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Background <p>Meningiomas are among the most prevalent central nervous system (CNS) tumors, with up to 20% of cases exhibiting recurrence or aggressive behavior. Hypoxia is a key driver of malignant transformation and therapeutic resistance, yet its molecular basis in meningioma remains poorly understood.</p> Methods <p>We conducted integrative transcriptomic and epigenomic profiling of IOMM-Lee cells (grade 3 meningioma) cultured under hypoxic (0.2% O₂) and normoxic conditions. RNA-sequencing and Illumina MethylationEPIC v2.0 data were analyzed in R using DESeq2 and minfi, respectively. Functional enrichment, transcription-factor binding analysis, and pathway mapping (clusterProfiler, enrichR) were performed. Findings were cross-validated in public meningioma datasets, in Indian meningioma patient cohort and cell line via RT-qPCR, and azacytidine-based demethylation assay. Functional role of the candidate gene was elucidated in vitro via cellular assays.</p> Results <p>Hypoxia triggered a canonical HIF1A-driven transcriptional program activating glycolytic and angiogenic pathways while downregulating genes associated with DNA repair and replication in meningioma. Several differentially expressed genes (DEGs) were identified as known oncogenes, tumor-suppressors, or associated with immune regulation and stemness. Promoter motif analysis identified <i>HIF1</i>,<i> SP1</i>,<i> TP53</i>,<i> BRCA1</i>, and <i>E2F1</i> as enriched transcriptional regulators. We validated hypoxia and HIF1-mediated regulation of some of the top DEGs. DNA-methylation analysis revealed epigenetic silencing of <i>RTN4IP1</i> and <i>ZBTB7C</i> under hypoxia, reversible upon azacytidine treatment. Integrative comparison with patient datasets highlighted <i>SLITRK2</i>,<i> PDE4C</i>,<i> SGCD</i>, and <i>LRP1B</i> as hypoxia-responsive genes associated with poor prognosis. Several hypoxia-regulated genes also showed significant correlation with known hypoxia biomarkers, <i>VEGFA</i> and <i>CA9</i>. <i>IGFBP3</i> and <i>NDRG1</i> were among the top hypoxia-associated upregulated genes, and <i>IGFBP3</i> expression was linked to advanced meningioma grades. Knockdown of <i>IGFBP3</i> via siRNA in hypoxia-treated IOMM-Lee cells was associated with reduced cell proliferation and migration.</p> Conclusions <p>This study presents the first integrated transcriptomic–epigenomic landscape of hypoxia in grade 3 meningioma, uncovering regulatory networks and candidate biomarkers with prognostic and therapeutic potential. These findings provide a foundation for future translational studies targeting hypoxia-driven tumor progression in meningioma.</p>

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Novel insights into hypoxia-driven transcriptomic and epigenetic landscapes in grade 3 meningioma

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年12月24日

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  • Mansi Dalal,
  • Ritanksha Joshi,
  • Priyadarshana Ajithkumar,
  • Jyotsna Singh,
  • Vaishali Suri,
  • Aniruddha Chatterjee,
  • Ritu Kulshreshtha

摘要

Background

Meningiomas are among the most prevalent central nervous system (CNS) tumors, with up to 20% of cases exhibiting recurrence or aggressive behavior. Hypoxia is a key driver of malignant transformation and therapeutic resistance, yet its molecular basis in meningioma remains poorly understood.

Methods

We conducted integrative transcriptomic and epigenomic profiling of IOMM-Lee cells (grade 3 meningioma) cultured under hypoxic (0.2% O₂) and normoxic conditions. RNA-sequencing and Illumina MethylationEPIC v2.0 data were analyzed in R using DESeq2 and minfi, respectively. Functional enrichment, transcription-factor binding analysis, and pathway mapping (clusterProfiler, enrichR) were performed. Findings were cross-validated in public meningioma datasets, in Indian meningioma patient cohort and cell line via RT-qPCR, and azacytidine-based demethylation assay. Functional role of the candidate gene was elucidated in vitro via cellular assays.

Results

Hypoxia triggered a canonical HIF1A-driven transcriptional program activating glycolytic and angiogenic pathways while downregulating genes associated with DNA repair and replication in meningioma. Several differentially expressed genes (DEGs) were identified as known oncogenes, tumor-suppressors, or associated with immune regulation and stemness. Promoter motif analysis identified HIF1, SP1, TP53, BRCA1, and E2F1 as enriched transcriptional regulators. We validated hypoxia and HIF1-mediated regulation of some of the top DEGs. DNA-methylation analysis revealed epigenetic silencing of RTN4IP1 and ZBTB7C under hypoxia, reversible upon azacytidine treatment. Integrative comparison with patient datasets highlighted SLITRK2, PDE4C, SGCD, and LRP1B as hypoxia-responsive genes associated with poor prognosis. Several hypoxia-regulated genes also showed significant correlation with known hypoxia biomarkers, VEGFA and CA9. IGFBP3 and NDRG1 were among the top hypoxia-associated upregulated genes, and IGFBP3 expression was linked to advanced meningioma grades. Knockdown of IGFBP3 via siRNA in hypoxia-treated IOMM-Lee cells was associated with reduced cell proliferation and migration.

Conclusions

This study presents the first integrated transcriptomic–epigenomic landscape of hypoxia in grade 3 meningioma, uncovering regulatory networks and candidate biomarkers with prognostic and therapeutic potential. These findings provide a foundation for future translational studies targeting hypoxia-driven tumor progression in meningioma.