Characterization of Gene Expression Programs and Their Dependence on Ligand Identity Within the Bone Morphogenetic Protein (BMP) Signaling Pathway

Signaling pathways have a central role in the development and homeostasis of an organism, as well as controlling cellular fate decisions. One very essential and well-established signaling pathway is the bone morphogenetic protein (BMP) signaling pathway, which is part of the Transforming Growth Factor-β (TGF-β) superfamily of proteins. The BMP pathway, as well as many other signaling pathways, exhibit a curious feature of bottleneck architecture, where many ligand variants converge and activate a small number of intracellular mediators which then diverge as they regulate many target genes. This intriguing architecture raises questions regarding the way information is processed by the cells and makes us wonder how such converging architectures could transduce information about the dose and combinatorial pattern of signaling ligands through a common signal transduction pathway. In this study, we use multiplexed single-cell RNA sequencing technology to analyze the transcriptional differences across an extensive set of ligand combinations and concentrations. By analyzing this high content dataset, we successfully identified distinct transcriptional programs that are controlled by the single BMP pathway, and the specific ligands that give rise to each program. Furthermore, we study the combinatorial logic by which multiple BMP signals, each regulating a distinct program, are integrated. Defining the set of response programs controlled by the BMP pathway would help us uncover fundamental principles of information encoding and decoding in similar bottleneck architectures and better understand the way extracellular information is perceived by individual cells and control their decision-making processes and fate.