In a recent study published in Nature Medicine, researchers investigated the impact of biological sex on protein levels and its genomic control by analyzing 1,277 proteomes of the human brain.
The prevalence rates of neurological and psychiatric disorders, such as schizophrenia, Parkinson's disease, and Alzheimer's disease, differ by sex. Genetic risks for these conditions also differ by sex.
The underlying reasons for these differences might originate from environmental, genetic, and physiologic factors. However, data on their underlying mechanisms is limited. Gene expression and splicing differences by sex have been reported across developmental stages.
About the study
In the present study, researchers assessed sex-based discrepancies in protein and messenger ribonucleic acid (mRNA) expression to elucidate biological mechanisms characterizing the influence of sex in brain diseases.
The team evaluated the impact of sex on protein levels and its genomic control at the protein and transcript levels by analyzing information obtained from 621 transcriptomes of the human brain donated by a sample of brain proteome contributors.
They also examined the relationship between sex-differentiated abundances in protein levels in the brain and various mental and neurological diseases. Proteomes from six regions of the brain in 1,277 European donors were analyzed, with the dorsolateral region of the prefrontal cortex (dPFC) accounting for 62% (n=793) proteomes.
X-chromosomal genotyping was utilized to predict the sex, which was subsequently matched to the self-reported sex. Before evaluating sex-biased expressions, the impact of molecular sequencing batches, post-mortem intervals, donor maturity, and medical diagnosis was calculated through linear regression modeling.
In addition, the team performed surrogate variable analysis (SVA) to determine hidden scientific or biological variables that could affect protein levels in the brain, such as cellular composition.
Since different regions of the brain might contain different types of cells with varied biological functioning, sex-based differences in protein levels were evaluated in the temporal cortex, parahippocampal gyrus, precuneus, middle gyrus of the frontal lobe, and premotor cortex.
To detect proteins exhibiting sex-biased protein distribution patterns across various brain regions, multivariate adaptive shrinkage (MASH) was used for protein estimation. In addition, the team determined the local false sign rates (LFSRs) for all proteins.
Subsequently, the team examined differences in the genomic control of protein levels between men and women by performing sex-stratified protein quantitative trait locus (sb-pQTL) evaluation in the dorsolateral prefrontal cortex, with the greatest number of participants that includes proteomic and genetic information (n=716), and investigated proteins coded by autosomes and X chromosomal genes.
The researchers examined genes with sex-differentiated expression in the human brain at both the messenger ribonucleic acid and protein levels. Sex-based protein quantitative trait loci (sb-pQTLs) and sb-eQTLs were compared to better understand the impact of sex on the genetic control of brain proteins and mRNAs.
A Sum of Single Effects (SuSiE) regression analysis was used to examine the likelihood of several independent causal variations within each identified gene.
For six psychiatric and neurological traits with available sex-stratified genome-wide association studies (GWAS) results, the team also performed sex-stratified proteome-wide association studies (PWAS) and colocalization analysis in each sex separately to identify proteins with evidence consistent with a causal role in one sex but not in the other.
Of the 10,198 proteins evaluated, 371 (4%) were encoded by genes on the X chromosome. The researchers found that 13% (n=1,354) of brain proteins were sex-differentiated, and two percent (n=150) had sb-pQTLs.
Among the 9,080 genes assessed in both the transcriptomic and proteomic profiles, 498 (5.5%) had sex-differentiated expression at both the mRNA and protein levels, and 76% displayed concordant sex-biased mRNA and protein expression. However, the impacts of sex on the genetic control of expression were more visible at the protein level.
An average of 25% of the putatively causative genes exhibited sex-differentiated protein abundance, with 12 putatively causal proteins having sb-pQTLs and controlling for four psychiatric qualities, one neurologic trait, and three brain structural features.
Three of the 12 causative genes showed skewed protein abundance: endoplasmic reticulum lectin 1 (ERLEC1), cloning and in situ localization of the human contactin gene (CNTN2), and GRB10-interacting GYF protein 2 (GIGYF2).
Further, 23 sex-specific causative proteins, 11 for females and 12 for men, were detected by combining sex-specific pQTLs with sex-stratified GWAS of six psychiatric and neurologic diseases. Forty-eight percent of the 9,080 genes assessed in the transcriptomic and proteomic profiles had sex-differentiated expression at the mRNA and protein levels.
The difference in the number of sb-eQTLs and sb-pQTLs could not be explained by inter-individual differences in mRNA levels or sample size. Sex-biased gene expression was observed in all six brain areas studied. Sex-biased pQTLs were prevalent for exonic and intergenic single nucleotide polymorphisms, whereas intronic single-nucleotide polymorphisms were depleted.
Proteins involved in cellular morphology, cell adhesion, actin filament organization, translation initiation, and branched-chain amino acid degradation were found among genes with concordant sex-biased expression between mRNA and protein.
For example, catenin delta 1 (CTNND1) is a causative gene in four psychiatric diseases (major depression, post-traumatic stress disorder, schizophrenia, and problematic alcohol use) and neuroticism, with sex-biased expression at both the transcript and protein levels in opposite directions.
Overall, the study findings showed that sex significantly influences protein and mRNA expression in the brain, particularly at the protein level, impacting psychiatric and neurologic disorders. The study identified potential causal genes with sex-differentiated or sex-biased protein expression, highlighting the importance of sex-aware mechanistic studies in understanding brain health and the underlying mechanisms for sex-based differences in brain diseases.