GSE134597
GSE GEOMusashi1 is a master regulator of aberrant translation in Group 3 medulloblastoma
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Summary
Pediatric medulloblastoma (MB) is the most common solid malignant brain neoplasm, with group 3 (G3) MB representing the most aggressive subgroup associated with a poor prognosis and a remarkable ability to resist upfront multimodal therapy. Despite a low mutational burden of disease and MYC amplification identified as a independent factor associated with poor survivorship, efforts to target the MYC has met with limited therapeutic success. Consequently alternative mediators associated with the aggressive phenotype of G3 MB continues as a common goal within the MB community. Here we show how the neural stem cell determinant Musashi 1 (MSI1) is a central and vital moderator of G3 MB in both a MYC amplified mouse model of G3 MB and patient derived xenografts (PDX). Specifically, we modified the MYC amplified and p53 mutated (MP) mouse model of G3 MB to generate Msi1 conditional knockout mice (Msi1flox/flox), which led to the observation that MSI1 is required for tumor initiation of MP tumors. To identify the translational potential of these findings, we employed shRNA against Msi1 in multiple PDX lines, observing a striking deficit in multiple key stem cell features including self-renewal, proliferation, and failure to progress through the cell cycle. Notably, Msi1 inhibition resulted in a failure of tumor initiation, translating to a significantly prolonged survival, reaffirming the essential role for MSI1 in G3 MB. To determine how MSI1 symphonizes the anarchic post-transcriptional landscape of G3MB, we differentially analyzed the MSI1 binding sites in normal neural stem cells and G3 MB and subsequently compared the MSI1-binding transcriptome, and proteome following Msi1 inhibition. Comparative analysis suggested an integral role for post-transcriptional regulators, such as MSI1 and its binding prey mRNA, as a therapeutic target. Here we propose the neural RNA binding protein MSI1, as a master regulator, hijacked from its normal neural developmental function, orchestrating the aberrant translational landscape of G3 MB.
Overall Design
shRNA against Msi1 in a patient-derived xenograft line.
Analysis (4 steps)
View Data Processing- RNA-sequencing reads were trimmed using cutadapt (v1.4.0) of adaptor sequences, and mapped to repetitive elements (RepBase v18.04) using the STAR (v2.4.0i).
- Reads did not map to repetitive elements were then mapped to the human genome (hg19).
- Using GENCODE (v19) gene annotations and featureCounts (v.1.5.0) to create read count matrices.
- The transcript RPKMs of input and polysome fractions were calculated from the read count matrices.
Supplementary Files (1)
GEO Samples (8)
Dataset Citations (1)
SRA Experiments (8) and Runs (8)
Total: 6305 MBSample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR9722509 | 27049883 | 2028741225 | 765.25 | GFP2_S26_L003_R1_001.fastq.gz, SRR9722509, SRR9722509.lite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR9722510 | 31217595 | 2341319625 | 888.88 | GFP2_poly_S32_L003_R1_001.fastq.gz, SRR9722510, SRR9722510.lite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR9722511 | 25201040 | 1890078000 | 717.25 | GFP3_S27_L003_R1_001.fastq.gz, SRR9722511, SRR9722511.lite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR9722512 | 25505134 | 1912885050 | 724.42 | GFP3_poly_S33_L003_R1_001.fastq.gz, SRR9722512, SRR9722512.lite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR9722513 | 27607231 | 2070542325 | 778.76 | MSI2_S29_L003_R1_001.fastq.gz, SRR9722513, SRR9722513.lite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR9722514 | 26897586 | 2017318950 | 778.82 | MSI2_poly_S35_L003_R1_001.fastq.gz, SRR9722514, SRR9722514.lite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR9722515 | 30718119 | 2303858925 | 868.16 | MSI3_S30_L003_R1_001.fastq.gz, SRR9722515, SRR9722515.lite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR9722516 | 27826166 | 2086962450 | 783.29 | MSI3_poly_S36_L003_R1_001.fastq.gz, SRR9722516, SRR9722516.lite | SRA |
Linked Publications (2)
Data Files (8)
| Accession | File Name | Stored Type | Output Type | Mapping Assembly | Size | Download | |
|---|---|---|---|---|---|---|---|
| — | GFP2_poly_S32_L003_R1_001.fastq.gz | RNA-Seq | 888.9 MB | link | |||
| — | GFP2_S26_L003_R1_001.fastq.gz | RNA-Seq | 765.2 MB | link | |||
| — | GFP3_poly_S33_L003_R1_001.fastq.gz | RNA-Seq | 724.4 MB | link | |||
| — | GFP3_S27_L003_R1_001.fastq.gz | RNA-Seq | 717.2 MB | link | |||
| — | MSI2_poly_S35_L003_R1_001.fastq.gz | RNA-Seq | 778.8 MB | link | |||
| — | MSI2_S29_L003_R1_001.fastq.gz | RNA-Seq | 778.8 MB | link | |||
| — | MSI3_poly_S36_L003_R1_001.fastq.gz | RNA-Seq | 783.3 MB | link | |||
| — | MSI3_S30_L003_R1_001.fastq.gz | RNA-Seq | 868.2 MB | link |