Fundamental limits on dynamic inference from single cell snapshots

Abstract

Single cell expression profiling reveals the molecular states of individual cells with unprecedented detail. However, because these methods destroy cells in the process of analysis, they cannot measure how gene expression changes over time. But some information on dynamics is present in the data: the continuum of molecular states in the population can reflect the trajectory of a typical cell. Many methods for extracting single cell dynamics from population data have been proposed. However, all such attempts face a common limitation: for any measured distribution of cell states, there are multiple dynamics that could give rise to it, and by extension, multiple possibilities for underlying mechanisms of gene regulation. Here, we describe the aspects of gene expression dynamics that cannot be inferred from a static snapshot alone and identify assumptions necessary to constrain a unique solution for cell dynamics from static snapshots. We translate these constraints into a practical algorithmic approach, Population Balance Analysis (PBA), which makes use of a method from spectral graph theory to solve a class of high dimensional differential equations. We use simulations to show the strengths and limitations of PBA, and then apply it to single-cell profiles of hematopoietic progenitor cells (HPCs). Cell state predictions from this analysis agree with HPC fate assays reported in several papers over the past two decades. By highlighting the fundamental limits on dynamic inference faced by any method, our framework provides a rigorous basis for dynamic interpretation of a gene expression continuum and clarifies best experimental designs for trajectory reconstruction from static snapshot measurements.\n\nSignificanceSeeing a snapshot of individuals at different stages of a process can reveal what the process would look like for a single individual over time. Biologists apply this principle to infer temporal sequences of gene expression states in cells from measurements made at a single moment in time. However, these inferences are fundamentally under-determined. Using a conservation law, we enumerate reasons that there is no unique dynamics associated with a single snapshot, limiting our ability to infer gene regulatory mechanisms. We then propose a method for dynamic inference that provides a unique dynamic solution under defined approximations and apply it to data from bone marrow stem cells. Overall, this study introduces formal biophysical approaches to single cell bioinformatics.\n\nClassificationBIOLOGICAL SCIENCES / Systems Biology