Abstract P2-11-22: Expression of milk whey protein genes in human breast carcinoma cells isolated by LCM impacts prediction of clinical outcomes

Background: Milk whey protein consumption has been associated with breast cancer prevention, therapy and treatment tolerance, and other studies detected these proteins or their mRNAs in breast cancer models or tissues. Our objectives are to ascertain expression of certain whey protein genes in human breast carcinoma cells isolated by Laser Capture Microdissection (LCM) and to determine if gene expression is related to risk of recurrence and overall survival in lesions with various ER/PR status. Genes selected were: LALBA (alpha-lactalbumin), LPO (lactoperoxidase), LTF (lactotransferrin), PAEP (progestogen associated endometrial protein or glycodelin) and SSP1 (secreted phosphoprotein 1 or osteopontin). This retrospective investigation is unique in that highly quantified ER and PR protein levels and ESR1 and PGR relative expression from pure populations of carcinoma cells were employed to stratify cancers into ER/PR subcategories to assess relationships of expression of candidate genes with clinical outcomes. Methods: This investigation of primary breast carcinomas from 170 postmenopausal and 77 premenopausal patients used a matchless deidentified dataset of quantified estrogen receptor (ER) and progestin receptor (PR) protein results with clinical follow-up. ER/PR protein levels, expressed as fmol/mg cytosol protein, were quantified earlier from each breast carcinoma with FDA-approved kits, either Radioligand-Binding Assay (LBA, NEN/DuPont) and/or enzyme immunoassay (EIA, Abbott Labs). Patients were treated with the standard of care at the time of diagnosis. The PixCell IleTM (ThermoFisher, Arcturus) LCM instrument was used to procure only carcinoma cells from tissue sections of de-identified, frozen biopsies, using protocols we employed earlier. Total RNA of each fixed specimen was extracted, purified and amplified to obtain relative expression levels of approximately 22,000 genes by microarray, providing an assessment of mRNA in carcinoma cells only. Relationships of relative gene expression, quantified ER/PR and other features of primary breast cancers were analyzed with clinical results using R software v4.2.0 (Vigorous Calisthenics) by Univariable Cox Regression, Kaplan Meier plots and various tests (i.e., Wilcoxon, Log Ranked, Spearman and/or Chi Square tests). Bidirectional elimination stepwise regression was also used to derive best predictors of patient outcomes. Results: Violin plots of expression distribution of each milk protein gene of 247 biopsies regardless of patient menopausal status revealed that LALBA and SSP1 were highly elevated (p < 0.001) in ER+ (n = 146) or PR+ (n = 146) breast cancer cells while PAEP was quite diminished (p < 0.001). No difference was observed in LPO expression in ER+ or PR+ cells and LTF was only elevated slightly (p < 0.05) in ER+ cells. Regardless of ER/PR status of breast cancer, LTF, LALBA, SSP1, AR and ESR1 gene expression levels were increased significantly in postmenopausal versus premenopausal patients while PAEP was decreased (p < 0.001). No difference was observed in LPO or PGR expression. Correlation matrices examined gene to gene and receptor protein to gene relationships. Using Kaplan Meier analyses of each gene alone with Log Ranked Tests of outcomes, only SSP1 expression was associated with clinical outcome, i.e., overexpression was associated with lower PFS and OS (p = < 0.05). Conclusions: Application of bidirectional elimination stepwise regression of gene expression of the five milk proteins collectively with ER/PR protein status of each carcinoma revealed that LALBA gene expression enhanced prediction of PFS in ER+ cancer while PAEP expression was associated with improved prediction of OS in ER+ carcinomas. We report that expression of LALBA and PAEP genes, largely associated with milk production in normal breast tissue, are also expressed in certain breast carcinomas and influence prediction of patient survival.

Citation Format: James L. Wittliff, Michael W. Daniels. Expression of milk whey protein genes in human breast carcinoma cells isolated by LCM impacts prediction of clinical outcomes [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-11-22.

Abstract P1-06-07: Enhanced differentiation of clinical behavior by breast carcinomas utilizing quantification of estrogen and progestin receptor proteins and gene expression subsets

Background: IHC analyses of clinical biomarkers for breast cancer management yield semi-quantitative results potentially complicated by variation in methods and interpretation. We are mining a comprehensive database established over four decades that contains deidentified results of quantified protein and RNA biomarkers with clinical outcomes to detect candidates for companion diagnostics and molecular targets. Assays were performed in a Reference Laboratory holding both CLIA and Commonwealth of Kentucky licenses. Methods: This retrospective investigation utilized ER/PR protein levels, expressed as fmol/mg cytosol protein, that were quantified for each of 2339 carcinoma biopsies with FDA-approved kits and cut-off values by radio-ligand binding assay (LBA, NEN/DuPont) and/or enzyme immunoassay (EIA, Abbott Labs). Of these, 454 specimens had both LBA and EIA results recorded. Biomarker results and de-identified clinical outcomes were examined using REMARK criteria. Gene expression, quantified biomarkers, features of primary breast cancers and clinical patient outcomes were analyzed by univariable and multivariable Cox regressions, Fisher’s Exact Test, Kaplan Meier plots and with R software v4.0.0. Microarray results of ~22,000 genes were obtained from RNA of LCM-procured breast carcinoma cells of 247 primary breast biopsies and expression levels of 85 cancer-associated genes were determined by RTqPCR of 278 specimens after RNA extraction and purification with established procedures. Results: Quantified levels of both ER and PR protein were expressed to a greater extent in primary carcinomas from post-menopausal patients compared to cancers from premenopausal women regardless of assay type (p = 0.005). ESR1 expression by microarray was only greater in LCM-procured carcinoma cells of post-menopausal patients while both ESR1 and PGR relative expression levels measured by qPCR were greater in tissue biopsies of post-menopausal women (p = 0.05). Box plots of untransformed EIA/LBA results of either ER (n=454) or PR (n=452) using specimens on which both quantifying assays were performed revealed a significant positive ER bias by EIA (median ratio=1.54) compared to that of PR (median ration=1.13). Transformed data of ratios confirmed this observation. Kaplan Meier plots of patient outcomes with ER or PR or both assessed by each assay type suggested LBA was a slightly better predictor. Microarray analyses of LCM-procured cells revealed 2994 genes distinguishing ER+ from ER- breast cancers of which ~200 genes were identified that differentiated 4 distinct molecular subtypes (2 ER+ and 2 ER-) exhibiting different outcomes upon Kaplan-Meier analyses. Expression levels of the 85 genes (including ERBB2), validated by qPCR with RNA from biopsy tissue sections, were evaluated relative to quantified levels of either ER or PR protein or both in primary breast cancer biopsies. Collectively, use of quantified ER/PR protein or ESR1/PGR expression with clinical outcomes enhanced identification of small molecular signatures and drug development candidates. Conclusions: Measurements of ER, PR and HER2 proteins with tests that quantify their levels as well as by microarray and qPCR assessment of ESR1, PGR and ERBB2 relative gene expression were correlated with prediction of clinical outcomes of breast carcinomas exhibiting various features (e.g., pathology classification, TNBC). Results reinforced importance of assessing levels of the clinically relevant biomarkers in a quantified fashion to enhance their use in breast cancer management and prediction of risk of recurrence. These investigations also revealed numerous over-expressed genes in carcinomas with poor clinical outcomes suggesting candidates for development of novel therapeutics.

Citation Format: James L Wittliff, Michael W. Daniels. Enhanced differentiation of clinical behavior by breast carcinomas utilizing quantification of estrogen and progestin receptor proteins and gene expression subsets [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 P1-06-07.

Abstract PS5-33: Androgen receptor gene expression and prediction of clinical outcomes of breast cancers exhibiting triple negative or triple positive breast carcinoma cells procured by LCM

Background: Clinical utility of AR, assessed by IHC of protein or by RT-qPCR of gene expression of intact tissue biopsies, has been the focus of many studies without uniform agreement. Due to cellular heterogeneity of most breast cancer biopsies, it is often unclear if measurements of AR and certain clinically relevant biomarkers accurately reflect their content in isolated cells. Using Laser Capture Microdissection (LCM) to procure only populations of breast carcinoma cells from tissue biopsies provides the inimitable opportunity to examine relationships of AR to a variety of parameters. Methods: We performed retrospective studies using a unique, de-identified dataset of ER/ESR1, PR/PGR and HER2/ERBB2 results with AR gene expression determined from LCM-procured carcinoma cells of biopsies from 247 breast cancer patients with associated clinical follow-up. ER/PR protein levels, expressed as fmol/mg cytosol protein, were quantified from each carcinoma biopsy with FDA-approved kits using enzyme immunoassay (EIA, Abbott Labs) or radio-ligand binding assay (NEN/DuPont). HER2 protein content of biopsies was quantified by EIA (Oncogene Sciences). Microarray analyses of ~22,000 genes were performed on RNA isolated, purified and amplified from LCM-procured carcinoma cells to assess relative gene expression. Biomarker results and de-identified clinical outcomes were examined using REMARK criteria in a CLIA licensed laboratory. Gene expression, quantified biomarkers, features of primary breast cancers and clinical outcomes were analyzed by univariable and multivariable Cox regressions, Fisher’s Exact Test, Kaplan Meier plots and with R software v4.0.0. Clinical relevance of gene expression was externally validated with SurvExpress. (Aguirre-Gamboa et al. PLoS One e742502013). Results: Using the median value of relative AR expression in LCM-procured carcinoma cells as a cutoff, elevated AR mRNA, when considered independently, was associated with the following (given as the means): older patients (61.1 vs 55.8 yo), relative expression of either ESR1 (0.2 vs -3.1), PGR (0.4 vs 0.0) or ERBB2 (0.7 vs -0.1) as well as longer PFS (63.7 vs 52.6 mos) and OS (72.4 vs 61.8 mos). Also, carcinoma cells with increased AR mRNA exhibited higher levels of ER protein (242.4 vs 106.5 fmol/mcp) or PR protein (313.8 vs 90.2 fmol/mcp). Whereas, HER2 protein status was not significantly different between AR median bifurcated groups). Neither patient race nor tissue pathology was examined in these analyses. Significantly, Kaplan Meier analyses clearly indicated that addition of AR gene expression to TNBC status (so called QNBC, Quadruple Negative Breast Cancer) did not alter either PFS (5 yr = 0.78 vs 0.79 % probability) nor OS (5 yr = 0.57 vs 0.56 %) of patients. Similarly, Kaplan Meier analyses also indicated that addition of AR gene expression to TPBC status (so called QPBC, Quadruple Positive Breast Cancer) did not alter PFS (5 yr = 0.87 vs 0.87 % probability) nor OS (5 yr = 0.67 vs 0.66 %) of patients. Also, no differences were ascertained for PFS nor for OS of patients at 10 yrs of outcomes between TNBC and QNBC breast cancers clearly indicating that AR gene expression does not contribute to the assessment of a patient’s clinical course. Conclusions: Collectively, when cancers were compared as TNBC versus TPBC status, expression results of ESR1, PGR and ERBB2 genes using LCM-procured carcinoma cells indicated poorer prognosis and overall survival of breast cancer patients with TNBC. However, inclusion of AR gene expression in either of these bifurcated groups ascertained from LCM-procured cells, did not alter patient PFS nor OS suggesting AR utility in clinical management appears to be unwarranted. Supported in part by grants to JLW from Phi Beta Psi Sorority Charity Trust.

Citation Format: James L Wittliff, Michael W. Daniels. Androgen receptor gene expression and prediction of clinical outcomes of breast cancers exhibiting triple negative or triple positive breast carcinoma cells procured by LCM [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS5-33.

Serine synthesis influences tamoxifen response in ER+ human breast carcinoma

Estrogen receptor-positive breast cancer (ER+ BC) is the most common form of breast carcinoma accounting for approximately 70% of all diagnoses. Although ER-targeted therapies have improved survival outcomes for this BC subtype, a significant proportion of patients will ultimately develop resistance to these clinical interventions, resulting in disease recurrence. Phosphoserine aminotransferase 1 (PSAT1), an enzyme within the serine synthetic pathway (SSP), has been previously implicated in endocrine resistance. Therefore, we determined whether expression of SSP enzymes, PSAT1 or phosphoglycerate dehydrogenase (PHGDH), affects the response of ER+ BC to 4-hydroxytamoxifen (4-OHT) treatment. To investigate a clinical correlation between PSAT1, PHGDH, and endocrine resistance, we examined microarray data from ER+ patients who received tamoxifen as the sole endocrine therapy. We confirmed that higher PSAT1 and PHGDH expression correlates negatively with poorer outcomes in tamoxifen-treated ER+ BC patients. Next, we found that SSP enzyme expression and serine synthesis were elevated in tamoxifen-resistant compared to tamoxifen-sensitive ER+ BC cells in vitro. To determine relevance to endocrine sensitivity, we modified the expression of either PSAT1 or PHGDH in each cell type. Overexpression of PSAT1 in tamoxifen-sensitive MCF-7 cells diminished 4-OHT inhibition on cell proliferation. Conversely, silencing of either PSAT1 or PHGDH resulted in greater sensitivity to 4-OHT treatment in LCC9 tamoxifen-resistant cells. Likewise, the combination of a PHGDH inhibitor with 4-OHT decreased LCC9 cell proliferation. Collectively, these results suggest that overexpression of serine synthetic pathway enzymes contribute to tamoxifen resistance in ER+ BC, which can be targeted as a novel combinatorial treatment option.

Abstract P1-09-03: Clinically relevant gene expression subsets deciphered from breast carcinomas classified by quantified expression levels of estrogen and progestin receptors

Background: Prior to standardization of IHC parameters by CAP/ASCO Guidelines in 2010 (Hammond et al., Arch Pathol Lab Med), ER/PR measurements were highly variable (e.g., fixation/staining, observer scoring). While serving as the National Reference Laboratory for NCI supported clinical trials by the NSABP, SWOG, CALGB, NCCTG, ECOG and SECSG, both EIA and radio-ligand binding assays (LBA) were employed that quantified ER/PR content and activities. Using ER/PR levels, we assessed relationships of qPCR expression of 85 candidate genes from 569 primary cancers with clinical outcomes to decipher molecular signatures that predict risk of recurrence.

Methods: This retrospective study used a unique dataset of de-identified ER/PR results of 1220 primary cancers from patients with clinical follow-up, stored in an IRB-approved Database. ER/PR protein levels, expressed as fmol/mg cytosol protein, were quantified earlier from each carcinoma with FDA-approved kits using either enzyme immunoassay (n = 751, Abbott Labs) or LBA (n = 552, NEN/DuPont). Relationships between ER/PR content assessed by LBA compared to that from EIA were examined. Results obtained from 1988-1996 and de-identified clinical outcomes were examined using REMARK criteria in a CLIA licensed laboratory. Gene expression, ER/PR quantified by LBA or EIA, features of primary breast cancers and clinical outcomes were analyzed by univariable and multivariable Cox regressions, Kaplan Meier plots and LASSO with R software v3.6.0. Gene expression levels were validated by qPCR while molecular signatures were externally validated with SurvExpress. (Aguirre-Gamboa et al. PLoS One e742502013).

Results: Examination of patient survival by Kaplan-Meier analyses using cancers classified by quantified ER or PR (regardless of by EIA or by LBA) revealed RFS and OS were related to increased content. Relationships RFS/OS with Kd values from LBA were examined. Also, differences in ER/PR status of carcinomas were associated with RFS and OS of patients (i.e., ER+/PR+ was related to increased RFS and OS while ER-/PR- status was associated with reduced RFS and OS). Univariable Cox regression of expression of each of the 85 genes identified 18 that predicted RFS while 22 genes predicted OS, confirmed by Kaplan-Meier Analyses. Multiple imputation by chained equations (‘MICE’, Zhang, Ann Transl Med. 2016) imputed missing qPCR values in order to utilize all 569 patients and 85 genes. With the ‘SGL’ package in R, an optimal L2 penalty determined the best fit LASSO model (algorithm sets minimum size for each beta coefficient and its associated gene to be included in the final Cox survival models). Sixteen gene subsets were deciphered according to quantified ER, PR or ER/PR status predicted either RFS or OS or both reflecting the increased or decreased hazard for a one unit change in a gene while controlling for other gene associations.

Conclusion: Expression of each gene in each of the 16 subsets exhibits a hazard ratio, when taken jointly, predicts either PFS or OS. Multidimensional portrayal of variation in the outcome PFS or OS is controlled by gene expression in the signature for an overall effect. Using expression results validated by qPCR, subsets of ER and/or PR related genes in primary lesions were identified that predict a patient's risk of recurrence and overall survival. Collectively, results suggest that gene expression profiles based on quantified ER/PR content of a biopsy serve as value-added biomarkers for assessing prognosis of breast carcinomas and identifying candidates for developing companion diagnostics.

Supported in part by grants to JLW from Phi Beta Psi Sorority Charity Trust, University of Louisville, Office of the EVPR, and a CTSP award, Commonwealth of Kentucky. WAS is the recipient of a fellowship from Bates College, ME.

Citation Format: James L Wittliff, William A. Stern, Zohair R. Hameed, Michael W. Daniels. Clinically relevant gene expression subsets deciphered from breast carcinomas classified by quantified expression levels of estrogen and progestin receptors [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 P1-09-03.

Relationships of protein biomarkers of the urokinase plasminogen activator system with expression of their cognate genes in primary breast carcinomas

Background

uPA, its receptor uPAR, and inhibitors PAI‐1 and PAI‐2 play key roles in membrane remodeling/invasion and in predicting response to chemotherapy. We identified novel relationships of these biomarkers with ER/PR that indicate clinical utility for assessing breast carcinoma outcomes.

Methods

Retrospective studies were performed with de‐identified results of (a) uPA, uPAR, and PAI‐1; (b) estrogen (ER) and progestin receptor (PR); and (c) clinical outcomes. Relative expression of 22 000 genes from microarray of RNA from LCM‐procured breast cancer cells was used with R Studio version 3.4.1.

Results

Primary ER/PR status was related to uPA, uPAR, or PAI‐1 levels. ER− or PR− cancers expressed elevated uPA, uPAR, and PAI2 mRNA compared to ER+ or PR+ cells. Inverse relationships between ER/PR protein and expression of uPA, uPAR, and PAI‐2 were observed, whereas HER2 status was unrelated. qPCR analyses showed RERG and NQO‐1 expressions were elevated in uPA− lesions, while CD34 and EDG‐1 were elevated in uPAR− cancers. ERBB4 was overexpressed in PAI‐1+ carcinomas. Cox regression analyses revealed relationships of ER/PR status and uPA system members with regard to clinical outcomes of breast cancer.

Conclusions

uPA, uPAR, PAI1, or PAI2 expression was increased in either ER− or PR− cancers similar to that of protein content in ER−/PR− carcinomas, suggesting sex hormones regulate the uPA system in breast cancer. Results revealed protein content of uPA system members was related to ER/PR status of primary lesions. Use of LCM‐procured carcinoma cells uncovered relationships between expression of known cancer−associated genes and protein content of uPA system members. Collectively, results indicate evaluation of ER and PR protein of primary breast cancers combined with analyses of uPA, uPAR, and PAI‐1 protein content improves assessment of clinical outcomes.

Abstract P6-07-04: Gene expression profiles of angiogenesis related cytokines and cognate receptors predict breast cancer progression and survival

Background: Angiogenesis plays a critical role in breast cancer development, invasion and metastasis, and VEGF, TGFß1, and IL10 genes and their cognate receptors are implicated in cancer behavior, mediating membrane and microenvironment remodeling. Our goal is to assess relationships of expression of these genes in LCM-procured carcinoma cells from primary breast cancers with clinical outcomes to predict risk of recurrence.

Methods: Gene expression determined by microarray and qPCR, ER/PR quantified by radio-ligand binding or EIA, features of primary breast cancers and clinical outcomes were performed by univariable and multivariable Cox regressions, Kaplan Meier plots and LASSO with R software v3.2.5. Microarray analyses of ˜22,000 genes utilized RNA isolated, purified and amplified from LCM-procured carcinoma cells. Gene expression was validated by qPCR while molecular signatures were externally validated with SurvExpress (Aguirre-Gamboa et al. PLoS One e74250, 2013).

Results: Univariable Cox regression of microarray results of cytokines and cognate receptor genes revealed IL10 expression was significant for prediction of Progression Free (PFS) or Overall Survival (OS) using an adjusted p-value of ≥ 0.30 (discovery cut-off). Without regard to ER/PR status, Kaplan Meier plots confirmed IL10 or TGFß1 expression was significant for predicting PFS and OS. Using ER+ cancers, IL10 or VEGF expression was related to PFS while only IL10R was related to OS of ER- cancers using univariable Cox regression. Validation by qPCR using tissue curls disclosed independent expression of either TGFß1 or VEGF predicted PFS and OS while that of TGFß1Rwas only related to PFS. IL10R expression only predicted OS of breast cancer patients. Violin plots of qPCR results indicated elevated expression of each of these six genes in ER+ primaries without regard to outcome. Multivariable Cox regression analyses of expression levels of cytokine-receptor gene pairs revealed that IL10-IL10R co-expression was highly significant for predicting OS. Strongly supportive, backwards selection (R software v3.2.5) utilizing microarray expression levels derived a significant model (molecular signature) consisting of IL10, IL10R and VEGFR genes for predicting OS. External validation of this 3-gene subset was accomplished utilizing patient data collected on SurvExpress. A second clinically relevant signature predicting OS in PR+ breast cancers was detected when TGFß1R expression was included with these 3 genes. Finally, backwards selection of qPCR data derived a significant 3-gene model composed of IL10R, TGFß1 and VEGF for predicting PFS that was undeniably validated by SurvExpress.

Conclusions: Using gene expression results derived from microarray analyses of LCM-procured breast carcinoma cells of primary lesions and validated by qPCR, subsets of angiogenesis related genes were identified that predict a patient's risk of recurrence and overall survival. Expression of candidate genes appears to be related to either/both ER or PR protein status of the primary lesion. Collectively, results suggest that expression of certain angiogenesis related genes may serve as biomarkers for assessing prognosis of breast carcinomas thus impacting clinical management.

Citation Format: Wittliff JL, Sereff SB, Smolenkova IA, Hameed ZR, Andres SA. Gene expression profiles of angiogenesis related cytokines and cognate receptors predict breast cancer progression and survival [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 P6-07-04.

Abstract 4622: Deciphering gene subsets associated with clinical outcomes of early stage breast carcinoma patients treated with Tamoxifen

NSABP Protocol B-09 reported primary breast carcinomas expressing estrogen (ER) and progestin receptors (PR) exhibited increased likelihood of response to Tamoxifen. However, some patients with early stage lesions relapse within 10 years. We identified a 5-gene model from 14 candidate expression profiles that improved differentiation of these patients (Kerr & Wittliff, Horm Canc 2:261-71, 2011). Goals are to examine relationships of clinical outcomes of patients whose carcinomas express individual genes and subsets of the models and externally validate their clinical utility. Procedures: De-identified primary breast carcinomas from 342 patients treated with Tamoxifen were used to assess clinical relevance of 14 candidate genes. Laser capture microdissection (LCM) was used previously to isolate carcinoma cells and assess 22,000 genes by microarray. qPCR validated expression of 14 candidate genes. Univariable Cox regression analyses were performed and Kaplan-Meier plots were constructed to assess relationships between either progression-free (PFS) or overall survival (OS) and expression of each gene using R Studio 1.0.143. Relationships of gene expression were segregated by ER/PR (quantified by EIA or radio-ligand binding) with clinical outcomes. SurvExpress evaluated performance externally of individual gene expression and signatures. Results: Univariable Cox regression of microarray results for 14 candidate genes from LCM-procured cancer cells of 247 biopsies without regard to ER/PR status indicated that RERG, ERRB4 and ESR1 were related to PFS while these 3 genes and EGFR and CAXII expression were associated with OS (adjusted p value < 0.30). Validation of individual gene expression of 274 intact tissue sections by qPCR revealed that 4 of these genes (exception of EGFR) as well as PGR, BCL2, SLC39A6, EDG-1, and CD34 were associated with PFS. Expression levels of each of these 9 candidate genes as well as PTGDS, SDF and NQO-1 were independently associated with OS. Kaplan-Meier plots assessed ability of each gene expression level to predict clinical outcomes (PFS/OS). Multivariate Cox regression, performed with backward conditional selection using either microarray data or qPCR results, revealed clinically relevant genes subsets for PFS and OS. SurvExpress, an online tool, was used to externally validate molecular signatures. Conclusions: We externally validated the 5-gene model composed of PGR, BCL2, ERBB4, RERG and CD34 that identified a subset of early stage, ER+ /PR+ breast cancers patients treated with Tamoxifen that exhibited high recurrence rates. ER, PR and HER2 proteins with gene expression were correlated with prediction of clinical outcomes. Clinically relevant molecular signatures identified gene candidates for development of companion diagnostics to their protein products to improve breast cancer management and prediction of risk of recurrence.

Citation Format: Zohair Riaz Hameed, Michael W. Daniels, D. Alan Kerr II, James L. Wittliff. Deciphering gene subsets associated with clinical outcomes of early stage breast carcinoma patients treated with Tamoxifen [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4622.

Abstract 1610: Expression of genes of the uPA system from LCM-procured breast carcinoma cells and their relationships with clinical outcomes

Introduction: The urokinase plasminogen activator (uPA), its receptor uPAR and serine protease inhibitors PAI-1 or PAI-2 play a key role in tissue membrane remodeling and invasion of basement membranes by induction of a fibrinolytic pathway. Earlier studies reported that uPA and PAI-1 protein levels assist in prediction of breast cancer response to chemotherapy. Our goal is to develop molecular signatures of candidate genes and identify novel relationships with these four protein biomarkers that demonstrate clinical utility for assessment of breast carcinoma outcomes. Methods: The retrospective study used de-identified tissue biopsies from primary breast cancers on which biomarker and clinical outcomes were stored in an IRB-approved Database. ELISA analyses of uPA, uPAR and PAI-1 performed using IMUBIND kits (American Diagnostica Inc.) used cutoff values previously reported. Estrogen (ER) and progestin receptor (PR) assays were performed either by EIA (Abbott Labs) or by radioligand binding (NEN/DuPont). Relative expression levels of 22,000 genes were determined by microarray using RNA extracted and amplified from Laser-Capture Microdissection (LCM) procured breast carcinoma cells. Univariable and multivariable Cox regression analyses, Kaplan-Meier plots, Violin and scatter grams were performed by R Studio version 3.4.1. External validation of gene subsets derived were performed with SurvExpress. Results: uPA and PAI-1 protein content of a carcinoma were predictive of overall survival (OS). Examination of biomarker gene expression by Violin plots revealed that either ER- or PR- breast cancers expressed elevated levels of UPA, UPAR and PAI2 compared to that of ER+ or PR+ carcinoma cells. Scatter grams suggested an inverse relationship between ER/PR protein levels and expression of UPA, UPAR and PAI2. Univariable Cox regression analyses indicated that PAI2 expression was associated with progression-free survival (PFS) and OS while UPA and PAI1 expression was only associated with OS with a p value < 0.3 (selected as the discovery limit). When carcinomas were sorted by biomarker levels, qPCR expression of RERG and NQO-1 were elevated in uPA- lesions while CD34 and EDG-1 were elevated in uPAR- cancers. However, ERBB4 expression was elevated in PAI-1+ carcinomas. Multivariate Cox regression, performed with backward conditional selection using microarray data with ER or PR status revealed clinically relevant genes for PFS and OS. SurvExpress, an online tool, validated gene subsets externally. Conclusions: Use of LCM-procured breast carcinoma cells in a nondestructive manner uncovered relationships between gene expression and either uPA, uPAR, PAI-1 or PAI-2 protein content of a lesion to reveal candidates for predicting clinical outcomes. Certain of these gene subsets appear related to patient prognosis when considered with ER/PR status of the carcinomas.

Citation Format: Seth B. Sereff, Michael W. Daniels, James L. Wittliff. Expression of genes of the uPA system from LCM-procured breast carcinoma cells and their relationships with clinical outcomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1610.

Abstract P1-01-12: Expression of autophagy related genes impacts clinical outcomes of human breast carcinoma and is associated with estrogen and progestin receptor status

The dual role of autophagy in breast cancer initiation, progression and responsiveness to various therapies is the focus of extensive studies. Our goal is to assess the relationship of expression of certain autophagy related genes in primary breast carcinomas to predict risk of recurrence. Our hypothesis includes the caveat that unique gene expression subsets will be deciphered by utilizing Laser Capture Microdissected breast carcinoma cells from tissue biopsies containing many cell types.

Methods: Comprehensive analyses of de-identified biomarker results, characteristics of 247 breast carcinoma specimens and clinical outcomes were performed by univariable Cox regressions, Kaplan Meier plots and LASSO with R software version 3.2.5. Microarray analyses were performed on RNA isolated from LCM-procured carcinoma cells to identify gene signatures associated with breast cancer behavior.

Results: Expression levels of 22 autophagy related genes analyzed by univariable Cox regression revealed that RB1CC1, KEAP1, ATG7, RUBCN, NOD2, HMOX1, BECN1, PIK3R4 were significant for predicting Progression Free Survival (PFS) at the discovery level of the adjusted p-value < 0.3. Of these, RB1CC1, KEAP1, & ATG7 were significant for Overall Survival (OS) without regard to ER/PR status. Using Kaplan Meier analyses, expression levels of each of 10 candidate genes predicted PFS of which expression of 6 of these genes also predicted OS using a median split cutoff without regard to ER/PR status. Applying LASSO computations without regard to ER/PR status of the primary breast cancer, a clinically relevant gene expression profile consisting of ATG7, BCL2, HMOX1, KEAP1, NOD2, PTEN, RB1CC1, and ULK4 predicted PFS. Collectively, expression of these 8 genes with TP53 and RUBCN predicted OS without regard to ER/PR status. Violin plots of relative gene expression of each of the 22 candidate genes known to be associated with autophagy pathways revealed that ATG7, ATG12, BCL2 and BECN1 were elevated in ER+ lesions while BCL2 and BECN1 were also elevated in PR+ breast carcinomas. Expression levels of 16 of the 22 autophagy related genes examined by univariable Cox regression were related to either ER or PR status of the primary lesion and predicted either PFS or OS. Refinement of clinically relevant gene subsets was accomplished by LASSO calculations in which either the ER or PR protein status of the primary breast carcinoma was considered. Of the genes in the molecular signatures derived, expression levels in breast carcinomas separated by either ER or PR status of the lesion were tested by Kaplan Meier analyses to assess relationships to PFS and OS.

Conclusions: Using gene expression results derived from microarray analyses of LCM-procured breast carcinoma cells of primary lesions, subsets of autophagy related genes were identified that predict a patient's risk of recurrence and overall survival. Expression of a number of candidate genes appears to be related to either/both the ER or PR protein status of the primary lesion. Collectively, results suggest that expression of certain autophagy related genes may serve as biomarkers for assessing prognosis of breast carcinoma thus impacting clinical management of breast cancer.

Citation Format: Wittliff JL, Hameed ZR, Daniels MW, Cheng A. Expression of autophagy related genes impacts clinical outcomes of human breast carcinoma and is associated with estrogen and progestin receptor status [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-01-12.

Expression of Genes for Methylxanthine Pathway-Associated Enzymes Accompanied by Sex Steroid Receptor Status Impacts Breast Carcinoma Progression

Consumption of methylxanthine alkaloids appears to induce activities by antagonizing adenosine receptors, implicated in breast cancer behavior in vitro. Our goal was to evaluate expression of genes for methylxanthine receptors and metabolizing enzymes to assess risk of breast carcinoma recurrence. Clinical outcomes, estrogen/progestin receptor results, and gene expression assays guided selection. RNA was isolated from laser capture microdissection-procured carcinoma cells for microarray using established protocols. Gene expression levels of eight methylxanthine receptors, eight metabolizing enzymes, and various phosphodiesterases were retrieved from microarray results. Univariable Cox regressions and Kaplan-Meier plots were determined for each gene with R software. Individually, lower expressions of PDE4A, CYP2A6, or CYP2E were related to decreased progression-free survival (PFS) and overall survival (OS). PDE1A over-expression predicted decreased PFS and OS. ADORA2B and RYR1 over-expressions predicted diminished OS. ER+ cancers exhibited lower ADORA1, ADORA2B, and RYR1 and elevated PDE4A, CYP2A6, and CYP2E expressions. Of PR+ carcinomas, diminished ADORA2B and RYR1 and elevated expressions of ADORA3, PDE4A, CYP2C8, and CYP2E were noted. Least absolute shrinkage and selection operator (LASSO) revealed that CYP2E, PDE1A, and PDE4A expressions collectively predicted PFS whereas ADORA1, CYP2E, PDE1A, PDE1B, and PDE4A expressions jointly predicted OS. Models were clinically significant when validated externally. LASSO also derived a six-gene model and five-gene model that predicted PFS of ER- or PR- carcinomas, respectively. Similarly, five-gene and four-gene models predicted OS in ER- or PR- carcinomas, respectively. Collectively, expression of genes involved in methylxanthine action and metabolism in single-cell types predicted clinical outcomes of breast carcinoma indicating promise for developing diagnostics and design of new therapeutics.

Abstract 1973: Novel relationships of expression of methylxanthine alkaloid receptor genes and risk of breast carcinoma recurrence

Consumption of methylxanthine alkaloids such as caffeine, theophylline and theobromine may induce breast pain. Caffeine appears to induce its biological activities by antagonizing adenosine receptors, which have been implicated in breast cancer cell behavior in vitro. Our goal is to evaluate expression of genes for methylxanthine receptors and metabolizing enzymes for assessing risk of breast cancer recurrence.

Procedures: De-identified primary cancers previously collected, stored and analyzed under stringent conditions were employed to amass an IRB-approved, de-identified comprehensive Database. Patient-related properties (e.g., nodal status, clinical outcome) and results from estrogen (ER) and progestin receptor (PR) analyses and gene expression assays guided selection. To decode clinical utility of gene expression profiles, Laser Capture Microdissection (PixCell IIe™ Arcturus/Thermo Fisher) was used previously to non-destructively collect carcinoma cells. RNA was extracted, amplified and analyzed by microarray (~ 22,000 genes).

Results: Gene expression levels of 8 methylxanthine receptors, 8 metabolizing enzymes and various phosphodiesterases were retrieved from microarray results of 247 breast biopsies. Univariable Cox regressions and Kaplan Meier plots were determined for each candidate gene with R software. Kaplan-Meier plots of PDE4A, CYP2A6 or CYP2E individually indicated lower expression was related to decreased progression free (PFS) and overall survival (OS) while PDE1A over-expression predicted decreased PFS and OS. ADORA2B and RYR1 over-expression was associated with lower OS. Gene expression was examined with ER or PR status without regard to clinical outcome. Breast cancers that were ER+ exhibited lower ADORA1, ADORA2B and RYR1 expression and elevated expression of PDE4A, CYP2A6 and CYP2E. PR+ carcinomas also exhibited decreased expression of ADORA2B and RYR1 expression. However, over-expression of ADORA3, PDE4A, CYP2C8 and CYP2E was observed in PR+ cancers. Analysis of variance (ANOVA) of carcinomas according to ER/PR status indicated ADORA2B expression was elevated in ER- cancers regardless of PR status. ANOVA also showed PDE4A was over expressed in ER+ carcinomas regardless of PR status. LASSO analysis revealed CYP2E, PDE1A and PDE4A expression taken jointly predicted PFS which was validated externally (Breast Cancer Meta-base) with SurvExpress.

Conclusions: Collectively, results suggest expression of genes involved in methylxanthine action and metabolism may be used to predict breast cancer behavior. Significantly, we identified gene expression signatures in single cell types that were highly associated with clinical outcome suggesting promise for development of novel prognostic tests for breast carcinoma management and design of new therapeutics.

Citation Format: Seth B. Sereff, Michael W. Daniels, James L. Wittliff. Novel relationships of expression of methylxanthine alkaloid receptor genes and risk of breast carcinoma recurrence [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1973. doi:10.1158/1538-7445.AM2017-1973

Abstract 2831: Identification of cell specific expression signatures using NGS global gene expression profiles from LCM procured breast carcinoma and adjacent stromal cells

Our goal is to determine relationships of gene expression profiles to patient-associated characteristics, breast carcinoma pathology and biomarker status with clinical outcome to improve assessment of prognosis and therapy selection.

Procedures: De-identified frozen tissue biopsies of human breast carcinomas which were collected and stored under stringently controlled conditions were employed. Patient-related features (e.g., age, race, menopausal status, nodal status, clinical treatment and response) and results from biochemical analyses of established tumor markers (e.g., estrogen and progestin receptors, EGF receptor, HER-2/neu oncoprotein) guided tissue selection. Structural integrity of a tissue was first evaluated by light microscopy of H&E stained sections. To decipher uniqueness and clinical utility of gene expression profiles from specific cell types, Laser Capture Microdissection (LCM) with a PixCell IIeTM (Arcturus®, Thermo Fisher Scientific) was used to non-destructively collect either carcinoma cells or adjacent stromal cells on CapSureTM LCM caps. A second intact serial tissue section was processed identically to that of the section used for LCM as a control. Each of the two independent cell captures from the same tissue section and the second intact tissue section were independently extracted for RNA. RNA was assessed for integrity, purified and subjected to novel analyses using the Ion AmpliSeqTM RNA Breast Cancer Research Panel containing 1174 genes. Sequencing workflow included templating on the Ion Chef TM System and multiplexed sequencing on the Ion S5TM XL sequencing system and Ion 540TM chip.

Results: Each sequencing library yielded approximately 4-5 million reads with a mapping rate of >98% that was achieved after alignment to the human transcriptome. Each sample was sequenced in triplicate with technical reproducibility near 99% with a mean of 1035 genes classified as detected. Cluster analyses of gene expression profiles revealed clear distinctions between stromal and carcinoma cells procured by LCM compared to intact tissue driven by strongly differentially expressed genes such as vimentin (VIM), MPRIP, stanniocalcin-2 (STC2) and estrogen receptor beta (ESR2).

Conclusions: Collectively, the results indicate that molecular signatures of breast carcinoma cells procured by LCM reveal unique gene expression profiles compared to those of the intact tissue section or the adjacent stromal cells. These novel findings are likely to discern molecular features unique to a breast carcinoma that may be related to clinical outcome to improve assessment of patient prognosis and therapy selection. Supported in part by a grant from the Phi Beta Psi Charity Trust (JLW & SAA) and a CTSP Award from the Commonwealth of Kentucky (JLW). For research use only.

Citation Format: Jeoffrey J. Schageman, Kristi Lea, Sarah A. Andres, Kelli S. Bramlett, James L. Wittliff. Identification of cell specific expression signatures using NGS global gene expression profiles from LCM procured breast carcinoma and adjacent stromal cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2831. doi:10.1158/1538-7445.AM2017-2831

Abstract 669: Quantification of estrogen (ER) and progestin receptor (PR) as well as HER2/neu proteins and gene expression improves discrimination of clinical behavior by triple positive breast carcinomas

IHC analyses of ER, PR and HER2 proteins are used as clinical biomarkers for breast cancer management. However, IHC provides semi-quantitative results sometimes complicated by variation in methods and interpretation. Our goal was to ascertain clinical use of these three analytes to predict breast cancer recurrence when analyses for gene expression and protein products were quantified.

Procedures: We examined ER and PR protein in 1059 de-identified carcinoma biopsies previously quantified by radio-ligand binding and/or enzyme immunoassay (EIA) using FDA approved reagents and HER2 oncoprotein determined by EIA to assess relationships between biomarker profiles and disease-free (DFS) and overall survival (OS) for 123 patients. Our comprehensive, IRB-approved Database also contained de-identified Microarray results obtained for ~ 22,000 genes from LCM-procured breast carcinoma cells of 247 primary breast biopsies. ESR1, PGR and ERBB2 gene expression levels were validated previously in 278 cancers by qPCR.

Results: Generalized Pair Plots of the three protein biomarkers indicated a relationship only between ER and PR supporting evidence that ER complexed with estrogenic ligands promotes synthesis of PR. Of the 8 possible combinations of the 3 protein biomarkers, only breast cancers exhibiting ER+PR+HER2+ (triple positive breast cancer, TPBCa) exhibited increased OS, whereas those with triple negative breast cancers (TNBCa) had decreased OS. TPBCa was exhibited by 32.5 % of specimens compared to TNBCa, which represented 7.3% of biopsies when biomarker proteins were quantified. Number of TPBCa was less when expression of the 3 genes (ESR1+/PGR+/ERBB2+) was measured by microarray or by qPCR while those of TNBCa increased. Furthermore, when TPBCa were identified by either microarray or by qPCR measurements, collectively increased ESR1, PGR and ERBB2 expression was associated with increased PFS and OS of patients. In contrast, biopsies that were ESR1-/PGR-/ERBB+ (14.1%) correlated with poor prognosis and overall survival using qPCR data, while those exhibiting ESR1-PGR+ERBB2- (14.1%) profiles by microarray results exhibited decreased PFS and OS. Influence of patient menopausal status on biomarker profiles was examined.

Conclusions: Quantitative measurements of ER, PR and HER2 proteins as well as microarray and qPCR assessment of ESR1, PGR and ERBB2 gene expression were correlated with prediction of clinical outcomes of breast carcinomas exhibiting Triple Positive Breast Cancers (TPBCa). Results reinforce importance of assessing levels of the three biomarkers in a quantified fashion to enhance their use in breast cancer management and prediction of risk of recurrence.

Citation Format: Zohair R. Hameed, Michael W. Daniels, D. Alan Kerr, James L. Wittliff. Quantification of estrogen (ER) and progestin receptor (PR) as well as HER2/neu proteins and gene expression improves discrimination of clinical behavior by triple positive breast carcinomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 669. doi:10.1158/1538-7445.AM2017-669

Abstract P3-05-11: Clinical outcomes of estrogen-receptor negative breast carcinoma are associated with protein hormone-cognate receptor gene expression

Background: Since certain protein hormones appear to be associated with progression of breast cancer cells in vitro, we employed a global approach by evaluating relationships between genes for these hormones and their cognate receptors in human breast cancer biopsies as independent predictors of risk of recurrence. Our goal is to derive clinically relevant molecular signatures correlating various ER/PR subtypes.

Methods: Microarray analyses of LCM-procured carcinoma cells from 247 de-identified biopsies determined expression of genes for 61 protein hormones (the ligands) and 81 cognate receptors. Total RNA was extracted, purified and amplified from cells to determine expression of 22,000 genes. Univariable and multivariable Cox regressions were determined using expression levels of each hormone/receptor gene. Kaplan-Meier plots were constructed with an adjusted p-value <0.30 (discovery cutoff) for each gene candidates with/without ER status of the lesion. Cox regression analyses with/without interaction models deciphered candidates of hormone-receptor complexes that predicted risk of recurrence as well as overall survival using clinical follow-up that extended as much as 12 years. LASSO was used to derive gene subsets to predict overall survival (OS) and progression free survival (PFS) within ER/PR subtypes.

Results: Expression levels of 7 genes for protein hormones and 10 receptor genes were significant for OS at an adjusted p-value of <0.30 while expression of 15 hormone and 19 receptor genes were significant for PFS without regard to ER/PR subtypes. When expression levels were considered with ER status only, 3 genes for ER+ lesions and 6 genes for ER- lesions were identified that predicted OS/PFS. Categorization of cancers according to combined ER and PR status revealed one gene for ER+/PR+, 3 genes for ER+/PR- and 2 genes for ER-/PR- associated with PFS/OS. After stratifying gene expression into above/below median for the linear predictor, Kaplan-Meier plots revealed patient groups with each signature for ER+/PR+, ER-/PR- and ER- lesions that exhibited significantly different survival. Molecular signatures comprising 16 genes for ER+/PR+ carcinomas, 10 genes for ER-/PR- lesions and 6 genes for ER- carcinomas predicted clinical outcomes with C-indices of 0.79, 0.76 and 0.71, respectively.

Conclusion: We revealed many breast carcinomas synthesize mRNA species for various protein hormones and their cognate receptors by determining gene expression directly on pure populations of these cells procured by LCM. We report a novel ten-gene ER-/PR- signature containing four genes in common with that of a six-gene ER- only signature that predicts breast cancer recurrence. Collectively, results of mRNA expression suggest that often breast carcinomas exhibit substantial elements of endocrine autonomy for regulating progression, warranting investigation of protein products of gene candidates in isolated populations of breast carcinoma cells.

Citation Format: Daniels MW, Wittliff JL, Brock GN. Clinical outcomes of estrogen-receptor negative breast carcinoma are associated with protein hormone-cognate receptor gene expression [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 P3-05-11.

Clinical outcomes linked to expression of gene subsets for protein hormones and their cognate receptors from LCM-procured breast carcinoma cells

PURPOSE

Certain peptide hormones and/or their cognate receptors influencing normal cellular pathways also have been detected in breast cancers. The hypothesis is that gene subsets of these regulatory molecules predict risk of breast carcinoma recurrence in patients with primary disease.

METHODS

Gene expression levels of 61 hormones and 81 receptors were determined by microarray with LCM-procured carcinoma cells of 247 de-identified biopsies. Univariable and multivariable Cox regressions were determined using expression levels of each hormone/receptor gene, individually or as a pair.

RESULTS

Molecular signatures for ER+/PR+, ER-/PR-, and ER- carcinoma cells deciphered by LASSO were externally validated at HRs (CI) of 2.8 (1.84-4.4), 1.53 (1.01-2.3), and 1.72 (1.15-2.56), respectively. Using LCM-procured breast carcinoma cells, a 16-gene molecular signature was derived for ER+/PR+ biopsies, whereas a 10-gene signature was deciphered for ER-/PR- cancers. Four genes, POMC, CALCR, AVPR1A, and GH1, of this 10-gene signature were identified in a 6-gene molecular signature for ER- specimens.

CONCLUSIONS

Applying these signatures, Kaplan-Meier plots definitively identified a cohort of patients with either ER-/PR- or ER- carcinomas that exhibited low risk of recurrence. In contrast, the ER+/PR+ signature identified a cohort of patients with high risk of breast cancer recurrence. Each of the three molecular signatures predicted clinical outcomes of breast cancer patients with greater accuracy than observed with either single-gene analysis or by ER/PR protein content alone. Collectively, our results suggest that gene expression profiles of breast carcinomas with suspected poor prognosis (ER-/PR-) have identified a subset of patients with decreased risk of recurrence.

Abstract P3-04-06: Expression of genes for peptide/protein hormones and their receptors in breast carcinomas as biomarkers predicting risk of recurrence

Background: Several reports have suggested expression of certain peptide/protein hormones in breast cancer cells appear to be related to clinical behavior. We have taken a global approach by evaluating relationships between genes for these hormones and their cognate receptor proteins as independent predictors of risk of recurrence.

Methods: Expression of genes for 55 peptide/protein hormones (the ligands) and 73 of their cognate receptor proteins were measured by microarray analyses of LCM-procured carcinoma cells from 247 breast carcinoma biopsies. Using an IRB-approved biorepository and comprehensive database, total RNA was extracted from carcinoma cells to determine expression levels of 22,000 genes. Univariate and multivariate Cox regressions with interaction were determined using expression values of each ligand and its cognate receptor with an interaction term.

Results: When pairs of hormone ligand and cognate receptor genes were evaluated by multivariate Cox regression with interaction, the following sets of genes were identified that predicted risk of breast cancer recurrence (INS/IGF2R, HAMP/SLC40A1, POMC/MC4R, GH1/GHR and VIP/VIPR2) and OS (CORT/SSTR5, VIP/VIPR2 and GHRH/GHRHR, based on unadjusted p-value for interaction term < 0.05). Since expression in situ of both hormone and receptor are necessary to elicit endocrine action, a unique alternative approach using the minimum expression value between ligand and receptor for each patient was applied. These results revealed that the complex of HAMP/SLC40A1 showed significance in both the interaction and minimum models, and was further investigated by splitting the ligand and receptor into low (below 1st quartile) and high (above 1st quartile) expression groups. The group consisting of high expression for both ligand and receptor was contrasted with the other three groups (low expression for ligand, receptor, or both). The higher expression group exhibited a better DFS (hazard ratio (HR) = 0.56 95% CI 0.37-0.84, p=0.004) and OS (HR = 0.59 95% CI 0.37-0.93, p=0.022).

Conclusion: As a result of determining gene expression directly on pure populations of breast carcinoma cells procured by LCM, we have demonstrated the many lesions synthesize mRNA species for a wide variety of peptide and protein hormones as well as for their cognate receptor proteins. Using clinical follow-up that extended as much as 12 years, univariate and multivariate Cox regression analyses with and without interaction models revealed a number of noteworthy candidates of hormone-receptor complexes that predicted risk of breast cancer recurrence as well as overall survival. Collectively, our results suggests that many breast carcinomas exhibit considerable endocrine autonomy for controlling progression, which warrants investigation of the protein products of the gene candidates in isolated populations of breast carcinoma cells.

Citation Format: Wittliff JL, Daniels MW, Brock GN. Expression of genes for peptide/protein hormones and their receptors in breast carcinomas as biomarkers predicting risk of recurrence. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P3-04-06.

Abstract P6-03-14: Expression of genes for aromatase inhibitor targets to discriminate invasive lobular from invasive ductal carcinomas of the breast using LCM-procured cells to complement endocrine biomarkers

Background: The BIG 1-98 trial and later the ABCSG 8 study reported that patients with invasive lobular carcinoma (ILC) exhibited better response to aromatase inhibitors (AIs) compared to those with invasive ductal carcinoma (IDC). Aromatase cytochrome P450 (CYP19) synthesizes estrogen from androgens and is the target of AI's. CYP19 substrates are generated by upstream enzymes including estrone sulfatase (SULT1E1) and 3b-hydroxysteroid dehydrogenase type 1 (HSD3B1). Enzymes of the aromatase pathway have been reported to be expressed in intact tissue biopsies of breast cancer. To learn more about the pathogenic mechanisms that may underlie the survival benefit of ILCs treated with AIs, we analyzed expression levels of key enzymes related to the aromatase pathway in ILC and IDC. Unlike previous studies, we determined gene expression levels directly on pure populations of carcinoma cells procured by laser capture microdissection, eliminating the contribution of non-cancerous cells.

Methods: Using an IRB-approved biorepository and database, total RNA was extracted from carcinoma cells of 247 de-identified biopsies to perform microarray analyses of 22,000 genes. Of the 247 samples, 16 were ILC, 13 were low grade IDC, 55 were intermediate grade IDC and 85 were high grade IDC, and 107 of these were hormone receptor positive. CYP19, HSD3B1 and SULT1E1 expression was directly detected in LCM-procured breast carcinoma cells of ILC and of IDC. Expression of other genes generally associated with the aromatase pathway, e.g., NADPH-cytochrome P450 reductase (POR), ATP-binding cassette gene (ABCG2), catechol-o-methyltransferase (COMT) and uridine-5'-diphosphate glucuronosyltransferase (UGT1A3 & UGT1A9) as well as HSD17B2 were assessed with LCM-procured cells. Estrogen receptor (ER) and progesterone receptor (PR) proteins were quantified by radio-ligand binding and EIA, and gene expression was validated by qPCR.

Results: Univariate Cox regression analyses indicated that ABCG2, HSD17B2and UGTA3 independently predicted disease free and/or overall survival of breast carcinomas. We found that CYP19 expression in carcinoma cells, as well as SULT1E1, COMT, POR, HSD17B2 and UTG1A3 expression, decreased as either ER or PR protein increased. HSD3B1 appeared to be over-expressed in ILC compared to IDC, however this difference did not approach statistical significance, likely due to the small sample size. No differences were seen in expression levels of CYP19 and SULT1E1 between ILC and IDC.

Conclusions: An inverse relationship between CYP19 and ER and PR expression levels was observed and suggests that synthesis of estrogens by breast cancer cells in situ plays a significant role in defining tumor biology. Our results also indicate overexpression of HSD3B1 in ILC, although not statistically significant. This finding suggests that HSD3B1 may be a key contributor to the increased benefit of AI therapy seen in ILC. Collectively our results suggest a comprehensive study is warranted to ascertain the molecular basis for differences in expression of genes directing estrogen synthesis in situ in relationship to AI therapeutic responses of histologic subtypes of breast carcinomas.

Citation Format: Sanders MAG, Daniels MW, Wittliff JL. Expression of genes for aromatase inhibitor targets to discriminate invasive lobular from invasive ductal carcinomas of the breast using LCM-procured cells to complement endocrine biomarkers. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P6-03-14.

Abstract P2-03-11: Interaction between smoking history and gene expression levels impacts survival of breast carcinoma patients

Our investigations explore the association of cigarette smoking on breast cancer risk of recurrence and progression, in contrast to studies that focused on tobacco use and risk of breast cancer occurrence. The goal was to decipher the interaction between smoking history and expression levels of 22 gene candidates selected from microarray data obtained from laser capture microdissected carcinoma cells from 247 de-identified patient tissue biopsies on disease recurrence and overall patient survival of breast cancer patients. qRT-PCR was used to determine expression levels for NAT1, NAT2, COMT, SOD1, SOD2, BRCA1, BRCA2, APOC1, ARID1B, CTNNBL1, MSX1, UBE2F, IRF2, NCOA1, LECT2, THAP4, RIPK1, AGPAT1, C7orf23, CENPN, CETN1 and YTHDC2 selected from a previous study for 50 breast cancer patients with a history of cigarette smoking and 51 patients who had never smoked. For smokers and non-smokers separately, L1-penalized multivariable Cox regression models were fit to predict patient disease-free and overall survival, with 1000 splits of the data into training (70%) and test (30%) sets to determine predictive accuracy based on the C-index. The LASSO penalty was used to perform variable selection in each of the training sets, and a permutation procedure was used to determine a significance threshold for the number of times a variable was kept in the model. Multivariable analyses using the LASSO revealed CENPN, CETN1, CYP1A1, IRF2, LECT2, and NCOA1 to be significant predictors for both disease recurrence and mortality among smokers. Additionally, COMT was highly associated with recurrence, and NAT1 and RIPK1 were associated with mortality. In contrast, only IRF2, CETN1, and CYP1A1 were significant for disease recurrence and mortality among non-smokers, with NAT2 additionally significant for survival. Median, 25th percentile, and 75th percentile for the C-indexes based on the gene expression models are given in Table 1.

Table 1. C-indexes for the Four Gene Expression Models Based on 1000 Test Data SetsPatient GroupOutcome25th PercentileMedian75th PercentileCurrent SmokersOverall Survival0.730.800.86Current SmokersRecurrence-free Survival0.670.730.78Never SmokedOverall Survival0.530.590.66Never SmokedRecurrence-free Survival0.510.590.66

Analysis of interaction between smoking status and gene expression values using the combined samples revealed significant interactions between smoking status and CYP1A1, LECT2, CETN1. Molecular signatures consisting of 7-8 genes were highly predictive for breast cancer recurrence and overall survival among smokers, with median C-index values of 0.8 and 0.73 for overall survival and recurrence, respectively. In contrast, the median C-index values for non-smokers was only 0.59. Hence, significant interactions between expression of crucial genes and cigarette smoking status appear to play a key role in predicting clinical outcomes of breast carcinoma patients. Supported in part by a grant from the Phi Beta Psi Charity Trust (TSK & JLW) and a Research of Women (ROW) grant to JLW from the EVP for Research and Innovation, University of Louisville.

Citation Format: James L Wittliff, Sarah A Andres, Mohammad A Alatoum, Katie E Bickett, Theodore S Kalbfleisch, Guy N Brock. Interaction between smoking history and gene expression levels impacts survival of breast carcinoma patients [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 P2-03-11.

Abstract P4-07-09: Breast cancer specific expression of miRNA deciphered using next generation sequencing of LCM procured cells

The objective of this study is to decipher miRNA expression profiles of laser capture microdissection (LCM)-procured carcinoma cells compared to those of intact serial sections of a breast cancer biopsy. Our hypothesis is that miRNA signatures discerned from specific carcinoma cell populations more precisely correlate with clinical behavior than that provided by conventional biomarkers of intact tissue biopsies. De-identified frozen biopsies of invasive ductal carcinomas of known grade and biomarker status containing 35-70% cancer were selected from an IRB-approved Biorepository (JLW). Serial tissue sections were stained with H & E and 12-15,000 carcinoma cells were collected from an adjacent section. RNA was extracted using PureLink RNA Mini Kit™ (Invitrogen), evaluated (Agilent Bioanalyzer) and sequenced for miRNA expression using the Ion Torrent™ System (Thermo Fisher). Total RNAs were enriched for small RNA species using mirVana miRNA™ kits (Thermo Fisher) and RNA libraries were constructed from 5 ng of enriched RNA using Ion Total RNA-Seq Kit v2. Barcodes were utilized to multiplex libraries for template preparation and sequencing on Proton PI™ chips as twelve-plex library pools. Each library was sequenced to an average of 30M reads on the Ion Proton™sequencer with the Ion PI™ chip. Sequence reads were aligned to miRNA precursor hairpins available from the miRBase (miRBase.org) miRNA repository. Aligned reads to each miRBase reference miRNA were then reported. Using the R statistical software package, DESeq (Bioconductor), counts for all libraries were normalized and relative expression was calculated. Mapping statistics (e.g., aligned reads (range 59-79%) and miRBase matches (range 69-85%)) were assessed for each library. Comparison of expressed miRNAs from intact tissue sections with those of cognate carcinoma cells procured by LCM revealed, in general, that smaller defined miRNA gene sets were expressed in isolated populations of carcinoma cells. miRNA expression patterns of experimental pairs (intact vs LCM-procured) using MA-plots were highly variable in carcinomas with different grades, suggesting a relationship to disease status. Gene frequency plots, comparing expression from intact tissue sections to that of LCM-procured cell population, revealed subsets of differently expressed miRNAs. To increase statistical power, a follow-up experiment was performed with triplicate libraries from 4 different representative carcinoma samples. In addition to miRNA sequencing, targeted RNA sequencing with an Ion AmpliSeq™ RNA panel was used to capture gene expression information from the12 additional samples. From these replicated libraries, we are able to combine mRNA and miRNA expression information to create an expected profile from these breast carcinoma tissue samples. Application of Next Generation Sequencing of miRNAs and Ion AmpliSeq™ RNA panels using LCM-procured cells and intact tissue provides an innovative approach for assessing differential expression of miRNA and mRNA levels involved in breast cancer behavior. Supported in part by a grant from the Phi Beta Psi Charity Trust (JLW & SAA) and a CTSP Award from the Commonwealth of Kentucky (JLW). For research use only.

Citation Format: Kelli S Bramlett, James L Wittliff, Jose G Cienfuegos, Sarah A Andres, Jeoffrey J Schageman. Breast cancer specific expression of miRNA deciphered using next generation sequencing of LCM procured cells [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 P4-07-09.

A systems biology approach identifies a regulatory network in parotid acinar cell terminal differentiation

OBJECTIVE

The transcription factor networks that drive parotid salivary gland progenitor cells to terminally differentiate, remain largely unknown and are vital to understanding the regeneration process.

METHODOLOGY

A systems biology approach was taken to measure mRNA and microRNA expression in vivo across acinar cell terminal differentiation in the rat parotid salivary gland. Laser capture microdissection (LCM) was used to specifically isolate acinar cell RNA at times spanning the month-long period of parotid differentiation.

RESULTS

Clustering of microarray measurements suggests that expression occurs in four stages. mRNA expression patterns suggest a novel role for Pparg which is transiently increased during mid postnatal differentiation in concert with several target gene mRNAs. 79 microRNAs are significantly differentially expressed across time. Profiles of statistically significant changes of mRNA expression, combined with reciprocal correlations of microRNAs and their target mRNAs, suggest a putative network involving Klf4, a differentiation inhibiting transcription factor, which decreases as several targeting microRNAs increase late in differentiation. The network suggests a molecular switch (involving Prdm1, Sox11, Pax5, miR-200a, and miR-30a) progressively decreases repression of Xbp1 gene transcription, in concert with decreased translational repression by miR-214. The transcription factor Xbp1 mRNA is initially low, increases progressively, and may be maintained by a positive feedback loop with Atf6. Transfection studies show that Xbp1 activates the Mist1 promoter [corrected]. In addition, Xbp1 and Mist1 each activate the parotid secretory protein (Psp) gene, which encodes an abundant salivary protein, and is a marker of terminal differentiation.

CONCLUSION

This study identifies novel expression patterns of Pparg, Klf4, and Sox11 during parotid acinar cell differentiation, as well as numerous differentially expressed microRNAs. Network analysis identifies a novel stemness arm, a genetic switch involving transcription factors and microRNAs, and transition to an Xbp1 driven differentiation network. This proposed network suggests key regulatory interactions in parotid gland terminal differentiation.

Temporal Expression of miRNAs in Laser Capture Microdissected Palate Medial Edge Epithelium from Tgfβ3(-/-) Mouse Fetuses

Clefting of the secondary palate is the most common birth defect in humans. Midline fusion of the bilateral palatal processes is thought to involve apoptosis, epithelial to mesenchymal transition, and cell migration of the medial edge epithelium (MEE), the specialized cells of the palate that mediate fusion of the palatal processes during fetal development. Data presented in this manuscript are the result of analyses designed to identify microRNAs that are expressed and regulated by TGFβ3 in developing palatal MEE. The expression of 7 microRNAs was downregulated and 1 upregulated in isolated MEE from wildtype murine fetuses on gestational day (GD) 13.5 to GD14.5 (prior to and during epithelial fusion of the palatal processes, respectively). Among this group were miRNAs linked to apoptosis (miR-378) and epithelial to mesenchymal transformation (miR-200b, miR-205, and miR-93). Tgfβ3(-/-) fetuses, which present with a complete and isolated cleft of the secondary palate, exhibited marked dysregulation of distinct miRNAs both in the palatal MEE and mesenchyme when compared to comparable wild-type tissue. These included, among others, miRNAs known to affect apoptosis (miR-206 and miR-186). Dysregulation of miRNAs in the mesenchyme underlying the palatal MEE of Tgfβ3(-/-) fetuses is also discussed in relation to epithelial-mesenchymal transformation of the MEE. These results are the first systematic analysis of the expression of microRNAs in isolated fetal palatal epithelium and mesenchyme. Moreover, analysis of the Tgfβ3 knockout mouse model has enabled identification of miRNAs with altered expression that may contribute to the cleft palate phenotype.

Co-expression of genes with estrogen receptor-α and progesterone receptor in human breast carcinoma tissue

Abstract Background: To detect genes associated with the expression of ESR1 and PGR - as well as of their protein products, estrogen receptor (ER) and progesterone receptor (PR) - 221 de-identified invasive ductal carcinomas of the breast were investigated. Our long-term goal is to decipher relationships between the expression of ER- and PR-associated genes and breast cancer behavior to improve diagnostics and identify new molecular targets for drug design.

MATERIALS AND METHODS

Frozen tissue sections were evaluated for structural integrity and pathology after hematoxylin and eosin staining. ER and PR protein levels were quantified by either enzyme immunoassay or radio-ligand binding assay. Total RNA preparations were reverse transcribed for qPCR measurements of ESR1, PGR and 31 gene candidates.

RESULTS

Both ESR1 and PGR expression levels were correlated with their cognate receptor protein expression (Pearson correlations of 0.82 and 0.68, p<0.001, respectively), to assess molecular relationships between clinically relevant biomarkers in tissue specimens. Coordinate expression of EVL, NAT1, TBC1D9, SCUBE2, RABEP1, SLC39A6, TCEAL1, FUT8, XBP1, PTP4A2 or GATA3 with either ESR1 or PGR was detected.

CONCLUSIONS

Examination of relationships between ESR1 and PGR gene expression and that of other genes of interest indicated: a high degree of correlation between ESR1 levels and expression of NAT1, SCUBE2, XBP1 and GATA3; and a high degree of correlation between PGR expression and that of NAT1, ESR1, SCUBE2 and RABEP1. These results suggest that direct relationships of these genes exist with estrogen and progestin receptor mediated pathways. Pathway analysis software provided additional evidence of gene interactions.

Gender-associated expression of tumor markers and a small gene set in breast carcinoma

Breast carcinomas in both genders share pathological features, although differences in incidence, prognosis and survival are reported. Expression of 33 genes was investigated in male and female breast carcinomas in association with ER, PR, HER-2/neu and EGF-receptor. Among 98 male breast cancers, 82 were ER+ and 78 were PR+. ER and PR protein levels were greater in males compared to females, although no differences were observed in ESR1 and PGR expression. A difference was observed in binding affinities of PR but not ER between genders. No differences were observed in HER-2/neu, EGFR protein, or patient age. Expression of NAT1, TBC1D9, IL6ST, RABEP1, PLK1 and LRBA was elevated in carcinomas of males compared to those of females, in which ER status appeared to be related to expression. Over-expression of protein products of these genes represents novel molecular targets for development of gender-specific therapeutics and companion diagnostics.

Abstract P4-04-03: A microgenomic approach using LCM procured breast cancer cells to identify clinically relevant gene signatures that underlie favorable response of ILC to aromatase inhibitors

Based on CGH analyses, invasive lobular carcinoma (ILC) is closely related to low grade invasive ductal carcinoma (IDC), and is genetically unrelated to intermediate and high grade invasive carcinomas (Pathol Res Pract 2005; 201:713). Results from the BIG 1-98 trial, showed that patients with ILC and luminal B (intermediate/high grade) IDC treated with Letrozole, an aromatase inhibitor (AI), had a significant improvement in overall survival, whereas patients with luminal A (low grade) IDC did not (Cancer Res 2012; 72(24 Suppl):Abstract nr S1-1). Despite genetic evidence suggesting a close relationship between ILC and low grade IDC, and disparity between ILC and intermediate and high grade IDC, a clinically relevant gene set underlying a tumor's biologic responsiveness to AIs likely exists. We are deciphering a gene subset that would differ in expression between low grade IDC and ILC, and would be shared by ILC and luminal B IDC. Identification of such a gene set should lead to a more robust marker for identifying AI responsive tumors rather than relying solely on histomorphology and/or immunohistochemistry for the pathologic diagnosis of ILC, since the distinction between ILC and IDC is not always straight forward in pathology practice.

Using 247 de-identified human breast carcinoma biopsies collected under standardized, stringent conditions, total RNA was extracted from carcinoma cells procured by laser capture microdissection to perform microarray analyses of approximately 22,000 genes to identify expression signatures associated with breast cancer characteristics. Of the 247 samples, 169 samples were used for the analysis and included 16 ILCs, 13 low grade IDCs, 55 intermediate grade IDCs and 85 high grade IDCs.

Preliminary analyses identified 1267 genes that were differentially expressed (p&lt;0.01) between cell samples from patients with IDC compared to those with ILC. Gene expression levels in breast cancer cells from patients with low grade IDC compared to those with ILC yielded 200 genes that were statistically differentially expressed (p&lt;0.01). When comparing high grade IDC to ILC, 149 of these genes were not differentially expressed indicating that this gene set may serve as a panel of candidate genes for identifying cancers responsive to AIs. Pathway analysis software (Ingenuity®) identified that these genes were associated with key molecular and cellular functions, e.g., cell-to-cell signaling, cell morphology, cell death and survival, cellular assembly and organization and carbohydrate metabolism. qPCR analyses are used to validate and refine the gene subset distinguishing ILC from low grade IDC. Our approach is revealing subtle molecular features that discriminate these lesions based on clinical behavior. Supported in part by a grant from the Phi Beta Psi Charity Trust.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P4-04-03.

Epigenetic analysis of laser capture microdissected fetal epithelia

Laser capture microdissection (LCM) is a superior method for nondestructive collection of specific cell populations from tissue sections. Although DNA, RNA, and protein have been analyzed from LCM-procured samples, epigenetic analyses, particularly of fetal, highly hydrated tissue, have not been attempted. A standardized protocol with quality assurance measures was established to procure cells by LCM of the medial edge epithelia (MEE) of the fetal palatal processes for isolation of intact microRNA for expression analyses and genomic DNA (gDNA) for CpG methylation analyses. MicroRNA preparations, obtained using the RNAqueous Micro kit (Life Technologies), exhibited better yields and higher quality than those obtained using the Arcturus PicoPure RNA Isolation kit (Life Technologies). The approach was validated using real-time polymerase chain reaction (PCR) to determine expression of selected microRNAs (miR-99a and miR-200b) and pyrosequencing to determine CpG methylation status of selected genes (Aph1a and Dkk4) in the MEE. These studies describe an optimized approach for employing LCM of epithelial cells from fresh frozen fetal tissue that enables quantitative analyses of microRNA expression levels and CpG methylation.

Characterization of estrogen response element binding proteins as biomarkers of breast cancer behavior

BACKGROUND

While investigating estrogen response element (ERE) binding properties of human estrogen receptor-α (hERα) in breast cancer cytosols, other ERE-binding proteins (ERE-BP) were observed.

DESIGN AND METHODS

Recognition properties of ERE-BP were evaluated by electrophoretic mobility shift assays (EMSA) with ERE sequences of the 5'-flanking region of the estrogen responsive gene vitellogenin A2 (VitA2). Cytosols were incubated 16 h, 4 °C with [32P]ERE sequences and separated by EMSA. A method of estimating ERE-BP levels was developed by measuring band intensity from EMSA profiles, expressed in digital light units (DLU)/μg protein and normalized to total DLU. ERE-BP were purified by affinity chromatography and EMSA, and then identified by mass spectrometry.

RESULTS

ERE-BP in cytosols did not supershift in the presence of anti-hERα or anti-hERβ antibodies recognizing different ER epitopes suggesting that they are not fragments of either receptor isoform. ERE-BP competed with hERα for binding to VitA2-ERE. Increased levels of ERE-BP DNA-binding activities measured in 310 cytosols prepared from breast cancer biopsies correlated with decreased patient survival. Strikingly, breast cancer patients with ER negative status and high ERE-BP expression exhibited the poorest disease-free and overall survival. After purification, ERE-BP were identified as Ku70 (XRCC6) and Ku80 (XRCC5) using mass spectrometry. ERE-BP were confirmed to be Ku70/80 by supershift assay.

CONCLUSION

Presence of these novel ERE-binding proteins in a breast carcinoma is a strong predictor of poor prognosis. Our results suggest that ERE-BP, identified as Ku70/Ku80, in cytosols prepared from breast carcinoma biopsies are useful biomarkers for assessing risk of breast cancer recurrence.

Interrogating differences in expression of targeted gene sets to predict breast cancer outcome

Background

Genomics provides opportunities to develop precise tests for diagnostics, therapy selection and monitoring. From analyses of our studies and those of published results, 32 candidate genes were identified, whose expression appears related to clinical outcome of breast cancer. Expression of these genes was validated by qPCR and correlated with clinical follow-up to identify a gene subset for development of a prognostic test.

Methods

RNA was isolated from 225 frozen invasive ductal carcinomas,and qRT-PCR was performed. Univariate hazard ratios and 95% confidence intervals for breast cancer mortality and recurrence were calculated for each of the 32 candidate genes. A multivariable gene expression model for predicting each outcome was determined using the LASSO, with 1000 splits of the data into training and testing sets to determine predictive accuracy based on the C-index. Models with gene expression data were compared to models with standard clinical covariates and models with both gene expression and clinical covariates.

Results

Univariate analyses revealed over-expression of RABEP1, PGR, NAT1, PTP4A2, SLC39A6, ESR1, EVL, TBC1D9, FUT8, and SCUBE2 were all associated with reduced time to disease-related mortality (HR between 0.8 and 0.91, adjusted p < 0.05), while RABEP1, PGR, SLC39A6, and FUT8 were also associated with reduced recurrence times. Multivariable analyses using the LASSO revealed PGR, ESR1, NAT1, GABRP, TBC1D9, SLC39A6, and LRBA to be the most important predictors for both disease mortality and recurrence. Median C-indexes on test data sets for the gene expression, clinical, and combined models were 0.65, 0.63, and 0.65 for disease mortality and 0.64, 0.63, and 0.66 for disease recurrence, respectively.

Conclusions

Molecular signatures consisting of five genes (PGR, GABRP, TBC1D9, SLC39A6 and LRBA) for disease mortality and of six genes (PGR, ESR1, GABRP, TBC1D9, SLC39A6 and LRBA) for disease recurrence were identified. These signatures were as effective as standard clinical parameters in predicting recurrence/mortality, and when combined, offered some improvement relative to clinical information alone for disease recurrence (median difference in C-values of 0.03, 95% CI of -0.08 to 0.13). Collectively, results suggest that these genes form the basis for a clinical laboratory test to predict clinical outcome of breast cancer.

Assessment of phytoestrogen and mycoestrogen recognition by recombinant human estrogen receptor-α using ligand titration arrays

INTRODUCTION

Exposure to phytoestrogens and mycoestrogens has emerged as a public health issue due to their potentially endocrine disruption activities resulting from direct interaction with sex-steroid hormone receptors. There is a significant requirement for comprehensive, reproducible methods to determine the extent of estrogen mimicry by compounds encountered in the environment to estimate risk:benefit ratios, particularly in humans.

OBJECTIVE

To develop a systematic approach for assessing recognition of chemically diverse compounds by human estrogen receptor proteins to aid in their assessment as endocrine disruptor compounds (EDCs).

METHODS

Recombinant human estrogen receptor-α protein (rhERα) was expressed in Saccharomyces cervisiae as an ubiquitin fusion under control of a CUP1 promoter and partially purified with heparin affinity chromatography in the unliganded state. A novel radio-ligand binding array was developed to evaluate structurally diverse compounds, both naturally occurring and synthetic, for estrogen binding activity and affinity.

RESULTS

Binding affinities of suspected estrogen mimics for rhERα were calculated over a range of [(3) H]estradiol-17β concentrations using Lundon OneSite® and Compete® software.

CONCLUSION

β-zearalanol, a mycoestrogen similar to zearalenone used as an ICCVAM validation substance for the in vitro estrogen receptor binding assays (ICCAM report), was employed as a model estrogen mimic to illustrate the approach, methods and calculations using these techniques.

Abstract 3457: Gender-associated expression of tumor markers and a small gene set in breast carcinoma

In 2011, carcinoma of the breast in men accounted for ∼1% of all breast cancers in the US, and approximately 450 male patients died from this disease. Although breast carcinomas in both genders share certain pathological features, notable differences have been observed regarding incidence, prognosis and survival. Results from microarray analyses in our studies and those of other reports were used to select 33 candidate genes to investigate in male breast carcinomas. Tumor marker results for 99 male breast cancers and ∼18,000 female breast carcinomas were extracted from our IRB-approved comprehensive database. Estrogen receptor (ER) and progestin receptor (PR) levels were determined by either radio-ligand binding (NEN/DuPont) or enzyme immunoassay (Abbott Labs). HER-2/neu levels were determined by either ELISA (Oncogene Science) or EIA (Triton Biosciences), and epidermal growth factor receptor (EGFR) levels were determined by an in-house radio-ligand competition assay. RNA was isolated from tissue sections of de-identified frozen biopsies from 12 male patients and 233 female patients using the RNeasy Mini kit (Qiagen) and analyzed for quality and quantity (Agilent Bioanalyzer). cDNA for qPCR measurements was prepared in Tris-HCl buffer with KCl, MgCl2, DTT (Invitrogen), dNTPs (Invitrogen), RNasin (Promega) and Superscript RT III (Invitrogen). qPCR reactions were performed using Power Sybr Green PCR Master Mix (Applied Biosystems), forward/reverse primers and cDNA obtained from the reverse transcription reaction. Relative gene expression was calculated by the ddCt method using β-actin as a reference and Universal Human Reference RNA (Stratagene) as a calibrator. Among 99 male breast cancers, 82 were ER positive and 78 exhibited PR. Levels of ER (P = 0.013) and PR (P &lt; 0.001) protein were greater in male breast cancers compared to biopsies from female patients, although no difference was observed in the expression of ESR1 and PGR genes that encode these receptors. In contrast, no differences were observed in either of the other conventional breast cancer biomarkers, HER-2/neu or EGFR protein, nor in patient age at diagnosis. However, there was a difference in the binding affinities (Kd value) of PR (P = 0.004) between the genders, which was not observed in ER between male and female breast cancer tissues. Furthermore, expression levels of six genes (NAT1, TBC1D9, IL6ST, RABEP1, PLK1 and LRBA) that we and others have suggested serve as indicators of risk of recurrence, were elevated in male breast cancer biopsies compared to those from female patients (P &lt; 0.05). Preliminary results suggest that over-expression of the protein product of one or more of the genes identified represents a molecular target that warrants further exploration for development of a gender specific therapeutic and companion diagnostic. Supported in part by a grant from Phi Beta Psi Charity Trust and a CTSP Award from the Commonwealth of Kentucky.

Citation Format: Sarah A. Andres, Irina A. Smolenkova, James L. Wittliff. Gender-associated expression of tumor markers and a small gene set in breast carcinoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3457. doi:10.1158/1538-7445.AM2013-3457

Expression of urokinase-type plasminogen activator (uPA), its receptor (uPAR), and inhibitor (PAI-1) in human breast carcinomas and their clinical relevance

Serine proteases convert plasminogen to plasmin which is involved in tissue remodeling under physiologic and pathophysiologic conditions, including breast carcinoma invasion and progression. Both urokinase-type plasminogen activator (uPA) and pro-uPA associate with uPA receptor (uPAR) on target cells, where plasminogen activator inhibitors (e.g., PAI-1) may modulate their activities. Expression levels of these factors were compared in breast carcinomas relative to patient characteristics, carcinoma features, and clinical outcome. uPA, uPAR, and PAI-1 were quantified by enzyme-linked immunosorbent assay (ELISA) in extracts of 226 biopsies while estrogen receptor (ER) and progestin receptor (PR) were determined by enzyme immunoassay (EIA) or radio-ligand binding. Each set of assays contained a novel reference specimen with known quantities of each of these five analytes. Levels in ng/mg protein of these biomarkers exhibited ranges: uPA (0-12.3); uPAR (0-19.5); PAI-1 (0-91.2). When considered independently, expression of uPA, uPAR, or PAI-1 was unrelated to patient age or menopausal status. Although no correlation was observed between each analyte with stage, grade, or ER/PR status, levels appeared to differ with pathology and nodal status. A dendrogram from hierarchical clustering of uPA, uPAR, and PAI-1 levels in 106 specimens revealed three clusters of breast cancer patients. Kaplan-Meier analyses of uPA, uPAR, and PAI-1 indicated a correlation with overall survival (OS), suggesting collective examination of these biomarkers is useful in predicting clinical outcome of breast cancer.

Relationships of ESR1 and XBP1 expression in human breast carcinoma and stromal cells isolated by laser capture microdissection compared to intact breast cancer tissue

Results from investigations of human genomics which utilize intact tissue biopsy specimens maybe compromised due to a host of uncontrolled variables including cellular heterogeneity of a sample collected under diverse conditions, then processed and stored using different protocols. To determine the cellular origin and assess relationships of mRNA expression of two genes reported to be co-expressed in human breast carcinoma (estrogen receptor-α, ESR1 and X-box binding protein 1, XBP1), gene expression analyses were performed with intact tissue sections and compared with those of laser capture microdissection (LCM)-procured carcinoma and stromal cells from serial sections of the same tissue. Frozen sections of human breast carcinomas were first evaluated for structural integrity and pathology after hematoxylin and eosin (H&E) staining. Total RNA preparations from intact tissue sections and LCM-procured carcinoma and stromal cells were reverse transcribed for measurements of ESR1 and XBP1 expression by quantitative PCR (qPCR). These results were compared with those obtained from microarray analyses of LCM-procured carcinoma cells. Levels of ESR1 and XBP1 were detected in the intact breast cancer tissue sections suggesting coordinate gene expression. Although coordinate expression of these genes was observed in the LCM-procured carcinoma cells, it was not discerned in LCM-procured stromal cells. The origin of coordinate expression of ESR1 and XBP1 observed in whole tissue sections of human breast cancer biopsies is due principally to their co-expression in carcinoma cells and not in the surrounding stromal cells as substantiated using LCM-procured cells. Collectively, a microgenomic process was established from human tissue preparation to RNA characterization and analysis to identify molecular signatures of specific cell types predicting clinical behavior.

Abstract 5267: Relationship between gene and tumor marker expression in primary breast carcinoma and lymph node metastases of the same patient

Purpose: Our goal is to develop genomics-based tests of primary breast carcinoma for assessing risk of recurrence by comparing gene and tumor marker expression of primary lesions with those of lymph node and distant metastases. Using microarray analyses from our studies and other reports, 32 candidate genes were selected from carcinoma and stromal cells, whose expression appears related to clinical outcome of breast cancer (Andres et al., Cancer Res 69(Suppl): 403s-404s, 2009). Expression of candidate genes was evaluated with estrogen (ER) and progestin receptor (PR) protein levels to ascertain their relationship during lymph node invasion.

Procedures: ER and PR levels were determined by either ligand binding or enzyme immunoassay. RNA was isolated from tissue sections of de-identified frozen biopsies of invasive ductal carcinoma using the RNeasy® Mini kit (Qiagen) and analyzed for quality and quantity (Agilent Bioanalyzer). cDNA for qPCR measurements was prepared in Tris-HCl buffer with KCl, MgCl2, DTT (Invitrogen), dNTPs (Invitrogen), RNasin® (Promega) and Superscript® RT III (Invitrogen). qPCR reactions were performed using Power Sybr® Green PCR Master Mix (Applied Biosystems), forward/reverse primers and cDNA obtained from the reverse transcription reaction. Relative gene expression was calculated by the ddCt method, using β-actin as a reference and Universal Human Reference RNA (Stratagene) as a calibrator.

Results: Although ER and PR protein levels varied between the primary and lymph node metastasis, no patient with an ER- or PR- primary exhibited a positive ER/PR result in the metastasis. Only 3 patients with an ER+ or PR+ primary exhibited a loss of receptor expression in the lymph node metastasis. Expression of 15 of 32 genes (EVL, GABRP, TRIM29, IL6ST, RABEP1, SLC39A6, FUT8, PFKP, XBP1, MCM6, YBX1, LRBA, GATA3, MAPRE2, CKS2) was discordant in most primary lesion-lymph node metastasis pairs. However, expression of NAT1, ESR1, ST8SIA1, TBC1D9, CENPA, PLK1, ATAD2, PTP4A2, CX3CL1 GMPS and SLC43A3 exhibited concordance in the majority of primary-metastasis pairs. Only 3 patients exhibited differences in expression levels of SCUBE2, TPBG, TCEAL1, DSC2, MELK and BUB1 in primary-nodal metastasis pairs.

Conclusions: To ascertain genomic changes in primary breast carcinomas and lymph node metastases, we compared levels of 32 candidate genes whose expression appears related to clinical outcome of breast cancer. Seldom was gene expression in the metastasis greater than that of the primary. Gene expression and biological activities of their protein products are used to classify subsets of primary breast cancers according to metastatic spread. These results serve as the foundation for developing a genomics-based test to predict risk of breast cancer recurrence. Supported in part by grants from Phi Beta Psi Charity Trust and a CTSP Grant from the Commonwealth of Kentucky.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5267. doi:10.1158/1538-7445.AM2011-5267

Abstract 4413: A 5-gene model predicts clinical outcome in ER+/PR+, early stage breast cancers treated with adjuvant tamoxifen

Purpose: Patients with primary breast carcinomas expressing of both estrogen (ERα) and progesterone receptors (PR) are more likely to respond to Tamoxifen therapy than those with ERα and PR negative cancers, especially in women with early stage lesions. However, a significant number of these patients exhibiting clinicopathologic features suggesting good response and prognosis will relapse within 10 years. Additional markers are needed to identify patients at risk for breast cancer recurrence after administrative hormone therapy.

Procedures: Ten candidate genes associated with estrogen signaling were selected from a group of 200 genes identified from microarray studies of laser capture microdissected breast carcinoma cells of ER positive breast cancers and combined with those for conventional biomarkers (ESR1, PGR, ERBB2). Carcinoma cell content and pathology of each biopsy was confirmed. Expression of this 13-gene subset was analyzed by RT-qPCR in de-identified frozen tissue specimens from early stage, ER+/PR+ breast cancers treated with adjuvant Tamoxifen. A multivariate model was created by Cox regression using a training set of tissue sections from 36 biopsy specimens, and then applied to an independent validation set of sections from 24 specimens.

Results: A 5-gene model was derived from the training set that exhibited significant correlations with both relapse-free and overall survival. Applying this model to Kaplan-Meier regression, patients were separated into low risk (100% relapse-free at 150 months) and high risk (60% relapse-free at 150 months) groups (P = 0.03). When this model was applied to the validation set, similar risk stratification was achieved for both relapse-free and overall survival (P = 0.01 and 0.04, respectively). No significant difference in clinical features (e.g., tumor grade, tumor size and nodal status) was observed between the high and low risk groups.

Conclusions: We developed a 5-gene model composed of PgR, BCL2, ERBB4 JM-a, RERG and CD34 that identified a subset of early stage, ER+/PR+ breast cancers patients treated with Tamoxifen that exhibited high recurrence rates, although their clinicopathologic features suggested good prognosis and response. Furthermore, absence of association of the 5-gene model with tumor grade suggests the gene expression profile provides clinically relevant predictive information independent of proliferation. Supported in part by grants from the Phi Beta Psi Sorority Charity Trust and a CTSP award from the Commonwealth of Kentucky. DAK was a recipient of a Graduate Fellowship from the Integrated Programs in Biomedical Sciences, University of Louisville, and the Spatola Graduate Fellowship from IMD3.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4413. doi:10.1158/1538-7445.AM2011-4413

Abstract 4163: Expression of estrogen response element binding proteins in human breast carcinoma improves prediction of clinical outcome

Purpose: Unique ERE-binding proteins (ERE-BP) were detected in cytosolic extracts of breast cancer while investigating estrogen receptor-α (hERα) recognition of ERE sequences. Our goal is to compare properties of these novel ERE-BP with those of hERα and hERβ, and determine their clinical relevance.

Procedures: Using de-identified tissue biopsies, cytosols were prepared in 40 mM Tris buffer, pH 7.4 with 1.5 mM EDTA, 10 mM Na2MoO4, 10% glycerol, 1 mM PMSF and 10 μM monothioglycerol while nuclear pellets were extracted in the same buffer with 0.4M NaCl and without 10 mM Na2MoO4. Extracts were incubated 16 hr, 4°C with [32P]ERE and separated by electrophoretic mobility shift (EMSA) and super-shift assays (SSA) with ERE sequences present in 5’-flanking regions of estrogen responsive genes. ERE-BP level was estimated from band intensity of an EMSA profile. ERE-BP was correlated with cancer features (e.g. pathology, stage, nodal status), patient characteristics (e.g., family history, age, race) and clinical outcome to determine ERE-BP status for predicting clinical behavior of breast cancer.

Results: Both recombinant hERα and ERE-BP reference specimens were developed as assay controls. Compared to cytosolic levels, ERE-BP exhibited higher expression in nuclear extracts. When either disease-free (DFS) or overall survival (OS) was analyzed as a function of above or below median ERE-BP expression using Kaplan-Meier plots, patients with biopsies in the above median group exhibited decreased DFS and OS compared to women in the below median group. Overall 5-year survival was 68% for the above median group and 85% for those in the below median group. No correlation of ERE-BP level was observed with patient age, race, stage, nodal status or tumor marker levels; however ERE-BP over-expression correlated with increased tumor grade. There was no difference in survival between patients with ERα positive cancer in either the above median ERE-BP or below median ERE-BP groups. However, patients with ERα negative cancers expressing high ERE-BP exhibited the poorest OS of any group. Five year OS for patients in the ERα negative/above median ERE-BP group was only 55% compared to 78% in the ERα negative/below median ERE-BP group suggesting clinically relevant subtypes of ER negative carcinomas.

Conclusions: Results support our hypothesis that presence of these novel ERE-binding proteins in a breast carcinoma is an indicator of clinical behavior. ERE-BP expression in combination with ERα negative status in breast cancer appears to provide an improved means of identifying patients at greatest risk of recurrence and decreased survival. Supported in part by NIH/NCI 1R43CA106059-01A1, Phi Beta Psi Charity Trust, a UofL Research on Women Grant and a CTSB grant from the Commonwealth of Kentucky. TLK is a recipient of a DOD BCRP Pre-doctoral Traineeship Award.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4163. doi:10.1158/1538-7445.AM2011-4163

American Society of Clinical Oncology/College of American Pathologists guideline recommendations for immunohistochemical testing of estrogen and progesterone receptors in breast cancer (unabridged version)

PURPOSE

To develop a guideline to improve the accuracy of immunohistochemical (IHC) estrogen receptor (ER) and progesterone receptor (PgR) testing in breast cancer and the utility of these receptors as predictive markers.

METHODS

The American Society of Clinical Oncology and the College of American Pathologists convened an international Expert Panel that conducted a systematic review and evaluation of the literature in partnership with Cancer Care Ontario and developed recommendations for optimal IHC ER/PgR testing performance.

RESULTS

Up to 20% of current IHC determinations of ER and PgR testing worldwide may be inaccurate (false negative or false positive). Most of the issues with testing have occurred because of variation in pre-analytic variables, thresholds for positivity, and interpretation criteria.

RECOMMENDATIONS

The Panel recommends that ER and PgR status be determined on all invasive breast cancers and breast cancer recurrences. A testing algorithm that relies on accurate, reproducible assay performance is proposed. Elements to reliably reduce assay variation are specified. It is recommended that ER and PgR assays be considered positive if there are at least 1% positive tumor nuclei in the sample on testing in the presence of expected reactivity of internal (normal epithelial elements) and external controls. The absence of benefit from endocrine therapy for women with ER-negative invasive breast cancers has been confirmed in large overviews of randomized clinical trials.

American Society of Clinical Oncology/College of American Pathologists guideline recommendations for immunohistochemical testing of estrogen and progesterone receptors in breast cancer (unabridged version)

PURPOSE

To develop a guideline to improve the accuracy of immunohistochemical (IHC) estrogen receptor (ER) and progesterone receptor (PgR) testing in breast cancer and the utility of these receptors as predictive markers.

METHODS

The American Society of Clinical Oncology and the College of American Pathologists convened an international Expert Panel that conducted a systematic review and evaluation of the literature in partnership with Cancer Care Ontario and developed recommendations for optimal IHC ER/PgR testing performance.

RESULTS

Up to 20% of current IHC determinations of ER and PgR testing worldwide may be inaccurate (false negative or false positive). Most of the issues with testing have occurred because of variation in pre-analytic variables, thresholds for positivity, and interpretation criteria.

RECOMMENDATIONS

The Panel recommends that ER and PgR status be determined on all invasive breast cancers and breast cancer recurrences. A testing algorithm that relies on accurate, reproducible assay performance is proposed. Elements to reliably reduce assay variation are specified. It is recommended that ER and PgR assays be considered positive if there are at least 1% positive tumor nuclei in the sample on testing in the presence of expected reactivity of internal (normal epithelial elements) and external controls. The absence of benefit from endocrine therapy for women with ER-negative invasive breast cancers has been confirmed in large overviews of randomized clinical trials.

American Society of Clinical Oncology/College of American Pathologists guideline recommendations for immunohistochemical testing of estrogen and progesterone receptors in breast cancer

PURPOSE

To develop a guideline to improve the accuracy of immunohistochemical (IHC) estrogen receptor (ER) and progesterone receptor (PgR) testing in breast cancer and the utility of these receptors as predictive markers.

METHODS

The American Society of Clinical Oncology and the College of American Pathologists convened an international Expert Panel that conducted a systematic review and evaluation of the literature in partnership with Cancer Care Ontario and developed recommendations for optimal IHC ER/PgR testing performance.

RESULTS

Up to 20% of current IHC determinations of ER and PgR testing worldwide may be inaccurate (false negative or false positive). Most of the issues with testing have occurred because of variation in preanalytic variables, thresholds for positivity, and interpretation criteria.

RECOMMENDATIONS

The Panel recommends that ER and PgR status be determined on all invasive breast cancers and breast cancer recurrences. A testing algorithm that relies on accurate, reproducible assay performance is proposed. Elements to reliably reduce assay variation are specified. It is recommended that ER and PgR assays be considered positive if there are at least 1% positive tumor nuclei in the sample on testing in the presence of expected reactivity of internal (normal epithelial elements) and external controls. The absence of benefit from endocrine therapy for women with ER-negative invasive breast cancers has been confirmed in large overviews of randomized clinical trials.

American Society of Clinical Oncology/College of American Pathologists guideline recommendations for immunohistochemical testing of estrogen and progesterone receptors in breast cancer

PURPOSE

To develop a guideline to improve the accuracy of immunohistochemical (IHC) estrogen receptor (ER) and progesterone receptor (PgR) testing in breast cancer and the utility of these receptors as predictive markers.

METHODS

The American Society of Clinical Oncology and the College of American Pathologists convened an international Expert Panel that conducted a systematic review and evaluation of the literature in partnership with Cancer Care Ontario and developed recommendations for optimal IHC ER/PgR testing performance.

RESULTS

Up to 20% of current IHC determinations of ER and PgR testing worldwide may be inaccurate (false negative or false positive). Most of the issues with testing have occurred because of variation in preanalytic variables, thresholds for positivity, and interpretation criteria.

RECOMMENDATIONS

The Panel recommends that ER and PgR status be determined on all invasive breast cancers and breast cancer recurrences. A testing algorithm that relies on accurate, reproducible assay performance is proposed. Elements to reliably reduce assay variation are specified. It is recommended that ER and PgR assays be considered positive if there are at least 1% positive tumor nuclei in the sample on testing in the presence of expected reactivity of internal (normal epithelial elements) and external controls. The absence of benefit from endocrine therapy for women with ER-negative invasive breast cancers has been confirmed in large overviews of randomized clinical trials.

American Society of Clinical Oncology/College Of American Pathologists guideline recommendations for immunohistochemical testing of estrogen and progesterone receptors in breast cancer

PURPOSE

To develop a guideline to improve the accuracy of immunohistochemical (IHC) estrogen receptor (ER) and progesterone receptor (PgR) testing in breast cancer and the utility of these receptors as predictive markers.

METHODS

The American Society of Clinical Oncology and the College of American Pathologists convened an international Expert Panel that conducted a systematic review and evaluation of the literature in partnership with Cancer Care Ontario and developed recommendations for optimal IHC ER/PgR testing performance.

RESULTS

Up to 20% of current IHC determinations of ER and PgR testing worldwide may be inaccurate (false negative or false positive). Most of the issues with testing have occurred because of variation in preanalytic variables, thresholds for positivity, and interpretation criteria.

RECOMMENDATIONS

The Panel recommends that ER and PgR status be determined on all invasive breast cancers and breast cancer recurrences. A testing algorithm that relies on accurate, reproducible assay performance is proposed. Elements to reliably reduce assay variation are specified. It is recommended that ER and PgR assays be considered positive if there are at least 1% positive tumor nuclei in the sample on testing in the presence of expected reactivity of internal (normal epithelial elements) and external controls. The absence of benefit from endocrine therapy for women with ER-negative invasive breast cancers has been confirmed in large overviews of randomized clinical trials.

Expression of small sets of genes in carcinoma and stromal cells predict clinical behavior of human breast cancer

Abstract #6146

Background: The Human Genome Project has provided opportunities to develop precise tests for diagnostics, therapy selection and monitoring. From reiterative analyses of various microarray studies, 14 genes expressed in human breast carcinoma cells procured from de-identified tissue sections by LCM and 18 genes predicted in adjacent stromal cells were identified, whose expression appears related to clinical outcome. An additional 11 genes were identified in estrogen receptor positive (ER+) breast cancer exhibiting different survival probabilities. These genes have been evaluated with qPCR and with a disposable TipChip array (Xceed Molecular) as candidates for development of a prognostic test measuring clinically relevant gene expression profiles.&#x2028; Materials and Methods: RNA was isolated from 118 frozen tissue biopsies using the RNeasy® Mini kit (Qiagen) and analyzed for quality and quantity using the Bioanalyzer (Agilent). cDNA for qPCR measurements was prepared in Tris-HCl buffer containing KCl, MgCl2, DTT (Invitrogen), dNTPs (Invitrogen), RNasin® (Promega) and Superscript® RT III (Invitrogen). qPCR reactions were performed using Power Sybr® Green PCR Master Mix (Applied Biosystems), forward/reverse primers and cDNA obtained from the reverse transcription reaction. Relative gene expression was calculated with the ddCt method, using β-actin as the housekeeping gene and Universal Human Reference RNA (Stratagene) as a calibrator. Prior to gene expression analyses, extensive QC experiments were conducted, e.g., qPCR reactions were performed in triplicate with duplicate wells in each 384-well plate, to ensure reproducibility.&#x2028; Results: Gene candidates were analyzed on the Ziplex® Automated Workstation (Xceed Molecular) with a TipChip array containing probes for 61 genes including normalization controls. Preliminary gene expression results by qPCR and the TipChip were comparable for many of the 43 candidate genes (r2 ≥ 0.5 with ESR1 = 0.6). These data were correlated with disease-free and over-all survival outcomes stored in our extensive IRB-approved database. Expression of SLC39A6, FUT8 and CX3CL1 in the carcinoma/stromal subset correlated independently with disease-free survival using Cox Regression analyses (p &lt; 0.02). Using the 13-gene subset derived from ER+ breast cancers, CAXII, ERBB4 and RERG correlated independently with recurrence (p &lt; 0.03). These genes, as well as BCL2, correlated independently with overall survival (p &lt; 0.02).&#x2028; Conclusion: Expression profiles of 21 of the 32 candidate genes from this gene subset predicted early breast cancer recurrence. In an ER+/PR+ subpopulation, ERBB4 and HER-2 gene expression correlated best with recurrence in a multivariate Cox model (p = 0.001). Collectively, results suggest that an expression test based on these genes will predict clinical outcome. Supported in part by grants from Phi Beta Psi Charity Trust, University of Louisville's Office of Technology Transfer and from Xceed Molecular Corp. SAA & DAK II are recipients of IPBIS Graduate Fellowships.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 6146.

Steroid receptor and growth factor receptor expression in human nonsmall cell lung cancers using cells procured by laser-capture microdissection

Few biomarkers exist for management of nonsmall cell lung cancers (NSCLC), although estrogen receptor (ERalpha and ERbeta) and EGF receptor (EGFR) expression has been related to clinical outcome. To circumvent problems of cellular heterogeneity in whole tissue, relative gene expression of ERalpha, ERbeta, EGFR, and HER-2 (c-erb-B2) was examined in pure lung carcinoma (LC) cells and normal epithelia by LCM. Cell-specific RNA was isolated and purified for RT-qPCR and microarray. Comparison of NSCLC cells to normal epithelia indicated increased levels of mRNA expression of ERbeta, ERalpha, EGFR, and HER-2 by 31%, 38%, 54%, and 62%, respectively, in LCs. The majority of NSCLC exhibiting low ERalpha and high HER-2 expression were from smokers. Although there was no correlation between ERbeta or EGFR expression and smoking history, there appeared to be an inverse relationship between levels of ERbeta and EGFR mRNAs in normal and neoplastic lung. Additionally, microarray analyses of LCM cells revealed >2,000 genes significantly altered in LC compared with normal epithelia. Herein, differences in NSCLC gene expression and normal lung cells were noted between specimens from gender and smoking groups. Microarray data revealed ERa expression was associated with alterations in <20 genes while ERbeta expression revealed >500 associated genes, suggesting a more prominent role for ERbeta in lung. HER-2 mRNA levels appeared associated with >1,000 genes, while EGFR mRNA levels were associated with far fewer genes. Collectively, results suggest quantitative genomic analyses of pure cell populations allow more accurate interpretation of LC status, which is being correlated with clinical outcome.

Potent Inhibitors of LXXLL-Based Protein-Protein Interactions

Protein-protein interactions between estrogen receptors, ERalpha and ERbeta, and their coactivators (CoAs) are an attractive target for drug intervention. This interaction is mediated by a small pentapeptide motif (LXXLL), termed the NR box. Based on this motif, a variety of cyclic and linear peptides were synthesized in order to gain a better understanding of the association of CoA proteins with the ER isoforms. Utilizing a time-resolved florescence-based coactivator interaction assay, we determined the abilities of these peptides to inhibit this interaction. Using molecular modeling and CD spectroscopy, we have examined the structural basis of their bioactivities with both hormone receptor isoforms. Either homocysteine or penicillamine was utilized as a substitute for cysteine in the disulfide-bridged peptides, while tertiary leucine and neopentyl glycine were used as the surrogates for the NR box leucines. The most potent disufide-bridged peptide (K(i)= 70 pM, with ERalpha) incorporates neopentyl glycine in the NR box, while the most active peptide in this series with ERbeta (K(i)=350 pM) incorporates tertiary leucine. Surprisingly, several linear peptides containing a single cysteine residue showed activities with low nanomolar K(i) values. Collectively, our results suggest a synthetic approach for designing potent and selective peptidomimetics for ERalpha and ERbeta interactions with CoA proteins effecting estrogen action.

Thioether side chain cyclization for helical peptide formation: inhibitors of estrogen receptor-coactivator interactions

Cystine, lanthionine, and cystathionine containing cyclic peptides incorporating the signature nuclear receptor (NR) box (LXXLL) motif have been synthesized and the abilities of these peptides to inhibit estrogen receptor (ER)-coactivator interactions have been determined. We found that helicity of these peptides directly correlated with their bioactivity. Cystathionine proved to be a redox-stable, isosteric replacement for the cystine disulfide. Cystathionine containing peptide 3 showed higher helical character and a lower inhibition constant (Ki, 7 nm) when compared with its cystine counterpart.

Helix-stabilized cyclic peptides as selective inhibitors of steroid receptor-coactivator interactions

The interaction between nuclear receptors and coactivators provides an arena for testing whether protein-protein interactions may be inhibited by small molecule drug candidates. We provide evidence that a short cyclic peptide, containing a copy of the LXXLL nuclear receptor box pentapeptide, binds tightly and selectively to estrogen receptor alpha. Furthermore, as shown by x-ray analysis, the disulfide-bridged nonapeptide, nonhelical in aqueous solutions, is able to adopt a quasihelical conformer while binding to the groove created by ligand attachment to estrogen receptor alpha. An i, i+3 linked analog, H-Lys-cyclo(d-Cys-Ile-Leu-Cys)-Arg-Leu-Leu-Gln-NH2 (peptidomimetic estrogen receptor modulator 1), binds with a Ki of 25 nM, significantly better than an i, i+4 bridged cyclic amide, as predicted by molecular modeling design criteria. The induction of helical character, effective binding, and receptor selectivity exhibited by this peptide analog provide strong support for this strategy. The stabilization of minimalist surface motifs may prove useful for the control of other macromolecular assemblies, especially when an amphiphilic helix is crucial for the strong binding interaction between two proteins.