Machine learning developed an intratumor heterogeneity signature for predicting prognosis and immunotherapy benefits in skin cutaneous melanoma.

IF 1.5 4区 医学 Q3 DERMATOLOGY Melanoma Research Pub Date : 2024-06-01 Epub Date: 2024-02-16 DOI:10.1097/CMR.0000000000000957
Wei Zhang, Shuai Wang
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Abstract

Intratumor heterogeneity (ITH) is defined as differences in molecular and phenotypic profiles between different tumor cells and immune cells within a tumor. ITH was involved in the cancer progression, aggressiveness, therapy resistance and cancer recurrence. Integrative machine learning procedure including 10 methods was conducted to develop an ITH-related signature (IRS) in The Cancer Genome Atlas (TCGA), GSE54467, GSE59455 and GSE65904 cohort. Several scores, including tumor immune dysfunction and exclusion (TIDE) score, tumor mutation burden (TMB) score and immunophenoscore (IPS), were used to evaluate the role of IRS in predicting immunotherapy benefits. Two immunotherapy datasets (GSE91061 and GSE78220) were utilized to the role of IRS in predicting immunotherapy benefits of skin cutaneous melanoma (SKCM) patients. The optimal prognostic IRS constructed by Lasso method acted as an independent risk factor and had a stable and powerful performance in predicting the overall survival rate in SKCM, with the area under the curve of 2-, 3- and 4-year receiver operating characteristic curve being 0.722, 0.722 and 0.737 in TCGA cohort. We also constructed a nomogram and the actual 1-, 3- and 5-year survival times were highly consistent with the predicted survival times. SKCM patients with low IRS scores had a lower TIDE score, lower immune escape score and higher TMB score, higher PD1&CTLA4 IPS. Moreover, SKCM patients with low IRS scores had a lower gene sets score involved in DNA repair, angiogenesis, glycolysis, hypoxia, IL2-STAT5 signaling, MTORC1 signaling, NOTCH signaling and P53 pathway. The current study constructed a novel IRS in SKCM using 10 machine learning methods. This IRS acted as an indicator for predicting the prognosis and immunotherapy benefits of SKCM patients.

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机器学习开发出肿瘤内异质性特征,用于预测皮肤黑色素瘤的预后和免疫疗法的疗效。
背景:肿瘤内异质性(ITH)是指肿瘤内不同肿瘤细胞和免疫细胞在分子和表型特征上的差异。ITH 与癌症进展、侵袭性、耐药性和癌症复发有关:方法:在癌症基因组图谱(The Cancer Genome Atlas,TCGA)、GSE54467、GSE59455 和 GSE65904 队列中,采用包括 10 种方法在内的整合机器学习程序来开发 ITH 相关特征(IRS)。包括肿瘤免疫功能障碍和排斥(TIDE)评分、肿瘤突变负荷(TMB)评分和免疫表观评分(IPS)在内的几项评分被用来评估IRS在预测免疫疗法获益方面的作用。两个免疫治疗数据集(GSE91061和GSE78220)被用来评估IRS在预测皮肤黑色素瘤(SKCM)患者免疫治疗获益中的作用:在TCGA队列中,用Lasso方法构建的最佳预后IRS作为一个独立的风险因素,在预测SKCM总生存率方面具有稳定而强大的性能,其2年、3年和4年接收者操作特征曲线下面积分别为0.722、0.722和0.737。我们还构建了一个提名图,实际的 1 年、3 年和 5 年生存时间与预测的生存时间高度一致。IRS评分较低的SKCM患者TIDE评分较低,免疫逃逸评分较低,TMB评分较高,PD1&CTLA4 IPS较高。此外,IRS得分低的SKCM患者在DNA修复、血管生成、糖酵解、缺氧、IL2-STAT5信号转导、MTORC1信号转导、NOTCH信号转导和P53通路中的基因组得分也较低:本研究利用 10 种机器学习方法构建了 SKCM 的新型 IRS。结论:本研究利用10种机器学习方法构建了SKCM的新型IRS,该IRS可作为预测SKCM患者预后和免疫治疗获益的指标。
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来源期刊
Melanoma Research
Melanoma Research 医学-皮肤病学
CiteScore
3.40
自引率
4.50%
发文量
139
审稿时长
6-12 weeks
期刊介绍: ​​​​​​Melanoma Research is a well established international forum for the dissemination of new findings relating to melanoma. The aim of the Journal is to promote the level of informational exchange between those engaged in the field. Melanoma Research aims to encourage an informed and balanced view of experimental and clinical research and extend and stimulate communication and exchange of knowledge between investigators with differing areas of expertise. This will foster the development of translational research. The reporting of new clinical results and the effect and toxicity of new therapeutic agents and immunotherapy will be given emphasis by rapid publication of Short Communications. ​Thus, Melanoma Research seeks to present a coherent and up-to-date account of all aspects of investigations pertinent to melanoma. Consequently the scope of the Journal is broad, embracing the entire range of studies from fundamental and applied research in such subject areas as genetics, molecular biology, biochemistry, cell biology, photobiology, pathology, immunology, and advances in clinical oncology influencing the prevention, diagnosis and treatment of melanoma.
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