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| Status |
Public on Nov 02, 2020 |
| Title |
Effects of EGF, cetuximab, trastuzumab and afatinib on gene expression in gastric cancer cell lines |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The antibody trastuzumab in combination with platin-fluoropyrimidine chemotherapy is the standard of care for patients with HER2-positive recurrent or metastatic gastric cancer. Alternative treatment options and biomarkers for prediction of therapy response are needed since some patients do not respond to trastuzumab therapy or develop acquired resistance. We compared the molecular effects of trastuzumab and other HER-targeting drugs cetuximab and afatinib. We also tested the hypothesis that the treatment-dependent regulation of a gene indicates its importance for response, and therefore it may be used as biomarker for patient stratification. The four gastric cancer cell lines Hs746T, MKN1, MKN7 and NCI-N87 were treated with EGF, cetuximab, trastuzumab or afatinib for 4 or 24 hours. The effect on gene expression was then measured by RNA sequencing and the resulting candidate biomarkers were tested in an available cohort of gastric cancer patients or were functionally analyzed in vitro. Treatment with afatinib resulted in the highest number of regulated genes, followed by cetuximab and trastuzumab. Although trastuzumab had little effects on gene expression, we identified BMF, HAS2 and SHB as candidate biomarkers for trastuzumab response. HAS2 and SHB were confirmed as potential predictive markers for trastuzumab therapy response in clinical specimens. AREG, EREG and HBEGF were identified as candidate biomarkers for afatinib and cetuximab treatment. The functional analysis confirmed HBEGF as resistance factor for cetuximab. By confirming HAS2, SHB and HBEGF as biomarkers for anti-HER therapies, we provide evidence that the regulation of gene expression after treatment can be used for biomarker discovery.
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| Overall design |
Gastric cancer cell lines were treated with EGF, cetuximab, trastuzumab and afatinib in biological triplicates
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| Contributor(s) |
Geffers R, Ebert K, Luber B, Zwingenberger G, Arnold R, Keller S |
| Citation(s) |
33115415, 35264144 |
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| Submission date |
Dec 03, 2019 |
| Last update date |
Mar 31, 2022 |
| Contact name |
Robert Geffers |
| E-mail(s) |
[email protected]
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| Phone |
+49 531-6181-3058
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| Organization name |
HCI - Helmholtz Centre for Infection Research
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| Department |
Dep. Molecular Bacteriology
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| Lab |
Genome Analytics
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| Street address |
Inhoffenstr. 7
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| City |
Braunschweig |
| ZIP/Postal code |
38124 |
| Country |
Germany |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (132)
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| Relations |
| BioProject |
PRJNA593206 |
| SRA |
SRP234536 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE141352_RAW.tar |
35.1 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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