B-RAF and N-RAS mutations are preserved during short time in vitro propagation and differentially impact prognosis

Abstract

In melanoma, the RAS/RAF/MEK/ERK signalling pathway is an area of great interest, because it regulates tumor cell proliferation and survival. A varying mutation rate has been reported for B-RAF and N-RAS, which has been largely attributed to the differential source of tumor DNA analyzed, e.g., fixed tumor tissues or in vitro propagated melanoma cells. Notably, this variation also interfered with interpreting the impact of these mutations on the clinical course of the disease. Consequently, we investigated the mutational profile of B-RAF and N-RAS in biopsies and corresponding cell lines from metastatic tumor lesions of 109 melanoma patients (AJCC stage III/IV), and its respective impact on survival. 97 tissue biopsies and 105 biopsy-derived cell lines were screened for B-RAF and N-RAS mutations by PCR single strand conformation polymorphism and DNA sequencing. Mutations were correlated with patient survival data obtained within a median follow-up time of 31 months. B-RAF mutations were detected in 55% tissues and 51% cell lines, N-RAS mutations in 23% tissues and 25% cell lines, respectively. There was strong concordance between the mutational status of tissues and corresponding cell lines, showing a differing status for B-RAF in only 5% and N-RAS in only 6%, respectively. Patients with tumors carrying mutated B-RAF showed an impaired median survival (8.0 versus 11.8 months, p = 0.055, tissues; 7.1 versus 9.3 months, p = 0.068, cell lines), whereas patients with N-RAS-mutated tumors presented with a favorable prognosis (median survival 12.5 versus 7.9 months, p = 0.084, tissues; 15.4 versus 6.8 months, p = 0.0008, cell lines), each in comparison with wildtype gene status. Multivariate analysis qualified N-RAS (p = 0.006) but not B-RAF mutation status as an independent prognostic factor of overall survival. Our findings demonstrate that B-RAF and N-RAS mutations are well preserved during short term in vitro propagation and, most importantly, differentially impact the outcome of melanoma patients.

Figure 1. Schematic presentation of the study flow.

Figure 2. Detection and identification of B-RAF and N-RAS mutations in melanoma cell lines and corresponding tissues by fluorescent capillary electrophoresis SSCP and DNA sequencing.

Migration patterns under non-denaturing conditions of single stranded fragments of exon 15 of the B-RAF gene with a T1799A mutation at codon 600 in the cell line Ma-Mel-36 (A) and the corresponding tumor tissue (B). Migration patterns for the B-RAF exon 15 fragments with wild type sequences in the cell line Ma-Mel-37a (C) and the corresponding tumor tissue (D). Panels (E) to (H) show sequence analyses of the cell lines and tumor tissues given in (A) to (D). Fluorescent capillary electrophoresis patterns for the N-RAS exon 2 sequence with a CAA>CGA mutation at codon 61 in the cell line Ma-Mel-05 (I) and the corresponding tumor tissue (J). Migration patterns for the N-RAS exon 2 fragments with wild-type sequences in the cell line Ma-Mel-59 (K) and the corresponding tumor tissue (L). Panels (M) to (P) show the confirmation of the mutations in the cell lines and tissues shown in (I) to (L) by sequence analysis.

Figure 3. Kaplan-Meier survival estimation for the whole patient population by mutational status.

Curves showing the overall survival of 109 metastatic melanoma patients starting from the time point of tumor biopsy. Survival probabilities were compared by the mutational status of B-RAF in tumor tissue biopsies (n = 97) (A) and biopsy-derived tumor cell lines (n = 105) (D), as well as N-RAS in tumor tissue biopsies (n = 97) (B) and biopsy-derived tumor cell lines (n = 105) (E). (C) and (F) differentiate patients harbouring B-RAF mutations (n = 52, tissues; n = 52, cell lines), patients harbouring N-RAS mutations (n = 21, tissues; n = 25; cell lines), and patients without mutations in both genes (n = 24, tissues; n = 27, cell lines). Statistical differences between groups were calculated using the log-rank test. Vertical bars indicate censored observations.

Figure 4. Kaplan-Meier survival estimation for stage IV patients only by mutational status.

Curves showing the overall survival starting with the time point of tumor biopsy in 82 metastatic melanoma patients who were in stage IV disease at that time. Survival probabilities were compared by the mutational status of B-RAF in tumor tissue biopsies (n = 70) (A) and biopsy-derived tumor cell lines (n = 80) (D), as well as N-RAS in tumor tissue biopsies (n = 70) (B) and biopsy-derived tumor cell lines (n = 80) (E). (C) and (F) differentiate patients harbouring B-RAF mutations (n = 43, tissues; n = 45, cell lines), patients harbouring N-RAS mutations (n = 12, tissues; n = 15; cell lines), and patients without mutations in both genes (n = 15, tissues; n = 20, cell lines). Statistical differences between groups were calculated using the log-rank test. Vertical bars indicate censored observations.