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Jacobs SA, Wang Y, Abraham J, Feng H, Montero AJ, Lipchik C, Finnigan M, Jankowitz RC, Salkeni MA, Maley SK, Puhalla SL, Piette F, Quinn K, Chang K, Nagy RJ, Allegra CJ, Vehec K, Wolmark N, Lucas PC, Srinivasan A, Pogue-Geile KL. NSABP FB-10: a phase Ib/II trial evaluating ado-trastuzumab emtansine (T-DM1) with neratinib in women with metastatic HER2-positive breast cancer. Breast Cancer Res 2024; 26:69. [PMID: 38650031 PMCID: PMC11036567 DOI: 10.1186/s13058-024-01823-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 04/11/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND We previously reported our phase Ib trial, testing the safety, tolerability, and efficacy of T-DM1 + neratinib in HER2-positive metastatic breast cancer patients. Patients with ERBB2 amplification in ctDNA had deeper and more durable responses. This study extends these observations with in-depth analysis of molecular markers and mechanisms of resistance in additional patients. METHODS Forty-nine HER2-positive patients (determined locally) who progressed on-treatment with trastuzumab + pertuzumab were enrolled in this phase Ib/II study. Mutations and HER2 amplifications were assessed in ctDNA before (C1D1) and on-treatment (C2D1) with the Guardant360 assay. Archived tissue (TP0) and study entry biopsies (TP1) were assayed for whole transcriptome, HER2 copy number, and mutations, with Ampli-Seq, and centrally for HER2 with CLIA assays. Patient responses were assessed with RECIST v1.1, and Molecular Response with the Guardant360 Response algorithm. RESULTS The ORR in phase II was 7/22 (32%), which included all patients who had at least one dose of study therapy. In phase I, the ORR was 12/19 (63%), which included only patients who were considered evaluable, having received their first scan at 6 weeks. Central confirmation of HER2-positivity was found in 83% (30/36) of the TP0 samples. HER2-amplified ctDNA was found at C1D1 in 48% (20/42) of samples. Patients with ctHER2-amp versus non-amplified HER2 ctDNA determined in C1D1 ctDNA had a longer median progression-free survival (PFS): 480 days versus 60 days (P = 0.015). Molecular Response scores were significantly associated with both PFS (HR 0.28, 0.09-0.90, P = 0.033) and best response (P = 0.037). All five of the patients with ctHER2-amp at C1D1 who had undetectable ctDNA after study therapy had an objective response. Patients whose ctHER2-amp decreased on-treatment had better outcomes than patients whose ctHER2-amp remained unchanged. HER2 RNA levels show a correlation to HER2 CLIA IHC status and were significantly higher in patients with clinically documented responses compared to patients with progressive disease (P = 0.03). CONCLUSIONS The following biomarkers were associated with better outcomes for patients treated with T-DM1 + neratinib: (1) ctHER2-amp (C1D1) or in TP1; (2) Molecular Response scores; (3) loss of detectable ctDNA; (4) RNA levels of HER2; and (5) on-treatment loss of detectable ctHER2-amp. HER2 transcriptional and IHC/FISH status identify HER2-low cases (IHC 1+ or IHC 2+ and FISH negative) in these heavily anti-HER2 treated patients. Due to the small number of patients and samples in this study, the associations we have shown are for hypothesis generation only and remain to be validated in future studies. Clinical Trials registration NCT02236000.
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Affiliation(s)
| | - Ying Wang
- NSABP Foundation, Pittsburgh, PA, USA
| | - Jame Abraham
- NSABP Foundation, Pittsburgh, PA, USA
- Cleveland Clinic, Weston/Taussig Cancer Institute, Cleveland, OH, USA
| | | | - Alberto J Montero
- NSABP Foundation, Pittsburgh, PA, USA
- Cleveland Clinic, Weston/Taussig Cancer Institute, Cleveland, OH, USA
- University Hospitals/Seidman Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | | | | | - Rachel C Jankowitz
- NSABP Foundation, Pittsburgh, PA, USA
- University of Pittsburgh, Pittsburgh, PA, USA
- University of Pennsylvania Perelman School of Medicine, State College, PA, USA
| | - Mohamad A Salkeni
- NSABP Foundation, Pittsburgh, PA, USA
- National Institutes of Health, Washington, DC, USA
- Virginia Cancer Specialists, Fairfax, VA, USA
| | | | - Shannon L Puhalla
- NSABP Foundation, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Fanny Piette
- International Drug Development Institute, Louvain-la-Neuve, Belgium
| | | | | | | | - Carmen J Allegra
- NSABP Foundation, Pittsburgh, PA, USA
- University of Florida Health, Gainesville, FL, USA
| | | | - Norman Wolmark
- NSABP Foundation, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Peter C Lucas
- NSABP Foundation, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Ashok Srinivasan
- NSABP Foundation, Pittsburgh, PA, USA
- Autism Impact Fund, Pittsburgh, PA, USA
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Maron SB, Chatila W, Walch H, Chou JF, Ceglia N, Ptashkin R, Do RKG, Paroder V, Pandit-Taskar N, Lewis JS, Biachi De Castria T, Sabwa S, Socolow F, Feder L, Thomas J, Schulze I, Kim K, Elzein A, Bojilova V, Zatzman M, Bhanot U, Nagy RJ, Lee J, Simmons M, Segal M, Ku GY, Ilson DH, Capanu M, Hechtman JF, Merghoub T, Shah S, Schultz N, Solit DB, Janjigian YY. Determinants of Survival with Combined HER2 and PD-1 Blockade in Metastatic Esophagogastric Cancer. Clin Cancer Res 2023; 29:3633-3640. [PMID: 37406106 PMCID: PMC10502449 DOI: 10.1158/1078-0432.ccr-22-3769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 02/21/2023] [Accepted: 06/30/2023] [Indexed: 07/07/2023]
Abstract
PURPOSE We report updated clinical outcomes from a phase II study of pembrolizumab, trastuzumab, and chemotherapy (PTC) in metastatic esophagogastric cancer in conjunction with outcomes from an independent Memorial Sloan Kettering (MSK) cohort. PATIENTS AND METHODS The significance of pretreatment 89Zr-trastuzumab PET, plasma circulating tumor DNA (ctDNA) dynamics, and tumor HER2 expression and whole exome sequencing was evaluated to identify prognostic biomarkers and mechanisms of resistance in patients treated on-protocol with PTC. Additional prognostic features were evaluated using a multivariable Cox regression model of trastuzumab-treated MSK patients (n = 226). Single-cell RNA sequencing (scRNA-seq) data from MSK and Samsung were evaluated for mechanisms of therapy resistance. RESULTS 89Zr-trastuzumab PET, scRNA-seq, and serial ctDNA with CT imaging identified how pre-treatment intrapatient genomic heterogeneity contributes to inferior progression-free survival (PFS). We demonstrated that the presence of intensely avid lesions by 89Zr-trastuzumab PET declines in tumor-matched ctDNA by 3 weeks, and clearance of tumor-matched ctDNA by 9 weeks were minimally invasive biomarkers of durable PFS. Paired pre- and on-treatment scRNA-seq identified rapid clearance of HER2-expressing tumor clones with expansion of clones expressing a transcriptional resistance program, which was associated with MT1H, MT1E, MT2A, and MSMB expression. Among trastuzumab-treated patients at MSK, ERBB2 amplification was associated with improved PFS, while alterations in MYC and CDKN2A/B were associated with inferior PFS. CONCLUSIONS These findings highlight the clinical relevance of identifying baseline intrapatient heterogeneity and serial ctDNA monitoring of HER2-positive esophagogastric cancer patients to identify early evidence of treatment resistance, which could guide proactive therapy escalation or deescalation.
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Affiliation(s)
- Steven B. Maron
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Walid Chatila
- Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York
| | - Henry Walch
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joanne F. Chou
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nicholas Ceglia
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Ryan Ptashkin
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Richard Kinh Gian Do
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Viktoriya Paroder
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neeta Pandit-Taskar
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jason S. Lewis
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Tiago Biachi De Castria
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Shalom Sabwa
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Fiona Socolow
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Lara Feder
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jasmine Thomas
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Isabell Schulze
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kwanghee Kim
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Arijh Elzein
- Department of Pharmacology, Weill Cornell Medicine Graduate School of Medical Sciences, New York, New York
| | - Viktoria Bojilova
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Matthew Zatzman
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Umesh Bhanot
- Precision Pathology Center, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Jeeyun Lee
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Marc Simmons
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michal Segal
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Geoffrey Yuyat Ku
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - David H. Ilson
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Marinela Capanu
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jaclyn F. Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Taha Merghoub
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Sohrab Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikolaus Schultz
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B. Solit
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Marie-Josée & Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yelena Y. Janjigian
- Department of Medicine, Gastrointestinal Oncology Service, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Weill Cornell Medical College, New York, New York
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Greenwald WW, He Y, Chen S, Jiang T, Valouev A, Min J, Barbacioru C, Gaile DP, Ma D, Kim Y, Tran G, Wu I, Jaimovich A, Raymond V, Nagy RJ, Chuang HY. Abstract 3758: Accurate epigenomic estimates of circulating tumor fraction in large-scale clinical data. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Liquid biopsy offers a rapid and non-invasive alternative to tissue biopsy for identifying biomarkers. More recently, its application has broadened to include assessment of early response to therapy (i.e. molecular response) and in the early-stage settings, detection of minimal residual disease (MRD) and early disease recurrence1. While circulating tumor fraction (cTF) estimated by somatic mutations is well associated with the tumor progression and prognosis, interference can occur from clonal hematopoiesis of indeterminate potential (CHIP), and for cell-free DNA (cfDNA) samples that lack detectable somatic mutations, somatic tumor fraction cannot be estimated. In this analysis, we demonstrate that epigenomic signatures accurately measure cTF using orthogonal analytes to somatic mutations and enable cTF estimation even in cases without detectable tumor driver variants.
Methods: To capture tumor-associated methylated cfDNA, we designed a custom assay of a broad genomic panel (15.2 Mb) targeting unmethylated regions in plasma cfDNA from healthy individuals. We profiled plasma samples from cancer patients with this panel, and utilized machine learning to integrate methylation signals into an estimate of cTF. We benchmarked the accuracy of methylation cTFs on real plasma samples, as well as in-vitro and in-silico titration datasets. Both titration data sets were generated by mixing cfDNA from patients with colorectal cancer (CRC) into the plasma from cancer-free donors, either via titration of CRC cfDNA into cfDNA from cancer-free donors for the in-vitro data, or via computationally mixing reads from CRC patients with those from cancer-free donors for the in-silico data.
Results: Our methylation cTF quantified a similar cTF to those derived from well-calibrated genomic tumor driver mutations; across the 670 stage I-IV CRC samples, a strong correlation (Pearson r=0.85) was observed between methylation logit(cTF) and genomic logit(cTF). The methylation cTF was capable of quantifying low cTFs: it quantified a cTF over 0.1% in >99% of the 270 in-vitro and 1,000 in-silico titration samples with true cTFs >0.1%. In contrast, when applied to 2,037 cancer-free samples, less than 5% of the samples resulted in estimated cTFs of >0.1%. Our methylation cTF was more robust than genomic cTF on the 62 in vitro titration samples with true cTFs between 0.3-1%, with a five fold lower coefficient of variation across methylation cTFs compared to genomic cTFs.
Conclusions: cTFs from methylated cfDNA may overcome the current limitations of somatic mutation based methods. Our methylation approach is capable of accurately detecting cTFs in tumor-driver positive and negative cases. As we estimate tumor-negative cases to be 30-50% of patients with stage I-III cancer and 15-20% of patients with stage IV cancer, our methylation approach may hold promise for providing better evaluation for patient care and management.
Citation Format: William W. Greenwald, Yupeng He, Sai Chen, Tingting Jiang, Anton Valouev, Jun Min, Catalin Barbacioru, Daniel P. Gaile, Dustin Ma, Yvonne Kim, Giao Tran, Indira Wu, Ariel Jaimovich, Victoria Raymond, Rebecca J. Nagy, Han-Yu Chuang. Accurate epigenomic estimates of circulating tumor fraction in large-scale clinical data [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 3758.
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Affiliation(s)
| | | | - Sai Chen
- 1Guardant Health, Redwood City, CA
| | | | | | - Jun Min
- 1Guardant Health, Redwood City, CA
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Chen S, Zhang S, Jiang T, Yen J, He Y, Jaimovich A, Kim Y, Ma D, Tran G, Gaile DP, Nagy RJ, Helman E, Chuang HY. Abstract 3763: Detection of tumor-associated gene inactivation in clinical blood draws via cell-free DNA methylation profiling. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Introduction: The ability to detect genome-wide epigenetic changes, such as DNA methylation, has expanded translational applications in oncology settings. Because these changes occur early in carcinogenesis, they can be used for early cancer detection when genomic technologies fall short due to lower sensitivity, and in the early and late-stage cancer setting for minimal residual disease detection, disease monitoring and therapy selection. In this analysis, we demonstrated our detection of differential methylations that classify cancer from healthy normals, as well as the quantification of promoter methylation, using a highly sensitive targeted assay that simultaneously captures both genomic alterations and methylation signatures in cell-free DNA (cfDNA).
Methods: Methylation signals were profiled with a broad genomic panel (15.2 Mb) targeting regions that are unmethylated in plasma cfDNA from cancer-free donors. The panel covers the promoter regions of 925 out of 1,217 known tumor suppressor genes (TSGs) (e.g. TP53, APC, RB1, PTEN), homologous recombination and repair (HRR) genes (e.g. ATM, BRCA1/2, CDK12, RAD51C/D). We applied our genomic and epigenomic assay on cfDNA from 1,968 colorectal cancer (CRC) patients, 480 patients with other 6 common cancers, and 2,037 cancer-free donors. To test the sensitivity of our epigenomic assay, we generated an in-silico dataset by computationally mixing reads from the cancer patients with those from cancer-free donors at a low tumor fraction (TF) of 0.1%.
Results: Among 62 clinically relevant TSG and HRR genes, 56 (90%) were differentially methylated (Wilcoxon p<0.05) between the 2,448 cancer vs. 2,037 cancer-free donor samples. In the in-silico dataset, 51 of the 56 differentially methylated genes remained statistically significant (Wilcoxon p<0.05) at 0.1% TF. In the 1,968 CRC patients, we observed a significant association (Fisher’s p<1e-05) between MLH1 promoter methylation and microsatellite instability (MSI-H): 70% of MSI-H samples has MLH1 promoter methylation above a predefined “high methylation” threshold, while only 7% of microsatellite-stable samples has MLH1 promoter methylation above this threshold. Our result is consistent with previous studies that 54-100% of CRC patients with MSI-H tumors harbor MLH1 promoter methylation.
Conclusion: We demonstrate that our assay can accurately detect cancer-driven DNA methylation across the genome in clinical plasma samples. Detection of differential methylation in cancerous versus non-cancerous tissues could allow for early cancer detection, leading to better survival and prediction of recurrence prior to imaging. The highly sensitive detection of promoter methylation shown with TSG, HRR, and MLH1 genes may provide orthogonal information to oncologists in therapeutic selection with high confidence.
Citation Format: Sai Chen, Shile Zhang, Tingting Jiang, Jennifer Yen, Yupeng He, Ariel Jaimovich, Yvonne Kim, Dustin Ma, Giao Tran, Daniel P. Gaile, Rebecca J. Nagy, Elena Helman, Han-Yu Chuang. Detection of tumor-associated gene inactivation in clinical blood draws via cell-free DNA methylation profiling [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 3763.
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Affiliation(s)
- Sai Chen
- 1Guardant Health, Redwood City, CA
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Yablonovitch A, Gnerre S, Yen J, Shell S, Helman E, Fairclough S, Nagy RJ, Odegaard J, Chudova D, Talasaz A. Abstract 537: NTRK1 fusion detection from clinical cfDNA NGS using a de novo fusion caller. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: NTRK rearrangements, though rare in common cancers, are clinically actionable targets with two FDA-approved drugs for pan-cancer indications, larotrectinib and entrectinib. Fusion detection from ctDNA provides an opportunity to facilitate screening for this biomarker, though technical challenges such as heterogeneity in fusion partners remain. To address this, we developed an assembly-based de novo fusion algorithm that does not rely on a fixed set of partner genes and applied it to >18,000 clinical samples to detect NTRK1 fusions.
Methods: A cohort of 18,867 patients across multiple cancer types (lung adenocarcinoma, breast cancer, and colorectal adenocarcinoma), plus 276 healthy control samples were previously tested with Guardant360(R), a CLIA-validated 74-gene cfDNA NGS-based assay. The median unique molecule coverage was approximately 3,000 molecules sequenced to 15,000x read depth. Samples were reanalyzed in silico using the de novo fusion algorithm: in brief, reads aligned to candidate fusion breakpoints were assembled into de Bruijn graphs. Resulting contigs were aligned to the reference and analytical filters were applied to achieve high specificity.
Results: NTRK1 fusions were detected in 0.13% of patients, a similar prevalence to what has been previously described in tissue (Rosen et al., 2020). No fusions were identified in 276 healthy control samples. When examining intergenic fusions, 53% of fusions included previously characterized partner genes (TPM3, TPR, LMNA, and TP53), while the remaining fusions contained novel partners.The majority of NTRK1 fusion partners (76%) were detected only once, consistent with previous studies. KRAS G12D and BRAF V600E were detected in 17% and 13% of NTRK1 fusion-positive patients, respectively, and occurred predominantly in the colorectal cohort; most variants (60%) were subclonal to the NTRK1 fusion, and have been previously shown to be associated with resistance to TRK inhibitors through downstream activation of the MAPK pathway. The on-target resistance variant NTRK1 G595R was detected in 8% of patients positive for NTRK1 fusions, all of which were subclonal to the fusion. EGFR L858R was detected in 13% of NTRK1 fusion-positive patients, all of which were clonal to the fusion and in the lung cohort, in accordance with previous studies showing NTRK1 fusions as a resistance mechanism to TKIs in EGFR-positive NSCLC (Xia et al., 2020).
Conclusions: NTRK1 fusions were detected in cfDNA at a similar prevalence to tissue NGS, demonstrating high sensitivity of plasma-based assays to detect these fusions. NTRK1 fusion partners were diverse, with the majority of partner genes observed only once across the cohort. Both clonal and subclonal NTRK1 rearrangements were detected, affirming that this biomarker can emerge as an oncogenic driver or as a mechanism of resistance.
Citation Format: Arielle Yablonovitch, Sante Gnerre, Jennifer Yen, Scott Shell, Elena Helman, Stephen Fairclough, Rebecca J. Nagy, Justin Odegaard, Darya Chudova, AmirAli Talasaz. NTRK1 fusion detection from clinical cfDNA NGS using a de novo fusion caller [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 537.
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Thompson JC, Carpenter EL, Silva BA, Rosenstein J, Chien AL, Quinn K, Espenschied CR, Mak A, Kiedrowski LA, Lefterova M, Nagy RJ, Katz SI, Yee SS, Black TA, Singh AP, Ciunci CA, Bauml JM, Cohen RB, Langer CJ, Aggarwal C. Serial Monitoring of Circulating Tumor DNA by Next-Generation Gene Sequencing as a Biomarker of Response and Survival in Patients With Advanced NSCLC Receiving Pembrolizumab-Based Therapy. JCO Precis Oncol 2021; 5:PO.20.00321. [PMID: 34095713 PMCID: PMC8169078 DOI: 10.1200/po.20.00321] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Revised: 01/07/2021] [Accepted: 02/09/2021] [Indexed: 01/13/2023] Open
Abstract
Although the majority of patients with metastatic non-small-cell lung cancer (mNSCLC) lacking a detectable targetable mutation will receive pembrolizumab-based therapy in the frontline setting, predicting which patients will experience a durable clinical benefit (DCB) remains challenging. MATERIALS AND METHODS Patients with mNSCLC receiving pembrolizumab monotherapy or in combination with chemotherapy underwent a 74-gene next-generation sequencing panel on blood samples obtained at baseline and at 9 weeks. The change in circulating tumor DNA levels on-therapy (molecular response) was quantified using a ratio calculation with response defined by a > 50% decrease in mean variant allele fraction. Patient response was assessed using RECIST 1.1; DCB was defined as complete or partial response or stable disease that lasted > 6 months. Progression-free survival and overall survival were recorded. RESULTS Among 67 patients, 51 (76.1%) had > 1 variant detected at a variant allele fraction > 0.3% and thus were eligible for calculation of molecular response from paired baseline and 9-week samples. Molecular response values were significantly lower in patients with an objective radiologic response (log mean 1.25% v 27.7%, P < .001). Patients achieving a DCB had significantly lower molecular response values compared to patients with no durable benefit (log mean 3.5% v 49.4%, P < .001). Molecular responders had significantly longer progression-free survival (hazard ratio, 0.25; 95% CI, 0.13 to 0.50) and overall survival (hazard ratio, 0.27; 95% CI, 0.12 to 0.64) compared with molecular nonresponders. CONCLUSION Molecular response assessment using circulating tumor DNA may serve as a noninvasive, on-therapy predictor of response to pembrolizumab-based therapy in addition to standard of care imaging in mNSCLC. This strategy requires validation in independent prospective studies.
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Affiliation(s)
- Jeffrey C. Thompson
- Division of Pulmonary, Allergy and Critical Care Medicine, Thoracic Oncology Group, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Erica L. Carpenter
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Benjamin A. Silva
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Jamie Rosenstein
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Austin L. Chien
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | | | | | | | | | | | | | - Sharyn I. Katz
- Department of Radiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Stephanie S. Yee
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Taylor A. Black
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Aditi P. Singh
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Christine A. Ciunci
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Joshua M. Bauml
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Roger B. Cohen
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Corey J. Langer
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Charu Aggarwal
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
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Palmero R, Taus A, Viteri S, Majem M, Carcereny E, Garde-Noguera J, Felip E, Nadal E, Malfettone A, Sampayo M, Riva F, Nagy RJ, Lanman RB, Faull I, Dix D, Karachaliou N, Rosell R. Biomarker Discovery and Outcomes for Comprehensive Cell-Free Circulating Tumor DNA Versus Standard-of-Care Tissue Testing in Advanced Non–Small-Cell Lung Cancer. JCO Precis Oncol 2021; 5:93-102. [DOI: 10.1200/po.20.00241] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Purpose Treatment guidelines for advanced non–small-cell lung cancer (aNSCLC) recommend broad molecular profiling for targeted therapy selection. This study prospectively assessed comprehensive next-generation sequencing (NGS) of cell-free circulating tumor DNA (cfDNA) compared with standard-of-care (SOC) tissue-based testing to identify guideline-recommended alterations in aNSCLC. PATIENTS AND METHODS Patients with treatment-naïve aNSCLC were tested using a well-validated NGS cfDNA panel, and results were compared with SOC tissue testing. The primary objective was noninferiority of cfDNA vs. tissue analysis for the detection of two guideline-recommended biomarkers ( EGFR and ALK) and an additional six actionable biomarkers. Secondary analyses included tissue versus cfDNA biomarker discovery, overall response rate (ORR), progression-free survival (PFS) to targeted therapy, and positive predictive value (PPV) of cfDNA. RESULTS The primary objective was met with cfDNA identifying actionable mutations in 46 patients versus 48 by tissue ( P < .05). In total, 0/186 patients were genotyped for all eight biomarkers with tissue, compared with 90.8% using cfDNA. Targetable alterations or KRAS were identified in 80.7% when cfDNA was used first versus 57.1% when tissue was used first. PPV for cfDNA-detected EGFR was 100.0% (25/25). ORR and PFS in patients receiving targeted therapy based on tissue or cfDNA were similar to those previously reported. Conclusion This prospective study confirms a previous report that comprehensive cfDNA testing is noninferior to SOC tissue testing in detecting aNSCLC-recommended biomarkers. Furthermore, cfDNA-based first-line therapy produced outcomes similar to tissue-based testing, demonstrating the clinical utility of comprehensive cfDNA genotyping as the initial genotyping modality in patients with treatment-naïve aNSCLC when tissue is insufficient or when all actionable biomarkers cannot be rapidly assessed.
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Affiliation(s)
| | - Alvaro Taus
- Hospital del Mar, Barcelona, Spain
- Universidad Autónoma de Barcelona (UAB), Barcelona, Spain
| | - Santiago Viteri
- Quirón Salud-Dexeus University Institute, IOR, Medical Oncology Department, Barcelona, Spain
| | | | - Enric Carcereny
- Institut Català d'Oncologia Badalona-Hospital Germans Trias i Pujol B-ARGO, Badalona, Spain
| | | | | | | | - Andrea Malfettone
- Medica Scientia Innovation Research—MEDSIR, Barcelona, Spain and Ridgewood, NJ
| | - Miguel Sampayo
- Medica Scientia Innovation Research—MEDSIR, Barcelona, Spain and Ridgewood, NJ
| | - François Riva
- Medica Scientia Innovation Research—MEDSIR, Barcelona, Spain and Ridgewood, NJ
| | | | | | - Iris Faull
- Guardant Health, South San Francisco, CA
| | - Daniel Dix
- Guardant Health, South San Francisco, CA
| | - Niki Karachaliou
- Catalan Institute of Oncology, Hospital Germans Trias I Pujol, Badalona, Spain
| | - Rafael Rosell
- Catalan Institute of Oncology, Hospital Germans Trias I Pujol, Badalona, Spain
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Grivas P, Lalani AKA, Pond GR, Nagy RJ, Faltas B, Agarwal N, Gupta SV, Drakaki A, Vaishampayan UN, Wang J, Barata PC, Gopalakrishnan D, Naik G, McGregor BA, Kiedrowski LA, Lanman RB, Sonpavde GP. Circulating Tumor DNA Alterations in Advanced Urothelial Carcinoma and Association with Clinical Outcomes: A Pilot Study. Eur Urol Oncol 2020; 3:695-699. [DOI: 10.1016/j.euo.2019.02.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 02/14/2019] [Indexed: 02/06/2023]
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9
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Negrao MV, Raymond VM, Lanman RB, Robichaux JP, He J, Nilsson MB, Ng PKS, Amador BE, Roarty EB, Nagy RJ, Banks KC, Zhu VW, Ng C, Chae YK, Clarke JM, Crawford JA, Meric-Bernstam F, Ignatius Ou SH, Gandara DR, Heymach JV, Bivona TG, McCoach CE. Molecular Landscape of BRAF-Mutant NSCLC Reveals an Association Between Clonality and Driver Mutations and Identifies Targetable Non-V600 Driver Mutations. J Thorac Oncol 2020; 15:1611-1623. [PMID: 32540409 DOI: 10.1016/j.jtho.2020.05.021] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/22/2020] [Accepted: 05/05/2020] [Indexed: 01/09/2023]
Abstract
INTRODUCTION Approximately 4% of NSCLC harbor BRAF mutations, and approximately 50% of these are non-V600 mutations. Treatment of tumors harboring non-V600 mutations is challenging because of functional heterogeneity and lack of knowledge regarding their clinical significance and response to targeted agents. METHODS We conducted an integrative analysis of BRAF non-V600 mutations using genomic profiles of BRAF-mutant NSCLC from the Guardant360 database. BRAF mutations were categorized by clonality and class (1 and 2: RAS-independent; 3: RAS-dependent). Cell viability assays were performed in Ba/F3 models. Drug screens were performed in NSCLC cell lines. RESULTS A total of 305 unique BRAF mutations were identified. Missense mutations were most common (276, 90%), and 45% were variants of unknown significance. F468S and N581Y were identified as novel activating mutations. Class 1 to 3 mutations had higher clonality than mutations of unknown class (p < 0.01). Three patients were treated with MEK with or without BRAF inhibitors. Patients harboring G469V and D594G mutations did not respond, whereas a patient with the L597R mutation had a durable response. Trametinib with or without dabrafenib, LXH254, and lifirafenib had more potent inhibition of BRAF non-V600-mutant NSCLC cell lines than other MEK, BRAF, and ERK inhibitors, comparable with the inhibition of BRAF V600E cell line. CONCLUSIONS In BRAF-mutant NSCLC, clonality is higher in known functional mutations and may allow identification of variants of unknown significance that are more likely to be oncogenic drivers. Our data indicate that certain non-V600 mutations are responsive to MEK and BRAF inhibitors. This integration of genomic profiling and drug sensitivity may guide the treatment for BRAF-mutant NSCLC.
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Affiliation(s)
- Marcelo V Negrao
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - Jacqulyne P Robichaux
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Junqin He
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Monique B Nilsson
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Patrick K S Ng
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bianca E Amador
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Emily B Roarty
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - Viola W Zhu
- Chao Family Comprehensive Cancer Center, Department of Medicine, Division of Hematology-Oncology, University of California Irvine, Orange, California
| | - Chun Ng
- Kaiser Permanente, Stockton, California
| | - Young Kwang Chae
- Robert H. Lurie Comprehensive Cancer Center, Division of Hematology-Oncology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | | | | | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sai-Hong Ignatius Ou
- Chao Family Comprehensive Cancer Center, Department of Medicine, Division of Hematology-Oncology, University of California Irvine, Orange, California
| | - David R Gandara
- Division of Hematology-Oncology, Department of Internal Medicine, University of California Davis Comprehensive Cancer Center, Sacramento, California
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Trever G Bivona
- Division of Hematology and Oncology, University of California San Francisco, San Francisco, California
| | - Caroline E McCoach
- Division of Hematology and Oncology, University of California San Francisco, San Francisco, California.
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10
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Janjigian YY, Maron SB, Chatila WK, Millang B, Chavan SS, Alterman C, Chou JF, Segal MF, Simmons MZ, Momtaz P, Shcherba M, Ku GY, Zervoudakis A, Won ES, Kelsen DP, Ilson DH, Nagy RJ, Lanman RB, Ptashkin RN, Donoghue MTA, Capanu M, Taylor BS, Solit DB, Schultz N, Hechtman JF. First-line pembrolizumab and trastuzumab in HER2-positive oesophageal, gastric, or gastro-oesophageal junction cancer: an open-label, single-arm, phase 2 trial. Lancet Oncol 2020; 21:821-831. [PMID: 32437664 DOI: 10.1016/s1470-2045(20)30169-8] [Citation(s) in RCA: 211] [Impact Index Per Article: 52.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/02/2020] [Accepted: 03/06/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND Addition of trastuzumab to first-line chemotherapy improves overall survival in patients with HER2-positive metastatic gastric cancer. We assessed the safety and activity of pembrolizumab in combination with trastuzumab and chemotherapy in first-line HER2-positive metastatic oesophagogastric (gastric, oesophageal, or gastroesophageal junction) cancer. METHODS This study was an investigator-initiated, open-label, non-randomised, single-arm, single centre, phase 2 trial in patients aged 18 years or older with HER2-positive metastatic oesophagogastric cancer. Eligible patients had measurable or evaluable non-measurable disease, Eastern Cooperative Oncology Group performance status of 0, 1, or 2, and left ventricular ejection fraction of at least 53%. Patients were eligible to receive an initial induction cycle of 200 mg flat dose of intravenous pembrolizumab and 8 mg/kg loading dose of intravenous trastuzumab. For subsequent cycles, patients received 130 mg/m2 of intravenous oxaliplatin or 80 mg/m2 of cisplatin on day 1, 850 mg/m2 of oral capecitabine twice a day for 2 weeks followed by 1 week off (or intravenous 5-fluorouracil, 800 mg/m2 per day on days 1-5), and a 200 mg flat dose of intravenous pembrolizumab, and 6 mg/kg of trastuzumab, administered on day 1 of each 3-week cycle. The primary endpoint was 6-month progression-free survival, defined as the proportion of patients alive and free of progression at 6 months, assessed in patients who received at least one dose of trastuzumab and pembrolizumab. The regimen would be considered worthy of further investigation if 26 or more of 37 patients were progression-free at 6 months. This trial is registered with ClinicalTrials.gov, NCT02954536, and is ongoing, but closed to enrolment. FINDINGS Between Nov 11, 2016, and Jan 23, 2019, 37 patients were enrolled. At the time of data cutoff on Aug 6, 2019, median follow-up among survivors was 13·0 months (IQR 11·7-23·5). The primary endpoint was achieved; 26 (70%; 95% CI 54-83) of 37 patients were progression-free at 6 months. The most common treatment-related adverse event of any grade was neuropathy, which was reported in 36 (97%) of 37 patients. The most common grade 3 or 4 adverse events were lymphocytopenia (seven [19%] patients with grade 3 and two [5%] with grade 4), grade 3 decreased electrolytes (six [16%] patients), and grade 3 anaemia (four [11%] patients). Serious adverse events occurred in two patients patients (both grade 3 nephritis leading to treatment discontinuation). Four patients discontinued pembrolizumab because of immune-related adverse events. There were no treatment-related deaths. INTERPRETATION Pembrolizumab can be safely combined with trastuzumab and chemotherapy and has promising activity in HER2-positive metastatic oesophagogastric cancer. A randomised phase 3 clinical trial assessing the efficacy and safety of pembrolizumab versus placebo in combination with trastuzumab and chemotherapy in first-line HER2-positive metastatic oesophagogastric cancer is underway. FUNDING Merck & Co.
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Affiliation(s)
- Yelena Y Janjigian
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
| | - Steven B Maron
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Walid K Chatila
- Marie-Josée & Henry R Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Tri-Institutional Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Brittanie Millang
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shweta S Chavan
- Marie-Josée & Henry R Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Carly Alterman
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Joanne F Chou
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michal F Segal
- Department of Nursing, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Z Simmons
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Parisa Momtaz
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marina Shcherba
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Geoffrey Y Ku
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Alice Zervoudakis
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Elizabeth S Won
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - David P Kelsen
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - David H Ilson
- Gastrointestinal Oncology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | | | | | - Ryan N Ptashkin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Mark T A Donoghue
- Marie-Josée & Henry R Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marinela Capanu
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Barry S Taylor
- Marie-Josée & Henry R Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David B Solit
- Marie-Josée & Henry R Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Genitourinary Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Nikolaus Schultz
- Marie-Josée & Henry R Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
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11
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Ledet EM, Lilly MB, Sonpavde G, Lin E, Nussenzveig RH, Barata PC, Yandell M, Nagy RJ, Kiedrowski L, Agarwal N, Sartor O. Comprehensive Analysis of AR Alterations in Circulating Tumor DNA from Patients with Advanced Prostate Cancer. Oncologist 2020; 25:327-333. [PMID: 32297439 PMCID: PMC7160408 DOI: 10.1634/theoncologist.2019-0115] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2019] [Accepted: 10/04/2019] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Somatic alterations in circulating tumor DNA (ctDNA) may be associated with treatment response or prognosis in prostate cancer (PCa). The goal was to characterize androgen receptor gene (AR) amplifications and mutations detected in ctDNA from patients with PCa and to further understand the somatic genetic heterogeneity of advanced prostate cancer. PATIENTS AND METHODS This study included a heterogeneous group of 892 patients with advanced PCa (predominantly castrate-resistant prostate cancer) with AR alterations detected in ctDNA that underwent next-generation sequencing of 54 to 73 genes via Guardant360 testing (Guardant Health, Inc., Redwood City, CA). Distribution and summary of AR alterations detected, the association of AR alterations with other genes, and a pathway analysis are reported. RESULTS The median absolute plasma copy number of AR amplifications was 3.3 (range, 1.2-165.2). Many patients had multiple AR mutations; a total of 112 unique mutations were identified in AR, including L702H (25%), T878A (14%), H875Y (11%), W742C (8%), W742L (4%), F877L (2%), and T878S (2%). Other ctDNA gene alterations in the Guardant assays included TP53 (50%), MYC (34%), BRAF (32%), PIK3CA (29%), MET (25%), CDK6 (26%), EGFR (24%), FGFR1 (21%), and APC (12%). Many of these non-AR alterations are not tissue verified in other studies. AR amplification cosegregated with alterations in MYC (p < .001), BRAF (p < .001), PIK3CA (p < .001), MET (p < .001), CDK6 (p < .001), EGFR (p < .001), FGFR1 (p = .391), and more. Alterations in APC were significantly associated with mutations in AR (p < .001). CONCLUSION Several AR alterations and concomitant non-AR alterations that associate with drug resistance were detected. These findings provide additional insights into the heterogeneity of advanced prostate cancer. IMPLICATIONS FOR PRACTICE The goal was to characterize androgen receptor gene (AR) amplifications and mutations detected in circulating tumor DNA (ctDNA) from patients with prostate cancer in relation to non-AR gene alterations detected in the ctDNA landscape. The study included 892 patients with prostate cancer with AR alterations in ctDNA. AR alterations were significantly associated with other gene alterations detected in ctDNA. The common AR mutations found are linked to resistance to abiraterone, enzalutamide, or bicalutamide. Characterization of the circulating AR landscape and gene alterations provides potential additional insight into the somatic genetic heterogeneity of advanced prostate cancer.
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Affiliation(s)
- Elisa M. Ledet
- Tulane Cancer CenterNew OrleansLouisianaUSA
- Tulane University School of MedicineNew OrleansLouisianaUSA
| | | | | | - Edwin Lin
- School of Medicine, University of UtahSalt Lake CityUtahUSA
| | | | | | - Mark Yandell
- Department of Human Genetics, University of UtahSalt Lake CityUtahUSA
| | | | | | - Neeraj Agarwal
- Huntsman Cancer Institute, University of UtahSalt Lake CityUtahUSA
| | - Oliver Sartor
- Tulane Cancer CenterNew OrleansLouisianaUSA
- Tulane University School of MedicineNew OrleansLouisianaUSA
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12
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Aggarwal C, Thompson JC, Chien AL, Quinn KJ, Hwang WT, Black TA, Yee SS, Christensen TE, LaRiviere MJ, Silva BA, Banks KC, Nagy RJ, Helman E, Berman AT, Ciunci CA, Singh AP, Wasser JS, Bauml JM, Langer CJ, Cohen RB, Carpenter EL. Baseline Plasma Tumor Mutation Burden Predicts Response to Pembrolizumab-based Therapy in Patients with Metastatic Non-Small Cell Lung Cancer. Clin Cancer Res 2020; 26:2354-2361. [PMID: 32102950 DOI: 10.1158/1078-0432.ccr-19-3663] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/13/2020] [Accepted: 02/12/2020] [Indexed: 12/22/2022]
Abstract
PURPOSE The role of plasma-based tumor mutation burden (pTMB) in predicting response to pembrolizumab-based first-line standard-of-care therapy for metastatic non-small cell lung cancer (mNSCLC) has not been explored. EXPERIMENTAL DESIGN A 500-gene next-generation sequencing panel was used to assess pTMB. Sixty-six patients with newly diagnosed mNSCLC starting first-line pembrolizumab-based therapy, either alone or in combination with chemotherapy, were enrolled (Clinicaltrial.gov identifier: NCT03047616). Response was assessed using RECIST 1.1. Associations were made for patient characteristics, 6-month durable clinical benefit (DCB), progression-free survival (PFS), and overall survival (OS). RESULTS Of 66 patients, 52 (78.8%) were pTMB-evaluable. Median pTMB was 16.8 mutations per megabase (mut/Mb; range, 1.9-52.5) and was significantly higher for patients achieving DCB compared with no durable benefit (21.3 mut/Mb vs. 12.4 mut/Mb, P = 0.003). For patients with pTMB ≥ 16 mut/Mb, median PFS was 14.1 versus 4.7 months for patients with pTMB < 16 mut/Mb [HR, 0.30 (0.16-0.60); P < 0.001]. Median OS for patients with pTMB ≥ 16 was not reached versus 8.8 months for patients with pTMB < 16 mut/Mb [HR, 0.48 (0.22-1.03); P = 0.061]. Mutations in ERBB2 exon 20, STK11, KEAP1, or PTEN were more common in patients with no DCB. A combination of pTMB ≥ 16 and absence of negative predictor mutations was associated with PFS [HR, 0.24 (0.11-0.49); P < 0.001] and OS [HR, 0.31 (0.13-0.74); P = 0.009]. CONCLUSIONS pTMB ≥ 16 mut/Mb is associated with improved PFS after first-line standard-of-care pembrolizumab-based therapy in mNSCLC. STK11/KEAP1/PTEN and ERBB2 mutations may help identify pTMB-high patients unlikely to respond. These results should be validated in larger prospective studies.
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MESH Headings
- Aged
- Aged, 80 and over
- Antibodies, Monoclonal, Humanized/administration & dosage
- Antineoplastic Agents, Alkylating/therapeutic use
- Antineoplastic Agents, Immunological/administration & dosage
- Biomarkers, Tumor/blood
- Biomarkers, Tumor/genetics
- Carcinoma, Non-Small-Cell Lung/blood
- Carcinoma, Non-Small-Cell Lung/drug therapy
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/pathology
- Female
- Humans
- Lung Neoplasms/blood
- Lung Neoplasms/drug therapy
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Male
- Middle Aged
- Mutation
- Neoplasm Metastasis
- Predictive Value of Tests
- Prospective Studies
- Survival Rate
- Treatment Outcome
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Affiliation(s)
- Charu Aggarwal
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania.
| | - Jeffrey C Thompson
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Austin L Chien
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | | | - Wei-Ting Hwang
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Taylor A Black
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Stephanie S Yee
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Theresa E Christensen
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Michael J LaRiviere
- Division of Radiation Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Benjamin A Silva
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | | | | | | | - Abigail T Berman
- Division of Radiation Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Christine A Ciunci
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Aditi P Singh
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Jeffrey S Wasser
- Neag Comprehensive Cancer Center, UConn Health, University of Connecticut, Farmington, Connecticut
| | - Joshua M Bauml
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Corey J Langer
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Roger B Cohen
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Erica L Carpenter
- Division of Hematology/Oncology, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
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13
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Dagogo-Jack I, Yoda S, Lennerz JK, Langenbucher A, Lin JJ, Rooney MM, Prutisto-Chang K, Oh A, Adams NA, Yeap BY, Chin E, Do A, Marble HD, Stevens SE, Digumarthy SR, Saxena A, Nagy RJ, Benes CH, Azzoli CG, Lawrence MS, Gainor JF, Shaw AT, Hata AN. MET Alterations Are a Recurring and Actionable Resistance Mechanism in ALK-Positive Lung Cancer. Clin Cancer Res 2020; 26:2535-2545. [PMID: 32086345 DOI: 10.1158/1078-0432.ccr-19-3906] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/22/2020] [Accepted: 02/17/2020] [Indexed: 12/15/2022]
Abstract
PURPOSE Most ALK-positive lung cancers will develop ALK-independent resistance after treatment with next-generation ALK inhibitors. MET amplification has been described in patients progressing on ALK inhibitors, but frequency of this event has not been comprehensively assessed. EXPERIMENTAL DESIGN We performed FISH and/or next-generation sequencing on 207 posttreatment tissue (n = 101) or plasma (n = 106) specimens from patients with ALK-positive lung cancer to detect MET genetic alterations. We evaluated ALK inhibitor sensitivity in cell lines with MET alterations and assessed antitumor activity of ALK/MET blockade in ALK-positive cell lines and 2 patients with MET-driven resistance. RESULTS MET amplification was detected in 15% of tumor biopsies from patients relapsing on next-generation ALK inhibitors, including 12% and 22% of biopsies from patients progressing on second-generation inhibitors or lorlatinib, respectively. Patients treated with a second-generation ALK inhibitor in the first-line setting were more likely to develop MET amplification than those who had received next-generation ALK inhibitors after crizotinib (P = 0.019). Two tumor specimens harbored an identical ST7-MET rearrangement, one of which had concurrent MET amplification. Expressing ST7-MET in the sensitive H3122 ALK-positive cell line induced resistance to ALK inhibitors that was reversed with dual ALK/MET inhibition. MET inhibition resensitized a patient-derived cell line harboring both ST7-MET and MET amplification to ALK inhibitors. Two patients with ALK-positive lung cancer and acquired MET alterations achieved rapid responses to ALK/MET combination therapy. CONCLUSIONS Treatment with next-generation ALK inhibitors, particularly in the first-line setting, may lead to MET-driven resistance. Patients with acquired MET alterations may derive clinical benefit from therapies that target both ALK and MET.
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Affiliation(s)
- Ibiayi Dagogo-Jack
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Satoshi Yoda
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Jochen K Lennerz
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital, Boston, Massachusetts
| | - Adam Langenbucher
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Jessica J Lin
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Marguerite M Rooney
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Kylie Prutisto-Chang
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Audris Oh
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Nathaniel A Adams
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Beow Y Yeap
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Emily Chin
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Andrew Do
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Hetal D Marble
- Department of Pathology, Center for Integrated Diagnostics, Massachusetts General Hospital, Boston, Massachusetts
| | - Sara E Stevens
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Subba R Digumarthy
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts
| | - Ashish Saxena
- Department of Medicine, Weill Cornell Medicine, New York, New York
| | | | - Cyril H Benes
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Christopher G Azzoli
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Michael S Lawrence
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Justin F Gainor
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Alice T Shaw
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts. .,Harvard Medical School, Boston, Massachusetts
| | - Aaron N Hata
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts. .,Harvard Medical School, Boston, Massachusetts
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14
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Kiedrowski LA, Juric D, Hardin AI, Price KS, Nagy RJ, Arteaga CL, O'Shaughnessy J, Bardia A, Cristofanilli M, Lanman RB. Abstract P4-10-15: PIK3CA mutational analysis using cell-free DNA next-generation sequencing detects activating mutations that may be missed with targeted hot-spot testing. Cancer Res 2020. [DOI: 10.1158/1538-7445.sabcs19-p4-10-15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: The FDA recently approved alpelisib, in combination with fulvestrant, for HR+/HER2- PIK3CA-mutated advanced/metastatic breast cancer after trials demonstrated improved clinical outcomes with this targeted combination. The companion diagnostic, the Qiagen Therascreen, is a PCR-based kit detecting 11 single nucleotide variant (SNV) mutations limited to 3 exons in the PIK3CA gene. However, other functionally significant mutations outside these hotspots, including activating SNVs and indels, have been reported, suggesting they confer PI3K dependence and, therefore, sensitivity to PI3K inhibitors. We explored the prevalence and spectrum of PIK3CA mutations that can be identified with more comprehensive testing methods.
Methods: We queried a large commercial laboratory database of clinical genomic test results from Guardant360 (Guardant Health, Inc) plasma cell-free DNA (cfDNA) next-generation sequencing (NGS) analysis of 74 genes detecting SNVs, indels, copy number amplifications, and fusions. This assay includes full exonic sequencing of PIK3CA. Clinical genomic results from patients with a diagnosis of advanced breast cancer who had at least one genomic alteration detected by Guardant360 between 11/25/2016 - 6/8/2019 were retrospectively analyzed.
Results: 6940 eligible samples from 5549 unique patients with advanced breast cancer were identified; some patients had samples submitted at multiple timepoints. Excluding duplicate mutations from serial sampling, a total of 2761 nonsynonymous PIK3CA SNVs were identified in 2095 unique patients (38%); 2435 of these 2761 (88%) detected in 1982 patients (36%) were predicted to be activating. 353/1982 (18%) mutation positive patients had >1 PIK3CA activating mutation detected. Among the 2435 activating SNVs, 626 (26%) were located outside the hotspots covered by the companion diagnostic test. These 626 occurrences included over 70 unique activating mutations, with 16 unique mutations observed in >10 patients each. The most common non-hotspot mutations included E726K (117 patients), N345K (83 patients), and E453K (48 patients). Additional analysis was performed to assess for PIK3CA indels; 118 PIK3CA indels were identified in 118/5549 unique patients (2%). Predicted activating indels were identified across the PIK3CA gene, including the C2 and kinase domains and in the linking region between the adapter binding and Ras-binding domains.
Conclusions: PIK3CA mutation analysis with PCR-based hotspot testing is limited to only the most common mutations and will miss as many as one-quarter of alterations that could potentially be targeted with alpelisib, an FDA-approved PI3Ka inhibitor. While additional data may be needed to determine the clinical response from targeting these alterations, molecular data and case reports suggest that these less common PIK3CA mutations are viable targets for a PI3K inhibitor. Comprehensive NGS, including plasma-based cfDNA testing, should be considered to identify the full spectrum of patients who may respond to PI3K targeted therapies.
Citation Format: Lesli A Kiedrowski, Dejan Juric, Aaron I Hardin, Kristin S Price, Rebecca J Nagy, Carlos L Arteaga, Joyce O'Shaughnessy, Aditya Bardia, Massimo Cristofanilli, Richard B Lanman. PIK3CA mutational analysis using cell-free DNA next-generation sequencing detects activating mutations that may be missed with targeted hot-spot testing [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-10-15.
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Affiliation(s)
| | - Dejan Juric
- 2Massachusetts General Hospital Cancer Center, Department of Medicine, Harvard Medical School, Boston, MA
| | | | | | | | | | | | - Aditya Bardia
- 2Massachusetts General Hospital Cancer Center, Department of Medicine, Harvard Medical School, Boston, MA
| | - Massimo Cristofanilli
- 5Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL
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15
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Gutierrez ME, Price KS, Lanman RB, Nagy RJ, Shah I, Mathura S, Mulcahy M, Norden AD, Goldberg SL. Genomic Profiling for KRAS, NRAS, BRAF, Microsatellite Instability, and Mismatch Repair Deficiency Among Patients With Metastatic Colon Cancer. JCO Precis Oncol 2019; 3:PO.19.00274. [PMID: 32923867 PMCID: PMC7448804 DOI: 10.1200/po.19.00274] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2019] [Indexed: 12/20/2022] Open
Abstract
PURPOSE Genomic testing is recognized in national guidelines as essential to guide appropriate therapy selection in metastatic colorectal cancer. Previous studies report adherence to testing guidelines is suboptimal, but current testing rates have not been assessed. This study reports testing rates in metastatic colon cancer (mCC) for guideline-recommended biomarkers in a US-based population. MATERIALS AND METHODS A retrospective review of data extracted from electronic medical records was performed to identify patients with pathologically confirmed mCC and describe patterns of guideline-aligned biomarker testing. Data were extracted from the electronic health records of 1,497 patients treated at 23 practices across the United States. Both community and academic centers were represented. RESULTS A total of 1,497 patients with mCC diagnosed between January 1, 2013 and December 31, 2017 were identified. Guideline-aligned biomarker testing rates for RAS, BRAF, and microsatellite instability/mismatch repair deficiency over this study period were 41%, 43%, and 51%, respectively. Patients were more likely to have guideline-aligned testing for RAS and BRAF if they were treated at an academic center, were diagnosed with de novo metastatic disease, and were female. In addition, patients < 65 years of age were more likely to have guideline-aligned RAS testing. Of the 177 patients (12% of cohort) who received anti-epidermal growth factor receptor therapy, only 50 (28%) had complete guideline-aligned biomarker testing. CONCLUSION Despite guideline recommendations and significant therapeutic implications, overall biomarker testing rates in mCC remain suboptimal. Adherence to guideline-recommended biomarker testing would potentially reduce exposure to expensive and ineffective therapies, resulting in improved patient outcomes.
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Affiliation(s)
- Martin E. Gutierrez
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ
| | | | | | | | | | | | | | | | - Stuart L. Goldberg
- John Theurer Cancer Center, Hackensack University Medical Center, Hackensack, NJ
- Cota Healthcare, New York, NY
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16
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Smyth LM, Piha-Paul SA, Won HH, Schram AM, Saura C, Loi S, Lu J, Shapiro GI, Juric D, Mayer IA, Arteaga CL, de la Fuente MI, Brufksy AM, Spanggaard I, Mau-Sørensen M, Arnedos M, Moreno V, Boni V, Sohn J, Schwartzberg LS, Gonzàlez-Farré X, Cervantes A, Bidard FC, Gorelick AN, Lanman RB, Nagy RJ, Ulaner GA, Chandarlapaty S, Jhaveri K, Gavrila EI, Zimel C, Selcuklu SD, Melcer M, Samoila A, Cai Y, Scaltriti M, Mann G, Xu F, Eli LD, Dujka M, Lalani AS, Bryce R, Baselga J, Taylor BS, Solit DB, Meric-Bernstam F, Hyman DM. Efficacy and Determinants of Response to HER Kinase Inhibition in HER2-Mutant Metastatic Breast Cancer. Cancer Discov 2019; 10:198-213. [PMID: 31806627 DOI: 10.1158/2159-8290.cd-19-0966] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/23/2019] [Accepted: 12/02/2019] [Indexed: 11/16/2022]
Abstract
HER2 mutations define a subset of metastatic breast cancers with a unique mechanism of oncogenic addiction to HER2 signaling. We explored activity of the irreversible pan-HER kinase inhibitor neratinib, alone or with fulvestrant, in 81 patients with HER2-mutant metastatic breast cancer. Overall response rate was similar with or without estrogen receptor (ER) blockade. By comparison, progression-free survival and duration of response appeared longer in ER+ patients receiving combination therapy, although the study was not designed for direct comparison. Preexistent concurrent activating HER2 or HER3 alterations were associated with poor treatment outcome. Similarly, acquisition of multiple HER2-activating events, as well as gatekeeper alterations, were observed at disease progression in a high proportion of patients deriving clinical benefit from neratinib. Collectively, these data define HER2 mutations as a therapeutic target in breast cancer and suggest that coexistence of additional HER signaling alterations may promote both de novo and acquired resistance to neratinib. SIGNIFICANCE: HER2 mutations define a targetable breast cancer subset, although sensitivity to irreversible HER kinase inhibition appears to be modified by the presence of concurrent activating genomic events in the pathway. These findings have implications for potential future combinatorial approaches and broader therapeutic development for this genomically defined subset of breast cancer.This article is highlighted in the In This Issue feature, p. 161.
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Affiliation(s)
- Lillian M Smyth
- Memorial Sloan Kettering Cancer Center, New York, New York.,St. Vincent's University Hospital, Dublin, Ireland
| | | | - Helen H Won
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Cristina Saura
- Vall d'Hebron University Hospital, Vall d'Hebrón Institute of Oncology (VHIO), Barcelona, Spain
| | - Sherene Loi
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Janice Lu
- University of Southern California Norris Comprehensive Cancer Center, Los Angeles, California
| | | | - Dejan Juric
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | | | - Carlos L Arteaga
- The University of Texas Southwestern Medical Center Harold C. Simmons Comprehensive Cancer Center, Dallas, Texas
| | | | - Adam M Brufksy
- University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, Pennsylvania
| | | | | | | | | | - Valentina Boni
- START Madrid Hospital Universitario HM Sanchinarro, Madrid, Spain
| | - Joohyuk Sohn
- Yonsei Cancer Center, University College of Medicine, Seoul, Korea
| | | | | | - Andrés Cervantes
- CIBERONC, Biomedical Research Institute INCLIVA, University of Valencia, Valencia, Spain
| | | | | | | | | | - Gary A Ulaner
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Komal Jhaveri
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | | | - Myra Melcer
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Yanyan Cai
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Grace Mann
- Puma Biotechnology, Inc., Los Angeles, California
| | - Feng Xu
- Puma Biotechnology, Inc., Los Angeles, California
| | - Lisa D Eli
- Puma Biotechnology, Inc., Los Angeles, California
| | | | | | | | - José Baselga
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Barry S Taylor
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - David M Hyman
- Memorial Sloan Kettering Cancer Center, New York, New York.
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17
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Fairclough SR, Kiedrowski LA, Lin JJ, Zelichov O, Tarcic G, Stinchcombe TE, Odegaard JI, Lanman RB, Shaw AT, Nagy RJ. Identification of osimertinib-resistant EGFR L792 mutations by cfDNA sequencing: oncogenic activity assessment and prevalence in large cfDNA cohort. Exp Hematol Oncol 2019; 8:24. [PMID: 31632838 PMCID: PMC6788107 DOI: 10.1186/s40164-019-0148-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 09/23/2019] [Indexed: 12/20/2022] Open
Abstract
Cell-free DNA (cfDNA) next-generation sequencing has the potential to capture tumor heterogeneity and genomic evolution under treatment pressure in a non-invasive manner. Here, we report the detection of EGFR L792 mutations, a non-covalent mechanism of osimertinib resistance, using Guardant360 cfDNA testing in a patient with metastatic EGFR-mutant non-small cell lung cancer (NSCLC) whose disease progressed on osimertinib. We subsequently analyzed a large cohort of over 1800 additional patient samples harboring an EGFR T790M mutation and identified a concomitant L792 mutation in a total of 22 (1.2%) cases. In vitro functional assays demonstrated that the EGFR L858R/T790M/L792F/H mutations conferred intermediate-level resistance to osimertinib. Further understanding of potential acquired resistance mechanisms to targeted therapy may help inform treatment strategy in EGFR-mutant NSCLC.
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Affiliation(s)
| | | | - Jessica J Lin
- 2Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, 55 Fruit St, Boston, MA 02114 USA
| | - Ori Zelichov
- NovellusDx, Jerusalem Biopark, Hadassah Ein-Kerem Medical Center Campus, Jerusalem, Israel
| | - Gabi Tarcic
- NovellusDx, Jerusalem Biopark, Hadassah Ein-Kerem Medical Center Campus, Jerusalem, Israel
| | | | | | - Richard B Lanman
- Guardant Health, Inc., 505 Penobscot Dr, Redwood City, CA 94063 USA
| | - Alice T Shaw
- 2Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, 55 Fruit St, Boston, MA 02114 USA
| | - Rebecca J Nagy
- Guardant Health, Inc., 505 Penobscot Dr, Redwood City, CA 94063 USA
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18
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Abraham J, Montero AJ, Jankowitz RC, Salkeni MA, Beumer JH, Kiesel BF, Piette F, Adamson LM, Nagy RJ, Lanman RB, Sperinde J, Huang W, Allegra CJ, Srinivasan A, Wang Y, Pogue-Geile KL, Lucas PC, Jacobs SA. Safety and Efficacy of T-DM1 Plus Neratinib in Patients With Metastatic HER2-Positive Breast Cancer: NSABP Foundation Trial FB-10. J Clin Oncol 2019; 37:2601-2609. [PMID: 31442103 PMCID: PMC6784849 DOI: 10.1200/jco.19.00858] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
PURPOSE Patients with human epidermal growth factor receptor 2 (HER2)–positive metastatic breast cancer eventually develop resistance to dual-antibody therapy with trastuzumab plus pertuzumab. Mechanisms of resistance have not been well elucidated. We evaluated the safety, tolerability, and efficacy of ado-trastuzumab emtansine (T-DM1) plus neratinib in patients who progressed on trastuzumab plus pertuzumab. PATIENTS AND METHODS In this 3 + 3 dose-escalation study, patients with metastatic breast cancer who progressed on trastuzumab, pertuzumab, and a taxane were treated with T-DM1 at 3.6 mg/kg intravenously every 3 weeks and dose-escalating neratinib at 120, 160, 200, or 240 mg/d orally. RESULTS Twenty-seven patients were treated across four dose-levels of neratinib. Dose-limiting toxicity in cycle 1 was grade 3 diarrhea in six patients and grade 3 nausea in one; no patient experienced grade 4 diarrhea, and there were no grade 5 toxicities. Other grade 3 to 4 toxicities included nausea (11%), dehydration (11%), electrolyte abnormality (19%), thrombocytopenia (15%), elevated transaminase levels (7%), and fatigue (7%). Twelve (63%) of 19 evaluable patients had an objective response. Responses occurred at all neratinib doses. Plasma cell–free DNA at baseline showed ERBB2 (HER2) amplification in 10 of 27 patients. Deep and more durable responses occurred in patients with cell-free DNA ERBB2 amplification. Two complete responders had high expression of total HER2 and p95HER2 in baseline tissue. CONCLUSION We report the recommended phase II dose of T-DM1 3.6 mg/kg and neratinib 160 mg/d for this combination. Possible resistance mechanisms to HER2 antibodies may be loss of the HER2 receptor and high expression of p95HER2. These data provide the basis for an ongoing phase II study to better define the activity of this regimen.
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Affiliation(s)
- Jame Abraham
- NSABP Foundation, Pittsburgh, PA.,Cleveland Clinic, Taussig Cancer Institute, Cleveland, OH
| | - Albert J Montero
- NSABP Foundation, Pittsburgh, PA.,Cleveland Clinic, Taussig Cancer Institute, Cleveland, OH
| | - Rachel C Jankowitz
- NSABP Foundation, Pittsburgh, PA.,University of Pittsburgh School of Medicine, Pittsburgh, PA.,UPMC Hillman Cancer Center, Pittsburgh, PA
| | | | - Jan H Beumer
- NSABP Foundation, Pittsburgh, PA.,UPMC Hillman Cancer Center, Pittsburgh, PA
| | - Brian F Kiesel
- NSABP Foundation, Pittsburgh, PA.,UPMC Hillman Cancer Center, Pittsburgh, PA
| | - Fanny Piette
- International Drug Development Institute, Louvain-la-Neuve, Belgium
| | | | | | | | - Jeff Sperinde
- Monogram Biosciences, Laboratory Corporation of America Holdings, South San Francisco, CA
| | - Weidong Huang
- Monogram Biosciences, Laboratory Corporation of America Holdings, South San Francisco, CA
| | - Carmen J Allegra
- NSABP Foundation, Pittsburgh, PA.,University of Florida Health, Gainesville, FL
| | | | | | | | - Peter C Lucas
- NSABP Foundation, Pittsburgh, PA.,University of Pittsburgh School of Medicine, Pittsburgh, PA
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19
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Maron SB, Chase LM, Lomnicki S, Kochanny S, Moore KL, Joshi SS, Landron S, Johnson J, Kiedrowski LA, Nagy RJ, Lanman RB, Kim ST, Lee J, Catenacci DVT. Circulating Tumor DNA Sequencing Analysis of Gastroesophageal Adenocarcinoma. Clin Cancer Res 2019; 25:7098-7112. [PMID: 31427281 DOI: 10.1158/1078-0432.ccr-19-1704] [Citation(s) in RCA: 132] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 07/01/2019] [Accepted: 08/14/2019] [Indexed: 12/20/2022]
Abstract
PURPOSE Gastroesophageal adenocarcinoma (GEA) has a poor prognosis and few therapeutic options. Utilizing a 73-gene plasma-based next-generation sequencing (NGS) cell-free circulating tumor DNA (ctDNA-NGS) test, we sought to evaluate the role of ctDNA-NGS in guiding clinical decision-making in GEA. EXPERIMENTAL DESIGN We evaluated a large cohort (n = 2,140 tests; 1,630 patients) of ctDNA-NGS results (including 369 clinically annotated patients). Patients were assessed for genomic alteration (GA) distribution and correlation with clinicopathologic characteristics and outcomes. RESULTS Treatment history, tumor site, and disease burden dictated tumor-DNA shedding and consequent ctDNA-NGS maximum somatic variant allele frequency. Patients with locally advanced disease having detectable ctDNA postoperatively experienced inferior median disease-free survival (P = 0.03). The genomic landscape was similar but not identical to tissue-NGS, reflecting temporospatial molecular heterogeneity, with some targetable GAs identified at higher frequency via ctDNA-NGS compared with previous primary tumor-NGS cohorts. Patients with known microsatellite instability-high (MSI-High) tumors were robustly detected with ctDNA-NGS. Predictive biomarker assessment was optimized by incorporating tissue-NGS and ctDNA-NGS assessment in a complementary manner. HER2 inhibition demonstrated a profound survival benefit in HER2-amplified patients by ctDNA-NGS and/or tissue-NGS (median overall survival, 26.3 vs. 7.4 months; P = 0.002), as did EGFR inhibition in EGFR-amplified patients (median overall survival, 21.1 vs. 14.4 months; P = 0.01). CONCLUSIONS ctDNA-NGS characterized GEA molecular heterogeneity and rendered important prognostic and predictive information, complementary to tissue-NGS.See related commentary by Frankell and Smyth, p. 6893.
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Affiliation(s)
- Steven B Maron
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Leah M Chase
- The University of Chicago Medical Center, Chicago, Illinois
| | | | - Sara Kochanny
- The University of Chicago Medical Center, Chicago, Illinois
| | - Kelly L Moore
- The University of Chicago Medical Center, Chicago, Illinois
| | - Smita S Joshi
- The University of Chicago Medical Center, Chicago, Illinois
| | - Stacie Landron
- The University of Chicago Medical Center, Chicago, Illinois
| | - Julie Johnson
- The University of Chicago Medical Center, Chicago, Illinois
| | - Lesli A Kiedrowski
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Rebecca J Nagy
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
| | - Richard B Lanman
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea
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20
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Cocco E, Schram AM, Kulick A, Misale S, Won HH, Yaeger R, Razavi P, Ptashkin R, Hechtman JF, Toska E, Cownie J, Somwar R, Shifman S, Mattar M, Selçuklu SD, Samoila A, Guzman S, Tuch BB, Ebata K, de Stanchina E, Nagy RJ, Lanman RB, Houck-Loomis B, Patel JA, Berger MF, Ladanyi M, Hyman DM, Drilon A, Scaltriti M. Resistance to TRK inhibition mediated by convergent MAPK pathway activation. Nat Med 2019; 25:1422-1427. [PMID: 31406350 PMCID: PMC6736691 DOI: 10.1038/s41591-019-0542-z] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 07/02/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Emiliano Cocco
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alison M Schram
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Amanda Kulick
- Program in Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sandra Misale
- Program in Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Helen H Won
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rona Yaeger
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Program in Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Pedram Razavi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryan Ptashkin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eneda Toska
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - James Cownie
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Romel Somwar
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sophie Shifman
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marissa Mattar
- Program in Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - S Duygu Selçuklu
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Aliaksandra Samoila
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sean Guzman
- Program in Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | | | - Elisa de Stanchina
- Program in Molecular Pharmacology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Rebecca J Nagy
- Department of Medical Affairs, Guardant Health Inc., Redwood City, CA, USA
| | - Richard B Lanman
- Department of Medical Affairs, Guardant Health Inc., Redwood City, CA, USA
| | - Brian Houck-Loomis
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Juber A Patel
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael F Berger
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Marc Ladanyi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Alexander Drilon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Weill Cornell Medical College, New York, NY, USA.
| | - Maurizio Scaltriti
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA. .,Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Dagogo-Jack I, Rooney M, Lin JJ, Nagy RJ, Yeap BY, Hubbeling H, Chin E, Ackil J, Farago AF, Hata AN, Lennerz JK, Gainor JF, Lanman RB, Shaw AT. Treatment with Next-Generation ALK Inhibitors Fuels Plasma ALK Mutation Diversity. Clin Cancer Res 2019; 25:6662-6670. [PMID: 31358542 DOI: 10.1158/1078-0432.ccr-19-1436] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/18/2019] [Accepted: 07/15/2019] [Indexed: 12/22/2022]
Abstract
PURPOSE Acquired resistance to next-generation ALK tyrosine kinase inhibitors (TKIs) is often driven by secondary ALK mutations. Here, we investigated utility of plasma genotyping for identifying ALK resistance mutations at relapse on next-generation ALK TKIs. EXPERIMENTAL DESIGN We analyzed 106 plasma specimens from 84 patients with advanced ALK-positive lung cancer treated with second- and third-generation ALK TKIs using a commercially available next-generation sequencing (NGS) platform (Guardant360). Tumor biopsies from TKI-resistant lesions underwent targeted NGS to identify ALK mutations. RESULTS By genotyping plasma, we detected an ALK mutation in 46 (66%) of 70 patients relapsing on a second-generation ALK TKI. When post-alectinib plasma and tumor specimens were compared, there was no difference in frequency of ALK mutations (67% vs. 63%), but plasma specimens were more likely to harbor ≥2 ALK mutations (24% vs. 2%, P = 0.004). Among 29 patients relapsing on lorlatinib, plasma genotyping detected an ALK mutation in 22 (76%), including 14 (48%) with ≥2 ALK mutations. The most frequent combinations of ALK mutations were G1202R/L1196M and D1203N/1171N. Detection of ≥2 ALK mutations was significantly more common in patients relapsing on lorlatinib compared with second-generation ALK TKIs (48% vs. 23%, P = 0.017). Among 15 patients who received lorlatinib after a second-generation TKI, serial plasma analysis demonstrated that eight (53%) acquired ≥1 new ALK mutations on lorlatinib. CONCLUSIONS ALK resistance mutations increase with each successive generation of ALK TKI and may be underestimated by tumor genotyping. Sequential treatment with increasingly potent ALK TKIs may promote acquisition of ALK resistance mutations leading to treatment-refractory compound ALK mutations.
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Affiliation(s)
- Ibiayi Dagogo-Jack
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Marguerite Rooney
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Jessica J Lin
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Beow Y Yeap
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Emily Chin
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Jennifer Ackil
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Anna F Farago
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Aaron N Hata
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Jochen K Lennerz
- Center for Integrated Diagnostics, Massachusetts General Hospital, Boston, Massachusetts
| | - Justin F Gainor
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | | | - Alice T Shaw
- Massachusetts General Hospital Cancer Center and Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts.
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22
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Cocco E, Kulick A, Misale S, Yaeger R, Razavi P, Won HH, Ptashkin R, Hechtman JF, Toska E, Cownie J, Somwar R, Shifman S, Mattar M, Selçuklu SD, Samoila A, Guzman S, Tuch BB, Ebata K, Stanchina ED, Nagy RJ, Lanman RB, Berger MF, Ladanyi M, Hyman DM, Drilon A, Scaltriti M, Schram AM. Abstract LB-118: Resistance to TRK inhibition mediated by convergent MAP kinase pathway activation. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-lb-118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: TRK inhibition is now standard of care for advanced pediatric and adult patients (pts) with TRK fusion solid tumors, regardless of origin. To date, TRK kinase domain mutations are the only known resistance mechanism, and next-generation TRK inhibitors active against these mutations such as LOXO-195 are being developed. We reasoned some pts will develop TRK-independent resistance and hypothesized that these pts will require unique therapeutic approaches.
Methods: Paired tumor biopsies and serial cell-free DNA (cfDNA) prospectively collected from pts with TRK fusion-positive cancers treated with first- and next-generation TRK inhibitors before treatment and at progression were sequenced. In parallel, pt-derived and engineered models were analyzed.
Results: Alterations involving upstream non-TRK receptor kinases and downstream MAPK pathway members were initially identified in tumors from 3 TRK fusion-positive gastrointestinal (GI) cancer pts who developed resistance to TRK inhibitors. Pt 1 with CTRC-NTRK1 pancreatic cancer developed temporally distinct emergent BRAF V600E and KRAS G12D mutations. Pt 2 with LMNA-NTRK1 colorectal cancer developed temporally distinct KRAS G12A and G12D mutations. Pt 3 with PLEKHA6-NTRK1 cholangiocarcinoma developed focal MET amplification. Phenocopying these clinical observations, pt-derived xenografts and primary cell lines developed BRAF and KRAS mutations following chronic TRK inhibition. Consistently, ectopic expression of these alterations conferred resistance to TRK inhibitors. Given that all 3 index pts had GI cancers, we expanded serial cfDNA sequencing to 5 additional TRK fusion-positive GI disease, identifying 3 with emergent MAPK alterations at progression, bringing the overall frequency of acquired MAPK alterations in GI cancers analyzed to 75% (6/8). To further evaluate whether these emergent alterations induced functional dependence on ERK signaling, pts 1-3 were treated with agents targeting these emergent alterations (dabrafenib + trametinib, LOXO-195 + trametinib, and LOXO-195 + crizotinib, respectively). Pt 1 achieved transient tumor regression, followed by outgrowth of KRAS-mutant disease. Pt 3 achieved a 4.5 months tumor regression. Sequencing at progression in pt 3 identified multiple acquired MET point mutations known to interfere with crizotinib binding.
Conclusions: These data suggest that a subset of TRK fusion-positive cancers will develop off-target mechanisms of resistance to TRK inhibition. Relative to other TRK fusion-positive tumors, GI cancers may have a higher propensity for developing these bypass alterations that demonstrate remarkable convergence on ERK signaling. A portion of these mechanisms may be managed with simultaneous targeting of the TRK and MAPK pathways, although additional modeling is required to determine if upfront treatment would confer more durable responses.
Citation Format: Emiliano Cocco, Amanda Kulick, Sandra Misale, Rona Yaeger, Pedram Razavi, Helen H. Won, Ryan Ptashkin, Jaclyn F. Hechtman, Eneda Toska, James Cownie, Romel Somwar, Sophie Shifman, Marissa Mattar, S Duygu Selçuklu, Aliaksandra Samoila, Sean Guzman, Brian B. Tuch, Kevin Ebata, Elisa de Stanchina, Rebecca J. Nagy, Richard B. Lanman, Michael F. Berger, Marc Ladanyi, David M. Hyman, Alexander Drilon, Maurizio Scaltriti, Alison M. Schram. Resistance to TRK inhibition mediated by convergent MAP kinase pathway activation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr LB-118.
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Affiliation(s)
| | - Amanda Kulick
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Sandra Misale
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Rona Yaeger
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Pedram Razavi
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Helen H. Won
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ryan Ptashkin
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Eneda Toska
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - James Cownie
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | - Romel Somwar
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | - Sean Guzman
- 1Memorial Sloan Kettering Cancer Center, New York, NY
| | | | | | | | | | | | | | - Marc Ladanyi
- 1Memorial Sloan Kettering Cancer Center, New York, NY
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23
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Tan I, Stinchcombe TE, Ready NE, Crawford J, Datto MB, Nagy RJ, Lanman RB, Gu L, Clarke JM. Therapeutic outcomes in non-small cell lung cancer with BRAF mutations: a single institution, retrospective cohort study. Transl Lung Cancer Res 2019; 8:258-267. [PMID: 31367539 DOI: 10.21037/tlcr.2019.04.03] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Background Data describing therapeutic outcomes in patients with non-small cell lung cancers (NSCLC) with BRAF mutations remains limited. Methods We conducted a retrospective cohort study of 31 patients with metastatic NSCLC treated at Duke University Hospital who had been identified by next-generation sequencing methods to bear a BRAF mutation in their tumor in order to evaluate clinical response to immunotherapy and chemotherapy. Results Sixty-five percent of patients identified in this cohort were current or former smokers. Fourteen (45.2%) of patients had a BRAF V600E mutation and 17 (54.8%) had a non-V600E mutation. Median progression-free survival (PFS) in the 23 patients who received first-line chemotherapy was 6.4 months [95% confidence interval (CI), 2.3 to 13.0]. Overall survival (OS) in patients who received first-line chemotherapy showed a median survival of 18 months (95% CI, 7.4 to 28.6). OS comparing patients who had never received immunotherapy at any point was 18.4 months (95% CI, 4.1 to NE) compared to 19.0 months (95% CI, 9.9 to 28.6) in those who had received immunotherapy. We did not find a statistically significant difference in OS in patients with BRAF V600E, BRAF amplification, or non-V600E mutations. There was also no difference in OS in patients treated with targeted BRAF inhibitors compared to those who were not treated with targeted BRAF inhibitors. Conclusions We describe therapeutic outcomes for patients with metastatic NSCLC with BRAF mutations treated with either cytotoxic chemotherapy or immunotherapy. Although the sample size is small, the survival curves do not suggest improved clinical activity in this population when treated with immunotherapy.
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Affiliation(s)
- Irena Tan
- Department of Internal Medicine, Duke University Medical Center, Durham, NC, USA
| | - Thomas E Stinchcombe
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA.,Division of Medical Oncology, Duke University Medical Center, Durham, NC, USA
| | - Neal E Ready
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA.,Division of Medical Oncology, Duke University Medical Center, Durham, NC, USA
| | - Jeffrey Crawford
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA.,Division of Medical Oncology, Duke University Medical Center, Durham, NC, USA
| | - Michael B Datto
- Department of Pathology, Duke University Medical Center, Durham, NC, USA
| | - Rebecca J Nagy
- Guardant Health, Inc., Penobscot Dr, Redwood City, CA, USA
| | | | - Lin Gu
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA
| | - Jeffrey M Clarke
- Duke Cancer Institute, Duke University Medical Center, Durham, NC, USA.,Division of Medical Oncology, Duke University Medical Center, Durham, NC, USA
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24
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Formisano L, Lu Y, Servetto A, Hanker AB, Jansen VM, Bauer JA, Sudhan DR, Guerrero-Zotano AL, Croessmann S, Guo Y, Ericsson PG, Lee KM, Nixon MJ, Schwarz LJ, Sanders ME, Dugger TC, Cruz MR, Behdad A, Cristofanilli M, Bardia A, O'Shaughnessy J, Nagy RJ, Lanman RB, Solovieff N, He W, Miller M, Su F, Shyr Y, Mayer IA, Balko JM, Arteaga CL. Aberrant FGFR signaling mediates resistance to CDK4/6 inhibitors in ER+ breast cancer. Nat Commun 2019; 10:1373. [PMID: 30914635 PMCID: PMC6435685 DOI: 10.1038/s41467-019-09068-2] [Citation(s) in RCA: 230] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 02/14/2019] [Indexed: 12/30/2022] Open
Abstract
Using an ORF kinome screen in MCF-7 cells treated with the CDK4/6 inhibitor ribociclib plus fulvestrant, we identified FGFR1 as a mechanism of drug resistance. FGFR1-amplified/ER+ breast cancer cells and MCF-7 cells transduced with FGFR1 were resistant to fulvestrant ± ribociclib or palbociclib. This resistance was abrogated by treatment with the FGFR tyrosine kinase inhibitor (TKI) lucitanib. Addition of the FGFR TKI erdafitinib to palbociclib/fulvestrant induced complete responses of FGFR1-amplified/ER+ patient-derived-xenografts. Next generation sequencing of circulating tumor DNA (ctDNA) in 34 patients after progression on CDK4/6 inhibitors identified FGFR1/2 amplification or activating mutations in 14/34 (41%) post-progression specimens. Finally, ctDNA from patients enrolled in MONALEESA-2, the registration trial of ribociclib, showed that patients with FGFR1 amplification exhibited a shorter progression-free survival compared to patients with wild type FGFR1. Thus, we propose breast cancers with FGFR pathway alterations should be considered for trials using combinations of ER, CDK4/6 and FGFR antagonists. Era+ breast cancer patients often develop resistance to endocrine therapy. Here, the authors show that FGFR1 amplification is a resistance mechanism to CDK4/6 inhibitor and endocrine therapy and that combined treatment with FGFR, CDK4/6, and anti-estrogens is a potential therapeutic strategy in Era+ breast cancer tumors.
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Affiliation(s)
- Luigi Formisano
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | - Yao Lu
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | | | - Ariella B Hanker
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA.,UTSW Simmons Cancer Center, Dallas, TX, 75230, USA.,Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | - Valerie M Jansen
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | - Joshua A Bauer
- Departments of Biochemistry, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | - Dhivya R Sudhan
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA.,UTSW Simmons Cancer Center, Dallas, TX, 75230, USA
| | - Angel L Guerrero-Zotano
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | - Sarah Croessmann
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | - Yan Guo
- Vanderbilt Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, 37232-6307, TN, USA
| | - Paula Gonzalez Ericsson
- Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | - Kyung-Min Lee
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | - Mellissa J Nixon
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | - Luis J Schwarz
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | - Melinda E Sanders
- Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA.,Departments of Pathology, Microbiology & Immunology, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | - Teresa C Dugger
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | | | - Amir Behdad
- Robert H Lurie Comprehensive Cancer Center, Chicago, 60611, IL, USA
| | | | - Aditya Bardia
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, 02114, MA, USA
| | - Joyce O'Shaughnessy
- Baylor University Medical Center, Texas Oncology, , US Oncology, Dallas, 75246, TX, USA
| | | | | | - Nadia Solovieff
- Novartis Institutes for Biomedical Research, Cambridge, 02139, MA, USA
| | - Wei He
- Novartis Institutes for Biomedical Research, Cambridge, 02139, MA, USA
| | - Michelle Miller
- Novartis Pharmaceuticals Corporation, East Hanover, 07936, NJ, USA
| | - Fei Su
- Novartis Pharmaceuticals Corporation, East Hanover, 07936, NJ, USA
| | - Yu Shyr
- Vanderbilt Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, 37232-6307, TN, USA
| | - Ingrid A Mayer
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA.,Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | - Justin M Balko
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA
| | - Carlos L Arteaga
- Departments of Medicine, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA. .,UTSW Simmons Cancer Center, Dallas, TX, 75230, USA. .,Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, 37232-6307, TN, USA.
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25
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Siravegna G, Sartore-Bianchi A, Nagy RJ, Raghav K, Odegaard JI, Lanman RB, Trusolino L, Marsoni S, Siena S, Bardelli A. Plasma HER2 ( ERBB2) Copy Number Predicts Response to HER2-targeted Therapy in Metastatic Colorectal Cancer. Clin Cancer Res 2019; 25:3046-3053. [PMID: 30808777 DOI: 10.1158/1078-0432.ccr-18-3389] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 12/10/2018] [Accepted: 02/04/2019] [Indexed: 01/14/2023]
Abstract
PURPOSE ERBB2 (HER2) amplification is an emerging biomarker in colon cancer, conferring sensitivity to combination anti-HER2 therapy. Measurement of HER2 copy number is typically performed using surgical specimens, but cell-free circulating tumor DNA (ctDNA) analysis may be a noninvasive alternative. We determined the sensitivity of plasma copy number (pCN) for detecting ERBB2 amplifications and whether pCN correlated with tissue-detected copy number. We also assessed response to HER2-targeted therapy based on pCN and suggest a pCN threshold predictive of response. EXPERIMENTAL DESIGN Forty-eight pretreatment and progression plasma samples from 29 HER2-positive patients in the HERACLES A clinical trial were tested using the Guardant360 cfDNA assay. We correlated ERRB2 pCN with progression-free survival (PFS) and best objective response (BOR) and applied an adjustment method based on tumor DNA shedding using the maximum mutant allele fraction as a surrogate for tumor content to accurately determine the pCN threshold predictive of response. RESULTS Forty-seven of 48 samples had detectable ctDNA, and 46 of 47 samples were ERBB2-amplified on the basis of cfDNA [2.55-122 copies; 97.9% sensitivity (95% confidence interval, 87.2%-99.8%)]. An adjusted ERBB2 pCN of ≥25.82 copies correlated with BOR and PFS (P = 0.0347). CONCLUSIONS cfDNA is a viable alternative to tissue-based genotyping in the metastatic setting. The cfDNA platform utilized correctly identified 28 of 29 (96.6%) of pretreatment samples as ERBB2-amplified and predicted benefit from HER2-targeted therapy. In this study, an observed pCN of 2.4 and an adjusted pCN of 25.82 copies of ERBB2 are proposed to select patients who will benefit from HER2-targeted therapy.
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Affiliation(s)
- Giulia Siravegna
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy.,Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Andrea Sartore-Bianchi
- Niguarda Cancer Center, ASST Grande Ospedale Metropolitano Niguarda, Milano, Milan, Italy.,Department of Oncology and Haematology-Oncology, University of Milan, Milano, Milan, Italy
| | | | - Kanwal Raghav
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - Livio Trusolino
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy.,Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | - Silvia Marsoni
- FIRC Institute of Molecular Oncology (IFOM), Milano, Milan, Italy
| | - Salvatore Siena
- Niguarda Cancer Center, ASST Grande Ospedale Metropolitano Niguarda, Milano, Milan, Italy. .,Department of Oncology and Haematology-Oncology, University of Milan, Milano, Milan, Italy
| | - Alberto Bardelli
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy. .,Department of Oncology, University of Torino, Candiolo, Torino, Italy
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26
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Abraham J, Puhalla SL, Sikov WM, Montero AJ, Salkeni MA, Razaq WA, Beumer JH, Kiesel BF, Buyse ME, Adamson LM, Srinivasan A, Pogue-Geile KL, Allegra CJ, Nagy RJ, Jacobs SA. Abstract PD3-04: Analysis of ERBB2 (HER2) amplification by ctDNA in a phase Ib dose-escalation trial evaluating trastuzumab emtansine (T-DM1) with neratinib in women with metastatic disease with initially diagnosed HER2+ breast cancer: NSABP FB-10. Cancer Res 2019. [DOI: 10.1158/1538-7445.sabcs18-pd3-04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background:
In this phase Ib study, the activity of T-DM1 plus N was assessed in patients (pt) previously treated with trastuzumab, pertuzumab, and a taxane (H+P+T). Several mechanisms of resistance have been hypothesized in pts progressing following H+P+T, including acquired alterations in the ERBB (HER) family proteins, reactivation of bypass or parallel pathways, or selective elimination of HER2-overexpressing clones. Loss of HER2 amp has been shown to occur in 25-35% of pts with residual tumor after neoadjuvant therapy or in metastatic disease after initial therapy with chemotherapy and HER2-targeted agents. Data on concordance of HER2 status between tissue and blood is limited. In 7 pts with cfDNA HER2 amp, concomitant tissue was concordant in all 7 pairs and response to anti-HER2 therapy occurred in 6. In our study we have retrospectively analyzed cfDNA in blood samples obtained at study entry.
Methods:
Eligible pts had prior H+P+T as neoadjuvant therapy, or 1st-line metastatic disease, measurable disease, ECOG PS ≤2, and adequate hematologic, renal, and liver function. Pts with stable brain metastases were eligible. Treatment consisted of T-DM1 3.6 mg/kg iv q3wk and N 120, 160, 200, or 240 mg/d using a 3+3 dose-escalation design. HER2+ was determined at initial diagnosis; tissue confirmation at study entry (after H+P+T progression) was not required. Blood was collected in for pharmacokinetic analyses of N peak and trough, and for cfDNA using the Guardant360 assay, which is a 73-gene next-generation cfDNA-sequencing panel that detects SNVs, indels, CNAs, and fusions, utilizing Digital Sequencing and custom bioinformatics methods for error correction. The cut-off for HER2 amp was a copy number of ≥2.0 established by Guardant based on training-set data.
Results:
There were 27 H+P+T-resistant pts enrolled and all pts had a blood sample analyzed for HER2 amp. Eighteen pts were evaluable for efficacy at 6 wks and 11 pts at 12 wks. Dose-limiting toxicity occurred in 6 pts during cycle 1, 1 pt was withdrawn for non-compliance, and 2 pts were withdrawn for disease complications. The recommended phase II dose of N was determined to be 160 mg/d. Responses were seen at all dose-levels of N. Pharmacokinetic analyses did not show a clear relationship with either peak or trough and dose-level. Ten pts showed HER2 amp in blood and 17 were non-amp. Of 18 pts evaluable after 2 cycles (6 wks), 12 pts had an objective response (7 amp; 5 non-amp) and 5 had progressive disease (1 amp; 4 non-amp). At 12 wks, there were 3 CRs and 8 PRs (7 amp; 4 non-amp). All CRs were in amp pts and lasted 364, 510, and 859+ days.
Conclusions:
HER2 amp as determined by cfDNA was found in 10 of 27 pts. The deeper and more prolonged (>12 wk) responses occurred in 7 of 10 amp HER2 pts v 4 of 17 non-amp HER2 pts (p=0.04). In our ongoing phase II study of this regimen concomitant tissue and blood will be analyzed to better understand potential benefit or lack of benefit, with continued use of anti-HER2 therapy after progression on anti-HER2 therapies.
Support: Puma Biotechnology, Inc.
Citation Format: Abraham J, Puhalla SL, Sikov WM, Montero AJ, Salkeni MA, Razaq WA, Beumer JH, Kiesel BF, Buyse ME, Adamson LM, Srinivasan A, Pogue-Geile KL, Allegra CJ, Nagy RJ, Jacobs SA. Analysis of ERBB2 (HER2) amplification by ctDNA in a phase Ib dose-escalation trial evaluating trastuzumab emtansine (T-DM1) with neratinib in women with metastatic disease with initially diagnosed HER2+ breast cancer: NSABP FB-10 [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr PD3-04.
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Affiliation(s)
- J Abraham
- NSABP Foundation, Pittsburgh; Cleveland Clinic Foundaion, Cleveland; University of Pittsburgh Medical Center, Pittsburgh; Women and Infants Hospital of RI, Providence; West Virginia Univerity, Morgantown; Peggy and Charles Stephenson Oklahoma Ca Ctr, Oklahoma City; UPMC Hillman Cancer Center, Pittsburgh; IDDI, Inc., San Francisco; NSABP/NRG Oncology, Pittsburgh; University of Florida, Gainesville; Guardant Health, Redwood City; University of Pittsburgh Cancer Institute, Univ of Pgh School of Medicine, Pittsburgh
| | - SL Puhalla
- NSABP Foundation, Pittsburgh; Cleveland Clinic Foundaion, Cleveland; University of Pittsburgh Medical Center, Pittsburgh; Women and Infants Hospital of RI, Providence; West Virginia Univerity, Morgantown; Peggy and Charles Stephenson Oklahoma Ca Ctr, Oklahoma City; UPMC Hillman Cancer Center, Pittsburgh; IDDI, Inc., San Francisco; NSABP/NRG Oncology, Pittsburgh; University of Florida, Gainesville; Guardant Health, Redwood City; University of Pittsburgh Cancer Institute, Univ of Pgh School of Medicine, Pittsburgh
| | - WM Sikov
- NSABP Foundation, Pittsburgh; Cleveland Clinic Foundaion, Cleveland; University of Pittsburgh Medical Center, Pittsburgh; Women and Infants Hospital of RI, Providence; West Virginia Univerity, Morgantown; Peggy and Charles Stephenson Oklahoma Ca Ctr, Oklahoma City; UPMC Hillman Cancer Center, Pittsburgh; IDDI, Inc., San Francisco; NSABP/NRG Oncology, Pittsburgh; University of Florida, Gainesville; Guardant Health, Redwood City; University of Pittsburgh Cancer Institute, Univ of Pgh School of Medicine, Pittsburgh
| | - AJ Montero
- NSABP Foundation, Pittsburgh; Cleveland Clinic Foundaion, Cleveland; University of Pittsburgh Medical Center, Pittsburgh; Women and Infants Hospital of RI, Providence; West Virginia Univerity, Morgantown; Peggy and Charles Stephenson Oklahoma Ca Ctr, Oklahoma City; UPMC Hillman Cancer Center, Pittsburgh; IDDI, Inc., San Francisco; NSABP/NRG Oncology, Pittsburgh; University of Florida, Gainesville; Guardant Health, Redwood City; University of Pittsburgh Cancer Institute, Univ of Pgh School of Medicine, Pittsburgh
| | - MA Salkeni
- NSABP Foundation, Pittsburgh; Cleveland Clinic Foundaion, Cleveland; University of Pittsburgh Medical Center, Pittsburgh; Women and Infants Hospital of RI, Providence; West Virginia Univerity, Morgantown; Peggy and Charles Stephenson Oklahoma Ca Ctr, Oklahoma City; UPMC Hillman Cancer Center, Pittsburgh; IDDI, Inc., San Francisco; NSABP/NRG Oncology, Pittsburgh; University of Florida, Gainesville; Guardant Health, Redwood City; University of Pittsburgh Cancer Institute, Univ of Pgh School of Medicine, Pittsburgh
| | - WA Razaq
- NSABP Foundation, Pittsburgh; Cleveland Clinic Foundaion, Cleveland; University of Pittsburgh Medical Center, Pittsburgh; Women and Infants Hospital of RI, Providence; West Virginia Univerity, Morgantown; Peggy and Charles Stephenson Oklahoma Ca Ctr, Oklahoma City; UPMC Hillman Cancer Center, Pittsburgh; IDDI, Inc., San Francisco; NSABP/NRG Oncology, Pittsburgh; University of Florida, Gainesville; Guardant Health, Redwood City; University of Pittsburgh Cancer Institute, Univ of Pgh School of Medicine, Pittsburgh
| | - JH Beumer
- NSABP Foundation, Pittsburgh; Cleveland Clinic Foundaion, Cleveland; University of Pittsburgh Medical Center, Pittsburgh; Women and Infants Hospital of RI, Providence; West Virginia Univerity, Morgantown; Peggy and Charles Stephenson Oklahoma Ca Ctr, Oklahoma City; UPMC Hillman Cancer Center, Pittsburgh; IDDI, Inc., San Francisco; NSABP/NRG Oncology, Pittsburgh; University of Florida, Gainesville; Guardant Health, Redwood City; University of Pittsburgh Cancer Institute, Univ of Pgh School of Medicine, Pittsburgh
| | - BF Kiesel
- NSABP Foundation, Pittsburgh; Cleveland Clinic Foundaion, Cleveland; University of Pittsburgh Medical Center, Pittsburgh; Women and Infants Hospital of RI, Providence; West Virginia Univerity, Morgantown; Peggy and Charles Stephenson Oklahoma Ca Ctr, Oklahoma City; UPMC Hillman Cancer Center, Pittsburgh; IDDI, Inc., San Francisco; NSABP/NRG Oncology, Pittsburgh; University of Florida, Gainesville; Guardant Health, Redwood City; University of Pittsburgh Cancer Institute, Univ of Pgh School of Medicine, Pittsburgh
| | - ME Buyse
- NSABP Foundation, Pittsburgh; Cleveland Clinic Foundaion, Cleveland; University of Pittsburgh Medical Center, Pittsburgh; Women and Infants Hospital of RI, Providence; West Virginia Univerity, Morgantown; Peggy and Charles Stephenson Oklahoma Ca Ctr, Oklahoma City; UPMC Hillman Cancer Center, Pittsburgh; IDDI, Inc., San Francisco; NSABP/NRG Oncology, Pittsburgh; University of Florida, Gainesville; Guardant Health, Redwood City; University of Pittsburgh Cancer Institute, Univ of Pgh School of Medicine, Pittsburgh
| | - LM Adamson
- NSABP Foundation, Pittsburgh; Cleveland Clinic Foundaion, Cleveland; University of Pittsburgh Medical Center, Pittsburgh; Women and Infants Hospital of RI, Providence; West Virginia Univerity, Morgantown; Peggy and Charles Stephenson Oklahoma Ca Ctr, Oklahoma City; UPMC Hillman Cancer Center, Pittsburgh; IDDI, Inc., San Francisco; NSABP/NRG Oncology, Pittsburgh; University of Florida, Gainesville; Guardant Health, Redwood City; University of Pittsburgh Cancer Institute, Univ of Pgh School of Medicine, Pittsburgh
| | - A Srinivasan
- NSABP Foundation, Pittsburgh; Cleveland Clinic Foundaion, Cleveland; University of Pittsburgh Medical Center, Pittsburgh; Women and Infants Hospital of RI, Providence; West Virginia Univerity, Morgantown; Peggy and Charles Stephenson Oklahoma Ca Ctr, Oklahoma City; UPMC Hillman Cancer Center, Pittsburgh; IDDI, Inc., San Francisco; NSABP/NRG Oncology, Pittsburgh; University of Florida, Gainesville; Guardant Health, Redwood City; University of Pittsburgh Cancer Institute, Univ of Pgh School of Medicine, Pittsburgh
| | - KL Pogue-Geile
- NSABP Foundation, Pittsburgh; Cleveland Clinic Foundaion, Cleveland; University of Pittsburgh Medical Center, Pittsburgh; Women and Infants Hospital of RI, Providence; West Virginia Univerity, Morgantown; Peggy and Charles Stephenson Oklahoma Ca Ctr, Oklahoma City; UPMC Hillman Cancer Center, Pittsburgh; IDDI, Inc., San Francisco; NSABP/NRG Oncology, Pittsburgh; University of Florida, Gainesville; Guardant Health, Redwood City; University of Pittsburgh Cancer Institute, Univ of Pgh School of Medicine, Pittsburgh
| | - CJ Allegra
- NSABP Foundation, Pittsburgh; Cleveland Clinic Foundaion, Cleveland; University of Pittsburgh Medical Center, Pittsburgh; Women and Infants Hospital of RI, Providence; West Virginia Univerity, Morgantown; Peggy and Charles Stephenson Oklahoma Ca Ctr, Oklahoma City; UPMC Hillman Cancer Center, Pittsburgh; IDDI, Inc., San Francisco; NSABP/NRG Oncology, Pittsburgh; University of Florida, Gainesville; Guardant Health, Redwood City; University of Pittsburgh Cancer Institute, Univ of Pgh School of Medicine, Pittsburgh
| | - RJ Nagy
- NSABP Foundation, Pittsburgh; Cleveland Clinic Foundaion, Cleveland; University of Pittsburgh Medical Center, Pittsburgh; Women and Infants Hospital of RI, Providence; West Virginia Univerity, Morgantown; Peggy and Charles Stephenson Oklahoma Ca Ctr, Oklahoma City; UPMC Hillman Cancer Center, Pittsburgh; IDDI, Inc., San Francisco; NSABP/NRG Oncology, Pittsburgh; University of Florida, Gainesville; Guardant Health, Redwood City; University of Pittsburgh Cancer Institute, Univ of Pgh School of Medicine, Pittsburgh
| | - SA Jacobs
- NSABP Foundation, Pittsburgh; Cleveland Clinic Foundaion, Cleveland; University of Pittsburgh Medical Center, Pittsburgh; Women and Infants Hospital of RI, Providence; West Virginia Univerity, Morgantown; Peggy and Charles Stephenson Oklahoma Ca Ctr, Oklahoma City; UPMC Hillman Cancer Center, Pittsburgh; IDDI, Inc., San Francisco; NSABP/NRG Oncology, Pittsburgh; University of Florida, Gainesville; Guardant Health, Redwood City; University of Pittsburgh Cancer Institute, Univ of Pgh School of Medicine, Pittsburgh
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Raghav KPS, Yaeger R, Loree JM, Dasari A, Morris VK, Kee BK, Raymond VM, Nagy RJ, Lanman RB, Strickler JH, Corcoran RB, Overman MJ, Kopetz S. Comprehensive landscape of gene amplifications (amps) in tissue and circulating tumor DNA (ctDNA) in metastatic colorectal cancer (mCRC). J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.4_suppl.604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
604 Background: Amps, as oncogenic and resistance drivers, have therapeutic implications, but unlike mutations, have been sparsely described in mCRC. Functional account is piecemeal due to vague definitions, limited data on co-occurring alterations and use of primary tissue samples nonrepresentative of tumor heterogeneity. Our aim was to define the amp landscape in mCRC using tissue and ctDNA sequencing. Methods: We performed systematic analyses of copy-number variation in 2 cohorts of mCRC patients (pts) [tissue (TC) (N = 1,134) and ctDNA (BC) (N = 3,218)] who had high sensitivity targeted sequencing with MSK-IMPACT (341-468 genes) or Guardant Health (70-73 genes) panel, respectively. For BC, plasma copy number was adjusted (ApCN) to account for variable tumor DNA shedding using max allele frequency and high amp (HAmp) was defined as > 4 copies (similar to predefined tissue cutoff). Results: 166 (15%) and 405 (13%) pts in TC and BC harbored amp in at least one of 18 genes assessed by both panels (Table). Amp prevalence for individual gene was similar in both cohorts ( r = 0.9; P < .01) with RTK amps ( EGFR, ERBB2, MET, FGFR1/2, PDGFRA) seen in 8% pts. Key RTK amps were enriched in RAS/BRAF wild type (RB WT) compared to mutant (RB MUT) (OR 3.5; P < .01) pts in both cohorts, in contrast to low prevalence RTK and non-RTK amps. Median ApCN was higher for RTKs in RB WT vs MUT cases ( ERBB2: 12 vs 5; P = .02). Using validated EGFRab exposure (EGFRi) ctDNA signature, we found that EGFRi pts had higher prevalence of EGFR, MET, BRAF, KRAS, PIK3CA and FGFR1 amps compared to EGFRab naïve pts. Conclusions: While individually uncommon, amps occur across key oncogenic pathways in mCRC and after adjusting for ctDNA shedding, are seen at similar prevalence in tissue and plasma. Amps in RTKs are seen in 10-12% of RB WT tumors, suggesting clinically relevant roles as oncogenic effectors and targets. After EGFRi, a number of amps emerge, including PIK3CA and FGFR1 amps, not previously implicated in acquired resistance. [Table: see text]
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Affiliation(s)
| | - Rona Yaeger
- Memorial Sloan Kettering Cancer Center, New York, NY
| | | | - Arvind Dasari
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Van K. Morris
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Bryan K. Kee
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | | | | | | | | | - Scott Kopetz
- The University of Texas MD Anderson Cancer Center, Houston, TX
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28
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Mody K, Kasi PM, Surapaneni PK, Bekaii-Saab TS, Ramanathan RK, Ahn DH, Mahipal A, Starr JS, Ritter A, McMillan J, Wylie N, Roberts A, Nagy RJ, Borad MJ. Landscape of circulating tumor DNA and tissue-based profiling in advanced cholangiocarcinoma. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.4_suppl.291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
291 Background: Cholangiocarcinoma (CCA) has limited treatment options. Genomic analyses have led to development of targeted therapies now in clinical trials, and may enable discovery of new treatment options. However, biopsy often yields limited tissue, thus hampering tissue-based profiling opportunities. Comparative data regarding circulating tumor DNA (ctDNA) analysis and tissue based profiling in CCA are limited. Methods: We performed ctDNA NGS analysis along with tissue based profiling in pts with advanced CCA (January 2015- February 2018). ctDNA analysis was performed using Guardant 360 (Guardant Health, CA) which detects single nucleotide variants, amplifications, fusions, and specific insertion/deletion mutations in up to 73 different genes and the majority of tissue based profiling using Foundation One. The mutant allele fraction (MAF) for detected alterations was calculated relative to wild type in ctDNA. Therapeutic relevance was defined as alterations within OncoKB levels 1-3B and R1. The study was conducted in accordance with Mayo Clinic IRB requirements. Results: Among 124 pts and 139 total samples, ctDNA NGS revealed at least one genomic alteration (excluding variants of uncertain significance and synonymous mutations) in 89% of pts. Median number of alterations per pt was 3 [range, 1-15], with a median MAF of 0.42% (range, 0.1% - 94.2%). The total number of unique alterations was 321. The most commonly altered genes: TP53 (31%), KRAS (11%), FGFR2 (7%), APC and PIK3CA (each 5%) and ARID1A (3%). Amplifications were noted in 14 genes: BRAF, CCND1, CCND2, CCNE1, CDK4, CDK6, EGFR, ERBB2, FGFR1, FGFR2, MET, MYC, PDGFRA, and PIK3CA. Tissue-based profiling was available in 57 (46%) pts, with a median of 63 days between liquid and tissue biopsy. IDH1, FGFR2, TP53 and KRAS were most common gene mutations found in pts who had both liquid and tissue biopsy done. (Comparative results to be shown). Conclusions: ctDNA plasma profiling of pts with advanced CCA is a feasible alternative method to gather comprehensive genomic data. Further larger cohort studies comparing landscape of alterations seen on ctDNA versus tissue-based assays are needed.
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Mody K, Kasi PM, Surapaneni PK, Borad MJ, Ahn DH, Mahipal A, Starr JS, Ritter A, McMillan J, Wylie N, Roberts A, Nagy RJ, Bekaii-Saab TS. Landscape of circulating tumor DNA profiling of advanced pancreatic cancer (PDAC). J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.4_suppl.289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
289 Background: PDAC has limited treatment options. Genomic analyses have led to development of targeted therapies now in several clinical trials, and may enable the discovery of new treatment options. However, biopsy often yields limited tissue, thus hampering tissue-based profiling opportunities. Data regarding circulating tumor DNA (ctDNA) profiling in PDAC during real time clinical practice is limited. Methods: We performed ctDNA NGS analysis in pts with advanced PDAC (December 2014–August 2018). ctDNA analysis was performed using Guardant 360 (Guardant Health, CA), which detects single nucleotide variants, amplifications, fusions, and specific insertion/deletion mutations in up to 73 different genes. The mutant allele fraction (MAF) for detected alterations was calculated relative to wild type in ctDNA. Therapeutic relevance (TR) was defined as possible treatments within OncoKB levels 1-3B and R1. The study was conducted in accordance with Mayo Clinic Institutional Review Board requirements. Results: Among 171 pts and 206 total samples, ctDNA NGS revealed at least one genomic alteration in 150 pts (88%). Median number of alterations per patient was 3 [range, 1-15]. The total number of unique alterations was 450 with the most commonly altered genes being: TP53 (181 alterations, 40%), followed by KRAS (118 alterations, 26%), CDKN2A (23 alterations, 5%), SMAD4 (15 alterations, 3%), EGFR (11 alterations, 2.4%), PIK3CA (9 alterations, 2%), GNAS (8 alterations, 1.5%). Amplifications were noted in 16 genes, including BRAF, CCND2, CCNE1, CDK4, CDK6, EGFR, ERBB2, FGFR1, FGFR2, KIT, KRAS, MET, MYC, PDGFRA, PIK3CA and RAF1. Therapeutically relevant alterations were seen in 95 pts of the 150 pts (63%). Tissue based profiling (Results to be shown) was done in 56 (33%) pts of total 171 pts with a median of 130 days between ctDNA and tissue biopsy. KRAS and TP53 were the most common gene mutations found in patients with both liquid and tissue biopsy results. Conclusions: ctDNA plasma profiling of pts with advanced PDAC is a feasible alternative method to gather comprehensive genomic data.
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Price KS, Kiedrowski LA, De Zarraga FI, Cusnir M, Lanman RB, Nagy RJ. The spectrum of activating EGFR mutations from cell-free DNA (cfDNA) in large pancreatic cancer cohort. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.4_suppl.237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
237 Background: Metastatic pancreatic cancer (mPC) is one of the deadliest cancers with a < 10% 5-year survival rate. Poor prognosis is well established with lack of response to or rapid progression on existing chemotherapy options. Targeted therapies, like EGFR-TKIs, have been shown to increase survival in other solid tumors like NSCLC with certain oncogenic drivers. Although treatment with the EGFR-TKI erlotinib, in combination with gemcitabine, is available for patients (pts) with mPC, the survival benefit is small in unselected patients. A better understanding of the spectrum of EGFR mutations in mPC may lead to improved therapy selection. Methods: We retrospectively reviewed genomic results from 2,938 consecutive mPC pt samples sent for ctDNA NGS analysis between 7/2014 - 9/2018 (Guardant Health, Inc.). All reported EGFR mutations were reviewed and activating mutations were determined based on literature review. Results: 19 EGFR activating mutations were identified in 16 unique pts (0.66% of total mPC pts with alterations detected). 3 mutations were identified in the extracellular domain and 16 mutations in the tyrosine kinase domain (3 in exon 18, 3 in exon 19, 6 in exon 20, 4 in exon 21). Alterations in exon 20 included 5 T790M mutations; two of these were reported at allelic frequencies suggestive of germline origin. Analysis of co-mutations revealed 7 pts with EGFR mutations that appeared subclonal relative to other potential drivers (4 KRAS, 2 ERBB2, 1 GNAS). The median number of alterations per sample was 4 (range 2-170) with the latter pt exhibiting a hypermutator phenotype. Multiple pts had more than one activating EGFR alteration including one who was found to have 4 EGFR sequence alterations (S768I, L861Q, T790M, p.Val769_Asp770insMet) plus EGFR amplification (plasma copy number 66.8). We will collect and report clinical details to characterize the treatment context for these pts. Conclusions: Activating EGFR mutations in mPC are rare but may present an opportunity for targeted therapy in this population. Further exploration is warranted to better understand the oncogenic activity of less common, subclonal, or co-occurring EGFR mutations and their sensitivity to EGFR-TKIs in mPC.
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31
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Sanchez-Vega F, Hechtman JF, Castel P, Ku GY, Tuvy Y, Won H, Fong CJ, Bouvier N, Nanjangud GJ, Soong J, Vakiani E, Schattner M, Kelsen DP, Lefkowitz RA, Brown K, Lacouture ME, Capanu M, Mattar M, Qeriqi B, Cecchi F, Tian Y, Hembrough T, Nagy RJ, Lanman RB, Larson SM, Pandit-Taskar N, Schöder H, Iacobuzio-Donahue CA, Ilson DH, Weber WA, Berger MF, de Stanchina E, Taylor BS, Lewis JS, Solit DB, Carrasquillo JA, Scaltriti M, Schultz N, Janjigian YY. EGFR and MET Amplifications Determine Response to HER2 Inhibition in ERBB2-Amplified Esophagogastric Cancer. Cancer Discov 2019; 9:199-209. [PMID: 30463996 PMCID: PMC6368868 DOI: 10.1158/2159-8290.cd-18-0598] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 10/05/2018] [Accepted: 11/15/2018] [Indexed: 01/10/2023]
Abstract
The anti-HER2 antibody trastuzumab is standard care for advanced esophagogastric (EG) cancer with ERBB2 (HER2) amplification or overexpression, but intrinsic and acquired resistance are common. We conducted a phase II study of afatinib, an irreversible pan-HER kinase inhibitor, in trastuzumab-resistant EG cancer. We analyzed pretreatment tumor biopsies and, in select cases, performed comprehensive characterization of postmortem metastatic specimens following acquisition of drug resistance. Afatinib response was associated with coamplification of EGFR and ERBB2. Heterogeneous 89Zr-trastuzumab PET uptake was associated with genomic heterogeneity and mixed clinical response to afatinib. Resistance to afatinib was associated with selection for tumor cells lacking EGFR amplification or with acquisition of MET amplification, which could be detected in plasma cell-free DNA. The combination of afatinib and a MET inhibitor induced complete tumor regression in ERBB2 and MET coamplified patient-derived xenograft models established from a metastatic lesion progressing on afatinib. Collectively, differential intrapatient and interpatient expression of HER2, EGFR, and MET may determine clinical response to HER kinase inhibitors in ERBB2-amplified EG cancer. SIGNIFICANCE: Analysis of patients with ERBB2-amplified, trastuzumab-resistant EG cancer who were treated with the HER kinase inhibitor afatinib revealed that sensitivity and resistance to therapy were associated with EGFR/ERBB2 coamplification and MET amplification, respectively. HER2-directed PET imaging and cell-free DNA sequencing could help guide strategies to overcome the emergence of resistant clones.See related commentary by Klempner and Catenacci, p. 166.This article is highlighted in the In This Issue feature, p. 151.
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Affiliation(s)
- Francisco Sanchez-Vega
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jaclyn F Hechtman
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Pau Castel
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Geoffrey Y Ku
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Yaelle Tuvy
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Helen Won
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christopher J Fong
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nancy Bouvier
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Gouri J Nanjangud
- Molecular Cytogenetics Core Facility, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Joanne Soong
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Efsevia Vakiani
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mark Schattner
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - David P Kelsen
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Robert A Lefkowitz
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Karen Brown
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Mario E Lacouture
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Marinela Capanu
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marissa Mattar
- Antitumor Assessment Core Facility, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Besnik Qeriqi
- Antitumor Assessment Core Facility, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | | | | | | | | | - Steven M Larson
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Neeta Pandit-Taskar
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Heiko Schöder
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - David H Ilson
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Wolfgang A Weber
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elisa de Stanchina
- Antitumor Assessment Core Facility, Molecular Pharmacology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Barry S Taylor
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jason S Lewis
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - David B Solit
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York
| | - Jorge A Carrasquillo
- Department of Radiology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maurizio Scaltriti
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nikolaus Schultz
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yelena Y Janjigian
- Department of Medicine, Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, New York.
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32
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Sonpavde G, Agarwal N, Pond GR, Nagy RJ, Nussenzveig RH, Hahn AW, Sartor O, Gourdin TS, Nandagopal L, Ledet EM, Naik G, Armstrong AJ, Wang J, Bilen MA, Gupta S, Grivas P, Pal SK, Lanman RB, Talasaz A, Lilly MB. Circulating tumor DNA alterations in patients with metastatic castration-resistant prostate cancer. Cancer 2019; 125:1459-1469. [PMID: 30620391 DOI: 10.1002/cncr.31959] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/13/2018] [Accepted: 11/19/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Because cell-free DNA (cfDNA) analysis facilitates the noninvasive genomic profiling of metastatic castration-resistant prostate cancer (mCRPC), the authors evaluated the association between cfDNA alterations and outcomes and evolution with therapy. METHODS Patients with mCRPC underwent cfDNA genomic profiling using Guardant360, which examines major cancer-associated genes. Clinical factors, therapy information, failure-free survival, and overall survival (OS) were obtained for select patients. The association between genomic alterations and outcomes was investigated. RESULTS Of 514 men with mCRPC, 482 (94%) had ≥1 circulating tumor DNA (ctDNA) alteration. The most common recurrent somatic mutations were in TP53 (36%), androgen receptor (AR) (22%), adenomatous polyposis coli (APC) (10%), neurofibromin 1 (NF1) (9%), epidermal growth factor receptor (EGFR), catenin beta-1 (CTNNB1), and AT-rich interactive domain-containing protein 1A (ARID1A) (6% each); and BRCA1, BRCA2, and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) (5% each) The most common genes with increased copy numbers were AR (30%), MYC (20%), and BRAF (18%). Clinical outcomes were available for 163 patients, 46 of whom (28.8%) were untreated for mCRPC. A higher number of ctDNA alterations, AR alterations, and amplifications of MYC and BRAF were associated with worse failure-free survival and/or OS. On multivariable analysis, MYC amplification remained significantly associated with OS. Prior therapy and serial profiling demonstrated the evolution of alterations in AR and other genes. CONCLUSIONS ctDNA frequently was detected in this large cohort of "real-world" patients with mCRPC, and the alterations appeared to be similar to previously reported tumor tissue alterations. A higher number of alterations, and AR and MYC alterations, appear to compromise clinical outcomes, suggesting a role for immune checkpoint inhibitors and novel AR and BET inhibitors in selected patients.
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Affiliation(s)
| | - Neeraj Agarwal
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | | | | | | | - Andrew W Hahn
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | | | | | | | | | - Gurudatta Naik
- University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, Alabama
| | | | - Jue Wang
- University of Arizona Cancer Center at Dignity Health St. Joseph's Hospital and Medical Center, Phoenix, Arizona
| | | | | | | | - Sumanta K Pal
- City of Hope Comprehensive Cancer Center, Duarte, California
| | | | | | - Michael B Lilly
- Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina
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Piotrowska Z, Isozaki H, Lennerz JK, Gainor JF, Lennes IT, Zhu VW, Marcoux N, Banwait MK, Digumarthy SR, Su W, Yoda S, Riley AK, Nangia V, Lin JJ, Nagy RJ, Lanman RB, Dias-Santagata D, Mino-Kenudson M, Iafrate AJ, Heist RS, Shaw AT, Evans EK, Clifford C, Ou SHI, Wolf B, Hata AN, Sequist LV. Landscape of Acquired Resistance to Osimertinib in EGFR-Mutant NSCLC and Clinical Validation of Combined EGFR and RET Inhibition with Osimertinib and BLU-667 for Acquired RET Fusion. Cancer Discov 2018; 8:1529-1539. [PMID: 30257958 PMCID: PMC6279502 DOI: 10.1158/2159-8290.cd-18-1022] [Citation(s) in RCA: 307] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/21/2018] [Accepted: 09/24/2018] [Indexed: 12/12/2022]
Abstract
We present a cohort of 41 patients with osimertinib resistance biopsies, including 2 with an acquired CCDC6-RET fusion. Although RET fusions have been identified in resistant EGFR-mutant non-small cell lung cancer (NSCLC), their role in acquired resistance to EGFR inhibitors is not well described. To assess the biological implications of RET fusions in an EGFR-mutant cancer, we expressed CCDC6-RET in PC9 (EGFR del19) and MGH134 (EGFR L858R/T790M) cells and found that CCDC6-RET was sufficient to confer resistance to EGFR tyrosine kinase inhibitors (TKI). The selective RET inhibitors BLU-667 and cabozantinib resensitized CCDC6-RET-expressing cells to EGFR inhibition. Finally, we treated 2 patients with EGFR-mutant NSCLC and RET-mediated resistance with osimertinib and BLU-667. The combination was well tolerated and led to rapid radiographic response in both patients. This study provides proof of concept that RET fusions can mediate acquired resistance to EGFR TKIs and that combined EGFR and RET inhibition with osimertinib/BLU-667 may be a well-tolerated and effective treatment strategy for such patients. SIGNIFICANCE: The role of RET fusions in resistant EGFR-mutant cancers is unknown. We report that RET fusions mediate resistance to EGFR inhibitors and demonstrate that this bypass track can be effectively targeted with a selective RET inhibitor (BLU-667) in the clinic.This article is highlighted in the In This Issue feature, p. 1494.
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Affiliation(s)
- Zofia Piotrowska
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Hideko Isozaki
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Jochen K Lennerz
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Justin F Gainor
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Inga T Lennes
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Viola W Zhu
- Chao Family Comprehensive Cancer Center, University of California Irvine School of Medicine, Orange, California
| | - Nicolas Marcoux
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | | | - Subba R Digumarthy
- Department of Radiology, Massachusetts General Hospital, Boston, Massachusetts
| | - Wenjia Su
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Satoshi Yoda
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Amanda K Riley
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Varuna Nangia
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Jessica J Lin
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | | | | | - Dora Dias-Santagata
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Mari Mino-Kenudson
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - A John Iafrate
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts
| | - Rebecca S Heist
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Alice T Shaw
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | | | | | - Sai-Hong I Ou
- Chao Family Comprehensive Cancer Center, University of California Irvine School of Medicine, Orange, California
| | - Beni Wolf
- Blueprint Medicines, Cambridge, Massachusetts
| | - Aaron N Hata
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.
| | - Lecia V Sequist
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts.
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Bahcall M, Awad MM, Sholl LM, Wilson FH, Xu M, Wang S, Palakurthi S, Choi J, Ivanova EV, Leonardi GC, Ulrich BC, Paweletz CP, Kirschmeier PT, Watanabe M, Baba H, Nishino M, Nagy RJ, Lanman RB, Capelletti M, Chambers ES, Redig AJ, VanderLaan PA, Costa DB, Imamura Y, Jänne PA. Amplification of Wild-type KRAS Imparts Resistance to Crizotinib in MET Exon 14 Mutant Non-Small Cell Lung Cancer. Clin Cancer Res 2018; 24:5963-5976. [PMID: 30072474 PMCID: PMC6279568 DOI: 10.1158/1078-0432.ccr-18-0876] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 06/19/2018] [Accepted: 07/23/2018] [Indexed: 01/06/2023]
Abstract
PURPOSE MET inhibitors can be effective therapies in patients with MET exon 14 (METex14) mutant non-small cell lung cancer (NSCLC). However, long-term efficacy is limited by the development of drug resistance. In this study, we characterize acquired amplification of wild-type (WT) KRAS as a molecular mechanism behind crizotinib resistance in three cases of METex14-mutant NSCLC and propose a combination therapy to target it. EXPERIMENTAL DESIGN The patient-derived cell line and xenograft (PDX) DFCI358 were established from a crizotinib-resistant METex14-mutant patient tumor with massive focal amplification of WT KRAS. To characterize the mechanism of KRAS-mediated resistance, molecular signaling was analyzed in the parental cell line and its KRAS siRNA-transfected derivative. Sensitivity of the cell line to ligand stimulation was assessed and KRAS-dependent expression of EGFR ligands was quantified. Drug combinations were screened for efficacy in vivo and in vitro using viability and apoptotic assays. RESULTS KRAS amplification is a recurrent genetic event in crizotinib-resistant METex14-mutant NSCLC. The key characteristics of this genetic signature include uncoupling MET from downstream effectors, relative insensitivity to dual MET/MEK inhibition due to compensatory induction of PI3K signaling, KRAS-induced expression of EGFR ligands and hypersensitivity to ligand-dependent and independent activation, and reliance on PI3K signaling upon MET inhibition. CONCLUSIONS Using patient-derived cell line and xenografts, we characterize the mechanism of crizotinib resistance mediated by KRAS amplification in METex14-mutant NSCLC and demonstrate the superior efficacy of the dual MET/PI3K inhibition as a therapeutic strategy addressing this resistance mechanism.
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Affiliation(s)
- Magda Bahcall
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Mark M Awad
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Frederick H Wilson
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Man Xu
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Stephen Wang
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Sangeetha Palakurthi
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Jihyun Choi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Elena V Ivanova
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Giulia C Leonardi
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Bryan C Ulrich
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Cloud P Paweletz
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Paul T Kirschmeier
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Masayuki Watanabe
- Department of Gastroenterological Surgery, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Mizuki Nishino
- Department of Radiology, Brigham And Women's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | | | | | - Marzia Capelletti
- Center for Hematologic Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Emily S Chambers
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Amanda J Redig
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Paul A VanderLaan
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Daniel B Costa
- Thoracic Oncology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
- Hematology/Oncology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts
| | - Yu Imamura
- Department of Gastroenterological Surgery, The Cancer Institute Hospital of Japanese Foundation for Cancer Research, Tokyo, Japan
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Pasi A Jänne
- Lowe Center for Thoracic Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts.
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, Massachusetts
- Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
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Jacobs MT, Mohindra NA, Shantzer L, Chen IL, Phull H, Mitchell W, Raymond VM, Banks KC, Nagy RJ, Lanman RB, Christensen J, Patel JD, Clarke J, Patel SP. Use of Low-Frequency Driver Mutations Detected by Cell-Free Circulating Tumor DNA to Guide Targeted Therapy in Non–Small-Cell Lung Cancer: A Multicenter Case Series. JCO Precis Oncol 2018; 2:1-10. [DOI: 10.1200/po.17.00318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Purpose To evaluate the clinical outcome of patients with non–small-cell lung cancer treated by targeting low variant allelic frequency (VAF) driver mutations identified through cell-free DNA (cfDNA) next-generation sequencing (NGS). Detection of driver mutations in cancer is critically important in the age of targeted therapy, where both tumor-based as well as cfDNA sequencing methods have been used for therapeutic decision making. We hypothesized that VAF should not be predictive of response and that low VAF alterations detected by cfDNA NGS can respond to targeted therapy. Patients and Methods A multicenter retrospective case review was performed to identify patients with non–small-cell lung cancer who received targeted molecular therapy on the basis of findings of low VAF alterations in cfDNA NGS. Mutations at low VAF were defined as < 0.2% mutated cfDNA molecules in a background of wild-type cfDNA. Results One hundred seventy-two patients underwent cfDNA NGS testing. Of the 172 patients, 12 were identified as having low VAF driver alterations and were considered for targeted therapy. The median progression-free survival (PFS) for all patients was 52 weeks (range, 17 to 88 weeks). For patients with EGFR exon 19 deletion (n = 7), the median PFS was 52 weeks (range, 17 to 60.5 weeks). For patients with EML4-ALK fusions (n = 3), the median PFS was 60 weeks (range, 18 to 88 weeks). The median overall survival for all patients after diagnosis was 57.6 weeks. Conclusion Targeted treatment response for driver mutations detected by cfDNA may be independent of VAF, even in relation to other higher VAF aberrations in plasma, and directly dependent on the underlying disease biology and ability to treat the patient with appropriate targeted therapy.
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Affiliation(s)
- Miriam T. Jacobs
- Miriam T. Jacobs, Washington University School of Medicine in St Louis, St Louis, MO; Nisha A. Mohindra, Northwestern University; Jyoti D. Patel, University of Chicago School of Medicine, Chicago, IL; Lindsey Shantzer and Jeffrey Clarke, Duke University Medical Center, Durham, NC; Ingrid L. Chen, Stony Brook University School of Medicine, Stony Brook, NY; Hardeep Phull, William Mitchell, and Sandip P. Patel, University of California, San Diego, La Jolla; Victoria M. Raymond, Kimberly C. Banks, Rebecca J
| | - Nisha A. Mohindra
- Miriam T. Jacobs, Washington University School of Medicine in St Louis, St Louis, MO; Nisha A. Mohindra, Northwestern University; Jyoti D. Patel, University of Chicago School of Medicine, Chicago, IL; Lindsey Shantzer and Jeffrey Clarke, Duke University Medical Center, Durham, NC; Ingrid L. Chen, Stony Brook University School of Medicine, Stony Brook, NY; Hardeep Phull, William Mitchell, and Sandip P. Patel, University of California, San Diego, La Jolla; Victoria M. Raymond, Kimberly C. Banks, Rebecca J
| | - Lindsey Shantzer
- Miriam T. Jacobs, Washington University School of Medicine in St Louis, St Louis, MO; Nisha A. Mohindra, Northwestern University; Jyoti D. Patel, University of Chicago School of Medicine, Chicago, IL; Lindsey Shantzer and Jeffrey Clarke, Duke University Medical Center, Durham, NC; Ingrid L. Chen, Stony Brook University School of Medicine, Stony Brook, NY; Hardeep Phull, William Mitchell, and Sandip P. Patel, University of California, San Diego, La Jolla; Victoria M. Raymond, Kimberly C. Banks, Rebecca J
| | - Ingrid L. Chen
- Miriam T. Jacobs, Washington University School of Medicine in St Louis, St Louis, MO; Nisha A. Mohindra, Northwestern University; Jyoti D. Patel, University of Chicago School of Medicine, Chicago, IL; Lindsey Shantzer and Jeffrey Clarke, Duke University Medical Center, Durham, NC; Ingrid L. Chen, Stony Brook University School of Medicine, Stony Brook, NY; Hardeep Phull, William Mitchell, and Sandip P. Patel, University of California, San Diego, La Jolla; Victoria M. Raymond, Kimberly C. Banks, Rebecca J
| | - Hardeep Phull
- Miriam T. Jacobs, Washington University School of Medicine in St Louis, St Louis, MO; Nisha A. Mohindra, Northwestern University; Jyoti D. Patel, University of Chicago School of Medicine, Chicago, IL; Lindsey Shantzer and Jeffrey Clarke, Duke University Medical Center, Durham, NC; Ingrid L. Chen, Stony Brook University School of Medicine, Stony Brook, NY; Hardeep Phull, William Mitchell, and Sandip P. Patel, University of California, San Diego, La Jolla; Victoria M. Raymond, Kimberly C. Banks, Rebecca J
| | - William Mitchell
- Miriam T. Jacobs, Washington University School of Medicine in St Louis, St Louis, MO; Nisha A. Mohindra, Northwestern University; Jyoti D. Patel, University of Chicago School of Medicine, Chicago, IL; Lindsey Shantzer and Jeffrey Clarke, Duke University Medical Center, Durham, NC; Ingrid L. Chen, Stony Brook University School of Medicine, Stony Brook, NY; Hardeep Phull, William Mitchell, and Sandip P. Patel, University of California, San Diego, La Jolla; Victoria M. Raymond, Kimberly C. Banks, Rebecca J
| | - Victoria M. Raymond
- Miriam T. Jacobs, Washington University School of Medicine in St Louis, St Louis, MO; Nisha A. Mohindra, Northwestern University; Jyoti D. Patel, University of Chicago School of Medicine, Chicago, IL; Lindsey Shantzer and Jeffrey Clarke, Duke University Medical Center, Durham, NC; Ingrid L. Chen, Stony Brook University School of Medicine, Stony Brook, NY; Hardeep Phull, William Mitchell, and Sandip P. Patel, University of California, San Diego, La Jolla; Victoria M. Raymond, Kimberly C. Banks, Rebecca J
| | - Kimberly C. Banks
- Miriam T. Jacobs, Washington University School of Medicine in St Louis, St Louis, MO; Nisha A. Mohindra, Northwestern University; Jyoti D. Patel, University of Chicago School of Medicine, Chicago, IL; Lindsey Shantzer and Jeffrey Clarke, Duke University Medical Center, Durham, NC; Ingrid L. Chen, Stony Brook University School of Medicine, Stony Brook, NY; Hardeep Phull, William Mitchell, and Sandip P. Patel, University of California, San Diego, La Jolla; Victoria M. Raymond, Kimberly C. Banks, Rebecca J
| | - Rebecca J. Nagy
- Miriam T. Jacobs, Washington University School of Medicine in St Louis, St Louis, MO; Nisha A. Mohindra, Northwestern University; Jyoti D. Patel, University of Chicago School of Medicine, Chicago, IL; Lindsey Shantzer and Jeffrey Clarke, Duke University Medical Center, Durham, NC; Ingrid L. Chen, Stony Brook University School of Medicine, Stony Brook, NY; Hardeep Phull, William Mitchell, and Sandip P. Patel, University of California, San Diego, La Jolla; Victoria M. Raymond, Kimberly C. Banks, Rebecca J
| | - Richard B. Lanman
- Miriam T. Jacobs, Washington University School of Medicine in St Louis, St Louis, MO; Nisha A. Mohindra, Northwestern University; Jyoti D. Patel, University of Chicago School of Medicine, Chicago, IL; Lindsey Shantzer and Jeffrey Clarke, Duke University Medical Center, Durham, NC; Ingrid L. Chen, Stony Brook University School of Medicine, Stony Brook, NY; Hardeep Phull, William Mitchell, and Sandip P. Patel, University of California, San Diego, La Jolla; Victoria M. Raymond, Kimberly C. Banks, Rebecca J
| | - James Christensen
- Miriam T. Jacobs, Washington University School of Medicine in St Louis, St Louis, MO; Nisha A. Mohindra, Northwestern University; Jyoti D. Patel, University of Chicago School of Medicine, Chicago, IL; Lindsey Shantzer and Jeffrey Clarke, Duke University Medical Center, Durham, NC; Ingrid L. Chen, Stony Brook University School of Medicine, Stony Brook, NY; Hardeep Phull, William Mitchell, and Sandip P. Patel, University of California, San Diego, La Jolla; Victoria M. Raymond, Kimberly C. Banks, Rebecca J
| | - Jyoti D. Patel
- Miriam T. Jacobs, Washington University School of Medicine in St Louis, St Louis, MO; Nisha A. Mohindra, Northwestern University; Jyoti D. Patel, University of Chicago School of Medicine, Chicago, IL; Lindsey Shantzer and Jeffrey Clarke, Duke University Medical Center, Durham, NC; Ingrid L. Chen, Stony Brook University School of Medicine, Stony Brook, NY; Hardeep Phull, William Mitchell, and Sandip P. Patel, University of California, San Diego, La Jolla; Victoria M. Raymond, Kimberly C. Banks, Rebecca J
| | - Jeffrey Clarke
- Miriam T. Jacobs, Washington University School of Medicine in St Louis, St Louis, MO; Nisha A. Mohindra, Northwestern University; Jyoti D. Patel, University of Chicago School of Medicine, Chicago, IL; Lindsey Shantzer and Jeffrey Clarke, Duke University Medical Center, Durham, NC; Ingrid L. Chen, Stony Brook University School of Medicine, Stony Brook, NY; Hardeep Phull, William Mitchell, and Sandip P. Patel, University of California, San Diego, La Jolla; Victoria M. Raymond, Kimberly C. Banks, Rebecca J
| | - Sandip P. Patel
- Miriam T. Jacobs, Washington University School of Medicine in St Louis, St Louis, MO; Nisha A. Mohindra, Northwestern University; Jyoti D. Patel, University of Chicago School of Medicine, Chicago, IL; Lindsey Shantzer and Jeffrey Clarke, Duke University Medical Center, Durham, NC; Ingrid L. Chen, Stony Brook University School of Medicine, Stony Brook, NY; Hardeep Phull, William Mitchell, and Sandip P. Patel, University of California, San Diego, La Jolla; Victoria M. Raymond, Kimberly C. Banks, Rebecca J
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Slavin TP, Banks KC, Chudova D, Oxnard GR, Odegaard JI, Nagy RJ, Tsang KWK, Neuhausen SL, Gray SW, Cristofanilli M, Rodriguez AA, Bardia A, Leyland-Jones B, Janicek MF, Lilly M, Sonpavde G, Lee CE, Lanman RB, Meric-Bernstam F, Kurzrock R, Weitzel JN. Identification of Incidental Germline Mutations in Patients With Advanced Solid Tumors Who Underwent Cell-Free Circulating Tumor DNA Sequencing. J Clin Oncol 2018; 36:JCO1800328. [PMID: 30339520 PMCID: PMC6286162 DOI: 10.1200/jco.18.00328] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
PURPOSE To determine the potential for detection of incidental germline cancer predisposition mutations through cell-free DNA (cfDNA) analyses in patients who underwent solid tumor somatic mutation evaluation. PATIENTS AND METHODS Data were evaluated from 10,888 unselected patients with advanced (stage III/IV) cancer who underwent Guardant360 testing between November 2015 and December 2016. The main outcome was prevalence of putative germline mutations identified among 16 actionable hereditary cancer predisposition genes. RESULTS More than 50 cancer types were studied, including lung (41%), breast (19%), colorectal (8%), prostate (6%), pancreatic (3%), and ovarian (2%). Average patient age was 63.5 years (range, 18 to 95 years); 43% were male. One hundred and fifty-six individuals (1.4%) had suspected hereditary cancer mutations in 11 genes. Putative germline mutations were more frequent in individuals younger than 50 years versus those 50 years and older (3.0% v 1.2%, respectively; P < .001). Highest yields of putative germline findings were in patients with ovarian (8.13%), prostate (3.46%), pancreatic (3.34%), and breast (2.2%) cancer. Putative germline mutation identification was consistent among 12 individuals with multiple samples. Patients with circulating tumor DNA copy number variation and/or reversion mutations suggestive of functional loss of the wild-type allele in the tumor DNA also are described. CONCLUSION Detection of putative germline mutations from cfDNA is feasible across multiple genes and cancer types without prior mutation knowledge. Many mutations were found in cancers without clear guidelines for hereditary cancer genetic counseling/testing. Given the clinical significance of identifying hereditary cancer predisposition for patients and their families as well as targetable germline alterations such as in BRCA1 or BRCA2, research on the best way to validate and return potential germline results from cfDNA analysis to clinicians and patients is needed.
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Affiliation(s)
- Thomas P. Slavin
- Thomas P. Slavin, Kar Wing Kevin Tsang, Susan L. Neuhausen, Stacy W. Gray, and Jeffrey N. Weitzel, City of Hope, Duarte; Kimberly C. Banks, Darya Chudova, Justin I. Odegaard, Rebecca J. Nagy, Christine E. Lee, and Richard B. Lanman, Guardant Health, Redwood City; Razelle Kurzrock, University of California, San Diego, Moores Cancer Center, San Diego, CA; Geoffrey R. Oxnard, Dana-Farber Cancer Institute; Aditya Bardia, Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA; Massimo Cristofanilli, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL; Angel A. Rodriguez, Houston Methodist Hospital; Funda Meric-Bernstam, The University of Texas MD Anderson Cancer Center, Houston, TX; Brian Leyland-Jones, Avera Cancer Institute, Sioux Falls, SD; Mike F. Janicek, Arizona Oncology Associates Gynecology Oncology, Scottsdale, AZ; Michael Lilly, Medical University of South Carolina, Charleston, SC; and Guru Sonpavde, The University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, AL
| | - Kimberly C. Banks
- Thomas P. Slavin, Kar Wing Kevin Tsang, Susan L. Neuhausen, Stacy W. Gray, and Jeffrey N. Weitzel, City of Hope, Duarte; Kimberly C. Banks, Darya Chudova, Justin I. Odegaard, Rebecca J. Nagy, Christine E. Lee, and Richard B. Lanman, Guardant Health, Redwood City; Razelle Kurzrock, University of California, San Diego, Moores Cancer Center, San Diego, CA; Geoffrey R. Oxnard, Dana-Farber Cancer Institute; Aditya Bardia, Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA; Massimo Cristofanilli, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL; Angel A. Rodriguez, Houston Methodist Hospital; Funda Meric-Bernstam, The University of Texas MD Anderson Cancer Center, Houston, TX; Brian Leyland-Jones, Avera Cancer Institute, Sioux Falls, SD; Mike F. Janicek, Arizona Oncology Associates Gynecology Oncology, Scottsdale, AZ; Michael Lilly, Medical University of South Carolina, Charleston, SC; and Guru Sonpavde, The University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, AL
| | - Darya Chudova
- Thomas P. Slavin, Kar Wing Kevin Tsang, Susan L. Neuhausen, Stacy W. Gray, and Jeffrey N. Weitzel, City of Hope, Duarte; Kimberly C. Banks, Darya Chudova, Justin I. Odegaard, Rebecca J. Nagy, Christine E. Lee, and Richard B. Lanman, Guardant Health, Redwood City; Razelle Kurzrock, University of California, San Diego, Moores Cancer Center, San Diego, CA; Geoffrey R. Oxnard, Dana-Farber Cancer Institute; Aditya Bardia, Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA; Massimo Cristofanilli, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL; Angel A. Rodriguez, Houston Methodist Hospital; Funda Meric-Bernstam, The University of Texas MD Anderson Cancer Center, Houston, TX; Brian Leyland-Jones, Avera Cancer Institute, Sioux Falls, SD; Mike F. Janicek, Arizona Oncology Associates Gynecology Oncology, Scottsdale, AZ; Michael Lilly, Medical University of South Carolina, Charleston, SC; and Guru Sonpavde, The University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, AL
| | - Geoffrey R. Oxnard
- Thomas P. Slavin, Kar Wing Kevin Tsang, Susan L. Neuhausen, Stacy W. Gray, and Jeffrey N. Weitzel, City of Hope, Duarte; Kimberly C. Banks, Darya Chudova, Justin I. Odegaard, Rebecca J. Nagy, Christine E. Lee, and Richard B. Lanman, Guardant Health, Redwood City; Razelle Kurzrock, University of California, San Diego, Moores Cancer Center, San Diego, CA; Geoffrey R. Oxnard, Dana-Farber Cancer Institute; Aditya Bardia, Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA; Massimo Cristofanilli, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL; Angel A. Rodriguez, Houston Methodist Hospital; Funda Meric-Bernstam, The University of Texas MD Anderson Cancer Center, Houston, TX; Brian Leyland-Jones, Avera Cancer Institute, Sioux Falls, SD; Mike F. Janicek, Arizona Oncology Associates Gynecology Oncology, Scottsdale, AZ; Michael Lilly, Medical University of South Carolina, Charleston, SC; and Guru Sonpavde, The University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, AL
| | - Justin I. Odegaard
- Thomas P. Slavin, Kar Wing Kevin Tsang, Susan L. Neuhausen, Stacy W. Gray, and Jeffrey N. Weitzel, City of Hope, Duarte; Kimberly C. Banks, Darya Chudova, Justin I. Odegaard, Rebecca J. Nagy, Christine E. Lee, and Richard B. Lanman, Guardant Health, Redwood City; Razelle Kurzrock, University of California, San Diego, Moores Cancer Center, San Diego, CA; Geoffrey R. Oxnard, Dana-Farber Cancer Institute; Aditya Bardia, Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA; Massimo Cristofanilli, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL; Angel A. Rodriguez, Houston Methodist Hospital; Funda Meric-Bernstam, The University of Texas MD Anderson Cancer Center, Houston, TX; Brian Leyland-Jones, Avera Cancer Institute, Sioux Falls, SD; Mike F. Janicek, Arizona Oncology Associates Gynecology Oncology, Scottsdale, AZ; Michael Lilly, Medical University of South Carolina, Charleston, SC; and Guru Sonpavde, The University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, AL
| | - Rebecca J. Nagy
- Thomas P. Slavin, Kar Wing Kevin Tsang, Susan L. Neuhausen, Stacy W. Gray, and Jeffrey N. Weitzel, City of Hope, Duarte; Kimberly C. Banks, Darya Chudova, Justin I. Odegaard, Rebecca J. Nagy, Christine E. Lee, and Richard B. Lanman, Guardant Health, Redwood City; Razelle Kurzrock, University of California, San Diego, Moores Cancer Center, San Diego, CA; Geoffrey R. Oxnard, Dana-Farber Cancer Institute; Aditya Bardia, Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA; Massimo Cristofanilli, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL; Angel A. Rodriguez, Houston Methodist Hospital; Funda Meric-Bernstam, The University of Texas MD Anderson Cancer Center, Houston, TX; Brian Leyland-Jones, Avera Cancer Institute, Sioux Falls, SD; Mike F. Janicek, Arizona Oncology Associates Gynecology Oncology, Scottsdale, AZ; Michael Lilly, Medical University of South Carolina, Charleston, SC; and Guru Sonpavde, The University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, AL
| | - Kar Wing Kevin Tsang
- Thomas P. Slavin, Kar Wing Kevin Tsang, Susan L. Neuhausen, Stacy W. Gray, and Jeffrey N. Weitzel, City of Hope, Duarte; Kimberly C. Banks, Darya Chudova, Justin I. Odegaard, Rebecca J. Nagy, Christine E. Lee, and Richard B. Lanman, Guardant Health, Redwood City; Razelle Kurzrock, University of California, San Diego, Moores Cancer Center, San Diego, CA; Geoffrey R. Oxnard, Dana-Farber Cancer Institute; Aditya Bardia, Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA; Massimo Cristofanilli, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL; Angel A. Rodriguez, Houston Methodist Hospital; Funda Meric-Bernstam, The University of Texas MD Anderson Cancer Center, Houston, TX; Brian Leyland-Jones, Avera Cancer Institute, Sioux Falls, SD; Mike F. Janicek, Arizona Oncology Associates Gynecology Oncology, Scottsdale, AZ; Michael Lilly, Medical University of South Carolina, Charleston, SC; and Guru Sonpavde, The University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, AL
| | - Susan L. Neuhausen
- Thomas P. Slavin, Kar Wing Kevin Tsang, Susan L. Neuhausen, Stacy W. Gray, and Jeffrey N. Weitzel, City of Hope, Duarte; Kimberly C. Banks, Darya Chudova, Justin I. Odegaard, Rebecca J. Nagy, Christine E. Lee, and Richard B. Lanman, Guardant Health, Redwood City; Razelle Kurzrock, University of California, San Diego, Moores Cancer Center, San Diego, CA; Geoffrey R. Oxnard, Dana-Farber Cancer Institute; Aditya Bardia, Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA; Massimo Cristofanilli, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL; Angel A. Rodriguez, Houston Methodist Hospital; Funda Meric-Bernstam, The University of Texas MD Anderson Cancer Center, Houston, TX; Brian Leyland-Jones, Avera Cancer Institute, Sioux Falls, SD; Mike F. Janicek, Arizona Oncology Associates Gynecology Oncology, Scottsdale, AZ; Michael Lilly, Medical University of South Carolina, Charleston, SC; and Guru Sonpavde, The University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, AL
| | - Stacy W. Gray
- Thomas P. Slavin, Kar Wing Kevin Tsang, Susan L. Neuhausen, Stacy W. Gray, and Jeffrey N. Weitzel, City of Hope, Duarte; Kimberly C. Banks, Darya Chudova, Justin I. Odegaard, Rebecca J. Nagy, Christine E. Lee, and Richard B. Lanman, Guardant Health, Redwood City; Razelle Kurzrock, University of California, San Diego, Moores Cancer Center, San Diego, CA; Geoffrey R. Oxnard, Dana-Farber Cancer Institute; Aditya Bardia, Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA; Massimo Cristofanilli, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL; Angel A. Rodriguez, Houston Methodist Hospital; Funda Meric-Bernstam, The University of Texas MD Anderson Cancer Center, Houston, TX; Brian Leyland-Jones, Avera Cancer Institute, Sioux Falls, SD; Mike F. Janicek, Arizona Oncology Associates Gynecology Oncology, Scottsdale, AZ; Michael Lilly, Medical University of South Carolina, Charleston, SC; and Guru Sonpavde, The University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, AL
| | - Massimo Cristofanilli
- Thomas P. Slavin, Kar Wing Kevin Tsang, Susan L. Neuhausen, Stacy W. Gray, and Jeffrey N. Weitzel, City of Hope, Duarte; Kimberly C. Banks, Darya Chudova, Justin I. Odegaard, Rebecca J. Nagy, Christine E. Lee, and Richard B. Lanman, Guardant Health, Redwood City; Razelle Kurzrock, University of California, San Diego, Moores Cancer Center, San Diego, CA; Geoffrey R. Oxnard, Dana-Farber Cancer Institute; Aditya Bardia, Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA; Massimo Cristofanilli, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL; Angel A. Rodriguez, Houston Methodist Hospital; Funda Meric-Bernstam, The University of Texas MD Anderson Cancer Center, Houston, TX; Brian Leyland-Jones, Avera Cancer Institute, Sioux Falls, SD; Mike F. Janicek, Arizona Oncology Associates Gynecology Oncology, Scottsdale, AZ; Michael Lilly, Medical University of South Carolina, Charleston, SC; and Guru Sonpavde, The University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, AL
| | - Angel A. Rodriguez
- Thomas P. Slavin, Kar Wing Kevin Tsang, Susan L. Neuhausen, Stacy W. Gray, and Jeffrey N. Weitzel, City of Hope, Duarte; Kimberly C. Banks, Darya Chudova, Justin I. Odegaard, Rebecca J. Nagy, Christine E. Lee, and Richard B. Lanman, Guardant Health, Redwood City; Razelle Kurzrock, University of California, San Diego, Moores Cancer Center, San Diego, CA; Geoffrey R. Oxnard, Dana-Farber Cancer Institute; Aditya Bardia, Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA; Massimo Cristofanilli, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL; Angel A. Rodriguez, Houston Methodist Hospital; Funda Meric-Bernstam, The University of Texas MD Anderson Cancer Center, Houston, TX; Brian Leyland-Jones, Avera Cancer Institute, Sioux Falls, SD; Mike F. Janicek, Arizona Oncology Associates Gynecology Oncology, Scottsdale, AZ; Michael Lilly, Medical University of South Carolina, Charleston, SC; and Guru Sonpavde, The University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, AL
| | - Aditya Bardia
- Thomas P. Slavin, Kar Wing Kevin Tsang, Susan L. Neuhausen, Stacy W. Gray, and Jeffrey N. Weitzel, City of Hope, Duarte; Kimberly C. Banks, Darya Chudova, Justin I. Odegaard, Rebecca J. Nagy, Christine E. Lee, and Richard B. Lanman, Guardant Health, Redwood City; Razelle Kurzrock, University of California, San Diego, Moores Cancer Center, San Diego, CA; Geoffrey R. Oxnard, Dana-Farber Cancer Institute; Aditya Bardia, Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA; Massimo Cristofanilli, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL; Angel A. Rodriguez, Houston Methodist Hospital; Funda Meric-Bernstam, The University of Texas MD Anderson Cancer Center, Houston, TX; Brian Leyland-Jones, Avera Cancer Institute, Sioux Falls, SD; Mike F. Janicek, Arizona Oncology Associates Gynecology Oncology, Scottsdale, AZ; Michael Lilly, Medical University of South Carolina, Charleston, SC; and Guru Sonpavde, The University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, AL
| | - Brian Leyland-Jones
- Thomas P. Slavin, Kar Wing Kevin Tsang, Susan L. Neuhausen, Stacy W. Gray, and Jeffrey N. Weitzel, City of Hope, Duarte; Kimberly C. Banks, Darya Chudova, Justin I. Odegaard, Rebecca J. Nagy, Christine E. Lee, and Richard B. Lanman, Guardant Health, Redwood City; Razelle Kurzrock, University of California, San Diego, Moores Cancer Center, San Diego, CA; Geoffrey R. Oxnard, Dana-Farber Cancer Institute; Aditya Bardia, Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA; Massimo Cristofanilli, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL; Angel A. Rodriguez, Houston Methodist Hospital; Funda Meric-Bernstam, The University of Texas MD Anderson Cancer Center, Houston, TX; Brian Leyland-Jones, Avera Cancer Institute, Sioux Falls, SD; Mike F. Janicek, Arizona Oncology Associates Gynecology Oncology, Scottsdale, AZ; Michael Lilly, Medical University of South Carolina, Charleston, SC; and Guru Sonpavde, The University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, AL
| | - Mike F. Janicek
- Thomas P. Slavin, Kar Wing Kevin Tsang, Susan L. Neuhausen, Stacy W. Gray, and Jeffrey N. Weitzel, City of Hope, Duarte; Kimberly C. Banks, Darya Chudova, Justin I. Odegaard, Rebecca J. Nagy, Christine E. Lee, and Richard B. Lanman, Guardant Health, Redwood City; Razelle Kurzrock, University of California, San Diego, Moores Cancer Center, San Diego, CA; Geoffrey R. Oxnard, Dana-Farber Cancer Institute; Aditya Bardia, Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA; Massimo Cristofanilli, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL; Angel A. Rodriguez, Houston Methodist Hospital; Funda Meric-Bernstam, The University of Texas MD Anderson Cancer Center, Houston, TX; Brian Leyland-Jones, Avera Cancer Institute, Sioux Falls, SD; Mike F. Janicek, Arizona Oncology Associates Gynecology Oncology, Scottsdale, AZ; Michael Lilly, Medical University of South Carolina, Charleston, SC; and Guru Sonpavde, The University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, AL
| | - Michael Lilly
- Thomas P. Slavin, Kar Wing Kevin Tsang, Susan L. Neuhausen, Stacy W. Gray, and Jeffrey N. Weitzel, City of Hope, Duarte; Kimberly C. Banks, Darya Chudova, Justin I. Odegaard, Rebecca J. Nagy, Christine E. Lee, and Richard B. Lanman, Guardant Health, Redwood City; Razelle Kurzrock, University of California, San Diego, Moores Cancer Center, San Diego, CA; Geoffrey R. Oxnard, Dana-Farber Cancer Institute; Aditya Bardia, Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA; Massimo Cristofanilli, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL; Angel A. Rodriguez, Houston Methodist Hospital; Funda Meric-Bernstam, The University of Texas MD Anderson Cancer Center, Houston, TX; Brian Leyland-Jones, Avera Cancer Institute, Sioux Falls, SD; Mike F. Janicek, Arizona Oncology Associates Gynecology Oncology, Scottsdale, AZ; Michael Lilly, Medical University of South Carolina, Charleston, SC; and Guru Sonpavde, The University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, AL
| | - Guru Sonpavde
- Thomas P. Slavin, Kar Wing Kevin Tsang, Susan L. Neuhausen, Stacy W. Gray, and Jeffrey N. Weitzel, City of Hope, Duarte; Kimberly C. Banks, Darya Chudova, Justin I. Odegaard, Rebecca J. Nagy, Christine E. Lee, and Richard B. Lanman, Guardant Health, Redwood City; Razelle Kurzrock, University of California, San Diego, Moores Cancer Center, San Diego, CA; Geoffrey R. Oxnard, Dana-Farber Cancer Institute; Aditya Bardia, Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA; Massimo Cristofanilli, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL; Angel A. Rodriguez, Houston Methodist Hospital; Funda Meric-Bernstam, The University of Texas MD Anderson Cancer Center, Houston, TX; Brian Leyland-Jones, Avera Cancer Institute, Sioux Falls, SD; Mike F. Janicek, Arizona Oncology Associates Gynecology Oncology, Scottsdale, AZ; Michael Lilly, Medical University of South Carolina, Charleston, SC; and Guru Sonpavde, The University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, AL
| | - Christine E. Lee
- Thomas P. Slavin, Kar Wing Kevin Tsang, Susan L. Neuhausen, Stacy W. Gray, and Jeffrey N. Weitzel, City of Hope, Duarte; Kimberly C. Banks, Darya Chudova, Justin I. Odegaard, Rebecca J. Nagy, Christine E. Lee, and Richard B. Lanman, Guardant Health, Redwood City; Razelle Kurzrock, University of California, San Diego, Moores Cancer Center, San Diego, CA; Geoffrey R. Oxnard, Dana-Farber Cancer Institute; Aditya Bardia, Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA; Massimo Cristofanilli, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL; Angel A. Rodriguez, Houston Methodist Hospital; Funda Meric-Bernstam, The University of Texas MD Anderson Cancer Center, Houston, TX; Brian Leyland-Jones, Avera Cancer Institute, Sioux Falls, SD; Mike F. Janicek, Arizona Oncology Associates Gynecology Oncology, Scottsdale, AZ; Michael Lilly, Medical University of South Carolina, Charleston, SC; and Guru Sonpavde, The University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, AL
| | - Richard B. Lanman
- Thomas P. Slavin, Kar Wing Kevin Tsang, Susan L. Neuhausen, Stacy W. Gray, and Jeffrey N. Weitzel, City of Hope, Duarte; Kimberly C. Banks, Darya Chudova, Justin I. Odegaard, Rebecca J. Nagy, Christine E. Lee, and Richard B. Lanman, Guardant Health, Redwood City; Razelle Kurzrock, University of California, San Diego, Moores Cancer Center, San Diego, CA; Geoffrey R. Oxnard, Dana-Farber Cancer Institute; Aditya Bardia, Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA; Massimo Cristofanilli, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL; Angel A. Rodriguez, Houston Methodist Hospital; Funda Meric-Bernstam, The University of Texas MD Anderson Cancer Center, Houston, TX; Brian Leyland-Jones, Avera Cancer Institute, Sioux Falls, SD; Mike F. Janicek, Arizona Oncology Associates Gynecology Oncology, Scottsdale, AZ; Michael Lilly, Medical University of South Carolina, Charleston, SC; and Guru Sonpavde, The University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, AL
| | - Funda Meric-Bernstam
- Thomas P. Slavin, Kar Wing Kevin Tsang, Susan L. Neuhausen, Stacy W. Gray, and Jeffrey N. Weitzel, City of Hope, Duarte; Kimberly C. Banks, Darya Chudova, Justin I. Odegaard, Rebecca J. Nagy, Christine E. Lee, and Richard B. Lanman, Guardant Health, Redwood City; Razelle Kurzrock, University of California, San Diego, Moores Cancer Center, San Diego, CA; Geoffrey R. Oxnard, Dana-Farber Cancer Institute; Aditya Bardia, Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA; Massimo Cristofanilli, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL; Angel A. Rodriguez, Houston Methodist Hospital; Funda Meric-Bernstam, The University of Texas MD Anderson Cancer Center, Houston, TX; Brian Leyland-Jones, Avera Cancer Institute, Sioux Falls, SD; Mike F. Janicek, Arizona Oncology Associates Gynecology Oncology, Scottsdale, AZ; Michael Lilly, Medical University of South Carolina, Charleston, SC; and Guru Sonpavde, The University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, AL
| | - Razelle Kurzrock
- Thomas P. Slavin, Kar Wing Kevin Tsang, Susan L. Neuhausen, Stacy W. Gray, and Jeffrey N. Weitzel, City of Hope, Duarte; Kimberly C. Banks, Darya Chudova, Justin I. Odegaard, Rebecca J. Nagy, Christine E. Lee, and Richard B. Lanman, Guardant Health, Redwood City; Razelle Kurzrock, University of California, San Diego, Moores Cancer Center, San Diego, CA; Geoffrey R. Oxnard, Dana-Farber Cancer Institute; Aditya Bardia, Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA; Massimo Cristofanilli, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL; Angel A. Rodriguez, Houston Methodist Hospital; Funda Meric-Bernstam, The University of Texas MD Anderson Cancer Center, Houston, TX; Brian Leyland-Jones, Avera Cancer Institute, Sioux Falls, SD; Mike F. Janicek, Arizona Oncology Associates Gynecology Oncology, Scottsdale, AZ; Michael Lilly, Medical University of South Carolina, Charleston, SC; and Guru Sonpavde, The University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, AL
| | - Jeffrey N. Weitzel
- Thomas P. Slavin, Kar Wing Kevin Tsang, Susan L. Neuhausen, Stacy W. Gray, and Jeffrey N. Weitzel, City of Hope, Duarte; Kimberly C. Banks, Darya Chudova, Justin I. Odegaard, Rebecca J. Nagy, Christine E. Lee, and Richard B. Lanman, Guardant Health, Redwood City; Razelle Kurzrock, University of California, San Diego, Moores Cancer Center, San Diego, CA; Geoffrey R. Oxnard, Dana-Farber Cancer Institute; Aditya Bardia, Massachusetts General Hospital Cancer Center and Harvard Medical School, Boston, MA; Massimo Cristofanilli, Robert H. Lurie Comprehensive Cancer Center of Northwestern University, Chicago, IL; Angel A. Rodriguez, Houston Methodist Hospital; Funda Meric-Bernstam, The University of Texas MD Anderson Cancer Center, Houston, TX; Brian Leyland-Jones, Avera Cancer Institute, Sioux Falls, SD; Mike F. Janicek, Arizona Oncology Associates Gynecology Oncology, Scottsdale, AZ; Michael Lilly, Medical University of South Carolina, Charleston, SC; and Guru Sonpavde, The University of Alabama at Birmingham Comprehensive Cancer Center, Birmingham, AL
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Croessmann S, Formisano L, Kinch LN, Gonzalez-Ericsson PI, Sudhan DR, Nagy RJ, Mathew A, Bernicker EH, Cristofanilli M, He J, Cutler RE, Lalani AS, Miller VA, Lanman RB, Grishin NV, Arteaga CL. Combined Blockade of Activating ERBB2 Mutations and ER Results in Synthetic Lethality of ER+/HER2 Mutant Breast Cancer. Clin Cancer Res 2018; 25:277-289. [PMID: 30314968 DOI: 10.1158/1078-0432.ccr-18-1544] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/05/2018] [Accepted: 10/09/2018] [Indexed: 01/02/2023]
Abstract
PURPOSE We examined the role of ERBB2-activating mutations in endocrine therapy resistance in estrogen receptor positive (ER+) breast cancer. EXPERIMENTAL DESIGN ERBB2 mutation frequency was determined from large genomic databases. Isogenic knock-in ERBB2 mutations in ER+ MCF7 cells and xenografts were used to investigate estrogen-independent growth. Structural analysis was used to determine the molecular interaction of HER L755S with HER3. Small molecules and siRNAs were used to inhibit PI3Kα, TORC1, and HER3. RESULTS Genomic data revealed a higher rate of ERBB2 mutations in metastatic versus primary ER+ tumors. MCF7 cells with isogenically incorporated ERBB2 kinase domain mutations exhibited resistance to estrogen deprivation and to fulvestrant both in vitro and in vivo, despite maintaining inhibition of ERα transcriptional activity. Addition of the irreversible HER2 tyrosine kinase inhibitor neratinib restored sensitivity to fulvestrant. HER2-mutant MCF7 cells expressed higher levels of p-HER3, p-AKT, and p-S6 than cells with wild-type HER2. Structural analysis of the HER2 L755S variant implicated a more flexible active state, potentially allowing for enhanced dimerization with HER3. Treatment with a PI3Kα inhibitor, a TORC1 inhibitor or HER3 siRNA, but not a MEK inhibitor, restored sensitivity to fulvestrant and to estrogen deprivation. Inhibition of mutant HER2 or TORC1, when combined with fulvestrant, equipotently inhibited growth of MCF7/ERBB2 V777L xenografts, suggesting a role for TORC1 in antiestrogen resistance induced by ERBB2 mutations. CONCLUSIONS ERBB2 mutations hyperactivate the HER3/PI3K/AKT/mTOR axis, leading to antiestrogen resistance in ER+ breast cancer. Dual blockade of the HER2 and ER pathways is required for the treatment of ER+/HER2 mutant breast cancers.
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Affiliation(s)
- Sarah Croessmann
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Luigi Formisano
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Lisa N Kinch
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, Texas
| | - Paula I Gonzalez-Ericsson
- Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Dhivya R Sudhan
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - Aju Mathew
- University of Kentucky Markey Cancer Center, Lexington, Kentucky
| | | | | | - Jie He
- Foundation Medicine, Inc., Cambridge, Massachusetts
| | | | | | | | | | - Nick V Grishin
- Howard Hughes Medical Institute, UT Southwestern Medical Center, Dallas, Texas.,Department of Biophysics, UT Southwestern Medical Center, Dallas, Texas.,Department of Biochemistry, UT Southwestern Medical Center, Dallas, Texas
| | - Carlos L Arteaga
- Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee. .,Breast Cancer Program, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee.,Department of Cancer Biology, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee.,Harold C. Simmons Cancer Center, UT Southwestern Medical Center, Dallas, Texas
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Jia J, Morse MA, Nagy RJ, Lanman RB, Strickler JH. Cell-Free DNA Profiling to Discover Mechanisms of Exceptional Response to Cabozantinib Plus Panitumumab in a Patient With Treatment Refractory Metastatic Colorectal Cancer. Front Oncol 2018; 8:305. [PMID: 30211110 PMCID: PMC6121109 DOI: 10.3389/fonc.2018.00305] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 07/19/2018] [Indexed: 01/06/2023] Open
Abstract
MET amplification is rare in treatment-naïve metastatic colorectal cancer (CRC) tumors, but can emerge as a mechanism of resistance to anti-EGFR therapies. Preclinical and clinical data suggest that patients with MET amplified tumors benefit from MET-targeted therapy. Cabozantinib is an inhibitor of multiple tyrosine kinases, included c-MET. Panitumumab is an inhibitor of EGFR. This report describes a patient with KRAS, NRAS, and BRAF wild-type metastatic CRC who experienced disease progression on all standard chemotherapy and anti-EGFR antibody therapy. The patient was enrolled in a clinical trial evaluating the combination of cabozantinib plus panitumumab. After only 6 weeks of treatment, the patient experienced a significant anti-tumor response. Although tumor tissue was negative for MET amplification, molecular profiling of cell-free DNA (cfDNA) revealed MET amplification. This case represents the first report showing the activity of cabozantinib in combination with panitumumab in a patient with metastatic CRC, and suggests that MET amplification in cfDNA may be a biomarker of response. A clinical trial targeting MET amplified metastatic CRC is currently underway.
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Affiliation(s)
- Jingquan Jia
- Department of Medicine, Duke University Medical Center, Durham, NC, United States
| | - Michael A. Morse
- Department of Medicine, Duke University Medical Center, Durham, NC, United States
| | | | | | - John H. Strickler
- Department of Medicine, Duke University Medical Center, Durham, NC, United States
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Odegaard JI, Vincent JJ, Mortimer S, Vowles JV, Ulrich BC, Banks KC, Fairclough SR, Zill OA, Sikora M, Mokhtari R, Abdueva D, Nagy RJ, Lee CE, Kiedrowski LA, Paweletz CP, Eltoukhy H, Lanman RB, Chudova DI, Talasaz A. Validation of a Plasma-Based Comprehensive Cancer Genotyping Assay Utilizing Orthogonal Tissue- and Plasma-Based Methodologies. Clin Cancer Res 2018; 24:3539-3549. [PMID: 29691297 DOI: 10.1158/1078-0432.ccr-17-3831] [Citation(s) in RCA: 276] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Revised: 03/15/2018] [Accepted: 04/20/2018] [Indexed: 11/16/2022]
Abstract
Purpose: To analytically and clinically validate a circulating cell-free tumor DNA sequencing test for comprehensive tumor genotyping and demonstrate its clinical feasibility.Experimental Design: Analytic validation was conducted according to established principles and guidelines. Blood-to-blood clinical validation comprised blinded external comparison with clinical droplet digital PCR across 222 consecutive biomarker-positive clinical samples. Blood-to-tissue clinical validation comprised comparison of digital sequencing calls to those documented in the medical record of 543 consecutive lung cancer patients. Clinical experience was reported from 10,593 consecutive clinical samples.Results: Digital sequencing technology enabled variant detection down to 0.02% to 0.04% allelic fraction/2.12 copies with ≤0.3%/2.24-2.76 copies 95% limits of detection while maintaining high specificity [prevalence-adjusted positive predictive values (PPV) >98%]. Clinical validation using orthogonal plasma- and tissue-based clinical genotyping across >750 patients demonstrated high accuracy and specificity [positive percent agreement (PPAs) and negative percent agreement (NPAs) >99% and PPVs 92%-100%]. Clinical use in 10,593 advanced adult solid tumor patients demonstrated high feasibility (>99.6% technical success rate) and clinical sensitivity (85.9%), with high potential actionability (16.7% with FDA-approved on-label treatment options; 72.0% with treatment or trial recommendations), particularly in non-small cell lung cancer, where 34.5% of patient samples comprised a directly targetable standard-of-care biomarker.Conclusions: High concordance with orthogonal clinical plasma- and tissue-based genotyping methods supports the clinical accuracy of digital sequencing across all four types of targetable genomic alterations. Digital sequencing's clinical applicability is further supported by high rates of technical success and biomarker target discovery. Clin Cancer Res; 24(15); 3539-49. ©2018 AACR.
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Affiliation(s)
| | | | | | | | | | | | | | - Oliver A Zill
- Guardant Health, Redwood City, California.,Genentech, South San Francisco, California
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Piotrowska Z, Hazar-Rethinam M, Rizzo C, Nadres B, Van Seventer EE, Shahzade HA, Lennes IT, Iafrate AJ, Dias-Santagata D, Leshchiner I, Jessop NA, Hu H, Digumarthy SR, Nagy RJ, Lanman RB, Moody S, Niederst MJ, Engelman JA, Hata AN, Corcoran RB, Sequist LV. Heterogeneity and Coexistence of T790M and T790 Wild-Type Resistant Subclones Drive Mixed Response to Third-Generation Epidermal Growth Factor Receptor Inhibitors in Lung Cancer. JCO Precis Oncol 2018; 2018. [PMID: 30123863 DOI: 10.1200/po.17.00263] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Purpose Third-generation epidermal growth factor receptor (EGFR) inhibitors like nazartinib are active against EGFR mutation-positive lung cancers with T790M-mediated acquired resistance to initial anti-EGFR treatment, but some patients have mixed responses. Methods Multiple serial tumor and liquid biopsies were obtained from two patients before, during, and after treatment with nazartinib. Next-generation sequencing and droplet digital polymerase chain reaction were performed to assess heterogeneity and clonal dynamics. Results We observed the simultaneous emergence of T790M-dependent and -independent clones in both patients. Serial plasma droplet digital polymerase chain reaction illustrated shifts in relative clonal abundance in response to various systemic therapies, confirming a molecular basis for the clinical mixed radiographic responses observed. Conclusion Heterogeneous responses to treatment targeting a solitary resistance mechanism can be explained by coexistent tumor subclones harboring distinct genetic signatures. Serial liquid biopsies offer an opportunity to monitor clonal dynamics and the emergence of resistance and may represent a useful tool to guide therapeutic strategies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Susan Moody
- Novartis Institutes for Biomedical Research, Cambridge, MA
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Siravegna G, Lazzari L, Crisafulli G, Sartore-Bianchi A, Mussolin B, Cassingena A, Martino C, Lanman RB, Nagy RJ, Fairclough S, Rospo G, Corti G, Bartolini A, Arcella P, Montone M, Lodi F, Lorenzato A, Vanzati A, Valtorta E, Cappello G, Bertotti A, Lonardi S, Zagonel V, Leone F, Russo M, Balsamo A, Truini M, Di Nicolantonio F, Amatu A, Bonazzina E, Ghezzi S, Regge D, Vanzulli A, Trusolino L, Siena S, Marsoni S, Bardelli A. Radiologic and Genomic Evolution of Individual Metastases during HER2 Blockade in Colorectal Cancer. Cancer Cell 2018; 34:148-162.e7. [PMID: 29990497 DOI: 10.1016/j.ccell.2018.06.004] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Revised: 04/18/2018] [Accepted: 06/07/2018] [Indexed: 02/07/2023]
Abstract
Targeting HER2 is effective in 24% of ERBB2 amplified metastatic colorectal cancer; however, secondary resistance occurs in most of the cases. We studied the evolution of individual metastases during treatment to discover spatially resolved determinants of resistance. Circulating tumor DNA (ctDNA) analysis identified alterations associated with resistance in the majority of refractory patients. ctDNA profiles and lesion-specific radiographic reports revealed organ- or metastasis-private evolutionary patterns. When radiologic assessments documented progressive disease in target lesions, response to HER2 blockade was retained in other metastases. Genomic and functional analyses on samples and cell models from eight metastases of a patient co-recruited to a postmortem study unveiled lesion-specific evolutionary trees and pharmacologic vulnerabilities. Lesion size and contribution of distinct metastases to plasma ctDNA were correlated.
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Affiliation(s)
| | - Luca Lazzari
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, TO, Italy; FIRC Institute of Molecular Oncology (IFOM), Milan, Italy; Department of Oncology, University of Torino, Candiolo, TO 10060, Italy
| | - Giovanni Crisafulli
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, TO, Italy; Department of Oncology, University of Torino, Candiolo, TO 10060, Italy
| | | | | | - Andrea Cassingena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan 20162, Italy
| | - Cosimo Martino
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, TO, Italy
| | | | | | | | - Giuseppe Rospo
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, TO, Italy
| | - Giorgio Corti
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, TO, Italy
| | | | - Pamela Arcella
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, TO, Italy
| | - Monica Montone
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, TO, Italy
| | - Francesca Lodi
- Department of Oncology, University of Torino, Candiolo, TO 10060, Italy
| | | | - Alice Vanzati
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan 20162, Italy
| | - Emanuele Valtorta
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan 20162, Italy
| | | | - Andrea Bertotti
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, TO, Italy; Department of Oncology, University of Torino, Candiolo, TO 10060, Italy
| | - Sara Lonardi
- Istituto Oncologico Veneto - IRCCS, Oncologia Medica 1, Padova 35128, Italy
| | - Vittorina Zagonel
- Istituto Oncologico Veneto - IRCCS, Oncologia Medica 1, Padova 35128, Italy
| | - Francesco Leone
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, TO, Italy; Department of Oncology, University of Torino, Candiolo, TO 10060, Italy
| | | | | | - Mauro Truini
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan 20162, Italy
| | - Federica Di Nicolantonio
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, TO, Italy; Department of Oncology, University of Torino, Candiolo, TO 10060, Italy
| | - Alessio Amatu
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan 20162, Italy
| | - Erica Bonazzina
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan 20162, Italy
| | - Silvia Ghezzi
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan 20162, Italy
| | - Daniele Regge
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, TO, Italy
| | - Angelo Vanzulli
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan 20162, Italy; Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan 20122, Italy
| | - Livio Trusolino
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, TO, Italy; Department of Oncology, University of Torino, Candiolo, TO 10060, Italy
| | - Salvatore Siena
- Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan 20162, Italy; Department of Oncology and Hemato-Oncology, Università degli Studi di Milano, Milan 20122, Italy
| | - Silvia Marsoni
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, TO, Italy; FIRC Institute of Molecular Oncology (IFOM), Milan, Italy; Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milan 20162, Italy
| | - Alberto Bardelli
- Candiolo Cancer Institute-FPO, IRCCS, Candiolo, TO, Italy; Department of Oncology, University of Torino, Candiolo, TO 10060, Italy.
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Schram AM, Selcuklu SD, Nagy RJ, Smyth LM, Eli LD, Cutler RE, Lalani AS, Hyman DM, Lanman RB. Abstract 5533: Cell-free DNA sequencing in ERBB2-mutant breast cancer patients treated with neratinib and fulvestrant: Exploratory analysis from the Phase 2 SUMMIT ‘basket' trial. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-5533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Mutations in ERBB2, encoding the HER2 protein, occur in up to 4% of breast cancers. A subset of ERBB2 mutations have been shown to have oncogenic potential through constitutive activation of the HER2 kinase. SUMMIT (NCT01953926) is a phase II ‘basket' study investigating the use of the irreversible pan-HER tyrosine kinase inhibitor neratinib, in combination with the estrogen degrader fulvestrant, for the treatment of patients with advanced hormone-positive breast cancers harboring ERBB2 mutations. We collected and sequenced serial samples of circulating cell-free DNA (cfDNA) from participating patients in order to identify biomarkers of response and resistance.
Methods: Patients were treated with neratinib 240 mg daily and fulvestrant at the labelled 500 mg dose. Plasma was collected and cfDNA was extracted from patients at baseline and on Day 1 of each cycle (occurring every 4 weeks). Next generation sequencing (NGS) was performed on cfDNA samples collected from 12 patients using the Guardant360 test (Guardant Health, CA), which identifies select point mutations, small insertions and deletions, copy number changes, and structural rearrangements in 73 genes. Paired samples were sequenced from 9 of the 12 patients, including baseline and progression samples from 7 patients. cfDNA NGS results were compared to pretreatment tissue NGS results obtained 0-6 years prior (median: 6 months).
Results: 90% (9/10) baseline cfDNA NGS detected the locally reported ERBB2 mutation identified by tissue NGS. In one patient with only a sample obtained at progression, the ERBB2 mutation was identified. No ERBB2 mutation was identified in a singular on-treatment sample obtained from a patient with continued response to therapy. Eight ERBB2 mutations were identified in the baseline cfDNA sample of one patient with a hypermutated tumor, 6 of which were not identified by tissue NGS. Emergence of at least one additional ERBB2 mutation was seen in 3/7 patients with paired baseline and progression samples, including patients with 2 and 5 acquired ERBB2 mutations. The ERBB2 mutant allele fraction (MAF) increased compared to baseline in 4/7 of patients at the time of progression and declined in 2/2 patients with continued response to therapy. cfDNA NGS detected mutations, unidentified by tissue NGS in 9/10 baseline samples and in 11/12 patients, including 5 ESR1 mutations in 3 patients.
Conclusion: cfDNA NGS was sensitive for the detection of ERBB2 mutations. MAF dynamics typically tracked response to, or progression on therapy, at the time of cfDNA collection. The emergence of additional ERBB2 mutations was common at the time of progression; however, no T798 gatekeeper mutation was observed. Many subclonal mutations were identified on cfDNA NGS that were not observed on tissue NGS.
Citation Format: Alison M. Schram, S. Duygu Selcuklu, Rebecca J. Nagy, Lillian M. Smyth, Lisa D. Eli, Richard E. Cutler, Alshad S. Lalani, David M. Hyman, Richard B. Lanman. Cell-free DNA sequencing in ERBB2-mutant breast cancer patients treated with neratinib and fulvestrant: Exploratory analysis from the Phase 2 SUMMIT ‘basket' trial [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 5533.
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Aguirre AJ, Nowak JA, Camarda ND, Moffitt RA, Ghazani AA, Hazar-Rethinam M, Raghavan S, Kim J, Brais LK, Ragon D, Welch MW, Reilly E, McCabe D, Marini L, Anderka K, Helvie K, Oliver N, Babic A, Da Silva A, Nadres B, Van Seventer EE, Shahzade HA, St Pierre JP, Burke KP, Clancy T, Cleary JM, Doyle LA, Jajoo K, McCleary NJ, Meyerhardt JA, Murphy JE, Ng K, Patel AK, Perez K, Rosenthal MH, Rubinson DA, Ryou M, Shapiro GI, Sicinska E, Silverman SG, Nagy RJ, Lanman RB, Knoerzer D, Welsch DJ, Yurgelun MB, Fuchs CS, Garraway LA, Getz G, Hornick JL, Johnson BE, Kulke MH, Mayer RJ, Miller JW, Shyn PB, Tuveson DA, Wagle N, Yeh JJ, Hahn WC, Corcoran RB, Carter SL, Wolpin BM. Real-time Genomic Characterization of Advanced Pancreatic Cancer to Enable Precision Medicine. Cancer Discov 2018; 8:1096-1111. [PMID: 29903880 DOI: 10.1158/2159-8290.cd-18-0275] [Citation(s) in RCA: 218] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 05/17/2018] [Accepted: 06/13/2018] [Indexed: 12/28/2022]
Abstract
Clinically relevant subtypes exist for pancreatic ductal adenocarcinoma (PDAC), but molecular characterization is not yet standard in clinical care. We implemented a biopsy protocol to perform time-sensitive whole-exome sequencing and RNA sequencing for patients with advanced PDAC. Therapeutically relevant genomic alterations were identified in 48% (34/71) and pathogenic/likely pathogenic germline alterations in 18% (13/71) of patients. Overall, 30% (21/71) of enrolled patients experienced a change in clinical management as a result of genomic data. Twenty-six patients had germline and/or somatic alterations in DNA-damage repair genes, and 5 additional patients had mutational signatures of homologous recombination deficiency but no identified causal genomic alteration. Two patients had oncogenic in-frame BRAF deletions, and we report the first clinical evidence that this alteration confers sensitivity to MAPK pathway inhibition. Moreover, we identified tumor/stroma gene expression signatures with clinical relevance. Collectively, these data demonstrate the feasibility and value of real-time genomic characterization of advanced PDAC.Significance: Molecular analyses of metastatic PDAC tumors are challenging due to the heterogeneous cellular composition of biopsy specimens and rapid progression of the disease. Using an integrated multidisciplinary biopsy program, we demonstrate that real-time genomic characterization of advanced PDAC can identify clinically relevant alterations that inform management of this difficult disease. Cancer Discov; 8(9); 1096-111. ©2018 AACR.See related commentary by Collisson, p. 1062This article is highlighted in the In This Issue feature, p. 1047.
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Affiliation(s)
- Andrew J Aguirre
- Dana-Farber Cancer Institute, Boston, Massachusetts. .,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Jonathan A Nowak
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Nicholas D Camarda
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts.,Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Richard A Moffitt
- Department of Biomedical Informatics, Department of Pathology, Stony Brook University, Stony Brook, New York
| | - Arezou A Ghazani
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts
| | | | - Srivatsan Raghavan
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Jaegil Kim
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | | | | | | | - Emma Reilly
- Dana-Farber Cancer Institute, Boston, Massachusetts
| | - Devin McCabe
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts.,Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Lori Marini
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts.,Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts
| | - Kristin Anderka
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts
| | - Karla Helvie
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts
| | - Nelly Oliver
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts
| | - Ana Babic
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Annacarolina Da Silva
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Brandon Nadres
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | | | | | | | - Kelly P Burke
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Thomas Clancy
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Surgery, Brigham and Women's Hospital, Boston, Massachusetts
| | - James M Cleary
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Leona A Doyle
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Kunal Jajoo
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Gastroenterology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Nadine J McCleary
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Jeffrey A Meyerhardt
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Janet E Murphy
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Kimmie Ng
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Anuj K Patel
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Kimberly Perez
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Michael H Rosenthal
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Douglas A Rubinson
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Marvin Ryou
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Gastroenterology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Geoffrey I Shapiro
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Ewa Sicinska
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Stuart G Silverman
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Rebecca J Nagy
- Department of Medical Affairs, Guardant Health, Inc., Redwood City, California
| | - Richard B Lanman
- Department of Medical Affairs, Guardant Health, Inc., Redwood City, California
| | | | | | - Matthew B Yurgelun
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Charles S Fuchs
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts.,Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Levi A Garraway
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts
| | - Gad Getz
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Jason L Hornick
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Bruce E Johnson
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts
| | - Matthew H Kulke
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Robert J Mayer
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Jeffrey W Miller
- Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Paul B Shyn
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts
| | - David A Tuveson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York; Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor, New York
| | - Nikhil Wagle
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts.,Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts
| | - Jen Jen Yeh
- Departments of Surgery and Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina
| | - William C Hahn
- Dana-Farber Cancer Institute, Boston, Massachusetts.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
| | - Ryan B Corcoran
- Harvard Medical School, Boston, Massachusetts.,Massachusetts General Hospital Cancer Center, Boston, Massachusetts
| | - Scott L Carter
- Dana-Farber Cancer Institute, Boston, Massachusetts. .,Broad Institute of Harvard and MIT, Cambridge, Massachusetts.,Joint Center for Cancer Precision Medicine, Dana-Farber Cancer Institute/Brigham and Women's Hospital, Boston, Massachusetts.,Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Brian M Wolpin
- Dana-Farber Cancer Institute, Boston, Massachusetts. .,Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts.,Harvard Medical School, Boston, Massachusetts
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Maron SB, Alpert L, Kwak HA, Lomnicki S, Chase L, Xu D, O'Day E, Nagy RJ, Lanman RB, Cecchi F, Hembrough T, Schrock A, Hart J, Xiao SY, Setia N, Catenacci DVT. Targeted Therapies for Targeted Populations: Anti-EGFR Treatment for EGFR-Amplified Gastroesophageal Adenocarcinoma. Cancer Discov 2018; 8:696-713. [PMID: 29449271 PMCID: PMC5984701 DOI: 10.1158/2159-8290.cd-17-1260] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 01/11/2018] [Accepted: 02/09/2018] [Indexed: 02/07/2023]
Abstract
Previous anti-EGFR trials in unselected patients with gastroesophageal adenocarcinoma (GEA) were resoundingly negative. We identified EGFR amplification in 5% (19/363) of patients at the University of Chicago, including 6% (8/140) who were prospectively screened with intention-to-treat using anti-EGFR therapy. Seven patients received ≥1 dose of treatment: three first-line FOLFOX plus ABT-806, one second-line FOLFIRI plus cetuximab, and three third/fourth-line cetuximab alone. Treatment achieved objective response in 58% (4/7) and disease control in 100% (7/7) with a median progression-free survival of 10 months. Pretreatment and posttreatment tumor next-generation sequencing (NGS), serial plasma circulating tumor DNA (ctDNA) NGS, and tumor IHC/FISH for EGFR revealed preexisting and/or acquired genomic events, including EGFR-negative clones, PTEN deletion, KRAS amplification/mutation, NRAS, MYC, and HER2 amplification, and GNAS mutations serving as mechanisms of resistance. Two evaluable patients demonstrated interval increase of CD3+ infiltrate, including one who demonstrated increased NKp46+, and PD-L1 IHC expression from baseline, suggesting an immune therapeutic mechanism of action. EGFR amplification predicted benefit from anti-EGFR therapy, albeit until various resistance mechanisms emerged.Significance: This paper highlights the role of EGFR inhibitors in EGFR-amplified GEA-despite negative results in prior unselected phase III trials. Using serial ctDNA and tissue NGS, we identified mechanisms of primary and acquired resistance in all patients, as well as potential contribution of antibody-dependent cell-mediated cytotoxicity to their clinical benefit. Cancer Discov; 8(6); 696-713. ©2018 AACR.See related commentary by Strickler, p. 679This article is highlighted in the In This Issue feature, p. 663.
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Affiliation(s)
- Steven B Maron
- Department of Medicine, University of Chicago, Chicago, Illinois
| | - Lindsay Alpert
- Department of Pathology, University of Chicago, Chicago, Illinois
| | - Heewon A Kwak
- Department of Pathology, University of Chicago, Chicago, Illinois
| | | | - Leah Chase
- Department of Medicine, University of Chicago, Chicago, Illinois
| | - David Xu
- Department of Medicine, University of Chicago, Chicago, Illinois
| | - Emily O'Day
- Department of Medicine, University of Chicago, Chicago, Illinois
| | | | | | | | | | | | - John Hart
- Department of Pathology, University of Chicago, Chicago, Illinois
| | - Shu-Yuan Xiao
- Department of Pathology, University of Chicago, Chicago, Illinois
| | - Namrata Setia
- Department of Pathology, University of Chicago, Chicago, Illinois
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Bardelli A, Siravegna G, Sartore-Bianchi A, Nagy RJ, Mussolin B, Cassingena A, Martino C, Lonardi S, Zagonel V, Leone F, Amatu A, Trusolino L, Odegaard J, Lanman RB, Marsoni S, Siena S. Plasma HER2 (ERBB2) copy number to predict response to HER2-targeted therapy in metastatic colorectal cancer. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.3506] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Alberto Bardelli
- Istituto di Candiolo, Fondazione del Piemonte per l'Oncologia, IRCCS, Candiolo, Italy
| | - Giulia Siravegna
- Istituto di Candiolo, Fondazione del Piemonte per l'Oncologia, IRCCS, Candiolo, Italy
| | | | | | - Benedetta Mussolin
- Istituto di Candiolo, Fondazione del Piemonte per l'Oncologia, IRCCS, Candiolo, Italy
| | | | - Cosimo Martino
- Istituto di Candiolo, Fondazione del Piemonte per l'Oncologia, IRCCS, Candiolo, Italy
| | | | - Vittorina Zagonel
- Department of Clinical and Experimental Oncology, Medical Oncology 1, Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy
| | - Francesco Leone
- Division of Medical Oncology, Candiolo Cancer Institute, University of Turin, FPO, IRCCS, Italy, Candiolo, Italy
| | - Alessio Amatu
- Grande Ospedale Metropolitano Niguarda, Milan, Italy
| | - Livio Trusolino
- Istituto di Candiolo, Fondazione del Piemonte per l'Oncologia, IRCCS, Candiolo, Italy
| | | | | | - Silvia Marsoni
- Istituto di Candiolo, Fondazione del Piemonte per l'Oncologia, IRCCS, Candiolo, Italy
| | - Salvatore Siena
- Department of Hematology and Oncology, Niguarda Cancer Center, Grande Ospedale Metropolitano Niguarda, Milano, Italy
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Mody K, Borad MJ, Bekaii-Saab TS, Yang JD, Ramanathan RK, Ahn DH, Mahipal A, Roberts A, Nagy RJ, Kasi PM. Real-time circulating tumor DNA profiling of advanced cholangiocarcinoma (CCA). J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.4089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | | | | | | | - Daniel H. Ahn
- Ohio State University Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH
| | - Amit Mahipal
- H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
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Tan I, Stinchcombe T, Ready NE, Datto MB, Nagy RJ, Gu L, Clarke JM. Therapeutic outcomes in non-small cell lung cancer with BRAF mutations: A single institution, retrospective cohort study. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.e21222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Irena Tan
- Duke University Medical Center, Durham, NC, US
| | - Tom Stinchcombe
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | | | - Lin Gu
- Cancer and Leukemia Group B Statistical Center, Durham, NC
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Arshad J, Roberts A, Nagy RJ, Wilky BA, Trent JC. Utility of circulating tumor DNA (ctDNA) in the management of patients with gastrointestinal stromal tumor (GIST): Analysis of 152 patients. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.11539] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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49
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Lee CE, Wells AM, Sheehy N, Nagy RJ, Lanman RB. Opportunities for provider education in the use and interpretation of liquid biopsy. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.11017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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50
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Medford A, Niemierko A, Moy B, Spring L, Malvarosa G, Younger J, Lanman RB, Nagy RJ, Corcoran RB, Isakoff SJ, Ellisen LW, Juric D, Bardia A. Molecular alterations in the Ras-Raf-Erk (MAPK) pathway in metastatic hormone receptor positive (HR+)/HER2- breast cancer: Incidence and impact on clinical outcomes. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.1021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
| | | | - Beverly Moy
- Massachusetts General Hospital Cancer Center, Boston, MA
| | | | | | | | | | | | | | | | | | - Dejan Juric
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA
| | - Aditya Bardia
- Massachusetts General Hospital Cancer Center, Boston, MA
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