DRPPM-EASY: A Web-Based Framework for Integrative Analysis of Multi-Omics Cancer Datasets

• Published in: Biology (Basel, Switzerland) Vol. 11; no. 2; p. 260
• Main Authors: Obermayer, Alyssa, Dong, Li, Hu, Qianqian, Golden, Michael, Noble, Jerald D, Rodriguez, Paulo, Robinson, Timothy J, Teng, Mingxiang, Tan, Aik-Choon, Shaw, Timothy I
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 08-02-2022; MDPI
• Subjects: Acute lymphoblastic leukemia; Cancer; CCLE; Clustering; Computer applications; Consortia; Datasets; DNA damage; Gene expression; Integration; Lymphatic leukemia; Lymphocytes T; Mass spectrometry; Metastases; multi-omics analysis; Ovarian cancer; p53 Protein; Phenotypes; Programming languages; Proteins; Proteomes; Proteomics; R Shiny application; RNA-seq; Scientific imaging; T-cell acute lymphoblastic leukemia; Technical Note; Transcriptomes; Transcriptomics; Tumor cell lines; User experience; multi-omics analysis; RNA-seq; proteomics; CCLE; R Shiny application; T-cell acute lymphoblastic leukemia
• ISSN: 2079-7737; 2079-7737
• DOI: 10.3390/biology11020260

High-throughput transcriptomic and proteomic analyses are now routinely applied to study cancer biology. However, complex omics integration remains challenging and often time-consuming. Here, we developed DRPPM-EASY, an R Shiny framework for integrative multi-omics analysis. We applied our application to analyze RNA-seq data generated from a USP7 knockdown in T-cell acute lymphoblastic leukemia (T-ALL) cell line, which identified upregulated expression of a TAL1-associated proliferative signature in T-cell acute lymphoblastic leukemia cell lines. Next, we performed proteomic profiling of the USP7 knockdown samples. Through DRPPM-EASY-Integration, we performed a concurrent analysis of the transcriptome and proteome and identified consistent disruption of the protein degradation machinery and spliceosome in samples with USP7 silencing. To further illustrate the utility of the R Shiny framework, we developed DRPPM-EASY-CCLE, a Shiny extension preloaded with the Cancer Cell Line Encyclopedia (CCLE) data. The DRPPM-EASY-CCLE app facilitates the sample querying and phenotype assignment by incorporating meta information, such as genetic mutation, metastasis status, sex, and collection site. As proof of concept, we verified the expression of TP53 associated DNA damage signature in TP53 mutated ovary cancer cells. Altogether, our open-source application provides an easy-to-use framework for omics exploration and discovery.