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ICBatlas: A Comprehensive Resource for Depicting Immune Checkpoint Blockade Therapy Characteristics from Transcriptome Profiles
Mei Yang1,2; Ya-Ru Miao1; Gui-Yan Xie1; Mei Luo1; Hui Hu1; Hang Fai Kwok3,4; Jian Feng5; Jian Feng1,2
2022-11-02
Source PublicationCancer Immunology Research
ISSN2326-6066
Volume10Issue:11Pages:1398-1406
Abstract

Immune checkpoint blockade (ICB) therapy provides remarkable clinical benefits for multiple cancer types. Much work is currently being conducted to investigate the mechanisms of ICB therapy at the transcriptional level. Integrating the data produced by these studies will help us give more insight into the transcriptomic features of ICB therapy. We collected the transcriptome and clinical data of ICB-treated patient samples from the Gene Expression Omnibus, ArrayExpress, The Cancer Genome Atlas, and dbGaP databases. On the basis of the clinical information, all samples are initially classified into response/nonresponse or pretreatment/on-treatment groups. Differential expression, pathway enrichment, and immune cell infiltration analyses are performed between the samples from different groups. We also introduce the Response Score (RS) calculated by integrating the variability degree and the frequency of the dysregulated genes in the responders to evaluate the impact of gene expression on the response. Finally, all the abovementioned contents are integrated into the ICBatlas database. ICBatlas provides the transcriptome features of ICB therapy through the analysis of 1,515 ICB-treated samples from 25 studies across nine cancer types. The data in ICBatlas include clinical outcomes, treatment-related genes, biological pathways, and immune cell infiltration. Users can investigate the abovementioned transcriptome features in the response (R vs. NR) or treatment (Pre vs. On) modules at the data set, cancer type, or immune checkpoint level and compare the degree of gene impact on the response in the RS module. ICBatlas is the first database to show the transcriptome features on ICB therapy in human cancers and freely available at http://bioinfo.life.hust.edu.cn/ICBatlas/.

KeywordAnti-pd-1 Safety Immunotherapy Predicts
DOI10.1158/2326-6066.CIR-22-0249
URLView the original
Indexed BySCIE
Language英語English
WOS Research AreaOncology ; Immunology
WOS SubjectOncology ; Immunology
WOS IDWOS:000879852200001
Scopus ID2-s2.0-85141888240
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Citation statistics
Document TypeJournal article
CollectionMinistry of Education Frontiers Science Center for Precision Oncology, University of Macau
Faculty of Health Sciences
Cancer Centre
Corresponding AuthorJian Feng; Jian Feng
Affiliation1.Huazhong Univ Sci & Technol, Coll Life Sci & Technol, Ctr Artificial Intelligence Biol, Hubei Bioinformat & Mol Imaging Key Lab,Key Lab Mo, Wuhan, Peoples R China
2.Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
3.Cancer Centre, Faculty of Health Sciences, University of Macau, Taipa, Macau
4.MoE Frontiers Science Center for Precision Oncology, University of Macau, Taipa, Macau
5.Department of Respiratory, Affiliated Hospital of Nantong University, Nantong, China
Recommended Citation
GB/T 7714
Mei Yang,Ya-Ru Miao,Gui-Yan Xie,et al. ICBatlas: A Comprehensive Resource for Depicting Immune Checkpoint Blockade Therapy Characteristics from Transcriptome Profiles[J]. Cancer Immunology Research, 2022, 10(11), 1398-1406.
APA Mei Yang., Ya-Ru Miao., Gui-Yan Xie., Mei Luo., Hui Hu., Hang Fai Kwok., Jian Feng., & Jian Feng (2022). ICBatlas: A Comprehensive Resource for Depicting Immune Checkpoint Blockade Therapy Characteristics from Transcriptome Profiles. Cancer Immunology Research, 10(11), 1398-1406.
MLA Mei Yang,et al."ICBatlas: A Comprehensive Resource for Depicting Immune Checkpoint Blockade Therapy Characteristics from Transcriptome Profiles".Cancer Immunology Research 10.11(2022):1398-1406.
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