One-pot method for preparing DNA, RNA, and protein for multiomics analysis II

Typical multiomics studies employ separate methods for DNA, RNA, and protein sample preparation, which is labor intensive, costly, and prone to sampling bias. We describe a method for preparing high-quality, sequencing-ready DNA and RNA, and either intact proteins or mass-spectrometry-ready peptides for whole proteome analysis from a single sample. This method utilizes a reversible protein tagging scheme to covalently link all proteins in a lysate to a bead-based matrix and nucleic acid precipitation and selective solubilization to yield separate pools of protein and nucleic acids. We demonstrate the utility of this method to compare the genomes, transcriptomes, and proteomes of four triple-negative breast cancer cell lines with different degrees of malignancy. These data show the involvement of both RNA and associated proteins, and protein-only dependent pathways that distinguish these cell lines. We also demonstrate the utility of this multiomics workflow for tissue analysis using mouse brain, liver, and lung tissue. To assess the quality and reproducibility of our novel multiomics sample preparation workflow, we prepared DNA, RNA, and peptides from four triple-negative breast cancer cell lines that exhibit different degrees of malignancy: MCF10A (non-tumorigenic), MCFNeoT (benign hyperplasia), MCFT1 (atypical hyperplasia), MCFCA1 (invasive cancer). Three biological replicates were carried out with each cell line.