Abstract A011: DPY30 regulates immunoediting by suppressing uncoordinated DNA replication in pancreatic cancer
Authors: Citron Francesca , Perelli Luigi , Balestrieri Chiara , Cecchetto Luca , Chu Yanshuo , Ho I-Lin , Zhang Li , Yen Er-Yen , Montanez Luis Castillo , Shah Rutvi , Attanasio Sergio , Srinivasan Sanjana , Dyke Charles , Chen Ko-Chien , Jiang Shan , Pan Jing , Gao Sisi , Wang Huamin , Yao Wantong , Wang Linghua , Pilato Mauro Di , Genovese Giannicola , Viale Andrea , Draetta Giulio 
Published: January 2024

Abstract
DNA replication is a tightly regulated, multi-step process orchestrated by licensing and replication factors that ensure the faithful duplication of the entire genome exclusively during S phase of the cell cycle. Although the mechanisms preventing uncoordinated DNA replication are well characterized, it remains unclear how cells counteract its potentially harmful effects when it does occur, especially in a context of oncogenic stress. Here, we identify DPY30, an understudied component of all COMPASS-like complexes, as a modulator of DNA replication. We found upregulated DPY30 expression in pancreatic ductal adenocarcinoma (PDAC) as well as a correlation between increasing DPY30 expression level and higher tumor grade and poor clinical outcomes. To investigate the role of DPY30 in DNA replication, we generated and characterized human- and mouse-derived PDAC cells silenced or knockout for DPY30 expression in vivo, within a context of increasing immune pressure. ATAC-Seq and ChIP-Seq were used to inform on the epigenetic landscape of PDAC cells silenced for DPY30 or WDR5 expression. Additionally, we conducted unbiased proteomics and transcriptomics analyses to uncover the underlying molecular mechanisms. The canonical function of COMPASS complexes is to regulate histone 3 lysine 4 (H3K4) methylation. Unexpectedly, DPY30 loss in PDAC cells did not affect H3K4 methylation patterns compared to WDR5 loss, the core member of the COMPASS-like complex. Transcriptomic data unveil a dysregulation of genes belonging to DNA replication and repair pathways in DPY30-silenced PDAC cells. This prompted unbiased proteomics analysis, which showed that DPY30 interacts with members of the DNA helicase, possibly stabilizing the DNA replication fork progression. We found that DPY30 overexpression, by preventing Geminin ubiquitylation, strongly stabilizes its expression, which in turn suppresses Cdt1 activity in late S-phase, buffering the risk of uncoordinated DNA replication in G2/M phase. Consistently, DPY30 loss resulted in DNA re-replication and chromosomal instability, as manifested by DNA fiber and metaphasic spread. In vivo, whole-exome sequencing analysis of DPY30-knockout tumors revealed that DPY30 loss markedly increased mutational burden in immunodeficient mice. In syngeneic models, DPY30 loss strongly inhibited tumor growth, prolonged survival, and increased T cell infiltration of tumors. Moreover, the immune system selectively cleared tumor cells with complex karyotypes, and we observed improved anti-tumor efficacy with DPY30 knockdown and anti-PD-1 treatment compared to either condition alone. In summary, our study has unveiled a previously unrecognized role for DPY30 in stabilizing the replisome machinery by preventing excessive DNA replication. In the context of PDAC, DPY30 sustains genome stability, providing a strong rationale for exploring DPY30 or its effector proteins as potential targets and suggesting that patients whose tumors carry low DPY30 expression might be successfully treated with immune checkpoint inhibitors.
Citation Format: Francesca Citron, Luigi Perelli, Chiara Balestrieri, Luca Cecchetto, Yanshuo Chu, I-Lin Ho, Li Zhang, Er-Yen Yen, Luis Castillo Montanez, Rutvi Shah, Sergio Attanasio, Sanjana Srinivasan, Charles Dyke, Ko-Chien Chen, Shan Jiang, Jing Pan, Sisi Gao, Huamin Wang, Wantong Yao, Linghua Wang, Mauro Di Pilato, Giannicola Genovese, Andrea Viale, Giulio Draetta. DPY30 regulates immunoediting by suppressing uncoordinated DNA replication in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Damage Repair: From Basic Science to Future Clinical Application; 2024 Jan 9-11; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2024;84(1 Suppl):Abstract nr A011.