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INTERNATIONAL CONGRESS OF

CancerGenetics

• New Molecular and Cellular Pathways of IDH1 Mutation in the Glioblastoma

• Fardad Danaee Fard,¹ Iman Safari,^2,*
  1. Independent Researcher
  2. Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen
  
  
  
• Introduction: Mutations in isocitrate dehydrogenase (IDH) 1 and 2 genes are key drivers of glioblastomas, particularly secondary glioblastomas in younger patients. These mutations are often prognostic for low-grade glioblastomas. While these mutations grant new functions to the enzymes, the exact molecular and cellular mechanisms linking them to glioblastoma pathogenesis remain unclear. To investigate this, we reanalyzed a single-cell RNA sequencing (scRNA-seq) dataset to compare cellular composition and gene expression patterns associated with these mutations.
• Methods: We analyzed a publicly available dataset (GSE103224) from 8 high-grade glioma tissues, including one with the p.R132H mutation in the IDH1 gene (mutant) and others without any mutation (wild type). Using the Seurat package, we performed standard analysis, including PCA, UMAP, and tSNE for dimensionality reduction. We corrected for batch effects related to mitochondrial gene percentages and clustered cells at a resolution of 0.6, regressing out cell cycle effects. Cells were annotated with SingleR and BlueprintEncodeData. We extracted and plotted cell counts and markers for mutant and wild type conditions using ggplot2. Gene ontology enrichment analysis was conducted with clusterProfiler and org.Hs.eg.db in R.
• Results: Our analysis shows that the R132H mutation in IDH1 significantly reduces the number of neurons, mesangial cells, fibroblasts, astrocytes, epithelial, and endothelial cells and increases adipocytes. Cyclin analysis showed adipocytes are mostly in the G1 phase, with upregulated genes related to microtubule movement and non-canonical Wnt signaling, and downregulated genes related to cell cycle inhibition. KEGG analysis indicated downregulation of apoptosis-related genes in adipocytes. Differential gene expression analysis revealed lower expression of MHC pathway, phagosome, and PI3K-AKT pathway genes in mutant tissue. Additionally, genes related to immune regulation, inflammation, and cytokine production were downregulated, while antigen presentation genes were upregulated when comparing mutant tissue to the wildtype in general. The mutation also appears to cause leukocyte death and negatively regulate innate immune responses and inflammation. Macrophages showed induction of immune response pathways and inhibition of cell proliferation and migration. Dendritic cells downregulated genes related to metabolism, cell proliferation, cytokine production, and proteolysis, but expressed genes related to brain development and ECM organization. CD4+ T cells upregulated genes related to negative regulation of cell development, neurogenesis, and nervous system development, while downregulating genes related to immune response and autophagy.
• Conclusion: The findings from our study provide insights into the cellular and molecular consequences of the R132H mutation in IDH1 gene. A broad impact on tissue homeostasis and cellular diversity was the initially-observed impact of the mutation. One potential explanation for these observations could be that this mutation might provide a selective advantage in some cell types. The functional analysis of these adipocytes revealed that they may face a block in cell cycle progression. The transcriptome profile of adipocytes points towards a complex regulatory mechanism that promotes proliferation while potentially inhibiting differentiation. The downregulation of apoptosis-related genes in adipocytes further supports the notion of enhanced cell survival in this cell type. This could contribute to the increased adipocyte count observed in the mutant samples. The differential gene expression analysis between mutant and wildtype tissues highlighted several key pathways affected by the R132H mutation, suggesting a compromised immune response. However, the upregulation of genes activating antigen presentation processes indicates a potential compensatory mechanism to maintain some level of immune surveillance. The mutation also appears to induce leukocyte cell death and negatively regulate innate immune responses and inflammatory reactions. The GO analysis of macrophages suggests a complex interplay between promoting immune responses and limiting tissue remodeling or repair processes. Similarly, the expression profile of dendritic cells in the mutant samples indicates a potential shift in the functional state of dendritic cells, possibly affecting their role in antigen presentation and immune activation. Lastly, the analysis of CD4+ T cells further highlight the broad immunomodulatory effects of the R132H mutation. In conclusion, the R132H mutation in IDH1 exerts widespread effects on various cell types and pathways, leading to altered cellular composition, immune responses, and potentially impacting tissue homeostasis and function.
• Keywords: Single-cell transcriptome, Glioblastoma, IDH1 mutation, clonal sequencing