A pluripotent stem cell atlas of multilineage differentiation revealsTMEM88as a developmental regulator of mammalian blood pressure

Abstract

This study develops a versatile cell multiplexing and data analysis platform to accelerate knowledge gain into mechanisms of cell differentiation. We engineer a cell barcoding system in human cells enabling multiplexed single-cell RNA sequencing for high throughput perturbation of customisable and versatile experimental conditions. This is coupled with a new computational analysis pipeline that overcomes the limitations of existing algorithms by using an unsupervised, genome-wide, orthogonal biological reference point to reveal the cell diversity and regulatory networks of any input scRNA-seq data set. We implement this pipeline by engineering transcribed barcodes into induced pluripotent stem cells and multiplex 62 independent experimental conditions comprising eight differentiation time points and nine developmental signalling perturbations with duplicates. We identify and deconstruct the temporal, signalling, and gene regulatory basis of multilineage iPSC differentiation into ectoderm, mesoderm, and endoderm cell types. This study provides a cellular and computational pipeline to study cell differentiation applicable to diverse fields of developmental biology, drug discovery, and disease modelling.

Inferring cell diversity in single cell data using consortium-scale epigenetic data as a biological anchor for cell identity

“…In our companion study, we demonstrate the utility of TRIAGE-Cluster by applying it on a multiplexed single cell atlas of iPSC differentiation data that integrates temporal data across eight time points and signalling data with nine developmental signalling perturbation [44]. 48 peaks were identified from the in vitro differentiation atlas data, and clustering performance was evaluated using a trajectory approach VIA which evaluates cell states relationship [45].…”

“…We provide a second analysis of paraxial mesoderm lineage cell types based on detailed dissection using TRIAGE-associated outputs ( Figure S5 ). Further examples of the data interpretation pipeline outlined here are provided for analysis of in vitro differentiation from pluripotency outlined in the companion paper [44]. The collective results of both studies including new data, software package downloads, and data analysis dashboard can be accessed online (http://cellfateexplorer.d24h.hk/).…”