Dataset Information

Characterization of Arginine Methylation in Cancer Cell using LC-MS/MS

ABSTRACT: Protein arginine methyltransferase 9 (PRMT9) activity has been observed to be elevated in cancer patients, including many types of leukemias, correlating with poor prognosis and decreased response to immune checkpoint inhibitors. By targeting PRMT9, we can eliminate PRMT9-proficient/immune-cold cancers via mechanisms such as Type-I Interferon associated immunity. Deleting PRMT9 resulted in a decrease in arginine methylation of regulators involved in RNA translation and DNA damage response. Through global proteomics and SILAC methyl(R) enrichment, we characterized arginine methylation changes in AML cell lines via LC-MS/MS.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

DISEASE(S): Acute Leukemia

SUBMITTER: Krystine Mansfield

LAB HEAD: Patrick Pirrotte

PROVIDER: PXD039441 | Pride | 2024-01-11

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	074_0003_02A_R_MethylSILAC1ug_18OCT19_CELL_HUM_LUM_0000_PA_120MIN_RS_RS_01.raw	Raw
	074_0003_02A_R_MethylSILAC1ug_18OCT19_CELL_HUM_LUM_0000_PA_120MIN_RS_RS_02.raw	Raw
	074_0003_02A_combined.zip	Other
	074_0003_03A_R_SILACGlobal_16DEC20_TIS_CHI_ECL_0000_01AA_240MIN_MNM_RS_02_FS_cv40.raw	Raw
	074_0003_03A_R_SILACGlobal_16DEC20_TIS_CHI_ECL_0000_01AA_240MIN_MNM_RS_02_FS_cv60.raw	Raw

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Project description:Protein methylation has been implicated in many important biological contexts including signaling, metabolism, and transcriptional control. Despite the importance of this post- translational modification, the global analysis of protein methylation by mass spectrometry-based proteomics has not been extensively studied due to the lack of robust, well-characterized techniques for methyl-peptidemethyl peptide enrichment. Here, to better investigate protein methylation, we optimized and compared two methods for methyl-peptidemethyl peptide enrichment: immunoaffinity purification (IAP) and high pH strong cation exchange (SCX). Comparison of these methods revealed that they are largely orthogonal for monomethyl arginine (MMA), suggesting that the usage of both techniques is required to provide a global view of protein methylation. Using both IAP and SCX, we investigated changes in protein methylation downstream of protein arginine methyltransferase 1 (PRMT1). Together, these techniques allowed us to quantify over ~1,000 arginine methylation sites on 407 proteins. Of these methylation sites, PRMT1 knockdown resulted in significant changes to 110 arginine methylation sites on 59 proteins. In contrast, zero lysine methylation sites were significantly changed upon PRMT1 knockdown. In PRMT1 knockdown cells, 24 MMA sites exhibited both significant downregulation (ie, putative PRMT1-mediated MMA targets) and 63 significant upregulation (ie, putative PRMT1-mediated ADMA targets). PRMT1 knockdown induced significant changes in asymmetric dimethyl arginine (ADMA), consistent with being PRMT1 targets. Additionally, We also observed that PRMT1 knockdown induced significant increases in symmetric dimethyl arginine (SDMA) methylation, suggesting that loss of PRMT1 activity allows scavenging of PRMT1 substrates by Type II PRMTs. Analysis of the subcellular localization and protein function of the significantly changing methyl-proteins revealed that the majority of PRMT1 substrates are localized to the nucleus and involved in RNA and DNA binding. Taken together, our results suggest that deep protein methylation profiling by mass spectrometry requires orthogonal enrichment techniques, identify novel PRMT1 methylation targets, and highlight in order to understand the dynamic interplay between methyltransferases in mammalian cells.

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Characterization of Arginine Methylation in Cancer Cell using LC-MS/MS

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