MET Copy Number Research Articles

Clinical-genomic characteristics in patients with EGFR-mutated non-small cell lung cancer harboring MET copy number gains after progression on EGFR-TKI: A report from LC-SCRUM-TRY.

8628 Background: MET amplification (amp) account for 10-15% of resistance mechanism in EGFR-mutated non-small cell lung cancer (NSCLC) to EGFR-tyrosine kinase inhibitor (TKI) treatment. MET copy number (CN) gains consists of MET focal amp and polysomy (poly), but the clinical characteristics and outcome of EGFR-TKI resistant NSCLC patients harboring MET amp, poly remains unclear. Methods: The clinical-genomic characteristics and treatment outcome ofEGFR-TKI resistant EGFR-mutated NSCLC registered in LC-SCRUM-TRY (UMIN000041957) were analyzed. Genetic resistant alterations were screened using next-generation sequencing (NGS) (Tissue; Oncomine Precision Assay [OPA] or Plasma; Guardant360 [G360]), and MET-fluorescence in-situ hybridization (FISH). MET amp was defined as MET CN ≥4 (OPA), MET CN ≥2.12 (G360) or MET/CEP7 ratio ≥2 (FISH). MET poly was defined as MET CN≥5 and MET/CEP7 ratio <2 by FISH. Results: A total of 1559 patients had been enrolled in LC-SCRUM-TRY between Sep 2020 and Jan 2024. Of 1537 analyzed samples, 666 (43%) were EGFR-TKI resistant samples. Of these, 92 (14%), 239 (36%) and 335 (50%) had MET amp, poly, and no CN gain (no CNG), respectively. Patient characteristics and treatment outcome with 1st line EGFR-TKI and platinum-based chemotherapy (PBC) post EGFR-TKI is summarized (Table 1). The overall response rate (ORR) of PBC post EGFR-TKI in the patients with MET amp, poly and no CNG was 41%, 29% and 31%, respectively (p=0.34), with median progression-free survival (mPFS) being 5.7 months, 6.8 months, and 6.7 months (p=0.02). In addition, 12 and 11 of patients with MET amp and poly were enrolled into clinical trial of MET-targeted therapy (MET-TKI, n=2; MET-antibody-drug conjugate [ADC], n=4; EGFR/MET-antibody, n=2), and MET non-targeted therapy (EGFR-TKI, n=5; other ADCs, n=10: immunotherapy; n=1). The ORR of MET-targeted therapy/MET non-targeted therapy were 60/0% for MET amp, and 0/33% for MET poly, respectively. Conclusions: Patients with shorter PFS with prior 1st line EGFR-TKI are more likely to have MET amp. The efficacy of standard PBC post EGFR-TKI in patients with MET CNG is limited. Current MET-targeted therapy may not be effective for EGFR-mutated NSCLC harboring MET poly after progression on EGFR-TKI. [Table: see text]

Abstract CT251: Savolitinib (savo) + osimertinib (osi) vs savo + placebo (PBO) in patients (pts) with EGFR-mutated (EGFRm), MET-amplified advanced NSCLC with progression on osi

Abstract Background Osi, an EGFR-TKI, is the preferred 1L treatment (tx) for EGFRm aNSCLC; however, resistance eventually develops in most pts. MET amplification is the most common known resistance mechanism to osi. Combining osi with savo, a MET-TKI, has shown antitumor activity in EGFRm, MET-amplified aNSCLC. We conducted a Phase II, double-blind, randomized study (NCT04606771) to assess the individual contribution of savo to the combination. Methods Pts with EGFRm (Ex19del, L858R), MET-amplified (MET gene copy ≥5 or MET/CEP7 ratio ≥2; central confirmation by FISH), aNSCLC with progression on ≥1 tx, including osi, were randomized (1:1) to savo 300 mg QD + osi 80 mg QD or savo 300 mg QD + PBO. Tx continued until PD, unacceptable AEs, or other discontinuation criterion. Primary endpoint: ORR per RECIST 1.1 (investigator-assessed). Efficacy was also assessed by exploratory, higher MET cutoffs (determined retrospectively): 3+ staining ≥90% tumor cells (IHC90+) and/or MET gene copy ≥10 (FISH10+). Plasma was collected for exploratory analyses. Results 30 pts were randomized (savo + osi n=14; savo + PBO n=16). Table shows efficacy data. Grade ≥3 AEs and sAEs occurred in: 3 (21%) and 4 (29%) pts receiving savo + osi; 5 (31%) and 3 (19%) pts receiving savo + PBO, respectively. Most common any-grade AEs with savo + osi vs savo + PBO were nausea (50% vs 19%), peripheral edema (36% vs 25%) and vomiting (21% vs 31%). Conclusion Savo + osi demonstrated clinical activity, with savo + PBO showing lower clinical activity. Clinical activity was observed in pts with higher MET cutoffs (FISH10+ and/or IHC90+). Due to small sample sizes, these data need to be interpreted with caution. Safety was consistent with known AE profiles of each tx. This study was terminated early as the contribution of savo to the savo + osi combination is being further assessed in SAVANNAH (NCT03778229), which uses a different savo dosing regimen and higher MET-amplification cutoffs. TABLE 1. NAND Savolitinib + osimertinib Savolitinib + placebo FISH10+ and/or IHC90+a (n=8) All patients(n=14) FISH10+ and/or IHC90+ a (n=7) All patients (n=16) ORR, % (95% CI)b 63 (24, 91) 57 (29, 82) 29 (4, 71) 13 (2, 38) Complete response, n (%)b 0 0 0 0 Partial response, n (%)b 5 (63) 8 (57) 2 (29) 2 (13) Median duration of response, weeks (95% CI) 30.6 (23.0, NC) 30.6 (18.9, NC) NR (12.4, NC) NR (12.4, NC) PFS events, n (%)c 4 (50) 9 (64) 5 (71) 13 (81) Median PFS, months (95% CI) 8.2 (4.1, NC) 7.4 (5.6, NC) 4.0 (1.3, NC) 1.6 (1.3, 4.1) aAs IHC was not used to determine pt eligibility, this subgroup does not comprise all randomized pts due to limited sample availability; bResponses included unconfirmed responses; cOnly included events that occurred within 2 missed visits of the last evaluable assessment. CI, confidence interval; FISH10+, FISH (MET copy number ≥10); IHC90+, immunohistochemistry overexpression (3+ staining intensity) in ≥90% of tumor cells; NC, not calculable; NR, not reached; ORR, objective response rate; PFS, progression-free survival. Citation Format: James Chih-Hsin Yang, Yuh-Min Chen, Ullas Batra, Kien Do, Piyada Sitthideatphaiboon, Pongwut Danchaivijitr, Kang-Yun Lee, Jarin Chindaprasirt, Cheng-Ta Yang, Gee-Chen Chang, Chaiyut Charoentum, Teerapat Ungtrakul, Juan Ignacio Hernandez Moran, Ryan Hartmaier, Matthew Haskins, Wanning Xu, Jonathan W. Riess. Savolitinib (savo) + osimertinib (osi) vs savo + placebo (PBO) in patients (pts) with EGFR-mutated (EGFRm), MET-amplified advanced NSCLC with progression on osi [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr CT251.

Clinical Implication of Concurrent Amplification of MET and FGFR2 in Metastatic Gastric Cancer.

c-mesenchymal epithelial transition factor receptor (c-MET) and fibroblast growth factor receptor 2 (FGFR2) amplification have been identified as factors associated with advanced stage and poor prognosis in gastric cancer (GC). While they are typically considered mutually exclusive, concurrent amplifications have been reported in a small subset of GC patients. in this retrospective study, we analyzed the clinical outcomes of GC patients with MET and FGFR2 amplification using the next-generation sequencing (NGS) database cohort at Samsung Medical Center, which included a total of 2119 patients between October 2019 and April 2021. Of 2119 cancer patients surveyed, the number of GC patients was 614 (29.0%). Out of 614 GC patients, 39 (6.4%) had FGFR2 amplification alone, 22 (3.6%) had MET amplification, and 2 GC patients (0.3%) had concurrent FGFR2 and MET amplification. Two patients with concurrent FGFR2 and MET amplification did not respond to first-line chemotherapy. These two patients had significantly shorter overall survival (3.6 months) compared to patients with FGFR2 or MET amplification alone (13.6 months and 8.4 months, respectively) (p = 0.004). Lastly, we tested the existence of FGFR2 and MET in tumor specimens from different organ sites. Initially, the NGS was tested in a primary tumor specimen from stomach cancer, where the MET copy number was 14.1 and the FGFR2 copy number was 5.3. We confirmed that both MET and FGFR2 were highly amplified in the primary tumor using FISH (MET-CEP7 ratio = 5 and FGFR2-CEP7 ratio = 3). However, although the MET copy number was normal in peritoneal seeding using FISH, FGFR2 remained amplified using FISH (FGFR2-CEP7 ratio = 7) with high FGFR2 protein overexpression. Hence, there was intra-patient molecular heterogeneity. our findings suggest that concurrent amplification of FGFR2 and MET in GC patients is associated with clinical aggressiveness and may contribute to non-responsiveness to chemotherapy or targeted therapy.

Clinical and molecular Characterization of NSCLCs with MET exon 14 skipping mutation coexist MET amplification.

e20506 Background: MET exon 14 skipping mutation (METex14) and MET amplification are the most prevalent molecular alterations associated with MET carcinogenesis in non-small cell lung cancer, with respective frequencies of 3-4% and 1-5%. Recent research indicates that patients with METex14 may also carry MET amplification, and that MET-TKI therapy has a higher response rate in this patient population. We evaluated the clinical and molecular characteristics of patients with altered or co-altered MET using NGS data of non-small cell lung cancer cases from Jiangsu Simcere diagnostic Co., ltd. Methods: During 2019-2021, samples from 33074 NSCLC patients underwent comprehensive genomic profiling (CGP) using hybrid-capture technology at the Simcere diagnostic laboratory (Nanjing, China). To detect gene mutations in tumor tissue or blood samples of patients, next-generation sequencing (NGS) was performed. MET amplification was defined as MET copy number greater than 2.25. Results: MET exon 14 skipping was found in 325 pts (0.98%), MET amplification was found in 136 pts (0.41%), and the co-alter population consisted of only 36 pts (0.11%). Receptor, Donor, D1010, Y1003, and other METex14 subtypes represented 12.0%, 36.6%, 24.6%, 0.2%, and 26.2%, respectively, of the population. Then, we divided MET-altered NSCLC patients into three groups: MET14 (carrying only METex14), AMP (carrying only MET amplification), and MET14&AMP (MET14 concomitant MET amplification). The differences in age, gender, TMB copy number, and MET copy number were then compared between these groups. Patients with AMP were considerably younger than those with METex14&AMP or AMP. (MET14&AMP: 69.0±9.27 vs AMP: 63.5±10.6, P = 0.032; MET14: 70.0±10.9, P < 0.001). The AMP group contained significantly more male patients than the MET14 group (68.0% vs. 54.5%, P = 0.019), but there were no significant differences between the remaining groups. In contrast to tissue-based TMB, the AMP group was significantly higher than the other two (AMP:17.059.5 vs MET 14: 2.945.79; P0.001; MET14&AMP: 3.650.63, P = 0.005). In spite of this, there was no statistically significant difference between the AMP and MET14 & AMP groups in terms of MET copy number or percentage of MET CN > = 10. Conclusions: In general, AMP pts are younger and have a higher TMB than co-alteration pts; however, there is no significant difference in MET CN between AMP and co-alteration pts; whether the coexisting group is sensitive to MET-TKI is unknown, and future research should focus on the treatment of co-alteration and AMP pts.

Abstract LB294: Baseline and on-treatment plasma-based genomics as a predictor of outcome in SAVANNAH: Savolitinib + osimertinib in EGFRm MET overexpressed/amplified NSCLC post-osimertinib

Abstract Savolitinib, an oral, potent, and highly selective MET-TKI, in combination with osimertinib, a 3rd-generation, irreversible, oral EGFR-TKI, may overcome common acquired MET-driven resistance following osimertinib treatment. The ongoing Ph2 SAVANNAH (NCT03778229) study is investigating this combination in pts with EGFRm NSCLC who have MET overexpression and/or amplification upon progressive disease (PD) post-osimertinib. Using plasma EGFRm as an estimate of tumor burden, we report exploratory analyses of progression-free survival (PFS) by plasma EGFRm clearance during treatment at Day (D) 22. Additionally, agreement between tissue (IHC/FISH) and plasma (NGS) testing for detecting MET overexpression and/or amplification is reported. Following central MET testing on tumor tissue collected upon PD post-osimertinib, eligible pts received oral savolitinib (300 or 600 mg QD, or 300 mg BID) + oral osimertinib 80 mg QD. MET overexpression was assessed by IHC (3+ staining in ≥50% of tumor cells [IHC50+]) and amplification by FISH (MET copy number ≥5 and/or MET:CEP7 ratio ≥2 [FISH5+]). Here, PFS analysis was performed in subgroups identified by exploratory higher biomarker cut-off levels of 3+ staining in ≥90% tumor cells (IHC90+) and/or MET copy number ≥10 (FISH10+). Plasma EGFRm (Ex19del/L858R only) analysis was conducted by ddPCR at D1 and every week thereafter for 4 weeks and at week 6. Plasma EGFRm clearance was defined as undetected EGFRm ctDNA at D22, where it was detected at D1. Baseline (BL) MET amplifications were determined via ctDNA NGS at D1. Agreement analysis was performed (DCO 27Aug2021). This analysis included 192 pts who received savolitinib 300 mg QD + osimertinib and had ≥2 post-BL RECIST scans. Of those with valid tissue FISH and IHC results and evaluable ctDNA at D1 (88% [169/192]), 124 pts had detectable plasma EGFRm. Plasma EGFRm clearance was assessed in 103 pts with detectable D1 plasma EGFRm who also had evaluable ctDNA at D22. Clearance was observed more frequently in pts with IHC90+ or FISH10+ tumors (42% [28/66]) than those with IHC90- and FISH10- tumors (16% [6/37]). Median PFS (95% CI) with vs without clearance was 11.0 (7.4, 13.0) vs 4.1 (2.7, 5.5) months in pts with IHC90+ or FISH10+ tumors. Agreement between tissue FISH and plasma NGS was assessed in 72 evaluable pts. Overall, 21 (29%) pts had MET FISH10+ tumors and 14 (19%) had plasma NGS focal MET amplification, with 11 being positive by both methods (positive percent agreement [PA]: 52%, negative PA: 94%, overall PA: 67%). Plasma EGFRm clearance was observed after 3 wks of savolitinib + osimertinib, particularly in pts with MET IHC90+ or FISH10+ tumors and was associated with improved PFS. Limited positive agreement between tissue- and BL plasma-based testing suggests IHC/FISH may be able to identify more pts likely to benefit from savolitinib + osimertinib. Citation Format: Ryan James Hartmaier, Aleksandra Markovets, Wanning Xu, Agata Baczynska, Alexander Todd, Myung-Ju Ahn. Baseline and on-treatment plasma-based genomics as a predictor of outcome in SAVANNAH: Savolitinib + osimertinib in EGFRm MET overexpressed/amplified NSCLC post-osimertinib [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 2 (Clinical Trials and Late-Breaking Research); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(8_Suppl):Abstract nr LB294.

Osimertinib + Savolitinib to Overcome Acquired MET-Mediated Resistance in Epidermal Growth Factor Receptor-Mutated, MET-Amplified Non-Small Cell Lung Cancer: TATTON.

The savolitinib + osimertinib combination represents a promising therapy in patients with MET-amplified/overexpressed, EGFRm advanced NSCLC with disease progression on a prior EGFR-TKI. Acquired resistance mechanisms to this combination include those via MET, EGFR, and KRAS. On-treatment ctDNA dynamics can predict clinical outcomes and may provide an opportunity to inform earlier decision-making. This article is highlighted in the In This Issue feature, p. 1.

Abstract 5103: Characterization of the genomic landscape and actionable mutations in Taiwanese prostate cancer patients

Abstract Background: Prostate Cancer (PCa) is the second most common male cancer worldwide and the most common cancer in males over 65 years old. PCa is the sixth most common cancer in Taiwan, and its incidence rate has increased gradually over the past 30 years. PAPR inhibitors are the only type of targeted drug approved by the FDA to treat advanced castration-resistant prostate cancer (CRPC) that has grown after the hormone therapy drugs. This study aimed to characterize the genomic profile of Taiwanese PCa and explore whether there are potential treatment guidances derived. Methods: Formalin-fixed paraffin-embedded (FFPE) tumor tissues from 99 patients diagnosed with PCa and collected at Chi-Mei Medical Center (CMMC) were subject to next-generation sequencing using ACTOnco® CGP panel that cover coding regions of 440 cancer-related genes. Genomic alterations (GAs) and signatures, including single nucleotide variations (SNVs), short insertions and deletions (InDels), copy-number variations (CNVs), fusion genes, tumor mutations burden (TMB), and microsatellite instability (MSI) status were retrieved. The gene mutation prevalence was compared with the Western population using the TCGA prostate cancer dataset. Results: A total of 1558 variants was identified, including 215 SNVs, 22 InDels, 1178 CN gain and 135 homozygous deletions. Similar to the Western population, the most frequently mutated genes were SPOP (21.2%), KMT2C (10.1%), MUC16 (8.1%), TP53 (6.1%), ARID2 (5.1%), IDH1 (5.1%), PTGS2 (5.1%). Further analysis showed that 12 patients harbored deleterious/likely deleterious mutations in genes implicated in homologous recombination (HRR) DNA repair pathway, including three BRCA2, two CDK12, BRAD1 and ARID1A, respectively, and one ATR, ATM and PALB2, respectively. All BRCA2 mutations were predicted to be germline origin and only one-third of 12 HRR mutants had a biallelic gene loss. Median TMB calculated from NGS data is 0.6 muts/Mb (range 0 to 4.5) and all samples are microsatellite-stable (MSS). Therapeutically actionable gene and pathway analysis revealed that up to 24.2% of patients harbored at least one aberration against FDA-approved targeted drugs, such as MET copy number (CN) gain (11.1%), mTOR pathway aberration (6.1%), HRR gene biallelic loss (4%), BRAF activating mutation (4%), IDH1 activating mutations (4%), EGFR CN gain (3.0%), FGFR1 CN gain (2.0%), MET fusion (1.0%) and BRAF fusion (1%). Conclusion: This CGP study unraveled the genomic profile of Taiwanese prostate cancers, and the results showed that GAs identified could serve as a potential biomarker to guide personalized, targeted therapies in one-fourth of patients. Citation Format: Kien Thiam Tan, Chia-Ling Wu, Yen-Jung Lu, Ka-Po Tse, Chien-Feng L Li. Characterization of the genomic landscape and actionable mutations in Taiwanese prostate cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5103.

Abstract LB515A: A MET targeting biparatopic antibody-drug conjugates (ADC), REGN5093-M114, has an antitumor efficacy in NSCLC harboring MET gene alterations

Abstract Introduction: Aberrations in MET occurs frequently in non-small cell lung cancer (NSCLC), via MET amplification or MET exon 14 skipping (METex14) mutation. Small-molecule tyrosine kinase inhibitors (TKIs) targeting MET have been developed, but durable response is invariably limited by the emergence of acquired resistance. In this study, we examined the preclinical activity of a MET x MET biparatopic antibody to a novel maytansinoid payload, REGN5093-M114, in MET-driven patient-derived models. Experimental Design: We had previously established patient-derived models from EGFR-TKIs resistant patients with MET-amplified or -overexpressed EGFR-mutant NSCLC. Patient-derived organoids (PDOs), patient-derived cells (PDCs), or ATCC cell lines were used for cell viability, apoptosis assay and western blots to investigate the activity of REGN5093-M114. In order to explore the predictive biomarker correlates of REGN5093-M114 and MET status, we investigated whole MET expression, surface MET expression by flow cytometry, MET amplification by copy number analysis. We evaluated the antitumor activity of REGN5093-M114 in patient-derived tumor xenograft (PDX) models from EGFR-mutant NSCLC patients with acquired resistance to osimertinib plus savolitinib, including acquired MET p.Y1230C mutation. Finally, we determined whether REGN5093-M114 is able to overcome acquired resistance to the MET-TKI, tepotinib, using PDC from METex14 mutant NSCLC patients. Result: In acquired MET-amplified EGFR-TKI resistant PDCs, PDOs, ATCC cell lines and PDX models, REGN5093-M114 alone exhibited a significant antitumor efficacy compared to MET-TKI or the MET x MET biparatopic antibody (REGN5093), but had no effect on some models with same MET copy number as the sensitive models. On the other hand, regardless of MET CNV, MET-overexpressed TKI-naïve EGFR mutant NSCLC cells showed a sensitive response to REGN5093-M114. Thus, we calculated the area under the curve plot for REGN5093-M114 by quantifying whole MET expression, surface MET expression, and MET CNV values for each cell line. As a result, the surface MET expression had the most predictive power on determining the efficacy of the REGN5093-M114. Notably, REGN5093-M114 potently reduced tumor growth of EGFR mutant NSCLC with PTEN loss or MET Y1230C mutation after progression on prior TATTON study. Furthermore, we demonstrated that the combined treatment of MET-TKI and REGN5093-M114 shows synergistic antitumor efficacy with a marked reduction of MET downstream signals and increased apoptotic proteins in the METex14 mutant NSCLC. Altogether, REGN5093-M114 is a potent candidate to overcome the current challenges faced in targeting MET pathway. Conclusion: REGN5093-M114 has the potential to be a novel therapeutic option in NSCLC harboring MET genetic alterations, and further clinical application is highly warranted. Citation Format: Seung Yeon Oh, Sun Min Lim, You Won Lee, Eun Ji Lee, Jae Hwan Kim, Seong Gu Heo, Mi Ra Yu, Min Hee Hong, Hye Ryun Kim, John DaSilva, Christopher Daly, Mi Ran Yun, Byoung Chul Cho. A MET targeting biparatopic antibody-drug conjugates (ADC), REGN5093-M114, has an antitumor efficacy in NSCLC harboring MET gene alterations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr LB515A.

Real-world (rw) analysis of quantitative MET copy number (CN) as a biomarker in NSCLC.

9123 Background: MET amplification (amp) can be a de novo driver or mechanism of resistance to targeted therapy. We explored the genomic landscape of MET amp NSCLC, including co-driver alterations and amplicon size, and its association with outcomes to MET tyrosine kinase inhibitors (TKIs) using rw data. Methods: Comprehensive genomic profiling (CGP) results from 64,521 tissue and 5,177 liquid NSCLC samples were queried for MET amp (focal amplicons ≥4 copies above specimen ploidy). Sub analysis comparing focal (≤20Mbp) and non-focal (> 20Mbp) amp was performed. Using the nationwide (̃280 US cancer clinics) de-identified EHR-derived Flatiron Health-Foundation Medicine aNSCLC clinicogenomic database (CGDB) linked to tissue CGP (8/2014-9/2021), we assessed co-driver presence ( EGFR, ALK, RET, ROS1, NTRK, BRAF, KRAS) prior to therapy exposure and outcomes to MET TKIs. Results: MET amp was detected in 2,102 (3.3%) NSCLC tissue samples (median CN of 11, range 6-168). Evaluating full gene focal amplicons as well as non-focal MET amps (n = 398, median CN 7), smaller amplicon size significantly correlated with higher CN (p < 0.001). In 5,177 liquid samples, MET amp was detected in 40 (0.77%) cases; frequency increased to 3.2% (33/1,033) in those with a tumor fraction above 10%. In the CGDB, 261 (3.2%) pts had NSCLC with MET amp (median CN 11). Among 241 pts with MET amp detected prior to receipt of any targeted therapy, MET amp co-occurred with another driver in 32 (13%) cases (81% KRAS, 16% EGFR, 3.1% BRAF) and with a MET exon 14 skipping alteration ( METex14) in 25 (10%). MET CN negatively correlated with the presence of a co-driver (median 11 with MET amp alone vs 9 with a non- METex14 co-driver, p < 0.001); however, MET CN was similar in MET amp cases with and without METex14 (median 11 for both, p = 0.60). Co-occurring non- METex14 drivers were detected in 26% of MET amp cases with CN < 8 and 19% with CN 8-9, but in only 9.1% with CN 10-20 and 2.6% with CN > 20. Tumor mutational burden was not significantly correlated with MET CN. In 14 cases with an EGFR or ALK co-driver and MET amp detected post-treatment with an EGFR or ALK TKI, median MET CN was 13. Of 241 targeted therapy naïve MET amp pts, 39 received a MET TKI after CGP (30 crizotinib, 9 capmatinib) and 26 had rw response assessment available. Excluding 5 pts with co- METex14, 12/21 (57%) pts had a partial response and median rwPFS was 3.6 months. This rw cohort analysis was underpowered to assess the relationship between CN and outcome. Conclusions: MET amp was detected in 3.3% of NSCLC tissue samples and 3.2% of high tumor fraction blood samples. In TKI-naïve pts, MET CN negatively correlated with the presence of a concurrent NSCLC driver. MET amp was associated with response to MET TKIs. Further studies evaluating MET CN, amplicon size and presence of other potential drivers in both blood and tissue, as predictive biomarkers for MET TKIs and potential combination strategies for targeting MET amp, are warranted.

Clinical response to tepotinib according to circulating tumor (ct) DNA biomarkers in patients with advanced NSCLC with high-level MET amplification (METamp) detected by liquid biopsy (LBx).

9121 Background: Tepotinib, a potent, highly selective, oral, MET inhibitor, showed meaningful activity in patients (pts) with NSCLC with high-level METamp by LBx in VISION. Exploratory biomarker analyses are presented herein. Methods: Pts had 0–2 prior therapy lines, high-level METamp by LBx (Guardant360; MET copy number ≥2.5), and no MET exon 14 skipping or EGFR/ ALK alterations. Pts received tepotinib 500 mg once daily (450 mg active moiety). Primary endpoint was objective response by independent review; data cut-off: Aug 20, 2021. Exploratory biomarker analysis included LBx at baseline (BL), on treatment, and end of treatment (EOT). Early molecular response (eMR) was defined as undetectable METamp 6–8 weeks on treatment. Results: 24 pts were enrolled (median age: 63.4 years [yrs]; smokers: 88%; ECOG PS 1: 88%; adenocarcinoma: 67%). Treatment duration was ≥1 yr in five pts and ≥2 yrs in two pts (both ongoing). Overall, objective response rate (ORR) was 41.7% (95% CI: 22.1, 63.4). Treatment-naïve pts (n=7) had an ORR of 71.4% (29.0, 96.3), median (m) DOR was 14.3 months (2.8, not estimable [ne]), and mPFS was 15.6 months (1.4, ne). BL biomarker analyses according to clinical benefit (CR/PR/SD [n=11] vs PD/NE [n=13]) showed association with better outcomes in pts with focal METamp, or without MYCamp or RB1 mutation (Table). MYCamp/ RB1 mutation was detected in 4/7 pts with neuroendocrine/not otherwise specified histology; MYCamp in 2/3 pts with neuroendocrine histology. Low BL ctDNA mutant allele frequency (MAF) was associated with better outcomes. 14 pts had eMRs (ORR 71.4%); persistent METamp (n=4) was associated with lack of clinical response. 2/9 pts with EOT biomarker profiles had emerging resistance mechanisms (MET kinase domain mutations Y1230 and D1228); both had METamp re-emergence. Treatment-related adverse events included edema (composite term; any grade: 46%; Grade 3: 13%) and constipation (any grade: 17%; Grade ≥3: 0%). Conclusions: Tepotinib showed meaningful activity, especially in first line, in the first trial of a MET inhibitor in EGFR WT NSCLC with high-level METamp to enroll based on a convenient LBx assay. BL biomarker analyses indicated focal METamp, MYC/RB1 WT, and low ctDNA MAF were associated with improved outcomes. Serial LBx could monitor molecular response and evaluate resistance. Clinical trial information: NCT02864992. [Table: see text]

Analysis of molecular characterization: Pancreatic ductal adenocarcinoma with hepatic metastases.

4129 Background: Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal solid tumors. Distant metastasis is the leading cause of cancer death. Approximately 50% of PDAC patients are discovered to have distant metastases, mainly in the liver. Chemotherapy is the main recommended treatment for metastatic PDACs, with a median survival time of only 4-6 months and the 5-year survival of 1%. Therefore, deciphering the molecular mechanisms of metastatic PDAC is urgently for exploring effective therapeutic targets. Methods: 93 normal-paired samples from patients with PDAC were analyzed using hybridization capture-based next generation sequencing. Somatic and germline mutations were identified including 500 genes associated with tumor development. Sequencing data were analyzed to call tumor specific single nucleotide variants (SNV), small insertions and deletions (InDels), copy number alterations (CNA) and gene fusions and rearrangements. Results: A total 93 patients with PDAC were analyzed, including hepatic metastases (15/93), lymph node metastases (1/93), colon metastases (1/93), pelvic metastases (1/93), and no distant metastasis (75/93). In PDAC patients without distant metastasis, the most frequent mutated gene was KRAS (72%), followed by TP53 (60%), CDKN2A (21%), SMAD4 (17%), ARID1A (11%), RNF43 (9%), and RBM10 (8%). In PDAC patients with hepatic metastases, we found that the most frequent one was KRAS (100%), followed by TP53 (87%), CDKN2A (40%), SMAD4 (40%), RNF43 (13%), and RBM10 (6%). Furthermore, four PDAC patients occurred KRAS copy number amplification, including 2 cases of hepatic metastases. And a hepatic metastases PDAC patient had ERBB2 and MET copy number amplification. We also found that seven no-metastasis patients carried pathogenic or likely pathogenic germline variants, including BRIP1, PALB2, RECQL, ATM, RAD50, FANCM and BRCA1. Conclusions: High frequency mutation genes in PDAC patients with hepatic metastases were highly consistent with those of no-metastasis patients. KRAS and TP53 gene co-mutations were extensively mutated in hepatic metastases patients. Our results revealed the molecular mechanisms driving PDAC hepatic metastases should be considered in further study.

MET Expression Level in Lung Adenocarcinoma Loosely Correlates with MET Copy Number Gain/Amplification and Is a Poor Predictor of Patient Outcome.

Simple SummaryMET is a proto-oncogene and plays an important role on tumor cell survival, proliferation, metastasis, and drug resistance. Patient with MET amplification has shown an inferior outcome comparing to patients without MET amplification. Fluorescence in situ hybridization (FISH) is often used to detect MET amplification, and immunohistochemistry (IHC) is often used to assess MET expression level. Though some institutions provide both tests, IHC is more readily available in most pathology laboratories and is cheaper than FISH. This study evaluated the correlation of MET expression level with MET copy number gain/amplification, and the MET overexpression with patient’s outcome. By studying 446 patients with lung adenocarcinoma, we found that the concordance of MET expression and MET copy number gain/amplification was low; high-level of MET expression was associated with inferior outcome, but it was not an independent poor prognostic factor. These findings indicate that IHC for MET expression can’t substitute FISH analysis for MET amplification.MET amplification has been associated with shorter survival in cancer patients, however, the potential correlation of MET overexpression with either MET amplification or patient outcome is controversial. The aim of this study was to address these questions by correlating MET expression level with MET copy number and patient outcome in a cohort of 446 patients who had a lung adenocarcinoma: 88 with MET amplification, 118 with polysomy 7, and 240 with negative results by fluorescence in situ hybridization. MET expression assessed by immunohistochemistry was semi-quantified by expression level: absent (0+), weak (1+), moderate (2+) and strong (3+); or by H-score: 0–99, 100–199, and ≥200. MET expression level or H-score was positively but weakly correlated with MET copy number or MET/CEP7 ratio. Strong expression of MET (3+ or H-score ≥ 200) was associated with a shorter overall survival, but it was not an independent hazard for survival by multivariant analysis. We conclude that MET expression is loosely correlated with MET copy number gain/amplification. Strong expression of MET does not independently predict patient outcome.

Comprehensive Genomic Profiling of Circulating Cell-Free DNA Distinguishes Focal MET Amplification from Aneuploidy in Diverse Advanced Cancers.

Amplification (amp) of MET can be observed in cases of focal gene copy number gain, such as MET-driven amp, or with a gain of chromosome 7, such as aneuploidy. Several studies have shown that only high-level focal MET amp (MET/CEP7 ratio ≥5) is oncogenic, with such tumors responding to targeted therapy. However, there are few reports on how to distinguish between focal amplification and aneuploidy using next-generation sequencing (NGS). A total of 1025 patients with advanced solid tumors (typically pre-treated) were tested with a non-invasive comprehensive cfDNA NGS panel (Guardant360) from July 2014 to June 2019. Since bioinformatics upgrades of Guardant360 were undergoing in September 2018, focal MET amp was determined by our independent algorithm using the cohorts tested before September 2018 (291 patients), and validation was performed in the remaining cohort (734 patients). MET alterations (alts) associated with aberrant signaling were found in 110 patients (10.7%) among nine different cancer types, most commonly in non-small cell (12.2%, 62/510) and small cell (33.3%, 3/9) lung cancers, gastroesophageal cancer (19.4%, 7/36), and prostate adenocarcinoma (15.6%; 5/32). Among 291 patients tested before September 2018, 37 (12.7%) had MET alts. Among these, 24 (64.9%) had amps, 5 (13.5%) had exon 14 skipping, and 13 (35.1%) had single nucleotide variants (SNVs). Co-alterations, such as amp + SNVs, were found in four samples (10.8%). Among 24 MET amps, 29.2% (7/24) were focal according to our algorithm. MET copy number was significantly higher with focal amp compared to non-focal amp (mean copy number 3.26 vs. 2.44, respectively, p = 0.00304). In 734 patients tested after September 2018, our definition of focal MET amp was detected in 4.2% (31/734). Overall, focal amplification based on our algorithm was 3.7% (=38/1025). This study describes an approach to distinguish focal and non-focal MET amplification using comprehensive genomic profiling of cfDNA in advanced cancer patients. Focal MET amp accounted for ~30% of all MET amp, which was found in 3.7% of patients with diverse cancers and was associated with a higher plasma copy number. Clinical studies are warranted to assess the clinical utility of targeted therapies for tumors with focal MET amplification detected by NGS of cfDNA.

Implementation of clinical sequencing for molecular profiling in patients with advanced cancer.

The advancement of cancer genomics has allowed for multiplex gene assays using next-generation sequencing (NGS) to be practically implemented, however, a clinical practice system remains to be established. We evaluated the feasibility of clinical sequencing using NGS-based multiplex gene assays between cooperating medical institutions in patients with advanced cancers. In this observational study, DNA and RNA samples prepared from existing tumor tissues were subjected to comprehensive genomic profiling using targeted sequencing. From January 2017 to March 2019, 36 samples from 33 patients were assessed. Of all patients, 27 (82%) had lung cancer, with the median age of 50 years (range 38-83). Multiplex gene panel tests were successfully carried out on 35/36 (97%) samples. Potentially actionable gene alterations were identified in 10/30 (33%) samples (3 HER2, 2 KRAS, 2 ALK, 1 PIK3CA, 1 RET, and 1 CDKN2A). In the 6 samples examined for resistant mechanisms, ALK I1171N mutation and MET copy number gain were detected in 2 patients with ALK rearrangement-positive lung cancer. Clinical sequencing using NGS-based multiplex gene assays between collaborating domestic medical institutions was feasible, with a success rate of > 97%. Overall, clinical sequencing benefits therapeutic decision-making in patients with advanced cancer.

Profiling genomic characteristics related to immunotherapy for gastric cancer with amplified MET.

e16066 Background: Gastric cancer (GCA) is one of the most deadly cancers all over the world, with an estimate of 26,560 new cases and 11,180 deaths in United States according to the cancer statistics of 2021. As immunotherapy has become available for GCA, it is necessary to distinguish patients who might be resistant to it. Methods: We identified 41 patients with amplified MET from a large Chinese cohort including 934 GCA (4.4% out of them) according to the ratio of purity adjusted copy number of MET and chromosome 7. Then, we comprehensively profiled genomic characteristics related to immunotherapy for GCA with amplified MET and compared them with other GCA. Results: First, mutated RNF43 and AXIN1 were much more prevalent in GCA with amplified MET. These two genes are components of Wnt pathway, whose aberrance is associated with resistance to immunotherapy. Second, carrier ratios of amplified CDK6 and CCND1 were much higher in GCA with amplified MET. These two genes play important roles in cell cycle pathway, while amplification of CCND1 has been recognized as a negatively predictive biomarker for immunotherapy. Third, we calculated mutational load of immunotherapy-related positively (mutated ATM, BRCA1, BRCA2, CHEK2, ERCC2, ERCC4, FANCA, KRAS, MLH1, MSH2, MSH6, NRAS, PALB2, PBRM1, PMS2, POLD1, POLE, RAD50 and TP53; deleted POLE) and negatively (mutated B2M, CTNNB1, DNMT3A, EGFR, JAK1, JAK2 and STK11; amplified CCND1, EGFR, FGF19, FGF3, FGF4, MDM2 and MDM4; deleted B2M, JAK2, PTEN and STK11) predictive biomarkers for GCA with amplified MET. We defined the mutational load as mean carrier ratio of point mutations or copy number variations (CNVs) appeared in a gene set. As is expected, the mutational load of point mutations in 19 positively predictive biomarkers in GCA with amplified MET was much lower than that in other GCA, whereas the mutational load of CNV in 11 negatively predictive biomarkers in GCA with amplified MET was much higher than that in other GCA. Finally, we found GCA with amplified MET possessed lower tumor mutational burden (TMB) and microsatellite instability (MSI), depleted somatic signature of defective DNA mismatch repair and higher copy number instability (CNI). Conclusions: Genomic characteristics of GCA with amplified MET are associated with adverse response to immunotherapy and thus it should be carefully evaluated when these patients are treated with immunotherapy.

The FAM3C locus that encodes interleukin-like EMT inducer (ILEI) is frequently co-amplified in MET-amplified cancers and contributes to invasiveness

BackgroundGene amplification of MET, which encodes for the receptor tyrosine kinase c-MET, occurs in a variety of human cancers. High c-MET levels often correlate with poor cancer prognosis. Interleukin-like EMT inducer (ILEI) is also overexpressed in many cancers and is associated with metastasis and poor survival. The gene for ILEI, FAM3C, is located close to MET on chromosome 7q31 in an amplification “hotspot”, but it is unclear whether FAMC3 amplification contributes to elevated ILEI expression in cancer. In this study we have investigated FAMC3 copy number gain in different cancers and its potential connection to MET amplifications.MethodsFAMC3 and MET copy numbers were investigated in various cancer samples and 200 cancer cell lines. Copy numbers of the two genes were correlated with mRNA levels, with relapse-free survival in lung cancer patient samples as well as with clinicopathological parameters in primary samples from 49 advanced stage colorectal cancer patients. ILEI knock-down and c-MET inhibition effects on proliferation and invasiveness of five cancer cell lines and growth of xenograft tumors in mice were then investigated.ResultsFAMC3 was amplified in strict association with MET amplification in several human cancers and cancer cell lines. Increased FAM3C and MET copy numbers were tightly linked and correlated with increased gene expression and poor survival in human lung cancer and with extramural invasion in colorectal carcinoma. Stable ILEI shRNA knock-down did not influence proliferation or sensitivity towards c-MET-inhibitor induced proliferation arrest in cancer cells, but impaired both c-MET-independent and -dependent cancer cell invasion. c-MET inhibition reduced ILEI secretion, and shRNA mediated ILEI knock-down prevented c-MET-signaling induced elevated expression and secretion of matrix metalloproteinase (MMP)-2 and MMP-9. Combination of ILEI knock-down and c-MET-inhibition significantly reduced the invasive outgrowth of NCI-H441 and NCI-H1993 lung tumor xenografts by inhibiting proliferation, MMP expression and E-cadherin membrane localization.ConclusionsThese novel findings suggest MET amplifications are often in reality MET-FAM3C co-amplifications with tight functional cooperation. Therefore, the clinical relevance of this frequent cancer amplification hotspot, so far dedicated purely to c-MET function, should be re-evaluated to include ILEI as a target in the therapy of c-MET-amplified human carcinomas.

Abstract CT127: A phase I study of cMET inhibitor bozitinib in patients with advanced NSCLC harboring cMET alterations

Abstract Introduction: Cellular mesenchymal-epithelial transition (cMET) dysregulation has been described in non-small-cell lung cancer (NSCLC) and implicated as a negative prognostic factor. It can occur as amplification, overexpression or mutations leading to exon 14 skipping. Bozitinib (PLB-1001, CBT-101) is a potent highly selective cMET inhibitor, which has demonstrated superior activity in both in vitro and in vivo NSCLC models. Methods: This was a phase I, open-label multicenter study conducted in locally advanced or metastatic NSCLC patients that included a dose-escalation (19 patients) and a dose-expansion phase (18 patients) (NCT02896231). A traditional 3+3 design was adopted for dose escalation. The primary objective was to characterize the safety and tolerability of single agent Bozitinib. The secondary objectives included pharmacokinetics (PK) analysis and antitumor activity assessed by RECIST v1.1. cMET dysregulation was defined by: IHC 3+ expression in >50% of tumor cells or gain of copy numbers (GCN) ≥5 or cMET/centromere ≥2.2 by FISH or MET copy number ≥2.25 or with exon 14 skipping by next-generation sequencing (NGS). Only central laboratory testing was acceptable. Patients≥18 years with locally advanced or metastatic NSCLC with an ECOG performance status ≤2 were enrolled. Those previously treated with cMET inhibitor or HGF targeting therapy were excluded. Patients were orally administrated with Bozitinib capsules in a total of 6 dose cohorts: 5 BID dose cohorts (50 mg BID, 100 mg BID, 150 mg BID, 200 mg BID and 275 mg BID), and 1 QD dose cohort (300 mg QD). The enrollment had been completed by October 31 2019 with 37 enrolled patients. Results: Of the 37 enrolled patients, with a median age of 61: 8 had overexpression; 11 had exon 14 skipping; 8 had amplification and 10 patients had more than 1 type of MET alterations. Bozitinib was generally well-tolerated in all cohorts. Treatment-related AEs of any grade were observed in 35 patients and those of ≥ grade 3 were observed in 10 patients (in 200mg BID, 275mg BID and 300mg QD groups), including ALT increase, AST increase, bilirubin increase and peripheral edema. Common AEs occurring in more than 20% of patients included: ALT increase (40.5%), AST increase (40.5%), bilirubin increase (40.5%), peripheral edema (32.4%) and QTc interval prolongation (18.9%). Bozitinib showed good linear PK characteristics, with dose-dependent increases in exposure and a half-life around 13.8-44.6h. 36 were included in the BOR analysis. One patient was excluded due to the development of brain metastases after first dose. This cohort presented an ORR of 30.6% (11/36) and a DCR of 94.4% (34/36). Sub-analysis of ORR for patients with overexpression, amplification and exon 14 skipping were 35.7%, 41.2% and 66.7%, respectively. ORR for patients with overexpression and amplification (N=6) was 50%. ORR for patients harboring both exon 14 skipping and amplification (N=4) was 100%. Conclusions: Based on safety profiles, PK and efficacy analyses, 200mg BID was determined to be RP2D. Bozitinib was well-tolerated with manageable safety profiles when administered at RP2D. Preliminary antitumor activity was observed in patients with exon 14 skipping and/or amplification, particularly in those with NGS-identified exon 14 skipping. Citation Format: Jinji Yang, Qing Zhou, Huajun Chen, Lin Wu, Jun Zhao, Renhua Guo, Yun Fan, Hepeng Shi, Weizhe Xue, Peilong Zhang, Han-Zhang Han, Xuan Lin, Shuyin Chen, Lu Zhang, Hao Liu, Xinru Mao, Bin Gan, Yilong Wu. A phase I study of cMET inhibitor bozitinib in patients with advanced NSCLC harboring cMET alterations [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 CT127.

Recurrence of ovarian squamous cell carcinoma with MET gene copy number variation: a case report and review of literature

BackgroundMalignant transformation such as ovarian squamous cell carcinoma (SCC) in ovarian mature cystic teratoma (OMCT) is a rare tumor. The gene mutation of ovarian SCC remains unclear. We herein report a recurrent case of ovarian squamous cell carcinoma with MET gene copy number variation.Case presentationA 60-year-old woman presented with recurrence of ovarian SCC 8 months after primary surgery. Adhesiolysis, right abdominal wall mass excision, prosthetics, enterectomy, enterostomy and partial cystectomy were performed by laparoscope. Pathologic examination demonstrated metastatic squamous cell carcinoma in ileocecus, rectum and abdominal wall muscle. MET gene copy number was elevated with copy number of six in this case. Postoperatively, the patient was treated with four cycles of combination chemotherapy with docetaxel and carboplatin. The patient was free of disease at 20 months’ follow-up.ConclusionsOptimal cytoreductive surgery combined with platinum-based chemotherapy is recommended currently for not only primary tumor but also recurrence. For patients with malignant transformation in OMCT, prompt diagnosis and individualized treatment are crucial for better prognosis. Increased copy number of MET may be correlated with her poor PFS and can be a potential therapeutic target for this case.

RELAY study of erlotinib (ERL) + ramucirumab (RAM) or placebo (PL) in EGFR-mutated metastatic non-small cell lung cancer (NSCLC): Biomarker analysis using circulating tumor DNA (ctDNA) in Japanese patients (pts).

9527 Background: The phase III RELAY study (NCT02411448) showed significantly improved progression-free survival (PFS) for RAM+ERL vs PL+ERL in 449 pts with previously untreated EGFR mutation-positive metastatic NSCLC (median PFS 19.4 vs 12.4 mo, HR 0.591 [95% CI 0.461–0.760], p<.0001). To understand baseline genetic mutations and treatment-emergent (TE) resistance mechanisms, this exploratory liquid biopsy substudy examined biomarkers in ctDNA from participating Japanese pts by next-generation sequencing (NGS) and droplet digital PCR (ddPCR). Methods: Plasma samples were collected at baseline, during treatment (Cycle 4, 13, and every 6 cycles to Cycle 53) and post-study treatment discontinuation (30-day follow-up [30d FU]). Mutations were assessed at baseline and 30d FU by NGS (Ion AmpliSeq Colon and Lung Cancer panel). EGFR mutations and MET and ERBB2 copy number (CN) were assessed at all time points by ddPCR. Baseline markers were analyzed in pts with any detectable baseline mutation (to confirm ctDNA presence; NGS N=84, ddPCR N=74). TE mutations were analyzed in pts with any detectable mutation at baseline and 30d FU (NGS N=26, ddPCR N=28). Among these pts, 81% and 57% for NGS and ddPCR, respectively, had progressed by 30d FU. Results: By plasma NGS, baseline EGFR activating mutations (exon 19 deletion or exon 21 [L858R] mutation) were detected in 83.3% of pts. Common co-occurring baseline mutations were TP53 (42.9%), PTEN (7.1%) and KRAS (6.0%). Baseline TP53 mutation rate was higher in men vs women (p=.02). No difference in PFS was detected by baseline TP53 status (interaction predictive p=.45, prognostic p=.33). TE mutations were detected in EGFR (including T790M), FGFR3, KRAS and TP53. Slightly higher rates of TE KRAS (p=.03) and TP53 (p=.07) mutations were detected in RAM+ERL than in PL+ERL. TE total EGFR mutations (p=.65) or TE T790M (p=.69) did not differ by arm. By ddPCR, baseline EGFR activating mutations were detected in all pts. T790M was detected at baseline in 2/37 pts/arm (5.4%) and was TE in 6/11 (55%) RAM+ERL pts and 7/17 (41%) PL+ERL pts. There was a trend (p=.054) for greater ERBB2 CN in RAM+ERL vs PL+ERL at Cycle 4. MET CN decreased slightly at Cycle 4 in both arms (significant in PL+ERL, p=.003). Biomarker levels by ddPCR across all time points will be presented. Conclusions: Though limited by sample size and likely inconsistent tumor shedding, this exploratory study identified potential differences in TP53, KRAS, ERBB2 and MET by demographics, treatment and/or time. Clinical trial information: NCT02411448 .

Detection of MET Alterations Using Cell Free DNA and Circulating Tumor Cells from Cancer Patients.

MET alterations may provide a potential biomarker to evaluate patients who will benefit from treatment with MET inhibitors. Therefore, the purpose of the present study is to investigate the utility of a liquid biopsy-based strategy to assess MET alterations in cancer patients. We analyzed MET amplification in circulating free DNA (cfDNA) from 174 patients with cancer and 49 healthy controls and demonstrated the accuracy of the analysis to detect its alteration in patients. Importantly, a significant correlation between cfDNA concentration and MET copy number (CN) in cancer patients (r = 0.57, p <10−10) was determined. Furthermore, we evaluated two approaches to detect the presence of MET on circulating tumor cells (CTCs), using the CellSearch® and Parsortix systems and monitored patients under anti-EGFR treatment (n = 30) combining both cfDNA and CTCs analyses. This follow-up provides evidence for the potential of MET CN assessment when patients develop resistance to anti-EGFR therapy and a significant association between the presence of CTCs MET+ and the Overall Survival (OS) in head and neck cancer patients (P = 0.05; HR = 6.66). In conclusion, we develop specific and noninvasive assays to monitor MET status in cfDNA/CTCs and demonstrate the utility of plasma MET CN determination as a biomarker for monitoring the appearance of resistance to anti-EGFR therapy.