Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis-enriched mutations in the A-kinase anchoring protein family (AKAPs)

Background: Tumor heterogeneity in breast cancer tumors is today widely recognized. Most of the available knowledge in genetic variation however, relates to the primary tumor while metastatic lesions are much less studied. Many studies have revealed marked alterations of standard prognostic and predictive factors during tumor progression. Characterization of paired primary- and metastatic tissues should therefore be fundamental in order to understand mechanisms of tumor progression, clonal relationship to tumor evolution as well as the therapeutic aspects of systemic disease. Methods: We performed full exome sequencing of primary breast cancers and their metastases in a cohort of ten patients and further confirmed our findings in an additional cohort of 20 patients with paired primary and metastatic tumors. Furthermore, we used gene expression from the metastatic lesions and a primary breast cancer data set to study the gene expression of the AKAP gene family. Results: We report that somatic mutations in A-kinase anchoring proteins are enriched in metastatic lesions. The frequency of mutation in the AKAP gene family was 10% in the primary tumors and 40% in metastatic lesions. Several copy number variations, including deletions in regions containing AKAP genes were detected and showed consistent patterns in both investigated cohorts. In a second cohort containing 20 patients with paired primary and metastatic lesions, AKAP mutations showed an increasing variant allele frequency after multiple relapses. Furthermore, gene expression profiles from the metastatic lesions (n = 120) revealed differential expression patterns of AKAPs relative to the tumor PAM50 intrinsic subtype, which were most apparent in the basal-like subtype. This pattern was confirmed in primary tumors from TCGA (n = 522) and in a third independent cohort (n = 182). Conclusion: Several studies from primary cancers have reported individual AKAP genes to be associated with cancer risk and metastatic relapses as well as direct involvement in cellular invasion and migration processes. Our findings reveal an enrichment of mutations in AKAP genes in metastatic breast cancers and suggest the involvement of AKAPs in the metastatic process. In addition, we report an AKAP gene expression pattern that consistently follows the tumor intrinsic subtype, further suggesting AKAP family members as relevant players in breast cancer biology.Peer reviewe

Intra-tumor heterogeneity in breast cancer has limited impact on transcriptomic-based molecular profiling

Background: Transcriptomic profiling of breast tumors provides opportunity for subtyping and molecular-based patient stratification. In diagnostic applications the specimen profiled should be representative of the expression profile of the whole tumor and ideally capture properties of the most aggressive part of the tumor. However, breast cancers commonly exhibit intra-tumor heterogeneity at molecular, genomic and in phenotypic level, which can arise during tumor evolution. Currently it is not established to what extent a random sampling approach may influence molecular breast cancer diagnostics. Methods: In this study we applied RNA-sequencing to quantify gene expression in 43 pieces (2-5 pieces per tumor) from 12 breast tumors (Cohort 1). We determined molecular subtype and transcriptomic grade for all tumor pieces and analysed to what extent pieces originating from the same tumors are concordant or discordant with each other. Additionally, we validated our finding in an independent cohort consisting of 19 pieces (2-6 pieces per tumor) from 6 breast tumors (Cohort 2) profiled using microarray technique. Exome sequencing was also performed on this cohort, to investigate the extent of intra-tumor genomic heterogeneity versus the intra-tumor molecular subtype classifications. Results: Molecular subtyping was consistent in 11 out of 12 tumors and transcriptomic grade assignments were consistent in 11 out of 12 tumors as well. Molecular subtype predictions revealed consistent subtypes in four out of six patients in this cohort 2. Interestingly, we observed extensive intra-tumor genomic heterogeneity in these tumor pieces but not in their molecular subtype classifications. Conclusions: Our results suggest that macroscopic intra-tumoral transcriptomic heterogeneity is limited and unlikely to have an impact on molecular diagnostics for most patients.Peer reviewe

The prognostic implication of latitude in uveal melanoma : a nationwide observational cohort study of all patients born in Sweden between 1947 and 1989

BACKGROUND: The incidence of uveal melanoma increases with latitude. In this study, we examine the importance of latitude for uveal melanoma prognosis. METHODS: All uveal melanoma patients born in Sweden between 1947 and 1990 were included (n = 745). The latitude of patients’ birthplaces and home counties at the time of uveal melanoma diagnosis were collected. For all latitudes, data on sunlight and UV intensity parameters, temperature, daytime length variations, and socioeconomic factors were added. The prognostic implication of birthplace latitude and of moving > 1 degree of latitude was examined with multivariate Cox regressions and competing risk analyses. FINDINGS: There were no significant differences in patient sex, age, tumor size, T-category, or BAP-1 immunoexpression between patients born in the south, central or northern regions of Sweden. Decreasing birthplace latitude was a predictor of uveal melanoma-related mortality in multivariate Cox regression. Patients that were born in southern regions or moved > 1 degree south between birth and diagnosis had higher incidence of uveal melanoma-related mortality in competing risk analysis. The sum of yearly sunshine hours, global sunlight radiation, average daily ultraviolet light intensity, average annual temperature, or net wealth were not predictors of uveal melanoma-related mortality. INTERPRETATION: Latitude is a prognostic factor in uveal melanoma. This does not seem to be related to variations in patient or tumor characteristics at presentation, in management, in sunlight intensity, in ultraviolet light irradiance, in temperature, or in wealth. Future studies should examine if periodical changes in daylight hours or other factors could explain the prognostic implication. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12672-022-00584-0

A Prognostic Score for the Prediction of Local Treatment Failure in Plaque Brachytherapy of Uveal Melanoma

Purpose: To develop a prognostic score that correlates to a low, medium, and high incidence of treatment failure after plaque brachytherapy of uveal melanoma (UM).Methods and Materials: All patients who have received plaque brachytherapy for posterior UM at St. Erik Eye Hospital in Stockholm, Sweden from 1995 through 2019 were included (n = 1636). Treatment failure was defined as tumor recurrence, lack of tumor regression, or any other condition requiring a secondary transpupillary thermotherapy (TTT), plaque brachytherapy, or enucleation. The total sample was randomized into 1 training and 1 validation cohort, and a prognostic score for the risk for treatment failure was developed.Results: In multivariate Cox regression, low visual acuity, tumor distance to the optic disc &amp; LE;2 mm, American Joint Committee on Cancer (AJCC) stage, and a tumor apical thickness of &amp;gt;4 (for Ruthenium-106) or &amp;gt;9 mm (for Iodine-125) were independent predictors of treatment failure. No reliable threshold could be identified for tumor diameter or cancer stage. In competing risk analyses of the validation cohort, the cumulative incidence of treatment failure, as well as of secondary enucleation, increased with the prognostic score: In the low, intermediate, and high-risk classes, the 10-year incidence of treatment failure was 19, 28, and 35% and of secondary enucleation 7, 19, and 25 %, respectively.Conclusions: Low visual acuity, American Joint Committee on Cancer stage, tumor thickness, and tumor distance to the optic disc are independent predictors of treatment failure after plaque brachytherapy for UM. A prognostic score was devised that identifies low, medium, and high risk for treatment failure. &amp; COPY; 2022 The Author(s). Published by Elsevier Inc. on behalf of American Society for Radiation Oncology. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).Funding Agencies|Swedish Cancer Society [CAN 2017/1029, 21 1788 Pj 01 H]; Swedish Eye Foundation [2022-05-02]; Region Stockholm [20 0798 Fk]; Karolinska Institutet [FS-2021-01131]; [20200356]</p