Fig. 4: Integration of proteomic, genomic and transcriptomic datasets identifies downstream mechanisms and targets of NCP26 inhibition.
From: Prolyl-tRNA synthetase as a novel therapeutic target in multiple myeloma
A Scatterplot of proteomic and RNAseq datasets depicting changes after 6 h of NCP26 exposure in AMO1 cells. Proteins highlighted in blue are proteins downregulated by NCP26, and highlighted in red are discussed in the text (P < 0.01). B Pathway analysis of downregulated proteins highlights processes related to cell cycle and mitosis. C Venn diagram illustrating overlap between downregulated gene transcripts (RNAseq) and proteins (LC/MS proteomics) after 6 h of NCP26 exposure plus CRISPR knockdown targets in MM. D STRING analysis of overlapping downregulated proteins (73, intersecting with CRISPR genes and RNAseq (11), or CRISPR (62)) establishes an NCP26 network of essential myeloma mechanisms in AMO1 cells. Cell cycle checkpoints are highlighted in green. Red label: protein overlap from all three datasets. E Subset of downregulated proteins upon NCP26 treatment containing proline-rich motifs. F AMO1 and RPMI 8226 cells were cultured with NCP26 for 6 h at the indicated doses. Whole-cell lysates were subjected to immunoblotting using indicated antibodies. G AMO1, RPMI 8226, and MM.1 S cells were transduced with shLuc or shEPRS (#1, #2) shRNAs. Whole-cell lysates were subjected to immunoblotting using indicated antibodies. H TCF3 knockdown results in anti-proliferative activity in MM cells. After puromycin selection of shRNA constructs, cells were cultured for 48 h, and growth was assessed by MTT assay. Data represent mean ± SD of triplicate cultures. ***P < 0.001.
