Ipilimumab and nivolumab combined with anthracycline-based chemotherapy in metastatic hormone receptor-positive breast cancer: a randomized phase 2b trial

BACKGROUND

Immune checkpoint inhibitors have shown minimal clinical activity in hormone receptor-positive metastatic breast cancer (HR+mBC). Doxorubicin and low-dose cyclophosphamide are reported to induce immune responses and counter regulatory T cells (Tregs). Here, we report the efficacy and safety of combined programmed cell death protein-1/cytotoxic T-lymphocyte-associated protein 4 blockade concomitant with or after immunomodulatory chemotherapy for HR+mBC.

METHODS

Patients with HR+mBC starting first-/second- line chemotherapy (chemo) were randomized 2:3 to chemotherapy (pegylated liposomal doxorubicin 20 mg/m2 every second week plus cyclophosphamide 50 mg by mouth/day in every other 2-week cycle) with or without concomitant ipilimumab (ipi; 1 mg/kg every sixth week) and nivolumab (nivo; 240 mg every second week). Patients in the chemo-only arm were offered cross-over to ipi/nivo without chemotherapy. Co-primary endpoints were safety in all patients starting therapy and progression-free survival (PFS) in the per-protocol (PP) population, defined as all patients evaluated for response and receiving at least two treatment cycles. Secondary endpoints included objective response rate, clinical benefit rate, Treg changes during therapy and assessment of programmed death-ligand 1 (PD-L1), mutational burden and immune gene signatures as biomarkers.

RESULTS

Eighty-two patients were randomized and received immune-chemo (N=49) or chemo-only (N=33), 16 patients continued to the ipi/nivo-only cross-over arm. Median follow-up was 41.4 months. Serious adverse events occurred in 63% in the immune-chemo arm, 39% in the chemo-only arm and 31% in the cross-over-arm. In the PP population (N=78) median PFS in the immune-chemo arm was 5.1 months, compared with 3.6 months in the chemo-only arm, with HR 0.94 (95% CI 0.59 to 1.51). Clinical benefit rates were 55% (26/47) and 48% (15/31) in the immune-chemo and chemo-only arms, respectively. In the cross-over-arm (ipi/nivo-only), objective responses were observed in 19% of patients (3/16) and clinical benefit in 25% (4/16). Treg levels in blood decreased after study chemotherapy. High-grade immune-related adverse events were associated with prolonged PFS. PD-L1 status and mutational burden were not associated with ipi/nivo benefit, whereas a numerical PFS advantage was observed for patients with a high Treg gene signature in tumor.

CONCLUSION

The addition of ipi/nivo to chemotherapy increased toxicity without improving efficacy. Ipi/nivo administered sequentially to chemotherapy was tolerable and induced clinical responses.

TRIAL REGISTRATION NUMBER

ClinicalTrials.gov Identifier: NCT03409198.

Circulating Tumor Cells in Breast Cancer Patients Treated by Neoadjuvant Chemotherapy: A Meta-analysis

Background

We conducted a meta-analysis in nonmetastatic breast cancer patients treated by neoadjuvant chemotherapy (NCT) to assess the clinical validity of circulating tumor cell (CTC) detection as a prognostic marker.

Methods

We collected individual patient data from 21 studies in which CTC detection by CellSearch was performed in early breast cancer patients treated with NCT. The primary end point was overall survival, analyzed according to CTC detection, using Cox regression models stratified by study. Secondary end points included distant disease-free survival, locoregional relapse-free interval, and pathological complete response. All statistical tests were two-sided.

Results

Data from patients were collected before NCT (n = 1574) and before surgery (n = 1200). CTC detection revealed one or more CTCs in 25.2% of patients before NCT; this was associated with tumor size (P < .001). The number of CTCs detected had a detrimental and decremental impact on overall survival (P < .001), distant disease-free survival (P < .001), and locoregional relapse-free interval (P < .001), but not on pathological complete response. Patients with one, two, three to four, and five or more CTCs before NCT displayed hazard ratios of death of 1.09 (95% confidence interval [CI] = 0.65 to 1.69), 2.63 (95% CI = 1.42 to 4.54), 3.83 (95% CI = 2.08 to 6.66), and 6.25 (95% CI = 4.34 to 9.09), respectively. In 861 patients with full data available, adding CTC detection before NCT increased the prognostic ability of multivariable prognostic models for overall survival (P < .001), distant disease-free survival (P < .001), and locoregional relapse-free interval (P = .008).

Conclusions

CTC count is an independent and quantitative prognostic factor in early breast cancer patients treated by NCT. It complements current prognostic models based on tumor characteristics and response to therapy.

Abstract 3049: Tracing the origin of disseminated tumor cells in breast cancer using single-cell sequencing

Background. Single-cell micro-metastases of solid tumors often occur in the bone marrow. These disseminated tumor cells (DTCs) may resist therapy and lay dormant or progress to cause overt bone and visceral metastases. The molecular nature of DTCs remains elusive, as well as when and from where in the tumor they originate. Here, we apply single-cell sequencing to identify and trace the origin of DTCs in breast cancer.

Results. We sequence the genomes of 63 single cells isolated from six non-metastatic breast cancer patients. By comparing the cells’ DNA copy number aberration (CNA) landscapes with those of the primary tumors and lymph node metastasis, we establish that 53% of the single cells morphologically classified as tumor cells are DTCs disseminating from the observed tumor. The remaining cells represent either non-aberrant ‘normal’ cells or ‘aberrant cells of unknown origin’ that have CNA landscapes discordant from the tumor. Further analyses suggest that the prevalence of aberrant cells of unknown origin is age-dependent, and that at least a subset is hematopoietic in origin. Evolutionary reconstruction analysis of bulk tumor and DTC genomes enables ordering of CNA events in molecular pseudo-time and traced the origin of the DTCs to either the main tumor clone, primary tumor subclones, or subclones in an axillary lymph node metastasis.

Conclusions. Single-cell sequencing of bone marrow epithelial-like cells, in parallel with intra-tumor genetic heterogeneity profiling from bulk DNA, is a powerful approach to identify and study DTCs, yielding insight into metastatic processes. A heterogeneous population of CNA-positive cells is present in the bone marrow of non-metastatic breast cancer patients, only part of which are derived from the observed tumor lineages.

Citation Format: Jonas Demeulemeester, Parveen Kumar, Elen K. Møller, Silje Nord, David C. Wedge, April Peterson, Randi R. Mathiesen, Renathe Fjelldal, Masoud Z. Esteki, Koen Theunis, Elia F. Gallardo, Jason Grundstad, Elin Borgen, Lars O. Baumbusch, Anne-Lise Børresen-Dale, Kevin P. White, Vessela N. Kristensen, Peter Van Loo, Thierry Voet, Bjørn Naume. Tracing the origin of disseminated tumor cells in breast cancer using single-cell sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3049. doi:10.1158/1538-7445.AM2017-3049

Tracing the origin of disseminated tumor cells in breast cancer using single-cell sequencing

BACKGROUND

Single-cell micro-metastases of solid tumors often occur in the bone marrow. These disseminated tumor cells (DTCs) may resist therapy and lay dormant or progress to cause overt bone and visceral metastases. The molecular nature of DTCs remains elusive, as well as when and from where in the tumor they originate. Here, we apply single-cell sequencing to identify and trace the origin of DTCs in breast cancer.

RESULTS

We sequence the genomes of 63 single cells isolated from six non-metastatic breast cancer patients. By comparing the cells' DNA copy number aberration (CNA) landscapes with those of the primary tumors and lymph node metastasis, we establish that 53% of the single cells morphologically classified as tumor cells are DTCs disseminating from the observed tumor. The remaining cells represent either non-aberrant "normal" cells or "aberrant cells of unknown origin" that have CNA landscapes discordant from the tumor. Further analyses suggest that the prevalence of aberrant cells of unknown origin is age-dependent and that at least a subset is hematopoietic in origin. Evolutionary reconstruction analysis of bulk tumor and DTC genomes enables ordering of CNA events in molecular pseudo-time and traced the origin of the DTCs to either the main tumor clone, primary tumor subclones, or subclones in an axillary lymph node metastasis.

CONCLUSIONS

Single-cell sequencing of bone marrow epithelial-like cells, in parallel with intra-tumor genetic heterogeneity profiling from bulk DNA, is a powerful approach to identify and study DTCs, yielding insight into metastatic processes. A heterogeneous population of CNA-positive cells is present in the bone marrow of non-metastatic breast cancer patients, only part of which are derived from the observed tumor lineages.

Abstract LB-051: Tumor heterogeneity and dissemination in breast cancer: Deep sequencing of single disseminated cells from bone marrow compared to primary tumor and lymph node metastases

Metastasis is the main cause of death amongst breast cancer patients. Our knowledge of the metastatic cascade and how to inhibit it is limited. Here we dissect the genetic profile of multiple single disseminated tumor cells (DTCs) taken at various time points after diagnosis, and compare them to their matched primary tumors and lymph node metastasis. We have previously published a method for studying CNAs in single DTCs by whole genome sequencing, where we compared two primary breast carcinomas to two corresponding DTCs. Copy number profiles from whole genome sequencing (WGS) from 40 DTCs were analyzed. The single cell whole genome amplified (WGA) DNA was used to generate WGS libraries, and the DTCs were subsequently sequenced on the Illumina HiSeq 2000. The WGS reads were trimmed for WGA adapters and aligned to GRCh37 human reference using Burrows-Wheeler Aligner (BWA). LogR values were calculated for genomic bins and corrected for% GC-bias and segmented using the piecewise constant fitting (PCF) algorithm (the penalty parameter, γ, was set to 25). Copy number was estimated per segment as 2logR × Ψ, where Ψ is the average ploidy. B allele frequency (BAF) was calculated for each known SNP position from dbSNP (dbSNP build 135) and somatic mutations read-outs generated. In this study we compared the mutation spectre and CNAs in six primary tumors, one with corresponding lymph node metastasis and single DTCs. In total, CN profile from 40 DTCs showed evidence of dissemination at both early and late stage of disease progression. At large, the copy number profile of the examined DTCs exhibited either a limited number of alterations, or a pattern similar to the primary tumor and lymph node metastasis suggesting continuous dissemination of single tumor cells throughout the tumor evolution. By demonstrating sub-clonality in the lymph node metastasis we provide novel insight into the metastatic process. Further, the correlation in aberration pattern between the lymph node metastasis and multiple DTCs, implies that cells found in the bone marrow may have originated from the lymph node metastasis. The DTCs exhibited common aberrations typically found in breast carcinomas, and several DTCs had deletion of 16q and17p, and gain of 1q, 8q. Certain DTCs exhibited CNAs not visible in the primary tumor or lymph node including gain of 9q, 14q, 19q and Xq, and loss of 2p, 6p, 8p, 18p and 19p. Two DTCs from time of diagnosis exhibited gain of the whole chromosome 5 that was not observed in the primary tumor or the lymph node. These results reveal the importance of assessing the sub-clonal genetic alterations in the primary tumor, as well as in the lymph node metastasis and DTCs, in order to evaluate patient treatment and prognosis.

Citation Format: Elen Møller, Parveen Kumar, Silje Nord, David Wedge, Peter van Loo, April Peterson, Randi R. Mathiesen, Renathe Fjelldal, Masoud Z. Esteki, Jason A. Grundstad, Elin Borgen, Lars O. Baumbusch, Anne-Lise Børresen-Dale, Kevin P. White, Thierry Voet, Bjørn Naume, Vessela N. Kristensen. Tumor heterogeneity and dissemination in breast cancer: Deep sequencing of single disseminated cells from bone marrow compared to primary tumor and lymph node metastases. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr LB-051. doi:10.1158/1538-7445.AM2015-LB-051

Next-generation sequencing of disseminated tumor cells

Disseminated tumor cells (DTCs) detected in the bone marrow have been shown as an independent prognostic factor for women with breast cancer. However, the mechanisms behind the tumor cell dissemination are still unclear and more detailed knowledge is needed to fully understand why some cells remain dormant and others metastasize. Sequencing of single cells has opened for the possibility to dissect the genetic content of subclones of a primary tumor, as well as DTCs. Previous studies of genetic changes in DTCs have employed single-cell array comparative genomic hybridization which provides information about larger aberrations. To date, next-generation sequencing provides the possibility to discover new, smaller, and copy neutral genetic changes. In this study, we performed whole-genome amplification and subsequently next-generation sequencing to analyze DTCs from two breast cancer patients. We compared copy-number profiles of the DTCs and the corresponding primary tumor generated from sequencing and SNP-comparative genomic hybridization (CGH) data, respectively. While one tumor revealed mostly whole-arm gains and losses, the other had more complex alterations, as well as subclonal amplification and deletions. Whole-arm gains or losses in the primary tumor were in general also observed in the corresponding DTC. Both primary tumors showed amplification of chromosome 1q and deletion of parts of chromosome 16q, which was recaptured in the corresponding DTCs. Interestingly, clear differences were also observed, indicating that the DTC underwent further evolution at the copy-number level. This study provides a proof-of-principle for sequencing of DTCs and correlation with primary copy-number profiles. The analyses allow insight into tumor cell dissemination and show ongoing copy-number evolution in DTCs compared to the primary tumors.

Abstract P1-08-21: Detection and monitoring of circulating endothelial cells, circulating tumor cells and disseminated tumor cells during neoadjuvant breast cancer treatment including bevacizumab

Background: Results from studies with bevacizumab in addition to traditional neoadjuvant therapy (NAT) indicate a need for predictive biomarkers. As a sub-study of the NeoAva study (a neoadjuvant study), the aim was to investigate the potential association between the presence of circulating endothelial cells (CECs) in peripheral blood (PB), circulating tumor cells (CTCs) in PB and disseminated tumor cells (DTCs) in bone marrow (BM) at different time points during NAT +/- bevacizumab and at one year follow-up, and therapy response.

Patients and methods: A total of 150 HER2-negative patients with cT2-4 (≥ 2.5cm) N0-3 M0 status were randomized to receive NAT with or without bevacizumab. In this sub-study, 90 patients have so far been analyzed. Of these, 82 received chemotherapy (FEC100→taxane) and 8 received endocrine therapy (letrozole) + / - bevacizumab. Therapy response was evaluated according to the RECIST criteria and achievement of pathological complete response (pCR). Number of CECs, CTCs and DTCs were assessed at baseline after 12 weeks, at surgery (after 24 weeks) and at one year follow-up. Blood samples were analyzed by CellSearch® to assess CEC and CTC counts. The detection of DTCs was performed by immunocytochemical analysis of 2 × 106 BM mononuclear cells.

Results: The pathological complete response rate was 10 out of 90 (11.1%), eight of these patients received bevacizumab. For bevacizumab-treated patients with a change in CEC counts from baseline to time of surgery below median change (27 CECs), 35% (6/17) achieved pCR compared to 6% (1/18) in the group with a CEC count-increase above median change (p = 0.035). The corresponding pCR rates for patients not receiving bevacizumab (median CEC change 131 CECs) were 0% (0/15) and 13% (2/14), respectively. Stepwise testing of thresholds for CEC changes in the bevacizumab-arm revealed significant associations to pCR for change-values between 20 and 40. CTC- and DTC-status or -changes were not associated with tumor response or CEC changes.

Conclusion:

The presented results indicate that the level of change in the number of circulating endothelial cells during neoadjuvant therapy including bevacizumab is associated with the pathological complete response rate in breast cancer patients. This supports additional testing of CECs as a surrogate marker for response to this treatment. The analyses will be up-dated with results from the rest of the included patients.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr P1-08-21.

Abstract P3-06-17: Detection and monitoring of circulating endothelial cells, circulating tumor cells and disseminated tumor cells during neoadjuvant treatment including an anti-angiogenic agent

Withdrawn by Author

Citation Information: Cancer Res 2012;72(24 Suppl):Abstract nr P3-06-17.

Persistence of disseminated tumor cells after neoadjuvant treatment for locally advanced breast cancer predicts poor survival

Introduction

Presence of disseminated tumor cells (DTCs) in bone marrow (BM) and circulating tumor cells (CTC) in peripheral blood (PB) predicts reduced survival in early breast cancer. The aim of this study was to determine the presence of and alterations in DTC- and CTC-status in locally advanced breast cancer patients undergoing neoadjuvant chemotherapy (NACT) and to evaluate their prognostic impact.

Methods

Bone marrow and peripheral blood were collected before NACT (BM1: n = 231/PB1: n = 219), at surgery (BM2: n = 69/PB2: n = 71), and after 12 months from start of NACT (BM3: n = 162/PB3: n = 141). Patients were included from 1997 to 2003 and followed until 2009 (or ten years follow-up). DTC- and CTC-status were determined by morphological evaluation of immunocytochemically detected cytokeratin-positive cells. The prognostic significance of DTCs/CTCs was assessed by univariate and multivariate Cox-regression analyses.

Results

Before NACT, DTCs and CTCs were detected in 21.2% and 4.9% of the patients, respectively. At surgery, 15.9% and 1.4% had DTC- and CTC-presence, compared to 26.5% and 4.3% at 12 months from start of NACT. Of patients for whom DTC results both before NACT and at 12 months were available, concordant results were observed in 68%, and 14 out of 65 had positive DTC-status at both time points. Presence of ≥ 1 DTC 12 months from start of NACT, but not at other time points, predicted reduced disease-free survival (DFS; HR 2.3, p = 0.003), breast cancer-specific survival (BCSS; HR 3.0, p < 0.001) and overall survival (OS; HR 2.8, p < 0.001). Before NACT, presence of ≥ 3 DTCs was also associated with unfavorable outcome, and reduced BCSS was observed for CTC-positive patients (HR 2.2, p = 0.046). In multivariate analysis, DTC status (</≥ 1 DTC) at 12 months after start of NACT remained as a prognostic factor for both DFS (HR 2.2, p = 0.005), BCSS (HR 2.6, p = 0.002) and OS (HR 2.6, p = 0.002). The survival for patients with change in DTC-status was determined by the DTC-status at 12 months.

Conclusion

Presence of DTCs after NACT indicated high risk for relapse and death, irrespective of the DTC-status before treatment. The results supports the potential use of DTC analysis as a monitoring tool during follow up, for selection of patients to secondary treatment intervention within clinical trials.

P4-06-05: Prognostic Impact of Disseminated and Circulating Tumor Cells in Patients Treated for Locally Advanced Breast Cancer

INTRODUCTION: Neoadjuvant systemic therapy (NST) in breast cancer patients is an established approach to reduce tumor size prior to surgery and to assess the clinical effect of therapy on the breast cancer disease. The current study was designed to identify primary tumor resistance factors to epirubicin and paclitaxel therapy in patients with locally advanced breast cancer (Chrisanthar et al PLoSOne 2008 and 2011). As a substudy, the incidence of disseminated tumor cells (DTCs) and circulating tumor cells (CTCs) before and after therapy, was investigated. The aim was to evaluate the prognostic impact of DTCs and CTCs as well as to evaluate the effect of NST on DTCs and CTCs.

PATIENTS AND METHODS: Patients with locally advanced non-inflammatory breast cancer (T3-4and/or N2) were included in the study. The patients were randomly allocated to primary treatment either with epirubicin 90mg/m2 or paclitaxel 200mg/m2, with cross-over design if no response/progression, followed by mastectomy and axillary dissection. Bone marrow (BM) aspiration and peripheral blood (PB) samples were collected before NST (BM1/PB1)(n=230), at the time of surgery (BM2/PB2)(n=69; logistic reasons caused reduced sampling) and 12 months after randomization (BM3/PB3)(n=162). Detection of DTCs/CTCs was performed by standard immunocytochemical analysis of 2×106 mononuclear cells stained for cytokeratin by AE1AE3 antibodies. Patient outcomes were evaluated over a 10-year follow-up period. Univariate and multivariable proportional hazards models were estimated to assess the prognostic significance of DTC for disease-free survival (DFS) and overall survival (OS).

RESULTS: Before NST (BM1) 21.3% were DTC positive, compared to 15.9% and 26.5% at BM2 and BM3, respectively. Of those that both had BM1 and BM3 performed, 68% concordance and 22% overlap among positive cases was observed. Presence of DTCs in BM3 predicted reduced DFS (HR 2.2; 95% CI 1.3−3.7; p=0.007) and OS (HR 3.0; 95% CI 1.8−5.2; p&gt;0.001). DTC status before NST had no impact on outcome. No difference in the results was observed after exclusion of patients with limited M1 status at diagnosis (25 and 13 of those analysed for BM1 and BM3, respectively). The incidence of CTCs before NST was 4.9 % compared to 1.4% and 4.3 % at PB2 and PB3, respectively. Presence of CTC before NST was associated with reduced overall survival (HR 2.4; 95% CI 1.2−5.0; p=0.018), but CTC status was not significant for DFS or at other time points. In the multivariable analysis, DTC status at BM3 remained as a prognostic factor for both DFS (HR 2.0; 95% CI 1.1−3.6) and OS (HR 2.1; 95% CI 1.04−4.2).

CONCLUSION: In patients with locally advanced breast cancer, the presence of CTCs at the time of diagnosis identified high risk patients. However, the sensitivity of the performed CTC analysis was too low for further interpretation. Presence of DTCs 12 months after neoadjuvant therapy increased the risk for relapse and death. The best clinical utility of DTC analysis appears to be as a monitoring tool during follow up, in a “window of opportunity” for selection of patients to secondary adjuvant treatment intervention within clinical trials.

Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P4-06-05.

High-resolution analyses of copy number changes in disseminated tumor cells of patients with breast cancer

The presence of disseminated tumor cells (DTCs) in bone marrow (BM) identifies breast cancer patients with less favorable outcome. Furthermore, molecular characterization is required to investigate the malignant potential of these cells. This study presents a single-cell array comparative genomic hybridization (SCaCGH) method providing molecular analysis of immunomorphologically detected DTCs. The resolution limit of the method was estimated using the cancer cell line SK-BR-3 on 44 and 244k arrays. The technique was further tested on 28 circulating tumor cells and four hematopoietic cells (HCs) from peripheral blood (n = 8 patients). The SCaCGH method was finally applied to 24 DTCs, three immunopositive cells morphologically classified as probable HCs from breast cancer patients and five HC controls from BM (n = 7 patients plus n = 1 healthy donor). The frequency of copy number changes of the DTCs revealed similarities with primary breast tumor samples. Three of the patients had available profiles for DTCs and the corresponding tumor tissue from primary surgery. More than two-third of the analyzed DTCs disclosed equivalent changes, both to each other and to the corresponding primary disease, whereas the rest of the cells showed balanced profiles. The probable HCs revealed either balanced profiles (n = 2) or changes comparable to the tumor tissue and DTCs (n = 1), indicating morphological overlap between HCs and DTCs. Similar aberration patterns were visible in DTCs collected at diagnosis and at 3 years relapse-free follow-up. SCaCGH may be a powerful tool for the molecular characterization of DTCs.