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Identification and validation of the cellular senescence-related molecular subtypes of triple negative breast cancer via integrating bulk and single-cell RNA sequencing data

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机构: [1]Minist Educa t Beijing, Dept Med Oncol, Peking Univ Canc Hosp & Inst, Key Lab Carcinogenesis & Translat Res, Beijing 100142, Peoples R China [2]Sun Yat sen Univ, Affiliated Hosp 8, Dept Thyroid Surg, Shenzhen 518000, Guangdong, Peoples R China [3]First Affiliated Hosp Soochow Univ, Depart ment Thyroid & Breast Surg, Suzhou 215000, Jiangsu, Peoples R China [4]Jining Med Univ, Affiliated Hosp, Dept Pathol, Jining 272000, Shandong, Peoples R China [5]Nanjing Univ Chinese Med, Yancheng TCM Hosp, Yancheng 224002, Jiangsu, Peoples R China [6]Shanghai Jiao Tong Univ, Sch Med, Shanghai Peoples Hosp 9, Dept Radiol, Shanghai, Peoples R China [7]Shanghai Jiao Tong Univ, Sch Med, Shanghai Peoples Hosp 1, Dept Med Oncol, Shanghai 200080, Peoples R China
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关键词: Immune checkpoint blockade cellular senescence triple-negative breast cancer scRNA-seq bioinfor-matics

摘要:
Patients with triple-negative breast cancer (TNBC) reportedly benefit from immune checkpoint blockade (ICB) therapy. However, the subtype-specific vulnerabilities of ICB in TNBC remain unclear. As the complex interplay between cellular senescence and anti-tumor immunity has been previously discussed, we aimed to identify markers related to cellular senescence that may serve as potential predictors of response to ICB in TNBC. We used three transcriptomic datasets derived from ICB-treated breast cancer samples at both scRNA-seq and bulk-RNA-seq lev-els to define the subtype-specific vulnerabilities of ICB in TNBC. Differences in the molecular features and immune cell infiltration among the different TNBC subtypes were further explored using two scRNA-seq, three bulk-RNA-seq, and two proteomic datasets. 18 TNBC samples were collected and utilized to verify the association between gene expression and immune cell infiltration by multiplex immunohistochemistry (mIHC). A specific type of cellular senescence was found to be significantly associated with response to ICB in TNBC. We employed the expression of four senescence-related genes, namely CDKN2A, CXCL10, CCND1, and IGF1R, to define a distinct senescence -related classifier using the non-negative matrix factorization approach. Two clusters were identified, namely the senescence-enriching cluster (C1; CDKN2AhighCXCL10highCCND1lowIGF1Rlow) and proliferating-enriching cluster (C2; CDKN2AlowCXCL10lowCCND1highIGF1Rhigh). Our results indicated that the C1 cluster responds better to ICB and be-haves with higher CD8+ T cell infiltration than the C2 cluster. Altogether, in this study, we developed a robust cellular senescence-related classifier of TNBC based on the expression of CDKN2A, CXCL10, CCND1, and IGF1R. This clas-sifier act as a potential predictor of clinical outcomes and response to ICB.

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出版当年[2022]版:
大类 | 3 区 医学
小类 | 3 区 肿瘤学
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大类 | 3 区 医学
小类 | 4 区 肿瘤学
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Q2 ONCOLOGY
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Q2 ONCOLOGY

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第一作者机构: [1]Minist Educa t Beijing, Dept Med Oncol, Peking Univ Canc Hosp & Inst, Key Lab Carcinogenesis & Translat Res, Beijing 100142, Peoples R China
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通讯机构: [6]Shanghai Jiao Tong Univ, Sch Med, Shanghai Peoples Hosp 9, Dept Radiol, Shanghai, Peoples R China [7]Shanghai Jiao Tong Univ, Sch Med, Shanghai Peoples Hosp 1, Dept Med Oncol, Shanghai 200080, Peoples R China [*1]Department of Medical Oncology, Shanghai First People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200080, China. [*2]Department of Radiology, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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