Prognosis and therapy in thyroid cancer by gene signatures related to natural killer cells

生物 自然杀伤细胞 免疫疗法 免疫系统 基因 计算生物学 肿瘤科 癌症研究 免疫学 遗传学 医学 细胞毒性T细胞 体外
作者
Jin Zhang,Yadong Han,Jiaxin Zhang,Zhao Ming Liu,Ran Li,Linjie Zhao
出处
期刊:Journal of Gene Medicine [Wiley]
卷期号:26 (1) 被引量:2
标识
DOI:10.1002/jgm.3657
摘要

Natural killer (NK) cells are crucial to cancer development and prognosis. However, the role of NK cell-related genes in immunotherapy and the tumor immune microenvironment (TIME) is not well understood. This study aimed to develop reliable risk signatures associated with NK cell-related genes for predicting thyroid cancer (THCA).The single-cell RNA sequencing (scRNA-seq) data from seven THCA samples (GSE184362) and bulk-RNA-seq data of 502 THCA patients (TCGA-THCA) were included. The scRNA-seq data was analyzed using the "Seurat" R package to identify differentially expressed genes in NK cells. The clustering analysis was carried out using the R package "ConsensusClusterPlus". The gene set variation analysis (GSVA) algorithm was applied to assess the variations in biological pathways among subtypes. The ESTIMATE algorithm was utilized to calculate the scores for stromal, immune and estimate variables. In addition, we used the single sample Gene Set Enrichment Analysis and CIBERSORT algorithms to assess the degree to which immune cells and pathways related to immunity were enriched based on the meta-cohort. In the TCGA-THCA cohort, the "glmnet" R package was used for the gene selection, and LASSO Cox analysis was used to construct prognostic features. The "maftools" R package was used to examine the somatic mutation landscape of THCA in both low- and high-risk groups.One-hundred and eighty-five NK cell marker genes were screened, and nine genes were associated with the THCA prognosis. KLF2, OSTF1 and TAPBP were finally identified and constructed a risk signature with significant prognostic value. KLF2 and OSTF1 were protective genes, and TAPBP was a risk gene. Patients at high risk had a considerably lower overall survival compared with those at low risk. Mutations in the TCGA-THCA cohort were predominantly C > T. Increased tumor mutation burden (TMB) levels were linked to overall survival. The low-risk H-TMB+ group had a better prognosis, while the high-risk L-TMB+ group had the worst prognosis.Natural killer cell-related genes KLF2, OSTF1 and TAPBP were used to develop a novel prognostic risk signature, offering a new perspective on the prognosis and treatment of THCA.
最长约 10秒,即可获得该文献文件

科研通智能强力驱动
Strongly Powered by AbleSci AI
科研通是完全免费的文献互助平台,具备全网最快的应助速度,最高的求助完成率。 对每一个文献求助,科研通都将尽心尽力,给求助人一个满意的交代。
实时播报
飘逸宛丝发布了新的文献求助10
刚刚
孟子豪完成签到,获得积分10
刚刚
1秒前
陈天佑发布了新的文献求助10
1秒前
美满远锋完成签到,获得积分10
1秒前
轻狂发布了新的文献求助10
1秒前
2秒前
健忘数据线完成签到 ,获得积分10
2秒前
3秒前
莫华龙发布了新的文献求助10
3秒前
俊逸书琴发布了新的文献求助10
4秒前
LY发布了新的文献求助10
4秒前
4秒前
5秒前
开放的白晴应助小广采纳,获得10
5秒前
88完成签到,获得积分10
5秒前
neinei完成签到,获得积分10
5秒前
柳柳柳柳关注了科研通微信公众号
5秒前
顾矜应助苹果不平采纳,获得10
6秒前
寻炉乡完成签到,获得积分10
6秒前
SS1988发布了新的文献求助10
6秒前
thousandlong发布了新的文献求助10
7秒前
觅兴完成签到,获得积分10
7秒前
8秒前
8秒前
9秒前
9秒前
waiting完成签到,获得积分10
9秒前
朴素睫毛膏完成签到 ,获得积分10
9秒前
还在考虑完成签到,获得积分10
9秒前
123完成签到,获得积分10
9秒前
9秒前
88发布了新的文献求助10
10秒前
10秒前
沉静盼易发布了新的文献求助10
10秒前
搜集达人应助pK采纳,获得10
11秒前
诸葛藏藏发布了新的文献求助30
11秒前
万能图书馆应助13223456采纳,获得10
11秒前
thousandlong完成签到,获得积分10
11秒前
朱白完成签到,获得积分10
11秒前
高分求助中
Production Logging: Theoretical and Interpretive Elements 2700
Mechanistic Modeling of Gas-Liquid Two-Phase Flow in Pipes 2500
Kelsen’s Legacy: Legal Normativity, International Law and Democracy 1000
Handbook on Inequality and Social Capital 800
Conference Record, IAS Annual Meeting 1977 610
Interest Rate Modeling. Volume 3: Products and Risk Management 600
Interest Rate Modeling. Volume 2: Term Structure Models 600
热门求助领域 (近24小时)
化学 材料科学 生物 医学 工程类 有机化学 生物化学 物理 纳米技术 计算机科学 内科学 化学工程 复合材料 基因 遗传学 物理化学 催化作用 量子力学 光电子学 冶金
热门帖子
关注 科研通微信公众号,转发送积分 3546888
求助须知:如何正确求助?哪些是违规求助? 3123917
关于积分的说明 9357332
捐赠科研通 2822504
什么是DOI,文献DOI怎么找? 1551513
邀请新用户注册赠送积分活动 723546
科研通“疑难数据库(出版商)”最低求助积分说明 713791