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Integrating human brain proteomes with genome-wide association data implicates novel proteins in post-traumatic stress disorder

Abstract

Genome-wide association studies (GWAS) have identified several risk loci for post-traumatic stress disorder (PTSD); however, how they confer PTSD risk remains unclear. We aimed to identify genes that confer PTSD risk through their effects on brain protein abundance to provide new insights into PTSD pathogenesis. To that end, we integrated human brain proteomes with PTSD GWAS results to perform a proteome-wide association study (PWAS) of PTSD, followed by Mendelian randomization, using a discovery and confirmatory study design. Brain proteomes (N = 525) were profiled from the dorsolateral prefrontal cortex using mass spectrometry. The Million Veteran Program (MVP) PTSD GWAS (n = 186,689) was used for the discovery PWAS, and the Psychiatric Genomics Consortium PTSD GWAS (n = 174,659) was used for the confirmatory PWAS. To understand whether genes identified at the protein-level were also evident at the transcript-level, we performed a transcriptome-wide association study (TWAS) using human brain transcriptomes (N = 888) and the MVP PTSD GWAS results. We identified 11 genes that contribute to PTSD pathogenesis via their respective cis-regulated brain protein abundance. Seven of 11 genes (64%) replicated in the confirmatory PWAS and 4 of 11 also had their cis-regulated brain mRNA levels associated with PTSD. High confidence level was assigned to 9 of 11 genes after considering evidence from the confirmatory PWAS and TWAS. Most of the identified genes are expressed in other PTSD-relevant brain regions and several are preferentially expressed in excitatory neurons, astrocytes, and oligodendrocyte precursor cells. These genes are novel, promising targets for mechanistic and therapeutic studies to find new treatments for PTSD.

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Fig. 1
Fig. 2: Results of the discovery PWAS of PTSD.
Fig. 3: Bar graph of single-cell-type enrichment for the 11 potential PTSD-causal genes.
Fig. 4: Expression of the 11 potential PTSD-causal genes in different PTSD-relevant brain regions.

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Data availability

—MVP PTSD GWAS summary statistics: dbGAP (phs001672.v6.p1)

—PGC-PTSD GWAS summary statistics: publicly available on the PGC website (https://www.med.unc.edu/pgc/download-results/) under for the benefit of the wider biomedical community.

—Proteomic datasets: genotypes, protein expression levels, expression covariates: https://www.synapse.org/#!Synapse:syn24872746—AMP-AD datasets: genotypes, transcript expression levels, expression covariates https://adknowledgeportal.synapse.org/Explore/Studies/DetailsPage?Study=syn22313785—CMC datasets: We downloaded the transcript weights from http://gusevlab.org/projects/fusion/, https://data.broadinstitute.org/alkesgroup/FUSION/WGT/CMC.BRAIN.RNASEQ.tar.bz2—Sc-RNAseq datasets: https://www.synapse.org/#!Synapse:syn21589957—Allen brain atlas https://human.brain-map.org/microarray/search

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Acknowledgements

We are grateful to the participants of the ROS, MAP, Mayo, Mount Sinai Brain Bank, and Banner Sun Health Research Institute Brain and Body Donation Program for their time and participation. We thank the Psychiatric Genomics Consortium PTSD working group for making the summary statistics from the published PTSD GWAS in Nievergelt et al. [16] available. We thank Jiaqi Liu for her assistance with creating the Fig. 3. The authors thank MVP staff, researchers, and volunteers, who have contributed to MVP, and especially participants who previously served their country in the military and now generously agreed to enroll in the study. (See https://www.research.va.gov/mvp/ for more details) The following NIH grants supported this work: P30 AG066511 (AIL), P50 AG025688 (AIL), R01 AG015819 (DAB), R01 AG017917 (DAB), R01 AG056533 (TSW, APW), VA 1IK4 BX005219 (APW), I01 BX005686 (APW). TSW is also supported by R56 AG060757, R56 AG062256, RF1 AG057470. NTS is also supported by R01 AG053960, R01 AG057911, R01 AG061800. DAB is also supported by RC2 AG036547, U01 AG046152, U01 AG061356. AIL is also supported by U01 AG046161, U01 AG061357. APW is also supported by U01 MH115484, VA I01 BX003853. CMN, MBS, KCK, KJR were supported by R01MH106595. The Brain and Body Donation Program has been supported by NIH, the Arizona Department of Health Services, the Arizona Biomedical Research Commission and the Michael J. Fox Foundation for Parkinson’s Research. The views expressed in this work do not necessarily represent the views of the Veterans Administration or the United States Government.

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TSW and APW wrote the first draft of the paper. DAB, AIL, and NTS obtained the data. ESG, YL, SMV, JG, DMD, AL, TSW, and APW performed data analysis. MSB, AXM, CMN, KCK, DFL, JG, MBS, KJR, DAB, AIL contributed to data interpretation. All authors critically edited and commented on the paper.

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Correspondence to Aliza P. Wingo.

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Wingo, T.S., Gerasimov, E.S., Liu, Y. et al. Integrating human brain proteomes with genome-wide association data implicates novel proteins in post-traumatic stress disorder. Mol Psychiatry 27, 3075–3084 (2022). https://doi.org/10.1038/s41380-022-01544-4

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