ABSTRACT: Purpose: Feeding larvae of fly models of polyQ and other neurodegenerative disorders on AR or RS supplemented food substantially suppressed neurodegeneration. With a view to gain further insight into the suppression of polyQ pathology by AR or RS, we expressed the UAS-127Q transgene using the predominantly eye-specific GMR-GAL4 driver and examined the transcriptomic changes in wild type and 127Q-expressing eye discs following feeding on AR or RS. In order to find out reason underlying the suppression of neurodegeneration by feeding of AR and RS, we checked difference in gene expression between eye discs expressing GMR-GAL4>UAS-127Q and wild type. Method: Eye disc RNA profiles of wandering late third instar larvae of GMR-GAL4>UAS-127Q and wild type larvae, reared on normal food or food supplemented with AR or RS since after hatching, were generated by sequencing, in triplicate, using Illumina Hiseq2500 platform using 51bp pair-end reads, 12 samples per lane and each sample run across 2 lanes of flowcell (Flowcell ID: C7K52ACXX).This resulted in a sequencing depth of 19-25 million reads. The resulting sequencing fastq files were mapped to the Drosophila genome (dm6) using Tophat with Bowtie. The aligned SAM/BAM file for each was processed for guided transcript assembly using Cufflink 2.1.1 and gene counts were determined. Mapped reads were assembled using Cufflinks. Transcripts from all samples were subjected to merge with Cuffmerge to get final transcriptome assembly across samples. In order to ascertain differential expression of transcripts between different samples, Cuffdiff 2.1.1 was used (Trapnell et al., 2012). Result: Using an optimized data analysis workflow, we mapped about 19-25 million sequence reads per sample to the Drosophila melanogaster genome (dm6) and identified 15,904 transcripts with cufflink workflow in each genotypes studied. The GMR-GAL4 driven UAS-127Q expression in eye discs reared on AR supplemented food resulted in 259 differential expression, with 147 genes being down-regulated and 112 up-regulated, when compared with those reared on normal food, however, when larvae from same genotype reared on RS supplemented food resulted in 1641 DEGs, with 846 genes being down-regulated and 795 up-regulated compared with larvae reared on normal food. In eye disc of wild type larvae reared on AR supplemented food resulted in 680 DEGs, with 470 genes being down-regulated and 205 up-regulated compared with those reared on normal food. Larvae from wild type reared on RS supplemented food resulted in 427 DEGs, with 264 genes being down-regulated and 163 up-regulated compared with those reared on normal food. Compared to only GMR-GAL4>UAS-127Q and wild type larval eye discs reared on normal food, total of 1691, with 799 gene were up-regulated while 892 were down-regulated. Conclusion: The present results not only re-inforce earlier findings from our lab that the Ayurvedic Amalaki Rasayana and Rasa-Sindoor are potent suppressors of neurodegeneration but also provide direct evidence that these general health-promoting formulations significantly alter expression of many genes in protein-aggregation-clearance pathways and thus eliminate the cause of proteinopathy so that cell death is inhibited while other normal cellular activities continue. These formulations, which have been used in Ayurvedic practice for thousands of years as health-promoting as well as curative supplements, do not have any side-effects. Therefore, we believe that these Ayurvedic formulations have a good potential to ameliorate the sufferings of polyQ and other neurodegenerative disorders.
