Table_7_An Intratumor Heterogeneity-Related Signature for Predicting Prognosis, Immune Landscape, and Chemotherapy Response in Colon Adenocarcinoma.csv

BackgroundColon adenocarcinoma (COAD) is a frequent malignancy of the digestive system with a poor prognosis and high mortality rate worldwide. Intratumor heterogeneity (ITH) is associated with tumor progression, poor prognosis, immunosuppression, and therapy resistance. However, the relationship between ITH and prognosis, the immune microenvironment, and the chemotherapy response in COAD patients remains unknown, and this knowledge is urgently needed.MethodsWe obtained clinical information and gene expression data for COAD patients from The Cancer Genome Atlas (TCGA) database. The DEPTH2 algorithm was utilized to evaluate the ITH score. X-tile software was used to determine the optimal cutoff value of the ITH score. The COAD patients were divided into high- and low-ITH groups based on the cutoff value. We analyzed prognosis, tumor mutation burden (TMB), gene mutations, and immune checkpoint expression between the high- and low-ITH groups. Differentially expressed genes (DEGs) in the high- and low-ITH groups were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses. We performed univariate Cox regression and least absolute shrinkage and selection operator (LASSO) regression analyses to screen the prognosis-related genes for the construction of an ITH-related prognostic signature. The nomogram was used to predict the overall survival (OS) of COAD patients. The protein–protein interaction (PPI) network was constructed by using the GeneMANIA database. Principal component analysis (PCA) and single-sample gene set enrichment analysis (ssGSEA) were employed to explore the differences in biological pathway activation status between the high- and low-risk groups. The proportion and type of tumor-infiltrating immune cells were evaluated by the CIBERSORT and ESTIMATE algorithms. Additionally, we assessed the chemotherapy response and predicted small-molecule drugs for treatment. Finally, the expression of the prognosis-related genes was validated by using the UALCAN database and Human Protein Atlas (HPA) database.ResultsThe OS of the high-ITH group was worse than that of the low-ITH group. A positive correlation between ITH and TMB was identified. In subgroups stratified by age, gender, and tumor stage, the OS of the low-ITH group remained better than that of the high-ITH group. There were dramatic differences in the mutated genes, single nucleotide variant classes, variant types, immune checkpoints and cooccurring and mutually exclusive mutations of the DEGs between the high- and low-ITH groups. Based on the DEGs between the high- and low-ITH groups, we constructed a five-gene signature consisting of CEACAM5, ENO2, GABBR1, MC1R, and SLC44A4. The COAD patients were divided into high- and low-risk groups according to the median risk score. The OS of the high-risk group was worse than that of the low-risk group. The nomogram was used to accurately predict the 1-, 3- and 5-year OS of COAD patients and showed good calibration and moderate discrimination ability. The stromal score, immune score, and ESTIMATE score of the high-risk group were significantly higher than those of the low-risk group, whereas tumor purity showed the opposite trend. The patients classified by the risk score had distinguishable sensitivity to chemotherapeutic drugs. Finally, two public databases confirmed that CEACAM5 and SLC44A4 were upregulated in normal tissues compared with COAD tissues, and ENO2, GABBR1, and MC1R were upregulated in COAD tissues compared with normal tissues.ConclusionOverall, we identified an ITH-related prognostic signature for COAD that was closely related to the tumor microenvironment and chemotherapy response. This signature may help clinicians make more personalized and precise treatment decisions for COAD patients.

背景：结肠腺癌（COAD）是全球范围内常见的消化系统恶性肿瘤，其预后不良，死亡率高。肿瘤内异质性（ITH）与肿瘤进展、不良预后、免疫抑制和耐药性相关。然而，ITH与预后、免疫微环境和化疗反应之间的关系在COAD患者中尚不清楚，这一知识亟需获得。
方法：我们从癌症基因组图谱（TCGA）数据库中获得了COAD患者的临床信息和基因表达数据。利用DEPTH2算法评估ITH评分。使用X-tile软件确定ITH评分的最佳截止值。根据截止值将COAD患者分为高ITH组和低ITH组。我们分析了高ITH组和低ITH组之间的预后、肿瘤突变负荷（TMB）、基因突变和免疫检查点表达。对高ITH组和低ITH组中的差异表达基因（DEGs）进行了基因本体（GO）和京都基因与基因组百科全书（KEGG）通路富集分析。我们进行了单变量Cox回归和最小绝对收缩和选择算子（LASSO）回归分析，以筛选预后相关基因，构建ITH相关的预后特征。使用列线图预测COAD患者的总生存期（OS）。通过GeneMANIA数据库构建蛋白质-蛋白质相互作用（PPI）网络。采用主成分分析（PCA）和单样本基因集富集分析（ssGSEA）探索高风险组和低风险组之间生物学通路激活状态的差异。通过CIBERSORT和ESTIMATE算法评估肿瘤浸润免疫细胞的组成和类型。此外，我们还评估了化疗反应并预测了小分子药物。最后，使用UALCAN数据库和人类蛋白质图谱（HPA）数据库验证了预后相关基因的表达。
结果：高ITH组的OS低于低ITH组。ITH与TMB之间存在正相关。在按年龄、性别和肿瘤阶段划分的亚组中，低ITH组的OS仍优于高ITH组。高ITH组和低ITH组之间的突变基因、单核苷酸变异类、变异类型、免疫检查点和DEGs的共发和互斥突变存在显著差异。基于高ITH组和低ITH组之间的DEGs，我们构建了一个包含CEACAM5、ENO2、GABBR1、MC1R和SLC44A4的五个基因特征。根据中位风险评分将COAD患者分为高风险组和低风险组。高风险组的OS低于低风险组。列线图用于准确预测COAD患者的1年、3年和5年OS，并显示出良好的校准和适中的区分能力。高风险组的间质评分、免疫评分和ESTIMATE评分显著高于低风险组，而肿瘤纯度则呈现相反趋势。根据风险评分分类的患者对化疗药物具有可区分的敏感性。最后，两个公共数据库证实，与COAD组织相比，CEACAM5和SLC44A4在正常组织中上调，而ENO2、GABBR1和MC1R在COAD组织中上调。
结论：总体而言，我们确定了一个与肿瘤微环境和化疗反应密切相关的COAD ITH相关预后特征。此特征可能有助于临床医生为COAD患者做出更加个性化和精确的治疗决策。