Global Ring Study to Investigate the Comparability of Total Assay Performance of Commercial Claudin 18 Antibodies for Evaluation in Gastric Cancer

Claudin 18.2 (CLDN18.2), the dominant isoform of CLDN18 in gastric tissues, is a highly specific tight junction protein of the gastric mucosa with variably retained expressions in gastric and gastroesophageal junction cancers. Additionally, CLDN18.2-targeted treatment with zolbetuximab, in combination with chemotherapy, has recently been assessed in 2 phase-III studies of patients with HER2-negative, locally advanced, unresectable, or metastatic gastric or gastroesophageal junction adenocarcinoma. These trials used the investigational VENTANA CLDN18 (43-14A) RxDx immunohistochemistry (IHC) assay on the Ventana BenchMark platform to identify patients eligible for CLDN18.2-targeted treatment. We report the findings of a global ring study evaluating the analytical comparability of concordance of the results of 3 CLDN18 antibodies (Ventana, LSBio, and Novus) stained on 3 IHC-staining platforms (Ventana, Dako, and Leica). A tissue microarray (TMA), comprising 15 gastric cancer cases, was stained by 27 laboratories across 11 countries. Each laboratory stained the TMAs using at least 2 of the 3 evaluated CLDN18 antibodies. Stained TMAs were assessed and scored using an agreed IHC-scoring algorithm, and the results were collated for statistical analysis. The data confirmed a high level of concordance for the VENTANA CLDN18 (43-14A; Ventana platform only) and LSBio antibodies on both the Dako and Leica platforms, with accuracy, precision, sensitivity, and specificity rates all reaching a minimum acceptable ≥85% threshold and good-to-excellent levels of concordance as measured by Cohen's kappa coefficient. The Novus antibody showed the highest level of variability against the reference central laboratory results for the same antibody/platform combinations. It also failed to meet the threshold for accuracy and sensitivity when used on either the Dako or Leica platform. These results demonstrated the reliability of IHC testing for CLDN18 expression in gastric tumor samples when using commercially available platforms with an appropriate methodology and primary antibody selection.

Clinico-pathologic relationships with Ki67 and its change with short-term aromatase inhibitor treatment in primary ER + breast cancer: further results from the POETIC trial (CRUK/07/015)

PURPOSE

Ki67 assessed at diagnosis (Ki67baseline) is an important prognostic factor in primary oestrogen receptor-positive (ER +) breast cancer. Proportional change in Ki67 after 2 weeks (∆Ki672week) is associated with clinical benefit from endocrine therapies and residual Ki67 (Ki672week) with recurrence-free survival. The aim was to define the association between Ki67baseline and after aromatase inhibitor (AI) exposure ∆Ki672week and Ki672week with key prognostic and biologic factors utilising data from the POETIC study.

PATIENTS AND METHODS

In POETIC 4480 postmenopausal patients with primary ER and/or PgR + breast cancer were randomised 2:1 to 2 weeks' presurgical AI (anastrozole or letrozole) or no presurgical treatment (control). Ki67 was measured centrally in core-cut biopsies taken prior to AI and in core-cuts or the excision biopsy at surgery. Relationships between the Ki67 and biologic factors were explored using linear regression.

RESULTS

Established associations of Ki67baseline with biologic factors including PgR status, tumour grade, tumour size, histological subtype, nodal status, and vascular invasion were confirmed in the HER2- subpopulation. In the HER2 + subpopulation only grade and tumour size were significantly associated with Ki67baseline. In control group Ki672week was 18% lower than Ki67baseline (p < 0.001) when Ki672week was measured in excision biopsies but not when measured in core-cuts. Median suppression by AIs (∆Ki672week) was 79.3% (IQR: -89.9 to -54.6) and 53.7% (IQR: -78.9 to -21.1) for HER2-negative and HER2-positive cases, respectively. Significantly less suppression occurred in PgR- vs PgR + and HER2 + vs HER2- tumours which remained apparent after adjustment for 2-week sample type.

CONCLUSIONS

The magnitude of this study allowed characterisation of relationships between Ki67baseline, ∆Ki672week and Ki672week with high degrees of confidence providing a reference source for other studies. Lower values of Ki67 occur when measured on excision biopsies and could lead to apparent but artefactual decreases in Ki67: this should be considered when either ∆Ki672week or Ki672week is used in routine clinical practice to aid treatment decisions or in clinical trials assessing new drug therapies.

Systematically higher Ki67 scores on core biopsy samples compared to corresponding resection specimen in breast cancer: a multi-operator and multi-institutional study

Ki67 has potential clinical importance in breast cancer but has yet to see broad acceptance due to inter-laboratory variability. Here we tested an open source and calibrated automated digital image analysis (DIA) platform to: (i) investigate the comparability of Ki67 measurement across corresponding core biopsy and resection specimen cases, and (ii) assess section to section differences in Ki67 scoring. Two sets of 60 previously stained slides containing 30 core-cut biopsy and 30 corresponding resection specimens from 30 estrogen receptor-positive breast cancer patients were sent to 17 participating labs for automated assessment of average Ki67 expression. The blocks were centrally cut and immunohistochemically (IHC) stained for Ki67 (MIB-1 antibody). The QuPath platform was used to evaluate tumoral Ki67 expression. Calibration of the DIA method was performed as in published studies. A guideline for building an automated Ki67 scoring algorithm was sent to participating labs. Very high correlation and no systematic error (p = 0.08) was found between consecutive Ki67 IHC sections. Ki67 scores were higher for core biopsy slides compared to paired whole sections from resections (p ≤ 0.001; median difference: 5.31%). The systematic discrepancy between core biopsy and corresponding whole sections was likely due to pre-analytical factors (tissue handling, fixation). Therefore, Ki67 IHC should be tested on core biopsy samples to best reflect the biological status of the tumor.

Analysis of secondary pharmacology assays received by the US Food and Drug Administration

Secondary pharmacology studies are a time-efficient and cost-effective method for determining the safety profile of a potential new drug before it enters human trials. The results of these multi-target screens are commonly submitted with Investigational New Drug (IND) applications, but there currently is little guidance on how such information is presented and which targets are chosen for testing. In this study, we expand on our previous analysis of secondary pharmacology reports by manually curating and analyzing all secondary pharmacology results received by the FDA received as part of an IND submission. A total of 1120 INDs submitted by 480 sponsors between 1999 and October 2020 were included in this study. The overall results were largely consistent with previous internal and external studies, showing that the most tested target in our set was the histamine 1 receptor (tested 938 times), the most hit target was sodium channel site 2 (hit 141 times), and the target with the highest hit percentage was the vesicular monoamine transporter 2 (hit 42.2% of the time). Additionally, this study demonstrated that improvements in the secondary pharmacology submission process, such as changes in formatting and nomenclature, could enhance the utility of these assays for regulatory review, including assisting with identifying the safety liabilities of a drug candidate early in development. This updated data set will allow FDA-industry collaborative working groups to continue developing the best methods for regulatory submission of secondary pharmacology data and evaluate the need for a standard target panel.

Cost-Effectiveness of PD-L1 Testing in Non-Small Cell Lung Cancer (NSCLC) Using In Vitro Diagnostic (IVD) Versus Laboratory-Developed Test (LDT)

INTRODUCTION

Accurate PD-L1 testing for non-small cell lung cancer (NSCLC) maximizes the benefits of immune checkpoint inhibitor (ICI) drugs like pembrolizumab. False negative test results deny ICI treatments to eligible patients, worsening clinical and economic outcomes, while false positives increase costs by using ICI treatments without their benefits. This study evaluates the cost-effectiveness of PD-L1 testing with an in vitro diagnostic (IVD) compared to a laboratory-developed test (LDT) for allocating patients with NSCLC to treatment with either pembrolizumab or chemotherapy using the German healthcare system as a model.

METHODS

We developed a decision analytical model to evaluate the cost-effectiveness of PD-L1 testing with a regulatory body approved IVD compared to an LDT from the national German healthcare payer (statutory health insurance system) perspective. Accuracy of PD-L1 testing was based on data from two independent proficiency testing programs. The 1-year model was based on outcomes data from the KEYNOTE-024 clinical trial and treatment patterns reflecting current German practices.

RESULTS

IVDs produced accurate PD-L1 testing results in 93% (752/811) of tested cases compared to 73% (492/672) with LDTs. Most misclassifications concerned false negatives, occurring in 21% of LDTs vs 7% of IVDs. Total costs of the IVD group (48,878 €) were 196 € higher than the LDT group (48,682 €). These costs incorporate testing, first- and second-line therapy, managing treatment-related grade 3+ adverse events (AEs), and end-of-life costs for those who died within the year. Total effectiveness (percentage of patients successfully diagnosed and prescribed the correct therapy per German treatment guidelines) was 19 percentage points higher for the IVD group (88%) compared to the LDT group (69%). These differences in costs and effects lead to an incremental cost-effectiveness ratio (ICER) of 1057 €.

CONCLUSION

Compared to LDT technology, on-label IVD use for PD-L1 testing is only slightly more costly and substantially more effective for aligning patients with PD-L1-positive NSCLC with ICI therapy according to German practice guidelines. Given these findings, changes to testing and reimbursement policies may be considered to maximize patient outcomes in NSCLC.

Abstract P4-05-01: Results from the first UK NEQAS ICC & ISH external quality assessment for Ki-67 demonstration in breast cancer

AIMS: We previously described use of digital image analysis (DIA) to improve objectivity and reproducibility in external quality assessment (EQA) for immunocytochemical (ICC) staining in pathology [1]. Here we extend the work and report on: (1) use in EQA of the proliferation marker, Ki-67 in breast cancer, (2) use of a commercial prototype cell-line microarray (CLMA). MATERIALS AND METHODS: 34 laboratories stained slides provided by UK NEQAS using their routine ICC methods and returned them for central review and analysis. Slides were provided in duplicate; 29 laboratories returned both and 5 one slide (N = 63). Centrally performed DIA used the Cognition Master Professional Suite (CogM, VMscope GmbH) to quantify Ki67 labelling index (LI) [2]. Qualitative assessment aimed to separate submissions that were not useful from those which could be reported. This followed UK NEQAS standard methods. Materials assessed comprised two different breast cancer samples and a Ki-67 CLMA (Karpas Prototype, Array Science). RESULTS: Descriptive statistics on Ki-67 scores for each sample are presented in Table 1.

Analysis of individual sample types for difference in Ki-67 expression associated with primary antibody showed the following: mean Ki-67 LI on breast cancer A had a range of 13.6% (K2, Leica Biosystems) to 17.6% (30-9, Ventana Medical Systems), but no significant difference was found for any primary antibody clone. For breast cancer sample B, the range was 2.0% (MIB-1, Dako Agilent) to 3.2% (30-9), and the difference was significant at P&lt;0.05. In contrast, the CLMA showed no significant difference in expression for either MIB-1 or 30-9 (K2 could not be reported).The Ki-67-positive Karpas cell line in the CLMA had a small nuclear size compared to that of ‘standard’ breast cancer, which led to undercalling by CogM and potentially other DIA software; it also demonstrated a restricted dynamic range of high staining intensity, which reduced its ability to demonstrate differential staining in response to methodological variations.When assessed qualitatively 11.1% of submissions were not reportable (fail), 12.7% were sub-optimal but were scoreable (borderline), 23.8% had minor defects (adequate) and 52.4% were optimally stained (good). For both breast cancer samples, but not for the CLMA these qualitative categories were associated with increasing Ki-67 LI scores. For breast cancer A the mean Ki-67 LI score for the non-reportable group was significantly different from all other categories, which were not significantly different from each other; for breast cancer B, significant differences were seen between the non-reportable group and the adequate and good groups only (all at P&lt;0.05). CONCLUSIONS: Centrally performed DIA of Ki-67 LI on breast cancer tissue samples produces additional information that allows the identification of statistically significant differences between primary antibodies (MIB-1 and 30-9). It also validates qualitative assessment by demonstrating significant differences between qualitative categories and is likely to be useful to identify lab-specific differences in staining performance in future rounds of EQA.The prototype CLMA produced using the Karpas cell-line did not demonstrate statistically significant differences between primary antibody clones or qualitative categories and is not a useful tool for use in EQA.REFERENCES: 1. Warrick N, et al. UK IBCS 2020. Breast Cancer Res Treat 180, 527-596 (2020)2. http://vmscope.com/index

BC_ABC_BCLMA_0%CLMA_5%CLMA_10%CLMA_20%CLMA_30%Number of values124125164165110165165Minimum0.30.00.00.01.93.30.025% Percentile11.31.00.01.74.07.613.5Median15.22.20.02.35.09.416.375% Percentile20.03.50.23.26.111.519.8Maximum32.212.112.09.111.721.335.995% CI of medianActual confidence level96.2%95.1%96.5%95.7%95.5%95.7%95.7%Lower confidence limit14.01.80.02.04.99.115.5Upper confidence limit16.62.60.02.65.59.817.1Mean15.72.50.42.65.510.017.1Std. Deviation6.52.11.71.42.23.35.7Std. Error of Mean0.60.20.10.10.20.30.4Lower 95% CI of mean14.52.20.22.45.09.516.2Upper 95% CI of mean16.82.90.72.85.910.518.0

Citation Format: Andrew Dodson, Dawn Wilkinson, Mitch Dowsett, Suzanne Parry. Results from the first UK NEQAS ICC & ISH external quality assessment for Ki-67 demonstration in breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P4-05-01.

Biomarkers of Response and Resistance to Palbociclib Plus Letrozole in Patients With ER+/HER2- Breast Cancer

PURPOSE

To determine (i) the relationship between candidate biomarkers of the antiproliferative (Ki67) response to letrozole and palbociclib alone and combined in ER⁺/HER2^- breast cancer; and (ii) the pharmacodynamic effect of the agents on the biomarkers.

EXPERIMENTAL DESIGN

307 postmenopausal women with ER⁺/HER2^- primary breast cancer were randomly assigned to neoadjuvant treatment with letrozole for 14 weeks; letrozole for 2 weeks, then letrozole+palbociclib to 14 weeks; palbociclib for 2 weeks, then letrozole+palbociclib to 14 weeks; or letrozole+palbociclib for 14 weeks. Biopsies were taken at baseline, 2 and 14 weeks and surgery at varying times after stopping palbociclib. Immunohistochemical analyses were conducted for Ki67, c-PARP, ER, PgR, RB1, CCNE1, and CCND1.

RESULTS

Higher baselines ER and PgR were significantly associated with a greater chance of complete cell-cycle arrest (CCCA: Ki67 <2.7%) at 14 weeks and higher baseline Ki67, c-PARP, and CCNE1 with a lower chance. The interaction with treatment was significant only for c-PARP. CCND1 levels were decreased c.20% by letrozole at 2 and 14 weeks but showed a tendency to increase with palbociclib. CCNE1 levels fell 82% (median) in tumors showing CCCA but were unchanged in those with no CCCA. Only 2/9 tumors showed CCCA 3-9 days after stopping palbociclib. ESR1 mutations were found in 2/4 tumors for which surgery took place ≥6 months after starting treatment.

CONCLUSIONS

High CCNE1 levels were confirmed as a biomarker of resistance to letrozole+palbociclib. Ki67 recovery within 3-9 days of discontinuing palbociclib indicates incomplete suppression of proliferation during the "off" week of its schedule.

Aggregation and analysis of secondary pharmacology data from investigational new drug submissions at the US Food and Drug Administration

Secondary pharmacology studies are utilized by the pharmaceutical industry as a cost-efficient tool to identify potential safety liabilities of drugs before entering Phase 1 clinical trials. These studies are recommended by the Food and Drug Administration (FDA) as a part of the Investigational New Drug (IND) application. However, despite the utility of these assays, there is little guidance on which targets should be screened and which format should be used. Here, we evaluated 226 secondary pharmacology profiles obtained from close to 90 unique sponsors. The results indicated that the most tested target in our set was the GABA benzodiazepine receptor (tested 168 times), the most hit target was adenosine 3 (hit 24 times), and the target with the highest hit percentage was the quinone reductase 2 (NQO2) receptor (hit 29% of the time). The overall results were largely consistent with those observed in previous publications. However, this study also identified the need for improvement in the submission process of secondary pharmacology studies by industry, which could enhance their utility for regulatory purpose. FDA-industry collaborative working groups will utilize this data to determine the best methods for regulatory submission of these studies and evaluate the need for a standard target panel.

A simple digital image analysis system for automated Ki67 assessment in primary breast cancer

AIMS

Ki67 is a well-established immunohistochemical marker associated with cell proliferation that has prognostic and predictive value in breast cancer. Quantitative evaluation of Ki67 is traditionally performed by assessing stained tissue slides with light microscopy. Automated image analysis systems have become available and, if validated, could provide greater standardisation and improved precision of Ki67 scoring. Here, we aimed to evaluate the use of the Cognition Master Professional Suite (CogM) image analysis software, which is a simple system for scoring Ki67 in primary breast cancer samples.

METHODS AND RESULTS

Sections from 94 core-cut biopsies, 20 excision specimens and 29 pairs of core-cut biopsies and excision specimens were stained for Ki67 with MIB1 antibody and the Dako EnVision FLEX Detection System. Stained slides were scanned to convert them to digital data. Computer-based Ki67 scoring was performed with CogM. Manual Ki67 scoring assessment was conducted on previously stained sections from the same biopsies with a clinically validated system that had been calibrated against the risk of recurrence. A high correlation between manual and digital scores was observed [r_Cores  = 0.92, 95% confidence interval (CI) 0.87-0.94, P < 0.0001; r_Excisions  = 0.95, 95% CI 0.86-0.98, P < 0.0001] and there was no significant bias between them (P = 0.45). There was also a high correlation of Ki67 scores between paired core-cut biopsies and excision specimens when CogM was used (r = 0.78, 95% CI 0.59-0.89, P < 0.0001).

CONCLUSIONS

CogM image analysis allows for standardised automated Ki67 scoring that accurately replicates previously clinically validated and calibrated manual scores.

The IHC4+C score: an affordable and reproducible non-molecular decision-aid in hormone receptor-positive breast cancer. Does it still hold value for patients in 2020?

AIM

The majority of women diagnosed with early breast cancer have hormone-receptor positive (HR+)/HER2-negative disease. Adjuvant endocrine therapy provides substantial risk reduction benefits in virtually all patients. The role of adjuvant chemotherapy in certain subsets of patients is equivocal. This paper sought to evaluate the role of the IHC4+C score to aid this clinical decision in addition to providing an overview of the current molecular and non- molecular tools available in the adjuvant setting.

METHODS

This prospective study included 53 post-operative HR+/HER2- negative early breast cancer patients selected from the multidiscipliniary team meeting between August 2017 and January 2020. IHC4+C testing was requested by clinicians for patients in whom the availability of the score may have impacted adjuvant decision-making. Adjuvant treatment decisions were recorded at three time points (prior and post IHC4+C scoring as well as the patient's final decision). The primary goal was the proportion of patients who were spared chemotherapy following the availability of IHC4+C scores to impact on clinicians' recommendations for adjuvant systemic therapy.

RESULTS

A total of 34 patients (64%) were initially recommended to undergo chemotherapy or to consider chemotherapy. With the availability of the IHC4+C score, only 17 patients (32%) underwent chemotherapy, demonstrating a substantial reduction in the frequency of chemotherapy prescribing.

CONCLUSION

This study demonstrates that when utilized appropriately in a multidisciplinary setting, the IHC4+C algorithm is an alternative, reproducible and affordable tool with a proven capacity to stratify risk and to spare a large proportion of patients from undergoing chemotherapy.

UK NEQAS ICC & ISH Ki-67 Data Reveal Differences in Performance of Primary Antibody Clones

We examined data from 374 laboratories staining for Ki-67 as part of external quality assessment over 8 runs between 2013 and 2017 (total data sets=2601). One of 5 primary antibodies was used for 94.8% of submissions, with MIB-1 (Agilent Dako) comprising 58.8% of the total. Examining assessment score as a continuous variable showed the 30-9 (Ventana) and K2 (Leica Biosystems) clones were associated with the highest mean scores (17.0; 95% confidence interval, 16.8-17.2 and 16.3; 95% confidence interval, 15.9-16.6, respectively). Stain quality was not significantly different between them. Both were associated with significantly better staining compared with MIB-1 (Agilent Dako), MM1 (Leica Biosystems), and SP6 from various suppliers (P<0.05). Similarly, categorical assessment of "Good" versus "Not good" staining quality showed that the 30-9 and K2 clones were both significantly associated with "Good" staining (both P<0.001). Other methodological parameters were examined for significant primary antibody-specific effects; none were seen for 30-9, K2, or SP6. The MM1 clone was more likely to be associated with good quality staining when it was used with Leica Biosystems sourced antigen retrieval, detection, and platform, all statistically significant at P<0.01. MIB-1 was more likely to be associated with good quality staining results when it was used with Agilent Dako antigen retrieval, detection, and staining platforms (P<0.0001), and less likely at the same significance level when used with Leica Biosystems reagents and equipment. The data presented here show the importance of not just primary antibody choice but also matching that choice to other methodological factors.

Assessment of Ki67 in Breast Cancer: Updated Recommendations From the International Ki67 in Breast Cancer Working Group

Ki67 immunohistochemistry (IHC), commonly used as a proliferation marker in breast cancer, has limited value for treatment decisions due to questionable analytical validity. The International Ki67 in Breast Cancer Working Group (IKWG) consensus meeting, held in October 2019, assessed the current evidence for Ki67 IHC analytical validity and clinical utility in breast cancer, including the series of scoring studies the IKWG conducted on centrally stained tissues. Consensus observations and recommendations are: 1) as for estrogen receptor and HER2 testing, preanalytical handling considerations are critical; 2) a standardized visual scoring method has been established and is recommended for adoption; 3) participation in and evaluation of quality assurance and quality control programs is recommended to maintain analytical validity; and 4) the IKWG accepted that Ki67 IHC as a prognostic marker in breast cancer has clinical validity but concluded that clinical utility is evident only for prognosis estimation in anatomically favorable estrogen receptor–positive and HER2-negative patients to identify those who do not need adjuvant chemotherapy. In this T1-2, N0-1 patient group, the IKWG consensus is that Ki67 5% or less, or 30% or more, can be used to estimate prognosis. In conclusion, analytical validity of Ki67 IHC can be reached with careful attention to preanalytical issues and calibrated standardized visual scoring. Currently, clinical utility of Ki67 IHC in breast cancer care remains limited to prognosis assessment in stage I or II breast cancer. Further development of automated scoring might help to overcome some current limitations.

Long-term outcome and prognostic value of Ki67 after perioperative endocrine therapy in postmenopausal women with hormone-sensitive early breast cancer (POETIC): an open-label, multicentre, parallel-group, randomised, phase 3 trial

Background

Preoperative and perioperative aromatase inhibitor (POAI) therapy has the potential to improve outcomes in women with operable oestrogen receptor-positive primary breast cancer. It has also been suggested that tumour Ki67 values after 2 weeks (Ki67_2W) of POAI predicts individual patient outcome better than baseline Ki67 (Ki67_B). The POETIC trial aimed to test these two hypotheses.

Methods

POETIC was an open-label, multicentre, parallel-group, randomised, phase 3 trial (done in 130 UK hospitals) in which postmenopausal women aged at least 50 years with WHO performance status 0–1 and hormone receptor-positive, operable breast cancer were randomly assigned (2:1) to POAI (letrozole 2·5 mg per day orally or anastrozole 1 mg per day orally) for 14 days before and following surgery or no POAI (control). Adjuvant treatment was given as per UK standard local practice. Randomisation was done centrally by computer-generated permuted block method (variable block size of six or nine) and was stratified by hospital. Treatment allocation was not masked. The primary endpoint was time to recurrence. A key second objective explored association between Ki67 (dichotomised at 10%) and disease outcomes. The primary analysis for clinical endpoints was by modified intention to treat (excluding patients who withdrew consent). For Ki67 biomarker association and endpoint analysis, the evaluable population included all randomly assigned patients who had paired Ki67 values available. This study is registered with ClinicalTrials.gov, NCT02338310; the European Clinical Trials database, EudraCT2007-003877-21; and the ISRCTN registry, ISRCTN63882543. Recruitment is complete and long-term follow-up is ongoing.

Findings

Between Oct 13, 2008, and April 16, 2014, 4480 women were recruited and randomly assigned to POAI (n=2976) or control (n=1504). On Feb 6, 2018, median follow-up was 62·9 months (IQR 58·1–74·1). 434 (10%) of 4480 women had a breast cancer recurrence (280 [9%] POAI; 154 [10%] control), hazard ratio 0·92 (95% CI 0·75–1·12); p=0·40 with the proportion free from breast cancer recurrence at 5 years of 91·0% (95% CI 89·9–92·0) for patients in the POAI group and 90·4% (88·7–91·9) in the control group. Within the POAI-treated HER2-negative subpopulation, 5-year recurrence risk in women with low Ki67_B and Ki67_2W (low–low) was 4·3% (95% CI 2·9–6·3), 8·4% (6·8–10·5) with high Ki67_B and low Ki67_2W (high–low) and 21·5% (17·1–27·0) with high Ki67_B and Ki67_2W (high–high). Within the POAI-treated HER2-positive subpopulation, 5-year recurrence risk in the low–low group was 10·1% (95% CI 3·2–31·3), 7·7% (3·4–17·5) in the high–low group, and 15·7% (10·1–24·4) in the high–high group. The most commonly reported grade 3 adverse events were hot flushes (20 [1%] of 2801 patients in the POAI group vs six [<1%] of 1400 in the control group) and musculoskeletal pain (29 [1%] vs 13 [1%]). No treatment-related deaths were reported.

Interpretation

POAI has not been shown to improve treatment outcome, but can be used without detriment to help select appropriate adjuvant therapy based on tumour Ki67. Most patients with low Ki67_B or low POAI-induced Ki67_2W do well with adjuvant standard endocrine therapy (giving consideration to clinical–pathological factors), whereas those whose POAI-induced Ki67_2W remains high might benefit from further adjuvant treatment or trials of new therapies.

Funding

Cancer Research UK.

Homologous recombination DNA repair deficiency and PARP inhibition activity in primary triple negative breast cancer

Triple negative breast cancer (TNBC) encompasses molecularly different subgroups, with a subgroup harboring evidence of defective homologous recombination (HR) DNA repair. Here, within a phase 2 window clinical trial, RIO trial (EudraCT 2014-003319-12), we investigate the activity of PARP inhibitors in 43 patients with untreated TNBC. The primary end point, decreased Ki67, occured in 12% of TNBC. In secondary end point analyses, HR deficiency was identified in 69% of TNBC with the mutational-signature-based HRDetect assay. Cancers with HRDetect mutational signatures of HR deficiency had a functional defect in HR, assessed by impaired RAD51 foci formation on end of treatment biopsy. Following rucaparib treatment there was no association of Ki67 change with HR deficiency. In contrast, early circulating tumor DNA dynamics identified activity of rucaparib, with end of treatment ctDNA levels suppressed by rucaparib in mutation-signature HR-deficient cancers. In ad hoc analysis, rucaparib induced expression of interferon response genes in HR-deficient cancers. The majority of TNBCs have a defect in DNA repair, identifiable by mutational signature analysis, that may be targetable with PARP inhibitors.

Abstract P5-02-01: Analytical validation and prognostic potential of an automated digital scoring protocol for Ki67: An International Ki67 Working Group study

Background: The nuclear proliferation biomarker Ki67 has multiple potential roles in breast cancer, including aiding decisions based on prognosis, but has unacceptable between-laboratory variability. Here we tested an open source and calibrated automated digital image analysis (DIA) platform to: (i) Assess inter-laboratory reproducibility of automated Ki67 measurement among 17 participating labs and compare those with standardized pathologist-based visual scoring. (ii) Investigate the comparability of Ki67 measurement across corresponding core biopsy and whole section cases. (iii) Test prognostic potential of the built Ki67 scoring algorithms on an independent cohort.

Methods: Two sets of 60 previously stained slides containing 30 core-cut biopsy and 30 corresponding whole tumor sections from 30 ER+ breast cancer cases were sent to 17 participating labs for automated assessment of average Ki67 expression. The blocks were centrally cut and stained for Ki67 using the Mib-1 antibody. The QuPath (open-source software) DIA platform was used to evaluate tumoral Ki67 expression. Calibration of the DIA method was performed in our previous study (Acs et al, Lab Invest 2019). A detailed guideline for building an automated Ki67 scoring algorithm was sent to the participating labs. Visual scoring of average Ki67 expression was performed by pathologists according to published standardized methods (Leung et al, NPJ Br Cancer 2016; Leung et al, Histopath 2019). Locked down DIA Ki67 scoring algorithms were applied to a validation cohort: 222 breast cancer cases from the Karolinska University Hospital in whole section format. Sufficient reproducibility to declare analytical validity was defined as an Intra Class Correlation (ICC) with lower limit of 95% credible interval (CI) &gt;0.80. Markov Chain Monte Carlo routines for generalized linear mixed models were used to estimate ICCs and calculate corresponding CIs.

Results: The same-section ICC was 0.902 (CI: 0.852-0.949) across 17 labs using calibrated DIA platform on core biopsy slides and 0.845 (CI: 0.778-0.912) on whole sections. The different-section ICC across the 17 labs was 0.873 (CI: 0.806-0.932) scoring on core biopsy slides and 0.777 (CI: 0.670-0.874) on whole sections. The pathologist-based visual Ki67 scoring showed ICC of 0.860 for all comparisons, respectively (CI: 0.795-0.927). Similar to what was observed for visual Ki67 scoring, the DIA scores are higher for core biopsy slides compared to paired whole sections (p≤0.001; median difference: 5.31%; IQR: 11.50%). Ki67 scores of all locked down DIA algorithms correlates significantly (p≤0.023) with outcome on the validation cohort (observed hazard ratios range: 2.518-2.922).

Conclusions: Automated Ki67 evaluation using a calibrated, open-source DIA platform (QuPath) met the pre-specified criterion of success on core biopsies but not on whole sections in the multi-institutional setting. The systematic discrepancy between core biopsy and corresponding whole sections was likely due to pre-analytical factors (tissue handling, fixation) and intratumor heterogeneity. We found that different algorithms built according to calibrated DIA methods had similar prognostic potential. Assessment of clinical utility is planned.

Citation Format: Balazs Acs, Samuel C.Y. Leung, Kelley M. Kidwell, Indu Arun, Renaldas Augulis, Sunil S. Badve, Yalai Bai, Anita L. Bane, John M.S. Bartlett, Jane Bayani, Gilbert Bigras, Annika Blank, Signe Borgquist, Henk Buikema, Martin C. Chang, Robin L. Dietz, Andrew Dodson, Anna Ehinger, Susan Fineberg, Cornelia M. Focke, Dongxia Gao, Allen M. Gown, Carolina Gutierrez, Johan Hartman, Judith C. Hugh, Zuzana Kos, Anne-Vibeke Lænkholm, Arvydas Laurinavicius, Richard M. Levenson, Rustin Mahboubi-Ardakani, Mauro G. Mastropasqua, Takuya Moriya, Sharon Nofech-Mozes, C. Kent Osborne, Liron Pantanowitz, Frédérique M. Penault-Llorca, Tammy Piper, Mary Anne Quintayo, Tilman T. Rau, Stefan Reinhard, Stephanie Robertson, Takashi Sakatani, Roberto Salgado, Melanie Spears, Jane Starczynski, Tomoharu Sugie, Bert van der Vegt, Giuseppe Viale, Shakeel Virk, Lila A. Zabaglo, Daniel F. Hayes, Mitch Dowsett, Torsten O. Nielsen, David L. Rimm, International Ki67 in Breast Cancer Working Group, BIG-NABCG. Analytical validation and prognostic potential of an automated digital scoring protocol for Ki67: An International Ki67 Working Group study [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P5-02-01.

Impact of aromatase inhibitor treatment on global gene expression and its association with antiproliferative response in ER+ breast cancer in postmenopausal patients

Background

Endocrine therapy reduces breast cancer mortality by 40%, but resistance remains a major clinical problem. In this study, we sought to investigate the impact of aromatase inhibitor (AI) therapy on gene expression and identify gene modules representing key biological pathways that relate to early AI therapy resistance.

Methods

Global gene expression was measured on pairs of core-cut biopsies taken at baseline and at surgery from 254 patients with ER-positive primary breast cancer randomised to receive 2-week presurgical AI (n = 198) or no presurgical treatment (control n = 56) from the POETIC trial. Data from the AI group was adjusted to eliminate artefactual process-related changes identified in the control group. The response was assessed by changes in the proliferation marker, Ki67.

Results

High baseline ESR1 expression associated with better AI response in HER2+ tumours but not HER2− tumours. In HER2− tumours, baseline expression of 48 genes associated with poor antiproliferative response (p < 0.005) including PERP and YWHAQ, the two most significant, and the transcription co-regulators (SAP130, HDAC4, and NCOA7) which were among the top 16 most significant. Baseline gene signature scores measuring cell proliferation, growth factor signalling (ERBB2-GS, RET/GDNF-GS, and IGF-1-GS), and immune activity (STAT1-GS) were significantly higher in poor AI responders. Two weeks of AI caused downregulation of genes involved in cell proliferation and ER signalling, as expected. Signature scores of E2F activation and TP53 dysfunction after 2-week AI were associated with poor AI response in both HER2− and HER2+ patients.

Conclusions

There is a high degree of heterogeneity in adaptive mechanisms after as little as 2-week AI therapy; however, all appear to converge on cell cycle regulation. Our data support the evaluation of whether an E2F signatures after short-term exposure to AI may identify those patients most likely to benefit from the early addition of CDK4/6 inhibitors.

Trial registration

ISRCTN, ISRCTN63882543, registered on 18 December 2007.

External quality assessment demonstrates that PD-L1 22C3 and SP263 assays are systematically different

PD‐L1 inhibitors are part of first line treatment options for patients with advanced non‐small cell lung cancer. PD‐L1 immunohistochemistry (IHC) assays act as either a companion or a complementary diagnostic. The purpose of this study is to describe the experience of external quality assurance (EQA) provider UK NEQAS ICC and ISH with the comparison of different PD‐L1 assays used in daily practice. Three EQA rounds (pilot, run A and run B) were carried out using formalin fixed paraffin embedded samples with sample sets covering a range of epitope concentrations, including ‘critical samples’ near to clinical threshold cut‐offs. An expert panel (n = 4) evaluated all returned slides simultaneously and independently on a multi‐header microscope together with the participants own in‐house control material. The tonsil sample was evaluated as ‘acceptable’ or ‘unacceptable’, and for the other samples the percentage of PD‐L1 stained tumour cells were estimated in predetermined categories (<1%, 1 to <5%, 5 to <10%, 10 to <25%, 25 to <50%, 50 to <80%, 80 to 100%). In the pilot and the two subsequent runs the number of participating laboratories was 43, 69 and 76, respectively. The pass rate for the pilot run was 67%; this increased to 81% at run A and 82% at run B. For two ‘critical samples’, in runs A and B, 22C3 IHC had significantly higher PD‐L1 expression than SP263 IHC (p < 0.001), whilst the PD‐L1 scores for the other six samples were similar for all assays. In run A the laboratory developed tests (LDTs) using 22C3 scored lower than the commercial 22C3 tests (p = 0.01). After the initial testing, improvement in performance of PD‐L1 IHC is shown for approved and LDT PD‐L1 assays. Equivalency of approved PD‐L1 22C3 and SP263 assays cannot be assumed as the scores cross the clinically relevant thresholds of 1% and 50% PD‐L1 expression.

Early Enrichment of ESR1 Mutations and the Impact on Gene Expression in Presurgical Primary Breast Cancer Treated with Aromatase Inhibitors

PURPOSE

To investigate the presence of ESR1 mutations in primary estrogen-receptor-positive (ER+) breast cancer treated with extended (>4 weeks) neoadjuvant (presurgical) aromatase inhibitor (NAI) therapy and to identify patients who may gain less benefit from aromatase inhibition (AI) alone based upon on-treatment changes in gene expression.

EXPERIMENTAL DESIGN

We evaluated ER, progesterone receptor, and Ki67 by immunostaining, ESR1 mutations by droplet-digital PCR and expression of over 800 key breast cancer genes in paired pre- and post-NAI tumor samples from 87 ER+ breast cancer patients.

RESULTS

Cell proliferation and estrogen-regulated genes (ERG) remained suppressed in most tumors indicative of persistent response to NAI. Enrichment of ESR1 mutations was found in five tumors and predominantly in patients receiving therapy for >6 months. ESR1-mutant tumors showed increased expression of ESR1 transcript and limited suppression of ERGs and proliferation-associated genes in response to NAI. ESR1 wild-type tumors with high residual proliferation (Ki67r ≥10%; 15/87 tumors) showed lower ESR1/ER expression pre- and post-therapy and lower ERGs. Tumors with ESR1 mutations or Ki67r ≥10% showed less inhibition of estrogen response, cell cycle, and E2F-target genes.

CONCLUSIONS

Ligand-independent ER signaling, as a result of ESR1 mutation or reduced ER dependence, identified after extended NAI therapy, can guide early selection of patients who would benefit from combination therapy.

Combination of mTORC1/2 inhibitor vistusertib plus fulvestrant in vitro and in vivo targets oestrogen receptor-positive endocrine-resistant breast cancer

Background

Endocrine therapies are still the main strategy for the treatment of oestrogen receptor-positive (ER+) breast cancers (BC), but resistance remains problematic. Cross-talk between ER and PI3K/AKT/mTORC has been associated with ligand-independent transcription of ER. We have previously reported the anti-proliferative effects of the combination of everolimus (an mTORC1 inhibitor) with endocrine therapy in resistance models, but potential routes of escape via AKT signalling can lead to resistance; therefore, the use of dual mTORC1/2 inhibitors has met with significant interest.

Methods

To address this, we tested the effect of vistusertib, a dual mTORC1 and mTORC2 inhibitor, in a panel of endocrine-resistant and endocrine-sensitive ER+ BC cell lines, with varying PTEN, PIK3CA and ESR1 mutation status. End-points included proliferation, cell signalling, cell cycle and effect on ER-mediated transcription. Two patient-derived xenografts (PDX) modelling endocrine resistance were used to assess the efficacy of vistusertib, fulvestrant or the combination on tumour progression, and biomarker studies were conducted using immunohistochemistry and RNA-seq technologies.

Results

Vistusertib caused a dose-dependent decrease in proliferation of all the cell lines tested and reduced abundance of mTORC1, mTORC2 and cell cycle markers, but caused an increase in abundance of EGFR, IGF1R and ERBB3 in a context-dependent manner. ER-mediated transcription showed minimal effect of vistusertib. Combined therapy of vistusertib with fulvestrant showed synergy in two ER+ PDX models of resistance to endocrine therapy and delayed tumour progression after cessation of therapy.

Conclusions

These data support the notion that models of acquired endocrine resistance may have a different sensitivity to mTOR inhibitor/endocrine therapy combinations.

Analytical validation of a standardised scoring protocol for Ki67 immunohistochemistry on breast cancer excision whole sections: an international multicentre collaboration

AIMS

The nuclear proliferation marker Ki67 assayed by immunohistochemistry has multiple potential uses in breast cancer, but an unacceptable level of interlaboratory variability has hampered its clinical utility. The International Ki67 in Breast Cancer Working Group has undertaken a systematic programme to determine whether Ki67 measurement can be analytically validated and standardised among laboratories. This study addresses whether acceptable scoring reproducibility can be achieved on excision whole sections.

METHODS AND RESULTS

Adjacent sections from 30 primary ER⁺ breast cancers were centrally stained for Ki67 and sections were circulated among 23 pathologists in 12 countries. All pathologists scored Ki67 by two methods: (i) global: four fields of 100 tumour cells each were selected to reflect observed heterogeneity in nuclear staining; (ii) hot-spot: the field with highest apparent Ki67 index was selected and up to 500 cells scored. The intraclass correlation coefficient (ICC) for the global method [confidence interval (CI) = 0.87; 95% CI = 0.799-0.93] marginally met the prespecified success criterion (lower 95% CI ≥ 0.8), while the ICC for the hot-spot method (0.83; 95% CI = 0.74-0.90) did not. Visually, interobserver concordance in location of selected hot-spots varies between cases. The median times for scoring were 9 and 6 min for global and hot-spot methods, respectively.

CONCLUSIONS

The global scoring method demonstrates adequate reproducibility to warrant next steps towards evaluation for technical and clinical validity in appropriate cohorts of cases. The time taken for scoring by either method is practical using counting software we are making publicly available. Establishment of external quality assessment schemes is likely to improve the reproducibility between laboratories further.

Comparison of protein expression between formalin-fixed core-cut biopsies and surgical excision specimens using a novel multiplex approach

PURPOSE

We evaluated whether multiplex protein quantification using antibody bar-coding with photocleavable oligonucleotides (NanoString) can be applied to evaluate protein expression in breast cancer FFPE specimens. We also assessed whether diagnostic core-cuts fixed immediately at time of procedures and surgical excision sections from routinely fixed breast cancers are affected by the same fixation related differences noted using immunohistochemistry (IHC).

METHODS

The expression of 26 proteins was analysed using NanoString technology in 16 pairs of FFPE breast cancer core-cuts and surgical excisions. The measurements yielded were compared with those by IHC on Ki67, PgR and HER2 biomarkers and pAKT and pERK1/2 phosphorylated proteins.

RESULTS

When considered irrespective of sample type, expression measured by the two methods was strongly correlated for all markers (p < 0.001; ρ = 0.69-0.88). When core-cuts and excisions were evaluated separately, the correlations between NanoString and IHC were weaker but significant except for pAKT in excisions. Surgical excisions showed lower levels of 8/12 phosphoproteins and higher levels of 4/13 non-phosphorylated proteins in comparison to core-cuts (p < 0.01). Reduced p4EBP1, pAMPKa, pRPS6 and pRAF1 immunogenicity in excisions was correlated with tumour size and mastectomy specimens showed lower p4EBP1 and pRPS6 expression than lumpectomy (p < 0.05).

CONCLUSIONS

Our study supports the validity of the new multiplex approach to protein analysis but indicates that, as with IHC, caution is necessary for the analysis in excisions particularly of phosphoproteins. The specimen type, tumour size and surgery type may lead to biases in the quantitative analysis of many proteins of biologic and clinical interest in excision specimens.

PIPA: A phase Ib study of β-isoform sparing phosphatidylinositol 3-kinase (PI3K) inhibitor taselisib (T) plus palbociclib (P) and fulvestrant (FUL) in PIK3CA-mutant (mt) ER-positive and taselisib (T) plus palbociclib (P) in PIK3CA-mutant (mt) ER-negative advanced breast cancer

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Background: PI3K and CDK4/6 inhibitors synergise in ER+ve and –ve PIK3CA-mt breast cancer (BC) models. Escalation phase of this study set recommended phase 2 dose (RP2D) at P 125mg on a 3/1 scheme plus T 2mg daily ( Lim, ASCO 2017). Here we present the results of expansion cohorts for PIK3CA-mt BC patients (pts). Methods: The primary objective was to assess the confirmed objective response rate (ORR) of the P + T + FUL triplet in pts with measurable PIK3CA-mt ER+ve HER2-ve advanced BC, with up to two prior lines of chemotherapy for advanced disease. PIK3CA mutation was assessed in tissue or plasma DNA analysis. Exploratory objectives included assessment of efficacy of P + T in a cohort of pts with PIK3CA-mt advanced ER-ve BC. Safety is reported overall for 44 patients including an additional cohort of 7 PIK3CA-unknown ER+ve BC pts treated with P + T + letrozole (LET). For the P + T + FUL triplet a Simon minmax design was used, with 6 responses in 25 patients required to declare efficacy. Results: We recruited 24 assessable patients with PIK3CA-mt ER+ve HER2-ve advanced BC, median age 57 (42-74), median 3 (1-9) prior therapy lines for advance disease, with 24 (100%) receiving prior endocrine therapy and 23 (96%) prior aromatase inhibitor. ORR was 33% (8/24, 95% CI 16-55%), with median progression free survival (PFS) 7.9m (95% CI 5.6-11.8). For the 11 assessable PIK3CA-mt ER-ve pts (8 HER2-ve, 3 HER2+ve) receiving P + T, ORR was 0% (0/11), clinical benefit rate (CBR) 27% (3/11) and median PFS 4.3m (95% CI 1.8-6.1). Most common AEs across all cohorts were neutropenia (80%), fatigue (50%), mucositis (50%) and thrombocytopenia (30%). Most common grade 3/4 AEs were neutropenia (57%) and rash (11%). Translational research is ongoing. Conclusions: The triplet of P + T + FUL has promising efficacy in pre-treated PIK3CA-mt ER+ve advanced BC. A subset of patients with PIK3CA-mt ER-ve advanced BC had clinical benefit from P + T. The combination of P + T +/- FUL/LET was well tolerated with anticipated AEs. Clinical trial information: NCT02389842.

Biomarker analysis of PALLET: A neoadjuvant trial of letrozole (L) ± palbociclib (P)

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Background: PALLET randomized 307 postmenopausal women with ER+ primary breast cancer to one of 4 treatment groups (3:2:2:2 ratio): A: L for 14wks; B: L for 2wks then L+P to 14wks; C: P for 2wks then L+P to 14wks; D: L+P for 14wks. This allowed a randomized 1:2 comparison of L (Group A) vs L+P (Groups B+C+D) at 14wks. P was given 125mg/d PO (21 days on, 7 days off). Adding P to L markedly enhanced Ki67 suppression and Complete Cell Cycle Arrest (CCCA, Ki67 < 2.7%) by 14wks but did not substantially increase clinical response. We now report exploratory analysis of the association of baseline expression of 6 pre-specified biomarkers involved in estrogen and CDK4/6 signaling with CCCA at 14wks and changes in their expression during therapy. Methods: Estrogen receptor (ER), progesterone receptor (PgR), RB and CCNE1 were measured by IHC and CCND1 by IHC and FISH (CCND1/CEP11 ratio≥2.0 amplified). Baseline biomarker values were available with 14wk Ki67 values in up to 64 patients for L alone and up to 124 patients for L+P. Of these 59% and 90%, respectively, achieved CCCA. Results: With L alone CCCA was significantly less frequent (indicating relative resistance) with low baseline PgR (odds ratio [OR] 0.22, 95%CI 0.05-0.96, p = 0.04) or high CCNE1 levels (OR 10.39, 95%CI 1.19-90.48, p = 0.03). With L+P CCCA was also significantly less frequent with high CCNE1 (OR 50.34 95%CI 5.12-495.34, p = 0.001) or with low baseline ER (OR 0.21 95%CI 0.08-0.60, p = 0.004). CCCA was not significantly different with either treatment according to CCND1 amplification status or expression overall. However, CCCA showed a tendency to being less frequent in non-amplified cases with low baseline cyclin-D1 expression when treated with L+P (p = 0.10). There were no significant changes in ER levels or CCND1 amplification over 14wks. By 14 wks PgR, RB, CCND1 and CCNE1 levels were significantly suppressed by L or L+P (geomeans PgR: -96.4% vs -94.9%; CCND1: -79.9% vs -70.7%; CCNE1: -68.2% vs -74.7%; RB: -23.5% vs 26.1%, respectively) and there was no significant difference between the treatments. Conclusions: These data support low ER, possibly indicating limited luminal status, and high CCNE1 as markers of poor Ki67 response to L+P in primary disease and are consistent with findings in studies in advanced disease. Clinical trial information: NCT02296801.

Abstract P2-07-02: A newly derived combined clinical treatment score and immunohistochemical-4 prognostic tool

AIM

To determine whether a modified Clinical Treatment Score (CTS) based on continuous tumor size and 5 lymph node categories provided more prognostic information in an independent test set than the original CTS with and without the Immunohistochemical-4 (IHC4) algorithm for prediction of residual distant recurrence risk over 10-years.

BACKGROUND

Risk of recurrence information in patients with estrogen receptor-positive (ER+), early breast cancer informs decision-making on chemotherapy use. The CTS and IHC4 algorithms provide such information, particularly when used in combination (IHC4+C). Their derivation in the translational cohort of the Arimidex Tamoxifen Alone or in Combination trial (TransATAC) was described by Cuzick et al in 2011. In the original model tumor size and nodal status were each classified into three categories, causing prognostic information to be lost.

METHODS

We modeled a novel CTSn algorithm on outcome data from patients in the anastrozole and tamoxifen arms in ATAC incorporating tumor size as a continuous variable and sub-dividing nodal status into five categories. IHC4n was re-derived in the TransATAC cohort independent of CTSn. Patients were chemotherapy-naïve. We compared ability to predict risk of residual distant recurrence of the new IHC4n+Cn model with that of the original one when tested in a training cohort and in a validation set of chemotherapy-naïve patients from the Tamoxifen vs. Exemestane Adjuvant Multicentre (TEAM) trial using Cox regression models and the C-index.

RESULTS

The ATAC training set for CTSn comprised 4056 patients, the TransATAC training set for IHC4n comprised 1125 patients; 2591 patients were in the TEAM validation set. Patients in the TEAM set were older (median age in TransATAC: 63.5, TEAM: 68.3 years), had a higher nodal-burden (node-positive in TransATAC: 29.4%, TEAM: 51.8%) and had more Grade 3 tumors (TransATAC: 18.3%, TEAM: 32.2%).

The new IHC4n+Cn was significantly prognostic, and non-significantly more prognostic than the original IHC4+C in both the training and validation cohorts. When assessed using the C-index statistic, IHC4n+Cn had a higher discriminatory ability than the original algorithm (Table 1).

Table 1 TransATAC (N=1125)TEAM (N=2591) HR* (95% CI)C-indexHR* (95% CI)C-indexOld Models    CTS2.26 (2.01-2.53)0.6811.88 (1.73-2.03)0.650IHC41.67 (1.46-1.91)0.6301.49 (1.35-1.63)0.604IHC4+C2.76 (2.40-3.18)0.7242.03 (1.87-2.21)0.671New Models    CTSn2.64 (2.26-3.09)0.7212.16 (1.96-2.39)0.687IHC4n1.74 (1.52-2.01)0.6421.51 (1.36-1.68)0.603IHC4n+Cn2.91 (2.47-3.42)0.7382.28 (2.06-2.51)0.695(*Hazard Ratio for change in one Standard Deviation).

CONCLUSION

By separately remodellng the part of the IHC4+C score based on clinicopathological characteristics using the whole ATAC chemo-naïve cohort, and the part that uses IHC-derived information in chemo-naïve TransATAC patients, we increased the precision of the individual risk estimates produced by both CTSn and IHC4n compared to those given by the original algorithms. The new IHC4n+Cn shows a trend for improved prognostic ability compared to the original IHC4+C. Like its predecessor, it relies on information that is readily available to clinicians and integrates it in an evidence-based way to improve prognostication in ER+ early breast cancer.

Citation Format: Dodson A, Sestak I, Bayani J, Dowsett M, Bartlett J, Cuzick J. A newly derived combined clinical treatment score and immunohistochemical-4 prognostic tool [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P2-07-02.

Abstract GS3-02: PALLET: A neoadjuvant study to compare the clinical and antiproliferative effects of letrozole with and without palbociclib

Background: CDK4/6 inhibitors, such as palbociclib, are used to treat ER+ metastatic breast cancer in combination with endocrine therapy with trials ongoing in patients with primary disease. No biomarkers exist to identify those who do/do not benefit from added CDK4/6 inhibition. PALLET is an investigator-initiated/led phase II randomized trial collaboration between UK and NSABP investigators evaluating the biological and clinical effects of palbociclib with letrozole combination as neoadjuvant therapy.

Methods: Postmenopausal women with ER+ primary breast cancer and tumors &gt;2.0cm (ultrasound) were randomized to one of 4 treatment groups (3:2:2:2 ratio): Group A: letrozole (2.5mg/d) for 14 weeks; Group B: letrozole for 2 weeks followed by letrozole + palbociclib to 14 weeks; Group C: palbociclib for 2 weeks followed by letrozole + palbociclib to 14 weeks; Group D: letrozole + palbociclib for 14 weeks. Palbociclib was given 125mg/d PO on a 21 days on, 7 days off schedule. Post-14 week treatment was at the discretion of the treating clinician including letrozole until surgery. Core-cut biopsies were taken at baseline, 2 weeks and 14 weeks. Co-primary endpoints for letrozole alone vs palbociclib groups (Group A vs Groups B+C+D) were: (i) change in Ki67 (IHC) between baseline and 14 weeks (log-fold change, Mann-Whitney test); (ii) clinical response (ultrasound) after 14 weeks (4 group, ordinal, Mann-Whitney test). Complete cell-cycle arrest (CCCA) (Ki67≤2.7%) was analyzed using a logistic regression model adjusting for recruitment region. Pre-specified exploratory biomarkers included c-PARP (apoptosis).

Results: 307 patients were recruited between 27 Feb 2015 and 08 Mar 2018; 103 were randomized to letrozole alone and 204 to letrozole + palbociclib. 279 (90.9%) patients were evaluable for 14 week clinical response. Clinical response was not significantly different between letrozole vs letrozole + palbociclib groups [(p=0.20; CR+PR 49.5% (46/93) vs 54.3% (101/186) and PD 5.4% (5/93) vs 3.2% (6/186)] nor was the small proportion of patients with pathological CR (1/87, 1.1% vs 6/180, 3.3%; p=0.43). 190 (61.9%) patients were evaluable for 14 week change in Ki67. The median log-fold change in Ki67 was greater with letrozole + palbociclib vs letrozole alone (-4.1 vs -2.2; p&lt;0.001) corresponding to a geometric mean change of -97.4% vs -88.5%. Similarly, a greater proportion of patients who received letrozole + palbociclib achieved CCCA (90% vs 59%, p&lt;0.001). 146 (47.6%) patients were evaluable for c-PARP and the log-fold change (suppression) was greater with letrozole + palbociclib vs letrozole alone (-0.80 vs -0.42; p=0.003) corresponding to a geometric mean change of -56.8% vs -31.4%. Other biomarkers of response / resistance are being evaluated. A higher proportion of patients had a grade ≥3 toxicity on letrozole + palbociclib than letrozole alone (49.8% vs 17.0%; p&lt;0.001) mainly due to asymptomatic neutropenia.

Conclusion: Adding palbociclib to letrozole markedly enhanced the suppression of malignant cell proliferation as assessed by Ki67 but did not substantially increase the clinical response of primary ER+ breast cancer over a 14-week period. Concurrent reductions in cell death may have reduced the speed of tumor shrinkage.

Citation Format: Dowsett M, Jacobs S, Johnston S, Bliss J, Wheatley D, Holcombe C, Stein R, McIntosh S, Barry P, Dolling D, Snowdon C, Perry S, Batten L, Dodson A, Martins V, Modi A, Cornman C, Puhalla S, Wolmark N, Julian T, Pogue-Geile K, Robidoux A, Provencher L, Boileau JF, Shalaby I, Thirlwell M, Fisher K, Huang Bartlett C, Koehler M, Osborne K, Rimawi M. PALLET: A neoadjuvant study to compare the clinical and antiproliferative effects of letrozole with and without palbociclib [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr GS3-02.

Abstract P4-15-01: Acquired ESR1 mutation and persistent expression of estrogen regulated genes in ER+ breast cancers on long-term neoadjuvant treatment with aromatase inhibitors

Background: Aromatase inhibitors (AI), which block the conversion of androgen to estrogen, are the mainstay therapy for estrogen receptor–positive (ER+) breast cancer (BC). However, many patients relapse.

Purpose: To identify molecular alterations associated with long-term neoadjuvant AI therapy of ER+ BC.

Methods: We retrospectively identified 137 patients diagnosed with ER+ BC and treated with neoadjuvant AI for at least 1 month at the Royal Marsden Hospital (2003–2016). Paired pre- (diagnosis) and post-AI (surgery) biopsies with &gt;40% invasive cell areas were available from 87 ER+ BC patients. In all samples, we evaluated ER, PR and Ki67 immunostaining, ESR1 hot-spot mutations by droplet digital PCR and expression of 801 genes associated with BC and response to endocrine therapy by NanoString.

Results: Mean time on neoadjuvant treatment was 26 weeks (range 5.6–92.3). Cell proliferation remained suppressed in most tumours indicating little evidence for acquired resistance: 56/87 (64%) showed residual Ki67 (Ki67r) &lt;2.7% (complete cell cycle arrest) and 14/87 (11.5%) had Ki67r&gt;10%. This was paralleled by reduced expression of proliferation genes, ER (immunostaining and gene expression) and estrogen-regulated genes (ERG) at surgery compared with the diagnostic samples (all p&lt;0.001). There was a weak positive correlation between AI duration and Ki67r and less reduction in proliferation genes, ESR1 and ERGs expression (p&lt;0.05; r=0.26-0.34). Pathway analysis revealed inhibition of cell cycle (e.g. reduced expression of several cyclins), E2F targets and estrogen response (e.g. reduced expression of ER downstream targets such as FOXM1). CDK genes showed a variable response: CDK1 and CDK2 decreasing, CDK4 increasing and no change in CDK6. Most notably, 6 surgical samples showed ESR1 mutations: one of these cases had the mutation at diagnosis. All 5 acquired mutations were detected in patients treated for &gt;6 months, giving a prevalence in this cohort of 5/34 (15%). Tumours with ESR1 mutations showed less suppression of ERGs (p=0.002) and proliferation (p=0.039) and increased ESR1 (p=0.016) expression at surgery compared with tumours without mutation. Pathway analysis confirmed lack of inhibition of estrogen response (FDR&gt;5%) and less inhibition of cell cycle [enrichment score: -0.49 vs -0.78) and E2F targets (-0.47 vs -0.8) in tumours with mutation. Tumours without ESR1 mutation but with Ki67r&gt;10% also showed reduced ERGs response (p=0.006) compared to tumours with Ki67r&lt;2.7%. Additionally, these tumours showed relative activation of cell cycle, estrogen response, E2F targets pathways and mTORC1 signalling (FDR&lt;1%).

Conclusion: Overall most tumours showed no evidence for the emergence of resistant disease after neoadjuvant AI therapy even after many months of treatment. However, we detected an enrichment of ESR1 mutations (15% of cases) after long-term treatment as a putative driver of ERG expression and proliferation and thus reduced AI response. Therefore, mutant ER appears to be associated with ligand-independent ERG activity supporting the clinical validity of dual blockade with a selective ER down-regulator combined with a CDK4/6 inhibitor targeting the RB/E2F axis in this scenario.

Citation Format: Leal MF, Haynes BP, Schuster E, Yeo B, Afentakis M, Dodson A, Buus R, Cheang MC, Martin L-A, Dowsett M. Acquired ESR1 mutation and persistent expression of estrogen regulated genes in ER+ breast cancers on long-term neoadjuvant treatment with aromatase inhibitors [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-15-01.

Randomized Phase II Study Evaluating Palbociclib in Addition to Letrozole as Neoadjuvant Therapy in Estrogen Receptor-Positive Early Breast Cancer: PALLET Trial

PURPOSE

CDK4/6 inhibitors are used to treat estrogen receptor (ER)-positive metastatic breast cancer (BC) in combination with endocrine therapy. PALLET is a phase II randomized trial that evaluated the effects of combination palbociclib plus letrozole as neoadjuvant therapy.

PATIENTS AND METHODS

Postmenopausal women with ER-positive primary BC and tumors greater than or equal to 2.0 cm were randomly assigned 3:2:2:2 to letrozole (2.5 mg/d) for 14 weeks (A); letrozole for 2 weeks, then palbociclib plus letrozole to 14 weeks (B); palbociclib for 2 weeks, then palbociclib plus letrozole to 14 weeks (C); or palbociclib plus letrozole for 14 weeks. Palbociclib 125 mg/d was administered orally on a 21-days-on, 7-days-off schedule. Core-cut biopsies were taken at baseline and 2 and 14 weeks. Coprimary end points for letrozole versus palbociclib plus letrozole groups (A v B + C + D) were change in Ki-67 (protein encoded by the  MKI67 gene; immunohistochemistry) between baseline and 14 weeks and clinical response (ordinal and ultrasound) after 14 weeks. Complete cell-cycle arrest was defined as Ki-67 less than or equal to 2.7%. Apoptosis was characterized by cleaved poly (ADP-ribose) polymerase.

RESULTS

Three hundred seven patients were recruited. Clinical response was not significantly different between palbociclib plus letrozole and letrozole groups ( P = .20; complete response + partial response, 54.3% v 49.5%), and progressive disease was 3.2% versus 5.4%, respectively. Median log-fold change in Ki-67 was greater with palbociclib plus letrozole compared with letrozole (-4.1 v -2.2; P < .001) in the 190 evaluable patients (61.9%), corresponding to a geometric mean change of -97.4% versus -88.5%. More patients on palbociclib plus letrozole achieved complete cell-cycle arrest (90% v 59%; P < .001). Median log-fold change (suppression) of cleaved poly (ADP-ribose) polymerase was greater with palbociclib plus letrozole versus letrozole (-0.80 v -0.42; P < .001). More patients had grade 3 or greater toxicity on palbociclib plus letrozole (49.8% v 17.0%; P < .001) mainly because of asymptomatic neutropenia.

CONCLUSION

Adding palbociclib to letrozole significantly enhanced the suppression of malignant cell proliferation (Ki-67) in primary ER-positive BC, but did not increase the clinical response rate over 14 weeks, which was possibly related to a concurrent reduction in apoptosis.

Breast cancer biomarkers in clinical testing: analysis of a UK national external quality assessment scheme for immunocytochemistry and in situ hybridisation database containing results from 199 300 patients

We describe a collated data set of results from clinical testing of breast cancers carried out between 2009 and 2016 in the United Kingdom and Republic of Ireland. More than 199 000 patient biomarker data sets, together with clinicopathological parameters were collected. Our analyses focused on human epidermal growth factor receptor-2 (HER2), oestrogen receptor (ER) and progesterone receptor (PR), with the aim of the study being to provide robust confirmatory evidence on known associations in these biomarkers and to uncover new data on previously undescribed or unconfirmed associations, thus strengthening the evidence-base in clinical breast cancer testing. Overall, 13.1% of tumours were HER2-positive; 10.6% in ER-positive tumours, and 25.5% in ER-negative tumours. Higher rates of HER2 positivity were significantly associated with patient age <56 years versus age ≥56 years, symptomatic versus screen-detected tumours, testing of involved axillary node versus primary breast cancer, invasive ductal carcinoma (not otherwise specified) versus other histological types, higher histological grade, increasing tumour size, increasing nodal involvement, ER-negative versus ER-positive tumour status, PR-negative versus PR-positive tumour status. Where ER status was known, 82.7% of tumours were ER-positive; 80.9% in women age <56 years, and 83.6% in those age ≥56 years (ER-positive cut-off ≥1.0% positive tumour cells or equivalent). Where PR status was known, 64.9% of tumours were PR-positive; 65.8% in women age <56 years, and 64.4% in women age ≥56 years (PR-positive cut off ≥10.0% or equivalent). These analyses of clinical test results provide contemporary benchmarking data for HER2, ER and PR positive rates.

Integration of Clinical Variables for the Prediction of Late Distant Recurrence in Patients With Estrogen Receptor-Positive Breast Cancer Treated With 5 Years of Endocrine Therapy: CTS5

Purpose Estimating risk of late distant recurrence (DR) is an important goal for managing women with hormone receptor-positive breast cancer after 5 years of endocrine treatment without recurrence. We developed and validated a simple clinicopathologic tool (Clinical Treatment Score post-5 years [CTS5]) to estimate residual risk of DR after 5 years of endocrine treatment. Patients and Methods The ATAC (Arimidex, Tamoxifen, Alone or in Combination) data set (N = 4,735) was used to create a prognostic score for post-5-year risk of DR. Validity of CTS5 (ATAC) was tested in the BIG 1-98 data set (N = 6,711). Time to late DR, 5 years after finishing scheduled endocrine therapy, was the primary end point. Cox regression models estimated the prognostic performance of CTS5 (ATAC). Results CTS5 (ATAC) was significantly prognostic for late DR in the ATAC cohort (hazard ratio, 2.47; 95% CI, 2.24 to 2.73; P < .001) and BIG 1-98 validation cohort (hazard ratio, 2.07; 95% CI, 1.88 to 2.28; P < .001). CTS5 (ATAC) risk stratification defined in the training cohort as low (< 5% DR risk, years 5 to 10), intermediate (5% to 10%), or high (> 10%) identified 43% of the validation cohort as low risk, with an observed DR rate of 3.6% (95% CI, 2.7% to 4.9%) during years 5 to 10. From years 5 to 10, 63% of node-negative patients were low risk, with a DR rate of 3.9% (95% CI, 2.9% to 5.3%), and 24% with one to three positive nodes were low risk, with a DR rate of 1.5% (95% CI, 0.5% to 3.8%). A final CTS5 for future use was derived from pooled data from ATAC and BIG 1-98. Conclusion CTS5 is a simple tool based on information that is readily available to all clinicians. CTS5 was validated as highly prognostic for late DR in the independent BIG 1-98 study. The final CTS5 algorithm identified 42% of women with < 1% per-year risk of DR who could be advised of the limited potential value of extended endocrine therapy.

Major Impact of Sampling Methodology on Gene Expression in Estrogen Receptor-Positive Breast Cancer

To investigate the impact of sampling methodology on gene expression data from primary estrogen receptor–positive (ER+) breast cancer biopsies, global gene expression was measured in core-cut biopsies at baseline and surgery from patients randomly assigned to receive either two weeks of presurgical aromatase inhibitor (AI; n = 157) or no presurgical treatment (n = 56). Those genes most markedly altered in the AI group (eg, FOS, DUSP1, RGS1, FOSB) were similarly altered in the no treatment group; some widely investigated genes that were apparently unaffected in the AI group (eg, MYC) were counter-altered in the control group, masking actual AI-dependent changes. In the absence of a control group, these artefactual changes would likely lead to the most affected genes being the erroneous focus of research. The findings are likely relevant to all archival collections of ER+ breast cancer.

Abstract P2-03-01: Analytical validation of a standardized scoring protocol for Ki67 assessed on breast excision whole sections: An international multicenter collaboration

Aims: (i) Determine whether between-observer reproducibility for Ki67 when assessed on whole sections according to a standardized scoring protocol is adequate for clinical application. (ii) Compare between-observer reproducibility of Ki67 scores assessed on hot-spots to scores using a global method that averages across a tissue section.

Background: The nuclear proliferation biomarker Ki67 has multiple potential roles in breast cancer, including aiding decisions based on prognosis, but unacceptable levels of between-laboratory variability have been observed. The International Ki67 in Breast Cancer Working Group has undertaken a systematic program to determine whether Ki67 measurement can be analytically validated and standardized across labs. In phase 1, variability in visual interpretation was identified as an important source of variability. Phases 2 and 3a showed that adherence to defined scoring methods substantially improved reproducibility in scoring tissue microarrays and core-cut biopsies. We now assess whether acceptable reproducibility can be achieved on whole sections.

Methods: Adjacent sections from 30 primary ER+ breast cancers were centrally stained for Ki67 to assemble 4 sets of 30 stained tumor sections, circulated around 23 labs in 12 countries. Ki67 was scored by 2 methods by all labs: (a) global: 4 fields of 100 tumor cells each were selected to reflect observed heterogeneity in nuclear staining (b) hot-spot: the field with highest Ki67 percentage of tumor cells with nuclear staining was selected and up to 500 cells scored. Ki67 scores were log2-transformed for statistical analyses and back-transformed for presentation. The primary objective was to assess whether either method could achieve an intraclass correlation coefficient (ICC) significantly greater than 0.8, considered substantial to almost-perfect reproducibility. Secondary objectives were to assess which method had highest observed ICC and to assess whether observers identified the same “hot-spots”.

Results: ICC for the global method was 0.87 (95%CI: 0.799-0.93), marginally meeting the prespecified success criterion. The ICC for the hot-spot method was 0.83 (95%CI: 0.74-0.90) and had a CI extending below the success criterion. Across the 23 labs, geometric mean value of the 30 scores ranged from 8.5 to 19.6 for the global method and from 12.8 to 30.3 for the hot-spot method. The overall mean (95% CI) of these values was 12.9 (11.9-14.0) and 20.9 (19.1-22.8), respectively. Visually, between-laboratory agreement in location of selected hot-spot varies between cases. The median times for scoring were 9 and 6 minutes for global and hot-spot methods respectively.

Conclusions: The global method marginally met the prespecified criterion of success; it should now be evaluated for clinical validity in appropriate cohorts of cases. The hot-spot method was observed to have slightly less reproducibility between labs. The time taken for scoring by either method is practical using counting software we are making publicly available. Establishment of external quality assessment schemes is likely to improve the reproducibility between labs further.

(Supported by a grant from the Breast Cancer Research Foundation)

Citation Format: Nielsen TO, Leung SCY, Zabaglo LA, Arun I, Badve SS, Bane AL, Bartlet JMS, Borgquist S, Chang MC, Dodson A, Ehinger A, Fineberg S, Focke CM, Gao D, Gown AM, Gutierrez C, Hugh JC, Kos Z, Lænkholm A-V, Mastropasqua MG, Moriya T, Nofech-Mozes S, Osborne CK, Penault-Llorca FM, Piper T, Sakatani T, Salgado R, Starczynski J, Sugie T, van der Vegt B, Viale G, Hayes DF, McShane LM, Dowsett M. Analytical validation of a standardized scoring protocol for Ki67 assessed on breast excision whole sections: An international multicenter collaboration [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-03-01.

Abstract GS6-01: Integration of clinical variables for the prediction of late distant recurrence in patients with oestrogen receptor positive breast cancer treated with 5 years of endocrine therapy

Background: The prediction of late distant recurrence (DR) is an important clinical goal for managing women with hormone receptor positive disease who have reached the end of 5 years' endocrine treatment without recurrence. Molecular profiles have produced conflicting results for the prediction of late DR. Here, we develop and validate a simple clinicopathological tool (Clinical Treatment Score post-5 years (CTS5)) to estimate the residual risk of DR after 5 years' endocrine treatment, which should help in discussions with patients about the potential benefits or not of continued endocrine therapy.

Patients and Methods: The ATAC dataset (N=4735) of postmenopausal women with oestrogen receptor (ER) positive breast cancer treated with 5 years' tamoxifen or anastrozole was used as a training cohort to establish a prognostic score for post-5-year risk of DR. CTS5 was based on five categories for nodal status, linear and quadratic terms for tumour size (capped at 30mm), three categories for grade, and continuous age. The validity of the CTS5 was tested in the BIG1-98 dataset (N=6711), which included postmenopausal women with ER-positive breast cancer treated with tamoxifen or letrozole (either monotherapy or sequential). Both cohorts included women who were alive and DR-free 5 years after randomization. Time to late DR, defined beginning at 5 years after ATAC or BIG 1-98 randomization, was the primary endpoint. Cox regression models estimated the prognostic performance of the CTS5. Hazard Ratios (HRs) are for a change of one Standard Deviation.

Results: The CTS5 model was a significant predictor for late DR in ATAC (HR=2.47 (95% CI, 2.24-2.73), P&lt;0.001) and performed better than the established 0-10 year CTS model (Cuzick et al., JCO, 2011). CTS5 was confirmed as highly predictive for late DR in the BIG1-98 validation cohort (HR=2.07 (1.88-2.28), P&lt;0.001). Of greatest importance was that CTS5 risk stratification defined in the training cohort as low (&lt;5% risk of DR during years 5-10), intermediate (5-10% risk), high (&gt;10% risk), identified 43% of the validation cohort as low risk, with an observed DR rate of 3.6% (95% CI 2.7-4.9) during years 5-10. Within nodal subgroups, 63% of node-negative were low risk with 3.9% (2.9-5.3) DR rate between years 5-10, and 24% having 1-3 nodes positive were low risk with 1.5% (0.5-3.8) DR rate between years 5-10. Separation of intermediate-risk from high-risk categories was also shown in the training set but improvements in calibration seem necessary for clinical utility for that assessment.

Conclusion: The CTS5 is a simple tool based on information that is readily available to all clinicians. It was more accurate in its prediction of DR risk in years 5-10 than the published CTS model. CTS5 was validated as highly prognostic for late DR in the independent BIG 1-98 study. The algorithm identified a subgroup of women with either node-negative disease or 1-3 positive nodes as having less than 1% per year risk of DR who could be advised of the limited value of extended endocrine therapy.

Citation Format: Sestak I, Regan M, Dodson A, Viale G, Thürlimann B, Colleoni M, Cuzick J, Dowsett M. Integration of clinical variables for the prediction of late distant recurrence in patients with oestrogen receptor positive breast cancer treated with 5 years of endocrine therapy [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr GS6-01.

Abstract P3-08-16: ER, PR and HER2 biomarkers in UK and Irish clinical breast cancer testing: analysis of results from &gt;168,000 patients

AIMS

To describe and analyse &gt;168,000 sets of results from clinical breast biomarker testing carried-out between 2009 and 2016 in the UK and Republic of Ireland, focussing on biological relationships. To present robust confirmatory evidence on known associations and provide new data on previously undescribed or unconfirmed ones.

BACKGROUND

Between Jan-2009 and Jan-2016 the UK National External Quality Assessment Scheme for Immunocytochemistry and In-situ Hybridisation (UK NEQAS ICC&ISH) collected results on clinical breast cancer testing, comprehensively for human epidermal growth factor receptor-2 (HER2) and optionally for estrogen receptor (ER) and progesterone receptor (PR), from most UK and Irish testing centres. Primary objectives were to assess and, where indicated achieve improvements in testing quality. The size and scope of the data-set is unparalleled in the literature and represent a significant reference resource for the breast cancer community.

METHODS

UK NEQAS ICC&ISH created and curated an on-line data-entry system allowing centres to systematically collect their own HER2, ER and PR results from clinical testing; for HER2, immunohistochemical (IHC) and in-situ hybridisation (ISH) data were collected; for ER and PR, IHC results could be entered according to local practise format. Tools and guidance were provided enabling centres to analyse their data for local audit and quality assurance. Clinicopathologic data was also collected, including: patient age at diagnosis, histological tumor type, tumor grade, site/stage (primary, recurrence, metastasis) and sample type (core, excision).

RESULTS

Data are present on 168,793 patients. 173 centres contributed ≥100 entries (96% of total). Median age was 62 years (IQR: 51-72). Tumor type was stated in 42%: 76% were invasive ductal, and 13% invasive lobular carcinoma. Grade was stated in 56%: 15% were Grade 1, 55% Grade 2 and 30% Grade 3. Site/stage was stated in 56%: 92% were primary, 2% recurrent and 6% metastatic. Sample type was stated in 70%: 75% were cores and 25%, excision.

Receptor statuses were available as follows; HER2 (100%): 87% negative, 13% positive; ER (45%): 15% negative, 85% positive; PR (31%): 29% negative, 71% positive.

HER2 data were available as follows; category by IHC: 91%; amplification status by ISH: 15%; HER2 gene/chromosome 17 (CEP17) ratio: 15% (86% of which were IHC 2+); HER2 gene copy number: 7%; CEP17 copy number: 7%.

HER2-positive rate was 24% in ER-negative and 11% in ER-positive cases. HER2-positive status was negatively associated with increasing ER positivity (rho -0.22, P&lt;0.001). 71% of HER2-positive cases were ER-positive and 29% were ER-negative. The HER2 2+ rate was 14% in ER-negative and 21% in ER-positive cases. Considering only IHC 2+ cases, median HER2 copy number was 5.4 in ER-negative and 4.4 in ER-positive disease.

Comprehensive description of significant associations for all parameters will be presented.

CONCLUSION

The unique size and scope of this data-set has allowed confirmation of known associations for HER2, ER and PR with clinicopathologic and biological characteristics in breast cancer to very high confidence levels, and has uncovered previously undescribed relationships in both ER-positive and ER-negative disease.

Citation Format: Dodson A, Parry S, Ibrahim M, Bartlett J, Dowsett M, Miller K. ER, PR and HER2 biomarkers in UK and Irish clinical breast cancer testing: analysis of results from &gt;168,000 patients [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-08-16.

Discordance between oncotype DX recurrence score and RSPC for predicting residual risk of recurrence in ER-positive breast cancer

PURPOSE

Oncotype DX, a gene expression assay widely employed to aid decision making on adjuvant chemotherapy use in patients with primary oestrogen receptor-positive (ER+) breast cancer, produces a recurrence score (RS) related to distant disease recurrence (DR) risk (RS%). In node-negative patients, RS can be integrated with clinicopathological parameters to derive RS-pathology-clinical (RSPC) that improves prognostic accuracy.

METHODS

Data were collected on patients having clinically indicated tests with an intermediate clinical risk of distant recurrence, and for whom the decision to prescribe chemotherapy remained unclear. Correlation between RS% and RSPC scores was examined. An agreement table was constructed using risk-categorised data. Association between RS%-derived categorical risk assignments and treatment recommendation was evaluated.

RESULTS

Data on 171 tests (168 patients) were available. Median DR risk by RS% was 11% (range 3-34%), by RSPC it was 15% (range 4-63%). Correlation between RS% and RSPC was 0.702 (p < 0.001). RS% classified 57.3% of cases as low-, 32.2% intermediate- and 10.5% high-risk for DR; by RSPC proportions were 33.9, 35.7, and 30.4%, respectively. The number of patients receiving chemotherapy recommendations was: 14/87 (16.1%) categorised as low-risk by RS%, 27/49 (55.1%) as intermediate-risk and 12/13 (92.3%) as high-risk. Of 149 patients recommended for endocrine treatment alone, 28 (18.8%) were categorised by RS% as low-risk but by RSPC as intermediate- or high-risk.

CONCLUSIONS

In this group of patients, RSPC assessed fewer patients as low-risk and more as high-risk than did RS%. The discordances between the scores indicate that RSPC estimates of risk should be considered when selecting patients for endocrine therapy alone.

Embryonic transcription factor SOX9 drives breast cancer endocrine resistance

The estrogen receptor (ER) drives the growth of most luminal breast cancers and is the primary target of endocrine therapy. Although ER blockade with drugs such as tamoxifen is very effective, a major clinical limitation is the development of endocrine resistance especially in the setting of metastatic disease. Preclinical and clinical observations suggest that even following the development of endocrine resistance, ER signaling continues to exert a pivotal role in tumor progression in the majority of cases. Through the analysis of the ER cistrome in tamoxifen-resistant breast cancer cells, we have uncovered a role for an RUNX2-ER complex that stimulates the transcription of a set of genes, including most notably the stem cell factor SOX9, that promote proliferation and a metastatic phenotype. We show that up-regulation of SOX9 is sufficient to cause relative endocrine resistance. The gain of SOX9 as an ER-regulated gene associated with tamoxifen resistance was validated in a unique set of clinical samples supporting the need for the development of improved ER antagonists.

School performance for children with cleft lip and palate: a population-based study

BACKGROUND

Educational attainment is important in shaping young people's life prospects. To investigate whether being born with orofacial cleft (OFC) affects school performance, we compared school test results between children born with and without OFC.

METHODS

Using record-linked datasets, we conducted a population-based cohort study of children liveborn in Western Australia 1980-2010 with a diagnosis of OFC on the Register of Developmental Anomalies, and a random sample of 6603 children born without OFC. We compared odds ratios for meeting national minimum standards in five domains (reading, numeracy, writing, spelling, grammar and punctuation), and adjusted OR (aOR) for children with cleft lip only (CLO), cleft lip and palate (CL + P) and cleft palate only (CPO) for each domain.

RESULTS

Results from two testing programs (WALNA and NAPLAN) were available for 3238 (89%) children expected to participate. Most met the national minimum standards. Compared with children without OFC, children with CPO were less likely to meet minimum standards for NAPLAN reading (aOR 0.57 [95%CI 0.34, 0.96]) grammar and punctuation (aOR 0.49 [95%CI 0.32, 0.76]), WALNA writing (aOR 0.66 [95%CI 0.47, 0.92]), and WALNA and NAPLAN numeracy (aOR 0.64 [95%CI 0.43, 0.95] and aOR 0.47 [95%CI 0.28, 0.82]), respectively. Children with CL + P had significantly lower odds for reaching the spelling standard in NAPLAN tests (aOR 0.52 [95%CI 0.29, 0.94]). Children with CLO had similar odds for reaching all minimum standards.

CONCLUSION

Children born with OFC, particularly children with CPO, should be monitored to identify learning difficulties early, to enable intervention to maximize school attainment.

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.

Acrylamide-forming potential of potatoes grown at different locations, and the ratio of free asparagine to reducing sugars at which free asparagine becomes a limiting factor for acrylamide formation

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Location of cultivation affects potato composition and acrylamide-forming potential.

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Effects of variety and storage interact with those of location.

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Dramatic differences in free asparagine concentration in potatoes grown at two sites.

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Concentration of reducing sugars is the primary determinant of acrylamide formation.

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Ratio of free asparagine to reducing sugars determines whether free asparagine affects acrylamide formation.

Acrylamide is produced from free asparagine and reducing sugars during high-temperature cooking and food processing, and potato products are major contributors to dietary acrylamide intake. The present study analysed twenty varieties of potatoes grown at two sites (Doncaster and Woburn) in the United Kingdom to assess the effect of location of cultivation on acrylamide-forming potential. Analysis of variance revealed a full site by variety nested within type (French fry, boiling and crisping) by storage interaction for acrylamide (p < 0.003, F-test), reducing sugars and total sugars (p < 0.001, F-test). There was much greater free asparagine in potatoes grown at the Doncaster site compared with the Woburn site. Modelling of the relationship between the ratio of free asparagine to reducing sugars and the levels of acrylamide identified a value of 2.257 ± 0.149 as the tipping point in the ratio below which free asparagine concentration could affect acrylamide formation.

Analytical validation of a standardized scoring protocol for Ki67: phase 3 of an international multicenter collaboration

Pathological analysis of the nuclear proliferation biomarker Ki67 has multiple potential roles in breast and other cancers. However, clinical utility of the immunohistochemical (IHC) assay for Ki67 immunohistochemistry has been hampered by unacceptable between-laboratory analytical variability. The International Ki67 Working Group has conducted a series of studies aiming to decrease this variability and improve the evaluation of Ki67. This study tries to assess whether acceptable performance can be achieved on prestained core-cut biopsies using a standardized scoring method. Sections from 30 primary ER+ breast cancer core biopsies were centrally stained for Ki67 and circulated among 22 laboratories in 11 countries. Each laboratory scored Ki67 using three methods: (1) global (4 fields of 100 cells each); (2) weighted global (same as global but weighted by estimated percentages of total area); and (3) hot-spot (single field of 500 cells). The intraclass correlation coefficient (ICC), a measure of interlaboratory agreement, for the unweighted global method (0.87; 95% credible interval (CI): 0.81–0.93) met the prespecified success criterion for scoring reproducibility, whereas that for the weighted global (0.87; 95% CI: 0.7999–0.93) and hot-spot methods (0.84; 95% CI: 0.77–0.92) marginally failed to do so. The unweighted global assessment of Ki67 IHC analysis on core biopsies met the prespecified criterion of success for scoring reproducibility. A few cases still showed large scoring discrepancies. Establishment of external quality assessment schemes is likely to improve the agreement between laboratories further. Additional evaluations are needed to assess staining variability and clinical validity in appropriate cohorts of samples.

Heterogeneity in global gene expression profiles between biopsy specimens taken peri-surgically from primary ER-positive breast carcinomas

BACKGROUND

Gene expression is widely used for the characterisation of breast cancers. Variability due to tissue heterogeneity or measurement error or systematic change due to peri-surgical procedures can affect measurements but is poorly documented. We studied the variability of global gene expression between core-cuts of primary ER+ breast cancers and the impact of delays to tissue stabilisation due to sample X-ray and of diagnostic core cutting.

METHODS

Twenty-six paired core-cuts were taken immediately after tumour excision and up to 90 minutes delay due to sample X-ray; 57 paired core-cuts were taken at diagnosis and 2 weeks later at surgical excision. Whole genome expression analysis was conducted on extracted RNA. Correlations and differences were assessed between the expression of individual genes, gene sets/signatures and intrinsic subtypes.

RESULTS

Twenty-three and 56 sample pairs, respectively, were suitable for analysis. The range of correlations for both sample sets were similar with the majority being >0.97 in both. Correlations between pairs for 18 commonly studied genes were also similar between the studies and mainly with Pearson correlation coefficients >0.6 except for a small number of genes, which had a narrow-dynamic range (e.g. MKI67, SNAI2). There was no systematic difference in intrinsic subtyping between the first and second sample of either set but there was c.15 % discordance between the subtype assignments between the pairs, mainly where the subtyping of individual samples was less certain. Increases in the expression of several stress/early-response genes (e.g. FOS, FOSB, JUN) were found in both studies and confirmed findings in earlier smaller studies. Increased expression of IL6, IGFBP2 and MYC (by 17 %, 14 % and 44 %, respectively) occurred between the samples taken 2 weeks apart and again confirmed findings from an earlier study.

CONCLUSIONS

There is generally good correlation in gene expression between pairs of core-cuts except where genes have a narrow dynamic range. Similar correlation coefficients to the average gene expression profiles of intrinsic subtype, particularly LumA and LumB, can lead to discordances between assigned subtypes. Substantial changes in expression of early-response genes occur within an hour after surgery and in IL6, IGFB2 and MYC as a result of diagnostic core-cut biopsy.

TRIAL REGISTRATION

Trial number CRUK/07/015 . Study start date September 2008.

Risk of recurrence estimates with IHC4+C are tolerant of variations in staining and scoring: an analytical validity study

AIMS

The IHC4+C score combines assessment of oestrogen receptor (ER), progesterone receptor (PgR), HER2 and Ki67 with clinicopathological parameters to identify the risk of distant disease recurrence in patients with breast cancer, so, aiding treatment decision-making on adjuvant chemotherapy. Despite low cost and wide availability, the reported use of IHC4+C remains limited; one explanation for this is the perception that immunohistochemistry (IHC)-based methods and assessment of them lack precision, reproducibility and portability. We examined the effects of decentralised testing and easily reproducible estimate-based scoring methods on IHC4+C scores to determine its suitability for wider adoption.

METHODS

Sections from a breast cancer tissue micro-array (TMA) were distributed to three centres undertaking diagnostic breast cancer IHC. Centres stained sections using their standard procedures, and returned them for central assessment. The results were compared with those obtained at IHC4+C's originating hospital (Royal Marsden Hospital (RMH)). In parallel, TMA sections stained at RMH were scored by a variety of simplified non-counting-based methods. The results were compared with those produced using counting.

RESULTS

There was a high degree of correlation between individual IHC results produced by external centres and those of RMH (r: 0.797-0.982), and between risk of distant recurrence scores derived from them (r: 0.972-0.984). Scoring methods for ER and PgR could be adapted to require less precision without significantly affecting correlation with counted results (r: 0.933 and 0.980, respectively), but correlation between estimating and counting for Ki67 was poorer (r: 0.855).

CONCLUSIONS

IHC4+C is tolerant of variation in staining and scoring methods. Although additional confirmatory comparative studies are required, these data support use of IHC4+C in clinical practice outside RMH.

Clinical utility of the IHC4+C score in oestrogen receptor-positive early breast cancer: a prospective decision impact study

BACKGROUND

Most oestrogen receptor (ER)-positive early breast cancer diagnosed today is highly curable with multimodality treatment. Systemic adjuvant treatments including endocrine therapy and chemotherapy have made a significant contribution to the increasing cure rates over the past three decades. However not all women will require chemotherapy. The IHC4+C score is a prognostic tool that integrates four immunohistochemical measures with clinicopathological features to estimate the residual risk of distant recurrence at 10 years in post-menopausal women with ER-positive breast cancer who have received 5 years of endocrine therapy. Retrospective studies indicate that the test can identify a set of women that are at such low risk of recurrence that chemotherapy can be of little benefit.

METHODS

In this study, 124 patients were prospectively selected from the multidisciplinary team meeting between January 2013 and April 2014 for IHC4+C testing. Adjuvant systemic treatment recommendations by clinicians were recorded without and with the availability of the score in addition to the patient's decision.

RESULTS

There was concordance in the MDT's recommendation without and with the availability of the score in 73% of cases. Clinicians recommended chemotherapy or at least its discussion to 74 (59%) patients, which fell to 32 (34%) patients after the IHC4+C score was made available, sparing one in four tested patients a chemotherapy recommendation, along with its toxicity and expense.

CONCLUSION

This decision impact study shows that when used by clinicians in the multidisciplinary team meeting for adjuvant decision-making, a significant proportion of patients are spared chemotherapy recommendations.