mRNA profiling reveals determinants of trastuzumab efficiency in HER2-positive breast cancer
Silvia von der Heyde1, Steve Wagner2, Alexander Czerny3
1Statistical Bioinformatics, Department of Medical Statistics, University Medical Center Göttingen, Göttingen, Germany; IndivuTest GmbH, Hamburg, Germany.
Abstract:
Intrinsic and acquired resistance to the monoclonal antibody drug trastuzumab is a major problem in the treatment of HER2-positive breast cancer. A deeper understanding of the underlying mechanisms could help to develop new agents. Our intention was to detect genes and single nucleotide polymorphisms (SNPs) affecting trastuzumab efficiency in cell culture. Three HER2-positive breast cancer cell lines with different resistance phenotypes were analyzed. We chose BT474 as model of trastuzumab sensitivity, HCC1954 as model of intrinsic resistance, and BTR50, derived from BT474, as model of acquired resistance. Based on RNA-Seq data, we performed differential expression analyses on these cell lines with and without trastuzumab treatment. Differentially expressed genes between the resistant cell lines and BT474 are expected to contribute to resistance. Differentially expressed genes between untreated and trastuzumab treated BT474 are expected to contribute to drug efficacy. To exclude false positives from the candidate gene set, we removed genes that were also differentially expressed between untreated and trastuzumab treated BTR50. We further searched for SNPs in the untreated cell lines which could contribute to trastuzumab resistance. The analysis resulted in 54 differentially expressed candidate genes that might be connected to trastuzumab efficiency. 90% of 40 selected candidates were validated by RT-qPCR. ALPP, CALCOCO1, CAV1, CYP1A2 and IGFBP3 were significantly higher expressed in the trastuzumab treated than in the untreated BT474 cell line. GDF15, IL8, LCN2, PTGS2 and 20 other genes were significantly higher expressed in HCC1954 than in BT474, while NCAM2, COLEC12, AFF3, TFF3, NRCAM, GREB1 and TFF1 were significantly lower expressed. Additionally, we inferred SNPs in HCC1954 for CAV1, PTGS2, IL8 and IGFBP3. The latter also had a variation in BTR50. 20% of the validated subset have already been mentioned in literature. For half of them we called and analyzed SNPs. These results contribute to a better understanding of trastuzumab action and resistance mechanisms.
Insights
Understanding trastuzumab resistance in HER2-positive breast cancer is key. This study identified genes and SNPs affecting trastuzumab efficiency, offering insights into treatment resistance mechanisms.
Area of Science:
- Oncology
- Molecular Biology
- Genetics
Background:
- Intrinsic and acquired resistance to trastuzumab poses a significant challenge in treating HER2-positive breast cancer.
- Identifying the genetic and molecular mechanisms underlying this resistance is crucial for developing more effective therapeutic strategies.
Purpose of the Study:
- To identify genes and single nucleotide polymorphisms (SNPs) that influence the efficacy of trastuzumab in HER2-positive breast cancer cell lines.
- To differentiate between mechanisms of intrinsic and acquired resistance to trastuzumab.
Main Methods:
- Differential gene expression analysis using RNA-Seq on three HER2-positive breast cancer cell lines with varying trastuzumab resistance phenotypes (sensitive, intrinsic resistance, acquired resistance).
- Identification and validation of candidate genes and SNPs associated with trastuzumab resistance using RT-qPCR.
- Bioinformatic analysis to detect SNPs in relevant genes within resistant cell lines.
Main Results:
- 54 differentially expressed candidate genes potentially linked to trastuzumab efficiency were identified, with 90% validated by RT-qPCR.
- Specific genes (e.g., ALPP, CAV1, IGFBP3) showed altered expression in response to trastuzumab treatment in sensitive cells.
- Several genes (e.g., GDF15, IL8, LCN2) were differentially expressed between resistant and sensitive cell lines, and SNPs were identified in genes like CAV1 and PTGS2.
Conclusions:
- The study identified novel candidate genes and SNPs contributing to trastuzumab resistance in HER2-positive breast cancer.
- These findings enhance the understanding of trastuzumab's mechanism of action and resistance pathways.
- The identified genetic markers may serve as potential targets for overcoming treatment resistance.
