Investigating the functional significance of genome-wide variants associated with antipsychotic treatment response in schizophrenia

Ovenden, Ellen Susan (2015-12)

Thesis (MSc)--Stellenbosch University, 2015.

Thesis

ENGLISH ABSTRACT: Schizophrenia is a debilitating disease affecting approximately 70 million people worldwide. Response to treatment, much like the disorder itself, is highly heritable, heterogeneous, and poorly understood. Only 50% of patients respond well to medication, and extensive research has provided limited improvement on this figure. Advances in genetic technologies coupled with massive increases in study sample size have the potential to explain the “missing heritability” of both schizophrenia and treatment response. Genome-wide association studies (GWAS) are at the forefront of complex trait research, but have had minimal success in terms of explaining the biology of psychiatric drug response. Despite the majority of GWAS “hits” being located in noncoding regions, functional interpretation is usually restricted to the closest gene. The Encyclopedia of DNA Elements (ENCODE) project has recently shown that noncoding variation is not just a functional proxy of adjacent coding regions, but can have complex and pervasive regulatory effects. This study aimed to investigate the functionality of noncoding single nucleotide polymorphisms (SNPs) in schizophrenia treatment response. A novel bioinformatics pipeline incorporated coding and noncoding variants implicated in treatment response, regions of linkage disequilibrium (LD), regulatory data, and biological pathway predictions. Firstly, the literature was mined to identify all variants associated via GWAS with antipsychotic response, after which publically available data was employed to find markers in LD with these variants. This larger group of variants was analysed with bioinformatic tools such as RegulomeDB and rSNPBase to determine regulatory potential. Thereafter, affected gene targets and pathways were identified with DAVID and GeneMANIA. In order to investigate the findings further, the top predicted regulatory variants and their GWAS partners were genotyped with TaqMan® OpenArray® in a South African first episode schizophrenia (FES) cohort and analysed for associations with treatment outcomes. The bioinformatic portion of this study implicated a region on chromosome 4q24 associated with treatment-refractory schizophrenia through involvement of the nuclear factor of kappa light polypeptide gene enhancer in B-cells 1 (NFKB1) gene. This gene is a master regulator involved in immunity and has over 200 gene targets. NFKB1 and immune dysregulation have both previously been implicated in schizophrenia, pointing to a genetic overlap between schizophrenia risk and antipsychotic treatment response. The most significant variants in the association analyses occurred at the 4q24 locus, with rs230493 and rs3774959 significantly associated with poor response in the negative symptom domain (P < 0.0001). These findings suggest a genetic link between persistent negative symptoms and treatment nonresponse. Additionally, a 14-variant haplotype containing these two polymorphisms was associated with 4.41% higher positive symptom severity. Not only do these results validate the importance of the 4q24 region in antipsychotic response, but they emphasise the overlap of schizophrenia risk and drug response, and the potential role of genomic dysregulation in undesirable treatment outcomes. NFKB1 and other associated genes should be studied in population-specific, replicative cohorts, in order to validate potential biomarkers of treatment response. This study illustrated the importance of thorough GWAS interpretation and inclusion of coding and noncoding variants to form biological hypotheses and better understand antipsychotic response.

AFRIKAANSE OPSOMMING: Skisofrenie is ʼn aftakelende siekte wat sowat 70 miljoen mense wêreldwyd raak. Behandelingsreaksie is, baie soos die siekte self, hoogs oorerflik en heterogeen, en word nog swak verstaan. Slegs 50% van pasiënte reageer goed op medikasie, en uitvoerige navorsing het slegs beperkte verbetering op hierdie syfer tot gevolg gehad. Vooruitgang in genetiese tegnologieë tesame met ʼn geweldige toename in studie-steekproefgrootte kan potensieel die “ontbrekende erflikheid” van sowel skisofrenie as behandelingsreaksie verklaar. Genoom-wye assosiasiestudies (GWAS) is aan die voorpunt van komplekse kenmerknavorsing, maar het tot dusver minimale sukses ten opsigte van die verklaring van die biologie van psigiatriese middelreaksie gehad. Ondanks die feit dat die meerderheid GWAS-trefpunte in niekoderende streke voorkom, is funksionele interpretasie gewoonlik tot die naaste geen beperk. Die Ensiklopedie van DNS-elemente- (ENCODE-)projek het onlangs bewys dat niekoderende variasie nie net ʼn funksionele sekundus van naasliggende koderende streke is nie, maar komplekse en deurdringende regulerende gevolge kan hê. Hierdie studie was daarop gemik om die funksionaliteit van niekoderende enkel-nukleotied-polimorfismes (ENPs) in skisofreniebehandelingsreaksie te ondersoek. ʼn Nuwe bioïnformatika-pyplyn het koderende en niekoderende variante wat by behandelingsreaksie betrek word, streke van koppelingsdisekwilibrium (KD), reguleringsdata, en biologiese padvoorspellings geïnkorporeer. Eerstens is die literatuur ondersoek om alle variante te identifiseer wat via GWAS met antipsigotika-reaksie geassosieer word, waarna algemeen beskikbare data gebruik is om merkers in KD met hierdie variante te vind. Hierdie groter groep variante is met bioïnformatika-hulpmiddels soos RegulomeDB en rSNPBase ontleed om reguleringspotensiaal te bepaal. Daarna is geaffekteerde geenteikens en paaie met DAVID en GeneMANIA geïdentifiseer. Ten einde die bevindings verder te ondersoek, is die top- voorspelde reguleringsvariante en hul GWAS-vennote met TaqMan® OpenArray® in ʼn Suid-Afrikaanse eerste-episode-skisofrenie-kohort gegenotipeer en vir assosiasies met behandelingsuitkomste ontleed. Die bioïnformatika-gedeelte van hierdie studie het ʼn streek op chromosoom 4q24 geïmpliseer wat deur betrokkenheid van die geen nukleêre-faktor-kappa ligte polipeptied geen bevorderaar in B-selle 1 (NFKB1) met behandelingsweerstandige skisofrenie geassosieer word. Hierdie geen, ʼn meester-reguleerder wat op immuniteit betrekking het, het meer as 200 geenteikens. NFKB1 en immuundisregulering is albei vantevore by skisofrenie geïmpliseer, wat op ʼn genetiese oorvleueling van skisofrenie-risiko en antipsigotika-behandelingsreaksie dui. Die mees beduidende variante in die assosiasie het by die 4q24-lokus voorgekom, met rs230493 en rs3774959 wat albei beduidend met swak ná-behandelingsreaksie in die negatiewe-simptoom-domein geassosieer was (P < 0.00001). Hierdie bevindings dui op ʼn genetiese verband tussen volhardende negatiewe simptome en niereaksie op behandeling. Daarbenewens is ʼn 14-variant-haplotipe wat hierdie twee polimorfismes bevat met ʼn 4.41% hoër graad positiewe simptome geassosieer. Hierdie resultate staaf nie net die belangrikheid van die 4q24-streek in antipsigotika-reaksies nie, maar beklemtoon ook die oorvleueling van skisofrenie-risiko en middelreaksie, en die potensiële rol van genoom-disregulering in ongewenste behandelingsuitkomste. NFKB1 en ander verwante gene moet in populasiespesifieke, repliseerbare kohorte bestudeer word ten einde potensiële biomerkers van behandelingsreaksie te staaf. Hierdie studie illustreer die waarde van deeglike GWAS-interpretasie en die insluiting van koderende en niekoderende variante om biologiese hipoteses te vorm en antipsigotika-reaksies beter te begryp.

Please refer to this item in SUNScholar by using the following persistent URL: http://hdl.handle.net/10019.1/97704
This item appears in the following collections: