基于 HLA-I 等位基因、新结合剂和细胞因子表达的癌症患者风险评估。
Risk assessment of cancer patients based on HLA-I alleles, neobinders and expression of cytokines.
发表日期:2023 Oct 18
作者:
Anjali Dhall, Sumeet Patiyal, Harpreet Kaur, Gajendra P S Raghava
来源:
COMPUTERS IN BIOLOGY AND MEDICINE
摘要:
癌症免疫疗法的进步在治疗癌症方面显示出显着的效果。为了设计有效的免疫疗法,根据患者的基因组图谱了解患者的免疫反应非常重要。然而,要做到这一点的分析需要熟练掌握生物信息学方法。快速发展的测序技术和统计方法给那些想要寻找不同癌症的生物标志物但不具备详细的编码或工具知识的科学家造成了障碍。在这里,我们提供基于网络的资源,使没有生物信息学专业知识的科学家能够获得不同水平的不同癌症类型的预后生物标志物。我们计算了 8346 名癌症患者的 20 种癌症类型的预后生物标志物。这些生物标志物的计算基于 i) 352 种 I 类人类白细胞抗原,ii) 660959 种肿瘤特异性 HLA1 新结合剂,以及 iii) 153 种细胞因子的表达谱。据观察,癌症患者的生存风险取决于某些类型的 HLA-I 等位基因的存在;例如,HLA-A*03:01的肝癌患者风险较低。我们的分析表明 HLA-I 等位基因的新结合物与某些类型癌症患者的总生存期具有高度相关性。例如,HLA-B*07:02 结合物与肺鳞状细胞癌的生存相关性为 0.49,与肾嫌色细胞患者的生存相关性为 -0.77。此外,我们根据细胞因子表达计算了预后生物标志物。少数细胞因子的较高表达有利于膀胱尿路上皮癌的生存,例如 IL-2,而 IL-5R 对于肾嫌色细胞患者的生存不利。 CancerHLA-I 维护原始和分析数据,可供公众免费访问 (https://webs.iiitd.edu.in/raghava/cancerhla1/)。版权所有 © 2023 Elsevier Ltd。保留所有权利。
Advancements in cancer immunotherapy have shown significant outcomes in treating cancers. To design effective immunotherapy, it's important to understand immune response of a patient based on its genomic profile. However, analyses to do that requires proficiency in the bioinformatic methods. Swiftly growing sequencing technologies and statistical methods create a blockage for the scientists who want to find the biomarkers for different cancers but don't have detailed knowledge of coding or tool. Here, we are providing a web-based resource that gives scientists with no bioinformatics expertise, the ability to obtain the prognostic biomarkers for different cancer types at different levels. We computed prognostic biomarkers from 8346 cancer patients for twenty cancer types. These biomarkers were computed based on i) presence of 352 Human leukocyte antigen class-I, ii) 660959 tumor-specific HLA1 neobinders, and iii) expression profile of 153 cytokines. It was observed that survival risk of cancer patients depends on presence of certain type of HLA-I alleles; for example, liver hepatocellular carcinoma patients with HLA-A*03:01 are at lower risk. Our analysis indicates that neobinders of HLA-I alleles have high correlation with overall survival of certain type of cancer patients. For example, HLA-B*07:02 binders have 0.49 correlation with survival of lung squamous cell carcinoma and -0.77 with kidney chromophobe patients. Additionally, we computed prognostic biomarkers based on cytokine expressions. Higher expression of few cytokines is survival favorable like IL-2 for bladder urothelial carcinoma, whereas IL-5R is survival unfavorable for kidney chromophobe patients. Freely accessible to public, CancerHLA-I maintains raw and analysed data (https://webs.iiitd.edu.in/raghava/cancerhla1/).Copyright © 2023 Elsevier Ltd. All rights reserved.