Abstract P5-11-02: Recurrent ESR1 fusions in primary tumors; a promising predictive factor for outcome to first-line endocrine therapy?

Introduction:

While fusion genes have been identified and are being utilized as prognostic and predictive markers in various types of cancer, their relevance still needs to be established and verified for breast cancer. Recently, recurrent estrogen receptor alpha (ESR1) fusion genes have been identified as putative endocrine resistance markers, but their predictive value for response to endocrine therapy has not yet been independently validated. Here we studied the presence of fusions of ESR1 exon 2 with exons 1 to 11 of CCDC170, resulting in constitutively activated CCDC170, of ESR1 exon 4 with AKAP12, a putative tumor-suppressor gene, and ESR1 exon 1 with C6orf211/ARMT1, a methyltransferase and their association with outcome in a large cohort of ESR1-positive metastatic breast cancer patients.

Methods:

Fusion gene mRNA levels were measured in 307 ESR1-positive primary tumors by quantitative reverse transcriptase PCR (RT-qPCR). If the RT-qPCR generated a positive Cq value, the expected fusion gene product sizes were validated by MultiNA. All patients in this study were hormone-naïve and all experienced a recurrence and subsequently received 1st line endocrine therapy. The association of the presence of ESR1 fusion genes in the primary tumor with disease-free interval (DFI) before, and progression-free survival (PFS) up to 36 months after start with 1st line tamoxifen (n=219) or aromatase inhibitors (n=88), were evaluated.

Results:

74 patients (24.1%) experienced a disease recurrence within one year after removal of the primary tumor (mean DFI; 34.8 months) and 257 patients (83.7%) progressed on 1st-line endocrine therapy within 3 years (mean PFS; 12.5 months).

For the tamoxifen cohort, ESR1-CCDC170 fusion transcripts were found in 84 patients, of which fusions restricted to exon 1, 4, 6, 10 and 11 of CCDC170 were present in 18 patients who all but one progressed within 3 years (mean PFS 9.1 months). Of note, overall, these 18 patients also had a reduced DFI. Similarly for the 7 patients with ESR1-AKAP12 fusions and the one patient with an ESR1- ARMT fusion; all these patients progressed within 3 years. But in contrast to the ESR1-CCDC170 fusion positive patients, these patients had a prolonged DFI {see Table).

Similar observations were made for the smaller AI cohort, though with the - with respect to their predictive value - most relevant ESR1-CCDC170 fusions restricted to exon 4, 5, 6 and 10 of CCDC170 and here we now also observed a decreased DFI for the 7 patients with ESR1-AKAP12 and the 3 patients with ESR1- ARMT1 fusions (see Table).

1st line tamoxifen (n=219)1st line AI (n=88)Fusion% positiveDFI (months) pos/allPFS (months) pos/allFusion% positiveDFI (months) pos/allPFS (months) pos/allE2-CCDC170 Exon 2 to 1/4/6/10/118.2%19.8/27.99.1/12.0E2-CCDC170 Exon 2 to 4/5/6/1012.5%32.4/51.910.5/13.8E2-AKAP123.2%33.1/27.711.9/12.0E2-AKAP128.0%23.6/54.710.3/12.0E2-ARMT10.5%(n=1)(n=1)E2-ARMT13.4%30.3/52.79.3/12.0

Conclusion:

Measuring recurrent ESR1 fusions in primary breast cancer might become a promising tool to identify patients with intrinsic resistance to endocrine therapy or aggressive disease biology. Importantly however, which fusions are relevant appears to depend on the type of endocrine therapy given.

Citation Format: Sieuwerts AM, Vitale SR, Bos M, Sleijfer S, Martens JW. Recurrent ESR1 fusions in primary tumors; a promising predictive factor for outcome to first-line endocrine therapy? [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P5-11-02.

Abstract P1-09-20: An optimized workflow to analyze ESR1 mutations in both circulating cell-free and circulating tumor cell DNA by digital PCR

Background

In metastatic breast cancer (MBC) patients ESR1 mutations (mESR1) in cell-free DNA (cfDNA) have been related to endocrine therapy (ET) resistance. Such mutations might also be detectable in circulating tumor cells (CTCs). Mutation detection in small amounts of cfDNA and in CTCs in a background of leukocytes is highly challenging. The current study evaluated how to reliably investigate mESR1 status in such minute amounts of cfDNA and in DNA from CellSearch-enriched CTCs.

Materials & Methods

Plasma (200 µL) and matched CellSearch-enriched CTC fractions of 7 healthy blood donors (HBD) and 29 MBC patients at baseline and after ET (≥ 5 CTC/7.5 mL) were evaluated. cfDNA was isolated from plasma with the QIAamp CNA kit and CTC-enriched DNA with the AllPrep kit (Qiagen). mESR1 status in both cfDNA and CTC-enriched DNA fractions was compared with or without whole genome amplification (repli-g WGA, Qiagen) or ESR1 target specific amplification. Quantitative PCR (qPCR) for wild type (WT) ESR1 was used to control the number of WT copies loaded into the chips for digital PCR (dPCR) analysis. The variant allele frequencies (VAF) of hotspot mutations for ESR1 (D538G, Y537S, Y537C and Y537N) were evaluated with mutation-specific Taqman assays by chip-based dPCR (QuantStudio 3D, Thermo Fischer Scientific).

Results

To allow inclusion of as many samples as possible, we successfully downscaled the volume of required plasma from 1 mL to 200 µL as this resulted in the same VAF. Sample-type specific thresholds for mESR1 presence were established (2% for the cell-free plasma samples, at which percentage all HBDs were negative, and 0.5% for the CTCs to allow identification of one mutated CTC-specific copy in a background of ~1,000 leukocytes).

WGA was unable to adequately amplify fragmented cfDNA, resulting in a too low DNA yield. However, locus-specific target pre-amplification of a 136 bp fragment covering all 4 different mutations followed by mutant specific dPCR performed well for both cfDNA and CTC DNA, but only if the loading of the pre-amplified product into the dPCR chips was optimized by qPCR for the number of WT ESR1 copies.

The most optimal results for dPCR data interpretation were obtained after: 1. including at least one positive sample in each dPCR session; 2. using a “safe loading window”, 3. loading and reading chips at least twice in QuantStudio 3D ; 4. critically evaluating the contribution by a non-specific “comet effect”; and 5. after loading the data in the software, performing at least two independent data analyses to exclude intra-observer variations.

Summary

Here we describe our workflow to assess mESR1 in a limited amount of plasma cfDNA or CellSearch enriched CTC DNA. This workflow has been successfully used to investigate the mESR1 VAF status in DNA from matched CTC DNA and cfDNA of MBC patients before start of 1st line endocrine therapy and at progression (see also abstract number 851017).

Citation Format: Vitale SR, Sieuwerts AM, Helmijr J, Beije N, van der Vlugt – Daane M, Foekens JA, Sleijfer S, Jansen MPHM, Martens JWM. An optimized workflow to analyze ESR1 mutations in both circulating cell-free and circulating tumor cell DNA by digital PCR [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-09-20.

Mechanisms of activation of the transcription factor Nrf2 by redox stressors, nutrient cues, and energy status and the pathways through which it attenuates degenerative disease

Nuclear factor-erythroid 2 p45-related factor 2 (Nrf2) regulates the basal and stress-inducible expression of a battery of genes encoding key components of the glutathione-based and thioredoxin-based antioxidant systems, as well as aldo-keto reductase, glutathione S-transferase, and

NAD(P)H

quinone oxidoreductase-1 drug-metabolizing isoenzymes along with multidrug-resistance-associated efflux pumps. It therefore plays a pivotal role in both intrinsic resistance and cellular adaptation to reactive oxygen species (ROS) and xenobiotics. Activation of Nrf2 can, however, serve as a double-edged sword because some of the genes it induces may contribute to chemical carcinogenesis by promoting futile redox cycling of polycyclic aromatic hydrocarbon metabolites or confer resistance to chemotherapeutic drugs by increasing the expression of efflux pumps, suggesting its cytoprotective effects will vary in a context-specific fashion. In addition to cytoprotection, Nrf2 also controls genes involved in intermediary metabolism, positively regulating those involved in NADPH generation, purine biosynthesis, and the β-oxidation of fatty acids, while suppressing those involved in lipogenesis and gluconeogenesis. Nrf2 is subject to regulation at multiple levels. Its ability to orchestrate adaptation to oxidants and electrophiles is due principally to stress-stimulated modification of thiols within one of its repressors, the Kelch-like ECH-associated protein 1 (Keap1), which is present in the cullin-3 RING ubiquitin ligase (CRL) complex CRLKeap1. Thus modification of Cys residues in Keap1 blocks CRLKeap1 activity, allowing newly translated Nrf2 to accumulate rapidly and induce its target genes. The ability of Keap1 to repress Nrf2 can be attenuated by p62/sequestosome-1 in a mechanistic target of rapamycin complex 1 (mTORC1)-dependent manner, thereby allowing refeeding after fasting to increase Nrf2-target gene expression. In parallel with repression by Keap1, Nrf2 is also repressed by β-transducin repeat-containing protein (β-TrCP), present in the Skp1-cullin-1-F-box protein (SCF) ubiquitin ligase complex SCFβ-TrCP. The ability of SCFβ-TrCP to suppress Nrf2 activity is itself enhanced by prior phosphorylation of the transcription factor by glycogen synthase kinase-3 (GSK-3) through formation of a DSGIS-containing phosphodegron. However, formation of the phosphodegron in Nrf2 by GSK-3 is inhibited by stimuli that activate protein kinase B (PKB)/Akt. In particular, PKB/Akt activity can be increased by phosphoinositide 3-kinase and mTORC2, thereby providing an explanation of why antioxidant-responsive element-driven genes are induced by growth factors and nutrients. Thus Nrf2 activity is tightly controlled via CRLKeap1 and SCFβ-TrCP by oxidative stress and energy-based signals, allowing it to mediate adaptive responses that restore redox homeostasis and modulate intermediary metabolism. Based on the fact that Nrf2 influences multiple biochemical pathways in both positive and negative ways, it is likely its dose-response curve, in terms of susceptibility to certain degenerative disease, is U-shaped. Specifically, too little Nrf2 activity will lead to loss of cytoprotection, diminished antioxidant capacity, and lowered β-oxidation of fatty acids, while conversely also exhibiting heightened sensitivity to ROS-based signaling that involves receptor tyrosine kinases and apoptosis signal-regulating kinase-1. By contrast, too much Nrf2 activity disturbs the homeostatic balance in favor of reduction, and so may have deleterious consequences including overproduction of reduced glutathione and NADPH, the blunting of ROS-based signal transduction, epithelial cell hyperplasia, and failure of certain cell types to differentiate correctly. We discuss the basis of a putative U-shaped Nrf2 dose-response curve in terms of potentially competing processes relevant to different stages of tumorigenesis.