Methylomic profiling in schizophrenia: towards an integrated genetic-epigenetic approach

Schizophrenia is a severe psychiatric disorder, characterized by psychotic symptoms, delusions and hallucinations, disorganisation, dysfunctional affective responses, and altered cognitive functioning. The social and economic consequences of schizophrenia are severe, eclipsing those of many other illnesses. With a lifetime prevalence rate of ~1%, schizophrenia contributes significantly to the global burden of disease, ranking among the top ten causes of disability in developed countries worldwide. Current approaches to understanding the causes of schizophrenia have focused primarily on uncovering a genetic contribution to the disorder, although identifying risk variants has not been straightforward. Furthermore, there is considerable heterogeneity across studies and the mechanism behind the action of genetic risk variants remains largely unknown. Despite considerable research effort, therefore, we are remain no closer to understanding the precise aetiology of SZ and a long way from realising the post-genomic promises of novel diagnostic and therapeutic strategies.

Sequencing the genome was, however, only the first step in our quest to understand how genes are expressed and regulated. Sitting above the DNA sequence is a second layer of information (the 'epigenome') that mediates the regulation of when and where genes are functionally transcribed. Unlike the DNA sequence, which is stable and strongly conserved, epigenetic processes can be highly dynamic: not only are they developmentally-regulated, but they can also be modified by exposure to a range of external environmental factors and stochastic events in the cell.

This study aims, for the first time, to systematically examine the role of epigenetic processes in schizophrenia, focusing on DNA methylation, a chemical modification to DNA that can directly influence gene transcription and function. We will use cutting-edge methods to examine genome-wide patterns of DNA methylation in several unique collections of samples. First, we will use a large collaborative collection of schizophrenia patients and controls. These samples have already been extensively studied at the genetic level, enabling us to undertake an integrated genetic-epigenetic approach to schizophrenia. Second, we will examine epigenetic differences within genetically-identical monozygotic twin-pairs, where one twin has schizophrenia and the other does not. Third, we will examine differences in brain tissue taken post-mortem from patients with schizophrenia. Finally, we will assess epigenetic changes across specific regions of the genome in individuals at high-risk for developing schizophrenia, tracking changes in DNA methylation with disease onset.

Our proposed integrated genetic-epigenetic approach brings together a world-class group of epigeneticists, geneticists, clinicians and bioinformaticians with the ultimate goal of identifying peripheral epigenetic biomarkers for schizophrenia and transforming diagnostic, therapeutic, and future aetiological approaches to the disease.

We propose a comprehensive genome-wide analysis of epigenetic dysfunction associated with schizophrenia (SZ) using cutting-edge methodologies to identify novel pathways involved in pathogenesis. We will examine genome-wide patterns of DNA methylation in a unique collection of samples. First, via collaboration with research groups involved in the UK10K consortium, we will undertake methylomic analysis using the Illumina Infinium 450K array in SZ samples (n=1700) and matched controls (n=1700) from ongoing genome-wide association study (GWAS) and exome sequencing projects, enabling us to perform an integrated epigenetic-genetic analytical strategy and representing the largest epigenome-wide association study yet undertaken. Specific SZ-associated differentially methylated regions (DMRs) will be verified and subsequently replicated in another set of samples using the Sequenom EpiTYPER platform and bisulfite pyrosequencing. Validated DMRs will also be examined longitudinally in a high-risk prodromal cohort to investigate epigenetic changes associated with the transition into disease. Second, we will examine genome-wide patterns of DNA methylation in MZ twin-pairs discordant for SZ using the largest collection of such samples ever assessed. This will enable us to examine the epigenome independent of any underlying genomic sequence variation and allow us to fully control for factors such as age, sex and the early (pre- and peri-natal) environment while providing further independent validation/replication for SZ-associated regions implicated in Aim 1. Third, we will use post-mortem brain samples obtained from SZ cases and controls to examine the extent to which disease-associated epigenetic marks detected in the periphery reflect changes occurring in functionally-relevant tissues. A key element of data analysis will involve the integration of epigenetic information with GWAS data, exome sequencing and other clinical/demographic data using novel methods developed in our lab.

In addition to other scientists (especially other and research groups investigating the aetiology of schizophrenia) the results of this project have the potential to impact on a number of other beneficiaries. These include patients suffering from schizophrenia, the pharmaceutical industry, health service providers, and academic groups investigating the causes of other complex disease phenotypes.

The social and economic consequences of schizophrenia are severe, eclipsing those of many other mental and somatic illnesses. With a lifetime prevalence rate of ~1%, the disorder contributes significantly to the global burden of disease, ranking among the top ten causes of disability in developed countries worldwide. Importantly, there is no cure for schizophrenia, and available treatments are often inefficient and characterized by severe side-effects. Given the dynamic and potentially-reversible nature of the epigenome, the outputs from this research could potentially nominate new targets for drug development for the treatment of schizophrenia. A number of pharmaceutical companies are actively developing so-called "epigenetic drugs" and could rapidly take advantage of these outputs. Our data may also highlight novel neurobiological pathways involved in schizophrenia, again stimulating the development of novel therapeutic interventions. Developing new treatments for schizophrenia will have subsequent benefits to the family and friends of affected individuals, and potentially boost the economy by enabling affected individuals to return to work.

Another positive output of this research may be the identification of potential blood biomarkers for risk of schizophrenia, which could have important public health implications. For example, if we are able to detect epigenetic changes in our high-risk prodromal samples, this could be used to develop tests for the disease before symptoms become manifest, resulting in more relevant and targeted interventions. Identifying biological correlates of schizophrenia may also help remove some of the stigma associated with the disease.

Finally, we hope that our novel integrated genetic-epigenetic approach to schizophrenia may stimulate similar research strategies to be adopted by academics working in the context of other complex disease phenotypes.