Proceedings of Oncobiology Symposiums
Proceedings of XIV Oncobiology Symposium

INTRODUCTION AND OBJECTIVES: Ovarian cancer (OV) has the highest mortality rate among all gynecological cancers, and the most prevalent OV subtype is the high grade serous ovarian carcinoma (HGSOC). The KRAB-ZNF protein family is characterized by the presence of a Zinc-finger domain, which grants the protein DNA-binding specificity, and a Krüppel-associated box domain, capable of recruiting proteins that work as scaffolding for chromatin-modifying protein complexes, generally acting as transcription repressors. ZNF429 codes for a poorly studied protein from this family and its expression shows an association with overall survival in HGSOC patients. Therefore, we aim to identify the mechanism by which ZNF429 impacts disease progression. MATERIAL AND METHODS: RNA sequencing (RNA-Seq), Clinical Proteomic Tumor Analysis Consortium (CPTAC) iTraq protein detection, and clinical data from The Cancer Genome Atlas (TCGA), Cancer Cell Line Encyclopedia (CCLE) RNA-Seq data, Chromatin Immunoprecipitation-exonuclease sequencing (ChIP-exo) data for ZNF429 (GSM2466552), and single-cell RNA-seq data from HGSOC were used to investigate the association between ZNF429 expression and patient overall survival and to identify genes potentially regulated by ZNF429 and their possible cell of origin. Samples and cell lineages were classified into High and Low expression groups according to ZNF429 expression profiles. Pathway enrichment analysis was performed through the WebGestalt website. RESULTS AND CONCLUSION: Bulk RNA-seq analysis indicated that high ZNF429 expression is associated with better prognosis in HGSOC (p < 0.0001, HR: 0.28, CI.95: 0.17~0.47). Differential expression analysis combined with ChIP-exo data revealed 355 peaks related to 141 unique differentially expressed genes (DEG). Of note, several of the downregulated genes were enriched in the “Extracellular matrix organization” pathway. TCGA proteomic data analysis indicated that several of these potential targets were downregulated also in the protein level in HGSOC samples expressing high levels of ZNF429. There was no difference in gene expression when ovarian cancer cell lines from CCLE were analyzed. This indicates that expression of ZNF429 possibly comes from non-malignant cells. Thus, we analyzed ovarian cancer single-cell RNA-seq data in order to identify the origin of ZNF429 and its targets. ZNF429 expression was detected in different cells, but potential targets were mostly expressed by fibroblasts. Thereby, we believe that ZNF429 acts as a transcription regulator in fibroblasts by modulating targets involved in extracellular matrix organization and thereby facilitating the spread of malignant cells, which could explain the association between ZNF429 expression and patient overall survival. We aim to validate these results in future investigations by analyzing samples from an INCA's cohort and also constructing knockout cell lines using CRISPR-CAS9.