Dataset Information

Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data

ABSTRACT: A quantitative time series of EGFR signaling was acquired using mass spectrometry-based phosphoproteomics to develop an algorithm that identifies signaling pathway structures. The study used Flp-In 293 cells expressing EGFR that were stimulated with EGF.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Epithelial Cell, Cell Culture

DISEASE(S): Disease Free

SUBMITTER: Anthony Gitter

LAB HEAD: Anthony Gitter

PROVIDER: PXD006697 | Pride | 2018-09-18

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20140214_pY_Flpin_EGFR_A_iTRAQ_1.pep.xml	Pepxml
	20140214_pY_Flpin_EGFR_A_iTRAQ_1.raw	Raw
	20140214_pY_Flpin_EGFR_A_iTRAQ_2.pep.xml	Pepxml
	20140214_pY_Flpin_EGFR_A_iTRAQ_2.raw	Raw
	20140215_Flpin_EGFR_A_iTRAQ_IMAC_f1.pep.xml	Pepxml

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Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data.

Köksal Ali Sinan AS Beck Kirsten K Cronin Dylan R DR McKenna Aaron A Camp Nathan D ND Srivastava Saurabh S MacGilvray Matthew E ME Bodík Rastislav R Wolf-Yadlin Alejandro A Fraenkel Ernest E Fisher Jasmin J Gitter Anthony A

Cell reports 20180901 13

We present a method for automatically discovering signaling pathways from time-resolved phosphoproteomic data. The Temporal Pathway Synthesizer (TPS) algorithm uses constraint-solving techniques first developed in the context of formal verification to explore paths in an interaction network. It systematically eliminates all candidate structures for a signaling pathway where a protein is activated or inactivated before its upstream regulators. The algorithm can model more than one hundred thousan ...[more]

PMID: 30257219

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Project description:Aberrant activation of Hedgehog (HH) signaling has been identified as a key etiologic factor of many human malignancies. Signal strength, target gene specificity, and oncogenic activity of HH signaling profoundly depend on interactions with other pathways such as epidermal growth factor receptor-mediated signaling which has been shown to cooperate with HH/GLI in basal cell carcinoma and pancreatic cancer. We demonstrate that the human medulloblastoma cell line Daoy possesses a fully inducible endogenous HH pathway. Treatment of Daoy cells with Sonic Hedgehog or Smoothened agonist induced expression of GLI1 protein and prevented processing of GLI3 to its repressor form. To study interactions between HH- and EGF-induced signaling in greater detail, time-resolved measurements were carried out and analyzed on the transcriptomic as well as proteomic level. Daoy cells responded to the co-treatment by downregulating GLI1, PTCH, and HHIP on the transcript level which was also seen when Amphiregulin (AREG) was used instead of EGF. The finding that EGFR signaling silences proteins acting as negative regulators of HH signaling is firstly described here as a novel crosstalk mechanism. Furthermore, combined EGFR/HH signaling maintains high GLI1 protein levels contrasting its downregulation on the transcript level. On the other hand, high level synergism was observed with respect to a strong and significant upregulation of numerous canonical EGF-targets with putative tumor-promoting properties such as MMP7, VEGFA, and IL-8. In conclusion, synergistic effects between EGFR and HH signaling can selectively induce a switch from a canonical HH/GLI profile to a modulated specific target gene profile pointing to more wide-spread, yet context-dependent, interactions between HH/GLI and growth factor receptor signaling in human malignancies. To study interactions between HH- and EGF-induced signaling, time-resolved measurements were carried out over a period of 24 h at 14 different time points after stimulation by EGF with and without additional stimulation by SHH. Furthermore, as a control, cells without any stimulation by EGF and SHH (control) and cells in the presents of SHH were analyzed. Overall, three biological replicates of 60 different treatment/timepoints were analyzed yielding 180 different samples.