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Methylome-wide association findings for major depressive disorder overlap in blood and brain and replicate in independent brain samples

Abstract

We present the first large-scale methylome-wide association studies (MWAS) for major depressive disorder (MDD) to identify sites of potential importance for MDD etiology. Using a sequencing-based approach that provides near-complete coverage of all 28 million common CpGs in the human genome, we assay methylation in MDD cases and controls from both blood (N = 1132) and postmortem brain tissues (N = 61 samples from Brodmann Area 10, BA10). The MWAS for blood identified several loci with P ranging from 1.91 × 10−8 to 4.39 × 10−8 and a resampling approach showed that the cumulative association was significant (P = 4.03 × 10−10) with the signal coming from the top 25,000 MWAS markers. Furthermore, a permutation-based analysis showed significant overlap (P = 5.4 × 10−3) between the MWAS findings in blood and brain (BA10). This overlap was significantly enriched for a number of features including being in eQTLs in blood and the frontal cortex, CpG islands and shores, and exons. The overlapping sites were also enriched for active chromatin states in brain including genic enhancers and active transcription start sites. Furthermore, three loci located in GABBR2, RUFY3, and in an intergenic region on chromosome 2 replicated with the same direction of effect in the second brain tissue (BA25, N = 60) from the same individuals and in two independent brain collections (BA10, N = 81 and 64). GABBR2 inhibits neuronal activity through G protein-coupled second-messenger systems and RUFY3 is implicated in the establishment of neuronal polarity and axon elongation. In conclusion, we identified and replicated methylated loci associated with MDD that are involved in biological functions of likely importance to MDD etiology.

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Acknowledgements

The current methylation study was supported by grant R01MH099110 from the National Institute of Mental Health. Tissues were received from five brain banks, including the Victorian Brain Bank, supported by The Florey Institute of Neuroscience and Mental Health, The Alfred and Victorian Forensic Institute of Medicine and funded by Australia’s National Health & Medical Research Council and Parkinson’s Victoria; the Stanley Medical Research Institute; The Netherlands Brain Bank, Netherlands Institute of Neuroscience, Amsterdam; the Harvard Brain Tissue Resource Center; and The Douglas – Bell Canada Brain Bank, Douglas Institute Research Center, Canada. Funding for NESDA was obtained from the Netherlands Organization for Scientific Research (Geestkracht program grant 10-000-1002); the Center for Medical Systems Biology (CSMB, NWO Genomics), Biobanking and Biomolecular Resources Research Infrastructure (BBMRI-NL), VU University’s Institutes for Health and Care Research (EMGO+) and Neuroscience Campus Amsterdam, University Medical Center Groningen, Leiden University Medical Center, National Institutes of Health (NIH, R01D0042157-01A, MH081802, Grand Opportunity grants 1RC2 MH089951 and 1RC2 MH089995). Part of the genotyping and analyses were funded by the Genetic Association Information Network (GAIN) of the Foundation for the National Institutes of Health. Computing was supported by BiG Grid, the Dutch e-Science Grid, which is financially supported by NWO.

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Correspondence to Karolina A. Aberg.

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B.W.J.H.P. has received research funding (non-related) from Jansen Research and Boehringer Ingelheim. The remaining authors declare that they have no conflict of interest.

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Aberg, K.A., Dean, B., Shabalin, A.A. et al. Methylome-wide association findings for major depressive disorder overlap in blood and brain and replicate in independent brain samples. Mol Psychiatry 25, 1344–1354 (2020). https://doi.org/10.1038/s41380-018-0247-6

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