Investigating differential expression in PTSD patients versus controls: An RNA-Seq study
Date
2017-12
Authors
Journal Title
Journal ISSN
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Publisher
Stellenbosch : Stellenbosch University
Abstract
ENGLISH ABSTRACT: Post-traumatic stress disorder (PTSD) is a debilitating neuropsychiatric disorder underpinned by complex, multi-factorial interactions including genetic and environmental factors. To date, most genetic studies have focused on specific candidate genes involved in PTSD and therefore lack a holistic view of the disorder. In this study, we aimed to utilise RNA-Seq to investigate molecular mechanisms and possible blood bio-signatures in South African PTSD patients.
Whole blood gene expression levels of South African mixed ancestry ethnicity (Coloured) individuals were compared between PTSD diagnosed (N = 19) and trauma-exposed control (N = 29) individuals. RNA from whole blood from each participant was subjected to RNA-Seq using the Illumina HiSeq 4000 platform at a sequencing depth of 50 million paired-end reads. Differentially expressed genes (p-value < 0.05) were further prioritized based on their involvement in disease phenotype, function, pathways and known gene/protein interactions using the semantic model of disease in BioOntological Relationship Graph (BORG) database. Furthermore, co-expression analysis of the prioritized candidate genes were carried out to investigate co-regulated differentially expressed gene sets between each groups.
A total of 556 differentially expressed genes were identified, of which 196 (21 up- and 175 downregulated) genes were identified as being possibly biologically relevant. Co-expression analysis revealed a network of four highly co-expressed, upregulated genes and a large co-expression network consisting of 36 downregulated genes. The four co-expressed upregulated genes (RPL6, RPS6, RPS3A and EEF1B2) and six highly connected co-expressed downregulated genes (DHX9, BCLAF1, THRAP3, EIF4G1, HSPA4 and MCL1) were identified as potentially relevant gene candidates contributing to the pathology of PTSD.
In conclusion, we were able to identify putative blood transcriptomic response in PTSD patients’ vs trauma-exposed controls. Additionally, a set of differentially expressed genes, possibly associated with molecular functions/mechanisms of PTSD were determined. These preliminary findings provide novel insight in underlying genetic expression of PTSD in South African population. Future transcriptomic studies using larger sample size will be instrumental in validating our findings, and should include miRNA profiling to identify a more robust signature of potential blood based biomarkers.
AFRIKAANSE OPSOMMING: Post-traumatiese stresversteuring (PTSV) is 'n neuropsigiatriese siekte wat bestaan uit komplekse, multi-faktoriaal interaksies. To top hede het meeste genetiese studies slegs gefokus op spesifieke kandidaat gene betrokke by PTSV. Hierdie kandidaat studies het dus nie 'n holistiese siening wat kan verkry word deur 'n hele-transkriptoom RNS-Sequencing (RNS-Seq) benadering nie. In hierdie voorlopige studie beoog ons om RNS-Seq aan te wend om molekulêre meganismes en moontlike bloed biomerkers in Suid-Afrikaanse PTSV patiente te ondersoek. In hierdie kontrole studie vergelyk vroulike, kleurling (gemengde afkoms) individue wat gediagnoseer is met PTSV (N = 19) met ‘n trauma blootgestelde kontrole (N = 29) groep. RNS was geisoleer vanaf vol bloed en gestuur vir RNS-Seq met behulp van die Illumina HiSeq 4000 platform op 'n opeenvolging diepte van 50 miljoen lees pare. Bioinformatika ontledings was toe uitgevoer, gevolg deur stroomaf mede-uitdrukking analise om mede-gereguleerde differensieel uitgedruk gene stelle tussen groepe te ondersoek. n Totaal van 556 differensieel uitgedruk gene was geïdentifiseer waarvan 196 (21 opreguleer en 175 onderreguleer) gene biologies relevant was gebaseer is op 'n ontologie gedryfde prioriteits benadering. Mede-uitdrukking analise het daarna 'n netwerk van vier hoogs mede-uitgedrukkings gene (opreguleer) en 'n groot mede-uitdrukking netwerk van 36 gene (onderreguleer) geïdentifiseer. Die vier mede-uitgespreek gene (RPL6, RPS6, RPS3A en EEF1B2) (opreguleer) en ses hoogs verbind mede-uitgespreek gene (DHX9, BCLAF1, THRAP3, EIF4G1, HSPA4 en MCL1) (onderreguleer) was geïdentifiseer as potensieel, relevante skakels wat bydra tot die patologie van PTSV. Hierdie hipotese-genererende studie dien as ondersteunende bewys dat 'n bloed transkriptomise reaksie betrokke by PTSV. Hierbenewens het die studie gene geidentifiseer wat moontlik betrokke is by die molekulêre onderbou van hierdie siekte. Toekomstige studies word egter aanbeveel om hierdie bevindinge te ondersteun en om miRNA profilering te gebruik vir die identifisering van meer robuuste, bloed gebaseer biomerkers vir PTSV.
AFRIKAANSE OPSOMMING: Post-traumatiese stresversteuring (PTSV) is 'n neuropsigiatriese siekte wat bestaan uit komplekse, multi-faktoriaal interaksies. To top hede het meeste genetiese studies slegs gefokus op spesifieke kandidaat gene betrokke by PTSV. Hierdie kandidaat studies het dus nie 'n holistiese siening wat kan verkry word deur 'n hele-transkriptoom RNS-Sequencing (RNS-Seq) benadering nie. In hierdie voorlopige studie beoog ons om RNS-Seq aan te wend om molekulêre meganismes en moontlike bloed biomerkers in Suid-Afrikaanse PTSV patiente te ondersoek. In hierdie kontrole studie vergelyk vroulike, kleurling (gemengde afkoms) individue wat gediagnoseer is met PTSV (N = 19) met ‘n trauma blootgestelde kontrole (N = 29) groep. RNS was geisoleer vanaf vol bloed en gestuur vir RNS-Seq met behulp van die Illumina HiSeq 4000 platform op 'n opeenvolging diepte van 50 miljoen lees pare. Bioinformatika ontledings was toe uitgevoer, gevolg deur stroomaf mede-uitdrukking analise om mede-gereguleerde differensieel uitgedruk gene stelle tussen groepe te ondersoek. n Totaal van 556 differensieel uitgedruk gene was geïdentifiseer waarvan 196 (21 opreguleer en 175 onderreguleer) gene biologies relevant was gebaseer is op 'n ontologie gedryfde prioriteits benadering. Mede-uitdrukking analise het daarna 'n netwerk van vier hoogs mede-uitgedrukkings gene (opreguleer) en 'n groot mede-uitdrukking netwerk van 36 gene (onderreguleer) geïdentifiseer. Die vier mede-uitgespreek gene (RPL6, RPS6, RPS3A en EEF1B2) (opreguleer) en ses hoogs verbind mede-uitgespreek gene (DHX9, BCLAF1, THRAP3, EIF4G1, HSPA4 en MCL1) (onderreguleer) was geïdentifiseer as potensieel, relevante skakels wat bydra tot die patologie van PTSV. Hierdie hipotese-genererende studie dien as ondersteunende bewys dat 'n bloed transkriptomise reaksie betrokke by PTSV. Hierbenewens het die studie gene geidentifiseer wat moontlik betrokke is by die molekulêre onderbou van hierdie siekte. Toekomstige studies word egter aanbeveel om hierdie bevindinge te ondersteun en om miRNA profilering te gebruik vir die identifisering van meer robuuste, bloed gebaseer biomerkers vir PTSV.
Description
Thesis (MSc)--Stellenbosch University, 2017.
Keywords
Post-traumatic Stress Disorder (PTSD), UCTD, Neuropsychiatric disorders, Nucleotide sequence