Real World Evaluation of the Prosigna/PAM50 Test in a Node-Negative Postmenopausal Swedish Population: A Multicenter Study

Simple Summary

Gene expression signatures can provide important information on the risk of recurrence in patients with hormone receptor positive early breast cancer, and they can guide postoperative treatment. We have investigated how the implementation of gene-expression-based risk signatures with the Prosigna^® test impacted patient management in Sweden. The two major conclusions of this study are that prognostic factors derived from routine pathology were poor predictors of the intrinsic subtype and the risk of recurrence score, and that gene-expression-based risk combined with clinicopathological biomarkers (tumor size, Ki67, tumor grade) spared patients from adjuvant chemotherapy, but also identified patients who would potentially benefit from this treatment.

Abstract

Molecular signatures to guide decisions for adjuvant chemotherapy are recommended in early ER-positive, HER2-negative breast cancer. The objective of this study was to assess what impact gene-expression-based risk testing has had following its recommendation by Swedish national guidelines. Postmenopausal women with ER-positive, HER2-negative and node negative breast cancer at intermediate clinical risk and eligible for chemotherapy were identified retrospectively from five Swedish hospitals. Tumor characteristics, results from Prosigna^® test and final treatment decision were available for all patients. Treatment recommendations were compared with the last version of regional guidelines before the introduction of routine risk signature testing. Among the 360 included patients, 41% (n = 148) had a change in decision for adjuvant treatment based on Prosigna^® test result. Out of the patients with clinical indication for adjuvant chemotherapy, 52% (n = 118) could avoid treatment based on results from Prosigna^® test. On the contrary, 23% (n = 30) of the patients with no indication were escalated to receive adjuvant chemotherapy after testing. Ki67 could not distinguish between the Prosigna^® risk groups or intrinsic subtypes and did not significantly differ between patients in which decision for adjuvant therapy was changed based on the test results. In conclusion, we report the first real-world data from implementation of gene-expression-based risk assessment in a Swedish context, which may facilitate the optimization of future versions of the national guidelines.

Remodeling of secretory lysosomes during education tunes functional potential in NK cells

Inhibitory signaling during natural killer (NK) cell education translates into increased responsiveness to activation; however, the intracellular mechanism for functional tuning by inhibitory receptors remains unclear. Secretory lysosomes are part of the acidic lysosomal compartment that mediates intracellular signalling in several cell types. Here we show that educated NK cells expressing self-MHC specific inhibitory killer cell immunoglobulin-like receptors (KIR) accumulate granzyme B in dense-core secretory lysosomes that converge close to the centrosome. This discrete morphological phenotype is independent of transcriptional programs that regulate effector function, metabolism and lysosomal biogenesis. Meanwhile, interference of signaling from acidic Ca²⁺ stores in primary NK cells reduces target-specific Ca²⁺-flux, degranulation and cytokine production. Furthermore, inhibition of PI(3,5)P₂ synthesis, or genetic silencing of the PI(3,5)P₂-regulated lysosomal Ca²⁺-channel TRPML1, leads to increased granzyme B and enhanced functional potential, thereby mimicking the educated state. These results indicate an intrinsic role for lysosomal remodeling in NK cell education.

Evolutionary history of metastatic breast cancer reveals minimal seeding from axillary lymph nodes

Metastatic breast cancers are still incurable. Characterizing the evolutionary landscape of these cancers, including the role of metastatic axillary lymph nodes (ALNs) in seeding distant organ metastasis, can provide a rational basis for effective treatments. Here, we have described the genomic analyses of the primary tumors and metastatic lesions from 99 samples obtained from 20 patients with breast cancer. Our evolutionary analyses revealed diverse spreading and seeding patterns that govern tumor progression. Although linear evolution to successive metastatic sites was common, parallel evolution from the primary tumor to multiple distant sites was also evident. Metastatic spreading was frequently coupled with polyclonal seeding, in which multiple metastatic subclones originated from the primary tumor and/or other distant metastases. Synchronous ALN metastasis, a well-established prognosticator of breast cancer, was not involved in seeding the distant metastasis, suggesting a hematogenous route for cancer dissemination. Clonal evolution coincided frequently with emerging driver alterations and evolving mutational processes, notably an increase in apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like-associated (APOBEC-associated) mutagenesis. Our data provide genomic evidence for a role of ALN metastasis in seeding distant organ metastasis and elucidate the evolving mutational landscape during cancer progression.

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.

Electronic supplementary material

The online version of this article (10.1186/s12885-018-4021-6) contains supplementary material, which is available to authorized users.

Abstract P6-01-04: Evolutionary analyses of matched primary and metastatic breast cancer reveal both linear and parallel progression with lack of axillary lymph node involvement

This abstract was withdrawn by the authors.

Abstract P6-07-09: Somatic mutations in A kinase anchoring proteins (AKAPs) in metastatic tumors - A potential characteristic of breast cancer metastasis

Introduction

Genomic heterogeneity in primary solid tumors has been extensively studied using deep sequencing technologies during the last decade. The heterogeneity of cancer tumors is today a well-established concept partly reflected in the low number of genes being recurrently mutated in over 10% of the tumors. However, most available data relates to the primary breast cancer tumors and little has been described about the mutational profiles of the metastatic lesions and their relation to its original malignant cell population. Prospective and retrospective studies have demonstrated that altered receptor status in the metastatic lesion occurs at high rates during cancer progression and is additionally affected by adjuvant therapy with major implications for management of the metastatic disease. Here, we report the exome sequences of paired primary and metastatic lesions from ten breast cancer patients.

Results

We found a marked heterogeneity of somatic mutations as well as chromosomal aberrations in the metastatic lesions. A number of mutated genes were enriched in the metastases including, significantly, members of the A-kinase anchoring protein family (AKAPs), p < 0.02; Fisher's exact test.

The enrichment of AKAP mutations in metastatic lesions was confirmed in an independent cohort containing 20 patients with paired primary and metastatic lesions, which showed the same mutational pattern. In total, 14 nonsynonymous mutations were found in ten of the fourteen AKAP family members. Out of the totally 30 patients examined, ten (30%) carried one or more mutations in AKAP genes either in primary tumor, metastasis, or both. In seven of these ten patients, the AKAP mutation was found uniquely in the metastatic lesion.

Several copy number variations (CNV), mostly deletions in regions containing AKAP genes were detected. For example, the down-regulation of AKAP12 is often associated with promoter hypermethylation or loss of its locus 6q24-25.2 and has been associated with tumor progression and metastasis. In our data deletion of the AKAP12 locus is present in six out of twenty patients.

Discussion

AKAPs are members of a protein family acting as anchors for Protein Kinase A (PKA) by specifically associate PKA regulatory subunits to cellular organelles and direct its active signal transduction spatially and temporally. Several of the AKAP members have been associated to cancer development and metastatic spread, mostly based on differential expression and effects on migration in in vitro assays but both polymorphisms and somatic mutations have been reported in human tumors.

Our findings indicate that in metastatic lesions, the primary tumor genome is extensively transformed, with enrichment of mutations in a distinct set of genes. Together, these findings suggest the involvement of AKAPs in the metastatic process and provide a potential avenue for targeted therapy directed at metastatic breast cancer. Molecular and genetic characterization of the metastatic lesions is not only important in the clinical setting but should also provide the means to reveal genetic patterns specific for the disseminated malignancy.

Citation Format: Kjällquist U, Erlandsson R, Alkodsi A, Tobin N, Karlsson E, Hatschek T, Hartman J, Linnarsson S, Bergh J. Somatic mutations in A kinase anchoring proteins (AKAPs) in metastatic tumors - A potential characteristic of breast cancer metastasis. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-07-09.

Myelodysplastic syndromes are propagated by rare and distinct human cancer stem cells in vivo

Evidence for distinct human cancer stem cells (CSCs) remains contentious and the degree to which different cancer cells contribute to propagating malignancies in patients remains unexplored. In low- to intermediate-risk myelodysplastic syndromes (MDS), we establish the existence of rare multipotent MDS stem cells (MDS-SCs), and their hierarchical relationship to lineage-restricted MDS progenitors. All identified somatically acquired genetic lesions were backtracked to distinct MDS-SCs, establishing their distinct MDS-propagating function in vivo. In isolated del(5q)-MDS, acquisition of del(5q) preceded diverse recurrent driver mutations. Sequential analysis in del(5q)-MDS revealed genetic evolution in MDS-SCs and MDS-progenitors prior to leukemic transformation. These findings provide definitive evidence for rare human MDS-SCs in vivo, with extensive implications for the targeting of the cells required and sufficient for MDS-propagation.

Highly multiplexed and strand-specific single-cell RNA 5' end sequencing

Single-cell analysis of gene expression is increasingly important for the analysis of complex tissues, including cancer, developing organs and adult stem cell niches. Here we present a detailed protocol for quantitative gene expression analysis in single cells, by the sequencing of mRNA 5' ends. In all, 96 cells are lysed, and their mRNA is converted to cDNA. By using a template-switching mechanism, a bar code and an upstream primer-binding sequence are introduced simultaneously with reverse transcription. All cDNA is pooled and then prepared for 5' end sequencing, including fragmentation, adapter ligation and PCR amplification. The chief advantage of this approach is the great reduction in cost and time, afforded by the early bar-coding strategy. Compared with previous methods, it is more suitable for large-scale quantitative analysis, as well as for the characterization of transcription start sites, but it is unsuitable for the detection of alternatively spliced transcripts. Sample preparation takes 3 d, and two sets of 96 cells can be prepared in parallel. Finally, the sequencing and data analysis can take an additional 4 d altogether.

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

Our understanding of the development and maintenance of tissues has been greatly aided by large-scale gene expression analysis. However, tissues are invariably complex, and expression analysis of a tissue confounds the true expression patterns of its constituent cell types. Here we describe a novel strategy to access such complex samples. Single-cell RNA-seq expression profiles were generated, and clustered to form a two-dimensional cell map onto which expression data were projected. The resulting cell map integrates three levels of organization: the whole population of cells, the functionally distinct subpopulations it contains, and the single cells themselves-all without need for known markers to classify cell types. The feasibility of the strategy was demonstrated by analyzing the transcriptomes of 85 single cells of two distinct types. We believe this strategy will enable the unbiased discovery and analysis of naturally occurring cell types during development, adult physiology, and disease.