Transcriptomic profiling of high- and low-spiking regions reveals novel epileptogenic mechanisms in focal cortical dysplasia type II patients

Abstract

Focal cortical dysplasia (FCD) is a malformation of the cerebral cortex with poorly-defined epileptogenic zones (EZs), and poor surgical outcome in FCD is associated with inaccurate localization of the EZ. Hence, identifying novel epileptogenic markers to aid in the localization of EZ in patients with FCD is very much needed. High-throughput gene expression studies of FCD samples have the potential to uncover molecular changes underlying the epileptogenic process and identify novel markers for delineating the EZ. For this purpose, we, for the first time performed RNA sequencing of surgically resected paired tissue samples obtained from electrocorticographically graded high (MAX) and low spiking (MIN) regions of FCD type II patients and autopsy controls. We identified significant changes in the MAX samples of the FCD type II patients when compared to non-epileptic controls, but not in the case of MIN samples. We found significant enrichment for myelination, oligodendrocyte development and differentiation, neuronal and axon ensheathment, phospholipid metabolism, cell adhesion and cytoskeleton, semaphorins, and ion channels in the MAX region. Through the integration of both MAX vs non-epileptic control and MAX vs MIN RNA sequencing (RNA Seq) data, PLP1, PLLP, UGT8, KLK6, SOX10, MOG, MAG, MOBP, ANLN, ERMN, SPP1, CLDN11, TNC, GPR37, SLC12A2, ABCA2, ABCA8, ASPA, P2RX7, CERS2, MAP4K4, TF, CTGF, Semaphorins, Opalin, FGFs, CALB2, and TNC were identified as potential key regulators of multiple pathways related to FCD type II pathology. We have identified novel epileptogenic marker elements that may contribute to epileptogenicity in patients with FCD and could be possible markers for the localization of EZ.

Transcriptome analyses of the cortex and white matter of focal cortical dysplasia type II: Insights into pathophysiology and tissue characterization

“…Interestingly, they found an upregulation of myelin-associated transcripts in FCD cases that had high electric activity, compared with controls from autopsies. In addition, Srivastava et al ( 15 ) found differential expression of lipid-biosynthesis enzymes between FCD and controls, which is similar to our finding concerning cholesterol biosynthesis-enzymes. Despite such similarity, caution is necessary when comparing our data and those from others due to particularities associated with sequencing methods and control selection.…”

“…The restricted sample size is a limitation of our study. However, it is noteworthy that the number of individuals with FCD is larger than in previous reports (14,15). In addition, despite the reduced sample sizes, we were able to validate the results regarding cholesterol and GPNMB at the protein level, which gives biological consistency to our findings.…”

“…The authors observed epigenetic regulation in genes involved in neuron cell migration. Moreover, the recent study by Srivastava et al ( 15 ) addressed the transcriptomes of 5 FCDs (IIa and IIb) and 2 controls, also considering gray and white matters concurrently. Interestingly, they found an upregulation of myelin-associated transcripts in FCD cases that had high electric activity, compared with controls from autopsies.…”

“…Overall, our results revealed different transcriptomic signatures in FCD type IIa and IIb lesions. Of note, the RNA-Seq method allowed us to obtain data not considered in previous studies focusing only on histopathological analyses of human FCD samples (13)(14)(15). Thus, such genetic data prompted us to further histopathologically and specifically investigate the expressions of cholesterol biosynthesis enzymes and GPNMB, which are respectively potential neuropathological biomarkers of a dysplastic brain cortex chronically exposed to seizures and of balloon cells.…”

“…In this context, we designed an original high throughput study by using RNA-Seq to perform transcriptome analysis ( 12 ) and identify differentially expressed mRNAs in the cortex and white matter of individuals with epilepsy due to FCD type IIa or IIb. Even though other authors investigated FCD transcriptome ( 13 – 15 ), the gray and white matters were studied as homogenates, gene expression protocols were different from ours and fewer FCD cases were considered. Moreover, we compared the transcriptome profiles of the two lesions with those obtained from brain samples from autopsied control individuals without a history of neurological disease.…”