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Lapin M, Huang HJ, Chagani S, Javle M, Shroff RT, Pant S, Gouda MA, Raina A, Madwani K, Holley VR, Call SG, Dustin DJ, Lanman RB, Meric-Bernstam F, Raymond VM, Kwong LN, Janku F. Monitoring of Dynamic Changes and Clonal Evolution in Circulating Tumor DNA From Patients With IDH-Mutated Cholangiocarcinoma Treated With Isocitrate Dehydrogenase Inhibitors. JCO Precis Oncol 2022; 6:e2100197. [PMID: 35171660 PMCID: PMC8865526 DOI: 10.1200/po.21.00197] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [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: 05/05/2021] [Revised: 09/25/2021] [Accepted: 01/06/2022] [Indexed: 12/21/2022] Open
Abstract
PURPOSE IDH mutations occur in about 30% of patients with cholangiocarcinoma. Analysis of mutations in circulating tumor DNA (ctDNA) can be performed by droplet digital polymerase chain reaction (ddPCR). The analysis of ctDNA is a feasible approach to detect IDH mutations. METHODS We isolated ctDNA from the blood of patients with IDH-mutated advanced cholangiocarcinoma collected at baseline, on therapy, and at progression to isocitrate dehydrogenase (IDH) inhibitors. RESULTS Of 31 patients with IDH1R132 (n = 26) or IDH2R172 mutations (n = 5) in the tumor, IDH mutations were detected in 84% of ctDNA samples analyzed by ddPCR and in 83% of ctDNA samples analyzed by next-generation sequencing (NGS). Patients with a low variant allele frequency of ctDNA detected by NGS at baseline had a longer median time to treatment failure compared to patients with high variant allele frequency of ctDNA (3.6 v 1.5 months; P = .008). Patients with a decrease in IDH-mutated ctDNA on therapy by ddPCR compared with no change/increase had a trend to a longer median survival (P = .07). Most frequent emergent alterations in ctDNA by NGS at progression were ARID1A (n = 3) and TP53 mutations (n = 3). CONCLUSION Detection of IDH mutations in ctDNA in patients with advanced cholangiocarcinoma is feasible, and dynamic changes in ctDNA can correspond with the clinical course and clonal evolution.
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Affiliation(s)
- Morten Lapin
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
- Department of Hematology and Oncology, Stavanger University Hospital, Stavanger, Norway
| | - Helen J. Huang
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Sharmeen Chagani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Milind Javle
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Rachna T. Shroff
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
- Division of Hematology/Oncology, University of Arizona Cancer Center, Tucson, AZ
| | - Shubham Pant
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Mohamed A. Gouda
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Anjali Raina
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kiran Madwani
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Veronica R. Holley
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - S. Greg Call
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Derek J. Dustin
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Lawrence N. Kwong
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Filip Janku
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX
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Ezeife DA, Spackman E, Juergens RA, Laskin JJ, Agulnik JS, Hao D, Laurie SA, Law JH, Le LW, Kiedrowski LA, Melosky B, Shepherd FA, Cohen V, Wheatley-Price P, Vandermeer R, Li JJ, Fernandes R, Shokoohi A, Lanman RB, Leighl NB. The economic value of liquid biopsy for genomic profiling in advanced non-small cell lung cancer. Ther Adv Med Oncol 2022; 14:17588359221112696. [PMID: 35923926 PMCID: PMC9340413 DOI: 10.1177/17588359221112696] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 04/05/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022] Open
Abstract
Background: Liquid biopsy (LB) can detect actionable genomic alterations in plasma circulating tumor circulating tumor DNA beyond tissue testing (TT) alone in advanced non-small cell lung cancer (NSCLC) patients. We estimated the cost-effectiveness of adding LB to TT in the Canadian healthcare system. Methods: A cost-effectiveness analysis was conducted using a decision analytic Markov model from the Canadian public payer (Ontario) perspective and a 2-year time horizon in patients with treatment-naïve stage IV non-squamous NSCLC and ⩽10 pack-year smoking history. LB was performed using the comprehensive genomic profiling Guardant360™ assay. Standard of care TT for each participating institution was performed. Costs and outcomes of molecular testing by LB + TT were compared to TT alone. Transition probabilities were calculated from the VALUE trial (NCT03576937). Sensitivity analyses were undertaken to assess uncertainty in the model. Results: Use of LB + TT identified actionable alterations in more patients, 68.5 versus 52.7% with TT alone. Use of the LB + TT strategy resulted in an incremental cost savings of $3065 CAD per patient (95% CI, 2195–3945) and a gain in quality-adjusted life-years of 0.02 (95% CI, 0.01–0.02) versus TT alone. More patients received chemo-immunotherapy based on TT with higher overall costs, whereas more patients received targeted therapy based on LB + TT with net cost savings. Major drivers of cost-effectiveness were drug acquisition costs and prevalence of actionable alterations. Conclusion: The addition of LB to TT as initial molecular testing of clinically selected patients with advanced NSCLC did not increase system costs and led to more patients receiving appropriate targeted therapy.
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Affiliation(s)
- Doreen A. Ezeife
- Department of Oncology, Tom Baker Cancer Center, 1331 29 St NW, Toronto, ON T2N 4N2, Canada University of Calgary, Calgary, AB, Canada
| | | | | | - Janessa J. Laskin
- BC Cancer, The University of British Columbia, Vancouver, BC, Canada
| | - Jason S. Agulnik
- Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Desiree Hao
- Tom Baker Cancer Center, Calgary, AB, Canada University of Calgary, Calgary AB, Canada
| | - Scott A. Laurie
- Ottawa Hospital Research Institute/Department of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Jennifer H. Law
- Princess Margaret Cancer Center, University of Toronto, Toronto, ON, Canada
| | - Lisa W. Le
- Princess Margaret Cancer Center, University of Toronto, Toronto, ON, Canada
| | | | - Barbara Melosky
- BC Cancer, The University of British Columbia, Vancouver, BC, Canada
| | | | - Victor Cohen
- Jewish General Hospital, McGill University, Montreal, QC, Canada
| | - Paul Wheatley-Price
- Ottawa Hospital Research Institute/Department of Medicine, University of Ottawa, Ottawa, ON, Canada
| | | | - Janice J. Li
- Princess Margaret Cancer Center, University of Toronto, Toronto, ON, Canada
| | - Roxanne Fernandes
- Princess Margaret Cancer Center, University of Toronto, Toronto, ON, Canada
| | - Aria Shokoohi
- BC Cancer, The University of British Columbia, Vancouver, BC, Canada
| | | | - Natasha B. Leighl
- Princess Margaret Cancer Center, University of Toronto, Toronto, ON, Canada
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Kingston B, Cutts RJ, Bye H, Beaney M, Walsh-Crestani G, Hrebien S, Swift C, Kilburn LS, Kernaghan S, Moretti L, Wilkinson K, Wardley AM, Macpherson IR, Baird RD, Roylance R, Reis-Filho JS, Hubank M, Faull I, Banks KC, Lanman RB, Garcia-Murillas I, Bliss JM, Ring A, Turner NC. Author Correction: Genomic profile of advanced breast cancer in circulating tumor DNA. Nat Commun 2021; 12:4479. [PMID: 34272402 PMCID: PMC8285402 DOI: 10.1038/s41467-021-24791-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Belinda Kingston
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Rosalind J Cutts
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Hannah Bye
- Centre for Molecular Pathology, Royal Marsden Hospital, London, UK
| | - Matthew Beaney
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Giselle Walsh-Crestani
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Sarah Hrebien
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Claire Swift
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | | | - Laura Moretti
- ICR-CTSU, The Institute of Cancer Research, London, UK
| | | | - Andrew M Wardley
- NIHR Manchester Clinical Research Facility at The Christie, Manchester Academic Health Science Centre & Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology Medicine & Health, University of Manchester, Manchester, UK
| | | | | | - Rebecca Roylance
- University College London Hospitals NHS Foundation Trust, London, UK
| | | | - Michael Hubank
- Centre for Molecular Pathology, Royal Marsden Hospital, London, UK
| | - Iris Faull
- Guardant Health, Inc., Redwood City, CA, USA
| | | | | | - Isaac Garcia-Murillas
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | - Alistair Ring
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK.
| | - Nicholas C Turner
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK.
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Page RD, Drusbosky L, Dada HI, Raymond VM, Daniel DB, Divers SG, Reckamp KL, Villalona-Calero MA, Odegaard JI, Lanman RB, Papadimitrakopoulou V, Leighl NB. Clinical outcomes for plasma-based comprehensive genomic profiling versus tissue testing in advanced lung adenocarcinoma. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.9027] [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
9027 Background: Somatic genomic testing is recommended by numerous expert guidelines to inform targeted therapy treatment for patients with advanced lung adenocarcinoma (aLUAD). The NILE study was a prospective observational study that demonstrated non-inferiority of cell-free circulating tumor DNA (cfDNA)-based tumor genotyping compared to tissue-based genotyping to find targetable genomic alterations in patients with newly diagnosed aLUAD. As the cohort has matured, clinical outcomes data can now be reported. Methods: This prospective, multicenter North American study (NCT03615443) enrolled patients with previously untreated aLUAD who had standard of care (SOC) tissue genotyping performed and concurrent comprehensive cfDNA analysis using the commercially available Guardant360 assay (Guardant Health, Redwood City, CA). After 12 months of study enrollment, objective response rates, disease control rate, and time to treatment data were collected for patients with targetable genomic alterations, as defined by NCCN guidelines, who were treated with physician’s choice of therapy. Results: Among 282 patients on the study, 89 (31.6%) had an actionable biomarker detected by tissue (21.3%) and/or cfDNA (27.3%) analysis. Sixty-one (68.5%) of these patients were treated with an FDA-approved targeted therapy guided by somatic genotyping results ( EGFR, ALK, ROS1). Thirty-three patients were eligible for clinical response evaluation and demonstrated an objective response rate of 58% and disease control rate of 94%. Twenty-five (76%) achieved a durable response > 6 months; 17 (52%) achieved a durable response > 12 months. Patients responded to targeted therapy regardless of the variant allele frequency of the target alteration. The time to treatment (TtT) was significantly faster for cfDNA-informed biomarker detection as compared to tissue genotyping (median 18 vs 31 days, respectively; p = 0.0008). Conclusions: This is the first prospective community-based study to find that cfDNA detects guideline-recommended biomarkers at a rate similar to tissue genotyping, and therapeutic outcomes based on plasma-based comprehensive genomic profiling are comparable to published tissue-based targeted therapy clinical outcomes. The NILE study complements and confirms findings in the prospective FLAURA and SLLIP studies, which exclusively enrolled at academic sites. Clinical trial information: NCT03615443.
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Affiliation(s)
- Ray D. Page
- The Center for Cancer and Blood Disorders, Fort Worth, TX
| | | | | | | | - Davey B. Daniel
- Sarah Cannon Research Institute, Tennessee Oncology-Chattanooga, Chattanooga, TN
| | | | | | | | | | | | | | - Natasha B. Leighl
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
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Kingston B, Cutts RJ, Bye H, Beaney M, Walsh-Crestani G, Hrebien S, Swift C, Kilburn LS, Kernaghan S, Moretti L, Wilkinson K, Wardley AM, Macpherson IR, Baird RD, Roylance R, Reis-Filho JS, Hubank M, Faull I, Banks KC, Lanman RB, Garcia-Murillas I, Bliss JM, Ring A, Turner NC. Genomic profile of advanced breast cancer in circulating tumour DNA. Nat Commun 2021; 12:2423. [PMID: 33893289 PMCID: PMC8065112 DOI: 10.1038/s41467-021-22605-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 03/16/2021] [Indexed: 12/31/2022] Open
Abstract
The genomics of advanced breast cancer (ABC) has been described through tumour tissue biopsy sequencing, although these approaches are limited by geographical and temporal heterogeneity. Here we use plasma circulating tumour DNA sequencing to interrogate the genomic profile of ABC in 800 patients in the plasmaMATCH trial. We demonstrate diverse subclonal resistance mutations, including enrichment of HER2 mutations in HER2 positive disease, co-occurring ESR1 and MAP kinase pathway mutations in HR + HER2- disease that associate with poor overall survival (p = 0.0092), and multiple PIK3CA mutations in HR + disease that associate with short progression free survival on fulvestrant (p = 0.0036). The fraction of cancer with a mutation, the clonal dominance of a mutation, varied between genes, and within hotspot mutations of ESR1 and PIK3CA. In ER-positive breast cancer subclonal mutations were enriched in an APOBEC mutational signature, with second hit PIK3CA mutations acquired subclonally and at sites characteristic of APOBEC mutagenesis. This study utilises circulating tumour DNA analysis in a large clinical trial to demonstrate the subclonal diversification of pre-treated advanced breast cancer, identifying distinct mutational processes in advanced ER-positive breast cancer, and novel therapeutic opportunities.
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Affiliation(s)
- Belinda Kingston
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Rosalind J Cutts
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Hannah Bye
- Centre for Molecular Pathology, Royal Marsden Hospital, London, UK
| | - Matthew Beaney
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Giselle Walsh-Crestani
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Sarah Hrebien
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | - Claire Swift
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | | | - Laura Moretti
- ICR-CTSU, The Institute of Cancer Research, London, UK
| | | | - Andrew M Wardley
- NIHR Manchester Clinical Research Facility at The Christie, Manchester Academic Health Science Centre & Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology Medicine & Health, University of Manchester, Manchester, UK
| | | | | | - Rebecca Roylance
- University College London Hospitals NHS Foundation Trust, London, UK
| | | | - Michael Hubank
- Centre for Molecular Pathology, Royal Marsden Hospital, London, UK
| | - Iris Faull
- Guardant Health, Inc., Redwood City, CA, USA
| | | | | | - Isaac Garcia-Murillas
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK
| | | | - Alistair Ring
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK.
| | - Nicholas C Turner
- The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, UK.
- Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, UK.
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Lanman RB, Hylkema L, Boone CM, Allée B, Castillo RO, Moreno SA, Flores MF, DeSilva U, Bingham B, Kemp BM. Ancient DNA analysis of archaeological specimens extends Chinook salmon's known historic range to San Francisco Bay's tributaries and southernmost watershed. PLoS One 2021; 16:e0244470. [PMID: 33857143 PMCID: PMC8049268 DOI: 10.1371/journal.pone.0244470] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/18/2021] [Indexed: 11/23/2022] Open
Abstract
Understanding a species’ historic range guides contemporary management and habitat restoration. Chinook salmon (Oncorhynchus tshawytscha) are an important commercial and recreational gamefish, but nine Chinook subspecies are federally threatened or endangered due to anthropogenic impacts. Several San Francisco Bay Area streams and rivers currently host spawning Chinook populations, but government agencies consider these non-native hatchery strays. Through the morphology-based analysis of 17,288 fish specimens excavated from Native American middens at Mission Santa Clara (CA-SCL-30H), Santa Clara County, circa 1781–1834 CE, 88 salmonid vertebrae were identified. Ancient DNA sequencing identified three separate individuals as Chinook salmon and the remainder as steelhead/rainbow trout (Oncorhynchus mykiss). These findings comprise the first physical evidence of the nativity of salmon to the Guadalupe River in San Jose, California, extending their documented historic range to include San Francisco Bay’s southernmost tributary watershed.
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Affiliation(s)
- Richard B. Lanman
- Guadalupe-Coyote Resource Conservation District, San Jose, California, United States of America
- Institute for Historical Ecology, Los Altos, California, United States of America
- * E-mail:
| | - Linda Hylkema
- University Operations, Cultural Resource Management Program, Santa Clara University, Santa Clara, California, United States of America
| | - Cristie M. Boone
- Albion Environmental, Inc., Santa Cruz, California, United States of America
| | - Brian Allée
- South Bay Clean Creeks Coalition, San Jose, California, United States of America
| | - Roger O. Castillo
- Salmon and Steelhead Restoration Group, Inc., San Jose, California, United States of America
| | - Stephanie A. Moreno
- Guadalupe-Coyote Resource Conservation District, San Jose, California, United States of America
| | - Mary Faith Flores
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Upuli DeSilva
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Brittany Bingham
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, United States of America
| | - Brian M. Kemp
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, United States of America
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7
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Pascual J, Cutts RJ, Kingston B, Hrebien S, Kilburn LS, Kernaghan S, Moretti L, Wilkinson K, Wardley AM, Macpherson IR, Baird RD, Roylance R, Hubank M, Walsh G, Faull I, Banks KC, Lanman RB, Garcia-Murillas I, Bliss JM, Ring A, Turner NC. Abstract PS5-02: Assessment of early ctDNA dynamics to predict efficacy of targeted therapies in metastatic breast cancer: Results from plasmaMATCH trial. Cancer Res 2021. [DOI: 10.1158/1538-7445.sabcs20-ps5-02] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: Early changes in circulating tumour DNA (ctDNA) levels may identify which patients respond to therapy earlier than imaging, with ctDNA levels falling rapidly in patients who respond to therapy. The plasmaMATCH trial assessed the utility of ctDNA testing with an error-corrected 73-gene targeted panel (Guardant360, Guardant Health) to allocate patients to four mutation matched therapy cohorts. ESR1-extended fulvestrant (A), HER2-neratinib +/- fulvestrant (B), AKT1-capivasertib + fulvestrant (C), AKT basket-capivasertib (D). Here, we report paired baseline and early on treatment ctDNA analysis from plasmaMATCH, to establish the optimal criteria for predicting progression free survival (PFS). Methods: In plasmaMATCH treatment cohorts, plasma samples were collected for ctDNA analysis pre-treatment at cycle 1-day 1 (C1D1) and cycle 2-day 1 (C2D1) timepoints, and sequenced with the Guardant 360 assay. Patients were included if they had a minimum of 14 days of treatment in the first cycle. Multiple different methods were investigated to integrate variant allele fractions (VAF) of mutations identified at each timepoint to estimate the level of ctDNA, including maximum VAF, mean VAF and weighted mean VAF, and weighted mean VAF of clonal mutations at C1D1. Variants with a VAF <0.3%, set as the limit of detection, in C1D1 were excluded. Genes frequently mutated in CHIP were excluded (GNAS, JAK2, IDH1, IDH2 and ATM) from the weighted mean VAF of clonal mutations method. The circulating DNA ratio (CDR) was calculated as the ratio of C2D1 level relative to C1D1 level. The optimal cut-point for predicting PFS was assessed by fitting a range of cutpoints for each VAF integration method, identifying the cut-point with the highest Harrell’s C-index. Results: A total of 142 patients were enrolled into plasmaMATCH cohorts A-D, 79 patients had samples sent for paired C1D1-C2D1 plasma ctDNA sequencing, 1 failed sequencing and 1 insufficient treatment, and 77 (54%) patients had assessable C1D1-C2D1 plasma ctDNA sequencing results (45 cohort A, 12 cohort B, 12 cohort C, 8 cohort D). A weighted mean of clonal mutations in C1D1 ctDNA sequencing was the optimal method for integrating VAF, with peak C-Index 0.67. At the optimal C-index cutoff of 0.132, median PFS with high ctDNA CDR was 2.4 months (95% CI 2.0-3.7) and with suppressed ctDNA CDR was 9.9 months (95% CI 7.0-13.7) (HR 4.3, 95% CI 2.4-7.6, p<0.0001). Early changes in ctDNA level were also predictive in cohorts A extended dose fulvestrant alone (HR 5.8, 95% CI 2.2-16, p=0.0001) and cohorts B-D of targeted therapy (HR 3.8, 95% CI 1.7-8.6, p=0.00063). In analysis that was not pre-planned, patients with undetectable ctDNA at C2D1 had a particularly good outcome (p<0.0001, table 1). Conclusions: We identify an optimal methodology for assessing early dynamic changes in ctDNA that predicts treatment efficacy in patients with metastatic breast cancer. This methodology will require validation in independent data-sets, and if validated would allow trials of adapting therapy on the basis of early ctDNA dynamics.
Table 1ctDNA dynamics categoryMedian PFS months (95%CI)6-month PFSORRUndetectable (N=11) CDR=018.2 (10.2-NA)91%9/11 (82%)Suppressed (N=14) CDR <0.132 and >05.4 (4.6-NA)48%6/14 (43%)High (N=52) CDR >=0.1322.4 (2.0-3.7)8%4/52 (8%)
Citation Format: Javier Pascual, Rosalind J Cutts, Belinda Kingston, Sarah Hrebien, Lucy S Kilburn, Sarah Kernaghan, Laura Moretti, Katie Wilkinson, Andrew M Wardley, Iain R Macpherson, Richard D Baird, Rebecca Roylance, Michael Hubank, Giselle Walsh, Iris Faull, Kimberly C Banks, Richard B Lanman, Isaac Garcia-Murillas, Judith M Bliss, Alistair Ring, Nicholas C Turner. Assessment of early ctDNA dynamics to predict efficacy of targeted therapies in metastatic breast cancer: Results from plasmaMATCH trial [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS5-02.
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Affiliation(s)
- Javier Pascual
- 1The Royal Marsden NHS Foundation Trust and The Institute of Cancer Research, London, United Kingdom
| | | | | | - Sarah Hrebien
- 2The Institute of Cancer Research, London, United Kingdom
| | - Lucy S Kilburn
- 2The Institute of Cancer Research, London, United Kingdom
| | | | - Laura Moretti
- 2The Institute of Cancer Research, London, United Kingdom
| | | | | | - Iain R Macpherson
- 4Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Richard D Baird
- 5Cancer Research UK Cambridge Centre, Cambridge, United Kingdom
| | - Rebecca Roylance
- 6University College London Hospitals NHS Foundation Trust, London, United Kingdom
| | - Michael Hubank
- 2The Institute of Cancer Research, London, United Kingdom
| | - Giselle Walsh
- 2The Institute of Cancer Research, London, United Kingdom
| | | | | | | | | | - Judith M Bliss
- 2The Institute of Cancer Research, London, United Kingdom
| | - Alistair Ring
- 1The Royal Marsden NHS Foundation Trust and The Institute of Cancer Research, London, United Kingdom
| | - Nicholas C Turner
- 1The Royal Marsden NHS Foundation Trust and The Institute of Cancer Research, London, United Kingdom
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8
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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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Lam VK, Zhang J, Wu CC, Tran HT, Li L, Diao L, Wang J, Rinsurongkawong W, Raymond VM, Lanman RB, Lewis J, Roarty EB, Roth J, Swisher S, Lee JJ, Gibbons DL, Papadimitrakopoulou VA, Heymach JV. Genotype-Specific Differences in Circulating Tumor DNA Levels in Advanced NSCLC. J Thorac Oncol 2020; 16:601-609. [PMID: 33388476 DOI: 10.1016/j.jtho.2020.12.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [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: 09/02/2020] [Revised: 12/03/2020] [Accepted: 12/13/2020] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Plasma-based circulating tumor DNA (ctDNA) is an established biomarker for molecular profiling with emerging applications in disease monitoring in multiple tumor types, including, NSCLC. However, determinants of ctDNA shedding and correlation with tumor burden are incompletely understood, particularly in advanced-stage disease. METHODS We retrospectively analyzed ctDNA-based and tissue-based genomic data and imaging from 144 patients with NSCLC. Tumor burden was quantified with computed tomography (CT) and brain magnetic resonance imaging for the overall cohort and 18F-fludeoxyglucose positron emission tomography-CT in a subset of patients. RESULTS There was a moderate but statistically significant correlation between ctDNA variant allele frequency and multiple imaging measures of tumor burden such as CT volume (rho = 0.34, p ≤ 0.0001) and metabolic tumor volume (rho = 0.36, p = 0.003). This correlation was strongest in KRAS-mutant tumors (rho = 0.56, p ≤ 0.001), followed by TP53 mutants (rho = 0.43, p ≤ 0.0001), and weakest in EGFR-mutated (EGFR+) tumors (rho = 0.24, p = 0.077). EGFR+ tumors with EGFR copy number gain had significantly higher variant allele frequency than EGFR+ without copy number gain (p ≤ 0.00001). In multivariable analysis, TP53 and EGFR mutations, visceral metastasis, and tumor burden were independent predictors of increased ctDNA shedding. CONCLUSIONS Levels of detectable ctDNA were affected not only by tumor burden but also by tumor genotype. The genotype-specific differences observed may be due to variations in DNA shedding and cellular turnover. These findings have implications for the emerging use of ctDNA in NSCLC disease monitoring and early detection.
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Affiliation(s)
- Vincent K Lam
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jianjun Zhang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Carol C Wu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hai T Tran
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lerong Li
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lixia Diao
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jing Wang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Waree Rinsurongkawong
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - Jeff Lewis
- Department of Thoracic/Head and Neck Medical Oncology, 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
| | - Jack Roth
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephen Swisher
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - J Jack Lee
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Don L Gibbons
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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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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11
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Charo LM, Eskander RN, Okamura R, Patel SP, Nikanjam M, Lanman RB, Piccioni DE, Kato S, McHale MT, Kurzrock R. Clinical implications of plasma circulating tumor DNA in gynecologic cancer patients. Mol Oncol 2020; 15:67-79. [PMID: 32881280 PMCID: PMC7782073 DOI: 10.1002/1878-0261.12791] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [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: 05/21/2020] [Revised: 07/21/2020] [Accepted: 08/27/2020] [Indexed: 12/17/2022] Open
Abstract
Molecular characterization of cancers is important in dictating prognostic factors and directing therapy. Next‐generation sequencing of plasma circulating tumor DNA (ctDNA) offers less invasive, more convenient collection, and a more real‐time representation of a tumor and its molecular heterogeneity than tissue. However, little is known about the clinical implications of ctDNA assessment in gynecologic cancer. We describe the molecular landscape identified on ctDNA, ctDNA concordance with tissue‐based analysis, and factors associated with overall survival (OS) in gynecologic cancer patients with ctDNA analysis. We reviewed clinicopathologic and genomic information for 105 consecutive gynecologic cancer patients with ctDNA analysis, including 78 with tissue‐based sequencing, enrolled in the Profile‐Related Evidence Determining Individualized Cancer Therapy (NCT02478931) trial at the University of California San Diego Moores Cancer Center starting July 2014. Tumors included ovarian (47.6%), uterine (35.2%), cervical (12.4%), vulvovaginal (2.9%), and unknown gynecologic primary (1.9%). Most ovarian and uterine cancers (86%) were high grade. 34% (N = 17) of ovarian cancers had BRCA alterations, and 22% (N = 11) were platinum sensitive. Patients received median 2 (range 0–13) lines of therapy prior to ctDNA collection. Most (75.2%) had at least one characterized alteration on ctDNA analysis, and the majority had unique genomic profiles on ctDNA. Most common alterations were TP53 (N = 59, 56.2% of patients), PIK3CA (N = 26, 24.8%), KRAS (N = 14, 13.3%), BRAF (N = 10, 9.5%), ERBB2 (N = 8, 7.6%), and MYC (N = 8, 7.6%). Higher ctDNA maximum mutation allele frequency was associated with worse OS [hazard ratio (HR): 1.91, P = 0.03], while therapy matched to ctDNA alterations (N = 33 patients) was independently associated with improved OS (HR: 0.34, P = 0.007) compared to unmatched therapy (N = 28 patients) in multivariate analysis. Tissue and ctDNA genomic results showed high concordance unaffected by temporal or spatial factors. This study provides evidence for the utility of ctDNA in determining outcome and individualizing cancer therapy in patients with gynecologic cancer.
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Affiliation(s)
- Lindsey M Charo
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Ramez N Eskander
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Ryosuke Okamura
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, University of California San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Sandip P Patel
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, University of California San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Mina Nikanjam
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, University of California San Diego Moores Cancer Center, La Jolla, CA, USA
| | | | - David E Piccioni
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, University of California San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Shumei Kato
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, University of California San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Michael T McHale
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego Moores Cancer Center, La Jolla, CA, USA
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, University of California San Diego Moores Cancer Center, La Jolla, CA, USA
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12
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Baumgartner JM, Riviere P, Lanman RB, Kelly KJ, Veerapong J, Lowy AM, Kurzrock R. Prognostic Utility of Pre- and Postoperative Circulating Tumor DNA Liquid Biopsies in Patients with Peritoneal Metastases. Ann Surg Oncol 2020; 27:3259-3267. [PMID: 32767050 DOI: 10.1245/s10434-020-08331-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [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: 06/30/2019] [Indexed: 12/14/2022]
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) is a promising technology for treatment selection, prognostication, and surveillance after definitive therapy. Its use in the perioperative setting for patients with metastatic disease has not been well studied. We characterize perioperative plasma ctDNA and its association with progression-free survival (PFS) in patients undergoing surgery for peritoneal metastases. PATIENTS AND METHODS We recruited 71 patients undergoing surgery for peritoneal metastases and evaluated their plasma with a targeted 73-gene ctDNA next-generation sequencing test before and after surgery. The association between perioperative ctDNA, as well as other patient factors, and PFS was evaluated by Cox regression. RESULTS ctDNA was detectable in 28 patients (39.4%) preoperatively and in 37 patients (52.1%) postoperatively. Patients with high ctDNA [maximum somatic variant allele fraction (MSVAF) > 0.25%] had worse PFS than those with low MSVAF (< 0.25%) in both the pre- and postoperative settings (median 4.8 vs. 19.3 months, p < 0.001, and 9.2 vs.15.0 months, p = 0.049, respectively; log-rank test). On multivariate analysis, high-grade histology [hazard ratio (HR) 3.42, p = 0.001], incomplete resection (HR 2.35, p = 0.010), and high preoperative MSVAF (HR 3.04, p = 0.001) were associated with worse PFS. Patients with new postoperative alterations in the context of preoperative alteration(s) also had a significantly shorter PFS compared with other groups (HR 4.28, p < 0.001). CONCLUSIONS High levels of perioperative ctDNA and new postoperative ctDNA alterations in the context of preoperative alterations predict worse outcomes in patients undergoing resection for peritoneal metastases. This may highlight a role for longitudinal ctDNA surveillance in this population.
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Affiliation(s)
- Joel M Baumgartner
- Department of Surgery, Division of Surgical Oncology, University of California, San Diego, La Jolla, CA, USA.
| | - Paul Riviere
- Center for Personalized Cancer Therapy, University of California, San Diego, La Jolla, CA, USA
| | | | - Kaitlyn J Kelly
- Department of Surgery, Division of Surgical Oncology, University of California, San Diego, La Jolla, CA, USA
| | - Jula Veerapong
- Department of Surgery, Division of Surgical Oncology, University of California, San Diego, La Jolla, CA, USA
| | - Andrew M Lowy
- Department of Surgery, Division of Surgical Oncology, University of California, San Diego, La Jolla, CA, USA
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy, University of California, San Diego, La Jolla, CA, USA
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13
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Mack PC, Banks KC, Espenschied CR, Burich RA, Zill OA, Lee CE, Riess JW, Mortimer SA, Talasaz A, Lanman RB, Gandara DR. Spectrum of driver mutations and clinical impact of circulating tumor DNA analysis in non-small cell lung cancer: Analysis of over 8000 cases. Cancer 2020; 126:3219-3228. [PMID: 32365229 PMCID: PMC7383626 DOI: 10.1002/cncr.32876] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/16/2019] [Accepted: 11/12/2019] [Indexed: 01/24/2023]
Abstract
BACKGROUND Circulating cell-free tumor DNA (ctDNA)-based mutation profiling, if sufficiently sensitive and comprehensive, can efficiently identify genomic targets in advanced lung adenocarcinoma. Therefore, the authors investigated the accuracy and clinical utility of a commercially available digital next-generation sequencing platform in a large series of patients with non-small cell lung cancer (NSCLC). METHODS Plasma-based comprehensive genomic profiling results from 8388 consecutively tested patients with advanced NSCLC were analyzed. Driver and resistance mutations were examined with regard to their distribution, frequency, co-occurrence, and mutual exclusivity. RESULTS Somatic alterations were detected in 86% of samples. The median variant allele fraction was 0.43% (range, 0.03%-97.62%). Activating alterations in actionable oncogenes were identified in 48% of patients, including EGFR (26.4%), MET (6.1%), and BRAF (2.8%) alterations and fusions (ALK, RET, and ROS1) in 2.3%. Treatment-induced resistance mutations were common in this cohort, including driver-dependent and driver-independent alterations. In the subset of patients who had progressive disease during EGFR therapy, 64% had known or putative resistance alterations detected in plasma. Subset analysis revealed that ctDNA increased the identification of driver mutations by 65% over standard-of-care, tissue-based testing at diagnosis. A pooled data analysis on this plasma-based assay demonstrated that targeted therapy response rates were equivalent to those reported from tissue analysis. CONCLUSIONS Comprehensive ctDNA analysis detected the presence of therapeutically targetable driver and resistance mutations at the frequencies and distributions predicted for the study population. These findings add support for comprehensive ctDNA testing in patients who are incompletely tested at the time of diagnosis and as a primary option at the time of progression on targeted therapies.
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Affiliation(s)
- Philip C. Mack
- Division of Hematology‐OncologyDepartment of Internal MedicineUniversity of California Davis Comprehensive Cancer CenterSacramentoCalifornia
- College of MedicineCalifornia Northstate UniversityElk GroveCalifornia
| | | | | | - Rebekah A. Burich
- Division of Hematology‐OncologyDepartment of Internal MedicineUniversity of California Davis Comprehensive Cancer CenterSacramentoCalifornia
| | - Oliver A. Zill
- Guardant Health, IncRedwood CityCalifornia
- Present address:
GenentechSouth San FranciscoCalifornia
| | | | - Jonathan W. Riess
- Division of Hematology‐OncologyDepartment of Internal MedicineUniversity of California Davis Comprehensive Cancer CenterSacramentoCalifornia
| | | | | | | | - David R. Gandara
- Division of Hematology‐OncologyDepartment of Internal MedicineUniversity of California Davis Comprehensive Cancer CenterSacramentoCalifornia
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14
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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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Agulnik J, Law JH, Juergens R, Laskin J, Laurie S, Hao D, Ezeife DA, Le LW, Kiedrowski LA, Lanman RB, Leighl NB. Abstract A26: Defining VALUE: Routine liquid biopsy in NSCLC diagnosis—a Canadian trial in progress. Clin Cancer Res 2020. [DOI: 10.1158/1557-3265.liqbiop20-a26] [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: Genotyping tumor tissue in time for clinical treatment decision-making has been challenging in advanced non-small cell lung cancer (NSCLC). Next-generation sequencing (NGS) of cell-free DNA (cfDNA) obtained from blood samples may improve diagnostic testing, with faster turnaround time (TAT) and potential cost savings. This study defines the added value of cfDNA versus tumor tissue genotyping in patients with advanced NSCLC in the Canadian public health care system.
Methods: Patients with advanced non-squamous NSCLC patients at 6 cancer centers across Canada are being recruited (BC, Alberta, Ontario, Quebec). Two cohorts are included: 1) treatment-naïve patients with ≤10 pack year smoking history (N=150) and 2) patients with known oncogenic drivers (e.g., EGFR, ALK, ROS1, BRAF) that have progressed on tyrosine kinase inhibitors (N=60). Consenting patients undergo peripheral blood draw and cfDNA NGS analysis using Guardant360™ (Guardant Health), a validated assay that detects alterations in 74 known cancer-associated genes, prior to starting treatment (Cohort 1) or next line of treatment (Cohort 2). Standard-of-care (SOC) tissue profiling is completed per institutional standards. Endpoints include response, progression-free survival, time-to-treatment failure, as well as time to treatment initiation, number of actionable genomic alterations identified, result TAT, patient-reported quality of life (EQ-5D), and willingness to pay. A decision-analytic model will be developed to perform a cost-consequence analysis of cfDNA versus tissue-based diagnostics.
Results: Between February and October 3, 2019, 49 patients (32 female, 17 male) were recruited to Cohort 1 and 31 (21 female, 10 male) to Cohort 2. Forty patients in Cohort 1 (81.6%) had ≥1 alteration detected, with a total of 145 genetic alterations detected in 36 genes. Of these, 68 were actionable with FDA-approved drugs and/or clinical trials available. The most frequent actionable alterations were in EGFR (33.8%), MET Exon 14 Skipping (7.4%), and EML4-ALK fusion (2.9%). Additional alterations included TP53 (29.4%), KRAS (8.8%), PIK3CA (4.4%), and STK11 (2.9%). In Cohort 2, 29 patients (93.5%, 29/31) had ≥1 alteration detected, with a total of 130 alterations in 33 genes. The most frequent alterations were in EGFR (46.0%), TP53 (9.5%), EML4-ALK fusion (6.3%), ALK mutations (4.8%), and BRAF, BRCA2, GNAS, KRAS, MET Exon 14 Skipping, NRAS, and PTEN (each 3.2%). In samples with alterations detected, the median number of alterations/patient was 3 (range 1-17). The median time to Guardant report was 8 days (range 5-27). Mutations detected in tissue, concordance, and time to result for SOC tissue profiling will be updated, along with incremental treatment options for patients.
Conclusion: Over 86% of advanced NSCLC patients had detectable cfDNA and at least 61 had actionable mutations. Blood-based testing may be an important cost-efficient addition to tissue-based testing in lung cancer to determine optimal treatment options.
Citation Format: Jason Agulnik, Jennifer H. Law, Rosalyn Juergens, Janessa Laskin, Scott Laurie, Desiree Hao, Doreen A. Ezeife, Lisa W. Le, Lesli A. Kiedrowski, Richard B. Lanman, Natasha B. Leighl. Defining VALUE: Routine liquid biopsy in NSCLC diagnosis—a Canadian trial in progress [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr A26.
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Affiliation(s)
| | | | | | | | - Scott Laurie
- 5Ottawa Hospital Regional Cancer Centre, Ottawa, ON, Canada,
| | - Desiree Hao
- 6Tom Baker Cancer Centre, Calgary, AB, Canada,
| | | | - Lisa W. Le
- 2Princess Margaret Cancer Centre, Toronto, ON, Canada,
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16
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Juergens RA, Ezeife DA, Laskin JJ, Agulnik JS, Hao D, Laurie SA, Law JH, Le LW, Kiedrowski LA, Shepherd FA, Cohen V, Shokoohi A, Vandermeer R, Li JJ, Hanson I, Fernandes R, Salvarrey AM, Lanman RB, Leighl NB. Demonstrating the value of liquid biopsy for lung cancer in a public health care system. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.15_suppl.3546] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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
3546 Background: Given the challenges of molecular profiling in patients with advanced lung cancer, this prospective study examines clinical outcomes and utility of liquid biopsy in treatment naive stage IV lung adenocarcinoma patients (Cohort 1) and in the setting of resistance to targeted therapy (Cohort 2; not reported here). Methods: This study is being conducted at 6 Canadian centres (NCT03576937) using Guardant 360 (G360), a validated cell-free DNA next-generation sequencing assay that identifies variants in 74 cancer-associated genes, including fusions and copy number gain. Cohort 1 (N = 150) includes patients with treatment-naïve advanced non-squamous lung carcinoma, ≤10 pack-year smoking history, and measurable disease. Patients received standard of care tumour tissue (TT) molecular profiling ( EGFR, ALK +/- ROS1) and liquid biopsy (LB). The primary endpoint was response rate to first-line therapy (RECIST 1.1); secondary endpoints include incremental targetable alterations identified through G360 ( EGFR, ALK, BRAF, ERBB2, KRAS (G12C), NTRK, MET (amplification, exon 14 skipping), RET, ROS1), turn-around time (TAT) and successful molecular profiling rates. Results: To date, 84 eligible patients with clinical data have been accrued to Cohort 1. Median age is 64 (range 23-91), 64% are female, 85% never smokers, 96% have adenocarcinoma. Actionable targets have been identified in 55% of patients using G360 ( EGFR/ALK in 37%), 39% using standard TT profiling. Eight EGFR/ALK aberrations were identified in TT but not LB, while 6 were identified in LB but not TT. TT profiling for EGFR/ALK was unsuccessful in 8% of patients (insufficient tissue, failed biopsy). Fourteen patients (17%) had no ctDNA alterations detected by G360 (low disease burden vs. non-shedding). Of 75 patients receiving first-line treatment, 57% received targeted therapy, 28% chemotherapy combinations, 11% checkpoint inhibitors and 4% were observed. Treatment decisions were informed by G360 alone in 37% and by G360+TT results in 27% (by physician report). Among 46 evaluable patients, ORR was 54% (25/46). Using G360, ORR was 75% (15/20) in those with actionable alterations and 38.5% (10/26) in those without. Using TT, ORR was 67% (14/21) in those with actionable alterations and 44% (11/25) in those without. Mean TAT was 7.9 days (SD+/-1.7) for LB vs 19.9 days (SD+/- 9.8) for TT. Conclusions: Liquid biopsy using G360 identifies actionable targets beyond tissue profiling alone in newly diagnosed lung cancer patients, has faster TAT and yields similar outcomes with targeted and non-targeted therapy. Clinical trial information: NCT03576937 .
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Affiliation(s)
| | | | | | | | - Desiree Hao
- Tom Baker Cancer Centre, Calgary, AB, Canada
| | | | | | - Lisa W Le
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | - Frances A. Shepherd
- Cancer Clinical Research Unit, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | | | | | | | | | - Inna Hanson
- Princess Margaret Cancer Centre, Toronto, ON, Canada
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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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Pairawan S, Hess KR, Janku F, Sanchez NS, Mills Shaw KR, Eng C, Damodaran S, Javle M, Kaseb AO, Hong DS, Subbiah V, Fu S, Fogelman DR, Raymond VM, Lanman RB, Meric-Bernstam F. Cell-free Circulating Tumor DNA Variant Allele Frequency Associates with Survival in Metastatic Cancer. Clin Cancer Res 2020; 26:1924-1931. [PMID: 31852833 PMCID: PMC7771658 DOI: 10.1158/1078-0432.ccr-19-0306] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [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: 02/09/2019] [Revised: 06/13/2019] [Accepted: 12/12/2019] [Indexed: 01/05/2023]
Abstract
PURPOSE Physicians are expected to assess prognosis both for patient counseling and for determining suitability for clinical trials. Increasingly, cell-free circulating tumor DNA (cfDNA) sequencing is being performed for clinical decision making. We sought to determine whether variant allele frequency (VAF) in cfDNA is associated with prognosis. EXPERIMENTAL DESIGN We performed a retrospective analysis of 298 patients with metastatic disease who underwent clinical comprehensive cfDNA analysis and assessed association between VAF and overall survival. RESULTS cfDNA mutations were detected in 240 patients (80.5%). Median overall survival (OS) was 11.5 months. cfDNA mutation detection and number of nonsynonymous mutations (NSM) significantly differed between tumor types, being lowest in appendiceal cancer and highest in colon cancer. Having more than one NSM detected was associated with significantly worse OS (HR = 2.3; P < 0.0001). VAF was classified by quartiles, Q1 lowest, Q4 highest VAF. Higher VAF levels were associated with a significantly worse overall survival (VAF Q3 HR 2.3, P = 0.0069; VAF Q4 HR = 3.8, P < 0.0001) on univariate analysis. On multivariate analysis, VAF Q4, male sex, albumin level <3.5 g/dL, number of nonvisceral metastatic sites >0 and number of prior therapies >4 were independent predictors of worse OS. CONCLUSIONS Higher levels of cfDNA VAF and a higher number of NSMs were associated with worse OS in patients with metastatic disease. Further study is needed to determine optimal VAF thresholds for clinical decision making and the utility of cfDNA VAF as a prognostic marker in different tumor types.
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Affiliation(s)
- Seyed Pairawan
- Department of Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kenneth R Hess
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Filip Janku
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Nora S Sanchez
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kenna R Mills Shaw
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cathy Eng
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Senthilkumar Damodaran
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Milind Javle
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ahmed O Kaseb
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David S Hong
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Vivek Subbiah
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Siqing Fu
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David R Fogelman
- Department of GI Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas.
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Breast Surgical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
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19
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Zheng ZY, Anurag M, Lei JT, Cao J, Singh P, Peng J, Kennedy H, Nguyen NC, Chen Y, Lavere P, Li J, Du XH, Cakar B, Song W, Kim BJ, Shi J, Seker S, Chan DW, Zhao GQ, Chen X, Banks KC, Lanman RB, Shafaee MN, Zhang XHF, Vasaikar S, Zhang B, Hilsenbeck SG, Li W, Foulds CE, Ellis MJ, Chang EC. Neurofibromin Is an Estrogen Receptor-α Transcriptional Co-repressor in Breast Cancer. Cancer Cell 2020; 37:387-402.e7. [PMID: 32142667 PMCID: PMC7286719 DOI: 10.1016/j.ccell.2020.02.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 11/15/2019] [Accepted: 02/06/2020] [Indexed: 12/18/2022]
Abstract
We report that neurofibromin, a tumor suppressor and Ras-GAP (GTPase-activating protein), is also an estrogen receptor-α (ER) transcriptional co-repressor through leucine/isoleucine-rich motifs that are functionally independent of GAP activity. GAP activity, in turn, does not affect ER binding. Consequently, neurofibromin depletion causes estradiol hypersensitivity and tamoxifen agonism, explaining the poor prognosis associated with neurofibromin loss in endocrine therapy-treated ER+ breast cancer. Neurofibromin-deficient ER+ breast cancer cells initially retain sensitivity to selective ER degraders (SERDs). However, Ras activation does play a role in acquired SERD resistance, which can be reversed upon MEK inhibitor addition, and SERD/MEK inhibitor combinations induce tumor regression. Thus, neurofibromin is a dual repressor for both Ras and ER signaling, and co-targeting may treat neurofibromin-deficient ER+ breast tumors.
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Affiliation(s)
- Ze-Yi Zheng
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Meenakshi Anurag
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Jonathan T Lei
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA; Interdepartmental Program in Translational Biology and Molecular Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Jin Cao
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Purba Singh
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Jianheng Peng
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA; Department of Physical Examination, the First Affiliated Hospital of Chongqing Medical University, Chongqing, P.R. China
| | - Hilda Kennedy
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Nhu-Chau Nguyen
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Yue Chen
- Adrienne Helis Malvin Medical Research Foundation, New Orleans, LA, USA
| | - Philip Lavere
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jing Li
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Xin-Hui Du
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA; Department of Bone and Soft Tissue, Zhengzhou University Affiliated Henan Cancer Hospital and College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, P. R. China
| | - Burcu Cakar
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Wei Song
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Beom-Jun Kim
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Jiejun Shi
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Sinem Seker
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Doug W Chan
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Guo-Qiang Zhao
- Department of Bone and Soft Tissue, Zhengzhou University Affiliated Henan Cancer Hospital and College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, P. R. China
| | - Xi Chen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | | | | | - Maryam Nemati Shafaee
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Xiang H-F Zhang
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Suhas Vasaikar
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Susan G Hilsenbeck
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Wei Li
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Charles E Foulds
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX, USA
| | - Matthew J Ellis
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA; Department of Medicine, Baylor College of Medicine, Houston, TX, USA.
| | - Eric C Chang
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA.
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20
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Robichaux JP, Elamin YY, Vijayan R, Nilsson MB, Hu L, He J, Zhang F, Pisegna M, Poteete A, Sun H, Li S, Chen T, Han H, Negrao MV, Ahnert JR, Diao L, Wang J, Le X, Meric-Bernstam F, Routbort M, Roeck B, Yang Z, Raymond VM, Lanman RB, Frampton GM, Miller VA, Schrock AB, Albacker LA, Wong KK, Cross JB, Heymach JV. Pan-Cancer Landscape and Analysis of ERBB2 Mutations Identifies Poziotinib as a Clinically Active Inhibitor and Enhancer of T-DM1 Activity. Cancer Cell 2020; 37:420. [PMID: 32183953 PMCID: PMC7241090 DOI: 10.1016/j.ccell.2020.03.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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21
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Agarwal A, Nassar A, Nagy R, Curran C, Abou Alaiwi S, Lanman RB, Talasaz A, Sweeney C, Sonpavde G. Circulating tumor (ct)-DNA alterations in patients with testicular germ cell tumors. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.6_suppl.415] [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
415 Background: Testicular germ cell tumors (GCT) infrequently harbor somatic mutations. ctDNA assessment allows the noninvasive genomic profiling of malignancies and may assist with understanding molecular evolution of resistance. We report ctDNA profiling of patients (pts) with testicular GCTs. Methods: 40 patients (pts) with advanced testicular GCTs from multiple institutions in the USA that underwent ctDNA analysis using the Guardant (G)-360 platform were eligible and a total of 48 samples were collected. 36 pts had one sample, 3 pts had 2 samples, 1 pt had 6 samples. De-identified demographic data were collected in addition to data for ctDNA alterations. G360 employed a CLIA-certified ctDNA panel that assessed single nucleotide variant and copy number alterations in 68 to 73 genes for potentially actionable genomic alterations. Variants reported at least 3 times in the Catalogue of Somatic Mutations in Cancer (COSMIC) database or found in OncoKB were considered pathogenic. Results: Of 40 patients with testicular GCTs, 13pts (33%) were post systemic therapy. The median age was 36 years (range 20-61). 199 ctDNA alterations were detected in 35 patients (87.5%) across 41 genes. Among the 199 alterations, 102 were believed to be pathogenic and detectable in 26 samples from 25 pts (62.5) (%). The most common pathogenic somatic alterations were KRAS (n = 16/102, 16%), TP53 (n = 16/102, 16%), CCND2 (n = 9/102, 9%), CDK6 (n = 9/102, 9%), MET (n = 9/102, 9%), and RAF1 (n = 6/102, 6%). Conclusions: ctDNA alterations were frequently detected in resistant testicular GCTs and appear similar to alterations previously described in tumor tissue analyses of testicular GCTs. Given that ctDNA offers a non-invasive means of profiling tumor DNA, further development of this promising modality is warranted to study the evolution of resistance to cisplatin-based chemotherapy and new potentially actionable alterations.
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Affiliation(s)
- Archana Agarwal
- Dana Farber Cancer Institute at St. Elizabeth's Medical Center, Brighton, MA
| | | | | | | | - Sarah Abou Alaiwi
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA
| | | | | | - Christopher Sweeney
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA
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22
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Nassar A, Agarwal A, Nagy R, Curran C, Abou Alaiwi S, McGregor BA, Talasaz A, Lanman RB, Sonpavde G. Genomic landscape of circulating tumor (ct)-DNA alterations in patients with penile cancer. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.6_suppl.6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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
6 Background: Penile cancer is a rare disease associated with HPV infection and harbors recurrent somatic genomic alterations in the ERBB (HER)-family, CDKN2A, TP53, NOTCH1 and PIK3CA. ctDNA assay allows the noninvasive genomic profiling of malignancies and may assist with understanding molecular evolution. To our knowledge, the genomic alterations observed in ctDNA for penile cancer have not been described before. We report ctDNA profiling of patients with advanced penile cancer. Methods: Sixteen pts with metastatic penile cancer from multiple institutions in the United States that underwent ctDNA analysis using the Guardant360 platform were eligible. Three patients had at least one serial ctDNA sample. De-identified demographic data were collected. Guardant 360 is CLIA-certified ctDNA panel that assesses single nucleotide variants and copy number alterations in 68 to 73 genes for potentially actionable genomic alterations. Variants seen at least 3 times in the Catalogue of Somatic Mutations in Cancer (COSMIC) database or reported in OncoKB were considered pathogenic. Results: The median age was 64 years (range 40-77). 4 pts (25%) were documented to be post platinum-based chemotherapy. Among the entire cohort, 51 ctDNA alterations were detected (median=2, range 0-6) in 15/16 patients (94%) across 21 genes (table). Of the 51 alterations, 24 (47%) were actionable and had approved targeted therapies in other cancers. Alterations were most frequently detected in TP53 (9/16, 56%), CDKN2A (5/16, 31%), and TERT promoter (5/16, 31%) (table). In 3 patients with serial samples, 9 novel pathogenic alterations were detected in the second sample including ATM, CDKN2A, ARID1A, CCND1, CDK6, EGFR, PDGFRA, PIK3CA, and SMAD4. Conclusions: ctDNA alterations in patients with advanced penile cancer were frequently detected and appeared similar to previously described tumor tissue analyses. New alterations found on serial ctDNA assays shed light on patterns of tumor evolution and may inform drug development for this challenging orphan malignancy.[Table: see text]
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Affiliation(s)
| | - Archana Agarwal
- Dana Farber Cancer Institute at St. Elizabeth's Medical Center, Brighton, MA
| | | | | | - Sarah Abou Alaiwi
- Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute, Boston, MA
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23
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Kiedrowski LA, Thomas RA, Vogelzang NJ, Sonpavde G, Gupta S, Gourdin TS, Faltas BM, Nagy R, Lanman RB, Grivas P. FGFR2/3 genomic alterations (GA) in cell-free (cf)DNA from patients (pts) with advanced urothelial carcinoma (aUC). J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.6_suppl.565] [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
565 Background: Erdafitinib is approved in pts with aUC with relevant FGFR2/3 GA. BLC2001 trials in pts with activating FGFR2/3 mutations reported 40% ORR to erdafitinib (49% for those with single nucleotide variants [SNVs] and 16% with fusions), 39% stable disease rate, and potentially reduced response to anti-PD-L1. Genomic profiling with plasma cfDNA next-generation sequencing (NGS) is increasingly used to identify targetable GA in pts with advanced solid tumors and presents a minimally invasive option for identification of FGFR2/3 GA. Methods: Genomic data from the Guardant360 database were queried from clinical results released from 10/19/15 - 8/28/19 for clinical samples submitted with diagnoses of aUC or related diagnoses (e.g. bladder cancer, renal pelvis carcinoma). All assays included FGFR2/3 fusions and complete sequencing of all critical exons harboring sensitizing FGFR2/3 SNVs. Results: 1349 results from 1096 unique pts were identified. Somatic GA were identified in 1192 tests (88%) from 997 pts. Fusions and/or nonsynonymous SNVs in FGFR2/3 were identified in 201 pts (20%); 141 pts (14%) had at least one characterized activating FGFR2/3 GA. Of 34 pts (3.4%) with FGFR3 fusions, partners included TACC3 (32), JAKMIP1 (1), and TNIP2 (1). Overall, most SNVs identified in FGFR3 were predicted to be activating (103/125, 82%) whereas in FGFR2 most were variants of uncertain significance (VUS; 62/72, 86%). Of 89 unique variants (59 in FGFR2, 30 in FGFR3), 19 (21%) were activating mutations (7 in FGFR2, 12 in FGFR3). The most common activating SNVs in FGFR3 were S249C (58 pts), Y373C (20) and R248C (10), and in FGFR2 was N549K (4). VUS in both genes were individually uncommon (no VUS recurring in >3 pts). Median copy number-adjusted clonality of SNVs in FGFR3 was higher than those in FGFR2 (0.80 vs 0.20); this remained true when limiting to only characterized activating mutations (0.84 vs 0.17). Conclusions: cfDNA NGS analysis identifies fusions and a broad spectrum of SNVs in FGFR2/3, including heterogeneous subclonal mutations, at a rate similar to reported tissue testing. cfDNA is a minimally invasive option for pts with aUC to assess candidacy for erdafitinib and clinical trials.
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Affiliation(s)
| | | | | | | | - Sumati Gupta
- Huntsman Cancer Institute-University of Utah Health Care, Salt Lake City, UT
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24
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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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Vidula N, Rich TA, Sartor O, Yen J, Hardin A, Nance T, Lilly MB, Nezami MA, Patel SP, Carneiro BA, Fan AC, Brufsky AM, Parker BA, Bridges BB, Agarwal N, Maughan BL, Raymond VM, Fairclough SR, Lanman RB, Bardia A, Cristofanilli M. Routine Plasma-Based Genotyping to Comprehensively Detect Germline, Somatic, and Reversion BRCA Mutations among Patients with Advanced Solid Tumors. Clin Cancer Res 2020; 26:2546-2555. [DOI: 10.1158/1078-0432.ccr-19-2933] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Revised: 12/17/2019] [Accepted: 02/03/2020] [Indexed: 11/16/2022]
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Raghav KPS, Wang XS, Xiao L, Dasari A, Morris VK, Johnson B, Shen JPY, Parseghian CM, Kee BK, Shureiqi I, Fogelman DR, Wolff RA, Raymond VM, Odegaard JI, Lanman RB, Overman MJ, Kopetz S. A randomized study evaluating tailoring of advanced/metastatic colorectal cancer (mCRC) therapy using circulating cell-free tumor DNA (ctDNA) (TACT-D). J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.4_suppl.tps277] [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
TPS277 Background: Identifying non-responders to expensive salvage therapies with modest benefits and substantial treatment related adverse events (TRAEs) (e.g. regorafenib/TAS102 in mCRC) is necessary to maximize benefits and limit toxicities. Serial ctDNA sequencing is reliable for tracking tumor dynamics and appears to predict resistance to therapy earlier than radiographic progression. Methods: TACT-D is a randomized study (N = 100) to validate the ability of changes in ctDNA (ΔctDNA) to predict resistance early and in limiting toxicities. We hypothesize that increase in ctDNA (measured by variant allele fraction) at 2 weeks (wk) into treatment can predict resistance earlier than standard radiographic means [at 8-12 wk] and detecting resistance early can enable prompt change in therapy resulting in reduction of TRAEs. Pts with mCRC eligible for either regorafenib/TAS102 are randomized 2:1 to either standard of care (SOC) or ctDNA arm. On SOC arm, treatment is given as per current paradigm i.e. for 8 wk and then restaging. On ctDNA arm, decision to continue therapy is based on ctDNA change between baseline and 2 weeks [ΔctDNA = ctDNA (C1D15 – C1D1)]. Increase in ctDNA triggers early radiographic staging (4 wk). Treatment is continued for disease stability/regression and discontinued for progression. Study has 2 co-primary endpoints: 1) Association of Δ ctDNA and radiographic progression [62 pts on SOC arm, have 94% power (2-sided α 0.05) to detect difference of 95% vs. 58% in progressive disease between pts with increase vs decrease in ctDNA] and 2) Compare proportion of pts experiencing TRAEs within 4 months between study arms [67 in SOC arm and 33 in ctDNA arm have 82% power (2-sided α 0.05) to detect a 30% decrease in toxicity]. Key secondary endpoints include: patient-reported outcomes (MD Anderson Symptom Inventory and PRO-CTCAE), OS, clinical events of special interest (hospitalizations/ER visits/medical interventions such as blood transfusions/IV hydration), clinical trial referral and cost effectiveness. Study is now actively accruing pts (NCT03844620). Funding: MD Anderson Cancer Center, Houston, TX & Guardant Health Inc., Redwood City, CA. Clinical trial information: NCT03844620.
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Affiliation(s)
| | | | - Lianchun Xiao
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - 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
| | - Benny Johnson
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Bryan K. Kee
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Imad Shureiqi
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Robert A. Wolff
- 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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Jia J, Niedzwiecki D, Arrowood C, Garett-Mead N, Nagy R, Lanman RB, Wright J, Nixon AB, Strickler JH. A phase II study of savolitinib (volitinib, AZD6094, HMPL-504) in subjects with MET amplified metastatic colorectal cancer (mCRC) detected by cell-free (cf)DNA. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.4_suppl.tps270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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
TPS270 Background: MET amplification (amp) is a well-described driver of acquired EGFR antibody (Ab) resistance and is found in 10-20% of pts with KRAS and NRAS wild-type mCRC treated with anti-EGFR Abs. Blood-based genomic profiling of cfDNA is a non-invasive and efficient means of identifying acquired MET amp in mCRC. Although the activity of anti-MET tyrosine kinase inhibitors (TKIs) in EGFR Ab refractory mCRC has been shown in preclinical and clinical studies, the clinical efficacy of anti-MET TKIs in pts with MET amplified mCRC is not well established. Savolitinib is a potent and highly selective oral small molecule anti-MET TKI that is currently under clinical development for MET-driven papillary renal cell carcinoma, NSCLC and gastric cancer. Methods: This single-arm phase II study will evaluate the clinical efficacy and tolerability of savolitinib in pts with MET amplified mCRC. Eligible pts include those with RAS wild-type mCRC who have been previously treated with 5-FU, oxaliplatin, irinotecan, an anti-VEGF Ab and an anti-EGFR Ab. Pts must have MET amp detected by Guardant360 (G360) cfDNA screening assay. Up to 150 patients will be screened to identify at least 15 pts for study accrual. Prior treatment with an anti-MET TKI or monoclonal Ab against c-MET or HGF is excluded. The primary objective is to estimate the objective response rate (ORR) for savolitinib. In this heavily pre-treated cohort an observed ORR of 20% is considered clinically meaningful and worthy of further study. Secondary objectives are to evaluate the efficacy (progression-free survival, duration of response), safety and tolerability. Correlation between tissue and blood-based biomarkers and clinical outcomes will be explored. Blood will be collected at baseline and each restaging to determine if savolitinib eliminates MET amp in cfDNA. Subjects will receive savolitinib at a dose of 600mg by mouth daily on 28-day cycles. Response will be assessed every 2 cycles (8 weeks) per RECIST version 1.1. This study was initiated on 1/30/2019. Recruitment is ongoing in the NCI Experimental Therapeutics Clinical Trials Network (ETCTN). Clinical trial information: NCT03592641.
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Affiliation(s)
- Jingquan Jia
- DUMC, Department of Medical Oncology, Durham, NC
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Benavides M, Alcaide J, Alvarez M, Torres E, Sevilla I, Gil Calle S, Reyna C, Alés I, Durán G, Wolman R, Cazorla M, Jimenez Gallego P, López I, Cantero A, Godoy A, Lanman RB, Faull I, Odegaard J, Kim IJ, Alba E. Clinical utility of comprehensive circulating tumor DNA (ctDNA) testing compared to standard-of-care (SoC) tissue testing in first-line (1L) metastatic colorectal cancer (mCRC) patients (pts). J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.4_suppl.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: 11/20/2022] Open
Abstract
15 Background: Accurate genotyping is mandatory for the management of mCRC pts. Tissue-based testing is still the SoC; however, is not available for all pts. and may be exhausted by serial testing, resulting in incomplete genotyping. We aimed to establish the validity of comprehensive non-invasive ctDNA testing in 1L mCRC pts for whom SoC tissue genotyping was available. Methods: 1L mCRC pts were tested with a comprehensive ctDNA test (Guardant360), a RAS ctDNA test (OncoBeam), and SoC tissue testing at the time of diagnosis. The primary endpoint was NCCN guideline biomarker discovery rate ( KRAS, NRAS, and BRAF mutations, ERBB2 amplification, and microsatellite instability). Results: In 91 evaluable pts, the biomarker discovery rate was 54.9% (50/91) for SoC tissue testing, 59.3% (54/91) for comprehensive ctDNA testing ( p= 0.0318 for non-inferiority vs. SoC), and 42.9% (39/91) for RAS ctDNA testing (inferiority not rejected vs. SoC). Both comprehensive and RAS ctDNA testing showed high positive agreement (85%, 44/52, and 86%, 31/36) and negative agreement (96%, 268/279, and 93%, 93/100) relative to SoC tissue testing at the gene level. Expanding genotyping beyond KRAS codon 12/13 mutations increased biomarker discovery rate by 56% for tissue testing (50/91 vs. 32/91, McNemar’s p< 0.0001) and by 64% for comprehensive ctDNA (54/91 vs. 33/91, McNemar’s p< 0.0001). Turnaround time was significantly shorter for comprehensive ctDNA testing vs. SoC tissue testing (mean 11.7 days vs. 23.0 days, paired T-test p= 0.0002). On retrospective analysis, 92% of biomarker-positive pts would have been identified at 2 weeks using the comprehensive ctDNA test for initial genotyping with reflex to tissue for biomarker-negative pts, whereas initial use of SoC tissue testing would have identified only 85% of positive pts at 4 weeks (Fisher’s exact p< 0.0001). Conclusions: As previously reported for lung cancer, comprehensive ctDNA testing in 1L mCRC identifies at least as many biomarker-positive pts as SoC tissue genotyping with high concordance to tissue and in half the turnaround time.
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Affiliation(s)
- Manuel Benavides
- Hospital Universitario Regional y Virgen de la Victoria, Málaga, Spain
| | | | - Martina Alvarez
- Hospital Universitario Regional y Virgen de la Victoria, Málaga, Spain
| | - Esperanza Torres
- Hospital Universitario Regional y Virgen de la Victoria, Málaga, Spain
| | - Isabel Sevilla
- Hospital Universitario Regional y Virgen de la Victoria, Málaga, Spain
| | - Silvia Gil Calle
- Hospital Universitario Regional y Virgen de la Victoria, Málaga, Spain
| | - Carmen Reyna
- Hospital Universitario Regional y Virgen de la Victoria, Málaga, Spain
| | - Inmaculada Alés
- Hospital Universitario Regional y Virgen de la Victoria, Málaga, Spain
| | - Gema Durán
- Hospital Universitario Regional y Virgen de la Victoria, Málaga, Spain
| | | | - Mireya Cazorla
- Hospital Universitario Regional y Virgen de la Victoria, Málaga, Spain
| | | | - Irene López
- Hospital Universitario Regional y Virgen de la Victoria, Málaga, Spain
| | - Alexandra Cantero
- Hospital Universitario Regional y Virgen de la Victoria, Málaga, Spain
| | - Ana Godoy
- Hospital Universitario Regional y Virgen de la Victoria, Málaga, Spain
| | | | | | | | | | - Emilio Alba
- Hospital Universitario Regional y Virgen de la Victoria, Málaga, Spain
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Henry J, Willis J, Parseghian CM, Raghav KPS, Johnson B, Dasari A, Stone D, Jeyakumar N, Coker O, Raymond VM, Lanman RB, Overman MJ, Kopetz S. NeoRAS: Incidence of RAS reversion from RAS mutated to RAS wild type. J Clin Oncol 2020. [DOI: 10.1200/jco.2020.38.4_suppl.180] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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
180 Background: RAS mutations are found in ~50% of patients (pts) with metastatic colorectal cancer (mCRC) and associated with resistance to anti-EGFR. Circulating tumor DNA (ctDNA) enables detection of resistant RASMUT arising from RASWT. Recently there has been interest in defining the converse: RASMUT tumors that revert to RASWT, with early results suggesting rates of ~7%. Clinical trials in this population are in development, though the incidence has not been validated with robust methodologies. Methods: 1) We identified 74 mCRC pts with baseline RASMUT and longitudinal ctDNA or tissue data enrolled in ATTACC (NCT01196130), a prospective genomic matching protocol utilizing paired tissue/ctDNA samples at baseline. We evaluated serial samples for RAS loss. 2) Using an external cohort of pts with mCRC and serial ctDNA with a targeted NGS assay sequencing all KRAS/ NRAS exons (Guardant360, Guardant Health), we screened pts for baseline RASMUT with no evidence of prior anti-EGFR exposure and evaluated for RAS loss. Results: 74 pts met criteria of RASMUT CRC with serial samples in ATTACC. Of these, 51 retained RASMUT. 22 pts had very low or absent levels of other clonal alterations such as APC or TP53 and are therefore unable to reliably detect RAS loss. One patient had true RAS loss with NRAS G13R, APC and TP53 mutations at baseline and persistent high-level APC and TP53 mutations without a detectable NRAS mutation, for an overall rate of RAS loss of 2% (1/52). In the second cohort we identified 162 pts, 34 of which had insufficient ctDNA to assess RAS loss on the serial sample as defined by loss of clonal alterations like APC and TP53. Of the remaining 128 patients, 11 had RAS loss (8.5%, with 1 NRAS, 10 KRAS). We next compared the relative mutant allele frequency (rMAF) between RAS retainers and RAS loss. The median baseline rMAF for pts who lost RAS was 0.74, compared to 0.86 in pts retaining RAS (p = 0.045). Conclusions: RAS reversion in mCRC from RASMUT to RASWT is uncommon and occurs at a rate between 2-8% in our two cohorts. RAS reversion is associated with a lower rMAF at baseline, suggesting subclonality. Liquid biopsies must be interpreted carefully, such that a determination of RAS mutation status is most informative in the presence of truncal APC and/or TP53 mutations.
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Affiliation(s)
- Jason Henry
- MD Anderson Hematology/Oncology Fellowship, Houston, TX
| | - Jason Willis
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Benny Johnson
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Arvind Dasari
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - David Stone
- University of Texas Health Science Center at Houston, Houston, TX
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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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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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Patel H, Okamura R, Fanta P, Patel C, Lanman RB, Raymond VM, Kato S, Kurzrock R. Clinical correlates of blood-derived circulating tumor DNA in pancreatic cancer. J Hematol Oncol 2019; 12:130. [PMID: 31801585 PMCID: PMC6894333 DOI: 10.1186/s13045-019-0824-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [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: 07/29/2019] [Accepted: 11/08/2019] [Indexed: 12/18/2022] Open
Abstract
Background Treatment outcomes for patients with advanced pancreatic ductal adenocarcinoma (PDAC) remain dismal. There are unmet needs for understanding the biologic basis of this malignancy using novel next-generation sequencing technologies. Herein, we investigated the clinical utility of circulating tumor DNA (ctDNA) (the liquid biopsy) in this malignancy. Methods ctDNA was analyzed in 112 patients with PDAC (54–73 genes) and tissue DNA in 66 patients (315 genes) (both clinical-grade next-generation sequencing). Number of alterations, %ctDNA, concordance between ctDNA and tissue DNA, and correlation of ctDNA results with survival were assessed. Results The most common genes altered in ctDNA were TP53 (46% of patients, N = 51) and KRAS (44%, N = 49). Median number of characterized ctDNA alterations per patient was 1 (range, 0–6), but patients with advanced PDAC had significantly higher numbers of ctDNA alterations than those with surgically resectable disease (median, 2 versus 0.5, P = 0.04). Overall, 75% (70/94) of advanced tumors had ≥ 1 ctDNA alteration. Concordance rate between ctDNA and tissue DNA alterations was 61% for TP53 and 52% for KRAS. Concordance for KRAS alterations between ctDNA and tissue DNA from metastatic sites was significantly higher than between ctDNA and primary tumor DNA (72% vs 39%, P = 0.01). Importantly, higher levels of total %ctDNA were an independent prognostic factor for worse survival (hazard ratio, 4.35; 95% confidence interval, 1.85–10.24 [multivariate, P = 0.001]). A patient with three ctDNA alterations affecting the MEK pathway (GNAS, KRAS, and NF1) attained a response to trametinib monotherapy ongoing at 6 months. Conclusions Our findings showed that ctDNA often harbored unique alterations some of which may be targetable and that significantly greater numbers of ctDNA alterations occur in advanced versus resectable disease. Furthermore, higher ctDNA levels were a poor prognostic factor for survival.
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Affiliation(s)
- Hitendra Patel
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, 3855 Health Sciences Drive, La Jolla, CA, 92093, USA
| | - Ryosuke Okamura
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, 3855 Health Sciences Drive, La Jolla, CA, 92093, USA.
| | - Paul Fanta
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, 3855 Health Sciences Drive, La Jolla, CA, 92093, USA
| | - Charmi Patel
- Department of Pathology, UC San Diego, La Jolla, CA, USA
| | - Richard B Lanman
- Department of Medical Affairs, Guardant Health, Inc., Redwood City, CA, USA
| | - Victoria M Raymond
- Department of Medical Affairs, Guardant Health, Inc., Redwood City, CA, USA
| | - Shumei Kato
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, 3855 Health Sciences Drive, La Jolla, CA, 92093, USA
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, 3855 Health Sciences Drive, La Jolla, CA, 92093, USA
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Espenschied CR, Yen JL, Nance T, Lanman RB, Banks KC. Abstract B028: Pan-cancer landscape of somatic BRCA1 and BRCA2 mutations detected in circulating tumor DNA. Mol Cancer Ther 2019. [DOI: 10.1158/1535-7163.targ-19-b028] [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: Frequencies of germline mutations in BRCA1 and BRCA2 (BRCA1/2) are well-described; however, existing data are incomplete regarding the cancer specific spectrum of somatic BRCA1/2 (sBRCA) mutations and co-occurrence of microsatellite instability (MSI), particularly when detected in circulating tumor DNA (ctDNA). To better elucidate potential target populations for PARP inhibitor (PARPi) monotherapy and combination PARPi-immunotherapy trials and provide data on the frequency of sBRCA mutations detected in ctDNA, we conducted a retrospective, IRB approved analysis of de-identified genomic results of advanced solid tumor patients (pts) who had clinical liquid biopsy testing (Guardant360) from 06-2018 to 05-2019. METHODS Cancer specific sBRCA inactivating mutation frequencies were calculated for cancer types with >50 patients tested; histological sub-types were compared to available TCGA inactivating sBRCA frequencies using Fisher’s exact or Chi-square test as appropriate. RESULTS Overall, 3388 pts were found to have one or more variant of uncertain significance (n=2338) and/or inactivating mutation (n=1050) in BRCA1/2. Of the 1050, 352 (33.5%) had only germline mutation(s) (gBRCA), 24 (2.3%) had both gBRCA and sBRCA, and 674 (64.2%) had sBRCA mutations only. Further analyses were limited to the 674 pts with sBRCA mutations only. Cancer specific sBRCA frequencies in uterine (5.1%), ovarian (5.0%), colorectal (CRC, 3.3%), lung squamous (3.1%), head and neck (2.9%), gastroesophageal (2.6%), melanoma (2.4%), urothelial (2.3%), breast (2.3%), lung adenocarcinoma (2.1%), and pancreatic (2.1%) cancers were not significantly different from TCGA while frequencies in prostate (3.7%, p=0.004) and renal cell (2.1%, p=0.02) cancers were significantly higher than TCGA. The mean (median) number of sBRCA mutations per pt was 1.1 (1) with 47 pts having >1 sBRCA mutation. Multiple sBRCA mutations were seen in pts with CRC (n=14), prostate (n=9), non-small cell lung (n=7), breast (n=6), uterine (n=3), ovarian (n=2), and other (n=5) cancers. Co-occurring MSI was detected in 44/468 (9.4%) pts with sBRCA inactivating mutation(s) tested. CONCLUSIONS ctDNA detected sBRCA mutations at frequencies consistent with, or above TCGA, indicating it is an effective method for identifying pts eligible for PARPi trials. Additional studies are ongoing to assess the clonality of the sBRCA mutations which may further impact PARPi trial considerations. Our cohort consists of advanced cancer pts, so the identification of sBRCA mutations in prostate cancer at a higher frequency than TCGA supports what is known about the association between gBRCA mutations and more aggressive, advanced stage cancer and suggests the possibility of a similar association for sBRCA in prostate and renal cell cancers. The co-occurrence of defective homologous recombination and mismatch repair has previously been reported in tissue sequencing studies, but numbers in those and the current study are small. Still, this co-occurrence sub-population may represent a unique molecular subtype in which to investigate combination PARPi-immunotherapy. In a one year period, standard of care ctDNA testing identified 1050 advanced cancer pts with BRCA mutations, two-thirds of which were somatic, occurring in over 30 cancer types, suggesting that PARPi therapies may have relevance in a broad range of cancers.
Citation Format: Carin R Espenschied, Jennifer L Yen, Tracy Nance, Richard B Lanman, Kimberly C Banks. Pan-cancer landscape of somatic BRCA1 and BRCA2 mutations detected in circulating tumor DNA [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics; 2019 Oct 26-30; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2019;18(12 Suppl):Abstract nr B028. doi:10.1158/1535-7163.TARG-19-B028
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Willis J, Lefterova MI, Artyomenko A, Kasi PM, Nakamura Y, Mody K, Catenacci DVT, Fakih M, Barbacioru C, Zhao J, Sikora M, Fairclough SR, Lee H, Kim KM, Kim ST, Kim J, Gavino D, Benavides M, Peled N, Nguyen T, Cusnir M, Eskander RN, Azzi G, Yoshino T, Banks KC, Raymond VM, Lanman RB, Chudova DI, Talasaz A, Kopetz S, Lee J, Odegaard JI. Validation of Microsatellite Instability Detection Using a Comprehensive Plasma-Based Genotyping Panel. Clin Cancer Res 2019; 25:7035-7045. [PMID: 31383735 DOI: 10.1158/1078-0432.ccr-19-1324] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/15/2019] [Accepted: 07/10/2019] [Indexed: 12/24/2022]
Abstract
PURPOSE To analytically and clinically validate microsatellite instability (MSI) detection using cell-free DNA (cfDNA) sequencing. EXPERIMENTAL DESIGN Pan-cancer MSI detection using Guardant360 was analytically validated according to established guidelines and clinically validated using 1,145 cfDNA samples for which tissue MSI status based on standard-of-care tissue testing was available. The landscape of cfDNA-based MSI across solid tumor types was investigated in a cohort of 28,459 clinical plasma samples. Clinical outcomes for 16 patients with cfDNA MSI-H gastric cancer treated with immunotherapy were evaluated. RESULTS cfDNA MSI evaluation was shown to have high specificity, precision, and sensitivity, with a limit of detection of 0.1% tumor content. In evaluable patients, cfDNA testing accurately detected 87% (71/82) of tissue MSI-H and 99.5% of tissue microsatellite stable (863/867) for an overall accuracy of 98.4% (934/949) and a positive predictive value of 95% (71/75). Concordance of cfDNA MSI with tissue PCR and next-generation sequencing was significantly higher than IHC. Prevalence of cfDNA MSI for major cancer types was consistent with those reported for tissue. Finally, robust clinical activity of immunotherapy treatment was seen in patients with advanced gastric cancer positive for MSI by cfDNA, with 63% (10/16) of patients achieving complete or partial remission with sustained clinical benefit. CONCLUSIONS cfDNA-based MSI detection using Guardant360 is highly concordant with tissue-based testing, enabling highly accurate detection of MSI status concurrent with comprehensive genomic profiling and expanding access to immunotherapy for patients with advanced cancer for whom current testing practices are inadequate.See related commentary by Wang and Ajani, p. 6887.
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Affiliation(s)
- Jason Willis
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | - Pashtoon Murtaza Kasi
- Division of Oncology/Hematology, Department of Internal Medicine, University of Iowa, Iowa City, Iowa
| | - Yoshiaki Nakamura
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | - Kabir Mody
- Division of Hematology and Medical Oncology, Mayo Clinic, Jacksonville, Florida
| | | | - Marwan Fakih
- Medical Oncology, City of Hope, Duarte, California
| | | | - Jing Zhao
- Guardant Health, Redwood City, California
| | | | | | - Hyuk Lee
- Division of Gastroenterology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyoung-Mee Kim
- Division of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Seung Tae Kim
- Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jinchul Kim
- Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | | | - Manuel Benavides
- Medical Oncology, Hospital Universitario Virgen de la Victoria, Malaga, Spain
| | - Nir Peled
- Division of Medical Oncology, Rabin Medical Center, Petach Tiqea, Israel
| | - Timmy Nguyen
- Hematology/Oncology, Cleveland Clinic Foundation, Weston, Florida
| | - Mike Cusnir
- Comprehensive Cancer Center, Mount Sinai Medical Center, Miami Beach, Florida
| | - Ramez N Eskander
- Center for Personalized Cancer Therapy, Division of Gynecologic Oncology, University of California San Diego Health Moores Cancer Center, La Jolla, California
| | - Georges Azzi
- Medical Oncology, Holy Cross Michael & Dianne Bienes Comprehensive Cancer Center, Fort Lauderdale, Florida
| | - Takayuki Yoshino
- Department of Gastroenterology and Gastrointestinal Oncology, National Cancer Center Hospital East, Kashiwa, Japan
| | | | | | | | | | | | - Scott Kopetz
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeeyun Lee
- Division of Hematology-Oncology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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Kim ST, Banks KC, Pectasides E, Kim SY, Kim K, Lanman RB, Talasaz A, An J, Choi MG, Lee JH, Sohn TS, Bae JM, Kim S, Park SH, Park JO, Park YS, Lim HY, Kim NKD, Park W, Lee H, Bass AJ, Kim K, Kang WK, Lee J. Impact of genomic alterations on lapatinib treatment outcome and cell-free genomic landscape during HER2 therapy in HER2+ gastric cancer patients. Ann Oncol 2019; 29:1037-1048. [PMID: 29409051 PMCID: PMC5913644 DOI: 10.1093/annonc/mdy034] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background To identify predictive markers for responders in lapatinib-treated patients and to demonstrate molecular changes during lapatinib treatment via cell-free genomics. Patients and methods We prospectively evaluated the efficacy of combining lapatinib with capecitabine and oxaliplatin as first line neoadjuvant therapy in patients with previously untreated, HER2-overexpressing advanced gastric cancer. A parallel biomarker study was conducted by simultaneously performing immunohistochemistry and next-generation sequencing (NGS) with tumor and blood samples. Results Complete response was confirmed in 7/32 patients (21.8%), 2 of whom received radical surgery with pathologic-confirmed complete response. Fifteen partial responses (46.8%) were observed, resulting in a 68.6% overall response rate. NGS of the 16 tumor specimens demonstrated that the most common co-occurring copy number alteration was CCNE1 amplification, which was present in 40% of HER2+ tumors. The relationship between CCNE1 amplification and lack of response to HER2-targeted therapy trended toward statistical significance (66.7% of non-responders versus 22.2% of responders harbored CCNE1 amplification; P = 0.08). Patients with high level ERBB2 amplification by NGS were more likely to respond to therapy, compared with patients with low level ERBB2 amplification (P = 0.02). Analysis of cfDNA showed that detectable ERBB2 copy number amplification in plasma was predictive to the response (100%, response rate) and changes in plasma-detected genomic alterations were associated with lapatinib sensitivity and/or resistance. The follow-up cfDNA genomics at disease progression demonstrated that there are emergences of other genomic aberrations such as MYC, EGFR, FGFR2 and MET amplifications. Conclusions The present study showed that HER2+ GC patients respond differently according to concomitant genomic aberrations beyond ERBB2, high ERBB2 amplification by NGS or cfDNA can be a positive predictor for patient selection, and tumor genomic alterations change significantly during targeted agent therapy.
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Affiliation(s)
- S T Kim
- Division of Hematology-Oncolog, Department of Medicine, Samsung Medical Center, Seoul, Korea; Sungkyunkwan University School of Medicine, Seoul, Korea
| | - K C Banks
- Department of Medical Affair, Guardant Health, Dana-Farber Cancer Institute, Boston, USA
| | - E Pectasides
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - S Y Kim
- Division of Hematology-Oncolog, Department of Medicine, Samsung Medical Center, Seoul, Korea; Sungkyunkwan University School of Medicine, Seoul, Korea
| | - K Kim
- Division of Hematology-Oncolog, Department of Medicine, Samsung Medical Center, Seoul, Korea; Sungkyunkwan University School of Medicine, Seoul, Korea
| | - R B Lanman
- Department of Medical Affair, Guardant Health, Dana-Farber Cancer Institute, Boston, USA
| | - A Talasaz
- Department of Medical Affair, Guardant Health, Dana-Farber Cancer Institute, Boston, USA
| | - J An
- Sungkyunkwan University School of Medicine, Seoul, Korea; Department of Surgery, Samsung Medical Center, Seoul, Korea
| | - M G Choi
- Sungkyunkwan University School of Medicine, Seoul, Korea; Department of Surgery, Samsung Medical Center, Seoul, Korea
| | - J H Lee
- Sungkyunkwan University School of Medicine, Seoul, Korea; Department of Surgery, Samsung Medical Center, Seoul, Korea
| | - T S Sohn
- Sungkyunkwan University School of Medicine, Seoul, Korea; Department of Surgery, Samsung Medical Center, Seoul, Korea
| | - J M Bae
- Sungkyunkwan University School of Medicine, Seoul, Korea; Department of Surgery, Samsung Medical Center, Seoul, Korea
| | - S Kim
- Sungkyunkwan University School of Medicine, Seoul, Korea; Department of Surgery, Samsung Medical Center, Seoul, Korea
| | - S H Park
- Division of Hematology-Oncolog, Department of Medicine, Samsung Medical Center, Seoul, Korea; Sungkyunkwan University School of Medicine, Seoul, Korea
| | - J O Park
- Division of Hematology-Oncolog, Department of Medicine, Samsung Medical Center, Seoul, Korea; Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Y S Park
- Division of Hematology-Oncolog, Department of Medicine, Samsung Medical Center, Seoul, Korea; Sungkyunkwan University School of Medicine, Seoul, Korea
| | - H Y Lim
- Division of Hematology-Oncolog, Department of Medicine, Samsung Medical Center, Seoul, Korea; Sungkyunkwan University School of Medicine, Seoul, Korea
| | - N K D Kim
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - W Park
- Samsung Genome Institute, Samsung Medical Center, Seoul, Korea
| | - H Lee
- Sungkyunkwan University School of Medicine, Seoul, Korea; Division of Gastroenterolog, Department of Medicine, Samsung Medical Center, Seoul, Korea
| | - A J Bass
- Division of Molecular and Cellular Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - K Kim
- Pathology and Translational Genomics, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - W K Kang
- Division of Hematology-Oncolog, Department of Medicine, Samsung Medical Center, Seoul, Korea; Sungkyunkwan University School of Medicine, Seoul, Korea
| | - J Lee
- Division of Hematology-Oncolog, Department of Medicine, Samsung Medical Center, Seoul, Korea; Sungkyunkwan University School of Medicine, Seoul, Korea.
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Kaseb AO, Sánchez NS, Sen S, Kelley RK, Tan B, Bocobo AG, Lim KH, Abdel-Wahab R, Uemura M, Pestana RC, Qiao W, Xiao L, Morris J, Amin HM, Hassan MM, Rashid A, Banks KC, Lanman RB, Talasaz A, Mills-Shaw KR, George B, Haque A, Raghav KPS, Wolff RA, Yao JC, Meric-Bernstam F, Ikeda S, Kurzrock R. Molecular Profiling of Hepatocellular Carcinoma Using Circulating Cell-Free DNA. Clin Cancer Res 2019; 25:6107-6118. [PMID: 31363003 PMCID: PMC9292132 DOI: 10.1158/1078-0432.ccr-18-3341] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [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: 10/12/2018] [Revised: 02/15/2019] [Accepted: 07/25/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Molecular profiling has been used to select patients for targeted therapy and determine prognosis. Noninvasive strategies are critical to hepatocellular carcinoma (HCC) given the challenge of obtaining liver tissue biopsies. EXPERIMENTAL DESIGN We analyzed blood samples from 206 patients with HCC using comprehensive genomic testing (Guardant Health) of circulating tumor DNA (ctDNA). RESULTS A total of 153/206 (74.3%) were men; median age, 62 years (range, 18-91 years). A total of 181/206 patients had ≥1 alteration. The total number of alterations was 680 (nonunique); median number of alterations/patient was three (range, 1-13); median mutant allele frequency (% cfDNA), 0.49% (range, 0.06%-55.03%). TP53 was the common altered gene [>120 alterations (non-unique)] followed by EGFR, MET, ARID1A, MYC, NF1, BRAF, and ERBB2 [20-38 alterations (nonunique)/gene]. Of the patients with alterations, 56.9% (103/181) had ≥1 actionable alterations, most commonly in MYC, EGFR, ERBB2, BRAF, CCNE1, MET, PIK3CA, ARID1A, CDK6, and KRAS. In these genes, amplifications occurred more frequently than mutations. Hepatitis B (HBV)-positive patients were more likely to have ERBB2 alterations, 35.7% (5/14) versus 8.8% HBV-negative (P = 0.04). CONCLUSIONS This study represents the first large-scale analysis of blood-derived ctDNA in HCC in United States. The genomic distinction based on HCC risk factors and the high percentage of potentially actionable genomic alterations suggests potential clinical utility for this technology.
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Affiliation(s)
- Ahmed O Kaseb
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
| | - Nora S Sánchez
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Shiraj Sen
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Robin K Kelley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Benjamin Tan
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
- Department of Radiology, Washington University School of Medicine, St. Louis, Missouri
| | - Andrea G Bocobo
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Kian H Lim
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri
- Department of Radiology, Washington University School of Medicine, St. Louis, Missouri
| | - Reham Abdel-Wahab
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Arizona Clinical Oncology Department, Assiut University Hospital, Assiut, Egypt
| | - Marc Uemura
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Wei Qiao
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lianchun Xiao
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeffrey Morris
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hesham M Amin
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Manal M Hassan
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Asif Rashid
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | | | | | - Kenna R Mills-Shaw
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Bhawana George
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Abedul Haque
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kanwal P S Raghav
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Robert A Wolff
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - James C Yao
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Funda Meric-Bernstam
- Sheikh Khalifa Bin Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sadakatsu Ikeda
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, University of California San Diego, Moores Cancer Center, La Jolla, California
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, University of California San Diego, Moores Cancer Center, La Jolla, California.
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Robichaux JP, Elamin YY, Vijayan RSK, Nilsson MB, Hu L, He J, Zhang F, Pisegna M, Poteete A, Sun H, Li S, Chen T, Han H, Negrao MV, Ahnert JR, Diao L, Wang J, Le X, Meric-Bernstam F, Routbort M, Roeck B, Yang Z, Raymond VM, Lanman RB, Frampton GM, Miller VA, Schrock AB, Albacker LA, Wong KK, Cross JB, Heymach JV. Pan-Cancer Landscape and Analysis of ERBB2 Mutations Identifies Poziotinib as a Clinically Active Inhibitor and Enhancer of T-DM1 Activity. Cancer Cell 2019; 36:444-457.e7. [PMID: 31588020 PMCID: PMC6944069 DOI: 10.1016/j.ccell.2019.09.001] [Citation(s) in RCA: 122] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/29/2019] [Accepted: 09/01/2019] [Indexed: 12/16/2022]
Abstract
We characterized the landscape and drug sensitivity of ERBB2 (HER2) mutations in cancers. In 11 datasets (n = 211,726), ERBB2 mutational hotspots varied across 25 tumor types. Common HER2 mutants yielded differential sensitivities to eleven EGFR/HER2 tyrosine kinase inhibitors (TKIs) in vitro, and molecular dynamics simulations revealed that mutants with a reduced drug-binding pocket volume were associated with decreased affinity for larger TKIs. Overall, poziotinib was the most potent HER2 mutant-selective TKI tested. Phase II clinical testing in ERBB2 exon 20-mutant non-small cell lung cancer resulted in a confirmed objective response rate of 42% in the first 12 evaluable patients. In pre-clinical models, poziotinib upregulated HER2 cell-surface expression and potentiated the activity of T-DM1, resulting in complete tumor regression with combination treatment.
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Affiliation(s)
- Jacqulyne P Robichaux
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yasir Y Elamin
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - R S K Vijayan
- Institute for Applied Cancer Science, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Monique B Nilsson
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lemei Hu
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Junqin He
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Fahao Zhang
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Marlese Pisegna
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Alissa Poteete
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Huiying Sun
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shuai Li
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - Ting Chen
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - Han Han
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - Marcelo Vailati Negrao
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jordi Rodon Ahnert
- Investigative Cancer Therapeutics, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Lixia Diao
- Department of Bioinformatics and Computational Biology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jing Wang
- Department of Hematopathology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiuning Le
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Funda Meric-Bernstam
- Investigative Cancer Therapeutics, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mark Routbort
- Department of Hematopathology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Brent Roeck
- Spectrum Pharmaceuticals, Irvine, CA 92618, USA
| | - Zane Yang
- Spectrum Pharmaceuticals, Irvine, CA 92618, USA
| | | | | | | | | | | | | | - Kwok-Kin Wong
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY 10016, USA
| | - Jason B Cross
- Institute for Applied Cancer Science, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA.
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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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Sánchez NS, Kahle MP, Bailey AM, Wathoo C, Balaji K, Demirhan ME, Yang D, Javle M, Kaseb A, Eng C, Subbiah V, Janku F, Raymond VM, Lanman RB, Mills Shaw KR, Meric-Bernstam F. Identification of Actionable Genomic Alterations Using Circulating Cell-Free DNA. JCO Precis Oncol 2019; 3:PO.19.00017. [PMID: 32923868 PMCID: PMC7448805 DOI: 10.1200/po.19.00017] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/30/2019] [Indexed: 12/20/2022] Open
Abstract
PURPOSE Cell-free DNA (cfDNA) next-generation sequencing is a noninvasive approach for genomic testing. We report the frequency of identifying alterations and their clinical actionability in patients with advanced/metastatic cancer. PATIENTS AND METHODS Prospectively consented patients had cfDNA testing performed. Alterations were assessed for therapeutic implications. RESULTS We enrolled 575 patients with 37 tumor types. Of these patients, 438 (76.2%) had at least one alteration detected, and 205 (35.7%) had one or more alterations of high potential for clinical action. In diseases with 10 or more patients enrolled, 50% or more had at least one alteration deemed of high potential for clinical action. Trials were identified in 80% of patients (286 of 357) with any alteration and in 92% of patients (188 of 205) with one or more alterations of high potential for clinical action of whom 57.6% (118 of 205) had 6 or more months of follow-up available. Of these patients, 10% (12 of 118) had received genomically matched therapy through enrollment in clinical trials (n = 8), off-label drug use (n = 3), or standard of care (n = 1). Although 88.6% of all patients had a performance status of 0 or 1 upon enrollment, the primary reason for not acting on alterations was poor performance status at next treatment change (28.1%; 27 of 96). CONCLUSION cfDNA testing represents a readily accessible method for genomic testing and allows for detection of genomic alterations in most patients with advanced disease. Utility may be higher in patients interested in investigational therapeutics with adequate performance status. Additional study is needed to determine whether utility is enhanced by testing earlier in the treatment course.
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Affiliation(s)
- Nora S. Sánchez
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Chetna Wathoo
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kavitha Balaji
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Dong Yang
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Milind Javle
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ahmed Kaseb
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Cathy Eng
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Vivek Subbiah
- The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Filip Janku
- The University of Texas MD Anderson Cancer Center, Houston, TX
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40
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Rotow JK, Gui P, Wu W, Raymond VM, Lanman RB, Kaye FJ, Peled N, Fece de la Cruz F, Nadres B, Corcoran RB, Yeh I, Bastian BC, Starostik P, Newsom K, Olivas VR, Wolff AM, Fraser JS, Collisson EA, McCoach CE, Camidge DR, Pacheco J, Bazhenova L, Li T, Bivona TG, Blakely CM. Co-occurring Alterations in the RAS-MAPK Pathway Limit Response to MET Inhibitor Treatment in MET Exon 14 Skipping Mutation-Positive Lung Cancer. Clin Cancer Res 2019; 26:439-449. [PMID: 31548343 DOI: 10.1158/1078-0432.ccr-19-1667] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 07/19/2019] [Accepted: 09/10/2019] [Indexed: 01/07/2023]
Abstract
PURPOSE Although patients with advanced-stage non-small cell lung cancers (NSCLC) harboring MET exon 14 skipping mutations (METex14) often benefit from MET tyrosine kinase inhibitor (TKI) treatment, clinical benefit is limited by primary and acquired drug resistance. The molecular basis for this resistance remains incompletely understood. EXPERIMENTAL DESIGN Targeted sequencing analysis was performed on cell-free circulating tumor DNA obtained from 289 patients with advanced-stage METex14-mutated NSCLC. RESULTS Prominent co-occurring RAS-MAPK pathway gene alterations (e.g., in KRAS, NF1) were detected in NSCLCs with METex14 skipping alterations as compared with EGFR-mutated NSCLCs. There was an association between decreased MET TKI treatment response and RAS-MAPK pathway co-occurring alterations. In a preclinical model expressing a canonical METex14 mutation, KRAS overexpression or NF1 downregulation hyperactivated MAPK signaling to promote MET TKI resistance. This resistance was overcome by cotreatment with crizotinib and the MEK inhibitor trametinib. CONCLUSIONS Our study provides a genomic landscape of co-occurring alterations in advanced-stage METex14-mutated NSCLC and suggests a potential combination therapy strategy targeting MAPK pathway signaling to enhance clinical outcomes.
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Affiliation(s)
- Julia K Rotow
- Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Philippe Gui
- Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Wei Wu
- Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | | | | | - Frederic J Kaye
- Department of Medicine, University of Florida, Gainesville, Florida
| | - Nir Peled
- Soroka Medical Center, Ben-Gurion University, Beer-Sheva, Israel
| | - Ferran Fece de la Cruz
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Brandon Nadres
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Ryan B Corcoran
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, Boston, Massachusetts
| | - Iwei Yeh
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.,Departments of Dermatology and Pathology, and Clinical Cancer Genomics Laboratory, University of California, San Francisco, California
| | - Boris C Bastian
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California.,Departments of Dermatology and Pathology, and Clinical Cancer Genomics Laboratory, University of California, San Francisco, California
| | - Petr Starostik
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida
| | - Kimberly Newsom
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, Florida
| | - Victor R Olivas
- Department of Medicine, University of California, San Francisco, California
| | - Alexander M Wolff
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California
| | - Eric A Collisson
- Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Caroline E McCoach
- Department of Medicine, University of California, San Francisco, California.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | | | | | | | - Tianhong Li
- Department of Internal Medicine, University of California, Davis, California
| | - Trever G Bivona
- Department of Medicine, University of California, San Francisco, California. .,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
| | - Collin M Blakely
- Department of Medicine, University of California, San Francisco, California. .,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California
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41
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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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42
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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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Choi MY, Kato S, Wang HY, Lin JH, Lanman RB, Kurzrock R. JAK2 V617F mutation in plasma cell-free DNA preceding clinically overt myelofibrosis: Implications for early diagnosis. Cancer Biol Ther 2019; 19:664-668. [PMID: 29565699 PMCID: PMC6067874 DOI: 10.1080/15384047.2018.1450120] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
A 52 year-old man with Erdheim-Chester Disease (ECD) (a non-Langerhans polyostotic sclerosing histiocytosis) had next-generation sequencing (NGS) performed as part of his diagnostic workup. In addition to the tissue BRAF V600E mutation that is found in over 50% of ECD cases, he was also found to have a JAK2 V617F alteration in cell-free circulating tumor DNA (ctDNA) (liquid biopsy). The latter was thought to be an "incidental" finding, perhaps due to clonal hematopoiesis (though this usually occurs in older individuals), as his blood counts were normal and he had no splenomegaly. Approximately 13 months after the ctDNA test showing JAK2 V617F, he developed anemia, thrombocytopenia, and splenomegaly. Marrow biopsy then showed megakaryocytic atypia and markedly increased marrow fibrosis, consistent with WHO grade 2 of 3 myelofibrosis. Therefore, the patient was determined to have ECD with a typical BRAF V600E mutation, as well as primary myelofibrosis, with the latter diagnosis manifesting clinically over one year after the JAK2 V617F was first detected in ctDNA. He recently was started on the JAK2 inhibitor ruxolitinib. This case demonstrates that genomic alterations detected by liquid biopsy for evaluation of specific malignancies already present may serve as an early harbinger of hematological disease.
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Affiliation(s)
- Michael Y Choi
- a Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine , University of California San Diego Moores Cancer Center , La Jolla , CA , USA
| | - Shumei Kato
- a Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine , University of California San Diego Moores Cancer Center , La Jolla , CA , USA
| | - Huan-You Wang
- b Department of Pathology , University of California San Diego , La Jolla , CA , USA
| | - Jonathan H Lin
- b Department of Pathology , University of California San Diego , La Jolla , CA , USA
| | | | - Razelle Kurzrock
- a Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine , University of California San Diego Moores Cancer Center , La Jolla , CA , USA
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44
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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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46
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Choi IS, Kato S, Fanta PT, Leichman L, Okamura R, Raymond VM, Lanman RB, Lippman SM, Kurzrock R. Genomic Profiling of Blood-Derived Circulating Tumor DNA from Patients with Colorectal Cancer: Implications for Response and Resistance to Targeted Therapeutics. Mol Cancer Ther 2019; 18:1852-1862. [PMID: 31320401 DOI: 10.1158/1535-7163.mct-18-0965] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 12/03/2018] [Accepted: 07/12/2019] [Indexed: 11/16/2022]
Abstract
Molecular profiling of circulating tumor DNA (ctDNA) is a promising noninvasive tool. Here, next-generation sequencing (NGS) of blood-derived ctDNA was performed in patients with advanced colorectal cancer. We investigated ctDNA-derived genomic alterations, including potential actionability, concordance with tissue NGS, and serial dynamics in 78 patients with colorectal cancer using a clinical-grade NGS assay that detects single nucleotide variants (54-73 genes) and selected copy-number variants, fusions, and indels. Overall, 63 patients [80.8% (63/78)] harbored ctDNA alterations; 59 [75.6% (59/78)], ≥1 characterized alteration (variants of unknown significance excluded). All 59 patients had actionable alterations potentially targetable with FDA-approved drugs [on-label and/or off-label (N = 54) or with experimental drugs in clinical trials (additional five patients); University of California San Diego Molecular Tumor Board assessment]: 45, by OncoKB (http://oncokb.org/#/). The tissue and blood concordance rates for common specific alterations ranged from 62.3% to 86.9% (median = 5 months between tests). In serial samples from patients on anti-EGFR therapy, multiple emerging alterations in genes known to be involved in therapeutic resistance, including KRAS, NRAS, BRAF, EGFR, ERBB2, and MET were detected. In conclusion, over 80% of patients with stage IV colorectal cancer had detectable ctDNA, and the majority had potentially actionable alterations. Concordance between tissue and blood was between 62% and 87%, despite a median of 5 months between tests. Resistance alterations emerged on anti-EGFR therapy. Therefore, biopsy-free, noninvasive ctDNA analysis provides data relevant to the clinical setting. Importantly, sequential ctDNA analysis detects patterns of emerging resistance allowing for precision planning of future therapy.
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Affiliation(s)
- In Sil Choi
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, California.,Department of Internal Medicine, Seoul National University Boramae Medical Center, Seoul, South Korea
| | - Shumei Kato
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, California.
| | - Paul T Fanta
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, California
| | - Lawrence Leichman
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, California
| | - Ryosuke Okamura
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, California
| | - Victoria M Raymond
- Department of Medical Affairs, Guardant Health, Inc., Redwood City, California
| | - Richard B Lanman
- Department of Medical Affairs, Guardant Health, Inc., Redwood City, California
| | - Scott M Lippman
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, California
| | - Razelle Kurzrock
- Center for Personalized Cancer Therapy and Division of Hematology and Oncology, Department of Medicine, UC San Diego Moores Cancer Center, La Jolla, California
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Devarakonda S, Sankararaman S, Herzog BH, Gold KA, Waqar SN, Ward JP, Raymond VM, Lanman RB, Chaudhuri AA, Owonikoko TK, Li BT, Poirier JT, Rudin CM, Govindan R, Morgensztern D. Circulating Tumor DNA Profiling in Small-Cell Lung Cancer Identifies Potentially Targetable Alterations. Clin Cancer Res 2019; 25:6119-6126. [PMID: 31300452 DOI: 10.1158/1078-0432.ccr-19-0879] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [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: 03/19/2019] [Revised: 05/15/2019] [Accepted: 07/02/2019] [Indexed: 01/11/2023]
Abstract
PURPOSE Patients with SCLC rarely undergo biopsies at relapse. When pursued, tissue obtained can be inadequate for molecular testing, posing a challenge in identifying potentially targetable alterations in a clinically meaningful time frame. We examined the feasibility of circulating tumor DNA (ctDNA) testing in identifying potentially targetable alterations in SCLC. EXPERIMENTAL DESIGN ctDNA test results were prospectively collected from patients with SCLC between 2014 and 2017 and analyzed. ctDNA profiles of SCLC at diagnosis and relapse were also compared. RESULTS A total of 609 samples collected from 564 patients between 2014 and 2017 were analyzed. The median turnaround time for test results was 14 days. Among patients with data on treatment status, there were 61 samples from 59 patients and 219 samples from 206 patients collected at diagnosis and relapse, respectively. The number of mutations or amplifications detected per sample did not differ by treatment status. Potentially targetable alterations in DNA repair, MAPK and PI3K pathways, and genes such as MYC and ARID1A were identifiable through ctDNA testing. Furthermore, our results support that it may be possible to reconstruct the clonal relationship between detected variants through ctDNA testing. CONCLUSIONS Patients with relapsed SCLC rarely undergo biopsies for molecular testing and often require prompt treatment initiation. ctDNA testing is less invasive and capable of identifying alterations in relapsed disease in a clinically meaningful timeframe. ctDNA testing on an expanded gene panel has the potential to advance our knowledge of the mechanisms underlying treatment resistance in SCLC and aid in the development of novel treatment strategies.
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Affiliation(s)
- Siddhartha Devarakonda
- Washington University School of Medicine, Saint Louis, Missouri
- Alvin J. Siteman Cancer Center, Saint Louis, Missouri
| | | | - Brett H Herzog
- Washington University School of Medicine, Saint Louis, Missouri
| | - Kathryn A Gold
- University of California San Diego School of Medicine, La Jolla, California
| | - Saiama N Waqar
- Washington University School of Medicine, Saint Louis, Missouri
- Alvin J. Siteman Cancer Center, Saint Louis, Missouri
| | - Jeffrey P Ward
- Washington University School of Medicine, Saint Louis, Missouri
- Alvin J. Siteman Cancer Center, Saint Louis, Missouri
| | | | | | - Aadel A Chaudhuri
- Washington University School of Medicine, Saint Louis, Missouri
- Alvin J. Siteman Cancer Center, Saint Louis, Missouri
| | | | - Bob T Li
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - John T Poirier
- Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Ramaswamy Govindan
- Washington University School of Medicine, Saint Louis, Missouri
- Alvin J. Siteman Cancer Center, Saint Louis, Missouri
| | - Daniel Morgensztern
- Washington University School of Medicine, Saint Louis, Missouri.
- Alvin J. Siteman Cancer Center, Saint Louis, Missouri
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48
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Rich TA, Reckamp KL, Chae YK, Doebele RC, Iams WT, Oh M, Raymond VM, Lanman RB, Riess JW, Stinchcombe TE, Subbiah V, Trevarthen DR, Fairclough S, Yen J, Gautschi O. Analysis of Cell-Free DNA from 32,989 Advanced Cancers Reveals Novel Co-occurring Activating RET Alterations and Oncogenic Signaling Pathway Aberrations. Clin Cancer Res 2019; 25:5832-5842. [PMID: 31300450 DOI: 10.1158/1078-0432.ccr-18-4049] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 05/06/2019] [Accepted: 07/02/2019] [Indexed: 12/11/2022]
Abstract
PURPOSE RET is an emerging oncogenic target showing promise in phase I/II clinical trials. An understudied aspect of RET-driven cancers is the extent to which co-occurring genomic alterations exist and how they may impact prognosis or therapeutic response. EXPERIMENTAL DESIGN Somatic activating RET alterations were identified among 32,989 consecutive patients with metastatic solid tumors tested with a clinical cell-free circulating tumor DNA (cfDNA) assay. This comprehensive next-generation sequencing (NGS) assay evaluates single-nucleotide variants, and select indels, fusions, and copy number gains in 68-73 clinically relevant cancer genes. RESULTS A total of 176 somatic activating RET alterations were detected in 170 patients (143 fusions and 33 missense mutations). Patients had non-small cell lung (NSCLC, n = 125), colorectal (n = 15), breast (n = 8), thyroid (n = 8), or other (n = 14) cancers. Alterations in other oncogenic signaling pathway genes were frequently identified in RET-positive samples and varied by specific RET fusion gene partner. RET fusions involving partners other than KIF5B were enriched for alterations in MAPK pathway genes and other bona fide oncogenic drivers of NSCLC, particularly EGFR. Molecular and clinical data revealed that these variants emerged later in the genomic evolution of the tumor as mechanisms of resistance to EGFR tyrosine kinase inhibitors. CONCLUSIONS In the largest cancer cohort with somatic activating RET alterations, we describe novel co-occurrences of oncogenic signaling pathway aberrations. We find that KIF5B-RET fusions are highly specific for NSCLC. In our study, only non-KIF5B-RET fusions contributed to anti-EGFR therapy resistance. Knowledge of specific RET fusion gene partner may have clinical significance.
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Affiliation(s)
| | - Karen L Reckamp
- Department of Medical Oncology & Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, California
| | - Young Kwang Chae
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Robert C Doebele
- Medical Oncology/Department of Medicine, University of Colorado Cancer Center, Aurora, Colorado
| | - Wade T Iams
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Michael Oh
- Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | | | | | - Jonathan W Riess
- Division of Hematology/Oncology, University of California Davis Comprehensive Cancer Center, Sacramento, California
| | | | - Vivek Subbiah
- Department of Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David R Trevarthen
- Department of Hematology/Oncology, Comprehensive Cancer Care and Research Institute of Colorado, Englewood, Colorado
| | | | | | - Oliver Gautschi
- University of Berne and Department of Medicine, Cantonal Hospital Lucerne, Lucerne, Switzerland
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49
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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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50
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Quinn K, Helman E, Nance T, Yen J, Latham J, Gleitsman K, Vijaya-Satya R, Artieri C, Artyomenko A, Sikora M, Chudova D, Lanman RB, Talasaz A. Abstract 3404: Landscape and genomic correlates of ctDNA-based tumor mutational burden across six solid tumor types. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3404] [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: Tumor mutational burden (TMB) has emerged as a predictive biomarker of response to immune checkpoint inhibitor (ICI) therapy. Current panel-based TMB algorithms aggregate signal from certain types of somatic variants (e.g. non-synonymous coding SNVs); however, delineating the contributions of these and other types of mutations may refine TMB calculation from gene panels. Moreover, early studies suggest other possible genomic correlates of patient outcome to ICI which may be complementary to TMB. Here, we explore the landscape of mutations comprising TMB and other genomic features correlating with TMB on a subset of several thousand late-stage plasma samples run on GuardantOMNITM (OMNI), a highly sensitive 500-gene cfDNA sequencing platform.
Methods: We developed a cfDNA-based TMB algorithm which is robust to variable tumor shedding levels and presence of clonal hematopoiesis. We assessed cfDNA-based TMB in over 1,000 plasma samples across six tumor types, including lung and prostate. We examine the contribution of nonsynonymous, synonymous, intronic SNVs, and indels to TMB score. We investigate correlations between TMB and additional genomic features, including chromosomal instability, loss of HLA-bearing chromosome 6p, microsatellite instability (MSI), and common oncogenic and resistance mutations.
Results: We found that the distribution of WES-calibrated TMB scores across this cohort of samples is consistent with TCGA, with median 10 mutations/Mb and upper-tertile of 14 mutations/Mb across tumor types. The number of non-synonymous coding SNVs per sample correlated highly with synonymous coding SNV and intronic SNV counts (Pearson’s r > 0.7 for each). Including this additional signal in TMB calculation improves clinical sensitivity by up to 5%. In MSS samples, indels were highly correlated with SNVs, indicating that both likely arise from a similar underlying mechanism. We found no clear correlation between high TMB and chromosomal instability, with high TMB samples exemplifying a range of tumor ploidies. TMB association with oncogenic drivers is consistent with existing literature, with lower median TMB in EGFR-driven lung tumors (p < 0.01), but little to no correlation between TMB and KRAS or PIK3CA driver status, or STK11 loss of function (p > 0.05), suggesting these latter events could be independent clinical biomarkers to TMB.
Conclusions: Panel-based TMB scores can leverage synonymous and non-coding mutations to strengthen the signal of exome-wide mutation load. As more patient outcome data becomes available, TMB algorithms and orthogonal biomarkers of tumor genome immunogenicity will evolve further for improved guidance of patient response to immunotherapy. Sequencing panels with high sensitivity for TMB, via large panel space, and the ability to detect copy-number variations and MSI-status, will be important for biomarker development and clinical applications.
Citation Format: Katie Quinn, Elena Helman, Tracy Nance, Jennifer Yen, John Latham, Kristin Gleitsman, Ravi Vijaya-Satya, Carlo Artieri, Alex Artyomenko, Marcin Sikora, Darya Chudova, Richard B. Lanman, AmirAli Talasaz. Landscape and genomic correlates of ctDNA-based tumor mutational burden across six solid tumor types [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 3404.
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