Longitudinal Circulating Tumor DNA Research Articles

232P Longitudinal circulating tumor DNA (ctDNA) analysis in the phase 1b MONALEESASIA study of ribociclib (RIB) + endocrine therapy (ET) in Asian patients (pts) with hormone receptor–positive (HR+)/human epidermal growth factor receptor 2–negative (HER2–) advanced breast cancer (ABC)

232P Longitudinal circulating tumor DNA (ctDNA) analysis in the phase 1b MONALEESASIA study of ribociclib (RIB) + endocrine therapy (ET) in Asian patients (pts) with hormone receptor–positive (HR+)/human epidermal growth factor receptor 2–negative (HER2–) advanced breast cancer (ABC)

90P Longitudinal circulating tumor DNA profiling of metastatic urothelial carcinoma in the POLARIS-03 trial

Noninvasive biomarkers for immune checkpoint inhibitors remain a compelling unmet medical need. POLARIS-03 is a multicenter phase II trial to evaluate the safety and efficacy of toripalimab (anti-PD-1) in refractory metastatic urothelial carcinoma (mUC). We assessed the predictive utility of longitudinal circulating tumor DNA (ctDNA) analysis from a single-institution biomarker cohort.

Longitudinal Circulating Tumor DNA Analysis in Blood and Saliva for Prediction of Response to Osimertinib and Disease Progression in EGFR-Mutant Lung Adenocarcinoma.

Simple SummaryctDNA assay is a promising non-invasive method to detect genomic alterations associated with lung cancer. In this prospective study of 25 patients with EGFR-mutant lung adenocarcinoma receiving osimertinib, ctDNA progression predated radiographic progression by 118 days in 11 of 20 patients with disease progression. Saliva-based ctDNA analysis and plasma NGS detected additional patients with ctDNA progression preceding clinical progression, suggesting the potential complementary roles of different ctDNA detection methodologies. Baseline mutant ctDNA level predicted progression-free survival while tumor volume measurements by volumetric CT did not. Serial ctDNA analysis of plasma and saliva is a clinically useful tool to monitor response and resistance to osimertinib.Background: We assessed whether serial ctDNA monitoring of plasma and saliva predicts response and resistance to osimertinib in EGFR-mutant lung adenocarcinoma. Three ctDNA technologies—blood-based droplet-digital PCR (ddPCR), next-generation sequencing (NGS), and saliva-based EFIRM liquid biopsy (eLB)—were employed to investigate their complementary roles. Methods: Plasma and saliva samples were collected from patients enrolled in a prospective clinical trial of osimertinib and local ablative therapy upon progression (NCT02759835). Plasma was analyzed by ddPCR and NGS. Saliva was analyzed by eLB. Results: A total of 25 patients were included. We analyzed 534 samples by ddPCR (n = 25), 256 samples by NGS (n = 24) and 371 samples by eLB (n = 22). Among 20 patients who progressed, ctDNA progression predated RECIST 1.1 progression by a median of 118 days (range: 61–272 days) in 11 (55%) patients. Of nine patients without ctDNA progression by ddPCR, two patients had an increase in mutant EGFR by eLB and two patients were found to have ctDNA progression by NGS. Levels of ctDNA measured by ddPCR and NGS at early time points, but not volumetric tumor burden, were associated with PFS. EGFR/ERBB2/MET/KRAS amplifications, EGFR C797S, PIK3CA E545K, PTEN V9del, and CTNNB1 S45P were key resistance mechanisms identified by NGS. Conclusion: Serial assessment of ctDNA in plasma and saliva predicts response and resistance to osimertinib, with each assay having supplementary roles.

Abstract LB054: Confirmation of target inhibition and anti-tumor activity of the SHP2 inhibitor RMC-4630 via longitudinal analysis of ctDNA in a phase 1 clinical study

Abstract RMC-4630 is a potent, selective, orally bioavailable allosteric inhibitor of SHP2, a central node in the RAS signaling pathway. Preclinical data have demonstrated that RMC-4630 can shrink tumors carrying certain mutations in the RAS pathway such as KRASG12C, NF1LOF, and BRAFClass3. Longitudinal circulating tumor DNA (ctDNA) was isolated from blood using GuardantOMNI in 80 patients with relapsed/refractory solid tumors in the phase 1 dose-escalation trial of RMC-4630 (NCT03634982) to characterize and confirm RAS pathway mutations and to evaluate molecular responses in patients receiving RMC-4630 monotherapy. Safety, PK and efficacy findings from this study are reported in a separate abstract. 78 of 80 patients had baseline somatic mutations detected in plasma, of which 60 were either KRASG12X, NF1LOF, or BRAFClass3; 48 of these 60 patients also had on-treatment ctDNA assessments and these patients constitute the population reported here. 9 of 48 patients (19%) had KRASG12C detected at baseline, available scan results and a ctDNA sample after 4 weeks of receiving RMC-4630. A decrease in KRASG12C variant allele frequency (VAF) was detected in 5/9 patients (56%) with clearance in 1 patient with a partial response. Decrease in KRASG12C VAF was associated with change in tumor volume (PCC=0.85, p=0.008), preceding scan results by approximately 1 month, suggesting that change in KRASG12C VAF may be an early measure of drug activity or possibly response. 5 of 48 patients (10%) had NF1LOF detected at baseline. A decrease, or stability in NF1LOF VAF on treatment compared to baseline was detected in 4 (80% of all NF1LOF patients). The decrease in NF1LOF VAF was not associated with change in tumor volume and may represent effects of RMC-4630 on a subclone harboring NF1LOF. One patient had a detectable BRAFClass3 mutation at baseline, which decreased in VAF on treatment compared to baseline. Of the remaining patients there were 12 KRASG12D, 9 KRASG12V and other KRASG12X. The majority progressed with an increase in VAF of all mutations including KRASG12X, suggesting that the KRASG12X-containing clone is responsible for escape from single agent RMC-4630. In most instances the increase in KRASG12X VAF in blood preceded determination of clinical progression. Longitudinal assessment of ctDNA indicates that some patients with RAS-addicted tumors undergo a molecular response on treatment with the SHP2 inhibitor RMC-4630. Citation Format: Josie L. Hayes, Marianna Koczywas, Sai-Hong Ignatius Ou, Pasi A. Janne, Jose M. Pacheco, Susanna Ulahannan, Judy S. Wang, Howard A. Burris, Jonathan W. Riess, Caroline McCoach, Michael S. Gordon, Anna Capasso, Ariel Chen, Richa Dua, Bojena Bitman, Martha Guerra, Hongfang Wang, Xiaolin Wang, Eric Haura. Confirmation of target inhibition and anti-tumor activity of the SHP2 inhibitor RMC-4630 via longitudinal analysis of ctDNA in a phase 1 clinical study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr LB054.

The prognostic value of longitudinal circulating tumor DNA profiling during osimertinib treatment.

BackgroundSerial profiling of circulating tumor DNA (ctDNA) could reflect dynamic molecular changes in response to treatment and potentially predict impending disease progression (PD). Herein, we investigated the molecular factors and dynamic changes in ctDNA that can serve as predictors of survival outcomes of patients with epidermal growth factor receptor (EGFR)-mutated advanced non-small cell lung cancer (NSCLC) who received osimertinib therapy after progression from prior EGFR inhibitor regimen.MethodsCapture-based targeted sequencing was performed on the baseline and longitudinal plasma samples collected from 72 and 57 patients, respectively, using a 168-gene panel.ResultsAnalysis revealed that inferior overall survival (OS) was correlated with various baseline molecular features including high allelic fraction (AF) of EGFR sensitizing mutations (P=0.045), high maximum AF (maxAF, P=0.060), or harboring concurrent genomic alterations such as copy number amplification (CNA) in EGFR (P=0.026) or in other genes (P=0.026), and genes involved in the cell cycle (P=0.004) or TP53 signaling pathway (P=0.032). Moreover, ctDNA clearance at first follow-up after 6 weeks of osimertinib therapy was correlated with significantly longer progression-free survival (PFS) (P=0.022) and OS (P=0.009). Molecular PD, reflected by the emergence of new mutation or increased AF of existing mutations, was detected at an average lead time of 2.5 months prior to radiological PD. Patients with molecular PD were more likely to harbor CNA (P=0.035) and TP53 mutations (P=0.023).ConclusionsMolecular factors derived from serial ctDNA profiling can serve as predictive and prognostic markers, which could allow early detection of PD, preceding imaging modalities by 2.5 months.

Abstract 2997: Longitudinal circulating tumor DNA (ctDNA) analysis predicts response and reveals the resistance mechanisms of ensartinib in ALK+ NSCLC patients (pts) progressed on crizotinib: Updated analysis of a phase II clinical trial

Abstract Introduction: In the previous phase II clinical trial (NCT03215693), ensartinib, a next generation (NG) ALK TKI, showed comparable efficacy to other NG ALK TKIs in the post-crizotinib setting. In the preplanned biomarker analysis, we investigated the efficacy and the resistance mechanisms of ensartinib via longitudinal ctDNA analysis. Methods: Pts with stage IIIB/IV ALK+ NSCLC, and had progressive disease (PD) after crizotinib were eligible. Plasma samples from this trial were prospectively collected for ctDNA analysis at baseline (BL), cycle 3 day 1 (C3D1) and the end of treatment (EOT). Plasma DNA was analyzed using a 212-gene sequencing panel. ctDNA amount was defined as the sum of variant allele fraction (VAF) of ALK fusions and mutations. Cox model was applied for multivariate analysis. Results: Between 9/2017 and 7/2019, 182 pts were enrolled in the trial. In total, 178 were included in the full analysis set (FAS), with a median PFS (mPFS) of 9.8 months (95% CI, 7.5 to 11.7 months). 169 pts were evaluable by independent review committee (IRC), with an ORR of 57.7% (95% CI, 50.2% to 65.3%). A total of 431 ctDNA samples were analyzed, including 168 at BL, 165 at C3D1, and 106 at EOT (8 overlappings between C3D1 and EOT). 168 (99.4%) pts had evaluable ctDNA at BL. The median ctDNA amount was 0.00704. The higher ctDNA amount was associated with liver metastases, bone metastases, and TP53 mutations. Tumor burden, as measured by the sum of the target lesions' longest diameters, also positively correlated with ctDNA amount (Pearson correlation 0.261; p < 0.001). Multivariable Cox regression revealed that high level of ctDNA amount and TP53 mutations at BL was significantly associated with poor PFS independently (p =0.020 and p < 0.001) (Table). 106 (62.7%) pts had evaluable ctDNA at both BL and EOT. Compared to baseline, the frequency of certain ALK mutations significantly increased at EOT, such as G1269A (7.5% vs 21.7%), G1202R (3.8% vs 17.0%) and E1210K (0% vs 10.4%). TP53 statusctDNA amountTP53 Wildtype TP53 Mutations Low amountHigh amount(n = 34)(n = 134)(n = 46)(n = 47)mPFS, months (95% CI) 11.7 (9.8, 14.0) 4.2 (3.0, 5.6)9.3 (5.6, 11.7) 4.2 (2.8, 5.5)HR (95% CI); p value2.50 (1.65, 3.79) ; p < 0.0012.34 (1.52, 3.61) ; p < 0.001 Consistent with the change in frequency, the abundance of G1269A, G1202R, and E1210K also trended to increase at EOT, while the abundance of C1156Y and I1171X had a downward trend in most pts. Conclusions: Consistent with previous reports, ensartinib showed high clinical efficacy. Longitudinal ctDNA analysis could be a powerful tool in predicting treatment outcomes and revealing resistant mechanisms of ensartinib. We observed G1269A, G1202R and E1210K as the major resistant mutations to ensartinib. Additional analyses are ongoing and results will be updated and reported in the meeting. Citation Format: Yunpeng Yang, Jie Huang, Tao Wang, Jianya Zhou, Jing Zheng, Jifeng Feng, Wu Zhuang, Jianhua Chen, Jun Zhao, Wei Zhong, Yanqiu Zhao, Yiping Zhang, Yong Song, Yi Hu, Zhuang Yu, Youling Gong, Yuan Chen, Feng Ye, Shucai Zhang, Lejie Cao, Yun Fan, Gang Wu, Yubiao Guo, Chengzhi Zhou, Kewei Ma, Jian Fang, Weineng Feng, Yunpeng Liu, Zhendong Zheng, Gaofeng Li, Ning Wu, Wei Song, Xiaoqing Liu, Shijun Zhao, Lieming Ding, Li Mao, Giovanni Selvaggi, Larry Zhu, Shanshan Xiao, Li Zhang. Longitudinal circulating tumor DNA (ctDNA) analysis predicts response and reveals the resistance mechanisms of ensartinib in ALK+ NSCLC patients (pts) progressed on crizotinib: Updated analysis of a phase II clinical trial [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 2997.

Abstract CT024: Utility of longitudinal circulating tumor DNA (ctDNA) modeling to predict RECIST-defined progression in first-line patients with epidermal growth factor receptor mutation-positive (EGFRm) advanced non-small cell lung cancer (NSCLC)

Abstract Circulating tumor DNA is released into the bloodstream from tumors and can reflect both intra-tumor heterogeneity and clonal evolution.1 As ctDNA levels are thought to reflect tumor burden, a decrease in ctDNA while on therapy may suggest treatment efficacy.2 We assessed whether longitudinal changes in ctDNA could supplement or improve RECIST-based measures for decision making during drug development. Plasma samples collected at regular intervals were analyzed to predict the risk of disease progression in patients with EGFRm (Ex19del or L858R) advanced NSCLC following initiation of first-line EGFR tyrosine kinase inhibitor (TKI) treatment in the FLAURA study (NCT02296125). Of 556 patients who received treatment (osimertinib 80 mg daily [QD] or comparator EGFR-TKI [gefitinib 250 mg QD or erlotinib 150 mg QD]), 353 (63%) had an available sample with detectable levels of ctDNA at baseline. Patients with both imaging and ctDNA samples at baseline and 3 additional timepoints (n=320, the analysis set) were divided (as implemented in caret R package)3 into training (n=259) and validation (n=61) cohorts. Clinical data from these patients (data cut-off: June 12 2017) were used to fit joint models of either ctDNA dynamics or sum of the longest tumor diameters (SLD) and progression-free survival (PFS). Longitudinal ctDNA levels were measured using droplet digital PCR (ddPCR; Biodesix®) for EGFR-TKI sensitizing mutations (Ex19del or L858R) in all available samples. Model covariates were selected based on their statistical significance for the longitudinal and hazard sub-models and were analyzed using JMbayes package as implemented in R software (3.5.1). Our analysis indicates that the joint model can independently characterize changes in ctDNA and SLD and can predict PFS in the validation cohort, using only ctDNA changes occurring within 6 weeks from the initiation of therapy. Similarly, in the training cohort, joint modelling indicates that the relationship between SLD and PFS using RECIST is consistent with the longitudinal ctDNA analysis. In the analysis set, our model estimated a PFS of 16.6 months (95% confidence interval [CI] 12.1, NC) for osimertinib (n=153) and 9.4 months (95% CI 8.0, 13.5) for comparator EGFR-TKI (n=167). Model-predicted PFS probability using either ctDNA or SLD data was similar, suggesting ctDNA dynamics may provide similar information to RECIST for clinical decision making. Based on this analysis, ctDNA dynamics could be utilized to predict RECIST-defined progression for decision making during drug development of treatments for patients with NSCLC.

Abstract A60: Phylogenetic analyses reveal variable patterns of tumor evolution in HGSOC

Abstract High-grade serous ovarian cancer (HGSOC) is the most common and difficult to treat ovarian cancer subtype. HGSOC is diagnosed typically at late stage when it has already metastasized to many tissues in peritoneal cavity. In order to gain understanding of ovarian cancer evolution and reasons for chemoresistance, patients’ sequencing and clinical data were extensively analyzed. We studied 124 cancerous samples from 30 HGSOC patients and sequenced whole genomes from multiple tissues collected at diagnosis (N=92), interval debulking surgery (N=17), and relapse (N=15), and in addition deep sequencing data (600 genes) from seven patients with longitudinal circulating tumor DNA (ctDNA). Subclones were identified using somatic mutations and copy number variants (CNV). Patients were divided into three primary therapy response groups (poor, intermediate, and good) using platinum free interval (PFI), primary therapy outcome, and residual tumor size after surgery. The poor response group consisted of patients having progressive disease. Phylogenetic analysis revealed clearly distinct evolutionary models in HGSOC. Briefly, patients can be first divided into two main groups based on genetic diversity between tissues at diagnosis and secondly into three subgroups by comparing them to patients’ relapse samples affected by chemotherapy. In our study 70% of patients fall into the model displaying high genetic diversity between tissues. Although genetic diversity did not correlate with clinical outcome, the number of subclones differed significantly between primary therapy response groups (ANOVA, p=0.013): good outcome patients had more subclones. Relapse or interval stage samples were available from ten patients. Four of them displayed static pattern, continuing the low genetic diversity detected at diagnosis. In this evolution model, subclonal composition is very similar in all the samples regardless of tissue or treatment stage. In the six other patients, we identified models with a) complete subclonal turnover (N=2), b) accumulation of novel mutations (N=2), or c) mixed pattern (N=2). Accumulation of novel mutations in the two patients (PFI 6.0 and 2.7 months) may result from the defective homologous recombination machinery identified by relapse-specific mutational signature (COSMIC signature SBS3). As a common feature of metastasis, evidence of polyclonal seeding was detected in almost all the patients. HGSOC tumors exhibit multiple distinct models of evolution. The most patients are highly genetically different. However, in a quarter of the patients tumors were quite static at diagnosis and half of them remained static even after chemotherapy despite obvious selection pressure. In the majority of cases, the largest number of changes were detected once influenced to chemotherapy. Because of inter-tissue heterogeneity and diverging nature of HGSOC on-time samples, for example through ctDNA, are needed to find optimal drug combinations for this moving target. Citation Format: Jaana Oikkonen, Nil Campamà Sanz, Antti Häkkinen, Yilin Li, Ingrid Schulman, Mikko Kivikoski, Kaisa Huhtinen, Sakari Hietanen, Seija E. Grénman, Johanna Hynninen, Rainer Lehtonen, Sampsa Hautaniemi. Phylogenetic analyses reveal variable patterns of tumor evolution in HGSOC [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr A60.

Comprehensive modeling of longitudinal circulating tumor DNA dynamics to predict clinical response to first-line immunotherapy and chemoimmunotherapy in advanced non-small cell lung cancer.

9525 Background: First-line immunotherapy (IO) and chemo-immunotherapy (chemo-IO) are approved for PD-L1-expressing advanced non-small cell lung cancer (NSCLC), but PD-L1 expression does not reliably predict therapeutic response. Therefore, accurate on-therapy response assessment is needed to guide clinical decision-making. Conventional radiographic imaging is the gold-standard, but may not capture the nature and timing of an immune-mediated response. We investigated whether comprehensive longitudinal circulating tumor DNA (ctDNA) dynamics could enhance prediction of clinical response. Methods: We conducted targeted error correction sequencing (TEC-Seq) of longitudinal plasma specimens and matched white blood cells (WBCs) in patients with NSCLC treated with first-line IO or chemo-IO. Plasma ctDNA variants were identified by filtering out clonal hematopoiesis (CH) and germline (GL) variants found in matched WBCs. Clinical and pathological data, including PD-L1 tumor proportion score (TPS), and imaging response by RECIST1.1 were assessed. ctDNA dynamics were modeled to predict durable clinical benefit (at 6 months), progression-free survival (PFS), and overall survival (OS). Results: A total of 143 longitudinal plasma and 24 white blood cell samples underwent TEC-Seq for 31 patients with NSCLC treated with IO (n = 17) or chemo-IO (n = 14). ctDNA variants were found in 77% (n = 24) of patients after filtering out CH and GL variants, which comprised 53% (n = 196 of 373) of all variants. Molecular response, signified by elimination of ctDNA variants, was detected in 32% (n = 10) of patients and associated with improved PFS (p = 0.0004, log rank) and OS (p = 0.017, log rank). Time to molecular response was shorter than time to best RECIST response (median 3 vs. 7.71 weeks, p = 0.048, Mann-Whitney U test). A logistic regression model incorporating molecular response, recrudescence, or emergence of new variants predicted durable clinical benefit (sensitivity 84%, specificity 76%, AUC 0.88) better than PD-L1 TPS (AUC 0.67, p = 0.046, bootstrap method). Conclusions: Comprehensive modeling of ctDNA variant dynamics predicts clinical outcome independent of PD-L1 status in patients with advanced NSCLC treated with first-line IO or chemo-IO. Verification of bona fide ctDNA variants by matched WBC sequencing is essential. Molecular response can be identified earlier than imaging response and could enable on-therapy decision-making to alter clinical outcomes.

Mechanisms of Acquired Resistance to Savolitinib, a Selective MET Inhibitor in MET-Amplified Gastric Cancer.

PURPOSESome gastric cancers harbor MET gene amplifications that can be targeted by selective MET inhibitors to achieve tumor responses, but resistance eventually develops. Savolitinib, a selective MET inhibitor, is beneficial for treating patients with MET-driven gastric cancer. Understanding the resistance mechanisms is important for optimizing postfailure treatment options.PATIENTS AND METHODSHere, we identified the mechanisms of acquired resistance to savolitinib in 3 patients with gastric cancer and MET-amplified tumors who showed a clinical response and then cancer progression. Longitudinal circulating tumor DNA (ctDNA) is useful for monitoring resistance during treatment and progression when rebiopsy cannot be performed.RESULTSUsing a next-generation sequencing 100-gene panel, we identified the target mechanisms of resistance MET D1228V/N/H and Y1230C mutations or high copy number MET gene amplifications that emerge when resistance to savolitinib develops in patients with MET-amplified gastric cancer.CONCLUSIONWe demonstrated the utility of ctDNA in gastric cancer and confirmed this approach using baseline tumor tissue or rebiopsy.

Clinical Implications of Monitoring ESR1 Mutations by Circulating Tumor DNA in Estrogen Receptor Positive Metastatic Breast Cancer: A Pilot Study

BACKGROUND: ESR1 mutations are frequently detected in ER+ MBC, and have been reported to be associated with endocrine therapy resistance. However, there are little researches to validate whether dynamic monitoring of ESR1 mutations could serve as a predictive plasma biomarker of acquired resistance to endocrine therapy. Therefore, in this study, we performed longitudinal circulating tumor DNA (ctDNA) detection to evaluate the clinical implications of monitoring ESR1 mutations. METHODS: We performed longitudinal dynamic mutation analyses of plasma samples from 45 patients with metastatic breast cancer (MBC) and sequencing paired biopsy tissues, using a targeted NGS panel of 425 genes. These patients were treated at the Second Affiliated Hospital of Dalian Medical University between January 2017 and February 2019 with written informed consent. RESULTS: Mutations profiles were highly concordant between plasma and paired tissue samples from 45 MBC patients (r = 0.96, P < 0.0001). ESR1 mutations were enriched in ER+ MBC patients after AI therapy (17.8%, 8/45). The median time from AI endocrine therapies to the initial detection of ESR1 mutation was 39 months (95% CI 21.32–57.57). Some hotspot mutations (Y537S (n = 5), Y537N (n = 1), D538G (n = 2), E380Q (n = 2)) and several rare mutations (L345SfsX7, 24fs, G344delinsGC) were identified in our cohort. In addition, we observed that two patients obtained multiple ESR1 mutations over the course of treatment (Y537N/Y537S/D538G, L345SfsX7/24fs/E380Q). Through dynamically monitoring ESR1 mutations by ctDNA, we demonstrated that the change of allele frequency of ESR1 mutations was an important biomarker, which could predict endocrine resistance of ER+ MBC in our study. We also observed that the combination of everolimus in four cases with acquired ESR1 mutations showed longer PFS than other therapies without everolimus. CONCLUSION: The dynamic monitoring of ESR1 mutations by ctDNA is a promising tool to predict endocrine therapy resistance in ER+ MBC patients.

Liquid biopsy: a powerful tool to monitor trastuzumab resistance in HER2-positive metastatic gastric cancer

Human epidermal growth factor receptor 2 (HER2) overexpression/amplification affects about 6.1%–23.0% of gastric cancer patients [1, 2]. All major guidelines recommend HER2 testing to guide the selection for trastuzumab treatment in metastatic gastric cancer (mGC) [3], because doublet chemotherapy with trastuzumab significantly improved overall survival (OS) in the crucial trastuzumab for gastric cancer trial (the ToGA trial) [4]. However, the unsatisfactory gain of median progression-free survival (PFS) stresses important issues of intrinsic and acquired resistance to HER2-targeted therapies [4]. Currently, the underlying molecular mechanism of trastuzumab resistance in mGC is still unclear, and the strategies to real time monitor resistance-specific aberrations are urgently needed. As circulating tumor DNA (ctDNA) carries the same genomic alterations that are present in the primary tumor [5, 6], liquid biopsy-based ctDNA profiling offers a unique opportunity for serially monitoring treatment response in a non-invasive manner, and has opened the door for identification the mechanisms of drug resistance. In a study recently published in Gut, titled “Liquid biopsies to track trastuzumab resistance in metastatic HER2-positive gastric cancer”, Wang et al. [7] demonstrated for the first time that longitudinal ctDNA sequencing could promisingly predict tumor shrinkage and progression in HER2 + mGC patients under trastuzumab treatment. Based on the detected molecular alterations from the ctDNA profiling, they further dissected various mechanisms of trastuzumab resistance (Fig. 1). Longitudinal circulating tumor DNA sequencing provides novel insights into gene alterations underlying trastuzumab resistance in HER2-positive metastatic gastric cancer. HER2+: HER2-positive; mGC: metastatic gastric cancer; ctDNA: circulating tumor DNA: Copy No.: copy number In this study, the authors sequenced 416 clinically relevant genes to determine the genomic profiles of GC patients. The molecular alterations, including copy number alterations, mutations and structural variations, detected in 78 paired plasma and tissue samples (46 from HER2+ patients and 32 from HER2− patients) were used to evaluate the consistency of detection between the “liquid” and “solid” biopsies. As expected, the alterations detected in plasma provided a good representation of the status in the tumor tissues. In particular, HER2 amplification status, the major marker of HER2 + GC, detected by plasma-based ctDNA sequencing was highly consistent with that by tissue-based sequencing and fluorescence in situ hybridisation. These findings indicated that plasma-based ctDNA profiling might provide insights into HER2 amplification in HER2 + GC. Further longitudinal analysis were perform in 97 time-course plasma samples collected from 24 HER2 + mGC patients to track the resistance during trastuzumab treatment. As compared to plasma carcinoembryonic antigen, the copy number variations (CNVs) of HER2 in ctDNA were better at tracking trastuzumab treatment response. Generally, the HER2 copy number decreased during treatment compared with baseline and levels of progressive disease (PD), indicating tumor shrinkage. Additionally, most patients with intrinsic resistance-related progression presented higher HER2 copy numbers at PD than baseline, while the patients with acquired resistance often had lower HER2 copy numbers at PD. From the same ctDNA profiles, the authors found evidence for reported mechanisms of trastuzumab resistance in 76.5% patients. They found that the patients with multiple resistance mechanisms (PIK3CA/R1/C3 and ERBB2/4 mutations) displayed much shorter PFS during trastuzumab treatment. These findings suggested that liquid biopsy-based ctDNA profiling can effectively capture the heterogeneity information about acquired resistance. Furthermore, they also observe several novel resistance mechanisms. One of them is the ERBB4 S774G mutation. This novel mutation can increase the sensitivity to trastuzumab treatment, suggesting for the first time that the mutation of ERBB4 play a critical role in mediating resistance to ERBB2 inhibitors in HER2 + GC. Another novel resistance mechanism is the emergence of NF1 mutations. Using in vitro and in vivo experiments, the authors demonstrated that NF1 was a resistance-related gene and could be used as a potential resistance marker of trastuzumab. NF1 lost (mutation or deletion) contributes to driving resistance of HER2-targeted therapy via elevating pMEK/ERK activation, whereas the combination of HER2 and MEK/ERK inhibitors might overcome trastuzumab resistance. This study has some obvious limitations. First, other rare genomic or even nongenomic mechanisms of trastuzumab resistance may have been missed by the 416-gene panel. Second, the relatively small number of patient enrolled does not allow drawing definitive conclusion on the predictive value of this liquid biopsy approach. Nevertheless, the study provides helpful information to monitor the treatment response of trastuzumab and develop therapeutic strategies for the HER2 + mGC patients with trastuzumab resistance. The author read and approved the final manuscript. Not applicable. The author declares no competing interests. Not applicable. Not applicable. Not applicable. Not applicable.

The Spatiotemporal Evolution of Lymph Node Spread in Early Breast Cancer.

Purpose: The most significant prognostic factor in early breast cancer is lymph node involvement. This stage between localized and systemic disease is key to understanding breast cancer progression; however, our knowledge of the evolution of lymph node malignant invasion remains limited, as most currently available data are derived from primary tumors.Experimental Design: In 11 patients with treatment-naïve node-positive early breast cancer without clinical evidence of distant metastasis, we investigated lymph node evolution using spatial multiregion sequencing (n = 78 samples) of primary and lymph node deposits and genomic profiling of matched longitudinal circulating tumor DNA (ctDNA).Results: Linear evolution from primary to lymph node was rare (1/11), whereas the majority of cases displayed either early divergence between primary and nodes (4/11) or no detectable divergence (6/11), where both primary and nodal cells belonged to a single recent expansion of a metastatic clone. Divergence of metastatic subclones was driven in part by APOBEC. Longitudinal ctDNA samples from 2 of 7 subjects with evaluable plasma taken perioperatively reflected the two major evolutionary patterns and demonstrate that private mutations can be detected even from early metastatic nodal deposits. Moreover, node removal resulted in disappearance of private lymph node mutations in ctDNA.Conclusions: This study sheds new light on a crucial evolutionary step in the natural history of breast cancer, demonstrating early establishment of axillary lymph node metastasis in a substantial proportion of patients. Clin Cancer Res; 24(19); 4763-70. ©2018 AACR.

Abstract 937: Longitudinal circulating-tumor DNA profiling of EGFR-mutated non-small cell lung cancer patients treated with EGFR-tyrosine kinase inhibitors

Abstract Background: In EGFR-mutant non-small cell lung cancer (NSCLC), progression disease (PD) under 1st-generation EGFR tyrosine kinase inhibitors (EGFR-TKIs) is driven by the EGFR T790M mutation in about 50% of cases. This mutation is targeted with osimertinib, a specific and potent inhibitor that also showed superior efficacy to that of 1st-generation EGFR-TKIs in the 1st-line treatment EGFR+ NSCLC. Strategy: We performed a longitudinal circulating-tumor DNA (ctDNA) analysis to evaluate 1) the dynamics of sensitizing or resistant mutations over time and 2) the genomic alterations associated with EGFR-TKI resistance, in NSCLC patients treated with either 1st-generation EGFR-TKIs (n=24) or with osimertinib (n=20). ctDNA sequencing was performed using InVisionSeq™, an amplicon-based NGS (36-gene panel) assay. Results: Sensitivity was 80% and 100% for the detection of EGFR-activating mutations and the EGFR T790M mutation, respectively, at PD in ctDNA vs tissue biopsies. The type of progression appears to influence the detection of EGFR mutations in plasma. Patients (pts) with exclusively brain or thoracic PD had significantly lower allelic fractions (AFs) of EGFR-activating mutations than pts with systemic PD (P=0.006). AFs of both EGFR-activating and EGFR T790M mutations were highest in patients with progressive metastases in liver or bone. High cell-free DNA load was associated with the presence of TP53 mutations regardless of the time under treatment (n=248 samples). The total number of mutations detected in ctDNA was higher in pts treated with osimertinib vs. 1st-generation EGFR-TKIs (P=0.004), suggesting a potential increase of tumor heterogeneity over time. We observed that the AFs of mutant ctDNA were correlated with response to treatment. Complete clearance of EGFR T790M (AF detection limit: 0.01%) was observed in pts who presented a partial response to osimertinib (n=17), of these, EGFR-activating mutations were found in 4/17 pts (AF:0.05-1.03%). PD was evidenced in 36/44 pts. Emergence of mechanisms of resistance, before the confirmation of clinical PD, was evidenced in 5 and 3 pts under erlotinib and osimertinib, respectively. PD to 1st-generation EGFR-TKIs was mainly driven by EGFR T790M (86%), followed by mutations in PIK3CA or PTEN. We detected the emergence of heterogeneous potential mechanisms of resistance to osimertinib in 3/9 cases, including mutations in EGFR, KRAS, BRAF as well as HER2 and MET amplification. We did not identify genomic drivers of resistance in 16/36 pts, despite evidence of clinical PD. These pts had either exclusive brain or thoracic progression. ctDNA WES will be performed in these samples. Conclusion: Our results suggest that ctDNA sequencing might be a complementary, noninvasive tool to monitor response to treatment and heterogeneous mechanisms of resistance in NSCLC pts treated with EGFR inhibitors. Citation Format: Sandra Ortiz-Cuaran, Aurélie Swalduz, Camille Léonce, Solène Marteau, Séverine Martinez, Gilles Clapisson, Virginie Avrillon, Luc Odier, Lionel Falchero, Pierre Fournel, Emma Green, Clive Morris, Maurice Pérol, Pierre Saintingy. Longitudinal circulating-tumor DNA profiling of EGFR-mutated non-small cell lung cancer patients treated with EGFR-tyrosine kinase inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 937.

Fusion detection and longitudinal circulating tumor DNA (ctDNA) profiling in ALK+ non-small cell lung cancer (NSCLC) patients.

e21031Background: Therapeutic response in ALK+ NSCLC is driven by heterogeneous mechanisms of resistance. Liquid biopsy (LB) offers a non-invasive approach to study the tumor genomic landscape unde...

Tracking the Evolution of Resistance to ALK Tyrosine Kinase Inhibitors through Longitudinal Analysis of Circulating Tumor DNA.

ALK rearrangements predict for sensitivity to ALK tyrosine kinase inhibitors (TKIs). However, responses to ALK TKIs are generally short-lived. Serial molecular analysis is an informative strategy for identifying genetic mediators of resistance. Although multiple studies support the clinical benefits of repeat tissue sampling, the clinical utility of longitudinal circulating tumor DNA analysis has not been established in ALK-positive lung cancer. Using a 566-gene hybrid-capture next-generation sequencing (NGS) assay, we performed longitudinal analysis of plasma specimens from 22 ALK-positive patients with acquired resistance to ALK TKIs to track the evolution of resistance during treatment. To determine tissue-plasma concordance, we compared plasma findings to results of repeat biopsies. At progression, we detected an ALK fusion in plasma from 19 (86%) of 22 patients, and identified ALK resistance mutations in plasma specimens from 11 (50%) patients. There was 100% agreement between tissue- and plasma-detected ALK fusions. Among 16 cases where contemporaneous plasma and tissue specimens were available, we observed 100% concordance between ALK mutation calls. ALK mutations emerged and disappeared during treatment with sequential ALK TKIs, suggesting that plasma mutation profiles were dependent on the specific TKI administered. ALK G1202R, the most frequent plasma mutation detected after progression on a second-generation TKI, was consistently suppressed during treatment with lorlatinib. Plasma genotyping by NGS is an effective method for detecting ALK fusions and ALK mutations in patients progressing on ALK TKIs. The correlation between plasma ALK mutations and response to distinct ALK TKIs highlights the potential for plasma analysis to guide selection of ALK-directed therapies.

Longitudinal circulating-tumor DNA profiling of EGFR-mutated lung adenocarcinoma patients treated with EGFR-tyrosine kinase inhibitors

Longitudinal circulating-tumor DNA profiling of EGFR-mutated lung adenocarcinoma patients treated with EGFR-tyrosine kinase inhibitors

Heterogeneity Underlies the Emergence of EGFRT790 Wild-Type Clones Following Treatment of T790M-Positive Cancers with a Third-Generation EGFR Inhibitor.

Rociletinib is a third-generation EGFR inhibitor active in lung cancers with T790M, the gatekeeper mutation underlying most first-generation EGFR drug resistance. We biopsied patients at rociletinib progression to explore resistance mechanisms. Among 12 patients with T790M-positive cancers at rociletinib initiation, six had T790-wild-type rociletinib-resistant biopsies. Two T790-wild-type cancers underwent small cell lung cancer transformation; three T790M-positive cancers acquired EGFR amplification. We documented T790-wild-type and T790M-positive clones coexisting within a single pre-rociletinib biopsy. The pretreatment fraction of T790M-positive cells affected response to rociletinib. Longitudinal circulating tumor DNA (ctDNA) analysis revealed an increase in plasma EGFR-activating mutation, and T790M heralded rociletinib resistance in some patients, whereas in others the activating mutation increased but T790M remained suppressed. Together, these findings demonstrate the role of tumor heterogeneity when therapies targeting a singular resistance mechanism are used. To further improve outcomes, combination regimens that also target T790-wild-type clones are required. This report documents that half of T790M-positive EGFR-mutant lung cancers treated with rociletinib are T790-wild-type upon progression, suggesting that T790-wild-type clones can emerge as the dominant source of resistance. We show that tumor heterogeneity has important clinical implications and that plasma ctDNA analyses can sometimes predict emerging resistance mechanisms.