Quantifying the neuronal and glial composition of the brain using DNA methylation profiles

To date, most epigenetic datasets have been generated on DNA samples isolated from bulk tissues. As the proportion of individual cell types within a sample can vary across individuals, systematic differences in cellular proportions that correlate with the phenotype of interest may manifest as differences in the overall epigenetic profile. Deconvolution algorithms calculate a series of continuous variables reflecting the underlying cellular heterogeneity of each sample from the bulk tissue profile that can be used to adjust for confounding in epigenome-wide association analyses. Here we provide novel reference profiles for brain cell types for use with reference based deconvolution algorithms. We used a FANS protocol recently described by our group to purify nuclei populations from prefrontal cortex tissue from 43 adult donors. Our initial gating strategy used an antibody against NeuN to isolate neuronal nuclei in combination with an antibody against SOX10 to separate oligodendrocyte nuclei from other glial nuclei. Subsequently, in a second gating strategy we additionally included an antibody against IRF8 to enrich microglia from the NeuNNeg/SOX10Neg fraction. Our third gating strategy used an antibody against SATB2 in place of NeuN to isolate excitatory neurons. We generated DNA methylation profiles using the Illumina EPIC array for NeuNPos (neuron-enriched; n = 28), NeuNNeg/SOX10Pos (oligodendrocyte-enriched; n = 24), NeuNNeg/SOX10Neg (microglia- and astrocyte-enriched; n = 21), NeuNNeg/SOX10Neg/IRF8Pos (microglia-enriched; n = 17), NeuNNeg/SOX10Neg/IRF8Neg, (astrocyte-enriched; n = 7), SATB2Pos (excitatory neuron-enriched; n = 9), and SATB2Neg (inhibitory neuron- and glial- enriched; n = 6) nuclei populations. We have demonstrated that these are applicable for use with established deconvolution algorithms to quantify the cellular heterogeneity of the cortex and other regions of the human brain from bulk DNAm data. These variables will be critical covariates to include in future epigenetic studies of brain disorders to minimise the risk of false positive associations and improve our understanding of the changes in the brain that underpin the development of psychiatric disorders and neurodegenerative diseases. Post-mortem prefrontal cortex (PFC) samples were processed using our optimized FANS protocol to purify nuclei populations from 42 adult donors. Our initial gating strategy used an antibody against NeuN (a robust marker of post-mitotic neurons) to isolate neuronal nuclei in combination with an antibody against SOX10 (a transcription factor involved in the differentiation of oligodendrocytes) to separate oligodendrocyte nuclei from other glial nuclei. Subsequently, in a second gating strategy we additionally included an antibody against IRF8 (a transcription factor that is upregulated in microglia(30)) to enrich microglia from the NeuNNeg/SOX10Neg fraction. Our third gating strategy used an antibody against SATB2 (a DNA binding protein involved in transcriptional regulation and chromatin remodeling which is expressed in excitatory neurons in the mature central nervous system) in place of NeuN . We generated DNAm profiles using the Illumina EPIC array for NeuNPos (neuron-enriched; n = 28), NeuNNeg/SOX10Pos (oligodendrocyte-enriched; n = 24), NeuNNeg/SOX10Neg (microglia- and astrocyte-enriched; n = 21), NeuNNeg/SOX10Neg/IRF8Pos (microglia-enriched; n = 17), NeuNNeg/SOX10Neg/IRF8Neg, (astrocyte-enriched; n = 7), SATB2Pos (excitatory neuron-enriched; n = 9), and SATB2Neg (inhibitory neuron- and glial- enriched; n = 6) nuclei populations.