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GSE134597

GSE GEO
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Musashi1 is a master regulator of aberrant translation in Group 3 medulloblastoma

Organism: Homo sapiens
Platform: GPL20301
Samples: 8
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Jul 21 2019
Last Updated: Jan 03 2023
Status: Public on Jul 19 2022
Contact: En-Ching,,Luo (UCSD)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA555800 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP215807

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
Processing steps for GSE134597
  1. 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).
  2. Reads did not map to repetitive elements were then mapped to the human genome (hg19).
  3. Using GENCODE (v19) gene annotations and featureCounts (v.1.5.0) to create read count matrices.
  4. The transcript RPKMs of input and polysome fractions were calculated from the read count matrices.

Supplementary Files (1)

GSE134597_msi_polysome_RPKM.csv.gz Download
GEO Samples (8)

Dataset Citations (1)

Characterization of an RNA binding protein interactome reveals a context-specific post-transcriptional landscape of MYC-amplified medulloblastoma.
PMID 36473869 · 2022 · Nature communications
Michelle M Kameda-Smith, Helen Zhu, En-Ching Luo, Yujin Suk, Agata Xella, Brian Yee, Chirayu Chokshi, Sansi Xing, Frederick Tan, Raymond G Fox, Ashley A Adile, David Bakhshinyan, Kevin Brown, William D Gwynne, Minomi Subapanditha, Petar Miletic, Daniel Picard, Ian Burns, Jason Moffat, Kamil Paruch, Adam Fleming, Kristin Hope, John P Provias, Marc Remke, Yu Lu, Tannishtha Reya, Chitra Venugopal, Jüri Reimand, Robert J Wechsler-Reya, Gene W Yeo, Sheila K Singh

SRA Experiments (8) and Runs (8)

Total: 6305 MB
SRX6480058 SRP215807 RNA-Seq SINGLE
GSM3957959: MB002_GFP_2; Homo sapiens; RNA-Seq
Sample: SRS5130164
BioProject: PRJNA555800
BioSample: SAMN12330740
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: patient-derived medulloblastoma cell
pdx line: MB002
shRNA: GFP
rna fraction: Total
Original files (1)
patient-derived medulloblastoma cell
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
SRX6480059 SRP215807 RNA-Seq SINGLE
GSM3957960: MB002_GFP_2_poly; Homo sapiens; RNA-Seq
Sample: SRS5130165
BioProject: PRJNA555800
BioSample: SAMN12330739
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: patient-derived medulloblastoma cell
pdx line: MB002
shRNA: GFP
rna fraction: Polysome
Original files (1)
patient-derived medulloblastoma cell
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
SRX6480060 SRP215807 RNA-Seq SINGLE
GSM3957961: MB002_GFP_3; Homo sapiens; RNA-Seq
Sample: SRS5130166
BioProject: PRJNA555800
BioSample: SAMN12330738
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: patient-derived medulloblastoma cell
pdx line: MB002
shRNA: GFP
rna fraction: Total
Original files (1)
patient-derived medulloblastoma cell
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
SRX6480061 SRP215807 RNA-Seq SINGLE
GSM3957962: MB002_GFP_3_poly; Homo sapiens; RNA-Seq
Sample: SRS5130167
BioProject: PRJNA555800
BioSample: SAMN12330737
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: patient-derived medulloblastoma cell
pdx line: MB002
shRNA: GFP
rna fraction: Polysome
Original files (1)
patient-derived medulloblastoma cell
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
SRX6480062 SRP215807 RNA-Seq SINGLE
GSM3957963: MB002_shMSI_2; Homo sapiens; RNA-Seq
Sample: SRS5130168
BioProject: PRJNA555800
BioSample: SAMN12330736
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: patient-derived medulloblastoma cell
pdx line: MB002
shRNA: shMSI
rna fraction: Total
Original files (1)
patient-derived medulloblastoma cell
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
SRX6480063 SRP215807 RNA-Seq SINGLE
GSM3957964: MB002_shMSI_2_poly; Homo sapiens; RNA-Seq
Sample: SRS5130169
BioProject: PRJNA555800
BioSample: SAMN12330735
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: patient-derived medulloblastoma cell
pdx line: MB002
shRNA: shMSI
rna fraction: Polysome
Original files (1)
patient-derived medulloblastoma cell
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
SRX6480064 SRP215807 RNA-Seq SINGLE
GSM3957965: MB002_shMSI_3; Homo sapiens; RNA-Seq
Sample: SRS5130170
BioProject: PRJNA555800
BioSample: SAMN12330734
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: patient-derived medulloblastoma cell
pdx line: MB002
shRNA: shMSI
rna fraction: Total
Original files (1)
patient-derived medulloblastoma cell
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
SRX6480065 SRP215807 RNA-Seq SINGLE
GSM3957966: MB002_shMSI_3_poly; Homo sapiens; RNA-Seq
Sample: SRS5130171
BioProject: PRJNA555800
BioSample: SAMN12330733
Platform: ILLUMINA
Instrument: Illumina HiSeq 4000
Organism: Homo sapiens
Sample attributes
source_name: patient-derived medulloblastoma cell
pdx line: MB002
shRNA: shMSI
rna fraction: Polysome
Original files (1)
patient-derived medulloblastoma cell
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