Patterns of genomic evolution in advanced melanoma

Genomic alterations occurring during melanoma progression and the resulting genomic heterogeneity between metastatic deposits remain incompletely understood. Analyzing 86 metastatic melanoma deposits from 53 patients with whole-exome sequencing (WES), we show a low branch to trunk mutation ratio and little intermetastatic heterogeneity, with driver mutations almost completely shared between lesions. Branch mutations consistent with UV damage indicate that metastases may arise from different subclones in the primary tumor. Selective gain of mutated BRAF alleles occurs as an early event, contrasting whole-genome duplication (WGD) occurring as a late truncal event in about 40% of cases. One patient revealed elevated mutational diversity, probably related to previous chemotherapy and DNA repair defects. In another patient having received radiotherapy toward a lymph node metastasis, we detected a radiotherapy-related mutational signature in two subsequent distant relapses, consistent with secondary metastatic seeding. Our findings add to the understanding of genomic evolution in metastatic melanomas.

As melanoma progresses, it evolves. Here, in advanced melanoma the authors study genomic evolution, highlighting trunk mutations dominated by the ultraviolet damage signature, common late truncal whole-genome duplication events, as well as selective copy number gain of mutant BRAF.

Abstract P4-09-04: Withdrawn

This abstract was withdrawn by the authors.

Abstract P5-08-05: The influence of doxorubicin on PTEN and PI3K-Akt-mTOR signaling in human breast cancer

Background:

De novo as well as acquired resistance are common features of anthracycline therapy in breast cancer. The PTEN tumor suppressor gene is frequently inactivated in human breast cancer, leading to induction of PI3K-Akt-mTOR signaling, which facilitates cell growth, survival, invasion and ultimately tumor progression. Upregulation of the PI3K-Akt-mTOR pathway has been suggested as a possible mechanism of anthracycline resistance, but there is limited data in the clinical setting, including its influence on PTEN expression.

Methods:

The early PTEN response to doxorubicin was assessed in vitro in MCF7 (estrogen receptor positive) and MDA-MB231 (triple negative) human breast cancer cell lines 24 hours after the initiation of chemotherapy. Tumor samples from thirty patients with locally advanced breast cancer were analyzed for PTEN expression levels and PI3K-Akt-mTOR signaling before and after neoadjuvant anthracycline therapy. The early effect of anthracyclines on PTEN expression is currently being evaluated in human breast cancer samples 24 hours after the initiation of chemotherapy. Mice bearing MCF7 and MDA-MB231 xenografts will be used to assess the potential of PI3K-Akt-mTOR signal transduction inhibitors in preventing anthracycline resistance.

Results:

PTEN expression was found to be profoundly downregulated in both MCF7 and MDA-MB231 cell lines, 24 hours after exposure to doxorubicin at their respective IC50. An increase in Akt1 protein levels in both cell lines was observed in the same setting. In 19 out of 30 human breast cancers PTEN levels increased after a median of 16 weeks neoadjuvant doxorubicin treatment. No difference between estrogen receptor positive and negative breast cancers was observed. The increase in PTEN was accompanied by an increase in fibrotic tissue in the tumor interior. There was no correlation between PTEN level or treatment-induced alterations in PTEN expression and response rates or recurrence-free survival (RFS). The results from our currently ongoing experiments will be presented.

Conclusion:

PTEN expression increases in the majority of human breast cancers during long-term exposure to doxorubicin. However, PTEN is greatly downregulated, with corresponding Akt1 increase, 24 hours after exposure to high doses of doxorubicin in vitro. These results indicate different effects of short- and long-term exposure to doxorubicin, which may be of importance to the development of anthracycline resistance, and to understand at what time a combinational approach with inhibitors of the PI3K-Akt-mTOR pathway will be beneficial. Current efforts are aimed at evaluating the potential of such inhibitors to counteract doxorubicin resistance in this setting.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P5-08-05.

RINF (CXXC5) is overexpressed in solid tumors and is an unfavorable prognostic factor in breast cancer

BACKGROUND

We have previously described the essential role of the retinoid-inducible nuclear factor (RINF) during differentiation of hematopoietic cells and suggested its putative involvement in myeloid leukemia and preleukemia. Here, we have investigated whether this gene could have a deregulated expression in malignant tissues compared with their normal tissues of origin and if this potential deregulation could be associated with important clinicopathological parameters.

PATIENTS AND METHODS

RINF messenger RNA expression was examined in biopsies from locally advanced breast tumors, metastatic malignant melanomas, and papillary thyroid carcinomas and compared with their paired or nonpaired normal reference samples. Further, the prognostic role of RINF expression was evaluated in locally advanced breast cancer.

RESULTS

RINF expression was significantly higher in all tumor forms (primary breast, and thyroid cancers and metastatic melanomas) as compared with normal control tissues (P < 0.001 for each comparison). Importantly, high levels of RINF expression correlated to a poor overall survival in breast cancer (P = 0.013). This finding was confirmed in three independent public microarray datasets (P = 0.043, n = 234; P = 0.016, n = 69; P = 0.001, n = 196) and was independent of tamoxifen therapy. Notably, high levels of RINF was strongly associated with TP53 wild-type status (P = 0.002) possibly indicating that high levels of RINF could substitute for TP53 mutations as an oncogenic mechanism during the malignant development of some cases of breast cancer.

CONCLUSIONS

Our data indicate that (i) RINF overexpression is associated with the malignant phenotype in solid tumors and (ii) RINF overexpression represents an independent molecular marker for poor prognosis in breast tumors.

Abstract P4-02-02: Epidermal Growth Factor Receptors (ErbB/HER) and the Ligand Neuregulin 1 (NRG1) Increase in Breast Tumors during Short Time Endocrine Treatment

Background: Cross-talk between estrogen receptor (ER) and growth factor signaling pathways has been suggested to play a role in development of resistance to endocrine treatment with tamoxifen or aromatase inhibitors (AIs). While HER-2/neu amplification has been associated with lack of endocrine sensitivity in ER+ breast cancer, recent data have suggestedanti-HER-2 therapy to enhance efficacy of AIs in a subset of HER-2/neu non-amplified breast cancers [1], and we found HER-2/neu upregulation in tumors responding to therapy with AIs [2]. Here, we aimed at exploring the effect of treatment with AIs on other components of the HER family, including NRG1, recently reported to be subject to silencing through promoter methylation in breast cancers [3].

Methods: Tumor biopsies were collected from 60 ER + breast cancers before and after 3 months treatment with the AIs, Anatrozole or Letrozole. Tumor biopsies after 2 weeks of treatment were available for 39 of the patients. RNA was extracted from the tumors and mRNA expression analysis of HER-1, HER-2/neu, HER-3, HER-4 and NRG1 were performed with gene-specific primers and probes by real-time PCR. Changes in mRNA expression during treatment were analyzed by Wilcoxon Sign Rank tests, and correlation between expression groups by Spearman correlation.

Results: Among HER-2/neu non-amplified tumors (n=56), we observed a significant increase in mRNA expression for HER-1 (40/50 tumors; mean increase 2.0-fold) and NRG1 (38/54 tumors; mean increase 2.9-fold) during treatment independent of treatment response (P&lt;0.001 for both). A non-significant increase in Her-2/neu was observed in 28/54 tumors (18/38 responders). Interestingly, individual alterations in tumor HER-2/neu correlated negatively to change in HER-1 (R=-0.414, p=0.001). Data on DNA methylation at the NRG1 gene will be presented. While no statistical significant increase or decrease in HER-3 or -4 were observed, individual variations in these two parameters were statistically correlated among individual tumors (R=0.621, P&lt;0.001).

Conclusions: Estrogen suppression with use of AIs significantly increased intratumor expression levels of HER-1 and NRG1 in HER-2/neu non-amplified tumors, while HER-2/neu increased in a subset of tumors. These findings suggest extensive cross-talks between estrogen stimulation and the HER system, indicating potential mechanisms of therapy resistance. The increase in NRG1 during treatment with AIs may represent a cellular response that leads to changes in its tumor suppressor activity. These findings merits further explorations.

1. Johnston, S., et al., Lapatinib combined with letrozole versus letrozole and placebo as first-line therapy for postmenopausal hormone receptor-positive metastatic breast cancer. J Clin Oncol, 2009. 27(33): p. 5538-46.

2. Flageng, M.H., et al., Nuclear receptor co-activators and HER-2/neu are upregulated in breast cancer patients during neo-adjuvant treatment with aromatase inhibitors. Br J Cancer, 2009. 101(8): p. 1253-60.

3. Chua, Y.L., et al., The NRG1 gene is frequently silenced by methylation in breast cancers and is a strong candidate for the 8p tumour suppressor gene. Oncogene, 2009. 28(46): p. 4041-52.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P4-02-02.

Breast cancer prognostication and prediction in the postgenomic era

Expanding knowledge, together with implementation of new techniques, has fuelled the area of translational medical research aiming at improving prognostication as well as prediction in cancer therapy. At the same time, new discoveries have revealed a biological complexity we were unaware of only a decade ago. Thus, we are faced with novel challenges with respect to how we may explore issues such as prognostication and predict drug resistance in vivo. While microarray analysis exploring expression of thousands of genes in concert represents a major methodological advancement, discoveries such as the finding of different mechanisms of epigenetic silencing, intronic mutations, that most gene transcripts in the human genome are subject to alternative splicing and that hypersplicing seems to be a tumour-related phenomenon, exemplifies a complex pathology that may not be explored with use of single analytical methods only. This paper discusses clinical settings for studying drug resistance in vivo together with a discussion of contemporary biology in this field. Notably, each individual parameter which has been found correlated to drug resistance in vivo so far represents either a direct drug target or a factor involved in DNA repair or apoptosis. On the basis of these findings, we suggest drug resistance may be explored on the basis of upfront biological hypotheses.