Deconvolution-derived cell-type expression targets for personal genome sequence-to-expression prediction
TL;DR
Results support deconvolution as a feasible approach for generating cell-type-resolved training targets, while showing that target quality and limited cohort size remain important constraints.
Abstract
Sequence-to-function models learn regulatory features from genomic sequence, but they remain limited in their ability to predict gene-expression differences among individuals. Cell-type-specific regulatory effects may be obscured in bulk RNA sequencing, whereas paired genotype and single-cell expression cohorts remain small. We evaluated whether deconvolution of bulk RNA-seq could provide scalable cell-type-specific targets for personal-genome expression prediction. GTEx v8 bulk RNA-seq from six tissues was deconvolved with BayesPrism using single-nucleus reference profiles, producing targets across 83 tissue–cell-type contexts. Deconvolved expression agreed with matched pseudobulked GTEx single-nucleus RNA-seq, with median donor-level Pearson correlations across genes ranging from 0.53 to 0.73 by tissue. We compared genotype-feature models, regressors trained on frozen Enformer representations, and fine-tuned Enformer and Borzoi models. Across random and nonlinear-enriched gene sets, sequence-derived approaches generally outperformed genotype-feature baselines, while frozen Enformer features were competitive with end-to-end fine-tuning. For the random gene set, Fisher-averaged Pearson correlations were 0.122–0.142 for sequence-derived approaches and 0.081–0.086 for genotype-feature baselines in a coverage-aware sensitivity analysis. Model performance was positively associated with deconvolution–pseudobulk agreement for sequence-derived models (r = 0.35–0.43 across tissue–cell-type contexts), suggesting that target reliability may constrain downstream prediction. Context-specific Enformer fine-tuning did not materially out-perform a shared, combined-context strategy. These results support deconvolution as a feasible approach for generating cell-type-resolved training targets, while showing that target quality and limited cohort size remain important constraints. Frozen pretrained representations provide a computationally efficient and competitive baseline for personal sequence-to-expression modeling.