Single-cell analysis of sex and gender differences in the human brain during development and disease

Abstract Sex and gender differences in human brain are of interest to society and science as numerous processes are impacted by them, including brain development, behavior, and the occurrence, prevalence, and therapeutic response of diseases. By assembling publicly accessible data from the in utero to elderly age in healthy, Alzheimer’s disease and multiple sclerosis samples, we thoroughly analyzed SG changes through brain development and brain disorders at a single-cell level. We identified and characterised SG-biased genes in ten key types of brain cells across nine age and illness groups, by analysing a total of 419,885 single-nucleus RNA- sequencing samples from 161 human brains (72 females, 89 males). SG-biased genes were located mostly on the autosomes and showed some enrichment for Y chromosome but not X. Most SG-biased genes were unique to cell types and were enriched for cell type specific markers. Furthermore, SG-biased genes showed little overlap across age and disease groups. Despite a very low gene overlap, there was a high functional overlap for SG-biased genes across cell types as well as across age and disease. Female-biased genes were enriched for brain-related processes, and male-biased genes were enriched for metabolic pathways. Mitochondrial genes were consistently female-biased. Both male- and female-biased genes were highly enriched for androgen (not estrogen) response elements and interestingly thymosin targets were enriched consistently only in male-biased genes. Finally, we have created a web resource with full characterisation of SG-biased genes at different thresholds for the scientific community, to validate findings and generate further new hypotheses, available at https://joshiapps.cbu.uib.no/SRB app/.