Department of Obstetrics and Gynecology, University of California, Los Angeles, Los Angeles, United States; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, United States
Feyiang Ma
Molecular Biology Institute, University of California, Los Angeles, Los Angeles, United States; Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
Austin Quach
Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
Anhyo Jeong
Department of Obstetrics and Gynecology, University of California, Los Angeles, Los Angeles, United States
Hannah L Sunshine
Department of Molecular, Cellular and Integrative Physiology, University of California, Los Angeles, Los Angeles, United States; Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, United States
Department of Biological Chemistry, University of California, Los Angeles, United States
Raphael Helaers
Human Molecular Genetics, de Duve Institute, University of Louvain, Brussels, Belgium
Xinmin Li
Department of Pathology and Laboratory Medicine, University of California, Los Angeles, United States
Matteo Pellegrini
Molecular Biology Institute, University of California, Los Angeles, Los Angeles, United States; Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
James A Wohlschlegel
Department of Biological Chemistry, University of California, Los Angeles, United States
Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, United States; Department of Cell and Developmental Biology, Northwestern University Feinberg School of Medicine, Chicago, United States
Environmental cues, such as physical forces and heterotypic cell interactions play a critical role in cell function, yet their collective contributions to transcriptional changes are unclear. Focusing on human endothelial cells, we performed broad individual sample analysis to identify transcriptional drifts associated with environmental changes that were independent of genetic background. Global gene expression profiling by RNA sequencing and protein expression by liquid chromatography–mass spectrometry directed proteomics distinguished endothelial cells in vivo from genetically matched culture (in vitro) samples. Over 43% of the transcriptome was significantly changed by the in vitro environment. Subjecting cultured cells to long-term shear stress significantly rescued the expression of approximately 17% of genes. Inclusion of heterotypic interactions by co-culture of endothelial cells with smooth muscle cells normalized approximately 9% of the original in vivo signature. We also identified novel flow dependent genes, as well as genes that necessitate heterotypic cell interactions to mimic the in vivo transcriptome. Our findings highlight specific genes and pathways that rely on contextual information for adequate expression from those that are agnostic of such environmental cues.
