Cell type and gene expression deconvolution with BayesPrism enables Bayesian integrative analysis across bulk and single-cell RNA sequencing in oncology

Inferring single-cell compositions and their contributions to global gene expression changes from bulk RNA sequencing (RNA-seq) datasets is a major challenge in oncology. Here we develop Bayesian cell proportion reconstruction inferred using statistical marginalization (BayesPrism), a Bayesian method to predict cellular composition and gene expression in individual cell types from bulk RNA-seq, using patient-derived, scRNA-seq as prior information. We conduct integrative analyses in primary glioblastoma, head and neck squamous cell carcinoma and skin cutaneous melanoma to correlate cell type composition with clinical outcomes across tumor types, and explore spatial heterogeneity in malignant and nonmalignant…

• DR
  Damon Runyon Cancer Research Foundation
• CF
  Croucher Foundation
• LR
  Liaoning Revitalization Talents Program

  Award: XLYC2002010
• NI
  National Institutes of Health

  Awards: U54-CA209975, R01-HG009309, P30-CA008748
• NH
  National Human Genome Research Institute

  Award: R01-HG009309
• NC
  National Cancer Institute

  Awards: CA008748, U2C-CA288284, CA209975, U54-CA209975, P30-CA008748