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Science Studies Use Single-Cell RNA Sequencing to Study Cell States, Apply Deep Phenotyping to Pregnancy

A computational method for predicting cellular differentiation states using single-cell RNA sequencing (scRNAseq) data is presented in this week's Science. In the report, scientists from Stanford University and their collaborators show that the number of detectably expressed genes per cell strongly associates with cellular differentiation status. Using this finding, they create a framework — dubbed CytoTRACE — for predicting relative differentiation states from single-cell transcriptomes. When applied to different tissues and organisms, CytoTRACE outperformed previous methods and nearly 19,000 annotated gene sets for resolving 52 experimentally determined developmental trajectories, they write. It also helped identify quiescent stem cells and revealed genes that contribute to breast tumorigenesis. "We envision that our approach will complement existing scRNAseq analysis strategies, with implications for the identification of immature cells and their developmental trajectories in complex tissues throughout multicellular life," the scientists state.

The application of deep phenotyping — a healthcare research approach that combines omics data with digital health data, clinical lab tests, and other information — during pregnancy can not only improve birth outcomes but also identify the antecedents of lifelong health and wellness, the Institute for Systems Biology's Leroy Hood and others write in Science Translational Medicine this week. Despite its potential, the time and costs associated with deep phenotyping limit its use in the clinic, the authors write. But pregnancy is uniquely suited to the approach since it involves frequent engagement with healthcare providers, has a relatively short duration, and is critically important to lifelong health. "Deep phenotyping of pregnancy, combined with data on neonates and infants … may usher in a comprehensive view on early developmental perturbations before they manifest as diseases," they state. "Realizing the immense potential of these approaches, when deployed during or after pregnancy, should facilitate collaborations for enhancement of pregnancy-focused, system-oriented transdisciplinary research and personalized clinical interventions that may vastly affect health and wellness during pregnancy and across the human life span."