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DNAJC9 expression in basal-like and luminal A breast cancer subtypes predicts worse survival

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Abstract

Background

This study aimed to analyze the role of genetic/epigenetic alterations and the prognostic value of the DNAJC9 gene in breast cancer.

Materials and methods

RT-PCR and Q-RT-PCR methods are used to examine DNAJC9 expression in breast cell lines. Survival ratios of breast cancer patients were evaluated by using bc-GenExMiner. Combined bisulfite restriction analysis and UALCAN in-silico tool were used to assess the methylation level of the DNAJC9 promoter. Mutations were searched with the help of Sanger Cosmic database and direct sequencing.

Results

DNAJC9 mRNA expression is significantly higher in basal-like, HER2-Enriched (HER2-E), luminal A and luminal B breast cancer subtypes compared to normal breast-like samples based on DNA microarray datasets (P < 0.001). Similar results were obtained in RNA-seq datasets, except for the luminal A breast cancer subtype (P > 0.1). We did not find any mutation at the core promoter region of DNAJC9 in breast cancer and normal cell lines. Mutations of DNAJC9 are infrequent in clinical samples (<%1). DNAJC9 promoter region is hypomethylated in tumor and normal samples. DNAJC9 expression is unfavorable for survival in basal-like and luminal A breast cancer subtypes.

Conclusions

Mutations or promoter hypomethylation do not appear to have a role in high DNAJC9 gene expression in breast cancer. DNAJC9 expression could be suggested as a novel biomarker in basal-like and luminal A breast cancer subtypes.

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Data availability

The primer sequences and the datasets used in our study are are provided in online resource file.

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Acknowledgements

We thank Dr. I. Yulug (Bilkent University, Ankara, Turkiye) for providing the cell lines.

Funding

This work was supported by Zonguldak Bulent Ecevit University (Zonguldak, Turkiye) (Grant No: 2020-50737594-02) to Dr. Tolga Acun.

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Authors and Affiliations

  1. Department of Molecular Biology and Genetics, Faculty of Science, Zonguldak Bulent Ecevit University, 67100, Zonguldak, Turkey

    Oya Incekara & Tolga Acun

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  1. Oya Incekara
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  2. Tolga Acun
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Contributions

Conceptualization: TA; Methodology: OI, TA; Formal analysis and investigation: OI, TA; Writing - original draft preparation: TA; Funding acquisition: TA; Supervision: TA.

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Correspondence to Tolga Acun.

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Incekara, O., Acun, T. DNAJC9 expression in basal-like and luminal A breast cancer subtypes predicts worse survival. Mol Biol Rep 50, 7275–7282 (2023). https://doi.org/10.1007/s11033-023-08654-4

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