Intrinsic Subtypes from the PAM50 Gene Expression Assay in a Population-Based Breast Cancer Survivor Cohort: Prognostication of Short- and Long-term Outcomes

ArticleinCancer Epidemiology Biomarkers & Prevention 23(5) · February 2014with14 Reads
DOI: 10.1158/1055-9965.EPI-13-1017 · Source: PubMed
Background: The PAM50, a gene expression assay to categorize breast tumors into intrinsic subtypes, has not been previously used to examine short- and long-term prognostication in a population-based cohort where treatment patterns and time of initial follow-up vary. Methods: In a stratified case-cohort design of 1,691 women from the LACE and Pathways breast cancer survivor cohorts, we used PAM50 to categorize tumors into Luminal A, Luminal B, HER2-enriched (E), Basal-like and Normal-like, and to examine risk of early and late recurrence and mortality by Cox proportional hazards regression. Results: Compared with Luminal A, cumulative risk of recurrence and breast cancer (BC) death was higher for Luminal B, Her2-E and Basal-like tumors at 2, 5 and 10 years. However, hazard ratios (HR) of BC death varied over time (<5 years (early) vs. >5 years (late)) for both Basal-like (HR 6.23 early vs.0.63 late) and HER2-E tumors (HR 2.97 early vs. HR 0.73 late) but not for Luminal B tumors where risk was elevated consistently (HR 2.67 early vs. HR 1.47 late). The contrast between Luminal B, HER2-E and Basal-like compared with Luminal A on early recurrence was stronger when subtype was defined by PAM50 than by immunohistochemistry markers (IHC). Conclusions: The PAM50 categorized intrinsic subtypes in a manner that more accurately predicts recurrence and survival, especially for luminal tumors, compared with commonly used methods that rely on traditional IHC clinical markers. Impact: The PAM50 is robust for use in epidemiological studies and should be considered when archived tumor tissues are available.
    • "During the last decade, it has become apparent that gene expression-based data in breast cancer can provide useful biological, prognostic, and predictive informa- tion [1, 2]. For example, the main intrinsic molecular subtypes of breast cancer (Luminal A, Luminal B, HER2- enriched, and Basal-like) are biologically and prognostically relevant [3][4][5][6]and have been associated with anthracycline and tamoxifen benefit in the adjuvant set- ting [7][8][9]. Importantly, the intrinsic subtypes are not fully recapitulated by the combined determination of pathology-based biomarkers such as estrogen receptor (ER), progesterone receptor (PR), Ki67, and HER2 [1, 3, 4,[9][10][11][12], all of which are currently being used in the clinical setting. "
    [Show abstract] [Hide abstract] ABSTRACT: Background: Predicting treatment benefit and/or outcome before any therapeutic intervention has taken place would be clinically very useful. Herein, we evaluate the ability of the intrinsic subtypes and the risk of relapse score at diagnosis to predict survival and response following neoadjuvant chemotherapy. In addition, we evaluated the ability of the Claudin-low and 7-TNBCtype classifications to predict response within triple-negative breast cancer (TNBC). Methods: Gene expression and clinical-pathological data were evaluated in a combined dataset of 957 breast cancer patients, including 350 with TNBC, treated with sequential anthracycline and anti-microtubule-based neoadjuvant regimens. Intrinsic subtype, risk of relapse score based on subtype and proliferation (ROR-P), the Claudin-low subtype and the 7-TNBCtype subtype classification were evaluated. Logistic regression models for pathological complete response (pCR) and Cox models for distant relapse-free survival (DRFS) were used. Results: Basal-like, Luminal A, Luminal B, and HER2-enriched subtypes represented 32.7 %, 30.6 %, 18.2 %, and 10.3 % of cases, respectively. Intrinsic subtype was independently associated with pCR in all patients, in hormone receptor-positive/HER2-negative disease, in HER2-positive disease, and in TNBC. The pCR rate of Basal-like disease was >35 % across all clinical cohorts. Neither the Claudin-low nor the 7-TNBCtype subtype classifications predicted pCR within TNBCs after accounting for intrinsic subtype. Finally, intrinsic subtype and ROR-P provided independent prognostic information beyond clinicopathological variables and type of pathological response. A 5-year DRFS of 97.5 % (92.8-100.0 %) was observed in these neoadjuvant-treated and clinically node-negative patients predicted to be low risk by ROR-P (i.e. 57.4 % of Luminal A tumors with clinically node-negative disease). Conclusions: Intrinsic subtyping at diagnosis provides prognostic and predictive information for patients receiving neoadjuvant chemotherapy. Although we could not exclude a survival benefit of neoadjuvant chemotherapy in patients with early breast cancer with clinically node-negative and ROR-low disease at diagnosis, the absolute benefit of cytotoxic therapy in this group might be rather small (if any).
    Full-text · Article · Dec 2015
    • "Taken together, these findings support the concept that the methylation status of the PREX1 promoter is causally linked to P-REX1 upregulation and associates with poor outcome of breast cancer patients, thus implying PREX1 methylation as a prognostic factor. Although basal-like tumors have the worse prognosis particularly within the first five years after diagnosis [47], most breast cancers belong to the luminal type. Therefore, survival correlations with P-REX1 expression most likely include luminal breast cancer patients as the largest population , thus arguing the possibility that PREX1 promoter methylation has prognostic value to predict outcome in this subset of patients. "
    [Show abstract] [Hide abstract] ABSTRACT: IntroductionThe Rac-GEF P-REX1 is a key mediator of ErbB signaling in breast cancer recently implicated in mammary tumorigenesis and metastatic dissemination. Although P-REX1 is essentially undetectable in normal human mammary epithelial tissue, this Rac-GEF is markedly up-regulated in human breast carcinomas, particularly of the luminal subtype. The mechanisms underlying P-REX1 up-regulation in breast ca-ncer are unknown. Towards the goal of dissecting the mechanistic basis of P-REX1 overexpression in breast cancer, in this study we focused on the analysis of methylation of the PREX1 gene promoter.Methods To determine the methylation status of the PREX1 promoter region, we used bisulfite genomic sequencing and pyrosequencing approaches. Re-expression studies in cell lines were carried out by treatment of breast cancer cells with the demethylating agent 5-aza-2¿-deoxycitidine. PREX1 gene methylation in different human breast cancer subtypes was analyzed from the TCGA database.ResultsWe found that the human PREX1 gene promoter has a CpG island located between ¿1.2 kb and +1.4 kb, and that DNA methylation in this region inversely correlates with P-REX1 expression in human breast cancer cell lines. A comprehensive analysis of human breast cancer cell lines and tumors revealed significant hypomethylation of the PREX1 promoter in ER-positive, luminal subtype, whereas hypermethylation occurs in basal-like breast cancer. Treatment of normal MCF-10A or basal-like cancer cells, MDA-MB-231 with the demethylating agent 5-aza-2¿-deoxycitidine in combination with the histone deacetylase inhibitor trichostatin A restores P-REX1 levels to those observed in luminal breast cancer cell lines, suggesting that aberrant expression of P-REX1 in luminal breast cancer is a consequence of PREX1 promoter demethylation. Unlike PREX1, the pro-metastatic Rho/Rac-GEF, VAV3, is not regulated by methylation. Notably, PREX1 gene promoter hypomethylation is a prognostic marker of poor patient survival.Conclusions Our study identified for the first time gene promoter hypomethylation as a distinctive subtype-specific mechanism for controlling the expression of a key regulator of Rac-mediated motility and metastasis in breast cancer.
    Full-text · Article · Sep 2014
    • "The most frequently diagnosed sub-type is Luminal A (51%), followed by Luminal B (29%), Basal (17%), HER2 (12.5%), and Claudin-low (2%). The importance of these molecular subtypes cannot be underestimated as they allow for prediction of therapeutic targets and they display distinct clinical courses (Caan et al., 2014). Women whose tumors fit the Luminal A profile have the best prognosis whereas those whose tumors have Luminal B or Basal profiles have poor prognosis. "
    [Show abstract] [Hide abstract] ABSTRACT: Nuclear receptors exert profound effects on mammary gland physiology and have complex roles in the etiology of breast cancer. In addition to receptors for classic steroid hormones such as estrogen and progesterone, the nuclear vitamin D receptor (VDR) interacts with its ligand 1α,25(OH)2D3 to modulate the normal mammary epithelial cell genome and subsequent phenotype. Observational studies suggest that vitamin D deficiency is common in breast cancer patients and that low vitamin D status enhances the risk for disease development or progression. Genomic profiling has characterized many 1α,25(OH)2D3 responsive targets in normal mammary cells and in breast cancers, providing insight into the molecular actions of 1α,25(OH)2D3 and the VDR in regulation of cell cycle, apoptosis, and differentiation. New areas of emphasis include regulation of tumor metabolism and innate immune responses. However, the role of VDR in individual cell types (i.e., epithelial, adipose, fibroblast, endothelial, immune) of normal and tumor tissues remains to be clarified. Furthermore, the mechanisms by which VDR integrates signaling between diverse cell types and controls soluble signals and paracrine pathways in the tissue/tumor microenvironment remain to be defined. Model systems of carcinogenesis have provided evidence that both VDR expression and 1α,25(OH)2D3 actions change with transformation but clinical data regarding vitamin D responsiveness of established tumors is limited and inconclusive. Because breast cancer is heterogeneous, analysis of VDR actions in specific molecular subtypes of the disease may help to clarify the conflicting data. The expanded use of genomic, proteomic and metabolomic approaches on a diverse array of in vitro and in vivo model systems is clearly warranted to comprehensively understand the network of vitamin D regulated pathways in the context of breast cancer.
    Full-text · Article · Jun 2014
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