ABSTRACT: Purpose: In order to describe how non- genetic factors may contribute to emergence of additional neurodegenerative disorders in mice with neuronal Gaucher Disease (nGD), full transcript mRNA sequencing was implemented with half brain in order to study differential gene expression between experimental groups: (Untreated) Control, CBE (Conduritol β epoxide ), SVNI (Sindbis virus), and CBE + SVNI Methods: Full transcript mRNA sequencing was implemented with half brain in order to study differential gene expression between experimental groups (biologilal triplicates in each group). We mapped 20 million sequence reads per sample to the mouse genome (GRCm38) and identified 16,903 transcripts. . All subjects were 28 days old. Half of the bisected brains were flash-frozen in liquid nitrogen and stored in -80C conditions until use. RNA was isolated using a RNeasy mini kit (Qiagen, Hilden, Germany). Extraction of RNA was performed at the Israeli Institute for Biological Research and the RNA was then transferred to the Weizmann Institute of Science for further analysis. Quality was examined with the Agilent 2200 TapeStation system (Agilent Technologies); RIN values of each sample were determined satisfactory for use in sequencing. Expression of mRNA was quantified using DESeq following normalization of library size with Pipeline. Gene lists were created by criteria based on an absolute linear fold change ≥ 2.0, *p ≤ 0.05. Enriched pathways in the resulting gene lists were analyzed with Ingenuity Pathway Analysis (IPA). Results: Our study represents the first full RNA transcriptome analysis of brains from of CBE-treated mice, with biological triplicates generated by RNA-seq technology. The CBE and CBE+SVNI conditions boast remarkably similar genetic profiles with no differentially expressed genes changed between them (fold change ≥ 2.0, *p ≤ 0.05). In CBE, SVNI, and CBE + SVNI conditions respectively, 501, 1724, and 554 genes were significantly upregulated compared to the control, while 5, 333, and 40 genes were significantly downregulated respectively (Fig. 2B). Surprisingly, 476 upregulated genes in the CBE condition were shared with SVNI, while only 25 genes were uniquely upregulated. No downregulated genes were shared between the two conditions (Fig. 2C). Here, we conclude that CBE and CBE+SVNI demonstrate nearly identical mRNA profiles while SVNI boasted highly differential genes compared to all other conditions. Conclusion: Half brain mRNA profiles of 28-day old untreated (Control), CBE-treated, SVNI-treated, and SVNI + CBE-treated mice were generated by deep sequencing, in triplicate, using Illumina Hiseq.
