Identifying Subpopulations of Cells in Single-Cell Transcriptomic Data: A Bayesian Mixture Modeling Approach to Zero Inflation of Counts.

In the study of single-cell RNA-seq (scRNA-Seq) data, a key component of the analysis is to identify subpopulations of cells in the data. A variety of approaches to this have been considered, and although many machine learning-based methods have been developed, these rarely give an estimate of uncertainty in the cluster assignment. To allow for this, probabilistic models have been developed, but scRNA-Seq data exhibit a phenomenon known as dropout, whereby a large proportion of the observed read counts are zero. This poses challenges in developing probabilistic models that appropriately model the data. We develop a novel Dirichlet process mixture model that employs both a mixture at the cell level to model multiple populations of cells and a zero-inflated negative binomial mixture of counts at the transcript level. By taking a Bayesian approach, we are able to model the expression of genes within clusters, and to quantify uncertainty in cluster assignments. It is shown that this approach outperforms previous approaches that applied multinomial distributions to model scRNA-Seq counts and negative binomial models that do not take into account zero inflation. Applied to a publicly available data set of scRNA-Seq counts of multiple cell types from the mouse cortex and hippocampus, we demonstrate how our approach can be used to distinguish subpopulations of cells as clusters in the data, and to identify gene sets that are indicative of membership of a subpopulation.

Immune Cell Networks Uncover Candidate Biomarkers of Melanoma Immunotherapy Response.

The therapeutic activation of antitumour immunity by immune checkpoint inhibitors (ICIs) is a significant advance in cancer medicine, not least due to the prospect of long-term remission. However, many patients are unresponsive to ICI therapy and may experience serious side effects; companion biomarkers are urgently needed to help inform ICI prescribing decisions. We present the IMMUNETS networks of gene coregulation in five key immune cell types and their application to interrogate control of nivolumab response in advanced melanoma cohorts. The results evidence a role for each of the IMMUNETS cell types in ICI response and in driving tumour clearance with independent cohorts from TCGA. As expected, 'immune hot' status, including T cell proliferation, correlates with response to first-line ICI therapy. Genes regulated in NK, dendritic, and B cells are the most prominent discriminators of nivolumab response in patients that had previously progressed on another ICI. Multivariate analysis controlling for tumour stage and age highlights CIITA and IKZF3 as candidate prognostic biomarkers. IMMUNETS provide a resource for network biology, enabling context-specific analysis of immune components in orthogonal datasets. Overall, our results illuminate the relationship between the tumour microenvironment and clinical trajectories, with potential implications for precision medicine.