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| Status |
Public on Sep 28, 2021 |
| Title |
RNA-seq analysis of transcriptomic changes in control (shLuc) and GEM knockdown (shGem) bone marrow LSK cells |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Cancers develop from the accumulation of somatic mutations, yet it remains unclear how oncogenic lesions cooperate to drive cancer progression. Using a mouse model harboring NRasG12D and EZH2 mutations that recapitulates leukemic progression, we employed single-cell RNA sequencing to map cellular composition and gene expression alterations in healthy or diseased bone marrows during leukemogenesis. At cellular level, NRasG12D induces myeloid-biased differentiation and EZH2-deficiency impairs myeloid cell maturation, whereas they cooperate to promote myeloid expansion with dysregulated transcriptional programs. At gene level, NRasG12D and EZH2-deficiency independently and synergistically control gene expression in single cells. We integrated results from histopathology, leukemia repopulation, and leukemia-initiating cell assays to validate transcriptome-based cellular profiles. We used this resource to relate developmental hierarchies to leukemia phenotypes, evaluated oncogenic cooperation at single-cell and single-gene levels, and identified GEM as a new regulator of leukemia-initiating cells. Our studies establish an integrative approach to deconvolute cancer evolution in vivo.
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| Overall design |
Lineage negative cells were transduced with shRNA virus against luciferase (shLuc) or GEM (shGem). Positively transduced cells (GFP+) were sorted by FACS 72 hours post-transduction and subjected to RNA-seq library preparation. RNA-seq library was prepared using the SMARTer stranded pico input total RNA-seq kit (Takara)
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| Contributor(s) |
Liu Y, Gu Z, Xu J |
| Citation(s) |
34732703 |
| |
| Submission date |
Jun 28, 2021 |
| Last update date |
Nov 30, 2021 |
| Contact name |
Jian Xu |
| E-mail(s) |
Jian.Xu@stjude.org
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| Phone |
9015955208
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| Organization name |
St. Jude Children's Research Hospital
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| Department |
Pathology
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| Street address |
262 Danny Thomas Place, MS 345
|
| City |
Memphis |
| State/province |
Tennessee |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (8)
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| This SubSeries is part of SuperSeries: |
| GSE179084 |
Analysis of Oncogenic Cooperation during Leukemia Progression by Single Cell RNA-seq |
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| Relations |
| BioProject |
PRJNA742109 |
| SRA |
SRP325918 |
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