Genotype-Epigenome-Phenotype Integration Reveals the Contributions of Peripheral Immune Cells to Bipolar Disorder Pathogenesis, Phenotypic Heterogeneity, and Therapy

Abstract Immune dysfunctions are believed to contribute to bipolar disorder (BD), yet their mechanistic basis remains unclear. To address this, we systematically characterize BD-associated epigenomic and genetic variation in peripheral blood immune cells by profiling and integrating 833 genome-wide maps of five histone modification marks across 180 individuals (88 Type I BD patients, 92 controls), coupled with whole-genome sequencing data and rich medical records. We annotate 450k candidate cis- regulatory elements (CREs) and identify differential CREs (dCREs) in BD patients, suggesting down-regulated adaptive and up-regulated innate immune response. We predict candidate BD driver genes in the circulating immune system, which frequently show matched brain activity mainly related to calcium signaling and endoplasmic reticulum (ER) transport, suggesting dysregulated synaptic transmission, neuronal plasticity, and ER stress. We find that candidate driver genes are often linked to BD GWAS variants through blood-specific eQTLs not found in any brain cell types, indicating potential causal roles of circulating immune cells in bipolar disorder. We then infer 24 latent factors of BD-differential CRE variation and use them to group the patients into five epigenomic subtypes, which also show distinct disease phenotypes, including infection and inflammation, osmotic laxative use and glucose intolerance, quetiapine use, and hypertension. We next associate immune-partitioned BD polygenic risk scores with patient epigenomic subtypes, revealing the genetic basis of BD patient heterogeneity captured by blood epigenomics. Lastly, by analyzing transcriptional responses to known pharmacological interventions in hematopoietic cells that enrich BD patient group-specific dysregulated genes, we identify drugs/compounds that could be repurposed for ameliorating BD-associated immune dysfunction in a patient group-dependent manner. Overall, based on our study of genotype-epigenome-phenotype integration, we infer a potentially causal role of immune cells in BD, offering insights into biomarkers, subtypes, and precision medicine interventions targeting peripheral immune dysfunction and thus advancing precision medicine in BD. Competing Interest Statement Mark A. Frye M.D. has received research support from Assurex Health, Breakthrough Discoveries for Thriving with Bipolar Disorder (BD2), Baszucki Brain Group, and Mayo Foundation; received CME Travel and Honoraria from Carnot Laboratories and has Financial Interest / Stock ownership / Royalties with Chymia LLC. Funding Statement This work was supported by the Mayo Clinic Center for Individualized Medicine. This study was supported, in part, by the Marriott Family Foundation, the Thomas and Elizabeth Grainger Fund in Bipolar Disorder Novel Therapeutics and Advanced Diagnostics, and the Mayo Clinic Center for Individualized Medicine; none had a role in the design, conduct, analysis, or submission of the study, collection, management, analysis, and interpretation of the data; preparation, review, or approval of the manuscript; and decision to submit the manuscript for publication. It was also supported by NIH grants DK126827 and DK84567 (Epigenomics and Spatial Biology Core) to T.O., and AG058002, MH109978, and MH119509 to M.K. Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The 180 participants (88 BD cases and 92 age and gender-matched controls) were from the Mayo Clinic Bipolar Disorder Biobank and the Mayo Clinic Biobank113, respectively. They had consented to research, including research using their EHR data26. This study was reviewed and approved by the Mayo Clinic Institutional Review Board and by the access committees from both biobanks. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Data availability Supplementary info and datasets are linked from https://data.broadinstitute.org/compbio1/BDBloodEpigenome/data. Since the raw sequencing data with genetic information are protected, application and authentication are needed before accessing the data.