Prognostic Characteristics and Immune Effects of N6-Methyladenosine and 5-Methylcytosine-Related Regulatory Factors in Clear Cell Renal Cell Carcinoma

Abstract

In recent years, methylation modification regulators have been found to have essential roles in various tumor mechanisms. However, the relationships between N6-methyladenosine (m6A) and 5-methylcytosine (m5C) regulators and clear cell renal cell carcinoma (ccRCC) remain unknown. This study investigated these relationships using the data from The Cancer Genome Atlas database. We calculated risk scores using a Lasso regression analysis and divided the patient samples into two risk groups (tumor vs. normal tissues). Furthermore, we used univariate and multivariate Cox analyses to determine independent prognostic indicators and explore correlations between the regulatory factors and immune infiltrating cell characteristics. Finally, quantitative reverse transcriptase–polymerase chain reaction (PCR) and The Human Protein Atlas were used to verify signature-related gene expression in clinical samples. We identified expression differences in 35 regulatory factors between the tumor and normal tissue groups. Next, we constructed a five-gene risk score signature (NOP2 nucleolar protein [NOP2], methyltransferase 14, N6-adenosine-methyltransferase subunit [METTL14], NOP2/Sun RNA methyltransferase 5 [NSUN5], heterogeneous nuclear ribonucleoprotein A2/B1 [HNRNPA2B1], and zinc finger CCCH-type containing 13 [ZC3H13]) using the screening criteria (p < 0.01), and then divided the cases into high- and low-risk groups based on their median risk score. We also screened for independent prognostic factors related to age, tumor grade, and risk score. Furthermore, we constructed a Norman diagram prognostic model by combining two clinicopathological characteristics, which demonstrated good prediction efficiency with prognostic markers. Then, we used a single-sample gene set enrichment analysis and the cell-type identification by estimating relative subsets of RNA transcripts (CIBERSORT) method to evaluate the tumor microenvironment of the regulatory factor prognostic characteristics. Moreover, we evaluated five risk subgroups with different genetic signatures for personalized prognoses. Finally, we analyzed the immunotherapy and immune infiltration response and demonstrated that the high-risk group was more sensitive to immunotherapy than the low-risk group. The PCR results showed that NSUN5 and HNRNPA2B1 expression was higher in tumor tissues than in normal tissues. In conclusion, we identified five m6A and m5C regulatory factors that might be promising biomarkers for future research.

RNA modification pattern‐based subtypes reveal heterogenous clinical outcomes and tumor immunity of clear cell renal cell carcinoma

“…Our team also identified m7G modification patterns in clear cell RCC 20 . Li et al also summarized the prognostic features and immune effects of N6‐methyladenosine and 5‐methylcytosine‐related regulators in clear cell RCC 21 . N1‐methyladenosine and Pseudouracil modifications have been poorly studied in RCC.…”

“…20 Li et al also summarized the prognostic features and immune effects of N6-methyladenosine and 5-methylcytosine-related regulators in clear cell RCC. 21 N1-methyladenosine and Pseudouracil modifications have been poorly studied in RCC. Since previous research only focused attention on a single RNA modification subtype, the global effects of various methylation modificationrelated regulators are not fully depicted.…”

The role of RNA modification in urological cancers: mechanisms and clinical potential

“…Recently, there has been a gradual increase in research on m 5 C and cancer, although the specific mechanism of action of m 5 C in some cancers remains unclear. In urological cancers, m 5 C is also in its infancy, and current and future studies will continue to explore the role and molecular mechanisms of m 5 C. Currently, models of m 5 C-related regulators for predicting cancer prognosis, including PCa, RCC, and BCa, are constantly being established [ 147 – 150 ]. It has been reported that the m 5 C methyltransferase NSUN2 is highly expressed in prostate cancer tissues and is associated with poor patient prognosis.…”

Vital roles of m5C RNA modification in cancer and immune cell biology

“…YBX1 negatively modulates ccRCC by binding and stabilizing PEBR1 mRNA, a tumor suppressor gene ( 104 ). Other m 5 C-related genes, such as DNMT3B, NSUN1, NSUN2 and NSUN5, are highly expressed in ccRCC patients and correlate with worse prognosis ( 110 , 111 , 132 ), while NSUN6 and TET2 mainly function as protective factors ( 111 ). Notably, the role of NSUN4 in ccRCC remains controversial, as studies have obtained opposing results ( 110 , 111 ).…”