Tear Fluid as a Biomarker for Parkinson’s Disease: Downregulation of DNA Repair Genes/Pathways via RNA-Seq Analysis (S37.007)

Abstract

<h3>Objective:</h3> We performed an RNA-Seq analysis of tears from 16 Parkinson’s Disease (PD) patients and 16 healthy, age-matched healthy controls (HC) to identify genes and pathways that may serve as biomarkers of PD. <h3>Background:</h3> We previously demonstrated that PD tears have significantly higher levels of oligomeric a-synuclein than HC tears. Analyses of hundreds of subjects demonstrated this biomarker predicted PD diagnosis, irrespective of disease duration (AUROC=0.76). To improve this model, we performed RNA-Seq on PD and HC tears. Pilot studies of brain and tears revealed ~74% of genes expressed in aged cortex were expressed in tears. <h3>Design/Methods:</h3> Schirmer’s Tear Strips were frozen at −80°C. RNA was extracted and evaluated for quantity and integrity (RIN). RNA-Seq libraries were prepared with the NEBNext Ultra II RNA Library Prep Kit and sequenced on an Illumina NovaSeq sequencer. FASTQ files were aligned with Tophat and transcripts were counted and compared with Cufflinks. Pathway analysis was performed using the Qiagen Ingenuity Pathway Analysis (IPA) software and unsupervised, hierarchical clustering of significantly affected pathways was tested with RStudio. <h3>Results:</h3> RNA-Seq analysis showed more genes were downregulated in PD tears (N=898) vs. upregulated (N=238). IPA analysis of downregulated genes revealed DNA repair pathways were significantly affected, and reflected the downregulation of 60 genes related to DNA excision repair, recombination, and damage in PD tears. These 60 genes included <i>HNRNPC</i>, <i>TARDBP</i>, <i>USP47</i>, <i>EZH2</i>, <i>FANCC.</i> Unsupervised hierarchical clustering of these 60 genes’ transcript levels (FPKMs) separated PD and HC with 83.9% accuracy (sensitivity 93.3% and specificity 75%). <h3>Conclusions:</h3> RNA-Seq may provide a useful strategy for PD diagnosis using tears, a non-invasive biofluid. Preliminary data suggests increased diagnostic accuracy compared to our tear investigations of oligomeric a-synuclein levels alone. Downregulation of DNA repair genes/pathways suggests that alterations observed in PD brains and dopaminergic neurons are also observed in tears <b>Disclosure:</b> Dr. Lew has received personal compensation in the range of $5,000-$9,999 for serving as a Consultant for Supernus. Dr. Lew has received personal compensation in the range of $5,000-$9,999 for serving as a Consultant for kyowa. Dr. Lew has received personal compensation in the range of $5,000-$9,999 for serving as a Consultant for neurocrine. Dr. Lew has received personal compensation in the range of $500-$4,999 for serving as a Consultant for Acorda. Dr. Lew has received personal compensation in the range of $500-$4,999 for serving as a Consultant for Acadia. Dr. Lew has received personal compensation in the range of $500-$4,999 for serving as a Consultant for RegenXBio. Dr. Lew has received personal compensation in the range of $10,000-$49,999 for serving on a Speakers Bureau for Neurocrine. Dr. Lew has received personal compensation in the range of $5,000-$9,999 for serving on a Speakers Bureau for Kyowa. Dr. Lew has received personal compensation in the range of $500-$4,999 for serving on a Speakers Bureau for acorda. The institution of Dr. Lew has received research support from MJFF. Dr. Lew has received research support from NIH. Miss Omidsalar has nothing to disclose. Miss Singh Kakan has nothing to disclose. Mr. Gerke has nothing to disclose. Ms. Tanveer has nothing to disclose. Dr. Feigenbaum has nothing to disclose. Dr. Tamadonfar has nothing to disclose. Sarah Hamm-Alvarez has received personal compensation in the range of $500-$4,999 for serving as a Consultant for Oyster Point. The institution of Sarah Hamm-Alvarez has received research support from Oyster Point. Dr. Hjelm has nothing to disclose.