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Exploring homologous recombination repair and base excision repair pathway genes for possible diagnostic markers in hematologic malignancies

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Abstract

Hematologic malignancies (HMs) are a collection of malignant transformations, originating from the cells in the bone marrow and lymphoid organs. HMs comprise three main types; leukemia, lymphoma, and multiple myeloma. Globally, HMS accounts for approximately 10% of newly diagnosed cancer. DNA repair pathways defend the cells from recurrent DNA damage. Defective DNA repair mechanisms such as homologous recombination repair (HRR), nucleotide excision repair (NER), and base excision repair (BER) pathways may lead to genomic instability, which initiates HM progression and carcinogenesis. Expression deregulation of HRR, NER, and BER has been investigated in various malignancies. However, no studies have been reported to assess the differential expression of selected DNA repair genes combinedly in HMs. The present study was designed to assess the differential expression of HRR and BER pathway genes including RAD51, XRCC2, XRCC3, APEX1, FEN1, PARP1, and XRCC1 in blood cancer patients to highlight their significance as diagnostic/ prognostic marker in hematological malignancies. The study cohort comprised of 210 blood cancer patients along with an equal number of controls. For expression analysis, q-RT PCR was performed. DNA damage was measured in blood cancer patients and controls using the comet assay and LORD Q-assay. Data analysis showed significant downregulation of selected genes in blood cancer patients compared to healthy controls. To check the diagnostic value of selected genes, the Area under curve (AUC) was calculated and 0.879 AUC was observed for RAD51 (p < 0.0001) and 0.830 (p < 0.0001) for APEX1. Kaplan–Meier analysis showed that downregulation of RAD51 (p < 0.0001), XRCC3 (p < 0.02), and APEX1 (p < 0.0001) was found to be associated with a significant decrease in survival of blood cancer patients. Cox regression analysis showed that deregulation of RAD51 (p < 0.0001), XRCC2 (p < 0.02), XRCC3 (p < 0.003), and APEX1 (p < 0.00001) was found to be associated with the poor prognosis of blood cancer patients. Comet assay showed an increased number of comets in blood cancer patients compared to controls. These results are confirmed by performing the LORD q-assay and an increased frequency of lesions/Kb was observed in selected genes in cancer patients compared to controls. Our results showed significant downregulation of RAD51, XRCC2, XRCC3, APEX1, FEN1, PARP1, and XRCC1 genes with increased DNA damage in blood cancer patients. The findings of the current research suggested that deregulated expression of HRR and BER pathway genes can act as a diagnostic/prognostic marker in hematologic malignancies.

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Acknowledgements

Higher Education Commission of Pakistan (HEC) and COMSATS University, Islamabad, provided financial and infrastructural support to the authors. The authors thank the patients and the personnel of the Pakistan Institute of Medical Sciences (PIMS) in Islamabad for their participation in study.

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  1. Cancer Genetics and Epigenetics Research Group, Department of Biosciences, COMSATS University, Park Road, Islamabad, Pakistan

    Sumaira Fida Abbasi, Ishrat Mahjabeen, Neelam Parveen, Imama Qamar, Maria Fazal Ul Haq, Rabia Shafique, Nadia Saeed, Nida Sarosh Ashraf & Mahmood Akhtar Kayani

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Contributions

All of the authors read and approved the final version of manuscript. SFA, NP and IQ collected and isolated the RNA samples. SFA, MFH, RS, NS and NSA performed the expression analysis study. IM and MFH performed statistical analyses of the data and draft of the manuscript. MAK and IM supervised the project and provided critical revisions. All the authors discussed the results and commented on the manuscript.

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Correspondence to Ishrat Mahjabeen.

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Communicated by Shuhua Xu.

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Abbasi, S.F., Mahjabeen, I., Parveen, N. et al. Exploring homologous recombination repair and base excision repair pathway genes for possible diagnostic markers in hematologic malignancies. Mol Genet Genomics 298, 1527–1543 (2023). https://doi.org/10.1007/s00438-023-02078-2

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