Systems biology analysis of mitogen activated protein kinase inhibitor resistance in malignant melanoma
Helma Zecena1, Daniel Tveit1, Zi Wang2,3
1Systems Biology and Cancer Metabolism, Program for Quantitative Systems Biology, University of California Merced, 2500 North Lake Road, Merced, CA, 95343, USA.
Background:
Kinase inhibition in the mitogen activated protein kinase (MAPK) pathway is a standard therapy for cancer patients with activating BRAF mutations. However, the anti-tumorigenic effect and clinical benefit are only transient, and tumors are prone to treatment resistance and relapse. To elucidate mechanistic insights into drug resistance, we have established an in vitro cellular model of MAPK inhibitor resistance in malignant melanoma.
Methods:
The cellular model evolved in response to clinical dosage of the BRAF inhibitor, vemurafenib, PLX4032. We conducted transcriptomic expression profiling using RNA-Seq and RT-qPCR arrays. Pathways of melanogenesis, MAPK signaling, cell cycle, and metabolism were significantly enriched among the set of differentially expressed genes of vemurafenib-resistant cells vs control. The underlying mechanism of treatment resistance and pathway rewiring was uncovered to be based on non-genomic adaptation and validated in two distinct melanoma models, SK-MEL-28 and A375. Both cell lines have activating BRAF mutations and display metastatic potential.
Results:
Downregulation of dual specific phosphatases, tumor suppressors, and negative MAPK regulators reengages mitogenic signaling. Upregulation of growth factors, cytokines, and cognate receptors triggers signaling pathways circumventing BRAF blockage. Further, changes in amino acid and one-carbon metabolism support cellular proliferation despite MAPK inhibitor treatment. In addition, treatment-resistant cells upregulate pigmentation and melanogenesis, pathways which partially overlap with MAPK signaling. Upstream regulator analysis discovered significant perturbation in oncogenic forkhead box and hypoxia inducible factor family transcription factors.
Conclusions:
The established cellular models offer mechanistic insight into cellular changes and therapeutic targets under inhibitor resistance in malignant melanoma. At a systems biology level, the MAPK pathway undergoes major rewiring while acquiring inhibitor resistance. The outcome of this transcriptional plasticity is selection for a set of transcriptional master regulators, which circumvent upstream targeted kinases and provide alternative routes of mitogenic activation. A fine-woven network of redundant signals maintains similar effector genes allowing for tumor cell survival and malignant progression in therapy-resistant cancer.
Insights
Malignant melanoma cells develop resistance to BRAF inhibitors through non-genomic adaptation, rewiring the MAPK pathway. This involves altered gene expression and metabolism, leading to tumor cell survival and progression despite treatment.
Area of Science:
- Oncology
- Molecular Biology
- Cancer Research
Background:
- Kinase inhibition targeting the mitogen-activated protein kinase (MAPK) pathway is a standard cancer therapy for patients with activating BRAF mutations.
- Tumors often develop transient anti-tumorigenic effects and resistance to MAPK inhibitors, leading to relapse.
- Understanding the mechanisms of drug resistance is crucial for improving cancer treatment outcomes.
Purpose of the Study:
- To establish an in vitro cellular model of MAPK inhibitor resistance in malignant melanoma.
- To elucidate the mechanistic insights into how melanoma cells acquire resistance to BRAF inhibitors.
- To identify potential therapeutic targets for overcoming treatment resistance.
Main Methods:
- Established a cellular model of vemurafenib (PLX4032) resistance in malignant melanoma.
- Utilized RNA-Seq and RT-qPCR arrays for transcriptomic expression profiling.
- Validated findings in two distinct BRAF-mutated melanoma cell lines (SK-MEL-28 and A375).
Main Results:
- Identified significant enrichment in melanogenesis, MAPK signaling, cell cycle, and metabolism pathways in resistant cells.
- Revealed non-genomic adaptation involving downregulation of tumor suppressors and upregulation of growth factors and metabolic pathways.
- Discovered perturbation of oncogenic transcription factors (forkhead box and hypoxia-inducible factor families).
Conclusions:
- Malignant melanoma exhibits significant MAPK pathway rewiring and transcriptional plasticity upon acquiring inhibitor resistance.
- Non-genomic adaptation and activation of alternative signaling routes circumvent BRAF inhibition.
- Targeting key transcriptional master regulators and redundant signaling networks may overcome therapeutic resistance.
Related Concept Videos
02:54Protein Kinases and Phosphatases
Protein kinases
Many proteins in the cell are regulated by phosphorylation, the addition of a phosphate group. A family of enzymes called kinases...
02:54Protein Kinases and Phosphatases
02:38Mitogens and the Cell Cycle
01:52Eukaryotic Transcription Inhibitors
Eukaryotic transcription inhibitors usually contain two distinct domains, a...
01:25cAMP-dependent Protein Kinase Pathways
01:26Treatment for Pulmonary Arterial Hypertension: Receptor Tyrosine Kinase Inhibitors and Calcium Channel Blockers
TKIs, such as imatinib (Gleevec), are particularly effective in tackling the growth and mitogenic factors that become upregulated in PAH patients. These factors contribute to the...