Investigation of the usefulness of liver-specific deconvolution method by establishing a liver benchmark dataset

Immune responses in the liver are related to the development and progression of liver failure, and precise prediction of their behavior is important. Deconvolution is a methodology for estimating the immune cell proportions from the transcriptome, and it is mainly applied to blood-derived samples and tumor tissues. However, the influence of tissue-specific modeling on the estimation results has rarely been investigated. Here, we constructed a system to evaluate the performance of the deconvolution method on liver transcriptome data. We prepared seven mouse liver injury models using small-molecule compounds and established a benchmark dataset with corresponding liver bulk RNA-Seq and immune cell proportions. RNA-Seq expression for nine leukocyte subsets and four liver-associated cell types were obtained from the Gene Expression Omnibus to provide a reference. We found that the combination of reference cell sets affects the estimation results of reference-based deconvolution methods and established a liver-specific deconvolution by optimizing the reference cell set for each cell to be estimated. We applied this model to independent datasets and showed that liver-specific modeling is highly extrapolatable. We expect that this approach will enable sophisticated estimation from rich tissue data accumulated in public databases and to obtain information on aggregated immune cell trafficking. Graphical Abstract