title: Long non-coding RNA and alternative splicing modulations in Parkinson's leukocytes identified by RNA sequencing.
abstract: The continuously prolonged human lifespan is accompanied by increase in neurodegenerative diseases incidence, calling for the development of inexpensive blood-based diagnostics. Analyzing blood cell transcripts by RNA-Seq is a robust means to identify novel biomarkers that rapidly becomes a commonplace. However, there is lack of tools to discover novel exons, junctions and splicing events and to precisely and sensitively assess differential splicing through RNA-Seq data analysis and across RNA-Seq platforms. Here, we present a new and comprehensive computational workflow for whole-transcriptome RNA-Seq analysis, using an updated version of the software AltAnalyze, to identify both known and novel high-confidence alternative splicing events, and to integrate them with both protein-domains and microRNA binding annotations. We applied the novel workflow on RNA-Seq data from Parkinson's disease (PD) patients' leukocytes pre- and post- Deep Brain Stimulation (DBS) treatment and compared to healthy controls. Disease-mediated changes included decreased usage of alternative promoters and N-termini, 5'-end variations and mutually-exclusive exons. The PD regulated FUS and HNRNP A/B included prion-like domains regulated regions. We also present here a workflow to identify and analyze long non-coding RNAs (lncRNAs) via RNA-Seq data. We identified reduced lncRNA expression and selective PD-induced changes in 13 of over 6,000 detected leukocyte lncRNAs, four of which were inversely altered post-DBS. These included the U1 spliceosomal lncRNA and RP11-462G22.1, each entailing sequence complementarity to numerous microRNAs. Analysis of RNA-Seq from PD and unaffected controls brains revealed over 7,000 brain-expressed lncRNAs, of which 3,495 were co-expressed in the leukocytes including U1, which showed both leukocyte and brain increases. Furthermore, qRT-PCR validations confirmed these co-increases in PD leukocytes and two brain regions, the amygdala and substantia-nigra, compared to controls. This novel workflow allows deep multi-level inspection of RNA-Seq datasets and provides a comprehensive new resource for understanding disease transcriptome modifications in PD and other neurodegenerative diseases.
authors.affiliation: Department of Medical Neurobiology, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem, Israel.
authors.forename: Lilach
authors.initials: L
authors.lastname: Soreq
authors.affiliation: Department of Biological Chemistry, The Life Sciences Institute, The Hebrew University of Jerusalem, Jerusalem, Israel; Genomnia srl, Lainate, Milan, Italy.
authors.forename: Alessandro
authors.initials: A
authors.lastname: Guffanti
authors.affiliation: Department of Pediatrics, Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America.
authors.forename: Nathan
authors.initials: N
authors.lastname: Salomonis
authors.affiliation: Genomnia srl, Lainate, Milan, Italy.
authors.forename: Alon
authors.initials: A
authors.lastname: Simchovitz
authors.affiliation: The Center for Functional and Restorative Neurosurgery, Department of Neurosurgery, Hadassah University Hospital, Jerusalem, Israel.
authors.forename: Zvi
authors.initials: Z
authors.lastname: Israel
authors.affiliation: Department of Medical Neurobiology, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem, Israel; The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, Israel.
authors.forename: Hagai
authors.initials: H
authors.lastname: Bergman
authors.affiliation: Department of Biological Chemistry, The Life Sciences Institute, The Hebrew University of Jerusalem, Jerusalem, Israel; The Edmond and Lily Safra Center for Brain Sciences (ELSC), The Hebrew University of Jerusalem, Jerusalem, Israel.
authors.forename: Hermona
authors.initials: H
authors.lastname: Soreq
mesh_terms: D017398:Alternative Splicing; D000679:Amygdala / Q000378:metabolism; D001931:Brain Mapping / Q000379:methods; D046690:Deep Brain Stimulation; D005260:Female; D020869:Gene Expression Profiling; D006801:Humans; D007962:Leukocytes / Q000378:metabolism*; D008297:Male; D035683:MicroRNAs; D020411:Oligonucleotide Array Sequence Analysis; D010300:Parkinson Disease / Q000097:blood*; D062085:RNA, Long Noncoding; D017423:Sequence Analysis, RNA / Q000379:methods*; D013378:Substantia Nigra / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D062085:RNA, Long Noncoding