GSE127743
GSE GEOIn vivo CRISPR screening unveils RNA binding protein dependencies for leukemic stem cells and identifies ELAVL1 as a potential therapeutic target [RNA-seq]
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Summary
RNA binding protein (RBP)-directed post-transcriptional control of stem cell fate represents an underexplored mechanism driving hematopoietic stemness and transformation. We show that a unique set of RBPs are specifically enriched in leukemic stem cells (LSCs) of human primary acute myeloid leukemia (AML) but repressed in normal hematopoietic stem cells. Using an in vivo CRISPR-Cas9-mediated screening approach, we identify 33 key RBPs specifically essential for LSC-mediated MLL-AF9/NrasG12D AML. Knock-down/genetic ablation of the hit RBP Elavl1 in genetically distinct leukemias significantly reduced LSC numbers, and hampered leukemic engraftment. In human AML we show impairment of LSC-driven in vivo leukemic reconstitution and selective depletion of AML progenitors upon ELAVL1 targeting, highlighting the potential clinical importance of our findings. Profiling of the leukemic ELAVL1-mRNA interactome revealed hematopoietic differentiation, RNA splicing and mitochondrial metabolism as major pathways impacted by ELAVL1. Altogether, this work demonstrates that Elavl1 and other RBPs are critical regulators of LSC-survival and self-renewal.
Overall Design
2x sgNTC, 2x sgELAVL1; Cells were transduced with lentiviral-packaged sgRNA targeting Elavl1 and, as control, Ano9. 72 hours following transduction live 7AAD- GFP+ cells were isolated.
Analysis (4 steps)
View Data Processing- Raw reads were trimmed using cutadapt (v1.14) using the following parameters: -O 5 --match-read-wildcards --times 2 -e 0.0 --quality-cutoff 6 -m 18 -b TCGTATGCCGTCTTCTGCTTG ATCTCGTATGCCGTCTTCTGCTTG CGACAGGTTCAGAGTTCTACAGTCCGACGATC GATCGGAAGAGCACACGTCTGAACTCCAGTCAC AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
- Trimmed reads were mapped to and filtered of mouse-specific repeat elements (RepBase 18.05) with STAR (2.4.0i) using the following parameters: --alignEndsType EndToEnd --genomeDir repbase --genomeLoad NoSharedMemory --outBAMcompression 10 --outFileNamePrefix condition1 --outFilterMultimapNmax 10 --outFilterMultimapScoreRange 1 --outFilterScoreMin 10 --outFilterType BySJout --outReadsUnmapped Fastx --outSAMattrRGline ID:foo --outSAMattributes All --outSAMmode Full --outSAMtype BAM Unsorted --outSAMunmapped Within --outStd Log --readFilesIn r1.fastq r2.fastq --runMode alignReads --runThreadN 8
- Reads unmapped to repeat elements were mapped to the mouse genome with STAR using the same parameters as the previous step, using an mm9 index in place of the repeat element index
- Subread featureCounts (-a gencode.vM1.annotation.gtf -s 2 -p -o counts.txt RN2c.bam) was used to count features using mouse annotations (Gencode vM1)
GEO Samples (4)
SRA Experiments (4) and Runs (4)
Total: 14062 MBSample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR8656542 | 34265485 | 6921627970 | 3583.32 | SRR8656542, SRR8656542.lite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR8656543 | 36245947 | 7321681294 | 3806.72 | SRR8656543, SRR8656543.lite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR8656544 | 33487256 | 6764425712 | 3490.88 | SRR8656544, SRR8656544.lite | SRA |
Sample attributes
Original files (1)
Runs (1)
| Run | Spots | Bases | Size (MB) | Files | Link |
|---|---|---|---|---|---|
| SRR8656545 | 30209390 | 6102296780 | 3181.5 | SRR8656545, SRR8656545.lite | SRA |