Adaptive Digital Tissue Deconvolution

Abstract

Motivation: The inference of cellular compositions from bulk and spatial transcriptomics data increasingly complements data analyses. Multiple computational approaches were suggested and recently, machine learning techniques were developed to systematically improve estimates. Such approaches allow to infer additional, less abundant cell types. However, they rely on training data which do not capture the full biological diversity encountered in transcriptomics analyses; data can contain cellular contributions not seen in the training data and as such, analyses can be biased or blurred. Thus, computational approaches have to deal with unknown, hidden contributions. Moreover, most methods are based on cellular prototypes which serve as a reference; e.g., a generic T-cell profile is used to infer the proportion of T-cells. It is well known that cells adapt their molecular phenotype to the environment and as such, pre-specified cell prototypes can distort the inference of cellular compositions. Results: We propose Adaptive Digital Tissue Deconvolution (ADTD) to estimate cellular proportions of pre-selected cell types together with possibly unknown and hidden background contributions. Moreover, ADTD adapts the prototypic reference profiles to the molecular environment of the cells, which allows one to resolve cell-type specific regulation from bulk transcriptomics data. The performance of ADTD was verified in simulation studies, and in an application to breast cancer data we demonstrate how ADTD can be used to gain insights into molecular differences between breast cancer sub-types. Availability and implementation: A python implementation of ADTD and a tutorial are available at https://doi.org/10.5281/zenodo.7548362

Virtual Tissue Expression Analysis

“…Recent methodologies fine-tune the reference profiles to the particular tissue type of interest [6, 7, 8, 9]. However, even with these advancements, the within-tissue diversity of cells still remains concealed.…”

“…When we have knowledge of cell type frequencies within the bulk tissue, it becomes feasible to attribute bulk gene expression of specific genes to individual cell types [10, 11, 12, 9].…”