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Fusion genes are involved in cancer, and their detection using RNA-Seq is insufficient given the relatively short reading length. Therefore, we proposed a shifted short-read clustering (SSC) method, which focuses on overlapping reads from the same loci and extends them as a representative sequence. To verify their usefulness, we applied the SSC method to RNA-Seq data from four types of cell lines (BT-474, MCF-7, SKBR-3, and T-47D). As the slide width of the SSC method increased to one, two, five, or ten bases, the read length was extended from 201 bases to 217 (108%), 234 (116%), 282 (140%), or 317 (158%) bases, respectively. Furthermore, fusion genes were investigated using STAR-Fusion, a fusion gene detection tool, with and without the SSC method. When one base was shifted by the SSC method, the reads mapped to multiple loci decreased from 9.7% to 4.6%, and the sensitivity of the fusion gene was improved from 47% to 54% on average (BT-474: from 48% to 57%, MCF-7: 49% to 53%, SKBR-3: 50% to 57%, and T-47D: 43% to 50%) compared with original data. When the reads are shifted more, the positive predictive value was also improved. The SSC method could be an effective method for fusion gene detection.

Tetramethylrhodamine (TAMRA)-phenyl azide is a chemical probe used to detect intracellular acrolein directly in live cells. Herein, we demonstrated that TAMRA is the optimum fluorophore for the probe. TAMRA-phenyl azide was used to reveal that high levels of acrolein are generated in a variety of breast cancer cells, regardless of the tumor subtype. These findings corroborate the analysis presented in our previous report, in which TAMRA-phenyl azide was used to label breast cancer tissues resected from breast cancer patients. Because high levels of acrolein were generated in all cancer cell types, we believe that acrolein detection may be useful as a general method for labeling cancerous tissues.

One-step nucleic acid amplification (OSNA) for CK19 mRNA is an intraoperative diagnostic procedure for detection of lymph node metastasis. Automated Gene Amplification Detector RD-200 and the LYNOAMP CK19 gene amplification reagent as components of a new OSNA system have been developed. As an improvement over a conventional system, the new system can analyze 14 samples per run, evaluate two lymph nodes in ~ 17 min, and reduce inhibition of reactions. This study was aimed at evaluating clinical performance of the new system by comparing it with performance of histopathological analysis and a conventional OSNA system. A total of 150 lymph nodes in 63 breast cancer patients (T1–3) who underwent sentinel lymph node biopsy or axillary lymph node dissection were examined intraoperatively with the new OSNA system, the conventional system, and histopathological analysis. In comparison with histopathological analysis, sensitivity, specificity, and concordance rate of the new system were 93.9, 98.8, and 96.7%, respectively. In comparison with the conventional system, similar corresponding values were obtained: 96.9, 98.8, and 98.0%, respectively. The results show that clinical performance of the new OSNA system is equivalent to that of histopathological diagnosis and the conventional OSNA system. The new system is superior to the conventional one because of processing of a greater number of samples, shorter testing time, and the absence of inhibited reactions.

Highlights • Whole exome sequencing can assess HRD status as well as the SNP array in breast cancer. • HRD scores were higher in tumors with the germline HRR gene mutations than in those with the somatic HRR gene mutations and the wild-type HRR genes, between which no difference was found. • Acquisition of LOH induced HRD status even in tumor with the somatic HRR gene mutations. • In the luminal subset, HRD-high tumors were associated with a favorable response to neoadjuvant paclitaxel followed by 5-fluorouracil/epirubicin/cyclophosphamide., Recent studies demonstrated that homologous repair deficiency (HRD) score is a useful marker for response to poly (ADP-ribose) polymerase inhibitors or platinum-based chemotherapy. We determined HRD scores and elucidated the clinicopathologic characteristics of HRD-high tumors and their response to non-platinum-based chemotherapy. Primary breast cancer patients (n = 120) were pre-operatively treated with paclitaxel followed by 5-fluorouracil/epirubicin/cyclophosphamide (P-FEC). Germline and somatic homologous recombination related gene mutations (gHRRm and sHRRm, respectively) and HRD scores were analyzed using whole exome sequencing (WES) in tumor tissues obtained before chemotherapy. Of 120 tumors, 30 were determined to be HRD-high tumors, significantly associated with high Ki-67 (P = 0.014), ER negativity (P = 0.007), and PR negativity (P = 0.021). Triple-negative cancers showed significantly higher HRD scores than the luminal, luminal-HER2, and HER2 subtypes (P = 0.023, 0.016, and 0.033, respectively). HRD scores were significantly higher in tumors with gHRRm than in those with sHRRm (P = 0.002) or wild-type HRR genes (P = 1.44e-4), but no significant difference was found in HRD scores between tumors with sHRRm and wild-type HRR genes (P = 0.206). HRD-high tumors had significantly (P = 0.003) higher pCR rates and higher near-pCR rates (P = 0.049) compared with those of the HRD-low tumors in all tumors and the luminal subtype, respectively. HRD-high tumors were associated with aggressive phenotypes and gHRRm, but not sHRRm. Our findings suggested that HRD scores might be useful in predicting response to P-FEC in the luminal subtype.

Summary Background Aromatase inhibitors are a standard of care for hormone receptor-positive locally advanced or metastatic breast cancer. We investigated whether the selective oestrogen receptor degrader fulvestrant could improve progression-free survival compared with anastrozole in postmenopausal patients who had not received previous endocrine therapy. Methods In this phase 3, randomised, double-blind trial, we recruited eligible patients with histologically confirmed oestrogen receptor-positive or progesterone receptor-positive, or both, locally advanced or metastatic breast cancer from 113 academic hospitals and community centres in 20 countries. Eligible patients were endocrine therapy-naive, with WHO performance status 0–2, and at least one measurable or non-measurable lesion. Patients were randomly assigned (1:1) to fulvestrant (500 mg intramuscular injection; on days 0, 14, 28, then every 28 days thereafter) or anastrozole (1 mg orally daily) using a computer-generated randomisation scheme. The primary endpoint was progression-free survival, determined by Response Evaluation Criteria in Solid Tumors version 1·1, intervention by surgery or radiotherapy because of disease deterioration, or death from any cause, assessed in the intention-to-treat population. Safety outcomes were assessed in all patients who received at least one dose of randomised treatment (including placebo). This trial is registered with ClinicalTrials.gov, number NCT01602380. Findings Between Oct 17, 2012, and July 11, 2014, 524 patients were enrolled to this study. Of these, 462 patients were randomised (230 to receive fulvestrant and 232 to receive anastrozole). Progression-free survival was significantly longer in the fulvestrant group than in the anastrozole group (hazard ratio [HR] 0·797, 95% CI 0·637–0·999, p=0·0486). Median progression-free survival was 16·6 months (95% CI 13·83–20·99) in the fulvestrant group versus 13·8 months (11·99–16·59) in the anastrozole group. The most common adverse events were arthralgia (38 [17%] in the fulvestrant group vs 24 [10%] in the anastrozole group) and hot flushes (26 [11%] in the fulvestrant group vs 24 [10%] in the anastrozole group). 16 (7%) of 228 patients in in the fulvestrant group and 11 (5%) of 232 patients in the anastrozole group discontinued because of adverse events. Interpretation Fulvestrant has superior efficacy and is a preferred treatment option for patients with hormone receptor-positive locally advanced or metastatic breast cancer who have not received previous endocrine therapy compared with a third-generation aromatase inhibitor, a standard of care for first-line treatment of these patients. Funding AstraZeneca.

The aim of the present study was to evaluate the promoter methylation status of SEPT9_v2 in breast cancer and to detect this methylated gene in circulating tumor DNA (ctDNA) in plasma. Bisulfite sequencing was performed with a next generation sequencer. Methylation of the SEPT9_v2 promoter was found in 67% (8/12) of breast cancer cell lines and 53% (10/19) of breast tumor tissue, but not in normal breast tissue (0/19). A clear inverse correlation was observed between the expression of SEPT9_v2 mRNA and the methylation index (MI) both in cell lines and breast cancer tissues. The MI of SEPT9_v2 was significantly higher in non-basal subtype of breast cancer (13.0%, n=84) than in basal subtype (3.0%, n=23) (P

PURPOSE This research aimed to establish a diagnostic technique for breast cancer using nipple discharge (ND), with the objective of preventive diagnosis. ND has been proposed as a source of secreted proteomes that reflect early pathological changes in the ductal-lobular epithelial microenvironment, and could thus provide breast-specific cancer biomarkers that could be accessed noninvasively as a new clinical diagnostic technique. EXPERIMENTAL DESIGN Minute amounts of ND from patients with and without breast cancer (n = 19 and 12, respectively) were collected at the hospital and kept frozen until just before use. They were analyzed using high-pH RP peptide fractionations/low-pH RP 2D nano-LC/ESI-MS/MS. Biomarker candidates were also investigated using Western blot analysis and sandwich ELISA on ND and/or sera. RESULTS We found distinct tendencies in protein expression and three candidate breast cancer biomarkers (carbonic anhydrase 2, catalase, and peroxiredoxin-2) whose levels differed significantly between ND specimens from patients with and without breast cancer. CONCLUSIONS AND CLINICAL RELEVANCE These tendencies in protein expression and markers provide new ways to identify breast cancer patients. Therefore, RP/RP 2D LC/MS/MS analyses of ND and the above three markers are supported as a new breast cancer diagnostic technique.

Anti-HER2-autoantibodies (HER2-AAbs) are found in breast cancer patients as well as healthy individuals. However, the clinical relevance of the antibodies is unknown. We established an enzyme-linked immunosorbent assay with high sensitivity and quantified serum HER2-AAbs in 100 healthy women, 100 untreated patients with ductal carcinoma in situ (DCIS), and 500 untreated patients with invasive breast carcinoma (IBC). The associations between the levels of HER2-AAbs and breast cancer risk, and recurrence-free survival, were examined. High levels of HER2-AAbs were significantly associated with a reduced risk of DCIS (odds ratio [OR] 0.19, P = 4.6 × 10(-7)) or IBC (OR 0.31, P = 3.7 × 10(-7)). Subgroup analysis of IBC revealed a stronger association of HER2-AAbs with a reduced risk of the hormone receptor (HR)(-)/HER2(+) subtype (OR 0.12) than the other subtypes (HR(+)/HER2(-) [OR = 0.32], HR(+)/HER2(+) [OR 0.38], and HR(-)/HER2(-) [OR 0.29]). When we set the cutoff of HER2-AAbs at 20 ng/mL, recurrence-free survival of HER2-AAb-positive patients (N = 74) was significantly better than that of HER2-AAb-negative patients (N = 426) (P = 0.015). Univariate and multivariate analyses demonstrated that HER2-AAbs, as well as histological grade, were independently and significantly (P = 0.0065 and 0.049, respectively) associated with recurrence-free survival. Our exploratory study suggests a protective effect of naturally occurring HER2-AAbs on the development of primary and recurrent breast cancer. Further studies on HER2-AAbs are warranted.

Introduction Luminal breast cancer patients show a relatively favorable prognosis when treated with adjuvant hormonal therapy alone. However, some of these patients develop recurrence and they might derive benefit from adjuvant chemotherapy. Although several genomic profilings successfully developed to decide whether to administer adjuvant chemotherapy, clinically practical prediction methods of recurrence sites do not exist. Our previous study showed a possible prediction of bone metastases by using two serum markers; TRACP-5b as a marker of bone metabolism; likelihood of bone metastases, and CRP as a marker of inflammation; likelihood of distant recurrence. The incidence of bone metastases was significantly higher in high risk patients(+/+) than in the others(odds ratio: 10.9, P=0.040). In this study, we examined the potential of the two-marker prediction in the newly enrolled luminal patients. Patients and methods One hundred sixty luminal patients who underwent surgery were enrolled in this study. Their serum levels of TRACP-5b and CRP were measured in a blinded manner at the R & D laboratory of Nittobo Medical Co., Ltd. In the preliminary study, we identified that the median value of TRACP-5b in the premenopausal patients was lower than in the postmenopausal patients. We adjusted the value of TRACP-5b in the premenopausal patients and the cutoff value of TRACP-5b from 334 to 396mU/dL. The cutoff value of CRP was same as previous study(0.016 mg/dL). The odds ratio between +/+ and the others were calculated using MedCalc statistical software. Results One hundred sixty patients stratified into four classes according to the value of TRACP-5b and CRP: +/+ (n=43), +/- (n=38), -/+ (n=42) and -/- (n=37). Six of the 160 patients developed bone metastases as the initial site of replase within five years from surgery. The Incidence of bone metastases was 9.3%(4/43) in the +/+ patients and 1.7%(2/117) in the others. The incidence was significantly higher in the +/+ patients than in the others(odds ratio: 5.9, 95% CI 1.31 to 33.46, p= 0.045). When the other relapses than bone metastases were included in the analysis, no significant difference was observed between the two groups (odds ratio: 0.4, 95% CI 0.02 to 7.43, P=0.521). TRACP-5b concentration alone could not classify the patients into two groups according to significantly different incidences of bone metastases(odds ratio: 13.7, 95% CI 0.76 to 247.22, P=0.076). Conclusion The results in here show that the prediction of bone metastases by the combination of TRACP-5b and CRP concentrations is clinically relevant in the luminal patients. Reliable prediction of bone metastases would be realized by combination of our prediction method and one of genomic profilings. We plan to increase the number of patients to provide sufficient statistical power to confirm this diagnostic potential. Citation Format: Shimoda M, Nishimukai A, Shibata N, Kikuchi W, Hutawatari H, Ishihara H, Miyoshi Y, Noguchi S. Prediction of bone metastases of breast cancer using combined markers of bone metabolism and inflammation. [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 P2-08-27.

Aim: The aim of this study was to elucidate the role of transforming growth factor β (TGFβ) in the resistance of HER2-positive breast cancer cells to anti-HER2 drugs including trastuzumab and lapatinib. Methods: A HER2-positive breast cancer cell line, SKBR3, was cultured in the presence or absence of TGFβ for 14 days. Subsequently, TGFβ-treated cells were cultured for seven days with or without the anti-HER2 drugs. Sensitivity to trastuzumab and lapatinib was estimated by the WST-8 cell viability assay or absolute cell counts using In Cell Analyzer (GE Healthcare). Proportion of CD44+ CD24– breast cancer stem cells was estimated by flow cytometry of cells immunostained with anti-CD44 and anti-CD24 antibodies. For clinical study, 33 patients with HER2-positive breast cancer receiving neoadjuvant paclitaxel plus trastuzumab in our institution were analyzed. Among the cases, 27 biopsy samples obtained before any treatment from 27 patients who completed 12 cycles of weekly paclitaxel and trastuzumab were subjected to CD24 immunohistochemistry. Results: SKBR3 cells cultured with TGFβ for 14 days exhibited decreased sensitivity to both trastuzumab and lapatinib. Time course study revealed that continuous stimulation for 14 days with TGFβ was required for the resistance to anti-HER2 drugs. Activation of SMAD3, a downstream target molecule of TGFβ, was enhanced over time, judged by the increase in phosphorylation and in nuclear translocation. During 14 day culture with TGFβ, proportion of CD44+ CD24– cells were dramatically increased, and mammosphere formation, another marker of breast cancer stem cells, was significantly enhanced compared to cells treated without TGFβ. Among four HER2-positive breast cancer cell lines, only SKBR3 cells showed increased proportion of CD44+ CD24– cells and resistance to the anti-HER2 drugs, while other two cell lines exhibited epithelial-mesenchymal transition (EMT) in response to TGFβ. To explore the possibility of targeting TGFβ-SMAD3 axis to overcome resistance to anti-HER2 therapy, we used SIS3, a specific inhibitor of SMAD3. Importantly, SIS3 completely restored the sensitivity to both trastuzumab and lapatinib of TGFβ-treated SKBR3 cells, with the decrease in the proportion of CD44+ CD24– cells. These in vitro results suggest that CD24 downregulation can be a surrogate marker of resistance to anti-HER2 therapy. To establish this, we evaluated the CD24 expression in tumor samples of breast cancer patients who received paclitaxel plus trastuzumab in the neoadjuvant setting. Weak CD24 expression in tumor cells in biopsy samples obtained before any treatment was significantly correlated with poorer response to the drugs. Conclusion: These data clearly indicate the importance of TGFβ-SMAD3 axis in the acquired resistance to anti-HER2 drugs. Moreover, resistance to anti-HER2 therapy is associated with the property of breast cancer stem cells rather than EMT. Targeting TGFβ-SMAD3 axis warrants further investigation for overcoming resistance to anti-HER2 therapeutics. Citation Format: Shimoda M, Chihara Y, Kagara N, Naoi Y, Shimomura A, Shimazu K, Kim SJ, Noguchi S. Importance of TGFβ-SMAD3 axis in resistance to anti-HER2 drugs. [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 P3-06-05.

AIM: We have previously reported that the serum concentration of anti-HER2 autoantibodies (HER2-AAb) is associated with favorable outcomes in patients with invasive breast cancer (Tabuchi et al., Breast Cancer Res Treat 157:55-63, 2016). This study aimed to investigate the prognostic impact of HER2-AAb by examining the tumor microenvironments for humoral immunity. PATIENTS AND METHODS: From 500 consecutive patients with invasive breast cancer (Ibid.), we selected those whose log-transformed HER2-AAb values were above mean + 2SD (high HER2-AAb group, N = 33) or below mean − 2SD (low HER2-AAb group, N = 20). Tumor formalin-fixed paraffin-embedded (FFPE) samples and regional lymph node FFPE samples prepared from the patients’ surgical specimens were subjected to immunohistochemistry. Tumor-infiltrating immune cells (ICs) localized inside the tumor, in the adjacent stroma, and in the tumor stroma were separately counted. Expression of some proteins in tumor cells (TCs) was evaluated by the percentages of tumor cells showing presence of those proteins. RESULTS: We confirmed in the selected patients that the recurrence-free interval of the high HER2-AAb group was significantly longer than that of the low HER2-AAb group (log-rank P = 0.017; hazard ratio = 0.12). Tumor-infiltrating CD20-positive ICs (intratumoral + adjacent stromal ICs, P < 0.001), IGKC-positive ICs (intratumoral + adjacent stromal ICs, P = 0.023), and CXCL13-positive ICs (total ICs, P = 0.044) were significantly greater in the high HER2-AAb group than in the low HER2-AAb group. CD4-positive ICs in B-cell follicles of the regional lymph nodes were also significantly greater in the high HER2-AAb group than in the low HER2-AAb group (P = 0.026). Tumor-infiltrating PD-L1-positive ICs, CD8-positive ICs, FOXP3-positive ICs, as well as CD8/FOXP3 ratios, were not significantly different between the two groups. The expression of CXCL13, HLA-A/B/C, and PD-L1 in TCs was not significantly different between the two groups. The repertoire of B-cell receptors in ICs was not significantly different between the two groups but was considered to be skewed. HER2 expression and gene amplification and the existence of HER2 missense mutations were similar between the two groups. CONCLUSIONS: Increased HER2-AAb concentration was associated with enhanced humoral immunity in tumor microenvironments. Our findings indicate that a patient subpopulation with enhanced humoral immunity protecting against breast cancer recurrence exists. The recognition site of HER2-AAb may not be located in the HER2 polypeptide, but may be located in modifying factors, such as sugar chains. Citation Format: Masafumi Shimoda, Yasufumi Sato, Yoshiaki Sota, Tomohiro Miyake, Tomonori Tanei, Naofumi Kagara, Yasuto Naoi, Kenzo Shimazu, Seung Jin Kim, Shinzaburo Noguchi. Association of autoantibodies to HER2 with tumor microenvironments for humoral immunity and prognosis in patients with breast cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1604.

To examine the correlation of qualitative and quantitative dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) results with 95-gene classifier or Curebest 95-gene classifier Breast (95GC) results for recurrence prediction in estrogen receptor-positive breast cancer (ERPBC).This retrospective study included 78 ERPBC patients (age range, 24-74 years) classified into high- (n = 33) and low- (n = 45) risk groups for recurrence based on 95GC and who underwent DCE-MRI between July 2006 and November 2012. For qualitative evaluation, mass shape, margin, and internal enhancement based on BI-RADS MRI lexicon and multiplicity were determined by consensus interpretation by 2 breast radiologists. For quantitative evaluation, mass size, volume ratios of the DCE-MRI kinetics, and both the kurtosis and the skewness of the intensity histogram for the whole mass in the initial and delayed phases were determined. Differences between the 2 risk-groups were analyzed using univariate logistic regression analyses and multiple logistic regression analyses. Receiver-operating characteristic curve cut-off values were used to define the groups.As for the qualitative findings, the difference between the 2 groups was not significant. For the quantitative data, the volume ratio of "medium" in the initial phase differed significantly between the 2 groups (P = .049). The volume ratio of "medium" (P = .006) and of "slow-persistent" (P = .005), and the delayed phase kurtosis (P = .012) in the univariate logistic regression analyses, and in the multiple logistic regression, volume ratio of "medium" >38.9% and delayed phase kurtosis >3.31 were identified as significant high-risk indicators (odds ratio, 5.83 and 3.55; 95% confidence interval, 1.58 to 21.42 and 1.24 to 10.15; P = .008 and P = .018, respectively).A high volume ratio of "medium" in the initial phase and/or high kurtosis in the delayed phase for quantitative evaluation could predict high ERPBC recurrence risk based on 95GC.

The use of formalin-fixed paraffin-embedded (FFPE) tumor tissues in flow cytometry (FCM)-based determination of tumor cell DNA content is more complicated than the use of fresh-frozen tissues. This study aimed to accurately measure tumor cell DNA content from FFPE tissues by separating tumor cells from stromal cells through FCM and investigating its prognostic impact. We separately measured the DNA contents of tumor cells and stromal cells by gating with pan-cytokeratin and vimentin (FCMC/V). We evaluated tumor cell DNA contents [DNA index (DI)] of 290 FFPE tumor tissues and classified them into low and high DI groups, using a cutoff DI value determined through an unbiased computational method. The distribution of DI was bimodal, and a cutoff value was determined at a DI of 1.26. The high-DI tumors were associated with aggressive phenotypes and had significantly worse distant recurrence-free intervals (DRFI) than low-DI tumors. Multivariate analysis revealed that lymph node metastasis, Ki67, and DI were independent factors affecting DRFI. Accordingly, patients with low-DI/low-Ki67 tumors had excellent outcomes compared with other tumor types. Multiploid tumors were associated with increased lymphocytic infiltration and aggressive phenotypes. The DI of FFPE tumors could be precisely determined through FCMC/V. A combination of DI and Ki67 analyses may be able to predict the prognoses of breast cancer patients with greater accuracy.

Circulating tumor DNA (ctDNA) is released from cancer cells by apoptosis or other mechanisms, and as tumor tissue contains both blood and lymphatic vessels, ctDNA can spread to local lymph nodes (LNs). We aimed to detect the tumor-derived free DNA in metastasis-free LNs in patients with breast cancers harboring the PIK3CA-H1047R mutation. One hundred twenty-three patients were evaluated and the PIK3CA-H1047R mutation was assayed in sentinel LNs (SLNs), non-SLNs without metastasis, and serum by digital PCR. The mutant DNA was more frequent in metastasis-free SLNs (21.6%) than in metastasis-free non-SLNs (8.6%; P = 0.038), and patients with mutation-positive SLNs were more likely to be positive for serum mutant DNA. Apoptosis in primary breast tumors was determined by TUNEL assay. The apoptotic index was significantly higher (P = 0.003) in patients with mutation-positive SLNs without metastasis (mean, 1.17%) than those with mutation-negative SLNs without metastasis (mean, 0.79%). It was also significantly higher (P = 0.006) in those with mutation-positive serum (mean, 1.41%) than in those with mutation-negative serum (mean, 0.86%). Furthermore, fragment size of PIK3CA-H1047R mutant DNA in metastatic-free SLN lysate used for the one-step nucleic acid amplification (OSNA) assay was short (

Fusion genes make for one of the mechanisms of tumorigenesis. The identification of fusion genes by RNA-Seq has attracted attention. Various methods for detecting fusion genes have been proposed, but their accuracy is not sufficient. One of the causes of this problem is the relatively short reading length in RNA-Seq data. Therefore, before mapping RNA-Seq data, we proposed a method, which is based on shifted short-read clustering (SSC), to identify shifted reads of the same origin and extend them as representative sequences. As a result, we assumed that the percentage of uniquely mapped reads would be increased, and the detection rates of the fusion genes could be improved. To verify these hypotheses, we applied the SSC method to RNA-Seq data from three cell lines (BT-474, MCF-7, and SKBR-3). When only one base was shifted, the average read lengths of BT-474, MCF-7, and SKBR-3 were extended from 201 to 223 bases (111%), 201 to 214 bases (106%), and 201 to 213 bases (106%), respectively. Furthermore, the effectiveness of the SSC method is demonstrated by comparing the performances of a fusion gene detection tool's results, STAR-Fusion, with and without the SSC method of the reads. The percentage of uniquely mapped reads of BT-474, MCF-7, and SKBR-3 were improved from 88% to 93%, 88% to 94%, and 92% to 95%, respectively. Finally, the fusion gene detection rates of BT-474, MCF-7, and SKBR-3 were increased from 48% to 57%, 49% to 53%, and 50% to 53% respectively. The SSC method is considered to be an effective method not only for improving the percentage of uniquely mapped reads but also for fusion gene detection.

Prediction models for late (> 5 years) recurrence in ER-positive breast cancer need to be developed for the accurate selection of patients for extended hormonal therapy. We attempted to develop such a prediction model focusing on the differences in gene expression between breast cancers with early and late recurrence. For the training set, 779 ER-positive breast cancers treated with tamoxifen alone for 5 years were selected from the databases (GSE6532, GSE12093, GSE17705, and GSE26971). For the validation set, 221 ER-positive breast cancers treated with adjuvant hormonal therapy for 5 years with or without chemotherapy at our hospital were included. Gene expression was assayed by DNA microarray analysis (Affymetrix U133 plus 2.0). With the 42 genes differentially expressed in early and late recurrence breast cancers in the training set, a prediction model (42GC) for late recurrence was constructed. The patients classified by 42GC into the late recurrence-like group showed a significantly (P = 0.006) higher late recurrence rate as expected but a significantly (P = 1.62 × E−13) lower rate for early recurrence than non-late recurrence-like group. These observations were confirmed for the validation set, i.e., P = 0.020 for late recurrence and P = 5.70 × E−5 for early recurrence. We developed a unique prediction model (42GC) for late recurrence by focusing on the biological differences between breast cancers with early and late recurrence. Interestingly, patients in the late recurrence-like group by 42GC were at low risk for early recurrence.

Loss of imprinting (LOI) of insulin-like growth factor 2 (IGF2) is thought to be implicated in the pathogenesis of some tumors by upregulating IGF2 mRNA but its role in the pathogenesis of fibroadenomas (FAs) and phyllodes tumors (PTs) of the breast is yet to be studied. LOI of IGF2 was investigated in 25 FAs and 17 PTs which were heterozygous for Apa I polymorphism, and was found to be present in 13 FAs and 12 PTs. IGF2 mRNA expression was more upregulated in FAs and PTs than in paired surrounding normal tissues and laser microdissection showed that IGF2 mRNA expression was significantly higher in the stromal than the epithelial cells. LOI was not associated with upregulation of IGF2 mRNA, nor were MED12 mutations and methylation status of the differentially methylated region 0 (DMR0) of IGF2. These results demonstrate that IGF2 mRNA expression is more upregulated in FAs and PTs than in normal tissues, especially in their stromal cells, but such an upregulation is not related to LOI of IGF2, and that hypomethylation of DMR0 is unlikely to be involved in induction of LOI.

Background Monthly goserelin 3.6 mg dosing suppresses estradiol (E2) production and has proven efficacy in pre-menopausal women with estrogen receptor (ER)-positive breast cancer. This non-inferiority study evaluated the efficacy and safety of 3-monthly goserelin 10.8 mg compared with monthly goserelin 3.6 mg. Methods This was a Phase 3, open-label, multicenter trial. Pre-menopausal women with ER-positive advanced breast cancer were randomized to 3-monthly goserelin 10.8 mg or monthly goserelin 3.6 mg; all patients received concomitant tamoxifen (20 mg daily). The primary endpoint was progression-free survival (PFS) rate at 24 weeks; non-inferiority was to be confirmed if the entire 95 % confidence interval (CI) for the treatment difference was above −17.5 %. Secondary endpoints included objective response rate (ORR), serum E2 levels, safety, and tolerability. Results In total, 222 patients were randomized (goserelin 10.8 mg, n = 109; goserelin 3.6 mg, n = 113). PFS rate at week 24 was 61.5 % (goserelin 10.8 mg) and 60.2 % (goserelin 3.6 mg); treatment difference (95 % CI) was 1.3 % (−11.4, 13.9), confirming non-inferiority of goserelin 10.8 mg compared with goserelin 3.6 mg. ORR was 23.9 % (goserelin 10.8 mg) and 26.9 % (goserelin 3.6 mg); treatment difference (95 % CI) was −3.0 % (−15.5, 9.7). At week 24, mean serum E2 concentrations were similar in the goserelin 10.8 mg and goserelin 3.6 mg groups (20.3 pg/mL and 24.8 pg/mL, respectively). Conclusion A regimen of 3-monthly goserelin 10.8 mg demonstrated non-inferiority compared with monthly goserelin 3.6 mg for PFS rate at 24 weeks, with similar pharmacodynamic and safety profiles, in pre-menopausal women with ER-positive breast cancer.

The aims of this study were to develop a multi-gene expression-based prediction model for pathological complete response (pCR) to neoadjuvant chemotherapy (NAC) and to evaluate its prognosis prediction for estrogen receptor (ER) positive breast cancers. The training set included the NAC-treated patients (n = 104) with ER+ breast tumors in our hospital and the validation set included the NAC-treated patients (n = 259) with ER+/HER2- breast tumors in the public database (GSE25066). Gene expression in the tumor biopsy specimens obtained before NAC was analyzed with DNA microarray, and the prediction model (MPCP155) for pCR was constructed for the training set by using the genes (155 probes) involved in the metabolic pathways which the pathway analysis identified as being significantly associated with pathological response. With MPCP155, the tumors in the validation set could be classified into low chemo-sensitive (low-CS) (pCR rate = 2.6%) and high-CS (pCR rate = 15.3%; P = 0.0006) groups. Furthermore, the low-CS group showed a significantly better prognosis than the high-CS group (P = 2.0E-6). Moreover, prognosis prediction by MPCP155 was independent of the residual cancer burden score. MPCP155 may be helpful for decision making regarding the indication for neoadjuvant chemotherapy. In addition, MPCP155 was found to be useful for prognosis prediction for NAC-treated patients with ER+/HER2- tumors.

ABSTRACT Kyoto Breast Cancer Consensus Conference, Kyoto, Japan, 18–20 February 2014 The loco-regional management of breast cancer is increasingly complex with application of primary systemic therapies, oncoplastic techniques and genetic testing for breast cancer susceptibility. Personalization of loco-regional treatment is integral to optimization of breast cancer care. Clinical and pathological tumor stage, biological features and host factors influence loco-regional treatment strategies and extent of surgical procedures. Key issues including axillary staging, axillary treatment, radiation therapy, primary systemic therapy (PST), preoperative hormonal therapy and genetic predisposition were identified and discussed at the Kyoto Breast Cancer Consensus Conference (KBCCC2014). In the first of a two part conference scene, consensus recommendations for axillary management are presented and focus on the following topics: indications for completion axillary lymph node dissection in primary surgical patients with ≤2 macrometastases or any sentinel nodal deposits after PST; the timing of sentinel lymph node biopsy in the context of PST; use of axillary irradiation as a component of primary treatment plans and the role of intraoperative node assessment in the post-Z0011 era.

ABSTRACT Kyoto Breast Cancer Consensus Conference, Kyoto, Japan, 18–20 February 2014 The loco-regional management of breast cancer is increasingly complex with application of primary systemic therapies, oncoplastic techniques and genetic testing for breast cancer susceptibility. Personalization of loco-regional treatment is integral to optimization of breast cancer care. Clinical and pathological tumor stage, biological features and host factors influence loco-regional treatment strategies and extent of surgical procedures. Key issues including axillary staging, axillary treatment, radiation therapy, primary systemic therapy (PST), preoperative hormonal therapy and genetic predisposition were identified and discussed at the Kyoto Breast Cancer Consensus Conference (KBCCC2014). In the second of a two part conference scene, consensus recommendations for radiation treatment, primary systemic therapies and management of genetic predisposition are reported and focus on the following topics: influence of both clinical response to PST and stage at presentation on recommendations for postmastectomy radiotherapy; use of regional nodal irradiation in selected node-positive patients and those with adverse pathological factors; extent of surgical resection following downstaging of tumors with PST; use of preoperative hormonal therapy in premenopausal women with larger, node-negative luminal A-like tumors and managing increasing demands for contralateral prophylactic mastectomy in patients with a unilateral sporadic breast cancer.

The purpose of this study was to evaluate whether the baseline breast MRI findings would be useful for the prediction for pathological complete response (pCR) by breast cancer patients to neoadjuvant chemotherapy. Primary breast cancer patients (stage II-III) preoperatively treated with sequential paclitaxel (12 cycles) and fluorouracil, epirubicin, and cyclophosphamide (4 cycles), followed by surgery were retrospectively enrolled, and 229 patients were eligible. Before chemotherapy, breast MRI studies were performed. Breast tumors were dichotomized into round + oval and irregular types based on MRI morphology. The round + oval tumors showed a significantly higher pCR rate than the irregular tumors (42.0% vs 17.3%; P < 0.001). In addition, PAM50 analysis revealed that basal and HER2-enriched tumors were significantly more prevalent among round + oval than irregular type tumors (P = 0.015). Baseline MRI morphology appears to be a significant predictor for pCR. The higher rate of the basal and HER2-enriched tumors among the round + oval tumors may explain their better chemo-sensitivity.

Accurate prediction of recurrence risk is of vital importance for tailoring adjuvant chemotherapy for individual breast cancer patients. Although recurrence risk has been assessed by means of examination of histological data and biomarkers (ER, PR, HER2, Ki67), such conventional examinations are not accurate enough to select subsets of patients who are at sufficiently low risk of recurrence to be spared adjuvant chemotherapy without comprising the prognosis. In the past two decades or so, comprehensive gene expression analysis technology has rapidly developed and made it possible to construct recurrence prediction models for breast cancer based on multi-gene expression in tumor tissues. These models include MammaPrint, Oncotype DX, PAM50 ROR, GGI, EndoPredict, BCI, and Curebest 95GC. In clinical practice, these multi-gene classifiers are mostly used for ER-positive and node-negative breast cancer patients for whom deciding the indication of adjuvant chemotherapy based on conventional histological examination findings alone is often difficult. This article briefly reviews these multi-gene expression-based classifiers with special emphasis on Curebest™ 95GC, which was developed by us for ER-positive and node-negative breast cancer patients.

Background Luteinizing hormone-releasing hormone (LH-RH) agonists provide effective adjuvant treatment for premenopausal women with endocrine-responsive breast cancer. Here, we investigated appropriate treatment durations of an LH-RH agonist, leuprorelin. Methods We conducted an open-label, randomized controlled pilot study to evaluate the safety and efficacy of leuprorelin subcutaneously administered every-3-months for 2 versus 3 or more, up to 5 years, together with daily tamoxifen for 5 years in premenopausal endocrine-responsive breast cancer patients. Primary endpoints were disease-free survival (DFS) and safety. Results Eligible patients (N = 222) were randomly assigned to receive leuprorelin for either 2 years (N = 112) or 3 or more years (N = 110) with tamoxifen for 5 years after surgery. Leuprorelin treatment for 3 or more years provided no significant difference in DFS rate over 2 years: 94.1 versus 91.8 % at 144 weeks (3 years) after the second year (week 96) and 90.8 versus 90.4 % at the fifth year (week 240). The overall survival rate was 100 % for both groups during the third through fifth year study period. There were no significant differences in the incidence of adverse events (AEs) between the 2 groups: most AEs were rated grade 1 or 2. Conclusions Adjuvant leuprorelin treatment for 3 or more years with tamoxifen showed a survival benefit and safety profile similar to that for 2 years in premenopausal endocrine-responsive breast cancer patients. No new safety signal was identified for long-term leuprorelin treatment. Longer follow-up observation is needed to determine the optimal duration of leuprorelin treatment.

Tumor-specific promoter hypermethylation of large tumor suppressor, homolog 2 (LATS2), a tumor suppressor gene, has been investigated using methylation-specific polymerase chain reaction (MSP) assays in different types of human cancer producing conflicting results. The aim of the present study was to evaluate the methylation status of the LATS2 promoter region using bisulfite sequencing with a next generation sequencer for breast cancer. In the 11 patients enrolled in the present study, the LATS2 promoter methylation index (MI) was uniformly high in tumor and normal tissues of the breast (median, 84.0 and 87.4%, respectively). The presence of LATS2 promoter hypermethylation was confirmed in isolated tumor cells and normal epithelial cells using the magnetic-activated cell sorting method. In situ hybridization for LATS2 messenger RNA (mRNA) revealed that the mRNA expression of LATS2 was higher in normal epithelial cells, compared with tumor cells, however, it was not significantly associated with LATS2 MI. In 12 breast cancer cell (BCC) lines and two normal breast cell lines, the LATS2 promoter was uniformly hypermethylated with no correlation between the mRNA expression of LATS2 and the LATS2 MI. In addition, treatment of the BCC lines with a demethylating reagent had minimal effect on the mRNA expression of LATS2 in any of these cell lines. These results demonstrated that LATS2 hypermethylation was not involved in silencing the mRNA expression of LATS2 mRNA. The lower mRNA expression level of LATS2 in tumor cells, compared with normal epithelial cells, suggested the possible involvement of downregulation in the mRNA expression of LATS2 in the pathogenesis of breast cancer. Therefore, the conflicting results previously reported for LATS2 promoter methylation in different types of cancer, detected using MSP assays may be attributable to the low fidelity of the MSP assay.

Background The phase III randomised FALCON trial (NCT01602380) demonstrated improved progression-free survival with fulvestrant 500 mg versus anastrozole 1 mg in endocrine therapy-naive postmenopausal women with hormone receptor-positive (HR+) locally advanced or metastatic breast cancer (LA/MBC). Furthermore, overall health-related quality of life (HRQoL) was maintained and comparable for fulvestrant and anastrozole. Here, we present additional analyses of patient-reported HRQoL outcomes from FALCON. Methods Women with endocrine therapy-naive HR+ LA/MBC were randomised 1:1 to fulvestrant (days 0, 14, 28, then every 28 d) or anastrozole (daily) until disease progression or discontinuation. HRQoL was assessed by FACT-B questionnaire (TOI and FACT-B total score) at randomisation and every 12 weeks during treatment. HRQoL data post-treatment (with or without progression) were also collected. Results In total, 462 patients were randomised (fulvestrant, n = 230; anastrozole, n = 232). Compliance to FACT-B overall ranged from 60.0 to 97.4%. Mean change from baseline in TOI and FACT-B total score remained broadly stable (approximately ± 3 points to week 132) and was similar between arms during treatment. HRQoL was also maintained in FACT-B subscales. Approximately one-third of patients had improved TOI (≥+6 points) and FACT-B (≥+8 points) total scores from baseline up to week 120 and 132, respectively, of treatment with fulvestrant (ranges 26.4–45.0% and 22.4–35.8%, respectively) and anastrozole (ranges 18.6–32.9%, and 22.7–37.9%, respectively). Conclusions Mean change from baseline in TOI and FACT-B total score was maintained for fulvestrant and anastrozole; similar proportions of patients in both arms had improved TOI and FACT-B total scores.

Liquid biopsy using digital PCR (dPCR) has been widely used for the screening of ESR1 mutations, since they are frequently identified in the hotspot. However, dPCR is limited to the known mutations. Therefore, we aimed to analyze the utility of next-generation sequencing (NGS) to discover novel ESR1 mutations.Whole exon sequencing of the ESR1 gene using NGS was performed in 16 primary and 47 recurrent tumor samples and 38 plasma samples from hormone receptor-positive metastatic breast cancer patients. Functional analyses were then performed for the novel mutations we detected.We identified no mutations in primary tumors and six mutations in five recurrent tumors, including three types of known mutations (Y537C, Y537N, and D538G) and two novel mutations (E279V and G557R). We also identified seven mutations in five plasma samples, including three types of known mutations (S463P, Y537S, and D538G) and one mutation not reported in COSMIC database (L536H). All nine patients with ESR1 mutations were treated with aromatase inhibitors (AIs) prior to sampling, and the mutations were frequently detected in patients who received AI treatments in the metastatic setting. Among the three novel mutations (E279V, L536H, and G557R), L536H, but not E279V and G557R, showed ligand-independent activity. All three mutant proteins showed nuclear localization and had no relation with non-genomic ER pathways.Although the molecular mechanisms of the E279V and G557R mutations remain unclear, our data suggest the utility of NGS as a liquid biopsy for metastatic breast cancer patients and the potential to identify novel ESR1 mutations.

The breast cancer susceptibility gene 1 (BRCA1) and glutathione S-transferase P1 (GSTP1) promoters are reportedly often methylated in breast cancer tissues. Their methylation status in surrounding normal breast tissues has not been examined thoroughly although this may well be important for a better understanding of breast carcinogenesis. In this study, BRCA1 and GSTP1 promoter methylation was examined by methylation-specific PCR assay. Patients with BRCA1-methylated (n = 15) or BRCA1-unmethylated (n = 15) tumors and those with GSTP1-methylated (n = 9) or GSTP1-unmethylated (n = 11) tumors were included in the present study. Methylation status of manually micro-dissected normal epithelial cells from the formalin-fixed paraffin-embedded sections of normal breast tissues adjacent to and distant from the tumors was examined at multiple sites (n = 1–5). Of the 15 patients with BRCA1-methylated tumors, 9 harbored BRCA1 promoter methylation in at least one site of the normal breast tissues. However, no BRCA1 promoter methylation was observed at any site of the normal tissues of the 15 patients with BRCA1-unmethylated tumors. No GSTP1 promoter methylation was observed in the normal tissues regardless of the methylation status of the tumors. The presence of BRCA1 promoter methylation in the normal tissues was confirmed in the epithelial cells enriched with the magnetic-activated cell sorting method. Our findings suggest that a small proportion of normal breast epithelial cells with BRCA1 promoter methylation can be precursor cells from which BRCA1-methylated breast tumors may originate. This does not apply to GSTP1 promoter methylation.

Background The 95-gene classifier (95-GC) can classify patients with estrogen receptor (ER)–positive and node-negative breast cancer into those with low and high risk of relapse with an accuracy similar to that of 21-GC (Oncotype DX). Because 95-GC uses RNA from fresh-frozen (FF) tumor tissues, we herein attempted to develop a gene classifier that is applicable to RNA from formalin-fixed paraffin-embedded (FFPE) tumor tissues. Patients and Methods 25 paired FF and FFPE tumor tissues were subjected to DNA microarray for gene-expression analysis. Of the 95 probes included in the 95-GC, 72 were selected for construction of the gene classifier for FFPE tumor tissues, because the gene expression detected by these 72 probes was well preserved in the FFPE tumor tissues. Results The 72-GC was constructed with these 72 probes for the training set comprising 549 FF tumor tissues and validated with 434 FF tumor tissues (relapse-free survival at 10 years was 91% for the low-risk and 74% for the high-risk group (P = 3.74 × 10−7). The predictive capability of 72-GC for prognosis was found to be comparable to that of 95-GC. The 25 paired FF and FFPE tumor tissues from each of 25 patients were classified into the same risk group by 72-GC for 23 patients (92% concordance). 72-GC using the FFPE tumor tissues showed that the prognosis for the low-risk group was significantly (P = .007) better than for the high-risk group. Conclusion 72-GC is comparable to 95-GC in terms of accuracy of prognosis prediction, and may be effective for FFPE tumor tissues.

In a previous study, we established a one-step methylation-specific polymerase chain reaction (OS-MSP) assay for the detection of methylated DNA (met-DNA) and total DNA levels in serum. For the present study, this OS-MSP assay was used for patients with breast cancer treated with neoadjuvant chemotherapy (NAC) in order to investigate the prognostic significance of met-DNA and total DNA levels. Following treatment with NAC and prior to surgery, serum samples obtained from 120 patients with stage II/III breast cancer were subjected to the OS-MSP assay for analysis of the glutathione S-transferase pi 1, Ras association (RalGDS/AF-6) domain family member 1 and retinoic acid receptor β2 genes. The detection of methylation in a minimum of one of these genes indicated a positive outcome of the assay. The total DNA content of the serum was also determined. Of the 120 stage II/III patients, seven (6%) were positive for met-DNA in serum and showed a significantly worse overall survival (OS) time compared with patients negative for met-DNA (n=113) (5-year OS, 43 vs. 85%; P=0.002). The patients with high total DNA levels in serum (n=40) also showed a significantly worse OS compared with those with low total DNA levels (n=80) (65 vs. 91%; P

Background: In the BOLERO-2 trial, everolimus (EVE), an inhibitor of mammalian target of rapamycin, demonstrated significant clinical benefit with an acceptable safety profile when administered with exemestane (EXE) in postmenopausal women with hormone receptor-positive (HR+) advanced breast cancer. We report on the incidence, time course, severity, and resolution of treatment-emergent adverse events (AEs) as well as incidence of dose modifications during the extended follow-up of this study. Patients and methods: Patients were randomized (2:1) to receive EVE 10 mg/day or placebo (PBO), with open-label EXE 25 mg/day (n = 724). The primary end point was progression-free survival. Secondary end points included overall survival, objective response rate, and safety. Safety evaluations included recording of AEs, laboratory values, dose interruptions/adjustments, and study drug discontinuations. Results: The safety population comprised 720 patients (EVE + EXE, 482; PBO + EXE, 238). The median follow-up was 18 months. Class effect toxicities, including stomatitis, pneumonitis, and hyperglycemia, were generally of mild or moderate severity and occurred relatively early after treatment initiation (except pneumonitis); incidence tapered off thereafter. EVE dose reduction and interruption (360 and 705 events, respectively) required for AE management were independent of patient age. The median duration of dose interruption was 7 days. Discontinuation of both study drugs because of AEs was higher with EVE + EXE (9%) versus PBO + EXE (3%).Conclusions: Most EVE associated AEs occur soon after initiation of therapy, are typically of mild or moderate severity, and are generally manageable with dose reduction and interruption. Discontinuation due to toxicity was uncommon. Understanding the time course of class-effect AEs will help inform preventive and monitoring strategies as well as patient education. © The Author 2014. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved., SCOPUS: ar.j, info:eu-repo/semantics/published

Background One-step nucleic acid amplification (OSNA) for cytokeratin 19 messenger RNA is an intraoperative diagnostic procedure for the detection of lymph node metastasis. Objective This study aimed to construct intraoperative nomograms using OSNA for the prediction of non-sentinel lymph node (NSLN) metastasis and four or more axillary lymph node (ALN) metastases. Methods Of the 4736 breast cancer patients (T1-3, N0) who underwent sentinel lymph node (SLN) biopsy and had SLNs examined intraoperatively with OSNA, 623 with SLN metastasis treated with completion ALN dissection (cALND) were retrospectively analyzed, and were randomly divided into training (n = 312) and validation (n = 311) sets. Results Of the clinicopathological parameters available preoperatively and intraoperatively, the multivariate analysis of the training set revealed that clinical tumor size and total tumor load (TTL) determined by OSNA were significantly associated with NSLN metastasis, and that clinical tumor size, number of macrometastatic SLNs, and TTL were significantly associated with four or more ALN metastases. Nomograms for NSLN metastasis and four or more ALN metastases were constructed using these parameters, and their area under the receiver operating characteristic curve (AUC) of the validation set were both 0.70, with a diagnostic accuracy similar to that of previously reported postoperative nomograms. Conclusions We constructed intraoperative nomograms using OSNA for the prediction of NSLN metastasis and four or more ALN metastases. These nomograms are as accurate as the conventional postoperative nomograms and might be helpful for decision making regarding the indication for cALND or the choice of adjuvant chemotherapeutic regimens and radiation field. Electronic supplementary material The online version of this article (10.1245/s10434-018-6633-0) contains supplementary material, which is available to authorized users.

542 Background: The TAILORx trial demonstrated that adjuvant endocrine and chemoendocrine therapies had similar efficacy in patients with hormone receptor-positive, HER2-negative, node-negative breast cancer with an Oncotype DX recurrence score (RS) of 11-25. However, a predictive strategy is needed to identify patients with intermediate RS who may benefit from adjuvant chemoendocrine therapy. Curebest 95GC Breast (95GC) is a 95-gene signature that can stratify patients into two groups with high (95GC-H) and low (95GC-L) groups to predict the risk of recurrence. Our primary objective was to show that 95GC can classify patients with intermediate RS into binary recurrence risk groups. Methods: Patients with ER-positive, HER2-negative, node-negative invasive breast cancer and RS 11-30 who underwent definitive surgery and adjuvant endocrine therapy were included. RNA was derived from archived formalin-fixed, paraffin-embedded samples, and 95GC was calculated as reported previously. The Fisher exact and Brunner-Munzel tests were used to compare variables between 95GC groups. A Kaplan-Meier estimate with a log-rank test was used for recurrence-free survival (RFS) analysis. Results: The analysis included 178 patients from five institutions. The 5-year RFS rate in patients with RS 18-30 was higher in the 95GC-L group (n = 129, 96.3%) than in the 95GC-H group (n = 49, 90.9%; p = 0.002), which was consistent with results in an independent Japanese population (n = 224; p < 0.001). RFS rates significantly differed between the groups among patients with RS 11-25 as well (95GC-L, 97.4%; 95GC-H, 87.1%; p = 0.001). RFS rates did not differ between patients with RS 18-25 (94.8%) and those with RS 26-30 (93.8%; p = 0.33). Conclusions: 95GC can predict recurrence risk in patients with ER-positive, HER2-negative, node-negative invasive breast cancer and intermediate RS. Further prospective retrospective studies in the TAILORx population are warranted to confirm that 95GC can identify patients who may benefit from adjuvant chemoendocrine therapy.

In article number 1801479, Shinzaburo Noguchi, Katsunori Tanaka, and co‐workers use a click‐to‐sense probe to detect acrolein, which is universally produced by cancer cells under oxidative stress, within five minutes at room temperature. All cancer types tested are imaged and discriminated through multiple cascade reactions in the living tissue of human patients. This probe can be used to quickly and accurately diagnose cancer morphology during breast‐conserving surgery, by reforming the conventional pathological methods.

Taxanes are among the drugs most commonly used for preoperative chemotherapy for breast cancer. Taxanes induce mitotic arrest and subsequent apoptosis. The spindle-assembly checkpoint (SAC) is known to be activated during mitosis, along with cyclin-dependent kinase-1 (CDK1), and is required for taxane-induced cell death. We hypothesized that CDK1 activity predicts response to taxane-containing chemotherapy. This study included breast cancer patients who received preoperative chemotherapy- taxane-containing treatment followed by anthracycline-based treatment-and then underwent surgery. Before starting taxane-containing chemotherapy, patients underwent fine-needle aspiration biopsy, and the biopsy samples were incubated in paclitaxel solution to measure CDK activity. Clinical were evaluated after taxane therapy, and pathological resposes were evaluated after completion of all preoperative chemotherapy. Thirty five patients were eligible for analysis of clinical response to taxane-containing therapy. Twenty-six patients had taxane-sensitive and 9 taxane-resistant tumors. Using a cut-off of CDK activity determined by the ROC analysis, patients were classified into SAC function and dysfunction groups. Univariate logistic regression analysis with clinicopathologic parameters showed that only CDK-based SAC functionality was significantly correlated with clinical response (P =0.017). No significant correlation was observed between SAC functionality and pathologic response. CDK-based SAC functionality significantly predicted clinical response (P =.0072, overall agreement = 71.4%), and this is a unique mechanism-based marker for predicting taxane chemosensitivity. Further, large prospective study is needed to determine CDK-based SAC functionality could be developed as a predictive biomarker.

Everolimus (EVE)+exemestane (EXE; n = 485) more than doubled median progression-free survival versus placebo (PBO) + EXE (n = 239), with a manageable safety profile and no deterioration in health-related quality-of-life (HRQOL) in patients with hormone-receptor-positive (HR(+)) advanced breast cancer (ABC) who recurred or progressed on/after nonsteroidal aromatase inhibitor (NSAI) therapy. To further evaluate EVE + EXE impact on disease burden, we conducted additional post-hoc analyses of patient-reported HRQOL.HRQOL was assessed using EORTC QLQ-C30 and QLQ-BR23 questionnaires at baseline and every 6 weeks thereafter until treatment discontinuation because of disease progression, toxicity, or consent withdrawal. Endpoints included the QLQ-C30 Global Health Status (QL2) scale, the QLQ-BR23 breast symptom (BRBS), and arm symptom (BRAS) scales. Between-group differences in change from baseline were assessed using linear mixed models with selected covariates. Sensitivity analysis using pattern-mixture models determined the effect of study discontinuation on/before week 24. Treatment arms were compared using differences of least squares mean (LSM) changes from baseline and 95% confidence intervals (CIs) at each timepoint and overall.Clinicaltrials.gov: NCT00863655.Progression-free survival, survival, response rate, safety, and HRQOL.Linear mixed models (primary model) demonstrated no statistically significant overall difference between EVE + EXE and PBO + EXE for QL2 (LSM difference = -1.91; 95% CI = -4.61, 0.78), BRBS (LSM difference = -0.18; 95% CI = -1.98, 1.62), or BRAS (LSM difference = -0.42; 95% CI = -2.94, 2.10). Based on pattern-mixture models, patients who dropped out early had worse QL2 decline on both treatments. In the expanded pattern-mixture model, EVE + EXE-treated patients who did not drop out early had stable BRBS and BRAS relative to PBO + EXE.HRQOL data were not collected after disease progression.These analyses confirm that EVE + EXE provides clinical benefit without adversely impacting HRQOL in patients with HR(+) ABC who recurred/progressed on prior NSAIs versus endocrine therapy alone.

The aromatase inhibitors exemestane and anastrozole are approved in Japan for first-line treatment of postmenopausal patients with advanced, hormone-receptor-positive breast cancer. This phase 3, randomized, double-blind study directly compared time to progression (TTP) for exemestane and anastrozole therapy in this patient population. Eligible patients were randomized to receive exemestane 25 mg or anastrozole 1 mg, each once daily. The primary endpoint was TTP based on assessment by an expert radiologic images review committee (ERIRC). Secondary endpoints included investigator-assessed TTP, time to treatment failure, overall survival, objective response rate, clinical benefit rate, and safety. A total 298 patients were randomized to receive exemestane (n = 149; mean age 63.4 years) or anastrozole (n = 149; mean age 64.0 years). Median ERIRC-assessed TTP was 13.8 and 11.1 months (hazard ratio = 1.007; 95 % confidence interval [CI]: 0.771, 1.317) and median investigator-assessed TTP was 13.8 and 13.7 months (hazard ratio = 1.059; 95 % CI: 0.816, 1.374) in the exemestane and anastrozole arms, respectively. Median overall survival was 60.1 months in the anastrozole arm and was not reached in the exemestane arm at data cutoff. The objective response rate was 43.9 % (95 % CI: 35.3, 52.8) and 39.1 % (95 % CI: 30.6, 48.1) in the exemestane and anastrozole arms, respectively. Treatment-related adverse events grade ≥3 occurred in 9.4 and 6.0 % of patients, and treatment-related serious adverse events occurred in 4.0 and 3.4 % of patients in the exemestane and anastrozole arms, respectively. In this study, the efficacy and safety profiles of exemestane were similar to those of anastrozole in Japanese patients with advanced, hormone-receptor-positive breast cancer; however, TTP non-inferiority of exemestane versus anastrozole was not confirmed.

Increased intratumoral expression of aromatase, the key enzyme for estrogen biosynthesis, is predicted to be of critical importance in the development of breast cancer. Recently, several germline rearrangements at 15q21 have been shown to cause overexpression of the aromatase gene CYP19A1 and resulting aromatase excess syndrome. To determine whether submicroscopic genomic rearrangements at 15q21 are involved in aromatase overexpression in breast cancer tissues, we investigated copy-number alterations in genomic DNA obtained from 44 tumor samples. Comparative genomic hybridization analysis identified no deletion or duplication at 15q21 in the 44 samples. These results, in conjunction with previous data, indicate that aromatase overexpression in breast cancer tissues is likely to result from a promoter switch of CYP19A1 and/or accumulation of CYP19A1-expressing cells, rather than from cryptic transactivation of CYP19A1 because of genomic rearrangements at 15q21.

BACKGROUND: The randomized, controlled BOLERO-2 (Breast Cancer Trials of Oral Everolimus) trial demonstrated significantly improved progression-free survival with the use of everolimus plus exemestane (EVE + EXE) versus placebo plus exemestane (PBO + EXE) in patients with advanced breast cancer who developed disease progression after treatment with nonsteroidal aromatase inhibitors. This analysis investigated the treatment effects on health-related quality of life (HRQOL). METHODS: Using the European Organisation for Research and Treatment of Cancer Quality of Life Questionnaire-Core 30 (EORTC QLQ-C30) questionnaire, HRQOL was assessed at baseline and every 6 weeks thereafter until disease progression and/or treatment discontinuation. The 30 items in 15 subscales of the QLQ-C30 include global health status wherein higher scores (range, 0-100) indicate better HRQOL. This analysis included a protocol-specified time to definitive deterioration (TDD) analysis at a 5% decrease in HRQOL versus baseline, with no subsequent increase above this threshold. The authors report additional sensitivity analyses using 10-point minimal important difference decreases in the global health status score versus baseline. Treatment arms were compared using the stratified log-rank test and Cox proportional hazards model adjusted for trial stratum (visceral metastases, previous hormone sensitivity), age, sex, race, baseline global health status score and Eastern Cooperative Oncology Group performance status, prognostic risk factors, and treatment history. RESULTS: Baseline global health status scores were found to be similar between treatment groups (64.7 vs 65.3). The median TDD in HRQOL was 8.3 months with EVE + EXE versus 5.8 months with PBO + EXE (hazard ratio, 0.74; P = .0084). At the 10-point minimal important difference, the median TDD with EVE + EXE was 11.7 months versus 8.4 months with PBO + EXE (hazard ratio, 0.80; P = .1017). CONCLUSIONS: In patients with advanced breast cancer who develop disease progression after treatment with nonsteroidal aromatase inhibitors, EVE + EXE was associated with a longer TDD in global HRQOL versus PBO + EXE. Cancer 2013. © 2013 American Cancer Society.

The combination of capecitabine and paclitaxel (XP) has demonstrated synergistic antitumor activity in preclinical models. The purpose of this phase II study was to evaluate the efficacy and safety of a monthly XP regimen in patients with metastatic breast cancer (MBC). Eligible patients had received one or fewer prior chemotherapy regimens for MBC. Patients received oral capecitabine of low dose (828 mg/m2 twice daily, days 1–21) plus paclitaxel (80 mg/m2, i.v., over 60 min, days 1, 8 and 15) every 28 days until disease progression or unacceptable toxicity. The primary endpoint was overall response rate (ORR). Progression-free survival (PFS), overall survival (OS) and safety were secondary endpoints. An exploratory analysis of efficacy according to hormone receptor (HR) status was performed. Forty-four patients were enrolled, and 43 patients were evaluable. ORR was 46.5 %. PFS and OS were 8.3 and 22.9 months, respectively. ORR was 45.5 % in patients with HR-positive tumors and 50 % in HR-negative cases. The most frequently observed grade 3/4 adverse events were neutropenia (27.9 %), leukopenia (11.6 %), hand-foot syndrome (HFS, 9.3 %) and fatigue (7.0 %). There were no discontinuations due to HFS. Monthly XP was an effective and well-tolerated regimen for the first- or second-line treatment for MBC.

Aims: This meta-analysis explores the relationship between the everolimus minimum (Cmin) and maximum (Cmax) exposure and the risk for pulmonary adverse events (AEs) in Japanese versus non-Japanese patients. Methods: Patient-level data from patients treated with daily everolimus in advanced solid tumor trials were evaluated using a Cox regression model, stratified by cancer type or treatment arm, with log-transformed time-averaged Cmin or Cmax as a time-varying covariate. Kaplan-Meier analysis was used to evaluate the relationship between pulmonary AEs and pharmacokinetic parameters. Results: Thirty studies were identified. In the Cmin population (n = 1,962), all-grade pulmonary AE incidence was significantly higher in Japanese versus non-Japanese patients (19.9 vs. 9.4%). Pharmacokinetic parameters were similar between Japanese and non-Japanese patients. A 2-fold increase in everolimus Cmin significantly increased the risk for the first any-grade pulmonary AE in Japanese (risk ratio: 1.824; 95% CI: 1.141-2.918) and non-Japanese patients (risk ratio: 1.406; 95% CI: 1.156-1.710). Conclusions: The risk for pulmonary AEs is related to everolimus exposure. Local monitoring and reporting differences might account for the significantly higher reported incidence of low-grade everolimus-associated pulmonary AEs in Japanese versus non-Japanese patients. Patients should be carefully monitored for early signs of pulmonary AEs, and appropriate medical management should be implemented.

Resistance against anti-HER2 drugs in HER2-positive breast cancer is a major obstacle to the improving prognosis. Transforming growth factor β (TGFβ) is a cytokine involved in the acquisition of more malignant phenotypes through epithelial-mesenchymal transition (EMT) and cancer stem cell (CSC) properties. The aim of this study was to investigate the effects of TGFβ and its downstream SMAD pathway on resistance to anti-HER2 drugs. HER2-positive breast cancer cell lines were stimulated with TGFβ for 14 days. Then, the sensitivity to trastuzumab and lapatinib and the expression levels of various EMT and CSC markers were examined. The correlation of nuclear SMAD3 expression in untreated breast tumor tissues with trastuzumab efficacy in neoadjuvant settings was examined. The effect of a small-molecule inhibitor of SMAD3 (SIS3) on resistance to anti-HER2 drugs was explored. We found that continuous activation of the TGFβ-SMAD3 pathway induced resistance to anti-HER2 drugs and CSC traits in HER2-positive breast cancer cells. The induction of drug resistance by TGFβ required strong activation of SMAD3. In fact, activated SMAD3 regulated multiple genes that harbor SMAD-binding elements and are involved in trastuzumab resistance. Nuclear SMAD3 expression in tumor tissue was inversely correlated with sensitivity to neoadjuvant treatment with trastuzumab. SIS3 not only prevented the acquisition of resistance to anti-HER2 drugs but also restored trastuzumab sensitivity in trastuzumab-resistant cells. This study indicates that the TGFβ-SMAD3 pathway plays an important role in the induction and maintenance of resistance to anti-HER2 drugs. Thus, SMAD3 is a potential therapeutic target that can inhibit resistance and restore sensitivity to anti-HER2 drugs.

Gene expression profiling has been increasingly used in clinical practice. Integration of expression data across multiple experiments provides better insight into the heterogeneity of the biology being examined. A problem of the data integration, an experimental batch from platform or laboratory sources, remains a barrier to systematically analyzing data across different datasets. Several methods (such as, ComBat) have been proposed to remove batch effects. However, these methods often make assumptions about ideal distribution of the underlying data. Difficulties might be expected when comparing datasets that have fundamentally different (dataset-dependent) distributions. For example, clinical datasets are often collected from patient samples with various disease stages or conditions. Therefore, we have compared several mathematical transformations across many datasets, including the nonparametric Z scaling transformation method (NPZ) we have proposed for clinical use. We selected 2,813 patients with available information on estrogen receptor (ER) status or human epidermal growth factor receptor 2 (HER2) status from 24 Affymetrix HG-U133 (GPL96) or Affymetrix HG-U133 plus 2.0 (GPL570) datasets in the Gene Expression Omnibus database. The microarray expression data were processed with one of the four following methods: Raw (background correction and log transformation only), Microarray Suite 5.0 (MAS5), frozen robust multiarray analysis (fRMA), and radius minimax (RMX). The normalized data were sequentially transformed by using one of the following five methods: untransformed (without transformation), single-array-based transformations (RANK, Z, NPZ, or YuGene). Finally, we compared the ER and HER2 statuses assessed by immunohistochemical (IHC) staining with mRNA expression. We found that single-array-based transformation in addition to normalization improved the concordance rates of the IHC staining. We demonstrated the influence of transformation by using breast cancer samples and showed that adding single-array-based transformations to microarray expression data resulted in stronger correlations with IHC staining.

Background We conducted an open-label, randomized controlled trial evaluating the appropriate treatment duration of leuprorelin acetate 3-month depot, TAP-144-SR (3M), administered postsurgically every 3 months for 2 years versus 3 or more (up to 5) years, in combination with tamoxifen, for 5 years in premenopausal endocrine-responsive breast cancer patients and reported similar survival benefit in the two treatment groups. We hereby present patient-reported quality of life (QOL) data obtained from this trial. Methods Three self-administered QOL questionnaires (QOL-ACD, QOL-ACD-B, FACT-ES subscale) were used, and the difference in QOL score changes between the two groups was analyzed using a mixed-effects model for repeated measures. Results Eligible patients (N = 222) were randomly assigned to a 2-year (2YG, N = 112) or 3-or-more-year treatment group (3YG, N = 110). The time courses of the three QOL scores during the trial period were similar in the two groups. The mean changes in the QOL scores from week 96 were largely stable through week 240 in the 3YG, but showed significantly greater improvement in the score changes from week 96 in the 2YG than the 3YG. Symptoms associated with menopause such as hot flashes and sweating contributed to these results. Menstruation recovery was associated with significantly greater improvement of these symptoms in the 2YG than the 3YG. Conclusions Patient-reported menopause-associated symptoms and QOL improved after discontinuation of the LH-RH agonist administration and menstruation recovery. QOL information should be a consideration in long-term treatment.

The aim of this study was to investigate the clinicopathological characteristics of GATA binding protein 3 (GATA3)-positive breast cancers as well as the association of GATA3 expression with response to chemotherapy.Tumor specimens obtained before neoadjuvant chemotherapy [paclitaxel followed by 5-fluorouracil/epirubicin/cyclophosphamide)] from breast cancer patients (n = 130) were subjected to immunohistochemical and mutational analysis of GATA3 and DNA microarray gene expression analysis for intrinsic subtyping.Seventy-four tumors (57%) were immunohistochemically positive for GATA3. GATA3-positive tumors were significantly more likely to be lobular cancer, estrogen receptor (ER)-positive, progesterone receptor (PgR)-positive, Ki67-negative, and luminal A tumors. Somatic mutations were found in only three tumors. Pathological complete response (pCR) was observed in 8 (11%) GATA3-positive tumors and in 22 (39%) GATA3-negative tumors. multivariate analysis showed that tumor size, human epidermal growth factor receptor 2 (her2), and gata3 were independent predictors of pcr.GATA3-positive breast cancers showed luminal differentiation characterized by high ER expression and were mostly classified as luminal-type tumors following intrinsic subtyping. Interestingly, GATA3 was an independent predictor of response to chemotherapy, suggesting that GATA3 might be clinically useful as a predictor of a poor response to chemotherapy.