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Choudhury NJ, Marra A, Sui JSY, Flynn J, Yang SR, Falcon CJ, Selenica P, Schoenfeld AJ, Rekhtman N, Gomez D, Berger MF, Ladanyi M, Arcila M, Rudin CM, Riely GJ, Kris MG, Heller G, Reis-Filho JS, Yu HA. Molecular Biomarkers of Disease Outcomes and Mechanisms of Acquired Resistance to First-Line Osimertinib in Advanced EGFR-Mutant Lung Cancers. J Thorac Oncol 2023; 18:463-475. [PMID: 36494075 PMCID: PMC10249779 DOI: 10.1016/j.jtho.2022.11.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/14/2022] [Accepted: 11/18/2022] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Preferred first-line treatment for patients with metastatic EGFR-mutant lung cancer is osimertinib, yet it is not known whether patient outcomes may be improved by identifying and intervening on molecular markers associated with therapeutic resistance. METHODS All patients with metastatic EGFR-mutant lung cancer treated with first-line osimertinib at the Memorial Sloan Kettering Cancer Center (n = 327) were identified. Available pretreatment and postprogression tumor samples underwent targeted gene panel sequencing and mutational signature analysis using SigMA algorithm. Progression-free survival (PFS) and overall survival were estimated using the Kaplan-Meier method. RESULTS Using multivariate analysis, baseline atypical EGFR (median PFS = 5.8 mo, p < 0.001) and concurrent TP53/RB1 alterations (median PFS = 10.5 mo, p = 0.015) were associated with shorter PFS on first-line osimertinib. Of 95 patients with postprogression biopsies, acquired resistance mechanisms were identified in 52% (off-target, n = 24; histologic transformation, n = 14; on-target, n = 12), with MET amplification (n = 9), small cell lung transformation (n = 7), and acquired EGFR amplification (n = 7), the most frequently identified mechanisms. Although there was no difference in postprogression survival on the basis of identified resistance (p = 0.07), patients with subsequent second-line therapy tailored to postprogression biopsy results had improved postprogression survival (hazard ratio = 0.09, p = 0.006). The paired postprogression tumors had higher tumor mutational burden (p = 0.008) and further dominant APOBEC mutational signatures (p = 0.07) compared with the pretreatment samples. CONCLUSIONS Patients with EGFR-mutant lung cancer treated with first-line osimertinib have improved survival with treatment adaptation on the basis of identified mechanisms of resistance at time of progression using tissue-based genomic analysis. Further survival gains may be achieved using risk-based treatment adaptation of pretreatment genomic alterations.
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Affiliation(s)
- Noura J Choudhury
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Antonio Marra
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jane S Y Sui
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jessica Flynn
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Soo-Ryum Yang
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Christina J Falcon
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Pier Selenica
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Adam J Schoenfeld
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Natasha Rekhtman
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Daniel Gomez
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael F Berger
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marc Ladanyi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Marie-Josee and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria Arcila
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Charles M Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Gregory J Riely
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Mark G Kris
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Glenn Heller
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jorge S Reis-Filho
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Helena A Yu
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York; Department of Medicine, Weill Cornell Medical College, New York, New York.
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Barr MP, Baird AM, Halliday S, Martin P, Allott EH, Phelan J, Korpanty G, Coate L, O’Brien C, Gray SG, Sui JSY, Hayes B, Cuffe S, Finn SP. Liquid Biopsy: A Multi-Parametric Analysis of Mutation Status, Circulating Tumor Cells and Inflammatory Markers in EGFR-Mutated NSCLC. Diagnostics (Basel) 2022; 12:diagnostics12102360. [PMID: 36292049 PMCID: PMC9600124 DOI: 10.3390/diagnostics12102360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 09/07/2022] [Accepted: 09/17/2022] [Indexed: 11/22/2022] Open
Abstract
The liquid biopsy has the potential to improve patient care in the diagnostic and therapeutic setting in non-small cell lung cancer (NSCLC). Consented patients with epidermal growth factor receptor (EGFR) positive disease (n = 21) were stratified into two cohorts: those currently receiving EGFR tyrosine kinase inhibitor (TKI) therapy (n = 9) and newly diagnosed EGFR TKI treatment-naïve patients (n = 12). Plasma genotyping of cell-free DNA was carried out using the FDA-approved cobas® EGFR mutation test v2 and compared to next generation sequencing (NGS) cfDNA panels. Circulating tumor cell (CTC) numbers were correlated with treatment response and EGFR exon 20 p.T790M. The prognostic significance of the neutrophil to lymphocyte ratio (NLR) and lactate dehydrogenase (LDH) was also investigated. Patients in cohort 1 with an EGFR exon 20 p.T790M mutation progressed more rapidly than those with an EGFR sensitizing mutation, while patients in cohort 2 had a significantly longer progression-free survival (p = 0.04). EGFR exon 20 p.T790M was detected by liquid biopsy prior to disease progression indicated by computed tomography (CT) imaging. The cobas® EGFR mutation test detected a significantly greater number of exon 20 p.T790M mutations (p = 0.05). High NLR and derived neutrophil to lymphocyte ratio (dNLR) were associated with shorter time to progression and worse survival outcomes (p < 0.05). High LDH levels were significantly associated with shorter time to disease progression (p = 0.03). These data support the use of liquid biopsy for monitoring EGFR mutations and inflammatory markers as prognostic indicators in NSCLC.
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Affiliation(s)
- Martin P. Barr
- Thoracic Oncology Research Group, Trinity St James’s Cancer Institute, St James’s Hospital, D08 W9RT Dublin, Ireland
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
- Correspondence: ; Tel.: +353-1-8963620
| | - Anne-Marie Baird
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
| | - Sophia Halliday
- Patrick G. Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, UK
| | - Petra Martin
- Thoracic Oncology Research Group, Trinity St James’s Cancer Institute, St James’s Hospital, D08 W9RT Dublin, Ireland
- Department of Medical Oncology, Midlands Regional Hospital, R35 NY51 Tullamore, Ireland
| | - Emma H. Allott
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
- Patrick G. Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast BT9 7AE, UK
| | - James Phelan
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
| | - Greg Korpanty
- Department of Medical Oncology, University Hospital Limerick, V94 F858 Limerick, Ireland
| | - Linda Coate
- Department of Medical Oncology, University Hospital Limerick, V94 F858 Limerick, Ireland
| | - Cathal O’Brien
- Cancer Molecular Diagnostics Laboratory, St James’s Hospital, D08 W9RT Dublin, Ireland
| | - Steven G. Gray
- Thoracic Oncology Research Group, Trinity St James’s Cancer Institute, St James’s Hospital, D08 W9RT Dublin, Ireland
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
| | - Jane S. Y. Sui
- Thoracic Oncology Research Group, Trinity St James’s Cancer Institute, St James’s Hospital, D08 W9RT Dublin, Ireland
| | - Brian Hayes
- Department of Histopathology, Cork University Hospital, T12 XF62 Cork, Ireland
- Department of Pathology, University College Cork, T12 DC4A Cork, Ireland
| | - Sinead Cuffe
- Thoracic Oncology Research Group, Trinity St James’s Cancer Institute, St James’s Hospital, D08 W9RT Dublin, Ireland
- Department of Medical Oncology, St James’s Hospital, D08 NHY1 Dublin, Ireland
| | - Stephen P. Finn
- Thoracic Oncology Research Group, Trinity St James’s Cancer Institute, St James’s Hospital, D08 W9RT Dublin, Ireland
- Department of Histopathology, St James’s Hospital, D08 RX0X Dublin, Ireland
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Sui JSY, Martin P, Keogh A, Murchan P, Ryan L, Nicholson S, Cuffe S, Broin PÓ, Finn SP, Fitzmaurice GJ, Ryan R, Young V, Gray SG. Altered expression of ACOX2 in non-small cell lung cancer. BMC Pulm Med 2022; 22:321. [PMID: 35999530 PMCID: PMC9396774 DOI: 10.1186/s12890-022-02115-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 08/16/2022] [Indexed: 12/24/2022] Open
Abstract
Peroxisomes are organelles that play essential roles in many metabolic processes, but also play roles in innate immunity, signal transduction, aging and cancer. One of the main functions of peroxisomes is the processing of very-long chain fatty acids into metabolites that can be directed to the mitochondria. One key family of enzymes in this process are the peroxisomal acyl-CoA oxidases (ACOX1, ACOX2 and ACOX3), the expression of which has been shown to be dysregulated in some cancers. Very little is however known about the expression of this family of oxidases in non-small cell lung cancer (NSCLC). ACOX2 has however been suggested to be elevated at the mRNA level in over 10% of NSCLC, and in the present study using both standard and bioinformatics approaches we show that expression of ACOX2 is significantly altered in NSCLC. ACOX2 mRNA expression is linked to a number of mutated genes, and associations between ACOX2 expression and tumour mutational burden and immune cell infiltration were explored. Links between ACOX2 expression and candidate therapies for oncogenic driver mutations such as KRAS were also identified. Furthermore, levels of acyl-CoA oxidases and other associated peroxisomal genes were explored to identify further links between the peroxisomal pathway and NSCLC. The results of this biomarker driven study suggest that ACOX2 may have potential clinical utility in the diagnosis, prognosis and stratification of patients into various therapeutically targetable options.
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Affiliation(s)
- Jane S Y Sui
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James's Hospital, Dublin, D08RX0X, Ireland.,Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Petra Martin
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James's Hospital, Dublin, D08RX0X, Ireland.,Midland Regional Hospital Tullamore, Tullamore, Ireland
| | - Anna Keogh
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James's Hospital, Dublin, D08RX0X, Ireland
| | - Pierre Murchan
- Department of Histopathology and Morbid Anatomy, Trinity College Dublin, Dublin, Ireland.,School of Mathematics, Statistics, and Applied Mathematics, National University of Ireland Galway, Galway, Ireland
| | - Lisa Ryan
- Department of Histopathology, Labmed Directorate, St. James's Hospital, Dublin, Ireland
| | - Siobhan Nicholson
- Department of Histopathology, Labmed Directorate, St. James's Hospital, Dublin, Ireland
| | - Sinead Cuffe
- HOPE Directorate, St James's Hospital, Dublin, Ireland
| | - Pilib Ó Broin
- School of Mathematics, Statistics, and Applied Mathematics, National University of Ireland Galway, Galway, Ireland
| | - Stephen P Finn
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James's Hospital, Dublin, D08RX0X, Ireland.,Department of Histopathology and Morbid Anatomy, Trinity College Dublin, Dublin, Ireland.,Department of Histopathology, Labmed Directorate, St. James's Hospital, Dublin, Ireland.,Cancer Molecular Diagnostics, Labmed Directorate, St. James's Hospital, Dublin, Ireland
| | - Gerard J Fitzmaurice
- Surgery, Anaesthesia and Critical Care Directorate, St James's Hospital, Dublin, Ireland
| | - Ronan Ryan
- Surgery, Anaesthesia and Critical Care Directorate, St James's Hospital, Dublin, Ireland
| | - Vincent Young
- Surgery, Anaesthesia and Critical Care Directorate, St James's Hospital, Dublin, Ireland
| | - Steven G Gray
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James's Hospital, Dublin, D08RX0X, Ireland. .,Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland. .,School of Biological Sciences, Technological University Dublin, Dublin, Ireland.
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Abstract
The receptor tyrosine kinase (RTK) c-MET plays important roles in cancer, yet despite being frequently overexpressed, clinical responses to targeting this receptor have been limited in the clinical setting. A singular significant challenge has been the accurate identification of biomarkers for the selection of responsive patients. However, recently mutations which result in the loss of exon 14 (called METex14 skipping) have emerged as novel biomarkers in non-small cell lung carcinomas (NSCLC) to predict for responsiveness to targeted therapy with c-MET inhibitors. Currently, the diverse genomic alterations responsible for METex14 skipping pose a challenge for routine clinical diagnostic testing. Next generation sequencing (NGS) is the current gold standard for identifying the diverse mutations associated with METex14, but the cost for such a procedure remains to some degree prohibitive as often NGS is requested on a case-by-case basis, and many hospitals may not even have the capacity or resources to conduct NGS.However, PCR-based approaches to detect METex14 have been developed which can be conducted in most routine hospital laboratories and may therefore allow a cost-effective approach to pre-screen patients that may respond to c-MET inhibitors prior to conducting NGS, or until all patients will have NGS conducted as routine practise. In this chapter, we describe one such PCR-based approach for screening samples for the detection of METex14 in NSCLC.
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Affiliation(s)
- Jane S Y Sui
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, Dublin, Ireland
- Department of Medical Oncology, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Stephen P Finn
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, Dublin, Ireland
- Department of Histopathology, Cancer Molecular Diagnostics, Labmed Directorate, St. James's Hospital, Dublin, Ireland
- Department of Histopathology and Morbid Anatomy, Trinity College Dublin, Dublin, Ireland
| | - Steven G Gray
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, St. James's Hospital, Dublin, Ireland.
- Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland.
- School of Biological Sciences, Dublin Institute of Technology, Dublin, Ireland.
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Abstract
Introduction: Small-cell lung cancer (SCLC) is an aggressive form of lung cancer that has a dismal prognosis. One of the factors hindering therapeutic developments for SCLC is that most SCLC is not surgically resected resulting in a paucity of material for analysis. To address this, significant efforts have been made by investigators to develop pre-clinical models of SCLC allowing for downstream target identification in this difficult to treat cancer.Areas covered: In this review, we describe the current pre-clinical models that have been developed to interrogate SCLC, and outline the benefits and limitations associated with each. Using examples we show how each has been used to (i) improve our knowledge of this intractable cancer, and (ii) identify and validate potential therapeutic targets that (iii) are currently under development and testing within the clinic.Expert opinion: The large numbers of preclinical models that have been developed have dramatically improved the ways in which we can examine SCLC and test therapeutic targets/interventions. The newer models are rapidly providing novel avenues for the design and testing of new therapeutics. Despite this many of these models have inherent flaws that limit the possibility of their use for individualized therapy decision-making for SCLC.
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Affiliation(s)
- Jane S Y Sui
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James's Hospital, Dublin, Ireland.,Department of Medical Oncology, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Petra Martin
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James's Hospital, Dublin, Ireland
| | - Steven G Gray
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James's Hospital, Dublin, Ireland.,Labmed Directorate, St. James's Hospital, Dublin, Ireland.,School of Biological Sciences, Dublin Institute of Technology, Dublin, Ireland
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