IRX1 is a novel gene, overexpressed in high-grade IDH-mutant astrocytomas

• Published in: Pathology, research and practice Vol. 245; p. 154464
• Main Authors: Sugur, Harsha S., Rao, Shilpa, Sravya, Palavalasa, Athul Menon, K., Arivazhagan, Arimappamagan, Mehta, Bhupesh, Santosh, Vani
• Format: Journal Article
• Language: English
• Published: Germany Elsevier GmbH 01-05-2023
• Subjects: Astrocytoma - genetics; Astrocytoma - pathology; Biomarkers; Brain Neoplasms - pathology; DNMT3A; Glioblastoma - pathology; High-grade IDH-mutant astrocytoma; Homeodomain Proteins - genetics; Homeodomain Proteins - metabolism; Humans; IRX1; Isocitrate Dehydrogenase - genetics; Mutation; Nanostring; Neoplasm Recurrence, Local; Prognosis; RNA, Messenger - genetics; TCGA mRNA sequencing data; Transcription Factors - genetics; IRX1; High-grade IDH-mutant astrocytoma; Prognosis; TCGA mRNA sequencing data; Nanostring; DNMT3A
• ISSN: 0344-0338; 1618-0631
• DOI: 10.1016/j.prp.2023.154464

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.
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.
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.
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.
•Amongst the higher grades A, IDH-mt., A3 tumours are known to be associated with a heterogenous clinical outcome.•Some molecular alterations have been associated with worse prognosis, indicating that further research in A3 is needed.•IRX1 is a novel gene overexpressed in high grade IDH-mutant astrocytomas with prognostic significance in A3 tumours.•IRX1 could serve as an aggressive biomarker for high grade IDH-mutant astrocytomas, useful for routine clinical practice.