Combined multiomics analysis reveals the mechanism of CENPF overexpression-mediated immune dysfunction in diffuse large B-cell lymphoma in vitro

Dan Yang; Jia Wang; Mingqiu Hu; Feng Li; Feifei Yang; Youcai Zhao; Yanli Xu; Xuezhong Zhang; Lijun Tang; Xiuqun Zhang

doi:10.3389/fgene.2022.1072689

Combined multiomics analysis reveals the mechanism of CENPF overexpression-mediated immune dysfunction in diffuse large B-cell lymphoma in vitro

Front Genet. 2022 Dec 30:13:1072689. doi: 10.3389/fgene.2022.1072689. eCollection 2022.

Authors

Dan Yang¹, Jia Wang², Mingqiu Hu¹, Feng Li¹, Feifei Yang¹, Youcai Zhao³, Yanli Xu¹, Xuezhong Zhang¹, Lijun Tang², Xiuqun Zhang¹

Affiliations

¹ Department of Hematology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China.
² Department of Nuclear Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.
³ Department of Pathology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China.

Abstract

Diffuse large B-cell lymphoma (DLBCL) is one of the most common aggressive B-cell lymphomas with significant heterogeneity. More than half of patients are cured, but 40%-45% still face relapse or develop drug resistance, and the mechanism is not yet known. In this study, Centrimeric protein F (CENPF) overexpression was found in several DLBCL patients with relapsed or refractory disease compared to patients with complete remission. Thus, the human DLBCL cell line SU-DHL-4 was chosen for this study, and CENPF was upregulated in that cell line by using an adenovirus in vitro. Mass spectrometry-based quantitative proteome analysis was first performed, and the results showed that the expression levels of various proteins were increased when CENPF was upregulated, and these proteins are mainly involved in cellular processes, biological regulation, immune system processes and transcriptional regulator activity. Bioinformatics data analysis revealed that the main enriched proteins, including UBE2A, UBE2C, UBE2S, TRIP12, HERC2, PIRH2, and PIAS, were involved in various ubiquitin-related kinase activities and ubiquitination processes. Thus, ubiquitinome analysis was further performed, and the results demonstrated that proteins in many immune-related cellular pathways, such as natural killer cell-mediated cytotoxicity, the T-cell receptor signaling pathway and the B-cell receptor signaling pathway, were significantly deubiquitinated after CENPF was upregulated in DLBCL cells. Furthermore, TIMER2.0 was also used to reveal the association between CENPF and immune infiltration in DLBCL. The results showed that CENPF expression was positively correlated with CD8⁺ T cells, NK cells and B lymphocytes in DLBCL samples but negatively correlated with regulatory T cells. Aberrant activation of CENPF may induce immune dysregulation in DLBCL cells by mediating protein deubiquitination in various immune signaling pathways, which leads to tumor escape of DLBCL, but further experimental validation is still needed.

Keywords: centrimeric protein F; diffuse large B-cell lymphoma; proteome; tumor escape; ubiquitination.