The role of genetic testing in evaluating surgical outcomes for pediatric focal cortical dysplasia associated with NPRL3 variant

Highlights

• •Epilepsy related to NPRL3 gene variants had high possibility to be drug‐resistant.
• •This report presents a rare case of FCD Ib associated with NPRL3 gene variants.
• •Accurrate surgical decision-making is challaging in NPRL3 gene variants.

Abstract

This case report describes a 5-year-and-10-month-old female patient who developed sleep-related hypermotor epilepsy, at the age of 2, exhibiting various forms of seizures since the age of 2. Initially, the seizures were controlled for one year with multiple anti-seizure medications; however, symptoms recurred when the patient was 3 years and 5 months old, leading to an increased seizure frequency and a poor response to combined drug therapy. Long-term video-EEG revealed discharges originating from the frontal lobe, while MRI and PET-CT scans indicated FCD in the left frontal region. The patient underwent left frontal epileptogenic focus resection at the age of 6, with pathological findings confirming FCD type 1b. Whole-exome sequencing of blood and brain tissue samples revealed NPRL3 gene variants. Although she remained seizure-free for one year post-surgery, the patient experienced a relapse, with follow-up EEG revealing multifocal discharges. These findings indicate that variants in the NPRL3 gene contribute to focal cortical dysplasia (FCD) and are frequently associated with drug-resistant epilepsy. For FCD 1b patients with NPRL3 gene variants, the risks and benefits of surgery should be carefully evaluated. This report explores the role of NPRL3 gene variants in FCD1b and their impact on surgical treatment, emphasizing the importance of comprehensive preoperative assessment and individualized therapeutic strategies.

1. Introduction

Focal cortical dysplasia (FCD) is a predominant cause of drug-resistant epilepsy, frequently diagnosed during childhood. FCD manifests as a range of clinical symptoms, including seizures, cognitive impairments, and behavioral issues. Patients exhibit significant variability in their responses to anti-seizure medications, which poses long-term challenges in treatment. Based on pathological characteristics, FCD is categorized into subtypes, with FCD type 1 often exhibiting subtle cortical abnormalities and indistinct boundaries with adjacent normal brain tissue. These characteristics complicate imaging-based diagnoses, frequently leading to misdiagnosis [1]. They also impede accurate surgical planning, increasing the risk of leaving residual lesions or excising excessive normal tissue, thereby heightening the likelihood of seizure recurrence post-surgery.

Recent genetic research has identified several genes, including DEPDC5, NPRL2, NPRL3, TSC1, TSC2, PIK3CA, and AKT3, as crucial regulators of the mTOR signaling pathway [2]. Studies increasingly highlight the role of the GATOR1 complex in negatively regulating the mTORC1 signaling pathway. The overactivation of this pathway contributes to cortical developmental abnormalities and epilepsy [3]. NPRL3, a component of the GATOR1 complex, modulates the mTOR signaling pathway, and its dysregulation has been associated with various types of epilepsy and cortical dysplasias. Research indicates that NPRL3 variants exhibit significant clinical heterogeneity, influencing seizure types, imaging abnormalities, and EEG features. This is particularly evident in familial focal epilepsy, where NPRL3 variants demonstrate notable genetic susceptibility [4].

This case report discusses a 5-year-10-month-old female patient who has experienced sleep-related hypermotor epilepsy since the age of 2. The uniqueness of this case is highlighted by the recurrence of seizures despite treatment with multiple anti-seizure medications, ultimately leading to a diagnosis of FCD1b caused by a variant in the NPRL3 gene. This report provides significant insights for the differential diagnosis of drug-resistant epilepsy cases, emphasizing the necessity of considering underlying genetic factors and their therapeutic implications.

2. Case presentation

The patient is a 5-year-and-10-month-old girl who began experiencing seizures at the age of 2. These seizures were initially characterized by three manifestations: (1) rightward gaze and unresponsiveness, followed by tonic tremors in the right upper limb and both lower limbs, lasting from 10 s to 1 min; (2) a sudden seeking of objects or people for hugging during sleep or upon waking, accompanied by altered consciousness, leading to bilateral upper limb tremors lasting several seconds; and (3) sudden gaze fixation, with or without altered consciousness and limb tremors, occurring multiple times daily (up to 20 episodes).

The initial treatment included levetiracetam, oxcarbazepine, and valproate, which successfully controlled the seizures for one year. However, at 3 years and 5 months of age, symptoms recurred, with seizures occurring during both wakefulness and sleep (1–8 episodes per day, each lasting approximately 5 s). Additional medications, including lamotrigine, perampanel, lacosamide, and clobazam, were subsequently administered but proved ineffective. Currently, seizure episodes primarily involve gaze fixation during sleep and unresponsiveness, occasionally accompanied by manual automatisms (4–5 episodes per day).

The developmental history indicates that the patient exhibited normal growth and development prior to the onset of the disease. However, by age 4, progressive delays in language, cognition, and fine motor skills became evident. Family history revealed a maternal cousin diagnosed with epilepsy. Physical examination showed normal consciousness and responsiveness, with no signs of pigmentary abnormalities or rashes. Systemic and neurological examinations were normal. Video EEG demonstrated interictal discharges, including spikes and sharp-slow waves, originating from the left frontal pole and region. The ictal EEG displayed fast rhythmic discharges in the left frontal and central areas (Fig. 1A). MRI indicated thickening at the base of the left superior frontal sulcus, and PET-CT revealed localized hypometabolism in that area (Fig. 2A). Family-based whole exome sequencing of blood samples identified a maternal splice-site variant c.318 + 1G > T in NPRL3 (Fig. 2B). By the age of 6, the patient continued to experience frequent seizures, and with parental consent, underwent a left frontal lobe epileptogenic focus resection. Pathological findings confirmed the diagnosis of FCD1b (Fig. 2C). Whole exome sequencing of the resected brain tissue identified a splice site variant in NPRL3 (Fig. 2D). Following surgery, the patient remained seizure-free for one year; however, seizures recurred, presenting as sudden gaze fixation accompanied by left manual automatisms during sleep. A review of the electroencephalogram (EEG) revealed multifocal discharges that activated during sleep in the interictal period, particularly in the temporal and central regions. In contrast, the ictal EEG indicated seizure onset originating from the right temporal region (Fig. 1B).

Fig. 1.

EEG of patient with NPRL3 variant.

Fig. 2.

Brain MRI, pathological and genetic results of patient with NPRL3 variant.

(A)(Aa-b) The interictal EEG revealed low-amplitude fast waves in the left frontal area, along with sharp waves and sharp slow waves in the same region. (Ac-e) The ictal EEG displayed low fast waves that evolved in the left frontal region. (B)(Ba) The interictal EEG exhibited slow waves in the right anterior temporal region. (Bb) The interictal EEG showed spike waves in the central region. (Bc-e) The ictal EEG demonstrated evolution in the right temporal region.

(A)(Aa-c) Preoperative epilepsy sequence MRI revealed thickening of the cortex in the left superior frontal sulcus. (d-f) PET-CT scans indicated low metabolic activity in the corresponding regions. (Ag-h) Brain MRI images were obtained following the resection of the left frontal lobe to address epilepsy. (B) The blood sample detected a maternal NPRL3 variant (c.318 + 1G > T), which was validated by Sanger sequencing. (C) A pathological biopsy of the lesion tissue was conducted post-resection of the left frontal lobe. (D)The NPRL3 variant (c.318 + 1G > T) was detected in the brain tissue specimen and validated by Sanger sequencing.

3. Discussion

This case presents a pediatric patient diagnosed with FCD1b associated with a variant in the NPRL3 gene, who exhibits sleep-related hypermotor epilepsy. Following several unsuccessful attempts to manage the condition with anti-seizure medications, the patient underwent resection of a seizure lesion in the left frontal lobe. Unfortunately, after a brief period of seizure freedom, seizures recurred from other regions of the brain. This outcome underscores the complexity and therapeutic challenges associated with this condition.

NPRL3 encodes the nitrogen permease regulator-like protein 3 (NPRL3), which is a crucial component of the GATOR1 complex that negatively regulates the mTORC1 signaling pathway, thereby maintaining cellular growth and metabolic balance [5]. Variants in the NPRL3 gene can lead to dysfunction of the GATOR1 complex, resulting in excessive activation of the mTORC1 pathway. This overactivation can adversely affect neuronal structure, disrupt synaptic communication, and hinder cortical development, ultimately leading to the occurrence of FCD and epilepsy [6]. Reported NPRL3 variants primarily consist of splice site or nonsense variations in exons 4, 6, and 8, which can affect mRNA splicing or protein function, thereby causing dysregulation of the mTOR pathway [7].

Variations in the NPRL3 gene exhibit significant clinical heterogeneity, with members of the same family carrying the same mutation displaying varying degrees of symptom severity [8]. This phenomenon was also observed in the present case. Recent studies have revealed that these phenotypic differences may stem from the “two-hit” pathogenic mechanism involving NPRL3-related FCD and epilepsy: a congenital germline variant serves as the first “hit,” while a subsequent somatic variation in another gene constitutes the second “hit.” The synergistic effects of both lead to the formation of FCD and the onset of epilepsy [9]. Although we performed whole-exome sequencing analysis on peripheral blood and pathological brain tissue specimens from surgical resections of patients, unfortunately, we did not detect any other pathogenic variants. However, due to the limitations of this detection technology, we cannot entirely exclude the possibility of variations in non-coding regions and low-frequency somatic variations associated with the GATOR1 gene complex.

Interestingly, the pathological results of this case show FCD type Ib, rather than the FCD type II pathological type associated with NPRL3 variations reported in most studies. This finding expands our understanding of the relationship between GATOR1 complex genes and the spectrum of cortical dysplasia. Although surgical treatment can significantly improve seizure control, long-term postoperative prognosis remains a unique challenge for carriers of NPRL3 variations. Research by Sahly et al [10] indicates that children with GATOR1 gene-related epilepsy often experience a seizure-free period post-surgery, but this state is typically difficult to maintain. In this study, all four children with NPRL3 variations experienced either recurrence or new-onset electrical seizures, including one patient with FCD type Ia who, despite undergoing left functional hemispherectomy, was found to have electrical seizures originating from the right frontal area upon follow-up EEG. The brief seizure-free period followed by recurrence in this patient is consistent with the typical postoperative characteristics of GATOR1-related epilepsy.There are two possible reasons for its recurrence: first, the unclear boundaries of FCD type Ib lesions leading to incomplete resection; second, the presence of 'silent' developmental malformations that were not detected by preoperative imaging. The latter is particularly likely, as the patient's electroencephalogram during recurrence showed a shift in the seizure origin to the right temporal lobe, with multifocal discharges during the interictal period. Studies indicate that approximately 30–40 % of FCD patients have MRI-negative lesions [1], and these 'silent' lesions may become activated after the initial surgery, resulting in new seizures. This situation is not uncommon in GATOR1-related epilepsy, where multiple epileptic foci may coexist but exhibit activity at different times. This also suggests that when assessing patients with GATOR1-related epilepsy, we should consider employing more sensitive imaging and electrophysiological examination methods to comprehensively evaluate potential epileptic foci. Meanwhile, long-term follow-up should be maintained postoperatively to remain vigilant for the possibility of activation of newly developed lesions.

Furthermore, considering the association between NPRL3 variants and hyperactivation of the mTOR pathway, mTOR inhibitors such as rapamycin may offer targeted therapeutic options for these patients [11]. Recent studies have demonstrated that mTOR inhibitors exhibit promising efficacy in treating mTOR pathway-related somatic overgrowth syndromes [12], potentially providing novel therapeutic strategies for patients with GATOR1-associated epilepsy.

4. Conclusions

This case highlights the crucial role of genetic diagnosis in planning epilepsy surgery. For patients with NPRL3 variants, a careful benefit-risk assessment is essential when determining the surgical approach and the extent of resection. Despite achieving initial seizure control, these patients encounter unique challenges due to the potential reactivation of “silent” lesions. Therefore, systematic postoperative monitoring and long-term follow-up are critical. Integrating genetic information into individualized surgical decision-making ultimately enhances treatment outcomes and improves the quality of life for this distinct patient population.

5. Statement on the use of generative AI and figures, images and artwork

All authors declare that generative AI has not been used to produce any part of this manuscript or figures/images.

Ethical statement

This study was conducted in accordance with the ethical standards of the Ethics Committee of Xi 'an Children's Hospital and with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards. The study protocol was approved by the the Ethics Committee of Xi 'an Children's Hospital (Approval No.20220620-16). Informed consent was obtained from all individual participants included in the study.

CRediT authorship contribution statement

Bei Li: Writing – original draft. Liang Liu: Data curation. Jianyun Su: Methodology, Investigation. Shanshan Jia: Resources, Project administration. Zhijing Wang: Validation, Supervision. Xia Li: Writing – review & editing. Siyu Zhao: Writing – review & editing.

Funding

This work was supported by Shaanxi Province Key Research and Development Program (No. 2023-YBSF-075) and Shaanxi Provincial Natural Science Basic Research Program (No. 2021JM-559).

Declaration of competing interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.