The coding and non-coding transcriptional landscape of subependymal giant cell astrocytomas

Abstract

Tuberous sclerosis complex (TSC) is an autosomal dominantly inherited neurocutaneous disorder caused by inactivating mutations in TSC1 or TSC2, key regulators of the mechanistic target of rapamycin complex 1 (mTORC1) pathway. In the CNS, TSC is characterized by cortical tubers, subependymal nodules and subependymal giant cell astrocytomas (SEGAs). SEGAs may lead to impaired circulation of CSF resulting in hydrocephalus and raised intracranial pressure in patients with TSC. Currently, surgical resection and mTORC1 inhibitors are the recommended treatment options for patients with SEGA. In the present study, high-throughput RNA-sequencing (SEGAs n = 19, periventricular control n = 8) was used in combination with computational approaches to unravel the complexity of SEGA development. We identified 9400 mRNAs and 94 microRNAs differentially expressed in SEGAs compared to control tissue. The SEGA transcriptome profile was enriched for the mitogen-activated protein kinase (MAPK) pathway, a major regulator of cell proliferation and survival. Analysis at the protein level confirmed that extracellular signal-regulated kinase (ERK) is activated in SEGAs. Subsequently, the inhibition of ERK independently of mTORC1 blockade decreased efficiently the proliferation of primary patient-derived SEGA cultures. Furthermore, we found that LAMTOR1, LAMTOR2, LAMTOR3, LAMTOR4 and LAMTOR5 were overexpressed at both gene and protein levels in SEGA compared to control tissue. Taken together LAMTOR1–5 can form a complex, known as the ‘Ragulator’ complex, which is known to activate both mTORC1 and MAPK/ERK pathways. Overall, this study shows that the MAPK/ERK pathway could be used as a target for treatment independent of, or in combination with mTORC1 inhibitors for TSC patients. Moreover, our study provides initial evidence of a possible link between the constitutive activated mTORC1 pathway and a secondary driver pathway of tumour growth.

Tuberous Sclerosis Complex as Disease Model for Investigating mTOR-Related Gliopathy During Epileptogenesis

“…Indeed, human tuber and SEGA tissue also display activation of inflammation in astrocytes, in particular, the toll-like receptor 4 (TLR-4), interleukin 1β (IL-1β), and complement pathways, as well as increased expression of IL-17, intercellular adhesion molecule 1, tumor necrosis factor α (TNF-α), and nuclear factor κB (NF-κB) ( 61 – 63 , 96 – 98 ). In particular, several large-scale RNA-sequencing studies confirmed that neuroinflammation is a hallmark of TSC-associated lesions, and the retrieved data were enriched for both astrocyte and microglial specific genes ( 21 , 63 , 99 , 100 ). Additionally, microRNAs (miRNAs) involved in the regulation of astrocytic inflammatory responses are upregulated in TSC ( 101 ).…”

Distinct DNA Methylation Patterns of Subependymal Giant Cell Astrocytomas in Tuberous Sclerosis Complex

“…The precise role of T-cells in SEGAs is still unknown, it could indicate a more responsive immune response to tumor cells but we also know that, neuroin ammation can increase the expression and activity of MMPs, which are increased in SEGAs and can play a role in tumorgenesis (Bongaarts et al 2020). The MAPK pathway has been shown to be an important pathway for SEGA growth and has been suggested as a novel target for therapy for patients with SEGA (Bongaarts et al 2019, Tyburczy et al 2010, Mi et al 2009). Therefore, the differences in methylation of this pathway between the two groups found in this study is interesting and could potentially re ect how these tumors would respond to MAPK inhibitors.…”

“…Data was processed as previously described (Bongaarts et al 2019). Brie y, sequence reads were trimmed and ltered using FastQC v0.11.5 (Babraham Institute, Babraham, Cambridgeshire, UK) and Trimmomatic v0.36 (Bolger, Lohse, and Usadel 2014).…”

“…Pathogenic loss of function mutations in TSC1 or TSC2 result in constitutive activation of the mTOR pathway and uncontrolled cell cycle progression (Chan et al 2004). Besides the mTOR pathway, the immune system, the Mitogen-activated protein kinase (MAPK) pathway and extracellular matrix (ECM) organization have been suggested to play a role in SEGA development based on gene expression studies (Bongaarts et al 2019, Martin et al 2017, Tyburczy et al 2010. However, the precise mechanisms behind these gene expression changes in SEGA are still largely unknown.…”

Targeting protein kinases for anti-glioma treatment

“…This group includes subependymal giant cell astrocytoma (SEGA), which is a rare, benign childhood neoplasm of grade I histological malignancy according to the WHO classification (WHO GI). SEGA tumours occur in approximately 10-20% of patients with tuberous sclerosis complex (TSC), which is a rare genetic condition [15,82].…”