Assessment of structural chromosomal instability phenotypes as biomarkers of carboplatin response in triple negative breast cancer: the TNT trial

BACKGROUND

In the TNT trial of triple negative breast cancer (NCT00532727), germline BRCA1/2 mutations were present in 28% of carboplatin responders. We assessed quantitative measures of structural chromosomal instability (CIN) to identify a wider patient subgroup within TNT with preferential benefit from carboplatin over docetaxel.

PATIENTS AND METHODS

Copy number aberrations (CNAs) were established from 135 formalin-fixed paraffin-embedded primary carcinomas using Illumina OmniExpress SNP-arrays. Seven published [allelic imbalanced CNA (AiCNA); allelic balanced CNA (AbCNA); copy number neutral loss of heterozygosity (CnLOH); number of telomeric allelic imbalances (NtAI); BRCA1-like status; percentage of genome altered (PGA); homologous recombination deficiency (HRD) scores] and two novel [Shannon diversity index (SI); high-level amplifications (HLAMP)] CIN-measurements were derived. HLAMP was defined based on the presence of at least one of the top 5% amplified cytobands located on 1q, 8q and 10p. Continuous CIN-measurements were divided into tertiles. All nine CIN-measurements were used to analyse objective response rate (ORR) and progression-free survival (PFS).

RESULTS

Patients with tumours without HLAMP had a numerically higher ORR and significantly longer PFS in the carboplatin (C) than in the docetaxel (D) arm [56% (C) versus 29% (D), PHLAMP,quiet = 0.085; PFS 6.1 months (C) versus 4.1 months (D), Pinteraction/HLAMP = 0.047]. In the carboplatin arm, patients with tumours showing intermediate telomeric NtAI and AiCNA had higher ORR [54% (C) versus 20% (D), PNtAI,intermediate = 0.03; 62% (C) versus 33% (D), PAiCNA,intermediate = 0.076]. Patients with high AiCNA and PGA had shorter PFS in the carboplatin arm [3.4 months (high) versus 5.7 months (low/intermediate); and 3.8 months (high) versus 5.6 months (low/intermediate), respectively; Pinteraction/AiCNA = 0.027, Padj.interaction/AiCNA = 0.125 and Pinteraction/PGA = 0.053, Padj.interaction/PGA = 0.176], whilst no difference was observed in the docetaxel arm.

CONCLUSIONS

Patients with tumours lacking HLAMP and demonstrating intermediate CIN-measurements formed a subgroup benefitting from carboplatin relative to docetaxel treatment within the TNT trial. This suggests a complex and paradoxical relationship between the extent of genomic instability in primary tumours and treatment response in the metastatic setting.

Evaluation of applying IHC4 as a prognostic model in the translational study of Intergroup Exemestane Study (IES): PathIES

BACKGROUND

Intergroup Exemestane Study (IES) was a randomised study that showed a survival benefit of switching adjuvant endocrine therapy after 2-3 years from tamoxifen to exemestane. This PathIES aimed to assess the role of immunohistochemical (IHC)4 score in determining the relative sensitivity to either tamoxifen or sequential treatment with tamoxifen and exemestane.

PATIENTS AND METHODS

Primary tumour samples were available for 1274 patients (27% of IES population). Only patients for whom the IHC4 score could be calculated (based on oestrogen receptor, progesterone receptor, HER2 and Ki67) were included in this analysis (N = 430 patients). The clinical score (C) was based on age, grade, tumour size and nodal status. The association of clinicopathological parameters, IHC4(+C) scores and treatment effect with time to distant recurrence-free survival (TTDR) was assessed in univariable and multivariable Cox regression analyses. A modified clinical score (PathIEscore) (N = 350) was also estimated.

RESULTS

Our results confirm the prognostic importance of the original IHC4, alone and in conjunction with clinical scores, but no significant difference with treatment effects was observed. The combined IHC4 + Clinical PathIES score was prognostic for TTDR (P < 0.001) with a hazard ratio (HR) of 5.54 (95% CI 1.29-23.70) for a change from 1st quartile (Q1) to Q1-Q3 and HR of 15.54 (95% CI 3.70-65.24) for a change from Q1 to Q4.

CONCLUSION

In the PathIES population, the IHC4 score is useful in predicting long-term relapse in patients who remain disease-free after 2-3 years. This is a first trial to suggest the extending use of IHC4+C score for prognostic indication for patients who have switched endocrine therapies at 2-3 years and who remain disease-free after 2-3 years.

Abstract P2-10-02: The impact of intrinsic subtypes and molecular features on aromatase inhibitor induced reduction of proliferation marker of Ki67 in primary ER+ breast cancer: A POETIC study (CRUK/07/015)

Background

Neoadjuvant endocrine therapy (NAE) is often a good option for postmenopausal (PM) women with estrogen receptor positive (ER+) breast cancers(BC). Fall in Ki67 is widely accepted as valid for predicting favorable tumor response to NAE and improved outcome. We report our planned correlative study to investigate if intrinsic subtype impacts on Ki67 changes (ΔKi67) as measured by immunohistochemistry. We also explored the correlation of several ER+ BC relevant molecular features at baseline(B) with ΔKi67.

Patients and methods

POETIC is a phase III, randomized 2:1 study for 4486 PM patients with ER+ BC to determine whether peri-operative aromatase inhibitor (AI) followed by standard adjuvant therapy improves outcome compared with standard adjuvant therapy alone. The proliferation rate was estimated as percentage (%) of cancer cells staining for Ki67. Primary biological endpoint was defined as two-week (2wk) change in Ki67 (2wkΔKi67): ln[(2wk Ki67+0.1)/(B Ki67+0.1)]. Secondary endpoint: “responders”, was % change of Ki67 defined as (2wk Ki67 – B Ki67) *100/B Ki67. “Responder” was defined as follows: reduction &lt;50% as poor (PR), 50-75% moderate and &gt;75% as good responder (GR).

Human whole genome expression(GE) Illumina BeadChips were performed. Data was obtained from 137 paired samples from the treatment group(T) and 49 pairs from the control(C) group with GE data passing quality check and baseline Ki67≥5% to minimise the impact of extreme values based on proportional ΔKi67. Intrinsic subtype and risk of recurrence(ROR) groups were calculated using PAM50. GE scores from Oncotype Dx, MammaPrint, p53 mutation/wildtype(Troester 2006), ER+ early response (ERE)(Hatzis 2011), estrogen-regulated genes subtypes (Oh 2006) and markers for 23 different immune cell types(Bindea 2013) were calculated. Associations of GE scores to endpoints of response were determined by Spearman correlation and chi-square tests. Bonferroni correction was used to control error rate with p&lt;0.0005 deemed significant.

Results

At B of the 137 paired T, 64% were Luminal A (LumA), 22% Luminal B (LumB), 9% as HER-2 enriched (HER2-E), 2% as Basal-like (BLBC) and 3% as Normal-like. Subtypes at B were associated with response, with LumA showing the biggest reduction of Ki67 (p=0.0001) and GR. All GE, except ERE, correlated significantly with 2wkΔKi67 and response: higher risk groups associated with lowest reduction rate. None of immune cell types correlated with 2wkΔKi67, except that tumors enriched with T-helper 1 cell type were associated with PR (p &lt; 0.000001).

Comparing subtypes between time-points, 85% of LumB and 42% of HER2-E were assigned instead as LumA at 2wk regardless of response. Of the 15 ROR defined high-risk group, only 33% were assigned instead as low-risk at 2wk.

Conclusion

Both LumA and LumB are endocrine sensitive. A fall of Ki67 was observed in majority of cases. Most tumors estimated as high-risk by molecular profiling showed less response and most remained moderate or high risk of recurrence on endocrine therapy. Whether molecular profiling at 2wk after starting AI predicts for long-term outcome in PM women with ER+ better than at diagnosis will need to be determined.

Citation Format: Cheang MCU, Morden J, Gao Q, Parker J, López-Knowles E, Detre S, Hills M, Zabaglo L, Tomiczek M, Mallon E, Robertson J, Smith I, Bliss J, Dowsett M, On Behalf of the POETIC Trialists. The impact of intrinsic subtypes and molecular features on aromatase inhibitor induced reduction of proliferation marker of Ki67 in primary ER+ breast cancer: A POETIC study (CRUK/07/015) [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 P2-10-02.

Abstract P2-09-02: True effect of aromatase inhibitor (AI) treatment on global gene expression (expr) changes in postmenopausal ER+ breast cancer (BC) patients: A POETIC study (CRUK/07/015)

BACKGROUND Gene expression (expr) analyses are increasingly used for characterising the pharmacodynamic response of primary BC. This includes assessing ER+ BC's dependence on estrogen (E) by measuring gene expr changes after AI-treatment. However, differences in tissue sampling and other preanalytic procedures between samples taken at diagnosis (D) and surgery (S), may lead to systematic artifactual changes that are falsely ascribed to the intervention. To identify genes whose expr is truly affected by AI, we measured global gene expr changes from paired core-cut biopsies at D and S from patients in the POETIC presurgical window trial.

METHODS In POETIC, 4486 postmenopausal women with primary ER+ BC were randomised 2:1 to receive perioperative AI (2 weeks pre + 2 weeks post surgery, termed Tr) or no perioperative treatment (termed Con), allowing gene expr changes to be compared between Tr and Con. RNA was extracted from paired RNA-later stored core-cuts of 56 Con and 157 Tr patients and arrayed on Illumina whole genome expr BeadChips. Raw data was extracted, transformed, normalised and batch-corrected. Probes not detected (p&gt;0.01) in &gt;=25% of samples were discarded. Impact of AI on genes was evaluated based on difference of the expr mean changes (log2(S/D)) of the Tr and Con samples.

RESULTS In the Con group, expr of 73 genes significantly changed (FDR&lt;5%); 70 of these changed by a similar magnitude in the Tr group, indicating their change was independent of AI therapy but would have been artifactually discovered as changed by AI in the absence on Con. The 8 genes most up-regulated in Tr were all among the 20 genes most up-regulated in Con: many were early-response or stress-associated genes. Three of the 8 most down-regulated in AI were the most down-regulated in Con: all were haemoglobin-related. Expr of some genes was changed in Con (eg MYC increase) but was unaffected in Tr. Such artifactual gene changes in Con tumors conceal true AI-induced changes that would not be detected in the absence of comparison with Con.

615 genes were down-regulated and 472 up-regulated in Tr but not Con. The majority of down-regulated genes were cell cycle or proliferation-associated or E-regulated, including ESR1, PDZK1, GREB1, HSPB1. Functional mapping showed changes in the regulation of cyclins and cyclin dependent kinases impacting on G1/S and G2/M. Of note, up-regulated genes included CDK6 (target for CDK4/6 inhibitors) and CCND2, involved in G1/S checkpoint regulation; SNAI2, TGFB3, TGFBR2, associated with tumour invasion and metastasis; and other genes involved in aryl hydrocarbon receptor, Glioblastoma Multiforme, HIPPO and p53 signalling.

CONCLUSION Expr of certain genes is altered by processes involved in presurgical window studies. In the absence of a Con group, these may be wrongly ascribed to an experimental intervention or wrongly considered as unaffected by the intervention (eg MYC in this study).

Down-regulation of E-responsive and proliferation genes was an expected response to AI but increased expr of genes such as SNAI2, CCND2 and CDK6 indicates immediate tumour re-wiring and provides mechanistic support for benefit from combination therapy with a CDK4/6 inhibitor.

Citation Format: Gao Q, López-Knowles E, Cheang MCU, Morden J, Martin L-A, Sidhu K, Evans D, Martins V, Dodson A, Skene A, Holcombe C, Mallon E, Abigail E, Bliss J, Robertson J, Smith I, Dowsett M. True effect of aromatase inhibitor (AI) treatment on global gene expression (expr) changes in postmenopausal ER+ breast cancer (BC) patients: A POETIC study (CRUK/07/015) [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 P2-09-02.

Abstract P2-08-16: Prognostic and predictive abilities of intrinsic subtype in hormone receptor-positive metastatic breast cancer from the EGF30008 phase III clinical trial

Background

Combination of letrozole and lapatinib improved progression-free survival (PFS) compared with letrozole and placebo in patients with hormone receptor-positive (HR+)/HER2+ metastatic breast cancer (MBC), but not HR+/HER2-negative (HER2-) disease (JCO 2009). However, HR+ disease is clinically and biologically heterogeneous with all intrinsic molecular subtypes (Luminal A, Luminal B, HER2-enriched [HER2E] and Basal-like) identified. Here, we tested retrospectively the prognostic and predictive ability of intrinsic subtype in tumor samples of the EGF30008 trial.

Methods

Expression profiling from FFPE tumor tissues was performed on the nCounter platform. Tumors were classified into each intrinsic subtype using the research-based PAM50 classifier (JCO 2009). Cox proportional hazard models for PFS and overall survival (OS) were used to generate point estimates of hazard ratios (HR) and corresponding 95% confidence intervals (CIs). Changes in likelihood ratio χ2 values were used to measure and compare the relative amount of information of each variable. Variables evaluated were: age, prior endocrine therapy, presence of visceral disease, number of metastatic sites, performance status, clinical HER2 status, and treatment. To determine whether the intrinsic subtypes were predictive of lapatinib benefit, we tested the interaction term of subtype by treatment arm in a Cox model that also included the main effects. Kaplan-Meier plots were used to depict the proportion of patients free from progression as a function of time.

Results

Tumor samples from 821 patients (63.8%) were profiled (85.7% primary and 14.3% metastatic tumor samples). Clinical-pathological features of this patient subset were well balanced compared with the original set. Within the entire cohort, all subtypes were identified: Luminal A (46.5%); Luminal B (29.7%); HER2E (7.4%); Basal-like (3.4%) and normal-like (12.9%). Within HER2+ disease, 28.6% of samples were HER2E. Intrinsic subtype was found the strongest prognostic factor independently associated with PFS and OS in all patients, and in patientswith HER2-negative or HER2+ disease (P&lt;0.0001). Median PFS and OS for each subtype within clinically HER2-negative disease were: Luminal A (16.85 and 45.0 months), Luminal B (10.97 and 37.0 months), HER2E (4.67 and 16.0 months) and Basal-like (4.14 and 23.0 months). Within clinically HER2-negative disease (n=644), 16 patients (2.5%) had HER2E disease. Patients with HER2-/HER2E disease benefited from lapatinib (6.5 vs 2.6 months; PFS HR =0.24, 95% CI: 0.07-0.86; P=0.019; HER2E vs not treatment interaction P=0.016). Finally, intrinsic subtype was not predictive of benefit from lapatinib within HER2+ disease.

Conclusions

HR-positive disease is biologically heterogeneous and intrinsic subtypes are strongly prognostic in a first-line MBC setting. HR+/HER2- disease with a HER2E profile may benefit from lapatinib. The clinical value of intrinsic subtyping in HR+ MBC warrants further investigation, but patients with Luminal A/HER2-negative MBC disease might be good candidates for letrozole monotherapy in the first-line setting regardless of visceral disease and number of metastases.

Citation Format: Prat A, Cheang MCU, Galván P, Nuciforo P, Paré L, Adamo B, Viladot M, Press MF, Gagnon R, Ellis C, Johnston S. Prognostic and predictive abilities of intrinsic subtype in hormone receptor-positive metastatic breast cancer from the EGF30008 phase III clinical trial. [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 P2-08-16.

Abstract P3-07-04: Intrinsic subtype and therapeutic response among early stage HER2-positive breast tumors from the North Central cancer treatment group (Alliance) N9831 trial

Importance: 20-25% of patients with early stage HER2-positive breast cancer develop tumor relapse after adjuvant trastuzumab. Identification of such patients is a key goal for clinical management decisions.

Objective: To assess molecular heterogeneity among early stage HER2-positive patients using the Prosigna™ algorithm, to define intrinsic subtypes, and to determine the clinical significance of such heterogeneity.

Design: The NanoString® platform was used to measure the abundance of the PAM50 subtype signature transcripts. Samples from the NCCTG (Alliance) N9831 trial were analyzed using the Prosigna™ algorithm to define intrinsic subtype and risk scores. Subtypes were evaluated for recurrence-free survival following chemotherapy with or without trastuzumab.

Setting: Samples were obtained from a multi-center randomized phase III trial of chemotherapy versus chemotherapy plus trastuzumab.

Participants: All tumors were centrally evaluated for HER2 positivity, defined as IHC 3+ and/or FISH &gt;2.0; 1392 patients were evaluated for molecular subtype.

Intervention(s): Patients received adjuvant chemotherapy (doxorubicin plus cyclophosphamide followed by paclitaxel) (n=484) or chemotherapy plus trastuzumab (n=908).

Main Outcome Measure(s): The primary outcome was recurrence-free survival as a function of subtype and treatment.

Results: Patients with HER2-positive tumors with HER2-enriched features comprised about 70% of the sample cohort, and these individuals received significant benefit from adjuvant trastuzumab (HR=0.68, 95%CI: 0.52, 0.89, p=0.005), as did the relatively fewer patients (291/1392) with Luminal-type tumors (HR=0.52, 95%CI: 0.32, 0.85, p=0.01). The sample cohort contained a small number of patients with tumors having Basal-like features (97/1392), and the data suggest that these individuals may have received less benefit from trastuzumab, beyond that received from chemotherapy alone (HR=1.06, 95%CI:0.53,2.13, p=0.87).

Conclusions: The majority of HER2-positive tumors are classified as HER2-enriched or Luminal using the Prosigna algorithm, and patients with such tumors benefit from adjuvant trastuzumab. About 10% of HER2-positive tumors exhibit Basal-like genomic features, and such tumors appear to recur at fairly similar frequency irrespective of treatment with chemotherapy or chemotherapy plus trastuzumab. Patients with HER2-positive/Basal-like tumors may represent a cohort that should be considered for enrollment in trials to evaluate emerging novel HER2-targeted agents, other targeted therapies, or combinations of both approaches.

Support provided in part by CA129949 and CA15083.

Citation Format: Perez EA, Ballman KV, Mashadi-Hossein A, Tenner KS, Kachergus JM, Norton N, Necela BM, Carr JM, Ferree S, Perou CM, Cheang MCU, Thompson EA. Intrinsic subtype and therapeutic response among early stage HER2-positive breast tumors from the North Central cancer treatment group (Alliance) N9831 trial. [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 P3-07-04.

Chemotherapy benefit for 'ER-positive' breast cancer and contamination of nonluminal subtypes—waiting for TAILORx and RxPONDER

BACKGROUND

Retrospective analyses of NSABP B20 and SWOG 8814 showed a large benefit of chemotherapy in patients with ER-positive tumors and high OncotypeDX Recurrence Score (RS≥31). However, it might be possible that both studies may be contaminated by non-luminal tumors, especially in high-risk RS group.

METHODS

We conducted simulations in order to obtain a better understanding of how the NSABP B20 and SWOG 8814 results would have been if non-luminal breast cancer would have been excluded. Simulations were done separately for the node-negative and node-positive cohorts.

RESULTS AND CONCLUSION

The results of the simulations suggest that the non-luminal tumors are augmenting the apparent benefit of chemotherapy, but do not appear to be responsible for the entire effect. These simulations could provide information about the potential influence of contamination by unexpected tumor subtypes on the future results of TAILORx and RxPONDER clinical trials.

Predicting response and survival in chemotherapy-treated triple-negative breast cancer

BACKGROUND

In this study, we evaluated the ability of gene expression profiles to predict chemotherapy response and survival in triple-negative breast cancer (TNBC).

METHODS

Gene expression and clinical-pathological data were evaluated in five independent cohorts, including three randomised clinical trials for a total of 1055 patients with TNBC, basal-like disease (BLBC) or both. Previously defined intrinsic molecular subtype and a proliferation signature were determined and tested. Each signature was tested using multivariable logistic regression models (for pCR (pathological complete response)) and Cox models (for survival). Within TNBC, interactions between each signature and the basal-like subtype (vs other subtypes) for predicting either pCR or survival were investigated.

RESULTS

Within TNBC, all intrinsic subtypes were identified but BLBC predominated (55-81%). Significant associations between genomic signatures and response and survival after chemotherapy were only identified within BLBC and not within TNBC as a whole. In particular, high expression of a previously identified proliferation signature, or low expression of the luminal A signature, was found independently associated with pCR and improved survival following chemotherapy across different cohorts. Significant interaction tests were only obtained between each signature and the BLBC subtype for prediction of chemotherapy response or survival.

CONCLUSIONS

The proliferation signature predicts response and improved survival after chemotherapy, but only within BLBC. This highlights the clinical implications of TNBC heterogeneity, and suggests that future clinical trials focused on this phenotypic subtype should consider stratifying patients as having BLBC or not.

Abstract P6-07-10: Luminal A vs. Basal-like Breast Cancer: time dependent changes in the risk of relapse in the absence of treatment

Background: Numerous retrospective analyses of prospective randomized clinical trials of patients treated with adjuvant tamoxifen and chemotherapy have demonstrated that the breast cancer intrinsic subtype Luminal A tumors generally have favorable early initial outcomes, while basal-like tumors are associated with a marked risk of early relapse. To determine the extended natural history of the intrinsic subtypes across two decades of follow up the PAM50 “non-commercial open source bioinformatics” qPCR assay was conducted on node negative tumors accrued through the Cooperative Breast Cancer Tissue Registry (CBCTR) from patients who did not receive systemic therapy.

Methods: Intrinsic subtype calls were obtained from 331 CBCTR cases treated with local interventions only. Tumors were classified into Luminal A (LumA), Luminal B (LumB), HER2-enriched (HER2-E) and Basal-like (BLBC), and correlated relapse-free (RFS). Patient survival and hazard rate were estimated using Kaplan-Meier plots and log-rank test. Multivariable Cox regression analyses were used to determine the significance of the intrinsic subtypes, adjusted with standard clinicopathological variables including tumor size, age at diagnosis, grade, radiation therapy treatment, centralized reviewed estrogen receptor, progesterone receptor and human epidermal growth factor 2 status measured by immunohistochemistry. Patients were diagnosed from 1978 to 1992, with a mean follow-up time of 13 years (range 0.5–31).

Results: Of the 331 tumors tested, 51% of cases were classified as LumA, 18% as LumB, 11% as HER2-E and 20% as BLBC. Although LumA was associated with the best outcome for the first 10-year of follow-up, the final number of RFS events were eventually comparable with those observed for BLBC with prolonged follow up (Table 1). In the multivariable Cox model, only BLBC tumors were associated with worse prognosis than LumA with borderline significance (Hazard ratio: 2.0 (95% CI 0.9–5), p = 0.07). BLBC had the highest hazard rates for the first 5 years (7% at first year to 5% at 5 yr), consistent with previous observations. Interestingly, in the absence of treatment, the slow growing LumA subtype had a gradual increase of hazard for an RFS event from 3% at 5 yrs to 4% at 10 yrs to 7% at 20 yrs. The hazard rates of LumA cross with those of BLBC at 10 years.

Abstract P4-16-02: A survival benefit from locoregional radiotherapy for node-positive and CMF treated breast cancer is most significant in Luminal A tumors

Background: Between 1978–1986, 318 premenopausal women treated with mastectomy for lymph node positive breast cancer, were randomized to CMF chemotherapy alone vs. CMF chemotherapy and adjuvant radiotherapy (RT) to the chest wall and regional lymph nodes. After 15 years of follow-up, post-mastectomy RT was associated with a statistically significant 29% relative risk reduction in mortality. Recent evidence suggests that Luminal A tumors, identified using hormone receptors and Ki67, have a particularly favorable prognosis. We retrospectively identified the Luminal A tumors from this clinical trial cohort to determine if the response to postmastectomy RT differed among Luminal A and non-Luminal A tumors.

Methods: 203 archival breast tumor samples from this study were used to construct a tissue microarray. Luminal A tumors were identified using an immunopanel consisting of: estrogen receptor, progestorone receptor, Her2, and Ki67. Luminal A tumors were defined as either ER or PR positive, Her2 negative, and Ki67 &lt; 14%. Kaplan-Meier estimates and the log-rank test were used to test the differences in locoregional relapse free survival (LRFS) and breast cancer specific survival (BCSS). Interaction between treatment and Luminal A/Non-luminal A were tested using Cox regression analysis.

Results: The intrinsic subtype was successfully determined in 144 breast tumors, and 49 were classified as Luminal A (34%). Survival outcomes at 10 years are summarized in Table 1:

Concordance among gene expression-based predictors for ER-positive breast cancer treated with adjuvant tamoxifen

BACKGROUND

ER-positive (ER+) breast cancer includes all of the intrinsic molecular subtypes, although the luminal A and B subtypes predominate. In this study, we evaluated the ability of six clinically relevant genomic signatures to predict relapse in patients with ER+ tumors treated with adjuvant tamoxifen only.

METHODS

Four microarray datasets were combined and research-based versions of PAM50 intrinsic subtyping and risk of relapse (PAM50-ROR) score, 21-gene recurrence score (OncotypeDX), Mammaprint, Rotterdam 76 gene, index of sensitivity to endocrine therapy (SET) and an estrogen-induced gene set were evaluated. Distant relapse-free survival (DRFS) was estimated by Kaplan-Meier and log-rank tests, and multivariable analyses were done using Cox regression analysis. Harrell's C-index was also used to estimate performance.

RESULTS

All signatures were prognostic in patients with ER+ node-negative tumors, whereas most were prognostic in ER+ node-positive disease. Among the signatures evaluated, PAM50-ROR, OncotypeDX, Mammaprint and SET were consistently found to be independent predictors of relapse. A combination of all signatures significantly increased the performance prediction. Importantly, low-risk tumors (>90% DRFS at 8.5 years) were identified by the majority of signatures only within node-negative disease, and these tumors were mostly luminal A (78%-100%).

CONCLUSIONS

Most established genomic signatures were successful in outcome predictions in ER+ breast cancer and provided statistically independent information. From a clinical perspective, multiple signatures combined together most accurately predicted outcome, but a common finding was that each signature identified a subset of luminal A patients with node-negative disease who might be considered suitable candidates for adjuvant endocrine therapy alone.

S5-2: PAM50 HER2−Enriched Subtype Enriches for Tumor Response to Neoadjuvant Anthracyclines/Taxane and Trastuzumab/Taxane Containing Regimens in HER2−Positive Breast Cancer

Background: Patients with clinically HER2−positive (clinHer2+) tumors often receive trastuzumab in combination with chemotherapy as their standard of care. This study sought to determine the predictive value of the HER2−enriched (HER2−E) molecular subtype for sensitivity to neoadjuvant anthracycline/taxane containing chemotherapy and a trastuzumab plus taxane-based regimen within clinHer2+ disease.

Materials and methods: Gene expression data on pre-treatment fresh-frozen tumor tissues were collected from a combined cohort of MDACC/I-SPY trial (GSE25055/65), and the XeNA trial (GSE22358). Patients from MDACC/I-SPY were treated with doxorubicin/cyclophosphamide (AC) or 5-fluorouracil/epirubicin or doxorubicin/C (FEC or FAC) sequentially with paclitaxel. All patients from XeNA received capecitabine/docetaxel (and trastuzumab if clinHer2+). Intrinsic subtypes were determined using PAM50. Chisquare test and multivariable logistic regression analysis were used to test significance of association between subtype and pathological complete response (pCR or residual cancer burden [RCB] 0/1) and residual disease (RD or RCB2/3) adjusted with pre-treatment tumor size. Kaplan Meier was used for distant relapse-free survival (DRFS) estimates.

Results: For the MDACC/I-SPY cohort (n=595), pCR rates for intrinsic subtypes were 3% (5/168) for LumA, 16% (14/90) for LumB, 33% (23/69) for HER2−E and 37% (76/208) for Basal-like. Tumors achieving RCB0/1 were significantly associated with better DFRS compared to those tumors with RCB 2/3, even within each intrinsic subtype. The 5-year DFRS for HER2−E with RCB0/1 and RCB2/3 was 100% and 31% (p=0.007), respectively. ClinHer2+ status was also significantly associated with pCR (34% vs. 19%, p=0.016). Strikingly, among the clinHer2+ tumors (n=47), 75% (12/16) of the responders were classified as HER2−E (Table 1A) and those tumors that were clinHer2+/HER2−E had 6 times odds to achieve pCR when compared to clinHer2+/non-HER2−E. In the XeNA trial (n=122), the HER2−E subtype was significantly associated with response, composing 85% (7/8) of the clinHer2+ who achieved a pCR. Finally, clinHer2+/HER2−E tumors were 34 times more likely to achieve pCR than clinHer2+/non-HER2−E tumors (Table1B).

Genomic predictors of response to doxorubicin versus docetaxel in primary breast cancer

Taxanes and anthracyclines improve the outcome of early breast cancer, although the benefit is limited to a small proportion of patients and are toxic. We prospectively looked for predictors of response to these drugs.

EXPERIMENTAL DESIGN

Four cycles of doxorubicin (75 mg/m²) or docetaxel (100 mg/m²) were compared as presurgical chemotherapy for breast cancer. Biomarkers were determined by immunohistochemistry and fluorescent in situ hybridization using prechemotherapy core biopsies. Tumors were also classified into one of the molecular intrinsic subtypes using an immunohistochemical panel of five biomarkers and genomic profiles. Single genes and intrinsic subtypes were correlated with response to doxorubicin versus docetaxel. Among the 204 evaluable patients, significant predictors of sensitivity in multivariate analysis were low topo2a expression and ER-negative status for doxorubicin and small tumor size and ER-negative status for docetaxel. Predictors of resistance in multivariate analysis were triple-negative status (ER/PgR/HER2 negative by IHC/FISH) for doxorubicin, and high TNM stage for docetaxel. Triple-negative tumors were associated with topo2a overexpression more than the other subtypes. In 94 patients with gene expression profiles, docetaxel was superior to doxorubicin in the basal-like subtype (good pathological response rate - PCR + class I of 56 vs. 0%; P = 0.034); no significant differences were observed in the other subtypes when comparing these two drugs. Low topo2a expression and ER-negative status were predictors of response to doxorubicin, while small tumor size and ER-negative status predicted response to docetaxel. Docetaxel was superior to doxorubicin in triple-negative/basal-like tumors, while no significant differences were seen in the remaining intrinsic subtypes.

Abstract PD07-09: Hypoxia (VEGF-S) Signature and CRYAB Predict Response to Neoadjuvant Anthracycline/Taxane Containing Chemotherapy within Triple Negative and Unselected Breast Tumors

Background: Aggressive breast tumors are a clinically challenge to manage. A VEGF-signature (VEGF-s) developed in vivo (Hu et al. BMC Med. 09) and the profile of the anti-apoptotic gene and regulator of tumor angiogenesis, CRYAB (Moyano et al. J Clin Invest 06; Dimberg et al. Blood 08), are both associated with distant metastasis. In this study, we sought to test if these two mechanistically related biomarkers predict pathological complete response(pCR) to anthracyline/taxane-based neoadjuvant chemotherapy.

Methods: Gene expression data of pre-treatment fresh frozen tumors were combined, 149 from the ISPY trial (Agilent 44K) and 225 from MD Anderson Cancer Center(MDACC) (Affymetrix HG U133A). Patients from I-SPY were treated with doxorubicin/cyclophosphamide followed by a taxane. Patients from MDACC were treated with paclitaxel followed by sequential fluorouracil-AC. Tumors were classified into intrinsic subtypes using PAM50(Parker et al. J Clin Oncol 09) and Claudin-low(CL) predictor(Prat et al., Submitted). Odds ratios of biomarkers to pCR were determined using logistic regression. Predictive values of multivariable models were estimated using receiver operating characteristic curve. Results: 319 patients had complete data; the pCR rate was similar between the datasets (ISPY 22%, MDACC 20%). Both the VEGF-s and CRYAB were highly expressed within Basal-like(BL) and CL (P&lt;0.0001); these two biomarkers were positively correlated with each other (r: 0.4, P&lt;0.001). In univariate analysis, both VEGF-s (P&lt;0.001) and CRYAB (P&lt;0.001) were significantly associated with pCR. A multivariable test including tumor size, grade, ER, Her2, intrinsic subtypes, VEGF-s and CRYAB, had an AUC value of 0.86 to predict pCR(Table 1). T stage, Her2, intrinsic subtypes and CRYABwere significant.

82 patients with triple-negative tumors within this combined cohort. In univariate analysis, T stage, grade or classifying tumors into BL vs not did not predict pCR; but VEGF-s (p= 0.04) and CRYAB (p = 0.02) were associated with pCR. Multivariable model, including VEGF-s, CRYAB and the clinical variables, had a predictive value of 0.71 to pCR(Table 1), which identified CRYAB as the most significant factor by likelihood ratio test.

Table 1: Multivariable logistic regression models to predict pCR.

Conclusion: VEGF-s and CRYAB expression are associated with aggressive subtypes and may possibly help to predict response of anthracycline/taxane-based neoadjuvant chemotherapy beyond ER, Her2, and intrinsic subtypes.