A nearest-neighbor based nonparametric test for viral remodeling in heterogeneous single-cell proteomic data

Abstract

An important problem in contemporary immunology studies based on single-cell protein expression data is to determine whether cellular expressions are remodeled postinfection by a pathogen. One natural approach for detecting such changes is to use nonparametric two-sample statistical tests. However, in single-cell studies direct application of these tests is often inadequate, because single-cell level expression data from processed uninfected populations often contain attributes of several latent subpopulations with highly heterogeneous characteristics. As a result, viruses often infect these different subpopulations at different rates, in which case the traditional nonparametric two-sample tests for checking similarity in distributions are no longer conservative. In this paper, we propose a new nonparametric method for Testing Remodeling under Heterogeneity (TRUH) that can accurately detect changes in the infected samples compared to possibly heterogeneous uninfected samples. Our testing framework is based on composite nulls and is designed to allow the null model to encompass the possibility that the infected samples, though unaltered by the virus, might be dominantly arising from underrepresented subpopulations in the baseline data. The TRUH statistic, which uses nearest neighbor projections of the infected samples into the baseline uninfected population, is calibrated using a novel bootstrap algorithm. We demonstrate the nonasymptotic performance of the test via simulation experiments and also derive the large sample limit of the test statistic which provides theoretical support toward consistent asymptotic calibration of the test. We use the TRUH statistic for studying remodeling in tonsillar T cells under different types of HIV infection and find that, unlike traditional tests which do not have any heterogeneity correction, TRUH based statistical inference conforms to the biologically validated immunological theories on HIV infection.