Statistically extracting cell-type specific information from human brain transcriptomic datasets captures the effects of age, manner of death, dissection, and psychiatric diagnosis
Hagenauer MG, Li JZ, Meng F, Walsh D, Bunney WE, Myers RM, Barchas JD, Schatzberg AF, Watson SJ, Akil H
Society for Neuroscience. 2016.
Most scientists would agree that psychiatric illness is unlikely to arise from pathological changes that occur uniformly across the entire brain. Despite this fact, the majority of transcriptomic analyses of the human brain are conducted using block-dissected tissue due to the difficulty of conducting single-cell level analyses on donated post-mortem brains. To address this challenge, we compiled a database of more than 3300 transcripts that were specifically-enriched in one of 10 primary brain cell types within published single-cell transcriptomic experiments. Using this database, we predicted the relative cell type composition for 157 human dorsolateral prefrontal cortex samples using Affymetrix microarray data from the Pritzker Neuropsychiatric Consortium, as well as for 841 samples spanning 160 brain regions included in an Agilent microarray dataset from the Allen Brain Atlas. These predictions were generated by averaging normalized expression levels across the transcripts specific to each primary cell type to create a “cell type index”. Using this method, we determined that the expression of cell type specific transcripts identified by different experiments, methodologies, and species clustered into three main cell type groups: neurons, oligodendrocytes, and astrocytes/support cells. Overall, the principal components of variation in the data were largely explained by the neuron to glia ratio of the samples. The relative balance of these cell types was influenced by a variety of demographic, pre- and post-mortem variables. In particular, age and prolonged anaerobic conditions around the time of death were associated with decreased neuronal content and increased astrocytic and endothelial content in the tissue, replicating the known vulnerability of neurons to adverse conditions and illustrating the proliferation of vasculature in a hypoxic environment. We also found that the red blood cell content was reduced in individuals who died in a manner that involved exsanguination. When comparing across brain regions, we were able to easily capture canonical cell type signatures - increased endothelial cells and vasculature in the choroid plexus, oligodendrocytes in the corpus callosum, astrocytes in the central glial substance, neurons and immature cells in the dentate gyrus, and interneurons in the globus pallidus. Finally, by including a set of “cell type indices” in a larger model examining the relationship between gene expression and neuropsychiatric illness, we were able to identify more provocative candidate molecules in relationship to major depressive disorder, bipolar disorder, and schizophrenia than using standard methodology.