Exploring the Significance of the Exon 4-Skipping Isoform of the ZNF217 Oncogene in Breast Cancer.

Philippe Clezardin,Lőrinc S Pongor,Jérôme Solassol,Diep T Le,Pascale A Cohen,Balázs Győrffy,Joël Lachuer,Julie Vendrell,Aurélie Bellanger,Anne Wierinckx

doi:10.3389/fonc.2021.647269

Abstract

Oncogene alternative splicing events can create distinct functional transcripts that offer new candidate prognostic biomarkers for breast cancer. ZNF217 is a well-established oncogene but its exon 4-skipping isoform (ZNF217-ΔE4) has never been investigated in terms of clinical or biological relevance. Using in silico RNA-seq and RT-qPCR analyses, we demonstrated for the first time the existence of ZNF217-ΔE4 transcripts in primary breast tumors, and a positive correlation between ZNF217-ΔE4 mRNA levels and those of the wild-type oncogene (ZNF217-WT). A pilot retrospective analysis revealed that, in the Luminal subclass, the combination of the two ZNF217 variants (the ZNF217-ΔE4-WT gene-expression signature) provided more information than the mRNA expression levels of each isoform alone. Ectopic overexpression of ZNF217-ΔE4 in breast cancer cells promoted an aggressive phenotype and an increase in ZNF217-WT expression levels that was inversely correlated with DNA methylation of the ZNF217 gene. This study provides new insights into the possible role of the ZNF217-ΔE4 splice variant in breast cancer and suggests a close interplay between the ZNF217-WT and ZNF217-ΔE4 isoforms. Our data suggest that a dual signature combining the expression levels of these two isoforms may serve as a novel prognostic biomarker allowing better stratification of breast cancers with good prognosis and aiding clinicians in therapeutic decisions.

Highlights

Breast cancer is the most frequent cancer in women, with an estimated 2.2 million new cases being diagnosed in 2020 worldwide, and the leading cause of cancer death in women (> 684,000 cases in 2020) [1]
Our analysis further discovered spliced alignments from exon 3 to exon 5, revealing the expression of the ZNF217-DE4 isoform in primary breast cancers
ZNF217-DE4 (E3-exon – exon 5 junction (E5)) mRNA levels in the primary breast tumors highlighted that the ZNF217-DE4 isoform mRNA expression levels are globally weaker than those of the ZNF217-WT isoform (Figures 1A, B)

Summary

Introduction

Breast cancer is the most frequent cancer in women, with an estimated 2.2 million new cases being diagnosed in 2020 worldwide, and the leading cause of cancer death in women (> 684,000 cases in 2020) [1]. The ZNF217 gene is located on chromosome 20q13.2, a region frequently amplified in many tumors, including those of the breast [2]. Previous studies highlighted that the ZNF217 oncogene is involved in both early and late stages of tumor progression [for review [3]]. Our previous work contributed to the demonstration that breast cancer cells possessing high ZNF217 expression levels display a more aggressive phenotype (e.g. increased cell proliferation, increased invasive properties and resistance to chemotherapy) [4, 5]. High ZNF217 mRNA levels in primary breast tumors are of bad prognosis and associated with shorter relapse free survival (RFS) and metastasis development [5, 6], with the most discriminatory prognostic power observed in Luminal breast cancers [7]

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