Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance
Genevieve Stein-O'Brien1,2, Luciane T Kagohara2, Sijia Li2
1Institute of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA.
Background:
Targeted therapies specifically act by blocking the activity of proteins that are encoded by genes critical for tumorigenesis. However, most cancers acquire resistance and long-term disease remission is rarely observed. Understanding the time course of molecular changes responsible for the development of acquired resistance could enable optimization of patients' treatment options. Clinically, acquired therapeutic resistance can only be studied at a single time point in resistant tumors.
Methods:
To determine the dynamics of these molecular changes, we obtained high throughput omics data (RNA-sequencing and DNA methylation) weekly during the development of cetuximab resistance in a head and neck cancer in vitro model. The CoGAPS unsupervised algorithm was used to determine the dynamics of the molecular changes associated with resistance during the time course of resistance development.
Results:
CoGAPS was used to quantify the evolving transcriptional and epigenetic changes. Applying a PatternMarker statistic to the results from CoGAPS enabled novel heatmap-based visualization of the dynamics in these time course omics data. We demonstrate that transcriptional changes result from immediate therapeutic response or resistance, whereas epigenetic alterations only occur with resistance. Integrated analysis demonstrates delayed onset of changes in DNA methylation relative to transcription, suggesting that resistance is stabilized epigenetically.
Conclusions:
Genes with epigenetic alterations associated with resistance that have concordant expression changes are hypothesized to stabilize the resistant phenotype. These genes include FGFR1, which was associated with EGFR inhibitors resistance previously. Thus, integrated omics analysis distinguishes the timing of molecular drivers of resistance. This understanding of the time course progression of molecular changes in acquired resistance is important for the development of alternative treatment strategies that would introduce appropriate selection of new drugs to treat cancer before the resistant phenotype develops.
Insights
Understanding cancer acquired resistance is key. This study reveals that while transcription changes rapidly, epigenetic alterations stabilize resistance over time, offering new therapeutic strategies for head and neck cancer.
Area of Science:
- Oncology
- Molecular Biology
- Genomics
Background:
- Targeted cancer therapies block tumorigenesis-critical proteins.
- Acquired therapeutic resistance limits long-term disease remission.
- Understanding resistance development dynamics is crucial for optimizing treatment.
Purpose of the Study:
- To investigate the temporal molecular changes during acquired resistance development.
- To analyze the dynamics of transcriptional and epigenetic alterations in response to therapy.
Main Methods:
- Utilized high-throughput omics data (RNA-sequencing, DNA methylation) weekly.
- Employed the CoGAPS algorithm to analyze time-course molecular changes.
- Applied PatternMarker statistic for heatmap-based visualization of omics data dynamics.
Main Results:
- Transcriptional changes occur immediately with therapeutic response or resistance.
- Epigenetic alterations emerge specifically with resistance development.
- DNA methylation changes show a delayed onset relative to transcription, stabilizing resistance.
Conclusions:
- Integrated omics analysis distinguishes the timing of molecular drivers of resistance.
- Epigenetic alterations stabilize the resistant phenotype, as seen with FGFR1.
- Understanding resistance progression aids in developing preemptive treatment strategies.
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