Leveraging large-scale datasets and single cell omics data to develop a polygenic score for cisplatin-induced ototoxicity

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dc.contributor.authorMiao, Deanne Nixie
dc.contributor.authorWilke, MacKenzie
dc.contributor.authorPham, John
dc.contributor.authorLadha, Feryal
dc.contributor.authorSingh, Mansumeet
dc.contributor.authorArsenio, Janilyn
dc.contributor.authorLuca, Emilia
dc.contributor.authorDabdoub, Alain
dc.contributor.authorYang, Wejian
dc.contributor.authorYang, Jun J.
dc.contributor.authorDrögemöller, Britt
dc.date.accessioned2024-11-22T18:02:37Z
dc.date.available2024-11-22T18:02:37Z
dc.date.issued2024-10-08
dc.date.updated2024-11-01T04:31:12Z
dc.description.abstractAbstract Background Cisplatin-induced ototoxicity (CIO), characterized by irreversible and progressive bilateral hearing loss, is a prevalent adverse effect of cisplatin chemotherapy. Alongside clinical risk factors, genetic variants contribute to CIO and genome-wide association studies (GWAS) have highlighted the polygenicity of this adverse drug reaction. Polygenic scores (PGS), which integrate information from multiple genetic variants across the genome, offer a promising tool for the identification of individuals who are at higher risk for CIO. Integrating large-scale hearing loss GWAS data with single cell omics data holds potential to overcome limitations related to small sample sizes associated with CIO studies, enabling the creation of PGSs to predict CIO risk. Results We utilized a large-scale hearing loss GWAS and murine inner ear single nuclei RNA-sequencing (snRNA-seq) data to develop two polygenic scores: a hearing loss PGS (PGSHL) and a biologically informed PGS for CIO (PGSCIO). The PGSCIO included only variants which mapped to genes that were differentially expressed within cochlear cells that showed differential abundance in the murine snRNA-seq data post-cisplatin treatment. Evaluation of the association of these PGSs with CIO in our target CIO cohort revealed that PGSCIO demonstrated superior performance (P = 5.54 × 10− 5) relative to PGSHL (P = 2.93 × 10− 3). PGSCIO was also associated with CIO in our test cohort (P = 0.04), while the PGSHL did not show a significant association with CIO (P = 0.52). Conclusion This study developed the first PGS for CIO using a large-scale hearing loss dataset and a biologically informed filter generated from cisplatin-treated murine inner ear snRNA-seq data. This innovative approach offers new avenues for developing PGSs for pharmacogenomic traits, which could contribute to the implementation of tailored therapeutic interventions. Further, our approach facilitated the identification of specific cochlear cells that may play critical roles in CIO. These novel insights will guide future research aimed at developing targeted therapeutic strategies to prevent CIO.
dc.identifier.citationHuman Genomics. 2024 Oct 08;18(1):112
dc.identifier.doi10.1186/s40246-024-00679-5
dc.identifier.urihttp://hdl.handle.net/1993/38677
dc.language.isoeng
dc.language.rfc3066en
dc.publisherBMC
dc.rightsopen accessen_US
dc.rights.holderThe Author(s)
dc.subjectCisplatin-induced ototoxicity
dc.subjectPharmacogenomics
dc.subjectPolygenic scores
dc.subjectSingle-nuclei RNA-sequencing
dc.titleLeveraging large-scale datasets and single cell omics data to develop a polygenic score for cisplatin-induced ototoxicity
dc.typeJournal Article
local.author.affiliationRady Faculty of Health Sciences::Max Rady College of Medicine::Department of Biochemistry and Medical Genetics
oaire.citation.issue112
oaire.citation.titleHuman Genomics
oaire.citation.volume18
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