New insights into DNA damage repair in pediatric acute myeloid leukemia provided by single-cell multi-omics analysis

Li Zhang¹Xing Wang²Yanli Liu³Yanchen Lin⁴Yanmei Chen^5*

• ¹Graduate School, Hebei North University, Zhangjiakou, China
• ²People's Hospital of Yilong Country, Nanchong, China
• ³Dongying Hospital of Traditional Chinese Medicine (Dongying Shengli Hospital), Dongying, China
• ⁴Hebei North University School of Graduate Studies, Zhangjiakou, China
• ⁵Yongchuan Hospital of Chongqing Medical University, Chongqing, China

Background: Pediatric acute myeloid leukemia (pAML) is a highly heterogeneous disease with a low incidence but poor prognosis and a high relapse rate. The pathogenesis, remission, and relapse of pAML are influenced by DNA damage repair (DDR), highlighting its importance in understanding and treating pAML. Compared with adult AML (aAML), most pAML patients lack effective targeted therapeutic options. Accordingly, there is an urgent need for further elucidation of pAML pathogenesis and DDR-based exploration of potential therapeutic targets for pAML.In this study, we employed single-cell RNA sequencing (scRNA-seq) to identify key pAML-related cell progenitors (Prog) associated with DDR. We then combined differential expression analysis, DNA methylation analysis with single-cell ATAC sequencing (scATAC-seq) and discovered that MAD2L2 and PCNA are key DDR genes correlated with pAML pathogenesis. In vitro experiments demonstrated that knockdown of PCNA and MAD2L2 resulted in reduced proliferation capacity and increased apoptosis rates in AML cell lines, suggesting these genes participate in tumorigenesis and progression. Our analyses indicated that the collective influence of MAD2L2 and PCNA on DDR in pAML may be mediated by Prog-binding zinc finger proteins, which interfere with the bypass replication of translesion synthesis (TLS).Furthermore, the demand for DDR is higher in pAML than in aAML. Additionally, the expression trends of key genes and signaling pathways were similar in the diagnosis and relapse of pAML, suggesting that the key genes are linked to the relapse mechanism of pAML with influence of DDR. Conclusion: The key DDR genes MAD2L2 and PCNA might interfere with DDR through Prog cell-bound zinc finger proteins, acting as the potential therapeutic targets in pAML.