighted a novel gene, NIMA-related kinase 1 (NEK1), as a major genetic contributor to ALS. In particular, loss-of-function genetic variants in NEK1 confer susceptibility to ALS in as many as 3% of all cases. While NEK1 is a well-characterized kinase implicated in multiple cellular functions including the DNA damage response, its specific role and function in the CNS remains unresolved. What also remains elusive is the cellular mechanism(s) that lead to NEK1-related ALS pathophysiology, and the causal relationship of NEK1 variants to ALS. In the present study, we will use mutant NEK1 cellular models, patient iPSC-derived neurons, CRISPR/Cas9 gene-editing approaches and ALS patient CNS tissue to elucidate how NEK1 genetic variants associated with ALS, contribute towards neuronal dysfunction and degeneration. To assess both the necessity and sufficiency of NEK1 genetic variants, we will use CRISPR/Cas9 to correct mutations in patient iPSC lines, as well as to introduce mutations into a healthy genetic background. In Aim 1 we will determine whether ALS- related NEK1 variants exhibit signatures of ALS pathophysiology, infer susceptibility to DNA damage and alter cytoskeletal homeostasis. In Aim 2 we will perform a global phosphoproteomic analysis in mutant NEK1 and isogenic control motor neurons to identify protein targets that are differentially phosphorylated. We will validate our findings in postmortem patient CNS tissue, as well as brain and spinal cord from mutant NEK1 mouse models. Our studies will shed light into the cellular mechanisms that are compromised by NEK1 haploinsufficiency in patients and will likely uncover potential therapeutic targets for a significant percentage of ALS patients.

In Project 2 we will determine the functional consequences of epilepsy-associated ion channel gene variants using human neurons differentiated from patient-specific induced pluripotent stem cells (iPSCs). We will initially focus on the SCN2A and KCNQ2 genes, which encode the voltage-gated Na+ (NaV1.2) and K+ (KV7.2) channels respectively. Mutations in SCN2A and KCNQ2 are responsible for monogenic early onset epileptic encephalopathy (EE) with overlapping clinical features and diverse severity. Collectively, variants in these two genes account for ~10% of all mutations identified in genetic epilepsy. The molecular pathogenic mechanisms responsible for the clinical manifestations of KCNQ2- and SCN2A-related epilepsies remain largely unknown. More importantly, no targeted therapeutic approach capable of diminishing seizure burden and improving developmental outcomes exists for these devastating neurological disorders. In Aim 1, we will use patient- specific cortical neurons to elucidate the functional consequences of epilepsy-associated KCNQ2 and SCN2A variants. We will specifically examine cortical excitatory and inhibitory neurons derived from existing patient- specific iPSC lines with pathogenic variants and corresponding isogenic control lines. We will use a combination of transcriptional profiling (single-cell RNA-sequencing) with electrophysiological approaches (whole cell patch clamp recording and high-throughput optogenetic recordings) to determine the impact of mutations on neuronal function and excitability. In Aim 2, we will assess the intrinsic excitability of patient neurons before and after treatment with NaV channel blockers and KV7 agonists that have clinical efficacy in the patients from whom the cells were derived. Our goal will be to rank the in vitro effectiveness of drugs in restoring normal neuron excitability for each genetic variant, and then to correlate the in vitro drug responses with the clinical responses to AEDs documented for these patients. This project entails a strategic collaboration between Dr. Kiskinis, whose lab focuses on using stem cell-based approaches to establish models of neurological disease, and Q-State Biosciences, Inc., which under the scientific leadership of Dr. McManus has been developing optogenetic technologies to enable high-throughput electrical recordings of human neurons and drug screening platforms for epilepsy syndromes. This project will work closely with the other Center teams, including Core A (Variant Prioritization and Curation Core), Project 1 (High-Throughput Functional Evaluation of Ion Channel Variants) and Project 3 (Development and Investigation of Murine Models of Channelopathy-associated Epilepsy). Core A is building tools to prioritize variants for experimental evaluation by the three Center projects. Correlation of findings from Project 2 with those of Projects 1 and 3 will help determine the reliability and accuracy of iPSC technology to predict in vivo physiology and pharmacology. Our findings will impact the field by demonstrating mechanistic effects of channelopathy-associated epilepsy variants, and by providing a systematic evaluation of human neuron platforms for precise drug selection.