Dynamic biomarkers in hormone receptor-positive/HER2-negative breast cancer trials: a new hope for precision oncology.

e15033 Background: In the Phase 3 CAPItello-291 trial (NCT04305496), the addition of capivasertib (a potent, selective pan-AKT inhibitor) to fulvestrant significantly improved progression-free survival in patients with HR+/HER2− advanced breast cancer, especially in those with PIK3CA/AKT1/PTEN-altered tumors identified using tissue biopsy-based FoundationOneCDx. Given the growing utility of circulating tumor DNA (ctDNA) and interest in liquid biopsy-based tests to detect PIK3CA/AKT1/PTEN alterations, we performed a retrospective analytical comparison of FoundationOneCDx and blood-based FoundationOneLiquidCDx NGS data. Methods: We utilized the FoundationCORE database of breast cancer cases profiled during routine clinical care with FoundationOneCDx and/or FoundationOneLiquidCDx (covering the same genomic regions). Analytical comparison of all pathogenic PIK3CA/AKT1/PTEN alterations as well as alterations defined in the CAPItello-291 protocol (CAPItello-291 alterations) was performed in paired data from cases with both tissue and liquid biopsies, sampled within 90 days of each other. Subgroup analysis was conducted based on ctDNA tumor fraction (TF). Data from liquid biopsies were analyzed for co-occurring mutations. Results: CAPItello-291 alterations were detected in 44.9% of 35,730 tissue biopsies and 34.3% of 7056 liquid biopsies profiled from Jan 2017–Jun 2023. In paired NGS data (n=289), the overall positive percent agreement (PPA) for CAPItello-291 alterations across ctDNA TF subgroups was: TF ≥10% (n=99): 92.5%; TF 1–10% (n=66): 97.1%; TF <1% (n=124): 33.9%. The PPA for all PIK3CA/AKT1/PTEN short variants (base substitutions, indels) analyzed was: ctDNA TF ≥10%: PIK3CA, 93.9%; AKT1, 100%; PTEN, 100%, and ctDNA TF 1–10%: PIK3CA, 96.3%; AKT1, 100%; PTEN, 100%. For PTEN biallelic deletions, the PPA was 50% (2/4) in cases with ctDNA TF ≥10%. In liquid biopsies with CAPItello-291 alterations (n=2421), the most frequent co-occurring mutations were in TP53 (49.9%), ESR1 (31.2%), CDH1 (23.7%), NF1 (13.0%), RB1 (12.8%), CHEK2 (12.4%), ATM (11.9%), FGF3 (11.4%), FGF19 (11.0%), and FGF4 (10.5%). Mutations in BRCA1 (2.4%), BRCA2 (4.8%), and PALB2 (1.3%) were also observed. Conclusions: PPA between liquid and tissue biopsy NGS data for the detection of PIK3CA/AKT1/PTEN short variants was high in cases with ctDNA TF ≥1%. Liquid biopsies offer a minimally invasive approach for the detection of some CAPItello-291 alterations. However, limitations posed by ctDNA TF <1% and sample and variant types should be considered. Together, these data can help clinicians make informed decisions regarding suitable diagnostic tests to determine patient eligibility for breast cancer therapies.

Comprehensive genomic profiling (CGP) of circulating tumor DNA (ctDNA) provides an opportunity to noninvasively monitor a patient’s tumor burden via liquid biopsy. Liquid biopsies can assess a patient’s mutational landscape through time and provide information on treatment response and relapse. It has become increasingly common to have paired genomic data analysis between liquid and tissue biopsies from the same patient. However, the impact of clinical, temporal, and biologic factors on percentage of positive agreement (PPA) of variant detection between these biopsies is unclear. For our study, we leveraged two databases containing CGP data from paired liquid and tissue biopsy specimens tested by Foundation Medicine (FMI): the FMI database (>1700 paired samples) and the Flatiron Health-Foundation Medicine Clinico-Genomic Database (CGDB). The CGDB is a subset of the FMI database linked with the Flatiron Health nationwide de-identified EHR-derived database, which includes demographic, treatment, and clinical outcomes information (>500 paired samples). We report pan-solid tumor and per-indication prevalence and PPA for variants commonly assayed in both liquid and tissue tests. We found that PPA depended on the tumor DNA concentration in plasma and tissue biopsies, as well as the amount of time between tests. We also investigated the effect of treatments administered in the time between liquid and tissue tests on the detected variants and observed some well-described resistance alterations at a higher frequency in liquid samples, including a higher prevalence of ESR1 point mutations in breast cancer, more EGFR T790M alterations in lung cancer, and frequent KRAS Q61H alterations in colorectal cancer. Liquid biopsies can also contain DNA shed from multiple metastatic sites. We observed evidence of this in the form of polyclonal resistance alterations, which may also account for differences in PPA over time. Our findings indicate that while PPA is generally high between samples, it may be influenced by factors such as intervening therapies, resistance, therapy efficacy, and polyclonality of liquid samples. Citation Format: Zoe June F. Assaf, Smruthy Sivakumar, Dexter X. Jin, Sophia L. Maund, Svetlana Lyalina, Guneet Walia, Ethan S. Sokol, Sally E. Trabucco. Pan-solid tumor comparison of variant detection in paired liquid and tissue biopsies [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr A17.

1028 Background: Tissue biopsy is recommended to confirm breast cancer (BC) recurrence. Liquid biopsy [including circulating tumour cells (CTCs) and circulating tumour DNA (ctDNA)] is a non-invasive approach for detecting cancer that may provide information to identify treatment choices and replace invasive biopsies. This ongoing study aims to assess the concordance between tissue and liquid biopsy testing in subjects presenting with suspicion of distant recurrence from BC. Methods: Patients with suspected metastatic BC were enrolled; tumour characteristics and treatment were recorded. Blood samples were collected within 30 days before tissue biopsy, or within 7-28 days after tissue biopsy and before any systemic or radiation treatment. Samples were shipped to EPIC Sciences and processed within 96 hours; after plasma isolation, nucleated cells were plated; slides and plasma were banked. CTCs were identified using Epic Sciences digital imaging and machine learning algorithms. Single-cell isolation for genomic ctDNA analysis was performed. Cell free DNA was analyzed using a validated NGS panel to detect ctDNA alterations. The presence of metastases was classified as suspicious, highly suspicious, definitely metastatic BC or other by the treating oncologist based on the patient's clinical presentation and biopsy pathology results. Epic Sciences classified samples into similar categories based on CTC and ctDNA assay results. These classifications were performed independently. Sensitivity of the Epic Sciences methodology to detect metastatic BC (as determined by the treating oncologist), and its false positive rate were calculated. Results: 100 patients were enrolled from June 2020 to October 2022; shipping delays precluded EPIC assays in six patients; 94 patients were analyzed. Of 83 cases deemed suspicious, highly suspicious, or definitely metastatic BC by the treating oncologist, 61 were also deemed so by Epic Sciences (sensitivity of 73.5%, 95% confidence interval, CI 63.1% - 81.9%). Of 66 cases assigned as suspicious, highly suspicious, or definitely metastatic BC by the Epic Sciences, 4 had new primary cancers (3 lung cancer, 1 hepatocarcinoma), for a false positive rate of 6.1% (95% CI 1.9% - 15.0%). One additional case was classified as un-specified adenocarcinoma (possibly breast) by the treating oncologist; resolution awaits further follow-up. Conclusions: Preliminary results show that 73.5% of distant BC recurrences were correctly identified by liquid biopsy. A small number of false positive results occurred in patients with other new primary cancers. Additional analyses with CTC characterization are ongoing. [Table: see text]

A fatal affair: Circulating tumor cell relationships that shape metastasis

Targeted gene panel sequencing of liquid and tissue biopsies reveals actionable genomic alterations in Ghanaian metastatic breast cancer cases

Background. Determining the non-inferiority margin is an essential step in the design and interpretation of non-inferiority trials, and this margin should be preferably justified on clinical and statistical grounds. Methods. After a PubMed search for phase III trials in advanced breast cancer (BC) or non-small cell lung cancer (NSCLC) published between January 1998 and December 2009 in 11 leading journals, non-inferiority trials were selected by manual search of the full papers. Results. Twenty-four of 195 trials had a primary non-inferiority hypothesis. When the two six-year study periods were compared, there were time trends within BC and NSCLC, with most non-inferiority trials in BC reported in the first six-year period, and vice-versa for NSCLC. The median sample size was larger for non-inferiority than superiority trials (p < 0.01). The choice of a non-inferiority margin was reportedly justified in only five cases. Non-inferiority trials were more likely than superiority trials to yield positive results (p < 0.001), as were trials in breast cancer (p = 0.02). Conclusions. Non-inferiority margins for cancer trials appear to be chosen mostly on historical grounds. Since nearly three-quarters of non-inferiority trials achieve their primary objective, the extent to which the choice of margins has influence on trial results remains to be determined.

Breast cancer is an increasingly recognized public health concern in developing countries. The clinical spectrum is heterogeneous but largely characterized at presentation by a more advanced stage, the presence of various adverse factors and low rate of survival. The quantum of ongoing clinical trials in breast cancer is low and inadequate to address the needs of these populations. There are several design challenges in setting up breast cancer trials in the developing world, the most notable being the aquisition of informed consent, inducement and/or coercion of participants, adequacy of control arms in randomized trials, tropical infections and ethnic variations in drug metabolism. The main implementation challenges include scarcity of infrastructure and skilled human resources, variable delivery of standard breast cancer care, inadequate breast cancer pathology standards and deficient regulatory framework in many regions. There are several opportunities for conducting clinical trials that include a lar...

Martine Piccart, Fabrice André, David Cameron, Peter Campbell, Lisa Carey, Stephen Friend, Charles Perou, Kamal Saini, Daniel Hayes. Among the most recent important developments in oncology is the advance in high-throughput technologies. These “omics” technologies are becoming increasingly robust, cheap, and widespread (1) and they have generated three sets of data that should change the way clinical trials are being designed and conducted. First, genomic characterization of breast cancer (BC) has shown that it includes a large number of rare genomic entities, driven by different molecular aberrations (2,3). Some BC subpopulations (such as HER2 mutated BC) are maybe rare enough to qualify as orphan diseases. As the categorization of molecular features continues to evolve, such fragmentation is increasing. Second, the genomic characterization of metastatic BC has shown that metastatic process and resistance to therapy follows a branched evolution, with the genomic landscapes of primary and metastatic BC being different (4,5). As illustration, it has been shown that metastatic BC is enriched for ESR1 mutations, with this aberration detected after resistance to endocrine therapy has occurred (6). Finally, these new technologies have opened new frontiers in the field of personalized medicine since it is now possible to sequence hundreds of genes for less than US$ 2000 with short turnaround times and these figures are expected to continue to decrease, while accuracy and reproducibility of sequencing techniques continue to improve. These three major advances are changing the way clinical trials are being designed and performed. One challenge is to prospectively test drugs against this large list of molecular aberrations in a cost- and time-effective manner. Considering the rarity of these genomic segments, the conventional strategy of large phase III “all comer” BC trials is unsuitable for testing drugs that are predicted to be efficacious only among a small fraction of BC patients. Therefore, innovative clinical trial designs are needed. There are three basic questions that need to be addressed: a. how to optimally screen patients for genomic alterations? b. how to design strategies that will improve outcome? c. how to translate findings generated in metastatic BC in the early-stage disease? Testing for single genetic alterations at progression is inefficient and likely to result in screen-failure of the majority of patients. There is thus a need for molecular screening using multiplex technologies in order to maximize the likelihood of a patient to be a candidate for a molecularly targeted therapy. Moreover, there is a need to scale-up the number of patients screened in order to identify enough patients with a rare genomic alteration to constitute a cohort for a therapeutic trial. Thanks to funding from different sources, including the Breast Cancer Research Foundation, the Breast International Group has embarked on an ambitious program called AURORA (Aiming to Understand the Molecular Aberrations in Metastatic Breast Cancer), involving molecular characterization of host DNA, primary and metastatic tumor samples. AURORA will provide the structure for a large international network capable of running biology-driven trials for rare subpopulations of BC. AURORA has an innovative design, being a longitudinal cohort study with downstream nested biology-driven clinical trials. A similar initiative is planned to roll out in the United States. Such programs could make recruitment into biology-driven trials logistically and financially feasible. Although performed at large scale, AURORA will not be linked with large phase III registration trials, so that a further scale-up will be needed to screen enough patients to run them in rare genomic populations. One possibility could be to use blood-based assays, and no longer biopsies, in large cohorts of patients treated in community hospitals, and to refer the ones presenting “rare” genomic alterations to comprehensive cancer centers. However, the implementation of such an approach requires proof that the mutational landscape of metastatic BC is accurately reflected in the blood (7). There is an ever-increasing list of targeted compounds under clinical development targeting rare molecular alterations (8). A new approach could be to test an algorithm for drug prediction and not the drugs themselves. SAFIR02 is an illustration of such a trial, where patients are randomized between standard of care and a panel of targeted therapies matched with the genomic alterations found. In this “multidrug arm” trial, the hypothesis is that the use of the technology + the algorithm + the targeted compound will improve outcome. It is unclear whether regulatory agencies will accept this “package” approach. Adaptive trial designs represent another innovative approach to accelerate successful clinical development of targeted agents. In this scenario, patients’ allocation to different treatment arms follows initial rules, with subsequent modifications taking place on the basis of continuous data generation during the study. In the setting of BC, this approach can be exemplified by the I-SPY 2 neoadjuvant clinical trial (9). The ultimate goal will be to test whether the use of genomics and targeted therapies could cure early-stage BC patients. To this end, several neoadjuvant or ‘window’ preoperative trials are being designed that will evaluate whether targeted therapies will eradicate not only “driver” events, but also “lethal minority clones”. These trials will require genomic testing for early-stage BC patients. Interest in trials performed in the neoadjuvant setting was recently boosted, after FDA suggested possible drug approvals based on pathological complete response (pCR) as a surrogate endpoint (10). In the adjuvant setting one major challenge is the intratumoural heterogeneity of BC, since residual micrometastatic BC may have different molecular characteristics than the primary or the metastatic disease that we can currently interrogate (11). Since most of the targeted therapies could lead to the induction of compensatory upregulation of alternative oncogenic signaling pathways, there is a need to design trials that aim to understand such resistance mechanisms (12). Obtaining tissues after relapse under targeted therapy shall thus be vital to design the further combination strategies. To address the lack of safety data for different combination strategies, “virtual phase I trials” based on models or simulations could be developed to inform us about the expected toxicities of combinations and the recommended doses for subsequent phase II “efficacy” trials. Because of the real diversity that will be uncovered in patient’s tumors when we use these NextGen omics approaches, we also will need to learn to more quickly share the findings that we generate in the trials being run internationally. If we wait to share the data and the insights till after the findings are published, we will not move quickly enough towards improved patient care. To enable sharing we must develop ways to provide credit and incentives that move beyond calculations based on H factors and who is first or last author. The platforms being built by Sage Bionetworks such as “SYNAPSE” are examples of how to provide the provenance to track who contributed what and when (http://sagebase.org/synapse-overview/). To conclude, while there have been genuine advances in basic and translational oncology, as well as elucidation of multiple candidate targeted therapies, the full potential of these advances has not been realized, partly as a result of outdated trial methodologies. Innovative approaches are needed to quickly test these molecules in smartly designed clinical trials.

Over the last two decades we have seen a number of important advances in the biological underpinnings of breast cancer that have had a significant impact either directly or indirectly on the management and ultimately on the prognostic outcome of this disease. First, we now know that breast cancer is a heterogeneous disease made up of a number of unique subtypes each with its own natural history and associated prognostic outcome [1]. Second, some of these subtypes have specific targets (including ER and HER2) that have associated unique targeted therapeutic agents that significantly impact the natural history of this disease [2]. Third, data indicate that these targets are not static with approximately 30% of tumors showing discordance in the expression of hormone receptor or HER2 between the primary and associated metastatic tumor [3]. The therapeutic implications of such discordance have understandably resulted in most oncologists seeking to biopsy metastatic sites whenever possible. Despite these advances we have a long way to go with current research focusing on looking for biomarkers that have a dual prognostic and predictive function. An ideal biomarker being one able to accurately predict for early recurrence or progression of disease, provide information to guide therapeutic decisions, reliably predict response to specific treatment, provide an easy platform for testing of markers such as ER and HER2 at various time points along a cancer history continuum, and allow for the identification of unique targets that would help specific drug development. Circulating tumor cells (CTCs) is one such biomarker that has been actively investigated over the last decade and has shown promising results in a number of malignancies including breast cancer. The presence of epithelial cells in the circulation that are similar in appearance to primary tumor cells was first described by TR Ashworth about 150 years ago in a woman with metastatic breast cancer [4]. These detectable cancer cells are CTCs that represent a rare cell population in the circulation usually representing less than 10 cells/ml. These cells can originate from either the primary or metastatic tumor tissue and require special enrichment techniques for their detection [5]. These techniques are based either on the biological properties of the CTCs such as protein secretion or cell surface antigen expression or are based on the physical characteristics of these cells such as presence of electric charges, size of the cell, density or deformability. Currently the only FDA approved CTC enumeration Using circulating tumor cells to guide therapy in breast cancer: could this replace biopsies?

Purpose Observational study evidence has associated overweight/obesity with decreased survival in women with breast cancer and with several other cancers. Although full-scale, definitive weight loss adjuvant intervention trials with cancer end points remain to be conducted, a number of randomized controlled trials have evaluated weight loss interventions in survivors of cancer in women. Findings from these trials in breast, endometrial, and ovarian cancer are reviewed. Methods A systematic review of randomized controlled clinical trials evaluating weight loss interventions was updated (for studies published 2013 to 2016), and clinical trials registers were searched for ongoing trials. Results Six new randomized trials in breast cancer survivors and two randomized trials in endometrial cancer survivors were identified. Evidence from these trials and the 10 earlier randomized trials in female cancer survivors provide support for the feasibility of recruiting women closer to the cancer diagnosis and efficacy for achieving weight loss, in particular with telephone-based interventions, and have identified the challenge of achieving significant weight loss in African American cancer survivors and of maintaining weight loss in any cancer survivor group. Seven ongoing randomized trials are evaluating the influence of weight loss interventions on cancer end points (five in breast cancer, one in ovarian cancer, and one in endometrial cancer). Conclusion After a decade of preliminary studies, ongoing randomized, controlled clinical trials will potentially provide definitive assessment of whether weight loss can improve breast cancer clinical outcome. Longer-term interventions (> 2 years' duration) may be needed to optimize weight loss maintenance and any potential benefits on cancer end points.

An adaptive treatment strategy (ATS) is a rule for adapting a treatment plan to a patient's history of previous treatments and the response to those treatments. The ongoing management of chronic disease defines an ATS, which may be implicit and hidden or explicit and well-specified. The ATS is characterized by the use of intermediate, early markers of response to dynamically alter treatment decisions, in order to achieve a favorable ultimate outcome. We illustrate the ATS concept and describe how the effect of initial treatment decisions depends on the performance of subsequent decisions at later stages. We show how to compare two or more ATSs, or to determine an optimal ATS, using a sequential multiple assignment randomized (SMAR) trial. Designers of clinical trials might find the ATS concept useful in improving the efficiency and ecological relevance of clinical trials.

Background: The ROME trial, a phase II multicenter study, enrolled 1,794 patients with advanced solid tumors. Centralized next-generation sequencing (NGS) was performed on both tissue and liquid biopsies using FoundationOne CDx and FoundationOne Liquid CDx. A centralized Molecular Tumor Board (MTB) reviewed results to identify actionable alterations, with 400 patients subsequently randomized to tailored therapy (TT) or standard-of-care (SoC). In this trial, TT improved objective response rate (ORR) and progression-free survival (PFS) in the Intention to Treat population (ITT) Methods: This exploratory analysis evaluated the concordance between tissue (T) and liquid (L) biopsy results in detecting actionable alterations in ITT population. Concordance was defined as the detection of the same significant alterations in both biopsy types; discordance indicated detection in only one. Survival outcomes (OS and PFS) were analyzed across concordance groups. Due to the exploratory nature of the analysis, statistical significance was not determined Results: Concordance between tissue (T) and liquid (L) biopsies was 49%, with actionable alterations detected exclusively in tissue biopsies in 35% of patients and exclusively in liquid biopsies in 16%. Of the 203 discordant cases, 21% were attributed to test failures, 35% to discordant high tumor mutational burden (hTMB) detection, 1% to microsatellite instability (MSI) discrepancies, and 43.3% to differences in the detection of molecular alterations. The PI3K/PTEN/AKT/mTOR and ERBB2 pathways showed the highest discordance rates. Test results guided therapeutic choices in 84% and 65% of cases for tissue biopsy and liquid biopsy, respectively. Patients in the concordant T+L group receiving tailored therapy (TT) experienced significantly improved survival outcomes. Median overall survival (OS) was 11.05 vs. 7.70 months in the standard-of-care (SoC) group (HR 0.74; 95% CI: 0.51-1.07), and median progression-free survival (PFS) was 4.93 vs. 2.80 months (HR 0.55; 95% CI: 0.40-0.76). In contrast, the survival benefit of TT was less pronounced or absent in patients with discordant results. Overall, OS was higher in the T+L group (11.05 months), followed by the tissue-only group (9.93 months), and the liquid-only group (4.05 months). PFS followed a similar pattern, with the longest PFS observed in the T+L group (4.93 months) compared to 3.06 months in the tissue-only group and 2.07 months in the liquid-only group. Conclusions: Although the concordance rate between tissue and liquid biopsies was only 49%, the substantial increase in detection of actionable alterations (over 60% with the addition of liquid biopsy) and significative improvement of survival outcomes observed with combined T+L concordance strongly emphasize the importance of integrating both biopsy modalities to enhance precision oncology approaches. Citation Format: Paolo Marchetti, Simone Scagnoli, Edoardo Crimini, Simona Pisegna, Sofia Verkhovskaia, Giuseppe Curigliano, Sara Lonardi, Valentina Guarneri, Chiara Cremolini, Umberto Malapelle, Ettore D. Capoluongo, Paolo A. Ascierto, Fabio Puglisi, Giancarlo Pruneri, Giulia D'Amati, Bruna Cerbelli, Mauro Biffoni, Giuseppe Tonini, Lucia Del Mastro, Andrea Botticelli. Combined tissue and liquid biopsy improves outcomes in advanced solid tumors: an exploratory analysis of the ROME trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6372.

Liquid Biopsy Versus Tissue Biopsy to Determine Front Line Therapy in Metastatic Non-Small Cell Lung Cancer (NSCLC)

A Combinatorial Investigation of the Response to Anti-angiogenic Therapy in Breast Cancer: New Strategies for Patient Selection and Opportunities for Reconsidering Anti-VEGF, Anti-PI3K and Checkpoint Inhibition

Trastuzumab beyond progression: a challenge to translational oncology?