title: Small RNA sequencing revealed dysregulated piRNAs in Alzheimer's disease and their probable role in pathogenesis.
abstract: PIWI-interacting RNAs (piRNAs), ∼23-36 nucleotide-long small non-coding RNAs, earlier believed to be germline-specific, have now been identified in somatic cells including neural cells. However, piRNAs have not yet been studied in the human brain (HB) and Alzheimer's disease (AD)-affected brain. In this study, by next-generation small RNA sequencing, 564 and 451 piRNAs were identified in the HB and AD-affected brain respectively. The majority of the neuronal piRNAs have intronic origin wherein primary piRNAs are mostly from the negative strand. piRNAs originating from the coding sequence of mRNAs and tRNAs are highly conserved compared to other genomic contexts. We found 1923 mRNAs significantly down-regulated in AD as the predicted targets of 125 up-regulated piRNAs. The filtering of targets based on our criteria coupled with pathway enrichment analysis of all the predicted targets resulted in five most significant AD-associated pathways enriched with four genes (CYCS, LIN7C, KPNA6, and RAB11A) found to be regulated by four piRNAs. The qRT-PCR study verified the reciprocal expression of piRNAs and their targets. This study provides the first evidence of piRNAs in the HB and AD which will provide the foundation for future studies to unravel the regulatory role of piRNAs in the human brain and associated diseases. The sequencing data have been submitted to the GEO database (Accession no. GSE85075).
authors.affiliation: RNAi and Functional Genomics Laboratory, Department of Life Science, National Institute of Technology Rourkela, Odisha, 769008, India. vivek.iitian@gmail.com mallickb@nitrkl.ac.in.
authors.forename: Jyoti
authors.initials: J
authors.lastname: Roy
authors.affiliation: Bioinformatics Centre, Bose Institute, Kolkata 700054, India.
authors.forename: Arijita
authors.initials: A
authors.lastname: Sarkar
authors.affiliation: Bioinformatics Centre, Bose Institute, Kolkata 700054, India.
authors.forename: Sibun
authors.initials: S
authors.lastname: Parida
authors.affiliation: Bioinformatics Centre, Bose Institute, Kolkata 700054, India.
authors.forename: Zhumur
authors.initials: Z
authors.lastname: Ghosh
authors.affiliation: RNAi and Functional Genomics Laboratory, Department of Life Science, National Institute of Technology Rourkela, Odisha, 769008, India. vivek.iitian@gmail.com mallickb@nitrkl.ac.in.
authors.forename: Bibekanand
authors.identifier: http://orcid.org/0000-0003-4311-0720
authors.initials: B
authors.lastname: Mallick
mesh_terms: D000544:Alzheimer Disease / Q000235:genetics*; D016022:Case-Control Studies; D005091:Exons; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007438:Introns; D034622:RNA Interference; D012333:RNA, Messenger / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics*; D012343:RNA, Transfer / Q000235:genetics; D059467:Transcriptome
chemical_list: D012333:RNA, Messenger; D034741:RNA, Small Interfering; D012343:RNA, Transfer