 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 19, 2024 |
| Title |
The SAGA complex maintains the oncogenic gene expression program in MYCN-amplified neuroblastoma [ChIP-Seq] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
|
| Summary |
Pediatric cancers are frequently driven by fusion or amplification events that result in aberrant transcription factor activity. As transcription factors themselves remain challenging to target, an emerging therapeutic approach for these cancers is to target epigenetic complexes that help maintain oncogenic transcriptional programs. It is therefore critical to identify the complete set of epigenetic modulators maintaining the oncogenic epigenetic landscape of pediatric cancers. Here, we used functional genomic screens to identify epigenetic complexes critical for viability in cell line models of MYCN-amplified neuroblastoma, a disease of dysregulated development driven by an aberrant oncogenic transcriptional program. We identified multiple genes within the transcriptional coactivator Spt-Ada-Gcn5-acetyltransferase (SAGA) complex as selective dependencies in MYCN-amplified neuroblastoma. Integrating ChIP-seq, ATAC-seq, and RNA-seq with targeted protein-degradation and gene editing tools, we characterized the DNA recruitment sites of the SAGA complex in neuroblastoma, and the consequences of SAGA complex lysine acetyltransferase (KAT) activity loss on histone acetylation and gene expression. We demonstrate that loss of SAGA KAT activity suppresses MYC and MYCN gene expression programs and impairs cell cycle progression. Further, we showed that the SAGA complex is pharmacologically targetable with a KAT2A/KAT2B proteolysis targeting chimera molecule that demonstrated significant activity in vitro and in vivo. Our findings expand our understanding of the histone modifying complexes that maintain the oncogenic transcriptional state in this disease and suggest therapeutic potential for inhibitors of SAGA KAT activity in MYCN-amplified neuroblastoma.
|
| |
|
| Overall design |
Investigate alterations in TADA2B binding after TADA2B loss (degradation dTAG v1 TADA2B vs. DMSO at 6 hours) in KELLY, NGP and NB1 neuroblastoma cells, one replicate per condition. Investigate alterations in MYCN, H3K27ac and H3K9ac binding after TADA2B loss (degradation dTAG v1 TADA2B vs. DMSO at 6 hours) in KELLY neuroblastoma cells, one replicate per condition. Investigate alterations in MYCN, H3K27ac and H3K9ac binding after KAT2A/KAT2B targeting (PROTAC GSK-699-1 vs. DMSO at 6 hours) in KELLY neuroblastoma cells, two replicates per condition.
|
| |
|
| Contributor(s) |
Stegmaier K, Alexe G |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Aug 24, 2022 |
| Last update date |
Apr 19, 2024 |
| Contact name |
Gabriela Alexe |
| E-mail(s) |
galexe@broadinstitute.org
|
| Organization name |
Broad Institute
|
| Department |
Computational Biology and Bioinformatics
|
| Street address |
415 Main St.
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (35)
|
| GSM6506050 |
KELLY-TADA2Bdeg cells, DMSO, HA antibody, 6 hours |
| GSM6506051 |
KELLY-TADA2Bdeg cells, DMSO, Input, 6 hours |
| GSM6506052 |
KELLY-TADA2Bdeg cells, dTAGv1, HA antibody, 6 hours |
| GSM6506053 |
KELLY-TADA2Bdeg cells, dTAGv1, Input, 6 hours |
| GSM6506054 |
NB1-TADA2Bdeg cells, DMSO, HA antibody, 6 hours |
| GSM6506055 |
NB1-TADA2Bdeg cells, DMSO, Input, 6 hours |
| GSM6506056 |
NB1-TADA2Bdeg cells, dTAGv1, HA antibody, 6 hours |
| GSM6506057 |
NB1-TADA2Bdeg cells, dTAGv1, Input, 6 hours |
| GSM6506058 |
NGP-TADA2Bdeg cells, DMSO, HA antibody, 6 hours |
| GSM6506059 |
NGP-TADA2Bdeg cells, DMSO, Input, 6 hours |
| GSM6506060 |
NGP-TADA2Bdeg cells, dTAGv1, HA antibody, 6 hours |
| GSM6506061 |
NGP-TADA2Bdeg cells, dTAGv1, Input, 6 hours |
| GSM6506062 |
KELLY cells, DMSO, H3K9ac antibody, 6 hours |
| GSM6506063 |
KELLY cells, dTAGv1 TADA2B, H3K9ac antibody, 6 hours |
| GSM6506066 |
KELLY cells, DMSO, H3K27ac antibody, 6 hours |
| GSM6506067 |
KELLY cells, dTAGv1 TADA2B, H3K27ac antibody, 6 hours |
| GSM6506070 |
KELLY cells, DMSO, MYCN antibody, 6 hours |
| GSM6506071 |
KELLY cells, dTAGv1 TADA2B, MYCN antibody, 6 hours |
| GSM6506074 |
KELLY cells, DMSO, Input, 6 hours |
| GSM6506075 |
KELLY cells, dTAGv1 TADA2B, Input, 6 hours |
| GSM7871847 |
PROTAC experiment, KELLY cells, DMSO, H3K27ac antibody, 6 hours, replicate 1 |
| GSM7871848 |
PROTAC experiment, KELLY cells, DMSO, H3K27ac antibody, 6 hours, replicate 2 |
| GSM7871849 |
PROTAC experiment, KELLY cells, DMSO, H3K9ac antibody, 6 hours, replicate 1 |
| GSM7871850 |
PROTAC experiment, KELLY cells, DMSO, H3K9ac antibody, 6 hours, replicate 2 |
| GSM7871851 |
PROTAC experiment, KELLY cells, DMSO, Input, 6 hours, replicate 1 |
| GSM7871852 |
PROTAC experiment, KELLY cells, DMSO, Input, 6 hours, replicate 2 |
| GSM7871853 |
PROTAC experiment, KELLY cells, DMSO, MYCN antibody, 6 hours, replicate 1 |
| GSM7871854 |
PROTAC experiment, KELLY cells, GSK6991, H3K27ac antibody, 6 hours, replicate 1 |
| GSM7871855 |
PROTAC experiment, KELLY cells, GSK6991, H3K27ac antibody, 6 hours, replicate 2 |
| GSM7871856 |
PROTAC experiment, KELLY cells, GSK6991, H3K9ac antibody, 6 hours, replicate 1 |
| GSM7871857 |
PROTAC experiment, KELLY cells, GSK6991, H3K9ac antibody, 6 hours, replicate 2 |
| GSM7871858 |
PROTAC experiment, KELLY cells, GSK6991, Input, 6 hours, replicate 1 |
| GSM7871859 |
PROTAC experiment, KELLY cells, GSK6991, Input, 6 hours, replicate 2 |
| GSM7871860 |
PROTAC experiment, KELLY cells, GSK6991, MYCN antibody, 6 hours, replicate 1 |
| GSM7871861 |
PROTAC experiment, KELLY cells, GSK6991, MYCN antibody, 6 hours, replicate 2 |
|
| This SubSeries is part of SuperSeries: |
| GSE211355 |
The SAGA complex maintains the oncogenic gene expression program in MYCN-amplified neuroblastoma |
|
| Relations |
| BioProject |
PRJNA873048 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE211953_ChIPSeq_KELLY_DMSO.H3K27ac_06h.bw |
289.9 Mb |
(ftp)(http) |
BW |
| GSE211953_ChIPSeq_KELLY_DMSO.H3K9ac_06h.bw |
121.5 Mb |
(ftp)(http) |
BW |
| GSE211953_ChIPSeq_KELLY_DMSO.Input.TADA2B_06h.bw |
266.4 Mb |
(ftp)(http) |
BW |
| GSE211953_ChIPSeq_KELLY_DMSO.Input_06h.bw |
381.7 Mb |
(ftp)(http) |
BW |
| GSE211953_ChIPSeq_KELLY_DMSO.MYCN_06h.bw |
312.1 Mb |
(ftp)(http) |
BW |
| GSE211953_ChIPSeq_KELLY_DMSO.TADA2B_06h.bw |
146.5 Mb |
(ftp)(http) |
BW |
| GSE211953_ChIPSeq_KELLY_dTAGv1.H3K27ac_06h.bw |
328.0 Mb |
(ftp)(http) |
BW |
| GSE211953_ChIPSeq_KELLY_dTAGv1.H3K9ac_06h.bw |
142.7 Mb |
(ftp)(http) |
BW |
| GSE211953_ChIPSeq_KELLY_dTAGv1.Input.TADA2B_06h.bw |
321.0 Mb |
(ftp)(http) |
BW |
| GSE211953_ChIPSeq_KELLY_dTAGv1.Input_06h.bw |
310.1 Mb |
(ftp)(http) |
BW |
| GSE211953_ChIPSeq_KELLY_dTAGv1.MYCN_06h.bw |
340.5 Mb |
(ftp)(http) |
BW |
| GSE211953_ChIPSeq_KELLY_dTAGv1.TADA2B_06h.bw |
103.8 Mb |
(ftp)(http) |
BW |
| GSE211953_ChIPSeq_NB1_DMSO.Input_06h.bw |
455.5 Mb |
(ftp)(http) |
BW |
| GSE211953_ChIPSeq_NB1_DMSO.TADA2B_06h.bw |
285.6 Mb |
(ftp)(http) |
BW |
| GSE211953_ChIPSeq_NB1_dTAGv1.Input_06h.bw |
438.9 Mb |
(ftp)(http) |
BW |
| GSE211953_ChIPSeq_NB1_dTAGv1.TADA2B_06h.bw |
305.9 Mb |
(ftp)(http) |
BW |
| GSE211953_ChIPSeq_NGP_DMSO.Input_06h.bw |
417.8 Mb |
(ftp)(http) |
BW |
| GSE211953_ChIPSeq_NGP_DMSO.TADA2B_06h.bw |
233.7 Mb |
(ftp)(http) |
BW |
| GSE211953_ChIPSeq_NGP_dTAGv1.Input_06h.bw |
430.8 Mb |
(ftp)(http) |
BW |
| GSE211953_ChIPSeq_NGP_dTAGv1.TADA2B_06h.bw |
362.7 Mb |
(ftp)(http) |
BW |
| GSE211953_PROTAC_ChIPSeq_KELLY_DMSO_06h_H3K27ac.bw |
165.4 Mb |
(ftp)(http) |
BW |
| GSE211953_PROTAC_ChIPSeq_KELLY_DMSO_06h_H3K9ac.bw |
133.6 Mb |
(ftp)(http) |
BW |
| GSE211953_PROTAC_ChIPSeq_KELLY_DMSO_06h_Input.bw |
258.0 Mb |
(ftp)(http) |
BW |
| GSE211953_PROTAC_ChIPSeq_KELLY_DMSO_06h_MYCN.bw |
72.3 Mb |
(ftp)(http) |
BW |
| GSE211953_PROTAC_ChIPSeq_KELLY_GSK6991_06h_H3K27ac.bw |
195.2 Mb |
(ftp)(http) |
BW |
| GSE211953_PROTAC_ChIPSeq_KELLY_GSK6991_06h_H3K9ac.bw |
152.7 Mb |
(ftp)(http) |
BW |
| GSE211953_PROTAC_ChIPSeq_KELLY_GSK6991_06h_Input.bw |
257.8 Mb |
(ftp)(http) |
BW |
| GSE211953_PROTAC_ChIPSeq_KELLY_GSK6991_06h_MYCN.bw |
130.7 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...