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IRX1 is a novel gene, overexpressed in high-grade IDH-mutant astrocytomas
Harsha S Sugur1, Shilpa Rao1, Palavalasa Sravya1
1Department of Neuropathology, National Institute of Mental Health and Neuro Sciences, Bangalore, Karnataka 560029, India.
Background:
IDH-mutant astrocytomas include CNS WHO grade 2 (A2), grade 3 (A3) and grade 4 (A4), of which A3 and A4 are high-grade. A3 has a heterogenous clinical outcome that cannot be explained entirely by the existing molecular biomarkers. We comprehensively studied the transcriptome profile of A3 to determine clinical significance.
Methods:
TCGA mRNA-sequencing data of A3 was analyzed to derive differentially expressed genes (DEG), which were short-listed using various approaches. mRNA expression of the short-listed genes was validated using NanoString platform on a uniformly treated and molecularly characterized A3 cohort. Protein expression of one prognostically significant gene, Iroquois-class homeodomain (IRX1) was assessed by immunohistochemistry and correlated with patient survival and tumor recurrence. IRX1 expression was also studied in different grades of astrocytoma. Since DNA methyltransferase 3 alpha (DNMT3A) influences IRX1 expression, its mutations were evaluated in a subset of tumors.
Results:
TCGA analysis identified 96 DEG in A3 tumours. 57 genes were short-listed and finally narrowed down to 14 genes. mRNA values of 12/14 genes validated in our cohort. On multiple-variable analysis, IRX1 was the most prognostically relevant gene, with respect to progression free survival of patients. Further, IRX1 immunoexpression was significantly higher in A3 and A4 when compared to A2 and glioblastoma. Higher IRX1 immunoexpression correlated with poor prognosis in patients with A3 tumours. Also, a higher IRX1 expression was associated with DNMT3A mutation.
Conclusion:
Our study identifies IRX1 as a novel biomarker overexpressed in high-grade IDH-mutant astrocytomas with prognostic significance in A3. DNMT3A mutation probably modulates IRX1 expression.
Insights
This study identifies IRX1 as a novel biomarker in high-grade IDH-mutant astrocytomas. Higher IRX1 expression correlates with poor prognosis in grade 3 astrocytoma patients.
Area of Science:
- Neuro-oncology
- Molecular Biology
- Genomics
Background:
- IDH-mutant astrocytomas (grades 2, 3, and 4) are classified by WHO, with grades 3 and 4 considered high-grade.
- Grade 3 astrocytoma exhibits heterogeneous clinical outcomes not fully explained by current molecular markers.
- This study aimed to analyze the transcriptome profile of grade 3 astrocytoma for clinical significance.
Purpose of the Study:
- To identify novel molecular biomarkers for IDH-mutant astrocytomas.
- To determine the prognostic significance of gene expression in grade 3 astrocytoma.
- To investigate the role of IRX1 and its relationship with DNMT3A in astrocytoma.
Main Methods:
- Differential gene expression analysis of TCGA mRNA-sequencing data for grade 3 astrocytomas.
- Validation of candidate genes using NanoString and immunohistochemistry.
- Correlation of IRX1 protein expression with patient survival, tumor recurrence, and DNMT3A mutations.
Main Results:
- 96 differentially expressed genes were identified in grade 3 astrocytomas, narrowed down to 14 validated genes.
- IRX1 emerged as the most prognostically significant gene for progression-free survival.
- Higher IRX1 immunoexpression was observed in grades 3 and 4 astrocytomas compared to grade 2 and glioblastoma, correlating with poor prognosis in grade 3 cases and associated with DNMT3A mutations.
Conclusions:
- IRX1 is identified as a novel biomarker overexpressed in high-grade IDH-mutant astrocytomas.
- IRX1 demonstrates prognostic significance in grade 3 astrocytomas.
- DNMT3A mutations likely modulate IRX1 expression in astrocytomas.
