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

Area of Science:

• Oncology
• Immunology
• Bioinformatics

Background:

• Immune checkpoint blockade (ICB) therapy offers significant clinical benefits across various cancer types.
• Understanding the transcriptional mechanisms underlying ICB therapy is crucial for improving treatment efficacy.
• Existing data on ICB therapy's transcriptomic features are fragmented across multiple repositories.

Purpose of the Study:

• To integrate and analyze transcriptomic and clinical data from ICB-treated patients to uncover key features of ICB therapy.
• To develop a comprehensive database, ICBatlas, for exploring these transcriptomic features.
• To provide insights into gene expression patterns related to treatment response and biological pathways.

Main Methods:

• Collected transcriptome and clinical data from ICB-treated samples across public databases (GEO, ArrayExpress, TCGA, dbGaP).
• Classified samples into response/nonresponse and pretreatment/on-treatment groups for comparative analyses.
• Performed differential expression, pathway enrichment, immune cell infiltration analyses, and introduced a Response Score (RS) for gene impact evaluation.

Main Results:

• Integrated data from 1,515 ICB-treated samples across 25 studies and nine cancer types into the ICBatlas database.
• ICBatlas provides comprehensive data including clinical outcomes, treatment-related genes, pathways, and immune cell infiltration.
• The database enables investigation of transcriptome features at dataset, cancer type, or immune checkpoint levels, and assesses gene impact on response via the RS module.

Conclusions:

• ICBatlas is the first database to present comprehensive transcriptome features of ICB therapy in human cancers.
• The database facilitates deeper understanding of ICB therapy mechanisms and response predictors.
• ICBatlas is freely available, promoting further research into optimizing ICB treatments.