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Subependymal giant cell astrocytomas are characterized by mTORC1 hyperactivation, a very low somatic mutation rate, and a unique gene expression profile


Subependymal giant-cell astrocytomas (SEGAs) are slow-growing brain tumors that are a hallmark feature seen in 5–10% of patients with Tuberous Sclerosis Complex (TSC). Though histologically benign, they can cause serious neurologic symptoms, leading to death if untreated. SEGAs consistently show biallelic loss of TSC1 or TSC2. Herein, we aimed to define other somatic events beyond TSC1/TSC2 loss and identify potential transcriptional drivers that contribute to SEGA formation. Paired tumor-normal whole-exome sequencing was performed on 21 resected SEGAs from 20 TSC patients. Pathogenic variants in TSC1/TSC2 were identified in 19/21 (90%) SEGAs. Copy neutral loss of heterozygosity (size range: 2.2–46 Mb) was seen in 76% (16/21) of SEGAs (44% chr9q and 56% chr16p). An average of 1.4 other somatic variants (range 0–7) per tumor were identified, unlikely of pathogenic significance. Whole transcriptome RNA-sequencing analyses revealed 190 common differentially expressed genes in SEGA (n = 16, 13 from a prior study) in pairwise comparison to each of: low grade diffuse gliomas (n = 530) and glioblastoma (n = 171) from The Cancer Genome Atlas (TCGA) consortium, ganglioglioma (n = 10), TSC cortical tubers (n = 15), and multiple normal tissues. Among these, homeobox transcription factors (TFs) HMX3, HMX2, VAX1, SIX3; and TFs IRF6 and EOMES were all expressed >12-fold higher in SEGAs (FDR/q-value < 0.05). Immunohistochemistry supported the specificity of IRF6, VAX1, SIX3 for SEGAs in comparison to other tumor entities and normal brain. We conclude that SEGAs have an extremely low somatic mutation rate, suggesting that TSC1/TSC2 loss is sufficient to drive tumor growth. The unique and highly expressed SEGA-specific TFs likely reflect the neuroepithelial cell of origin, and may also contribute to the transcriptional and epigenetic state that enables SEGA growth following two-hit loss of TSC1 or TSC2 and mTORC1 activation.

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Fig. 1: MRI images and histologic features of SEGAs.
Fig. 2: Germline and somatic alterations in SEGAs.
Fig. 3: Comparison of RNA-Seq expression of SEGAs to other brain tumors and cortical tubers.
Fig. 4: Box plots for the top six DE (upregulated) TFs in SEGA compared to TCGA tumors (2463 tumors of 27 different histologic types), gangliogliomas and cortical tubers.
Fig. 5: Box plots for the top six DE (upregulated) TFs in SEGA compared to GTEx human normal tissues (~8500 samples from 30 normal tissue types, v6p release).
Fig. 6: Representative images of IRF6 immunohistochemistry.
Fig. 7: Representative images of SIX3 immunohistochemistry.
Fig. 8: Representative images of VAX1 immunohistochemistry.

Data availability

Access to data which are not available within the article and Supplementary material, can be provided by the authors upon request (direct contact to KG or DJK).


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The authors thank all subjects who participated in this study; the clinicians who referred and evaluated the patients and the neurosurgeons who performed the surgical resections; as well as Karthik V. Karnik and Edward R. Kwiatkowski for their work on customized code for MPS analysis, as well as Yana Stackpole for assistance with Qlucore analysis; Stichting Kinderen Kankervrij; Stichting AMC Foundation; Stichting TSC Fonds (EA, AB).


This work was supported by the Engles Family Fund for Research in TSC and LAM.

Author information




KG: conceptualized the study, performed experiments, analyzed and interpreted high throughput data, wrote and submitted the paper for publication. ZZ, JK, KDW, MET, DM, JSP, ZH, LT, HL, GG, and MSL: executed experiments or/and performed high throughput analyses: AB, WP, BG, MN, MM, and EA: contributed material; SA: selected a subset of the pediatric cases, evaluated their histology, and provided biospecimens. KK, SJ, MR, EAT, MM, HL, OD, KLL, DWE, MS, and EA: evaluated the patients/biospecimens or/and provided clinical data. DMM: provided biospecimens, performed pathology analysis of the tumors and contributed to experimental design; DJK: conceptualized and supervised the study, reviewed and interpreted data and contribute to paper preparation. All authors read and commented on the paper.

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Correspondence to Krinio Giannikou or David J. Kwiatkowski.

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Giannikou, K., Zhu, Z., Kim, J. et al. Subependymal giant cell astrocytomas are characterized by mTORC1 hyperactivation, a very low somatic mutation rate, and a unique gene expression profile. Mod Pathol 34, 264–279 (2021).

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