Abstract GS5-05: ZNF689 deficiency promotes intratumor heterogeneity and resistance to immune checkpoint blockade in triple-negative breast cancer

Abstract

Abstract Background: Triple-negative breast cancer (TNBC) is an aggressive disease characterized by remarkable intratumor heterogeneity (ITH), which poses a significant therapeutic challenge. However, the key determinants and underlying mechanisms of ITH in TNBC remain to be fully elucidated. Methods: We used multi-omics data from our cohort (n = 260) and The Cancer Genome Atlas (n = 134) cohort to comprehensively characterize ITH at the genetic and histologic levels. Transcriptomic differences between high ITH and low ITH tumors were compared to identify the core genes contributing ITH in TNBC. Xenograft models were used to examine the role of key determinants in TNBC ITH. The molecular mechanism was investigated by mass spectrometry, coimmunoprecipitation, pull-down, RNA-seq, long interspersed element-1 (LINE-1) reporter, ATAC-seq, luciferase reporter assays, chromatin immunoprecipitation, flow cytometry and coculture assay. Results: We found that high ITH was associated with poor patient survival and immune checkpoint blockade (ICB) resistance, which were validated in four independent ICB-treated trials. Further analysis indicated zinc finger protein 689 (ZNF689) deficiency as an important determinant of TNBC ITH. Mechanistically, the ZNF689-TRIM28 complex directly bound to the promoter of LINE-1, inducing H3K9me3-mediated transcriptional silencing. ZNF689 deficiency reactivated LINE-1 retrotransposition to exacerbate genomic instability, which promoted ITH. ZNF689 deficiency-induced ITH inhibited antigen presentation and CD8+ T cell infiltration, leading to ICB resistance. Pharmacological inhibition of LINE-1 retrotransposition reduced ITH, augmented antitumor immunity, and eventually sensitized ZNF689-deficient tumors to ICB. Consistently, ZNF689 expression positively correlated with favorable prognosis and ICB responsiveness in clinical samples. Conclusions: Our study uncovers a new mechanism underlying ZNF689 deficiency-induced ITH and suggests LINE-1 inhibition combined with ICB as a novel treatment strategy in TNBC. Citation Format: Li-Ping Ge, Xi Jin, Gen-Hong Di, Yi-Zhou Jiang, Zhi-Ming Shao. ZNF689 deficiency promotes intratumor heterogeneity and resistance to immune checkpoint blockade in triple-negative breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr GS5-05.