Donny (2022-01-22 21:24):
#paper doi:10.1016/j.ccell.2021.04.014 Conserved pan-cancer microenvironment subtypes predict response to immunotherapy 这是一篇MD Anderson和Boston Gene去年做的泛癌免疫分型的论文,作者先定义了20多个涉及肿瘤免疫相关特征的基因集,然后使用UCSC Xena的TCGA多种瘤种样本的TOIL RSEM标准化后的基因表达数据,使用ssGSEA算法计算特征基因集的富集打分,并针对瘤种内样本进行MAD标准化,并使用Louvain聚类进而将所有样本分为四大免疫亚型,分别是:免疫富集型、免疫富集纤维化型、纤维化型和免疫沙漠型。这四种分型依次表现为免疫浸润减少,免疫原性降低。这四个分型同时和之前所做的TCIA数据库的6种亚型分型基本一致,也从通路活性、关键肿瘤免疫指标、生存分析、HE免疫细胞数量、临床免疫治疗队列疗效等进行了多方面的佐证。
IF:48.800Q1 Cancer cell, 2021-06-14. DOI: 10.1016/j.ccell.2021.04.014 PMID: 34019806
Conserved pan-cancer microenvironment subtypes predict response to immunotherapy
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Abstract:
The clinical use of molecular targeted therapy is rapidly evolving but has primarily focused on genomic alterations. Transcriptomic analysis offers an opportunity to dissect the complexity of tumors, including the tumor microenvironment (TME), a crucial mediator of cancer progression and therapeutic outcome. TME classification by transcriptomic analysis of >10,000 cancer patients identifies four distinct TME subtypes conserved across 20 different cancers. The TME subtypes correlate with patient response to immunotherapy in multiple cancers, with patients possessing immune-favorable TME subtypes benefiting the most from immunotherapy. Thus, the TME subtypes act as a generalized immunotherapy biomarker across many cancer types due to the inclusion of malignant and microenvironment components. A visual tool integrating transcriptomic and genomic data provides a global tumor portrait, describing the tumor framework, mutational load, immune composition, anti-tumor immunity, and immunosuppressive escape mechanisms. Integrative analyses plus visualization may aid in biomarker discovery and the personalization of therapeutic regimens.
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