Thymidine kinase activity levels in serum can identify HR+ metastatic breast cancer patients with a low risk of early progression (SWOG S0226)

BACKGROUND

Some patients with metastatic breast cancer (MBC) stay on endocrine therapy (ET) for years and others progress quickly. Serum thymidine kinase activity (TKa), an indicator of cell-proliferation, is a potential biomarker for monitoring ET and predicting MBC outcome. We have previously reported TKa as being prognostic in MBC in SWOG S0226. Here, new data on progression within 30/60 days post sampling, with a new, FDA approved version of DiviTum®TKa highlighting differences vs. a Research Use Only version is reported.

METHODS

1,546 serum samples from 454 patients were assessed, collected at baseline and at 4 subsequent timepoints during treatment. A new predefined cut-off tested the ability to predict disease progression. A new measuring unit, DuA (DiviTum® unit of Activity) is adopted.

RESULTS

A DiviTum®TKa score <250 DuA provides a much lower risk of progression within 30/60 days after blood draw, the negative predictive value (NPV) was 96.7% and 93.5%, respectively. Patients <250 DuA experienced significantly longer progression-free survival and overall survival, demonstrated at baseline and for all time intervals.

CONCLUSIONS

DiviTum®TKa provides clinically meaningful information for patients with HR+ MBC. Low TKa levels provide such a high NPV for rapid progression that such patients might forego additional therapy added to single agent ET.Trial registration: NCT00075764.

Abstract P4-02-04: Serial monitoring of circulating tumor cells and circulating tumor DNA in metastatic lobular breast cancer identifies intra-tumor heterogeneity and precision and immuno-oncology biomarkers of therapeutic importance

Clinical decisions on precision and immuno-oncology therapies are based on predictive biomarkers commonly obtained from a single metastatic biopsy or archived primary tumor tissue. Circulating genomic biomarkers offer a minimally invasive approach to monitor intra-patient tumor heterogeneity and detect in real-time the clinically-relevant evolving clonal architecture. Although currently underutilized, we hypothesize that single-cell DNA next generation sequencing (scNGS) of circulating tumor cells (CTC) is a particularly well-suited method to complement biomarker information obtained from tissue and cell-free circulating tumor DNA (ctDNA). In this study we analyzed 113 individual CTC, 21 ctDNA, and 15 white blood cells (WBC) samples, from 15 CTC-positive lobular breast cancer patients, four of whom had CTC available at both metastatic baseline and after progression on a variety of therapies chosen at their physician’s discretion. Clinical NGS data from 15 tumor tissue biopsies obtained using a ~1700-gene DNA panel and whole transcriptome sequencing were available for comparison. CTC were enriched with the CellSearch® system and isolated as single cells with the DEPArray™ system. Whole genome amplified CTC and WBC, as well as ctDNA underwent scNGS with the Oncomine Comprehensive Assay covering ~500 genes and 1.1Mb of genomic space to detect mutations, copy number alterations, tumor mutation burden (TMB) and microsatellite instability (MSI). 99.1% of single cells and 95.2% of ctDNA samples were informative, with a mean sequencing depth of 664x. Using our previously developed, CTC-based precision medicine reporting platform, MI-CTCSeq, CTC in 9 of 15 patients (60%) had mutations that were actionable by FDA-approved targeted therapies including in the oncogenes PIK3CA and FGFR2 and HER2. 3 of these 9 patients (33%) harbored actionable alterations not shared between all 3 analyte types (tissue, CTC and ctDNA). These included 3 actionable mutations found in CTC and ctDNA only, 1 in tissue and ctDNA only, and 1 in ctDNA only. However, 2 of those ctDNA mutations were identified near the limit of detection and with a priori knowledge of their presence from tissue or CTC. Further, 1 patient with plentiful CTC had no detectable ctDNA and one patient’s tissue biopsy was inadequate for sequencing while both liquid biopsy analytes were abundant. 13 patients (87%) displayed intra-patient, inter-CTC genomic heterogeneity of putative driver mutations. 1 of 4 (25%) patients with CTC available in &gt;1 timepoint displayed fluctuations in their CTC subclonal makeup between timepoints. Data from this patient’s 2 tissue biopsies, 3 ctDNA samples, and 27 individual CTC over 4 timepoints combined to reveal in unprecedented detail inter-metastatic lesion and inter-CTC heterogeneity and tumor evolution in response to endocrine and immunotherapy selective pressures. ScNGS of CTC helped provide an additional level of detail not appreciated by sequencing of the other two analyte types. In another patient, CTC were composed of 2 subclones which were indistinguishable by ctDNA, 1 of which appears to have not been sampled by the tissue biopsy. Using a novel method, we enabled detection of single-cell CTC TMB and MSI. CTC TMB scores (dichotomized as above/below 10 mutations/Mb) were 100% concordant with those measured in the corresponding tissue biopsies. Further, in a novel observation, we detected intra patient, inter-CTC heterogeneity of TMB and MSI, which has potential implications for immunotherapy response and development of resistance. Taken together, these data support the non-invasive biomarker interrogation and monitoring by liquid biopsy that incorporates CTC scNGS and complements tissue in informing precision and immuno-oncology approaches. This may have important implications for appropriate treatment selection and identification of therapeutic resistance mechanisms.

Citation Format: Andi Cani, Emily Dolce, Alissa Turnbull, Kevin Hu, Chia-Jen Liu, Elizabeth Darga, Dan Robinson, Yi-Mi Wu, Dafydd G. Thomas, Costanza Paoletti, Scott Tomlins, James Rae, Aaron Udager, Arul Chinnaiyan, Erin F. Cobain, Daniel F. Hayes. Serial monitoring of circulating tumor cells and circulating tumor DNA in metastatic lobular breast cancer identifies intra-tumor heterogeneity and precision and immuno-oncology biomarkers of therapeutic importance [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 P4-02-04.

Abstract OT2-16-05: Safety Analyses of NRG BR004: A Randomized, Double-blind, Phase III Trial of Taxane/Trastuzumab/Pertuzumab with Atezolizumab or Placebo in First-line HER2-Positive Metastatic Breast Cancer (MBC)

Background: The CLEOPATRA trial established trastuzumab, pertuzumab and a taxane (THP) as a standard of care for first line metastatic, HER2-positve breast cancer with median progression-free survival (PFS) of 18.7 months and median OS of 57 months. NRG BR004 was a phase III, placebo-controlled trial designed to determine whether the addition of the PD-L1 inhibitor, atezolizumab, to THP would improve progression-free survival (PFS), relative to THP/placebo in patients with newly documented HER2-positive measurable metastatic breast cancer.

Methods: BR004 was designed to detect an improvement in the primary endpoint of PFS in patients with measurable disease from 16.5 to 22.5 months with addition of atezolizumab (HR 0.733). A sample size of 600 would provide 80% power with a type I error rate of 0.05 to detect such an improvement when 326 PFS events had been reported. Monthly accrual was projected at 30 patients per month with completion of accrual in 24 months. In addition to routine monitoring of safety data by the IDMC every 6 months, a formal analysis of the toxicity data was to be performed 16 weeks after the 100th patient had been randomized with review by the IDMC.

Results: First patient was randomized on May 1, 2019, and after 37 months 190 patients had been randomized. Several amendments were not successful in addressing the low accrual rate. The IDMC began regular monitoring of safety and accrual data in July 2020 and reviewed the formal safety analysis in February 2022. As of the February 2022 IDMC meeting, four Grade 5 adverse events (AEs) had been reported (2 occurring in 2020 and 2 in 2021), one of which occurred in a patient with evolving liver failure due to rapid disease progression at the start of therapy. The recommendation was to continue without modification, but notice was given the Grade 5 AEs had occurred on the same treatment arm without unblinding. When additional Grade 5 AEs occurred on 3/4/2022 and 4/27/2022 both on the same study arm with none reported on the other arm, accrual was held until the IDMC could review updated safety data, narratives of the Grade 5 AEs and the overall context of the trial. There was no evidence of clinically important imbalances between Grade 3 and Grade 4 AEs between the arms., Based on an uncertain but material safety signal, the ongoing accrual challenges, and determination that the clinical question being addressed was no longer sufficiently compelling, the IDMC recommended that the trial should be permanently closed to further enrollment. Summary safety data from 187 treated patients are provided in the Table. A decision was made to discontinue atezolizumab/placebo in patients receiving the investigational component of the trial therapy and unblind investigators and patients. The study will continue to collect information on PFS events, deaths and late immune AEs through April of 2024 when PFS and OS will be analyzed.

Conclusions: The imbalance in Grade 5 AEs which occurred on BR004 coupled with continued poor accrual and the changing landscape in HER2+ MBC resulted in early closure of enrollment and unblinding of patients. Follow-up continues to assess PFS, OS and monitor for delayed immune AEs.

Support: U10CA180868, -189867, -180822; U24CA196067; and Genentech.

Abstract 611: Assessment of tumor mutation burden and microsatellite instability by single-cell circulating tumor cell genomic profiling

The success of immune checkpoint inhibitors rests on biomarkers such as tumor mutation burden (TMB) and microsatellite instability (MSI), both FDA-approved predictors of anti PD-1/L1 therapy benefit. Tissue biopsies often collected once in the metastatic setting through an invasive procedure, or archived primary tumor tissue often collected much prior to treatment consideration, are the specimen types of choice for biomarker identification. The tissue sample originates from a limited region of one disease site, which may limit its usefulness given intra-patient tumor heterogeneity. TMB and MSI measurement by liquid biopsy, including proteins, circulating tumor cells (CTC), and cell-free circulating tumor DNA (ctDNA), is an attractive, minimally-invasive way to obtain a real-time picture of the entire disease. While TMB and MSI assessment from ctDNA have been reported, their measurement can be limited by low ctDNA tumor fraction. Single-cell next generation sequencing of CTC, on the other hand, is a particularly well-suited, but largely unexplored method of measuring TMB and MSI to complement tissue and ctDNA for better overall specificity of detection. In this proof-of-concept study, we show the ability to detect single-cell TMB and MSI. We analyzed 14 CTC and 4 ctDNA samples from 6 metastatic breast cancer patients, as well as 3 single cells and 1 cell pellet sample each from HCT-116 (MSI-High) and WiDr (MSI-Low) cell lines. CTC and cell line cells were enriched with the CellSearch® system and/or isolated with the DEPArray™ system. Whole genome amplified single-cell DNA was sequenced with the Oncomine Comprehensive Assay covering ~500 genes and 1.1Mb of genomic space. TMB and MSI scores obtained in CTC and ctDNA were compared to those measured in matched clinical tissue biopsies. Single-cell TMB scores and MSI status were assessable in all CTC tested. CTC TMB scores were highly concordant with the matched tissue samples (r=1.00), as were ctDNA TMB scores (r=0.98) in patients with assessable TMB scores in both biospecimen types compared. Importantly, TMB was detectable in CTC from one patient whose tissue sample was inadequate for clinical sequencing, and from another patient with inadequate, low tumor fraction ctDNA. Intriguingly, one patient harbored 3 TMB-high and 2 TMB-low CTC, potentially indicating intra-patient TMB heterogeneity. The known MSI-low status from clinical tumor tissue sequencing was correctly detected in CTC and ctDNA from all patients. MSI status and scores from single cells of HCT-116 and WiDr cell lines purified with the DEPArray™ system (mimicking CTC isolation), perfectly matched that of the corresponding cell pellet samples (r=1.00). Taken together, these data suggest the potential validity and continued interrogation of potential utility of CTC TMB and MSI detection to complement tissue and ctDNA in guiding checkpoint inhibitor immunotherapy.

Citation Format: Andi K. Cani, Emily M. Dolce, Chia-Jen Liu, Brittany Rupp, Elizabeth P. Darga, Costanza Paoletti, Dafydd G. Thomas, Yi-Mi Wu, Dan R. Robinson, Sunitha Nagrath, Arul M. Chinnaiyan, Scott A. Tomlins, Aaron M. Udager, John M. Carethers, Erin F. Cobain, Daniel F. Hayes. Assessment of tumor mutation burden and microsatellite instability by single-cell circulating tumor cell genomic profiling [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 611.

Abstract 1700: Serial monitoring of single-cell circulating tumor cell genomics in metastatic lobular breast cancer to identify precision and immuno-oncology biomarkers with therapeutic implications

Clinical decisions for precision and immuno-oncology therapies are based on predictive biomarkers commonly obtained from a single metastatic biopsy, or from archived primary tumor material. Circulating genomic biomarkers present a minimally invasive way to monitor the intra-patient tumor heterogeneity and its fluctuations in order to provide a real-time evaluation of the changing clonal architecture with potential therapeutic implications. Single-cell DNA next generation sequencing (scNGS) of circulating tumor cells (CTC) is a particularly well-suited method of unraveling and monitoring that heterogeneity to complement biomarker information obtained from tissue and cell-free circulating tumor DNA (ctDNA). In this proof-of-concept study we analyzed 123 CTC, 15 white blood cells (WBC), and ctDNA from 15 CTC-positive lobular breast cancer patients, five of whom had CTC available at both metastatic baseline and after progression on a variety of therapies chosen at their physician’s discretion. CTC were enriched with the CellSearch® system and isolated as single cells with the DEPArray™ system. Whole genome amplified CTC DNA underwent scNGS with the Oncomine Comprehensive Assay covering ~500 genes and 1.1Mb of genomic space to detect mutations, copy number alterations, tumor mutation burden (TMB) and microsatellite instability (MSI). 99.1% of cells were informative, with a mean sequencing depth of 664x. Using our previously developed, CTC-based precision medicine reporting platform, MI-CTCSeq, multiple CTC in seven of 15 patients (47%) had mutations that were actionable by FDA-approved targeted therapies including in the oncogenes PIK3CA (alpelisib) and FGFR2 (erdafitinib). 13 patients (87%) displayed intra-patient, inter-CTC genomic heterogeneity of putative driver mutations. Two of five (40%) patients with CTC at both baseline and progression displayed fluctuations in their CTC subclonal makeup between timepoints. One of the two harbored a baseline ESR1 (estrogen receptor α) p.D538G activating mutation that largely disappeared at progression and was replaced by a CTC subclone with a different ESR1 activating mutation, p.Y537S. Intriguingly, this patient’s CTC also harbored an FGFR2 p.K659M mutation in an actionable “hotspot” at progression, which was absent at baseline, suggesting potential utility of serial monitoring by CTC scNGS. TMB scores and MSI status in CTC were highly concordant with those measured in clinical tissue biopsies. Taken together, these data suggest the non-invasive interrogation of the CTC genomic landscape and its serial monitoring to inform precision and immuno-oncology treatments in real time.

Citation Format: Andi K. Cani, Emily M. Dolce, Elizabeth P. Darga, Kevin Hu, Chia-Jen Liu, James M. Rae, Daffyd G. Thomas, Scott A. Tomlins, Arul M. Chinnaiyan, Aaron M. Udager, Costanza Paoletti, Erin F. Cobain, Daniel F. Hayes. Serial monitoring of single-cell circulating tumor cell genomics in metastatic lobular breast cancer to identify precision and immuno-oncology biomarkers with therapeutic implications [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 1700.

Management of early stage HER2 positive breast cancer and increased implementation of axillary imaging to improve identification of nodal metastasis

BACKGROUND AND OBJECTIVES

Given the significant benefit of targeted therapies for HER2+ breast cancer patients in both the neoadjuvant and adjuvant settings, it is critical to identify all eligible patients for these treatments. We sought to investigate cT1cN0 HER2+ patients to determine the rate of postsurgical nodal positivity, and to identify presurgical factors associated with nodal positivity. We hypothesize there is a subset of underdiagnosed HER2+ patients who would benefit from preoperative axillary imaging and inclusion in neoadjuvant chemotherapy regimens.

METHODS

We performed a 10-year retrospective analysis of T1 HER2+ breast cancer patients. Clinicopathologic characteristics were evaluated based on surgical nodal data.

RESULTS

We identified 38 patients with cT1cN0 HER2+ cancer. Of this cohort, 24% had positive lymph nodes on final pathology. High tumor grade (p = 0.035) on core needle biopsy and the presence of lymphovascular invasion (p = 0.0036) were associated with an increased likelihood of lymph node positivity. The majority (66%) of lymph node positive patients were clinically T1c.

CONCLUSIONS

We identified a 24% nodal positivity rate in clinically node negative T1 HER2+ breast cancer patients. In particular, HER2+ patients with high-grade T1c cancers should undergo preoperative diagnostic axillary imaging to expand potential benefit from targeted therapies.

RB expression confers sensitivity to CDK4/6 inhibitor-mediated radiosensitization across breast cancer subtypes

Standard radiation therapy (RT) does not reliably provide locoregional control for women with multinode-positive breast cancer and triple-negative breast cancer (TNBC). We hypothesized that CDK4/6 inhibition (CDK4/6i) would increase the radiosensitivity not only of estrogen receptor–positive (ER⁺) cells, but also of TNBC that expresses retinoblastoma (RB) protein. We found that CDK4/6i radiosensitized RB WT TNBC (n = 4, radiation enhancement ratio [rER]: 1.49–2.22) but failed to radiosensitize RB-null TNBC (n = 3, rER: 0.84–1.00). RB expression predicted response to CDK4/6i + RT (R² = 0.84), and radiosensitization was lost in ER⁺/TNBC cells (rER: 0.88–1.13) after RB1 knockdown in isogenic and nonisogenic models. CDK4/6i suppressed homologous recombination (HR) in RB WT cells but not in RB-null cells or isogenic models of RB1 loss; HR competency was rescued with RB reexpression. Radiosensitization was independent of nonhomologous end joining and the known effects of CDK4/6i on cell cycle arrest. Mechanistically, RB and RAD51 interact in vitro to promote HR repair. CDK4/6i produced RB-dependent radiosensitization in TNBC xenografts but not in isogenic RB1-null xenografts. Our data provide the preclinical rationale for a clinical trial expanding the use of CDK4/6i + RT to difficult-to-control RB-intact breast cancers (including TNBC) and nominate RB status as a predictive biomarker of therapeutic efficacy.

PD-L1 expression on circulating tumor cells and platelets in patients with metastatic breast cancer

Background

Immune checkpoint inhibition is effective in several cancers. Expression of programmed death-ligand 1 (PD-L1) on circulating tumor or immune effector cells could provide insights into selection of patients for immune checkpoint inhibition.

Methods

Whole blood was collected at serial timepoints from metastatic breast cancer patients and healthy donors for circulating tumor cell (CTC) and platelet PD-L1 analysis with a phycoerythrin-labeled anti-human PD-L1 monoclonal antibody (Biolegend clone 29E.2A3) using the CellSearch^® assay. CTC PD-L1 was considered positive if detected on at least 1% of the cells; platelet PD-L1 was considered positive if ≥100 platelets per CellSearch frame expressed PD-L1.

Results

A total of 207 specimens from 124 metastatic breast cancer patients were collected. 52/124 (42%) samples at timepoint-1 (at or close to time of progressive disease) had ≥5 CTC/7.5ml whole blood. Of those, 21 (40%) had positive CTC PD-L1. In addition, platelet PD-L1 expression was observed in 35/124 (28%) at timepoint-1. Platelet PD-L1 was not detected in more than 70 specimens from 12 healthy donors. Platelet PD-L1 was associated with ≥5 CTC/7.5ml whole blood (p = 0.0002), less likely in patients with higher red blood cell counts (OR = 0.72, p<0.001) and a history of smoking tobacco (OR = 0.76, p<0.001). Platelet PD-L1 staining was not associated with tumor marker status, recent procedures or treatments, platelet-affecting drugs, or CTC PD-L1 expression.

Conclusion

PD-L1 expression was found in metastatic breast cancer patients on both CTC and platelets in an independent fashion. Inter-patient platelet PD-L1 expression was highly heterogeneous suggesting that it is a biological event associated with cancer in some but not all patients. Taken together, our data suggest that CTC and platelet PD-L1 expression could play a role in predicting which patients should receive immune checkpoint inhibition and as a pharmacodynamics biomarker during treatment.

Evaluating Serum Thymidine Kinase 1 in Patients with Hormone Receptor-Positive Metastatic Breast Cancer Receiving First-line Endocrine Therapy in the SWOG S0226 Trial

PURPOSE

Serum thymidine kinase 1 (sTK1) activity is associated with poor prognosis in metastatic breast cancer (MBC). We assessed the prognostic effect of sTK1 in patients with hormone receptor-positive MBC treated on a prospective randomized trial of anastrozole (A) versus A plus fulvestrant (A + F).

PATIENTS AND METHODS

sTK1 was assessed in 1,726 serums [baseline (BL), cycles 2, 3, 4, and 7] using the DiviTum assay. A prespecified cutoff of ≥200 Du/L was considered high. Progression-free survival (PFS) and overall survival (OS) were analyzed by Kaplan-Meier, log-rank tests, and Cox regression.

RESULTS

BL sTK1 was elevated in 171 (40%) of 432 patients. Patients with high versus low BL sTK1 had significantly worse PFS [median 11.2 vs. 17.3 months, HR = 1.76; 95% confidence interval (CI; 1.43-2.16); P < 0.0001] and OS [median 30 vs. 58 months, HR = 2.38; 95% CI (1.91-2.98); P < 0.0001]. OS was significantly better for patients with high sTK1 who did not have prior adjuvant tamoxifen and who received A + F versus A alone [median 46 vs. 21 months, HR = 0.58; 95% CI (0.38-0.87); P = 0.0087]. Patients with low sTK1 had no difference in outcomes by therapy (P = 0.44). At serial timepoints, high versus low sTK1 had significantly worse subsequent PFS and OS [at cycle 2: PFS HR = 1.70, 95% CI (1.34-2.17); P < 0.0001, OS HR = 2.51, 95% CI (1.93-3.26); P < 0.0001].

CONCLUSIONS

High sTK1 at BL and subsequent timepoints is associated with worse prognosis in patients with MBC starting first-line endocrine therapy (ET). Patients with low sTK1 at BL have comparable outcomes on single-agent or combination ET.

Assessment of Clinical Benefit of Integrative Genomic Profiling in Advanced Solid Tumors

Question

What is the clinical utility of genomic profiling for patients with advanced solid tumors?

Findings

In this cohort study of 1015 patients who underwent integrative genomic profiling, a high rate of pathogenic germline variants and a subset of patients who derive substantial clinical benefit from sequencing information were identified.

Meaning

These findings support (1) directed germline testing for inherited cancer predisposition in all patients with advanced cancer and (2) use of integrative genomic profiling as a component of standard of care for patients with cancer of unknown origin and other rare malignant neoplasms.

Importance

Use of next-generation sequencing (NGS) to identify clinically actionable genomic targets has been incorporated into routine clinical practice in the management of advanced solid tumors; however, the clinical utility of this testing remains uncertain.

Objective

To determine which patients derived the greatest degree of clinical benefit from NGS profiling.

Design, Setting, and Participants

Patients in this cohort study underwent fresh tumor biopsy and blood sample collection for genomic profiling of paired tumor and normal DNA (whole-exome or targeted-exome capture with analysis of 1700 genes) and tumor transcriptome (RNA) sequencing. Somatic and germline genomic alterations were annotated and classified according to degree of clinical actionability. Results were returned to treating oncologists. Data were collected from May 1, 2011, to February 28, 2018, and analyzed from May 1, 2011, to April 30, 2020.

Main Outcomes and Measures

Patients’ subsequent therapy and treatment response were extracted from the medical record to determine clinical benefit rate from NGS-directed therapy at 6 months and exceptional responses lasting 12 months or longer.

Results

During the study period, NGS was attempted on tumors from 1138 patients and was successful in 1015 (89.2%) (MET1000 cohort) (538 men [53.0%]; mean [SD] age, 57.7 [13.3] years). Potentially clinically actionable genomic alterations were discovered in 817 patients (80.5%). Of these, 132 patients (16.2%) received sequencing-directed therapy, and 49 had clinical benefit (37.1%). Exceptional responses were observed in 26 patients (19.7% of treated patients). Pathogenic germline variants (PGVs) were identified in 160 patients (15.8% of cohort), including 49 PGVs (4.8% of cohort) with therapeutic relevance. For 55 patients with carcinoma of unknown primary origin, NGS identified the primary site in 28 (50.9%), and sequencing-directed therapy in 13 patients resulted in clinical benefit in 7 instances (53.8%), including 5 exceptional responses.

Conclusions and Relevance

The high rate of therapeutically relevant PGVs identified across diverse cancer types supports a recommendation for directed germline testing in all patients with advanced cancer. The high frequency of therapeutically relevant somatic and germline findings in patients with carcinoma of unknown primary origin and other rare cancers supports the use of comprehensive NGS profiling as a component of standard of care for these disease entities.

Abstract OT-29-01: Tenacity: A phase 2, multicenter, open-label, single-arm study of AL101 monotherapy in patients with notch-activated triple negative breast cancer

Background: There is an urgent need to identify new therapeutic strategies for triple-negative breast cancer (TNBC), a sub-type associated with poor prognosis. The Notch pathway is activated during mammary gland development and has been implicated as a key driver in breast cancer (Collu, 2007). The frequency of Notch mutations or gene rearrangements was reported at 5 to 16% in TNBC tumors and over-expression of Notch was associated with worse overall survival (Robinson, 2011; Stoeck, 2014; Wang, 2015). AL101 is a potent and selective inhibitor of gamma secretase-mediated Notch signaling. In preclinical models, AL101 exerts its antitumor activity through direct inhibition of cell proliferation and indirectly via inhibition of tumor angiogenesis. In TNBC patient-derived xenograft (PDX) tumor models, the presence of activating Notch mutations/fusions correlated with robust response to AL101 monotherapy (ASCO 2019, Abstr 1064). AL101 has been studied in three Phase 1 studies in more than 200 subjects with various cancers (ASCO 2018, Abstr 2515) and is currently being studied in a Phase 2 study for patients with Adenoid Cystic Carcinoma with Notch activating mutations (ACCURACY- NCT03691207). Preliminary data reported from this trial showed clear signs of clinical activity along with a favorable safety profile (ESMO 2019, Abstr 3568). Trial design: The TENACITY study is an open-label, international, multicenter, single arm Phase 2, Simon two-stage optimal design for targeted therapy study of AL101 monotherapy in subjects with Notch-activated recurrent or metastatic TNBC who have received ≤ 3 lines of prior therapy. Patients with stable, asymptomatic CNS metastases are eligible. Notch activation will be determined by Next Generation Sequencing (NGS) of tumor DNA/RNA to detect somatic mutations and gene rearrangements. Target enrollment is 67 subjects. The design will include a lead-in cohort of 6 subjects to ascertain safety of AL101, 6 mg weekly (QW). After the 6th subject completes 4 weeks of therapy, safety will be assessed and subsequent dosage of AL101 will be determined (continue at 6 mg QW versus reduction to 4 mg QW). The primary endpoint is overall response rate (ORR), based on RECIST v1.1 as assessed by the treating investigator. The study design has 80% power with type I error level of 5% to detect an ORR of 23%. Key Secondary endpoints include progression free survival, clinical benefit rate, duration of response, overall survival and quality of life. Study will open to enrollment in July 2020. For further information on this trial, email chen.d@ayalapharma.com or visit clinicaltrials.gov (NCT04461600).

Citation Format: Tiffany A Traina, Erin F Cobain, Ella Evron, Chen Duksin, Gary Gordon. Tenacity: A phase 2, multicenter, open-label, single-arm study of AL101 monotherapy in patients with notch-activated triple negative 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 OT-29-01.

Clinical Applications of Circulating Tumor Cells in Breast Cancer

The development of metastatic disease accounts for the vast majority of cancer-related deaths in solid tumor malignancies. Distant metastases primarily develop as a result of tumor cell dissemination through the circulatory system.

Young Women with Breast Cancer: Fertility Preservation Options and Management of Pregnancy-Associated Breast Cancer

BACKGROUND

Breast cancer is the most common malignancy diagnosed in women of childbearing age. A breast cancer diagnosis in this young patient population can be uniquely complex to navigate when considering the potential impact of fertility loss associated with specific gonadotoxic therapies. Another unique challenge for young breast cancer patients is pregnancy-associated breast cancer (PABC), which occurs in approximately 1 of every 3000 pregnancies. Pregnancy adds a layer of complexity to breast cancer treatment planning as many therapies can affect the developing fetus. These two clinical challenges require nuanced multidisciplinary approaches to facilitate optimal treatment outcomes. We sought to review and summarize the management strategy options for both fertility preservation and PABC.

METHODS

A guideline and literature review was performed for fertility preservation, young patients with breast cancer, and pregnancy-associated breast cancer.

RESULTS

Fertility preservation options, both established and experimental, are detailed. Suggested clinical practice guidelines for PABC are also presented, which delineate breast cancer treatment recommendations based on pregnancy trimester.

CONCLUSION

A multidisciplinary approach to patient care, including oncologists and early referral to reproductive specialists, can provide young breast cancer patients with options for fertility preservation. Under the guidance of a multidisciplinary treatment team, PABC can also be diagnosed and treated to permit the best possible outcomes for the mother and the developing fetus.

Abstract P2-09-26: Frequency and mechanisms of elevated somatic mutation burden in metastatic breast cancer and response to immune checkpoint blockade

Background: Immune checkpoint blockade (ICB) is effective in the treatment of various malignancies. Thus far, however, results in breast cancer have been mixed. Elevated tumor mutational load, and subsequent increased likelihood of forming immunogenic neoantigens, has been correlated with response to ICB. Mutational load observed in breast cancers varies widely. However, most studies have assessed mutational load using primary tumors. Few studies have explored the frequency of high mutational load, molecular mechanisms accounting for this phenomenon, and its potential impact on response to ICB in metastatic breast cancer (MBC).

Methods: From 2011-2016, 124 patients (pts) with MBC of varying subtypes underwent research biopsy of their metastatic disease for whole genome, exome and transcriptome sequencing of tumor and matched normal sample through the Michigan Oncology Sequencing Center (Mi-OncoSeq). Those pts with elevated somatic mutation load were defined as having greater than 10 mutations per megabase of targeted sequencing and mutational signatures accounting for high mutation load were noted. Pts treated subsequently with ICB were followed to assess response.

Results: Twelve MBC pts had high mutation load (10% of cohort). Eight pts had estrogen receptor (ER) positive MBC and 4 pts had metastatic triple negative breast cancer (TNBC). In 5 cases, a clear mutational signature accounting for high mutation load was evident. Two TNBC cases harbored an APOBEC mutational signature in addition to 1 TNBC and 2 ER positive tumors displaying a microsatellite instability signature (MSI-H). Among the tumors with MSI-H signature, 1 case was associated with a pathogenic germline alteration in MLH1. Two pts were subsequently treated with ICB on a clinical trial. One pt came off study after 3 months due to progressive brain metastases and another had partial response to therapy lasting 7 months.

Conclusions: Elevated somatic mutation burden in MBC is observed in approximately 10% of pts, and is detected in both ER positive and TNBC. Since high mutation burden has been associated with increased likelihood of response to ICB, identification of this genomic feature could have important therapeutic implications for MBC pts.

Citation Format: Cobain EF, Robinson DR, Wu Y-M, Lonigro R, Vats P, Rabban E, Kumar-Sinha C, Schott AF, Smerage JB, Morikawa A, Burness ML, Van Poznak CH, Griggs J, Wicha M, Hayes DF, Chinnaiyan AM. Frequency and mechanisms of elevated somatic mutation burden in metastatic breast cancer and response to immune checkpoint blockade [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P2-09-26.

Indications for prognostic gene expression profiling in early breast cancer

OPINION STATEMENT

Breast cancer is a heterogeneous disease. While breast cancer mortality has dropped substantially over the past three decades due to early detection and adjuvant systemic therapy (AST), the risk of recurrence is highly dependent upon numerous factors including tumor size, involvement of regional lymph nodes, histologic grade, expression of hormone receptors (estrogen and progesterone), and human epidermal growth factor receptor 2 (HER2) amplification. We use these factors to determine which early breast cancer (EBC) patients should be treated with AST, including endocrine therapy (ET), chemotherapy, and HER2-directed treatments. While these factors aid in this determination, it remains challenging to identify those patients unlikely to benefit from adjuvant chemotherapy, resulting in over-treatment of patients. Given this dilemma, there has been great interest in the development of prognostic and predictive gene expression profiles. The most extensively studied profile, the 21-gene recurrence score (Oncotype Dx®), estimates 10-year risk of breast cancer recurrence in patients with estrogen receptor (ER)-positive, HER2-negative, node-negative EBC and is likely predictive of chemotherapy benefit. This assay has established analytic validity, clinical validity, and clinical utility for this patient group and, therefore, is indicated in this patient population to help inform decisions regarding administration of adjuvant chemotherapy. Several other assays may have utility in this clinical context or perhaps to identify patients who do not require extended adjuvant ET. These assays include the following: PAM 50 Risk of Recurrence (ROR) Score (Prosigna™), Breast Cancer Index, and EndoPredict®.

Abstract 1723: IKZF1/CDKN2A co-deletion predicts shorter survival in adult B-ALL

B lymphoblastic leukemia (B-ALL) in adults has a higher risk of relapse and lower long-term survival than pediatric B-ALL. Prognostic biomarkers are needed for better risk-stratification and therapy selection. Microarray-based genome-wide profiling studies in pediatric patients have revealed recurrent abnormalities in B-cell development and cell cycle regulation. IKZF1 alterations convey a negative prognostic impact in pediatric B-ALL, but their significance is not well characterized in adult B-ALL. CDKN2A alterations have also been associated with a poorer prognosis in adult Ph+ ALL, possibly by mediating resistance to targeted therapy. The copy number landscape of adult B-ALL has not been fully assessed, and given its inferior prognosis, may be distinct from its pediatric counterpart. We identified 70 adult B-ALL patients (median age 45 years, range 18-83) from 1998-2013 at three institutions. DNA was isolated from formalin-fixed, paraffin-embedded (FFPE) diagnostic bone marrow clots and assessed with the OncoScan FFPE Express genome-wide single nucleotide polymorphism (SNP) assay (Affymetrix). Copy number alteration (CNA) analysis was performed using Nexus Software V7 (Biodiscovery) and in-house coding. The most frequent CNAs called by the software were manually verified for probe evidence. Clinical data available on this cohort included age, gender, hematologic laboratory values at presentation, CSF involvement, receipt of allogeneic transplant, cytogenetic profile, presence of t(9;22), event-free survival (EFS), and overall survival (OS). Estimated median survival time of the entire adult B-ALL patient cohort was 29 months. Recurrent deletions in the diagnostic samples were noted at several loci, including CDKN2A (47%), IKZF1 (40%), PAX5 (24%), BTG1 (17%), and BTLA (14%). Recurrent gains were identified at the following loci: ERG (30%), ETS2 (21%), MYB (20%), UBASH3B (20%), PRKCH (19%), CDK6 (17%), and ETV6 (16%). No individual CNA heralded a significant prognostic impact in the entire cohort or in subgroup analyses stratified by presence of t(9;22) for either EFS or OS, though this could be due to our relatively smaller sample size in contrast to pediatric studies that have observed a prognostic impact at some of these loci. However, the combination of both CDK2NA and IKZF1 deletions (26%) correlated with a significantly worse overall survival than having only one or neither of these deletions (both vs CDKN2A only: p = 0.028, both vs IKZF1 only: p = 0.027, both vs neither deleted: p = 0.048). Age was the only other covariate significant in univariate analyses for OS, yet IKZF1/CDKN2A co-deletion remained significant in multivariate analysis adjusting for age. Adult B-ALL demonstrates frequent CDKN2A deletions, IKZF1 deletions, and CDKN2A/IKZF1 co-deletions. To our knowledge, the negative prognostic impact of the CDKN2A/IKZF1 co-deletion is a novel finding in adult B-ALL and requires further validation in larger cohorts.

Citation Format: Shiven Patel, Clinton C. Mason, Martha J. Glenn, Christian N. Paxton, Sara T. South, Melissa H. Cessna, Julie Asch, Erin F. Cobain, Dale L. Bixby, Lauren B. Smith, Joshua D. Schiffman, Rodney R. Miles. IKZF1/CDKN2A co-deletion predicts shorter survival in adult B-ALL. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1723. doi:10.1158/1538-7445.AM2015-1723