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

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 central nervous system TSC is characterized by cortical tubers, subependymal nodules and subependymal giant cell astrocytomas (SEGAs). SEGAs may lead to the impaired circulation of cerebrospinal fluid 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. Here, we performed RNA-Seq and small RNA-Seq on SEGAs (n=19) and periventricular controls (n=8) to gain a better understanding of the underlying molecular basis of SEGAs, so that novel treatment targets could be identified.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

1 Dataset 3 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001005932	This data set contains small RNA-sequencing and RNA-sequencing data from subependymal giant cell astrocytomas (SEGA) resected from tuberous sclerosis complex patients. Small RNA-sequencing and RNA-sequencing were performed on the same set of SEGAs (n=19) and periventricular controls (n=8). For full details on library preparation and patients please refer to the paper "The coding and non-coding transcriptional landscape of subependymal giant cell astrocytomas." (PMID: 31834371 DOI: 10.1093/brain/awz370).	Illumina HiSeq 2500	27

Publications	Citations
The coding and non-coding transcriptional landscape of subependymal giant cell astrocytomas. Bongaarts A, van Scheppingen J, Korotkov A, Mijnsbergen C, Anink JJ, Jansen FE, Spliet WGM, den Dunnen WFA, Gruber VE, Scholl T, Samueli S, Hainfellner JA, Feucht M, Kotulska K, Jozwiak S, Grajkowska W, Buccoliero AM, Caporalini C, Giordano F, Genitori L, Coras R, Blümcke I, Krsek P, Zamecnik J, Meijer L, Scicluna BP, Schouten-van Meeteren AYN, Mühlebner A, Mills JD, Aronica E. Brain 143: 2020 131-149	22
Dysregulation of the MMP/TIMP Proteolytic System in Subependymal Giant Cell Astrocytomas in Patients With Tuberous Sclerosis Complex: Modulation of MMP by MicroRNA-320d In Vitro. Bongaarts A, de Jong JM, Broekaart DWM, van Scheppingen J, Anink JJ, Mijnsbergen C, Jansen FE, Spliet WGM, den Dunnen WFA, Gruber VE, Scholl T, Hainfellner JA, Feucht M, Borkowska J, Kotulska K, Jozwiak S, Grajkowska W, Buccoliero AM, Caporalini C, Giordano F, Genitori L, Scicluna BP, Schouten-van Meeteren AYN, van Vliet EA, Mühlebner A, Mills JD, Aronica E. J Neuropathol Exp Neurol 79: 2020 777-790	9
MAPK inhibitor sensitivity scores predict sensitivity driven by the immune infiltration in pediatric low-grade gliomas. Sigaud R, Albert TK, Hess C, Hielscher T, Winkler N, Kocher D, Walter C, Münter D, Selt F, Usta D, Ecker J, Brentrup A, Hasselblatt M, Thomas C, Varghese J, Capper D, Thomale UW, Hernáiz Driever P, Simon M, Horn S, Herz NA, Koch A, Sahm F, Hamelmann S, Faria-Andrade A, Jabado N, Schuhmann MU, Schouten-van Meeteren AYN, Hoving E, Brummer T, van Tilburg CM, Pfister SM, Witt O, Jones DTW, Kerl K, Milde T. Nat Commun 14: 2023 4533	10