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Supplementary Data from Differential Survival and Therapy Benefit of Patients with Breast Cancer Are Characterized by Distinct Epithelial and Immune Cell Microenvironments

Flow chart of patients with BRCA1/2 alterations submitted to the study team between September 2016 and December 2019, and reasons for drop-out, rejection or screen failure. Abbreviations: VUS = Variant of Unknown Significance, LOH = Loss of Heterozygosity.

Purpose:In breast cancer, pathologic complete response (pCR) to neoadjuvant systemic therapy (NST) is associated with favorable long-term outcome. Trastuzumab emtansine as additional adjuvant therapy improves recurrence-free survival of patients with HER2-positive breast cancer without pCR, but it is uncertain whether all patients without pCR need additional therapy. We evaluated the prognostic value of residual disease after trastuzumab-based NST in patients with HER2-positive breast cancer using Residual Cancer Burden (RCB), Neoadjuvant Response Index (NRI), and Neo-Bioscore.Experimental Design:We included patients with stage II or III HER2-positive breast cancer treated with trastuzumab-based NST and surgery at The Netherlands Cancer Institute between 2004 and 2016. RCB, NRI, and Neo-Bioscore were determined. Primary endpoint was 5-year recurrence-free interval (RFI). A 3% difference compared with the pCR group was considered acceptable as noninferiority margin on the 5-year RFI estimate, based on a proportional hazards model, and its lower 95% confidence boundary.Results:A total of 283 women were included. Median follow-up was 67 months (interquartile range 44–100). A total of 157 patients (56%) with pCR (breast and axilla) had a 5-year RFI of 92% (95% CI, 88–97); patients without pCR had a 5-year RFI of 80% (95% CI, 72–88). Patients with an RCB = 1 (N = 40, 15%), an NRI score between 0.75 and 0.99 (N = 30, 11%), or a Neo-Bioscore of 0 to 1 (without pCR; N = 28, 11%) have a 5-year RFI that falls within a predefined noninferiority margin of 3% compared with patients with pCR.Conclusions:The RCB, NRI, and Neo-Bioscore can identify patients with HER2-positive breast cancer with minimal residual disease (i.e., RCB = 1, NRI ≥ 0.75, or Neo-Bioscore = 0–1) after NST who have similar 5-year RFI compared with patients with pCR.

Pharmacokinetics: Z-endoxifen levels per taselisib dose level

Purpose:Extensive work in preclinical models has shown that microenvironmental cells influence many aspects of cancer cell behavior, including metastatic potential and their sensitivity to therapeutics. In the human setting, this behavior is mainly correlated with the presence of immune cells. Here, in addition to T cells, B cells, macrophages, and mast cells, we identified the relevance of nonimmune cell types for breast cancer survival and therapy benefit, including fibroblasts, myoepithelial cells, muscle cells, endothelial cells, and seven distinct epithelial cell types.Experimental Design:Using single-cell sequencing data, we generated reference profiles for all these cell types. We used these reference profiles in deconvolution algorithms to optimally detangle the cellular composition of more than 3,500 primary breast tumors of patients that were enrolled in the SCAN-B and MATADOR clinical trials, and for which bulk mRNA sequencing data were available.Results:This large data set enables us to identify and subsequently validate the cellular composition of microenvironments that distinguish differential survival and treatment benefit for different treatment regimens in patients with primary breast cancer. In addition to immune cells, we have identified that survival and therapy benefit are characterized by various contributions of distinct epithelial cell types.Conclusions:From our study, we conclude that differential survival and therapy benefit of patients with breast cancer are characterized by distinct microenvironments that include specific populations of immune and epithelial cells.

Supplementary Figure from Patients with Rare Cancers in the Drug Rediscovery Protocol (DRUP) Benefit from Genomics-Guided Treatment

Time to progression per patient in a swimmers plot (all patients, N=30)

This file contains details on all late grade {greater than or equal to} 2 esophageal adverse events (I) and esophageal metabolic activity six weeks post-treatment (II).

Purpose:Patients with rare cancers (incidence less than 6 cases per 100,000 persons per year) commonly have less treatment opportunities and are understudied at the level of genomic targets. We hypothesized that patients with rare cancer benefit from approved anticancer drugs outside their label similar to common cancers.Experimental Design:In the Drug Rediscovery Protocol (DRUP), patients with therapy-refractory metastatic cancers harboring an actionable molecular profile are matched to FDA/European Medicines Agency–approved targeted therapy or immunotherapy. Patients are enrolled in parallel cohorts based on the histologic tumor type, molecular profile and study drug. Primary endpoint is clinical benefit (complete response, partial response, stable disease ≥ 16 weeks).Results:Of 1,145 submitted cases, 500 patients, including 164 patients with rare cancers, started one of the 25 available drugs and were evaluable for treatment outcome. The overall clinical benefit rate was 33% in both the rare cancer and nonrare cancer subgroup. Inactivating alterations of CDKN2A and activating BRAF aberrations were overrepresented in patients with rare cancer compared with nonrare cancers, resulting in more matches to CDK4/6 inhibitors (14% vs. 4%; P ≤ 0.001) or BRAF inhibitors (9% vs. 1%; P ≤ 0.001). Patients with rare cancer treated with small-molecule inhibitors targeting BRAF experienced higher rates of clinical benefit (75%) than the nonrare cancer subgroup.Conclusions:Comprehensive molecular testing in patients with rare cancers may identify treatment opportunities and clinical benefit similar to patients with common cancers. Our findings highlight the importance of access to broad molecular diagnostics to ensure equal treatment opportunities for all patients with cancer.

Purpose:The strategy of combining endocrine therapy with PI3K-mTOR inhibition has shown promise in estrogen receptor (ER)–positive breast cancer, but new agents and combinations with a better therapeutic index are urgently needed. Taselisib is a potent, selective, beta-isoform–sparing PI3 kinase inhibitor.Patients and Methods:30 patients with ER-positive, metastatic breast cancer who had failed prior endocrine therapy were treated with escalating doses of taselisib (2 or 4 mg in an intermittent or continuous schedule) combined with tamoxifen 20 mg once daily in this phase 1b study using a “rolling six” design.Results:Taselisib combined with tamoxifen was generally well tolerated, with treatment-emergent adverse events as expected for this class of drugs, including diarrhea (13 patients, 43%), mucositis (10 patients, 33%), and hyperglycemia (8 patients, 27%). No dose-limiting toxicities were observed. Objective responses were seen in 6 of 25 patients with RECIST-measurable disease (ORR 24%). Median time to disease progression was 3.7 months. Twelve of 30 patients (40%) had disease control for 6 months or more. Circulating tumor (ct)DNA studies using next-generation tagged amplicon sequencing identified early indications of treatment response and mechanistically relevant correlates of clinical drug resistance (e.g., mutations in KRAS, ERBB2) in some patients.Conclusions:Taselisib can be safely combined with tamoxifen at the recommended phase 2 dose of 4 mg given once daily on a continuous schedule. Preliminary evidence of antitumor activity was seen in both PIK3CA mutant and wild-type cancers. The randomized phase 2 part of POSEIDON (testing tamoxifen plus taselisib or placebo) is currently recruiting.

This file contains details on loco-regional control, progression free survival and overall survival split by treatment arm.

This file contains Supplementary Methods: radiotherapy details (I), treatment schedules (II), definition of Dose Limiting Toxicity (III) and a schedule of assessments (IV).

Supplementary data to Steenbruggen TG, van Seijen M, Janssen LM, van Ramshorst MS, van Werkhoven E, Vrancken Peeters MJTDF, et al. Prognostic value of residual disease after neoadjuvant therapy in HER2-positive breast cancer evaluated by Residual Cancer Burden, Neoadjuvant Response Index & Neo-Bioscore. Table S1, Table S2, Table S3, Table S4, Text and legend Figure S1

This file contains details on the pharmacokinetic profile (I) and parameters (II) of olaparib.

Purpose:To identify an MTD of olaparib, a PARP inhibitor, in combination with loco-regional radiotherapy with/without cisplatin for the treatment of non–small cell lung cancer (NSCLC).Patients and Methods:Olaparib dose was escalated in two groups: radiotherapy (66 Gy/24 fractions in 2.75 Gy/fraction) with and without daily cisplatin (6 mg/m2), using time-to-event continual reassessment method with a 1-year dose-limiting toxicity (DLT) period. The highest dose level with a DLT probability Results:Twenty-eight patients with loco-regional or oligometastatic disease (39%) were treated: 11 at olaparib 25 mg twice daily and 17 at 25 mg once daily. The lowest dose level with cisplatin was above the MTD due to hematologic and late esophageal DLT. The MTD without cisplatin was olaparib 25 mg once daily. At a latency of 1–2.8 years, severe pulmonary adverse events (AE) were observed in 5 patients across all dose levels, resulting in 18% grade 5 pulmonary AEs. Exploratory analyses indicate an association with the radiation dose to the lungs. At the MTD, olaparib reduced PAR levels by more than 95% and abolished radiation-induced PARylation. Median follow-up of survivors was 4.1 years. Two-year loco-regional control was 84%, median overall survival in patients with locally advanced NSCLC was 28 months.Conclusions:Combined mildly hypofractionated radiotherapy and low-dose daily cisplatin and olaparib was not tolerable due to esophageal and hematologic toxicity. Severe pulmonary toxicity was observed as well, even without cisplatin. More conformal radiotherapy schedules with improved pulmonary and esophageal sparing should be explored.

Supplementary Table from Patients with Rare Cancers in the Drug Rediscovery Protocol (DRUP) Benefit from Genomics-Guided Treatment

Supplementary Table 1

This file contains details on pulmonary function changes in diffusion tests (I) and spirometry tests (II), and the incidence of severe pulmonary adverse events by treatment arm (III).

Figure S1 from Prognostic Value of Residual Disease after Neoadjuvant Therapy in HER2-Positive Breast Cancer Evaluated by Residual Cancer Burden, Neoadjuvant Response Index, and Neo-Bioscore

Supplementary Methods Text

Supplementary Table from Differential Survival and Therapy Benefit of Patients with Breast Cancer Are Characterized by Distinct Epithelial and Immune Cell Microenvironments

This file contains the radiation doses to organs at risk (I) and details on systemic treatment (II).

Supplementary Figure from Differential Survival and Therapy Benefit of Patients with Breast Cancer Are Characterized by Distinct Epithelial and Immune Cell Microenvironments

This file contains details on DLT (I) and DLT probabilities according to TITE-CRM in the CCRT arm (II) and (SC)RT study arm (III).

Taselisib pharmacokinetics in combination with tamoxifen

PIK3CA mutations detected at baseline (in samples from 8 out of 30 patients)

Supplementary Legend

Background Pertuzumab greatly improves pathologic complete response (pCR) rates in early stage HER2-positive breast cancer. Long-term benefit of pertuzumab, however, is less well established, as follow-up of the NEOSPHERE and APHINITY trials did not show clear improvement in overall survival, although patients with high risk of recurrence (e.g. node positive) appeared to benefit. Since its long-term benefit remains uncertain, we compared outcome of patients treated with or without pertuzumab in a quasi-random experiment using real-world data. Methods We identified all patients with stage II-III HER2-positive breast cancer in the Netherlands treated with neoadjuvant trastuzumab containing chemotherapy between November 2013 and January 2016 from the nationwide Netherlands Cancer Registry. During this period, reimbursement of pertuzumab in the Netherlands was pending and pertuzumab was only available as trial medication for patients in 37 hospitals that participated in the TRAIN-2 study. This setting created a unique opportunity to compare two quasi-random cohorts of patients treated with or without pertuzumab. We used logistic regression analysis to evaluate the association between pertuzumab use and pCR (ypT0/is, ypN0) and Kaplan-Meier estimates and Cox regression analysis for the association with overall survival (OS). Multivariate analyses included age, cT-status, cN-status, hormone receptor (HR) status and grade. Multiple imputation was used to impute missing data for multivariate analysis. Results We identified 1,124 eligible patients of whom 453 (40%) had received pertuzumab. Baseline characteristics were comparable with and without pertuzumab: 61% of tumors were cT2, 22% cT3, 66% were node positive and 62% ER and/or PR-positive. Grade was missing for 17% in patients treated with and 46% in patients treated without pertuzumab and therefor imputed. PCR in breast and axilla could be determined in 1,091 patients. Pertuzumab use improved pCR rates (65% vs 41%, adjusted odds ratio [aOR] 3.01; 95% confidence interval [CI] 2.29-3.97; p Conclusion This real-world quasi-experiment confirms the efficacy of pertuzumab to achieve a pCR in stage II and III HER2-positive breast cancer. In addition, these data suggest a small absolute overall survival benefit with pertuzumab, most prominently in hormone receptor negative and node positive tumors. Despite the unique setting of two quasi-random cohorts treated with or without pertuzumab and very similar baseline characteristics, residual confounding cannot be fully excluded. Breast cancer specific evaluation and translational work including central revision of tumor grade for missing cases is pending. pCR (%)3-yr OS (%)Ptzno PtzPtzno PtzaHR (95%CI)Overall65%41%98%95%0.61 (0.38-1.00)HR-positive51%32%98%97%0.70 (0.36-1.33)HR-negative86%55%97%92%0.54 (0.26-1.13)cN071%46%99%100%0.54 (0.14-2.00)cN+62%38%97%93%0.65 (0.39-1.09) Citation Format: Anna van der Voort, Marte Liefaard, Mette van Ramshorst, Erik van Werkhoven, Astrid Scholten, Jelle Wesseling, Marie-Jeanne Vrancken Peeters, Linda de Munck, Gabe Sonke. Pathologic complete response and 3-year survival with or without pertuzumab using real-world data of stage II and III HER2-positive breast cancer [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS10-07.

To this day, targeted treatment options for patients with triple negative metastatic breast cancer (TNBC) are still virtually absent. Previously, we showed that elevated expression of the tyrosine kinase FER is an independent prognosticator that correlates with poor survival of high-grade and basal/TNBC patients. Here, we show that high FER levels are also associated with improved outcome after adjuvant taxane-based combination chemotherapy, in high-risk, HER2-negative patients. In TNBC cells, we observed a causal relation between high FER levels and sensitivity to taxanes. Our proteomics and mechanistic studies demonstrated that FER regulates endosomal recycling, a microtubule-dependent process that underpins breast cancer cell invasion. Using chemical genetics, we identified DCTN2 as a novel FER substrate. Our work indicates that the DCTN2 tyrosine 6 is essential for tubular recycling domains development in early endosomes and subsequent propagation of TNBC cell invasion in 3D. In conclusion, we show that high FER expression promotes endosomal recycling and represents a candidate predictive marker for benefit of adjuvant taxane-containing chemotherapy in high-risk patients, including TNBC patients. Citation Format: Sandra Tavares, Nalan Liv, Milena Pasolli, Mark Opdam, Max Ratze, Manuel Saornil, Lilian Sluimer, Rutger Hengeveld, Robert van Es, Erik van Werkhoven, Harmjan Vos, Holger Rehmann, Boudewijn Burgering, Hendrika Oosterkamp, Susanne Lens, Judith Klumperman, Sabine Linn, Patrick Derksen. FER regulates endosomal recycling and is a candidate predictor for taxane benefit in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB203.

Introduction: Early signs of clinical activity are an important factor in the decision to advance development of novel targeted drugs. Response Evaluation Criteria In Solid Tumors (RECIST) has limited value however, as many patients with relatively slowly growing tumors will end up in the Stable Disease (SD) group, obscuring the distinction between a slow natural course of disease or treatment effect. Furthermore, when determining therapeutic efficacy across tumor types using progression free survival, there is also no correction for the individual tumor's natural growth rate. To address this, we developed the Time To Progression (TTP) ratio, a novel clinical trial efficacy endpoint that is based on volumetrics and an intra-patient control. Methods: A prospective multicenter biomarker discovery study (CPCT-03, NCT01566279) was designed. Unselected cancer patients, without regular treatment options, were included and received treatment with the mTOR inhibitor everolimus. Treatment response was determined using both RECIST and the volumetric TTP ratio. The TTP ratio was defined as TTP1/TTP2, i.e. the quotient of the time to a prospectively determined ?30% volumetric increase in target lesions or occurrence of new lesions before treatment (TTP1) and on-treatment (TTP2). Response was classified as a TTP ratio of Results: Seventy-three patients were included, of whom 59 patients started treatment with everolimus. A TTP ratio could be determined in 43 of these patients (73%). According to RECIST, 35 patients (59%) had SD and one patient demonstrated a partial response (PR), while only 21 patients (36%) met the pre-specified criteria for treatment success according to our volumetric TTP ratio. Whereas RECIST (SD+PR) and TTP ratio were both correlated with OS (p rank test), TTP ratio also differentiated which patients had a longer median OS within the SD RECIST group (n = 28). TTP ratio responders had a median OS of 11 months (95% CI 4.4-17.6), compared to 5 months (95%CI 3.2-6.8) for non-responders (p = 0.0496, log-rank test). The inter-observer agreement (Krippendorff's alpha) for volumetric measurements was 0.78 (95%CI 0.70-0.87) for a total of 199 evaluated scans. Conclusion: These results suggest that volumetric TTP ratio is a reliable method to determine response, with a high inter-observer agreement. The TTP ratio correlates to OS and distinguishes which patients within the RECIST SD group had longer survival, which could be interpreted as a sign of clinical benefit. The TTP ratio may be an important tool to guide early clinical drug development and deserves further investigation. Citation Format: Fleur Weeber, Geert A. Cirkel, Christa G.M. Gadellaa - van Hooijdonk, Sander Bins, Marlous Hoogstraat, Erik van Werkhoven, Stefan M. Willems, Marijn van Stralen, Wouter B. Veldhuis, Nicolle J.M. Besselink, Neeltje Steeghs, Maja J. de Jonge, Marlies H.G. Langenberg, Edwin Cuppen, Jan H. Schellens, Stefan Sleijfer, Martijn P.J.K. Lolkema, Emile E. Voest. The time to progression ratio: a new individualized volumetric parameter for early detection of clinical benefit of targeted therapies. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr CT113.