- Email: [email protected]
GENOME-EDITING OF THE RERE SUPER-ENHANCER ALTERS EXPRESSION OF GENES IN INDEPENDENT SCHIZOPHRENIA GWAS REGIONS
EXOME-WIDE ASSOCIATION STUDY IDENTIFIES NOVEL SUSCEPTIBILITY GENES FOR PERSONALITY TRAITS associated with disease. Leveraging on the considerable investment in Genome-Wide Association Studies (GWAS) we are examining genome-wide patterns of DNA methylation across multiple cohorts with the aim of undertaking an integrated genetic-epigenetic approach to schizophrenia. Methods: DNA methylation profiled in whole blood samples from five schizophrenia case-control cohorts using the Illumina 450 K HumanMethylation array (total n = 3,200 samples). Each sample was also genotyped and polygenic scores for schizophrenia calculated. We performed two parallel Epigenome-Wide Association Studies (EWAS) to identify methylomic variation associated with 1) schizophrenia diagnosis and 2) polygenic burden calculated from the results of latest PGC schizophrenia GWAS, combing the results from each individual cohort by meta-analysis. Results: Differentially Methylated Positions (DMPs) associated with schizophrenia identified in each cohort showed consistent direction of effects across other datasets. Combing the results across the five cohorts, we identified 3,911 schizophrenia-associated DMPs annotated to 2,307 genes. This included further replication of 305/365 DMPs identified in our previous schizophrenia EWAS and an additional 2,434 novel DMPs. Furthermore, we identify overlap in regions characterized by differential DNA methylation and loci nominated in the largest GWAS of schizophrenia conducted by the PGC. Finally, we show how DNA methylation quantitative trait loci in combination with Bayesian co-localization analyses can be used to annotate extended genomic regions nominated by studies of schizophrenia, and to identify potential regulatory variation causally involved in disease. Discussion: This study represents the largest integrated analysis of genetic and epigenetic variation in schizophrenia. Combining data from multiple cohorts has enabled us to identify novel DMPs associated with both diagnosis and elevated polygenic burden for schizophrenia. We demonstrate the utility of using a polygenic risk score to identify molecular variation associated with etiological variation, and of using DNA methylation quantitative trait loci to refine the functional and regulatory variation associated with schizophrenia risk variants. Finally, we present strong evidence for the co-localization of genetic associations for schizophrenia and differential DNA methylation.
Disclosure: Nothing to disclose. http://dx.doi.org/10.1016/j.euroneuro.2017.08.006
6. GENOME-EDITING OF THE RERE SUPER-ENHANCER ALTERS EXPRESSION OF GENES IN INDEPENDENT SCHIZOPHRENIA GWAS REGIONS n
Cathy Barr , Yu Feng, Aidan Dineen, Ambalika Sarkar, Karen Wigg The Krembil Research Institute
S783
Background: The majority of associated markers for complex genetic traits reside in gene regulatory regions, particularly enhancers and super-enhancers. Enhancers can reside megabases from the gene they regulate (target gene) and their targets are often not the nearest gene. Thus, the assumption that the gene nearest a GWAS-significant marker will be the risk gene will in many cases be incorrect. Methods: To identify the target genes of enhancers with GWAS significant markers, we analyzed Capture-HiC data selecting enhancers for functional studies using CRISPR/ Cas9 in human neural precursor cells (hNPCs). The impact on expression was measured by RT-qPCR and RNA-seq in the edited versus the mock-transfected cells. Results: We selected the super-enhancer spanning the 3’ end of the RERE gene for study, the site of 12 GWAS significant SNPs for schizophrenia. Capture-HiC data indicate interactions of the super-enhancer with RERE (co-repressor/co-activator involved in retinoic acid signaling), PARK7 (Parkinsons 7, protects neurons from oxidative stress) and PER3 (Period 3). These 3 genes are transcription co-regulators or transcription factors. Using CRISPR/Cas9, we deleted a 2 kb region of the super-enhancer in hNPCs and analyzed the transcriptome by RNA-seq. We identified 107 genes that were differentially expressed, including 14 regulated by retinoic acid. Importantly, 3 of these are located in independent GWAS regions for schizophrenia. Discussion: Capture-HiC provides important new leads in pinpointing the target genes of enhancer-mediated regulation emanating from the GWAS findings and functional studies confirm altered expression of interacting genes. We are currently differentiating the CRISPR/Cas9 edited NPCs to neurons to examine the impact of the edits on differentiation and neuronal phenotypes. The finding of altered expression of genes in independent GWAS regions is an important new lead in understanding the regulation of schizophrenia risk genes.
Disclosure: Nothing to disclose. http://dx.doi.org/10.1016/j.euroneuro.2017.08.007
1:30 p.m. - 3:00 p.m. Saturday Afternoon Oral Session: Autism Spectrum Disorder 7. A GENETIC FIRST APPROACH TO DISSECTING THE HETEROGENEITY OF AUTISM: PHENOTYPIC COMPARISON OF AUTISM RISK COPY NUMBER VARIANTS n
Samuel Chawner ,1, Joanne Doherty1, Hayley Moss2, Carrie Bearden3, Wendy Chung4, Sarah Curran5, Jeremy Hall1, Sébastien Jacquemont6, Wendy Kates7, Jacob Vorstman8, Michael Owen9, Marianne Van Den Bree1 1
Cardiff University Cardiff University School of Medicine 3 University of California, Los Angeles 4 Columbia University 2
Disclosure: Nothing to disclose. http://dx.doi.org/10.1016/j.euroneuro.2017.08.006
6. GENOME-EDITING OF THE RERE SUPER-ENHANCER ALTERS EXPRESSION OF GENES IN INDEPENDENT SCHIZOPHRENIA GWAS REGIONS n
Cathy Barr , Yu Feng, Aidan Dineen, Ambalika Sarkar, Karen Wigg The Krembil Research Institute
S783
Background: The majority of associated markers for complex genetic traits reside in gene regulatory regions, particularly enhancers and super-enhancers. Enhancers can reside megabases from the gene they regulate (target gene) and their targets are often not the nearest gene. Thus, the assumption that the gene nearest a GWAS-significant marker will be the risk gene will in many cases be incorrect. Methods: To identify the target genes of enhancers with GWAS significant markers, we analyzed Capture-HiC data selecting enhancers for functional studies using CRISPR/ Cas9 in human neural precursor cells (hNPCs). The impact on expression was measured by RT-qPCR and RNA-seq in the edited versus the mock-transfected cells. Results: We selected the super-enhancer spanning the 3’ end of the RERE gene for study, the site of 12 GWAS significant SNPs for schizophrenia. Capture-HiC data indicate interactions of the super-enhancer with RERE (co-repressor/co-activator involved in retinoic acid signaling), PARK7 (Parkinsons 7, protects neurons from oxidative stress) and PER3 (Period 3). These 3 genes are transcription co-regulators or transcription factors. Using CRISPR/Cas9, we deleted a 2 kb region of the super-enhancer in hNPCs and analyzed the transcriptome by RNA-seq. We identified 107 genes that were differentially expressed, including 14 regulated by retinoic acid. Importantly, 3 of these are located in independent GWAS regions for schizophrenia. Discussion: Capture-HiC provides important new leads in pinpointing the target genes of enhancer-mediated regulation emanating from the GWAS findings and functional studies confirm altered expression of interacting genes. We are currently differentiating the CRISPR/Cas9 edited NPCs to neurons to examine the impact of the edits on differentiation and neuronal phenotypes. The finding of altered expression of genes in independent GWAS regions is an important new lead in understanding the regulation of schizophrenia risk genes.
Disclosure: Nothing to disclose. http://dx.doi.org/10.1016/j.euroneuro.2017.08.007
1:30 p.m. - 3:00 p.m. Saturday Afternoon Oral Session: Autism Spectrum Disorder 7. A GENETIC FIRST APPROACH TO DISSECTING THE HETEROGENEITY OF AUTISM: PHENOTYPIC COMPARISON OF AUTISM RISK COPY NUMBER VARIANTS n
Samuel Chawner ,1, Joanne Doherty1, Hayley Moss2, Carrie Bearden3, Wendy Chung4, Sarah Curran5, Jeremy Hall1, Sébastien Jacquemont6, Wendy Kates7, Jacob Vorstman8, Michael Owen9, Marianne Van Den Bree1 1
Cardiff University Cardiff University School of Medicine 3 University of California, Los Angeles 4 Columbia University 2