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

• Published in: Communications biology Vol. 7; no. 1; p. 324
• Main Authors: Biedka, Stephanie, Alkam, Duah, Washam, Charity L., Yablonska, Svitlana, Storey, Aaron, Byrum, Stephanie D., Minden, Jonathan S.
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 14.03.2024; Nature Publishing Group; Nature Portfolio
• Subjects: 38; 38/22; 38/23; 38/90; 38/91; 631/1647/2230; 631/337/2019; 631/67; 82; 82/58; 82/83; Animals; Biological analysis; Biomedical and Life Sciences; Deoxyribonucleic acid; DNA; DNA - genetics; DNA sequencing; Genomes; Life Sciences; Malignancy; Mass Spectrometry - methods; Mass spectroscopy; Mice; Multiomics; Peptides; Proteins; Proteome - metabolism; Proteomes; Ribonucleic acid; RNA; RNA - genetics; Scientific imaging; Solubilization; Transcriptomes; Tumor cell lines
• ISSN: 2399-3642; 2399-3642
• DOI: 10.1038/s42003-024-05993-1

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. The authors present a method utilizing the reversible protein tag ProMTag to prepare high-quality, sequencing-ready DNA and RNA, and either intact proteins or mass spectrometry-ready peptides for whole proteome analysis from a single sample.