RNA sequencing-based single sample predictors of molecular subtype and risk of recurrence for clinical assessment of early-stage breast cancer

Multigene assays for molecular subtypes and biomarkers can aid management of early invasive breast cancer. Using RNA-sequencing we aimed to develop single-sample predictor (SSP) models for clinical markers, subtypes, and risk of recurrence (ROR). A cohort of 7743 patients was divided into training and test set. We trained SSPs for subtypes and ROR assigned by nearest-centroid (NC) methods and SSPs for biomarkers from histopathology. Classifications were compared with Prosigna in two external cohorts (ABiM, n = 100 and OSLO2-EMIT0, n = 103). Prognostic value was assessed using distant recurrence-free interval. Agreement between SSP and NC for PAM50 (five subtypes) was high (85%, Kappa = 0.78) for Subtype (four subtypes) very high (90%, Kappa = 0.84) and for ROR risk category high (84%, Kappa = 0.75, weighted Kappa = 0.90). Prognostic value was assessed as equivalent and clinically relevant. Agreement with histopathology was very high or high for receptor status, while moderate for Ki67 status and poor for Nottingham histological grade. SSP and Prosigna concordance was high for subtype (OSLO-EMIT0 83%, Kappa = 0.73 and ABiM 80%, Kappa = 0.72) and moderate and high for ROR risk category (68 and 84%, Kappa = 0.50 and 0.70, weighted Kappa = 0.70 and 0.78). Pooled concordance for emulated treatment recommendation dichotomized for chemotherapy was high (85%, Kappa = 0.66). Retrospective evaluation suggested that SSP application could change chemotherapy recommendations for up to 17% of postmenopausal ER+/HER2-/N0 patients with balanced escalation and de-escalation. Results suggest that NC and SSP models are interchangeable on a group-level and nearly so on a patient level and that SSP models can be derived to closely match clinical tests.

Abstract P2-08-11: How reliable are biomarkers assessed on a core needle biopsy? A study of paired core needle biopsies and surgical specimens in early breast cancer

Background: The conventional biomarkers estrogen receptor (ER), progesterone receptor (PgR), human epidermal growth factor receptor 2 (HER2), Ki67, and Nottingham histologic grade (NHG) are used to classify breast cancer into its molecular subtypes, determine prognosis, and guide treatment. A preoperative core needle biopsy (CNB) is used to confirm the diagnosis and invasiveness of a breast lesion and forms the basis for characterizing the tumor in the case of neoadjuvant primary treatment, emphasizing the importance of obtaining reliable biomarker assessment from a diagnostic CNB. Aim: The aim of this study was to determine the similarity between biomarker status assessed on a CNB compared to a medically untreated surgical specimen. Methods: Paired CNB and surgical specimens from 267 patients that were part of the prospective Sweden Cancerome Analysis Network- Breast (SCAN-B) cohort were studied. The concordance for the five biomarkers: ER, PgR, Ki67, HER2 and molecular subtype, between paired CNB and surgical specimen were investigated using immunohistochemistry (IHC) and gene expression-based analytical methods (GEX). IHC data were collected from patient medical records and gene expression was measured by RNA sequencing. Cohen’s kappa and Mcnemar’s test were used to compare the concordance of biomarkers.Results: Moderate to very good levels of concordance were observed between the biomarker status obtained on a CNB compared with the paired surgical specimen for IHC (κappa range 0.474-0.917) and GEX (κappa range 0.528-0.776), respectively. However, a significant drift from low to high Ki67 status and from negative to positive HER2 status between the CNB and surgical specimen was observed when using IHC and GEX, respectively (McNemar p < 0.05 for both comparisons). Moderate to good concordance levels of biomarker status were generally obtained when comparing GEX and IHC status measured from the same type of sample (κappa range 0.484-0.649) except for Ki67 which consistently displayed poor concordance levels between IHC and GEX for both CNB and surgical specimen comparisons (κappa range 0.158-0.198). Notably, a significant shift from positive to negative ER status and high to low Ki67 status was observed when comparing IHC with GEX classification (McNemar p <0.001 for both comparisons). Conclusion: The tissue sampling and the method of biomarker analysis may affect the results of biomarker status and ultimately affect treatment decisions. The implications of using a preoperative CNB to determine biomarker status, prognosis, and treatment choice should be taken into consideration in neoadjuvant treatment settings.

Citation Format: Hani Saghir, Srinivas Veerla, Martin Malmberg, Lisa Rydén, Anna Ehinger, Lao Saal, Johan Vallon-Christersson, Åke Borg, Cecilia Hegardt, Ingrid Hedenfalk, Susanne Dieroff-Hay, Christer Larsson, Niklas Loman, Siker Kimbung. How reliable are biomarkers assessed on a core needle biopsy? A study of paired core needle biopsies and surgical specimens in 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 P2-08-11.

Abstract OT2-30-01: Nordictrip, a translational randomized phase-3study exploring the effect of the addition of capecitabine to carboplatinum-based chemotherapy in early “triple negative” breast cancer, ClinicalTrials.gov Identifier: NCT04335669

Background: A striking heterogeneity combined with an absence of highly efficient targeted treatments necessitates a continued effort to optimize the choice of chemotherapy for patients with triple negative breast cancer (TNBC). Neoadjuvant therapy has become the standard of care for high risk TNBC in order to potentially reduce breast and axillary surgery, start medical treatment early, allow genomic screening and guide post neoadjuvant therapy. Much attention is drawn to the use of immunotherapy in early TNBC, but there is also interesting data suggesting a potential to optimize the use of conventional chemotherapy. According to one meta-analysis including data from nine randomized controlled trials, the addition of platinum salts in the preoperative setting increases the pathologic complete response (pCR) rate in TNBC (Poggio 2018). A second meta-analysis, evaluating the effect of capecitabine in early breast cancer indicates an additional benefit from adding capecitabine to conventional chemotherapy in terms of an increased recurrence-free survival in the subset of TNBC (Mackelenbergh SABCS 2019). An adjuvant trial in TNBC suggests that the beneficial effect of capecitabine may be confined to patients with a non-basal like phenotype of TNBC (Lluch 2020), a subset that correlates with the homologous repair non-deficient subset which constitutes 41 % of TNBC in a mainly south Swedish population based cohort (Staaf 2019). The effect of capecitabine in platinum treated early TNBC is unknown. Objectives: We are conducting a multi-center randomized controlled trial evaluating the effect on the pCR rate by the addition of capecitabine to optimal platinum based and dose dense preoperative chemotherapy in early TNBC. Method: 820 patients (pts) with early TNBC stage 1 (≥20 mm) - 3 will be randomized 1:1 between two treatment arms A and B. A: Epirubicine Cyclophosphamide (EC) q2w x 4 followed by Carboplatin AUC 5 q3w with weekly paclitaxel x 12. B: Epirubicine Cyclophosphamide with capecitabine daily for two weeks (CEX) q3w x 4 followed by Carboplatin AUC 5 q3w with weekly paclitaxel x 12 The primary endpoint is pCR rate in the different treatment strata, and the primary translational endpoint will be the potential difference of treatment effect stratified for HRD-status in the primary tumor. Secondary endpoints include IDFS in subsets of TNBC, eg according to gene-expression-based subtypes of TNBC (Lehmann 2011, Burstein 2015), and germline mutation status of hereditary breast cancer genes. Tumor material for genotypig is collected at baseline, at surgery and optionally after two treatment cycles. Sequential blood samples are collected for tsDNA analysis during and after treatment termination. Results: The trial, which is a collaborative effort between the national breast cancer groups in the participating countries, has been postponed by the pandemic but is now recruiting according to plan. So far 56 patients out of 820 have been recruited at 15 sites in Sweden and Denmark. Additional Sites in Sweden, Denmark, Iceland and Finland are preparing to join the study. For update please see: www.NordicTrip.se; E-mail address: Nordictrip.onkologi@skane.se

Citation Format: Niklas Loman, Barbro Linderholm, Johan Ahlgren, Siker Kimbung, Lina Zander, Heidi Grill Magnusson, Eva-Christin Kjellman, Ann Julia Raaberg, Maj-Britt Raaby Jensen, Åke Borg, Johan Staaf, Anders Ståhlberg, Pär-Ola Bendahl, Anne-Vibeke Laenkholm, Minna Tanner, Olöf Bjarnadóttir, Oskar Johannsson, Bent Ejlertsen, Henrik Lindman. Nordictrip, a translational randomized phase-3study exploring the effect of the addition of capecitabine to carboplatinum-based chemotherapy in early “triple negative” breast cancer, ClinicalTrials.gov Identifier: NCT04335669 [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 OT2-30-01.

High CYP27A1 expression is a biomarker of favorable prognosis in premenopausal patients with estrogen receptor positive primary breast cancer

27-hydroxycholesterol (27HC), synthesized from cholesterol by the enzyme CYP27A1, differentially impacts estrogen receptor positive (ER+) breast cancer (BC) cell growth depending on estrogen levels. This study examined the association between CYP27A1 expression and prognosis in a cohort of 193 premenopausal patients with lymph node-negative primary BC with limited exposure to adjuvant systemic cancer treatments. In multivariable analyses among patients with ER+ tumors, high CYP27A1 protein and mRNA expressions were associated with four- and eight-fold reductions in the incidence of distant recurrence-free survival events: HR_adj = 0.26, 95% CI = 0.07-0.93 and HR_adj = 0.13, 95% CI = 0.03-0.60, respectively. In vitro studies revealed that 27HC treatment potently inhibited ER+ BC cell proliferation under lipid-depleted conditions regardless of estradiol levels, transcriptionally mediated through the downregulation of ER signaling with a concomitant upregulation of cholesterol export. Importantly, if validated, these results may have implications for adjuvant treatment decisions in premenopausal patients, especially when de-escalation of therapy is being considered.

CYP27A1 expression is associated with risk of late lethal estrogen receptor-positive breast cancer in postmenopausal patients

Background

27-Hydroxycholesterol (27HC) stimulates estrogen receptor-positive (ER+) breast cancer (BC) progression. Inhibiting the sterol 27-hydroxylase (CYP27A1) abrogates these growth-promoting effects of 27HC in mice. However, the significance of CYP27A1 expression on BC biology and prognosis is unclear.

Methods

Intratumoral CYP27A1 expression in invasive BC was measured by immunohistochemistry in two Swedish population-based cohorts (n = 645 and n = 813, respectively). Cox proportional hazards models were used to evaluate the association between CYP27A1 expression and prognosis.

Results

CYP27A1 was highly expressed in less than 1/3 of the tumors. High CYP27A1 expression was more frequent among high-grade tumors lacking hormone receptor expression and with larger tumor sizes. Over a median of 12.2 years follow-up in cohort 1, high CYP27A1 expression was associated with impaired survival, specifically after 5 years from diagnosis among all patients [overall survival (OS), HR_adjusted = 1.93, 95%CI = 1.26–2.97, P = 0.003; breast cancer-specific survival (BCSS), HR_adjusted = 2.33, 95%CI = 1.28–4.23, P = 0.006] and among patients ≥ 55 years presenting with ER+ tumors [OS, HR_adjusted = 1.99, 95%CI = 1.24–3.21, P = 0.004; BCSS, HR_adjusted = 2.78, 95%CI = 1.41–5.51, P = 0.003].

Among all patients in cohort 2 (median follow-up of 7.0 years), CYP27A1 expression was significantly associated with shorter OS and RFS in univariable analyses across the full follow-up period. However after adjusting for tumor characteristics and treatments, the association with survival after 5 years from diagnosis was non-significant among all patients [OS, HR_adjusted = 1.08, 95%CI = 0.05–2.35, P = 0.83 and RFS, HR_adjusted = 1.22, 95%CI = 0.68–2.18, P = 0.50] as well as among patients ≥ 55 years presenting with ER+ tumors [OS, HR_adjusted = 0.46 95% CI = 0.11–1.98, P = 0.30 and RFS, HR_adjusted = 0.97 95% CI = 0.44–2.10, P = 0.93].

Conclusion

CYP27A1 demonstrated great potentials as a biomarker of aggressive tumor biology and late lethal disease in postmenopausal patients with ER+ BC. Future studies should investigate if the benefits of prolonged endocrine therapy and cholesterol-lowering medication in BC are modified by CYP27A1 expression.

Transcriptomic and functional pathway features were associated with survival after pathological complete response to neoadjuvant chemotherapy in breast cancer

Pathological complete response (pCR) after neoadjuvant chemotherapy (NAC) has been proposed as a surrogate endpoint for the prediction of long-term survival in breast cancer (BC); however, an increased pCR rate has not clearly correlated with improved survival. We hypothesized that some transcriptomic and functional pathway features correlate with survival after pCR in BC. We utilized 2 published NAC cohorts, 105 women with gene expression data before, "Baseline", and that changed during NAC, "Delta", and TCGA database with 1068 BC patients to investigate the relationship between the efficacy of NAC and survival utilizing differentially expressed-mRNAs, construction and analysis of the mRNA-hub gene network, and functional pathway analysis. In mRNA expression profiling, S100A8 was a gene involved in survival after pCR in Baseline and NDP was a gene involved in recurrence after pCR in Delta. In functional pathway analysis, we found multiple pathways involved in survival after pCR. In mRNA-hub gene analysis, HSP90AA1, EEF1A1, APP, and HSPA4 were related to recurrence in BC patients with pCR due to NAC. TP53, EGFR, CTNNB1, ERBB2, and HSPB1 may play a significant role in survival for patients with pCR. Interestingly, high HSP90AA1, HSPA4, S100A8, and TP53, and low EEF1A1, EGFR, and CTNNB1 expressing tumors have significantly worse overall survival in TCGA BC cohort. We demonstrated the genes and functional pathway features associated with pCR and survival utilizing the bioinformatics approach to public BC cohorts. Some genes involved in recurrence after pCR due to NAC also served as prognostic factors in primary BC.

Abstract P3-08-21: High CYP27A1 expression at protein and transcript level predicts favorable outcome in node negative, premenopausal breast cancer

Background: Experimental evidence suggests that pathogenicity caused by cholesterol in breast cancer is partly elicited by 27-hydroxycholesterol (27HC), a primary cholesterol metabolite produced by the sterol 27-hydroxylase cytochrome p450 27A1 (CYP27A1). Targeting CYP27A1 abrogated the adverse effects of cholesterol and 27HC in preclinical studies. The prognostic relevance of CYP27A1 expression in patients with breast cancer is however not clearly defined. Previous studies suggest that the intratumoral expression of CYP27A1 might have diverse effects on prognosis depending on menopausal status. The aim of this study was to comprehensively evaluate the impact of both CYP27A1 protein and mRNA expression on tumor pathobiology and prognosis in pre-menopausal, node-negative breast cancer.

Materials and Methods: CYP27A1 expression at the protein and transcript level was evaluated in a prospective cohort of 237 premenopausal women with node-negative, primary invasive breast cancer. Protein and mRNA expression were assessed by immunohistochemistry (IHC) and in situ hybridization technique-RNAscope, respectively. Associations of CYP27A1 expression with tumor pathological features and prognosis were assessed with chi-square test and Cox regression models, respectively. Multivariable models were adjusted for age, hormone receptor status, Ki67, and histological grade.

Results: CYP27A1 protein was overexpressed in 28% and CYP27A1 mRNA in 23% of the tumors. The concordance between CYP27A1 protein and mRNA expression was 77.8% (rs=0.430). Among the discordant cases, 13.9% were only positive by IHC. Elevated expression of both protein and mRNA was significantly associated with aggressive tumor pathological features like high histological grade and high Ki67 expression (P<0.001). In multivariable Cox regression analyses, overexpression of CYP27A1 protein was independently prognostic for more than a factor-two reduced risk of disease recurrence (Recurrence-Free Survival (RFS): HR=0.40, 95% CI=0.23-0.86; Distant Recurrence-Free Survival (DRFS): HR=0.40, 95% CI=0.16-0.95). High CYP27A1 expression conferred even stronger protective effect for patients with estrogen receptor (ER) positive tumors when the analyses were stratified by ER status (RFS: HR=0.18, 95% CI=0.06-0.55; DRFS: HR=0.20, 95% CI=0.06-0.81). Likewise, high CYP27A1 mRNA expression was also independently prognostic for a longer RFS (HR=0.40, 95% CI=0.2-0.8), DRFS (HR=0.28; 95%CI=0.1-0.7) and in addition better overall survival (OS) (HR=0.20, 95% CI=0.08-0.60) in the overall population and in the subgroup of patients with ER positive tumors (OS: HR=0.14; 95% CI=0.03-0.65; RFS: HR= 0.22; 95% CI= 0.07-0.68; DRFS: HR=0.16; 95% CI=0.03-0.73).

Conclusion: These results indicate that high intratumoral expression of CYP27A1 is a strong indicator for an extensive recurrence-free interval and overall survival in premenopausal women with ER positive, lymph node-negative breast cancer. CYP27A1 transcript expression may serve as an even more sensitive prognostic biomarker.

Citation Format: Maria Inasu, Pär Ola Bendahl, Mårten Fernö, Per Malmström, Signe Borgquist, Siker Kimbung. High CYP27A1 expression at protein and transcript level predicts favorable outcome in node negative, premenopausal breast cancer [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 P3-08-21.

Abstract P2-08-26: High expression of CYP27A1 in breast cancer is associated with poor tumor pathological features and may differentially predict prognosis depending on menopausal status

Background: Pre-clinical and epidemiological data strongly link high cholesterol with breast cancer progression and poor prognosis. It was recently uncovered that the pathogenicity of cholesterol in breast cancer is directly propagated by 27-hydroxycholesterol (27HC), an oxysterol produced when cholesterol is hydroxylated by cytochrome P450, family 27, subfamily A, polypeptide 1 (CYP27A1) during bile acid synthesis. 27HC promotes breast tumor growth and metastasis via interactions with the estrogen receptor (ER) and liver x receptors respectively. Consequently, pharmaceutical approaches that directly interfere with CYP27A1 activity have been proposed to mitigate the adverse impact of 27HC in breast cancer. However, CYP27A1 expression or deregulation in clinical breast cancer is not well characterised. The aim of this study was to comprehensively describe the impact of tumor-specific expression of CYP27A1 protein on clinical breast cancer pathobiology and prognosis.

Methods: CYP27A1 expression in tumor cells was evaluated by immunohistochemistry in two independent population based cohorts including female patients with primary invasive breast cancer diagnosed between 1991 and 2010 (cohort 1) and between 2002 and 2012 (cohort 2). Staining was evaluable in 645 and 813 cases in cohort 1 and cohort 2, respectively. Associations between CYP27A1 expression with tumor pathological factors and survival were assessed by using logistic and Cox regression models respectively. Multivariable models adjusted for age at diagnosis, nodal status, histological grade, tumor size, ER and BMI.

Results: CYP27A1 was overexpressed in 21% and 28% in cohort 1 and cohort 2 respectively. High CYP27A1 expression was significantly associated with adverse tumor pathological features including negative hormone receptor (ER and PgR) status and histological grade 3 in both cohorts and with larger tumors (>20 mm) in cohort two only (p<0.05, for all comparisons). In multivariable Cox regression analyses, overexpression of CYP27A1 was neither independently prognostic for recurrence-free survival (cohort 2: HR=1.3, 95% CI= 0.88 – 1.9) nor overall survival (cohort 1: HR=1.3, 95% CI= 0.88 – 1.9 and Cohort 2: HR=1.3, 95% CI= 0.81 – 2.0, respectively). Upon stratification for menopausal status using age at diagnosis (< 50 years vs ≥ 50 years) as surrogate, the relationship between CYP27A1 expression and prognosis remained non-significant for older (postmenopausal) patients. Interestingly, among younger (premenopausal) women, elevated CYP27A1 expression was independently prognostic for shorter time to recurrence or death (HR=3.3, 95% CI= 1.5 – 7.4; cohort 2).

Conclusions: Collectively, these results indicate that intratumoral CYP27A1 expression supports the notion that 27HC plays an important pathological role in breast cancer progression but tumor cell-specific CYP27A1 expression is not sufficient to independently predict overall survival in postmenopausal patients. Further sufficiently sized studies are needed to clarify the prognostic significance of CYP27A1 in younger and presumably premenopausal patients and evaluate its role as a treatment predictive factor.

Citation Format: Kimbung S, Stålhammar T, Inasu M, Nodin B, Elebro K, Tryggvadottir H, Jirström K, Rose C, Ingvar C, Jernström H, Borgquist S. High expression of CYP27A1 in breast cancer is associated with poor tumor pathological features and may differentially predict prognosis depending on menopausal status [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 P2-08-26.

Afadin cooperates with Claudin-2 to promote breast cancer metastasis

Tabariès et al. show that signaling downstream from a Claudin-2/Afadin complex enables the efficient formation of breast cancer metastases.

Claudin-2 promotes breast cancer liver metastasis by enabling seeding and early cancer cell survival. We now demonstrate that the PDZ-binding motif of Claudin-2 is necessary for anchorage-independent growth of cancer cells and is required for liver metastasis. Several PDZ domain-containing proteins were identified that interact with the PDZ-binding motif of Claudin-2 in liver metastatic breast cancer cells, including Afadin, Arhgap21, Pdlim2, Pdlim7, Rims2, Scrib, and ZO-1. We specifically examined the role of Afadin as a potential Claudin-2-interacting partner that promotes breast cancer liver metastasis. Afadin associates with Claudin-2, an interaction that requires the PDZ-binding motif of Claudin-2. Loss of Afadin also impairs the ability of breast cancer cells to form colonies in soft agar and metastasize to the lungs or liver. Immunohistochemical analysis of Claudin-2 and/or Afadin expression in 206 metastatic breast cancer tumors revealed that high levels of both Claudin-2 and Afadin in primary tumors were associated with poor disease-specific survival, relapse-free survival, lung-specific relapse, and liver-specific relapse. Our findings indicate that signaling downstream from a Claudin-2/Afadin complex enables the efficient formation of breast cancer metastases. Moreover, combining Claudin-2 and Afadin as prognostic markers better predicts the potential of breast cancer to metastasize to soft tissues.

Statins: a role in breast cancer therapy?

Statin drugs have been used for more than two decades to treat hypercholesterolemia and as cardio-preventive drugs, resulting in a marked decrease in cardiovascular morbidity and mortality worldwide. Statins halt hepatic cholesterol biosynthesis by inhibiting the rate-limiting enzyme in the mevalonate pathway, hydroxymethylglutaryl-coenzyme A reductase (HMGCR). The mevalonate pathway regulates a host of biochemical processes in addition to cholesterol production. Attenuation of these pathways is likely responsible for the myriad benefits of statin therapy beyond cholesterol reduction - the so-called pleiotropic effects of statins. Chief amongst these purported effects is anti-cancer activity. A considerable body of preclinical, epidemiologic and clinical evidence shows that statins impair proliferation of breast cancer cells and reduce the risk of breast cancer recurrence. Potential mechanisms for this effect have been explored in laboratory models, but remain poorly understood and require further investigation. The number of clinical trials assessing the putative clinical benefit of statins in breast cancer is increasing. Currently, a total of 30 breast cancer/statin trials are listed at the global trial identifier website clinicaltrials.gov. Given the compelling evidence from performed trials in a variety of clinical settings, there have been calls for a clinical trial of statins in the adjuvant breast cancer setting. It would be imperative for such a trial to incorporate tumour biomarkers predictive of statin response in its design and analysis plan. Ongoing translational clinical trials aimed at biomarker discovery will help identify, which breast cancer patients are most likely to benefit from adjuvant statin therapy, and will add valuable clinical knowledge to the field.

Insensitivity to atorvastatin is associated with increased accumulation of intracellular lipid droplets and fatty acid metabolism in breast cancer cells

Apart from the relevant lipid-lowering effects, statins have demonstrated significant, although heterogeneous, anti-tumor activities in preventing breast cancer (BC) progression. To characterize the critical pathways behind the diverse responses to therapy, we investigated statin-induced changes in regulation of lipid metabolism and abundance of neutral lipid-containing cytoplasmic lipid droplets (LDs) in BC cells displaying different sensitivity to atorvastatin. Following atorvastatin treatment, accumulated LD levels inversely mirrored the marginal anti-proliferative effects in a dose and time-dependent manner in the less-sensitive BC cells. Transcriptional profiling excluded dysregulation of lipid uptake and efflux as specific mechanisms associated with differences in LD accumulation and anti-proliferative effects of atorvastatin. Notably, significant upregulation of genes involved in unsaturated fatty acid metabolism [stearoyl-CoA desaturase (SCD)] and cholesterol biosynthesis [3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR)], were associated with atorvastatin insensitivity. Taken together, the increased ability to store neutral lipids in LDs as consequence of atorvastatin treatment likely confers a proliferative advantage to BC cells and may serve as potential biomarker of statin resistance in BC. Contributions of cholesterol biosynthesis and unsaturated fatty acid metabolism to LD formation should be thoroughly explored for better understanding of the molecular mechanisms underlying statin-induced effects against BC progression.

High expression of cholesterol biosynthesis genes is associated with resistance to statin treatment and inferior survival in breast cancer

There is sufficient evidence that statins have a protective role against breast cancer proliferation and recurrence, but treatment predictive biomarkers are lacking. Breast cancer cell lines displaying diverse sensitivity to atorvastatin were subjected to global transcriptional profiling and genes significantly altered by statin treatment were identified. Atorvastatin treatment strongly inhibited proliferation in estrogen receptor (ER) negative cell lines and a commensurate response was also evident on the genome-wide transcriptional scale, with ER negative cells displaying a robust deregulation of genes involved in the regulation of cell cycle progression and apoptosis. Interestingly, atorvastatin upregulated genes involved in the cholesterol biosynthesis pathway in all cell lines, irrespective of sensitivity to statin treatment. However, the level of pathway induction; measured as the fold change in transcript levels, was inversely correlated to the effect of statin treatment on cell growth. High expression of cholesterol biosynthesis genes before treatment was associated with resistance to statin therapy in cell lines and clinical biopsies. Furthermore, high expression of cholesterol biosynthesis genes was independently prognostic for a shorter recurrence-free and overall survival, especially among ER positive tumors. Dysregulation of cholesterol biosynthesis is therefore predictive for both sensitivity to anti-cancer statin therapy and prognosis following primary breast cancer diagnosis.

Adipocytes and Obesity-Related Conditions Jointly Promote Breast Cancer Cell Growth and Motility: Associations With CAP1 for Prognosis

The global increase in overweight and obesity rates represent pressing public health concerns associated with severe comorbidities, amongst a rising incidence and impaired outcome of breast cancer. Yet, biological explanations for how obesity affects breast cancer are incompletely mapped. Herein, the joint impact by differentiated 3T3-L1 adipocytes and obesity-related metabolic conditions on breast cancer cells was evaluated in vitro and adipocyte-derived mediators assessed. Adipokine receptor expression was explored among breast cancer cell lines (n = 47) and primary breast tumors (n = 1,881), where associations with survival outcomes were investigated. Adipocytes and metabolic complications jointly stimulated breast cancer cell proliferation and motility, with phenotype-specific differences. Resistin was among the top modulated adipokines secreted by 3T3-L1 adipocytes under obesity-associated metabolic conditions compared with normal physiology. The newly identified resistin receptor, CAP1, was expressed across a large panel of breast cancer cell lines and primary breast tumors. CAP1 was associated with poor tumor characteristics with higher CAP1 expression among estrogen receptor (ER)-negative tumors, relative to ER-positive tumors (P = 0.025), and higher histological grades (P = 0.016). High CAP1 tumor expression was associated with shorter overall survival (adjusted hazard ratio [HR_adj] 1.54; 95% confidence interval [CI], 1.11-2.13) and relapse-free survival (HR_adj 1.47; 95% CI, 1.10-1.96), compared with low or intermediate CAP1 expression, particularly among ER-positive tumors or lymph node positive tumors. Together, these translational data demonstrate that the adipocyte secretome promote breast cancer cell proliferation and motility and highlight a potential role of CAP1 regarding breast cancer outcome-results that warrant further investigation to elucidate the obesity-breast cancer link in human pathology.

Gene expression modules in primary breast cancers as risk factors for organotropic patterns of first metastatic spread: a case control study

BACKGROUND

Metastases from primary breast cancers can involve single or multiple organs at metastatic disease diagnosis. Molecular risk factors for particular patterns of metastastic spread in a clinical population are limited.

METHODS

A case-control design including 1357 primary breast cancers was used to study three distinct clinical patterns of metastasis, which occur within the first six months of metastatic disease: bone and visceral metasynchronous spread, bone-only, and visceral-only metastasis. Whole-genome expression profiles were obtained using whole genome (WG)-DASL assays from formalin-fixed paraffin-embedded (FFPE) samples. A systematic protocol was developed for handling FFPE samples together with stringent data quality controls to identify robust expression profiling data. A panel of published and novel gene sets were tested for association with these specific patterns of metastatic spread and odds ratios (ORs) were calculated.

RESULTS

Metasynchronous metastasis to bone and viscera was found in all intrinsic breast cancer subtypes, while immunohistochemically (IHC)-defined receptor status and specific IntClust subgroups were risk factors for visceral-only or bone-only first metastases. Among gene modules, those related to proliferation increased the risk of metasynchronous metastasis (OR (95% CI) = 2.3 (1.1-4.8)) and visceral-only first metastasis (OR (95% CI) = 2.5 (1.2-5.1)) but not bone-only metastasis (OR (95% CI) = 0.97 (0.56-1.7)). A 21-gene module (BV) was identified in estrogen-receptor-positive breast cancers with metasynchronous metastasis to bone and viscera (area under the curve = 0.77), and its expression increased the risk of bone and visceral metasynchronous spread in this population. BV was further orthogonally validated with NanoString nCounter in primary breast cancers, and was reproducible in their matched lymph nodes metastases and an external cohort.

CONCLUSION

This case-control study of WG-DASL global expression profiles from FFPE tumour samples, after careful quality control and RNA selection, revealed that gene modules in the primary tumour have differing risks for clinical patterns of metasynchronous first metastases. Moreover, a novel gene module was identified as a putative risk factor for metasynchronous bone and visceral first metastatic spread, with potential implications for disease monitoring and treatment planning.

Assessment of early response biomarkers in relation to long-term survival in patients with HER2-negative breast cancer receiving neoadjuvant chemotherapy plus bevacizumab: Results from the Phase II PROMIX trial

Pathologic complete response (pCR) is a predictor for favorable outcome after neoadjuvant treatment in early breast cancer. Modulation of gene expression may also provide early readouts of biological activity and prognosis, offering the possibility for timely response-guided treatment adjustment. The role of early transcriptional changes in predicting response to neoadjuvant chemotherapy plus bevacizumab was investigated. One-hundred-and-fifty patients with large, operable and locally advanced HER2-negative breast cancer received epirubicin and docetaxel, with the addition of bevacizumab. Patients underwent tumor biopsies at baseline, after Cycle 2 and at the time of surgery. The primary end point, pCR, and its relation with the secondary endpoints event-free survival (EFS), overall survival (OS) and gene expression profiles, are reported. The pCR rate was 13% (95% CI 8.6-20.2), with significantly more pCRs among triple-negative [28% (95% CI 14.8-45.4)] than among hormone receptor positive (HR+) tumors [9% (95% CI 4.6-16.3); (OR = 3.9 [CI = 1.5-10.3])]. pCR rates were not associated with EFS or OS. PAM50 subtypes significantly changed after Cycle 2 (p = 0.03) and an index of absolute changes in PAM50 correlations between these time-points was associated with EFS [HR = 0.62 (CI = 0.3-1.1)]. In univariable analyses, signatures for angiogenesis, proliferation, estrogen receptor signaling, invasion and metastasis, and immune response, measured after Cycle 2, were associated with pCR in HR+ tumors. Evaluation of changes in molecular subtypes and other signatures early in the course of neoadjuvant treatment may be predictive of pCR and EFS. These factors may help guide further treatment and should be considered when designing neoadjuvant trials.

Impact of 27-hydroxylase (CYP27A1) and 27-hydroxycholesterol in breast cancer

The impact of systemic 27-hydroxycholesterol (27HC) and intratumoral CYP27A1 expression on pathobiology and clinical response to statins in breast cancer needs clarification. 27HC is an oxysterol produced from cholesterol by the monooxygenase CYP27A1, which regulates intracellular cholesterol homeostasis. 27HC also acts as an endogenous selective estrogen receptor (ER) modulator capable of increasing breast cancer growth and metastasis. 27HC levels can be modulated by statins or direct inhibition of CYP27A1, thereby attenuating its pro-tumorigenic activities. Herein, the effect of statins on serum 27HC and tumor-specific CYP27A1 expression was evaluated in 42 breast cancer patients treated with atorvastatin within a phase II clinical trial. Further, the associations between CYP27A1 expression with other primary tumor pathological features and clinical outcomes were studied in two additional independent cohorts. Statin treatment effectively decreased serum 27HC and deregulated CYP27A1 expression in tumors. However, these changes were not associated with anti-proliferative responses to statin treatment. CYP27A1 was heterogeneously expressed among primary tumors, with high expression significantly associated with high tumor grade, ER negativity and basal-like subtype. High CYP27A1 expression was independently prognostic for longer recurrence-free and overall survival. Importantly, the beneficial effect of high CYP27A1 in ER-positive breast cancer seemed limited to women aged ≤50 years. These results establish a link between CYP27A1 and breast cancer pathobiology and prognosis and propose that the efficacy of statins in reducing serum lipids does not directly translate to anti-proliferative effects in tumors. Changes in other undetermined serum or tumor factors suggestively mediate the anti-proliferative effects of statins in breast cancer.

Abstract P4-03-15: Joint influence by paracrine adipocyte signals and metabolic conditions on breast cancer

Background: The growing global population of overweight and obese people represents a pressing public health concern. A higher percentage of body fat is linked to an altered metabolic state and an increased risk of chronic metabolic disorders and cancer. Although, the mechanistic explanations for how obesity affects the development, progression and prognosis of cancer is incompletely mapped.

Purpose: To investigate the joint influence by adipocytes and metabolic pressure on breast cancer cell expansion.

Experimental Design: In vitro differentiated 3T3-L1 adipocytes were exposed to metabolic glucoselow/high and insulinlow/high pressure in order to mimic normal, pre-diabetic, overt diabetic and late diabetic conditions. Adipocyte-conditioned medium was collected and paracrine effects by adipocyte-derived factors on estrogen receptor (ER)-positive (T47D, MCF-7) and ER-negative (MDA-MB-231) breast cancer cell proliferation, molecular adaptations, and cell motility were subsequently analyzed using sulforhodamine B, Western immunoblotting and migration assays.

Results: Under normal metabolic conditions, adipocytes stimulated the growth of ER+ (1.1-2.0-fold; P<0.001) and to a greater extent, ER- breast cancer cells (3.1-fold; P<0.001), compared with controls. The joint effects by adipocyte paracrine signals and higher metabolic pressure (overt or late diabetic conditions), further enhanced the proliferative response in both ER+ and ER- cells (1.3-3.5-fold; P<0.01), compared with controls. Furthermore, adipocyte-derived factors induced morphological changes, protrusion extensions and cell migration in the low invasive T47D cells. Additional acquisition of molecular epithelial-mesenchymal transition features were observed in breast cancer cells following co-culturing with adipocyte-derived factors.

Conclusion: These study results support the hypothesis that paracrine signals by adipocytes significantly stimulate the proliferation and induction of a more motile phenotype of human breast cancer cells, which is further enhanced under obesity-associated metabolic conditions.

Citation Format: Rosendahl AH, Bergqvist M, Lettiero B, Kimbung S, Borgquist S. Joint influence by paracrine adipocyte signals and metabolic conditions on breast cancer [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 P4-03-15.

Abstract P6-02-04: Atorvastatin insensitivity is associated with increased lipid droplets accumulation and fatty acid metabolism in breast cancer cells

Lipophilic statins, including atorvastatin, may exert significant antiproliferative and proapoptotic effects in breast cancer as demonstrated in both clinical trials and cell models. However, heterogeneity in treatment response still remains a noteworthy challenge to be addressed. In this regard, we previously proposed a multigene signature including genes involved in cholesterol biosynthesis, which were dysregulated upon atorvastatin treatment and was shown to predict statin responsiveness in breast cancer (BC) cell lines and primary tumors. To further delineate the molecular mechanisms underlying this variability, we sought to characterize the differential statin-induced effects on intracellular lipid regulation observed in BC cell lines based on their sensitivity to atorvastatin treatment. BC cells were classified as insensitive (MCF-7 and T47D) or sensitive (MDA-MB-231) to atorvastatin by virtue of growth inhibition rate consequent to treatment with doses ranging up to 10 μM. Under complete culture conditions, atorvastatin-induced decrease in cell proliferation was inversely correlated to a progressive accumulation of neutral lipids in lipid droplets (LDs) in the insensitive cells following 72 hours treatment. Interestingly, in the sensitive MDA-MB-231 cells no significant change in LDs formation was observed despite the very potent antiproliferative effects (60% impairment of growth). However, in correspondence of severe inhibition of growth rate of at least 80% by atorvastatin treatment, MDA-MB-231 cells displayed a consistent reduction in LDs accumulation, suggesting beneficial effects of LDs biosynthesis on proliferation of BC cells. Transcriptional profiling of genes involved in lipid metabolism using microarrays and validated by qRT-PCR ruled out the likelihood that atorvastatin treatment altered lipid uptake and export mechanisms in sensitive cells in the presence of exogenous lipid supply. Nevertheless, gene ontology analysis indicated that an induction of cell stress responses was likely associated to atorvastatin sensitivity. Significant deregulation of genes involved in the fatty acid metabolic process, including biosynthesis of monounsaturated fatty acids (MUFAs), and cholesterol biosynthesis were instead linked to atorvastatin insensitivity. Accordingly, we found that the magnitude of the induction of the mRNAs of stearoyl-CoA desaturase (SCD), the key effector in MUFAs metabolism, and 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR), the established target of statins, were consistently lower in sensitive cells compared to the insensitive counterpart in response to atorvastatin treatment. Therefore, we suggest that the ability to significantly increase the number of stored neutral lipids in response to statin treatment may likely confer a proliferative advantage to BC cells. Our results also identified MUFAs metabolism as an attractive pathway to be further investigated in view of finding promising biomarkers for unraveling the molecular basis of statin sensitivity in breast cancer.

Citation Format: Lettiero B, Kimbung S, Borgquist S. Atorvastatin insensitivity is associated with increased lipid droplets accumulation and fatty acid metabolism in breast cancer cells [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 P6-02-04.

Contrasting breast cancer molecular subtypes across serial tumor progression stages: biological and prognostic implications

The relevance of the intrinsic subtypes for clinical management of metastatic breast cancer is not comprehensively established. We aimed to evaluate the prevalence and prognostic significance of drifts in tumor molecular subtypes during breast cancer progression. A well-annotated cohort of 304 women with advanced breast cancer was studied. Tissue microarrays of primary tumors and synchronous lymph node metastases were constructed. Conventional biomarkers were centrally assessed and molecular subtypes were assigned following the 2013 St Gallen guidelines. Fine-needle aspirates of asynchronous metastases were transcriptionally profiled and subtyped using PAM50. Discordant expression of individual biomarkers and molecular subtypes was observed during tumor progression. Primary luminal-like tumors were relatively unstable, frequently adopting a more aggressive subtype in the metastases. Notably, loss of ER expression and a luminal to non-luminal subtype conversion was associated with an inferior post-recurrence survival. In addition, ER and molecular subtype assessed at all tumor progression stages were independent prognostic factors for post-recurrence breast cancer mortality in multivariable analyses. Our results demonstrate that drifts in tumor molecular subtypes may occur during tumor progression, conferring adverse consequences on outcome following breast cancer relapse.

Clinical and molecular complexity of breast cancer metastases

Clinical oncology is advancing toward a more personalized treatment orientation, making the need to understand the biology of metastasis increasingly acute. Dissecting the complex molecular, genetic and clinical phenotypes underlying the processes involved in the development of metastatic disease, which remains the principal cause of cancer-related deaths, could lead to the identification of more effective prognostication and targeted approaches to prevent and treat metastases. The past decade has witnessed significant progress in the field of cancer metastasis research. Clinical and technological milestones have been reached which have tremendously enriched our understanding of the complex pathways undertaken by primary tumors to progress into lethal metastases and how some of these processes might be amenable to therapy. The aim of this review article is to highlight the recent advances toward unraveling the clinical and molecular complexity of breast cancer metastases. We focus on genes mediating breast cancer metastases and organ-specific tropism, and discuss gene signatures for prediction of metastatic disease. The challenges of translating this information into clinically applicable tools for improving the prognostication of the metastatic potential of a primary breast tumor, as well as for therapeutic interventions against latent and active metastatic disease are addressed.

Transcriptional Profiling of Breast Cancer Metastases Identifies Liver Metastasis-Selective Genes Associated with Adverse Outcome in Luminal A Primary Breast Cancer

PURPOSE

The complete molecular basis of the organ-specificity of metastasis is elusive. This study aimed to provide an independent characterization of the transcriptional landscape of breast cancer metastases with the specific objective to identify liver metastasis-selective genes of prognostic importance following primary tumor diagnosis.

EXPERIMENTAL DESIGN

A cohort of 304 women with advanced breast cancer was studied. Associations between the site of recurrence and clinicopathologic features were investigated. Fine-needle aspirates of metastases (n = 91) were subjected to whole-genome transcriptional profiling. Liver metastasis-selective genes were identified by significance analysis of microarray (SAM) analyses and independently validated in external datasets. Finally, the prognostic relevance of the liver metastasis-selective genes in primary breast cancer was tested.

RESULTS

Liver relapse was associated with estrogen receptor (ER) expression (P = 0.002), luminal B subtype (P = 0.01), and was prognostic for an inferior postrelapse survival (P = 0.01). The major variation in the transcriptional landscape of metastases was also associated with ER expression and molecular subtype. However, liver metastases displayed unique transcriptional fingerprints, characterized by downregulation of extracellular matrix (i.e., stromal) genes. Importantly, we identified a 17-gene liver metastasis-selective signature, which was significantly and independently prognostic for shorter relapse-free (P < 0.001) and overall (P = 0.001) survival in ER-positive tumors. Remarkably, this signature remained independently prognostic for shorter relapse-free survival (P = 0.001) among luminal A tumors.

CONCLUSIONS

Extracellular matrix (stromal) genes can be used to partition breast cancer by site of relapse and may be used to further refine prognostication in ER positive primary breast cancer.

Abstract P6-08-03: Transcriptional profiling of breast cancer metastases identifies liver metastasis-selective genes associated with adverse outcome in luminal A primary breast cancer

Background: The site of relapse is associated with the prognosis of metastatic breast cancer, but our understanding of the molecular determinants of organ-specificity of metastasis is incomplete. This study aimed to provide additional insight into the biology of breast cancer liver metastases and to identify liver metastasis-selective genes associated with outcome in primary breast cancer.

Methods: A cohort of 304 women with locally advanced and metastatic breast cancer was studied. Estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2) and Ki67 expression were quantified in primary tumors (N=217) by immunohistochemistry and in situ hybridization on tissue microarrays, and molecular subtypes were assigned according to the 2013 St Gallen guidelines. In addition, fine-needle aspirates of metastases (N=91) were subjected to whole genome transcriptional profiling.

Results: Liver relapse was significantly associated with ER positivity (P&lt;0.002) and the luminal B-like subtype (P&lt;0.01) and was prognostic of an inferior post-relapse survival (P&lt;0.001). Transcriptional profiling revealed that the major variation in the transcriptional landscape of breast cancer metastases was associated with the expression of hormone receptors and the tumor molecular subtype. However, liver metastases displayed unique transcriptional fingerprints, characterized by down-regulation of extracellular matrix (i.e. stromal) genes involved in adhesion and skeletal development. Importantly, we identified a subset of 17 liver metastasis-selective genes that displayed significantly decreased expression in primary tumors of high histological grade (grade 3) and of the luminal B and basal subtypes (P&lt;0.001). This 17-gene signature was significantly and independently prognostic of shorter relapse-free (P =0.001) and overall (P=0.03) survival among patients with ER positive primary tumors. Remarkably, the 17-gene signature remained an independent predictor of shorter relapse-free survival (P=0.004) among patients with luminal A primary tumors.

Conclusion: These results highlight a possible role of stroma-related genes in breast cancer liver metastasis biology and validate the prognostic relevance of extracellular matrix/stromal genes in hormone receptor positive primary breast cancer, specifically of the luminal A subtype.

Citation Format: Siker Kimbung, Ida Johansson, Anna Danielsson, Srinivas Veerla, Suzanne Egyhazi, Jonas Bergh, Zakaria Einbeigi, Barbro Linderholm, Elisabet Lidbrink, Niklas Loman, Per Malmström, Martin Söderberg, Thomas M Walz, Mårten Fernö, Thomas Hatschek, Ingrid Hedenfalk, the TEX Study Group. Transcriptional profiling of breast cancer metastases identifies liver metastasis-selective genes associated with adverse outcome in luminal A primary breast cancer [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P6-08-03.

Statin-induced anti-proliferative effects via cyclin D1 and p27 in a window-of-opportunity breast cancer trial

Purpose

Cholesterol lowering statins have been demonstrated to exert anti-tumoral effects on breast cancer by decreasing proliferation as measured by Ki67. The biological mechanisms behind the anti-proliferative effects remain elusive. The aim of this study was to investigate potential statin-induced effects on the central cell cycle regulators cyclin D1 and p27.

Experimental design

This phase II window-of-opportunity trial (Trial registration: ClinicalTrials.gov NCT00816244, NIH) included 50 patients with primary invasive breast cancer. High-dose atorvastatin (80 mg/day) was prescribed to patients for two weeks prior to surgery. Paired paraffin embedded pre- and post-statin treatment tumor samples were analyzed using immunohistochemistry for the expression of estrogen receptor (ER), progesterone receptor (PR), human epidermal growth factor receptor 2 (HER2), and the cell cycle regulators cyclin D1 and p27. Corresponding frozen tumor sample pairs were analyzed for expression of the genes coding for cyclin D1 and p27, CCND1 and CDKN1B, respectively.

Results

Forty-two patients completed all study parts, and immunohistochemical evaluation of ER and PR was achievable in 30 tumor pairs, HER2 in 29 tumor pairs, cyclin D1 in 30 tumor pairs and p27 in 33 tumor pairs. The expression of ER, PR and HER2 did not change significantly following atorvastatin treatment. Cyclin D1 expression in terms of nuclear intensity was significantly decreased (P = 0.008) after statin treatment in paired tumor samples. The protein expression of the tumor suppressor p27, evaluated either as the fraction of stained tumor cells or as cytoplasmic intensity, increased significantly (P = 0.03 and P = 0.02, respectively). At the transcriptional level, no significant differences in mRNA expression were detected for cyclin D1 (CCND1) and p27 (CDKN1B). However, CCND1 expression was lower in tumors responding to atorvastatin treatment with a decrease in proliferation although not significantly (P = 0.08).

Conclusions

We have previously reported statin-induced anti-proliferative effects in breast cancer. This study suggests that cell cycle regulatory effects may contribute to these anti-proliferative effects via cyclin D1 and p27.

Electronic supplementary material

The online version of this article (doi:10.1186/s12967-015-0486-0) contains supplementary material, which is available to authorized users.

Global Transcriptional Changes Following Statin Treatment in Breast Cancer

BACKGROUND

Statins purportedly exert antitumoral effects, but the underlying mechanisms are currently not fully elucidated. The aim of this study was to explore potential statin-induced effects on global gene expression profiles in primary breast cancer.

EXPERIMENTAL DESIGN

This window-of-opportunity phase II trial enrolled 50 newly diagnosed breast cancer patients prescribed atorvastatin (80 mg/day) for 2 weeks presurgically. Pre- and posttreatment tumor samples were analyzed using Significance Analysis of Microarrays (SAM) to identify differentially expressed genes. Similarly, SAM and gene ontology analyses were applied to gene expression data derived from atorvastatin-treated breast cancer cell lines (MCF7, BT474, SKBR3, and MDAMB231) comparing treated and untreated cells. The Systematic Motif Analysis Retrieval Tool (SMART) was used to identify enriched transcription factor-binding sites. Literature Vector Analysis (LitVAn) identified gene module functionality, and pathway analysis was performed using GeneGo Pathways Software (MetaCore; https://portal.genego.com/).

RESULTS

Comparative analysis of gene expression profiles in paired clinical samples revealed 407 significantly differentially expressed genes (FDR = 0); 32 upregulated and 375 downregulated genes. Restricted filtration (fold change ≥1.49) resulted in 21 upregulated and 46 downregulated genes. Significantly upregulated genes included DUSP1, RHOB1, GADD45B, and RGS1. Pooled results from gene ontology, LitVAn and SMART analyses identified statin-induced effects on the apoptotic and MAPK pathways among others. Comparative analyses of gene expression profiles in breast cancer cell lines showed significant upregulation of the mevalonate and proapoptotic pathways following atorvastatin treatment.

CONCLUSIONS

We report potential statin-induced changes in global tumor gene expression profiles, indicating MAPK pathway inhibition and proapoptotic events.

Molecular subtyping of serous ovarian tumors reveals multiple connections to intrinsic breast cancer subtypes

OBJECTIVE

Transcriptional profiling of epithelial ovarian cancer has revealed molecular subtypes correlating to biological and clinical features. We aimed to determine gene expression differences between malignant, benign and borderline serous ovarian tumors, and investigate similarities with the well-established intrinsic molecular subtypes of breast cancer.

METHODS

Global gene expression profiling using Illumina's HT12 Bead Arrays was applied to 59 fresh-frozen serous ovarian malignant, benign and borderline tumors. Nearest centroid classification was performed applying previously published gene profiles for the ovarian and breast cancer subtypes. Correlations to gene expression modules representing key biological breast cancer features were also sought. Validation was performed using an independent, publicly available dataset.

RESULTS

5,944 genes were significantly differentially expressed between benign and malignant serous ovarian tumors, with cell cycle processes enriched in the malignant subgroup. Borderline tumors were split between the two clusters. Significant correlations between the malignant serous tumors and the highly aggressive ovarian cancer signatures, and the basal-like breast cancer subtype were found. The benign and borderline serous tumors together were significantly correlated to the normal-like breast cancer subtype and the ovarian cancer signature derived from borderline tumors. The borderline tumors in the study dataset, in addition, also correlated significantly to the luminal A breast cancer subtype. These findings remained when analyzed in an independent dataset, supporting links between the molecular subtypes of ovarian cancer and breast cancer beyond those recently acknowledged.

CONCLUSIONS

These data link the transcriptional profiles of serous ovarian cancer to the intrinsic molecular subtypes of breast cancer, in line with the shared clinical and molecular features between high-grade serous ovarian cancer and basal-like breast cancer, and suggest that biomarkers and targeted therapies may overlap between these tumor subsets. The link between benign and borderline ovarian cancer and luminal breast cancer may indicate endocrine responsiveness in a subset of ovarian cancers.

Claudin-2 is an independent negative prognostic factor in breast cancer and specifically predicts early liver recurrences

BACKGROUND

Predicting any future metastatic site of early-stage breast cancer is important as it significantly influences the prognosis of advanced disease. This study aimed at investigating the potential of claudin-2, over-expressed in breast cancer liver metastases, as a biomarker for predicting liver metastatic propensity in primary breast cancer.

METHODS

Claudin-2 expression was analyzed in two independent cohorts. Cohort 1 included 304 women with metastatic breast cancer diagnosed between 2002 and 2007, while cohort 2 included 237 premenopausal women with early-stage node-negative breast cancer diagnosed between 1991 and 1994. Global transcriptional profiling of fine-needle aspirates from metastases was performed, followed by immunohistochemical analyses in archival primary tumor tissue. Associations between claudin-2 expression and relapse site were assessed by univariable and multivariable Cox regression models including conventional prognostic factors. Two-sided statistical tests were used.

RESULTS

CLDN2 was significantly up-regulated (P < 0.001) in liver metastases compared to other metastatic sites. Claudin-2 protein was more frequently expressed in primary tumors from patients who subsequently developed liver metastases (P = 0.02) and high expression was associated with a shorter metastasis-free interval (cohort 1, HR = 1.4, 95% CI = 1.0-1.9; cohort 2, HR = 2.2, 95% CI = 1.3-3.5). Specifically, a significantly shorter interval between primary tumor diagnosis and liver-specific recurrence was observed among patients with high levels of claudin-2 expression in the primary tumor (cohort 1, HR = 2.3, 95% CI = 1.3-3.9).

CONCLUSION

These results suggest a novel role for claudin-2 as a prognostic biomarker with the ability to predict not only the likelihood of a breast cancer recurrence, but more interestingly, the liver metastatic potential of the primary tumor.

Abstract B8: Molecular subtyping of epithelial ovarian cancer reveals connections to intrinsic breast cancer subtypes

Aim: Epithelial ovarian cancer is one of the most lethal female cancers. It is a heterogeneous group of neoplasms and the different histologic subtypes are thought to constitute separate disease entities. Efforts have been made to characterize ovarian cancers further and molecular subgroups that correlate to clinical features have been reported, but are still not in clinical use (Tothill et al., Clin Cancer Res, 2008). The subgroups, called C1-C6, represent serous and endometrioid ovarian tumors with the C1-C2 and C4-C5 subgroups characterizing high-grade serous tumors and correlated to a worse prognosis. The C3 and C6 subtypes represent borderline and low-grade tumors and show a favorable prognosis.

We aimed to further outline and refine the genetic differences between malignant, benign and borderline ovarian tumors and to investigate similarities between ovarian cancer and the well described intrinsic subtypes of breast cancer (Perou et al., Nature, 2000).

Materials and methods: Global gene expression profiling (Illumina HT-12 bead arrays) was applied to 72 fresh-frozen serous ovarian tumors (37 adenocarcinomas, 17 adenomas, 5 borderline tumors,13 biological replicates) collected in the ovarian tumor tissue biobank at Skane University Hospital, Sweden (2004-2011). We performed nearest centroid classification of our tumors for the molecular subtypes of ovarian cancer (“C-signatures”) as well as for the intrinsic subgroups of breast cancer (luminal A, luminal B, basal-like, normal-like, and HER2) using the genes from Hu et al. (BMC Genomics, 2006). The results were validated by performing nearest centroid classification of the intrinsic breast cancer subtypes and the C-signatures on the ovarian tumors in the Tothill cohort as well.

Results: Our malignant tumors correlated significantly to the basal-like breast cancer subtype (p&lt;0.001) and to the ovarian C1, C2 and C4 signatures (p=0.020). The basal-like tumors, in turn, correlated significantly to the C2 and C4 signatures (p=0.019 and p=0.001, respectively), thus supporting a link between molecular subtypes of ovarian and breast cancers. The borderline and benign tumors showed a significant correlation to the normal-like breast cancer subtype and the ovarian C3 signature, and these signatures also correlated significantly with each other (p&lt;0.001). These findings were supported when the breast cancer subtypes were applied to the Tothill cohort; the basal-like subtype correlated significantly to the C2 signature and the normal-like subtype to the C3 signature (p&lt;0.001). Of interest, there was a tendency towards worse prognosis among malignant tumors that correlated to the basal-like breast cancer subtype compared to the other malignant tumors, which is in line with similar findings in breast cancer. All reported p-values are calculated using Fischer's Exact Test.

Conclusion: Both epithelial ovarian cancers and breast cancers are heterogeneous diseases, nevertheless they share many similarities such as hormonal influence and varying long-term prognosis. Our novel findings support a link between previously reported molecular subtypes in ovarian cancer and the well-established intrinsic subtypes of breast cancer, which could potentially be of use for further investigations of biomarkers in ovarian cancer and new thinking regarding the use of chemotherapeutic agents as well as targeted treatments.

Citation Format: Jenny-Maria Jönsson, Mev Dominguez-Valentin, Ida Johansson, Siker Kimbung, Mats Jönsson, Anna Måsbäck, Susanne Malander, Mef Nilbert. Molecular subtyping of epithelial ovarian cancer reveals connections to intrinsic breast cancer subtypes. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: From Concept to Clinic; Sep 18-21, 2013; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2013;19(19 Suppl):Abstract nr B8.

Abstract B58: Claudin-2 is an independent negative prognostic factor in breast cancer and specifically predicts early liver recurrences

Background: The liver is the third most frequent breast cancer metastatic site and hepatic metastases confer an inferior prognosis relative to bone and lung metastases. Metastatic sites differ depending on the phenotype of the primary tumor, but the mechanisms driving this organ-specific tropism are not well understood. The scarcity of clinical samples from liver metastases has greatly impeded the development of a human liver metastasis gene signature for predicting the likelihood of liver metastasis after adjuvant therapy and identifying biomarkers for liver-specific recurrence from breast cancer.

Objectives: This study was designed to provide a description of the transcriptional landscape of breast cancer site-specific metastases and to investigate the role of claudin-2 (CLDN2) expression in breast cancer progression and prediction of liver recurrences.

Methods: Global transcriptional profiling of breast cancer metastatic lesions (n=92) from different anatomical sites was performed and genes differentially expressed between liver metastases versus other metastatic sites were identified. Immunohistochemical (IHC) staining of CLDN2 protein was performed on tissue microarrays of primary tumors and matched lymph node metastases present at the time of primary diagnosis in a cohort of patients with metastatic disease (n=192), and was validated in an independent cohort of node-negative breast cancer patients (n=208).

Results: Unsupervised principal component analyses and hierarchical clustering showed that the previously described and well-known intrinsic subtypes constituted the strongest discriminator between the metastatic lesions, and in addition revealed that liver metastases displayed a unique gene expression profile. Gene ontology analyses of genes significantly altered in the liver compared to other sites revealed a down-regulation of extracellular matrix remodeling, tight-junctions and focal adhesion genes in the liver. Remarkably, however, CLDN2 (a tight-junction family member) was found to be up-regulated in the liver metastases (P&lt;0.001). IHC staining for CLDN2 in primary tumors and matched lymph node metastases revealed that it was more frequently expressed in lymph node metastases compared to primary tumors (P=0.001). Also, consistent with mRNA expression levels, high protein expression was more frequently observed in tumors from patients who eventually developed a liver metastasis (p=0.02). Interestingly, high expression of CLDN2 in the primary tumor was associated with a shorter time to recurrence at any site (HR=1.42; 95% CI=1.0-1.9) and with breast cancer specific death (HR=1.42; 95% CI=0.98-2.1). Specifically, high expression of CLDN2 in the primary tumor was associated with shorter progression to liver metastasis (HR=2.28; 95% CI=1.3-3.9). CLDN2 remained a significant prognostic factor for relapse free and liver metastasis free survival in multivariate analyses adjusting for known breast cancer prognostic factors. Furthermore, evaluation of CLDN2 expression in an independent cohort confirmed its negative prognostic value for early recurrences (HR=2.15; 95% CI=1.3-3.5).

Conclusions: These results suggest that the intrinsic subtypes of primary breast cancers are to a large extent maintained in recurrences, and further that liver metastases may be notably different and represent a distinct entity with a separate underlying biology compared to other metastases. In addition, a potential role of CLDN2 in the development of breast cancer liver metastases is highlighted and identifies CLDN2 as a novel negative prognostic factor in breast cancer which specifically predicts time to liver recurrence.

Citation Format: Siker Kimbung, Mårten Fernö, Per Malmström, Thomas Hatschek, Ingrid Hedenfalk. Claudin-2 is an independent negative prognostic factor in breast cancer and specifically predicts early liver recurrences. [abstract]. In: Proceedings of the AACR Special Conference on Tumor Invasion and Metastasis; Jan 20-23, 2013; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2013;73(3 Suppl):Abstract nr B58.

Abstract P1-05-07: Prognostic relevance of Claudin-2 expression in metastatic breast cancer

The site of relapse is known to be a strong prognostic factor of survival from metastatic breast cancer. The liver is the third most frequent site affected and patients with hepatic metastases have an inferior prognosis relative to patients with bone and lung metastases. Predicting the likelihood of liver metastasis after adjuvant therapy of primary breast cancer is challenging. The aim of this study was to identify and characterize genes associated with breast cancer liver metastases. We thus performed global transcriptional profiling of 120 metastatic lesions from different anatomical sites from breast cancer patients enrolled in a randomized clinical trial1 and found that while the expression of other matrix remodelling and tight-junction molecules was down-regulated in liver metastases, Claudin-2 (CLDN2) was significantly up-regulated (p = 0.001). Furthermore, high expression of CLDN2 was also observed amongst patients diagnosed with a liver metastasis, irrespective of the specific site of the metastasis that was profiled, compared to patients without hepatic metastases (p = 0.001). We further investigated the prognostic significance of CLDN2 protein expression by immunohistochemical staining of primary tumours and matched lymph node metastases from a larger cohort of patients (n∼200) with metastatic breast cancer. We found CLDN2 to be significantly more frequently expressed in lymph node metastases compared to primary tumours (p = 0.013). Also, consistent with mRNA expression levels, more frequent expression of CLDN2 protein was observed in the primary tumours of patients who eventually developed a liver metastasis (p = 0.027). Interestingly, high expression of CLDN2 in the primary tumour was associated with a shorter time to recurrence (p = 0.032). Specifically, high expression of CLDN2 in the primary tumour was associated with a shorter progression to liver metastasis (p = 0.002). These data highlight a potential role of CLDN2 in the development and prognosis of breast cancer liver metastases.

1. Hatschek, T., et al. Individually tailored treatment with epirubicin and paclitaxel with or without capecitabine as first-line chemotherapy in metastatic breast cancer: a randomized multicenter trial. Breast Cancer Res Treat. 2012, 131(3):939–47.

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P1-05-07.

Abstract 3386: Molecular profiling of breast cancer organ-specific metastases

Background: Breast cancer molecular subtypes preferentially metastasize to specific organs, but the underlying molecular mechanisms are not well understood. While several studies have attempted to delineate these mechanisms by making predictions from primary tumours, the likelihood of missing further relevant biological differences which may be enriched or distinctively present in the metastases cannot be overlooked. In addition, survival after relapse is influenced by the anatomical location of the metastasis, with visceral involvement associated with the poorest survival, suggesting that differences in biology and response to treatment may exist. However, the scarcity of clinical material from metastatic lesions has largely prevented detailed molecular characterization of breast cancer site-specific metastases. Material and Methods: We performed global gene expression profiling on 122 fine needle aspirates of metastatic lesions from different anatomical sites obtained from breast cancer patients treated within the Swedish randomized trial (TEX) of chemotherapy for metastatic breast cancer. Sub-classification was performed using unsupervised hierarchical clustering, while differentially expressed genes and modulated pathways in metastases from different sites and sub-classes were identified using Significance Analysis of Microarrays (SAM) analysis. Breast cancer survival after relapse was also compared between patients. Results: We confirmed the observation that breast cancer metastasis to visceral organs is associated with the poorest outcome. Molecularly, samples were sub-classified into groups with strong correlations with the previously described breast cancer intrinsic subtypes and also striking overlap with pathological characteristics of the primary tumour. Metastasis pairs from the same individual were more similar to each other than to independent metastatic lesions from other patients. More interestingly, liver metastases formed a unique sub-cluster which could be distinguished from the other sites by the expression of several genes (and pathways) involved in focal adhesion, matrix remodelling, and wnt signalling. Conclusions: Our data suggest that breast cancer molecular subtypes and primary tumour characteristics are to a large extent maintained in recurrences and further that liver metastases may be notably different and represent a distinct entity with a separate underlying biology which may hence require specific targeted therapeutic management.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3386. doi:1538-7445.AM2012-3386

Abstract P6-15-04: Targeting the PI3K Pathway Enhances the Effect of PARP-1 Inhibition in BRCA1 Deficient Breast Cancer Cells

Background: Available targeted therapies have improved the prognosis for many women diagnosed with breast cancer. However, more than 15% of cases do not benefit from these targeted agents. Amongst these are tumours with Breast cancer 1 (BRCA1) dysfunction, triple-negative and basal-like breast cancers, which remain a treatment challenge and are associated with a poor outcome. New approaches to specifically target these groups of breast tumors are needed. The DNA damage repair defects associated with lack of BRCA1 confers sensitivity to poly-(ADP-ribose) polymerase 1 (PARP-1) inhibitors. Furthermore, most BRCA1 mutated tumours do not express the phosphatase and tensin homolog (PTEN) implying activation of the phosphatidylinositol-3 kinase (PI3K) pathway which promotes cell survival and resistance to apoptosis. The aim of this study was to investigate if co-targeting the PI3K pathway can improve the response of BRCA1 mutated cells to PARP-1 inhibition.

Material and methods:, Two BRCA1 and PTEN deficient breast cancer cell lines; MDA-MB-436 and SUM149, were treated with the PARP-1 inhibitor AG14361 (1-(4-dimethylaminomethyl-phenyl)-8-9-dihydro-7H-2,7,9a-benzo[cd]azulen-6-one) and the PI3K inhibitor LY294002 (2-(4-morpholinyl)-8-phenyl-chromone), as single agents and in combination. Cytotoxicity was estimated using the sulpho-rhodamine B assay while cell cycle phase distribution and DNA integrity were analyzed by flow cytometry.

Results: AG14361 induced DNA damage leading to G2/M arrest and decreased viability. LY294002, on the other hand, affected the cell cycle by arresting cells in G1. Importantly, combining AG14361 with LY294002 further decreased survival (P&lt;0.001) with a concomitant decrease in G2/M (P&lt;0.05).

Discussion: This observation may indicate a combination specific up-regulation of apoptosis and suggests that LY294002 potentiates the effects of AG14361. Our results may represent an improved selective targeted treatment strategy for BRCA1 deficient breast cancers and other cancers with DNA damage repair defects and activated PI3K signalling.

Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P6-15-04.