Metastasis-Specific CpG Island DNA Hypermethylation of the Long Non-Coding RNA Gene 00404 in Renal Cell Carcinoma

<b>Background/Objectives:</b> Alterations in long non-protein-coding RNAs (lncRNAs) are known to influence cellular proliferation, apoptosis, and metastasis in human cancers, including renal cell carcinoma (RCC). <b>Methods:</b> Using pyrosequencing, we analyzed DNA methylation (DNAm) at 23 loci within the <i>LINC00404</i> CpG island across 28 human cancer cell line models, 181 RCC tumor tissues, 154 paired tumor-adjacent normal tissues (adNs), and 194 metastatic tissue samples. <b>Results:</b> Our analysis revealed that all CpG sites exhibited tumor-specific hypermethylation (all <i>p</i> ≤ 1.4 × 10^-5). Moreover, primary RCC tissues with distant metastases (M1) and metastatic tissue samples (Mtx) showed significant hypermethylation compared to RCC without distant metastases (M0). Notably, DNAm in Mtx displayed a significant increase in 22 CpG sites, compared to 12 CpG sites in the M1/M0 comparison, suggesting that DNAm in Mtx differs both qualitatively and quantitatively. <b>Conclusions:</b> Given that elevated levels of DNAm were also observed in the majority of cell line models, our findings suggest that <i>LINC00404</i> may play a pivotal role in the malignant development and progression of RCC metastasis, as well as in other human cancers.