| dc.description.abstract | Breast cancer is the most predominant form of cancer in females worldwide. High throughput gene expression analysis has led to classification of breast cancer into distinct molecular subtypes (Parker et al., 2009; Perou et al., 2000). Several genetic and epigenetic changes can contribute to the variable phenotypic outcomes of breast cancer. Histone variants are the key player of epigenetic regulation in cancer, of which H2A.Z is the most studied in breast cancer (Buschbeck & Hake, 2017). H2A.Z.1 and H2A.Z.2.1 are isoforms expressed from two genes, H2AFZ and H2AFV respectively, that differ in only three amino acids. H2A.Z.2.2 is the alternative spliced isoform of H2AFV. H2A.Z.1 has been reported to be overexpressed in breast cancer (Hua et al., 2008). However, the contribution of H2A.Z.2.1 and H2A.Z.2.2 isoforms in breast cancer is not known. An RNA-binding protein QKI plays a key role in posttranscriptional events, including alternative splicing and controls the metabolism of the RNA transcript of several genes, including a histone variant macroH2A.1. Whether QKI has a role in the regulation of H2A.Z isoforms in breast cancer is unclear. Using publicly available data, I bioinformatically analyzed the expression level of QKI and H2A.Z isoforms and their correlation with survival in different breast cancer subtypes. H2A.Z.1 and H2A.Z.2.1 were upregulated in more aggressive breast cancer, whereas H2A.Z.2.2 was downregulated compared to the normal tissue adjacent to the tumor. All the QKI isoforms were downregulated in breast cancer compared to the normal tissues. High levels of H2A.Z.1 and QKI-5 expressions were correlated with poor patient survival. However, high H2A.Z.2.1/H2A.Z.2.2 expression levels were correlated with a good patient prognosis. The identification of QKI binding sites in the pre-mRNAs of H2AFZ and H2AFV indicates the possibility that QKI may target and bind and regulate their expression. For experimental validation, I applied the siRNA-mediated knockdown and overexpression of QKI in a panel of breast cancer cell lines to determine the role of this splicing protein in the regulation of H2A.Z isoforms. A reduction of all the H2A.Z mRNA was observed in all the breast cancer cell lines upon knockdown of QKI. The reduction of H2A.Z.1 protein was also detected in stable Ty-H2A.Z.1 MCF-7 cells with the knockdown of QKI. However, not all the QKI isoforms regulated H2A.Z isoforms, and different QKI isoforms behave differently across breast cancer subtypes. Among the QKI isoforms, QKI-5 showed an effect on the H2A.Z.1 and H2A.2.1 mRNA in luminal B subtype. Overexpression of QKI-6 showed an effect on H2A.Z.1 and H2A.Z.2.1 mRNA level in HER2 and on H2A.Z.1 mRNA level in basal and luminal A subtypes. Whereas, QKI-7 was associated with increased H2A.Z.1 mRNA in the basal subtype. We also observed a reduced level of QKI with the knockdown of H2A.Z.1 in the stable Ty-H2A.Z.1-MCF-7 breast cancer cell line. Though we cannot confirm the effect of QKI on H2AFV splicing, other regulatory mechanisms of QKI may influence H2A.Z mRNA. We conclude that different QKI isoforms may have distinct roles in the regulation of H2A.Z isoforms and that this varies with the breast cancer cell types. | eng |