Time-course RNAseq of Pancreatic cell lines with ERK inhibitor treatment
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ABSTRACT:
PROVIDER: PRJEB25806 | ENA |
REPOSITORIES: ENA
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Project description:Mutational activation of the KRAS oncogene is a major genetic driver of pancreatic ductal adenocarcinoma (PDAC) growth. KRAS-dependent PDAC growth is mediated primarily through persistent activation of the RAF-MEK-ERK mitogen-activated protein kinase (MAPK) cascade, one of the most extensively studied cancer signaling networks. While substrates of RAF and MEK kinases are highly restricted, ERK1/2 has been attributed to over 1,000 substrates. In this study, we used the highly selective ERK1/2 inhibitor, SCH772984, and proteomic and phosphoproteomic analyses to extend the repertoire of ERK-dependent phosphosites and phosphoproteins in PDAC. We validated the specificity of SCH772984 in our cell lines using multiplexed inhibitor beads coupled with mass spectrometry (MIB/MS). We then performed phosphoproteomics and global proteomics in a panel of PDAC cell lines and identified 5,117 ERK-dependent phosphosites on 2,252 proteins, of which 88% and 67%, respectively, were not previously associated with ERK. We then utilized our recently annotated serine/threonine kinome motif database to dissect the phosphoproteome and reveal an expansive ERK-regulated kinase network. We found that ERK- and immediate downstream kinase RSK-substrate motifs predominated after one hour of ERK inhibition, whereas cell cycle regulatory cyclin-dependent kinase motifs predominated by 24 h, reflecting a highly dynamic ERK-dependent phosphoproteome. We find compensatory activation of HIPK, CLK, PKN, PAK, and DYRK family kinases. Finally, using the genome-wide CRISPR-Cas9 dataset in the Cancer Dependency Map portal (DepMap), we determined that approximately 18% of ERK dependent phosphoproteins are essential for pancreatic cancer growth, and these are enriched in nuclear proteins. Together, our findings provide a system-wide profile of the mechanistic basis for ERK-driven pancreatic cancer growth.
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Project description:Mutational activation of the KRAS oncogene is a major genetic driver of pancreatic ductal adenocarcinoma (PDAC) growth. KRAS-dependent PDAC growth is mediated primarily through persistent activation of the RAF-MEK-ERK mitogen-activated protein kinase (MAPK) cascade, one of the most extensively studied cancer signaling networks. While substrates of RAF and MEK kinases are highly restricted, ERK1/2 has been attributed to over 1,000 substrates. In this study, we used the highly selective ERK1/2 inhibitor, SCH772984, and proteomic and phosphoproteomic analyses to extend the repertoire of ERK-dependent phosphosites and phosphoproteins in PDAC. We validated the specificity of SCH772984 in our cell lines using multiplexed inhibitor beads coupled with mass spectrometry (MIB/MS). We then performed phosphoproteomics and global proteomics in a panel of PDAC cell lines and identified 5,117 ERK-dependent phosphosites on 2,252 proteins, of which 88% and 67%, respectively, were not previously associated with ERK. We then utilized our recently annotated serine/threonine kinome motif database to dissect the phosphoproteome and reveal an expansive ERK-regulated kinase network. We found that ERK- and immediate downstream kinase RSK-substrate motifs predominated after one hour of ERK inhibition, whereas cell cycle regulatory cyclin-dependent kinase motifs predominated by 24 h, reflecting a highly dynamic ERK-dependent phosphoproteome. We find compensatory activation of HIPK, CLK, PKN, PAK, and DYRK family kinases. Finally, using the genome-wide CRISPR-Cas9 dataset in the Cancer Dependency Map portal (DepMap), we determined that approximately 18% of ERK dependent phosphoproteins are essential for pancreatic cancer growth, and these are enriched in nuclear proteins. Together, our findings provide a system-wide profile of the mechanistic basis for ERK-driven pancreatic cancer growth.
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Project description:Fgf signaling via Erk activation has been associated with both neural induction and the generation of a primed state for the differentiation of embryonic stem cells (ESCs) to all somatic lineages. To dissect the role of Erk in both ESC self-renewal and lineage specification we explore the requirements for this pathway in various in vitro differentiation settings. A combination of pharmacological inhibition of Erk signaling and genetic loss of function experiments reveal a role for Erk signaling in suppressing endodermal differentiation, but not neural specification. Activation of Erk signaling in ESCs de-represses primitive endoderm (PrE) gene expression as a consequence of inhibiting the pluripotent/epiblast network. The early response to Erk activation correlates with functional PrE priming while sustained Erk activity results in PrE differentiation. Taken together, our results suggest that Erk signaling suppresses pluripotent gene expression to enable endodermal differentiation. We use microarray analysis to determine the transcription response to Erk1/2 in mouse embryonic stem cells across a 24 hour window of time Mouse ESCs carrying a tamoxifen inducible constitutively active c-Raf fusion protein were stimulated for 6 time points (30minutes, 1 hour, 2 hours, 4 hours, 8 hours, and 24 hours) in the presence of 250nM PD173074. Uninduced (0h hours) and DMSO only treated cells served as controls.
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