ICBatlas: A Comprehensive Resource for Depicting Immune Checkpoint Blockade Therapy Characteristics from Transcriptome Profiles.

Cancer Immunol Res

Center for Artificial Intelligence Biology, Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China.

Published: November 2022

AI Article Synopsis

  • Immune checkpoint blockade (ICB) therapy has shown significant benefits for various cancers, prompting investigations into its effects at the transcriptional level to better understand these mechanisms.
  • Researchers gathered transcriptome and clinical data from multiple databases, categorizing samples based on their treatment response and analyzing gene expression, pathways, and immune cell presence.
  • The resulting ICBatlas database consolidates data from 1,515 ICB-treated samples across nine cancer types, allowing users to explore how gene expression impacts treatment response, clinical outcomes, and related biological pathways.

Article 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/.

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Source
http://dx.doi.org/10.1158/2326-6066.CIR-22-0249DOI Listing

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