Sex differences in brain protein expression and disease
Open accessAbstract
Most complex human traits differ by sex, but we have limited insight into the underlying mechanisms. Here, we investigated the influence of biological sex on protein expression and its genetic regulation in 1,277 human brain proteomes. We found that 13.2% (1,354) of brain proteins had sex-differentiated abundance and 1.5% (150) of proteins had sex-biased protein quantitative trait loci (sb-pQTLs). Among genes with sex-biased expression, we found 67% concordance between sex-differentiated protein and transcript levels; however, sex effects on the genetic regulation of expression were more evident at the protein level. Considering 24 psychiatric, neurologic and brain morphologic traits, we found that an average of 25% of their putatively causal genes had sex-differentiated protein abundance and 12 putatively causal proteins had sb-pQTLs. Furthermore, integrating sex-specific pQTLs with sex-stratified genome-wide association studies of six psychiatric and neurologic conditions, we uncovered another 23 proteins contributing to these traits in one sex but not the other. Together, these findings begin to provide insights into mechanisms underlying sex differences in brain protein expression and disease.
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Additional brain pQTL studies exist but generally have smaller sample sizes or analyze fewer proteins.
“Additional brain pQTL studies exist but generally have smaller sample sizes or analyze fewer proteins (15, 16).”
From Low overlap of plasma and CSF protein quantitative trait loci affects protein discovery for neurological disease (2026) · cites this paper as [15]
The Results section, ‘Sex differences in genetic control of brain protein abundance’ (page unavailable), confirms that this is a brain pQTL study, so it supports the existence of an additional study. Our copy does not compare its sample size or number of proteins analyzed with other brain pQTL studies, so it does not establish the claim that such studies generally have smaller samples or analyze fewer proteins. (LLM, conf=0.83)
Experimental — accuracy not yet measuredPrior work examined the effect of biological sex on protein expression and its genetic regulation in human brain proteomes.
“Our prior work examined the effect of biological sex on protein expression and its genetic regulation in human brain proteomes.”
From Unraveling sex differences in Alzheimer's disease and related endophenotypes with brain proteomes (2025) · cites this paper as [24]
These findings are in line with prior work showing robust differences in brain protein expression by sex.
“These findings are in line with our prior work showing robust differences in brain protein expression by sex.”
From Unraveling sex differences in Alzheimer's disease and related endophenotypes with brain proteomes (2025) · cites this paper as [24]
32 of 428 (7.5%) of the CSF index pQTLs and 61 of 480 (12.7%) of the plasma pQTLs also analyzed in the brain-based mass spectrometry pQTL analysis had opposite directions of effect (P<0.05).
“In addition, 32 of 428 (7.5%) of the CSF index pQTLs and 61 of 480 (12.7%) of the plasma pQTLs also analyzed in the brain-based mass spectrometry pQTL analysis (15) had opposite directions of effect (P < 0.05).”
From Low overlap of plasma and CSF protein quantitative trait loci affects protein discovery for neurological disease (2026) · cites this paper as [15]
We extended and validated these differences in larger plasma pQTL datasets [Fenland and deCODE Genetics] and brain pQTL resources.
“We extended and validated these differences in larger plasma pQTL datasets [Fenland (9) and deCODE Genetics (10)] and brain pQTL resources (15, 16).”
From Low overlap of plasma and CSF protein quantitative trait loci affects protein discovery for neurological disease (2026) · cites this paper as [15]
The FUT8 pQTL is concordant between CSF and brain (neurological contexts) and discordant in the deCODE study.
“The pQTL is concordant between CSF and brain (neurological contexts) (15) and discordant in the deCODE study.”
From Low overlap of plasma and CSF protein quantitative trait loci affects protein discovery for neurological disease (2026) · cites this paper as [15]
The citation is attached to the CSF–brain concordance claim, not the separate deCODE comparison. The Results section on genetic control of brain protein abundance reports brain pQTLs, but our copy yields no passage about a FUT8 pQTL being concordant between CSF and brain (searched: FUT8, CSF, cerebrospinal fluid, and concordance). (LLM, conf=0.72)
Experimental — accuracy not yet measuredWe did not observe an association at this variant for GBA in the brain, potentially because of a lack of power to detect rare variant effects.
“We did not observe an association at this variant for GBA in the brain (15), potentially because of a lack of power to detect rare variant effects.”
From Low overlap of plasma and CSF protein quantitative trait loci affects protein discovery for neurological disease (2026) · cites this paper as [15]
The Methods (Genetic data; page unavailable) say variants with a minor allele frequency below 5% were excluded, and the Discussion (page unavailable) notes limited power in sex-stratified analyses. Neither passage reports a result for GBA or the variant in the citing sentence. Searches for GBA and rare-variant effects found no passage addressing that specific nonassociation. (LLM, conf=0.73)
Experimental — accuracy not yet measuredEvidence of colocalization between miR-QTLs and host gene eQTLs (coloc PP.H4 > 0.5) was found for 17 of 106 miRNA-host pairs.
“Considering the 106 miRNA-host pairs (103 mature miRNAs from 77 precursors in 71 host genes) for which the miRNA had miR-QTLs and the host gene had eQTLs, we found evidence of colocalization between miR-QTLs and host gene eQTLs (coloc PP.H4 > 0.5) for 17 pairs and no evidence of colocalization for 89 pairs (Supplementary Table 9).”
From Mapping the microRNA landscape in the older adult brain and its genetic contribution to neuropsychiatric conditions (2024) · cites this paper as [21]
No evidence of colocalization between miR-QTLs and host gene eQTLs was found for 89 of 106 miRNA-host pairs.
“Considering the 106 miRNA-host pairs (103 mature miRNAs from 77 precursors in 71 host genes) for which the miRNA had miR-QTLs and the host gene had eQTLs, we found evidence of colocalization between miR-QTLs and host gene eQTLs (coloc PP.H4 > 0.5) for 17 pairs and no evidence of colocalization for 89 pairs (Supplementary Table 9).”
From Mapping the microRNA landscape in the older adult brain and its genetic contribution to neuropsychiatric conditions (2024) · cites this paper as [21]
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- Authors
- Wingo, A. P., Liu, Y., Gerasimov, E. S., Vattathil, S. M., Liu, J., Cutler, D. J., Epstein, M. P., Blokland, G. A. M., Thambisetty, M., Troncoso, J. C., Duong, D. M., Bennett, D. A., Levey, A. I., Seyfried, N. T., & Wingo, T. S.
- Affiliations
- Emory University (US)
- Maastricht University (NL)
- National Institutes of Health (US)
- Johns Hopkins University (US)
- Rush University Medical Center (US)
- Corresponding author
- Wingo, Aliza P.
- Wingo, Thomas S.
- ORCID
- Venue
- Nature Medicine
- Published
- 2023-08-31
- Volume
- 29
- Issue
- 9
- Pages
- 2224-2232
- ISSN
- 1078-8956 (ISSN-L)
- 1546-170X
- PMC
- PMC10504083
- OpenAlex
- W4386324900
- Cited by
- 94
- References
- 71
- Citations by year
- 2026: 27 · 2025: 40 · 2024: 26 · 2023: 1
- FWCI
- 24.06
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Nature Medicine (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Research Publications (Maastricht University) (publishedVersion, cc-by)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Funders
- U.S. Department of Veterans Affairs (IK4BX005219, I01 BX005686, I01BX003853, IK2 CX000601)
- National Institutes of Health (1rf1ag071170-01)
- National Institute on Aging (R01AG017917, R01AG056533, RF1 AG071170, U19AG033655, R01AG015819, P30AG010161, U01AG061357, U01AG061356, U54AG065187, P30AG066507, R01AG072120, R01AG079170, R01AG075827, R01AG087250, P30AG066511, P30AG072975)
- Topics
- Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Sex and Gender in Healthcare
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Keywords
- sex differences, brain proteome, sex-biased gene expression, protein abundance, mental illness, neurological disorders
- MeSH terms
- Brain, Female, Humans, Male, Phenotype, Sex Characteristics, Multifactorial Inheritance, Genome-Wide Association Study
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