Estrogen receptor splice variants as a potential source of false-positive estrogen receptor status in breast cancer diagnostics

Delineating intra-tumoral heterogeneity and tumor evolution in breast cancer using precision-based approaches

The burden of breast cancer continues to increase worldwide as it remains the most diagnosed tumor in females and the second leading cause of cancer-related deaths. Breast cancer is a heterogeneous disease characterized by different subtypes which are driven by aberrations in key genes such as BRCA1 and BRCA2, and hormone receptors. However, even within each subtype, heterogeneity that is driven by underlying evolutionary mechanisms is suggested to underlie poor response to therapy, variance in disease progression, recurrence, and relapse. Intratumoral heterogeneity highlights that the evolvability of tumor cells depends on interactions with cells of the tumor microenvironment. The complexity of the tumor microenvironment is being unraveled by recent advances in screening technologies such as high throughput sequencing; however, there remain challenges that impede the practical use of these approaches, considering the underlying biology of the tumor microenvironment and the impact of selective pressures on the evolvability of tumor cells. In this review, we will highlight the advances made thus far in defining the molecular heterogeneity in breast cancer and the implications thereof in diagnosis, the design and application of targeted therapies for improved clinical outcomes. We describe the different precision-based approaches to diagnosis and treatment and their prospects. We further propose that effective cancer diagnosis and treatment are dependent on unpacking the tumor microenvironment and its role in driving intratumoral heterogeneity. Underwriting such heterogeneity are Darwinian concepts of natural selection that we suggest need to be taken into account to ensure evolutionarily informed therapeutic decisions.

Distinct Neoadjuvant Chemotherapy Response and 5-Year Outcome in Patients With Estrogen Receptor-Positive, Human Epidermal Growth Factor Receptor 2-Negative Breast Tumors That Reclassify as Basal-Type by the 80-Gene Signature

The 80-gene molecular subtyping signature (80-GS) reclassifies a proportion of immunohistochemistry (IHC)-defined luminal breast cancers (estrogen receptor–positive [ER+], human epidermal growth factor receptor 2–negative [HER2–]) as Basal-Type. We report the association of 80-GS reclassification with neoadjuvant treatment response and 5-year outcome in patients with breast cancer.

Identity exposed: genomic assay unmasks TNBC-like breast cancer tumors disguised as HR+ #NBRST

Lost but Not Least-Novel Insights into Progesterone Receptor Loss in Estrogen Receptor-Positive Breast Cancer

Estrogen receptor α (ERα) and progesterone receptor (PgR) are crucial prognostic and predictive biomarkers that are usually co-expressed in breast cancer (BC). However, 12-24% of BCs present ERα(+)/PgR(-) phenotype at immunohistochemical evaluation. In fact, BC may either show primary PgR(-) status (in chemonaïve tumor sample), lose PgR expression during neoadjuvant treatment, or acquire PgR(-) phenotype in local relapse or metastasis. The loss of PgR expression in ERα(+) breast cancer may signify resistance to endocrine therapy and poorer outcomes. On the other hand, ERα(+)/PgR(-) BCs may have a better response to neoadjuvant chemotherapy than double-positive tumors. Loss of PgR expression may be a result of pre-transcriptional alterations (copy number loss, mutation, epigenetic modifications), decreased transcription of the PGR gene (e.g., by microRNAs), and post-translational modifications (e.g., phosphorylation, sumoylation). Various processes involved in the down-regulation of PgR have distinct consequences on the biology of cancer cells. Occasionally, negative PgR status detected by immunohistochemical analysis is paradoxically associated with enhanced transcriptional activity of PgR that might be inhibited by antiprogestin treatment. Identification of the mechanism of PgR loss in each patient seems challenging, yet it may provide important information on the biology of the tumor and predict its responsiveness to the therapy.

Estrogens and Progestogens in Triple Negative Breast Cancer: Do They Harm?

Triple-negative breast cancers (TNBC) occur more frequently in younger women and do not express estrogen receptor (ER) nor progesterone receptor (PR), and are therefore often considered hormone-insensitive. Treatment of premenopausal TNBC patients almost always includes chemotherapy, which may lead to premature ovarian insufficiency (POI) and can severely impact quality of life. Hormone replacement therapy (HRT) is contraindicated for patients with a history of hormone-sensitive breast cancer, but the data on safety for TNBC patients is inconclusive, with a few randomized trials showing increased risk-ratios with wide confidence intervals for recurrence after HRT. Here, we review the literature on alternative pathways from the classical ER/PR. We find that for both estrogens and progestogens, potential alternatives exist for exerting their effects on TNBC, ranging from receptor conversion, to alternative receptors capable of binding estrogens, as well as paracrine pathways, such as RANK/RANKL, which can cause progestogens to indirectly stimulate growth and metastasis of TNBC. Finally, HRT may also influence other hormones, such as androgens, and their effects on TNBCs expressing androgen receptors (AR). Concluding, the assumption that TNBC is completely hormone-insensitive is incorrect. However, the direction of the effects of the alternative pathways is not always clear, and will need to be investigated further.

Molecular intrinsic versus clinical subtyping in breast cancer: A comprehensive review

Breast cancer is a heterogeneous disease manifesting diversity at the molecular, histological and clinical level. The development of breast cancer classification was centered on informing clinical decisions. The current approach to the classification of breast cancer, which categorizes this disease into clinical subtypes based on the detection of estrogen receptor, progesterone receptor, human epidermal growth factor receptor 2, and proliferation marker Ki67, is not ideal. This is manifested as a heterogeneity of therapeutic responses and outcomes within the clinical subtypes. The newer classification model, based on gene expression profiling (intrinsic subtyping) informs about transcriptional responses downstream from IHC single markers, revealing deeper appreciation for the disease heterogeneity and capturing tumor biology in a more comprehensive way than an expression of a single protein or gene alone. While accumulating evidences suggest that intrinsic subtypes provide clinically relevant information beyond clinical surrogates, it is imperative to establish whether the current conventional immunohistochemistry-based clinical subtyping approach could be improved by gene expression profiling and if this approach has a potential to translate into clinical practice.

Current concepts in breast cancer genomics: An evidence based review by the CGC breast cancer working group

BACKGROUND

Genomic abnormalities in breast cancer have been described according to diverse conceptual frameworks, including histologic subtypes, clinical molecular subtypes, intrinsic DNA, RNA, and epigenetic profiles, and activated molecular pathways.

METHODS

The Cancer Genomics Consortium (CGC) Breast Cancer Workgroup performed an evidence based literature review to summarize current knowledge of clinically significant genomic alterations in breast cancer using CGC levels of evidence. Targetable or disease-defining alterations were prioritized.

RESULTS

We summarized genomic alterations in breast cancer within a framework of existing clinical tools for diagnosis, risk stratification, and therapeutic management. Using CGC levels of evidence, we catalog copy number profiles, gene expression profiles, and mutations in clinically significant genes. We also describe emerging molecular markers such as methylation profiling and immunotherapy biomarkers.

CONCLUSION

A summary of currently available information on breast cancer genomics will enhance precision medicine by serving as an interpretive resource for clinical laboratory geneticists, providing a foundation for future practice guidelines, and identifying knowledge gaps to address in future research.

Current immunoassay methods and their applications to clinically used biomarkers of breast cancer

Breast cancer is the leading cause of cancer-related mortality worldwide, with a higher incidence in developed countries. The biomarkers for breast cancer such as estrogen receptor, progesterone receptor, human epidermal growth factor receptor 2, CA (cancer antigen) 15-3, CA 27.29, and carcinoembryonic antigen have been recommended for use in the laboratory based on the guidelines of American and European societies. Immunoassays have been frequently and consistently used to detect these clinically established biomarkers of breast cancer. Despite the higher accessibility of serum biomarkers, including CA 15-3, CA 27.29, and CEA, compared to tissue markers, variations in immunoassays affect their standardization and clinical utility. When reviewing the immunoassays used to detect these serum markers, we found that the most frequently used immunoassay was enzyme-linked immunosorbent assay, followed by electrochemiluminescent immunoassay, and then chemiluminescence immunoassay for CA 15-3 and CEA. Meanwhile, the chemiluminescence immunoassay was the most common technique for CA27.29. The electrochemiluminescent immunoassay and monoclonal fluorometric assay have become the preferred methods in 2010-2019 compared to 2000-2009. Analytical and clinical performance factors such as sensitivity, specificity, detection limit, hazard risk to laboratory personnel, speed, and economic feasibility influenced these changes in user preference. When using the immunoassays, there should be a comprehensive understanding of the principles, advantages, vulnerability, and precautions for interpretation. In the future, a combination of immunological biomarkers and genetic platforms will benefit patients with breast cancer by facilitating prognosis prediction and guiding therapeutic intervention.

Estrogen receptor variants in ER-positive basal-type breast cancers responding to therapy like ER-negative breast cancers

Immunohistochemically ER-positive HER2-negative (ER+HER2−) breast cancers are classified clinically as Luminal-type. We showed previously that molecular subtyping using the 80-gene signature (80-GS) reclassified a subset of ER+HER2− tumors to molecular Basal-type. We report here that molecular reclassification is associated with expression of dominant-negative ER variants and evaluate response to neoadjuvant therapy and outcome in the prospective neoadjuvant NBRST study (NCT01479101). The 80-GS reclassified 91 of 694 (13.1%) immunohistochemically Luminal-type tumors to molecular Basal-type. Importantly, all 91 discordant tumors were classified as high-risk, whereas only 66.9% of ER+/Luminal-type tumors were classified at high-risk for disease recurrence (i.e., Luminal B) (P < 0.001). ER variant mRNA (ER∆3, ER∆7, and ERα-36) analysis performed on 84 ER+/Basal tumors and 48 ER+/Luminal B control tumors revealed that total ER mRNA was significantly lower in ER+/Basal tumors. The relative expression of ER∆7/total ER was significantly higher in ER+/Basal tumors compared to ER+/Luminal B tumors (P < 0.001). ER+/Basal patients had similar pathological complete response (pCR) rates following neoadjuvant chemotherapy as ER−/Basal patients (34.3 vs. 37.6%), and much higher than ER+/Luminal A or B patients (2.3 and 5.8%, respectively). Furthermore, 3-year distant metastasis-free interval (DMFI) for ER+/Basal patients was 65.8%, significantly lower than 96.3 and 88.9% for ER+/Luminal A and B patients, respectively, (log-rank P < 0.001). Significantly lower total ER mRNA and increased relative ER∆7 dominant-negative variant expression provides a rationale why ER+/Basal breast cancers are molecularly ER-negative. Identification of this substantial subset of patients is clinically relevant because of the higher pCR rate to neoadjuvant chemotherapy and correlation with clinical outcome.

Multimodal Assessment of Estrogen Receptor mRNA Profiles to Quantify Estrogen Pathway Activity in Breast Tumors

BACKGROUND

Molecular markers have transformed our understanding of the heterogeneity of breast cancer and have allowed the identification of genomic profiles of estrogen receptor (ER)-α signaling. However, our understanding of the transcriptional profiles of ER signaling remains inadequate. Therefore, we sought to identify the genomic indicators of ER pathway activity that could supplement traditional immunohistochemical (IHC) assessments of ER status to better understand ER signaling in the breast tumors of individual patients.

MATERIALS AND METHODS

We reduced ESR1 (gene encoding the ER-α protein) mRNA levels using small interfering RNA in ER⁺ MCF7 breast cancer cells and assayed for transcriptional changes using Affymetrix HG U133 Plus 2.0 arrays. We also compared 1034 ER⁺ and ER^- breast tumors from publicly available microarray data. The principal components of ER activity generated from these analyses and from other published estrogen signatures were compared with ESR1 expression, ER-α IHC, and patient survival.

RESULTS

Genes differentially expressed in both analyses were associated with ER-α IHC and ESR1 mRNA expression. They were also significantly enriched for estrogen-driven molecular pathways associated with ESR1, cyclin D1 (CCND1), MYC (v-myc avian myelocytomatosis viral oncogene homolog), and NFKB (nuclear factor kappa B). Despite their differing constituent genes, the principal components generated from these new analyses and from previously published ER-associated gene lists were all associated with each other and with the survival of patients with breast cancer treated with endocrine therapies.

CONCLUSION

A biomarker of ER-α pathway activity, generated using ESR1-responsive mRNAs in MCF7 cells, when used alongside ER-α IHC and ESR1 mRNA expression, could provide a method for further stratification of patients and add insight into ER pathway activity in these patients.

Molecular subtyping improves diagnostic stratification of patients with primary breast cancer into prognostically defined risk groups

Combined use of MammaPrint and a molecular subtyping profile (BluePrint) identifies disease subgroups with marked differences in long-term outcome and response to neo-adjuvant therapy. The aim of this study was to evaluate the prognostic value of molecular subtyping using MammaPrint and BluePrint in women with early-stage breast cancer (BC) treated at US institutions following National Comprehensive Cancer Network standard guidelines. Tumor samples were collected from stage 1-2B consecutively diagnosed BC patients (n = 373) who underwent lumpectomy or mastectomy with an axillary staging procedure between 1992 and 2010 at two institutes (NorthShore University HealthSystem and Fox Chase Cancer Center) in the United States of America, with a median follow-up time of 9.5 years. MammaPrint low-risk patients had a 10-year DMFS of 96 % (95 %CI 92.8–99.4), while MammaPrint high-risk patients had a 10-year DMFS of 87 % (95 %CI 81.9–92.1) with a hazard ratio of 3.62 (95 %CI 1.38–9.50) (p = 0.005). Uni- and multivariate analyses included age, tumor size, grade, ER, and Her2; in multivariate analysis, MammaPrint reached near-significance (HR 3.01; p 0.08). When comparing BluePrint molecular subtyping with clinical stratification, the prognosis (10-year DMFS) was significantly different in 10-year DMFS between the different molecular subtypes (p < 0.001). This retrospective study with 10-year follow-up data provides valuable insight into prognosis of patients with primary BC comparing clinical with molecular subtyping. The BluePrint molecular stratification assay identifies patients with significantly different outcomes compared with standard clinical molecular stratification.

Synergy of urokinase‑type plasminogen activator receptor isomer (D1D2) and integrin α5β1 causes malignant transformation of hepatic cells and the occurrence of liver cancer

The aim of the present study was to investigate the correlations and possible synergy among the urokinase‑type plasminogen activator receptor (uPAR) isomer D1D2 and integrin α5β1 expression levels, malignant transformation in hepatic cells and the occurrence of liver cancer. The expression site and concentration of uPAR (D1D2) were analyzed using polymerase chain reaction and in situ hybridization at the gene level in 60 samples of hepatocellular carcinoma (HCC) tissues, 60 samples of para‑carcinoma tissues and 25 samples of normal liver tissues. The mRNA levels of uPAR (D1D2) and integrin α5β1 were markedly increased para‑carcinoma tissue and liver cancer tissue as compared with those in normal tissue. The grey values of the three groups were significantly different (P<0.05). In situ hybridization revealed that the expression levels of uPAR (D1D2) and integrin α5β1 in the cytoplasm and the positive rate of the two molecules in the HCC tissue were significantly higher than those in the para-carcinoma and normal liver tissues, and the expression levels were positively correlated (rs1=0.257, P<0.05; rs2=0.261, P<0.05). The results suggested that uPAR (D1D2) mRNA overexpression may be due to changes in the conformation of the uPAR isomer. Synergy of uPAR (D1D2) mRNA and integrin α5β1 interaction may result in abnormal signal transduction in liver cells and ultimately liver cell abnormal clonal hyperplasia and malignant transformation.

An epigenomic approach to therapy for tamoxifen-resistant breast cancer

Tamoxifen has been a frontline treatment for estrogen receptor alpha (ERα)-positive breast tumors in premenopausal women. However, resistance to tamoxifen occurs in many patients. ER still plays a critical role in the growth of breast cancer cells with acquired tamoxifen resistance, suggesting that ERα remains a valid target for treatment of tamoxifen-resistant (Tam-R) breast cancer. In an effort to identify novel regulators of ERα signaling, through a small-scale siRNA screen against histone methyl modifiers, we found WHSC1, a histone H3K36 methyltransferase, as a positive regulator of ERα signaling in breast cancer cells. We demonstrated that WHSC1 is recruited to the ERα gene by the BET protein BRD3/4, and facilitates ERα gene expression. The small-molecule BET protein inhibitor JQ1 potently suppressed the classic ERα signaling pathway and the growth of Tam-R breast cancer cells in culture. Using a Tam-R breast cancer xenograft mouse model, we demonstrated in vivo anti-breast cancer activity by JQ1 and a strong long-lasting effect of combination therapy with JQ1 and the ER degrader fulvestrant. Taken together, we provide evidence that the epigenomic proteins BRD3/4 and WHSC1 are essential regulators of estrogen receptor signaling and are novel therapeutic targets for treatment of Tam-R breast cancer.

Drug resistance to targeted therapies: déjà vu all over again

A major limitation of targeted anticancer therapies is intrinsic or acquired resistance. This review emphasizes similarities in the mechanisms of resistance to endocrine therapies in breast cancer and those seen with the new generation of targeted cancer therapeutics. Resistance to single-agent cancer therapeutics is frequently the result of reactivation of the signaling pathway, indicating that a major limitation of targeted agents lies in their inability to fully block the cancer-relevant signaling pathway. The development of mechanism-based combinations of targeted therapies together with non-invasive molecular disease monitoring is a logical way forward to delay and ultimately overcome drug resistance development.