Construction of a risk prediction model using m6A RNA methylation regulators in prostate cancer: comprehensive bioinformatic analysis and histological validation
机构:[1]Department of Urology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China.临床科室泌尿外科首都医科大学附属北京同仁医院首都医科大学附属同仁医院[2]Beijing Advanced Innovation Center for Big Data‑Based Precision Medicine, Beihang University & Capital Medical University, Beijing Tongren Hospital, Beijing 100730, China.首都医科大学附属北京同仁医院首都医科大学附属同仁医院[3]Department of Urology, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100020, China.北京朝阳医院
Background Epigenetic reprogramming reportedly has a crucial role in prostate cancer (PCa) progression. RNA modification is a hot topic in epigenetics, and N6-methyladenosine (m6A) accounts for approximately 60% of RNA chemical modifications. The aim of this study was to evaluate the m6A modification patterns in PCa patients and construct a risk prediction model using m6A RNA regulators. Materials and methods Analyses were based on the levels of 25 m6A regulators in The Cancer Genome Atlas (TCGA). Differentially expressed gene (DEG) and survival analyses were performed according to TCGA-PRAD clinicopathologic and follow-up information. To detect the influences of m6A regulators and their DEGs, consensus clustering analysis was performed, and tumor mutational burden (TMB) estimation and tumor microenvironment (TME) cell infiltration were assessed. mRNA levels of representative genes were verified using clinical PCa data. Results Diverse expression patterns of m6A regulators between tumor and normal (TN) tissues were detected regarding Gleason score (GS), pathological T stage (pT), TP53 mutation, and survival comparisons, with HNRNPA2B1 and IGFBP3 being intersecting genes. HNRNPA2B1 was upregulated in advanced stages (GS > 7, pT3, HR > 1, and TP53 mutation), as verified using clinical PCa tissue. Three distinct m6A modification patterns were identified through consensus clustering analysis, but no significant difference was found among these groups in recurrence-free survival (RFS) analysis. Six DEGs of m6A clusters (m6Aclusters) were screened through univariate Cox regression analysis. MMAB and PAIAP2 were intersecting genes for the five clinical factors. MMAB, which was upregulated in PCa compared with TN, was verified using clinical PCa samples. Three distinct subgroups were established according to the 6 DEGs. Cluster A involved the most advanced stages and had the poorest RFS. The m6A score (m6Ascore) was calculated based on the 6 genes, and the low m6Ascore group showed poor RFS with a negative association with infiltration for 16 of 23 immune-related cells. Conclusion We screened DEGs of m6Aclusters and identified 6 genes (BAIAP2, TEX264, MMAB, JAGN1, TIMM8AP1, and IMP3), with which we constructed a highly predictive model with prognostic value by dividing TCGA-PRAD into three distinct subgroups and performing m6Ascore analysis. This study helps to elucidate the integral effects of m6A modification patterns on PCa progression.
基金:
This study was supported by the National Natural Science Foundation of
China (Grant Nos. 81772698 and 82072833 to Hao Ping) and the Open
Research Fund from Beijing Advanced Innovation Center for Big Data-Based
Precision Medicine, Beijing Tongren Hospital, Beihang University & Capital
Medical University (Grant No. BHTR-KFJJ-202005 to Hao Ping).
第一作者机构:[1]Department of Urology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China.
通讯作者:
通讯机构:[1]Department of Urology, Beijing Tongren Hospital, Capital Medical University, Beijing 100730, China.[2]Beijing Advanced Innovation Center for Big Data‑Based Precision Medicine, Beihang University & Capital Medical University, Beijing Tongren Hospital, Beijing 100730, China.
推荐引用方式(GB/T 7714):
Quan Yongjun,Zhang Xiaodong,Ping Hao.Construction of a risk prediction model using m6A RNA methylation regulators in prostate cancer: comprehensive bioinformatic analysis and histological validation[J].CANCER CELL INTERNATIONAL.2022,22(1):doi:10.1186/s12935-021-02438-1.
APA:
Quan, Yongjun,Zhang, Xiaodong&Ping, Hao.(2022).Construction of a risk prediction model using m6A RNA methylation regulators in prostate cancer: comprehensive bioinformatic analysis and histological validation.CANCER CELL INTERNATIONAL,22,(1)
MLA:
Quan, Yongjun,et al."Construction of a risk prediction model using m6A RNA methylation regulators in prostate cancer: comprehensive bioinformatic analysis and histological validation".CANCER CELL INTERNATIONAL 22..1(2022)