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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 19, 2021 |
| Title |
Transcriptional profiling of estrogen receptor fusion genes in breast cancer cell lines |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Genomic analysis has recently identified multiple ESR1 gene translocations in estrogen receptor-alpha positive (ERα+) metastatic breast cancer (MBC) that encode chimeric proteins whereby the ESR1 ligand binding domain (LBD) is replaced by C-terminal sequences from many different gene partners. Here we functionally screened 15 ESR1 fusions and identified 10 that promoted estradiol-independent cell growth, motility, invasion, EMT and resistance to fulvestrant. RNA sequencing identified a gene expression pattern specific to functionally active ESR1 gene fusions that was subsequently reduced to a diagnostic 24-gene signature. This signature was further examined in 20 ERα+ patient-derived xenografts (PDXs) and in 55 ERα+ MBC samples. The 24-gene signature successfully identified cases harboring ESR1 gene fusions and also accurately diagnosed the presence of activating ESR1 LBD point mutations. Therefore, the 24-gene signature represents an efficient approach to screening samples for the presence of diverse somaticESR1 mutations and translocations that drive endocrine treatment failure in MBC.
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| Overall design |
RNA-seq of stable T47D breast cancer cells expressing HA-tagged ESR1 constructs and YFP control in hormone deprived media, -/+ E2. (ESR1-e6 denotes ESR1 fusion containing the first 6 exons of ESR1)
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| Contributor(s) |
Ellis MJ, Lei JT, Gou X, Anurag M |
| Citation(s) |
34711608 |
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| Submission date |
Dec 17, 2021 |
| Last update date |
Feb 14, 2022 |
| Contact name |
Jonathan Thomas Lei |
| E-mail(s) |
jlei@bcm.edu
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| Organization name |
Baylor College of Medicine
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| Department |
Medicine - Lester and Sue Smith Breast Center
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| Lab |
Eric C. Chang Lab
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| Street address |
1 Baylor Plaza
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (42)
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| GSM5740192 |
ESR1-e6>YAP1, +E2 |
| GSM5740193 |
ESR1-e6>PCDH11X |
| GSM5740194 |
ESR1-e6>PCDH11X, +E2 |
| GSM5740195 |
ESR1-e6>DAB2 |
| GSM5740196 |
ESR1-e6>DAB2, +E2 |
| GSM5740197 |
ESR1-e6>GYG1 |
| GSM5740198 |
ESR1-e6>GYG1, +E2 |
| GSM5740199 |
ESR1-e6>SOX9 |
| GSM5740200 |
ESR1-e6SOX9, +E2 |
| GSM5740201 |
ESR1-e6>ARNT2 |
| GSM5740202 |
ESR1-e6>ARNT2, +E2 |
| GSM5740203 |
ESR1-e6>PCMT1 |
| GSM5740204 |
ESR1-e6>PCMT1, +E2 |
| GSM5740205 |
ESR1-e6>ARID1B |
| GSM5740206 |
ESR1-e6>ARID1B, +E2 |
| GSM5740207 |
ESR1-e6 |
| GSM5740208 |
ESR1-e6, +E2 |
| GSM5740209 |
ESR1-WT |
| GSM5740210 |
ESR1-WT, +E2 |
| GSM5740211 |
YFP_rep2 |
| GSM5740212 |
YFP_rep2, +E2 |
| GSM5740213 |
ESR1-e6>ARNT2-e2 |
| GSM5740214 |
ESR1-e6>ARNT2-e2, +E2 |
| GSM5740215 |
ESR1-e6>LPP |
| GSM5740216 |
ESR1-e6>LPP, +E2 |
| GSM5740217 |
ESR1-e6>NCOA1 |
| GSM5740218 |
ESR1-e6>NCOA1, +E2 |
| GSM5740219 |
ESR1-e6>TCF12 |
| GSM5740220 |
ESR1-e6>TCF12, +E2 |
| GSM5740221 |
ESR1-e6>CLINT1 |
| GSM5740222 |
ESR1-e6>CLINT1, +E2 |
| GSM5740223 |
ESR1-e6>GRIP1 |
| GSM5740224 |
ESR1-e6>GRIP1, +E2 |
| GSM5740225 |
ESR1-e6>TNRC6B |
| GSM5740226 |
ESR1-e6>TNRC6B, +E2 |
| GSM5740227 |
ESR1-Y537S |
| GSM5740228 |
ESR1-Y537S, +E2 |
| GSM5740229 |
ESR1-D538G |
| GSM5740230 |
ESR1-D538G, +E2 |
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| Relations |
| BioProject |
PRJNA789898 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE191158_RAW.tar |
92.1 Mb |
(http)(custom) |
TAR (of RESULTS) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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