Biology subjects

Kabekkodu, S. P.

Publications and source records attributed to Kabekkodu, S. P..

3 recordsLinked to original sources

bioRxiv2025

Promoter DNA Methylation Epigenetically Regulates the Tumor-Suppressor Function of the miR-379/656 (C14MC) Cluster in Hepatocellular Carcinoma

Hepatocellular carcinoma (HCC) is a leading cause of cancer-related mortality. Several microRNAs (miRNAs) play key roles in HCC development and progression. The role of epigenetic processes like DNA methylation in the regulation of miRNAs is critical to HCC pathogenesis. In this study, we show that the miR-379/656 cluster (C14MC) acts as a tumor suppressor cluster and is epigenetically regulated by DNA methylation. We demonstrated that C14MC is downregulated in HCC cell lines through nCounter assay and in clinical samples from The Cancer Genome Atlas (TCGA) liver hepatocellular carcinoma tissues. The C14MC promoter was identified and characterized through cloning and dual luciferase assay. Furthermore, we demonstrated that the loss of C14MC tumor suppressor function is directly regulated by the hypermethylation of promoter-bound CpGs, as shown in artificial methylation experiments. The reactivation of specific C14MC miRNAs, like miR-299-5p and miR-376c-3p via mimics, abrogated the expression of several target oncogenes, including PARP1, SPP1, RAD21, and CENPA that regulate critical molecular pathways such as the p53 signaling and NF-kappa B signaling pathways in HCC. Additionally, overexpression of miR-299-5p and miR-376c-3p inhibited HCC cell migration and invasion, suggesting that overexpression of candidate C14MC miRNAs can mitigate cancer hallmarks in HCC cells. Furthermore, we checked for the clinical correlation of C14MC targets and their target genes in terms of survival outcomes and identified the key genes associated with prognostic potential in HCC. We conclude from our experimental findings that C14MC is a tumor-suppressor miRNA cluster and is regulated epigenetically by methylation in HCC. Several of these miRNAs and their targets can be used for early HCC diagnosis and prognosis. Thus, targeting C14MC can be useful in HCC management.

cancer biology↗

bioRxiv2024

Mitochondrial genome-encoded mitomiRs regulate cellular plasticity and susceptibility to ferroptosis in triple-negative breast cancer

Ferroptosis is a distinct form of regulated cell death promoted by iron-dependent lipid peroxidation. The metabolic plasticity of cancer cells determines their sensitivity to ferroptosis. Although mitochondrial dysfunction contributes to metabolic reprogramming in cancer cells, its role in ferroptosis remains to be identified. We identified that the mitochondrial genome encodes 13 miRNAs (mitomiRs) that are highly expressed in breast cancer cell lines and patient-derived tumor samples. Expression analysis revealed that mitomiRs are upregulated in basal-like triple-negative breast cancer (TNBC) cells compared to mesenchymal stem-like TNBC cells. Interestingly, 11 out of the 13 mitomiRs bind to the 3'UTR of zinc finger E-box-binding homeobox 1 (ZEB1), a transcription factor, involved in epithelial to mesenchymal transition (EMT) in breast cancer. Using mitomiR-3 mimic, inhibitor and sponges, we confirmed that mitomiR-3 indeed regulate ZEB1 expression in TNBC cells. Increased mesenchymal features in TNBC contributed to vulnerability to pro-ferroptotic metabolic reprogramming sensitizing to cell death in in vitro and in vivo models. Some of the challenges associated with pro-ferroptotic drugs includes lack of cancer cell specificity, low targeting ability, normal tissue toxicity contributing to their limited clinical application as cancer therapeutics. Here, we identified mitomiRs which are highly expressed in TNBC subtypes with low expression in normal breast cells making them an ideal candidate for selective inhibition for targeted therapy. Further, we demonstrated that the inhibition of mitomiRs in triple-negative breast cancer cells promote pro-ferroptotic metabolic reprogramming which can be exploited as novel vulnerability for targeted ferroptotic induction in cancer cells avoiding the normal tissue toxicity. Collectively, our results indicate a novel mechanism of mitochondrial miRNA mediated ferroptosis sensitivity in TNBC subtypes which could be exploited to develop potential miRNA-based therapeutics.

cancer biology↗

bioRxiv2023

MiR-4521 perturbs FOXM1-mediated DNA damage response in breast cancer

Forkhead (FOX) transcription factors are involved in cell cycle control, cellular differentiation, maintenance of tissues, and aging. Mutation or aberrant expression of FOX proteins is associated with developmental disorders and cancers. FOXM1, an oncogenic transcription factor, is a promoter of cell proliferation and accelerated development of breast adenocarcinomas, squamous carcinoma of the head, neck, and cervix, and nasopharyngeal carcinoma. High FOXM1 expression is correlated with chemoresistance in patients treated with doxorubicin and Epirubicin by enhancing the DNA repair in breast cancer cells. Here, we showed that FOXM1 is a direct target of miR-4521 in breast cancer. Overexpression of miR-4521 significantly downregulated FOXM1 expression in breast cancer cells. FOXM1 regulates cell cycle progression and DNA damage response in breast cancer. We showed that miR-4521 expression leads to increased ROS levels and DNA damage in breast cancer cells. FOXM1 plays a critical role in ROS scavenging and promotes stemness which contributes to drug resistance in breast cancer. We observed that breast cancer cells stably expressing miR-4521 lead to cell cycle arrest, impaired FOXM1 mediated DNA damage response leading to increased cell death in breast cancer cells. Additionally, miR-4521-mediated FOXM1 downregulation perturbs cell proliferation, invasion, cell cycle progression, and epithelial-to-mesenchymal progression (EMT) in breast cancer. High FOXM1 expression has been associated with radio and chemoresistance contributing to poor patient survival in multiple cancers, including breast cancer. Our study showed that FOXM1 mediated DNA damage response could be targeted using miR-4521 mimics as a novel therapeutic for breast cancer.

cancer biology↗