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Proteomic Sensors for Quantitative, Multiplexed, and Spatial Monitoring of Kinase Signaling

ABSTRACT: Proteomic Kinase Activity Sensors (ProKAS) is a new technology developed to allow for quantitative and multiplexed analyses of kinase signaling in living cells with spatial resolution. Kinase sensors are expressed in cells as part of a ProKAS construct, which uses signal peptides to localize to specific subcellular regions. The kinase sensors are targets for phosphorylation by specific kinases due to their amino acid sequences, which are derived from phosphoproteomic data or designed de novo using PSPA data that indicates kinase motif preferences. Includes data generated for revisions.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: William Comstock

LAB HEAD: Marcus Smolka

PROVIDER: PXD065795 | Pride | 2025-10-02

REPOSITORIES: Pride

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			Action	DRS
	102521_EJS_DMSOvsCPT_HCT_F01.mzXML	Mzxml
	102521_EJS_DMSOvsCPT_HCT_F01.pep.xml	Pepxml
	102521_EJS_DMSOvsCPT_HCT_F01.raw	Raw
	102521_EJS_DMSOvsCPT_HCT_F02.mzXML	Mzxml
	102521_EJS_DMSOvsCPT_HCT_F02.pep.xml	Pepxml

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Project description:Maintenance of genetic integrity is essential for survival of all organisms. Activating transcription factor 3 (ATF3) is a member of the c-AMP response element binding (CREB)/ATF family of transcription factors, and is highly inducible by various stress conditions including DNA damage. However, downstream targets and molecular basis underlying pleiotropic effects of ATF3 on the cell fate have been largely unknown. To identify ATF3 targets in the human genome, we carried out chromatin immunoprecipitation-microarray (ChiP-on-chip) and knockdown-expression profiling analysis using two models where ATF3 was either transiently induced or constitutively expressed. We show that ATF3 binds to an unexpectedly large number of targets; 5,984 promoters in HCT116 cells treated with an alkylating agene methyl methanesulfonate (MMS) and 1,423 promoters in LNCaP cells constitutively expressing ATF3. Importantly, targets of MMS-induced ATF3 are highly enriched not only for CREB/ATF motifs but also for binding sites of several stress sensors including DDIT3/CHOP, Egr1, and c-Ets which are concomitantly induced by MMS. Stress-induced ATF3 affects broad but select biological processes including cell cycle, cell death, adhesion, biosynthesis, and receptor signaling pathways. In addition, ATF3 binds to as many as 40% of the p53 targets and preferentially enhances MMS-induced activation of proapoptotic genes such as DR4, DR5, and PUMA, consistent with the proapoptotic effect of ATF3. These data shed new light on the co-regulatory function of ATF3 in the stress-induced transcription factor network. The comprehensive list of genomic targets of ATF3 will facilitate further understanding the role of ATF3 in determining life and death of cells under both physiological and tumour-associated stress conditions. Maintenance of genetic integrity is fundamental to survival of all organisms. DNA damage can be caused by various agents in environment and elicits complex responses in the cell. ATF3 is one of the transcription factors activated by various stress conditions including DNA damage, and has been shown to have pleiotropic effects on life and death of cells depending on the context of experimental conditions. It has been largely unknown, however, which genes and pathways are regulated by stress-induced ATF3. Here we attempted to answer this question by chromatin immunoprecipitation-microarray analysis of downstream targets of ATF3. We show that ATF3 binds to an unexpectedly large number of promoters (nearly 6,000) in a human colorectal cancer cell lineHCT116 treated with an alkylating agent methyl methanesulfonate. Interestingly, the ATF3 targets are highly enriched for binding sites of other stress sensors shedding light on a transcriptional co-regulatory network of DNA damage response. We further show that ATF3 regulates expression of genes in select biological processes including cell cycle, cell death, adhesion, metabolism, signal transduction, and the p53 pathway. The comprehensive list of ATF3 targets provides new insight into a highly inter-connected network of stress-induced transcription factors around ATF3. ChIP-chip samples: Comparison of ATF3-IP and whole genome DNA (control) Gene expression samples: HCT116 cells pre-transfected with either control siRNA or ATF3 knockdown siRNA and stimulated by methyl methanesulfonate (MMS) for 0, 6, 12, and 24 hours

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Proteomic Sensors for Quantitative, Multiplexed, and Spatial Monitoring of Kinase Signaling

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