Dataset Information

Human Pilocytic Astrocytoma Single Cell RNA Sequencing

ABSTRACT:

Pilocytic astrocytoma (PA), the most common childhood brain tumor, is a low-grade glioma with a single driver BRAF rearrangement. Here, we perform scRNAseq in six PAs using methods that enabled detection of the rearrangement. When compared to higher-grade gliomas, a strikingly higher proportion of the PA cancer cells exhibit a differentiated, astrocyte-like phenotype. A smaller proportion of cells exhibit a progenitor-like phenotype with evidence of proliferation. These express a mitogen-activated protein kinase (MAPK) program that was absent from higher-grade gliomas. Immune cells, especially microglia, comprise 40% of all cells in the PAs and account for differences in bulk expression profiles between tumor locations and subtypes. These data indicate that MAPK signaling is restricted to relatively undifferentiated cancer cells in PA, with implications for investigational therapies directed at this pathway.

Note that 931 out of 1234 samples in the Sequence Read Archive (SRA) passed QC and have transcript count data available from the Broad Institute Single Cell Portal. The transcript count data can be found at https://singlecell.broadinstitute.org/single_cell/study/SCP271/pilocytic-astrocytoma-single-cell-rna-seq#study-download

PROVIDER: phs001854 | dbGaP |

REPOSITORIES: dbGaP

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			Action	DRS
	GapExchange_phs001854.v1.p1.xml	Xml
	dbGaPEx2.1.5.xsd	Other
	Study_Report.phs001854.BRAF_PilocyticAstrocytomas.v1.p1.MULTI.pdf	Pdf
	manifest_phs001854.BRAF_PilocyticAstrocytomas.v1.p1.c1.DS-NDR-MDS.pdf	Pdf
	datadict_v2.xsl	Other

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Project description:Purpose: Gene expression analyses comparing tumors of different behaviors have been used for the identification of genes that have a role in the growth and maintenance of tumors, with the aim of both understanding the molecular basis of tumorigenesis and identifying novel potential therapeutic targets. We have here used this approach to identify the underlying gene expression differences between highly invasive glioblastoma multiforme and typically benign pilocytic astrocytomas. Experimental Design: We performed cDNA microarray analyses comparing astrocytomas of polar grade: grade I, pilocytic astrocytoma (PA), the non-invasive and most frequent pediatric tumor, with grade IV, the highly infiltrative glioblastoma multiforme (GBM) Results: Despite the significant clinical and pathological differences between the two tumor types, only 63 genes were found to exhibit two-fold or greater over-expression in GBM as compared with PA. A functional classification of the GBM over-expressed genes indicated that more than 50% are related to the regulation of the cell cycle and mitosis. Microarray data was validated by RQ-PCR testing six over-expressed genes in GBM related to PA: MELK, AUKB, ASPM, PRC1, IL13RA2 and KIAA0101. The differential expression was confirmed for all six genes, showing at least a 5 fold increase in the average expression levels in GBM compared to PA. Of the over expressed genes, that which exhibited the most statistically significant difference is Maternal Embryonic Leucine zipper Kinase (MELK). We undertook a more detailed investigation of the expression of this serine/threonine kinase gene in astrocytomas in the light of its role in the regulation of multipotent neural progenitor proliferation and previous suggestions that this may be a oncogenic target of general importance. In an examination of more than 100 tumors of the central nervous system we found progressively higher expression of MELK in GBM with astrocytoma grade and a noteworthy uniformity of high level expression in GBM. This latter feature probably explains the lack of observed association of MELK expression with survival of GBM patients. Over-expression at a similar level to GBM was also observed in medulloblastoma. We found neither gene methylation nor amplification to be a factor in MELK expression but were able to demonstrate that MELK knockdown in malignant astrocytoma cell lines caused a reduction in proliferation and anchorage-independent growth in in vitro assays. Conclusions: Our results indicate that GBM and PA differ by the expression of surprisingly few genes. Among them, MELK may play a key role in differentiating these two tumor types and represent an important therapeutic target for the management of the most frequent brain tumors in adult and children. Keywords: Comparizon of CNS tumors of different grades.

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Human Pilocytic Astrocytoma Single Cell RNA Sequencing

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