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

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 GEO, ArrayExpress, TCGA, and dbGaP databases. Based on the clinical information, all samples are initially classified into response/non-response or pre-treatment/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 1515 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 dataset, 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/.

IP-score correlated to endogenous tumour antigen peptide processing: A candidate clinical response score algorithm of immune checkpoint inhibitors therapy in multiple cohorts

“…Immunotherapy cohorts were acquired from the Immune Checkpoint Blockade Therapy Atlas (ICBatlas) ( 25 ). ICBatlas is a database that provides complete expression resources and functional analyses for ICB therapy patients.…”

The cell stress and immunity cycle in cancer: Toward next generation of cancer immunotherapy

“…ICBs have greatly improved cancer patients' outcomes, nevertheless a major subset of patients still fail to sufficiently respond while experiencing potential adverse effects. 147,148 Therefore, multiple predictive biomarkers are being tested to select only those patients who are likely to respond to immunotherapies, as leverage for adverse effects. 149 More details about biomarkers currently used are described in Box 1.…”

“…However, the early clinical response rates to these new ICBs are relatively more mixed, with only the combination of PD1 and LAG3 co‐blockade gaining approval for melanoma patients in the past few years. ICBs have greatly improved cancer patients' outcomes, nevertheless a major subset of patients still fail to sufficiently respond while experiencing potential adverse effects 147,148 . Therefore, multiple predictive biomarkers are being tested to select only those patients who are likely to respond to immunotherapies, as leverage for adverse effects 149 .…”

Comprehensively analysis of the FGD family with potential effects on prognosis and immune infiltration in lung adenocarcinoma

“…IPSs for LUAD patients were downloaded from TCIA database (30). The ICBatlas database was utilized to assess the expression of the FGD genes in NSCLC patients treated with ICB (31). KMplotter and ROCplotter (32) were used to analyze the expression of FGD genes in patients with other types of cancer treated with ICB.…”