基于多组学分析的肉瘤预后标志物的开发和验证。

BACKGROUND: In sarcomas, the DNA copy number and DNA methylation exhibit genomic aberrations. Transcriptome imbalances play a driving role in the heterogeneous progression of sarcomas. However, it is still unclear whether abnormalities of DNA copy numbers are systematically related to epigenetic DNA methylation, thus, a comprehensive analysis of sarcoma occurrence and development from the perspective of epigenetic and genomics is required. METHODS: RNASeq, copy number variation (CNV), methylation data, clinical follow-up information were obtained from The Cancer Genome Atlas (TCGA) and GEO database. The association between methylation and CNV was analyzed to further identify methylation-related genes (MET-Gs) and CNV abnormality-related genes (CNV-Gs). Subsequently DNA copy number, methylation, and gene expression data associated with the MET-Gs and CNV-Gs were integrated to determine molecular subtypes and clinical and molecular characteristics of molecular subtypes. Finally, key biomarkers were determined and validated in independent validation sets. RESULTS: A total of 5354 CNV-Gs and 4042 MET-Gs were screened and showed a high degree of consistency. Four molecular subtypes (iC1, iC2, iC3, and iC4) with different prognostic significances were identified by multiomics cluster analysis, specifically, iC2 had the worst prognosis and iC4 indicated an immune-enhancing state. Three potential prognostic markers (ENO1, ACVRL1 and APBB1IP) were determined after comparing the molecular characteristics of the four molecular subtypes. The expression of ENO1 gene was significantly correlated with CNV, and was noticeably higher in iC2 subtype with the worst prognosis than any other subtypes. The expressions of ACVRL1 and APBB1IP were negatively correlated with methylation, and were high-expressed in the iC4 subtype with the most favorable prognosis. In addition, the number of silent/nonsilent mutations and neoantigens in iC2 subtype were significantly more than those in iC1/iC3/iC4 subtype, and the same trend was also observed in CNV Gain/Loss. CONCLUSION: The current comprehensive analysis of genomic and epigenomic regulation provides new insights into multilayered pathobiology of sarcomas. Four molecular subtypes and three prognostic markers developed in this study improve the current understanding of the molecular mechanisms underlying sarcoma.

背景：在肉瘤中，DNA 拷贝数和 DNA 甲基化表现出基因组异常。转录组失衡在肉瘤的异质性进展中起着驱动作用。然而，目前尚不清楚 DNA 拷贝数的异常是否与表观遗传 DNA 甲基化系统相关，因此，需要从表观遗传学和基因组学的角度综合分析肉瘤的发生和发展。

方法：从 TCGA 和 GEO 数据库中获取了 RNAseq、拷贝数变异（CNV）、甲基化数据和临床随访信息。分析了甲基化与 CNV 的相关性，以进一步鉴定甲基化相关基因（MET-Gs）和 CNV 异常相关基因（CNV-Gs）。随后，整合与 MET-Gs 和 CNV-Gs 相关的 DNA 拷贝数、甲基化和基因表达数据，以确定分子亚型以及分子亚型的临床和分子特征。最后，在独立验证集中确定和验证关键生物标志物。

结果：筛选出 5354 个 CNV-Gs 和 4042 个 MET-Gs，两者具有高度一致性。通过多组学聚类分析鉴定了 4 个具有不同预后意义的分子亚型（iC1、iC2、iC3 和 iC4），其中 iC2 预后最差，iC4 表现出免疫增强状态。通过比较四个分子亚型的分子特征，确定了三个潜在的预后标志物（ENO1、ACVRL1 和 APBB1IP）。ENO1 基因的表达与 CNV 显著相关，在预后最差的 iC2 亚型中明显高于其他任何亚型。ACVRL1 和 APBB1IP 的表达与甲基化呈负相关，在预后最佳的 iC4 亚型中高表达。此外，iC2 亚型中的沉默/非沉默突变和新抗原数量明显多于 iC1/iC3/iC4 亚型，CNV Gain/Loss 也呈现相同趋势。

结论：目前对基因组和表观基因组调控的综合分析为肉瘤的多层次病理生物学提供了新的见解。本研究中开发的四个分子亚型和三个预后标志物提高了对肉瘤分子机制的现有认识。