Doctor of Philosophy (PhD)
Immunology, Pathology & Infectious Disease
Melanoma, Vemurafenib, Drug Resistance, Cell Line Authentication, Proto-Oncogene Proteins B-raf
Melanoma is the deadliest form of skin cancer, and incidence has continued to increase. Half of all melanomas have a BRAF V600E mutation and respond to MAPK pathway inhibitors, including BRAF inhibitor therapy or BRAF/MEK inhibitor combination therapy, but nearly all patients develop treatment resistance. Melanoma cell lines produce variable results as models of MAPK pathway inhibitor resistance. To better understand how the genomic similarity of a melanoma cell line to patient-derived tumors affects resistance mechanisms, differences in DNA mutations and copy-number alterations were compared between melanoma cell lines profiled by the Cancer Cell Line Encyclopedia and cutaneous melanoma tumors profiled by The Cancer Genome Atlas. Melanoma cell lines were ranked according to significantly different features combined into a patient similarity score. Vemurafenib-resistance was induced in three single-cell clones: high similarity SKMEL5, intermediate similarity SKMEL28, and low similarity HS695T. MEK, Erk, and Akt phosphorylation varied between single-cell clones derived from the same cell line. PDGFRβ phosphorylation was significantly increased in resistant HS695T clones. Single‑cell clones were analyzed by RNA-sequencing to determine DEGs associated with vemurafenib treatment and resistance. The vemurafenib-resistant single-cell clones from the three different cell lines were then compared to aggregated public data from patients with cutaneous melanoma that were on treatment or resistant to MAPK pathway inhibitors. Resistant patients had few DEGs relative to baseline patients. The patient similarity score showed no association with the similarity of enriched KEGG pathways in patients or the enrichment of genes from the cell lines for DEGs detected in patients. Vemurafenib‑resistant cell lines shared more features with patients on treatment with MAPK pathway inhibitors than with resistant patients. Overall, the genetic similarity of melanoma cell lines to patient tumors did not predict better utility as a pre-clinical model, and precision was low between single-cell clones from the same parental cell line.
Luebker, Stephen, "Gene Expression Profiling of MAPK Pathway Inhibitor Resistance in Cutaneous Melanoma: Can Bioinformatics Be Used to Select Better Melanoma Cell Lines?" (2021). Theses & Dissertations. 568.
Amino Acids, Peptides, and Proteins Commons, Cancer Biology Commons, Cells Commons, Dermatology Commons, Diagnosis Commons, Genetic Phenomena Commons, Genetic Processes Commons, Genomics Commons, Medical Cell Biology Commons, Medical Genetics Commons, Medical Molecular Biology Commons, Oncology Commons, Skin and Connective Tissue Diseases Commons, Therapeutics Commons