Proteome-wide identification of arginine methylation in colorectal cancer tissues from patients

Yongchul Lim; Ju Yeon Lee; Su Jin Ha; Suyeun Yu; Jung Kyong Shin; Hee Cheol Kim

doi:10.1186/s12953-020-00162-8

Proteome-wide identification of arginine methylation in colorectal cancer tissues from patients

Proteome Sci. 2020 May 19:18:6. doi: 10.1186/s12953-020-00162-8. eCollection 2020.

Authors

Yongchul Lim^#¹, Ju Yeon Lee^#², Su Jin Ha¹, Suyeun Yu³, Jung Kyong Shin¹, Hee Cheol Kim¹

Affiliations

¹ 1Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, 81, Irwon-ro, Gangnam-gu, Seoul, 135-710 South Korea.
² 2Korea Basic Science Institute, Research Center for Bioconvergence Analysis, Ochang, South Korea.
³ 3Department of Preventive Medicine, College of Medicine, Korea University, Seoul, South Korea.

^# Contributed equally.

Abstract

Background: Protein arginine methylation reaction is catalyzed by protein arginine methyltransferase (PRMT) and the modification is implicated in various diseases including cancer. Currently, thousands of arginine methylation sites have been identified using high-resolution mass spectrometry-based proteomics technology. However, identification of arginine methylation using clinical samples at proteome level has not been reported yet. The objective of the present study was to identify, monomethyl-arginine (MMA) and asymmetric dimethyl-arginine (ADMA) sites in colorectal cancer (CRC) tissues at proteome level.

Methods: Pooled CRC tissue samples from 10 patients with stage II and III were digested by trypsin and these digests were further processed and lyophilized. Using monomethyl- or asymmetric dimethyl arginine (MMA or ADMA, respectively) motif kits, methylarginine-containing peptides were enriched and subsequently analyzed by high-resolution LC-MS/MS. DLD1 and HCT116 colon cancer cells were treated with type I PRMTs inhibitor (MS023) alone or combined with SN-38, and the effect of the drugs on CRC cell proliferation and apoptosis was measured by water-soluble tetrazolium salt (WST-1) assay and FACS analysis, respectively.

Results: In the present study, 455 MMA sites of 272 proteins and 314 ADMA sites of 155 proteins were identified from CRC tissues acquired from patients. In addition, 216 methylation sites and 75 substrates for PRMTs were newly identified. These results reveal the significant presence of MMA and ADMA sites on nucleic acid binding proteins and protein complexes involved in transcription. To investigate the effect of protein arginine methylation in CRC proliferation and apoptosis, MS023 was treated to two CRC cell lines. After 48 h treatment with various concentrations of MS023, CRC cell proliferation was significantly suppressed, with concomitant apoptosis induction. Furthermore, MS023 treatment significantly enhanced the inhibitory effect of SN-38 on CRC cell proliferation.

Conclusion: This work reports the first comprehensive analysis of arginine methylation with clinical sample and suggests that type I PRMTs are potential therapeutic targets for drug discovery in CRC.

Keywords: Arginine methylation; Colorectal cancer; Immunoaffinity purification; Mass spectrometry; Type I PRMTs.