Silencing of tumor-suppressor genes (TSGs) by DNA promoter hypermethylation is an early event in carcinogenesis; hence, TSGs may serve as early tumor biomarkers. We determined the promoter methylation levels of p16^INK4a, RASSF1A, TIMP3, and PCQAP/MED15 TSGs in salivary DNA from oral cancer (OC) and oropharyngeal cancer (OPC) patients, using methylation-specific PCR coupled with densitometry analysis. We assessed the association between DNA methylation of individual TSGs with OC and OPC risk factors. The performance and the clinical validity of this quadruple-methylation marker panel were evaluated in discriminating OC and OPC patients from healthy controls using the CombiROC web tool. Our study reports that RASSF1A, TIMP3, and PCQAP/MED15 TSGs were significantly hypermethylated in OC and OPC cases compared to healthy controls. DNA methylation levels of TSGs were significantly augmented by smoking, alcohol use, and betel quid chewing, indicating the fact that frequent exposure to risk factors may drive oral and oropharyngeal carcinogenesis through TSG promoter hypermethylation. Also, this quadruple-methylation marker panel of p16^INK4a, RASSF1A, TIMP3, and PCQAP/MED15 TSGs demonstrated excellent diagnostic accuracy in the early detection of OC at 91.7% sensitivity and 92.3% specificity and of OPC at 99.8% sensitivity and 92.1% specificity from healthy controls.

Background Prostate cancer (PCa) is a commonly diagnosed cancer. Genome-wide association studies have implicated Iroquois homeobox 4 (IRX4) in PCa susceptibility, yet its functional roles remain unclear. We discovered a 78-amino acid micropeptide (miPEP, IRX4_PEP1), encoded from the alternative start site within the IRX4 gene. The miPEPs, encoded through short open reading frames (sORFs) have emerged as regulators of diverse biological processes. However, the significance of miPEPs in prostate tumorigenesis and therapy response remains unexplored to date. Here, we demonstrated the unique role of IRX4_PEP1 in PCa. Methods The role of IRX4_PEP1 was evaluated in PCa in vitro via functional assays and comprehensive pathway analysis. The interacting partners of IRX4_PEP1 were identified using an immunoprecipitation assay, and the impact of IRX4_PEP1 on PCa stem cells was assessed through a stem cell enrichment assay. Additionally, the expression of IRX4_PEP1 was evaluated in PCa patient samples for its potential diagnostic and prognostic significance. Results Here we show IRX4_PEP1 promotes PCa cell proliferation, migration, and invasion by interacting with heterogeneous nuclear ribonucleoprotein K (HNRPK). Notably, IRX4_PEP1 dysregulates Wnt signalling by interacting with Catenin beta 1 (β catenin; CTNB1), elevating PCa stemness markers, and fostering docetaxel resistance. Clinically, IRX4_PEP1 expression is elevated in PCa tissues and correlates positively with disease aggressiveness. CTNNB1, HNRNPK levels, and ssGSEA enrichment score of WNT/CTNB1 signalling correlate positively with IRX4_PEP1 in PCa tissues. Conclusions These findings highlight IRX4_PEP1 role in PCa stemness and chemoresistance, suggesting it as a therapeutic target and potential diagnostic marker.

Prostate cancer (PCa) is the second most common cancer affecting men worldwide. PCa shows a broad-spectrum heterogeneity in its biological and clinical behavior. Although androgen targeted therapy (ATT) has been the mainstay therapy for advanced PCa, it inevitably leads to treatment resistance and progression to castration resistant PCa (CRPC). Thus, greater understanding of the molecular basis of treatment resistance and CRPC progression is needed to improve treatments for this lethal phenotype. The current study interrogated both proteomics and transcriptomic alterations stimulated in AR antagonist/anti-androgen (Bicalutamide and Enzalutamide) treated androgen-dependent cell model (LNCaP) in comparison with androgen-independent/castration-resistant cell model (C4-2B). The analysis highlighted the activation of MYC and PSF/SFPQ oncogenic upstream regulators in response to the anti-androgen treatment. Moreover, the study revealed anti-androgen induced genes/proteins related to transcription/translation regulation, energy metabolism, cell communication and signaling cascades promoting tumor growth and proliferation. In addition, these molecules were found dysregulated in PCa clinical proteomic and transcriptomic datasets, suggesting their potential involvement in PCa progression. In conclusion, our study provides key molecular signatures and associated pathways that might contribute to CRPC progression despite treatment with anti-androgens. Such molecular signatures could be potential therapeutic targets to improve the efficacy of existing therapies and/or predictive/prognostic value in CRPC for treatment response.

Alternative splicing (AS) is tightly regulated to maintain genomic stability in humans. However, tumor growth, metastasis and therapy resistance benefit from aberrant RNA splicing. Iroquois-class homeodomain protein 4 (IRX4) is a TALE homeobox transcription factor which has been implicated in prostate cancer (PCa) as a tumor suppressor through genome-wide association studies (GWAS) and functional follow-up studies. In the current study, we characterized 12 IRX4 transcripts in PCa cell lines, including seven novel transcripts by RT-PCR and sequencing. They demonstrate unique expression profiles between androgen-responsive and nonresponsive cell lines. These transcripts were significantly overexpressed in PCa cell lines and the cancer genome atlas program (TCGA) PCa clinical specimens, suggesting their probable involvement in PCa progression. Moreover, a PCa risk-associated SNP rs12653946 genotype GG was corelated with lower IRX4 transcript levels. Using mass spectrometry analysis, we identified two IRX4 protein isoforms (54.4 kDa, 57 kDa) comprising all the functional domains and two novel isoforms (40 kDa, 8.7 kDa) lacking functional domains. These IRX4 isoforms might induce distinct functional programming that could contribute to PCa hallmarks, thus providing novel insights into diagnostic, prognostic and therapeutic significance in PCa management.