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Low-grade glioma risk SNP rs11706832 is associated with type I interferon response pathway genes in cell lines
Umeå University, Faculty of Medicine, Department of Radiation Sciences, Oncology.
Umeå University, Faculty of Medicine, Department of Radiation Sciences, Oncology.ORCID iD: 0000-0002-6754-2571
Umeå University, Faculty of Medicine, Department of Radiation Sciences, Oncology.
Umeå University, Faculty of Science and Technology, Department of Chemistry.ORCID iD: 0000-0001-9347-5790
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2023 (English)In: Scientific Reports, E-ISSN 2045-2322, Vol. 13, article id 6777Article in journal (Refereed) Published
Abstract [en]

Genome-wide association studies (GWAS) have contributed to our understanding of glioma susceptibility. To date, 25 risk loci for development of any of the glioma subtypes are known. However, GWAS studies reveal little about the molecular processes that lead to increased risk, especially for non-coding single nucleotide polymorphisms (SNP). A particular SNP in intron 2 of LRIG1, rs11706832, has been shown to increase the susceptibility for IDH1 mutated low-grade gliomas (LGG). Leucine-rich repeats and immunoglobulin-like domains protein 1 (LRIG1) is important in cancer development as it negatively regulates the epidermal growth factor receptor (EGFR); however, the mechanism responsible for this particular risk SNP and its potential effect on LRIG1 are not known. Using CRISPR-CAS9, we edited rs11706832 in HEK293T cells. Four HEK293T clones with the risk allele were compared to four clones with the non-risk allele for LRIG1 and SLC25A26 gene expression using RT-qPCR, for global gene expression using RNA-seq, and for metabolites using gas chromatography-mass spectrometry (GC–MS). The experiment did not reveal any significant effect of the SNP on the expression levels or splicing patterns of LRIG1 or SLC25A26. The global gene expression analysis revealed that the risk allele C was associated with upregulation of several mitochondrial genes. Gene enrichment analysis of 74 differentially expressed genes in the genome revealed a significant enrichment of type I interferon response genes, where many genes were downregulated for the risk allele C. Gene expression data of IDH1 mutated LGGs from the cancer genome atlas (TCGA) revealed a similar under expression of type I interferon genes associated with the risk allele. This study found the expression levels and splicing patterns of LRIG1 and SLC25A26 were not affected by the SNP in HEK293T cells. However, the risk allele was associated with a downregulation of genes involved in the innate immune response both in the HEK293T cells and in the LGG data from TCGA.

Place, publisher, year, edition, pages
Springer Nature, 2023. Vol. 13, article id 6777
National Category
Cancer and Oncology Medical Genetics
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URN: urn:nbn:se:umu:diva-208211DOI: 10.1038/s41598-023-33923-4ISI: 000984494600021PubMedID: 37185361Scopus ID: 2-s2.0-85154566176OAI: oai:DiVA.org:umu-208211DiVA, id: diva2:1757527
Available from: 2023-05-16 Created: 2023-05-16 Last updated: 2023-09-05Bibliographically approved

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Rosenbaum, AdamDahlin, Anna M.Andersson, UlrikaBjörkblom, BennyWu, Wendy Yi-YingHedman, HåkanWibom, CarlMelin, Beatrice S.

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Rosenbaum, AdamDahlin, Anna M.Andersson, UlrikaBjörkblom, BennyWu, Wendy Yi-YingHedman, HåkanWibom, CarlMelin, Beatrice S.
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OncologyDepartment of Chemistry
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