Circulating Tumor DNA Dynamics Research Articles

Abstract PO1-05-07: Circulating tumor DNA dynamics in acelERA Breast Cancer: a Phase II study of giredestrant for estrogen receptor-positive, HER2-negative, previously treated advanced breast cancer

Abstract BACKGROUND Giredestrant (GIR) is a highly potent, oral, selective estrogen receptor antagonist and degrader (SERD) that exhibits robust estrogen receptor (ER) occupancy. The Phase II, randomized, open-label acelERA Breast Cancer (BC) study (NCT04576455) assessed GIR vs physician’s choice of endocrine therapy (PCET) in second- or third-line ER-positive, HER2-negative advanced BC (ER+, HER2– aBC). The study did not reach statistical significance for the primary endpoint of investigator-assessed progression-free survival (PFS); however, the benefit of GIR was of larger magnitude among patients (pts) with ESR1-mutated tumors (ESR1m; a common cause of acquired resistance to endocrine therapy [ET]). We present an exploratory biomarker analysis of circulating tumor (ct)DNA dynamics. METHODS Pts (n = 303) were randomized 1:1 to GIR or PCET (75% of pts had fulvestrant [FUL]; 25%, an aromatase inhibitor). Partial response (PR), stable disease (SD), and progressive disease (PD) were categorized by RECIST v1.1. Plasma samples taken at Cycle 1, Day 1 (C1D1; n = 229), while on treatment (tx) at C2D1 (n = 220), and at the end of therapy (EOT; n = 155) were evaluated with the FoundationOne Liquid CDx next-generation sequencing assay. Gene mutations were defined as variants with known or likely impact on protein function. Composite tumor fraction (cTF) was defined as the total estimated tumor ctDNA content in each sample, and was only evaluable for a subset of samples (137 C1D1; 136 C2D1; 99 EOT). cTF or ESR1 mutant allele frequency (MAF) changes were calculated as a percent change from C1D1. ESR1m clonality was estimated as variant tumor fraction/estimated tumor fraction. Statistical significance was evaluated using the Mann–Whitney test. RESULTS The overall mutation landscape remained relatively unchanged with GIR tx at C2D1 or EOT, except for ESR1m prevalence, which declined from 43% at C1D1 to 26% on tx and 27% at EOT. With PCET, ESR1m prevalence decreased from 34% at C1D1 to 29% on tx, but increased to 43% by EOT. There were no concordant changes for other top mutated genes in this study, including PIK3CA, TP53, or DNMT3A. cTF decreased on tx in 38/65 (59%) and 32/59 (54%) of evaluable pts with GIR and PCET, respectively; the median change from C1D1 was –23% with GIR compared with –5% with PCET or –15% with FUL. The median change in cTF levels on tx with GIR was significantly greater in pts with a PR (–88%) vs PD (+6%, p = 0.002) or SD (–19%, p = 0.004). The degree of cTF decline on tx with GIR was significantly higher in pts with baseline ESR1m (median change –58%) vs no ESR1m detected (+5%, p = 0.012). Pts with a clonal ESR1m had higher levels of cTF decline on tx vs pts with subclonal ESR1m, suggesting cTF dynamics are a function of tumor heterogeneity. ESR1 MAF decreased on tx in 93% of pts with baseline ESR1m on GIR, vs 60% with PCET and 70% with FUL. ESR1 MAF decline on tx was significantly higher with GIR vs PCET at both C2D1 and EOT (p < 0.0001). The average ESR1 MAF decline on tx with GIR was greater in pts with a PR (–97%) vs PD (–54%, p = 0.025) or SD (–48%, p = 0.051), and all seven GIR-treated pts with a PR showed a near or total loss of ESR1 MAF by C2D1. The ESR1m variants D538G and Y537X had a significantly greater decline in MAF on tx with GIR vs PCET or FUL (p < 0.0001). CONCLUSIONS Data show that cTF and ESR1m ctDNA dynamics were associated with clinical response to GIR in ER+, HER2– aBC. ESR1 MAF decline was significantly greater with GIR vs PCET or FUL. ESR1 MAF declined to a greater degree with GIR compared with cTF, which is consistent with the larger magnitude of PFS benefit seen with GIR in pts with ESR1m tumors. The specific ESR1 variants D538G and Y537X showed greater sensitivity to GIR compared with PCET or FUL. Citation Format: Ann Collier, Aditya Bardia, Joo Hyuk Sohn, Elgene Lim, Marianna Chavez, Miguel Martín, Jorge Martinalbo, Pablo Perez-Moreno, Heather Moore. Circulating tumor DNA dynamics in acelERA Breast Cancer: a Phase II study of giredestrant for estrogen receptor-positive, HER2-negative, previously treated advanced breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO1-05-07.

Abstract PO2-14-06: CIRCULATING TUMOR DNA DYNAMICS IN THE FIRST TREATMENT LINE OF THE SONIA TRIAL

Abstract Background and objective: CDK4/6 inhibitors (CDK4/6i) improve the outcome of patients with ER+/HER2- advanced breast cancer when added to endocrine therapy in the first line or second line of treatment. The recently reported SONIA trial shows no difference in progression free survival after two lines of treatment (PFS2), overall survival (OS) or quality of life benefit of CDK4/6i in first-line compared to second-line, while adverse events are substantially higher when CDK4/6i is added in the first-line. However, a subgroup of patients shows early progression on endocrine mono-treatment and not all patients respond equally well to CDK4/6i. This highlights the need for early response markers during the first weeks of treatment to reduce unnecessary toxicity while providing the most optimal care. In this SONIA side study, we aim to investigate whether we could identify patients who will progress rapidly during first line of therapy by using circulating tumor DNA (ctDNA) dynamics. Methods: Blood samples were obtained from patients included in the SONIA trial in both the first line CDK4/6i + aromatase inhibitor (AI) combination arm (arm A) and the first line AI monotherapy arm (arm B) at three time points: before start, after two weeks and after three months of first line treatment. Cell free DNA (cfDNA) was isolated from all samples and subsequently baseline cfDNA was sequenced with the Oncomine™ Breast cfDNA Assay v2 (Thermofisher), a focused NGS panel of 10 genes. Dedicated dPCR assays were used to track an identified driver mutation over time. Results: Blood samples of 332 patients (206 in arm A and 126 in arm B) before start of first line treatment and after two weeks of treatment were obtained. At baseline, in 142 of the 332 (42.7%) patients at least one somatic mutation was detected. In 30 patients two or more mutations were identified, in which case the mutation with the highest variant allele frequency (VAF) was followed over time. The most frequently mutated genes were PIK3CA (102 patients (30.7% of the total included cohort)), TP53 (32 patients (9.6%)), SF3B1 (8 patients (2.4%) and ESR1 (6 patients (1.8%)). The median observed VAF at baseline was 4.1% (IQR: 1.5%-13.1%). Of the 142 patients with detectable ctDNA at baseline, 141 patients and 100 patients, respectively, had blood samples taken after 2 weeks and after 3 months of treatment. After two weeks, the VAF of the tracked mutation was increased in 15.2% (14/92) of the patients in arm A and in 18.4% (9/49) of the patients in arm B. At the same time 40.2% (37/92) of the patients in arm A and 34.7% (17/49) of the patients in arm B had cleared ctDNA. No difference was observed between the arms for both an increase in VAF (P=0.63, Chi-square test) and ctDNA clearance (P=0.52, Chi-square test). After 3 months an increased VAF of the tracked mutation compared to baseline was observed in 6.3% (4/64) of the patients in arm A and 8.3% (3/36) of the patients in arm B. At this timepoint 59.4% (38/64) of the patients in arm A and 61.1% (22/36) of the patients in arm B had cleared ctDNA. No difference was observed between the arms for both ctDNA clearance (P=0.86, Chi-square test) and increase in VAF (P=0.70, Chi-square test) after three months. Conclusions: ctDNA was detected at baseline in almost half of the patients in the SONIA study. Compared to baseline, a decreasing number of patients had an elevation of the VAF of the tracked mutation and an increasing number of patients showed ctDNA clearance from 2 weeks to 3 months after start of treatment. There was no difference between the two arms observed regarding ctDNA dynamics. Interestingly, irrespective of treatment arm, about 1/3rd of patients remained ctDNA-positive even after 3 months of treatment. Associations of these ctDNA data with the clinical outcome data are currently being evaluated and will be presented at the meeting. Citation Format: Elisabeth M Jongbloed, Stefania Stella, Lotte van Bergen, Corine Beaufort, Jean Helmijr, Vanja de Weerd, Frans Erdkamp, Joan Heijns, Yvonne Kamm, Anne-Marie van Riel, Quirine van Rossum-Schornagel, Maurice Jansen, Inge RHM Konings, Gabe Sonke, John WM Martens, Agnes Jager, Saskia M Wilting. CIRCULATING TUMOR DNA DYNAMICS IN THE FIRST TREATMENT LINE OF THE SONIA TRIAL [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-14-06.

Circulating Tumor DNA Dynamics Fail to Predict Efficacy of Poly(ADP-ribose) Polymerase/VEGFR Inhibition in Patients With Heavily Pretreated Advanced Solid Tumors.

Cell-free circulating tumor DNA (ctDNA) has shown its potential as a quantitative biomarker for longitudinal monitoring of response to anticancer therapies. However, ctDNA dynamics have not been studied in patients with heavily pretreated, advanced solid tumors, for whom therapeutic responses can be weak. We investigated whether changes in ctDNA could predict clinical outcomes in such a cohort treated with combined poly(ADP-ribose) polymerase/vascular endothelial growth factor receptor inhibitor therapy. Patients with metastatic pancreatic ductal adenocarcinoma (PDAC), triple-negative breast cancer (TNBC), small-cell lung cancer (SCLC), or non-small-cell lung cancer (NSCLC) received up to 7 days of cediranib 30 mg orally once daily monotherapy lead-in followed by addition of olaparib 200 mg orally twice daily. Patients had progressed on a median of three previous lines of therapy. Plasma samples were collected before and after cediranib monotherapy lead-in and on combination therapy at 7 days, 28 days, and every 28 days thereafter. ctDNA was quantified from plasma samples using a multigene mutation-based assay. Radiographic assessment was performed every 8 weeks. ctDNA measurements were evaluable in 63 patients. The median baseline ctDNA variant allele fractions (VAFs) were 20%, 28%, 27%, and 34% for PDAC, TNBC, SCLC, and NSCLC, respectively. No association was observed between baseline VAF and radiographic response, progression-free survival, or overall survival (OS). Similarly, no association was found between ctDNA decline and radiographic response or survival. However, an increase in ctDNA at 56 days of combination therapy was associated with disease progression and inferior OS in a landmark analysis. ctDNA levels or dynamics did not correlate with radiographic response or survival outcomes in patients with advanced metastatic malignancies treated with olaparib and cediranib.

Circulating Tumor DNA Dynamics as Early Outcome Predictors for Lisocabtagene Maraleucel as Second-Line Therapy for Large B-Cell Lymphoma from the Phase 3 TRANSFORM Study

Background: While the prognostic value of MRD using ultrasensitive circulating tumor DNA (ctDNA) assays after first-line immunochemotherapy for DLBCL has been shown (Roschewski M, et al. Blood 2022;140[suppl 1]:785), its relevance to outcomes after second-line (2L) treatment with CD19-directed CAR T cell therapy remains unclear. The phase 3 TRANSFORM study (NCT03575351) showed statistically significant and clinically meaningful improvements in event-free survival (EFS), CR rate, and PFS for lisocabtagene maraleucel (liso-cel) compared with standard of care (SOC) for patients (pts) with primary refractory or early relapsed large B-cell lymphoma (LBCL) eligible for autologous HSCT (Kamdar M, et al. Lancet 2022; Abramson JS, et al. Blood 2023). Here, we report longitudinally measured ctDNA levels from TRANSFORM as a prospective measure of disease burden and describe the predictive value of ctDNA after 2L liso-cel therapy for LBCL. Methods: From the original randomized population (n = 184), 551 plasma samples from 160 pts (liso-cel, n = 79; SOC, n = 81) were used for ctDNA assessment in a blinded manner by Phased Variant (PV) Enrichment and Detection Sequencing (PhasED-Seq) at Foresight Diagnostics. Tumor-derived PVs were identified directly from baseline plasma samples taken at screening without use of tumor tissue; matched DNA from peripheral blood mononuclear cells was used to censor germline variants and clonal hematopoiesis. PVs were used to longitudinally assess ctDNA on the day of liso-cel infusion; at Day 15; and Months 1, 2, 3, and 12 after infusion. For the SOC arm, only pretreatment samples were evaluated. ctDNA levels were compared with baseline characteristics, responses by Lugano 2014 criteria, and EFS. Pts/samples were reported as having detectable MRD when ctDNA levels exceeded a detection threshold (≈1:10 6 cell-free DNA molecules) corresponding to 98% specificity. Results: PVs were identified from 136 of 160 pts (85%) with evaluable pretreatment samples from the liso-cel and SOC treatment arms. The remaining samples had lower disease burden (sum of product of diameters[SPD]; 13%) or failed quality check (2%). Pretreatment ctDNA levels varied widely (median [IQR]: 136 [35‒696] haploid genome equivalents/mL) and were correlated with disease indices portraying higher-risk disease, including stage ( P = 0.02), age-adjusted International Prognostic Index ( P < 0.0001), disease burden (SPD; P < 0.0001), and LDH ( P < 0.0001). Serial ctDNA levels were evaluated after liso-cel infusion in 63 pts. Achieving undetectable ctDNA was associated with achieving CR and longer EFS at all time points after liso-cel infusion. ctDNA levels decreased rapidly in pts who achieved CR at Month 3, with 50% (17/34) having undetectable ctDNA by Day 15 after liso-cel infusion. Conversely, 89% of pts (16/18) with PD at Month 3 still had detectable ctDNA at Day 15 with lower levels of ctDNA clearance. These results highlight significant enrichment of undetectable ctDNA observed as early as Day 15 after infusion between pts with Month 3 CR versus PD ( P = 0.006). ctDNA clearance in pts who achieved CR at Month 3 continued to deepen further over time, with undetectable ctDNA rates of 63%, 74%, and 86% at 1, 3, and 12 months after liso-cel infusion, respectively. Furthermore, most pts in CR by PET/CT had undetectable ctDNA at paired time points (71%), confirming that pts achieving CR also achieved durable molecular remission. In the cases with discordant CR and ctDNA results, detection of residual ctDNA was significantly prognostic for shorter EFS at all respective response assessments (fraction of CR cases with residual ctDNA at 1 month and Log-rank test P value for EFS: 47% [15/32], P = 0.011; 3 months: 26% [9/34], P = 0.025; 12 months: 13% [4/31], P = 0.003). Conclusions: Achieving undetectable ctDNA in the first 3 months and as early as 15 days after liso-cel infusion was significantly associated with durable clinical benefit. Conversely, detectable ctDNA captured relapse risk unmeasured by imaging. These results demonstrate the potential clinical value of ctDNA monitoring as a biomarker for disease surveillance and as an early predictor of clinical benefit of liso-cel treatment for LBCL, which could guide and accelerate future clinical trials.

O4-5 Circulating tumor DNA dynamics as an early predictor of recurrence in patients with radically resected colorectal cancer: GALAXY study in the CIRCULATE-Japan

O4-5 Circulating tumor DNA dynamics as an early predictor of recurrence in patients with radically resected colorectal cancer: GALAXY study in the CIRCULATE-Japan

Circulating Tumor DNA Dynamics as Prognostic Markers in Locally Advanced and Metastatic Esophageal Squamous Cell Carcinoma

Esophageal squamous cell carcinoma (ESCC) is a deadly disease with frequent recurrence. There are unmet needs for prognostic biomarkers for dynamically monitoring disease progression and detecting minimal residual disease. To examine whether circulating tumor DNA is clinically useful as a prognostic biomarker for ESCC recurrence and patient survival. This single-center, population-based cohort study consecutively enrolled 147 patients receiving curative (n = 74) or palliative (n = 73) treatment at the surgery and clinical oncology departments of Queen Mary Hospital in Hong Kong from August 1, 2016, to September 31, 2021. Patients were followed up for 2 years. Plasma samples were collected at different longitudinal time points for a prospective circulating tumor DNA (ctDNA) next-generation sequencing profiling study of 77 actionable genes. Patients were treated with up-front surgery, neoadjuvant chemoradiotherapy plus surgery with or without adjuvant therapy, or palliative chemotherapy (CT). Detection of circulating tumor DNA (ctDNA), progression-free survival (PFS), and overall survival (OS). A total of 478 serial plasma samples from 147 patients with locoregional or metastatic ESCC were prospectively analyzed. Among the 74 patients in the curative group (median [range] age, 66 [46-85] years; 56 [76.0%] male), 44 (59.5%) relapsed and 36 (48.6%) died. For patients receiving curative surgical treatment, a high ctDNA level (hazard ratio [HR], 7.84; 95% CI, 1.87-32.97; P = .005) and ctDNA alterations (HR, 5.71; 95% CI, 1.81-17.97; P = .003) at 6 months postoperation were independently associated with poor OS. Among patients receiving neoadjuvant chemoradiotherapy, postneoadjuvant ctDNA alterations were associated with poor PFS (HR, 3.16; 95% CI, 1.17-8.52; P = .02). In the 73 patients in the palliative group (median [range] age, 63 [45-82] years; 63 [86.0%] male), 71 (97.3%) had disease relapse and 68 (93.2%) died. Detectable pre-CT NFE2L2 alterations were independently associated with PFS (HR, 2.99; 95% CI, 1.35-6.61; P = .007) and OS (HR, 28.39; 95% CI, 7.26-111.03; P = 1.52 × 10-6), whereas high ctDNA levels (HR, 2.41; 95% CI, 1.18-4.95; P = .02) and alterations in pre-cycle III ctDNA (HR, 1.99; 95% CI, 1.03-3.85; P = .04) showed weaker associations with PFS. Alterations in pre-CT ctDNA were independently associated with OS (HR, 4.46; 95% CI, 1.86-10.69; P = 7.97 × 10-4). The findings of this cohort study indicate that prognostic models incorporating ctDNA features are useful in ESCC. Both ctDNA level and NFE2L2 alterations pre-CT and before cycle III were found to be important prognostic factors in palliative groups, and ctDNA alterations after treatment and at 6 months after surgery may define high-risk groups for recurrence in the curative group. High-risk patients can benefit by a timely switch to the next therapeutic options.

Early Circulating Tumor DNA Dynamics and Efficacy of Lorlatinib in Patients With Treatment-Naive, Advanced, ALK-Positive NSCLC

IntroductionCirculating tumor DNA (ctDNA) has been used as a biomarker for prognostication and response to treatment. Here, we evaluate ctDNA as a potential biomarker for response to lorlatinib, a third-generation ALK tyrosine kinase inhibitor in patients with treatment-naive, advanced, ALK-positive NSCLC in the ongoing phase 3 CROWN study (NCT03052608). MethodsMolecular responses were calculated using mean variant allele frequency (VAF), longitudinal mean change in VAF (dVAF), and ratio to baseline. Efficacy assessments (progression-free survival [PFS] and objective response rate) were paired with individual patient ctDNA and analyzed for association. ResultsCompared with baseline, mean VAF at week 4 was decreased in both treatment arms. Considering all detected somatic variants, a reduction in dVAF (≤0) was associated with a longer PFS in the lorlatinib arm. The hazard ratio (HR) for a dVAF less than or equal to 0 versus more than 0 was 0.50 (95% confidence interval [CI]: 0.23–1.12) in the lorlatinib arm. A similar association was not observed for crizotinib (HR = 1.00, 95% CI: 0.49–2.03). Comparing molecular responders with nonresponders, patients treated with lorlatinib who had a molecular response had longer PFS (HR = 0.37, 95% CI: 0.16–0.85); patients treated with crizotinib who had a molecular response had similar PFS as those without a molecular response (HR = 1.48, 95% CI: 0.67–3.30). ConclusionsIn patients with treatment-naive, advanced, ALK-positive NSCLC, early ctDNA dynamics predicted better outcome with lorlatinib but not with crizotinib. These results suggest that ctDNA may be used to monitor and potentially predict efficacy of lorlatinib treatment.

Circulating tumor DNA dynamics as an early predictor of recurrence in patients with radically resected colorectal cancer: Updated results from GALAXY study in the CIRCULATE-Japan.

3521 Background: Postoperative circulating tumor DNA (ctDNA)-based molecular residual disease (MRD) is reported to be associated with a high risk of recurrence. Here, we present an updated analysis and the lead time interval (LTI) of ctDNA positivity to radiographic recurrence in patients (pts) with radically resected colorectal cancer (CRC), stage II-IV in the observational GALAXY study. Methods: Serial ctDNA was analyzed using personalized tumor-informed assay (Signatera bespoke multiplex-PCR NGS assay) at 1 (4-week MRD time point), 3, 6, 9, 12, 18, and 24 months after surgery until recurrence, and CT scans were conducted every 6 months. The primary endpoint was disease-free survival (DFS), defined as the time between the date of surgery and date of diagnosis with relapse or death due to any cause. The LTI was defined from the first ctDNA positive date at post-surgery to radiographic recurrence. Results: Among 3,615 CRC pts who were enrolled between May 2020 and April 2022 in GALAXY study, 2,083 pts that met the inclusion criteria were analyzed in this report. The median follow-up period was 16.3 months. Of 2,083 pts analyzed, 286 (14%) were ctDNA-positive at 4-weeks MRD time point and 1,797 (86%) were ctDNA-negative. Pts with ctDNA-positivity at 4-weeks MRD timepoint demonstrated an inferior DFS and were 12 times more likely to recur, compared to ctDNA-negative pts (HR:12, 95CI: 9.1-15%; p < 0.0001). We further combined ctDNA status with BRAF V600E status at 4-week MRD time point and observed that pts with ctDNA-positivity and BRAF V600E mutation showed significantly shorter DFS compared to ctDNA-positive pts with BRAF wild-type (p < 0.001). Whereas, in pts with ctDNA-negativity no significant difference in DFS was observed (p = 0.306). On performing ctDNA dynamics analysis between 4-weeks to 12 weeks, compared to pts who remained ctDNA-negative (N = 1529), a significantly shorter DFS was observed for pts who converted from ctDNA-negative to positive (N = 112, HR: 14.5, 95%CI: 8.8-23.8%, p < 0.0001) or who remained positive (N = 124, HR: 25.4, 95%CI: 18.3-35.3; p < 0.0001). Radiographic recurrence was observed in 186 pts (46%). Of these, 121 pts (65%) had CT imaging performed every 6 months, as per the protocol. The median LTI was 142 days (IQR, 43-189 days). Conclusions: Our study builds on the existing evidence from the recently published, prospective GALAXY study. ctDNA status at MRD time point post-surgery is prognostic of patient outcomes and is the most significant risk factor regardless of BRAF V600E status. ctDNA positivity predicted radiologic recurrence several months ahead of clinical recurrence. Pts with positive postoperative ctDNA should be examined carefully due to a high risk of recurrence. ctDNA-guided adjuvant strategy will further be established by ongoing randomized VEGA and ALTAIR studies in the CIRCULATE-Japan. Clinical trial information: UMIN000039205 .

ASO Visual Abstract: Early Circulating Tumor DNA Dynamics Predict Neoadjuvant Therapy Response and Recurrence in Colorectal Liver Metastases-A Prospective Study.

ASO Visual Abstract: Early Circulating Tumor DNA Dynamics Predict Neoadjuvant Therapy Response and Recurrence in Colorectal Liver Metastases-A Prospective Study.

Early Circulating Tumor DNA Dynamics Predict Neoadjuvant Therapy Response and Recurrence in Colorectal Liver Metastases: A Prospective Study.

For patients with colorectal liver metastases (CRLM) who receive neoadjuvant therapy (NAT), reliable indicators that can early and accurately predict treatment response are lacking. This study was conducted to prospectively investigate the potential of early circulating tumor DNA (ctDNA) dynamics as a precise predictor of NAT response and recurrence in CRLM. This study prospectively enrolled 34 patients with CRLM who received NAT, with blood samples collected and subjected to deep targeted panel sequencing at two time points: 1 day before the first and the second cycles of NAT. Correlations of ctDNA mean variant allele frequency (mVAF) dynamics and treatment response were assessed. The performance of early ctDNA dynamics in predicting treatment response was assessed and compared with those of carcinoembryonic antigen (CEA) and cancer antigen 19-9 (CA19-9). The baseline ctDNA mVAF was significantly associated with pre-NAT tumor diameter (r = 0.65; P < 0.0001). After one cycle of NAT, the ctDNA mVAF declined remarkably (P < 0.0001). The dynamic change in ctDNA mVAF of 50% or more was significantly correlated with better NAT responses. The discriminatory capacity of ctDNA mVAF changes was superior to that of CEA or CA19-9 in predicting radiologic response (area under the curve [AUC], 0.90 vs 0.71 vs 0.61) and pathologic tumor regression grade (AUC, 0.83 vs 0.64 vs 0.67). The early changes in ctDNA mVAF but not CEA or CA19-9 were an independent indicator of recurrence-free survival (RFS) (hazard ratio, 4.0; P = 0.023). For CRLM patients receiving NAT, an early ctDNA change is a superior predictor of treatment response and recurrence compared with conventional tumor markers.

Circulating Tumor DNA Dynamics and Treatment Outcome of Regorafenib in Metastatic Colorectal Cancer.

Circulating tumor DNA (ctDNA) is emerging as a valuable non-invasive tool to identify tumor heterogeneity and tumor burden. This study investigated ctDNA dynamics in metastatic colorectal cancer patients treated with regorafenib. In this prospective biomarker study, plasma cell-free DNA (cfDNA) samples obtained at baseline, at the first response evaluation after 2 cycles of treatment, and at the time of progressive disease were sequenced using a targeted next-generation sequencing platform which included 106 genes. A total of 285 blood samples from 110 patients were analyzed. Higher baseline cfDNA concentration was associated with worse progression-free survival (PFS) and overall survival (OS). After 2 cycles of treatment, variant allele frequency (VAF) in the majority of ctDNA mutations decreased with a mean relative change of -31.6%. Decreases in the VAF of TP53, APC, TCF7L2, and ROS1 after 2 cycles of regorafenib were associated with longer PFS. We used the sum of VAF at each time point as a surrogate for the overall ctDNA burden. A reduction in sum (VAF) of ≥ 50% after 2 cycles was associated with longer PFS (6.1 vs. 2.7 months, p=0.002), OS (11.3 vs. 5.9 months, p=0.001), and higher disease control rate (86.3% vs. 51.1%, p < 0.001). VAF of the majority of the ctDNA mutations increased at the time of disease progression, and VAF of BRAF increased markedly. Reduction in ctDNA burden as estimated by sum (VAF) could be used to predict treatment outcome of regorafenib.

Prospective Study of Perioperative Circulating Tumor DNA Dynamics in Patients Undergoing Hepatectomy for Colorectal Liver Metastases.

To evaluate the association of perioperative ctDNA dynamics on outcomes after hepatectomy for CLM. Prognostication is imprecise for patients undergoing hepatectomy for CLM, and ctDNA is a promising biomarker. However, clinical implications of perioperative ctDNA dynamics are not well established. Patients underwent curative-intent hepatectomy after preoperative chemotherapy for CLM (2013-2017) with paired prehepatectomy/postoperative ctDNA analyses via plasma-only assay. Positivity was determined using a proprietary variant classifier. Primary endpoint was recurrence-free survival (RFS). Median follow-up was 55 months. Forty-eight patients were included. ctDNA was detected before and after surgery (ctDNA+/+) in 14 (29%), before but not after surgery (ctDNA+/-) in 19 (40%), and not at all (ctDNA-/-) in 11 (23%). Adverse tissue somatic mutations were detected in TP53 (n = 26; 54%), RAS (n = 23; 48%), SMAD4 (n = 5; 10%), FBXW7 (n = 3; 6%), and BRAF (n = 2; 4%). ctDNA+/+ was associated with worse RFS (median: ctDNA+/+, 6.0 months; ctDNA+/-, not reached; ctDNA-/-, 33.0 months; P = 0.001). Compared to ctDNA+/+, ctDNA+/- was associated with improved RFS [hazard ratio (HR) 0.24 (95% confidence interval (CI) 0.1-0.58)] and overall survival [HR 0.24 (95% CI 0.08-0.74)]. Adverse somatic mutations were not associated with survival. After adjustment for prehepatectomy chemotherapy, synchronous disease, and ≥2 CLM, ctDNA+/- and ctDNA-/- were independently associated with improved RFS compared to ctDNA+/+ (ctDNA+/-: HR 0.21, 95% CI 0.08-0.53; ctDNA-/-: HR 0.21, 95% CI 0.08-0.56). Perioperative ctDNA dynamics are associated with survival, identify patients with high recurrence risk, and may be used to guide treatment decisions and surveillance after hepatectomy for patients with CLM.

Circulating tumor DNA dynamics and response to immunotherapy in colorectal cancer.

Circulating tumor DNA (ctDNA) is increasingly being investigated as a tool to detect minimal residual disease in resected, stage I-III colorectal cancer. Recent ctDNA studies have indicated that detection of ctDNA following surgery for resectable colorectal cancer confers a significantly higher risk of recurrence than those with negative ctDNA postoperatively. In those with postoperative ctDNA positivity, clearance of minimal residual disease with adjuvant chemotherapy is a positive prognostic indicator. Lastly, ctDNA has demonstrated superior sensitivity to the conventional blood tumor marker carcinoembryonic antigen (CEA) and can offer median lead times of up to 11 months for radiographic detection of recurrence during the surveillance of resected, stage I-III colorectal cancer. In metastatic colorectal cancer (mCRC), there is growing evidence to suggest that plasma ctDNA can be used to monitor tumor response to conventional chemotherapy as well. The present case series demonstrated that plasma ctDNA is a predictor of tumor response to immunotherapy in patients with mCRC that are microsatellite stable or microsatellite instability high. Plasma ctDNA could serve as a dynamic marker of immunotherapy response even in colorectal tumors that were CEA non-producers. Overall, these findings add to ongoing efforts to establish the role of plasma ctDNA in monitoring response to immunotherapy in CRC.

Circulating tumor DNA dynamics on front-line chemotherapy with bevacizumab or cetuximab in metastatic colorectal cancer: A biomarker analysis for acquired genomic alterations in CALGB/SWOG 80405 (Alliance) randomized trial.

193 Background: Enhanced understanding of the evolving clonal architecture under treatment stress is crucial to optimizing care and developing effective therapies in metastatic colorectal cancer (mCRC). Emergence of genomic alterations (GAs) [mutations (muts) and amplifications (amps)] in RAS, BRAF, EGFR, ERBB2, and MET have been recognized as key resistance mechanisms to anti-EGFR therapy in later lines in mCRC. Data regarding occurrence of these GAs under selective pressure in the first line setting is lacking. Methods: CALGB/SWOG 80405 was a randomized trial of bevacizumab (bev) vs cetuximab (cet) in first line mCRC. Patients (pts) with paired plasma samples (pre-treatment and post-progression) available for circulating tumor DNA (ctDNA) testing were included in this substudy. Sequencing of ctDNA was performed by Guardant360 assay in a CLIA-certified environment to detect GAs in 73 genes. RAS/BRAF status [mut vs. wild type (wt)] was based on clonal muts [pre-defined cutoff of relative MAF (rMAF) ≥ 25%] in ctDNA. Only samples with ≥1 GA were analyzed to minimize false negatives. The primary objective was to determine and compare prevalence of acquired GAs between study arms: bev (anti-VEGF) and cet (anti-EGFR). Descriptive statistics and Fisher’s exact test were used. Results: Baseline characteristics of ctDNA cohort were similar to the 80405 population. Among 133 randomized RAS/BRAF wt pts, 11 (15.3%) and 5 (8.2%) developed acquired GAs (OR 2.0, P = 0.29), in bev and cet arm, respectively. Key comparative data for pts with regard to acquired pathogenic GAs are shown in the table. Conclusions: In this randomized mCRC cohort, the ctDNA profile of acquired GAs with front line anti-EGFR chemotherapy appears to be strikingly distinct from that seen with later lines of therapy. Acquisition of GAs, classically associated with EGFR resistance in later line, was not only rare with upfront cet-chemotherapy but also comparable to bev-containing (anti-VEGF) regimen. The mechanisms of acquired resistance appear to differ when anti-EGFR therapy is administered in combination with highly active first line chemotherapy. Our findings have critical translational relevance to the timing and value of ctDNA-guided anti-EGFR rechallenge in mCRC pts, especially in those treated with anti-EGFR therapy upfront.[Table: see text]

Association of circulating tumor DNA dynamics with clinical outcomes in the adjuvant setting for patients with colorectal cancer from an observational GALAXY study in CIRCULATE-Japan.

9 Background: Circulating tumor DNA (ctDNA)-based molecular residual disease (MRD) has the potential to select patients who may benefit more from standard-of-care (SOC) adjuvant chemotherapy (ACT) by accurately assessing recurrence-risk post-surgery and by evaluating ACT efficacy. Here we present an analysis from GALAXY study, an observational study monitoring MRD, to evaluating the association of ctDNA dynamics with a short-term clinical outcome and ACT efficacy. Methods: A personalized tumor-informed assay (Signatera bespoke multiplex-PCR NGS assay) was used for post-surgical MRD detection in colorectal cancer (CRC) patients. Six-month disease-free survival (6M-DFS) rates were analyzed excluding patients enrolled in associated phase III trials (VEGA and ALTAIR). Results: Total 1,365 CRC patients enrolled between June 2020 and April 2021 were included in this analysis; 116 pStage I, 478 pStage II, 503 pStage III, and 268 oligomet resectable pStage IV (16% [42/268] received neoadjuvant chemotherapy). 6M-DFS rate by ctDNA dynamics from 4w to 12w were 98% in ‘negative to negative’ group (N = 618), 59% in ‘negative to positive’ (N = 32), 100% in ‘positive to negative’ (N = 58), and 45% in ‘positive to positive’ (N = 78), with a significant difference between ‘positive to negative’ and ‘positive to positive’ groups with hazard ratio (HR) of 52.3 (95% CI: 7.2-380.5; p &lt; 0.001), with a median follow-up time of 6.6 months. Further, out of 188 patients who were MRD+ at 4w with available MRD status at 12w, 95 received SOC ACT (80/95 received fluoropyrimidine [FP] + oxaliplatin and 15 received FP alone) by an investigator’s decision. ctDNA clearance rate at 12w was significantly higher in ACT vs. non-ACT; 57% (54/95) vs. 8% (7/93) in pStage I-IV (p &lt; 0.001), and 58% (42/72) vs. 11% (4/37) in pStage II-III (p &lt; 0.001). In addition, ctDNA clearance rate at 24w was also significantly higher in ACT vs. non-ACT; 26% (7/27) vs. 0% (0/30) in pStage I-IV (p = 0.003), and 33% (7/21) vs. 0% (0/15) in pStage II-III (p = 0.03). Cumulative incidence of ctDNA clearance was significantly higher in ACT vs. non-ACT (67% vs. 7% by 24w; cumulative HR = 17.1; 95% CI: 6.7-43.4, p &lt; 0.001). Among 4w-MRD+ patients, 6M-DFS rate was significantly higher in ACT vs. non-ACT; 84% vs. 34% (HR = 0.15; 95% CI: 0.078-0.25; p &lt; 0.001), which was seen in all stages, including pStage II. Conclusions: This analysis from the GALAXY study, is the largest MRD study to date, demonstrating the association of ctDNA dynamics with improved clinical outcomes in MRD+ patients. Our study shows that stratifying post-surgical treatment decisions using the assay can identify patients likely to benefit from ACT across all stages, including pStage II. ctDNA-guided adjuvant strategy will further be established by ongoing randomized VEGA and ALTAIR studies and will be presented in the future conferences. Clinical trial information: jRCT1031200006.

Circulating tumor DNA dynamics analysis in a xenograft mouse model with esophageal squamous cell carcinoma.

BACKGROUNDIt remains unclear which factors, such as tumor volume and tumor invasion, influence circulating tumor DNA (ctDNA), and the origin of ctDNA in liquid biopsy is always problematic. To use liquid biopsies clinically, it will be very important to address these questions.AIMTo assess the origin of ctDNA, clarify the dynamics of ctDNA levels, assess ctDNA levels by using a xenograft mouse after treatment, and to determine whether tumor volume and invasion are related to ctDNA levels.METHODSTumor xenotransplants were established by inoculating BALB/c-nu/nu mice with the TE11 cell line. Groups of mice were injected with xenografts at two or four sites and sacrificed at the appropriate time point after xenotransplantation for ctDNA analysis. Analysis of ctDNA was performed by droplet digital PCR, using the human telomerase reverse transcriptase (hTERT) gene.RESULTSMice given two-site xenografts were sacrificed for ctDNA at week 4 and week 8. No hTERT was detected at week 4, but it was detected at week 8. However, in four-site xenograft mice, hTERT was detected both at week 4 and week 6. These experiments revealed that both tumor invasion and tumor volume were associated with the detection of ctDNA. In resection experiments, hTERT was detected at resection, but had decreased by 6 h, and was no longer detected 1 and 3 d after resection.CONCLUSIONWe clarified the origin and dynamics of ctDNA, showing that tumor volume is an important factor. We also found that when the tumor was completely resected, ctDNA was absent after one or more days.

Circulating Tumor DNA Dynamics Predict Prognosis of Locally Advanced Non-Small Cell Lung Cancer Patients Treated With Definitive Chemoradiotherapy

Locally advanced non-small cell lung cancer (LA-NSCLC) has strong tumor heterogeneity. Postradiotherapy concentration of circulating tumor DNA (ctDNA) has been demonstrated a promising prognostic biomarker of LA-NSCLC and might be helpful in assisting consolidation decision-making. However, it is widely acknowledged that many biomarkers are specific to certain patient populations. Therefore, we performed this prospective study in Chinese patients with LA-NSCLC to evaluate the prognostic role of ctDNA.We consecutively enrolled patients with unresectable LA-NSCLC. Plasma samples were prospectively collected at different time point if obtained (1) baseline (pretreatment), (2) the fourth week during radiotherapy (RT), and (3) one-month post RT. All plasma specimens were subjected to next-generation sequencing panel of 474 cancer-related genes. Plasma samples with at least 1 variant detected were defined as ctDNA+. A landmark analysis was used to assess predictive value of ctDNA clearance at the time point of one-month post RT. Nonparametric test was used to compare ctDNA concentrations among groups. The Kaplan-Meier method was used to estimate survival distributions, Cox model to estimate hazard ratios and confidence intervals, and log-rank test to estimate P value.A total of 35 patients treated with definitive chemoradiotherapy (CRT) were enrolled. The median follow-up from diagnosis was 16 months. At baseline timepoint, 21 patients with ctDNA+ and 14 patients with ctDNA-. For ctDNA+ patients, ctDNA concentration (ng/ml) was significantly higher with increasing clinical stage (stage IIIA vs stage IIIB vs stage IIIC, 0.345 vs 0.580 vs 3.630, P = 0.007). Both progression free survival (PFS) and overall survival (OS) was not significantly different between ctDNA- and ctDNA+ group at baseline timepoint. However, at the time point of one-month post RT, patients with ctDNA- had significantly higher PFS (median: NA vs 7 months; HR 0.205, 95% CI: 0.066∼0.637; P = 0.002) and OS (HR 0.065, 95% CI: 0.008∼0.541; P = 0.001). Kinetic changes in ctDNA concentrations were analyzed in 16 pts with matching baseline and one-month post RT specimens. Of these 16 cases with detectable ctDNA at baseline, 50% (8/16) became undetectable at one-month post RT ("ctDNA clearance"), all these 8 patients were alive and nonrecurrent during the following-up. ctDNA clearance was associated with significantly higher PFS (P = 0.003) and OS (P = 0.016) compared with ctDNA residual patients.For LA-NSCLC receiving CRT, ctDNA concentration was significantly higher with increasing clinical stage (IIIA vs IIIB vs IIIC). Baseline ctDNA+/- seemed not a prognosis factor, whereas ctDNA- or ctDNA clearance at the time of one-month post RT was associated with significantly superior PFS and OS. More enrolled patients are needed to update and validate these results.NCT04014465.

A phase 1/2 study of the combination of acalabrutinib and vistusertib in patients with relapsed/refractory B-cell malignancies

In a phase 1b study of acalabrutinib (a covalent Bruton tyrosine kinase (BTK) inhibitor) in combination with vistusertib (a dual mTORC1/2 inhibitor) in patients with relapsed/refractory diffuse large B-cell lymphoma (DLBCL), multiple ascending doses of the combination as intermittent or continuous schedules of vistusertib were evaluated. The overall response rate was 12% (3/25). The pharmacodynamic (PD) profile for acalabrutinib showed that BTK occupancy in all patients was >95%. In contrast, PD analysis for vistusertib showed variable inhibition of phosphorylated 4EBP1 (p4EBP1) without modulation of AKT phosphorylation (pAKT). The pharmacokinetic (PK)/PD relationship of vistusertib was direct for TORC1 inhibition (p4EBP1) but did not correlate with TORC2 inhibition (pAKT). Cell-of-origin subtyping or next-generation sequencing did not identify a subset of DLBCL patients with clinical benefit; however, circulating tumor DNA dynamics correlated with radiographic response. These data suggest that vistusertib does not modulate targets sufficiently to add to the clinical activity of acalabrutinib monotherapy. Clinicaltrials.gov identifier: NCT03205046.

Preliminary results of BEAVER: An investigator-initiated phase II study of binimetinib and encorafenib for the treatment of advanced solid tumors with non-V600E BRAF mutations (mts).

e15038 Background: Recurring oncogenic non-V600E BRAF mts have been identified in many cancer types. Preclinical data indicate that some BRAF non-V600E mts can be targeted with BRAF + MEK inhibitors. BEAVER is an investigator-initiated study designed to test the safety and efficacy of binimetinib and encorafenib (B+E) in patients (pts) with non-V600E BRAF mts. Methods: Key eligibility criteria are: pts with advanced solid tumors with BRAF non-V600E activating (class 1 and 2) or inhibitory (class 3) mts, and no prior BRAF/MEK inhibitors. Pts receive binimetinib (45mg PO BID) and encorafenib (450mg PO daily) on a 28-day cycle until intolerable toxicity or progression. The primary objective is OR rate (ORR) as per RECIST 1.1. In this Simon 2-stage trial, ≥1 of 7 pts need to have an objective response (OR) before commencing second stage of study (26 pts total). Secondary objectives include: safety, DCR, PFS, and OS. Exploratory objectives include: genomic profiling of tumors, evaluating circulating tumor DNA dynamics and development of patient derived xenograft (PDX) models. Results: From June 2019 to Feb 2021, 12 pts were screened and 9 pts enrolled; 9 are evaluable for safety and 8 for efficacy. Tumor types were melanoma and colon (n=2 each), as well as gallbladder, lung, breast and uterine cancers (n=1 each). Median age was 62 yrs (range 40-72). Median number of prior treatments was 2 (range 0-6). 1 pt had a class 1, 3 pts had class 2, and 5 pts had class 3, non-V600E BRAF mts. The median number of cycles was 2 (range: 1-7). Common treatment-related adverse events were mostly grade ≤ 2, and included: Blurred vision (78%), fatigue (67%), nausea (44%), vomiting (33%), and rash (33%). Dose reductions were required in 4/9 pts (44%) due to: blurred vision (22%), central serous retinopathy (11%), malaise (11%) and increased lipase (11%). Drug-related grade 3 AEs occurred in 2/9 pts and included: malaise (11%), confusion (11%), fatigue (11%) and increased lipase (11%). All eye toxicities were reversible with dose interruption. ORR was 12.5% (1/8) with one unconfirmed PR in a melanoma pt (BRAF G469S), treated for 6.5 months. One gallbladder cancer pt (BRAF D594N) had SD, and 6 pts had PD as best response. Genomic profiling was performed on archival tumors for 8 pts. Two PDX models were established. Responses to B+E in PDX models mirrored responses in 2 corresponding pts who had PD. Genomic and molecular profiling of pt tumors and corresponding PDXs identified multiple potential mechanisms of B+E resistance including: activation of EGFR and Akt pathways and inactivation of NF1 and Rb1. Conclusions: Preliminary data confirmed the safety of B+E and showed preliminary evidence of anti-tumor activity in advanced cancer pts with non-V600E BRAF mts. This study met the criterion for advancing to stage 2. Enrolment in the BEAVER trial and correlative biomarker analyses are ongoing. Clinical trial information: NCT03839342.

Circulating tumor DNA dynamics and recurrence risk in patients undergoing curative intent resection of colorectal cancer liver metastases: A prospective cohort study.

BackgroundIn patients with resectable colorectal liver metastases (CRLM), the role of pre- and postoperative systemic therapy continues to be debated. Previous studies have shown that circulating tumor DNA (ctDNA) analysis, as a marker of minimal residual disease, is a powerful prognostic factor in patients with nonmetastatic colorectal cancer (CRC). Serial analysis of ctDNA in patients with resectable CRLM could inform the optimal use of perioperative chemotherapy. Here, we performed a validation study to confirm the prognostic impact of postoperative ctDNA in resectable CRLM observed in a previous discovery study.Methods and findingsWe prospectively collected plasma samples from patients with resectable CRLM, including presurgical and postsurgical samples, serial samples during any pre- or postoperative chemotherapy, and serial samples in follow-up. Via targeted sequencing of 15 genes commonly mutated in CRC, we identified at least 1 somatic mutation in each patient’s tumor. We then designed a personalized assay to assess 1 mutation in plasma samples using the Safe-SeqS assay. A total of 380 plasma samples from 54 patients recruited from July 2011 to Dec 2014 were included in our analysis. Twenty-three (43%) patients received neoadjuvant chemotherapy, and 42 patients (78%) received adjuvant chemotherapy after surgery. Median follow-up was 51 months (interquartile range, 31 to 60 months). At least 1 somatic mutation was identified in all patients’ tumor tissue. ctDNA was detectable in 46/54 (85%) patients prior to any treatment and 12/49 (24%) patients after surgery. There was a median 40.93-fold (19.10 to 87.73, P < 0.001) decrease in ctDNA mutant allele fraction with neoadjuvant chemotherapy, but ctDNA clearance during neoadjuvant chemotherapy was not associated with a better recurrence-free survival (RFS). Patients with detectable postoperative ctDNA experienced a significantly lower RFS (HR 6.3; 95% CI 2.58 to 15.2; P < 0.001) and overall survival (HR 4.2; 95% CI 1.5 to 11.8; P < 0.001) compared to patients with undetectable ctDNA. For the 11 patients with detectable postoperative ctDNA who had serial ctDNA sampling during adjuvant chemotherapy, ctDNA clearance was observed in 3 patients, 2 of whom remained disease-free. All 8 patients with persistently detectable ctDNA after adjuvant chemotherapy have recurred. End-of-treatment (surgery +/− adjuvant chemotherapy) ctDNA detection was associated with a 5-year RFS of 0% compared to 75.6% for patients with an undetectable end-of-treatment ctDNA (HR 14.9; 95% CI 4.94 to 44.7; P < 0.001). Key limitations of the study include the small sample size and the potential for false-positive findings with multiple hypothesis testing.ConclusionsWe confirmed the prognostic impact of postsurgery and posttreatment ctDNA in patients with resected CRLM. The potential utility of serial ctDNA analysis during adjuvant chemotherapy as an early marker of treatment efficacy was also demonstrated. Further studies are required to define how to optimally integrate ctDNA analyses into decision-making regarding the use and timing of adjuvant therapy for resectable CRLM.Trial registrationACTRN12612000345886.