Integrative analysis of key candidate genes and signaling pathways in autoimmune thyroid dysfunction related to anti-CTL
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PRECLINICAL STUDIES
Integrative analysis of key candidate genes and signaling pathways in autoimmune thyroid dysfunction related to anti-CTLA-4 therapy by bioinformatics Ying Zhang 1 & Francesca Garofano 1 & Xiaolong Wu 1 & Matthias Schmid 2 & Peter Krawitz 3 & Markus Essler 4 & Ingo G. H. Schmidt-Wolf 1 Received: 31 March 2020 / Accepted: 14 May 2020 # The Author(s) 2020
Summary Cytotoxic T lymphocyte-associated antigen-4 (CTLA-4), the first immune checkpoint to be targeted clinically, has provided an effective treatment option for various malignancies. However, the clinical advantages associated with CTLA-4 inhibitors can be offset by the potentially severe immune-related adverse events (IRAEs), including autoimmune thyroid dysfunction. To investigate the candidate genes and signaling pathways involving in autoimmune thyroid dysfunction related to anti-CTLA-4 therapy, integrated differentially expressed genes (DEGs) were extracted from the intersection of genes from Gene Expression Omnibus (GEO) datasets and text mining. The functional enrichment was performed by gene ontology (GO) annotation and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis. Protein-protein interaction (PPI) network, module enrichment, and hub gene identification were constructed and visualized by the online Search Tool for the Retrieval of Interacting Genes (STRING) and Cytoscape software. A total of 22 and 17 integrated human DEGs in hypothyroidism and hyperthyroidism group related to anti-CTLA-4 therapy were identified, respectively. Functional enrichment analysis revealed 24 GO terms and 1 KEGG pathways in the hypothyroid group and 21 GO terms and 2 KEGG pathways in the hyperthyroid group. After PPI network construction, the top five hub genes associated with hypothyroidism were extracted, including ALB, MAPK1, SPP1, PPARG, and MIF, whereas those associated with hyperthyroidism were ALB, FCGR2B, CD44, LCN2, and CD74. The identification of the candidate key genes and enriched signaling pathways provides potential biomarkers for autoimmune thyroid dysfunction related to anti-CTLA-4 therapy and might contribute to the future diagnosis and management of IRAEs for cancer patients. Keywords Immune checkpoint blockade . CTLA-4 . Autoimmune thyroid dysfunction . Differentially expressed genes . Signaling pathway
Introduction Electronic supplementary material The online version of this article (https://doi.org/10.1007/s10637-020-00952-z) contains supplementary material, which is available to authorized users. * Ingo G. H. Schmidt-Wolf [email protected] 1
Department of Integrated Oncology, Center for Integrated Oncology (CIO), University Hospital Bonn, Venusberg-Campus 1, D-53127 Bonn, Germany
2
Institute for Medical Biometry, Computer Science and Epidemiology, University Hospital Bonn, Bonn, Germany
3
Institute for Genomic Statistics and Bioinformatics of Medical School University Bonn, Bonn, Germany
4
Department of Nuclear Medicine, University Hospital Bonn, Bonn, Germany
Immune checkpoint blockade represents o
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