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RNA Sequencing of Intraoperative Peritumoral Tissues Reveals Potential Pathways Involved in Glioma-Related Seizures

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Abstract

Tumor-induced changes in the peritumoral neocortex play a crucial role in generation of seizures. This study aimed to investigate the molecular mechanisms potentially involved in peritumoral epilepsy in low-grade gliomas (LGGs). Intraoperative peritumoral brain tissues resected from LGG patients with seizures (pGRS) or without seizures (pGNS) were used for RNA sequencing (RNA-seq). Comparative transcriptomics was performed to identify differentially expressed genes (DEGs) in pGRS compared to pGNS using deseq2 and edgeR packages (R). Gene set enrichment analysis (GSEA) using Gene Ontology terms and Kyoto Encyclopedia of Genes & Genomes (KEGG) pathways was performed using the clusterProfiler package (R). The expression of key genes was validated at the transcript and protein levels in the peritumoral region using real-time PCR and immunohistochemistry, respectively. A total of 1073 DEGs were identified in pGRS compared to pGNS, of which 559 genes were upregulated and 514 genes were downregulated (log2 fold-change ≥ 2, padj < 0.001). The DEGs in pGRS were highly enriched in the “Glutamatergic Synapse” and “Spliceosome” pathways, with increased expression of GRIN2A (NR2A), GRIN2B (NR2B), GRIA1 (GLUR1), GRIA3 (GLUR3), GRM5, CACNA1C, CACNA1A, and ITPR2. Moreover, increased immunoreactivity was observed for NR2A, NR2B, and GLUR1 proteins in the peritumoral tissues of GRS. These findings suggest that altered glutamatergic signaling and perturbed Ca2+ homeostasis may be potential causes of peritumoral epilepsy in gliomas. This explorative study identifies important genes/pathways that merit further characterization for their potential involvement in glioma-related seizures.

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Data Availability

The RNA sequencing data is available in the NCBI’s Sequence Read Archive repository (BioProject: PRJNA940602). Reviewer’s link: https://dataview.ncbi.nlm.nih.gov/object/PRJNA940602?reviewer=bdon1ns3l8937bbgtre5ki34ji.

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Funding

This study was generously supported by grants from the Office of the Principal Scientific Adviser to the Government of India vide sanction number: Prn.SA/Epilep/2017(G). The funder had no role in study design, data analysis, or decision to publish.

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Authors and Affiliations

  1. Department of Neurology, AIIMS, New Delhi, India

    Krishan Kumar & Manjari Tripathi

  2. Department of Biophysics, All India Institute of Medical Sciences (AIIMS), New Delhi, 110029, India

    Vivek Dubey, Syeda S. Zaidi & Jyotirmoy Banerjee

  3. ICMR-National Institute of Pathology, New Delhi, India

    Fouzia Siraj

  4. Department of Pathology, AIIMS, New Delhi, India

    Mehar Chand Sharma

  5. Department of Neurosurgery, AIIMS, New Delhi, India

    P. Sarat Chandra & Ramesh Doddamani

  6. Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, India

    Aparna Banerjee Dixit

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  1. Krishan Kumar
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  3. Syeda S. Zaidi
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  9. Aparna Banerjee Dixit
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  10. Jyotirmoy Banerjee
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Contributions

KK designed the research, performed the experiments, analyzed the data, and wrote the paper; VD and SSZ performed the experiments; MT performed pre-surgical evaluation of patients; FS and MCS analyzed histopathological data; PSC performed surgery and provided tissue samples; RD, ABD, and JB designed the research, analyzed the data, and wrote the paper.

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Correspondence to Aparna Banerjee Dixit or Jyotirmoy Banerjee.

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The study was approved by institutional ethics committee (IEC) of All India Institute of Medical Sciences, New Delhi, and all the methods were performed in accordance with the relevant guidelines and regulations. A prior informed written consent was obtained from all subjects.

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Kumar, K., Dubey, V., Zaidi, S.S. et al. RNA Sequencing of Intraoperative Peritumoral Tissues Reveals Potential Pathways Involved in Glioma-Related Seizures. J Mol Neurosci 73, 437–447 (2023). https://doi.org/10.1007/s12031-023-02125-y

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