Abstract PD9-05: Stromal tumor-infiltrating lymphocytes identify early-stage triple-negative breast cancer patients with favorable outcomes at 10-year follow-up in the absence of systemic therapy: a pooled analysis of 1835 patients

Background: The prognostic value of stromal tumor-infiltrating lymphocytes (TILs) as a biomarker for triple-negative breast cancer (TNBC) has been extensively demonstrated in patients (pts) receiving (neo)adjuvant systemic therapy. In addition, several small studies suggest that a subset of pts with early-stage TNBC and high TILs have excellent long-term outcomes, even in the absence of systemic therapy [1-3]. However, data on the absolute risk of TNBC recurrence according to TIL levels in the absence of systemic therapy are limited and critical to inform the design of future systemic therapy de-escalation clinical trials.

Methods: We conducted an individual patient data pooled analysis of 12 international cohorts of pts with TNBC treated with locoregional therapy but no systemic therapy. TNBC was defined as tumors with estrogen and progesterone receptor of < 1% and HER2 negative (IHC 0, 1+ or IHC 2+ and FISH negative) per local evaluation. TILs were locally assessed in hematoxylin & eosin-stained slides according to the International Immuno-Oncology Biomarker Working Group guidelines (www.tilsinbreastcancer.org). We used the Kaplan-Meier method to assess survival outcomes according to prespecified TIL thresholds: 30% and 50%. Confidence intervals (CI) for survival probabilities were calculated using a percentile bootstrap method. The primary endpoint was invasive disease-free survival (iDFS, STEEP 2.0 definition). Key secondary outcomes included recurrence-free survival (RFS), distant disease-free survival (DDFS) and overall survival (OS).

Results: 1,835 pts diagnosed with TNBC between 1982 and 2017 who did not receive systemic therapy were included. The median age at diagnosis was 56 (IQR 38-71). Menopausal status was known in 1,184 women, of whom 78% were post-menopausal. The median tumor size was 2.0 cm (IQR 1.2-2.6). Most pts (87%) had no axillary lymph node involvement (N0). Most tumors were invasive ductal carcinoma (74%) and grade 3 (70%). The median level of TILs was 15% (IQR 5-40). The median duration of follow-up was 30.4 years (95% CI 29.9, 31.1). A total of 950 (52%) iDFS, 828 (45%) RFS, 767 (42%) DDFS events, and 604 (33%) deaths were observed. In multivariable analyses, higher TILs were independently associated with improved iDFS, RFS, DDFS, and OS beyond clinicopathological factors (likelihood ratio p< 10e-6). Each 10% increment in stromal TILs was associated with an 8% (95% CI: 6-11), 10% (95% CI: 7-13), and 13% (95% CI: 10-15) reduction in the risk of experiencing an iDFS, RFS or DDFS event, and with a 12% (95% CI: 9-15) reduction in the risk of death. iDFS, RFS, DDFS and OS rates according to different TIL thresholds and nodal status are shown in the Table. Of note, the RFS estimates (which exclude second non-breast primaries and contralateral breast cancers) were consistently higher than the iDFS counterparts (which include both), consistent with a high rate of contralateral breast cancers and second primary tumors in this cohort. Notably, patients with node-negative—and especially stage I—TNBC with high TILs had excellent survival rates at 10-year follow-up.

Conclusion: TILs are highly prognostic in pts with systemically untreated early-stage TNBC. Pts with pN0 (and especially stage I) TNBC with high TILs exhibited very favorable long-term outcomes even in the absence of systemic therapy. These data define the natural history of TIL-rich TNBC pts and are crucial to identifying the optimal patient population for future chemotherapy and immunotherapy de-escalation clinical trials.

References:

[1] Leon-Ferre et al, 2017, PMID: 28913760

[2] Park et al, 2019, PMID: 31566659

[3] de Jong et al, 2022, PMID: 35353548

Table 5 and 10-year survival endpoints according TIL level, nodal status, and stage

Citation Format: Roberto A. Leon-Ferre, Sarah Flora Jonas, Roberto Salgado, Sherene Loi, Vincent De Jong, Jodi M. Carter, Torsten Nielson, Samuel Leung, Nazia Riaz, Giuseppe Curigliano, Carmen Criscitiello, Vincent Cockenpot, Matteo Lambertini, Vera Suman, Barbro Linderholm, John WM Martens, Carolien HM van Deurzen, Mieke Timmermans, Tatsunori Shimoi, Shu Yazaki, Masayuki Yoshida, Sung-Bae Kim, Hee Jin Lee, Maria Vittoria Dieci, Guillaume Bataillon, Anne Salomon, Fabrice Andre, Marleen Kok, Sabine Linn, Matthew P. Goetz, Stefan Michiels. Stromal tumor-infiltrating lymphocytes identify early-stage triple-negative breast cancer patients with favorable outcomes at 10-year follow-up in the absence of systemic therapy: a pooled analysis of 1835 patients [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD9-05.

Abstract PD6-11: PD6-11 Evaluation of the Sensitivity to Endocrine Therapy Index (SET2,3) in Early Male Breast Cancer: Results from an analysis in the EORTC 10085/TBCRC/BIG/NCTN International Male Breast Cancer Program

Introduction Breast cancer is uncommon in men. Almost all male breast cancers are hormone receptor-positive, HER2-negative, although the pathogenesis is not always attributable to an endocrine condition. A few studies have compared biological characteristics or molecular signatures with breast cancers in women. We sought to evaluate whether hormone receptor-related gene expression is different in cancers from men compared to equivalent cancers from women. SET2,3 index measures non-proliferative hormone receptor-related transcriptional activity in the cancer (SET-ER/PR index) and adjusts this for a Baseline Prognosis Index (BPI) that combines the measurements of tumor and nodal stage with a 4-gene molecular subtype (ESR1, PGR, ERBB2, and AURKA). Methods We received aliquots of total RNA from male patients with breast cancer included in the retrospective cohort study of the EORTC 10085/BCG/TBCRC/BIG/NCTN International Male Breast Cancer Program (NCT01101425). SET2,3 assay was performed using the QuantiGene assay (Thermo Fisher) using bead-based hybridization and laser spectroscopy (Luminex). The statistical analyses were performed by the EORTC statistician. The primary objective of the study was the assessment of the prognostic value of the SET2,3 index score in patients with early-stage hormone receptor-positive, HER2-negative male breast cancer, treated with endocrine therapy. Clinical outcomes (recurrence-free survival – RFS; overall survival – OS) were estimated by Kaplan-Meier curves and secondarily compared using multivariable Cox models adjusted for continuous SET2,3 index, tumor size, nodal status, age, and chemotherapy and radiotherapy use. An exploratory analysis to compare the SET2,3 index scores distribution in female and male breast cancer patients was also performed using results from the same assay performed on cancers from women selected on the same inclusion criteria. Due to the low numbers of male patients treated with neoadjuvant treatment (N=6), this analysis was restricted to patients treated with adjuvant treatment (n=315 male and 660 female). Results Of the 321 male patients with breast cancer analyzed, treated between 1990 and 2010, 211 (65.7%) were categorized as high SET2,3 index score, reflecting a high endocrine activity in the cancer and low risk of recurrence, and 110 patients (34.3%) categorized as being low score, reflecting low endocrine activity and high risk of recurrence. At 5 years, the RFS was 75.0% (95% CI, 67.4-81.1) in the high SET2,3 group versus 60.7% (95% CI, 49.1-70.5) in the low SET2,3 group (HR univariate, 0.49; 95% CI, 0.34-0.70; P< 0.0001). The 5-year OS rate among patients with a high SET2,3 index was 84.3% (95% CI, 45.5-73.8), in contrast of 67.8% (95% CI, 56.6-76.7) in the low SET2,3 group (HR univariate, 0.44; 95% CI, 0.30-0.65; P< 0.0001). SET2,3 was independently prognostic for OS, but not RFS in multivariable Cox models. In patients classified as low SET2,3, the addition of neo/adjuvant chemotherapy to adjuvant endocrine therapy was associated with 5-year OS of 76.0% (95% CI, 59.5-86.4) and in patients who received endocrine therapy alone the 5-year OS was 61.3% (95% CI, 45.5-73.8), an absolute difference of 14.7 percentage points. Overall, we did not observe a difference in the distributions (median, interquartile range) of SET2,3 index between men (2.4, 1.9–2.6) and women (2.3, 2.0–2.7). Conclusion SET2,3 index measurements of endocrine-related transcriptional activity in male patients with breast cancer were not different from measurements in female patients with breast cancer. SET2,3 was prognostic in male breast cancer and our exploratory analysis suggests that chemotherapy might improve the poor prognosis for men with breast cancer that has low SET2,3 index. This study was funded by the Breast Cancer Research Foundation (BCRF).

Citation Format: Danielle B. Zakon, Coralie Poncet, Fatima Cardoso, Neven Anouk, Vicente Valero, Stefan Aebi, Kim Benstead, Oliver Bogler, Lissandra Dal Lago, Judith Fraser, Carmela Caballero, Ingrid A. Hedenfalk, Larissa A. Korde, Barbro Linderholm, John WM Martens, Lavinia P. Middleton, Melissa Murray, Catherine M. Kelly, Cecilia Nilsson, Monika Nowaczyk, Stephanie Peeters, Melanie Beauvois, Peggy Porter, Carolien P. Schroder, Isabel T. Rubio, Kathryn Ruddy, Christi van Asperen, Danielle Van Den Weyngaert, Carolien HM van Deurzen, Elise van Leeuwen-Stok, Joanna M. Vermeij, John MS Bartlett, Antonio C. Wolff, Sharon H. Giordano, W. Fraser Symmans. PD6-11 Evaluation of the Sensitivity to Endocrine Therapy Index (SET2,3) in Early Male Breast Cancer: Results from an analysis in the EORTC 10085/TBCRC/BIG/NCTN International Male Breast Cancer Program [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD6-11.

Abstract P2-03-14: Tumor-agnostic measurement of ctDNA levels in first line ER+, HER2- metastatic breast cancer patients as a marker for survival

INTRODUCTION: Circulating tumor cell (CTC) count and levels of circulating tumor DNA (ctDNA) have proven their individual prognostic value in metastatic breast cancer (MBC). Whereas CTCs can be quantified by enumeration, levels of ctDNA are often expressed as the variant allele frequency of the dominant mutation. The modified fast aneuploidy screening test-sequencing system (mFAST-SeqS) estimates ctDNA-load by measuring chromosomal aneuploidy instead of mutations. The mFAST-SeqS method is cheap and provides a comprehensive overview of the tumor genome without prior knowledge on genomic tumor aberrations. Previously, we showed in a small MBC cohort (n=50), heterogeneous with regard to subtype and line of treatment, that the mFAST-SeqS-derived genome-wide aneuploidy score (GWA-score) was an independent prognostic biomarker (1). Our current aim was to provide evidence for the prognostic value of GWA-score in a homogeneous cohort of estrogen receptor positive (ER+), HER2 negative (HER2-) MBC patients, starting first line treatment with an aromatase inhibitor.

MATERIALS & METHODS: CTCs were enumerated using the CellSearch-system (Menarini) and screened for ctDNA fraction using mFAST-SeqS in ER+, HER2- MBC patients, starting with first line aromatase inhibitors. CTC-count was divided into high (CTChigh) and low (CTClow) using the validated cut-off of 5 CTCs/7.5 ml blood; similarly GWA-score was divided in high (GWAhigh)and low (GWAlow) based on the previously described cut-off of 5 (2). PFS and OS were estimated using Kaplan-Meier. Cox regression was used for uni- and multivariable analysis.

RESULTS: One hundred and thirty-four patients were included in this analysis. Mean age was 68 (range 40-90). Median follow up was 26 months. Sixty-five samples had both scores low and 30 both high, 25 samples were CTChigh/GWAlow and 14 were CTClow/GWAhigh. PFS and OS were not significantly different between CTChigh versus CTClow groups (p=0.07 and p=0.26, median PFS 15 vs 24 months, median OS 45 vs 49 months). However, PFS and OS were significantly different between GWAhigh versus GWAlow groups (p < 0.01 for both, median PFS 11 vs 24 months, median OS 31 vs 51 months). In multivariate analysis, GWA-score was a significant prognostic factor for both PFS and OS while presence of visceral disease was also prognostic for OS (table 1).

CONCLUSIONS: In patients treated with aromatase inhibitors in the first line of treatment, GWA-score was an independent prognostic marker for a worse PFS and OS and may have added value beyond CTC-count.

1. Verschoor, N., et al., Abstract P2-01-17: Circulating tumor cell count and levels of circulating tumor DNA are complementary prognostic biomarkers in metastatic breast cancer - A pilot study. Cancer Research, 2022. 82(4_Supplement): p. P2-01-17-P2-01-17.

2. Belic, J., et al., mFast-SeqS as a Monitoring and Pre-screening Tool for Tumor-Specific Aneuploidy in Plasma DNA. Adv Exp Med Biol, 2016. 924: p. 147-155.

Table 1: Uni- and multivariate Cox regression for PFS and OS

Citation Format: Noortje Verschoor, Jaco Kraan, Vanja de Weerd, Ngoc M Van, Agnes Jager, Stefan Sleijfer, John WM Martens, Saskia M Wilting. Tumor-agnostic measurement of ctDNA levels in first line ER+, HER2- metastatic breast cancer patients as a marker for survival [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-03-14.

Abstract P3-09-18: The association between genomic alterations and body mass index in patients with early breast cancer

Background: High body mass index (BMI) is an established risk factor for developing breast cancer (BC), especially estrogen receptor (ER)-positive, and also has been associated with adverse survival. Still, patients with BC are currently treated independently of their BMI given limited understandings of the association between BC biology and patient adiposity. In this study, using retrospective data retrieved from two large BC studies, we aimed to identify genomic alterations of primary BC that are associated with BMI in the most common histological BC subtype - invasive carcinoma of no special type (NST). Patients, Data and Methods: Clinicopathological and genomic alteration data were retrieved from two study cohorts: METABRIC (Pereira et al. 2016) and ICGC (Nik-Zainal et al. 2016), with BMI recorded at the time of diagnosis and represented as either a continuous variable or a categorical variable of three categories - lean, overweight and obese. Stratification according to ER and HER2 status resulted in two focused subgroups: NST ER+/HER2- (n=392) and NST ER-/HER2- (n=152). Mutations classified as oncogenic using a set of predefined criteria were used to determine gene-level mutation status. Copy number alteration (CNA) calls were distinguished into three event types: amplification, hemizygous deletion and homozygous deletion. We used multivariable Firth’s logistic regression models with the presence of a genomic alteration as the response variable, BMI as the predicting variable of interest, and data cohort (METABRIC vs ICGC), age group (≤50 vs >50) and tumor grade (I & II vs III) as covariates, to assess the associations between BMI and recurrent gene-level genomic alterations, including gene mutations and CNAs. In a similar manner, we performed multivariable linear regression analysis, adjusting for age and tumor grade, to evaluate the associations of BMI with mutational signatures (MS) and tumor mutational burden in the ICGC NST subsets where these data are available. Results: Considering BMI as a categorical variable, we observed in the NST ER+/HER2- subgroup that PIK3CA was significantly less frequently mutated in obese compared to lean patients (33% vs 46%, odds ratio (OR) = 0.57 (95% confidence interval = (0.33, 0.97)), p = .039), while PTEN and TBX3 showed an increased frequency in overweight (6% vs 1%, OR = 4.14 (1.1, 22.34), p = .034) and obese (8% vs 1%, OR = 7.41 (1.82, 70.65), p = .008) patients, respectively. Regression analyses with BMI as a continuous variable revealed an increased prevalence of mutations in CDH1 and TBX3 genes as BMI increases by 1kg/m2 (OR = 1.14 (1.05, 1.24), p = .002, and OR = 1.13 (1.04, 1.22), p = .005, respectively) in patients with NST ER+/HER2- BC. No associations between BMI and oncogenic mutations was observed in the NST ER-/HER2- subgroup. Interrogation of gene-level CNAs in both subgroups demonstrated differences according to BMI in the prevalence of CNAs affecting a number of genes, many of which are known or have been presented with evidence to be involved in regulation of or regulated by hallmark pathways of BC, such as the MAPK/ERK, JAK/STAT and Wnt/β-catenin signaling pathways. We report a strong positive association between the single-base substitution signature 1 (SBS1), an age-correlated MS, and both continuous (coefficient (coef) = 18.3 (7.7, 28.9), p < .001) and categorical BMI (obese vs lean, coef = 336.3 (187.9, 484.8), p < .001) in the ICGC NST ER+/HER2- subgroup. Conclusion: This exploratory retrospective study suggests that the genomic profiles of primary BC may differ according to BMI. Clinical implications of these differences, especially the decreased prevalence of PIK3CA mutations in obese patients in the context of alpelisib, warrant further investigation. These results however indicate that patient adiposity should be taken into account in the era of personalized medicine.

Citation Format: Ha-Linh Nguyen, Tatjana Geukens, Marion Maetens, Karen Van Baelen, Maxim De Schepper, Sophia Leduc, Edoardo Isnaldi, Sam Aparicio, Ake Borg, Jane Brock, Annegien Broeks, Carlos Caldas, Andrew Green, Hazem Khout, Eyfjörð Jórunn, Stian Knappskog, Savitri Krishnamurthy, Sunil Lakhani, Anita Langerod, John WM Martens, Leigh Murphy, Serena Nik-Zainal, Colin Purdie, Emad Rakha, Andrea Richardson, Anne Salomon, Peter Simpson, Christos Sotiriou, Paul Span, Benita Kiat-Tee Tan, Alastair Thompson, Stefania Tommasi, Marc Van de Vijver, Steven Van Laere, Alain Viari, Giuseppe Floris, Elia Biganzoli, François Richard, Christine Desmedt. The association between genomic alterations and body mass index in patients with early breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-09-18.

Abstract P2-01-17: Circulating tumor cell count and levels of circulating tumor DNA are complementary prognostic biomarkers in metastatic breast cancer - A pilot study

Background and aim Minimally invasive liquid biopsies, usually referring to the analysis of tumor-derived material such as circulating tumor cells (CTC) and circulating tumor DNA (ctDNA), have already proven their individual prognostic value in metastatic breast cancer. Whereas CTCs can be quantified by enumeration, levels of ctDNA are often expressed as the variant allele frequency of the dominant mutation, determined by rather costly targeted next generation sequencing. The modified fast aneuploidy screening test-sequencing system (mFAST-SeqS) represents a fast and cost-effective assay to estimate the fraction of ctDNA by measuring chromosomal aneuploidy instead of mutations. Next to the low costs (EUR 50, USD 60) additional advantages of the mFAST-SeqS method include the independency of mutational status of the tumor and the comprehensive overview of the tumor genome. Our aim was to investigate the potential concordance and complementarity between CTC-count and the mFAST-SeqS-based genome-wide aneuploidy score (GWA score). Material and methods Consecutive blood samples obtained from ER positive, Her2 negative metastatic breast cancer patients, starting a new line of therapy, (n=23) were enumerated for CTCs using the CellSearch-system (Menarini Silicon Biosystems, Bologna, Italy) and screened for the percentage of ctDNA using mFAST-SeqS. This method provides a GWA-score by amplification of long interspaced nuclear elements (LINE-1 elements) throughout the genome and calculating the overall deviation from the average profile in normal controls. Spearman correlation between CTC-count and GWA-score was calculated. For survival analysis, CTC-count was divided into high (CTChigh) and low (CTClow) using 5 CTCs/7.5 ml blood as the cut-off as before; similarly GWA-score was divided in high (GWAhigh)and low (GWAlow) based on the previously described cut-off of 5. Kaplan-Meier analysis was performed to assess overall survival (OS) in subgroups. Results Mean patient age was 58 (range 42-78). Median follow up was 15 months (range 0-37). Median number of previous treatment lines of patients was 2 (range 0-11). Median CTC-count was 22 (range 0-4438) and median GWA-score was 3.94 (range 0.87-114.31). The Spearman correlation coefficient between CTC count and GWA-score was 0.44 (p=0.02). 3 out of 20 patients were alive at end of follow-up. OS was significantly different in the CTChigh group versus the CTClow group (p=0.01, log-rank test, median OS 31 and 7 months, respectively), as well as in the GWAhigh versus the GWAlow group (p =0.01, log-rank test, median OS 27 and 7 months). There was concordance in 12 out of 23 samples (52.2%). 4 samples had both scores low and 8 both high, 9 samples were CTChigh/GWAlow and 2 were CTClow/GWAhigh. OS was significantly different in these groups (p < 0.01, log-rank test), with a median OS of 6 months in the group with both scores high, a median OS of 18 months for the cases with a discordant score and median OS not reached in the group with both scores low.Conclusions Our pilot study confirmed that both CTC-count and mFAST-SeqS GWA-score are prognostic and indicate that a combination of these measurements may yield complementary prognostic value. It should be noted however that the sample size was limited thus far. Our current preliminary results will be extended to 98 cases, results of which will be presented at the meeting.

Citation Format: Noraly Verschoor, Elisabeth M Jongbloed, Jaco Kraan, Vanja de Weerd, Ngoc M Van, Agnes Jager, Stefan Sleijfer, Saskia M Wilting, John WM Martens. Circulating tumor cell count and levels of circulating tumor DNA are complementary prognostic biomarkers in metastatic breast cancer - A pilot study [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-01-17.

Abstract P3-03-03: Inflammatory breast cancer exhibits amplification and transcriptional activation of MYC in conjunction with NOTCH and TGFβ signaling

Inflammatory breast cancer (IBC) is an aggressive and poorly characterized breast cancer subtype with few targets available for molecular therapy. Several attempts aimed at characterizing the disease at the genomic, transcriptomic and proteomic level. Together, these studies suggest that MYC is central to the biology of IBC. Here, we analyzed data sets from patient samples and preclinical models to corroborate this hypothesis.

Genomic and transcriptomic profiles were obtained using next-generation sequencing and Affymetrix GeneChip analysis on a series of 101 and 137 samples from patients with IBC. In addition, non-IBC (nIBC) control samples were included from our own repositories (N=252) as well as from publicly available data sets (i.e. TCGA and METABRIC). Finally, RNA-sequencing and peptide phosphorylation data from preclinical IBC and nIBC models, both with and without TGFβ treatment, were explored.

Apart from TP53 and ERBB2, MYC is the 3rd most frequently mutated gene with single nucleotide variants, indels and amplifications found in 22% of 101 patients. Furthermore, MYC mutations are mutually exclusive with alterations in the NOTCH genes (i.e. NOTCH1, -2, -3, and -4 and CREBBP). At the gene expression level, a MYC activation score is elevated in IBC as compare to nIBC and correlates with a NOTCH activation signature. Genes overexpressed in IBC are enriched for various sets of MYC target genes and are associated with MYC amplifications in TCGA and METABRIC samples. In preclinical models, MYC target genes are particularly responsive to TGFβ treatment in IBC cells but not in nIBC cells and analysis of peptide phosphorylation patterns suggest this interaction may be regulated via PTK2B.

The present data suggest that MYC could be an important driver of IBC biology, which corroborates with the recent observation that MYC is an important hub in the signal transduction network of SUM149 and -190 cells. Furthermore, our data reveal that MYC activation is linked to NOCTH and TGFβ signaling. In earlier studies it was demonstrated that lymphovascular tumor emboli in the Mary-X mouse model of IBC exhibit NOTCH3 addition with downstream MYC overexpression, indicating that NOTCH/MYC signaling could be crucial for metastatic progression in IBC. In this context, it should be noted that an allele associated with metastatic risk in IBC patients resides at the 8q24 locus that harbors the MYC gene.

Citation Format: Charlotte Rypens, François Bertucci, Patrice Viens, John WM Martens, Marcel Smid, Carolien Schröder, Naoto T Ueno, Massimo Cristofanilli, Piet Dirix, Peter Vermeulen, Luc Dirix, Steven Van Laere. Inflammatory breast cancer exhibits amplification and transcriptional activation of MYC in conjunction with NOTCH and TGFβ signaling [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P3-03-03.

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.

Body mass index and breast cancer survival: a Mendelian randomization analysis

Background

There is increasing evidence that elevated body mass index (BMI) is associated with reduced survival for women with breast cancer. However, the underlying reasons remain unclear. We conducted a Mendelian randomization analysis to investigate a possible causal role of BMI in survival from breast cancer.

Methods

We used individual-level data from six large breast cancer case-cohorts including a total of 36 210 individuals (2475 events) of European ancestry. We created a BMI genetic risk score (GRS) based on genotypes at 94 known BMI-associated genetic variants. Association between the BMI genetic score and breast cancer survival was analysed by Cox regression for each study separately. Study-specific hazard ratios were pooled using fixed-effect meta-analysis.

Results

BMI genetic score was found to be associated with reduced breast cancer-specific survival for estrogen receptor (ER)-positive cases [hazard ratio (HR) = 1.11, per one-unit increment of GRS, 95% confidence interval (CI) 1.01-1.22, P = 0.03). We observed no association for ER-negative cases (HR = 1.00, per one-unit increment of GRS, 95% CI 0.89-1.13, P = 0.95).

Conclusions

Our findings suggest a causal effect of increased BMI on reduced breast cancer survival for ER-positive breast cancer. There is no evidence of a causal effect of higher BMI on survival for ER-negative breast cancer cases.

High-throughput automated scoring of Ki67 in breast cancer tissue microarrays from the Breast Cancer Association Consortium

Automated methods are needed to facilitate high-throughput and reproducible scoring of Ki67 and other markers in breast cancer tissue microarrays (TMAs) in large-scale studies. To address this need, we developed an automated protocol for Ki67 scoring and evaluated its performance in studies from the Breast Cancer Association Consortium. We utilized 166 TMAs containing 16,953 tumour cores representing 9,059 breast cancer cases, from 13 studies, with information on other clinical and pathological characteristics. TMAs were stained for Ki67 using standard immunohistochemical procedures, and scanned and digitized using the Ariol system. An automated algorithm was developed for the scoring of Ki67, and scores were compared to computer assisted visual (CAV) scores in a subset of 15 TMAs in a training set. We also assessed the correlation between automated Ki67 scores and other clinical and pathological characteristics. Overall, we observed good discriminatory accuracy (AUC = 85%) and good agreement (kappa = 0.64) between the automated and CAV scoring methods in the training set. The performance of the automated method varied by TMA (kappa range= 0.37-0.87) and study (kappa range = 0.39-0.69). The automated method performed better in satisfactory cores (kappa = 0.68) than suboptimal (kappa = 0.51) cores (p-value for comparison = 0.005); and among cores with higher total nuclei counted by the machine (4,000-4,500 cells: kappa = 0.78) than those with lower counts (50-500 cells: kappa = 0.41; p-value = 0.010). Among the 9,059 cases in this study, the correlations between automated Ki67 and clinical and pathological characteristics were found to be in the expected directions. Our findings indicate that automated scoring of Ki67 can be an efficient method to obtain good quality data across large numbers of TMAs from multicentre studies. However, robust algorithm development and rigorous pre- and post-analytical quality control procedures are necessary in order to ensure satisfactory performance.

SIAH2 protein expression in breast cancer is inversely related with ER status and outcome to tamoxifen therapy

Our previous study demonstrated that high mRNA levels for Seven in Absentia Homolog 2 (SIAH2) correlated with high Estrogen Receptor (ER) mRNA levels and with longer progression-free survival (PFS) after first-line tamoxifen. Others showed high SIAH2 protein levels in ER-negative breast cancer associated with an unfavorable relapse-free survival. In the current study, we investigated SIAH2 protein expression to clarify the discrepancy between protein and mRNA findings and to determine its diagnostic value in breast cancer patients. Tissue microarrays (TMAs) containing core specimens of primary breast tumors were immunohistochemically stained for SIAH2 protein. The TMAs analyzed a cohort of 746 patients with primary breast cancer (PBC) and a cohort of 245 patients with ER-positive metastatic breast cancer (MBC) treated with first-line tamoxifen. SIAH2 staining was scored for intensity and proportion of positive tumor cells and evaluated for its relationship with metastasis-free survival (MFS) and PFS. Multivariate survival analyses included traditional prognostic or predictive factors, respectively. The PBC-cohort had 263 patients with high SIAH2 protein expression and decreased expression of ER protein and mRNA levels (P = 0.005 and P = 0.003, respectively). High SIAH2 levels correlated with significant unfavorable MFS in lymph node negative, ER-positive breast cancer patients. The MBC-cohort had 86 patients with increased SIAH2 protein expression. High SIAH2 expression was associated with an unfavorable PFS after first-line tamoxifen in multivariate analyses (HR = 1.45; 95% CI, 1.07-1.96; P = 0.015). In conclusion, SIAH2 protein expression is especially observed in ER-negative tumors. Its prognostic value in breast cancer does not add to current prognostic markers. The proportion of SIAH2-positive cells can be used as biomarker to predict tamoxifen treatment failure in MBC patients.

Common germline polymorphisms associated with breast cancer-specific survival

INTRODUCTION

Previous studies have identified common germline variants nominally associated with breast cancer survival. These associations have not been widely replicated in further studies. The purpose of this study was to evaluate the association of previously reported SNPs with breast cancer-specific survival using data from a pooled analysis of eight breast cancer survival genome-wide association studies (GWAS) from the Breast Cancer Association Consortium.

METHODS

A literature review was conducted of all previously published associations between common germline variants and three survival outcomes: breast cancer-specific survival, overall survival and disease-free survival. All associations that reached the nominal significance level of P value <0.05 were included. Single nucleotide polymorphisms that had been previously reported as nominally associated with at least one survival outcome were evaluated in the pooled analysis of over 37,000 breast cancer cases for association with breast cancer-specific survival. Previous associations were evaluated using a one-sided test based on the reported direction of effect.

RESULTS

Fifty-six variants from 45 previous publications were evaluated in the meta-analysis. Fifty-four of these were evaluated in the full set of 37,954 breast cancer cases with 2,900 events and the two additional variants were evaluated in a reduced sample size of 30,000 samples in order to ensure independence from the previously published studies. Five variants reached nominal significance (P <0.05) in the pooled GWAS data compared to 2.8 expected under the null hypothesis. Seven additional variants were associated (P <0.05) with ER-positive disease.

CONCLUSIONS

Although no variants reached genome-wide significance (P <5 x 10(-8)), these results suggest that there is some evidence of association between candidate common germline variants and breast cancer prognosis. Larger studies from multinational collaborations are necessary to increase the power to detect associations, between common variants and prognosis, at more stringent significance levels.

Refined histopathological predictors of BRCA1 and BRCA2 mutation status: a large-scale analysis of breast cancer characteristics from the BCAC, CIMBA, and ENIGMA consortia

INTRODUCTION

The distribution of histopathological features of invasive breast tumors in BRCA1 or BRCA2 germline mutation carriers differs from that of individuals with no known mutation. Histopathological features thus have utility for mutation prediction, including statistical modeling to assess pathogenicity of BRCA1 or BRCA2 variants of uncertain clinical significance. We analyzed large pathology datasets accrued by the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA) and the Breast Cancer Association Consortium (BCAC) to reassess histopathological predictors of BRCA1 and BRCA2 mutation status, and provide robust likelihood ratio (LR) estimates for statistical modeling.

METHODS

Selection criteria for study/center inclusion were estrogen receptor (ER) status or grade data available for invasive breast cancer diagnosed younger than 70 years. The dataset included 4,477 BRCA1 mutation carriers, 2,565 BRCA2 mutation carriers, and 47,565 BCAC breast cancer cases. Country-stratified estimates of the likelihood of mutation status by histopathological markers were derived using a Mantel-Haenszel approach.

RESULTS

ER-positive phenotype negatively predicted BRCA1 mutation status, irrespective of grade (LRs from 0.08 to 0.90). ER-negative grade 3 histopathology was more predictive of positive BRCA1 mutation status in women 50 years or older (LR = 4.13 (3.70 to 4.62)) versus younger than 50 years (LR = 3.16 (2.96 to 3.37)). For BRCA2, ER-positive grade 3 phenotype modestly predicted positive mutation status irrespective of age (LR = 1.7-fold), whereas ER-negative grade 3 features modestly predicted positive mutation status at 50 years or older (LR = 1.54 (1.27 to 1.88)). Triple-negative tumor status was highly predictive of BRCA1 mutation status for women younger than 50 years (LR = 3.73 (3.43 to 4.05)) and 50 years or older (LR = 4.41 (3.86 to 5.04)), and modestly predictive of positive BRCA2 mutation status in women 50 years or older (LR = 1.79 (1.42 to 2.24)).

CONCLUSIONS

These results refine likelihood-ratio estimates for predicting BRCA1 and BRCA2 mutation status by using commonly measured histopathological features. Age at diagnosis is an important variable for most analyses, and grade is more informative than ER status for BRCA2 mutation carrier prediction. The estimates will improve BRCA1 and BRCA2 variant classification and inform patient mutation testing and clinical management.

Abstract 1611: 4-protein signature predicts outcome to tamoxifen treatment in estrogen receptor positive recurrent breast cancer

Tamoxifen is one of the most frequently used drugs in the treatment of estrogen receptor positive breast cancer. Although tamoxifen significantly increases patient survival in the adjuvant setting, a major factor that decreases its efficacy in the recurrent setting is drug resistance. The aim of our study is to identify a protein signature predicting outcome of tamoxifen treatment using high resolution mass spectrometry.

A total of 112 snap frozen breast tumor tissues were gathered from patients that had received tamoxifen as first line treatment upon recurrence. Samples were divided into a discovery (n= 56; Erasmus Medical Center) and validation sets (n=56; multi-center cohort). Based on progression of disease from start of tamoxifen therapy, patients were categorized having either Good (time-to-progression; ttp&gt;6 months) or Poor (ttp&lt;6 months) outcome. Approximately 4,000 tumor cells (∼200ng protein) were microdissected from each tissue, which were lysed and subsequently trypsin-digested. MS analyses were performed on a nano-liquid chromatography LTQ-Orbitrap mass spectrometer. Protein identification and quantitation were performed through MaxQuant. Significantly differentially abundant proteins (p&lt;0.05) were filtered through multivariate analysis and used to build a predictor for tamoxifen outcome.

A total of 2741 proteins were identified in both datasets. Comparative proteome analysis showed differential expression of 99 proteins in the discovery set. A subset of 4 proteins (PDCD4, OCIAD1, G3BP2, and CGN) derived from the multivariate model was selected to develop a predictor for tamoxifen outcome. The 4 protein abundances in the discovery samples were used to build a receiver operating characteristic curve, in which Youden J was selected as grouping cutoff. Group prediction was tested in the validation set through log rank test, which resulted in a significant ttp difference (p=0.004; HR=2.33, 95% CI [1.30-4.16]) between Good and Poor outcome. Our signature significantly predicts Poor outcome patients with 86.7% sensitivity, 41.46% specificity, 35.1% PPV, and 89.5% NPV in the multi-center cohort. OCIAD1, PDCD4, and CGN were significantly enriched in patients with Good outcome, while G3BP2 was more abundant in patients with Poor outcome. We are currently validating these results by immunohistochemistry in a large independent cohort. In addition, we are developing a targeted, multiplexed, quantitative MS-based assay for larger scale clinical validation.

Our 4-protein signature significantly predicts outcome to tamoxifen treatment for recurrent breast cancer. Large scale clinical validation will enable more tailored treatment of breast cancer patients with advanced ER+ disease. In addition, our findings may help elucidate the mechanisms underlying endocrine therapy resistance in recurrent breast cancer.

Citation Format: Tommaso De Marchi, NingQing Liu, Mila Tjoa, Christoph Stingl, Marcel Smid, Maxime P. Look, Mieke A. Timmermans, Rene BH Braakman, Mark Opdam, Sabine Linn, Paul Span, Fred CGJ Sweep, John WM Martens, Theo M. Luider, John A. Foekens, Arzu Umar. 4-protein signature predicts outcome to tamoxifen treatment in estrogen receptor positive recurrent breast cancer. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 1611. doi:10.1158/1538-7445.AM2014-1611

Abstract S6-05: High levels of APOBEC3B, a DNA deaminase and an enzymatic source of C-to-T transitions, are a validated marker of poor outcome in estrogen receptor-positive breast cancer

Two recent observations have connected the innate immune DNA cytosine deaminase APOBEC3B to the genetic evolution of breast cancer. First, APOBEC3B was shown to be up-regulated in the majority of breast cancers, and, in breast cancer cell lines, its activity was causally linked to a doubling of the number of C-to-T transitions over time and to a delay in cell cycle progression (1). Second, sequencing of the complete genome of 21 breast cancers independently suggested that APOBEC deaminase activity could be responsible for 2 of 5 mutational imprints identified, which involved clustered (also called kataegis) and dispersed C-to-T transition mutations in the context of 5’TC dinucleotide motifs (2).

In the current study, we addressed a possible association of APOBEC3B expression with outcome in clinical breast cancer. For this we measured using real-time RT-PCR APOBEC3B mRNA levels in 1,491 primary invasive breast cancers and correlated these levels with disease-free survival (DFS), metastasis-free survival (MFS) and overall survival (OS) using univariate and multivariable Cox regression analysis. In addition, we independently validated our findings in available gene expression datasets with appropriate follow-up.

In univariate analyses including all patients, increasing levels of APOBEC3B mRNA analyzed as a continuous variable were significantly associated with shorter DFS, MFS and OS (Hazard Ratio [HR] = 1.29, 1.31 and 1.36, respectively, all P&lt;0.001). To determine the relation of APOBEC3B mRNA expression with the natural course of the disease without the potential confounding effects of systemic adjuvant therapy, we restricted our next analyses to MFS in 829 patients with lymph node-negative disease who had not received any (neo)adjuvant systemic therapy. This analysis showed that APOBEC3B mRNA expression was, in univariate, and in multivariable analysis, including the traditional prognostic factors (age, menopausal status, tumor size, grade and steroid hormone receptors), a marker of pure prognosis specifically in patients with estrogen receptor-positive (ER+) disease (univariate HR = 1.30; P = 0.003; multivariate HR = 1.22, P = 0.042).

To substantiate and validate our findings, we analysed 4 independent available datasets containing in total 5,760 breast cancer cases in which APOBEC3B mRNA expression was measured by probes on microarrays and found that higher APOBEC3B mRNA expression (dichotomised by mean) was significantly associated with poor outcome in all 4 cohorts ([Metabric, 1,491 ER+ cases, HR = 1.82; P&lt;0.001], [Affymetrix compiled dataset-1, 2,407 cases, HR = 2.22; P = 0.001], and [BIG 1-98; 1,207 cases, HR = 2.13; P&lt;0.001 of late recurrence&gt;5 years], and [Affymetrix dataset-2, 643 ER+ cases, HR = 2.04; P = 0.001]).

Altogether, our analyses show that APOBEC3B mRNA - and as a result likely DNA deamination – is a validated predictor of poor outcome in breast cancer, supporting the notion that APOBEC3B is a potentially interesting clinical target for therapeutic intervention to prevent breast cancer progression and metastasis, particularly in ER+ disease.

1. Burns, M.B. et al. Nature 494, 366-70 (2013); 2. Nik-Zainal, S. et al. Cell 149, 979-93 (2012).

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr S6-05.

Abstract P4-09-03: Comparative proteomic analysis identifies a 15-protein signature related to clinical outcome of triple negative breast cancer

Withdrawn by Author

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P4-09-03.

P5-14-14: The Presence of a Fibrotic Focus Adds Significant Prognostic Information to the Prognostic 76-Gene Relapse Score in Lymph Node Negative Breast Cancer

Introduction: The fibrotic focus (FF) is a practical, easily assessable and reproducible integrative histological prognostic parameter in breast cancer. Its prognostic value has been shown before (Van den Eynden et al. Histopathology 2007). In this study we investigated whether the assessment of the FF adds prognostic information to the relapse score based on gene expression analysis of 76 genes as previously described (Wang et al. Lancet 2005).

Materials and Methods: All patients of 2 previous prognostic breast cancer gene expression studies for whom FFPE slides of the tumor were available (Wang et al. Lancet 2005 and Yu et al. BMC Cancer 2007) were selected, leading to a study population of 176 lymph node negative breast cancer patients. The presence and size (&lt;1/3 or &gt;1/3 of tumor area) of a FF were assessed on standard HE slides. These data were compared to the 76-gene relapse score, to standard clinicopathological variables and to metastasis-free survival.

Results: A small and large FF were found in 31 (17.6%) and 20 (11.4%) of patients, respectively. In 120 (68.2%) patients there was no FF and in 5 patients the presence of a FF could not be assessed due to insufficient FFPE material. 64 (36.4%) and 112 (63.6%) patients had respectively a good and poor prognostic 76-gene relapse score. There was a significant correlation between the presence of a FF and a poor 76-gene relapse score, 18 of 20 patients with a large FF had a poor relapse score (p = 0.03). Patients with a tumor with a FF and especially with a large FF had a significantly reduced metastasis free survival (Log rank p&lt;0.001). The same was true for patients with a poor 76-gene relapse score (Log rank p&lt;0.001). When only patients with a poor relapse score were taken into account, patients with a tumor with a large FF had a significantly decreased metastasis-free survival compared to patients without a FF or with a small FF (Log rank p=0.005). In patients with a good relapse score, the number of patients with a FF was too small for a separate analysis. In a multivariate Cox regression model for metastasis-free survival including age, ER and PR status, T stage, the FF and the 76-gene relapse score status, the FF (OR 1.5, p=0.02) and the relapse score status (OR 3.4, p = 0.001) were significant independent prognostic factors. Comparable results were found if the presence of a FF was dichotomized in large FF versus no or a small FF.

Conclusion: The assessment of the presence and size of a FF adds independent significant prognostic information to the prognostic 76-gene expression signature, especially in selecting a subgroup of patients with a very poor prognosis. Since the assessment of the FF is practical, easy, reproducible and cheap it should be considered to become part of the standard pathological examination of breast cancer resection specimens.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P5-14-14.

High miR-26a and low CDC2 levels associate with decreased EZH2 expression and with favorable outcome on tamoxifen in metastatic breast cancer

For patients with metastatic breast cancer, we previously described that increased EZH2 expression levels were associated with an adverse outcome to tamoxifen therapy. Main objective of the present study is to investigate miR-26a and miR-101 levels, which both target EZH2, for their association with molecular pathways and with efficacy of tamoxifen as first-line monotherapy for metastatic breast cancer. Expression levels were measured using quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) in primary breast cancer specimens of 235 estrogen receptor-α (ER)-positive patients. Pathway analysis was performed on microarray data available for 65 of these tumors. Logistic regression and Cox uni- and multivariate analysis were performed to relate expression levels with clinical benefit and time to progression (TTP). Increasing levels of miR-26a were significantly (P < 0.005) associated with both clinical benefit and prolonged TTP, whereas miR-101 was not. Cell cycle regulation and CCNE1 and CDC2 were the only significant overlapping pathway and genes differentially expressed between tumors with high and low levels of miR-26a and EZH2, respectively. In addition, increasing mRNA levels of CCNE1 (P < 0.05) and CDC2 (P < 0.001) were related to poor outcome. Multivariate analysis revealed miR-26a and CDC2 as an optimal set of markers associated with outcome on tamoxifen therapy, independently of traditional predictive factors. To summarize, only miR-26a levels are related with treatment outcome. Cell cycle regulation is the only overlapping pathway linked to miR-26a and EZH2 levels. Low mRNA levels of EZH2, CCNE1, and CDC2, and high levels of miR-26a are associated with favorable outcome on tamoxifen.

Insecticidal activity of a bacterial crystal protein expressed by a recombinant baculovirus in insect cells

Baculoviruses are insect pathogens with a relatively slow speed of action, and this has limited their use as control agents of insect pests. Introduction into baculoviruses of genes which code for proteins interfering specifically with insect metabolism or metamorphosis, such as toxins, hormones, and enzymes, may enhance the pathogenicity of these viruses. The complete insecticidal crystal protein gene cryIA(b) of Bacillus thuringiensis subsp. aizawai 7.21 was engineered into the nuclear polyhedrosis virus of Autographa californica (AcNPV) in place of the polyhedrin gene. In infected Spodoptera frugiperda cells, the cryIA(b) gene was expressed at a high level without interference with AcNPV production. The crystal protein was found in the cytoplasm of S. frugiperda cells, mainly as large crystals with an ultrastructure similar to that of B. thuringiensis crystals. Infected-cell extracts inhibited feeding of the large cabbage white Pieris brassicae. The toxicity of the crystal protein expressed by AcNPV recombinants was comparable with that of the crystal protein expressed by a corresponding Escherichia coli recombinant.

Abstract SY01-04: High-end proteomics enables identification of breast cancer therapy resistance predictive proteins

A spectrum of treatment options is available for breast cancer patients, the choice of which is mainly dependent on factors such as steroid hormone receptor and HER2/neu status, age, menopausal status, tumor size, grade, and lymph node status. Tamoxifen is an anti-estrogenic agent that has been widely and successfully used in the treatment of breast cancer over the past decades [1]. Tamoxifen inhibits the estrogen receptor α (ERα), which is expressed in approximately 70% of all breast tumors. When diagnosed at an early stage, breast cancer can be effectively treated with adjuvant tamoxifen. Next to endocrine treatment, adjuvant chemotherapy is often administered as well to improve survival. However, this success rate drops severely in advanced disease due to therapy-resistance. Approximately 50% of patients with metastatic breast cancer have no benefit from tamoxifen due to intrinsic resistance. While the other half of patients initially responds well to therapy and shows objective response (OR), eventually almost all patients develop progressive disease (PD) due to acquired resistance [2, 3]. First-line chemotherapy is more frequently used on ER- tumors, and on ER+ tumors where endocrine treatment failed or was no option to begin with. Despite the proven success of chemotherapy in primary tumors, in the advanced setting therapy-resistance eventually occurs. In general, patients with advanced disease only have a 5-year survival of approximately 20%.

The major issue in the treatment of breast cancer is that currently available clinical and biochemical markers can insufficiently predict the type of therapy response. Therefore, identification of new protein targets that can better predict therapy efficacy, and ultimately improve patient cure rate is crucial and a major focus of our research.

For our biomarker discovery studies we use primary breast tumor tissues from patients, of which we have long term clinical follow up. In addition, we perform laser capture microdissection on these heterogenic tissues to obtain relatively pure populations of tumor epithelial and stromal cells. By doing, so we end up with minute amounts of material, typically less than 1 μg protein, to be used in our comparative proteomics studies. This requires the use of robust proteomics platforms that offer exceptional sensitivity and dynamic range of detection in a high-throughput, accurate, and reproducible fashion.

One such technological platform is FTICR MS in combination with nLC, which has the possibility to separate in one single analysis large numbers of peptides (&gt;10³) with extremely high mass resolving power (&gt;100,000), and mass measurement accuracy (~1 ppm), with a dynamic range up to 10exp4, and a high peak capacity offered by nLC [4]. The nLC-FTICR platform in combination with the accurate mass and time (AMT) tag approach has allowed for high-throughput and sensitive studies of complex protein mixtures [5]. This approach initially utilizes conventional LC-MS/MS measurements to establish a reference database of AMT tags specific for a particular proteome sample (e.g. breast cancer tissue). Each tag consists of a theoretical mass calculated from the peptide sequence, an LC normalized elution time value, and an indicator of quality. The AMT tag database serves as a “look-up table” for identifying peptides in subsequent quantitative LC-MS analyses. Substituting routine LC-MS/MS analyses (shotgun approach) with LC-FTICR MS analyses (AMT tag approach) significantly increases overall throughput and sensitivity, while reducing sample requirements [6]. Additionally, quantitative intensity information related to the protein's abundance can be discerned from these MS analyses.

We have used the AMT tag approach for the identification of a putative tamoxifen therapy-resistance protein profile. In this study, primary tumor tissues responsive (n=27) and resistant (n=28) to first-line tamoxifen treatment were subjected to laser capture microdissection, and ~4,000 tumor cells were collected per tissue. nLC-FTICR MS was performed for protein biomarker discovery, and putative markers were verified through targeted MS/MS using Orbitrap. Differential abundance of our top candidate, EMMPRIN, was validated in an independent sample set using tissue microarray (TMA). High EMMPRIN levels were found in therapy-resistant tumors, which correlated with poor outcome on first-line tamoxifen treatment [7].

We are currently in the process of validating other putative profile proteins by means of immunohistochemistry using our TMA in cases where suitable antibodies are available. For other proteins, we are developing quantitative MS-based assays using multiple reaction monitoring (MRM). In addition, we are applying a similar comparative proteomics strategy for the identification of chemotherapy-resistance associated markers proteins.

In order to bring these validated marker proteins one step closer to clinical applicability, quantitative MRM assays may prove to be an invaluable tool for large-scale, multi-center validation studies.

[1] EBCTCG, Effects of chemotherapy and hormonal therapy for early breast cancer on recurrence and 15-year survival: an overview of the randomised trials. Lancet 2005, 365, 1687-1717.

[2] Clarke, R., Liu, M. C., Bouker, K. B., Gu, Z. et al., Antiestrogen resistance in breast cancer and the role of estrogen receptor signaling. Oncogene 2003, 22, 7316-7339.

[3] Massarweh, S., Schiff, R., Resistance to endocrine therapy in breast cancer: exploiting estrogen receptor/growth factor signaling crosstalk. Endocr. Relat. Cancer. 2006, 13 Suppl 1, S15-24.

[4] Qian, W. J., Camp, D. G., 2nd, Smith, R. D., High-throughput proteomics using Fourier transform ion cyclotron resonance mass spectrometry. Expert. Rev. Proteomics. 2004, 1, 87-95.

[5] Pasa-Tolic, L., Masselon, C., Barry, R. C., Shen, Y. et al., Proteomic analyses using an accurate mass and time tag strategy. Biotechniques 2004, 37, 621-624, 626-633, 636 passim.

[6] Umar, A., Luider, T. M., Foekens, J. A., Pasa-Tolic, L., NanoLC-FT-ICR MS improves proteome coverage attainable for approximately 3000 laser-microdissected breast carcinoma cells. Proteomics 2007, 7, 323-329.

[7] Umar, A., Kang, H., Timmermans, A. M., Look, M. P. et al., Identification of a putative protein profile associated with tamoxifen therapy resistance in breast cancer. Mol Cell Proteomics 2009, 8, 1278-1294.

Citation Format: Ljiljana Pasa-tolic, Theo M. Luider, John WM Martens, John A. Foekens, Arzu Umar. High-end proteomics enables identification of breast cancer therapy resistance predictive proteins [abstract]. In: Proceedings of the AACR 101st Annual Meeting 2010; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr SY01-04

DNA methylation as a biomarker in breast cancer

In cancer, epigenetic changes such as covalent addition of methyl groups to the genomic DNA itself are more prominent than genetic changes. Cytosine–phosphate–guanosine (CpG) methylation negatively affects gene transcription of an adjacent gene. It is thought that DNA methylation significantly contributes to all hallmarks of cancer. Next to being a potential therapy target, DNA methylation is an emerging field of biomarkers. Technically, DNA provides a stable and robust analyte that is particularly suitable for clinical applications. Moreover, there are numerous potential human DNA sources that could facilitate integration of methylation tests in clinical practice. In breast cancer, DNA methylation has shown promise as a potential biomarker for early detection, therapy monitoring, assessment of prognosis or prediction of therapy response. In particular, paired-like homeodomain transcription factor 2 (PITX2) DNA methylation has been validated using a robust assay for paraffin-embedded tissue for clinically relevant outcome prediction in early breast cancer patients treated by adjuvant tamoxifen therapy.

Pathway analysis of gene signatures predicting metastasis of node-negative primary breast cancer

Background

Published prognostic gene signatures in breast cancer have few genes in common. Here we provide a rationale for this observation by studying the prognostic power and the underlying biological pathways of different gene signatures.

Methods

Gene signatures to predict the development of metastases in estrogen receptor-positive and estrogen receptor-negative tumors were identified using 500 re-sampled training sets and mapping to Gene Ontology Biological Process to identify over-represented pathways. The Global Test program confirmed that gene expression profilings in the common pathways were associated with the metastasis of the patients.

Results

The apoptotic pathway and cell division, or cell growth regulation and G-protein coupled receptor signal transduction, were most significantly associated with the metastatic capability of estrogen receptor-positive or estrogen-negative tumors, respectively. A gene signature derived of the common pathways predicted metastasis in an independent cohort. Mapping of the pathways represented by different published prognostic signatures showed that they share 53% of the identified pathways.

Conclusion

We show that divergent gene sets classifying patients for the same clinical endpoint represent similar biological processes and that pathway-derived signatures can be used to predict prognosis. Furthermore, our study reveals that the underlying biology related to aggressiveness of estrogen receptor subgroups of breast cancer is quite different.

NF-1C, Sp1, and Sp3 are essential for transcription of the human gene for P450c17 (steroid 17alpha-hydroxylase/17,20 lyase) in human adrenal NCI-H295A cells

Cytochrome P450c17 catalyzes steroid 17alpha-hydroxylase and 17,20 lyase activities, which are required for the biosynthesis of cortisol and sex steroids. Human P450c17 is expressed in a cAMP-responsive, cell-specific, developmentally programmed fashion, but little is known about its transcriptional regulation. Expression of deletion mutants of up to 2,500 bp of human 5'-flanking DNA in human adrenal NCI-H295A cells indicated that most regulatory activity was confined to the first 227 bp. Deoxyribonuclease I footprinting of the proximal promoter identified the TATA box, an steroidogenic factor-1 site, and three previously uncharacterized sites at -107/85, at -178/-152, and at -220/-185. EMSAs and methylation interference assays suggested that the -107/-85 site and the -178/-152 site bind members of the NF-1 (nuclear factor-1) family of transcription factors. An NF-1 consensus sequence generated similar DNA/protein complexes, and antibodies against NF-1C2/CTF2 supershifted the complexes formed by the -107/-85 site, the -178/-152 site, and the NF-1 consensus site. Western blots of nuclear extracts from NCI-H295A cells probed with this NF-1 antiserum identified two NF-1 isoforms between 50 and 55 kDa. The presence of NF-1C2 (CTF2) and CTF5 in NCI-H295A cells was demonstrated by RT-PCR and sequencing. Mutation of both the -107/-85 and the -178/-152 NF-1 sites reduced basal transcription by half. Supershift assays showed that the ubiquitous proteins Sp1 and Sp3 both bind to the -227/-184 region, and that mutation of their binding sites reduced transcription by 75%. Mutation of the Sp1/Sp3 site plus the two NF-1 sites eliminated almost all detectable transcription. Thus, Sp1 and Sp3 binding to the -227/-184 site and NF-1C proteins binding to the -107/-85 and the -178/-152 sites are crucial for adrenal transcription of the human gene for P450c17.

Enzymatic activities of P450c17 stably expressed in fibroblasts from patients with the polycystic ovary syndrome

Polycystic ovary syndrome (PCOS) is a common endocrine disorder affecting approximately 5-10% of women of reproductive age. The clinical features of PCOS include oligo/anovulation, hyperandrogenemia, and hyperinsulinemia. Because P450c17 is the single enzyme catalyzing both 17alpha-hydroxylase and 17,20-lyase activities in the ovary and adrenal, some have suggested that defects in P450c17 may cause the hyperandrogenism of PCOS. Previous studies have shown that serine hyperphosphorylation of P450c17 increases the enzyme's 17,20-lyase activity, thereby favoring androgen production, and that serine phosphorylation of the insulin receptor beta-chain (IR-beta) inhibits IR-beta tyrosine phosphorylation, causing insulin resistance in vitro. We previously suggested that a gain of function mutation in a single serine kinase might cause the hyperandrogenism and insulin resistance observed in PCOS patients by excessive phosphorylation of both P450c17 and IR-beta. To test this hypothesis, we obtained fibroblasts from nine previously studied patients: three controls, three PCOS patients with normal levels of IR-beta serine phosphorylation, and three PCOS patients with increased levels of IR-beta serine phosphorylation. Initial studies showed that such skin fibroblasts could not be transfected effectively by calcium phosphate, diethylaminoethyl-dextran, lipofection or adenovirus procedures. Therefore, we employed a retroviral infection system to stably express human P450c17 in the primary cultures of fibroblast cells from the PCOS patients and controls and measured the resulting 17alpha-hydroxylase and 17,20-lyase activity. The cells were analyzed in a blinded fashion until the study was complete. The 17alpha-hydroxylase and 17,20-lyase activities in each cell line correlated well with the amount of P450c17 protein expressed, but there was no correlation between either enzymatic activity (or their ratio) with the clinical phenotype of the cells' donors even when results were corrected for the number of P450c17 complementary DNA inserts per cell line. Overnight incubation with 1 micromol/L insulin also did not affect enzymatic activity. Thus, we were unable to find evidence for the hypothesis that in PCOS a single abnormal kinase hyperphosphorylates both IR-beta, causing insulin resistance, and P450c17, causing hyperandrogenism. However, because fibroblasts do not normally express either P450c17 or the accessory proteins needed for its optimal activity, these results cannot exclude a role for serine phosphorylation in the hyperandrogenism and insulin resistance of PCOS.

A limited repertoire of mutations of the luteinizing hormone (LH) receptor gene in familial and sporadic patients with male LH-independent precocious puberty

Herein, we report mutation analysis of the LH receptor gene in 17 males with LH-independent precocious puberty, of which 8 were familial and 9 had a negative family history. A total of 7 different mutations (all previously reported) were detected in 12 patients. Among 10 European familial male-limited precocious puberty (FMPP) patients who had a LH receptor gene mutation, none had the Asp578Gly mutation, which is responsible for the vast majority of cases in the U.S. The restricted number of activating mutations of the LH receptor observed in this and other studies of FMPP strongly suggests that an activating phenotype is associated with very specific sites in the receptor protein. Clinical follow-up of the 5 patients who did not have LH receptor mutations shows that such cases most likely do not have true FMPP. LH receptor mutation analysis provides a sensitive tool for distinguishing true FMPP from other causes of early-onset LH-independent puberty in males.

Distinct gene arrangement in the Buzura suppressaria single-nucleocapsid nucleopolyhedrovirus genome

The genome organization of the Buzura suppressaria single-nucleocapsid nucleopolyhedrovirus (BusuNPV) was largely elucidated and compared to those of other baculoviruses. A detailed physical map was constructed for the restriction enzymes BamHI, BglI, BglII, EcoRI, HindIII, KpnI, PstI, XbaI and XhoI. The 120.9 kbp viral genome was cloned as restriction fragments into a plasmid library from which about 43.5 kbp of dispersed sequence information was generated. Fifty-two putative open reading frames homologous to those of other baculoviruses were identified and their location in the genome of BusuNPV was determined. Although the gene content of BusuNPV is similar to that of Autographa californica multiple-nucleocapsid nucleopolyhedrovirus, Bombyx mori nucleopolyhedrovirus and Orgyia pseudotsugata multiple-nucleocapsid nucleopolyhedrovirus, the gene order is, however, significantly different from that observed in the other viruses, which have a high degree of collinearity. A new approach (GeneParityPlot) was developed to represent the differences in gene order among baculoviruses when limited sequence information is available and to take advantage of the high degree of gene conservation. The data obtained show that BusuNPV is a distinct baculovirus species and the analyses suggest that gene distribution along baculovirus genomes may be used as a phylogenetic marker.

Activating and inactivating mutations in LH receptors

The glycoprotein hormones luteinizing hormone (LH) and human chorionic gonadotropin (hCG), both of which act through the LH receptor, play an important role in the regulation of both male and female gonadal function. Testicular androgen production by the Leydig cells is almost entirely dependent on LH/hCG action, while in the ovary LH triggers both oestrogen and progestin secretion and ovulation of the Graaffian follicles. In this review we discuss the various mutations that have been found in the LH receptor gene in the human and the lessons that can be learned from the phenotypes of the carriers of these mutations.

A homozygous mutation in the luteinizing hormone receptor causes partial Leydig cell hypoplasia: correlation between receptor activity and phenotype

Leydig cell hypoplasia (LCH) is characterized by a decreased response of the Leydig cells to LH. As a result, patients with this syndrome display aberrant male development ranging from complete pseudohermaphroditism to males with micropenis but with otherwise normal sex characteristics. We have evaluated three brothers with a mild form of LCH. Analysis of their LH receptor (LHR) gene revealed a homozygous missense mutation resulting in a substitution of a lysine residue for a isoleucine residue at position 625 of the receptor. In vitro analysis of this mutant LHR, LHR(I625K), in HEK293 cells indicated that the signaling efficiency was significantly impaired, which explains the partial phenotype. We have compared this mutant LHR to two other mutant LHRs, LHR(A593P) and LHR(S616Y), identified in a complete and partial LCH patient, respectively. Although the ligand-binding affinity for all three mutant receptors was normal, the hormonal response of LHR(A593P) was completely absent and that of LHR(S616Y) and LHR(I625K) was severely impaired. Low cell surface expression explained the reduced response of LHR(S616Y), while for LHR(I625K) this diminished response was due to a combination of low cell surface expression and decreased coupling efficiency. For LHR(A593P), the absence of a reduced response resulted from both poor cell surface expression and a complete deficiency in coupling. Our experiments further show a clear correlation between the severity of the clinical phenotype of patients and overall receptor signal capacity, which is a combination of cell surface expression and coupling efficiency.

Inhibin interferes with activin signaling at the level of the activin receptor complex in Chinese hamster ovary cells

To gain more insight in the mechanism of action of inhibin, we studied the effect of inhibin on activin signaling in Chinese hamster ovary cells. Inhibin specifically counteracted activin-induced expression of a plasminogen activator inhibitor 1 promoter element (3TP) and of the junB gene, but was ineffective when the responses were induced by transforming growth factor-beta. This indicates that inhibin acts only on the activin-specific part of these signaling cascades. Using a constitutively active activin type IB receptor we determined whether inhibin acted at the level of the activin-receptor complex or downstream of it. The mutant activin receptor stimulated the expression of the 3TP promoter in the absence of activin. This stimulation was insensitive to inhibin, indicating that inhibin acts exclusively at or upstream of this activin type I receptor. In addition, competition studies using labeled activin showed that inhibin displaced activin from the activin type II receptors, especially from the activin type IIB receptor, but not from the type I receptors. In conclusion, these data show that in Chinese hamster ovary cells inhibin acts directly at the activin receptor complex, most likely through displacement of activin from the activin type II receptor.

Characterization of the ecdysteroid UDP-glucosyltransferase gene of a single nucleocapsid nucleopolyhedrovirus of Buzura suppressaria

A putative ecdysteroid UDP-glucosyltransferase (egt) gene was identified in the single nucleocapsid nucleopolyhedrovirus of Buzura suppressaria (BusuNPV). This is the first egt gene to be characterized in a SNPV, suggesting that egt genes are prevalent in nucleopolyhedroviruses and possibly in all baculoviruses. The open reading frame (ORF) of the gene is 1539 nucleotides (nt) long, encoding a putative protein (EGT) of 513 amino acids (aa) with a M of 58922. The 5' noncoding region contains three possible TATA boxes. A polyadenylation signal, AATAAA, was found downstream of the translation stop codon. A putative signal peptide of 16 residues was present at the N-terminus of the EGT. The BusuNPV egt gene has a high degree of nucleotide and amino acid sequence homology to multiple nucleocapsid (M) NPV egt genes, the highest being to the Spodoptera exigua MNPV egt. A phylogenetic tree of eleven known EGTs was constructed using maximum parsimony analysis.

Characterization of baculovirus insecticides expressing tailored Bacillus thuringiensis CryIA(b) crystal proteins

Full-length, truncated, and mature forms of the CryIA(b) insecticidal crystal protein gene of Bacillus thuringiensis were engineered into the p10 locus of Autographa californica nuclear polyhdrosis virus (AcNPV). A signal sequence of Heliothis virescens juvenile hormone esterase was introduced at the N-terminus of these constructs to induce secretion. All recombinants, except those containing the mature toxin, produced high levels of CryIA(b) ICPs in insect cells. Thirty percent of the intracellular protoxin was N-glycosylated, suggesting that the protoxin was translocated across the ER membrane. Secretion into the medium, however, was limited. The production of the mature toxin was poor as a result of its cytotoxicity to insect cells. In a bioassay against second instar Spodoptera exigua larvae, using a recombinant expressing the Androctonus australis scorpion toxin gene in the same p10 locus as a positive control, the median survival time of AcNPV recombinants expressing the various B. thuringiensis CryIA(b) ICP constructs was not significant different from that of wild-type AcNPV. This suggests that production and/or secretion of B. thuringiensis (pro)toxins by AcNPV p10 recombinant viruses does not increase insecticidal activity since (i) the protoxins produced are inactive and not likely to be activated in vivo; (ii) secretion of the B. thuringiensis protoxins is poor; and (iii) production of the mature toxins results in cytotoxicity.

Mapping and characterization of the entomocidal domain of the Bacillus thuringiensis CryIA(b) protoxin

The amino acid sequences necessary for entomocidal activity of the CryIA(b) protoxin of Bacillus thuringiensis were determined. Introduction of stop codons behind codons Arg601, Phe604 or Ala607 showed that amino acid residues C-terminal to Ala607 are not required for insecticidal activity and that activation by midgut proteases takes place distal to Ala607. The two shortest polypeptides, deleted for part of the highly conserved beta-strand, were prone to proteolytic degradation, explaining their lack of toxicity. Apparently, this beta-strand is essential for folding of the molecule into a stable conformation. Proteolytic activation at the N-terminus was investigated by removing the first 28 codons, resulting in a translation product extending from amino acid 29 to 607. This protein appeared to be toxic not only to susceptible insect larvae such as Manduca sexta and Heliothis virescens, but also to Escherichia coli cells. An additional mutant, encoding only amino acid residues 29-429, encompassing the complete putative pore forming domain, but lacking a large part of the receptor-binding domain, was similarly toxic to E. coli cells. This suggests a role for the N-terminal 28 amino acids in rendering the toxin inactive in Bacillus thuringiensis, and indicates that the cytolytic potential of the pore forming domain is only realized after proteolytic removal of these residues by proteases in the insect gut. In line with this hypothesis are results obtained with a mutant protein in which Arg28 at the cleavage site was replaced by Asp. This substitution prevented the protein from being cleaved by trypsin in vitro, and reduced its toxicity to M. sexta larvae.

Passage of Autographa californica nuclear polyhedrosis virus through the midgut epithelium of Spodoptera exigua larvae

A special recombinant of Autographa californica multicapsid nuclear polyhedrosis virus (AcNPV) was designed to study the early histopathological events of baculovirus infection in Spodoptera exigua larvae. This recombinant contained a Drosophila melanogaster heat shock 70 promoter driving an Escherichia coli beta-galactosidase (Lac-Z) reporter gene to monitor the presence of early viral gene expression and a second reporter gene, the E. coli beta-glucuronidase (GUS) gene, under control of the very late AcNPV p10 promoter to monitor viral replication. In S. exigua larvae, permissive Spodoptera spp. cultured cells, and nonpermissive D. melanogaster cultured cells early viral gene expression was indicated by the appearance of Lac-Z as early as 3 hr p.i. Late viral gene expression was indicated by the appearance of GUS and occurred only in the permissive cultured cells and larvae. Early and late viral gene expression could be detected simultaneously using differential enzyme histochemistry. Analysis of infected S. exigua larvae revealed that midgut columnar cells and, at a low frequency, midgut regenerative cells were the primary sites of infection. Parental nucleocapsids were apparently transported through columnar cells to underlaying regenerative cells before virus replication and progeny production. Infection of tissues beside the midgut epithelium was not detected prior to viral replication within the midgut, suggesting that infection of the midgut is an important prelude to systemic infection.