Longitudinal Circulating Tumor DNA Research Articles

Evolutionary Pressures Shape Undifferentiated Pleomorphic Sarcoma Development and Radiotherapy Response.

Radiotherapy is an integral component in the treatment of many types of cancer, with approximately half of cancer patients receiving radiotherapy. Systemic therapy applies pressure that can select for resistant tumor subpopulations, underscoring the importance of understanding how radiation impacts tumor evolution to improve treatment outcomes. We integrated temporal genomic profiling of 120 spatially distinct tumor regions from 20 patients with undifferentiated pleomorphic sarcomas (UPS), longitudinal circulating tumor DNA (ctDNA) analysis, and evolutionary biology computational pipelines to study UPS evolution during tumorigenesis and in response to radiotherapy. Most unirradiated UPS displayed initial linear evolution followed by subsequent branching evolution with distinct mutational processes during early and late development. Metrics of genetic divergence between regions provided evidence of strong selection pressures during UPS development that further increased during radiotherapy. Subclone abundance changed following radiotherapy with subclone contraction tied to alterations in calcium signaling, and inhibiting calcium transporters radiosensitized sarcoma cells. Finally, ctDNA analysis accurately measured subclone abundance and enabled non-invasive monitoring of subclonal changes. These results demonstrate that radiation exerts selective pressures on UPS and suggest that targeting radioresistant subclonal populations could improve outcomes after radiotherapy.

Longitudinal circulating tumor DNA monitoring in predicting response to short-course radiotherapy followed by neoadjuvant chemotherapy and camrelizumab in locally advanced rectal cancer: data from a Phase Ⅲ clinical trial (UNION).

This study, conducted as part of a multicenter phase III clinical trial, aimed to assess the utility of circulating tumor DNA (ctDNA)-based minimal residual disease (MRD) in comparing the efficacy of short-course and long-course chemoradiotherapy (CRT) for locally advanced rectal cancer (LARC). A total of 244 plasma samples from 79 LARC patients undergoing neoadjuvant therapy (NAT) before surgery were collected at various time points. Targeted deep sequencing using a novel MRD panel was performed. During NAT, ctDNA levels declined significantly. Baseline ctDNA-MRD status did not correlate significantly with treatment response. Notably, compared to long-course radiotherapy, microsatellite instability increased significantly after short-course radiotherapy (shortRT). Additionally, ctDNA negativity or lower levels were significantly associated with pathological complete response (pCR). Clearance of ctDNA and MRD after shortRT correlated significantly with pCR. A predictive model based on ctDNA-MRD, combined with carcinoembryonic antigen (CEA), outperformed models using only MRD or only CEA in predicting pCR/non-pCR. These findings provide insights into NAT for LARC and highlight ctDNA-based MRD assessment's potential in tailoring treatment strategies, emphasizing the need for personalized approaches.

Neoadjuvant and adjuvant osimertinib in stage IA-IIIA, EGFR-mutant non-small cell lung cancer (NORA).

Treatment with adjuvant osimertinib for three years is the standard-of-care for resected stage IB-IIIA non-small cell lung cancer (NSCLC) harboring epidermal growth factor receptor (EGFR)-mutations. The role of neoadjuvant osimertinib in the perioperative setting is yet to be elucidated in the NeoADAURA study (NCT04351555). This is a single center, pilot study of patients with clinical stage IA-IIIA NSCLC (AJCC 8th edition) harboring an activating EGFR mutation (Exon 19 deletion, L858R) (NCT04816838). Patients were treated with two 28-day cycles of neoadjuvant osimertinib followed by surgical resection and 3 years of adjuvant osimertinib. The primary endpoint was objective response rate (ORR) after 2 cycles of neoadjuvant treatment. Secondary endpoints included pathologic complete response (pCR) rate and major pathologic response (MPR) rate. Exploratory objectives included the correlation of longitudinal circulating tumor DNA (ctDNA) testing (Signatera) and response to neoadjuvant osimertinib. A total of 25 patients were enrolled and treated with neoadjuvant osimertinib, and all patients received surgical resection with R0 resection. The ORR was 44% (n=11) all of which were partial responses. Fourteen patients (56%) showed stable disease (SD) following neoadjuvant osimertinib. MPR and PCR rates were 24% (n=6) and 0%, respectively. None of the patients received adjuvant chemotherapy. The median disease free survival (DFS) was not reached at a median follow-up of 31 months (range, 13.8-38.6 months). Six patients (30%) were ctDNA-positive at baseline and achieved clearance after 1 cycle of neoadjuvant osimertinib. There were no grade 3 adverse events (AEs) during neoadjuvant treatment. Two cycles of neoadjuvant osimertinib did not meet its primary endpoint of ORR. Neoadjuvant osimertinib is a feasible approach with a manageable safety profile in resectable EGFR-mutant NSCLC.

Circulating tumor DNA status and dynamics predict recurrence in patients with resected extrahepatic cholangiocarcinoma

Surgery is the only curative therapeutic option for resectable extrahepatic cholangiocarcinoma, but recurrence is common, and prognosis is poor. There is an unmet clinical need for improved decision-making regarding adjuvant chemotherapy (ACT). Herein, we evaluated the usefulness of monitoring longitudinal circulating tumor DNA (ctDNA) for molecular residual disease (MRD) in patients from the STAMP trial, which compares the efficacy of adjuvant capecitabine (CAP) vs. gemcitabine plus cisplatin (GemCis). Between July 2017 and November 2020, 101 patients were randomized 1:1 to receive GemCis (n= 50) or CAP (n= 51). Efficacy outcomes were analyzed with an extended follow-up of 19 months from the previous report. From a biomarker cohort of 89 patients, longitudinal plasma samples (n= 254) were prospectively collected post-surgery before ACT, and on-ACT at 12 and 24 weeks from cycle 1 day 1 (C1D1). ctDNA was evaluated using a personalized, tumor-informed, 16-plex PCR next-generation sequencing assay and was correlated with clinical outcomes. In the extended follow-up analysis, median disease-free survival (DFS) and overall survival did not significantly differ between the CAP and GemCis groups. Significantly inferior DFS was associated with ctDNA positivity before ACT (hazard ratio [HR] 1.8; p= 0.029), on-ACT at 12 weeks from C1D1 (HR 7.72; p <0.001), on-ACT at 24 weeks from C1D1 (HR 5.24; p <0.001), and anytime post-surgery (HR 3.81; p <0.001). Analysis of pre-treatment to on-treatment ctDNA dynamics revealed that serially ctDNA-negative patients exhibited a significantly longer DFS compared to those with sustained ctDNA positivity (HR 6.7; p <0.001) or those who turned ctDNA positive (HR 5.8; p <0.001). In patients with resected extrahepatic cholangiocarcinoma, ctDNA status and dynamics predicted recurrence during adjuvant therapy, and may help optimize clinical decision-making. The findings from this study highlight the critical role of ctDNA as a prognostic biomarker and monitoring tool for patients with resected extrahepatic cholangiocarcinoma. By demonstrating the superiority of ctDNA to predict disease recurrence compared to conventional biomarkers such as cancer antigen 19-9 and carcinoembryonic antigen, this study underscores its potential in guiding decision-making during adjuvant chemotherapy. These results may be crucial to refine post-surgical treatment strategies and improve patient outcomes. The practical application of ctDNA monitoring could lead to more personalized treatment approaches, enabling timely interventions based on molecular residual disease status. NCT03079427.

413P Longitudinal circulating tumor DNA (ctDNA) dynamics in phase I/IIa study of the first-in-class CDK4-selective inhibitor, PF-07220060, in combination with endocrine therapy in patients with HR+/HER2− metastatic breast cancer (mBC) who progressed on prior CDK4/6 inhibitors

413P Longitudinal circulating tumor DNA (ctDNA) dynamics in phase I/IIa study of the first-in-class CDK4-selective inhibitor, PF-07220060, in combination with endocrine therapy in patients with HR+/HER2− metastatic breast cancer (mBC) who progressed on prior CDK4/6 inhibitors

Genomic alterations associated with resistance and circulating tumor DNA dynamics for early detection of progression on CDK4/6 inhibitor in advanced breast cancer.

Combined CDK4/6 inhibitor (CDK4/6i) and endocrine therapy significantly improves outcome for patients with estrogen receptor-positive (ER+) metastatic breast cancer, but drug resistance and thus disease progression inevitably occur. Herein, we aimed to identify genomic alterations associated with combined CDK4/6i and endocrine therapy resistance, and follow the levels of specific mutations in longitudinal circulating tumor DNA (ctDNA) for early detection of progression. From a cohort of 86 patients with ER+ metastatic breast cancer we performed whole exome sequencing or targeted sequencing of paired tumor (N = 8) or blood samples (N = 5) obtained before initiation of combined CDK4/6i and endocrine therapy and at disease progression. Mutations in oncogenic genes at progression were rare, while amplifications of growth-regulating genes were more frequent. The most frequently acquired alterations observed were PIK3CA and TP53 mutations and PDK1 amplification. Longitudinal ctDNA dynamics of mutant PIK3CA or private mutations revealed increased mutation levels at progression in 8 of 10 patients (80%). Impressively, rising levels of PIK3CA-mutated ctDNA were detected 4-17 months before imaging. Our data add to the growing evidence supporting longitudinal ctDNA analysis for real-time monitoring of CDK4/6i response and early detection of progression in advanced breast cancer. Further, our analysis suggests that amplification of growth-related genes may contribute to combined CDK4/6i and endocrine therapy resistance.

Safety and anti-tumor activity of BAY 2927088 in patients with HER2-mutant NSCLC: Results from an expansion cohort of the SOHO-01 phase I/II study.

LBA8598 Background: HER2 ( ERBB2) mutations have been reported in approximately 2-4% of patients (pts) with NSCLC, with exon 20 insertions being the most common. BAY 2927088 is an oral, reversible tyrosine kinase inhibitor that potently inhibits mutant HER2 and mutant EGFR in preclinical models. Encouraging objective responses were observed in pts with NSCLC harboring a HER2-activating mutation and treated with BAY 2927088 in the dose-escalation/backfill part of the Phase I/II SOHO-01 trial (NCT05099172). More recently the FDA has granted Breakthrough Therapy designation for BAY 2927088 for previously treated pts with advanced NSCLC and activating HER2 mutations. Here we report the safety, anti-tumor activity, and longitudinal circulating tumor DNA (ctDNA) data in a cohort of pts treated with BAY 2927088 from the expansion part of this trial. Methods: Pts with advanced NSCLC harboring a HER2-activating mutation and who experienced disease progression after at least 1 systemic therapy, but naïve to HER2-targeted therapy, were enrolled and received BAY 2927088 at 20 mg twice daily. Plasma samples were collected at baseline and several on-treatment time points for longitudinal ctDNA profiling using next-generation sequencing (NGS; Oncomine Precision Assay). Results: As of February 19, 2024, 34 pts were treated with BAY 2927088, with a median follow-up of 8 months. Median age was 62 years, 68% were female, 74% had never smoked, and 53% had received ≥2 lines of systemic anti-cancer therapy. Median duration of treatment with BAY 2927088 was 7.1 months (range 0.2-9.2). Treatment was ongoing in 17 pts (50%). Ten pts had a dose reduction, 8 had dose interruptions, and 3 discontinued study treatment due to a drug-related adverse event. The most common adverse events were diarrhea (85%; mainly grade 1-2) and rash (47%; grade 1-2). In 33 pts evaluable for efficacy, responses were observed in 23 (objective response rate 70%; 95% CI 51.3, 84.4) and 5 (15%) had stable disease for a disease control rate of 82% (95% CI 64.5, 93.0). Responses were rapid (median time to response 5.7 weeks) and durable (median duration of response not reached). Median progression-free survival was 8.1 months (95% CI 4.4, not evaluable). In a subset of 20 pts with successful paired (baseline, on-treatment) blood NGS and detectable HER2 ctDNA at baseline, 19/20 (95%) had a decrease in ctDNA and 1 pt with progressive disease had an increase in ctDNA; 15/20 (75%) had no detectable ctDNA after 6 weeks of treatment (including 3/4 pts with stable disease). Conclusions: BAY 2927088 led to rapid, substantial, and durable responses in pts with pretreated HER2-mutant NSCLC. The safety profile was consistent with previously reported data. These data support the further clinical development of BAY 2927088 in pts with HER2-mutant NSCLC. Clinical trial information: NCT05099172 .

Longitudinal circulating tumor DNA monitoring in predicting response to short-course neoadjuvant radiotherapy in locally advanced rectal cancer: Data from a phase III clinical trial (UNION).

LBA3606 Background: The data presented here is from a multicenter, randomized, open-label, controlled Phase III clinical study evaluating the feasibility of short-course radiotherapy (shortRT) sequentially combined with camrelizumab and chemotherapy as neoadjuvant therapy (NAT) for locally advanced rectal cancer (LARC)(UNION). Our aim is to explore the value of circulating tumor DNA (ctDNA)-based minimal residual disease (MRD) in assessing the comparative efficacy of short-course and long-course chemoradiotherapy (CRT). Methods: A total of 244 plasma samples from 79 LARC patients, who underwent NAT prior to curative surgery, were collected at baseline (C1), on-NAT (C2), post-NAT (C3), and post-surgery (C4). Deep targeted panel sequencing of 556 cancer-related genes was performed. The changes in genomic features and ctDNA-MRD status during treatment were monitored, and the relationship between these changes and treatment response were explored. Results: During NAT, the ctDNA-MRD positivity rate showed significant declining trends. Patients with high baseline TMB tend to show a significant inclination towards major pathological response and tumor regression grade 0/1 after NAT, while there is no significant correlation observed between baseline ctDNA-MRD status and treatment response. Interestingly, compared to long-course radiotherapy, microsatellite instability is more pronounced after shortRT ( P=0.042), and ctDNA negativity is significantly associated with pathological complete response (pCR) ( P=0.022). Furthermore, both ctDNA clearance ( P=0.049) and MRD clearance ( P=0.015) after shortRT are significantly correlated with pCR. A risk scoring predictive model based on ctDNA-MRD was established, with achieving the highest C-index at the C2 time point. This model, combining MRD clearance and CEA, outperforms models using only MRD clearance (AUC=0.917, 95% CI=0.753 to 1.000) or only CEA (AUC=0.733, 95% CI=0.449 to 1.000), demonstrating superior performance in predicting pCR/non-pCR (AUC=0.983, 95% CI=0.937 to 1.000). Conclusions: These findings offers valuable insights into the dynamic landscape of NAT for LARC management and emphasize the potential of ctDNA-based MRD assessment as a valuable tool for tailoring treatment strategies. The differences observed between shortCRT and longCRT regimens underscore the need for personalized treatment approaches. Overall, our study contributes valuable insights into optimizing treatment decision-making and predicting treatment response in LARC patients, ultimately advancing the field of rectal cancer management.

Longitudinal circulating tumor DNA (ctDNA) analysis during treatment (Tx) of locally advanced resectable (LAR) gastric or gastroesophageal junction (G/GEJ) adenocarcinoma (ADENOCA): The PLAGAST prospective biomarker study.

4028 Background: After surgery, patients (pts) with LAR G/GEJ ADENOCA have a high recurrence risk despite Tx. Here, we investigate the ability of ctDNA to predict Tx response and improve risk stratification in a sub-cohort of pts from the PLAGAST prospective study (NCT02674373). Methods: Plasma samples were prospectively collected at baseline (before neoadjuvant therapy (NAT)/before surgery for NAT-naive pts), during-NAT, post-NAT, and post-surgery within 2-12 weeks, before adjuvant Tx [molecular residual disease (MRD) window]. Retrospective ctDNA analysis was performed using a clinically validated personalized, tumor-informed 16-plex PCR assay (Signatera, Natera Inc.). ctDNA results were evaluated for their correlation to recurrence-free survival (RFS) and overall survival (OS). Results: Between 07/2015 and 12/2022,plasma samples (n=283) were collected from 63 pts with LAR (≥cT2 and/or cN+), G (N=38/63; 60%) and GEJ (N=25/63; 40%) ADENOCA, median (m) age: 66 years (range: 34-86), and mfollow-up: 31 months (mo) (range: 2-93). ctDNA-clearance from baseline to during-NAT (N=30) or post-NAT (N=28), and MRD (N=50) window was associated with longer RFS and OS. Persistent ctDNA positivity (+ve) during-NAT was associated with a mRFS of 13.3mo vs. not reached (NR) for pts who achieved ctDNA-clearance (HR=4; p=0.032), and a mOS of NR for both groups, with 24mo OS rate at 95.6% vs. 58.6% (HR=5.85; p=0.097), respectively. ctDNA clearance post-NAT was associated with a mRFS of 7.79 vs. 52.04 mo (HR= 3.69; p=0.019) and a mOS of 18.9mo vs. NR (HR=8.78; p=0.007) for ctDNA-cleared vs. pts who did not clear, respectively. During the MRD window, mRFS of 3.57mo vs. NR (HR=12.94; p&lt;0.0001) and mOS of 8.59mo vs. NR (HR=14.54; p&lt;0.0001) was observed for ctDNA+ve and ctDNA negative pts, respectively. ctDNA dynamics revealed pts with early ctDNA clearance (during NAT) had the best outcomes, followed by pts who cleared ctDNA post-NAT, while pts who remained ctDNA+ve at baseline, during-NAT, and post-NAT had worse RFS and OS (24mo RFS rate of 75% vs. 48% vs. NR and 24mo OS rate of 100% vs. 80% vs. 17%, respectively). Of note, pts who achieved ctDNA clearance post-NAT correlated with tumor regression grade (TRG) 1/2/3 when compared to a TRG score of 4/5 in pts who were unable to clear ctDNA post-NAT (p=0.0345). Conclusions: Tumor-informed ctDNA results were predictive of NAT response and correlated with long-term outcomes with early ctDNA clearance associated with superior RFS and OS; meanwhile persistent ctDNA+ve post-NAT/pre-surgery/during MRD correlated with inferior OS and/or RFS as well as poor pathological response. In this initial analysis of the PLAGAST study, longitudinal ctDNA monitoring was prognostic of patient outcomes and may guide NAT clinical decision-making in pts with LAR G/GEJ ADENOCA. Clinical trial information: NCT02674373 .

Improving Prediction of Survival and Progression in Metastatic Non-Small Cell Lung Cancer After Immunotherapy Through Machine Learning of Circulating Tumor DNA.

To use modern machine learning approaches to enhance and automate the feature extraction from the longitudinal circulating tumor DNA (ctDNA) data and to improve the prediction of survival and disease progression, risk stratification, and treatment strategies for patients with 1L non-small cell lung cancer (NSCLC). Using IMpower150 trial data on patients with untreated metastatic NSCLC treated with atezolizumab and chemotherapies, we developed a machine learning algorithm to extract predictive features from ctDNA kinetics, improving survival and progression prediction. We analyzed kinetic data from 17 ctDNA summary markers, including cell-free DNA concentration, allele frequency, tumor molecules in plasma, and mutation counts. Three hundred and ninety-eight patients with ctDNA data (206 in training and 192 in validation) were analyzed. Our models outperformed existing workflow using conventional temporal ctDNA features, raising overall survival (OS) concordance index to 0.72 and 0.71 from 0.67 and 0.63 for C3D1 and C4D1, respectively, and substantially improving progression-free survival (PFS) to approximately 0.65 from the previous 0.54-0.58, a 12%-20% increase. Additionally, they enhanced risk stratification for patients with NSCLC, achieving clear OS and PFS separation. Distinct patterns of ctDNA kinetic characteristics (eg, baseline ctDNA markers, depth of ctDNA responses, and timing of ctDNA clearance, etc) were revealed across the risk groups. Rapid and complete ctDNA clearance appears essential for long-term clinical benefit. Our machine learning approach offers a novel tool for analyzing ctDNA kinetics, extracting critical features from longitudinal data, improving our understanding of the link between ctDNA kinetics and progression/mortality risks, and optimizing personalized immunotherapies for 1L NSCLC.

Characterization of mutational signatures demonstrating adaptive mutability post anti-EGFR therapy in a real-world metastatic colorectal cancer cohort.

3545 Background: Clinical benefit from anti-EGFR therapy (EGFRi) for RAS/RAF WT metastatic colorectal cancer (mCRC) is limited by secondary mutations in mitogen-activated protein kinases. The source of these new clones has been debated. In contrast to the outgrowth of pre-existing rare subclones, a new model, termed adaptive mutability, proposes the transient loss of DNA repair genes and concurrent induction of error-prone polymerase repair mechanisms (Russo et al Science, ’19). However, clinical evidence for this effect in a large patient cohort is lacking. Using longitudinal circulating tumor DNA (ctDNA) in a real-world cohort, we sought to explore mutational signatures and assess the presence of adaptive mutability in mCRC patients after EGFRi treatment. Methods: 288 patients from Guardant Health’s GuardantINFORM database with mCRC who received EGFRi and underwent longitudinal ctDNA NGS testing by Guardant360 (Redwood City, CA) between December 2014 and March 2023 were included. We extracted de novo single-nucleotide variant mutational signatures from the somatic ctDNA mutations per-cohort level, comparing pre- to post-treatment mutational profiles. Extracted mutational signatures were compared against COSMIC catalogue. Results: Of the 288 patients identified, 99.7% (287/288) were MSS/MSI-L prior to treatment. Pre-treatment, patients had a mean and median of 3 reportable variants per sample, with 30.2% (87/288) samples with &gt;5 variants. Post-treatment, patients had a mean of 5 and a median of 4 reportable variants, with 64.6% (186/288) of patients with &gt;5 variants. Overall mean shift in reportable variants between pre- and post-EGFRi was 5 variants, with a median of 4 changes. In comparing pre- and post-EGFRi cohorts for new mutations, three mutational signatures emerged: SBS17b, SBS15, and SBS3. SBS15 is associated with mismatch repair (MMR) deficiency and classically seen in MSI-H tumors, though notably this cohort was overwhelmingly MSS. SBS15 has been associated with polymerase epsilon exonuclease (POLE) defects and likely reflects repair by alternate error-prone polymerases such as Polι, Polλ, and Polκ. SBS3 has been associated with homologous recombination (HR) deficiency. SBS17b has been associated with exposure to 5-FU based chemotherapy in CRC patients, which was co-administered in many of the EGFRi treated patients. Conclusions: New mutations arising with EGFR inhibition demonstrate strong evidence for adaptive mutability, showcasing loss of mismatch repair and HR fidelity, and reliance on error-prone polymerases. This is the first large cohort to indirectly demonstrate evidence for this genomic mechanism underlying secondary acquired resistance. Further validation of the adaptive mutability signatures may support therapeutic strategies leveraging this vulnerability to extend benefit from targeted therapies.

Longitudinal circulating tumor DNA monitoring for detection of molecular residual disease in patients with advanced germ cell tumors.

e17022 Background: Germ cell malignancies, commonly manifesting as testicular cancer, is one of the most common malignancies in men 15 to 45 years of age, with the incidence doubling over the past 40 years. When identified promptly and treated with a multidisciplinary approach, germ cell tumors have an excellent prognosis with cure rate &gt;90% and 5-year survival rate &gt;95%. Treatment involves radical orchiectomy for diagnostic and therapeutic purposes. Further management includes active surveillance, adjuvant chemotherapy, retroperitoneal lymph node dissection (RLND), and radiation therapy. While AFP, B-HCG, and LDH are good biomarkers, they are not sensitive or specific for detecting molecular residual disease (MRD). B-HCG is detected in &lt;30% of individuals with seminoma and B-HCG and AFP are detected in 50–60% of patients with non-seminomatous tumors. We describe the use of circulating tumor DNA (ctDNA) for detection of MRD in advanced germ cell malignancy, especially when baseline biomarkers are negative. Methods: This is a retrospective analysis of 20 patients with testicular cancer treated at Rush University Medical Center who monitored closely for MRD. Signatera (Natera Inc.), a personalized tumor-informed ctDNA assay, was utilized for detection and quantification of ctDNA in patients’ plasma samples, measured at MRD (1-12 weeks post-orchiectomy) and regular intervals thereafter, regardless of treatment modality. Event free survival (EFS) was determined, defined as the period from radical orchiectomy to date of radiographic progression of disease. Results: There was a total of 20 patients (35% seminoma, 65% non-seminoma) with 2 of the patients having extragonadal disease. The mean age was 32.2 years old with IQR (28-36). Post operatively, 20% underwent RLND, 10% were on surveillance, 53% received post-orchiectomy chemotherapy, 6.7% of patients underwent autologous stem cell transplant. The median follow up time is 1.14 years. Two patients had positive ctDNA despite negative baseline traditional biomarkers. There were 23.3% (7/30) of patients that had evidence of radiographic progression. Of the patients with progression, serial ctDNA monitoring had high rates of concordance (85%, 6/7) of ctDNA positivity with biomarker positivity and radiographic progression. Conclusions: Overall, ctDNA correlated with, and sometimes even preceded, traditional biomarkers and radiographic findings of disease progression. The ctDNA positivity of 2 patients in this cohort despite negative baseline AFP, B-HCG, and LDH, highlights the sensitivity and specificity of ctDNA for MRD compared to more traditional biomarkers. Serial monitoring of ctDNA offers valuable insights into germ cell tumor disease status, including presence of MRD, and there is a need for prospective studies to guide treatment escalation and de-escalation in germ cell tumors.

Longitudinal circulating tumor DNA kinetics and correlation with patient outcomes in metastatic melanoma.

e21538 Background: Previous studies have shown circulating tumor DNA (ctDNA) to be an accurate noninvasive method for detecting minimal residual disease and predicting therapeutic response. This study aims to investigate if positive ctDNA and subsequent clearance kinetics may be used as a predictive and prognostic tool in patients with stage IV metastatic melanoma. Non-clearance of ctDNA may be associated with poorer outcomes for progression-free survival (PFS) and overall survival (OS). Methods: In this retrospective analysis of preexisting data from a cohort of 27 patients with stage IV melanoma treated at Rush University, longitudinal ctDNA plasma samples collected between 05/01/2020 and 01/01/2024 were analyzed. A tumor-informed ctDNA assay (SignateraTM, reported in mean tumor molecules per mL (MTM/ml), low limit of detection of 0.01% variant allele frequency) was used for detection and quantification of ctDNA in plasma samples. Progression was determined based off of radiographic studies, overall survival was determined by time from stage IV diagnosis to patient death. Results: A total of 192 ctDNA timepoints were analyzed. The median number of ctDNA timepoints per patient was 5 (range 1-26). 8 patients were identified whose initial ctDNA result was negative and remained negative throughout their treatment course; 5/8 of these patients had baseline negative values available prior to the initiation of treatment. 19 patients had at least 1 positive ctDNA result at any given time; 1/19 of these patients was ctDNA-negative at baseline, 7/19 were positive at baseline, and 11/19 did not have baseline values available. The PFS rate was higher for ctDNA-negative patients compared to ctDNA-positive patients (62.5% vs. 57.9%). The OS rate was also higher for ctDNA-negative patients compared to ctDNA-positive patients (75% vs. 52.6%). Of the ctDNA-positive patients, those who achieved persistent clearance or had decreasing values of ctDNA had higher PFS rates when compared to ctDNA-positive patients who neither downtrended nor achieved clearance (71.4% and 66.7% vs. 22.9%). Patients who achieved persistent clearance or had decreasing values of ctDNA also had higher OS rates when compared to ctDNA-positive patients who neither downtrended nor achieved clearance (71.4% and 100% vs. 33.3%). Conclusions: Within the limitations of a small sample size, our data suggests that for patients with stage IV melanoma, a positive ctDNA result is associated with poorer outcomes for PFS and OS, when compared to patients with negative ctDNA results. Additionally, ctDNA-positive patients who achieved persistent clearance or downtrending ctDNA values showed more favorable outcomes for PFS and OS than ctDNA-positive patients who did not. [Table: see text]

Personalized circulating tumor DNA monitoring improves recurrence surveillance and management after curative resection of colorectal liver metastases: a prospective cohort study.

Approximately 60% of patients with colorectal liver metastases (CRLM) experience relapse within 2 years after radical resection, previous studies have proven that repeat local treatment (LT) could prolong survival, however, it is difficult to seize the window for LT due to the lack of a high-sensitive surveillance method. In this study, the authors aim to examine the value of longitudinal circulating tumor DNA (ctDNA) in guiding adjuvant chemotherapy, optimizing clinical surveillance strategy, and thereby improving CRLM outcomes. The authors conducted a prospective clinical trial using a personalized, tumor-informed ctDNA assay to monitor 60 CRLM patients undergoing resection with curative intent. Formalin-fixed paraffin-embedded tumor samples were collected after surgery. Blood samples were collected before surgery, 30 days after surgery (post-OP), and every third month until relapse or up to 2 years. A total of 394 plasma samples from 60 eligible patients were analyzed, with a median follow-up time of 31.3 months. Landmark analyses revealed that detectable ctDNA at post-OP (HR, 4.8), postadjuvant chemotherapy (HR, 6.0), and end-of-treatment (HR, 5.6) were associated with higher recurrence risk ( P <0.001). Post-OP ctDNA positivity served as the only independent prognostic marker in the multivariant analysis (HR, 5.1; P <0.001). Longitudinal ctDNA analysis identified relapsed patients at both sensitivity and specificity of 100%. Most (75%) patients were found with radiological relapse within 6 months after the first detectable ctDNA with a median lead time of 3.5 months. In relapsed patients, 73.2% had oligometastatic disease and 61% were liver-restricted, of which 72.0% received repeat LTs, and 60.0% achieved a secondary no evidence of disease status. Longitudinal ctDNA monitoring assists in early prediction of relapse, and thereby improves survival of CRLM patients by increased secondary resection rate and secondary no evidence of disease rate.

Longitudinal circulating tumor DNA monitoring for detection of molecular residual disease in patients with penile squamous cell carcinoma.

11 Background: Penile squamous cell carcinoma (SCC) is an extremely rare, aggressive disease, representing 0.4-0.6% of all malignancies in males in the U.S. and Europe. Early diagnosis is imperative, as lymphatic spread is associated with a dismal prognosis. The estimated 5-year survival rate in patients with pelvic lymph node involvement is 0%. Moreover, there are limited treatment options that carry significant toxicity risks. Accurate biomarkers to evaluate treatment response and guide treatment to improve outcomes are needed. Molecular residual disease monitoring with circulating tumor DNA (ctDNA) may be helpful in these scenarios. Methods: This is a retrospective analysis of a cohort of 7 patients with advanced HPV-unassociated penile SCC treated at Rush University Medical Center who monitored closely for molecular residual disease (MRD). Signatera (Natera Inc.), a personalized tumor-informed ctDNA assay, was utilized for detection and quantification of ctDNA in patients’ plasma samples, measured at regular intervals. Progression of disease was based on radiographic imaging. Results: In our cohort, personalized, tumor-informed ctDNA assays were designed for 100% (7/7) of the patients. ctDNA was detectable in at least one time point in all of the patients. One patient underwent partial penectomy and lymph node (LN) dissection with 1/11 LN involved. He is being monitored without adjuvant treatment and has sustained ctDNA clearance. Another patient underwent surgery, and had positive post-operative ctDNA. He was treated with adjuvant TIP (paclitaxel, ifosfamide, and cisplatin) with subsequent ctDNA clearance. In 3 of the patients, ctDNA was checked at regular intervals and rising ctDNA prompted imaging studies that showed progression. These patients proceeded to second line treatment options. The remaining 2 patients are non-surgical candidate with LN positivity, who will begin treatment with TIP and monitoring of ctDNA after each cycle of chemotherapy. Twenty-eight percent (2/7) of patients remain alive with sustained ctDNA clearance. Twenty-eight percent (2/7) of patients remain alive with ctDNA positivity, planned to initiate treatment and monitoring of ctDNA at regular intervals. Forty-three percent (3/7) of patients who had persistent ctDNA positivity are now deceased. Conclusions: Our data suggests that a personalized, tumor-informed ctDNA assay is not only useful for MRD monitoring, but also highly predictive of treatment response and imaging-based progression in patients with penile SCC. In our sample, MRD status correlated with both radiographic progression and clinical outcomes. Prospective studies are needed to better understand how ctDNA can be used to guide neoadjuvant and adjuvant approaches, including treatment intensification or de-escalation, in patients with penile SCC.

Brentuximab Vedotin, Nivolumab, Doxorubicin, and Dacarbazine (AN+AD) for Early-Stage Classical Hodgkin Lymphoma (SGN35-027 Part C)

Introduction Brentuximab vedotin (BV) with AVD is approved in classical Hodgkin lymphoma (cHL) and has demonstrated statistically significant improvement in 6-year overall survival (OS) as compared with ABVD; associated neuropathy and neutropenia may be related to overlapping mechanisms of BV and vinblastine (Ansell 2022). A study in nonbulky early-stage cHL showed preserved efficacy with improved safety when omitting vinblastine in the BV-AD regimen (Abramson 2023). Here, we present results of a phase 2 trial adding nivolumab to the BV-AD regimen without radiation in patients (pts) with nonbulky early-stage cHL (SGN35-027 Part C). Methods SGN35-027 (NCT03646123) Part C enrolled pts with Ann Arbor stage I or II cHL without bulky disease, defined as those with a single node or nodal mass with a &amp;lt;10-cm diameter on computed tomography imaging. Pts received 4 cycles of AN+AD (BV 1.2 mg/kg [A], nivolumab 240 mg [N], doxorubicin 25 mg/m 2 [A], and dacarbazine 375 mg/m 2 [D] intravenously on days 1 and 15 of each 28-day cycle). Per protocol, G-CSF prophylaxis was not required for subjects receiving the treatment regimen. The primary endpoint is complete response (CR) rate at end of treatment (EOT). Secondary endpoints include progression-free survival (PFS), overall response rate (ORR), duration of response (DOR), and duration of complete response (DOCR), as well as safety and tolerability. The Lugano Classification Revised Staging System for malignant lymphoma (Cheson 2014) incorporating Lymphoma Response to Immunomodulatory Therapy Criteria (LYRIC) for nodal non-Hodgkin and Hodgkin Lymphomas (Cheson 2016) per investigator was used to assess disease response and progression. Exploratory endpoints include baseline and longitudinal circulating tumor DNA analysis on a subset of pts. Results Part C has completed enrollment with 154 pts having received at least 1 dose of study treatment. The majority of treated pts were white (84%), aged &amp;lt;65 years (92%), and female (55%), and presented with nonbulky stage I (11%) or II (89%) cHL. Median age was 31.0 years (range, 18-77). All findings were based on a data cutoff of 22 May 2023. Among 150 efficacy evaluable pts, the ORR was 98% (95% CI, 94.3-99.6) and the CR rate was 93% (95% CI, 87.3-96.3) at EOT (Table 1). Among all pts treated (N = 154), the ORR was 95% (95% CI, 90.9-98.2) and the CR rate was 90% (95% CI, 84.4-94.4) at EOT. With a median follow-up of 15.2 months, 3 of 154 pts (2%) had progressive disease (at 12.5, 16.4, and 24.0 months) and no deaths occurred. The PFS rate at 12 months was 100% (95% CI, 100-100) (Figure 1). A total of 99.2% of pts (95% CI, 94.3-99.9) had a DOR of least 12 months, and 97.2% (95% CI, 91.5-99.1) had a DOCR of at least 12 months. The planned treatment course of 4 cycles was completed by 94% of pts. Forty-four percent received G-CSF, primarily for primary prophylaxis, for 1 or more cycles. Three percent of pts discontinued treatment (all drugs) due to treatment-emergent adverse events (TEAEs). No events of febrile neutropenia were reported. Thirty four percent of pts experienced grade ≥3 treatment-related TEAEs, and 3% experienced grade ≥3 treatment-related peripheral sensory neuropathy. The most common grade ≥3 treatment-related TEAEs were neutropenia (9%), increased alanine aminotransferase (ALT) (7%), and increased aspartate aminotransferase (5%). Treatment-emergent immune-mediated adverse events (IMAEs) occurred in 22% of pts, and grade ≥3 treatment-emergent IMAEs occurred in 7% of pts. The most common treatment-emergent IMAE of any grade was hypothyroidism (6%). Twelve percent of pts experienced treatment-related serious TEAEs. The most common treatment-related serious TEAEs were pyrexia (3%), increased ALT (1%), and peripheral sensory neuropathy (1%). Conclusions Results from SGN35-027 Part C show promising efficacy and an acceptable safety profile for BV and nivolumab in combination with chemotherapy (AN+AD) for pts with nonbulky early-stage cHL. Pts had high ORR (98%) and CR rates (93%) at EOT, and a 12-month PFS of 100% with a median follow-up of 15.2 months. There was a low incidence of grade 3 or higher neuropathy and there were no cases of febrile neutropenia. AN+AD demonstrates encouraging efficacy in nonbulky early-stage cHL and may avoid toxicities associated with radiation, bleomycin, and vinblastine. Follow-up of Part C is ongoing with 92% of pts in long-term follow-up.

Neratinib+ fulvestrant+ trastuzumab for HR-positive, HER2-negative, HER2-mutant metastatic breast cancer: outcomes and biomarker analysis from the SUMMIT trial.

HER2 mutations are targetable alterations in patients with hormone receptor-positive (HR+) metastatic breast cancer (MBC). In the SUMMIT basket study, patients with HER2-mutant MBC received neratinib monotherapy, neratinib+ fulvestrant, or neratinib+ fulvestrant+ trastuzumab (N+ F+ T). We report results from 71 patients with HR+, HER2-mutant MBC, including 21 (seven in each arm) from a randomized substudy of fulvestrant versus fulvestrant+ trastuzumab (F+ T) versus N+ F+ T. Patients with HR+ HER2-negative MBC with activating HER2 mutation(s) and prior cyclin-dependent kinase 4/6 inhibitor (CDK4/6i) therapy received N+ F+ T (oral neratinib 240 mg/day with loperamide prophylaxis, intramuscular fulvestrant 500 mg on days 1, 15, and 29 of cycle 1 then q4w, intravenous trastuzumab 8mg/kg then 6 mg/kg q3w) or F+ T or fulvestrant alone. Those whose disease progressed on F+ T or fulvestrant could cross-over to N + F + T. Efficacy endpoints included investigator-assessed objective response rate (ORR), clinical benefit rate (RECIST v1.1), duration of response, and progression-free survival (PFS). Plasma and/or formalin-fixed paraffin-embedded tissue samples were collected at baseline; plasma was collected during and at end of treatment. Extracted DNA was analyzed by next-generation sequencing. ORR for 57 N+ F+ T-treated patients was 39% [95% confidence interval (CI) 26% to 52%); median PFS was 8.3months (95% CI 6.0-15.1 months). No responses occurred in fulvestrant- or F+ T-treated patients; responses in patients crossing over to N+ F+ T supported the requirement for neratinib in the triplet. Responses were observed in patients with ductal and lobular histology, 1 or ≥1 HER2 mutations, and co-occurring HER3 mutations. Longitudinal circulating tumor DNA sequencing revealed acquisition of additional HER2 alterations, and mutations in genes including PIK3CA, enabling further precision targeting and possible re-response. The benefit of N+ F+ T for HR+ HER2-mutant MBC after progression on CDK4/6is is clinically meaningful and, based on this study, N+ F+ T has been included in the National Comprehensive Cancer Network treatment guidelines. SUMMIT has improved our understanding of the translational implications of targeting HER2 mutations with neratinib-based therapy.

Longitudinal circulating tumor DNA monitoring for detection of molecular residual disease in patients with surgically resected stage II/III melanoma.

9582 Background: Over the past decade, advances in immunotherapy (IO) have dramatically improved overall survival (OS) for patients with metastatic melanoma. Immune checkpoint inhibitors and BRAF/MEK inhibitors also became standard of care for surgically resected stage III melanoma, and most recently pembrolizumab was approved for stage IIB/C patients. Although the phase III trials that led to their respective approvals met their primary endpoints for relapse-free survival, no benefit in OS has been observed. Given that a large proportion of early-stage melanoma patients are cured with surgery alone, the decision to proceed with adjuvant therapy should be weighed against the risk of potential life-altering toxicity. There is a high unmet need to develop biomarkers to accurately select patients who are most likely to benefit from adjuvant IO while sparing a group of low risk patients from unnecessary treatment. In this study, we evaluated the prognostic value of personalized, tumor-informed circulating tumor DNA (ctDNA) testing in patients with resectable stage II/III melanoma. Methods: In this real-world study, longitudinal plasma samples (n = 159) were analyzed in real-time from 45 stage IIA-IIID cutaneous melanoma patients treated at Rush University between 03/30/2021 and 01/12/2023. A personalized, tumor-informed ctDNA assay (Signatera bespoke, mPCR-NGS assay) was used for detection and quantification of ctDNA in plasma samples. Results: Personalized, tumor-informed ctDNA assays were successfully designed for 93% (42/45) of patients using tissue samples from either surgical resection (14/42, 33%) or biopsy (26/42, 67%; 16 shave, 10 excisional, 1 punch, 1 core). ctDNA was detectable at one or more time points in 36% (15/42) of patients. We observed a higher ctDNA-positivity rate in stage III patients (11/20, 55%) compared to stage II patients (4/22, 18%). Twelve of the 15 ctDNA-positive patients received adjuvant IO/treatment escalation after a positive ctDNA result; 6 patients had sustained ctDNA clearance, 2 had transient clearance, and 4 continue to receive adjuvant IO and follow-up ctDNA testing. Radiographic recurrence was observed in 7/42 patients, 6 of whom were ctDNA-positive. Ninety-six percent (26/27) of patients with persistent ctDNA-negativity remain clinically and radiographically progression-free. Conclusions: Our data suggest that molecular residual disease detection using a personalized, tumor-informed ctDNA assay is highly prognostic in melanoma patients undergoing curative resection. Sustained clearance of ctDNA was achieved with adjuvant therapy in a subset of this cohort. Prospective studies evaluating the utility of ctDNA to aid clinical decision-making regarding adjuvant treatment intensification or de-escalation are warranted.

Longitudinal circulating tumor DNA monitoring in patients with esophageal squamous cell carcinoma.

3041 Background: The clinical utility of longitudinal monitoring with circulating tumor DNA (ctDNA) as a prognostic and a predictive biomarker was recently reported in patients with resectable colorectal cancer (Kotani D, et al. Nature Medicine 2023). Here we report a prospective, observational study of longitudinal ctDNA monitoring in patients with esophageal squamous cell carcinoma (ESCC) receiving neoadjuvant chemotherapy (NAC) followed by surgery. Methods: Patients with ESCC planned for NAC followed by curative surgery, were prospectively enrolled in this study. As per the protocol, plasma samples were collected at 7 timepoints: pre-NAC, post-NAC, and 4,12, 24, 36, and 48-weeks after surgery. CT scans were conducted every 3 months. Longitudinal ctDNA testing was performed using a personalized, tumor-informed ctDNA assay (Signatera, bespoke mPCR, NGS assay). In this initial report, ctDNA results at 3 time points (pre-NAC, post-NAC, and 4 weeks post-surgery) were analyzed and their association with clinical outcomes and tumor regression grade (TRG) scores were assessed. Results: So far, a total of 83 blood samples from 28 patients with ESCC were collected serially at pre-NAC (N=28), post-NAC (N=27), and post-surgical (N=28) time points. Pre-NAC ctDNA was detectable in 96.4% patients (27/28), and detection rates decreased at the post-NAC (37%; 10/27) and post-surgical (11%; 3/28) timepoints. ctDNA-positivity post-NAC and post-surgery was associated with a significantly shorter recurrence free survival (RFS) with HR of 7.0 (95% CI: 1.4-35.0; p = 0.02) and HR of 14 (95% Cl 3.0-62; p &lt;0.001), respectively. Notably, patients who achieved ctDNA clearance with NAC had favorable RFS as compared to the patients who did not (HR=0.15, 95% CI: 0.03 – 0.75; p = 0.02). Post-NAC ctDNA was also associated with tumor regression grade (TRG) score. None of the patients with TRG3 score (N=3) were ctDNA positive, whereas 7.7% (1/13) patients in the TRG2 category and 81.8% (9/11) in the TRG1 category were ctDNA-positive. Conclusions: Our study demonstrates a strong correlation between ctDNA status and clinical outcomes in ESCC patients. Assessment of ctDNA may be useful monitoring in patients with ESCC post NAC/surgery and may be used in the future to direct post-surgical management in this patient population. Clinical trial information: UMIN000042003 .

A longitudinal circulating tumor DNA-based model associated with survival in metastatic non-small-cell lung cancer

One of the great challenges in therapeutic oncology is determining who might achieve survival benefits from a particular therapy. Studies on longitudinal circulating tumor DNA (ctDNA) dynamics for the prediction of survival have generally been small or nonrandomized. We assessed ctDNA across 5 time points in 466 non-small-cell lung cancer (NSCLC) patients from the randomized phase 3 IMpower150 study comparing chemotherapy-immune checkpoint inhibitor (chemo-ICI) combinations and used machine learning to jointly model multiple ctDNA metrics to predict overall survival (OS). ctDNA assessments through cycle 3 day 1 of treatment enabled risk stratification of patients with stable disease (hazard ratio (HR) = 3.2 (2.0–5.3), P < 0.001; median 7.1 versus 22.3 months for high- versus low-intermediate risk) and with partial response (HR = 3.3 (1.7–6.4), P < 0.001; median 8.8 versus 28.6 months). The model also identified high-risk patients in an external validation cohort from the randomized phase 3 OAK study of ICI versus chemo in NSCLC (OS HR = 3.73 (1.83–7.60), P = 0.00012). Simulations of clinical trial scenarios employing our ctDNA model suggested that early ctDNA testing outperforms early radiographic imaging for predicting trial outcomes. Overall, measuring ctDNA dynamics during treatment can improve patient risk stratification and may allow early differentiation between competing therapies during clinical trials.