Imputing Single-Cell Protein Abundance in Multiplex Tissue Imaging

Multiplex tissue imaging are a collection of increasingly popular single-cell spatial proteomics and transcriptomics assays for characterizing biological tissues both compositionally and spatially. However, several technical issues limit the utility of multiplex tissue imaging, including the limited number of molecules (proteins and RNAs) that can be assayed, tissue loss, and protein probe failure. In this work, we demonstrate how machine learning methods can address these limitations by imputing protein abundance at the single-cell level using multiplex tissue imaging datasets from a breast cancer cohort. We first compared machine learning methods’ strengths and weaknesses for imputing single-cell protein abundance. Machine learning methods used in this work include regularized linear regression, gradient-boosted regression trees, and deep learning autoencoders. We also incorporated cellular spatial information to improve imputation performance. Using machine learning, single-cell protein expression can be imputed with mean absolute error ranging between 0.05-0.3 on a [0,1] scale. Finally, we used imputed data to predict whether single cells were more likely to come from pre-treatment or post-treatment biopsies. Our results demonstrate (1) the feasibility of imputing single-cell abundance levels for many proteins using machine learning; (2) how including cellular spatial information can substantially enhance imputation results; and (3) the use of single-cell protein abundance levels in a use case to demonstrate biological relevance.