Expression of m6A Reader Protein YTHDC2 in Non-small Cell Lung Cancer in a Chinese Clinical Cohort

Summary

This study evaluates YTHDC2 expression in non-small cell lung cancer using bioinformatics and qRT-PCR. While database analyses suggest downregulation and prognostic relevance, clinical validation shows no significant difference. Findings highlight inconsistencies, indicating limited diagnostic accuracy and the need for further validation before clinical application.

Abstract

Non-small cell lung cancer (NSCLC) remains a leading cause of cancer-related mortality worldwide, with limited biomarkers available for early diagnosis and prognosis. N6-methyladenosine (m6A) RNA modification and its reader proteins, such as YTHDC2, play critical roles in gene regulation and tumorigenesis. This study aims to evaluate the expression profile of YTHDC2 in NSCLC tissues using bioinformatics and quantitative real-time PCR (qRT-PCR), assess the relationship between YTHDC2 and clinicopathological characteristics, and explore its potential clinical and biological relevance for future research. Gene expression and survival data from databases were analyzed for prognostic accuracy. YTHDC2 expression was quantified in NSCLC tissues in a Chinese clinical cohort, and clinicopathological characteristics were analyzed. Public database analyses showed that YTHDC2 was downregulated in NSCLC tissues (p < 0.05) and was associated with patient survival, although its prognostic performance was poor (AUC ≈ 0.5). qRT-PCR analysis of 19 paired tumor and adjacent normal tissues showed no statistically significant difference (p = 0.537) in YTHDC2 expression between cancer and adjacent tissues. Collectively, public database analyses suggest that YTHDC2 may be downregulated and have potential prognostic relevance in NSCLC, but independent clinical validation in our cohort did not confirm significant differential expression. These findings highlight substantial heterogeneity between large-scale datasets and real-world cohorts, indicating that YTHDC2 is unlikely to serve as a reliable standalone diagnostic or prognostic biomarker and may require integration with additional molecular markers for clinical applicability.

Introduction

Non-small cell lung cancer (NSCLC), encompassing squamous cell carcinoma and adenocarcinoma, is the most frequently diagnosed lung cancer and a leading cause of global cancer mortality¹. Global cancer statistics show that lung cancer is one of the main causes of cancer deaths². Recent developments in diagnosis, surgery, radiotherapy, and molecular targeted therapy have not improved the prognosis of NSCLC significantly because the primary diagnosis occurs in the late stage, and the disease is often asymptomatic in the early stages³. This underscores the need for new biomarkers to identify, prognost....

Protocol

The study was approved by the Ethical Committee of Hainan Medical University (approval number HMC1984.24) and was in accordance with the Declaration of Helsinki (as revised in 2013).

Study subjects

A study of 50 lung cancer patients diagnosed between 2017 and 2024 at Sanya Central Hospital in Hainan Province was conducted using the Chinese Medical Association Clinical Guidelines for the Diagnosis and Treatment of Lung Cancer (2024 Edition). CSCO staging (2024) aligned with the AJCC 8th Edition for cross-study comparability, as validated in Chinese cohorts¹², with two indepen....

Results

Expression of the YTHDC2 gene in tumors based on the TCGA database

Figure 3 illustrates the association between NSCLC and YTHDC2 by examining YTHDC2 expression levels across different cancers using the GDC tool in the TCGA database.

Expression of the YTHDC2 gene in NSCLC in the GEPIA database

483 lung adenocarcinoma tissue samples, 347 normal lung tissue samples, 486 lung squ.......

Discussion

YTHDC2, the largest N6-methyladenosine (m6A) binding protein in the YTH family, is unique for its ATP-dependent RNA helicase activity, distinguishing it as a key regulator of RNA metabolism¹³. Unlike other YTH family members, YTHDC2 is found in both the nucleus and the cytoplasm, where it regulates mRNA translation and RNA stability¹⁴. Previous experimental studies have shown that YTHDC2 suppresses lung adenocarcinoma (LUAD) progression by inhibiting ADIRF and MRPL12 mRNA e.......

Materials

List of materials used in this article

Name	Company	Catalog Number	Comments
Custom Primers and Probes	Sangon Biotech Co., Ltd., Shanghai, China	Custom synthesis	Primer and probe sequences listed in Table 6
DNase I	Magen Biotechnology Co., Ltd., Guangzhou, China	DNase I (HiPure FFPE RNA Kit)	Removal of genomic DNA contamination
ESTIMATE algorithm	Yoshihara et al.	R package (Version 1.0.13)	Tumor purity estimation
FFPE RNA Extraction Kit	Magen Biotechnology Co., Ltd., Guangzhou, China	HiPure FFPE RNA Kit (R4130-02)	RNA extraction from FFPE tissue
GDC Data Portal	National Cancer Institute (NCI), NIH, USA	https://portal.gdc.cancer.gov	Download of TCGA datasets
GEPIA web server	Peking University, China	http://gepia.cancer-pku.cn	Gene expression analysis
Kaplan–Meier Plotter	Semmelweis University, Hungary	https://kmplot.com	Survival analysis
Microcentrifuge	Eppendorf AG, Hamburg, Germany	5424 R	RNA purification procedures
NanoDrop Spectrophotometer	Thermo Fisher Scientific, Waltham, MA, USA	NanoDrop 2000/2000c	RNA quantification
Probe-based qPCR Master Mix	Thermo Fisher Scientific, Waltham, MA, USA	TaqMan Universal PCR Master Mix II (4440040)	Quantitative PCR amplification
R Statistical Software	R Foundation for Statistical Computing, Vienna, Austria	Version 4.4.1	Statistical analyses and ROC analysis
Real-time PCR System	Bio-Rad Laboratories, Hercules, CA, USA	CFX Opus 96	Quantitative real-time PCR
Reverse Transcription Kit	Thermo Fisher Scientific, Waltham, MA, USA	RevertAid First Strand cDNA Synthesis Kit (K1622)	cDNA synthesis
RNA Purification Column	Magen Biotechnology Co., Ltd., Guangzhou, China	HiPure Mini Column I	Silica membrane RNA purification column
RNase-Free Water	Magen Biotechnology Co., Ltd., Guangzhou, China	RNase-Free Water	RNA elution
SPSS Statistics	IBM Corp., Armonk, NY, USA	IBM SPSS Statistics Version 27.0	Statistical analyses
survivalROC package	CRAN (R Foundation for Statistical Computing)	Version 1.0.3.1	Time-dependent ROC analysis
TCGA database	National Cancer Institute (NCI), NIH, USA	https://portal.gdc.cancer.gov	Public cancer genomics database
Wash Buffer RW1	Magen Biotechnology Co., Ltd., Guangzhou, China	Buffer RW1	RNA purification wash buffer
Wash Buffer RW2	Magen Biotechnology Co., Ltd., Guangzhou, China	Buffer RW2	RNA purification wash buffer