Circulating Tumor Cells Prediction in Hormone Receptor Positive HER2-Negative Advanced Breast Cancer: A Retrospective Analysis of the MONARCH 2 Trial

BACKGROUND

The MONARCH 2 trial (NCT02107703) showed the efficacy of abemaciclib, a cyclin-dependent kinase 4 & 6 inhibitor (CDK4/6i), in combination with fulvestrant for hormone receptor-positive, HER2-negative metastatic breast cancer (MBC). The aim of this analysis was to explore the prediction of circulating tumor cells (CTCs) stratification using machine learning for hypothesis generation of biomarker-driven clinical trials.

PATIENTS AND METHODS

Predicted CTCs were computed in the MONARCH 2 trial through a K nearest neighbor (KNN) classifier trained on a dataset comprising 2436 patients with MBC. Patients were categorized into predicted Stage IVaggressive (pStage IVaggressive, ≥5 predicted CTCs) or predicted Stage IVindolent (pStage IVindolent, <5 predicted CTCs). Prognosis was tested in terms of progression-free-survival (PFS) and overall survival (OS) through Cox regression.

RESULTS

Patients classified as predicted pStage IVaggressive and predicted pStage Stage IVindolent were, respectively, 183 (28%) and 461 (72%). After multivariable Cox regression, predicted CTCs were confirmed as independently associated with prognosis in terms of OS, together with ECOG performance status, liver involvement, bone-only disease, and treatment arm. Patients in the pStage Stage IVindolent subgroup treated with abemaciclib experienced the best prognosis both in terms of PFS and OS. The treatment effect of abemaciclib on OS was then explored through subgroup analysis, showing a consistent benefit across all subgroups.

CONCLUSION

This study is the first analysis of CTCs modeling for stage IV disease stratification. These results show the need to expand biomarker profiling in combination with CTCs stratification for improved biomarker-driven drug development.

Interplay between ESR1/PIK3CA codon variants, oncogenic pathway alterations and clinical phenotype in patients with metastatic breast cancer (MBC): comprehensive circulating tumor DNA (ctDNA) analysis

BACKGROUND

although being central for the biology and druggability of hormone-receptor positive, HER2 negative metastatic breast cancer (MBC), ESR1 and PIK3CA mutations are simplistically dichotomized as mutated or wild type in current clinical practice.

METHODS

The study analyzed a multi-institutional cohort comprising 703 patients with luminal-like MBC characterized for circulating tumor DNA through next generation sequencing (NGS). Pathway classification was defined based on previous work (i.e., RTK, RAS, RAF, MEK, NRF2, ER, WNT, MYC, P53, cell cycle, notch, PI3K). Single nucleotide variations (SNVs) were annotated for their oncogenicity through OncoKB. Only pathogenic variants were included in the models. Associations among clinical characteristics, pathway classification, and ESR1/PIK3CA codon variants were explored.

RESULTS

The results showed a differential pattern of associations for ESR1 and PIK3CA codon variants in terms of co-occurring pathway alterations patterns of metastatic dissemination, and prognosis. ESR1 537 was associated with SNVs in the ER and RAF pathways, CNVs in the MYC pathway and bone metastases, while ESR1 538 with SNVs in the cell cycle pathway and liver metastases. PIK3CA 1047 and 542 were associated with CNVs in the PI3K pathway and with bone metastases.

CONCLUSIONS

The study demonstrated how ESR1 and PIK3CA codon variants, together with alterations in specific oncogenic pathways, can differentially impact the biology and clinical phenotype of luminal-like MBC. As novel endocrine therapy agents such as selective estrogen receptor degraders (SERDS) and PI3K inhibitors are being developed, these results highlight the pivotal role of ctDNA NGS to describe tumor evolution and optimize clinical decision making.

Genetic Alterations Detected by Circulating Tumor DNA in HER2-Low Metastatic Breast Cancer

PURPOSE

About 50% of breast cancers are defined as HER2-low and may benefit from HER2-directed antibody-drug conjugates. While tissue sequencing has evaluated potential differences in genomic profiles for patients with HER2-low breast cancer, genetic alterations in circulating tumor DNA (ctDNA) have not been well described.

EXPERIMENTAL DESIGN

We retrospectively analyzed 749 patients with metastatic breast cancer (MBC) and ctDNA evaluation by Guardant360 from three academic medical centers. Tumors were classified as HER2-low, HER2-0 (IHC 0) or HER2-positive. Single-nucleotide variants, copy-number variants, and oncogenic pathways were compared across the spectrum of HER2 expression. Overall survival (OS) was evaluated by HER2 status and according to oncogenic pathways.

RESULTS

Patients with HER2-low had higher rates of PIK3CA mutations [relative risk ratio (RRR), 1.57; P = 0.024] compared with HER2-0 MBC. There were no differences in ERBB2 alterations or oncogenic pathways between HER2-low and HER2-0 MBC. Patients with HER2-positive MBC had more ERBB2 alterations (RRR, 12.43; P = 0.002 for amplification; RRR, 3.22; P = 0.047 for mutations, in the hormone receptor-positive cohort), fewer ERS1 mutations (RRR, 0.458; P = 0.029), and fewer ER pathway alterations (RRR, 0.321; P < 0.001). There was no difference in OS for HER2-low and HER2-0 MBC [HR, 1.01; 95% confidence interval (CI), 0.79-1.29], while OS was improved in HER2-positive MBC (HR, 0.32; 95% CI, 0.21-0.49; P < 0.001).

CONCLUSIONS

We observed a higher rate of PIK3CA mutations, but no significant difference in ERBB2 alterations, oncogenic pathways, or prognosis, between patients with HER2-low and HER2-0 MBC. If validated, our findings support the conclusion that HER2-low MBC does not represent a unique biological subtype.

Genomic Complexity Predicts Resistance to Endocrine Therapy and CDK4/6 Inhibition in Hormone Receptor-Positive (HR+)/HER2-Negative Metastatic Breast Cancer

PURPOSE

Clinical biomarkers to identify patients unlikely to benefit from CDK4/6 inhibition (CDK4/6i) in combination with endocrine therapy (ET) are lacking. We implemented a comprehensive circulating tumor DNA (ctDNA) analysis to identify genomic features for predicting and monitoring treatment resistance.

EXPERIMENTAL DESIGN

ctDNA was isolated from 216 plasma samples collected from 51 patients with hormone receptor-positive (HR+)/HER2-negative (HER2-) metastatic breast cancer (MBC) on a phase II trial of palbociclib combined with letrozole or fulvestrant (NCT03007979). Boosted whole-exome sequencing (WES) was performed at baseline and clinical progression to evaluate genomic alterations, mutational signatures, and blood tumor mutational burden (bTMB). Low-pass whole-genome sequencing was performed at baseline and serial timepoints to assess blood copy-number burden (bCNB).

RESULTS

High bTMB and bCNB were associated with lack of clinical benefit and significantly shorter progression-free survival (PFS) compared with patients with low bTMB or low bCNB (all P < 0.05). Dominant APOBEC signatures were detected at baseline exclusively in cases with high bTMB (5/13, 38.5%) versus low bTMB (0/37, 0%; P = 0.0006). Alterations in ESR1 were enriched in samples with high bTMB (P = 0.0005). There was a high correlation between bTMB determined by WES and bTMB determined using a 600-gene panel (R = 0.98). During serial monitoring, an increase in bCNB score preceded radiographic progression in 12 of 18 (66.7%) patients.

CONCLUSIONS

Genomic complexity detected by noninvasive profiling of bTMB and bCNB predicted poor outcomes in patients treated with ET and CDK4/6i and identified early disease progression before imaging. Novel treatment strategies including immunotherapy-based combinations should be investigated in this population.

Cyclin-Dependent Kinase 4/6 Inhibitors Beyond Progression in Metastatic Breast Cancer: A Retrospective Real-World Biomarker Analysis

PURPOSE

As the continuation beyond progression (BP) of cyclin-dependent kinase 4/6 inhibitors (CDK4/6i) is becoming increasingly attractive for the treatment of patients with hormone receptor (HR)-positive, human epidermal growth factor receptor 2 (HER2)-negative metastatic breast cancer (MBC), the definition of resistance factors is crucial. The aim of the study was to investigate the impact of CDK 4/6i BP and to explore potential genomic stratification factors.

MATERIALS AND METHODS

We retrospectively analyzed a multi-institutional cohort of patients with HR-positive HER2-negative MBC characterized for circulating tumor DNA through next-generation sequencing before treatment start. Differences across subgroups were analyzed by chi-square test, and survival was tested by univariable and multivariable Cox regression. Further correction was applied by propensity score matching.

RESULTS

Among the 214 patients previously exposed to CDK4/6i, 172 were treated with non-CDK4/6i-based treatment (non-CDK) and 42 with CDK4/6i BP. Multivariable analysis showed a significant impact of CDK4/6i BP, TP53 single-nucleotide variants, liver involvement, and treatment line on both progression-free survival (PFS) and overall survival (OS). Propensity score matching confirmed the prognostic role of CDK4/6i BP both for PFS and OS. The favorable impact of CDK4/6i BP was consistent across all subgroups, and a differential benefit was suggested for ESR1-mutated patients. ESR1 and RB1 mutations were more represented in the CDK4/6i BP subgroup with respect to CDK4/6i upfront.

CONCLUSION

The study highlighted a significant prognostic impact of the CDK4/6i BP strategy with a potential added benefit in patients with ESR1 mutations suggesting the need for an extensive biomarker characterization.

Abstract 1031: Specific gene alterations of HER2 positive single circulating tumor cell (CTC) compared to autologous leukocytes in metastatic breast cancer (MBC)

Introduction: Monitoring of CTC in MBC showed ability to predict treatment resistance and outcome. HER2 is one of the most important tumor markers which is associated with rapid cell division and the metastasis and prognosis of MBC in the clinic. More recently, we reported single CTC gene mutation is a key point to distinguish metastasis capability in MBC (2022 AACR and 2022 ASCO). Herein, we report specific gene alterations in HER2+ single CTC compared to autologous leukocytes in MBC.

Methods: Whole blood sample (7.5ml/each) was collected from MBC patient before therapy. CTC enumeration was performed in FDA approved CellSearch™ System and then the single HER2+ CTC and leukocytes were isolated by using DEPArrayTM System (Menarini). The single cell DNA was isolated and then the initial library was prepared by using Ampli1™ Whole Genome Amplification, Ampli1™ QC Kit (Menarini) and AMPure XP kit (Beckman Coulter). The exome capture was performed by TruSeq DNA Exome kit (illumine). The sequencing was prepared by NextSeq 500 mid output V2.5 kit and was performed on the NextSeq 500 (Illumina).

Results: We identified 107 CTCs including 55 HER2+ CTCs and 14 CTC-clusters. Autologous single HER2+ CTC (HER2+CK+CD45−, Group 1), HER2+CK−CD45+ leukocyte (Group 2) and HER2−CK−CD45+ leukocyte (Group 3) were isolated and sequenced respectively. The sequencing data was processed following the GATK pipeline and annotated using SnpEff. There were 486,119 counts (56.69%) for intron variants, 175,819 counts (20.51%) for intergenic variants, 70,334 counts (8.20%) for exon variants, 50,370 counts (5.87%) for downstream genes, 45,915 counts (5.36%) for upstream genes and others (3.37%) in HER2+ CTC. Meanwhile, there were 71,848 (8.76%) and 0 counts for exon variants found in Group 2 and Group 3 respectively. There were 79 gene variants ((SNP and Ins-Del) identified to have the highest impact effect (≥20) on HER2+ CTC chromosome, when there were 85 and 0 highest impact gene variants were identified in Group 2 and Group 3 respectively. The specific gene alterations in Group 1 compared to Group 2 includes CCNA2, FOLH1, BRD4, SAMHD1, CYP17A1, IDE, HPGDS and CTNNB1 Among the top 50 high impact gene variants, there were 26 genes alteration sites are same in both Group 1 and Group 2, including FECH, HDAC8, CYP11B2, TTN(6 sites), RAN, CD207, HK1, CASP1(2 sites), BRCA1, PIK3CG (3 sites), APEX1(4 sites), KIF11, SIRT5 (2 sites), XYLB and CHKA.

Conclusion: Genomic characterization of HER2 positive single CTCs elucidated specific gene alterations associated with disease metastasis compared to autologous leukocytes in MBC. The newfound HER2+CK−CD45+ cells with gene alterations maybe a new kind of cancer transformed leukocytes which need further validation. Specific gene alterations will help to develop novel drugs aimed at the eradication of CTCs using molecularly driven therapies for disease metastasis.

Citation Format: Qiang Zhang, Lorenzo Gerratana, Zhe Ji, Xinkun Wang, Paolo D’Amico, Seema Singhal, Youbin Zhang, Andrew A. Davis, Ami N. Shah, William Gradishar. Specific gene alterations of HER2 positive single circulating tumor cell (CTC) compared to autologous leukocytes in metastatic breast cancer (MBC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1031.

Abstract 6744: Cell-free DNA detection of alterations in the MAPK pathway in metastatic hormone receptor positive breast cancer: A multi-institutional analysis of incidence and clinical outcomes

Background Alterations in the MAPK pathway are known mechanisms for tumorigenesis in multiple solid tumors. While not major drivers in early breast cancers, activating MAPK pathway alterations have been invoked as potential resistance mechanisms in advanced hormone receptor positive (HR+) breast cancer. While MAPK pathway mutations are believed to be relatively rare in breast cancer, the accessibility of cell-free DNA (cfDNA) analysis allows for evaluation of their prevalence, co-occurring mutations, and associated clinical outcomes. In this study, we evaluated the incidence of MAPK pathway alterations and impact on clinical outcomes among patients with metastatic breast cancer (MBC).

Methods Plasma was collected in patients with HR+ MBC at the Massachusetts General Hospital and Washington University in St. Louis, and cfDNA was analyzed via the Guardant 360 assay, a 74-gene next generation sequencing panel. The impact of MAPK pathway alterations on progression-free survival (PFS) and overall survival (OS) was analyzed using multivariable Cox regression analysis, adjusting for age, number of prior therapies, visceral metastases, de novo metastases, and PIK3CA alterations. PFS and OS were evaluated in the overall study population, as well as in subgroups that received endocrine therapy + CDK4/6 inhibitor, endocrine monotherapy and chemotherapy.

Results Out of 647 HR+ MBC patients, 103 (16%) had non-synonymous mutations in the MAPK pathway detected in cfDNA. Median age was similar (61.9 and 60.7) in MAPK-altered and non-altered patients, respectively. Both groups had received a median of 2 prior lines of therapy (p=0.08). MAPK pathway alterations included NF1 (n = 45, 7.0%), KRAS (n = 22, 3.4%), BRAF (n = 22, 3.4%), MAPK1 (n = 8, 1.2%), MAP2K1 (n = 6, 0.9%), NRAS (n = 5, 0.8%), RAF1 (n = 5, 0.8%), HRAS (n = 4, 0.6%), ARAF (n = 4, 0.6%), MAP2K2 (n = 4, 0.6%), RIT1 (n = 3, 0.5%), and MAPK3 (n = 2, 0.3%). Mutant allele fractions ranged from 0.03 to 26. Co-alterations in PIK3CA occurred in 49% (n = 51), TP53 in 41% (n = 42), and ESR1 in 27% (n = 28). In multivariable analysis, patients with MAPK-altered HR+ MBC had significantly poorer median PFS, 7.6 months vs 11.5 months (HR: 1.6; p = 0.005; 95% CI: 1.2-2.2). There was no statistically significant impact on outcomes when stratifying by treatment type.

Conclusions MAPK pathway alterations are associated with a significantly poorer PFS among patients with HR+ MBC. Further research is needed to independently validate these observations and evaluate the impact of genotype-directed therapy targeting MAPK-altered, HR+ MBC.

Citation Format: Arielle J. Medford, Andrzej Niemierko, Whitney L. Hensing, Andrew A. Davis, Katherine Clifton, Jennifer C. Keenan, Lesli Kiedrowski, Ami N. Shah, Lorenzo Gerratana, Massimo Cristofanilli, Aditya Bardia. Cell-free DNA detection of alterations in the MAPK pathway in metastatic hormone receptor positive breast cancer: A multi-institutional analysis of incidence and clinical outcomes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6744.

Abstract 2220: Dynamic development of ESR1 mutations in circulating tumor DNA (ctDNA) is associated with prognosis of patients with metastatic breast cancer (MBC)

Background: Relapse and endocrine resistance are major clinical challenges in the management of patients with MBC because it is a dynamic phenomenon including development of ESR1 mutations. The monitoring of ctDNA and circulating tumor cells (CTCs) in patients with MBC may predict metastasis and prognosis. We previously reported that ctDNA can be used to evaluate tumor heterogeneity (2022 AACR-#1950 and 2022 ASCO-#1057). Here, we report that dynamic ctDNA ESR1 mutations is a key point associated with a shorter survival, which may help to elucidate prognosis in patients with MBC.

Methods: This study included 406 hormone receptors positive MBC patients who received systemic treatment under an IRB-approved clinical trial (NU16B06) at Northwestern University Robert H Lurie Comprehensive Cancer Center. Plasma samples were collected from each patient at multiple time points: before treatment (Time point 1), and then 3 months (Time point 2), 6 months (Time point 3), 9 months (Time point 4), 12 months (Time point 5) and 24 months (Time point 6) after initiation of systemic treatment respectively. Plasma ctDNA was isolated using a Qiagen circulating nucleic acid kit, and then was analyzed using the Guardant360 Health next-generation sequencing (NGS)-based assay. All statistical analyses were conducted Mann-Whitney U test by IBM SPSS version 23.0.

Results: Of the 406 patients, ESR1 mutations were found in 18 hotspots from 59 patients (ESR1Mut, 14.5%) at either time points. There were 347 patients without any mutation (ESR1WT, 85.5%). Among the 59 patients who have ESR1 mutations, 41 (69.5%) patients have ESR1 mutations at only one time point, 6 patients (10.2%) have ESR1 mutations at 2 time pints, 5 patients (8.5%) have ESR1 mutations at 3 time points, 2 patients (3.3%) have ESR1 mutations at 4 time points, and 5 patents (8.5%) have ESR1 mutations for 5 time points respectively. The median survival times for patients in ESR1WT group is 11.5 years compared to 6.4 years for patients in ESR1Mut group (P=0.0134). This result indicated that patients without ESR1 mutations at any time point have 1.81 times longer median survival time than patients who have ESR1 mutations at any time point. Furthermore, 41 patients who have ESR1 mutation at only one time point have longer survival time (7.1 years) compared to 18 patients who have ESR1 mutation at more than 2 time points (5.1 years) (P&lt;0.01).

Conclusions: Dynamic development of ctDNA ESR1 mutations at different time points during the treatment significantly correlated with prognosis and survival of patients with metastatic breast cancer. Longitudinal dynamics of ESR1 mutation for treatment monitoring may offer important message for minimal residual disease and expand the early predictive role of prognosis for clinical decision-making in metastatic breast cancer.

Citation Format: Qiang Zhang, Jianhua Jiao, Lorenzo Gerratana, Paolo D’Amico, Seema Singhal, Youbin Zhang, Andrew A. Davis, Ami N. Shah, William Gradishar. Dynamic development of ESR1 mutations in circulating tumor DNA (ctDNA) is associated with prognosis of patients with metastatic breast cancer (MBC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2220.

Trajectories of participation in daily life among individuals newly diagnosed with cancer: A 5-month longitudinal study

PURPOSE

To determine how participation in daily life is impacted during the first six months following a new cancer diagnosis and to identify risk factors for participation restrictions. Patient-reported outcomes (PROs) were used to suggest referrals to rehabilitation services.

METHODS

Participants (n = 123) were adults (> 18 years) with the newly diagnosed primary brain, breast, colorectal, or lung cancer. PROs were collected at baseline (within 30 days of diagnosis/treatment initiation), two and five months post baseline. Daily life participation was assessed through the community participation indicators (CPI) (score range: 0-1) and patient-reported outcome measurement information system (PROMIS) ability to participate, (score range: 20-80; mean: 50, SD: 10). PROMIS-43 profile was also completed. Linear mixed-effect models with random intercept evaluated change in participation over time.

RESULTS

The baseline total sample mean CPI score was 0.56; patients reported mildly impaired participation based on PROMIS scores (baseline: 46.19, 2-month follow-up: 44.81, 5 months: 44.84). However, no statistically significant changes in participation were observed over the study period. Risk factors for lower participation included receiving chemotherapy, lower physical function, higher anxiety and fatigue, and reduction in employment, p < 0.05. PROs indicated that roughly half of the participants may benefit from physical or occupational therapy or mental health support, but only 20-36% were referred by their medical team.

CONCLUSION

People newly diagnosed with cancer experience impaired participation, but they are infrequently referred to supportive services such as rehabilitation. The use of PROs to assess participation, physical function, and mental health can promote access to supportive care services by identifying patients who may benefit from rehabilitation beyond those identified through routine clinical care.

Abstract P2-26-06: Association between CK+/CD45+ circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) alterations in advanced breast cancer patients

Background: Circulating tumor cells (CTCs) in breast cancer (BC) are commonly defined as epithelial cells (EPCAM and cytokeratin (CK) positive), lacking the universal blood cell marker CD45. Nonetheless, CTCs expressing both CK and CD45 (= dual-positive, DP cells) can be observed in the blood of cancer patients. Early evidence suggests that DP cells might derive from the fusion of tumor cells and macrophages, and we have previously demonstrated that they present aberrant genomes and are associated with worse prognosis in BC [1,2]. Here, to further investigate the mechanisms/pathways underlying their presence, we analyzed the association between DP cells and circulating tumor DNA (ctDNA) alterations. Methods: Blood samples were collected from patients with advanced BC (aBC), before starting a new line of therapy. All patients were enrolled in a prospective clinical trial. For CTC and DP cells analysis, 7.5 ml of blood collected in CellSave® tubes was processed with the FDA-approved CellSearch® platform (positivity cutoffs were ≥1 cell for DPcells and ≥5 cells for CTCs). For ctDNA analysis, plasma was collected from Streck stabilizing tubes and analyzed with the Guardant360™ NGS platform for the detection of somatic single nucleotide variants (SNVs), insertions/deletions (indels), gene fusions/rearrangements and copy number variations (CNVs), which were then classified into pathways based on previously defined profiles generated on the Cancer Genome Atlas database (RTK, RAS, RAF, MEK, NRF2, ER, WNT, MYC, P53, cell cycle, notch, PI3K). Associations between ctDNA-detected gene alterations and circulating cell types were analyzed through chi square test, while mutant allele frequency (MAF) and number of detected alterations (NDA) were tested by Mann Whitney test. Results: We analyzed blood samples from 169 patients with luminal-like (n=80), HER2+ (n=34) and triple-negative (n=52) aBC. DPcells were detected in 85 patients (50.3 %, range 0-53), of which 40 (47 %) were CTC-positive and 45 (53%) CTC-negative. Somatic ctDNA alterations were detected in all analyzed samples. In the overall population, the presence of ≥1 DPcell was associated with SNVs in the cell cycle pathway (p = 0.043), a numerically higher incidence was also observed for CNVs in this pathway. SNVs and CNVs in the cell cycle pathway were associated with CTCs ≥ 5 as well (p = 0.005 and p = 0.003, respectively). Moreover, associations with CTCs ≥ 5 were observed for RTK SNVs and CNVs (p = 0.041 and p = 0.046, respectively), PI3K SNVs and CNVs (p = 0.006 and p = 0.007, respectively), MYC SNVs and CNVs (p = 0.042). No associations were observed in terms of MAF and NDA. In the luminal-like subgroup an association was highlighted for CNVs in the cell cycle pathway, p = 0.038. CTCs ≥ 5 were associated with PI3K SNVs (p = 0.031). In the triple-negative subgroup DPcells were associated with SNVs in the RAF pathway (p = 0.041), whereas CTCs ≥ 5 were associated with PI3K SNVs and CNVs (p = 0.044 and p = 0.024, respectively) and RTK SNVs (p = 0.008). In the HER2 positive subgroup, a higher MAF and number of detected SNVs was observed for samples with ≥1 DPcell (p = 0.0286 and p = 0.0099, respectively). Conclusions: The study analyzed ctDNA features associated with canonical and CK+/CD45+ CTCs, showing differential gene alteration profiles. Cell cycle pathway SNVs were common in both CTC populations, while other pathways (RTK, PI3K, MYC and RAF) were significantly altered in a mutually exclusive pattern. These results suggest that DPcells might have a different biological meaning compared to canonical CTCs. More studies need to be conducted to better characterize this understudied CTC subpopulation and understand their specific contribution to cancer progression. References: 1) Reduzzi C. et al., Semin Cancer Biol. 2020;60:344-350. DOI:10.1016/j.semcancer.2019.10.008 2) Reduzzi C. et al., Journal of Clinical Oncology 40, no. 16_suppl (June 01, 2022) 1093-1093. DOI: 10.1200/JCO.2022.40.16_suppl.1093

Citation Format: Carolina REDUZZI, Lorenzo Gerratana, Youbin Zhang, Maroua MANAI, Paolo D’Amico, Andrew A. Davis, Jeannine Donahue, Ami N. Shah, Massimo Cristofanilli. Association between CK+/CD45+ circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) alterations in advanced breast cancer patients [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-26-06.

Abstract P4-01-18: Real-world second-line treatment patterns and associated clinical outcomes for 2795 patients with advanced HR+ HER2- breast cancer treated with first-line CDK4/6 inhibitors

Background: CDK4/6 inhibitors (CDK4/6i) are standard first-line (1L) regimens for HR+/HER2- advanced breast cancer (aBC). Recent data from the randomized phase II MAINTAIN trial reported a PFS benefit for patients (pts) who received a new endocrine therapy plus ribociclib (ribo) versus new endocrine therapy alone) following progression on CDK4/6i as compared to pts who received endocrine therapy alone. However, second-line (2L) treatment patterns and patient outcomes following 1L CDK4/6i are relatively undescribed. Here we describe real-world 2L treatment patterns following 1L CDK4/6i and associated clinical outcomes from a large clinical genomics database.

Methods: Real-world evidence (RWE) was sourced from the GuardantINFORM (Guardant Health) database which comprises aggregated commercial payer health claims and de-identified records from over 207,000 pts with comprehensive circulating tumor DNA (ctDNA) results via Guardant360 (G360) from 2014 to 2021. Pts with HR+/HER2- aBC with &gt;1 claim of CDK4/6i and &gt;1 claim for treatment after the index G360 test were included. Real-world time to treatment discontinuation (rwTTD) and real-world time to next treatment (rwTTNT) were assessed in months as proxies for progression-free survival. Real-world overall survival (rwOS) was also reported in months.

Results: 2,795 pts met criteria for inclusion; 2,361 (84.5%) were treated with 1L palbociclib (palbo), 271 (9.7%) with 1L abemaciclib (abema) and 163 (5.8%) with 1L ribo. Chemotherapy (chemo,35.5%) and endocrine-only therapy (32.8%) were the most common 2L therapy regardless of the 1L CDK4/6i agent (Table 1). Other 2L agents included endocrine backbone change (14.7%) or CDK4/6i change (7.7%). Endocrine backbone changes were observed more frequently (15.6%) in pts receiving 1L palbo while CDK4/6i changes were more frequent in pts receiving abema (14.0%) or ribo (22.0%). Pts treated with 2L CDK4/6i had improved rwTTNT, rwTTD and rwOS compared to 2L chemo regardless of 1L agent [rwTTNT: 10.2 (95% CI: 7.2-11.7) vs. 7.2 (6.5-8.1); rwTTD: 6.8 (95% CI: 5.8-8.5) vs. 4.3 (95% CI:3.9-4.7); rwOS: NR (95% CI: 40.0-NR) vs. 34.8 (95% CI: 31.3-37.2)]; improvement in rwTTNT, rwTTD and rwOS were also observed for pts with 2L endocrine backbone changes compared to chemo [rwTTNT: 8.5 (95% CI: 7.2-9.6) vs. 7.2 (6.5-8.1); rwTTD: 6.9 (95% CI: 5.8-7.9) vs. 4.3 (95% CI:3.9-4.7); rwOS: 63.4 (95% CI: 51.2-NR) vs. 34.8 (95% CI: 31.3-37.2)]. Pts treated with 2L alpelisib had the shortest rwOS regardless of 1L CDK4/6i agent used [any 1L: NR (95% CI: 23.6-NR)].

Conclusions: A variety of 2L regimens following 1L CDK4/6i were observed, with an improvement in rwTTNT, rwTTD and rwOS in pts receiving 2L CDK4/6i or 2L endocrine backbone change only relative to 2L chemo. These data are hypothesis generating, and the observed improvement may be secondary to therapy choice versus pts who received 2L chemo having more aggressive disease. Larger randomized trials are ongoing to study sequencing and efficacy of 2L treatments following 1L CDK4/6i.

Table 1. Distribution of 2L therapies by 1L CDK4/6i agent.

Citation Format: Katherine K. Clifton, Seth A. Wander, Cynthia Ma, Andrew A. Davis, Caroline Weipert, Nicole Zhang, Leslie Bucheit. Real-world second-line treatment patterns and associated clinical outcomes for 2795 patients with advanced HR+ HER2- breast cancer treated with first-line CDK4/6 inhibitors [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P4-01-18.

Abstract P3-05-08: Prevalence and prognosis of ER-loss in advanced invasive lobular carcinoma

Introduction: Estrogen receptor (ER) loss occurs in about 20% of recurrent breast cancers (BC) and is associated with unresponsiveness to endocrine therapy (ET) and poor prognosis. Prior studies evaluating ER-loss included predominately patients with invasive ductal carcinoma (IDC), and therefore the impact of ER-loss in invasive lobular carcinoma (ILC) is unknown. In this retrospective analysis, using real-world data, we aimed to determine the prevalence and clinical significance of ER-loss in ILC. Methods: Advanced BC were molecularly profiled at Caris Life Sciences (Phoenix, AZ) with NextGen Sequencing of DNA (592-gene panel or whole-exome sequencing), RNA (whole transcriptome sequencing, WTS) and immunohistochemistry (IHC) of select markers. A large real-world evidence (RWE) database combining Caris’ molecular data with clinical information obtained from insurance claims data (CODEai) was interrogated and overall survival (OS) was calculated from time of tissue collection to last patient contact. A tumor was considered to have ER-loss if therapies approved only for ER-positive BC were prescribed prior to obtaining a negative ER IHC result. OS was compared using Kaplan-Meier estimates for defined patient cohorts; significance was determined as p values &lt; 0.05. For molecular analyses, Fisher-Exact or Chi-Square tests were used to determine p values. Correction for multiple comparisons was performed using Benjamini-Hochberg to calculate q values. Results: The RWE database included 24,824 patients with advanced BC. At the time of tissue collection for molecular profiling, 6,786 advanced BC patients had been previously treated with ET (with or without mTOR or CDK4/6 inhibitors), of whom 1,338 had data available on histologic classification and ER IHC. The final analytical cohort included 263 patients with ILC and 1,075 with IDC. ER-loss was identified in 11.4% of ILC (n=30/263) and 19.6% (n=210/1075) of IDC (p=0.0017). In ILC, ER-loss was associated with significantly worse OS (HR: 1.75, 95%CI: 1.10-2.79, p=0.016) compared with no ER-loss. In the cohort of patients with ER-loss, patients with ILC had significantly worse OS compared with IDC (HR=2.03, 95% CI: 1.267-3.251, p=0.003). Further, when 1,016 tumors with ER-loss (regardless of histology) were stratified by the median OS (mOS=11mo), positive PD-L1 expression (34% vs. 22%, p=0.04, q=0.22), HER2 IHC positivity (16% vs. 7.8%, p=0.003, q=0.08) and HER2 amplification (16% vs. 4.7%, p=0.0006, q=0.04) were enriched in patients with longer mOS; while amplification of TEFB (0.38% vs. 2.6%, p=0.047, q=0.23) and MYB (0.38% vs. 2.6%, p=0.047, q=0.23) were enriched in patients with shorter mOS. WTS identified 197 differentially expressed genes, the majority of which were enriched in patients with longer mOS (q&lt; 0.05). Conclusions: In this large real-word dataset, ER-loss likely occurred in 11.4% of ILC and was associated with worse OS compared to both patients with IDC and ER-loss and ILC without ER-loss. Our analysis had several limitations; notably, our definition of ER-loss was based on prior treatment, we could not distinguish between de novo or recurrent metastatic disease and time of tissue collection was not standardized during the course of treatment. Thus, additional studies are needed to confirm these findings. However, this study does suggest that ER-loss occurs in a subset of patients with ILC and has poor prognostic implications.

Citation Format: Whitney L. Hensing, Joanne Xiu, W. Michael Korn, Stephanie L. Graff, Irene Kang, Evanthia T. Roussos Torres, Arielle L. Heeke, Andrew A. Davis, Nusayba A. Bagegni, Katherine K. Clifton, Ron Bose, Cynthia Ma, Foluso O. Ademuyiwa. Prevalence and prognosis of ER-loss in advanced invasive lobular carcinoma [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P3-05-08.

Abstract OT3-11-01: TK IMPACT: Treatment Monitoring of Hormone Receptor Positive (HR+), HER2 Negative (HER2-) Metastatic Breast Cancer (MBC) Patients Receiving CDK 4/6 Inhibitors (CDK4/6i) with DiviTum® Thymidine Kinase 1 Activity

Background: CDK 4/6i have altered the therapeutic landscape of HR+, HER2- MBC, improving progression free and overall survival (PFS and OS) compared to endocrine therapy (ET) alone. Despite durable responses to CDK 4/6i in a large majority of patients, treatment response monitoring in this population has historically included numerous serial blood-based and imaging studies at frequent time points. There is a growing global interest in utilizing novel non-invasive biomarker-driven disease monitoring assessments to improve patient outcomes and reduce health care costs. Thymidine kinase 1 (TK1), a key cell-cycle regulated enzyme important for nucleotide metabolism during DNA synthesis, is regulated by the E2F pathway, downstream of CDK 4/6. Studies have shown that DiviTum® TK1 activity (TKa) may serve as both a prognostic and predictive biomarker of CDK 4/6i treatment response (McCartney et al, Clin Canc Res, 2020; Malorni et al, Eur J Cancer, 2022; Bagegni et al, Breast Cancer Res, 2017). Early TKa suppression within 2 weeks (wk) post CDK 4/6i therapy initiation is associated with improved PFS, suggesting a subgroup of patients who may be able to de-escalate imaging frequency. Elevated TKa at baseline and post CDK 4/6i may identify patients with CDK 4/6i-resistant disease and disease progression (PD) requiring early therapy modification. TK IMPACT is a prospective, single-arm trial designed to assess the impact of incorporation of DiviTum® TKa on a physician’s decision regarding subsequent timing of routine disease monitoring modalities in patients with advanced HR+, HER2- MBC receiving ET plus CDK 4/6i (NCT04968964). Methods: Blood sample collections will be analyzed using DiviTum® TKa at baseline (bl), wk 2, 4, 6, 8, and Q 4 wks thereafter beginning at wk 8 during the first 24-wk time period of study enrollment (+/- 3 days); followed by Q 12 wks thereafter, until PD or 36 months, whichever occurs first. Optional repeat TKa within 2-4 wks (+/-3 days) is permitted in case of rising TKa. Research blood (bl, wk 2, 12, 24, 48, and PD) and optional archival tumor tissue collection at diagnosis and PD will be obtained for correlatives. The investigator will record intended imaging modalities and timing prior to receipt of TKa, followed by documentation of any changes in imaging testing interval after receipt of TKa. Key eligibility criteria include postmenopausal women age ≥18 years with HR+, HER2- MBC, to initiate (Cohort 1) or are currently receiving (≤24 months, Cohort 2) any FDA approved first line ET plus CDK 4/6i with a life expectancy &gt; 6 months. The primary endpoint is any physician-reported intended change in imaging testing interval post TKa by study cohort, within the first 48-wk period of study participation. Key secondary endpoints are concordance rate between TKa values and progression status at first on-study imaging and longitudinal TKa dynamics. Key exploratory endpoints include plasma and tumor tissue-based biomarkers of CDK 4/6i response and resistance. A total of 40 patients will be enrolled (n=20/Cohort). The expected change rate is 20% with a 95% Wilson confidence interval of 0.105~0.248 across all patients and if within each cohort, with a 95% Wilson confidence interval of 0.081~0.416 for N=20. N=40 allows the lower limit of the 95% CI &gt; 10% and that of the N=20 in Cohort 1 to be ~10%, indicating some clinically meaningful influence of TKa progression on patient management. The study is open to accrual and has presently enrolled 5 patients.

Citation Format: Nusayba A. Bagegni, Isabella Grigsby, Leslie Nehring, Jingqin Luo, Jennifer Powers Carson, David W. Gibson, Meghan Horvath, Katherine K. Clifton, Foluso O. Ademuyiwa, Rama Suresh, Ashley Frith, Andrew A. Davis, Lindsay L. Peterson, Ron Bose, Amy Williams, Mattias Bergqvist, Cynthia Ma. TK IMPACT: Treatment Monitoring of Hormone Receptor Positive (HR+), HER2 Negative (HER2-) Metastatic Breast Cancer (MBC) Patients Receiving CDK 4/6 Inhibitors (CDK4/6i) with DiviTum® Thymidine Kinase 1 Activity [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr OT3-11-01.

Abstract PD10-01: PD10-01 Impact of ESR1 mutations on Selective Estrogen Receptor Degraders and Modulators: an integrated liquid-biopsy and pharmacodynamics approach

Background: ESR1 hotspot mutations (HS) (i.e. 380, 536, 537, and 538) are important drivers of resistance to aromatase inhibitors, but the differential impact of genomic variants (HS vs non-HS) on response to endocrine therapies (ET) under clinical development, such as novel oral Selective Estrogen Receptor Degraders and Modulators (SERDs and SERMs), is not known. The aim of the study was to evaluate the impact of non-HS ESR1 mutations on the pharmacodynamics of SERDs and SERMs as an additional ET resistance mechanism. Materials and Methods: The study analyzed a multi-institutional cohort of 1008 patients with hormone receptor positive metastatic breast cancer characterized by circulating tumor DNA (ctDNA). Pathway classification was defined based on previous work (i.e. RTK, RAS, RAF, MEK, NRF2, ER, WNT, MYC, p53, Cell Cycle, Notch, PI3K). Single nucleotide variations (SNVs) were annotated through OncoKB; co-occurrence was tested by Fisher’s exact test. A structure-based computational strategy was used to create 3D-models of ESR1 mutants and predict changes in binding affinity (dAff) across approved and experimental drugs. A positive dAff reflects a lower affinity of the drug for mutant ESR1 compared with wild type and thus a potential for a reduced response. Results: Among the total 680 detected ESR1 mutations, 633 were missense, and 631 were gain-of-function. The most frequent mutations were in codon 537 (N=305), followed by 538 (N=224). No significant MAF differences were observed across ESR1 variants (P=0.0829). The L391F mutation resulted in an increased binding affinity for Lasofoxifene (LAS) (dAff -0.34), Giredestrant (GIR) (dAff -0.18), Elacestrant (ELA) (dAff -0.08) and Amcenestrant (AMC) (dAff -0.41), while a decreased binding affinity was observed for 4OH-Tamoxifen (TAM) (dAff 0.01), Imlunestrant (IML) (dAff 0.15), Fulvestrant (FUL) (dAff 0.43), and Camizestrant (CAM) (dAff 0.02). V392F decreased binding affinity for TAM (dAff 0.05), LAS (dAff 0.13), IML (dAff 0.11), GIR (dAff 0.11), FUL (dAff 0.04), CAM (dAff 0.05), AMC (dAff 0.06) but not for ELA (dAff -0.01). F404L decreased binding affinity for FUL (dAff 0.07), ELA (dAff 0.73), and CAM (dAff 0.26), while it increased binding affinity for TAM (dAff -0.27), LAS (dAff -0.02), IML (dAff -0.05), GIR (dAff -0.69), and AMC (dAff -2.01). G415E increased binding affinity for LAS, (dAff -0.15) GIR (dAff -0.02) and ELA (dAff -0.08), while it decreased binding affinity for TAM (dAff 0.11), IML (dAff 0.09), FUL (dAff 0.29), CAM (dAff 0.19) and AMC (dAff 0.10). Mutations in codon 537 did not affect dAff for TAM, GIR, and ELA; a significant decrease in binding affinity was observed for FUL and AMC, whereas it was increased for LAS. Mutational co-occurrence was tested between ESR1 mutations in FUL docking sites and oncogenic pathways. Significant associations were observed for cell cycle SNVs (P=0.047), Notch SNVs (P=0.020), and ER SNVs (P&lt; 0.001). Within these pathways, significant single-gene associations were observed for FBXW7 SNVs (P=0.020), ESR1 SNVs (P&lt; 0.001), and GATA3 SNVs (P= 0.016). Given the highly significant co-occurrence of non-HS with other ESR1 mutations, combined models were examined. The Y537/F404 combination resulted in decreased binding affinity for FUL and increased binding affinity for LAS, while L536/F404 decreased binding affinity for TAM and increased binding affinity for IML, ELA, and AMC. Notably, L540/F404 restored the FUL-ESR1 interaction resulting in an increased binding affinity (dAff -2.1). Conclusions: The study suggests that genomic variability in drug targets detectable through ctDNA may modulate therapeutic response. Preclinical models are under development to investigate the combined endocrine resistance mechanism suggested by the significant co-occurrence between ESR1 mutations in SERDs/SERMs docking sites and ESR1 hotspot mutations and provide valuable additional insights for drug development and future treatment algorithms.

Citation Format: Lorenzo Gerratana, Rossana Roncato, Mattia Sturlese, Andrew A. Davis, Marko Velimirovic, Carolina REDUZZI, Katherine K. Clifton, Whitney L. Hensing, Ami N. Shah, Charles S. Dai, Paolo D’Amico, Arielle J. Medford, Alessandra Franzoni, Linda Cucciniello, Firas Wehbe, Seth A. Wander, Barbara Belletti, William Gradishar, Amir Behdad, Giuseppe Damante, Cynthia Ma, Fabio Puglisi, Aditya Bardia, Massimo Cristofanilli. PD10-01 Impact of ESR1 mutations on Selective Estrogen Receptor Degraders and Modulators: an integrated liquid-biopsy and pharmacodynamics approach. [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD10-01.

Abstract P3-06-06: Real-world analysis of adverse events of patients with triple negative breast cancer receiving therapy per KEYNOTE-522

Background: KEYNOTE-522 was a randomized, double-blind, placebo-controlled phase 3 trial which resulted in the FDA approval of pembrolizumab with neoadjuvant chemotherapy for patients (pts) with newly diagnosed, high-risk, early-stage triple negative breast cancer (TNBC). Given the improvement in pathological complete response (pCR) and event-free survival rates, this regimen has emerged as standard-of-care (SOC) therapy. Adverse events in pts on this treatment regimen in clinical practice is unknown and understanding the real-world toxicity of this regimen is critical.

Methods: In this IRB approved retrospective, single-center study we examined pts with early-stage TNBC who received planned treatment per KEYNOTE-522 per SOC from 2021-present. This regimen includes a year of pembrolizumab combined with 4 cycles of neoadjuvant carboplatin/paclitaxel followed by 4 cycles of doxorubicin/cyclophosphamide. Number and length of treatment delays, treatment related toxicities of all grades, and pCR rate were collected from the electronic medical record.

Results: Of the 87 identified pts, 2 were excluded due to locally recurrent or metastatic disease and 6 did not receive immunotherapy due to concerns for toxicity or patient preference. Of the 79 pts who initiated treatment with chemotherapy and immunotherapy, median age of the cohort was 52 (27-77). 9 pts had a BRCA1 mutation and 1 pt had a BRCA2 mutation. 41 (51.9%) had T1-2 disease and 38 (48.1%) had T3-4 disease. 37 (46.8%) pts had N0 disease and 42 (53.2%) had N1-3 disease. 15 pts had baseline comorbidities, including heart disease, kidney disease, type II DM, and/or peripheral neuropathy. 68 pts (86.1%) had baseline ECOG 0, 9 (11.4%) had ECOG 1, and 2 (2.5%) had ECOG 2. At the time of analysis, 70 pts (88.6%) were receiving active treatment, of which 47 (67.1%) had completed ≥50% of the planned neoadjuvant therapy. Of pts completing ≥50% of planned neoadjuvant therapy and pts off therapy (N=56), 31 (55.4%) had 1 or more hospitalizations and 23 (41.1%) had 1 or more emergency room visits. 30 pts had treatment delays (53.6%) and 21 pts (37.5%) had dose reductions. Rates of adverse events are presented in Table 1. Of the 79 analyzed pts, 35 have undergone surgery. pCR rate was 45.7% (N=16). 8 (22.9%) pts had RCB-I, 4 (11.4%) pts had RCB-II, 3 (8.6%) pts had RCB-III, and 4 (11.4%) pts had residual disease without RCB calculation. Updated analysis will be included at time of presentation.

Conclusions: In this single-center retrospective study of pts receiving chemoimmunotherapy for TNBC, we found higher rates of grade 3 toxicity, including nausea, fatigue, neutropenia, diarrhea, peripheral neuropathy, and hypothyroidism, and lower pCR rate than was reported in the KEYNOTE-522 trial. This may reflect a more heterogeneous population of pts treated in routine clinical practice who are typically less fit than pts on clinical trials. Additionally, pts in this study had higher T stages (48.1% with T3-4 disease vs 26.0% in trial) and node positive disease (53.7% with N1-3 disease vs 48.8% in trial). Limitations include immaturity of data and small sample size; however, these data warrant validation through longer-term follow-up and multicenter validation.

Adverse Events in pts receiving Keynote-522 regimen as SOC and on clinical trial

Citation Format: Mara Hofherr, Jennifer Hedgecorth, Foluso O. Ademuyiwa, Lindsay L. Peterson, Nusayba A. Bagegni, Rama Suresh, Ashley Frith, Ron Bose, Katherine Weilbaecher, Cynthia Ma, Andrew A. Davis, Katherine K. Clifton. Real-world analysis of adverse events of patients with triple negative breast cancer receiving therapy per KEYNOTE-522 [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P3-06-06.

Abstract P5-02-07: Cell-free DNA detection of GATA3 mutations in metastatic hormone receptor positive breast cancer: a retrospective, observational multi-institutional analysis

Background GATA3 mutations (GATA3mut) have been reported in 10-20% of hormone receptor positive (HR+) breast cancers. It has been shown that targeting GATA3mut HR+ breast cancer with MDM2 inhibitors invokes synthetic lethality. MDM2 is an E3 ubiquitin ligase that targets p53 for degradation, and research suggests that restoring p53 by blocking MDM2 may be effective in treating GATA3mut HR+ breast cancer. One potential mechanism of this efficacy has been shown to be through the PI3K-AKT pathway. We thus sought to characterize the GATA3mut landscape in a multi-institutional cell-free DNA (cfDNA) analysis and to determine the association between GATA3mut and TP53 mutations, as well as alterations in the PI3K-AKT pathway and the impact of GATA3 on survival. Methods We analyzed cfDNA data collected at the Massachusetts General Hospital and at Washington University in St Louis via Guardant360, a next generation sequencing assay that analyzed up to 74 genes during the study period. The association of GATA3mut and co-mutations as well as number of prior therapies was estimated using Pearson’s chi-squared test for categorical variables, two-sample Wilcoxon rank-sum test for continues variables, and multivariable logistic regression. The impact of GATA3mut and GATA3 wildtype (WT) on progression-free survival (PFS) and overall survival (OS) was analyzed using multivariable Cox regression analysis, adjusting for age, number of prior therapies, visceral metastases, and de novo metastases. PFS and OS were evaluated in the overall study population, as well as in subgroups of patients that received endocrine monotherapy and chemotherapy. Results Out of 647 patients with HR+ MBC, 10% (n = 68) had non-synonymous GATA3 mutations. Among these 68 GATA3mut patients, 37% (n = 25) were mutations in exon 5, all but two of which were in the second zinc finger, and 62% (n = 42) were in exon 6. 62% (n = 42) were frameshift mutations, 20% (n = 14) were indels, and 18% (n = 12) were point mutations. Median mutant allele fraction (MAF) of GATAmut was 0.95% (range 0.03 – 30.5%). There was no statistically significant association of GATA3mut with the number of prior therapies, PR status, or the presence of ESR1, TP53, or PI3K-AKT pathway mutations. In the GATA3mut population, TP53 co-mutations (n = 21) were found with a median MAF of 0.6%. PI3K-AKT pathway alterations occurred in 47% (n=32) of GATA3mut patients (PIK3CA n = 27; AKT n = 2; PTEN n = 3). In the combined cohort, there was no significant difference in PFS or OS after adjusting for visceral metastases, de novo disease, number of prior therapies, and age. In a cohort of 80 patients that received endocrine monotherapy (GATA3 WT n = 74, GATA3mut n = 6), GATA3mut were associated with borderline worse PFS (HR 2.6; p = 0.061) and worse OS (HR 4.5; p = 0.009). There was no statistically significant difference in PFS or OS in a subgroup that received chemotherapy. Conclusions GATA3 mutations can be identified via cfDNA in patients with HR+ MBC. Co-mutations in TP53 occurred at overall low MAF. Further research is needed to characterize the functional impact of these low level TP53 co-mutations and develop therapeutic strategies to target GATA3 mutant MBC.

Citation Format: Arielle J. Medford, Marko Velimirovic, Andrzej Niemierko, Whitney L. Hensing, Andrew A. Davis, Katherine K. Clifton, Jennifer C. Keenan, Charles S. Dai, Lesli A. Kiedrowski, Ami N. Shah, Lorenzo Gerratana, Laura M. Spring, Leif Ellisen, Robert C. Doebele, Massimo Cristofanilli, Aditya Bardia. Cell-free DNA detection of GATA3 mutations in metastatic hormone receptor positive breast cancer: a retrospective, observational multi-institutional analysis [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-02-07.

Abstract PD13-09: PD13-09 Clinical outcomes of patients with HR+ HER2- advanced breast cancer with early progression on CDK4/6 inhibitors

Background: CDK4/6 inhibitors (CDK4/6i) paired with endocrine therapy (ET) are considered first-line (1L) therapy for patients (pts) with HR+ HER2- advanced breast cancer (aBC). A minority of pts will demonstrate primary resistance to CDK4/6i, as characterized by early progression. Thymidine kinase 1 (TK1) is a cell-cycle regulated enzyme downstream of CDK4/6 and involved in nucleotide metabolism during DNA synthesis. Prior studies have shown TK1 may serve as a biomarker of response to CDK4/6i, with early TK1 activity (TK1a) suppression after initiation of CDK 4/6i therapy associated with improved PFS. Lack of TK1a suppression may be associated with primary resistance to CDK4/6i. In this study, we aim to analyze response to subsequent lines of therapy and overall survival (OS) of pts with early progression on 1L CDK4/6i. Methods: Pts with HR+ HER2- aBC from a phase II trial of an alternative schedule of palbociclib (palbo alt dosing trial NCT 3007979) and from a retrospective palbociclib study were included in this analysis. Pts in the palbo alt dosing trial underwent baseline and C1D15 TK1a analysis after initiation on CDK4/6i. C1D15 TK1a suppression was defined at TK1a &lt; 30 Du/L. Pts in the retrospective palbociclib study included pts receiving palbo as part of their standard of care 1L therapy for HR+ HER2- aBC at Washington University in Saint Louis from 2016 to 2021. Clinical information, including treatment start and stop dates on each of the next-line therapies, were collected from the electronic medical record. PFS was estimated by the treatment duration on a specified treatment regimen. Early progression on CDK4/6i was defined as PFS &lt; 6 mo. Best response was defined as next line of therapy with the numerically longest PFS. OS was defined as time to death from the initiation of CDK4/6i. Results: Of the 54 pts enrolled on the palbo alt dosing trial, 51 pts were evaluable for clinical benefit and 46 pts were evaluable for TK1a suppression rate at C1D15. 7 pts (15.2%) were found without TK1a suppression at C1D15. This lack of TK1a suppression on palbo was associated with a significantly shorter PFS (median PFS=3.1 mo) compared to not reached in pts with TK1a suppression at C1D15. We conducted clinical analysis on N=26 pts who exhibited early progression on CDK4/6i which included 10 pts from the palbo alt dosing trial and 16 from the retrospective study. The average subsequent line of therapies in this cohort was 3, with the most common second line (2L) therapy being chemotherapy (N=17, 65.4%) and ET (N=8, 30.8%). The median PFS for pts receiving 2L chemotherapy and ET was 4.09 mo and 3.64 mo, respectively. 10 pts received both chemotherapy and ET with 7 (70.0%) achieving best response with chemotherapy compared to 3 pts (30.0%) who achieved best response with ET. The median OS for the cohort was 14.6 mo. Conclusions: Early progression on CDK4/6i is associated with a particularly poor prognosis. In our cohort, the median OS was far below the expected median OS for pts receiving 1L palbo as reported in the PALOMA-2 trial (14.6 mo vs 53.9 mo). Early progression on CDK4/6i is associated with more aggressive disease which may respond more favorably to chemotherapy, as demonstrated by best response to therapy. Further prospective studies are warranted to explore this treatment approach.

Citation Format: Katherine K. Clifton, Shana N. Thomas, Jingqin Luo, Jing Xi, Nusayba A. Bagegni, Foluso O. Ademuyiwa, Rama Suresh, Ashley Frith, Andrew A. Davis, Ron Bose, Katherine Weilbaecher, Whitney L. Hensing, Timothy Pluard, Massimo Cristofanilli, Hyo S. Han, Adam M. Brufsky, Kevin Kalinsky, Shom Goel, Seth A. Wander, Lindsay L. Peterson, Cynthia Ma. PD13-09 Clinical outcomes of patients with HR+ HER2- advanced breast cancer with early progression on CDK4/6 inhibitors [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr PD13-09.

Abstract P3-06-07: Phase Ib/II study to evaluate safety and tolerability of cabiralizumab in combination with nivolumab and neoadjuvant chemotherapy in patients with localized triple-negative breast cancer

Background: Neoadjuvant immune checkpoint inhibition (ICI) in combination with chemotherapy is approved for patients with high-risk, early-stage triple-negative breast cancer (TNBC) based on improved outcomes in the KEYNOTE-522 trial. However, some patients have primary resistant disease and do not achieve a pathological complete response (pCR), while others experience significant toxicity. Tumor-associated macrophages (TAMs) are a potential resistance mechanism for ICIs and are dependent on colony-stimulating factor 1 receptor (CSF1R). Therefore, we examined the addition of cabiralizumab, a CSF1R inhibitor, to neoadjuvant paclitaxel, carboplatin, and nivolumab to assess the safety, tolerability, and changes in the tumor microenvironment (TME) in patients with early-stage TNBC. Methods: This is a phase Ib/II, single-institution, randomized controlled clinical trial (NCT04331067) in patients with newly diagnosed Stage II-III TNBC. The primary endpoints include: (1) to determine the safety of a 12-week neoadjuvant regimen of paclitaxel (80 mg/m2 IV q week) + carboplatin (AUC5 IV q3 weeks) + nivolumab (240 mg IV q2 weeks) with or without cabiralizumab (4 mg/kg IV q2 weeks) and (2) to evaluate the effect of cabiralizumab on TAMs and changes in tumor infiltrating lymphocytes (TILs) in the TME between baseline and an on-treatment biopsy after 4 weeks of therapy. Adjuvant treatment is per investigator’s choice. Secondary objectives include evaluation of pCR rate and recurrence-free survival. Paired tissue and bone marrow biopsies are collected for evaluation of the TME and disseminated tumor cells, respectively. The study was designed to enroll 50 patients, including a 12-patient safety lead-in cohort. Here, we report the planned interim analysis of the safety lead-in cohort. Results: Between December 2020 and May 2022, we enrolled 12 patients to the safety lead-in, including 6 patients in each arm. 5 of 12 patients (41.7%) enrolled are underrepresented minorities, including 4 Black patients and 1 Hispanic patient. 2 of 6 patients in the nivolumab arm experienced grade 3 severe toxicity, including 1 patient who developed sepsis and 1 who developed peripheral neuropathy. 3 of 6 patients in the nivolumab + cabiralizumab arm developed grade 3 severe toxicity including 2 patients who experienced myositis and 1 patient who developed periorbital edema. Of the first 10 patients enrolled, 5 had a pCR (2 pCR in cabiralizumab arm, 3 pCR in non-cabiralizumab arm) and 3 had non-pCR (1 RCB-1 and 1 RCB-3 in cabiralizumab arm, 1 RCB-1 in non-cabiralizumab arm). 2 patients came off study prior to surgery (1 due to toxicity and 1 due to missing study visits). Data from the final 2 patients still on treatment will be available at the time of presentation. Discussion: Full safety, pathologic, and clinical response data in the safety lead-in cohort for patients with early-stage TNBC receiving neoadjuvant chemotherapy + nivolumab with or without cabiralizumab, will be presented.

Citation Format: Andrew A. Davis, Leonel Hernandez-Aya, Jingqin Luo, Mateusz Opyrchal, Foluso O. Ademuyiwa, Nusayba A. Bagegni, Katherine K. Clifton, Jill Anderson, Trish Hammerschmidt, Leslie Nehring, David DeNardo, Mark Watson, Rebecca Aft, Cynthia Ma, Katherine Weilbaecher. Phase Ib/II study to evaluate safety and tolerability of cabiralizumab in combination with nivolumab and neoadjuvant chemotherapy in patients with localized triple-negative breast cancer [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P3-06-07.

Modeling the Prognostic Impact of Circulating Tumor Cells Enumeration in Metastatic Breast Cancer for Clinical Trial Design Simulation

Despite the strong prognostic stratification of circulating tumor cells (CTCs) enumeration in metastatic breast cancer (MBC), current clinical trials usually do not include a baseline CTCs in their design. This study aimed to generate a classifier for CTCs prognostic simulation in existing datasets for hypothesis generation in patients with MBC. A K-nearest neighbor machine learning algorithm was trained on a pooled dataset comprising 2436 individual MBC patients from the European Pooled Analysis Consortium and the MD Anderson Cancer Center to identify patients likely to have CTCs ≥ 5/7 mL blood (StageIVaggressive vs StageIVindolent). The model had a 65.1% accuracy and its prognostic impact resulted in a hazard ratio (HR) of 1.89 (Simulatedaggressive vs SimulatedindolentP < .001), similar to patients with actual CTCs enumeration (HR 2.76; P < .001). The classifier's performance was then tested on an independent retrospective database comprising 446 consecutive hormone receptor (HR)-positive HER2-negative MBC patients. The model further stratified clinical subgroups usually considered prognostically homogeneous such as patients with bone-only or liver metastases. Bone-only disease classified as Simulatedaggressive had a significantly worse overall survival (OS; P < .0001), while patients with liver metastases classified as Simulatedindolent had a significantly better prognosis (P < .0001). Consistent results were observed for patients who had undergone CTCs enumeration in the pooled population. The differential prognostic impact of endocrine- (ET) and chemotherapy (CT) was explored across the simulated subgroups. No significant differences were observed between ET and CT in the overall population, both in terms of progression-free survival (PFS) and OS. In contrast, a statistically significant difference, favoring CT over ET was observed among Simulatedaggressive patients (HR: 0.62; P = .030 and HR: 0.60; P = .037, respectively, for PFS and OS).

Abstract 1950: A novel ESR1 mutation assay for single circulating tumor cell by application of DEPArray࣪ System and Digital Droplet PCR

Introduction: Although circulating tumor cells (CTC) display the same spatial and temporal heterogeneity as the primary tumor, they represent a privileged window to disclose mechanisms of metastases. ESR1 mutations are a major mechanism of acquired endocrine resistance in metastatic breast cancer (MBC). We previously reported that ESR1 mutations in circulating tumor DNA (ctDNA) was associated with worse prognosis in MBC (2020 ASCO). Herein, we report a new ultra-high sensitivity approach of ESR1 mutations assay for single CTC by using DEPArray system and Droplet Digital PCR (ddPCR).

Methods: Whole blood sample (7.5ml/each) was collected from stage IV MBC patients and then CTC enumeration was performed in CellSearch™ System by targeting the EpCAM antigen (2020 AACR #3120). The single CTC and single white blood cell (WBC) were then isolated from CellSearch cartridges by using DEPArray࣪ System (Menarini). The single CTC DNA was isolated by QIAamp DNA Micro Kit (Qiagen). ESR1 mutations hotspots including p.E380Q, p.Y537S and p.D538G were analyzed by using QX200™ ddPCR System (Annealing/Extension=58 °C, 40 cycles) and the corresponding probes (Mutation-FAM and Wild type-HEX mixed) for p.E380Q-dHsaMDS500014536, p.Y537-dHsaMDS975379796, p.D538G- dHsaMDS460485301 respectively (Bio-Rad). Meanwhile, corresponding plasma ctDNA was analyzed by Guardant 360 Health NGS-based assay for a 73 genes panel for single nucleotide variants.

Results: Positive controls (using 0.00000325ng pure positive DNA) and negative control (using water) were performed in each ddPCR assay. In cohort 1: total of 8 samples including 4 single CTC samples and 4 single WBC samples were collected using the DEPArray system. Wild type ESR1 (p.E380Q, p.Y537S and p.D538G) was detected in all 4 single CTC samples and 4 single WBC samples. There were 3 copies, 3.4 copies, 1.6 copies and 1.8 copies of p.E380Q mutation droplets found in 4 single CTC samples when there were no p.Y537S or p.D538G mutations found in these samples. There was no ESR1 mutation found in the corresponding ctDNA. In cohort 2: Two samples including 4 CTCs and 100 CTCs were collected from CellSearch cartridges. There were 0.09 vs 1 copies (8.25%) and 0.1 vs 0.31 copies (24.39%) of p.E380Q mutation droplets found in these two samples respectively, compared to ctDNA results of 1.80% and 0 respectively. Furthermore, there was 0.08 vs 0.67 copies (10.66%) of p.D538G mutation droplets were found in the sample including 100 CTCs compared to 12.70% mutations detected in the corresponding ctDNA.

Conclusion: Our new approach verified the feasibility of ESR1 mutations assay in very low amount DNA from single CTCs with high sensitivity even when ESR1 mutation could be found in CTCs but not ctDNA. This approach may offer a strong evidence for early disease metastasis, efficacy of individualized treatment monitoring and personalizing cancer therapy for precision medicine.

Citation Format: Qiang Zhang, Paolo D'Amico, Marwa Manai, Carolina Reduzzi, Andrew A. Davis, Lorenzo Gerratana, Weijun Qin, Jianhua Jiao, Saya L. Jacob, Jeannine Donahue, Youbin Zhang, Lisa Flaum, Massimo Cristofanilli, Leonidas C. Platanias, Ami N. Shah, William Gradishar. A novel ESR1 mutation assay for single circulating tumor cell by application of DEPArray࣪ System and Digital Droplet PCR [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1950.

Dual tissue and plasma testing to improve detection of actionable variants in patients with solid cancers

3017

Background: Next generation sequencing (NGS) of tumor tissue and plasma (circulating tumor DNA [ctDNA]) are used clinically to identify actionable genomic alterations, with implications for treatment selection and disease surveillance. Early studies have observed that solid tumor tissue and ctDNA testing may capture both overlapping and complementary alterations. Using the Tempus database, we examined whether dual tissue and ctDNA testing, “dual testing”, improved identification of actionable variants compared with either modality alone. Methods: We used Tempus Lens to retrospectively analyze 3153 de-identified stage 4 patients (breast [N = 644], colorectal [N = 841], non-small cell lung cancer (NSCLC) [N = 1232], and prostate [N = 436]). Each patient had dual testing—Tempus xF (ctDNA, 105 panel genes) and Tempus xT (tumor tissue, 595-648 panel genes), representing 6306 total samples. Samples were defined as concurrent if biopsied ≤30 days apart and longitudinal if plasma was collected between 31–365 days after tissue biopsy. All analyses were limited to single nucleotide variants and insertions/deletions that met the limit of detection criteria for both assays (104 genes). Indication matched actionable variants were defined by OncoKB Level 1 and 2 evidence, or R1 within both xF and xT (13 genes). Results: Of the 3153 patients with dual testing, 37% (1168) had actionable variants identified by at least one test. 94% (1100/1168) of these patients had variants identified via solid tumor profiling alone, 73% (856) had variants identified via ctDNA profiling alone, and 64% (745) had perfectly concordant variants. Thus, dual testing identified additional variants in 36% (423/1168) of these patients compared to any singular test. Of the 423 patients who had additional actionable alterations discovered through dual testing, ctDNA revealed unique alterations—which were not found in solid tissue testing—in 22% (95/423) of patients. Of these patients, 72% (68/95) had all actionable variants identified solely from ctDNA. Of the 251 patients with additional alterations identified by concurrent dual testing, 24% (61/251) had unique alterations identified in plasma. Similarly, of the 172 patients with additional alterations identified by longitudinal dual testing, 20% (34/172) had unique alterations identified in ctDNA alone. Conclusions: In the largest study of its kind, we show that dual tumor tissue and ctDNA testing—with samples collected either concurrently or longitudinally—identified more patients with actionable alterations than single modality testing alone and therefore should be considered as part of routine NGS testing. Additional studies to explore the genetic and intra-patient tumor heterogeneity of these variants as well as the impact of time between tissue and plasma sampling assessments and implications for timing of therapeutic recommendations are underway.

CK+/CD45+ (dual-positive) circulating cells are associated with prognosis in patients with advanced breast cancer

1093

Background: Circulating tumor cells (CTCs) expressing epithelial markers (EPCAM, cytokeratin (CK)) and lacking CD45 (a leukocyte marker) have been associated with poor outcome in many cancer types. Nonetheless, the presence of cells expressing both CK and CD45 (CK+/CD45+), circulating in the blood of cancer patients (pts) have also been reported, but not widely investigated. Early evidence indicates that circulating dual-positive cells (DPcells) are hybrids deriving from the fusion of tumor cells and macrophages. We previously reported that it is possible to detect DPcells in the blood of pts with metastatic breast cancer (BC) and that they are associated with shorter progression-free survival (PFS), in pts with <5 CK+/CD45- CTCs. Here, we investigated the impact of DPcells on overall survival (OS) in pts with advanced BC (aBC). Methods: Blood samples (7.5 ml) were collected from aBC pts before starting a new therapy and processed with the FDA-approved CellSearch platform for CTCs and DPcells enumeration. The prognostic role of CTCs and DPcells was assessed through the Kaplan-Meier method using the log-rank test. Single DPcells were isolated using the DEPArray platform and underwent whole genome amplification and lowpass whole genome sequencing (Ampli1 WGA and Ampli1 Lowpass kits). Results: Blood samples from 341 pts with luminal (n=168), HER2+ (n=76) and triple negative (n=88) BC were analyzed. Of these, 131 samples (38.4%) contained ≥5 CTCs (CTCpos), whereas DPcell were detected in 152 samples (44.6%, range 0-53), of which 66 (43.4%) were CTCpos and 86 (56.6%) CTCneg. Overall, DPcells were associated with a shorter OS: median OS 24.5 vs 35.0 months, p=0.046. However, when analyzing CTCpos and CTCneg separately, only the latter group showed a difference in OS according to DPcells presence. In particular, among CTCneg pts, those with ≥4 DPcells showed a 2.3-fold shorter OS (26.7 vs 60.6 months, p=0.025). Moreover, pts with ≥4 DPcells were less likely to experience a 6-months PFS clinical benefit (p=0.015). Interestingly, in the analysis by BC subtype, DPcells were confirmed to be associated with worse OS only in pts with triple negative BC (median OS 11.5 vs 16.9, p=0.048). To explore the exiology of DPcells, 2 out of 3 cells analyzed after single-cell isolation from 1 patient were confirmed to have copy number alterations (CNA) consistent with malignant cells. CNA and mutational profiling of additional single DPcells and CTCs are ongoing. Conclusions: DPcells are associated with worse OS in aBC pts, with the prognostic impact primarily in pts with <5 CTCs and triple negative BC. This suggests that DPcells might be an alternative way of tumor dissemination in specific pts, in which CK+/CD45- CTCs are less prevalent. More studies are needed to better elucidate DPcell clinical significance in BC, and to confirm their fusion-hybrid origin.

Defining resistance mechanisms to CDK4/6 inhibition in hormone receptor-positive HER2-negative metastatic breast cancer (MBC) through a machine learning approach applied to circulating tumor DNA (ctDNA)

3055

Background: Although cyclin-dependent kinase 4/6 inhibitors (CDK4/6i) are a primary treatment for hormone receptor-positive/HER2 negative MBC, data regarding resistance mechanisms are still an unmet need. The aim of the study was to highlight new resistance pathways using machine learning (ML) to detect multiparametric patterns in complex datasets. Methods: The study retrospectively analyzed a cohort of 610 hormone receptor positive HER2 negative MBC patients (pts) at Northwestern University, Massachusetts General Hospital and Washington University in St. Louis between 2015-2020 with baseline ctDNA testing by Guardant360. Pathways were defined based on previous work (Sanchez-Vega F et al, Cell. 2018) (i.e., RTK, RAS, RAF, MEK, NRF2, ER, WNT, MYC, P53, cell cycle, notch, PI3K). Only pathogenic variants according to OncoKB were included in the models. Associations among single nucleotide (SNVs) and copy number (CNVs) variations, pathway classification and previous exposure to CDK4/6i were explored through logistic regression and Gradient boosted machines (GBMs) ML algorithm. Results: at baseline, 322 pts (52.8%) were previously treated with CDK4/6i. The most detected pathway alterations were SNVs in PI3K (37.1%), P53 (31.8%), ER (29.2%) and RTK (22.3%). After stepwise logistic regression, RB1, NF1 and ESR1 SNVs were associated with previous exposure to CDK4/6i (respectively OR: 3.55 P = 0.017; OR: 3.06 P = 0.026 and OR: 1.82 P < 0.001), while SNVs in the ER pathway were associated with CDK4/6i (1.56 P < 0.001). Two GBMs models were designed based on gene variants (training AUC: 0.695, cross validation AUC: 0.631) and oncogenic pathways (training AUC: 0.713, cross validation AUC: 0.619). The highest relative importance (RI) was observed for ESR1 SNVs (RI: 35.35), TP53 SNVs (RI: 11.33), NF1 SNVs (RI: 3.45), SMAD4 SNVs (RI: 3.39) and RB1 SNVs (RI: 3.33). Alterations at a pathway level with the highest RI were ER SNVs (RI: 33.50), P53 SNVs (RI: 14.98), PI3K SNVs (RI: 14.40), RTK SNVs (RI: 10.55), RTK CNVs (RI: 10.26), cell cycle CNVs (RI: 6.99), cell cycle SNVs (RI: 6.77) and RAS SNVs (RI: 6.54). Of the previously highlighted pathway alterations, a significant impact on PFS after ctDNA collection was observed among de novo pts treated with CDK4/6i (165 pts) for ER SNVs (P < 0.0001), RTK SNVs (P = 0.0011), RTK CNVs (P = 0.0006), Cell cycle CNVs (P = 0.0010) and Cell cycle SNVs (P = 0.0143). No impact was observed on PFS for pts who had not received a CDK4/6i-based regimen. Conclusions: The combination of ctDNA-based datasets and machine learning algorithms defined novel resistance pathways for patients treated with CDK4/6i. Although preliminary, these results suggest that alterations of the ER, RTK and Cell cycle pathways might be crucial to optimize treatment strategy and drug development.

ESR1 mutations in circulating tumor DNA (ctDNA) are associated with CTCs and increased hormone receptors in metastatic tumor tissues of patients with metastatic breast cancer (MBC)

1057

Background: The monitoring of ctDNA and circulating tumor cells (CTCs) in patients with MBC predicts metastasis and prognosis. We previously reported that HER2 and ESR1 alterations in ctDNA were associated with predicted metastasis in MBC (2019 ASCO#1036). Furthermore, ctDNA can be used to evaluate tumor heterogeneity (2020 ASCO #1028). Here, we report that baseline ctDNA ESR1 mutation is a key point associated with tumor tissue characteristics and CTCs, which may help to elucidate disease resistance in MBC. Methods: This study included 288 hormone receptors positive MBC patients who received systemic treatment under an IRB-approved clinical trial (NU16B06) at NU Lurie Cancer Center (2016-2021). Baseline plasma ctDNA was analyzed by Guardant360 NGS for ESR1 mutations. CTC enumerations were performed by using 7.5ml blood in CELLTRACKS (Menarini). Estrogen receptor (ER), progesterone receptor (PR), HER2 and Ki67 in each patient’s biopsy tumor tissue before surgery, surgical tumor tissue and metastatic tumor tissue were evaluated by NU PathCore. Kruskal-Wallis was used for statistics. Results: Of the 288 patients, ESR1 mutations were found in 18 hotspots from 38 patients (ESR1Mut, 13.19%) and there were 250 patients without any mutation (ESR1WT, 86.81%). Median of Total CTCs (/7.5ml) and HER2+ CTCs (/7.5ml) were significantly increased in ESR1Mut group compared to ESR1WT group, total CTCs were 8.0 vs 1.0 (P=0.006) and HER2+ CTCs were 1.5 vs 0 (P=0.014), respectively. There were significant differences on hormone receptors expression (positive cells %) in tumor tissues between ESR1Mut group and ESR1WT group: 1) ESR1Mut group has significant higher expression in ER and PR in biopsy tumor tissues. The mean of ER in ESR1+group was 90.48% vs 48.18% in ESR1WT group (p<0.001). The mean of PR in ESR1Mut group was 40.86% vs 25.60% in ESR1WT group (p<0.001). Meanwhile, there is not significant difference on HER2 expression in ESR1Mut group compared ESR1WTgroup; 2) In the surgical tumor tissues, the mean ER was 97.64% in ESR1Mut group which was significantly higher than 47.90% in ESR1WT group (p<0.001), while the PR was 45.33% and 24.32%, respectively; 3) In metastatic tumor tissues, the mean of ER in ESR1Mut group was 84.75% vs 34.89% in ESR1WTgroup (p<0.001) and the mean of PR in ESR1Mut group was 32.25% vs 9.33% in ESR1WT group (p<0.001). Furthermore, median of Ki67 in ESR1Mut group is 28.33% which was significantly higher than 18.75% in ESR1WT group (p<0.01). Conclusions: Baseline ctDNA ESR1 mutations not only had higher total CTCs and HER2+ CTCs but also significantly correlated with high hormone receptors and proliferation in tumor metastatic tumor tissues. The synergy of ctDNA ESR1 mutation and tissue pathological characteristics expands the early predictive role of ctDNA monitoring metastatic prognosis for clinical decision-making.

Targeted Treatment for High-Risk Early-Stage Triple-Negative Breast Cancer: Spotlight on Pembrolizumab

Triple-negative breast cancer (TNBC) is a biologically aggressive yet heterogeneous disease that disproportionately affects younger women and women of color compared to other breast cancer subtypes. The paucity of effective targeted therapies and the prevalence of chemotherapeutic resistance in high-risk, early-stage TNBC pose significant clinical challenges. Deeper insights into the genomic and immune landscape have revealed key features of TNBC, including intrinsic genomic instability, DNA repair deficiency, and potentially an immunogenic tumor microenvironment. These advances led to landmark trials with immune checkpoint inhibitors in the advanced-stage setting, which subsequently translated into immunotherapy-based clinical trials in the early-stage setting and recent promising results. Pembrolizumab, an anti-programmed death 1 (PD-1) monoclonal antibody, was investigated in combination with platinum-, taxane- and anthracycline-based neoadjuvant chemotherapy followed by adjuvant pembrolizumab monotherapy for patients with high-risk, early-stage TNBC in the randomized, double-blind, placebo-controlled phase 3 KEYNOTE-522 trial. In July 2021, the US Food and Drug Administration (FDA) granted approval for pembrolizumab based on marked improvement in pathologic complete response rate and 3-year event-free survival compared to neoadjuvant chemotherapy alone. This advance immediately altered the longstanding treatment paradigm. Here, we review the impact of pembrolizumab plus chemotherapy for the treatment of patients with high-risk, early-stage TNBC, and discuss immunotherapy-related toxicity considerations, key immunomodulatory biomarkers under active investigation, and remaining clinical questions for future research directions.

Abstract P2-07-02: Genomic predictors of rapid progression to first line endocrine and CDK4/6 inhibitor combination therapy in patients with estrogen receptor positive (ER+) HER-2 negative (HER2-) advanced breast cancer (ABC)

Background: Endocrine therapy with CDK 4/6 inhibitors (ET/CDK4/6i) represents the 1st line therapy for ER+/HER2- ABC. While majority of patients derive clinical benefit with combination therapy, a subset have refractory disease with progression within 6 months. However, predictive biomarkers for rapid progression are lacking. In this study, we evaluated genomic profiles associated with rapid disease progression on ET/CDK4/6i. Methods: We identified 77 patients who received 1st line ET/CDK4/6i combination therapy (AI or SERD with one of the 3 approved CDK4/6is) and had ctDNA analysis performed via plasma based genotyping utilizing the commercially available Guardant360 assay at three sites: Washington University in St. Louis, MO, Northwestern University (Chicago, IL), and Massachusetts General Hospital (Boston, MA). We aimed to look at the differences in patient characteristics and genomic profiles of the tumors assessed from baseline ctDNA specimens between the patients with rapid progression (time to progression TTP&lt;=6 months) vs others. In particular, we focused on growth factor receptors (FGFR, EGFR) given that previous studies have shown that activation of FGFR1 and EGFR signaling may be implicated in resistance to endocrine based therapy in breast cancer. Time to progression was estimated by using Cox regression. Variable associations were estimated via logistic regression. Results: In the combined cohort, FGFR1 amplification (FGFR1amp) was detected in 15/77 patients (19.5%). FGFR1amp was seen in 5/10 (50%) of patients with rapid progression, consistent with existing knowledge that FGFR1amp contributes to resistance to CDK4/6i and/or ET. Presence of FGFR1amp was independently associated with shorter TTP (11.2 vs. 34.7 months, HR=3.14, p=0.02). EGFR mutations (EGFRmut) were detected in 8/77 (10.4%) patients, 3 of which were found among patients with rapid progression and another 5 among those with TTP&lt;=15 months. Presence of EGFRmut was also associated with shorter TTP (8.5 vs. 31.7 months, HR=6.50, p&lt;0.001) in multivariable analysis. Of the 4 patients with shortest TTP (&lt;3 months) 3 harbored both FGFR1amp and EGFRmut. In another 3 patients we observed FGFR1amp and co-activation of genes implicated in G1/S phase cell cycle transition, suggesting that FGFR1 amplified cells may require a co-activating downstream event that ultimately, via multiple pathway cross-talk, renders them resistant to ET/CDK4/6 inhibition. Patients with FGFR1 amplified tumors were younger compared to those without FGFR1amp (54.3 vs. 62.7 years, p=0.04). Presence of FGFR1amp was associated with presence of liver (p=0.01) but not bone or lung metastases which could be one of the explanations why patients with higher liver tumor burden are more resistant to ET/CDK4/6i inhibition. PIK3CA and TP53 gene mutations in our cohort were frequent (found in 41% and 30% of the patients, respectively) but were independently not associated with TTP (PIK3CAmut+ HR=1.31, p=0.55, TP53mut+ HR=0.67, p=0.36). ESR1 mutations were rarely encountered (9%) as the cohort had only been exposed to adjuvant endocrine therapy. Conclusions: These findings highlight how ctDNA can be used for patient stratification prior to initiation of first line of therapy in ER+/HER2- ABC since it is evident that not all patients derive the same benefit from ET/CDK4/6i. Certain genomic alterations, particularly in FGFR1, EGFR, and G1/S phase cell cycle transition are associated with rapid progression to 1st line ET/CDK4/6i therapy, and highlight the need for clinical trials investigating combination/novel therapies for this subgroup of patients with HR+/HER2- ABC. Our findings are hypothesis-generating and require further exploration in larger datasets.

Citation Format: Marko Velimirovic, Lorenzo Gerratana, Andrew A Davis, Whitney L Hensing, Katherine Clifton, Ami N Shah, Paolo D'Amico, Charles S Dai, Elyssa N Denault, Cynthia X Ma, Seth A Wander, Dejan Juric, Massimo Cristofanilli, Bruce A Chabner, Aditya Bardia. Genomic predictors of rapid progression to first line endocrine and CDK4/6 inhibitor combination therapy in patients with estrogen receptor positive (ER+) HER-2 negative (HER2-) advanced breast cancer (ABC) [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-07-02.

Abstract PD14-01: Comprehensive molecular characterization of patients with metastatic invasive lobular carcinoma (ILC): Using real-world data to describe this unique clinical entity

Background: ILC is the second most common type of breast cancer and accounts for approximately 10% of all invasive breast cancers. A hallmark of ILC is the lack of E-cadherin (CDH1) expression, which is frequently used to discriminate between lesions with borderline ductal and lobular histologies. While the genomic landscape of primary ILCs has been well described, less is known about patients (pts) with metastatic-ILC (mILC). Better characterization of the genomic landscape associated with mILC is critical for identifying biomarkers that may provide new insight into ILC tumor biology and ultimately improve long-term outcomes in pts with mILC. Methods: We retrospectively analyzed de-identified next-generation sequencing (NGS) data from 150 advanced/metastatic pts with ILC and 51 with mixed lobular/ductal histology, defined using the histology of the sequenced biopsy. Diagnoses were abstracted from pathology reports submitted at the time of sequencing. We used the stage documented closest in time to biopsy collection, and samples were excluded if the staging date was unknown or exceeded 180 days after the biopsy date. Our dataset consisted of samples that were molecularly profiled using the Tempus xT solid tumor assay (DNA-seq of 595-648 genes at 500x coverage, full-transcriptome RNA-seq). The mutations identified for this study include somatic single-nucleotide variants and insertions/deletions. Furthermore, we examined the co-mutational landscape of CDH1-mutant disease and investigated transcript-level expression variation. Results: Mutations in CDH1 occurred in 65.3% of all mILC samples (98/150). CDH1 expression was similar between CDH1-mutant and WT mILC samples (Wilcoxon rank sum test, p=0.8). The median tumor mutational burden (TMB) score was significantly higher in CDH1-mutant samples (Wilcoxon rank-sum test, p=0.010). CDH1-mutant samples were more likely to have a high TMB (≥10 mutations/MB) when compared with the wild-type CDH1 cohort (10% vs. 6.2%), but this difference was not statistically significant (Fisher’s Exact test, p=0.5). Additionally, we observed that the ER+ subtype was more frequent in CDH1-mutant samples, although this difference was not statistically significant (97% vs 88%; Fisher’s exact test, p=0.063). PIK3CA mutations were enriched in CDH1-mutant mILC (Table 1). TBX3 and NCOR1 mutations were also mildly enriched in CDH1-mutant mILC, but these results were not significant when correcting for multiple testing (Table 1). CDH1-mutant mixed histology pts had lower CDH1 expression than WT pts (p&lt;0.001, Wilcoxon rank sum exact test). PIK3CA mutations were enriched in CDH1-mutant mixed histology pts, but this difference was not statistically significant (50% vs. 31%; p=0.3, Fisher’s exact test). Log10 CDH1 expression across all mILC pts was lower than in mixed histology pts (3.01 vs 3.53; p&lt;0.001, Wilcoxon rank-sum test). Conclusions: Our real-world dataset illustrates that the molecular landscape of CDH1-mutant mILC pts is distinct from CDH1-WT mILC pts. Additionally, mILC differs from mixed histology at a transcriptional level, with lower CDH1 expression regardless of CDH1 mutational status. Our findings suggest a use for CDH1 RNA expression levels in reclassifying mixed histology samples as mILC. Additionally, therapies targeting PIK3CA may be further investigated for their actionability in CDH1-mutant mILC cases.

Table 1.Frequency of co-mutations in CDH1-mutant vs. WT mILC cohortsGenesCDH1-mutant (n=98)CDH1 WT (n=52)p-value1q-value2n (%)n (%)PIK3CA53 (54%)6 (12%)&lt;0.001&lt;0.001TBX313 (13%)0 (0%)0.0040.13NCOR111 (11%)0 (0%)0.0090.21Pearson’s Chi-squared test; Fisher’sexact test. 2Falsediscovery rate correction for multiple testing

Citation Format: Andrew A Davis, Amir Behdad, Kayla Viets Layng, Firas Wehbe, Lorenzo Gerratana, Elizabeth Mauer, Alex Barrett, Ami N Shah, Paolo D’Amico, Lisa Flaum, William J Gradishar, Leonidas C Platanias, Massimo Cristofanilli. Comprehensive molecular characterization of patients with metastatic invasive lobular carcinoma (ILC): Using real-world data to describe this unique clinical entity [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr PD14-01.

Abstract P2-02-05: Dynamic circulating tumor cell changes in enumeration and HER2 expression during systemic therapy for metastatic breast cancer

Introduction: CTCs are tumor cells that circulate in the blood of patient with primary and MBC and, are responsible for seeing of metastasis. The monitoring of CTCs in MBC emerged as strong prognostic and possible predictive biomarker in oncology over the past couple of decades. Meanwhile, overexpression of HER2 protein has been associated with rapid cell division and worse prognosis of MBC. Here we report a significant correlation between dynamic CTCs enumeration and CTCs-HER2 expression during the systemic therapies, with potential implication to understand treatment resistance. Methods: A total of 298 whole blood samples (7.5ml/each) were collected from 149 patients with stage IV breast cancer (2016-2020) at the Northwestern University Robert H Lurie Comprehensive Cancer Center, before (Baseline) and 3 months after (Time point 2) initiation of systemic treatment. CTC enumerations were performed using the FDA approved CellSearch™ system (Menarini) which is specific for the intracellular protein cytokeratin (CK) in epithelial cells, DAPI stains the cell nucleus, anti-CD45-APC is specific for leukocytes, and anti-HER-2/neu-FLU is specific for HER-2/neu antigen. The CTCs were classified as CK+, EpCAM+, DAPI+ and CD45-. We developed a criteria for evaluation of HER2 expression by 4 different categories (0,1+,2+,3+) based on expression intensity in our lab (present in 2021 ASCO). In this study we included CTCs with all intensities of HER2 expression (1+ to 3+) which was standardized in our lab. Mann-Whitney U test was used for statistics. Results: Of the 149 baseline samples, CTC≥1 were found in 101 patients (67.8%). A change in CTCs between baseline and time point 2 for these 101 patients: Three groups were identified: Group 1: 33patients (33%) with increase CTCs; Group 2: 64 patients (63%) with decreased CTC; Group 3: 4 patients (4%) with no change The median increase of total CTCs and HER2+ CTCs in Group 1 were 7.0 and 2.0, respectively; the median decrease of total CTCs and HER2+ CTCs in Group 2 were 9.5 and 2.0, respectively. The change of HER2+ CTCs was significantly correlated with the change of total CTCs after systemic therapy, with the correlation coefficient as rs=0.662 (p&lt;0.001) for these 101 patients. A significant positive correlation between HER2+ CTCs and total CTCs were found in both Group 1 and Group 2, rs=0.717 (p&lt;0.001) and rs=0.604 (p&lt;0.001) respectively. Furthermore, the ratio of HER2+ CTCs (HER2+ CTCs/total CTCs) in both Group 1 and Group 2 was also significantly correlated with total CTCs after therapy with the corresponding correlation coefficient as rs=0.536 (p&lt;0.001) and rs=0.388 (p&lt;0.001) in Group 1 and Group 2, respectively. Conclusion: Our study demonstrated that dynamic changes of CTCs after systemic therapies, are positively correlated with the HER2 expression in CTCs in different levels of baseline CTCs amounts. Observation of HER2 expression and ratio in CTCs during the course of systemic therapy is useful in monitoring therapy efficacy and potential disease progress.

Citation Format: Qiang Zhang, Weijun Qin, Paolo D'Amico, Andrew A. Davis, Jianhua Jiao, Lorenzo Gerratana, Saya L. Jacob, Youbin Zhang, Jeannine Donahue, Wenan Qiang, Ami N Shah, Amir Behdad, Lisa Flaum, William Gradishar, Leonidas C Platanias, Massimo Cristofanilli. Dynamic circulating tumor cell changes in enumeration and HER2 expression during systemic therapy for metastatic breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-02-05.

Abstract PD6-08: Exploring the interplay among ESR1/PIK3CA codon variants, oncogenic pathway alterations and clinical phenotype of metastatic breast cancer (MBC) through circulating tumor DNA (ctDNA) next-generation sequencing (NGS)

Background: High throughput genomic technologies such as NGS are enhancing the ability to dynamically characterize MBC but their role in describing biological evolution of multiple mutations together remains unclear. ESR1 and PIK3CA are central mutations related to the biology and druggability of hormone-receptor positive, HER2 negative (luminal-like) MBC. The aim of this study was to explore the interplay between oncogenic pathway alterations and ESR1 and PIK3CA codon variants on the impact and clinical phenotype of luminal-like MBC. Methods: The study retrospectively analyzed a multi-institutional cohort comprising 1047 MBC patients (pts) characterized for ctDNA through NGS before treatment start at Northwestern University (Chicago, IL), Massachusetts General Hospital (Boston, MA) and Washington University in St. Louis between 2015-2020. The analysis was then focused on luminal-like MBC. Pathway classification was defined based on previous work (Sanchez-Vega F et al, Cell. 2018) (i.e., RTK, RAS, RAF, MEK, NRF2, ER, WNT, MYC, P53, cell cycle, notch, PI3K). Single nucleotide variations (SNVs) were annotated for their oncogenicity through OncoKB and ClinVar. Only pathogenic variants were included in the models. Associations among, pathway classification, and ESR1/PIK3CA codon variants were explored through stepwise logistic regression. Overall survival (OS) was tested through Cox regression. Results: The luminal-like cohort comprised 702 pts. ESR1 mutations were detected in 166 pts (24%) and PIK3CA in 214 pts (31%). The most common ESR1 gene mutations were found in codons 537 (31%), 538 (21%), 536 (8%) and 380 (7%), while alterations in codons 1047 (38%), 545 (25%), and 542 (20%) were the most common for PIK3CA. Other pathogenic SNVs were observed in 33% and 17% of pts for ESR1 and PIK3CA, respectively with the former being polyclonal. SNVs alterations were mainly observed in the PI3K (35%), P53 (32%), ER (28%), RAS (8%), RTK (8%) and cell cycle (5%) pathways, while copy number variations (CNVs) were detected in the RTK (15%), cell cycle (11%), MYC (7%) PI3K (6%) and RAF (5%) pathways. ESR1 537 variants were associated with alterations in the ER and WNT pathways, 538 with cell cycle, 380 with P53 and ER, 536 with RTK. PIK3CA 1047 variants were associated with alterations in the RTK and P53 pathways, 542 with RTK, RAS and RAF, E545 with PI3K, RAS, cell cycle and P53. 1047 and 542 were also associated with CNVs in the PI3K pathway. Independent prognostic factors in terms of OS were ESR1 537/380 codon variants (HR 1.94 P = 0.001 and HR 2.29 P = 0.047), SNVs in the RAS, cell cycle, and P53 pathways (HR 1.74 P = 0.003 HR 1.84 P = 0.009 and HR 1.56 P &lt; 0.001) and CNVs in the cell cycle pathway (HR 1.96 P &lt; 0.001). Conclusions: This study demonstrated how ESR1 and PIK3CA codon variants, together with alterations in specific oncogenic pathways, can differentially impact the biology and clinical phenotype of luminal-like MBC. As novel endocrine therapy agents such as selective estrogen receptor degraders (SERDs) and PI3K inhibitors are being developed, these results highlight the pivotal role of ctDNA NGS to describe tumor evolution and optimize clinical decision making.

Odds Ratio95% Confidence IntervalPESR1 Y537ER SNVs3.341.487.530.004WNT SNVs6.251.4127.740.016ESR1 D538cell cycle SNVs5.221.7915.230.003ESR1 E380P53 SNVs4.801.4116.310.012ER SNVs5.331.3321.400.018ESR1 L536RTK CNVs4.511.1517.690.031PIK3CA H1047RTK SNVs3.751.708.290.001P53 SNVs2.611.584.34&lt; 0.001PI3K CNVs6.082.4515.08&lt; 0.001PIK3CA E542RTK SNVs5.001.9412.880.001RAS SNVs3.651.369.770.01RAF SNVs6.011.0733.870.042PI3K CNVs6.302.2917.36&lt; 0.001PIK3CA E545PI3K SNVs2.881.276.530.011RAS SNVs2.871.186.980.02cell cycle SNVs3.071.088.740.035NRF2 SNVs21.431.29356.520.033P53 SNVs3.752.046.89&lt; 0.001

Citation Format: Lorenzo Gerratana, Andrew A Davis, Marko Velimirovic, Katherine Clifton, Whitney L Hensing, Ami N Shah, Charles S Dai, Carolina Reduzzi, Paolo D’Amico, Qiang Zhang, Firas Wehbe, Seth Wander, William J Gradishar, Amir Behdad, Fabio Puglisi, Cynthia X Ma, Aditya Bardia, Massimo Cristofanilli. Exploring the interplay among ESR1/PIK3CA codon variants, oncogenic pathway alterations and clinical phenotype of metastatic breast cancer (MBC) through circulating tumor DNA (ctDNA) next-generation sequencing (NGS) [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr PD6-08.

Abstract P2-14-05: Emerging molecular variants by circulating tumor DNA after immunotherapy in metastatic breast cancer

Introduction: Immune checkpoint inhibition (ICI) in advanced malignancies offers a novel therapeutic approach, often with a more favorable toxicity profile and, in a subset of patients, the allure of a durable response. Unfortunately, the majority of patients with metastatic breast cancer (MBC) treated with a PD-(L)1 inhibitor progress rapidly. Mechanisms of resistance to and emerging genomic alterations after receiving ICI in MBC have not been well described. We aimed to describe the genomic profile of post-ICI therapy for MBC through the lens of circulating tumor DNA (ctDNA). Methods: Under an IRB-approved protocol, we retrospectively collected data from patients (pts) with MBC who had ctDNA analysis by the Guardant 360® assay (Redwood, CA) as part of their routine care between January 2015 and December 2020. We abstracted the demographic, clinical, pathologic, and therapeutic history for these patients. We identified patients who received ICI therapy and a ctDNA analysis within 6 months of completing therapy and, when possible, a paired ctDNA assay no more than 6 months prior to starting ICI. CtDNA variants were annotated by pathogenicity based on the OncoKB classification (Chakravarty et al, JCO PO 2017, date accessed 5/2021). The variant allele frequency (VAF) for a ctDNA sample was determined by the VAF for the dominant alteration in that sample. Results: Of 473 pts with MBC and ctDNA analysis, 49 received ICI therapy. Twenty-four pts had post-immune therapy ctDNA analysis, of whom 17 had paired pre- and post-immune therapy samples. For those with post-ICI ctDNA, the median age was 55 years, and breast cancer subtype was hormone receptor-positive, HER2-negative in 6 pts (25%), HER2-positive in 2 pts (8%), and triple negative in 16 pts (67%). Patients received a median of 2.5 lines of therapy for MBC prior to receiving immune therapy. Eighteen pts (75%) received pembrolizumab and 6 pts (25%) received atezolizumab as standard therapy for 4 pts, a clinical trial for 12 pts, and off label (based on molecular tumor board considerations or physician discretion) for 5 pts. Concurrent therapies were nab-paclitaxel (n=4, 17%), capecitabine (n=10, 42%), carboplatin (n=4, 17%), anti-HER2 (n=2, 8%), liposomal doxorubicin (n=1, 4%), and monotherapy (n=3, 13%). The median time from completing ICI to ctDNA collection was 16 days. In the post-ICI samples, the most common alterations were in TP53 (22%), PIK3CA (7%), KIT (4%), MYC (4%), and PTEN (4%). Across post-ICI samples, 72.46% of alterations were oncogenic or likely oncogenic (n=100). The median VAF in the post-ICI samples was 9.7% (interquartile range [IQR]: 2.2%-23%) compared to 2.8% (IQR: 0.5%-4.8%) in the pre-ICI samples. The median number of detected alterations per ctDNA analysis was 5 (IQR: 3-7) in the post-ICI samples and 2 (IQR: 2-5) in the pre-ICI samples. Among the 17 pts with paired samples, 15 pts had new alterations (44 total alterations gained), of which 68% were oncogenic or likely oncogenic. Twenty-nine alterations detected in the pre-ICI samples were no longer detected in the post-ICI samples. The new alterations were 50% SNV, 48% amplifications, and 2% deletions, and the most common new oncogenic or likely oncogenic alterations were in TP53 in 29%, PTEN in 18%, PIK3CA in 18%, KIT in 18%, and EGFR in 18%. Conclusions: Pathogenic alterations, particularly in the PTEN-PIK3CA-AKT pathway, continue to emerge after ICI treatment. Prospective, standardized evaluation of post-ICI tumor molecular profile in MBC can give insight into rational therapy sequencing approaches and/or novel combinations aimed at delaying resistance to ICI therapy.

Citation Format: Anthony K Kang, Ami N Shah, Neelima Katam, Andrew A Davis, Lorenzo Gerratana, Shruti Chandra, Saya Jacob, Meilynn Shi, Jeeven Srivastava, Paolo D’Amico, Carolina Reduzzi, Michael Gurley, Firas Wehbe, Qiang Zhang, Amir Behdad, Massimo Cristofanilli. Emerging molecular variants by circulating tumor DNA after immunotherapy in metastatic breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-14-05.

Abstract P2-08-04: Progressive metastatic breast cancer with no detectable circulating tumor DNA: Evaluating limitations of this highly sensitive tool

Background: Circulating tumor DNA (ctDNA) is being evaluated as a tool to monitor disease and guide therapy escalation and de-escalation in advanced breast cancer. The patient, disease, and treatment characteristics that influence whether tumor DNA is isolated and sequenced from the bloodstream are not well understood. We aimed to describe patient and disease characteristics of cases with undetectable ctDNA levels despite progressive metastatic breast cancer (MBC). Methods: We retrospectively identified patients (pts) with MBC who had ctDNA evaluation by the Guardant 360 assay (Redwood City, CA) as part of their routine care from 2015-2020. We correlated the ctDNA assay with the disease status at collection. We identified the patient cohort with no detectable ctDNA despite evaluation at the time of progressive disease but prior to the initiation of a new therapy (ND ctDNA/PD) and compared the clinical, pathologic, and molecular features of this group to those with detected ctDNA. Differences were tested by two proportion z-tests. Results: Of 1151 ctDNA samples collected among 473 pts with MBC, 87 (7.5%) samples had no detectable (ND) ctDNA. 54 of 87 samples with ND ctDNA were collected at a time of stable or responding disease or after a new line of therapy was started, leaving only 33 ctDNA evaluations (2.8%) among 30 pts with ND ctDNA despite collection at the time of PD prior to new therapy. Among this group there were 14 pts (47%) with HR+ HER-, 11 pts (37%) with HER2+, and 5 pts (17%) with TN MBC. This compared to 254 pts (60%) with HR+ HER2-, 82 pts (19%) with HER2+, and 85 pts (20%) with TN MBC and detectable ctDNA. HER2-positive MBC was more common in the ND ctDNA/PD group than detectable ctDNA group (p-0.02). In the ND ctDNA/PD group, the median time from MBC diagnosis to ctDNA evaluation was 7 months and pts had received a median of 0.5 prior lines of therapy for MBC. Four pts (13%) had lobular breast cancer, 24 pts (80%) had recurrent disease, 14 pts (47%) had visceral metastases, and 12 pts (40%) had oligometastatic disease. Sites of metastases at the time of ND ctDNA/PD were bone n=16 (53%), lung n=7 (23%), liver n=6 (20%), lymph node n=11 (37%), skin and soft tissue n=5 (17%), and CNS n=5 (17%). When compared to those with detectable ctDNA these differences in characteristics were not statistically significant, although numerically pts with ND ctDNA had more CNS disease (17% vs 10%) and less liver disease (20% vs 32%). At the time of ND ctDNA, the site of progression was bone n=14 (47%), CNS n=5 (17%), lymph node n=9 (30%), lung n=7 (23%), and liver n=5 (17%). There was a single site of progression in 20 pts (67%). 16 of 30 pts had repeat ctDNA analysis of which 9 pts had subsequent detectable ctDNA with a median VAF of 0.3%, a median of 1 alteration per sample, and oncogenic or likely oncogenic alterations in TP53 in 3 pts and BRCA1, CCNE1, CDH1, and PIK3CA in 1 pt each. Seven had tissue NGS, all of which showed multiple oncogenic alterations. The remaining 22 pts with ND ctDNA but no PD were responding to therapy based on imaging or had already started a new therapy since the last progression. This group also had a high proportion of HER2+ MBC (n=7, 32%) and low proportion with visceral disease (n=6, 27%) Conclusions: Although ctDNA is a highly sensitive tool to detect active MBC (&lt;3% of samples had ND ctDNA), its sensitivity may be less in some clinical scenarios, including HER2+ MBC, when there are limited sites of progression, or when there is isolated CNS progression.

Citation Format: Ami N Shah, Lorenzo Gerratana, Shruti Chandra, Dhruvika Mukhija, Neelima Katam, Anthony K Kang, Andrew A Davis, Millen Srivastava, Saya Jacob, Paolo D'Amico, Qiang Zhang, Carolina Reduzzi, Michael Gurley, Firas Wehbe, William J Gradishar, Amir Behdad, Massimo Cristofanilli. Progressive metastatic breast cancer with no detectable circulating tumor DNA: Evaluating limitations of this highly sensitive tool [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-08-04.

Abstract PD14-04: Circulating tumor DNA characterization of invasive lobular carcinoma in patients with metastatic breast cancer

Background:Invasive lobular carcinoma (ILC) is the second most common histology of breast cancer, accounting for approximately 10-15% of cases. Prior studies have demonstrated that loss of E-cadherin, as well as alterations in tissue including CDH1, FOXA1, TBX3 and PTEN loss, that were more commonly observed in Luminal A ILC, while GATA3 was more commonly observed in invasive ductal carcinoma (IDC) (Ciriello et al., Cell 2015). However, data regarding the characterization of circulating tumor DNA (ctDNA) in patients (pts) with metastatic ILC are limited. We hypothesized that there would be distinct mutational profiles between pts with metastatic ILC and IDC that could be characterized using ctDNA. Methods:This retrospective cohort study included de-identified clinical, pathological, and ctDNA data from pts with metastatic breast cancer (MBC) combined under a data use agreement and approved by the institutional review boards of three sites: Washington University in St. Louis (MO), Northwestern University (Chicago, IL), and Massachusetts General Hospital (Boston, MA). All pts included in the study had ctDNA testing per standard of care with plasma-based genotyping performed by Guardant360 (Redwood City, CA) between 2015-2020. Histological classification (ILC vs. IDC) was defined based on review of pathology reports from the primary tumor or from breast biopsies of de novo MBC, and additional clinical and pathological variables were obtained via electronic medical record review. Single nucleotide variants (SNVs) were annotated using OncoKB and ClinVar and only pathogenic variants were included. Mutational profiles were compared across histologic subtypes using Fisher’s exact test to assess differences in alteration frequency across subtypes. Multivariable analysis was performed. Results:A total of 994 pts with MBC underwent ctDNA testing and were included in the analysis. 10.7% of pts had ILC (N=106) and 89.3% had IDC (N=888). 89.4% of ILC cases were categorized as hormone-receptor positive (HR+) compared with 67.1% of IDC cases. Pts with ILC had a lower frequency of triple-negative (6.7% vs. 17.7%) and HER2 positive (3.9% vs. 15.2%) breast cancer compared with IDC. Pts with ILC had a significantly higher number of pathogenic SNVs compared with IDC (mean 4.45 vs. 2.77; P=0.0037). In contrast, pts with ILC had a significantly lower number of copy number alterations as compared to pts with IDC (mean 0.40 vs. 1.03; P=0.0017). No differences were observed in mutant allele frequency between pts with ILC and IDC. The 5 most common alterations observed in pts with ILC were the following: PIK3CA, TP53, ESR1, ERBB2, and ARID1A. Alterations in AR, BRAF, CDH1, ERBB2, FGFR2, IDH2, KRAS, NF1, PIK3CA, SMAD4, and TERT were significantly higher in ILC than IDC (all P&lt;0.05). In contrast, mutations in GATA3, and amplifications in ERBB2 and MYC were significantly more common in pts with IDC (all P&lt;0.05). In multivariable analysis, mutations in BRAF, CDH1, ERBB2, IDH2, TERT remained significantly higher in ILC, while amplification of MYC was significantly higher in IDC (all P&lt;0.05). After restricting the analysis to pts with HR+ HER2 negative MBC, the following genes were significant in multivariate analysis: CDH1 and ERBB2 for pts with ILC and MYC amplification for pts with IDC (all P&lt;0.05). Discussion:In this large, multi-institutional dataset, pts with metastatic ILC were characterized by a significantly higher number of SNVs in ctDNA compared to pts with IDC, suggesting higher mutational burden. We report several alterations that were significantly different in ILC vs. IDC. These results demonstrate the ctDNA profile of pts with ILC, and future studies should explore serial plasma-based genotyping to track ILC evolution to develop targeted precision medicine based therapeutic approaches for this unique subset of pts with MBC.

Citation Format: Andrew A Davis, Lorenzo Gerratana, Katherine Clifton, Marko Velimirovic, Whitney L Hensing, Ami N Shah, Paolo D’Amico, Carolina Reduzzi, Qiang Zhang, Charles S Dai, Elyssa N Denault, Nusayba A Bagegni, Mateusz Opyrchal, Foluso O Ademuyiwa, Ron Bose, William J Gradishar, Amir Behdad, Cynthia X Ma, Aditya Bardia, Massimo Cristofanilli. Circulating tumor DNA characterization of invasive lobular carcinoma in patients with metastatic breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr PD14-04.

Abstract P2-01-01: Genetic alterations detected by circulating tumor DNA (ctDNA) in HER2-low metastatic breast cancer (MBC)

Introduction: Approximately 40-50% of breast cancers are characterized by low HER2 expression (HER2-low), defined as immunohistochemistry (IHC) 1+ or 2+ and HER2 fluorescence in situ hybridization (FISH) unamplified, encompassing a large and heterogeneous subgroup that may confer benefit from novel HER2 directed therapies. Circulating tumor DNA (ctDNA) has emerged as a minimally invasive technique to detect cancer-specific gene aberrations. Genetic alterations in ctDNA of HER2-low MBC have not been well described, and we hypothesized that HER2-low MBC may have a distinct genomic profile, beyond standard histopathologic features. Methods: This retrospective cohort study included patients with MBC treated at Washington University in St. Louis, Northwestern University (Chicago, IL) and Massachusetts General Hospital (Boston, MA) who had undergone ctDNA analysis during the course of treatment using the commercially available Guardant360® assay. HER2 expression was evaluated by IHC/FISH according to ASCO/CAP guidelines on metastatic tissue biopsies (or primary breast tumor tissue if a metastatic site biopsy was not available). Tumors were classified as HER2-low (IHC 1+ or 2+/FISH negative), HER2-0 (IHC 0) or HER2-positive (IHC 3+ or IHC 2+/FISH amplified). Clinicopathologic characteristics and ctDNA genetic alterations for HER2-low MBC were described and compared with the HER2-0 and HER2-positive subgroups. Chi-square and Fisher’s exact tests were used for categorical variables. Logistical regression was performed for multivariable analyses. Results: A total of 991 patients with MBC were analyzed, including 160 (16.1%) HER2-positive, 351 (35.4%) HER2-0, and 480 (48.4%) HER2-low MBC. The majority (89.2%) of HER2-low MBC were estrogen-receptor positive (ER+). Compared with HER2-0 MBC, HER2-low MBC had a significantly higher incidence of PIK3CA mutations (OR 1.54, p=0.027). PDGFRA and MYC amplifications were also more common among HER2-low MBC (2.3% vs 0.28% and 8.1% vs 4.6%, respectively), although not significantly associated with this subtype in multivariable analysis. Within the ER+ MBC cohort, those with HER2-low also had higher rates of PIK3CA mutations (OR 1.66, p=0.012) and MYC amplification (OR 2.29, p=0.034), as compared to HER2-0. Compared with HER2-positive, HER2-low MBC had significantly lower rates of ERBB2 alterations (OR 0.26, p=0.0076 for ERBB2 mutations and OR 0.022, p&lt;0.001 for ERBB2 amplification). ESR1, AKT1, and RB1 mutations were more common in HER2-low compared with HER2-positive MBC (14.0% vs 6.9%; 3.1% vs none; 3.1% vs none, respectively), but were not significant in multivariable analysis. Conclusions: Among patients with ER+ MBC, HER-low had a higher incidence of PIK3CA mutations and MYC amplification compared to HER2-0 MBC, and both of these alterations have been implicated as mechanisms of endocrine resistance. We did not demonstrate a high incidence of ERBB2 alterations in patients with HER2-low MBC. To our knowledge, this is the first study to describe genetic alterations detected by ctDNA in patients with HER2-low MBC. Given the emergence of novel HER2-targeted antibody drug conjugates with clinical activity in HER2-low MBC, these findings may guide combination treatment strategies and patient selection for future studies. Further studies are needed to confirm whether HER2-low MBC represents a truly unique biologic subtype.

Citation Format: Whitney L Hensing, Lorenzo Gerratana, Katherine Clifton, Marko Velimirovic, Ami Shah, Paolo D'Amico, Carolina Reduzzi, Qiang Zhang, Charles S Dai, Nusayba A Bagegni, Mateusz Opyrchal, Foluso O Ademuyiwa, Bose Ron, Amir Behdad, Cynthia X Ma, Aditya Bardia, Massimo Cristofanilli, Andrew A Davis. Genetic alterations detected by circulating tumor DNA (ctDNA) in HER2-low metastatic breast cancer (MBC) [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-01-01.

Abstract P2-01-08: Esr1 Y537 mutations are associated with increased baseline circulating tumor cells enumeration for patients with estrogen receptor positive metastatic breast cancer

Introduction: Estrogen Receptor (ER)-positive breast cancer is the most frequent breast cancer subtype. Endocrine therapy (ET) targeting the ER pathway including CDK4/6 inhibitors represents the main initial therapeutic approach. However, clinical resistance associated with progression of disease caused by ESR1 mutations is a recognized an important mechanism of ET resistance. ESR1 mutations, most often detected from liquid biopsies, have been consistently associated with a worse outcome and are being currently evaluated as a potential biomarker to guide therapeutic decisions. Here we reported a new finding on the association between ESR1 amino acid Y537 mutations in ctDNA and circulating tumor cells (CTC) in metastatic breast cancer (MBC). Methods: The study included 158 ER positive MBC patients enrolled under an IRB-approved trial (NU16B06) at Lurie Cancer Center, Northwestern University. The patients received systemic treatments in 2016-2020. Whole blood samples (7.5ml/each) were collected in EDTA tubes from patients who were longitudinally characterized for CTCs before therapy (baseline). CTCs enumeration were performed in FDA approved CELLTRACKS ANALYZERII® System (Menarini) by using CXC Kit contains antibodies targeting 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. The CTCs were classified based on morphology and correct phenotype as CK+, DAPI+ and CD45-. Plasma ctDNA was isolated using a Qiagen circulating nucleic acid kit, and then was analyzed using the Guardant360 next-generation sequencing (NGS)-based assay. In this study, only patients with ESR1 mutations were included for statistical analyses of correlation between the hotspot mutation with the endocrine therapy resistance by using Causal Inference approach. All statistical analyses were conducted Mann-Whitney U test by IBM SPSS version 23.0. Results: ESR1 mutations were detected in 40 out of 158 patients at baseline. ESR1 Y537(N/C/S) mutations were detected in 13 patients, among which there were 9 patients who only had the Y537(N/C/S) mutations and no other ESR1 hotspot mutations (Group 1) and there were 4 patients who had polyclonal ESR1 mutations. In the latter cohort, there were 17 ESR1 amino acid mutations detected in 31 patients (Group 2) including Q314, T347T, N359I, K362N, E380Q, V392I, G442R, F461I, S463P, S464, I487M, K520K, M528V, L536H, D538G, D545D and Q565. There were no any ESR1 mutations detected in the other 118 patients (Group 3). The CTC&gt;5/7.5mL (Stage IV aggressive) were found in 66.7%, 38.7% and 29.3% patients in Group 1, Group 2 and Group 3 respectively. The median total CTCs was 26.0/7.5mL in MBC patients with ESR1 Y537(N/C/S) mutations (Group 1). The median of total CTCs was 2.0/7.5mL in the MBC patients with polyclonal ESR1 mutations but not on Y537 (N/C/S) (Group 2), and it was 1.0/7.5mL in the group of metastatic breast cancer without ESR1 mutations (Group 3). The median total CTCs in Group 1 was significantly higher than Group 2 (Mann-Whitney U, P&lt;0.05) and Group 3 (P=0.009), which indicated that Y537(N/C/S) mutations were correlated with higher baseline CTCs. Conclusions: In this study, we demonstrated a correlation between presence of ESR1 Y537 mutations and increased CTCs (higher Stage IV aggressive cases) in patients with HR+ MBC, These preliminary data may suggest a critical role of ESR1 Y537 mutations in the metastatic process, also indicating that different ESR1 amino acids mutations may play different roles on disease progress. Larger validation studies are needed to confirm that evaluation of ESR1 Y537 variant together with CTCs numeration is an accurate tool to identify endocrine-refractory disease.

Citation Format: Qiang Zhang, Jianhua Jiao, Paolo D'Amico, Andrew A. Davis, Weijun Qin, Lorenzo Gerratana, Saya L. Jacob, Youbin Zhang, Jeannine Donahue, Wenan Qiang, Ami N. Shah, Lisa Flaum, William Gradishar, Leonidas C. Platanias, Massimo Cristofanilli. Esr1 Y537 mutations are associated with increased baseline circulating tumor cells enumeration for patients with estrogen receptor positive metastatic breast cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-01-08.

Abstract P2-02-06: Her2-low ctcs in breast cancer: Pipeline for phenotypic driven, single-cell collection and molecular analysis

Background The presence of circulating tumor cells (CTCs) expressing HER2 at low score (HER2-low) in the peripheral blood of metastatic breast cancer (MBC) patients has been associated with resistance to treatment and more aggressive metastatic behavior. However, the biological intrinsic nature of HER2-low CTCs remains unexplored. Considering the technical challenges beyond the selective collection of immunophenotype-specific CTCs, we developed a pipeline to individually capture HER2-low CTCs to perform single-cell molecular analysis. Methods 4 different breast cancer cell lines (MDA-MB-231, T47D, MDA-MB-453, SKBR3), that are known to express HER2 at different immunohistochemistry scores (respectively classified as 0, 1+, 2+, 3+), were spiked (around 500 cells each) in healthy donor blood tubes (7.5 ml). Samples were subsequently enriched through the CellSearch™ (Menarini Silicon Biosystems, Bologna, Italy), HER2 stained using the CellSearch CTC Kit and analyzed with the ACCEPT tool (Zeune et al., 2017). Enriched cells were additionally characterized by the DEPArray NxT™ Cell Browser and subsequently collected in pooled and single cells. The HER2 signal-intensity scores (fluorescein isothiocyanate, FITC mean), detected by both tools in each cell line, was compared using the nonparametric Mann-Whitney U test. The optimal cut-offs to distinguish HER2 1+ from HER2 0 and HER2 2+ cells were calculated performing Receiving Operator Curves (ROC). Results Detected mean intensities retrieved from CellSearch™ and analyzed with the ACCEPT tool were respectively 0.34 (MDA-MB-231, 0), 1.44 (T47D, 1+), 15.28 (MDA-MB-453, 2+) 166 (SKBR3, 3+), resulting in the possibility to discriminate both 2+ and 3+ cells from 1+ and 0 (P &lt; 0.00001). No statistical significance has been observed between 1+ and 0 (P=0.19). Conversely, HER2 signal-intensity scores detected with the Cell Browser were: 3.69 (0), 4.38 (1+), 6.28 (2+) and 42.82 (3+). These results allow DEPArray Nxt to efficiently differentiate each single cell line, in particular HER2 1+ cells from both 0 and 2+ (P &lt; 0.00001), enabling the collection of these specific cells. The area under the ROC was 0.7 and 0.72 (respectively 0 vs 1+ and 1+ vs 2+) and the optimal calculated cut-offs were 3.23 (lower) and 4.61 (higher). Conclusions HER2-low CTCs can be detected and separately collected using predetermined intensity cut-offs. Downstream single-cell or pooled collection can be subsequently performed. Further molecular characterizations, as DNA genome sequencing, could highlight the underlying altered pathways responsible for resistance to treatment and molecular patterns accountable for worse prognosis.

Citation Format: Paolo D'Amico, Carolina Reduzzi, Wenan Qiang, Qiang Zhang, Lorenzo Gerratana, Ami N Shah, Andrew A Davis, Anthony Kang, Meilynn Shi, Youbin Zhang, Saya Jacob, Amir Behdad, Giuseppe Curigliano, Massimo Cristofanilli. Her2-low ctcs in breast cancer: Pipeline for phenotypic driven, single-cell collection and molecular analysis [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-02-06.

Positive predictive value of ERBB2 copy number gain by tissue or circulating tumor DNA next-generation sequencing across advanced cancers

BACKGROUND

The correlation of ERBB2 copy number gain (CNG) from tissue or circulating tumor DNA (ctDNA) by next-generation sequencing (NGS) with standard HER2 tissue evaluation is not well understood.

MATERIALS AND METHODS

We retrospectively identified patients with ERBB2 CNG on commercial NGS. We described their clinical-pathologic features and calculated the positive predictive value (PPV) of ERBB2 CNG by NGS for HER2-positivity by IHC and FISH testing.

RESULTS

176 patients had NGS revealing an ERBB2 CNG (112 by tumor tissue and 91 by ctDNA). The cancer subtypes with the most cases with ERBB2 CNG by NGS were breast (n = 67), non-small cell lung (n = 25), colorectal (n = 18), gastroesophageal (n = 17), pancreatic (n = 11), and uterine (n = 11). The PPV of ERBB2 CNG in determining HER2 positivity by standard IHC/FISH definitions was 88% for tissue NGS (n = 57) and 80% for ctDNA (n = 47). The PPV among breast cancer patients for tissue NGS was 97% (n = 35) and ctDNA was 93% (n = 39). However, for non-breast cancer cases, the PPV of ERBB2 amplification by tissue NGS dropped to 76% (n = 22) and by ctDNA to 44% (n = 7).

CONCLUSIONS

ERBB2 CNG by NGS is detected in numerous malignancies for which HER2 testing is not standard. Detection of ERBB2 CNG by tissue NGS and ctDNA has a high PPV for true HER2-positivity by standard IHC and/or FISH testing in breast cancer.

Single-Cells Isolation and Molecular Analysis: Focus on HER2-Low CTCs in Metastatic Breast Cancer

Simple Summary

While the concept of HER2-low expression is gaining momentum in the scientific landscape of breast cancer research, HER2-low circulating tumor cells (CTCs) also have promising relevance as biomarkers. Unveiling the biological features behind this recently highlighted evidence on CTCs might achieve both goals of speeding up the interpretation of the general understanding of HER2-low expressing breast cancer and declaring their independent biological and predictive value. If, on the one hand, studying CTCs allows to drill down more easily to a single cell resolution, on the other hand, CTC collection still remains a challenging procedure. In order to improve and standardize this process, we developed a structured pipeline for HER2-low CTC detection and collection. We defined and validated the optimal thresholds to select this specific subtype of CTCs using breast cancer cell lines of known HER2 expression. Our study represents the technical and procedural milestone that will allow a standardized collection process for future molecular investigations.

Abstract

Although the detection of CTCs expressing HER2 at low intensity (HER2-low CTCs) has been shown to have a negative prognostic value in metastatic breast cancer (MBC) patients, the biological intrinsic nature of HER2-low CTCs remains unexplored. Considering the technical challenges behind the selective collection of immunophenotype-specific CTCs, we developed a pipeline to individually capture HER2-low CTCs. Four different breast cancer cell lines (MDA-MB-231, T47D, MDA-MB-453, and SKBR3), that are known to express HER2 at different immunohistochemistry levels (respectively classified as 0, 1+, 2+, and 3+), were spiked in healthy donor blood tubes (7.5 mL) and processed with the CellSearch^® (Menarini Silicon Biosystems, Bologna, Italy) for enrichment and the DEPArray NxT^™ for single cell selection. The HER2 signal-intensities of each cell line was compared using the nonparametric Mann–Whitney U test. The optimal cut-offs to distinguish HER2 1+ from 0 and 2+ cells were calculated performing the Receiver operating characteristic (ROC) curve. Median HER2 signal-intensities detected with the DEPArray NxT^™ were: 2.59 (0), 3.58 (1+), 5.23 (2+) and 38.37 (3+). DEPArray NxT efficiently differentiated each single cell line (p < 0.001). The area under the ROC curve was 0.69 and 0.70 (respectively 0 vs. 1+ and 1+ vs. 2+) and the optimal calculated cut-offs were 2.85 (lower) and 4.64 (upper). HER2-low CTCs can be detected and separately collected using predetermined intensity cut-offs. This study will allow standardized single-cell or pooled collection of HER2-low CTCs for downstream molecular analyses.

Commercial ctDNA Assays for Minimal Residual Disease Detection of Solid Tumors

The detection of circulating tumor DNA via liquid biopsy has become an important diagnostic test for patients with cancer. While certain commercial liquid biopsy platforms designed to detect circulating tumor DNA have been approved to guide clinical decisions in advanced solid tumors, the clinical utility of these assays for detecting minimal residual disease after curative-intent treatment of nonmetastatic disease is currently limited. Predicting disease response and relapse has considerable potential for increasing the effective implementation of neoadjuvant and adjuvant therapies. As a result, many companies are rapidly investing in the development of liquid biopsy platforms to detect circulating tumor DNA in the minimal residual disease setting. In this review, we discuss the development and clinical implementation of commercial liquid biopsy platforms for circulating tumor DNA minimal residual disease detection of solid tumors. Here, we aim to highlight the technological features that enable highly sensitive detection of tumor-derived genomic alterations, the factors that differentiate these commercial platforms, and the ongoing trials that seek to increase clinical implementation of liquid biopsies using circulating tumor DNA-based minimal residual disease detection.

Cell-free DNA comparative analysis of the genomic landscape of first-line hormone receptor-positive metastatic breast cancer from the US and China

PURPOSE

Meaningful comparison of mutational landscapes across ethnic groups requires the use of standardized platform technology. We have used a harmonized NGS-based liquid biopsy assay to explore the differential genomic landscape of patients with initially hormone receptor-positive (HR+), HER2-negative MBC of first line metastasis or primary Stage IV at diagnosis from the United States (US) and China (CN).

METHODS

Plasma circulating tumor DNA (ctDNA) from 27 US patients and 65 CN patients was sequenced using the harmonized CLIA-certified, 152-gene PredicineCare™ liquid biopsy assay. Kaplan-Meier survival analysis was performed to analyze the correlation between genomic alterations and progression-free survival (PFS), and p-values were calculated using the log-rank test.

RESULTS

All patients in the CN cohort received chemotherapy and/or hormonal therapy, while 85.2% (23/27) patients in the US cohort received hormonal therapy plus CDK4/6 inhibitors. Mutations were detected in 23 of 27 (85%) US patients and 54 of 65 (83%) CN patients. The prevalence of AKT1 (P = 0.008) and CDH1 (P = 0.021) alterations were both higher in the US vs. CN cohort. In addition, FGFR1 amplification were more frequent in the CN vs. US cohort (P = 0.048). PTEN deletions (P = 0.03) and ESR1 alterations (P = 0.02) were associated with shorter PFS in the CN cohort, neither of these associations were observed in the US cohort. Interestingly, a reduced association between PTEN deletion and PFS was observed in patients receiving CDK4/6 inhibitor treatment.

CONCLUSION

The differential prevalence of ctDNA-based alterations such as FGFR1, AKT1, and CDH1 was observed in initially HR+/HER2- MBC patients in the US vs. CN. In addition, the association of PTEN deletions with shorter PFS was found in the CN but not the US cohort. The differential genomic landscapes across the two ethnic groups may reflect biologic differences and clinical implications.

ICAM1 initiates CTC cluster formation and trans-endothelial migration in lung metastasis of breast cancer

Circulating tumor cell (CTC) clusters mediate metastasis at a higher efficiency and are associated with lower overall survival in breast cancer compared to single cells. Combining single-cell RNA sequencing and protein analyses, here we report the profiles of primary tumor cells and lung metastases of triple-negative breast cancer (TNBC). ICAM1 expression increases by 200-fold in the lung metastases of three TNBC patient-derived xenografts (PDXs). Depletion of ICAM1 abrogates lung colonization of TNBC cells by inhibiting homotypic tumor cell-tumor cell cluster formation. Machine learning-based algorithms and mutagenesis analyses identify ICAM1 regions responsible for homophilic ICAM1-ICAM1 interactions, thereby directing homotypic tumor cell clustering, as well as heterotypic tumor-endothelial adhesion for trans-endothelial migration. Moreover, ICAM1 promotes metastasis by activating cellular pathways related to cell cycle and stemness. Finally, blocking ICAM1 interactions significantly inhibits CTC cluster formation, tumor cell transendothelial migration, and lung metastasis. Therefore, ICAM1 can serve as a novel therapeutic target for metastasis initiation of TNBC.

Circulating tumor cell (CTC) clusters are more efficient at mediating metastasis as compared to single cells and are associated with poor prognosis in breast cancer. Here, the authors show that ICAM1 is enriched in CTC clusters and its loss suppresses cell-cell interaction and CTC cluster formation, and propose ICAM1 as a therapeutic target for treating breast cancer metastasis.

Longitudinal Dynamics of Circulating Tumor Cells and Circulating Tumor DNA for Treatment Monitoring in Metastatic Breast Cancer

Liquid biopsy-based biomarkers, including circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA), are increasingly important for the characterization of metastatic breast cancer (MBC). The aim of the study was to explore CTCs and ctDNA dynamics to better understand their potentially complementary role in describing MBC.

METHODS

The study retrospectively analyzed 107 patients with MBC characterized with paired CTCs and ctDNA assessments and a second prospective cohort, which enrolled 48 patients with MBC. CTCs were immunomagnetically isolated and ctDNA was quantified and then characterized through next-generation sequencing in the retrospective cohort and droplet digital polymerase chain reaction in the prospective cohort. Matched pairs variations at baseline, at evaluation one (EV1), and at progression were tested through the Wilcoxon test. The prognostic role of ctDNA parameters was also investigated.

RESULTS

Mutant allele frequency (MAF) had a significant decrease between baseline and EV1 and a significant increase between EV1 and progression. Number of detected alterations steadily increased across timepoints, CTCs enumeration (nCTCs) significantly increased only between EV1 and progression. MAF dynamics across the main altered genes was then investigated. Plasma DNA yield did not vary across timepoints both in the retrospective cohort and in the prospective cohort, while the short fragments fraction showed a potential role as a prognostic biomarker.

CONCLUSION

nCTCs and ctDNA provide complementary information about prognosis and treatment benefit. Although nCTCs appeared to assess tumor biology rather than tumor burden, MAF may be a promising biomarker for the dynamic assessment of treatment response and resistance.

Correlation between different levels of HER2 expression in circulating tumor cells (cHER2 ratio) and metastatic behavior in stageIVaggressive breast cancer

3036

Background: The presence of HER2 expressing (HER2+) circulating tumor cells (CTCs) occurs often in metastatic breast cancer (MBC) patients (pts). We have previously showed that the ratio among CTCs expressing high level of HER2 and the total number of HER2+ CTCs (circulating HER2 ratio, cHer2 ratio) has a prognostic role in MBC patients. Here we further investigate the role of the cHER2 ratio in the process of metastatic spread. Methods: Under IRB-approved study we prospectively analyzed blood samples of patients with MBC enrolled before starting a new line of therapy. Samples were collected from pts treated at Northwestern University (Chicago, IL) between 2016 and 2020. CTCs were enumerated through CellSearch (Menarini Silicon Biosystems, Bologna, Italy) and characterized for HER2 expression using the CellSearch CXC Kit. HER2+ CTCs were divided in 3 different categories (1+,2+,3+) leaning on fluorescence intensity. Pts with <5 CTCs (stage IV indolent) were excluded from the analysis. The cHER2 ratio, defined as the sum of 2+ CTCs and 3+ CTCs divided by the total number of HER2+ CTCs, was used to split the remaining pts in 2 different cohorts: cHER2 ratio high (> 0.75) (cHER2high) and cHER2 ratio low (≤0.75) (cHER2low). The frequency of each metastatic site (i.e. liver, lung, central nervous system, bone, lymph nodes, skin/soft tissue, serosa) and the total number of different sites involved (1-7, ≤2 and >2 sites) were compared among the two sub-populations and analyzed through Fisher exact test. Results: Out of 98 pts enrolled, 77 were classified as cHER2low and 21 as cHER2high. We observed a higher frequency of oligometastatic pts (≤2 sites involved) in the cHER2high cohort (16, 76%), compared to only 29 (37%) in the cHER2low (p<0.005). Moreover, the cHER2 ratio was associated with a tropism toward specific sites of disease spread with higher incidence of liver, lung and lymph nodes metastases in the cHER2low cohort (p<0.05). No other statistical associations were observed in respect of specific organ tropism. The frequency of involvement for each metastatic site among the two cohorts are reported in the table. Conclusions: Measuring CTCs enumeration and HER2 expression we identified two cohorts, cHER2high and cHER2low, associated with distinct patterns of metastatic spread. The cHER2low pts were correlated to multiple sites of metastatic involvement, with particular tropism toward liver, lung and lymph nodes. These results confirm the prognostic role of the cHER2 ratio, suggesting a peculiar biological meaning of the HER2+ 1+ CTCs.[Table: see text]

Landscape of GATA3 mutations identified from circulating tumor DNA clinical testing and their impact on disease outcomes in estrogen receptor-positive (ER+) metastatic breast cancers treated with endocrine therapies

1065

Background: The GATA3 gene encodes for a transcription factor (TF) that plays a pivotal role in the development of breast tissue. Breast tumors with lower GATA3 expression have worse prognosis compared to tumors with higher expression. However, the consequences of somatic GATA3 mutations ( GATA3mut) on clinical outcomes in metastatic breast cancer (MBC) remain poorly understood. Further, GATA3 TF interferes with FOXA1 and ER to enhance transcription of ER-responsive genes, but the role of GATA3mut in altering downstream transcriptional activity and its effects on response to anti-estrogens remains unclear. Methods: We retrospectively identified ctDNA next-generation sequencing results from 101 ER+/HER2- patients with MBC treated with either selective estrogen receptor degraders (SERDs) alone or a combination of SERDs and CDK4/6 inhibitors at Massachusetts General Hospital (Boston, MA) and Northwestern University (Chicago, IL). Associations between GATA3mut, patient and tumor characteristics, and prior treatments were assessed using logistic regression. Clinical outcomes were estimated through Cox proportional hazards regression. Results: GATA3mut were observed in 13 patients (13%), each with a single GATA3 variant. These mutations were detected in exon 4 (M294K), exon 5 that includes Zn-finger-2 motif (T327fs, R331fs, N334K, D336fs, c.925-3_925-2del splice acceptor variant), and exon 6 (K358fs, P409fs, M416fs, G431fs, M439fs, V440fs). All mutations except for M294K were insertion/deletion frameshift mutations that result in either elongation or truncation of the protein, potentially with heterogenous downstream effects. GATA3mut were the only detectable alteration in 4 patients. The most commonly co-occurring mutations with GATA3mut were ESR1mut in 7/13 (53.8%) and PIK3CAmut in 6/13 (46%) patients. Presence of GATA3mut was associated with prior exposure to chemotherapy (OR = 1.09, 95%CI [1.01 - 1.10], p = 0.03). Patients with GATA3mut tumors had shorter PFS compared to GATA3wild tumors (4.1 vs. 6.7 months, in both univariate and multivariate analysis controlled for presence of ESR1mut: HR = 2.22 95%CI [1.12 – 4.38], p = 0.02). OS was also significantly shorter in patients harboring GATA3mut compared to GATA3wild (14.1 vs. 27.1 months, multivariate analysis: HR = 2.30 95%CI [1.04 – 5.11], p = 0.04). Conclusions: GATA3mut in breast cancer tend to be grouped within exons 5 and 6, and they likely contribute to acquired resistance to endocrine-based therapies in MBC. Our study showed that patients with GATA3mut ER+ MBC have worse prognosis compared to those who were GATA3wild. Larger studies are needed to further stratify and ascertain functional effects of different GATA3 mutations and explore GATA3 gene or its translational product as a possible druggable target.

Uncovering the differential impact of ESR1 and PIK3CA codon variants on the clinical phenotype of metastatic breast cancer (MBC) through circulating tumor DNA (ctDNA) next-generation sequencing (NGS)

1033

Background: The exposure to endocrine therapy (ET) can induce the onset of ESR1 gene alterations that have an impact on not only treatment resistance but also clinical phenotype. We previously demonstrated the potential of liquid biopsy in describing the metastatic behavior of MBC. The aim of this study was to explore the different clinical phenotype across the main ESR1 and PIK3CA codon variants. Methods: The study retrospectively analyzed a cohort of 501 MBC patients (pts) characterized for ctDNA through NGS before treatment start at Northwestern University (Chicago, IL), Massachusetts General Hospital (Boston, MA), CRO National Cancer Institute (Aviano, IT) and ASUFC Hospital (Udine, IT) between 2014 and 2020. Associations between clinical characteristics and ESR1 and PIK3CA codon variants were explored through logistic regression corrected for sites and ESR1/ PIK3CA status. Survival was tested through Cox regression both for progression-free survival (PFS) and overall survival (OS). Results: Of the total 501 pts, 289 (58%) were diagnosed with hormone-receptor positive (HRpos) MBC, 114 (23%) with HER2-positive MBC, and 93 (19%) with triple-negative MBC. ESR1 mutations were detected in 71 pts (14%) and PIK3CA in 154 pts (31%). The most represented ESR1 gene mutations were found in codons 380 (9%), 536 (23%), 537 (34%), and 538 (34%), while alterations in codons 542 (19%), 545 (21%), and 1047 (60%) were the most common for PIK3CA. As expected, ESR1 mutations were found only in HRpos pts previously exposed to ET (P < 0.001). No significant differences were observed for PIK3CA. After multivariable analysis, ESR1mutations were confirmed as highly associated with liver and bone metastases (OR 3.31, P < 0.001 and OR 5.09, P < 0.001). Moreover, an association with lung (OR 2.07, P = 0.010) was observed in this cohort. After multivariable analysis, codon 537 mutations were associated with bone involvement (OR 12.97, P = 0.014), codon 538 with liver (OR 4.73, P = 0.010), and codon 536 with soft tissue (OR 5.84, P = 0.006) and liver (OR 4.06, P = 0.048). PIK3CA mutations were associated with bone (OR 2.61, P < 0.001) and lung metastases (OR 1.62, P = 0.044). Specifically, codon 1047 mutations were the primary driver (OR 3.14, P = 0.001 and OR 1.97, P = 0.019). In HRpos MBC, baseline mutations in ESR1 codon 537 and 538 had a negative impact on OS (HR 3.73, P < 0.010 and HR 2.99, P < 0.021), while 380 and 536 had a negative impact on PFS (HR 18.98, P < 0.001 and HR 2.60, P = 0.015). No impact was observed across PIK3CA gene variants. Conclusions: This study showed the different tumor biology across ESR1 and PIK3CA gene variants. As novel selective estrogen receptor degraders (SERDS) and PIK3CA inhibitors are gaining momentum as new ET options in MBC, these results highlight the future pivotal role of ctDNA NGS in refining tumor biology characterization.

Circulating tumor DNA (ctDNA) as a tool to help guide germline testing in patients with solid malignancies

10602

Background: As the use of circulating tumor DNA (ctDNA) is more widely implemented, incidental identification of pathogenic variants reflecting germline alterations in cancer predisposition genes will occur more frequently. Such mutations are expected to have a high mutant allele frequency (MAF) or occur in genes typically associated with inherited syndromes. When a similar analysis was conducted by our group, we found that MAF of about 30% or greater in BRCA1/ 2 was associated with confirmed putative germline mutations in patients with breast cancer (Jacob et al & Davis et al, SABCS 2020). In this study, we extended this analysis to non-breast malignancies. Methods: Patients with non-breast solid malignancies and ctDNA testing between 2015-2020 were retrospectively identified from Northwestern Medicine. All ctDNA was analyzed using Guardant 360 (Guardant Health, Inc. Redwood City, Ca). Patients with ctDNA samples with mutations at high MAF (>30%) and those with BRCA1/2 mutations at any MAF were identified. We reviewed these charts for referral to genetic counselors and/or CLIA-approved germline testing. Descriptive analysis was reported for these findings. Genetic alterations were classified as pathogenic or of unknown significance based on OncoKB (Chakravarty et al, JCO PO 2017). Results: We identified ctDNA samples of 548 patients with non-breast solid malignancies, of whom 56 had gene mutations occurring at high MAF (>30%). Predominant cancer subtypes were lung (48%), colorectal (21%), pancreatic (7%), ovarian (3.5%), prostate (3.5%), and gastroesophageal (3.5%). The most common gene mutations identified were TP53 (46%), BRCA1/2 (18%), EGFR (18%), APC (13%), and KRAS (9%). 87.5% were pathogenic and 12.5% were of unknown significance. 11 patients (19.6%) had germline testing of whom 6 tested positive. These germline mutations were in BRCA2 (n = 3), EGFR, APC, and TP53. In addition to the 10 patients with BRCA1/2 mutations at high MAF (>30%), we identified 70 patients with BRCA1/2 mutations at low MAF ( < 30%). 54% were pathogenic and 46% were of unknown significance. 11 patients (14%) had germline testing of whom 3 tested positive for BRCA2, all at high MAF. 1 patient with a BRCA2 mutation at low MAF of 1.4% tested positive for a different germline BRCA2 variant. Conclusions: In patients with advanced cancers, ctDNA analysis can reveal variants with MAF >30% that are reflective of a germline mutation. Unfortunately the rate of genetic testing in these patients was low (20%). Future studies with germline testing in patients with high MAF variants would help understand the prevalence of germline variants. This can facilitate developing a more standardized approach for genetic counselor referral to identify families that may benefit from interventions for early detection or prevention of future cancers.

The Establishment of New Thresholds for PLND-Validated Clinical Nomograms to Predict Non-Regional Lymph Node Metastases: Using 68Ga-PSMA PET/CT as References

Purpose

PLND (pelvic lymph node dissection)-validated nomograms are widely accepted clinical tools to determine the necessity of PLND by predicting the metastasis of lymph nodes (LNMs) in pelvic region. However, these nomograms are in lacking of a threshold to predict the metastasis of extrareolar lymph nodes beyond pelvic region, which is not suitable for PLND. The aim of this study is to evaluate a threshold can be set for current clinical PLND-validated nomograms to predict extrareolar LN metastases beyond pelvic region in high-risk prostate cancer patients, by using ⁶⁸Ga-PSMA PET/CT as a reference to determine LN metastases (LNMs).

Experimental Design

We performed a retrospective analysis of 57 high-risk treatment-naïve PC patients in a large tertiary care hospital in China who underwent ⁶⁸Ga-PSMA-617 PET/CT imaging. LNMs was detected by ⁶⁸Ga-PSMA-617 PET/CT and further determined by imaging follow-up after anti-androgen therapy. The pattern of LN metastatic spread of PC patients were evaluated and analyzed. The impact of ⁶⁸Ga-PSMA PET/CT on clinical decisions based on three clinical PLND-validated nomograms (Briganti, Memorial Sloan Kettering Cancer Center, Winter) were evaluated by a multidisciplinary prostate cancer therapy team. The diagnostic performance and the threshold of these nomograms in predicting extrareolar LNMs metastasis were evaluated via receiver operating characteristic (ROC) curve analysis.

Results

LNMs were observed in 49.1% of the patients by ⁶⁸Ga-PSMA PET/CT, among which 65.5% of LNMs were pelvic-regional and 34.5% of LNMs were observed in extrareolar sites (52.1% of these were located above the diaphragm). The Briganti, MSKCC and Winter nomograms showed that 70.2%-71.9% of the patients in this study need to receive ePLND according to the EAU and NCCN guidelines. The LN staging information obtained from ⁶⁸Ga-PSMA PET/CT would have led to changes of planned management in 70.2% of these patients, including therapy modality changes in 21.1% of the patients, which were mainly due to newly detected non-regional LNMs. The thresholds of nomograms to predict non-regional LNMs were between 64% and 75%. The PC patients with a score >64% in Briganti nomogram, a score >75% in MSKCC nomogram and a score >67% in Winter nomogram were more likely to have non-regional LNMs. The AUCs (Area under curves) of the clinical nomograms (Briganti, MSKCC and Winter) in predicting non-regional LNMs were 0.816, 0.830 and 0.793, respectively.

Conclusions

By using ⁶⁸Ga-PSMA PET/CT as reference of LNM, the PLND-validated clinical nomograms can not only predict regional LNMs, but also predict non-regional LNMs. The additional information from ⁶⁸Ga-PSMA PET/CT may provide added benefit to nomograms-based clinical decision-making in more than two-thirds of patients for reducing unnecessary PLND. We focused on that a threshold can be set for current clinical PLND-validated nomograms to predict extrareolar LN metastases with an AUC accuracy of about 80% after optimizing the simple nomograms which may help to improve the efficiency for PC therapy significantly in clinical practice.

Abstract PS2-26: Evaluating the pathogenicity of emerging genomic aberrations detected by circulating tumor DNA over the course of metastatic breast cancer

Introduction: Previously reported data from our group and others have demonstrated an increase in genomic complexity and number of alterations over the course of treatment in MBC. Our study aims to categorize the pathogenicity of genomic aberrations found on serial ctDNA evaluations in MBC to explore the relevance of emerging mutations. Methods: Patients with MBC and ctDNA next-generation sequencing (NGS) analysis by Guardant360 (Guardant Health, Redwood City, CA) completed from 2015 to 2019 were retrospectively identified with an IRB-approved protocol. Clinical-pathologic features and time point for progression of disease were abstracted from review of the electronic medical record. Among the 255 patients with ctDNA analysis, 85 patients had serial ctDNA analysis from baseline and at subsequent progression of disease (PD1) and 27 had repeat ctDNA analysis at next progression (PD2). Genomic alterations were classified as oncogenic, likely oncogenic, predictive oncogenic, likely benign, inconclusive, unknown significance, and synonymous based on categorization by OncoKB.org (Chakravarty et al, JCO PO 2017). Oncogenic, likely oncogenic, and predicted oncogenic were considered ‘pathogenic’ while the remainder were ‘not known pathogenic’. Two-sample t-tests for difference of means (α = 0.05) was used for analysis of changes in pathogenic proportions and mutant allele frequencies (MAF). Results: The median age was 53.8 years, 41 patients had hormone receptor positive (HR+) HER2-negative, 22 had HER2+, and 22 had triple negative (TN) MBC. The median and interquartile range (IQR) of the time of MBC diagnosis to first ctDNA collection was 10 mo (0.3-23.1 mo), from baseline ctDNA to analysis at the time of disease progression (PD1) was 6.7 mo (3.6-12.5 mo), and from PD1 to second progression (PD2) was 4.6 mo (3.1-8.5 mo). At baseline 66% of alterations were pathogenic (38.4% oncogenic, 27.6% likely oncogenic, 26.5% unknown significance). The proportion of pathogenic variants did not significantly change over time: 62% at PD1 (p=0.41) and 56% at PD2 (p=0.19). The percent of pathogenic alterations by disease subtype at baseline and PD1 was 66% and 60% in HR+ HER2-, 73% and 57% in HER2+, and 62% and 71% in TN. 57% and 70% of patients had a new pathogenic alteration at PD1 and PD2, respectively. The most frequently detected new pathogenic alterations at the time of disease progression were TP53, PIK3CA, ESR1, FGFR1, and MYC, which occurred in 28%, 18%, 15%, 12%, and 11% of patients, respectively. Among genes that were altered in at least 10% of patients, the aberrations were very likely to be pathogenic (&gt;75% of alterations pathogenic) for TP53, PIK3CA, ESR1, MYC, BRAF, FGFR1, often pathogenic (50-75% of alterations pathogenic) for NF1, KIT, GATA3, ERBB2, EGFR, CCNE1, PDGFRA, and often not known pathogenic (&lt;50% of alterations pathogenic) for MET, AR, ARID1A, and BRCA2. When comparing the mean MAF of pathogenic and not known pathogenic alterations, paired by gene, the MAF was not significantly different for pathogenic alterations except for GATA3 (p=0.03). Conclusion: The continued emergence of pathogenic mutations at times of progression without a corresponding increase in the proportion of pathogenic variants suggests that new pathogenic mutations may arise as a result of increased tumor genomic instability over time, although these findings require confirmation in larger datasets. The large proportion of patients who present with new pathogenic variants at disease progression supports the utility of ctDNA to track tumor evolution. Additionally, this study highlights the importance of considering the pathogenicity of genomic alterations, as over one-third of aberrations in MBC were not known to be pathogenic.

Citation Format: Ami N Shah, Andrew A Davis, Saya Jacob, Lorenzo Gerratana, Brian Finkelman, Shruti Chandra, Neelima Katam, Firas Wehbe, Jeeven Srivastava, Ashwin Sunderraj, Qiang Zhang, Leonidas Platanias, Amir Behdad, William Gradishar, Massimo Cristofanilli. Evaluating the pathogenicity of emerging genomic aberrations detected by circulating tumor DNA over the course of 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 PS2-26.

Abstract PS2-08: Identification of incidental putative germline variants in circulating tumor DNA

Background: Circulating tumor DNA (ctDNA) has emerged as a potential tool for detecting disease recurrence, monitoring response to therapy, and identifying resistance mutations in the peripheral blood. With increased frequency of testing, there is an unmet need to recognize putative germline variants in ctDNA, and the probability that these variants are associated with inherited conditions. Here, we evaluated a large cohort of breast cancer patients who underwent ctDNA evaluation to determine the type and frequency of ctDNA mutations identified with confirmed germline testing.

Methods: We reviewed ctDNA testing from a single institution (Northwestern University). All breast cancer patients who had next-generation sequencing (NGS) performed by Guardant Health (Redwood City, CA) from 2015-2020 were included in this retrospective study. An allele frequency cutoff of 30% was pre-established as a threshold to review patient charts to determine whether genetic counseling and germline testing were performed, along with the timeframe of this testing (e.g. before or after ctDNA evaluation). Clinical information including demographics, pathology, tissue NGS testing, and germline testing were collected. Descriptive analyses and statistical associations were performed using STATA.

Results: The initial cohort consisted of 520 patients with breast cancer who underwent ctDNA testing. From this, we identified 84 patients (16.2%) who had at least one variant with allele frequency ≥30%. The most common variants identified were the following: TP53 (34%), PIK3CA (27%), BRCA1 (9%), BRCA2 (8%), and AKT1 (4%). Guardant360 classified 99% of these variants as pathogenic and 1% as a variant of unknown significance. Germline positivity using a separate CLIA-approved test for this indication was confirmed at the following frequencies: BRCA1 (2 of 8 positive, 25%), BRCA2 (2 of 5 positive, 40%), PIK3CA (0 of 5 positive), and TP53 (0 of 26 positive). In total, 14% of patients with ctDNA allele frequency ≥30% had a confirmed germline mutation. Lower age at breast cancer diagnosis was significantly associated with the probability of germline testing prior to ctDNA evaluation (P=0.0001). For patients who had a variant with allele frequency ≥30%, 24.3% never received genetic counseling or germline testing.

Conclusion: High allele frequency ctDNA variants (≥30%) were present in 16% of patients who underwent ctDNA evaluation with 14% of these variants confirmed as true germline variants. Consenting patients for ctDNA testing should include the possibility of identifying putative germline variants, and criteria should be established to refer patients for subsequent genetic counseling and germline testing, given the potential implications for patients and their family members.

Citation Format: Andrew A Davis, Michael C Burns, Lorenzo Gerratana, Paolo D'Amico, Saya Jacob, Ami Shah, Neelima Katam, Firas Wehbe, Qiang Zhang, Elena Vagia, Lisa Flaum, Kalliopi P. Siziopikou, Leonidas C Platanias, Amir Behdad, William J Gradishar, Massimo Cristofanilli. Identification of incidental putative germline variants in circulating tumor DNA [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 PS2-08.