|
| Status |
Public on Jul 10, 2017 |
| Title |
PHF6 regulates B-cell identity in acute lymphoblastic leukemia [RNA-Seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Inactivating mutations in the zinc finger gene PHF6 are seen in approximately 40% of adult T-cell acute lymphoblastic leukemias (T-ALLs) and 3% of adult acute myeloid leukemias (AMLs). The absence of PHF6 mutations in B-cell lineage malignancies has led to the hypothesis that PHF6 may act as a lineage-specific tumor suppressor gene. Here, we demonstrate that PHF6 plays a critical role in regulating B-cell identity in the context of B-cell precursor acute lymphoblastic leukemia (preB-ALL). Transplantation of Phf6 knockout preB-ALL cells (hereafter referred to as Phf6KO cells) into immunocompetent syngeneic recipients resulted in the development of a fully penetrant lymphoma-like disease. Strikingly, the resulting lymphomas showed robust up-regulation of the canonical T-cell marker CD4, suggesting that Phf6KO cells adopt a T-cell program in the context of leukemogenesis. RNA sequencing analysis revealed numerous differentially expressed (DE) genes in Phf6WT and Phf6KO cells, including a significant down-regulation of genes and gene sets involved in pathways important for B-cell development. Chromatin immunoprecipitation followed by high-throughput sequencing analysis revealed that PHF6 co-localizes with H3K27ac signals close to the transcription start sites (TSSs) and enhancer regions of a significant proportion of DE genes. Notably, regions flanking the TSS of DE genes showed significant enrichment for binding sites of several well-described master regulators of B-cell development, including PU.1, EGR-1, EBF-1, NF-kB, TCF3 and TCF12. We found that PHF6 and TCF12 physically interact in preB-ALL cells, suggesting that these factors act synergistically in the establishment and maintenance of B-cell identity. In addition, we found that a human PHF6 mutant T-ALL cell line has an incompletely rearranged IGH locus, strongly suggesting that T-ALL can have a B-cell origin. These findings reveal an essential role for PHF6 in the establishment and maintenance of B-cell identity in preB-ALL by directly activating genes that are crucial for B-cell lineage commitment and maintenance. Collectively, these results indicate that loss of function of PHF6 in preB-ALL leads to an unstable cellular state in which cells acquire alternate developmental programs (such as the T-lineage program) to survive, potentially explaining the apparent absence of PHF6 mutations in human B cell-lineage malignancies.
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| |
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| Overall design |
Gene expression profiles by RNA-Seq of 3 Phf6 wild-type preB-ALL cells, 3 shPhf6 preB-ALL cells, 6 Phf6 knockout (2 different sgRNAs) preB-ALL cells
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| Contributor(s) |
Soto-Feliciano YM, Hemann MT |
| Citation(s) |
28607179 |
| |
| Submission date |
Feb 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Michael Hemann |
| E-mail(s) |
hemann@mit.edu
|
| Phone |
6173240199
|
| Organization name |
Massachusetts Institute of Technology
|
| Department |
Koch Institute
|
| Lab |
Hemann Lab
|
| Street address |
500 Main St, Building 76 Room 301
|
| City |
Cambridge |
| State/province |
Massachusetts |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL13112 |
Illumina HiSeq 2000 (Mus musculus) |
|
| Samples (12)
|
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| This SubSeries is part of SuperSeries: |
| GSE77457 |
PHF6 regulates B-cell identity in acute lymphoblastic leukemia |
|
| Relations |
| BioProject |
PRJNA310412 |
| SRA |
SRP069174 |
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