The CTBP2-PCIF1 complex regulates m6Am modification of mRNA in head and neck squamous cell carcinoma
Kang Li, … , Qianming Chen, Demeng Chen
Kang Li, … , Qianming Chen, Demeng Chen
Published August 29, 2023
Citation Information: J Clin Invest. 2023;133(20):e170173. https://doi.org/10.1172/JCI170173.
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Research Article Cell biology Oncology

The CTBP2-PCIF1 complex regulates m6Am modification of mRNA in head and neck squamous cell carcinoma

Abstract

PCIF1 can mediate the methylation of N6,2′-O-dimethyladenosine (m6Am) in mRNA. Yet, the detailed interplay between PCIF1 and the potential cofactors and its pathological significance remain elusive. Here, we demonstrated that PCIF1-mediated cap mRNA m6Am modification promoted head and neck squamous cell carcinoma progression both in vitro and in vivo. CTBP2 was identified as a cofactor of PCIF1 to catalyze m6Am deposition on mRNA. CLIP-Seq data demonstrated that CTBP2 bound to similar mRNAs as compared with PCIF1. We then used the m6Am-Seq method to profile the mRNA m6Am site at single-base resolution and found that mRNA of TET2, a well-known tumor suppressor, was a major target substrate of the PCIF1-CTBP2 complex. Mechanistically, knockout of CTBP2 reduced PCIF1 occupancy on TET2 mRNA, and the PCIF1-CTBP2 complex negatively regulated the translation of TET2 mRNA. Collectively, our study demonstrates the oncogenic function of the epitranscriptome regulator PCIF1-CTBP2 complex, highlighting the importance of the m6Am modification in tumor progression.

Authors

Kang Li, Jie Chen, Caihua Zhang, Maosheng Cheng, Shuang Chen, Wei Song, Chunlong Yang, Rongsong Ling, Zhi Chen, Xiaochen Wang, Gan Xiong, Jieyi Ma, Yan Zhu, Quan Yuan, Qi Liu, Liang Peng, Qianming Chen, Demeng Chen

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Figure 4

m6Am-Seq identifies TET2 as a target of CTBP2 and PCIF1.

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m6Am-Seq identifies TET2 as a target of CTBP2 and PCIF1. (A) Venn diagra...
(A) Venn diagram shows the integration of PCIF1-dependent modified genes and CTBP2-dependent modified genes; 382 genes are consistently modified by PCIF1 and CTBP2. (B) The top consensus m6Am motif identified in SCC25 cells with or without PCIF1 KO (left) and SCC25 cells with or without CTBP2 KO (right). (C) Bar plots showing the top 5 GO terms (Biological Process, DAVID) for PCIF1-dependent modified genes (top) and CTBP2-dependent modified genes (bottom). (D) Scatterplot of the translation ratios (TRs) in PCIF1-WT and PCIF1-KO SCC25 cells. TRs were calculated by division of the ribosome-binding transcript signals by input RNA-Seq signals. The PCIF1-WT SCC25 cell group served as the NC group. (E) Cumulative distribution plot of the translation efficiency (TE) distribution in cells with or without PCIF1 KO. (F) Bar plots showing the top 5 GO terms of genes with increased TRs. (G) Venn diagram shows the intersection of genes in GO Biological Process terms (regulation of transcription) from genes with increased TRs (left) and PCIF1- and CTBP2-dependent modified genes (right). (H and I) Representative images of PCIF1-dependent modified (H) and CTBP2-dependent modified (I) single m6Am sites on the transcripts of TET2. The 2 adenosine residues with a high score (red bars) were defined as m6Am sites.