Abstract PS2-05: Genetic profiling for circulating tumor cell clusters to unveil molecular drivers of metastasis

Introduction: Although CTCs display the same spatial and temporal heterogeneity as the primary tumor, they represent a privileged window to disclose mechanisms of metastases. A portion of CTCs may form clusters that contain two or more CTCs bound together which were reported to have up to 50-fold of potential of forming distant metastasis in MBC as compared to individual CTCs (Aceto N. Cell, 2015). However, genomic characterization of CTCs-clusters compared to single CTCs remain largely unknown. We previously reported single CTC sequencing for HER2+ CTCs (2020 AACR #3120). Herein, we report a new finding of heterogeneity profiling for CTC-clusters compared to single CTCs, which would be helpful to evaluate the MBC metastasis capability and treatment in clinic. Methods: Whole blood sample (7.5ml/each) was collected from stage III/IV MBC patients before therapy. CTC enumeration was performed using the FDA-cleared CellSearch™ System (Menarini) targeting the EpCAM antigen for capturing CTCs which were then stained by Anti-CK-PE, DAPI, anti-CD45-APC and anti-HER2-FITC. The CTC-clusters and single CTCs were isolated using DEPArrayTM System (Menarini). DNA was isolated from CTC-clusters and single CTCs by ArcturusTM PicoPureTM DNA Extraction kit. The initial library was prepared by SMARTer® PicoPLEX® Gold Single Cell DNA-Seq Kit, and the exome capture was performed by Twist Human Core Exome EF Multiplex Complete Kit. The sequencing was prepared by NextSeq 500 mid output V2.5 kit and was performed on the NextSeq 500 (Illumina). It was a paired end run, 75×75 bps run with dual indexing. Results: We identified 107 CTCs by CellSearch™, including 93 single CTCs, 14 CTC-clusters and 145 WBCs. Autologous CTC-clusters (CK+DAPI+CD45-, Group 1), single CTCs (CK+DAPI+CD45-, Group 2), and leukocytes (CK-DAPI+CD45+, Group 3) were sequenced respectively. The sequencing data was processed following the GATK pipeline and annotated using SnpEff. There were 60,638 counts (6.77%) and 70,334 counts (8.20%) for exon variants in CTC-clusters and single CTCs respectively, 507,595 counts (56.69%) and 486,119 counts (56.69%) for intron variants, 194,026 (21.67%) and 175,819 counts (20.51%) for intergenic variants, 54,174 counts (6.05%) and 50,370 counts (5.87%) for downstream genes, 51,716 counts (5.78%) and 45,915 counts (5.36%) for upstream genes, and 3.04% and 3.37% of others variants in CTC-clusters and single CTCs respectively. Meanwhile, there was 0 count for exon and intron variants found in Group 3. There were 60 and 79 gene variants (SNP and Ins-Del) identified to have the highest impact effect (≥20) on CTC-clusters and single CTC exons respectively, which affect significantly on the functional proteins coding. Among the top 50 high impact gene variants in each group, there were 25 gene alteration sites were similar in Group 1 and 2, including XYLB, RAN, QPCT, HPGDS, HDAC8, GABBR2, CYP11B2 and CHKA. Specific to Group 1, there were 25 gene alterations which were primarily related to cellular proliferation and tumor promotion (AMD1), liver drug clearance (CES1), tissue remodeling (CHI3L1), immune cytokine signaling (JAK1) and metabolism (ASRGL1). Meanwhile, there are 25 specific gene alterations in Group 2 compared to Group 1, which were associated with nucleotide-excision repair (DDB1 and FAN1) chromosome positioning (KIF11), cell growth, differentiation, mitotic cycle, oncogenic transformation (PTPN3 and MAPK14), apoptosis (CASP1) and cell growth (CTNNB1). Conclusion: Genomic characterization of CTC-clusters compared to autologous single CTCs and leukocytes elucidated new specific gene alterations in CTC-clusters associated with most aggressive disease metastasis in MBC, which will help to gain new insights on the molecular mechanisms associated with the metastasis and find new molecularly driven therapies for disease metastasis.

Citation Format: Qiang Zhang, Lorenzo Gerratana, Paolo D'Amico, Andrew A. Davis, Saya Liz Jacob, Xinkun Wang, Zhe Ji, Zheng Cai, Elena Vagia, Wenan Qiang, Ami Shah, Youbin Zhang, Lisa Flaum, Firas Wehbe, Amir Behdad, William Gradishar, Leonidas Platanias, Massimo Cristofanilli. Genetic profiling for circulating tumor cell clusters to unveil molecular drivers of metastasis [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 PS2-05.

Abstract PS2-06: The detection and enumeration of circulating tumor cells (CTCs) and circulating endothelial cells (CECs) in metastatic breast cancer

Introduction: Circulating tumor cells (CTCs) are the roots of metastasis which is the main cause for death in metastatic breast cancer (MBC). CTCs enumeration is strongly prognostic in advanced disease and can stratify patients in two distinct disease, Stage IV aggressive and Stage IV indolent. In the former disease, the detection of CTC clusters and HER2-expression increase prognostic and predictive value. The metastatic cascade is a complex, regulated process involving immune cells and endothelial cells for progression and neoangiogenesis. Circulating endothelial cells (CECs) from the inner wall of blood vessels are shed into the blood stream during formation of blood vessels which is considered a sensitive marker of endothelial damage in pathological conditions such as cancer. CECs have been also studied as a biomarker for tumor progression and monitoring anti-angiogenic therapeutic effects in MBC. We evaluated the concomitant detection of CTCs and CECs in MBC patients, along with expression of HER2 in CTCs that may offer an interesting clue to elucidate the metastasis mechanisms. Methods: Whole blood samples (7.5ml/each) were collected from 14 stage IV MBC patients before systemic therapy. CTCs enumeration was performed in FDA approved CELLTRACKS System (Menarini) by using CTC Kit contains specific antibodies targeting the EpCAM for capturing CTCs, anti-CK-PE (for epithelial cells), DAPI (for nucleus), anti-CD45-APC (for leukocytes), and anti-HER-2/neu-FLU. The CTCs were classified as CK+, EpCAM+, DAPI+ and CD45-. Meanwhile, the same patients’ blood samples (4.0ml/each) were processed for CEC analyzed by using CEC kit which immunomagnetically captures CD146+ cells, and then stains the cells for CD105-PE (specific for protein endolgin), CD45-APC, nucleus-DAPI. The positive CECs were classified as CD 146+, CD105+, DAPI+ and CD45-. The associations between CTCs, HER2 expression and CECs were evaluated. Results: The average age of patients was 53.1. Subtypes of Luminal, HER2 positive and TNBC were 64.2% 7.2% and 28.6% respectively. Distant metastasis were found in 13 out of 14 patients, including bone (7), liver (5), Lymph nodes (5) and Pleura (2). CTCs were found positive (≥5, Stage IV aggressive) in 5 patients (range: 5-47, mean=24), and HER expression was identified in all 5 of these cases with a range of numbers between 1 and 7 (mean=4.2). The ratios of HER+ CTC/total ratios were 8.51%, 17.95%, 20%, 30.77%, and 33.33%. HER2 expression were defined officially in our lab according to the percentile of positive HER2 CTCs/Total CTCs and the expression intensity as - (<20%), + (20-39%), ++ (40-59%) and +++ (≥60%) respectively. There were 9 patients (%) were identified as CTCs negative (<5, Stage IV indolent) with the mean=1, and HER+ CTCs were found in only 2 patients with Stage IV indolent. Meanwhile, CECs were found in all 14 patients with a range of numbers between 4 to 115. There were an average of 33 CECs in Stage IV aggressive disease, compared to 53 CECs in Stage IV indolent. The average of CECs were 53.44, 12 and 37.25 in Luminal, HER2 positive and TNBC groups respectively. On the other hand, patients with HER2+ CTCs had an average of 50 CECs which is significantly higher than average of 41 CECs in patients without HER2+ CTCs. Moreover, there were average of 94.5, 56 and 40.22 CECs were found in groups when HER2 expression was ++/+++, above + and - respectively. The results demonstrated that although CTC enumeration have a reverse correlation with CECs numbers, HER2 expression in CTCs was significantly related with high CECs numbers. Conclusions: Our data provides the first evidence of potential association between CTCs and CECs in metastatic breast cancer. The association between HER2 expression and CECs offers a potential new insight to mechanism connections between CECs and disease metastasis in MBC.

Citation Format: Qiang Zhang, Paolo D'Amico, Jeannine Donahue, Lorenzo Gerratana, Andrew A. Davis, Saya Liz Jacob, Zheng Cai, Elena Vagia, Wenan Qiang, Ami N. Shah, Katy Kerby, Lisa Flaum, Youbin Zhang, Firas Wehbe, Amir Behdad, William Gradishar, Leonidas Platanias, Massimo Cristofanilli. The detection and enumeration of circulating tumor cells (CTCs) and circulating endothelial cells (CECs) in metastatic 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 PS2-06.

Abstract PS2-20: Prognostic value of baseline circulating tumor cells (CTCs) enumerations is for stage III and stage IV breast cancer

Introduction: Prognosis of metastatic breast cancer (MBC) is initially predicted by the cancer’s characteristics based on AJCC TNM system, including the size of the cancer tumor, invasion into nearby tissue, lymph nodes and other parts of the body beyond the breast. Although additional information including hormone-receptor status, HER2 status, and possibly Oncotype DX score contributed to improve prognostic evaluation, predicting clinical outcomes and treatment benefit for MBC is still a challenge in clinic because of the clinical and biologically heterogeneous condition. We recently reported that CTCs enumeration can classify MBC in two distinct prognostic groups independently of clinical and molecular characteristics (Crit Rev Oncol Hematol. 2019). Moreover, our group reported that CTCs is associated with HER2 expression in MBC which may indicate more aggressive tumor (2019 AACR #1919). Here we compared CTCs enumeration of Stage III and Stage IV, which would be helpful to evaluate the MBC metastasis capability and treatment in clinic. Methods: The study included 38 specimens prospectively collected under IRB-approved protocol from 38 patients with Stage III MBC, and 254 specimens from 254 patients with stage IV MBC who received standard systemic treatments based on disease subtypes at NMH (2016-2020). Duplicate whole blood samples (7.5ml/each) were collected in EDTA tubes from these patients who were longitudinally characterized for CTCs before therapy (baseline). CTCs enrichment and enumeration were performed in FDA approved semi-automated fluorescence CELLTRACKS ANALYZERII® System (Menarini) by using CELLSEARCH® CXC Kit contains antibodies targeting the Epithelial Cell Adhesion Molecule (EpCAM) antigen for capturing CTCs, anti-CK-PE which is specific for the intracellular protein cytokeratin in epithelial cells, DAPI for staining the cell nucleus, anti-CD45-APC is specific for leukocytes (2019 ASCO #1036). The CTCs were classified based on morphology and correct phenotype as CK+, DAPI+ and CD45-. Kruskal-Wallis test was used for statistics. Results: Patients were classified as Luminal, HER2 positive and TNBC disease subtypes in 46.6%, 46.7% and 6.7% respectively in Stage III patients, and 54%, 18% and 28% respectively in Stage IV patients. The patients at age above 50 were 26.% in Stage III group and 68% in Stage IV group respectively. IBC patients represented 61.5% and 33.5% of Stage III and Stage IV patients respectively. Metastasis in liver, lung and bone were diagnosed in 40.7%, 40.2% and 62.8% in Stage IV patients. CTC negative (<5 CTCs) and positive (≥5CTCs) patients were identified in 32/38 (84.22%, group 1) and 6/38 (15.78%, group 2) respectively in Stage III patients, and 149/254 (59%, Stage IV indolent ) and 105/254 (41%, Stage IV aggressive ) respectively in Stage IV patients. Patients in Group 1 have a significantly less recurrence probability than patients in Group 2 (p=0.015). Correspondingly, patients with Stage IV indolent also had significantly longer survival than patients with Stage aggressive disease (p=0.0021). When comparing the all population, Group 1 patients still have the highest survival probability (p=0.00057) within 47 months follow-up survey. More interesting, there was no any CTC-clusters found in all Stage III patients when there were 28 out of 254 stage IV patients (11.02%) were detected with CTC-clusters, who had the worst prognosis in compared to either Stage IV patients without CTC-clusters or Stage III patients (p=0.00035). Conclusions: In this study, we showed that enumeration of baseline CTC and CTC-clusters correlated with worse prognosis even the patients were pathologically diagnosed for the same stage, which provided an additional measure to predict disease recurrence after systemic therapies especially for Stage III MBC patients.

Citation Format: Qiang Zhang, Zheng Cai, Lorenzo Gerratana, Paolo D'Amico, Andrew A. Davis, Saya Liz Jacob, Elena Vagia, Ami N Shah, Lisa Flaum, Youbin Zhang, Wenan Qiang, Firas Wehbe, Amir Behdad, William Gradishar, Leonidas C Platanias, Massimo Cristofanilli. Prognostic value of baseline circulating tumor cells (CTCs) enumerations is for stage III and stage IV 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 PS2-20.

Abstract PS2-33: Investigating oncogenic signaling pathways in inflammatory metastatic breast cancer (MBC) though circulating tumor DNA (ctDNA) next-generation sequencing (NGS)

Background: Inflammatory breast cancer (IBC) has a distinctive and aggressive clinical behavior but its underlying biological characteristics have not been fully elucidated. The extended analysis of somatic alterations in The Cancer Genome Atlas (TCGA) highlighted canonical oncogenic pathways that were consistently represented across different tumor subtypes. The aim of this study was to translate such pathway-based characterization to the clinical setting through ctDNA NGS to dissect IBC’s biology and prognosis.

Methods: The study retrospectively analyzed 255 metastatic breast cancer (MBC) patients (pts) treated and characterized for ctDNA at Northwestern University (Chicago, IL). ctDNA was analyzed using the Guardant360 NGS assay (Guardant Health). Only non-synonymous alterations were analyzed. Pathway classification was defined based on prior work (Sanchez-Vega F et al, Cell. 2018). Associations among clinical characteristics, pathway classification, and IBC were explored through uni- and multivariate logistic regression; survival was tested though uni- and multivariate Cox regression both for progression-free survival (PFS) and overall survival (OS).

Results: Of 255 enrolled pts, 124 (48%) were diagnosed with hormone receptor positive (HR pos) MBC, 75 (30%) with HER2-positive (HER2_pos) MBC and 56 (22%) with triple negative (TNBC) MBC. IBC was diagnosed in 74 pts (30%). Receptor-tyrosine kinase, RTK (130 pts, 51%), p53 (130 pts, 51%), PI3K/Akt (116 pts, 46%), and cell cycle (91 pts, 36%) were the most often altered pathways. The multivariate model highlighted the association of IBC with HER2_pos (OR: 2.19; 95%CI: 1.09 - 4.38; P=0.0276), an increased number of alterations in the p53 pathway (OR: 2.05; 95%CI: 1.12 - 3.75; P=0.0197) and a decreased number of alterations in the RAS pathway (OR: 0.34; 95%CI: 0.14 - 0.80; P=0.0137). Decreased alterations in the ER pathway were borderline significant (OR: 0.48; 95%CI: 0.22 - 1.03; P=0.0584). Only cell cycle alterations had an impact on PFS for IBC (HR: 2.20; 95%CI: 1.18 - 4.08; P=0.0127), while p53 and Wnt had an impact on nonIBC (respectively HR: 2.00; 95%CI: 1.23 - 3.25; P=0.0052 and HR: 3.40; 95%CI: 1.20 - 9.64; P=0.0212). The univariate model showed a significant impact on OS RAF, ER, and cell cycle pathways alterations for IBC, the role of ER and cell cycle pathways alterations was confirmed in the multivariate model (respectively HR: 6.19; 95%CI: 1.63 - 23.48; P=0.0073 and HR: 3.79; 95%CI: 1.04 - 13.75; P=0.0431). The multivariate model showed a prognostic impact only for p53 in the nonIBC subgroup (HR: 2.20; 95%CI: 1.11 - 4.36; P=0.0237)

Conclusion: The ctDNA-based oncogenic signaling pathway characterization showed different biological and prognostic features across IBC and nonIBC MBC patients. Alterations of the p53 pathway were more likely to be present in IBC pts, while alterations in the RAS pathway were less represented in this cohort. ER and cell cycle pathways’ alterations impacted the OS of IBC MBC patients. Although preliminary, these results suggest a more comprehensive biological characterization based on ctDNA for treatment selection and clinical decision-making.

Main alterations and pathwayGeneNumber of alterations%PathwayTP5318815.58p53PIK3CA14111.68PI3K/AktERBB2725.97RTKESR1705.8ERMYC574.72MycFGFR1463.81RTKEGFR453.73RTKCCNE1383.15Cell cycleMET322.65RTKNF1322.65RAS

Citation Format: Lorenzo Gerratana, Andrew A Davis, Marco Mina, Saya L Jacob, Qiang Zhang, Ami N Shah, Paolo D’Amico, Neelima Katam, Firas Wehbe, Elena Vagia, Lisa Flaum, Leonidas Platanias, Amir Behdad, Fabio Puglisi, William J Gradishar, Giovanni Ciriello, Massimo Cristofanilli. Investigating oncogenic signaling pathways in inflammatory metastatic breast cancer (MBC) though circulating tumor DNA (ctDNA) next-generation sequencing (NGS) [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 PS2-33.

The Use of Serial Circulating Tumor DNA to Detect Resistance Alterations in Progressive Metastatic Breast Cancer

PURPOSE

Circulating tumor DNA (ctDNA) is a promising tool for noninvasive longitudinal monitoring of genomic alterations. We analyzed serial ctDNA to characterize genomic evolution in progressive metastatic breast cancer.

EXPERIMENTAL DESIGN

This was a retrospective cohort between 2015 and 2019 obtained under an Institutional Review Board-approved protocol at Northwestern University (Chicago, IL). ctDNA samples were analyzed with Guardant360 next-generation sequencing (NGS) assay. A total of 86 patients had at least two serial ctDNA collections with the second drawn at first post-NGS progression (PN1) by imaging and clinical assessment. A total of 27 participants had ctDNA drawn at second post-NGS clinical progression (PN2). We analyzed alterations, mutant allele frequency (MAF), number of alterations (NOA), and sites of disease on imaging in close proximity to ctDNA evaluation. Matched pairs' variations in MAF, NOA, and alterations at progression were tested through Wilcoxon test. We identified an independent control cohort at Massachusetts General Hospital (Boston, MA) of 63 patients with serial ctDNA sampling and no evidence of progression.

RESULTS

We identified 44 hormone receptor-positive, 20 HER2⁺, and 22 triple-negative breast cancer cases. The significant alterations observed between baseline and PN1 were TP53 (P < 0.0075), PIK3CA (P < 0.0126), AR (P < 0.0126), FGFR1 (P < 0.0455), and ESR1 (P < 0.0143). Paired analyses revealed increased MAF and NOA from baseline to PN1 (P = 0.0026, and P < 0.0001, respectively). When compared with controls without progression, patients with ctDNA collection at times of progression were associated with increased MAF and NOA (P = 0.0042 and P < 0.0001, respectively).

CONCLUSIONS

Serial ctDNA testing identified resistance alterations and increased NOA and MAF were associated with disease progression. Prospective longitudinal ctDNA evaluation could potentially monitor tumor genomic evolution.

Mass spectrometry-based serum proteomic signature as a potential biomarker for survival in patients with non-small cell lung cancer receiving immunotherapy

Background

VeriStrat test is a serum assay which uses a mass spectrometry (MS)-based proteomic signature derived from machine learning. It is currently used as a prognostic marker for patients with non-small cell lung cancer (NSCLC) receiving chemotherapy. However, little is known about its role for NSCLC patients receiving immune checkpoint inhibitors (ICIs).

Methods

This is a retrospective study that includes 47 patients with advanced stage NSCLC without an activating EGFR mutation, who underwent the VeriStrat test from 2016 to 2018. Spectra from blood samples were evaluated to assign patients into the VeriStrat ‘Good’ (VS-G) or VeriStrat ‘Poor’ (VS-P) risk group. The clinical outcomes of 32 patients who received programmed cell death 1 (PD-1) inhibitors nivolumab or pembrolizumab were analyzed by VeriStrat status.

Results

The VS-G group demonstrated significantly higher progression-free survival (PFS) and overall survival (OS) compared to the VS-P group among overall NSCLC patients regardless of treatment (median PFS of 7.1 vs. 4.2 months, P=0.013, and median OS, not reached vs. 17.2 months, P=0.012). Among NSCLC patients treated with ICIs, VS-G classification was associated with significantly increased PFS in comparison to VS-P classification (median PFS of 6.2 vs. 3.0 months, P=0.012), while the differences in OS trended towards significance (median OS, not reached vs. 16.5 months P=0.076). Multivariate analysis showed that the VeriStrat status was significantly correlated with PFS and OS in NSCLC patients treated with ICIs (P=0.017, P=0.034, respectively).

Conclusions

MS-based serum proteomic signature has potential as a biomarker for survival outcome in NSCLC patients receiving immunotherapy.

Abstract 5526: Serum proteomic scores for understanding response and mechanisms of resistance to immune checkpoint inhibitors in non-small cell lung cancer

Background:

Understanding of biological processes associated with response and resistance to immune checkpoint inhibitors (ICI) with or without chemotherapy is limited. We used serum-based, proteomic scores at baseline and after treatment initiation to explore mechanisms of early resistance for patients with non-small cell lung cancer (NSCLC) treated with ICI.

Methods:

Under an ongoing clinical protocol, 43 patients with advanced NSCLC were consented and serum samples were prospectively collected at two timepoints: baseline and approximately 3 weeks after treatment initiation with ICI (median 22 [IQR, 21 - 26] days). Samples were analyzed, blinded to clinical data, using MALDI-ToF mass spectrometry. Protein Set Enrichment Analysis (PSEA) approach applied to mass-spectral data was used to assign biological scores characterizing activation of 10 processes of interest (e.g., Type 1 immunity (Th1), complement, interferon (IFN)-gamma). Statistical associations with clinical response data using RECIST, progression-free survival (PFS), and overall survival (OS) were examined. The distribution of each PSEA score at baseline and 3 weeks was compared for patients with progression of disease (PD) as best response or PFS &lt;6 months classified as “Early PD" vs. patients with best response of SD, PR or CR and PFS ≥6 months as “no Early PD” using mixed effect models, with no adjustments for multiple comparisons.

Results:

Of the 43 participants, 28 received ICI with chemotherapy and 15 received as monotherapy. 31 of 43 patients (72%) were treatment naïve at baseline blood collection. PSEA scores measured at 3 weeks after initiation of systemic therapy showed significant differences between the Early PD (N=25) and no Early PD (N=18) groups in complement activation, IFN-gamma, Th1, and immune tolerance. In contrast, no differences in PSEA scores were observed in baseline measurements. For three biological processes (complement, IFN-gamma, immune tolerance), the differences in PSEA scores between the Early and no Early PD groups were more prominent with measurements at 3 weeks (Pinteraction &lt; 0.05).

Conclusions:

Collectively, these data demonstrate the potential utility of serum-based, proteomic scores to provide insight into mechanisms for early disease progression for patients treated with ICI. We identified several resistance mechanisms including complement activation, IFN-gamma signaling, and immune tolerance. The observed associations were more prominent after one cycle of treatment, suggesting that for a subset of patients early changes in the blood after treatment initiation may provide insight into mechanisms of resistance to ICI.

Citation Format: Andrew A. Davis, Jonghanne Park, Wade T. Iams, Michael S. Oh, Robert W. Lentz, Heinrich Roder, Joanna Roder, Senait Asmellash, Lelia Net, Julia Grigorieva, Nisha Mohindra, Victoria Villaflor, Young Kwang Chae. Serum proteomic scores for understanding response and mechanisms of resistance to immune checkpoint inhibitors in non-small cell lung cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5526.

Abstract 5527: Serum proteomic scores for understanding the mechanisms of immune-related adverse events (irAEs) in non-small cell lung cancer

Background:

Understanding of biological processes associated with irAEs for patients treated with immune checkpoint inhibitors (ICI) is limited. We used serum-based, proteomic scores at baseline and after treatment initiation to explore mechanisms of irAEs for patients with non-small cell lung cancer (NSCLC) treated with ICI.

Methods:

Under an ongoing clinical protocol, 43 patients with advanced NSCLC were consented and serum samples were prospectively collected at two timepoints: baseline and approximately 3 weeks after treatment initiation with ICI (median 22 [IQR, 21 - 26] days). Samples were analyzed, blinded to clinical data, using MALDI-ToF mass spectrometry. Protein Set Enrichment Analysis (PSEA) approach applied to mass-spectral data was used to assign biological scores characterizing activation of 10 processes of interest (e.g., Type 1 immunity, complement, interferon (IFN)-gamma). irAEs after initiation of ICI with or without chemotherapy were classified per standard definitions. Patients were classified into two groups based on irAEs of any grade: irAE positive and negative.

Results:

Of the 43 participants, 28 received ICI with chemotherapy and 15 received monotherapy. 18 of 43 patients (42%) were determined to have irAEs. These included the following: 9 pneumonitis, 3 thyroiditis, 3 adrenal insufficiency, 1 arthritis, 1 flare of pre-existing psoriasis, 1 mucositis, 1 colitis, 1 myocarditis, and 1 hepatitis (2 patients had both thyroiditis and adrenal insufficiency, 1 patient had both mucositis and pneumonitis). The median timeframe between treatment initiation and development of irAEs was 105 days [IQR, 42 - 169 days]. PSEA scores measured at 3 weeks after initiation of systemic therapy showed significant differences between irAE positive and negative groups in the following processes: extracellular matrix remodeling, complement activation, IFN-gamma signaling, and immune tolerance (P&lt;0.05 for PSEA scores of each pathway identified). These processes did not show any significant differences in PSEA scores at baseline. However, the changes in PSEA scores of all processes analyzed from baseline to 3 weeks after treatment initiation were not significantly different between the two groups.

Conclusions:

Our findings demonstrate that serum-based, proteomic scores can provide insight into understanding early mechanisms for the development of irAEs in patients treated with ICI. In particular, we identified several mechanisms associated with the development of irAEs, including extracellular matrix remodeling, complement activation, IFN-gamma signaling, and immune tolerance. These associations were not present at baseline and were only observed after treatment initiation, suggesting that early changes in the blood may provide insight into prediction of irAEs.

Citation Format: Andrew A. Davis, Jonghanne Park, Leeseul Kim, Gahyun Gim, Wade T. Iams, Michael S. Oh, Robert W. Lentz, Heinrich Roder, Joanna Roder, Senait Asmellash, Lelia Net, Julia Grigorieva, Nisha Mohindra, Victoria Villaflor, Young Kwang Chae. Serum proteomic scores for understanding the mechanisms of immune-related adverse events (irAEs) in non-small cell lung cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5527.

Landscape of circulating tumour DNA in metastatic breast cancer

BACKGROUND

We describe the genomic landscape of circulating tumour DNA (ctDNA) across pathological subtypes of metastatic breast cancer.

METHODS

255 clinically annotated patients with ctDNA testing by Guardant360 were stratified into HR+, HER2+, and TNBC cohorts. Frequency and heterogeneity of alterations were reported. Paired ctDNA and tissue sequencing were compared for a subset of patients. The association of ctDNA and metastatic sites of disease on imaging was also assessed.

FINDINGS

89% of patients had at least one ctDNA alteration detected. The most common single nucleotide variants (SNVs) for HR+ patients were PIK3CA, ESR1, and TP53. For HER2+, these were TP53, PIK3CA, and ERBB2 with ERBB2 as the most frequent copy number variant (CNV). For TNBC, the most common SNVs were TP53 and PIK3CA, and the most frequent CNVs were MYC, CCNE1, and PIK3CA. TNBC patients had a significantly higher mutant allele frequency (MAF) of the highest variant compared to HR+ or HER2+ patients (P<0.05). Overall, alterations in PIK3CA, ESR1, and ERBB2 were observed in 39.6%, 16.5%, and 21.6% of patients, respectively. Agreement between blood and tissue was 79-91%. MAF and number of alterations were significantly associated with number of metastatic sites on imaging (P<0.0001).

INTERPRETATION

These data demonstrate the genetic heterogeneity of metastatic breast cancer in blood, the high prevalence of clinically actionable alterations, and the potential to utilise ctDNA as a surrogate for tumour burden on imaging.

FUNDING

Lynn Sage Cancer Research Foundation, OncoSET Precision Medicine Program, and REDCap support was funded by the National Institutes of Health UL1TR001422.

Circulating tumor DNA (ctDNA) to evaluate stage III and stage IV metastatic breast cancer (MBC), describe tumor heterogeneity, and outcome

1028

Background: MBC is a challenging clinical condition treated with palliative intent due to tumor heterogeneity. We reported in 2019 ASCO that the correlation of HER2 and ESR1 mutations of ctDNA with CTCs results in worse prognosis in MBC. Here we reported that ctDNA mutations is a key point which is different between Stage III and Stage IV, and it would be helpful to evaluate the MBC metastasis and outcome. Methods: This study included 33 Stage III and 204 Stage IV MBC patients who received systemic treatments at NMH (2016-2019). Plasma ctDNA before treatment was isolated from patients and then was analyzed by Guardant 360 Health NGS-based assay for a 73 genes panel for genomic alterations including single nucleotide variants, insertions/deletions, gene fusions/rearrangements and copy number variations. Causal Inference with Ensembel Learning was used for statistical analyses. Results: Among stage III patients, 40% are luminal, 44% are HER2+ and 16% are TNBC, while in stage IV 50% patients are luminal, 20% are HER2+ and 30% are TNBC. The major differences in ctDNA between two stages lie in several genes including PIK3CA, ERBB2 and KRAS. On the top of the list is PIK3CA, which is detected in 2 out of 33 stage III patients (1 luminal, 1 HER2+) (6.06%) in baseline, each of them carries 1 mutation on PIK3CA (E542K, E545G). In 43 out of 204 stage IV patients (21.57%) who carry this gene, 15 show 1 amplification, 34 have 1 mutation (mainly H1047R, E542K, E545K and H1047L), 11 have 2 mutations (E542K/E726K, D454N/D1029N, E545K/D1017H, E545K/L287L, H1047R/E453K, H1047R/N426S and P539R/H1047R), and 1 has 3 mutations (E542Q/D454N/D1029N and E545K/E726K/R93Q). On treatment effects, PIK3CA is found to be very detrimental on prognosis and on its effects on the treatment outcome. Patients without any mutation in PIK3CA live 2.65 times longer than those with more than one mutations on PIK3CA ( p-value = 4.47e-06, CI = [1.731, 3.926]). PIK3CA, ESR1, TP53 and ARID1A are found to significantly affect liver metastasis when RET, FBXW7, ERBB2, CCND2, BRAF and MET are found to be associated with lung metastasis for both stages. EGFR, KIT and ARID1A are associated with CNS metastasis. Conclusions: We elucidated that ctDNA mutations on PIK3CA and other genes dramatically increased in Stage IV patients compared to Stage III patients which provides a new insight on the Stage III and Stage IV MBC determination. New set of genes especially PIK3CA are identified to correlate with metastasis and affect the outcome which may also be reliably used to monitor the response to therapy.

Cell-free DNA comparative analysis of hormone receptor-positive, first-line metastatic breast cancer genomic landscape in the United States and China

1059

Background: Metastatic breast cancer (MBC) is a heterogeneous disease associated with known somatic mutations of variable biological value in different subtypes. Furthermore, the clinical evolution of the disease demonstrates clonal evolution resulting in disease resistance more accurately detected using blood-based sequencing. Few studies have explored differences in genomic features of tumors across populations. Here, we performed circulating tumor DNA (ctDNA) sequencing to compare the genomic landscape of patients with hormone-receptor positive MBC at time of first recurrence or de-novo metastatic diagnosis in the United States (US) and China. Methods: Twenty-three US patients from Northwestern University and 65 Chinese patients from Peking University had ctDNA sequencing from plasma performed using the harmonized CLIA-certified, 152-gene PredicineCARE assay in laboratories in the US and China, respectively. The data analysis was conducted in China. Institutional Review Boards at each site approved the study. Fisher’s exact test was performed to compare mutational frequencies across populations. Results: Median age of patients at MBC diagnosis was 51 in the US cohort and 55 in the Chinese cohort. 87% of US patients and 82% of Chinese patients had received prior therapy for primary breast cancer, including endocrine therapy. Mutations were detected in 17 of 23 (74%) US patients and 59 of 65 (91%) Chinese patients. CNAs were observed in 57% of US patients and 58% of Chinese patients. The most common mutations detected in US patients were TP53 (26%), PIK3CA (22%), AKT1 (22%), CDH1 (17%), PTEN (13%), and ESR1 (9%) vs. PIK3CA (46%), TP53 (35%), ESR1 (12%), and BRCA2 (11%) in Chinese patients. Frequency of AKT1 and CDH1 mutations were significantly higher in the US population (P < 0.05), while PIK3CA mutations were higher in the Chinese population (P < 0.05). CNA gains in CCND3 and CDK4 were significantly higher in the US cohort, and FGFR1 was significantly more common in the Chinese cohort (all P < 0.05). Conclusions: To our knowledge, this is a first cross-regional comparison study in HR+ MBC patients in the US and China using a harmonized cfDNA NGS platform. At a population level, there were notable differences observed in somatic variants in two cohorts. Future sequencing efforts and clinical trials should include patients of diverse ethnic backgrounds to explore the impact of differences in genomic landscape on probability of benefit from treatments. A larger validation cohort is required to confirm these findings.

Association of financial conflicts of interest with academic success among junior faculty in hematology and oncology

2080

Background: Financial conflict of interest (COI) represents a complex issue in hematology and oncology. Little is known about when COIs develop during a career and if these correlate with early career success. We evaluated self-reported COIs for junior faculty members at 10 academic cancer centers and examined if these financial relationships with industry correlated with measures of academic career success. Methods: The study evaluated 229 assistant professors from the top 10 cancer centers based on the 2018 US News Cancer rankings. Faculty characteristics were determined from hospital websites including the number of years since completing fellowship. Data regarding National Institute of Health (NIH) funding were obtained. Industry funds (Sunshine Act funds; SAF) were identified from the Centers for Medicare & Medicaid Services (CMS) Open Payments database from 2013-2017. Self-reported COIs were obtained from the American Society of Clinical Oncology (ASCO) or American Society of Hematology (ASH) disclosures databases, and through review of disclosures from recent publications. Measures of academic success included h-index and number of publications. We assessed the influence of number of COIs and SAF received on measures of academic success. Results: Of the 229 included faculty, 45% were female, 39% graduated fellowship in 2015 or later, 35% were double-boarded, 40% had dual degrees and 15% received NIH funding. Approximately 46% of faculty had at least 1 COI. COIs (ASCO/ASH) were positively correlated with COIs self-reported in publications and total SAF (Spearman correlations 0.57 and 0.54, both P < 0.01). The development of COIs and the number of SAF increased with years in practice (Spearman correlations 0.37 and 0.28, both P < 0.01). COIs and SAF correlated with h-index (Spearman correlation 0.40 and 0.41, both P < 0.01). After adjusting for years since fellowship, linear regression demonstrated that log-transformed h-index and number of publications were associated with SAF (P < 0.01) and COIs (ASCO/ASH) (P = 0.01). Conclusions: Financial COIs were present in nearly half of the faculty and increased with more time since completing fellowship. Measures of academic success were positively correlated with COIs (ASCO/ASH) and SAF. These data suggest that cultivating industry relationships may aid faculty in establishing early academic success.

The landscape of genomic alterations detected in serial circulating tumor DNA (ctDNA) in clinical progressive metastatic breast cancer

1084

Background: Metastatic breast cancer (MBC) is associated with genomic evolution, representing a challenge at clinical progression. While tissue and blood next-generation sequencing (NGS) allows for the baseline detection of alterations, non-invasive longitudinal assessment of ctDNA can provide a tool for monitoring tumor evolution. We characterized genomic changes using serial ctDNA testing in patients with clinical progression. Methods: Patient data was obtained under an IRB-approved protocol and ctDNA was collected at Northwestern University between 2015-2019. All ctDNA samples were analyzed using the Guardant360 NGS assay. Of 255 patients with MBC, 86 had at least two serial ctDNA collections with the second collection drawn at first progression (P1) by imaging and clinical assessment. Participants were followed until second clinical progression (P2). We analyzed type of alterations, mutant allele frequency (MAF), number of alterations (NOA), and sites of disease on imaging in close proximity to ctDNA evaluation. Matched pairs variations in MAF and NOA at P1 and P2 were tested through Wilcoxon test. Results: We identified 44 HR+, 20 HER2+ and 22 TNBC cases. Median lines of therapy were 3 (interquartile range (IQR): 1-6) for HR+, 3 (IQR: 1-5) for HER2+, and 2 (IQR: 1-4) for TNBC. The most likely alterations between baseline to P1 were TP53 (p < 0.0075), PIK3CA (p < 0.0126), AR (p < 0.0126), FGFR1 (p < 0.0455) and ESR1 (p < 0.0143). In the HR+ subset , ESR1 was statistically more likely at P1. ESR1 at P1 was also associated with development of new liver lesions (p < 0.0320). ERBB2 mutation at P1 was associated with new lung (p < 0.0050) or bone lesions (p < 0.0030). Increase in NOA was observed between baseline and P1 (p < 0.0001), P1 and P2 (p < 0.0001), and baseline to P2 (p < 0.0004). MAF was increased between baseline and P2 (p < 0.0480). Conclusions: Serial ctDNA testing identified resistance alterations ( TP53, PIK3CA, AR, ESR1, FGFR1), with some mutations indicating new sites of disease ( ESR1, ERBB2). Heterogeneity of ctDNA was significantly associated with progressive disease. Prospective evaluation of the impact of serial ctDNA testing on treatment decisions is needed to expand the role of precision medicine in MBC. [Table: see text]

ERBB2 amplifications and mutations in 109 advanced breast cancer patients by next-generation sequencing

3565

Background: In advanced breast cancer (ABC) HER2 status is based on ASCO/CAP immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) criteria. Next generation sequencing (NGS) of tissue and blood can detect aberrations in ERBB2 such as copy number gain/amplifications (cng/amp) and mutations. Methods: We retrospectively identified patients (pts) seen at Northwestern University between 2015 and 2019 with ABC and an alteration in ERBB2 identified by tissue and/or circulating tumor DNA (ctDNA) NGS. We included pts with testing by Guardant360, TempusX, and/or FoundationOne platforms. NGS reports were evaluated for non-synonymous mutations and cng/amp. HR and HER2 status were determined based on the most recent pathologic assessment. Mutations were categorized as pathologic if they were consider oncogenic (level 1-2 evidence with direct functional data), likely oncogenic, or predicted oncogenic, based on OncoKB (Chakravarty et al., JCO PO 2017). Results: 109 cases of ABC (6 locally advanced, 103 metastatic) with ERBB2 alterations were identified. Tissue NGS was available from 43%, ctDNA from 72%, and both from 19%. The positive predictive value (PPV) of ERBB2 amp/cng by tissue NGS to predict HER2+ using the gold standard as IHC/FISH was 94% (33/35). The PPV of ERBB2 amp by ctDNA was 93% (40/43). ERBB2 mutations were detected in 52 pts. Of these, 23 pts were considered to harbor pathologic ERBB2 mutations, (19 oncogenic, 2 likely oncogenic, 1 predicted oncogenic) detected by ctDNA and tissue in 4, ctDNA in 16, and tissue in 3 pts. The most frequently detected mutations were V777L and S310. Four pts had co-mutations of ERBB2 V777L and S310F. Disease subtype among those with ERBB2 pathologic mutations was HR+ HER2- in 57%, HER2+ in 26%, and triple negative in 17%. In all patients with serial ctDNA analysis and pathologic ERBB2 mutations, the mutation was detected on the first analysis. Pathologic ERBB2 mutation represented the mutant with the highest mutant allele frequency (MAF) in 30% and top 3 highest MAF in an additional 35%. PIK3CA was co-mutated in 48%. Conclusions: The PPV of ERBB2 amp/cng by tissue and ctDNA NGS was high, and has potential utility for cancers where HER2 IHC/FISH is not standardly assessed or cases where biopsy is challenging. ERBB2 pathologic mutations were found in all breast cancer subtypes. When present, they were identified on the initial ctDNA analysis and often represented a significant clone, supporting its role as a ‘driver mutation’.

Novel Neoadjuvant Treatment Strategies for Triple-Negative Breast Cancer

Triple-negative breast cancer (TNBC), which accounts for approximately 10% to 15% of breast cancers, remains the most aggressive subtype and is characterized by early disease relapse for a subset of patients. TNBC remains a clinical challenge, given the lack of effective targeted treatments such as endocrine therapy for hormone receptor-positive (HR+) tumors or therapies against HER2.

Early Assessment of Molecular Progression and Response by Whole-genome Circulating Tumor DNA in Advanced Solid Tumors

Treatment response assessment for patients with advanced solid tumors is complex and existing methods require greater precision. Current guidelines rely on imaging, which has known limitations, including the time required to show a deterministic change in target lesions. Serial changes in whole-genome (WG) circulating tumor DNA (ctDNA) were used to assess response or resistance to treatment early in the treatment course. Ninety-six patients with advanced cancer were prospectively enrolled (91 analyzed and 5 excluded), and blood was collected before and after initiation of a new, systemic treatment. Plasma cell-free DNA libraries were prepared for either WG or WG bisulfite sequencing. Longitudinal changes in the fraction of ctDNA were quantified to retrospectively identify molecular progression (MP) or major molecular response (MMR). Study endpoints were concordance with first follow-up imaging (FFUI) and stratification of progression-free survival (PFS) and overall survival (OS). Patients with MP (n = 13) had significantly shorter PFS (median 62 days vs. 310 days) and OS (255 days vs. not reached). Sensitivity for MP to identify clinical progression was 54% and specificity was 100%. MP calls were from samples taken a median of 28 days into treatment and 39 days before FFUI. Patients with MMR (n = 27) had significantly longer PFS and OS compared with those with neither call (n = 51). These results demonstrated that ctDNA changes early after treatment initiation inform response to treatment and correlate with long-term clinical outcomes. Once validated, molecular response assessment can enable early treatment change minimizing side effects and costs associated with additional cycles of ineffective treatment.

Abstract PD8-03: Clinico-pathological and molecular features in young women with metastatic breast cancer

Introduction: Advanced breast cancer can be more aggressive and portend a worse prognosis in the younger population (age &lt; 50). While several studies have outlined clinico-pathologic features and molecular features of primary disease in young women with breast cancer, data in the metastatic setting remain scarce. Thus, the goal of this study was to explore the underlying clinic-pathologic and molecular profile of young women with metastatic breast cancer.

Methods: We conducted a retrospective analysis of 138 females with metastatic breast cancer treated at Northwestern Medicine who provided consent for serial evaluation of circulating biomarkers. Patient were divided into two cohorts based on age at the time of metastasis, namely premenopausal (defined as age &lt; 50) and postmenopausal (age ≥ 50). CellSearch™ immunomagnetic kit (Menarini Silicon Biosystems) was utilized to enumerate circulating tumor cells (CTCs), and the CellSearch™ CXC Kit (in 7.5 cc whole blood) characterized CTC HER2 expression. Circulating tumor DNA (ctDNA) was sequenced using the Guardant360 next-generation sequencing (NGS) assay (Guardant Health). When available, tissue samples from the primary and metastatic site(s) were sequenced using FoundationOne and/or Tempus xT NGS assays. Associations were drawn using Pearson’s χ2 test, independent samples T-tests, and multivariate logistic regression.

Results: Of the 138 women, 54 (39%) were premenopausal with median age of 42 (range: 28-49), and 84 (61%) were postmenopausal with median age of 57 (range: 50-81). For the premenopausal cohort, 96% had invasive ductal carcinoma, 2% invasive lobular carcinoma and 2% mixed/unknown, compared to postmenopausal with 74%, 19% and 7% respectively, p=0.003. No statistically significant association was observed based on disease subtype (HR+/HER2-, HR+/HER2+, HR-/HER2+, TNBC), correspondingly stratified as 46%, 17%, 9%, 28% (premenopausal) and 57%, 10%, 13% 20% (postmenopausal). In total, 39% of the premenopausal and 40% of the postmenopausal patients had inflammatory breast cancer (IBC). Among patients initially diagnosed with non-metastatic disease, time (years) to metastasis was 2.76 (95% CI 2.11 to 3.41) for the premenopausal and 6.08 (95% CI 4.89 to 7.27) for the postmenopausal cohort, p=0.0001. Statistically significant associations were found when comparing the NGS datasets, derived from serial collection of ctDNA +/- tissue samples. Specifically, the premenopausal group had a higher incidence of GATA3 (11 vs 6 cases; p=0.017) alterations, but a lower incidence of NF1 (1 vs 18; p&lt;0.001) and RB1 (1 vs 9; p=0.049) alterations. Most common gene alterations included TP53 (67%), PIK3CA (45%), ERBB2 (26%), GATA3 (26%), MYC (24%), FGFR1 (19%) and ESR1 (17%) for the younger cohort, versus TP53(67%), PIK3CA (39%), ESR1 (27%), NF1 (27%), MYC (23%), ERBB2 (23%) and FGFR1 (20%) for the postmenopausal cohort. There were no statistically significant differences between the cohorts in terms of total number of ctDNA alterations at baseline draw (median[IQR]: 3[1-7] premenopausal group; 5[2-7] postmenopausal group), presence of ≥5 CTCs (54%; 46% of total cases, respectively), occurrence of CTC clusters (26%; 24%), or HER2+ CTC expression (44%; 45%).

Conclusion: Our data reveal that premenopausal women diagnosed with metastatic breast cancer had a more rapid progression to metastasis and differ from their postmenopausal counterparts in both their pathologic profile (almost exclusively invasive ductal carcinoma) and molecular profile (notably, gene alteration frequencies of NF1, RB1 and GATA3), which could have significant implications in developing targeted treatment paradigms for younger women. Additionally, CTC prevalence in the metastatic setting differs from earlier stage breast cancer data showing a higher proportion of ≥5 CTCs in postmenopausal patients.

Citation Format: Kristen Carroll, Ami M Shah, Lorenzo Gerratana, Chenyu Lin, Andrew A Davis, Qiang Zhang, Youbin Zhang, Lisa Flaum, Amir Behdad, Leonidas C Platanias, William J Gradishar, Massimo Cristofanilli. Clinico-pathological and molecular features in young women with metastatic breast cancer [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 PD8-03.

Abstract P5-01-10: Next generation sequencing-based gene variant-oriented characterization in metastatic breast cancer: An innovative analysis using ctDNA

Introduction: Novel high throughput genomic technologies are enhancing the ability to dynamically characterize cancer on a granular level. Although Next Generation Sequencing (NGS) is becoming part of the common practice, little is known on the role of a characterization on a gene variant level. Large heterochromatic regions or blocks are a characteristic feature in the autosomes 1, 9, 16 and the blocks contain about 10% of the human genome. The heterochromatic regions consist of highly repetitive DNA of the classes Sat I to IV. Thus, these specific regions are preferential positions for genome instability. The aim of this study was to explore the feasibility of a gene variant-oriented characterization for variants interplay discovery and to explore the role of chromosome stability in gene variants incidence. Methods: This study analyzed a pilot cohort of 35 metastatic breast cancer (MBC) patients (pts) treated and characterized for CTCs and circulating tumor DNA (ctDNA) at Northwestern University (Chicago, IL). ctDNA was analyzed using the PredicinePLUS™ NGS 180-gene panel (Predicine Inc, CA). Associations between gene variants and clinico-molecular characteristics were tested through Fisher’s exact test. Chromosomes 1, 9, 16 where defined as instable (instable_chr) based on the presence of highly repeated sequences. Results: An overall set of 35 samples was analyzed, and the main variants were detected in the ARID1A (40%), ATM (20%), DNMT3A (37%), ESR1 (20%), PIK3CA (26%), and TP53 (49%) genes. A total of 448 gene variants were detected through the NGS panel and across them, ARID1A accounted for 5.13%, ATM 2.23%, DNMT3A 4.91%, ESR1 4.02%, PIK3CA 2.23%, and TP53 for 6.03%. Among the genes mutated, the DNMT3A:c.2644C&gt;T, DNMT3A:c.2645G&gt;A, ESR1:c.1138G&gt;C,ESR1:c.1609T&gt;A, ESR1:c.1610A&gt;C, ESR1:c.1613A&gt;G, PIK3CA:c.1624G&gt;A were the most detected. Thirty-eight copy number variations (CNV) and 3 splicing variants were observed. Notably, 55.6% of detected variants were found in instable_chr. No significant differences were observed between instable_chr variants and MBC subtype. Interestingly, ARID1Aaberrations were significantly linked to ATM, ESR1 (P=0.006) and PIK3CA with ESR1 (P= 0.019). Consistently with literature, ATM and TP53 variants were mutually exclusive (P&lt;0.0001). Intriguingly, both ATM and TP53 were associated with a higher incidence of variants affecting genes in instable_chr. Conclusions: MBC is often described as a non-gene-addicted disease, rendering the onset of gene variants a multi-factor phenomenon. The present results suggest a role for both chromosomal intrinsic instability and DNA repair impairment in this process, with a potential down-stream selection mediated by treatment resistance. Future studies are warranted to further validate this proof of concept approach.

Citation Format: Lorenzo Gerratana, Qiang Zhang, Ami N Shah, Alessandra Franzoni, Jianjun Yu, Shidong Jia, Andrew A Davis, Youbin Zhang, Firas Wehbe, Amir Behdad, Leonidas C Platanias, William J Gradishar, Massimo Cristofanilli. Next generation sequencing-based gene variant-oriented characterization in metastatic breast cancer: An innovative analysis using ctDNA [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 P5-01-10.

Abstract P3-01-05: Liquid biopsy methods and machine learning modeling to understand organ tropism and metastatization behavior of metastatic breast cancer

Background: Liquid biopsy provides a growing amount of real-time data about prognosis and the genomic landscape of metastatic breast cancer (MBC) and its comprehensive analysis is an emerging clinical need. Machine Learning (ML) data-driven models are able to “learn” information about a system and to adaptively improve their performance by directly observing its data. This enables the discovery of hidden patterns in complex heterogeneous and high dimensional data. The aim of this study was to explore the combination of clinical characteristics, circulating tumor DNA-detected aberrations (ctDNA) and CTC enumeration in estimating target organs more susceptible to MBC involvement using a ML modeling approach. Methods: The study retrospectively analyzed 88 MBC patients (pts) treated and characterized for CTCs and circulating tumor DNA (ctDNA) at Northwestern University (Chicago, IL) independently from treatment line. Blood samples were collected at baseline, concomitantly with imaging. CTCs were isolated through the CellSearch™ kit (Menarini Silicon Biosystems, PA), while ctDNA was analyzed using the Guardant360™ NGS-based assay (Guardant Health, CA). All features were normalized and included in a random forest algorithm implemented in Python (Scikit learn, BSD license), node splitting criterion for the decision tree classifiers was varied using Gini index and entropy. Hyperparameters of the random forest were then optimized including number of trees and the minimum leaf size by implementing hyperparameter grid search using 10-fold cross validation. Results: The median number of lines at baseline collection was 1 (interquartile range: 1-3), while the median number of metastatic sites was 3 (inter quartile range: 1-3) with the most observed sites being bone (37%), lymph nodes (29%), lung (27%) and liver (25%). The cohort consisted of 43% hormone receptor positive (HRpos), 32% TNBC, and 25% HER2-positive MBC. In the overall population, continuous CTC number (n_CTC), inflammatory breast cancer diagnosis (IBC), and aberrations in ESR1, KITand CDK4were the main features linked to liver metastases (AUC: 0.842), n_CTC, ESR1, PIK3CA, CCNE1and CDK6were the features linked to bone involvement (AUC: 0.770), while PIK3CA, METand MYC, were linked to lung organotropism (AUC: 0.701). Factors linked to the metastatization net combination pattern were then explored within each MBC subtype. Intriguingly, AR, n_CTC, TP53and ESR1were the main drivers in HRpos MBC (Mean per class error0.46), while EGFR, KITand NOTCH1were the main features in TNBC (Mean per class error 0.605). Consistently, n_CTC, ERBB2, PIK3CAwere the driving features among HER2 positive MBC pts (Mean per class error 0.87). Conclusions: This novel analysis demonstrates that liquid biopsy integrating both CTCs enumeration and genomic characterization by ctDNA could prove useful in a detailed description of the metastatic process, allowing a more tailored monitoring and therapeutic approach. Intriguingly, features linked to Epithelial to Mesenchymal transition were found to be a potential driver of the metastatization behavior, underlining the need to further elucidate the clinical impact of this process.

Citation Format: Lorenzo Gerratana, Andrew A Davis, Maurizio Polano, Qiang Zhang, Ami N Shah, Chenyu Lin, Debora Basile, Giuseppe Toffoli, Firas Wehbe, Fabio Puglisi, Amir Behdad, Leonidas C Platanias, William J Gradishar, Massimo Cristofanilli. Liquid biopsy methods and machine learning modeling to understand organ tropism and metastatization behavior of metastatic breast cancer [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 P3-01-05.

Abstract P5-01-08: Landscape of circulating tumor DNA (ctDNA) in metastatic breast cancer

Background: The clinical utility of routine clinical assessment of ctDNA in metastatic breast cancer (MBC) has not been clearly established. Recently, the Food and Drug Administration approved alpelisib (Piqray®) with a ctDNA-based companion diagnostic. Therefore, there is significant interest in describing the landscape of ctDNA alterations and establishing further clinical utility of this assessment.

Methods: We retrospectively identified ctDNA data from a single institution (Northwestern University). All patients had next-generation sequencing performed by Guardant Health (Redwood City, CA) from 2015-2019 for clinical evaluation, and patients were consented for participation in a prospective registry study. Reports were evaluated for type of genomic alterations, number of alterations, and mutant allele frequency (MAF) of the dominant clone. Clinical information including demographics, pathology, imaging, treatment, and response data were collected via patient chart review. Associations were tested through Fisher’s exact test or Kruskal-Wallis test as statistically appropriate. Matched paired samples were investigated through McNemar test.

Results: The cohort consisted of 255 patients with MBC. In total, 371 ctDNA reports were reviewed, including 116 patients with serial assessments. Baseline ctDNA evaluation occurred at a median of 3 lines of therapy (interquartile range (IQR): 1 - 5). Median number of alterations was 4 (IQR: 2-7), while median MAF was 4% (IQR: 0.6% - 17.9%). Across the entire cohort, PIK3CA and TP53 were the most commonly detected mutations, while MYC, FGFR1, PIK3CA, and ERBB2 were the most commonly detected amplifications. 40% of patients had PIK3CA aberrations observed in the analyzed plasma samples (28% amplification, 22% H1047R, 11% E542K), which was independent of breast cancer subtype. In the subset of patients with hormone-receptor positive (HR+) breast cancer, 30% of patients had ESR1 mutations (27% D538G, 19% Y537S, 12% Y537N, 11% E380Q). Patients with triple negative breast cancer (TNBC) had statistically higher MAF compared to HR+ or HER2+ breast cancer (P&lt;0.05). However, there were no differences in the number of alterations observed in each subtype. When examining the mutational profile of subtypes across lines of therapy, only ESR1 and FGFR1 were associated with collection beyond the first line of therapy for HR+ patients (P=0.003 and P&lt;0.025, respectively). The mutational profiles of TNBC and HER2+ subtypes did not vary by lines of therapy at baseline blood collection. Number of genomic alterations detected increased incrementally with increasing lines of therapy (P&lt;0.01), with specific genes more likely to be altered beyond the first line (ESR1, FGFR1, NF1). Higher MAF and number of genomic alterations were also significantly associated with number of metastatic sites on imaging (both P&lt;0.001). In the subset of patients with serial blood collections, across all patients, the following genomic alterations were significantly more likely to emerge over time in paired samples: APC, BRAF, CCNE1, ERBB2, MET, MYC, NF1 (all P&lt;0.05 with Q values corrected for multiplicity).

Conclusion: Liquid biopsy evaluation using ctDNA identified clinically meaningful genomic alterations at high frequency. In addition, our data indicate the potential clinical utility of ctDNA as a surrogate for tumor burden on imaging based on the observed correlation with lines of therapy received and sites of disease. Serial assessment of ctDNA demonstrated clonal evolution, particularly in the HR+ cohort, and identified resistant clones. Validation with an independent cohort is warranted.

Citation Format: Andrew A Davis, Saya Jacob, Lorenzo Gerratana, Ami N Shah, Firas Wehbe, Neelima Katam, Qiang Zhang, Lisa Flaum, Kalliopi Siziopikou, Leonidas C Platanias, William J Gradishar, Amir Behdad, Massimo Cristofanilli. Landscape of circulating tumor DNA (ctDNA) in metastatic breast cancer [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 P5-01-08.

Abstract P4-05-18: Molecular portraits of metastatic breast cancer using tissue next-generation sequencing

Introduction: Tumor sequencing efforts in breast cancer have historically focused on primary tissue samples. With the development of biomarker-based clinical trials and FDA-approved indications for anti-neoplastic agents in metastatic breast cancer (MBC), there is a deeper interest in elucidating genomic profiles of metastatic disease. We aimed to describe mutational profiles, tumor mutational burden (TMB), and microsatellite instability (MSI) status by subtype in a cohort of patients with MBC. Methods: We conducted a retrospective analysis of genomic data from 198 patients with MBC who had next generation sequencing (NGS) of tumor tissue by the TEMPUS assay (TEMPUS, Chicago, IL). The majority of patients (n=115) were treated at Northwestern Medicine. Tumors were sequenced to a minimum of 500x depth with classification of genomic alterations as actionable mutations, pathogenic mutations without known treatment, germline alterations, variants of unknown significance, copy number alterations, and chromosomal rearrangements. TMB was defined as nonsynonymous mutations per megabase (mut/MB) sequenced. Statistical analysis of TMB by subtype was conducted using independent samples T-tests. Associations were tested through two-sided Fisher’s exact test. Results: The cohort of 198 MBC patients had a median age of 51 years (range 23-88) and 52% were white, 9% black, 4% Asian, and 36% unknown. By histology, 52% had invasive ductal carcinoma, 5% had invasive lobular carcinoma, and the remainder of cases were unknown or other. The biopsy site of sequenced tissue was primary breast site in 35% and a metastatic site in the remaining. Sixty nine percent had hormone receptor positive (HR+), 21.3% had triple negative (TN), and 17.2% had HER2-positive (HER2+) MBC. Of the patients with MSI testing (n=183), 180 were MSI-stable, 3 were MSI-equivocal, and none were MSI-high. The median TMB in the whole cohort was 1.8 mut/MB (interquartile range 0.2-2.8), with a median of 2.9 (1.6-4.2) in TN compared to 1.7 (1.0-2.3) in HR+, and 1.4 (0.2-2.5) in HER2+ MBC. The mean TMB for the whole cohort and by TN, HR+, and HER2+ subtypes were 3.0, 4.8, 2.4 and 2.4, respectively. The difference in TMB was statistically significant for TN compared to HR+ (p=0.0006) and equivocal for TN compared to HER2+ (p=0.05). The most frequently seen aberrations in HR+ MBC were PIK3CA (34%), followed by TP53 (28%), ERBB2 (23%), GATA3 (23%), PTEN (13%). In HER2+ MBC alterations were seen in ERBB2 (70%), CDK12 (47%), TP53 (40%), PIK3CA (23%), ABCC3 (16%), PTEN (16%). In TN MBC TP53 (81%), KMT2C (19%), ZFHX3 (16%), PIK3CA (16%), and NCOR2 (14%) were most frequently altered. When comparing the three disease subtypes (HR+, HER2+, TN), statistically significant associations were found with TP53 mutations, most commonly observed in TN cases followed by HER2+ cases (p&lt;0.00001), and ERBB2 amplifications, most commonly observed in HER2+ cases (p&lt;0.00001). PIK3CA alterations were least frequently exhibited with TN compared to HR+ and/or HER2+ tumors (p=0.01). HR+ tumors had a greater proportion of GATA3 (p &lt; 0.0001), and ESR1 (p=0.034) alterations compared to HR- tumors. Conversely, HER2+ tumors had a greater proportion of CKD12 (p&lt; 0.0001) amplifications compared to HER- tumors. ​ Conclusions: MBC demonstrates a rich mutational profile with variations by subtype. Although TMB is lower than in several other solid malignancies, TMB greater than 10 mut/MB was observed in each subgroup, with TN MBC enriched for a higher TMB than HR+ MBC.

Citation Format: Ami N Shah, Andrew A Davis, Kristen J Carroll, Firas Wehbe, Amir Behdad, Massimo Cristofanilli. Molecular portraits of metastatic breast cancer using tissue next-generation sequencing [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 P4-05-18.

Abstract P5-01-13: Longitudinal changes in whole-genome (WG) cell-free DNA (cfDNA) and methylation as a blood-based biomarker to identify early disease progression in advanced breast cancer

Background: Liquid biopsies have potential clinical utility as dynamic biomarkers for treatment response in advanced breast cancer. We evaluated a plasma-only assay to track serial changes in WG cfDNA to identify disease progression prior to routine imaging.

Methods: We prospectively enrolled and serially collected blood from 25 patients with advanced breast cancer. Blood was drawn and collected in Streck tubes prior to start of a new treatment, after the first cycle (median 22 days), and/or second cycle (median 52 days). 4 mL of plasma was separated from peripheral blood, after which cfDNA was isolated from plasma and used to prepare libraries (11 with bisulfite conversion) for WG sequencing (median 20x depth). Based on a patient-specific profile of WG features, including copy-number alterations and cfDNA fragment length, the fraction of tumor-derived cfDNA (ctDNA) was quantified over the initial course of treatment. For a subset of the cohort (11 of 25 patients), we also quantified changes in genome-wide methylation levels from baseline to subsequent timepoints to classify patients as progressors or non-progressors. Imaging was performed per standard practice with treatment response determined by an independent radiologist according to RECIST 1.1 guidelines.

Results: Median age of patients in the cohort was 65 (range 30-83) and included all subtypes—HR+ (n=14), HR+ & HER2+ (n=6), and triple negative (n=5). 52% of patients were on their third line of therapy (range 1-5). On-study therapies were chemotherapy alone (8), targeted + hormone therapy (5), hormone therapy alone (4), targeted + chemotherapy (5), targeted therapy alone (1), or immune checkpoint + HDAC inhibitors (2). Patients with predicted progression by cfDNA (n=5), indicated by an increase in tumor fraction at either post-treatment blood collection, had worse progression-free survival (median 67 days) compared to patients who did not show an increase (n=20; median 207 days) (hazard ratio 7.9, [95% CI 2.2-28.5], log-rank p=3 × 10-4). For the patients who were predicted to progress, the ctDNA assay preceded clinical evaluation by a median of 53 days. All patients with predicted progression were later confirmed to progress at the first follow-up evaluation (5/5, 100% positive predictive value). For the remaining patients, 15 of 20 did not progress (75% negative predictive value). Therefore, sensitivity for the assay was 50% and specificity was 100%. Comparing molecular predictions for 11 of 25 patients based on genomic versus methylation features, 8 non-progressors were classified correctly by both types of features. For the 3 progressors, 2 were predicted correctly based solely on methylation, increasing the sensitivity to detect progression early in the treatment course.

Conclusions: Analyzing ctDNA early in the course of a new therapy holds promise to identify patients with early disease progression across multiple types of treatment. The assay accurately identified patients with no durable clinical benefit earlier, indicating potential clinical utility to change therapy and to limit unnecessary side effects and costs associated with ineffective treatments, if validated in a prospective clinical trial.​ Finally, integrating methylation-based changes with information about genomic alterations may increase performance of ctDNA-based response monitoring.

Citation Format: Andrew A Davis, David Chan, Michael S Oh, Robert W Lentz, Neil Peterman, Alex Robertson, Rohith Srivas, Abhik Shah, Nicole Lambert, Ayse Tezcan, Haluk Tezcan, Young Kwang Chae. Longitudinal changes in whole-genome (WG) cell-free DNA (cfDNA) and methylation as a blood-based biomarker to identify early disease progression in advanced breast cancer [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 P5-01-13.

Abstract P2-11-09: Characterization of metastatic breast cancer through a novel next generation sequencing platform for hypothesis generation on endocrine resistance

Introduction: Notwithstanding the increasing efficacy of systemic therapy, metastatic breast cancer (MBC) is still an incurable disease. The prolonged exposure to endocrine therapy will result in acquired resistance with consequent disease progression. Understanding the underlying mechanisms of resistance is therefore crucial for early resistance detection and for treatment choice optimization. The aim of this study was a comprehensive characterization through circulating tumor DNA analysis (ctDNA) for hypothesis generation on endocrine resistance. Methods: This retrospective study analyzed a pilot cohort of 35 metastatic breast cancer (MBC) patients (pts) treated and evaluated for ctDNA at Northwestern University (Chicago, IL). ctDNA was analyzed using the PredicinePLUS™ NGS 180-gene panel (Predicine Inc, CA). Endocrine resistance was defined as a relapse during the first 2 years of adjuvant endocrine therapy or progressive disease within endocrine therapy (ET) for MBC. Associations between clinico-pathological characteristics and gene variants were tested though Fisher’s exact test. Results: The study included 27 hormone receptor positive MBC (HR+) pts, 5 HER2 positive and 1 Triple Negative MBC (TNBC) patient. Among HR+ pts, 24 received ET in previous lines, including 21 cases treated with an aromatase inhibitor (AI)-based backbone, while 14 received an ET association with CDK4/6 inhibitors. Fifteen were classified as endocrine resistant according to clinical criteria. In the subgroup of pts previously treated with AI, the main detectable gene variants wereTP53 (48%), PIK3CA (26%), GNAS (30%), ESR1 (25%), CDH1 (22%), BRCA2(22%), ARID1A (41%) and AR (52%). Notably, TP53 and ESR1 aberrations were mainly polygenic (ESR1:c.1138G&gt;C, c.1261A&gt;C, c.1551G&gt;A c.1607T&gt;C, c.1609T&gt;A, c.1610A&gt;C, c.1610A&gt;G, c.1613A&gt;G, c.172G&gt;A; TP53:c.1024C&gt;T, c.473G&gt;A, c.524G&gt;A, c.536A&gt;G, c.559G&gt;A, c.586C&gt;T, c.587G&gt;C, c.638G&gt;A, c.659A&gt;G, c.713G&gt;A, c.772del), while the main genes showing copy number variations were in BRCA2 (Loss), JAK2 (Loss), PPP2R2A (Loss), RB1 (Loss), SERPINB3 and SERPINB4 (Gain). Moreover, among the totally detected 448 gene variants, only ESR1 mutations were associated with previous AI prescription (P=0.030). Conclusion:The present study offers an insight on the mutational landscape of MBC patients treated with endocrine therapy alone or associated with CDK4/6 inhibitors. ESR1 mutations were confirmed as the predominant resistance factor and were mainly polygenic. New promising targets such as SERPINB3, SERPINB4, ARID1A and AR add new intriguing clues on the potential role of Epithelial to Mesenchymal transition in endocrine resistance and warrant further investigation on a larger, prospective, cohort.

Citation Format: Lorenzo Gerratana, Qiang Zhang, Andrew A Davis, Ami N Shah, Jianjun Yu, Shidong Jia, Youbin Zhang, Firas Wehbe, Amir Behdad, Leonidas C Platanias, William J Gradishar, Massimo Cristofanilli. Characterization of metastatic breast cancer through a novel next generation sequencing platform for hypothesis generation on endocrine resistance [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 P2-11-09.

The role of PD-L1 expression as a predictive biomarker: an analysis of all US Food and Drug Administration (FDA) approvals of immune checkpoint inhibitors

The development of immune checkpoint inhibitors has changed the treatment paradigm for advanced cancers across many tumor types. Despite encouraging and sometimes durable responses in a subset of patients, most patients do not respond. Tumors have adopted the PD-1/PD-L1 axis for immune escape to facilitate tumor growth, which can be leveraged as a potential target for immune checkpoint inhibitors. On this basis, PD-L1 protein expression on tumor or immune cells emerged as the first potential predictive biomarker for sensitivity to immune checkpoint blockade. The goal of our study was to evaluate PD-L1 as a predictive biomarker based on all US Food and Drug Administration (FDA) drug approvals of immune checkpoint inhibitors. We evaluated the primary studies associated with 45 FDA drug approvals from 2011 until April 2019. In total, there were approvals across 15 tumor types. Across all approvals, PD-L1 was predictive in only 28.9% of cases, and was either not predictive (53.3%) or not tested (17.8%) in the remaining cases. There were 9 FDA approvals linked to a specific PD-L1 threshold and companion diagnostic: bladder cancer (N = 3), non-small cell lung cancer (N = 3), triple-negative breast cancer (N = 1), cervical cancer (N = 1), and gastric/gastroesophageal junction cancer (N = 1) with 8 of 9 (88.9%) with immune checkpoint inhibitor monotherapy. The PD-L1 thresholds were variable both within and across tumor types using several different assays, including approvals at the following PD-L1 thresholds: 1, 5, and 50%. PD-L1 expression was also measured in a variable fashion either on tumor cells, tumor-infiltrating immune cells, or both. In conclusion, our findings indicate that PD-L1 expression as a predictive biomarker has limitations and that the decision to pursue testing must be carefully implemented for clinical decision-making.

Abstract 1351: A novel application of DEPArrayTM NxT System to isolate circulating tumor cell (CTC)-clusters from patients with metastatic breast cancer (MBC)

Introduction: CTCs play a critical role in MBC, and a portion of CTCs may form clusters that contain two or more CTCs bound together which were reported to have up to 50-fold of potential of forming distant metastasis in MBC as compared to individual CTCs. However, genomic characterization of CTCs-clusters remain largely because the enrichment of CTC-clusters is technically challenging. Herein, we describe a novel isolation workflow to select CTC-clusters expressing specific biomarkers for patients with MBC.

Methods: Whole blood samples (7.5ml/each) were collected from 5 patients with stage III/IV BCa patients. CTC enumeration was performed with the FDA approved CELLTRACKS ANALYZERII® System (Menarini) by using CTC Kit targeting the Epithelial Cell Adhesion Molecule antigen for capturing CTCs, and immunofluorescent staining reagents including Anti-CK-PE (specific for epithelial cells), DAPI (for nucleus), anti-CD45-APC (specific for leukocyte), and anti-HER-2/neu-FLU. Or, using CXC kit includes anti-CCR5-PE. After confirming CTCs-clusters, both CTCs and CTC-clusters were enriched from Celltracks cartridge and were loaded into DEPArrayTM NxT cartridge, and then were isolated and sorted by using fluorescent imaging based DEPArrayTM NxT System.

Results: All these samples were identified having CTCs (≥ 5, between 34 to 208 CTCs) with CTC-clusters (between 1 to 16) by CellSearch analysis. The images of CTCs and CTC-clusters were displayed in CellBrowserTM by the DEPArrayTM NxT System. According to multiple channels assigned for PE, DAPI, APC and FITC, the CTCs and CTC-clusters were classified and then sorted based on morphology and correct phenotype as CK+, EpCAM+, DAPI+ and CD45-, with additional markers of HER2 or CCR5. The targeted CTCs and CTC-clusters were routed, parked and then recovered under the direction of Recovery ManagerTM. By using this technique, we successfully recovered and harvested 27/34 (DEPArray harvest/CellSearch diagnosis), 54/151, 57/115, 75/196, and 115/208 CTCs from each CellSearch cartridge sample respectively. Meanwhile, we collected 1/1 (100%), 6/16 (37.5%), 1/1 (100%), 3/11 (27.3%), and 4/4 (100%) of CTC-clusters respectively, as each CTC-cluster includes average of 2.85 CTCs. CTC-clusters at diameter as much as 45µm could be routed and recovered smoothly. Furthermore, CTC-Clusters with biomarkers of interest such as HER2+ or CCR5+ expression were separated into different tubes. The white blood cells from the same samples were also selected successfully as the controls.

Conclusions: We first reported a new workflow for CTC-clusters isolation. With further optimization, this feasible and reliable strategy will help streamline isolation of single CTC and CTC-clusters in MBC patients for genomic analysis providing the opportunity to gain new insights on the molecular mechanisms associated with the metastasis process.

Citation Format: Qiang Zhang, Lorenzo Gerratana, Ami N. Shah, Andrew A. Davis, Lisa Flaum, Youbin Zhang, Amir Behdad, Firas Wehbe, William Gradishar, Leonidas Platanias, Massimo Cristofanilli. A novel application of DEPArrayTM NxT System to isolate circulating tumor cell (CTC)-clusters from patients with metastatic breast cancer (MBC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1351.

Abstract 2279: Serial changes in tumor-derived whole-genome cfDNA fraction to identify early disease progression prior to imaging

Background:

Response to cancer treatment is usually determined by clinical exam and imaging assessment. Here, we analyzed changes in tumor-derived whole-genome cell-free DNA (cfDNA) at baseline and after treatment initiation to determine response to treatment prior to routine imaging.

Methods:

We prospectively enrolled and serially collected blood from 54 patients with metastatic malignancies (21 lung, 20 breast, 13 other tumor types). Baseline blood samples were drawn prior to initiation of a new treatment and at one or two additional time points, after the first cycle (median 21 days) and the second cycle (median 42 days). 4 mL of plasma was separated from peripheral blood collected in Streck Cell-Free DNA Blood Collection Tubes, and cfDNA was isolated from plasma aliquots using Qiagen QIAmp extraction kits. To prepare sequencing libraries, a method optimized for whole genome sequencing (WGS) was used based on the Kapa HyperPrep chemistry. WGS was performed at approximately 25X depth on the Illumina HiSeq X. Based on a patient-specific profile of whole genome features, changes in the fraction of tumor-derived cfDNA were quantified over the initial course of treatment. Imaging was performed per standard practice with treatment response determined by RECIST.

Results:

Median number of prior treatment lines was 1 [range 0-6]. Patients were treated with the following therapies: chemotherapy (27), immunotherapy (14), hormone therapy (7), or targeted therapy (6). For the entire cohort, patients with predicted progression by cfDNA (n=11), indicated by an increase in tumor fraction at either post-treatment blood collection, had worse event-free survival compared to patients that did not show an increase (n=43) (hazard ratio 8.0, [95% CI 3.4-19.2], log-rank p=4.5 x 10-8). For the patients who were predicted to progress, the cfDNA assay preceded clinical evaluation by a median of 39 days. Median progression-free survival was 62 days for patients with predicted progression versus 232 days for others. All patients with predicted progression were later confirmed to progress at the first follow-up evaluation (11/11, 100% positive predictive value). For the remaining patients, 32 of 43 did not progress (74% negative predictive value). Therefore, sensitivity for the assay was 50% and specificity was 100%.

Conclusions:

Analyzing tumor-derived cfDNA early in the course of a new therapy holds promise to identify patients with early disease progression across a variety of tumor histologies and types of treatment. Early identification of patients who are not benefitting from treatment will enable initiation of other potentially effective therapies, and reduce unnecessary side effects and cost associated with these treatments. Further studies are warranted to validate these findings in larger cohorts and to confirm the histology and treatment-independent nature of the approach.

Citation Format: Andrew A. Davis, Wade T. Iams, David Chan, Michael S. Oh, Robert W. Lentz, Neil Peterman, Alex Robertson, Abhik Shah, Rohith Srivas, Nicole Lambert, Tim Wilson, Peter George, Becky Wong, Ayse Tezcan, Ram Yalamanchili, Ken Nesmith, John C. Spinosa, Haluk Tezcan, Young Kwang Chae. Serial changes in tumor-derived whole-genome cfDNA fraction to identify early disease progression prior to imaging [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2279.

Abstract 408: Expression of CCR5 associated with HER2 in circulating tumor cells (CTCs) is a novel biomarker for patients with metastatic breast cancer (MBC)

Introduction: The Chemokine C-C motif ligand 5 (CCL5) and its receptor 5 (CCR5) play a significant role in solid tumors, particularly triple negative breast cancer (TNBC) and HER2+ subtypes with prognostic implications. CCL5-CCR5 axis was reported to govern cancer stem cells expansion and play key role in MBC progression. Our group recently reported that overexpression of HER2 was associated with CTC-clusters which caused poor prognosis of patients with MBC. Herein, we first reported the expression of CCR5 in CTCs of MBC patients, and described the correlation between CCR5 and HER2 expression in CTCs.

Methods: Whole blood samples (7.5ml/each) were collected from stage III/IV MBC patients before systemic therapy. CTCs enumeration was performed in FDA approved CELLTRACKS ANALYZERII® System (Menarini) by using CTC Kit contains antibodies targeting the Epithelial Cell Adhesion Molecule (EpCAM) antigen for capturing CTCs, and immunofluorescent staining reagents including anti-CK-PE (specific for epithelial cells), DAPI (for nucleus), anti-CD45-APC (specific for leukocytes), and anti-HER-2/neu-FLU. The CTCs were classified as CK+, EpCAM+, DAPI+ and CD45-. After confirming CTCs were positive by CellSearch system, CCR5 expression were evaluated by using CXC kit for multiple staining includes anti-CCR5-PE (R&D Systems), Anti-CK-FITC, DAPI and Anti-CD45-APC. The correlation between HER2 expression and CCR5 expression was analyzed by Kruskal-Wallis test was used for statistics.

Results: CTCs were found positive (≥5) in all seven MBC patients with a range of numbers between 124 and 442, and HER expression was identified in 6 out 7 cases (between 57 and 149 total cells). The ratios of HER2+ CTCs/total CTCs were varied between 28.5% and 88.1%. Meanwhile, CCR5 expression were found in 3 out 7 patients (Group 1), with CCR5+ CTCs/ total CTCs ratios were 4.45%, 43.1% and 59.1% respectively. There were 4 patients without CCR5 expression in CTCs (Group 2). The average HER2+ CTCs was 127.6 with HER2+ CTC/Total CTC as average of 59.4% in Group 1, which were significantly higher in compared with the corresponding numbers as 80.3 and 29.97% respectively in Group 2, which indicated that upregulation of CCR5 was positively associated with high level of HER2 expression in CTCs.

Conclusions: Our data provides the first evidence of strong expression of CCR5 in CTCs of MBC as potential new marker. The significant correlation between overexpression of HER2 in CTCs and high level of CCR5 indicated that CCR5 may contributes to more aggressive MBC subtypes with HER2 expression, which promotes carcinogenesis and metastasis at least partly by maintaining and increasing cancer stem cells leading to increased invasion. We conclude that the further understanding of the molecular interactions of CCR5 and HER2 in CTCs will be important to elucidate the mechanism of metastasis of MBC and predict prognosis.

Citation Format: Qiang Zhang, Lorezo Gerratana, Ami N. Shah, Andrew A. Davis, Lisa Flaum, Youbin Zhang, Richard G. Pestell, Firas Wehbe, Amir Behdad, Leonidas Platanias, William Gradishar, Massimo Cristofanilli. Expression of CCR5 associated with HER2 in circulating tumor cells (CTCs) is a novel biomarker for patients with metastatic breast cancer (MBC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 408.

Emerging Role of Genomics and Cell-Free DNA in Breast Cancer

OPINION STATEMENT

Precision Medicine is gaining momentum as the future gold standard healthcare strategy as it enables treatment optimization and consequently a potential improvement for quality of life and survival. This paradigm shift was possible thanks to new high-throughput genomics technologies, which provide prognostic and predictive information on tumor biology and potential treatment options, as standard pathological procedures are unable to capture both spatial and temporal tumor heterogeneity. As a result of decreasing costs, both solid and liquid-based genomics have an increasingly important role in clinical trials' screening procedures and are gradually being incorporated into clinical practice. Notwithstanding the great potential, its clinical utility is still a matter of debate and clinicians need to be aware of caveats in interpreting resulting data.

Whole-genome cell-free DNA (cfDNA) changes as a dynamic blood-based biomarker for early response assessment of advanced tumors

3041

Background: Liquid biopsies have potential clinical utility as dynamic biomarkers for treatment response. We analyzed serial changes in whole-genome (WG) cfDNA to identify patients with disease progression prior to routine imaging. Methods: We prospectively collected clinical data and blood from 69 advanced cancer patients (28 lung, 25 breast, 16 other). Blood was collected at baseline prior to initiation of a new treatment and at one or two additional timepoints (median 21 and 42 days). We isolated plasma cfDNA and prepared sequencing libraries for WG sequencing or WG bisulfite sequencing (median depth 20X). We quantified changes in the fraction of tumor-derived cfDNA over the initial course of treatment to predict progression vs. no progression. Treatment response at first post-treatment imaging was determined by RECIST 1.1 and clinical assessment. Study endpoints were agreement with first post-treatment imaging and progression-free survival (PFS) by cfDNA prediction. Results: Median age of patients was 70 and 59% were female. Patients were treated with the following therapies: chemotherapy (37), immunotherapy (17), endocrine (9), or targeted therapy (6). Patients with predicted progression by cfDNA (14), indicated by an increase in tumor fraction at either post-treatment blood collection, had shorter PFS (median 63 days) compared to patients without an increase (N = 55; median 255 days), with hazard ratio of 10.3 (95% confidence interval 4.6-23.4, log-rank P = 1x10-11). Positive predictive value was 100% for disease progression and negative predictive value was 78%. These findings were consistent in subset analyses of patients with lung (log-rank P = 2x10-5), breast (log-rank P = 3x10-4), and those treated with immunotherapy (log-rank P = 5x10-6). Conclusions: Our results show the ability to detect early disease progression with high fidelity using WG cfDNA prior to first imaging. These findings were consistent across multiple tumor types and treatments, including immunotherapy patients. Once validated, this dynamic, predictive, blood-based biomarker could aid in clinical decision making for early treatment change as a novel and cost-effective approach.

A prospective study tracking longitudinal changes in genome-wide cell-free DNA (cfDNA) methylation to identify early nonresponders to cancer treatment

3042

Background: Methylation is an epigenetic modification linked to cancer pathogenesis. The aim was to determine if changes in cfDNA methylation patterns before and after initiation of treatment could predict non-response to treatment prior to routine imaging and clinical follow-up. Methods: We prospectively collected clinical data and blood from 28 patients with metastatic malignancies (13 lung, 11 breast, 4 other). Blood was drawn prior to start of a new treatment, after first cycle (median 30 days), and/or second cycle (median 57 days). We performed whole-genome (WG) bisulfite sequencing (median depth 18X) on plasma cfDNA to determine methylation levels. By tracking how methylation levels deviate from unaffected individuals, from baseline to subsequent timepoints, we classified patients as either progressors (greater deviance) or non-progressors. Treatment response at first follow-up imaging (FUI) was determined by RECIST 1.1. Study endpoints were agreement with first FUI and progression-free survival (PFS) by cfDNA classification. Results: The cohort consisted of 68% females and the median age was 70. Main treatment regimens were chemo- (N = 12), immuno- (6), endocrine (5), or targeted-therapy (5). PFS was significantly shorter (log-rank p = 8 x 10-7) in patients classified as progressors by cfDNA (N = 8; median: 62 days) compared to non-progressors (N = 20, median: 263 days). For patients classified as progressors, the cfDNA assay preceded imaging and clinical evaluation by a median of 34 days. 7 out of 8 patients classified as cfDNA progressors were later confirmed to progress at first follow-up evaluation (88% positive predictive value). The one patient who was classified as progressor based on cfDNA was stable based on FUI (day 93 of treatment) but was later confirmed as progression on day 128 by FUI. For the remaining patients, 18 of 20 did not progress (90% negative predictive value). Thus, sensitivity for the assay for identifying progression was 78% and specificity was 95%. Conclusions: Our results show that WG cfDNA methylation change is a novel signature with potential to identify patients whose treatment regimen is ineffective prior to imaging.

Association of HER2 alterations and ESR1 mutations in cell-free DNA (cfDNA) with circulating tumor cells (CTCs), multiple metastasis, and prognosis in stage III/IV breast cancer (BCa)

1036

Background: The monitoring of CTCs and cfDNA in metastatic BCa showed ability to predict treatment resistance and survival. Here we report a highly significant correlation between HER2 alterations and ESR1 mutations of cfDNA with CTCs and prognosis of BCa, which may help to predict disease recurrence and treatment benefit. Methods: A total of 85 blood samples (7.5ml/each) were collected from 85 patients with stage III/IV BCa who received treatments at Northwestern RHLCCC. CTC enumeration was performed in FDA approved CELLTRACKS ANALYZERII System (Menarini). Plasma cfDNA was analyzed using Guardant360 NGS-based assay including a 73-gene panel for genomic alterations or mutations. We previously reported cut-off of 5.7% (2018 ASCO) was used to dichotomize the prognostic value of cfDNA percentage. Kruskal-Wallis test was used for statistics. Results: Of the 85 whole samples analyzed, there were 72 samples and 67 samples without ESR1 mutations (ESR1-) and HER2 alterations ( HER2-) respectively, and there are 13 samples and 18 samples that had ESR1 mutations ( ESR1+) and HER2 alterations ( HER2+, 10 amplified, 7 mutated, 1 for both) respectively. CTC positive (≥5) were detected in 13/57 ESR1-HER2- samples (Group 1) and 5/15 ESR1- HER2+ samples (Group 2), 7 /10 ESR1+ HER2- samples (Group 3), 3/3 ESR1+ HER2+ samples (Group 4). The median CTCs number/sample in Group 3 (15 CTCs) and Group 4 (12 CTCs) were significantly higher than Group 1 (0 CTC) and Group 2 (2 CTCs) (P = 0.0020). There were a significant higher average metastasis sites in Group 3 (3 sites) and Group 4 (3 sites) in compared to Group 1 (2 sites) and Group 2 (1 site) (P = 0.0035). Furthermore, patients in Group 4 ( ESR1+ HER2+) has the worst prognosis in compared to other groups (P = 0.0151) on overall survival. Conclusions: Both ESR1 mutations and HER2 alterations in cfDNA contribute to CTCs detection and disease metastasis sites independently, when ESR1 mutations plays a major role. The synergy of ESR1 mutation and HER2 alteration expands the predictive role of liquid biopsy tests monitoring the metastatic prognosis and endocrine resistance for clinical decision-making.

Clinical implication of monitoring PD-L1+ circulating tumor cells (CTCs) in patients with non-small cell lung cancer (NSCLC) receiving immunotherapy

e14044

Background: CTCs not only constitute a cellular component of liquid biopsy for dynamic, longitudinal information of malignancies, but also pose a continuous threat to seed new metastasis. Detection of these cells can help identify patients with residual disease and poor prognosis. However, it is unknown if heterogeneous CTCs can be profiled to monitor cancer stemness and immunotherapy response for patients. Limited clinical data exist for monitoring CTCs for markers of cancer stem cells, such as CD44 or CD166, and immunotherapy therapeutic targets including PD-L1. We hypothesized that dynamic monitoring of CTC positivity for these markers would correlate with responses to immune checkpoint inhibitor treatment for patients with NSCLC. Methods: As part of a prospective analysis of peripheral blood cells, 30 patients with NSCLC undergoing immunotherapy (pembrolizumab or atezolizumab) or combination therapy with chemotherapy had blood samples collected at 3-4 week intervals for up to 24 weeks. Peripheral blood mononuclear cells were isolated and analyzed for CD45, to identify non-leukocyte putative CTCs, CD166 and CD44, to identify cancer stem cell markers among potential CTCs, and PD-L1. Patients were evaluated for response based on RECIST criteria. Statistical analysis was performed using one-way ANOVA on samples from each time point. Results: A decrease in PD-L1+ CD45- cells (CTCs) at the second interval was most strongly associated with initial response. In contrast, increasing number of PD-L1+ CD45- cells were found among patients with progressive disease as compared to those with stable disease or a partial response (p = 0.01). (1) CD45- cells, (2) CD44+; CD45- cells and (3) CD166+; CD45- cells demonstrated no significant association with clinical outcomes. Baseline PD-L1 level on CTCs did not correlate with the PD-L1 level on tissue. Conclusions: We report the feasibility and potential clinical significance of monitoring surface markers on CTCs in the blood before and after initiation of immunotherapy. Our findings that PD-L1+ CTCs increased among non-responders to immunotherapy warrant further validation. Testing is ongoing to evaluate how these changes predict long-term outcome to treatment for patients.

Can the enumeration of circulating tumor cells (CTCs) and the characterization of circulating tumor DNA (ctDNA) provide insight into organ tropism in metastatic breast cancer (MBC)?

3038

Background: Liquid biopsy provides real-time data about prognosis and actionable mutations in MBC. The aim of this study was to explore the combination of ctDNA analysis and CTCs enumeration in estimating target organs more susceptible to MBC involvement. Methods: This retrospective study analyzed 85 MBC patients (pts) characterized for both CTCs and ctDNA at baseline. CTCs were isolated through the CellSearch kit (Menarini Silicon Biosystems, PA), while ctDNA was analyzed using the Guardant360 NGS-based assay (Guardant Health, CA). Pts with ≥ 5 CTC/7.5 ml of blood were defined as Stage IV aggressive as previously reported (Cristofanilli et al 2019). Statistical associations were explored through uni- and multivariate logistic regression and Fisher’s exact test. Results: 37% of pts were diagnosed with hormone receptor positive (HRpos) MBC, 26% with HER2-positive MBC and 37% with triple negative MBC (TNBC), 28 pts (33%) were defined as stage IV aggressive. The most observed metastatic sites were bone (37%), lymph nodes (29%), lung (27%) and liver (25%). In multivariate analysis, IBC and ESR1 mutations were the only significant factors associated with liver metastases (respectively, OR 0.12, P = 0.038 and OR 24.01, P = 0.019), while no associations were found with respect to lung localizations. Intriguingly, all HRpos MBC pts with ESR1 mutations had bone metastases (P = 0.022), while IBC and Stage IV aggressive were independently associated with bone metastases (respectively OR 0.10, P = 0.006 and OR 19.92, P = 0.003). FGFR1 and NF1 were associated with lymph node localizations (OR 3.68, P = 0.046, OR 4.39, P = 0.031, respectively), while CDK6 and TP53 alterations were associated with serosal involvement (OR 14.34, P = 0.029, OR 0.08, P = 0.031, respectively). Notably, TNBC and IBC were both associated with soft tissue spreading (respectively OR 3.7, P = 0.011, OR 2.79, P = 0.018). Conclusions: These results suggest that ctDNA and CTCs enumeration could give useful insights on MBC organotropism, suggesting a possible role for future monitoring strategies that dynamically focus on high-risk organs defined by tumor biology.

Clinical Implications of Circulating Tumor DNA Tumor Mutational Burden (ctDNA TMB) in Non-Small Cell Lung Cancer

BACKGROUND

Tissue tumor mutational burden (TMB) has emerged as a potential biomarker predicting response to anti-programmed cell death-1 protein receptor (PD-1)/programmed cell death-1 protein ligand (PD-L1) therapy, but few studies have explored using circulating tumor DNA (ctDNA) TMB in non-small cell lung cancer (NSCLC).

MATERIALS AND METHODS

A total of 136 patients with NSCLC with ctDNA testing were retrospectively evaluated from a single institution, along with a validation cohort from a second institution. ctDNA TMB was derived using the number of detected mutations over the DNA sequencing length.

RESULTS

Higher ctDNA TMB was significantly correlated with smoking history (p < .05, chi-squared test). Among patients treated with immune checkpoint inhibitors (n = 20), higher ctDNA TMB was significantly correlated with shorter progressive free survival (PFS) and overall survival (OS; 45 vs. 355 days; hazard ratio [HR], 5.6; 95% confidence interval [CI], 1.3-24.6; p < .01, and OS 106 days vs. not reached; HR, 6.0; 95% CI, 1.3-27.1; p < .01, respectively). In a small independent validation cohort (n = 12), there was a nonsignificant numerical difference for higher ctDNA TMB predicting shorter OS but not PFS. ctDNA TMB was not correlated with RECIST tumor burden estimation in the subset of patients treated with immune checkpoint blockade.

CONCLUSION

The findings indicate that higher ctDNA TMB, at the current commercial sequencing length, reflects worse clinical outcomes.

IMPLICATIONS FOR PRACTICE

Biomarkers to identify patients who will respond to immune checkpoint blockade are critical. Tissue tumor mutational burden (TMB) has emerged as a viable biomarker to predict response to anti-PD-1/PD-L1 therapy, but few studies have explored the meaning and potential clinical significance of noninvasive, blood-based TMB. Here, we investigated circulating tumor DNA (ctDNA) TMB and present data demonstrating that current ctDNA TMB may reflect tumor burden and that ctDNA panels with a greater number of mutations may be necessary to more accurately reflect tissue TMB.

Abstract P5-17-03: How is inflammatory breast cancer (IBC) different? Integration of clinico-pathological features and circulating tumor cells (CTCs)-based biomarkers for disease and prognostic assessment

Background: Since IBC is rare and burdened by a particularly unfavorable prognosis, biomarkers able to enhance diagnosis and risk assessment are of pivotal importance and a current unmet need. The aim of this study is to integrate standard clinico-pathological features with CTCs-based biomarkers for a more objective and detailed characterization of IBC.

Methods: This study analyzed retrospectively 251 Advanced Breast Cancer (BC) patients (pts) longitudinally characterized for CTCs and CTCs-based biomarkers at Thomas Jefferson University (Philadephia, PA) and Northwestern University (Chicago. IL). CTCs were enumerated through the CellSearch system (Menarini Silicon Biosystems), and characterized for HER2 expression using the CellSearch CXC Kit. Pts were defined as stage IV aggressive based on the previously reported ≥5 CTCs cut-off (Davis et al. 2018). Associations between clinical features, CTC-derived biomarkers and IBC were tested through uni and multivariate logistic regression. Survival was tested though log-rank test.

Results: Within the analyzed cases, 46% were diagnosed with IBC and among them, 38% was stage IV aggressive. CTC clusters (CTC_CL) were detectable in 12.5% of pts and HER2 positive CTCs (HER2_CTC) in 29.5%. Notably, IBC patients (pts) had a significantly lower CTC count with respect to non-IBC (median 2.5 vs 0 respectively for non-IBC and IBC; P=0.019). BC subtype (HER2 positive BC: OR 2.97; Triple negative BC: OR 2.13), liver and bone involvement (liver: OR 0.46; bone involvement: OR 0.31) were the only significant clinico-pathological features associated with IBC at univariate logistic regression. Interestingly, a marginal significance was observed for soft tissue involvement (OR 1.65, 95%CI 0.95 - 2.87, P=0.07). Stage IV aggressive and presence of HER2_CTC at baseline were moreover inversely associated with IBC. The multivariate model confirmed the significant association between IBC and HER2 positive BC subtype (OR 2.64, 95%CI 1.08 - 6.48, P=0.034), absence of bone involvement (OR 0.31, 95%CI 0.14 - 0.68, P=0.003) and absence of HER2_CTC (OR 0.38, 95%CI 0.15 - 0.98, P=0.045). The baseline detection of CTC_CL was a strong predictor of prognosis for OS in IBC pts (median OS (mOS) 7.6 months (mts) vs not reached (NR) respectively for detectable vs non-detectable CTC_CL; P&lt;0.0001), while a trend was observed for HER2_CTC (mOS 9.9 mts vs NR respectively for detectable vs non-detectable HER2_CTC; P&lt;0.082). Pts negative for CTC_CL at baseline had higher odds of developing CTC_CL in later time-points if stage IV aggressive (OR 12.27, 95%CI 2.10 - 71.57, P=0.005). Despite no baseline factors were significantly associated with the onset of HER2_CTC in later time-points, a trend (P=0.05) was observed for patients without lymph node involvement (OR: 5) and with bone involvement (OR: 4.3).

Conclusion: HER2_CTC and in particular CTC_CL are promising prognostic predictors in IBC. Stage IV aggressive IBC pts could benefit from a longitudinal CTCs assessment, being more prone to develop CTC_CL and therefore at higher risk of rapid disease progression. Probably due to the tropism for soft tissue, IBC is characterized by a lower number of HER2_CTC.

Citation Format: Gerratana L, Zhang Q, Wang C, Shah A, Davis AA, Ye Z, Zhang Y, Abu-Khalaf M, Flaum L, Strickland K, Rossi G, Behdad A, Gradishar W, Platanias L, Yang H, Cristofanilli M. How is inflammatory breast cancer (IBC) different? Integration of clinico-pathological features and circulating tumor cells (CTCs)-based biomarkers for disease and prognostic assessment [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 P5-17-03.

Abstract P3-01-08: HER2-negative metastatic breast cancer with HER2-positive circulating tumor cells (CTCs): A new CTC-defined HER2-positive subgroup

Introduction: CTCs can overexpress HER2 discordant from tumor HER2 expression. We aimed to describe characteristics of a CTC-defined group of pts with metastatic breast cancer (MBC) that is tumor HER2- and CTC HER2+ (HER2 tumor- CTC+).

Methods: We retrospectively analyzed data from pts treated at Northwestern University who had serial evaluation of CTCs and circulating tumor DNA (ctDNA). We included pts with pathologically confirmed HER2- MBC and HER2+ CTCs. CTCs were enumerated with the CellSearch immunomagnetic kit (Menarini Silicon Biosystems), HER2 expression on CTCs was determined using the CellSearch CXC Kit in 7.5 cc whole blood, and ctDNA was analyzed using the Guardant360 NGS assay (Guardant Health).

Results: Among 98 pts with HER2- MBC and CTC analysis, 46 (47%) had at least 1 HER2+ CTC. In this cohort the median age was 53. At initial BC diagnosis, 80% had early stage or locally advanced BC and 20% had de-novo metastatic disease. Baseline histology was 65% ductal, 20% lobular, 2% mixed ductal and lobular, and 13% unknown. Pathology of metastatic tumor was hormone receptor positive (HR+)/HER2- in 78% and triple negative in 22%. Detailed HER2 immunohistochemistry (IHC) and FISH results from metastases were available from 63% of pts of whom 72% had an IHC score of 0 or 1 and 28% had an IHC score of 2 with negative FISH testing. The median time from the most recent pathologic metastatic tumor assessment to the detection of a HER2+ CTC was 6.5 mo. Twenty-two pts had simultaneous (within 8 weeks) HER2- tumor confirmation and HER2+ CTC detection. The median lines of endocrine therapy (ET) for MBC prior to detection of HER2+ CTCs was 1 (range 0-5, 41% no ET, 17% 1 line, 41% &gt;2 lines). Pts received a median of 2 (range 0-10) prior systemic therapies for MBC prior to detection of HER2+ CTCs, (20% 0 lines, 41% 1-3 lines, and 39% &gt;4 lines). Among these 46 pts, CTCs were analyzed longitudinally in 104 samples, with HER2+ CTCs detected in 77 samples. Number of HER2+ CTCs at initial detection ranged from &lt;5 in 24%, 5-50 in 43%, and &gt;50 in 33%, with a median of 11.5 HER2+ CTCs. CTC clusters were noted in 37% of pts. At initial detection the proportion of CTCs that were HER2+ was 0-25% in 13% of pts, 26-50% in 46% of pts, and 51-100% in 41% of pts. Seven pts had ERBB2 aberrations in ctDNA. Of 12 pts with tumor sequencing, 2 had ERBB2 mutations, 1 had ERBB3 amplification, and 1 had overexpression of ERBB3 RNA. After detection of HER2+ CTCs, 18 pts received HER2 directed therapy (with chemotherapy in 13 pts, with endocrine therapy in 4 pts, and as monotherapy in 1 pt). Imaging demonstrated a partial response or stable disease in 9 pts (clinical benefit rate 50%), including in 1 pt with trastuzumab monotherapy, progressive disease in 8 pts, and not evaluated in 1 pt.

Conclusions: HER2+ CTCs are frequently detected simultaneously or soon after HER2- tumor assessment in MBC. Within this newly defined subgroup, the several responses seen with HER2 targeted therapy serve as a proof of concept that HER2 tumor- CTC+ patients can benefit from HER2 targeted therapy. Future studies are needed to determine a clinically relevant threshold for HER2+ CTCs to guide further study of HER2 therapy combinations in HER2 tumor- CTC+ pts.

Citation Format: Shah AN, Gerratana L, Zhang Q, Davis AA, Zhang Y, Flaum L, Behdad A, Platanias L, Gradishar WJ, Cristofanilli M. HER2-negative metastatic breast cancer with HER2-positive circulating tumor cells (CTCs): A new CTC-defined HER2-positive subgroup [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 P3-01-08.

Abstract P3-01-19: HER2-positive circulating tumor cells (CTCs) in advanced breast cancer (BC): A feature independent of BC subtype

Introduction: HER2 overexpression is observed on CTCs in advanced BC (ABC), but their significance is not known. We aimed to describe clinical, pathologic, and molecular associations with HER2 overexpression on CTCs in ABC patients (pts).

Methods: We conducted a retrospective analysis of data from ABC pts treated at Thomas Jefferson University and Northwestern University who had evaluation of CTCs and circulating tumor DNA (ctDNA). CTCs were enumerated with the CellSearch immunomagnetic kit (Menarini Silicon Biosystems), HER2 expression on CTCs was evaluated using the CellSearch CXC Kit, and ctDNA was analyzed using the Guardant360 NGS assay (Guardant Health). Associations with the presence of HER2+ CTCs were explored through univariate and multivariate logistic regression. Kruskal-Wallis testing evaluating HER2+ CTCs as a continuous variable was also conducted to confirm consistency of findings. Time to development of HER2+ CTCs was evaluated using Cox proportional hazards regression analysis.

Results: Baseline CTCs were evaluated in 209 pts (10% stage III, 90% stage IV) of whom 41% had no detectable CTCs, 23% had 1-4 CTCs, and 36% had &gt;5 CTCs (stage IV aggressive). Twelve percent had CTC clusters. At least 1 HER2+ CTC was seen in 33% of pts at baseline draw. Of 39 patients with HER2+ BC, only 18% had HER2+ CTCs. Of patients with HER2+ CTCs, 55% had hormone receptor positive BC, 28% had triple negative BC, and 18% had HER2+ BC. On univariate logistic analysis, BC subtype or HER2 status was not associated with the presence of HER2+ CTCs. IBC pts represented 52% of pts and were less likely to have HER2+ CTCs (OR 0.40 95% CI 0.19-0.84). Bone metastases were associated with an increased likelihood of HER2+ CTCs (OR 2.46, 95% CI 1.12-5.38); however, other sites of metastases and number of metastatic sites were not correlated with HER2+ CTCs. Aggressive disease features including &gt;5 CTCs and presence of CTC clusters were strongly associated with HER2+ CTCs (OR 15.72, 95% CI 6.89-35.8 and 8.97, 95% CI 3.23-24.89, respectively). Of 168 pts with ctDNA analysis, ERRB2 aberrations were seen in 22% of pts and were significantly associated with HER2+ CTCs (OR of 3.74, 95% CI 1.45-9.63). On multivariate analysis, the associations with &gt;5 CTCs and ERBB2 alterations in ctDNA remained statistically significant. The associations of HER2+ CTCs with bone disease, &gt;5 CTCs, CTC clusters, and ERBB2 alterations in ctDNA, and the inverse relationship with IBC were consistent when HER2+ CTCs were evaluated as a continuous variable with Kruskal-Wallis testing. Among pts without HER2+ CTCs at baseline, the time to detection of HER2+ CTCs correlated with the presence of bone metastases (HR 3.40, 95% CI 1.14-10.19), &gt;5 CTCs (3.77, 95% CI 1.33-10.70), and visceral disease (HR 3.00, 95% CI 1.07-8.44).

Conclusions: HER2+ CTCs are common in ABC, independent of HER2 status of the tumor, and, in fact, common in the luminal BC. HER2+ CTCs were also strongly associated with CTC characteristics of aggressive disease with poor survival (CTCs clusters and &gt;5 CTCs) and ERBB2 aberrations in ctDNA. Further studies will be investigating the role of HER2+ CTCs in endocrine resistance and the potential of anti-HER2 therapy in this unique CTC-defined setting.

Citation Format: Shah AN, Gerratana L, Davis AA, Zhang Q, Zhang Y, Rossi G, Wang C, Strickland K, Yang H, Flaum L, Abu-Khalaf M, Behdad A, Ye Z, Platanias L, Gradishar WJ, Cristofanilli M. HER2-positive circulating tumor cells (CTCs) in advanced breast cancer (BC): A feature independent of BC subtype [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 P3-01-19.

Abstract P5-17-02: Dissecting the biology of inflammatory breast cancer (BC) through cell free DNA and a circulating tumor cells (CTC)-derived signature

Background: The biological characteristics conferring Inflammatory BC's (IBC) distinctive and aggressive clinical features are currently not fully clarified. The aim of this study is to dissect IBC's biology through the integration of DNA and CTC-based circulating biomarkers.

Methods: This study retrospectively analyzed 251 Advanced BC (ABC) patients (pts) treated and longitudinally characterized for CTCs and circulating tumor DNA (ctDNA) at Thomas Jefferson University (Philadephia, PA) and Northwestern University (Chicago, IL). CTCs were enumerated through CellSearch (Menarini Silicon Biosystems), and characterized for HER2 expression using the CellSearch CXC Kit, while ctDNA was analyzed using the Guardant360 NGS assay (Guardant Health) and its percentage (%ctDNA) was classified based on the previously reported cut-off of 5.7% (Gerratana et al 2018). A subset of 117 pts was further characterized for circulating cell-free DNA (ccfDNA) through Qubit® dsDNA HS quantitation Assay (Thermo Fisher Scientific) and quantitative real-time PCR assay for ALU DNA repeats on chromosome 1.Associations between clinical characteristics, CTCs-derived biomarkers and IBC were explored through Fisher's exact test; survival was tested though Cox regression and log-rank test.

Results: Of the total 251 pts, 115 were diagnosed with IBC. Among the 117 patients characterized for ccfDNA, 70 had IBC. Median ccfDNA was 1.59 for IBC (IQR 1.02-3.19) and 2.37 for non-IBC (nIBC) (IQR 1.13-3.52), P=0.27. Consistent results were observed for %ctDNA levels (median value: 2 vs 1.6). The impact on OS of ccfDNA after log transformation was significant for the total population (HR 1.73 95%CI: 1.11-2.69) but not in IBC pts (HR 1.40 95%CI: 0.84-2.34). On the other hand, ctDNA high pts had a significantly worse OS (nIBC: HR 5.34 95%CI: 1.70-18.81 P=0.004; IBC: HR 4.05 95%CI: 1.91-8.58 P&lt; 0.001). In the ctDNA high subgroup no differences in total number of CTCs were observed between IBC and nIBC, while significantly lower CTCs were observed in ctDNA low IBC pts (P=0.0097). The ctDNA low IBC subgroup had a higher incidence of HER2 positive BC (P=0.003) and a significantly lower incidence of CTCs clusters (P=0.006), HER2 positive CTCs (P=0.041). Notably, no associations were observed with stage at baseline, number of metastatic sites, liver, lung and visceral involvement. On the other hand, the ctDNA_high IBC subgroup was characterized by a lower incidence in liver, bone and visceral involvement (P=0.017, P=0.014 and P=0.03 respectively) and a marginally high incidence in soft tissue involvement (0.084). Moreover, IBC diagnosis conferred a significantly worse prognosis only in the ctDNA low subgroup (OS at 12 months nIBC: 100% vs IBC: 70%; P=0.049), while no differences were observed in the ctDNA_high subgroup (OS at 12 months nIBC: 29% vs IBC: 26%; P=0.767).

Conclusion: ctDNA is able to stratify BC according to aggressiveness independently from the sites and type of metastases, both in the IBC and nIBC subgroups. IBC has a distinctive CTCs/ctDNA-based signature, in particular ctDNAlow pts have a lower incidence of HER2 positive CTCs and CTC clusters. This signature is probably due to predominant lymphatic metastatic spread and aggressive phenotype.

Citation Format: Gerratana L, Zhang Q, Wang C, Shah A, Davis AA, Ye Z, Zhang Y, Abu-Khalaf M, Flaum L, Strickland K, Rossi G, Behdad A, Gradishar W, Platanias L, Yang H, Cristofanilli M. Dissecting the biology of inflammatory breast cancer (BC) through cell free DNA and a circulating tumor cells (CTC)-derived signature [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 P5-17-02.

The clinical use of circulating tumor cells (CTCs) enumeration for staging of metastatic breast cancer (MBC): International expert consensus paper

BACKGROUND

The heterogeneity of metastatic breast cancer (MBC) necessitates novel biomarkers allowing stratification of patients for treatment selection and drug development. We propose to use the prognostic utility of circulating tumor cells (CTCs) for stratification of patients with stage IV disease.

METHODS

In a retrospective, pooled analysis of individual patient data from 18 cohorts, including 2436 MBC patients, a CTC threshold of 5 cells per 7.5 ml was used for stratification based on molecular subtypes, disease location, and prior treatments. Patients with ≥ 5 CTCs were classified as Stage IVaggressive, those with < 5 CTCs as Stage IVindolent. Survival was analyzed using Kaplan-Meier curves and the log rank test.

RESULTS

For all patients, Stage IVindolent patients had longer median overall survival than those with Stage IVaggressive (36.3 months vs. 16.0 months, P < 0.0001) and similarly for de novo MBC patients (41.4 months Stage IVindolent vs. 18.7 months Stage IVaggressive, p < 0.0001). Moreover, patients with Stage IVindolent disease had significantly longer overall survival across all disease subtypes compared to the aggressive cohort: hormone receptor-positive (44 months vs. 17.3 months, P < 0.0001), HER2-positive (36.7 months vs. 20.4 months, P < 0.0001), and triple negative (23.8 months vs. 9.0 months, P < 0.0001). Similar results were obtained regardless of prior treatment or disease location.

CONCLUSIONS

We confirm the identification of two subgroups of MBC, Stage IVindolent and Stage IVaggressive, independent of clinical and molecular variables. Thus, CTC count should be considered an important tool for staging of advanced disease and for disease stratification in prospective clinical trials.

Association of Tumor Mutational Burden With DNA Repair Mutations and Response to Anti-PD-1/PD-L1 Therapy in Non-Small-Cell Lung Cancer

PURPOSE

To examine clinical predictors of tumor mutational burden (TMB), to explore the association between TMB and DNA repair mutations, and to analyze TMB as a biomarker for response to immune checkpoint blockade in non-small-cell lung cancer.

PATIENTS AND METHODS

TMB scores were determined retrospectively for 72 consecutive patients at our institution with next-generation sequencing comprehensive genomic profiling testing by Foundation Medicine. TMB scores were correlated with a number of clinical variables and presence of DNA repair mutations. Thirty-four patients were treated with anti-programmed cell death 1 (PD-1)/programmed death ligand 1 (PD-L1) therapies, and survival analyses based on TMB score were performed. In addition, tissue immunohistochemical analysis was performed for a subset of patients.

RESULTS

History of smoking, but not other clinical variables, including prior treatment lines, stage of disease, and number of metastatic sites, predicted higher TMB score. Higher TMB score was significantly associated with greater number of DNA repair mutations. In the subset of patients treated with immune checkpoint blockade, higher TMB score significantly predicted overall survival, but not progression-free survival (hazard ratio = 0.10, P = .003; hazard ratio 1.1, P = .84, respectively). In a small subset of patients, PD-1/PD-L1 staining did not independently predict progression-free survival or overall survival.

CONCLUSION

Tissue TMB was significantly associated with smoking history and number of DNA repair mutations. TMB is a promising biomarker for response to anti-PD-1/PD-L1 therapy, with higher TMB score predicting longer overall survival.

Path toward Precision Oncology: Review of Targeted Therapy Studies and Tools to Aid in Defining "Actionability" of a Molecular Lesion and Patient Management Support

Precision medicine trials and targeted therapies have shifted to the forefront of oncology. Although targeted therapies have shown initial promise, implementation across the broad landscape of oncology has many challenges. These limitations include an incomplete understanding of the functional significance of variant alleles as well as the need for clinical research and practice models that are more patient-centered and account for the complexity of individual patient tumors. Furthermore, successful implementation of targeted therapies will also be predicated on efforts to standardize the framework for patient management support. Here, we review current implementations of targeted therapies in precision oncology and discuss how "actionability" is defined for molecular targets in cancer therapeutics. We also comment on the growing need for bioinformatics tools and data platforms to complement advances in precision oncology. Finally, we discuss current frameworks for integrating precision oncology into patient management and propose an integrated model that combines features of molecular tumor boards and decision support systems. Mol Cancer Ther; 16(12); 2645-55. ©2017 AACRSee related article by Pilié et al., p. 2641.

Abstract 3644: Blood tumor mutational burden (bTMB) from circulating tumor DNA (ctDNA) as a biomarker for both mutational status and tumor burden in non-small cell lung cancer (NSCLC)

Background:

Tissue tumor mutational burden (tTMB) has emerged as a viable biomarker for response to immune checkpoint blockade (ICB) in multiple histologies including NSCLC. Blood TMB (bTMB) is a novel summative measure of ctDNA genomic alterations in the peripheral blood. Few studies have examined the clinical utility and correlation of bTMB with tumor burden and survival.

Methods:

We identified 53 patients, retrospectively, who had paired blood (Guardant Health) and tissue (Foundation Medicine) next-generation sequencing testing. bTMB was determined by taking the number of reported mutations over the sequencing length of ctDNA. bTMB was calculated for research purposes and has not been approved for clinical use. From the cohort, 36 patients had baseline CT scans with measurable scores by RECIST version 1.1. Survival analyses by quartile were performed for the subset of patients (N=18 PFS, N=19 OS) treated with ICB.

Results:

bTMB was significantly correlated with baseline RECIST tumor burden estimations (p=0.010, Pearson Correlation, r=0.42, Table 1). There was a trend toward mutant allele frequency (MAF) of the highest clone in blood correlating with RECIST score (p=0.061). No significant correlation was found when comparing blood and tissue TMB scores in paired patients (p=0.70). In the subset of patients treated with ICB, higher bTMB was significantly associated with shorter PFS (HR 1.81 [1.03-3.18], p=0.038) and OS (HR 2.23 [1.09-4.58], p=0.029).

Conclusions:

This study demonstrated the feasibility and clinical utility of bTMB. Our findings may indicate that bTMB reflects tumor shedding into the blood as a surrogate for tumor burden and heterogeneity given the correlation with RECIST scores. In survival analyses, higher bTMB predicted shorter survival, which also reflects bTMB as a biomarker for tumor burden. Prospective studies are necessary to study bTMB in larger cohorts of patients treated with ICB.

Correlation CoefficientPRECIST-Blood TMB r = 0.424P = 0.010RECIST-Tissue TMB r = 0.238P = 0.198RECIST-MAFr = 0.316P = 0.061MAF-Blood TMB r = 0.182P = 0.289MAF-Tissue TMB r = 0.336P = 0.065Tissue TMB-Blood TMB r = 0.073P = 0.695

Citation Format: Andrew A. Davis, Carlos Galvez, Alan Pan, Nisha Mohindra, Victoria Villaflor, Young Kwang Chae. Blood tumor mutational burden (bTMB) from circulating tumor DNA (ctDNA) as a biomarker for both mutational status and tumor burden in non-small cell lung cancer (NSCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3644.

Complexity of Delivering Precision Medicine: Opportunities and Challenges

Precision medicine has emerged as a tool to match patients with the appropriate treatment based on the precise molecular features of an individual patient's tumor. Although examples of targeted therapies exist resulting in dramatic improvements in patient outcomes, comprehensive genomic profiling of tumors has also demonstrated the incredible complexity of molecular alterations in tissue and blood. These sequencing methods provide opportunities to study the landscape of tumors at baseline and serially in response to treatment. These tools also serve as important biomarkers to detect resistance to treatment and determine higher likelihood of responding to particular treatments, such as immune checkpoint blockade. Federally funded and publicly available data repositories have emerged as mechanisms for data sharing. In addition, novel clinical trials are emerging to develop new ways of incorporating molecular matched therapy into clinical trials. Various challenges to delivery of precision oncology include understanding the complexity of advanced tumors based on evolving "omics" and treatment resistance. For physicians, determining when and how to incorporate genetic and molecular tools into clinic in a cost-effective manner is critical. Finally, we discuss the importance of well-designed prospective clinical trials, biomarkers such as liquid biopsies, the use of multidisciplinary tumor boards, and data sharing as evidence-based medicine tools to optimally study and deliver precision oncology to our patients.

Concordance between genomic alterations assessed by next-generation sequencing in tumor tissue or circulating cell-free DNA

Genomic analysis of tumor tissue is the standard technique for identifying DNA alterations in malignancies. Genomic analysis of circulating tumor cell-free DNA (cfDNA) represents a relatively non-invasive method of assessing genomic alterations using peripheral blood. We compared the concordance of genomic alterations between cfDNA and tissue biopsies in this retrospective study. Twenty-eight patients with advanced solid tumors with paired next-generation sequencing tissue and cfDNA biopsies were identified. Sixty-five genes were common to both assays. Concordance was defined as the presence or absence of the identical genomic alteration(s) in a single gene on both molecular platforms. Including all aberrations, the average number of alterations per patient for tissue and cfDNA analysis was 4.82 and 2.96, respectively. When eliminating alterations not detectable in the cfDNA assay, mean number of alterations for tissue and cfDNA was 3.21 and 2.96, respectively. Overall, concordance was 91.9–93.9%. However, the concordance rate decreased to 11.8–17.1% when considering only genes with reported genomic alterations in either assay. Over 50% of mutations detected in either technique were not detected using the other biopsy technique, indicating a potential complementary role of each assay. Across 5 genes (TP53, EGFR, KRAS, APC, CDKN2A), sensitivity and specificity were 59.1% and 94.8%, respectively. Potential explanations for the lack of concordance include differences in assay platform, spatial and temporal factors, tumor heterogeneity, interval treatment, subclones, and potential germline DNA contamination. These results highlight the importance of prospective studies to evaluate concordance of genomic findings between distinct platforms that ultimately may inform treatment decisions.

Abstract P2-02-21: The utility and correlation of circulating tumor cells (CTCs) and cell-free circulating tumor DNA (ctDNA) based on HER2 positivity

Background:

CTCs are well-established prognostic and predictive biomarkers for metastatic breast cancer (MBC) and other solid tumors. ctDNA is emerging as a quantitative blood-based biomarker for monitoring genomic alterations and disease progression. We evaluated the clinical utility and correlation of these liquid biopsy molecular tools in a cohort of MBC patients.

Methods:

CTC samples were obtained from an ongoing, prospective study of blood based prognostic biomarkers for breast cancer patients. At this time, 71 patients and 98 total samples have been collected. CTC enumeration was performed using the CellSearchTM platform (Menarini, IT). Within this cohort, MBC patients who had ctDNA testing were identified. ctDNA testing was performed using Guardant360TM (Guardant Health, CA), a digital next-generation sequencing technology. Two groups were analyzed: (1) HER2-negative patients with CTC ≥ 5 in 7.5 ml of blood (2) HER2-positive patients who had been treated with HER2 targeted therapy.

Results:

22 samples (N=16 patients) were found with CTC ≥ 5 (range 8-904) and concurrent ctDNA testing (median timeframe between collection 0 days, range 0-42 days). There was a significant association between number of CTCs and the total number of genomic alterations detected in ctDNA (paired two sample t-test, p=0.012). In addition, CTC enumeration was significantly correlated with somatic alteration burden of the dominant clone (paired two sample t-test, p=0.023). The most common alterations detected in the blood were TP53 (55% of patients, 18 total mutations), PIK3CA (41% of patients, 15 total mutations), and ESR1 (32% of patients, 14 total mutations). For patients with HER2 positivity receiving HER2-targeted therapies (N=16 samples from 11 patients), only 18.8% of samples had detectable CTCs (all less than 5) as compared to 75.0% of samples with detectable ctDNA alterations. In N=12 samples with detectable ctDNA mutations, mean number of genomic alterations was 4.4 with mean somatic mutation burden of 2.95%.

 CTCs detectedctDNA detectedCTC ≥ 5Mean number of ctDNA alterations+Mean somatic alteration burden+HER2- (only cases with CTC ≥ 5)100% (22/22)100% (22/22)100%6.716.1%HER2+ (all cases)18.8% (3/16)75.0% (12/16)0%4.42.95%+excludes ctDNA samples without detected genomic alterations

Conclusions:

In HER2-negative MBC patients, CTC enumeration was significantly correlated with the number of ctDNA genomic alterations and somatic alteration burden, indicating the potential for ctDNA as a prognostic, quantitative biomarker of tumor burden. In patients with HER2 positivity, ctDNA may be a more sensitive liquid biopsy tool given the rarity of detecting CTCs detection in this population using the CellSearchTM system. In HER2-positive patients, consideration of size-dependent selection of CTCs using filtration of cells that have undergone epithelial-mesenchymal transition may improve detection in this subgroup.

Citation Format: Davis AA, Zhang Y, Behdad A, Taxter T, Strickland K, Santa-Maria C, Flaum L, Cruz MR, Platanias LC, Gradishar WJ, Cristofanilli M. The utility and correlation of circulating tumor cells (CTCs) and cell-free circulating tumor DNA (ctDNA) based on HER2 positivity [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 P2-02-21.

Overexpression of adhesion molecules and barrier molecules is associated with differential infiltration of immune cells in non-small cell lung cancer

Immunotherapy is emerging as a promising option for lung cancer treatment. Various endothelial adhesion molecules, such as integrin and selectin, as well as various cellular barrier molecules such as desmosome and tight junctions, regulate T-cell infiltration in the tumor microenvironment. However, little is known regarding how these molecules affect immune cells in patients with lung cancer. We demonstrated for the first time that overexpression of endothelial adhesion molecules and cellular barrier molecule genes was linked to differential infiltration of particular immune cells in non-small cell lung cancer. Overexpression of endothelial adhesion molecule genes is associated with significantly lower infiltration of activated CD4 and CD8 T-cells, but higher infiltration of activated B-cells and regulatory T-cells. In contrast, overexpression of desmosome genes was correlated with significantly higher infiltration of activated CD4 and CD8 T-cells, but lower infiltration of activated B-cells and regulatory T-cells in lung adenocarcinoma. This inverse relation of immune cells aligns with previous studies of tumor-infiltrating B-cells inhibiting T-cell activation. Although overexpression of endothelial adhesion molecule or cellular barrier molecule genes alone was not predictive of overall survival in our sample, these genetic signatures may serve as biomarkers of immune exclusion, or resistance to T-cell mediated immunotherapy.