501 Background: In the NATALEE clinical trial, RIB + NSAI significantly improved invasive disease–free survival (iDFS) vs NSAI alone in patients (pts) with stage II/III HR+/HER2− EBC. We report on the prognostic and predictive value of baseline gene exp in NATALEE. Methods: Pts were randomized 1:1 to RIB + NSAI or NSAI alone. Men and premenopausal women received goserelin. Eligible pts had anatomical stage IIA (if N0 with additional risk factors [G3, or G2 with Ki67 ≥20% or high genomic risk] or N1 [1-3 axillary lymph nodes]), IIB, or III disease per AJCC (8th ed). Gene exp in surgical samples was profiled by NanoString BC360 panel. PAM50-based intrinsic subtype × treatment (tx) interaction was estimated by likelihood ratio test. Prognostic and predictive effects of PAM50 subtypes and genomic risk/proliferation signature scores created from gene exp data were assessed with Cox proportional hazards models. Differences in genomic risk and proliferation scores were analyzed by Wilcoxon test. Associations between gene exp and RIB benefit were estimated with Cox models. Results: In all, 3022 baseline surgical samples were analyzed. iDFS benefit with RIB + NSAI was consistent in the biomarker (hazard ratio [HR], 0.72) and intent-to-treat populations (HR, 0.71). PAM50 subtype distribution was comparable across tx arms and differed between N0 and N1-N3 in pts with luminal A (LumA; 50% vs 68%), luminal B (lumB; 41% vs 26%), and basal-like (BSL; 6.4% vs 2.5%) disease, with similar percentages for HER2-enriched (HER2E; 2.5% vs 3.0%). PAM50 subtypes were strongly prognostic (HRs vs LumA: LumB, 1.39; HER2E, 2.62; BSL, 3.92). RIB had benefit across all PAM50 subtypes (HRs: LumA, 0.77; LumB, 0.71; HER2E, 0.50; BSL, 0.42), with no significant subtype × tx interaction ( P = .34). Higher genomic risk signature or proliferation signature scores showed a trend for increased RIB benefit, again with no significant interaction. Pts with N0 vs N1-N3 had significantly higher genomic risk scores and proliferation scores. Exploratory analysis of the predictive effect of gene exp on RIB benefit identified several genes for which higher (eg, CEACAM6 , NOD2 , and GPX3) or lower exp (eg, GATA3 , SLC39A6 , and MAPT ) was associated with increased RIB benefit. Conclusions: In this analysis of NATALEE, which examined the largest dataset of surgical tumor samples from any adj CDK4/6i trial in HR+/HER2− EBC, RIB had benefit across all PAM50 subtypes, with a trend for increased benefit in pts with higher genomic risk signature or proliferation signature scores. Baseline exp levels of several genes were associated with differential RIB benefit in EBC, showing potential predictive and prognostic value. The findings reinforce the therapeutic benefit of RIB in combination with ET across HR+/HER2− EBC populations. Clinical trial information: NCT03701334 .

PURPOSE:Patients with platinum-resistant/platinum-refractory high-grade serous ovarian cancer (HGSOC) without a BRCA mutation have poor prognosis and limited treatment options. We report efficacy and biomarker data from EPIK-O, which investigated alpelisib + olaparib versus single-agent chemotherapy in these patients. PATIENTS AND METHODS:EPIK-O was an open-label, phase III trial that randomly assigned patients with platinum-resistant/platinum-refractory HGSOC with no germline or known somatic BRCA mutation 1:1 to alpelisib 200 mg once daily + olaparib 200 mg twice daily or treatment of physician's choice (TPC; paclitaxel 80 mg/m2 once weekly or pegylated liposomal doxorubicin 40-50 mg/m2 once every 28 days). Patients had 1-3 previous systemic therapies. Previous bevacizumab was required (unless contraindicated); previous poly(adenosine diphosphate-ribose) polymerase inhibitors were allowed. Primary end point was progression-free survival (PFS) per RECIST 1.1 (blinded independent review committee [BIRC]). Secondary efficacy end points included overall response rate (ORR; per BIRC), duration of response (per BIRC), and overall survival (OS; key secondary end point). RESULTS:A total of 358 patients (alpelisib + olaparib [n = 180], TPC [n = 178]) were included. The median follow-up time was 9.3 months. At data cutoff (April 21, 2023), 33 (18.3%) and 30 (16.9%) patients remained on treatment with alpelisib + olaparib and TPC, respectively. The median PFS (BIRC) was 3.6 versus 3.9 months (hazard ratio [HR], 1.14 [95% CI, 0.88 to 1.48]; one-sided P = .84) for alpelisib + olaparib versus TPC. The ORR was 15.6% (95% CI, 10.6% to 21.7%) versus 13.5% (95% CI, 8.8% to 19.4%). The median OS was 10.0 versus 10.6 months (HR, 1.22; 95% CI, 0.87 to 1.71). The safety profile of alpelisib + olaparib was consistent with that observed for the individual agents. CONCLUSION:The primary objective, PFS improvement, was not met in EPIK-O. No new or unexpected adverse events were observed. Biomarker analyses provided new insights for responders to alpelisib + olaparib.

Background: The phase 2 RIGHT Choice study showed a statistically significant median progression-free survival (mPFS) benefit with 1L RIB + ET vs combo CT (HR, 0.61; 95% CI: 0.43-0.87; P = .003) in pts with clinically aggressive HR+/HER2− ABC (Lu Y-S, et al. J Clin Oncol. Published online May 21, 2024). This exploratory analysis of the RIGHT Choice study examined efficacy of RIB + ET vs combo CT by intrinsic subtype and gene/signature expression levels. Methods: Pre/perimenopausal pts with no prior systemic therapy for aggressive HR+/HER2− ABC were randomized 1:1 to RIB + letrozole/anastrozole + goserelin or physician's choice of combo CT. Baseline tumor samples (n = 49) from pts enrolled in the trial were microdissected and underwent gene expression profiling by NanoString nCounter BC360 and PanCancer IO 360 panels. High and low baseline gene/signature expression levels were defined as greater and less than or equal to the median level, respectively. Results: Of the available samples from the RIB arm (n = 27), 6 (22.2%) were luminal A, 14 (51.9%) were luminal B, 6 (22.2%) were HER2E, and 1 (3.7%) was basal-like; in the CT arm (n = 22), 11 (50.0%) were luminal A, 9 (40.9%) were luminal B, and 2 (9.1%) were HER2E. The mPFS in the RIB vs CT arms was 32.5 mo vs not reached (NR) (HR, 0.88; 95% CI: 0.20-3.91) in luminal A, 38.0 vs 21.7 mo (HR, 0.64; 95% CI: 0.18-2.20) in luminal B, and 17.4 vs 8.0 mo (HR, 0.23; 95% CI: 0.03-1.66) in HER2E subtype. In the combined luminal B/HER2E set, which are known to be associated with poor prognosis, the mPFS was 38.0 vs 18.4 mo with RIB + ET vs combo CT (HR, 0.58; 95% CI: 0.21-1.62). In the RIB arm, pts with high ESR1 expression showed longer mPFS vs pts with low ESR1 expression (high vs low expression, mPFS, HR [95% CI]; 38.0 vs 32.5 mo, 0.52 [0.16-1.66]). Pts in the RIB arm with low expression of tumor inflammation or immune-related genes/cells, such as tumor inflammatory signature (TIS; BC360 panel) and T-cell (IO 360 panel) expression, had a longer mPFS than pts with high expression of these signatures (low vs high expression, mPFS, HR [95% CI]: TIS, NR vs 11.4 mo, 0.17 [0.04-0.76]; T cells, NR vs 10.3 mo, 0.2 [0.05-0.76]). In contrast to the results in the RIB arm, pts with low expression of immune-related genes/cells in the CT arm had a shorter mPFS than those with high expression of these genes (low vs high expression, mPFS, HR [95% CI]: TIS, 15.0 mo vs NR, 2.08 [0.62- 6.93]; T cells, 12.8 vs 18.4 mo, 1.8 [0.57-5.71]). For most other immune-related genes/cells expressions and signatures, a comparable consistent trend in PFS benefit for low vs high expression levels was observed, with a higher PFS benefit for low gene expression in the ribociclib arm, and a higher PFS benefit for high gene expression in the CT arm. Conclusions: This exploratory analysis showed a trend towards PFS benefit with RIB + ET vs combo CT in pts with luminal B/HER2E intrinsic subtypes, which are associated with poor prognosis. This analysis also suggest a more pronounced trend for PFS benefit with RIB + ET in pts with low baseline expression levels of immune-related genes. Contrary results in the CT arm suggest that these signatures warrant further studies on their potential predictive value. These data are hypothesis generating and should be interpreted with caution due to small sample sizes. Citation Format: Yen-Shen Lu, Chia-Lang Hsu, Eznal Izwadi Bin Mohd Mahidin, Sudeep Gupta, Erhan Gökmen, Elena Artamonova, Huang-Chun Lien, Hamdy Azim, Yoon-Sim Yap, Yesim Eralp, Seock-Ah Im, Fei Su, Yogesh Chattar, Estelle Roux, Melissa Gao, Nagi S. El Saghir. First-line (1L) ribociclib (RIB) + endocrine therapy (ET) vs combination chemotherapy (combo CT) in clinically aggressive HR+/HER2- advanced breast cancer (ABC): a subgroup analysis of RIGHT Choice by intrinsic subtype & gene & signature expression [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2024; 2024 Dec 10-13; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2025;31(12 Suppl):Abstract nr PS2-06.

Supplemental Table 1. Representativeness of study participants

Supplemental Table 3. Multivariable analysis of treatment benefit by subtype

Immune-related adverse events (irAEs) impact outcomes, with most research focusing on early prediction (baseline data), rather than near-term prediction (one cycle before the occurrence of irAEs and the current cycle). We aimed to explore the near-term predictive value of neutrophil/lymphocyte ratio (NLR), platelet/lymphocyte ratio (PLR), absolute eosinophil count (AEC) for severe irAEs induced by PD-1 inhibitors. Data were collected from tumor patients treated with PD-1 inhibitors. NLR, PLR, and AEC data were obtained from both the previous and the current cycles of irAEs occurrence. A predictive model was developed using elastic net logistic regression Cutoff values were determined using Youden's Index. The predicted results were compared with actual data using Bayesian survival analysis. A total of 138 patients were included, of whom 47 experienced grade 1-2 irAEs and 18 experienced grade 3-5 irAEs. The predictive model identified optimal alpha and lambda through 10-fold cross-validation. The Shapiro-Wilk test, Kruskal-Wallis test and logistic regression showed that only current cycle data were meaningful. The NLR was statistically significant in predicting irAEs in the previous cycle. Both NLR and AEC were significant predictors of irAEs in the current cycle. The model achieved an area under the ROC curve (AUC) of 0.783, with a sensitivity of 77.8% and a specificity of 80.8%. A probability >= 0.1345 predicted severe irAEs. The model comprising NLR, AEC, and sex may predict the irAEs classification in the current cycle, offering a near-term predictive advantage over baseline models and potentially extending the duration of immunotherapy for patients.

Supplemental Table 2. Patient characteristics by subtype

1012 Background: In ML-3, ribociclib (RIB) demonstrated a significant PFS/OS benefit over placebo (PBO) in pts with HR+/HER2− ABC. We report associations of on-tx ∆ctDNA with OS/PFS and tumor size and of ctDNA detectability with radiological progression. Methods: Pts were randomized 2:1 to RIB or PBO + fulvestrant as 1st- or 2nd-line tx. ctDNA levels were measured by NGS at cycle 1 day 1 (C1D1), C4D1, C8D1, and every 8 cycles until end of tx. Analyses included: Wilcoxon rank sum text to compare ∆ctDNA from C1D1 to C4D1; Kaplan-Meier method to visualize relationship of ctDNA with PFS/OS; Cox proportional hazards model for associations of ctDNA and tumor metrics (objective response rate, best % change, % change at 1st tumor evaluation); Fisher’s exact test to compare ctDNA detectability between arms; and ∆ctDNA across time points to assess lead time between ctDNA level-based and radiological progression. Results: Overall, 534/726 (73.6%) pts had paired C1/C4 measurements. Rates of detectable (+) and undetectable (−) ctDNA at C1 and C4 were: C1+/C4+, 33.0%; C1+/C4−, 34.5%; C1−/C4−, 27.5%; and C1−/C4+, 5.1%. RIB vs PBO had a larger % decrease in ctDNA level from C1 to C4 (P=0.003). Pts with better best overall response also had larger ctDNA decreases from C1 to C4 (P<0.0001). On-tx ∆ctDNA from C1 to C4 correlated with PFS/OS (P<0.0001; Table). C1-/C4-, C1+/C4-, and C1+/C4+ strongly correlated with PFS within response categories (PR, SD, NCRNPD). C1-to-C4 % ∆ctDNA was only moderately correlated with tumor size change (best % change, r=0.41; change at 1st evaluation, r=0.32; both P<0.001). Univariate/multivariate analyses showed significant correlations between ctDNA metrics (% change, detection pattern at C4D1) and PFS/OS. ctDNA detection and % change generally remained significantly associated with PFS/OS even after adjusting for change in tumor size. In a longitudinal analysis of pts who cleared ctDNA at C4D1 (C4–), the median lead time between ctDNA progression and radiological progression was 8.2 mo (IQR 4.5–15.6). Conclusions: On-tx ∆ctDNA from C1 to C4 was correlated with PFS/OS even after adjusting for tumor size changes, suggesting that ctDNA and tumor dynamics capture distinct aspects of tumor tx responses. Decreases in ctDNA were greater with RIB vs PBO, mirroring ML-3 efficacy readouts but at a much earlier timepoint. This longitudinal analysis of ctDNA in ML-3 suggests that detecting ∆ctDNA is a sensitive way to monitor progression and may be a potential surrogate for efficacy in HR+/HER2− ABC. Clinical trial information: NCT02422615 . [Table: see text]

Supplemental Figure 1: CONSORT diagrams of the MONALEESA (ML) trials.

In 2020, Novartis Pharmaceuticals Corporation and the U.S. Food and Drug Administration (FDA) started a 4-year scientific collaboration to approach complex new data modalities and advanced analytics. The scientific question was to find novel radio-genomics-based prognostic and predictive factors for HR+/HER- metastatic breast cancer under a Research Collaboration Agreement. This collaboration has been providing valuable insights to help successfully implement future scientific projects, particularly using artificial intelligence and machine learning. This tutorial aims to provide tangible guidelines for a multi-omics project that includes multidisciplinary expert teams, spanning across different institutions. We cover key ideas, such as "maintaining effective communication" and "following good data science practices," followed by the four steps of exploratory projects, namely (1) plan, (2) design, (3) develop, and (4) disseminate. We break each step into smaller concepts with strategies for implementation and provide illustrations from our collaboration to further give the readers actionable guidance.

Abstract Background There is increasing interest in the use of liquid biopsies, but data on longitudinal analyses of circulating tumor DNA (ctDNA) remain relatively limited. Here, we report a longitudinal ctDNA analysis of MONALEESASIA, a phase Ib trial evaluating the efficacy and safety of ribociclib plus endocrine therapy (ET) in Asian patients with hormone receptor–positive, human epidermal growth factor receptor-2–negative advanced breast cancer. Methods MONALEESASIA enrolled premenopausal and postmenopausal Japanese and postmenopausal non-Japanese Asian patients. All patients received ribociclib with ET (letrozole, fulvestrant, or tamoxifen with goserelin). ctDNA was analyzed using a targeted next-generation sequencing panel of 572 cancer-related genes and correlated by best overall response (BOR). Results Five hundred seventy-four cell-free DNA samples from 87 patients were tested. The most frequently altered genes at baseline included PIK3CA (29%) and TP53 (22%). Treatment with ribociclib plus ET decreased ctDNA in most patients at the first on-treatment time point, regardless of dose or ET partner. Patients with partial response and stable disease had lower ctDNA at baseline that remained low until data cutoff if no progressive disease occurred. Most patients with progressive disease as the best response had higher ctDNA at baseline that remained high at the end of treatment. For patients with partial response and stable disease with subsequent progression, ctDNA increased towards the end of treatment in most patients, with a median lead time of 83 days (14–309 days). In some patients with BOR of partial response who experienced disease progression later, specific gene alterations and total ctDNA fraction increased; this was sometimes observed concurrently with the development of new lesions without a change in target lesion size. Patients with alterations in PIK3CA and TP53 at baseline had shorter median progression-free survival compared with patients with wild-type PIK3CA and TP53, 12.7 and 7.3 months vs 19.2 and 19.4 months, respectively (P = .016 and P = .0001, respectively). Conclusions Higher ctDNA levels and PIK3CA and TP53 alterations detected at baseline were associated with inferior outcomes. On-treatment ctDNA levels were associated with different patterns based on BOR. Longitudinal tracking of ctDNA may be useful for monitoring tumor status and detection of alterations with treatment implications. Trial registration ClinicalTrials.gov NCT02333370 . Registered on January 7, 2015.

In the context of cancer, clonal hematopoiesis of indeterminate potential (CHIP) is associated with the development of therapy-related myeloid neoplasms and shorter overall survival. Cell-free DNA (cfDNA) sequencing is becoming widely adopted for genomic screening of patients with cancer but has not been used extensively to determine CHIP status because of a requirement for matched blood and tumor sequencing. We present an accurate classification approach to determine the CH status from cfDNA sequencing alone, applying our model to 4324 oncology clinical cfDNA samples. Using this method, we determined that 30.3% of patients in this cohort have evidence of CH, and the incidence of CH varies by tumor type. Matched RNA sequencing data show evidence of increased inflammation, especially neutrophil activation, within the tumors and tumor microenvironments of patients with CH. In addition, patients with CH had evidence of neutrophil activation systemically, pointing to a potential mechanism of action for the worse outcomes associated with CH status. Neutrophil activation may be one of many mechanisms, however, because patients with estrogen receptor–positive breast cancer harboring TET2 frameshift mutations had worse outcomes but similar neutrophil frequencies to patients without CH. Together, these data show the feasibility of detecting CH through cfDNA sequencing alone and an application of this method, demonstrating increased inflammation in patients with CH both systemically and in the tumor microenvironment.

TPS1125 Background: RIB and PAL are CDK4/6 inhibitors with demonstrated efficacy in terms of progression-free survival (PFS) and similar tolerability in pts with HR+/HER2- ABC when combined with endocrine therapy (ET). Only RIB has demonstrated a consistent, statistically significant, and clinically meaningful overall survival (OS) benefit across the MONALEESA (ML) phase III trials, while PALOMA trials failed to achieve similar outcome. Given effective treatments (Tx) may change underlying tumor biology (TB), it is hypothesized that RIB changes TB, enabling a better response to subsequent therapy and thus improving OS. RNA-based intrinsic subtyping reflects differences in TB and has strong prognostic and predictive value in HR+/HER2- ABC. Non-Luminal subtypes, as HER2-E and basal-like (BL), are relatively endocrine-resistant and have poorer prognosis than luminal. Tumors can switch subtypes over time to a more aggressive and less endocrine-responsive biology, which may also be reversed by effective Tx. A retrospective analysis of pooled data from ML 2/3/7 trials showed that HER2-E tumors had surprising benefit from RIB, while BL tumors did not. Pre/clinical data and indirect comparisons suggest that RIB may outperform PAL in HER2-E. Thus, choosing pts with HER2-E tumors as a means of a well defined TB with relative endocrine resistance provides the right setup for HARMONIA study to explore likely differential re-sensitization to endocrine therapy with RIB vs. PAL and ultimately testing which CDK4/6i prepares best for continued response and OS benefit. In addition, HARMONIA explores the value of earlier Tx with chemotherapy (paclitaxel) + anti PD-1 (tislelizumab) in pts with BL tumors to leverage learnings from treating ET-insensitive triple-negative BC. Methods: This is an international, multicenter, randomized, open-label, phase III study, using prospective pre-selection based on TB in pts with HR+/HER2- ABC, with HER2-E tumors (main cohort) and with BL tumors (exploratory cohort). HER2-E cohort will randomized pts 1:1 to RIB+ET (letrozole or fulvestrant) or PAL+ET. As per recent protocol amendment, BL cohort pts will be treated with paclitaxel plus tislelizumab, an anti PD-1 monoclonal antibody, pts may be offered to try RIB + ET first, and will remain eligible for paclitaxel + tislelizumab upon progression. Primary endpoint (EP): PFS per RECIST v1.1. Secondary EP: OS, PFS2, clinical benefit rate, duration and time to response, quality of life, and exploratory EP, including subtype switching between primary and metastatic tumor, and after trial Tx. Interim and primary EP analysis will be performed after 224 and 310 PFS events are observed (~80% power using one-sided 5% α). HARMONIA will recruit in Spain (55 sites), Portugal (5), and US (35) within SOLTI & AFT network. Clinical trial information: NCT05207709 .

Supplementary Figure 1 from RG7204 (PLX4032), a Selective BRAFV600E Inhibitor, Displays Potent Antitumor Activity in Preclinical Melanoma Models

Supplementary Methods, Tables 1-3, Figure Legend from RG7204 (PLX4032), a Selective BRAFV600E Inhibitor, Displays Potent Antitumor Activity in Preclinical Melanoma Models

Supplementary Figure 1 from RG7204 (PLX4032), a Selective BRAF^V600E Inhibitor, Displays Potent Antitumor Activity in Preclinical Melanoma Models

A bstract In 2020, Novartis Pharmaceuticals Corporation and the U.S. Food and Drug Administration (FDA) started a 4-year scientific collaboration to find novel radiogenomics-based prognostic and predictive factors for HR+/HER2-metastatic breast cancer under a Research Collaboration Agreement. This manuscript aims to detail the guiding principles and methodology for this study. We include a discussion of internal and external clinical, genomics, imaging datasets, data processing workflows, and machine learning model development strategies. We also prospectively define our success criteria to ensure robust scientific outputs. Disclosure This publication reflects the views of the authors and should not be construed to represent FDA’s views or policies.