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 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.

A phase II study of palbociclib plus letrozole plus trastuzumab as neoadjuvant treatment for clinical stages II and III ER+ HER2+ breast cancer (PALTAN)

Patients with ER+/HER2+ breast cancer (BC) are less likely to achieve pathological complete response (pCR) after chemotherapy with dual HER2 blockade than ER-/HER2+ BC. Endocrine therapy plus trastuzumab is effective in advanced ER+/HER2+ BC. Inhibition of CDK4/6 and HER2 results in synergistic cell proliferation reduction. We combined palbociclib, letrozole, and trastuzumab (PLT) as a chemotherapy-sparing regimen. We evaluated neoadjuvant PLT in early ER+/HER2+ BC. Primary endpoint was pCR after 16 weeks. Research biopsies were performed for whole exome and RNA sequencing, PAM50 subtyping, and Ki67 assessment for complete cell cycle arrest (CCCA: Ki67 ≤ 2.7%). After 26 patients, accrual stopped due to futility. pCR (residual cancer burden-RCB 0) was 7.7%, RCB 0/I was 38.5%. Grade (G) 3/4 treatment-emergent adverse events occurred in 19. Among these, G3/4 neutropenia was 50%, hypertension 26.9%, and leucopenia 7.7%. Analysis indicated CCCA in 85% at C1 day 15 (C1D15), compared to 27% at surgery after palbociclib was discontinued. Baseline PAM50 subtyping identified 31.2% HER2-E, 43.8% Luminal B, and 25% Luminal A. 161 genes were differentially expressed comparing C1D15 to baseline. MKI67, TK1, CCNB1, AURKB, and PLK1 were among the genes downregulated, consistent with CCCA at C1D15. Molecular Signatures Database gene-sets analyses demonstrated downregulated processes involved in proliferation, ER and mTORC1 signaling, and DNA damage repair at C1D15, consistent with the study drug's mechanisms of action. Neoadjuvant PLT showed a pCR of 7.7% and an RCB 0/I rate of 38.5%. RNA sequencing and Ki67 data indicated potent anti-proliferative effects of study treatments. ClinicalTrials.gov- NCT02907918.

Loneliness, social isolation, and social support in older adults with active cancer during the COVID-19 pandemic

Introduction

The COVID-19 pandemic has had a considerable impact on mental health. The social distancing and stay-at-home orders have likely also impacted loneliness, social isolation, and social support. Older adults, particularly those with comorbidities such as cancer, have a greater potential to be impacted. Here we assessed loneliness, social isolation, and social support in older adults undergoing active cancer treatment during the pandemic.

Materials and methods

A mixed methods study in which quantitative data and qualitative response items were collected in parallel was conducted in 100 older adults with cancer. Participants completed a survey by telephone with a series of validated questionnaires to assess the domains of loneliness, social isolation, and social support as well as several open-ended questions. Baseline demographics and geriatric assessments were summarized using descriptive statistics. Bivariate associations between social isolation and loneliness and social support and loneliness were described using Spearman correlation coefficients. Conventional content analysis was performed on the open-ended questions.

Results

In a population of older adults with cancer, 3% were noted to be severely lonely, although 27% percent screened positive as having at least one indicator of loneliness by the University of California, Los Angeles (UCLA) Three Item Loneliness Scale. There was a significant positive correlation between loneliness and social isolation (r = +0.52, p < 0.05) as well as significant negative correlation between loneliness and social support (r = −0.49, p < 0.05). There was also a significant negative correlation between loneliness and emotional support (r = −0.43, p < 0.05). There was no significant association between loneliness and markers of geriatric impairments, including comorbidities, G8 score or cognition.

Discussion

Reassuringly, in this cohort we found relatively low rates of loneliness and social isolation and high rates of social support. Consistent with prior studies, loneliness, social isolation, and social support were found to be interrelated domains; however, they were not significantly associated with markers of geriatric impairments. Future studies are needed to study if cancer diagnosis and treatment may mediate changes in loneliness, social isolation, and social support in the context of the pandemic as well as beyond.

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.

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 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 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 P2-13-01: Phase 2 study of neoadjuvant palbociclib, letrozole, and trastuzumab in patients with ER+ HER2+ breast cancer (PALTAN)

Background Patients (pts) with ER+ HER2+ breast cancer (BC) are less likely to achieve pathological complete response (pCR) after neoadjuvant chemotherapy with dual HER2 blockade than pts with ER- HER2+ BC. Endocrine therapy (ET) plus trastuzumab is effective in advanced ER+ HER2+ BC, but pCR rate is low in the neoadjuvant setting. Inhibition of CDK4/6 and HER2 results in synergistic reduction in cell proliferation in preclinical studies. We therefore combined ET with CDK4/6 inhibition and trastuzumab in ER+ HER2+ BC as a chemotherapy-sparing regimen. Methods We evaluated the efficacy of palbociclib, letrozole, trastuzumab (PLT) in the neoadjuvant setting for pts with stages II or III ER+ HER2+ BC. Primary endpoint was pCR after 16 weeks of therapy. We assumed null of 15% pCR and pCR ≥ 30% warrants further investigation. To achieve 80% power at 1-sided 0.05 significance, 48 pts were to be enrolled. Evaluable population included pts who completed Cycle (C) 1 unless discontinued due to treatment-emergent adverse events (TEAEs) prior to completing C1. All who received one dose on study were considered evaluable for toxicity. Biopsies were collected at baseline (BL), C1 day 15 (C1D15), and surgery for RNA sequencing and central Ki67 assessment, for PAM50 subtype distribution, complete cell cycle arrest (CCCA: Ki67 ≤2.7%) at C1D15 and surgery, and treatment induced signaling changes. Results Accrual stopped early due to futility. 26 pts accrued were evaluable for efficacy and toxicity. pCR (residual cancer burden- [RCB] 0) was 7.7% (95% CI 0.9 - 25.1%) and RCB 0/I was 38.5% (95% CI 20.2 - 59.4%). TEAEs (n= 337) were seen in all pts (71.5% grade [G] 1, 19.3% G2, 8.6% G3, 0.6% G4); the most common were leukopenia (7.7%), neutropenia (7.1%), anemia (5.9%). G3/4 TEAEs occurred in 19 pts (73.1%). Among the 19, incidence of G3/4 neutropenia was 50%, hypertension 26.9%, leucopenia 7.7%. TEAEs (hypertension, ventricular tachycardia, pulmonary edema) leading to treatment discontinuation were reported in 1 pt. Two pts had at least one SAE. No treatment-related deaths occurred. Pt reported outcomes using NCI PRO-CTCAE revealed no differences in appetite, nausea, respiratory symptoms, edema, palpitations, rashes and dry skin, or concentration from BL to end of C4. Pts had worsening hair loss from BL to end of C4. Ki67 analysis indicated CCCA in 78% at C1D15, compared to 18% at surgery after only P had been discontinued approximately 4 weeks prior to surgery. RNA sequencing was performed on available biopsies collected at BL (N=16), C1D15 (N=5), and surgery (N=2) from 16 pts. Among 16 BL samples, PAM50 subtyping identified 5 (31.3%) basal-like, 2 (12.5%) HER2-E, 6 (37.5%) Lum B, and 3 (18.8%) normal. Subtype switching to Lum A at C1D15 (N=3, 1 each with HER2-E, Lum B, and normal at BL) or normal (N=2, 1 basal and 1 HER2-E at BL) was observed. 161 genes were differentially expressed (FDR p&lt;0.05); 145 downregulated and 16 upregulated comparing C1D15 to BL. MKI67, TK1, CCNB1, AURKB, PLK1 were among the downregulated genes, consistent with CCCA for majority of the samples at C1D15 by Ki67. Analysis of the Molecular Signatures Database Hallmark gene-sets comparing C1D15 and BL samples demonstrated downregulated biological processes involved in proliferation (E2F targets, G2M checkpoint, MYC targets, mitotic spindle), signaling (Estrogen response, mTORC1 signaling), and DNA damage (DNA repair) at C1D15, consistent with the mechanisms of action of the study drugs. E2F targets were higher in BL samples of RCB II/III, compared to RCB I (FDR p=0.042). Conclusions PALTAN did not meet its primary endpoint of pCR. Neoadjuvant PLT showed a pCR of 7.7% but was well tolerated. RNA sequencing and Ki67 data indicated potent anti-proliferative effects of study treatments, despite significant heterogeneity of intrinsic subtypes. Clinical trial information: NCT02907918.

Citation Format: Foluso O Ademuyiwa, Donald Northfelt, Tracey O'Connor, Ellis Levine, Jingqin Luo, Yu Tao, Jeremy Hoog, Marie Laury, Tracy Summa, Trish Hammerschmidt, Zhanfang Guo, Ashley Frith, Katherine Weilbaecher, Mateusz Opyrchal, Rebecca Aft, Katherine Clifton, Rama Suresh, Nusayba Bagegni, Ian S Hagemann, Cynthia X Ma. Phase 2 study of neoadjuvant palbociclib, letrozole, and trastuzumab in patients with ER+ HER2+ breast cancer (PALTAN) [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 P2-13-01.

NCCN Guidelines® Insights: Older Adult Oncology, Version 1.2021

The NCCN Guidelines for Older Adult Oncology address specific issues related to the management of cancer in older adults, including screening and comprehensive geriatric assessment (CGA), assessing the risks and benefits of treatment, preventing or decreasing complications from therapy, and managing patients deemed to be at high risk for treatment-related toxicity. CGA is a multidisciplinary, in-depth evaluation that assesses the objective health of the older adult while evaluating multiple domains, which may affect cancer prognosis and treatment choices. These NCCN Guidelines Insights focus on recent updates to the NCCN Guidelines providing specific practical framework for the use of CGA when evaluating older adults with cancer.

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.

Mutation profile differences in younger and older patients with advanced breast cancer using circulating tumor DNA (ctDNA)

PURPOSE

Little is known regarding the mutation profiles of ctDNA in the older adult breast cancer population. The objective of this study is to assess differences in mutation profiles in the older adult breast cancer population using a ctDNA assay as well as assess utilization of testing results.

METHODS

Patients with advanced breast cancer underwent molecular profiling using a plasma-based ctDNA NGS assay (Guardant360) between 5/2015 and 10/2019 at Siteman Cancer Center. The profiling results of a multi-institutional database of patients with advanced breast cancer who had undergone molecular profiling were obtained. Associations between mutations and age group (≥ 65 vs. < 65) were examined using a Fisher's exact test.

RESULTS

In the single-institutional cohort, 148 patients (69.2%) were < 65 years old and 66 patients (30.8%) ≥ 65 years old. ATM, BRAF, and PIK3CA mutations were found more frequently in older patients with ER + HER2- breast cancers (p < 0.01). In the multi-institutional cohort, 5367 (61.1%) were < 65 years old and 3417 (38.9%) ≥ 65 years old. ATM, PIK3CA, and TP53 mutations were more common in the older cohort (p < 0.0001) and MYC and GATA3 mutations were less common in the older cohort (p < 0.0001). CtDNA testing influenced next-line treatment management in 40 (19.8%) patients in the single-institutional cohort.

CONCLUSION

When controlling for subtype, results from a single institution were similar to the multi-institutional cohort showing that ATM and PIK3CA were more common in older adults. These data suggest there may be additional molecular differences in older adults with advanced breast cancers.

Mutation profile differences in younger and older patients with advanced breast cancer using circulating tumor DNA (ctDNA)

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Background: Although the noninvasive nature of ctDNA testing is attractive in an older adult population, less is known regarding the mutation profiles of ctDNA in the older adult breast cancer population as this population is often excluded from studies. Previous tissue testing has shown differences in mutation profiles between older and younger adults with breast cancer. The objective of this study is to assess differences in mutation profiles in the older and younger adult breast cancer population using a ctDNA assay. Methods: Patients (pts) with advanced breast cancer underwent molecular profiling using a plasma-based ctDNA NGS assay (Guardant360) between 5/2015-10/2019 at Siteman Cancer Center. Clinicopathological histories were obtained from the medical record. The results of a multicenter database of pts with advanced breast cancer who had undergone molecular profiling using Guardant360 were obtained. Associations between mutations and age were measured using a Fisher’s exact test. Results: In the single institution cohort, of the 214 patients who underwent testing, 148 (69.16%) were < 65 and 66 (30.84%) ≥ 65 years-old. The most frequently mutated genes in age < 65 pts were TP53 (48.65%), PIK3CA (35.81%), and ESR1 (30.41%) while the most frequently mutated genes in age≥65 pts were PIK3CA (56.06%), TP53 (51.52%), ESR1 (25.76%), and ATM (21.21%). ATM, BRAF and PIK3CA mutations were found more frequently in age≥ 65 pts with ER+ HER2- breast tumors (p < 0.01). MYC and ESR1 mutations were not significantly associated with age, overall or within subtype. Overall ctDNA resulted in change in management in 19.8% pts (40/202). In the larger multicenter cohort, of the 8803 pts who underwent testing, 5367 (61.0%) were < 65 and 3417 (38.8%) ≥ 65 years-old. ATM, ESR1 and PIK3CA mutations were more common in age≥65 pts (p < 0.0001) and MYC mutations were less common in age≥65 pts (p < 0.0001). Conclusions: This study found that ctDNA is a feasible, attractive alternative to traditional biopsies and may identify actionable mutations in older adults with breast cancer. When controlling for subtype, results from a single institution were similar to the larger multicenter cohort showing ATM and PIK3CA were more common in the older adult population. This data suggests there may be additional molecular differences between breast cancer in older compared to younger adults that warrants further investigation.

Identification of Actionable Fusions as an Anti-EGFR Resistance Mechanism Using a Circulating Tumor DNA Assay

PURPOSE

Gene fusions are established oncogenic drivers and emerging therapeutic targets in advanced colorectal cancer. This study aimed to detail the frequencies and clinicopathological features of gene fusions in colorectal cancer using a circulating tumor DNA assay.

METHODS

Circulating tumor DNA samples in patients with advanced colorectal cancer were analyzed at 4,581 unique time points using a validated plasma-based multigene assay that includes assessment of fusions in FGFR2, FGFR3, RET, ALK, NTRK1, and ROS1. Associations between fusions and clinicopathological features were measured using Fisher's exact test. Relative frequencies of genomic alterations were compared between fusion-present and fusion-absent cases using an unpaired t test.

RESULTS

Forty-four unique fusions were identified in 40 (1.1%) of the 3,808 patients with circulating tumor DNA detected: RET (n = 6; 36% of all fusions detected), FGFR3 (n = 2; 27%), ALK (n = 10, 23%), NTRK1 (n = 3; 7%), ROS1 (n = 2; 5%), and FGFR2 (n = 1; 2%). Relative to nonfusion variants detected, fusions were more likely to be subclonal (odds ratio, 8.2; 95% CI, 2.94 to 23.00; P < .001). Mutations associated with a previously reported anti-epidermal growth factor receptor (anti-EGFR) therapy resistance signature (subclonal RAS and EGFR mutations) were found with fusions in FGFR3 (10 of 12 patients), RET (nine of 16 patients), and ALK (seven of 10 patients). For the 27 patients with available clinical histories, 21 (78%) had EGFR monoclonal antibody treatment before fusion detection.

CONCLUSION

Diverse and potentially actionable fusions can be detected using a circulating tumor DNA assay in patients with advanced colorectal cancer. Distribution of coexisting subclonal mutations in EGFR, KRAS, and NRAS in a subset of the patients with fusion-present colorectal cancer suggests that these fusions may arise as a novel mechanism of resistance to anti-EGFR therapies in patients with metastatic colorectal cancer.

Association between gene fusions and anti-EGFR resistance signature in colorectal cancer

3564

Background: Acquired resistance to anti-EGFR therapy in metastatic colorectal cancer (mCRC) has been characterized by a circulating tumor DNA (ctDNA) signature including any sub-clonal RAS mutation, co-existing RAS mutations, or co-existing EGFR mutations. Here, we investigated if fusions in ctDNA are associated with this anti-EGFR signature for CRC patients (pts). Methods: 4289 advanced stage CRC pts underwent molecular profiling using a plasma-based NGS assay that included FGFR2, FGFR3, RET, ALK, NTRK1, and ROS1 fusions. Available clinical histories were reviewed. Correlations between fusions and clinicopathological features were measured with a Fischer exact test. Relative frequencies of genomic alterations were compared between fusion-present vs -absent cases with an unpaired t-test. Clonality for a given alteration was called for a relative variant allele frequency (rVAF) > 50 %, while subclonal was defined as < 50% rVAF. Results: 44 unique fusions were detected in 40 (1.1%) of the 3808 pts with alterations present: RET (N = 16), FGFR3 (N = 12), ALK (N = 10), NTRK1 (N = 3), ROS1 (N = 2), and FGFR2 (N = 1). Relative to non-fusion variants detected, fusions were more likely to be subclonal (OR 8.2, p < 0.0001). Mutations associated with a previously reported anti-EGFR resistance were found in FGFR3 (7/12 pts), RET (7/15 pts) and ALK (5/10 pts). In fusion-present cases, co-existing RAS mutations were more likely to be subclonal than non-fusion cases (OR 14, p < 0.0001). EGFR mutations were more common in fusion present cases (OR 3.7, p = 0.0001) and predominantly subclonal (97%). EGFR mutations aggregated to ectodomain sites (85%) previously linked to acquired anti-EGFR resistance. For 27 pts with available clinical histories, 21 (78%) received anti-EGFR treatment prior to ctDNA testing. Conclusions: Actionable fusions using a ctDNA NGS assay were predominantly subclonal and co-existed with subclonal RAS and EGFR mutations. These clinicopathologic features are consistent with a previously validated signature linked to resistance to anti-EGFR therapies in CRC. We hypothesize that fusions may arise as a previously undescribed mechanism of acquired resistance to anti-EGFR therapies in CRC pts.

Progression-free survival (PFS) and toxicities of palbociclib in a geriatric population

PURPOSE

Over 40% of newly diagnosed metastatic breast cancer patients are ≥ 70 years old; however, this population is less likely to be represented in clinical trials. The objective of this study was to analyze PFS, dose reductions, dose delays, and toxicity in a geriatric population receiving palbociclib in a non-trial setting.

METHODS

Patients with metastatic breast cancer receiving palbociclib in any line of therapy were identified from a cohort of 845 patients at a large academic institution. Dose delays, dose reductions, and toxicities were retrospectively extracted from the medical record. Data were analyzed using Fischer's exact test for categorized variables and T test/Wilcoxon rank-sum test for continuous variables. PFS and OS were analyzed using the Kaplan-Meier method.

RESULTS

605 patients who met eligibility criteria were included. 160 patients were ≥ 65 years old and 92 patients were ≥ 70 years old. Patients ≥ 70 had a significantly increased number of dose reductions (p = 0.03) and dose delays (p = 0.02) compared to the younger patients. There was no significant increase in toxicities, including neutropenic fever, infections, or hospitalizations, in the ≥ 70 cohort (p = 0.3). The ≥ 70 cohort had a significantly improved PFS as compared to the younger cohort (p = 0.02); however, age was no longer a significant variable in the multivariate analysis.

CONCLUSIONS

Palbociclib was well tolerated in the geriatric population and there was no difference in PFS between older and younger patients. These results are reassuring as palbociclib becomes the frontline standard of care therapy for patients.

Prognostic Factors in Patients with Metastatic Breast Cancer with Bone-Only Metastases

This article describes the association between pain attributable to bone metastasis and location, as well as number and type of bone metastases at time of bone metastasis diagnosis in metastatic breast cancer patients with bone‐only metastases. The resulting outcomes analysis should allow for earlier interventions or identification for clinical trial involvement.

Background.

Patients with metastatic breast cancer with bone‐only metastases (BOM) are a unique patient population without consensus regarding high‐risk characteristics, which we sought to establish.

Methods.

We identified 1,445 patients with BOM followed for at least 6 months at MD Anderson Cancer Center from January 1, 1997, to December 31, 2015.

Results.

Seventy‐one percent (n = 936) of the 1,325 patients with BOM with available pain characterization were symptomatic at time of BOM diagnosis. Pain was more common in patients with lytic compared with blastic or sclerotic metastases (odds ratio [OR], 1.79; 95% confidence interval [CI,] 1.26–2.53) and multiple versus single bone metastases (OR, 1.37; 95% CI, 1.03–1.83). Poorer overall survival (OS) was also noted in patients with multiple bone metastases (median OS, 4.80 years; 95% CI, 4.49–5.07) compared with single bone metastasis (median OS, 7.54 years; 95% CI, 6.28–10.10) and in patients with metastases in both the axial and appendicular skeleton (median OS, 4.58 years; 95% CI, 4.23–4.96) compared with appendicular‐only (median OS, 6.78 years; 95% CI, 5.26–7.96) or axial‐only metastases (median OS, 5.62 years; 95% CI, 4.81–6.69). Black/non‐Hispanic patients had poorer outcomes, and patients aged 40–49 years at time of breast cancer diagnosis had significantly better OS compared with both younger and older patient groups.

Conclusion.

Overall, several risk features for decreased OS were identified, including multiple bone metastases and both axial and appendicular skeleton involvement. Multiple bone metastases and lytic bone metastases were associated with increased pain.

Implications for Practice.

Patients with metastatic breast cancer and bone‐only metastases (BOM) represent a poorly characterized patient subset. The ability to identify unique patient characteristics at time of BOM diagnosis associated with increased morbidity or mortality would allow for recognition of patients who would benefit from more aggressive therapy. In this study, the largest sample of patients with BOM thus far reported is characterized, highlighting several higher‐risk BOM groups, including those with multiple bone metastases and bone metastases in both the axial and appendicular skeleton at time of BOM diagnosis. In addition to tailoring current practices for these high‐risk patients, ongoing studies of these patients are indicated.

Breast cancer phenotype in patients with hereditary gene mutations other than BRCA1 and BRCA2

e13121

Background: Use of multi-gene panel (MGP) testing for hereditary breast cancer (BC) has increased significantly. Unlike in case of TNBC diagnosed before age 60 and ordering BRCA testing; for MGP testing, healthcare providers depend on personal and/or family history of cancer as tumor phenotype and on patient characteristics for non-BRCA hereditary BC genes which are not well described. Therefore, we planned to evaluate tumor phenotype of BCs associated with hereditary gene mutations other than BRCA 1 and BRCA2. Methods: Consecutive patients with invasive BC who are in a prospective cohort study and who underwent MGP testing based on published criteria as clinically indicated were included in the study. All patients’ breast pathology slides were reviewed by breast pathologists at our institution. For statistical analysis: Patients’ demographic and clinical characteristics were summarized using descriptive statistics such as frequency distribution, mean (± s.d.) and median (range). SAS version 9.4 and S-Plus version 8.04 were used to carry out the computations for all analyses. Institutional IRB approval was obtained. Results: Between 2013 and 2017, 1607 patients underwent MGP testing and 347 were found to be positive for a pathogenic variant. For the study purposes we included only patients with invasive breast cancer (N = 146). Median age was 45.1 yrs (Range: 25-78). Genetics testing results were as follows: BRCA1: 38 (26%), BRCA2: 37 (25%), CHEK2 15 (10%), PALB2: 12 (8%) , ATM: 12 (8%), TP53: 9 (6%), CDH1 : 5 (3%), PTEN: 3 (2%), BRIP1: 3 (2%), and 12 patients (8%) positive for other genes (CDKN2A, MUTYH, PMS2, APC, BARD1, MLH1, NBN, RAD51C, and SDHD). Tumor phenotype by gene mutation in shown in table 1. Conclusions: Several hereditary BC genes are associated with ER positive BC which could have implications for chemoprevention, while others associated with ER neg/TNBC that could have therapeutic implications. These findings and implications need to be further studied in larger cohorts. [Table: see text]

Adjuvant or neoadjuvant chemotherapy in early stage triple negative breast cancer (TNBC) comparison of outcomes in both BRCA positive and BRCA negative patients

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Background: NSABP Protocol B-18 was a randomized trial which found no statistically significant difference in overall survival (OS) in patients (pts) receiving neoadjuvant (NAC) or adjuvant chemotherapy (AC), however outcome was not analyzed by breast cancer subtypes. Subsequent retrospective studies in TNBC reported conflicting results with an initial study showing a significant OS benefit with AC and later studies showing a trend toward improved survival with NAC. Furthermore, studies have not included a significant number of pts with BRCA mutations. This study aims to analyze outcomes of AC versus NAC in pts with early stage TNBC with and without BRCA germline mutations. Methods: Pts with stage I or II TNBC who had BRCA testing were identified from a prospective cohort study of 4027 pts at MD Anderson Cancer Center. Clinical, demographic, genetic test results, chemotherapy, recurrence, survival data were collected. OS and disease free survival (DFS) were estimated using the Kaplan-Meier method, and log-rank tests were used to compare groups. Results: 305 pts with stage I and II TNBC who met eligibility criteria were included in the analysis. Pts who received both NAC and AC or no chemotherapy were excluded. 181 received AC (59.3%) and 124 received NAC (40.7%). The majority of the pts were less than 50 years old (236, 77.4%) and white (194, 63.8%). 134 were BRCA positive (44.1%) and 170 were BRCA negative (55.9%). The majority of the pts received an anthracycline and taxane regimen (223, 73.1%). There was no significant association between OS or DFS and treatment with NAC versus AC in the overall cohort. Furthermore, there were no significant differences between pt subgroups (NAC BRCA positive, NAC BRCA negative, AC BRCA positive, and AC BRCA negative) with respect to either OS or DFS. Conclusions: NAC versus AC with standard anthracycline and taxane containing regimens results in similar DFS and OS survival amongst pts with stage I and II TNBC regardless of BRCA status. Further studies are needed to evaluate whether similar results are observed with newer agents, such as platinums, PARP inhibitors and other targeted agents.

Characterization of bone only metastasis (BOM) patients (pts) with respect to tumor subtypes (TS)

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Background: Metastatic breast cancer (MBC) pts with BOM are a unique population with limited characterization. Our goal was to characterize the TS of BOM pts, evaluating differences in sites and types of bone metastases (BM), treatment, and survival. Methods: We identified pts followed at MD Anderson Cancer Center from 01/01/1997 to 12/31/2015 for at least 6 months with a BOM diagnosis as first site of metastasis (met). TS was assessed by initial biopsy immunohistochemistry (IHC) (Table 1) with hormone receptor (HR) + defined as ER or PR >10%. Results: We identified 1445 pts with BOM, 1049 with initial biopsy IHC available to group into TS (Table 1). Among BOM pts, the majority had multiple BM at diagnosis (1141/79%), most in both the axial (Ax) and appendicular (App) skeleton (53%). Of the 808 pts with BM categorized on imaging at diagnosis, the majority were lytic (389/48%), with 21% sclerotic, 18% mixed, and 12% blastic. Time from breast cancer diagnosis to first met differed significantly by TS, χ2(3) = 94.33, P< .0001, with median time to met longer for pts with blastic (3.08 years; 95% CI 2.03, 4.24) versus lytic lesions (1.75 years; 95% CI 1.27, 2.17). Conclusions: BOM patients are a unique MBC subpopulation, more commonly found in luminal TS patients. Our study demonstrates prognostic differences in BOM pts specific to TS and emphasizes the need for further study of BOM patients. [Table: see text]