| Literature DB >> 34178026 |
Bingzhou Guo1, Hongliang Zhang2, Jinliang Wang3, Rilige Wu4,5, Junyan Zhang4,5, Qiqin Zhang6, Lu Xu7, Ming Shen7, Zhibo Zhang8, Fangyan Gu9, Weiliang Zeng1, Xiaodong Jia10, Chengliang Yin11.
Abstract
BACKGROUND: N6-methyladenosine (m6A) RNA modification is vital for cancers because methylation can alter gene expression and even affect some functional modification. Our study aimed to analyze m6A RNA methylation regulators and m6A-related genes to understand the prognosis of early lung adenocarcinoma.Entities:
Keywords: RNA methylation regulators; lung adenocarcinoma; m6A; m6A-related genes; prognostic signature
Year: 2021 PMID: 34178026 PMCID: PMC8226131 DOI: 10.3389/fgene.2021.656114
Source DB: PubMed Journal: Front Genet ISSN: 1664-8021 Impact factor: 4.599
Clinical information of the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) datasets.
| >61 | 104 | 104 | 251 |
| ≤61 | 122 | 24 | 149 |
| Female | 121 | 63 | 217 |
| Male | 105 | 65 | 183 |
| Alive | 191 | 76 | 278 |
| Dead | 35 | 52 | 122 |
| Stage I | 168 | 92 | 280 |
| Stage II | 58 | 36 | 120 |
FIGURE 1Random survival forest analysis. (A,B) random survival forests variable hunting analysis reveals the error rate for the data as a function of trees and uses the associated score to filter N6-methyladenosine (m6A) RNA methylation regulators and m6A-related genes. (C) Receiver operating characteristic (ROC) for selected prognostic signature from all 255 signatures.
FIGURE 2Evaluation of the risk predictive model in the training set and test set. (A–C) The distribution of m6A RNA methylation regulators and m6A-related gene expression level, patients’ survival status, and risk score between high- and low-risk group.
Prognosis of the three genes in the signature.
| ENSG00000047188 | YTHDC2 | YTH domain containing 2 | −2.02 | 0.00 | low |
| ENSG00000139168 | ZCRB1 | zinc finger CCHC-type and RNA binding motif containing 1 | 1.73 | 0.00 | high |
| ENSG00000248144 | ADH1C | alcohol dehydrogenase 1C (class I), gamma polypeptide | −1.96 | 0.00 | low |
FIGURE 3m6A RNA methylation regulators and m6A-related genes signature predict overall survival of patients of LUAD. (A–C) Kaplan–Meier survival curves classify patients into high- and low-risk groups by the m6A RNA methylation regulators and m6A-related genes signature in the training dataset (GSE31210), and test dataset (GSE50081 and TCGA). P values were calculated by log-rank test. (D–F) m6A RNA methylation regulators and m6A-related genes signatures were used for predicting survival in 1, 3, and 5 years by TimeROC analysis.
Clinical information and signature Chi-square table.
| Age | 0.89 | |||
| ≤61 | 62 | 60 | ||
| >61 | 51 | 53 | ||
| Gender | 0.18 | |||
| Female | 66 | 55 | ||
| Male | 47 | 58 | ||
| Pathological stage | 0.00 | |||
| I | 97 | 71 | ||
| II | 16 | 42 | ||
| Age | 0.82 | |||
| ≤61 | 11 | 13 | ||
| >61 | 53 | 51 | ||
| Gender | 1.00 | |||
| Female | 31 | 32 | ||
| Male | 33 | 32 | ||
| Pathological stage | 0.03 | |||
| I | 52 | 40 | ||
| II | 12 | 24 | ||
| Age | 0.00 | |||
| ≤61 | 60 | 89 | ||
| >61 | 140 | 111 | ||
| Gender | 0.69 | |||
| Female | 111 | 106 | ||
| Male | 89 | 94 | ||
| Pathological stage | 0.10 | |||
| I | 148 | 132 | ||
| II | 52 | 68 | ||
Univariable and multivariable Cox regression analysis of the signature and clinical information with lung adenocarcinoma (LUAD) survival.
| Age | >61 vs. ≤61 | 1.43 | 0.73 | 2.78 | 0.29 | 1.49 | 0.76 | 2.92 | 0.24 |
| Sex | Male vs. female | 1.52 | 0.78 | 2.96 | 0.22 | 1.03 | 0.51 | 2.08 | 0.92 |
| Pathological stage | II vs. I | 4.23 | 2.17 | 8.24 | 0.00 | 2.73 | 1.35 | 5.50 | 0.00 |
| Signature | High risk vs. low risk | 20.48 | 4.91 | 85.43 | 0.00 | 16.24 | 3.85 | 68.58 | 0.00 |
| Age | >61 vs. ≤61 | 2.09 | 0.89 | 4.89 | 0.09 | 2.04 | 0.86 | 4.80 | 0.10 |
| Sex | Male vs. female | 1.35 | 0.78 | 2.34 | 0.29 | 1.51 | 0.86 | 2.64 | 0.15 |
| Pathological stage | II vs I, | 2.53 | 1.45 | 4.44 | 0.00 | 2.09 | 1.17 | 3.73 | 0.01 |
| Signature | High risk vs. low risk | 2.40 | 1.36 | 4.23 | 0.00 | 2.23 | 1.24 | 4.02 | 0.01 |
| Age | >61 vs. ≤61 | 1.20 | 0.83 | 1.75 | 0.33 | 1.34 | 0.91 | 1.96 | 0.14 |
| Sex | Male vs. female | 1.03 | 0.72 | 1.47 | 0.87 | 1.03 | 0.72 | 1.48 | 0.88 |
| Pathological stage | II vs. I | 2.49 | 1.73 | 3.57 | 0.00 | 2.40 | 1.66 | 3.45 | 0.00 |
| Signature | High risk vs. low risk | 1.57 | 1.09 | 2.26 | 0.01 | 1.50 | 1.03 | 2.18 | 0.04 |
FIGURE 4Functional annotation and protein–protein interaction for the genes with significant prognosis. (A,B) Function prediction (BP, biological process; CC, cellular component). (C) Protein–protein interaction.
FIGURE 5Expression and genetic alterations of the three predictive genes. (A) The expression profiles of the three genes in the Oncomine database. (B) The representative protein expression of the three genes in LUAD and normal lung tissue in the Human Protein Atlas database. Data of ZCRB1 were not found in the database. (C) Genetic alterations of the three genes in LUAD in the cBioportal for Cancer Genomics.
FIGURE 6The expression of the three predictive genes in cancers via Tumor IMmune Estimation Resource (TIMER, https://cistrome.shinyapps.io/timer/). (A) YTHDC2 expression level in tumor tissues vs normal tissues. (B) ZCRB1 expression level in tumor tissues vs normal tissues. (C) ADH1C expression level in tumor tissues vs normal tissues. ACC, adrenocortical carcinoma; BLCA, bladder carcinoma; BRCA, breast carcinoma; CESC, cervical squamous cell carcinoma and endocervical adenocarcinoma; CHOL, cholangio carcinoma; COAD, colon adenocarcinoma; DLBC, lymphoid neoplasm diffuse large B-cell lymphoma; ESCA, esophageal carcinoma; GBM, glioblastoma multiforme; HNSC, head and neck squamous cell carcinoma; KICH, kidney chromophobe; KIRC, kidney renal clear cell carcinoma; KIRP, kidney renal papillary cell carcinoma; LAML, acute myeloid leukemia; LGG, brain lower grade glioma; LIHC, liver hepatocellular carcinoma; LUAD, lung adenocarcinoma; LUAC, lung squamous cell carcinoma; MESO, mesothelioma; OV, ovarian serous cystadenocarcinoma; PAAD, pancreatic adenocarcinoma; PCPG, pheochromocytoma and paraganglioma; PRAD, prostate adenocarcinoma; READ, rectum adenocarcinoma; SARC, sarcoma; SKCM, skin cutaneous melanoma; STAD, stomach adenocarcinoma; TGCT, testicular germ cell tumors; THCA, thyroid carcinoma; THYM, thymoma; UCEC, uterine corpus endometrial carcinoma; UCS, uterine carcinosarcoma; UVM, uveal melanoma.
FIGURE 7Compare the low and high expression of the three predictive genes in overall survival in (A) GSE31210 dataset, (B) GSE50081 dataset, and (C) TCGA dataset.