Integrated, High-Throughput, Multiomics Platform Enables Data-Driven Construction of Cellular Responses and Reveals Global Drug Mechanisms of Action

Abstract

An understanding of how cells respond to perturbation is essential for biological applications; however, most approaches for profiling cellular response are limited in scope to pre-established targets. Global analysis of molecular mechanism will advance our understanding of the complex networks constituting cellular perturbation and lead to advancements in areas, such as infectious disease pathogenesis, developmental biology, pathophysiology, pharmacology, and toxicology. We have developed a high-throughput multiomics platform for comprehensive, de novo characterization of cellular mechanisms of action. Platform validation using cisplatin as a test compound demonstrates quantification of over 10 000 unique, significant molecular changes in less than 30 days. These data provide excellent coverage of known cisplatin-induced molecular changes and previously unrecognized insights into cisplatin resistance. This proof-of-principle study demonstrates the value of this platform as a resource to understand complex cellular responses in a high-throughput manner.

RNA sequencing and proteomics approaches reveal novel deficits in the cortex of Mecp2-deficient mice, a model for Rett syndrome

“…The median relative abundance of multiple peptides used for protein-level quantification was applied to determine the overall relative protein abundance of the Mecp2 Jae/y mice versus WT. Statistical significance of protein-level differences was determined using an unpaired t -test for all the peptides used to quantify each protein using a p -value cutoff of p < 0.1 as previously applied [ 54 ].…”

“…Ingenuity® Pathway Analysis (IPA®; Qiagen) was used to identify significant biological pathways in both RNA-Seq and proteomics data sets. A list of detected genes and detected proteins (including post-translational modifications) was used as the data input for both individual and comparison pathway analyses, using a q < 0.05 cutoff for the gene pathway and p < 0.1 cutoff for the protein pathway analyses [ 54 ] such that only significant genes/proteins were considered for significant pathways. The “User dataset” option was chosen to use each individual detected gene/protein data set as the “reference set” for which to generate significant pathways.…”

Multi-Omic Analysis Reveals Disruption of Cholesterol Homeostasis by Cannabidiol in Human Cell Lines

“…Recent advances in mass spectrometry-based omics has enabled nearly comprehensive identification and quantification of cellular proteomes and metabolomes (Blum et al, 2018). Multi-omic profiling strategies that combine mass spectrometry based proteomics with next generation sequencing-based transcriptomics can reveal critical and unexpected insights into the mechanisms of drug action in human cell lines (Hafner et al, 2019;Norris et al, 2017). In this study, we used multi-omic profiling, in combination with FRET-based biosensor microscopy screening, to examine the mode of CBD action in human neuroblastoma and keratinocyte cells.…”

Quantitative Systems Pharmacology for Neuroscience Drug Discovery and Development: Current Status, Opportunities, and Challenges

“…68 A promising new approach, promoted by the Defense Advanced Research Projects Agency (DARPA) and still in its infancy, is to use time-resolved, untargeted multi-omic measurements to infer a drug MoA, which in its first application presented a putative resistance mechanism for cisplatin. 69 Identifying the target or pathways involved is highly desirable but not required by regulatory agencies, as efficacy and safety are sufficient to approve a drug. However, such knowledge can greatly aid in establishing a biomarker of target engagement to help determine compound dosing, guide preclinical toxicology studies, and provide the opportunity to pivot to a target-based discovery program.…”