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Bruno R, Poma AM, Panozzi M, Lenzini A, Elia G, Zirafa CC, Aprile V, Ambrogi MC, Baldini E, Lucchi M, Melfi F, Chella A, Sbrana A, Alì G. Early-Stage Non-Small Cell Lung Cancer: Prevalence of Actionable Alterations in a Monocentric Consecutive Cohort. Cancers (Basel) 2024; 16:1410. [PMID: 38611088 PMCID: PMC11010971 DOI: 10.3390/cancers16071410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 03/26/2024] [Accepted: 03/31/2024] [Indexed: 04/14/2024] Open
Abstract
Early-stage (ES) non-small cell lung cancer (NSCLC) is diagnosed in about 30% of cases. The preferred treatment is surgery, but a significant proportion of patients experience recurrence. Neoadjuvant and adjuvant chemotherapy has a limited clinical benefit. EGFR tyrosine kinase inhibitors and immunotherapy have recently opened new therapeutic scenarios. However, only a few data are available about the ES-NSCLC molecular landscape and the impact of oncogene addiction on therapy definition. Here, we determined the prevalence of the main lung cancer driver alterations in a monocentric consecutive cohort. Molecular analysis was performed on 1122 cases, including 368 ES and 754 advanced NSCLC. The prevalence of actionable alterations was similar between early and advanced stages. ES-NSCLC was significantly enriched for MET exon-14 skipping alterations and presented a lower prevalence of BRAF p.(V600E) mutation. PD-L1 expression levels, evaluated according to actionable alterations, were higher in advanced than early tumors harboring EGFR, KRAS, MET alterations and gene fusions. Taken together, these results confirm the value of biomarker testing in ES-NSCLC. Although approved targeted therapies for ES-NSCLC are still limited, the identification of actionable alterations could improve patients' selection for immunotherapy, favoring the enrollment in clinical trials and allowing a faster treatment start at disease recurrence.
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Affiliation(s)
- Rossella Bruno
- Unit of Pathological Anatomy, University Hospital of Pisa, Via Roma 67, 56126 Pisa, Italy;
| | - Anello Marcello Poma
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Savi 10, 56126 Pisa, Italy; (A.M.P.); (A.L.); (G.E.); (V.A.); (M.C.A.); (M.L.); (G.A.)
| | - Martina Panozzi
- Unit of Pathological Anatomy, University Hospital of Pisa, Via Roma 67, 56126 Pisa, Italy;
| | - Alessandra Lenzini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Savi 10, 56126 Pisa, Italy; (A.M.P.); (A.L.); (G.E.); (V.A.); (M.C.A.); (M.L.); (G.A.)
| | - Gianmarco Elia
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Savi 10, 56126 Pisa, Italy; (A.M.P.); (A.L.); (G.E.); (V.A.); (M.C.A.); (M.L.); (G.A.)
| | - Carmelina Cristina Zirafa
- Minimally Invasive and Robotic Thoracic Surgery, Department of Surgical, Medical, Molecular and Critical Care Pathology, University Hospital of Pisa, Via Paradisa 2, 56124 Pisa, Italy; (C.C.Z.); (F.M.)
| | - Vittorio Aprile
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Savi 10, 56126 Pisa, Italy; (A.M.P.); (A.L.); (G.E.); (V.A.); (M.C.A.); (M.L.); (G.A.)
| | - Marcello Carlo Ambrogi
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Savi 10, 56126 Pisa, Italy; (A.M.P.); (A.L.); (G.E.); (V.A.); (M.C.A.); (M.L.); (G.A.)
| | - Editta Baldini
- Medical Oncology, Hospital of Lucca, 55100 Lucca, Italy;
| | - Marco Lucchi
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Savi 10, 56126 Pisa, Italy; (A.M.P.); (A.L.); (G.E.); (V.A.); (M.C.A.); (M.L.); (G.A.)
| | - Franca Melfi
- Minimally Invasive and Robotic Thoracic Surgery, Department of Surgical, Medical, Molecular and Critical Care Pathology, University Hospital of Pisa, Via Paradisa 2, 56124 Pisa, Italy; (C.C.Z.); (F.M.)
| | - Antonio Chella
- Unit of Pneumology, University Hospital of Pisa, Via Roma 67, 56126 Pisa, Italy; (A.C.); (A.S.)
| | - Andrea Sbrana
- Unit of Pneumology, University Hospital of Pisa, Via Roma 67, 56126 Pisa, Italy; (A.C.); (A.S.)
| | - Greta Alì
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, Via Savi 10, 56126 Pisa, Italy; (A.M.P.); (A.L.); (G.E.); (V.A.); (M.C.A.); (M.L.); (G.A.)
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2
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Chen P, Liu Y, Wen Y, Zhou C. Non-small cell lung cancer in China. Cancer Commun (Lond) 2022; 42:937-970. [PMID: 36075878 PMCID: PMC9558689 DOI: 10.1002/cac2.12359] [Citation(s) in RCA: 143] [Impact Index Per Article: 71.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 07/21/2022] [Accepted: 08/24/2022] [Indexed: 04/08/2023] Open
Abstract
In China, lung cancer is a primary cancer type with high incidence and mortality. Risk factors for lung cancer include tobacco use, family history, radiation exposure, and the presence of chronic lung diseases. Most early-stage non-small cell lung cancer (NSCLC) patients miss the optimal timing for treatment due to the lack of clinical presentations. Population-based nationwide screening programs are of significant help in increasing the early detection and survival rates of NSCLC in China. The understanding of molecular carcinogenesis and the identification of oncogenic drivers dramatically facilitate the development of targeted therapy for NSCLC, thus prolonging survival in patients with positive drivers. In the exploration of immune escape mechanisms, programmed cell death protein 1 (PD-1)/programmed death-ligand 1 (PD-L1) inhibitor monotherapy and PD-1/PD-L1 inhibitor plus chemotherapy have become a standard of care for advanced NSCLC in China. In the Chinese Society of Clinical Oncology's guidelines for NSCLC, maintenance immunotherapy is recommended for locally advanced NSCLC after chemoradiotherapy. Adjuvant immunotherapy and neoadjuvant chemoimmunotherapy will be approved for resectable NSCLC. In this review, we summarized recent advances in NSCLC in China in terms of epidemiology, biology, molecular pathology, pathogenesis, screening, diagnosis, targeted therapy, and immunotherapy.
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Affiliation(s)
- Peixin Chen
- School of MedicineTongji UniversityShanghai200092P. R. China
- Department of Medical OncologyShanghai Pulmonary HospitalSchool of MedicineTongji UniversityShanghai200433P. R. China
| | - Yunhuan Liu
- Department of Respiratory and Critical Care MedicineHuadong HospitalFudan UniversityShanghai200040P. R. China
| | - Yaokai Wen
- School of MedicineTongji UniversityShanghai200092P. R. China
- Department of Medical OncologyShanghai Pulmonary HospitalSchool of MedicineTongji UniversityShanghai200433P. R. China
| | - Caicun Zhou
- School of MedicineTongji UniversityShanghai200092P. R. China
- Department of Medical OncologyShanghai Pulmonary HospitalSchool of MedicineTongji UniversityShanghai200433P. R. China
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3
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Diefenbach RJ, Lee JH, Stewart A, Menzies AM, Carlino MS, Saw RPM, Stretch JR, Long GV, Scolyer RA, Rizos H. Anchored Multiplex PCR Custom Melanoma Next Generation Sequencing Panel for Analysis of Circulating Tumor DNA. Front Oncol 2022; 12:820510. [PMID: 35494035 PMCID: PMC9039342 DOI: 10.3389/fonc.2022.820510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
Detection of melanoma mutations using circulating tumor DNA (ctDNA) is a potential alternative to using genomic DNA from invasive tissue biopsies. To date, mutations in the GC-rich TERT promoter region, which is commonly mutated in melanoma, have been technically difficult to detect in ctDNA using next-generation sequencing (NGS) panels. In this study, we developed a custom melanoma NGS panel for detection of ctDNA, which encompasses the top 15 gene mutations in melanoma including the TERT promoter. We analyzed 21 stage III and IV melanoma patient samples who were treatment-naïve or on therapy. The overall detection rate of the custom panel, based on BRAF/NRAS/TERT promoter mutations, was 14/21 (67%) patient samples which included a TERT C250T mutation in one BRAF and NRAS mutation negative sample. A BRAF or NRAS mutation was detected in the ctDNA of 13/21 (62%) patients while TERT promoter mutations were detected in 10/21 (48%) patients. Co-occurrence of TERT promoter mutations with BRAF or NRAS mutations was found in 9/10 (90%) patients. The custom ctDNA panel showed a concordance of 16/21 (76%) with tissue based-detection and included 12 BRAF/NRAS mutation positive and 4 BRAF/NRAS mutation negative patients. The ctDNA mutation detection rate for stage IV was 12/16 (75%) and for stage III was 1/5 (20%). Based on BRAF, NRAS and TERT promoter mutations, the custom melanoma panel displayed a limit of detection of ~0.2% mutant allele frequency and showed significant correlation with droplet digital PCR. For one patient, a novel MAP2K1 H119Y mutation was detected in an NRAS/BRAF/TERT promoter mutation negative background. To increase the detection rate to >90% for stage IV melanoma patients, we plan to expand our custom panel to 50 genes. This study represents one of the first to successfully detect TERT promoter mutations in ctDNA from cutaneous melanoma patients using a targeted NGS panel.
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Affiliation(s)
- Russell J Diefenbach
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia.,Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
| | - Jenny H Lee
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia.,Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.,Department of Medical Oncology, Chris O'Brien Lifehouse, Sydney, NSW, Australia
| | - Ashleigh Stewart
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia.,Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
| | - Alexander M Menzies
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.,The Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Department of Medical Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Sydney, NSW, Australia
| | - Matteo S Carlino
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.,The Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Crown Princess Mary Cancer Centre, Westmead and Blacktown Hospitals, Sydney, NSW, Australia
| | - Robyn P M Saw
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.,The Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - Jonathan R Stretch
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
| | - Georgina V Long
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.,The Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Department of Medical Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Sydney, NSW, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia
| | - Richard A Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia.,The Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia.,Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia.,Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and NSW Health Pathology, Sydney, NSW, Australia
| | - Helen Rizos
- Macquarie Medical School, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW, Australia.,Melanoma Institute Australia, The University of Sydney, Sydney, NSW, Australia
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4
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Dealing with NSCLC EGFR mutation testing and treatment: A comprehensive review with an Italian real-world perspective. Crit Rev Oncol Hematol 2021; 160:103300. [PMID: 33744362 DOI: 10.1016/j.critrevonc.2021.103300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 01/12/2023] Open
Abstract
Since their discovery, relevant efforts have been made to optimize the detection approaches to EGFR mutations as well as the clinical management of EGFR-mutated NSCLC. The recent shift from single gene testing to novel comprehensive detection platforms along with the development of new generation tyrosine kinase inhibitors, targeting both common and uncommon EGFR-mutations, is leading to a progressive increase in the number of patients who may benefit from targeted approaches, with subsequent impact on their long-term survival and quality of life. However, a prompt and adequate implementation of the most recent diagnostic and treatment advances in the routine practice often remains critical to be specifically addressed. In this review we provide a complete and updated overview of the different detection platforms and therapeutic options currently available for the clinical management of advanced EGFR-positive NSCLC, summarizing scientific evidence and describing molecular testing as well as treatment practice in the real-word scenario.
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Diefenbach RJ, Lee JH, Menzies AM, Carlino MS, Long GV, Saw RPM, Howle JR, Spillane AJ, Scolyer RA, Kefford RF, Rizos H. Design and Testing of a Custom Melanoma Next Generation Sequencing Panel for Analysis of Circulating Tumor DNA. Cancers (Basel) 2020; 12:E2228. [PMID: 32785074 PMCID: PMC7465941 DOI: 10.3390/cancers12082228] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/27/2020] [Accepted: 08/07/2020] [Indexed: 12/17/2022] Open
Abstract
Detection of melanoma-associated mutations using circulating tumor DNA (ctDNA) from plasma is a potential alternative to using genomic DNA from invasive tissue biopsies. In this study, we developed a custom melanoma next-generation sequencing (NGS) panel which includes 123 amplicons in 30 genes covering driver and targetable mutations and alterations associated with treatment resistance. Analysis of a cohort of 74 stage III and IV treatment-naïve melanoma patients revealed that sensitivity of ctDNA detection was influenced by the amount of circulating-free DNA (cfDNA) input and stage of melanoma. At the recommended cfDNA input quantity of 20 ng (available in 28/74 patients), at least one cancer-associated mutation was detected in the ctDNA of 84% of stage IV patients and 47% of stage III patients with a limit of detection for mutant allele frequency (MAF) of 0.2%. This custom melanoma panel showed significant correlation with droplet digital PCR (ddPCR) and provided a more comprehensive melanoma mutation profile. Our custom panel could be further optimized by replacing amplicons spanning the TERT promoter, which did not perform well due to the high GC content. To increase the detection rate to 90% of stage IV melanoma and decrease the sensitivity to 0.1% MAF, we recommend increasing the volume of plasma to 8 mL to achieve minimal recommended cfDNA input and the refinement of poorly performing amplicons. Our panel can also be expanded to include new targetable and treatment resistance mutations to improve the tracking of treatment response and resistance in melanoma patients treated with systemic drug therapies.
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Affiliation(s)
- Russell J. Diefenbach
- Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (R.J.D.); (J.H.L.)
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
| | - Jenny H. Lee
- Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (R.J.D.); (J.H.L.)
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
| | - Alexander M. Menzies
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Medical Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Sydney, NSW 2065, Australia
| | - Matteo S. Carlino
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Crown Princess Mary Cancer Centre, Westmead and Blacktown Hospitals, Sydney, NSW 2145, Australia
| | - Georgina V. Long
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Medical Oncology, Northern Sydney Cancer Centre, Royal North Shore Hospital, Sydney, NSW 2065, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
| | - Robyn P. M. Saw
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Melanoma and Surgical Oncology, Royal Prince Alfred Hospital, Sydney, NSW 2050, Australia
| | - Julie R. Howle
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Crown Princess Mary Cancer Centre, Westmead and Blacktown Hospitals, Sydney, NSW 2145, Australia
| | - Andrew J. Spillane
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Breast and Melanoma Surgery Department, Division of Surgery, Royal North Shore Hospital, Sydney, NSW 2065, Australia
| | - Richard A. Scolyer
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Tissue Pathology and Diagnostic Oncology, Royal Prince Alfred Hospital and New South Wales Health Pathology, Sydney, NSW 2050, Australia
| | - Richard F. Kefford
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
- Sydney Medical School, The University of Sydney, Sydney, NSW 2006, Australia
- Department of Clinical Medicine, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Helen Rizos
- Department of Biomedical Sciences, Faculty of Medicine, Health and Human Sciences, Macquarie University, Sydney, NSW 2109, Australia; (R.J.D.); (J.H.L.)
- Melanoma Institute Australia, The University of Sydney, Sydney, NSW 2065, Australia; (A.M.M.); (M.S.C.); (G.V.L.); (R.P.M.S.); (J.R.H.); (A.J.S.); (R.A.S.); (R.F.K.)
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6
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Genome-wide haplotype association study identifies risk genes for non-small cell lung cancer. J Theor Biol 2018; 456:84-90. [PMID: 30096405 DOI: 10.1016/j.jtbi.2018.08.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 08/05/2018] [Accepted: 08/06/2018] [Indexed: 02/07/2023]
Abstract
Lung cancer is the leading cause of cancer-related death worldwide. Most lung cancer is non-small cell lung cancer (NSCLC), in which malignant cells form in the lung epithelium. Mutations in multiple genes and environmental factors both contribute to NSCLC, and although some NSCLC susceptibility genes have been characterized, the pathogenesis of this disease remains unclear. To identify genes conferring NSCLC risk and determine their associated pathological mechanism, we combined genome-wide haplotype associated analysis with gene prioritization using 224,677 SNPs in 37 NSCLC cell lines and 116 unrelated European individuals. Five candidate genes were identified: ESR1, TGFBR1, INSR, CDH3, and MAP3K5. All of these have previously been implicated in NSCLC, with the exception of CDH3, which can therefore be considered a novel indicator of NSCLC risk. Functional annotation confirmed the relationship between these five genes and NSCLC. Our findings are indicative of the underlying pathological mechanisms of NSCLC and provide information to support future directions in diagnosing and treating NSCLC.
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7
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Kriegsmann J, Casadonte R, Kriegsmann K, Longuespée R, Kriegsmann M. Mass spectrometry in pathology - Vision for a future workflow. Pathol Res Pract 2018; 214:1057-1063. [PMID: 29910062 DOI: 10.1016/j.prp.2018.05.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 04/23/2018] [Accepted: 05/11/2018] [Indexed: 02/09/2023]
Abstract
Mass spectrometric (MS) techniques are applied in various areas of medical diagnostics. For the detection of microbiological germs and genetic mutations, MS is a method used in routine. Since MS also allows the analysis of proteins and peptides, it seems an ideal candidate to supplement histopatholological diagnostics. Matrix-assisted laser desorption/ionization time-of-flight Imaging MS links molecular analysis of numerous analytes with morphological information about their spatial distribution in cells or tissues. Herein, we review principle MS techniques as well as potential applications in pathology and discuss our vision for a future workflow.
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Affiliation(s)
- Jörg Kriegsmann
- MVZ for Histology, Cytology and Molecular Diagnostics Trier, Trier, Germany; Proteopath GmbH, Trier, Germany
| | | | - Katharina Kriegsmann
- Department of Hematology, Oncology and Rheumatology, University Hospital Heidelberg, Heidelberg, Germany
| | - Rémi Longuespée
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Mark Kriegsmann
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.
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8
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Malapelle U, Mayo-de-Las-Casas C, Molina-Vila MA, Rosell R, Savic S, Bihl M, Bubendorf L, Salto-Tellez M, de Biase D, Tallini G, Hwang DH, Sholl LM, Luthra R, Weynand B, Vander Borght S, Missiaglia E, Bongiovanni M, Stieber D, Vielh P, Schmitt F, Rappa A, Barberis M, Pepe F, Pisapia P, Serra N, Vigliar E, Bellevicine C, Fassan M, Rugge M, de Andrea CE, Lozano MD, Basolo F, Fontanini G, Nikiforov YE, Kamel-Reid S, da Cunha Santos G, Nikiforova MN, Roy-Chowdhuri S, Troncone G. Consistency and reproducibility of next-generation sequencing and other multigene mutational assays: A worldwide ring trial study on quantitative cytological molecular reference specimens. Cancer Cytopathol 2017; 125:615-626. [PMID: 28475299 DOI: 10.1002/cncy.21868] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 02/23/2017] [Accepted: 03/10/2017] [Indexed: 02/05/2023]
Abstract
BACKGROUND Molecular testing of cytological lung cancer specimens includes, beyond epidermal growth factor receptor (EGFR), emerging predictive/prognostic genomic biomarkers such as Kirsten rat sarcoma viral oncogene homolog (KRAS), neuroblastoma RAS viral [v-ras] oncogene homolog (NRAS), B-Raf proto-oncogene, serine/threonine kinase (BRAF), and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α (PIK3CA). Next-generation sequencing (NGS) and other multigene mutational assays are suitable for cytological specimens, including smears. However, the current literature reflects single-institution studies rather than multicenter experiences. METHODS Quantitative cytological molecular reference slides were produced with cell lines designed to harbor concurrent mutations in the EGFR, KRAS, NRAS, BRAF, and PIK3CA genes at various allelic ratios, including low allele frequencies (AFs; 1%). This interlaboratory ring trial study included 14 institutions across the world that performed multigene mutational assays, from tissue extraction to data analysis, on these reference slides, with each laboratory using its own mutation analysis platform and methodology. RESULTS All laboratories using NGS (n = 11) successfully detected the study's set of mutations with minimal variations in the means and standard errors of variant fractions at dilution points of 10% (P = .171) and 5% (P = .063) despite the use of different sequencing platforms (Illumina, Ion Torrent/Proton, and Roche). However, when mutations at a low AF of 1% were analyzed, the concordance of the NGS results was low, and this reflected the use of different thresholds for variant calling among the institutions. In contrast, laboratories using matrix-assisted laser desorption/ionization-time of flight (n = 2) showed lower concordance in terms of mutation detection and mutant AF quantification. CONCLUSIONS Quantitative molecular reference slides are a useful tool for monitoring the performance of different multigene mutational assays, and this could lead to better standardization of molecular cytopathology procedures. Cancer Cytopathol 2017;125:615-26. © 2017 American Cancer Society.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | | | | | - Rafael Rosell
- Catalan Institute of Oncology, Badalona, Spain
- Instituto Oncológico Dr Rosell (IOR), Quirón-Dexeus University Institute, Barcelona, Spain
| | - Spasenija Savic
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Michel Bihl
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Lukas Bubendorf
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Manuel Salto-Tellez
- Molecular Pathology Programme, Centre for Cancer Research and Cell Biology Queen's University Belfast, Belfast, United Kingdom
| | - Dario de Biase
- Department of Pharmacy and Biotechnology - University of Bologna, Bologna, Italy
| | | | - David H Hwang
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Rajyalakshmi Luthra
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Birgit Weynand
- Department of Pathology, Universitair Ziekenhuis Leuven, Leuven, Belgium
| | - Sara Vander Borght
- Department of Pathology, Universitair Ziekenhuis Leuven, Leuven, Belgium
| | - Edoardo Missiaglia
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Massimo Bongiovanni
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | | | | | | | - Alessandra Rappa
- Division of Pathology, European Institute of Oncology, Milan, Italy
| | - Massimo Barberis
- Division of Pathology, European Institute of Oncology, Milan, Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Nicola Serra
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Elena Vigliar
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Matteo Fassan
- Department of Medicine (DIMED), Surgical Pathology Unit University of Padua, Padua, Italy
| | - Massimo Rugge
- Department of Medicine (DIMED), Surgical Pathology Unit University of Padua, Padua, Italy
| | | | - Maria D Lozano
- Department of Pathology, University Clinic of Navarra, Pamplona, Spain
| | - Fulvio Basolo
- Department of Surgical, Medical and Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - Gabriella Fontanini
- Department of Surgical, Medical and Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - Yuri E Nikiforov
- Department of Pathology and Laboratory Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Suzanne Kamel-Reid
- Department of Laboratory Medicine and Pathobiology, University Health Network, Toronto, Ontario, Canada
| | - Gilda da Cunha Santos
- Department of Laboratory Medicine and Pathobiology, University Health Network, Toronto, Ontario, Canada
| | - Marina N Nikiforova
- Department of Pathology and Laboratory Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Sinchita Roy-Chowdhuri
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
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9
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Thomas De Montpréville V, Ghigna MR, Lacroix L, Lemoine A, Besse B, Mercier O, Fadel É, Dorfmuller P, Le Chevalier T. EGFR and KRAS molecular genotyping for pulmonary carcinomas: Feasibility of a simple and rapid technique implementable in any department of pathology. Pathol Res Pract 2017; 213:793-798. [DOI: 10.1016/j.prp.2017.03.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Accepted: 03/24/2017] [Indexed: 12/16/2022]
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10
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Ess S, Herrmann C, Frick H, Krapf M, Cerny T, Jochum W, Früh M. Epidermal growth factor receptor and anaplastic lymphoma kinase testing and mutation prevalence in patients with advanced non-small cell lung cancer in Switzerland: A comprehensive evaluation of real world practices. Eur J Cancer Care (Engl) 2017; 26. [DOI: 10.1111/ecc.12721] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2017] [Indexed: 11/29/2022]
Affiliation(s)
- S.M. Ess
- Cancer Registry St. Gallen-Appenzell; Cancer League Eastern Switzerland; St. Gallen Switzerland
| | - C. Herrmann
- Cancer Registry St. Gallen-Appenzell; Cancer League Eastern Switzerland; St. Gallen Switzerland
- Department of Public Health; University of Basel; Basel Switzerland
- Swiss Tropical and Public Health Institute; Basel Switzerland
| | - H. Frick
- Cancer Registry St. Gallen-Appenzell; Cancer League Eastern Switzerland; St. Gallen Switzerland
| | - M. Krapf
- Cancer Registry St. Gallen-Appenzell; Cancer League Eastern Switzerland; St. Gallen Switzerland
- University of Bern; Bern Switzerland
| | - T. Cerny
- Department of Internal Medicine; Division Medical Oncology; Kantonsspital St. Gallen; St. Gallen Switzerland
| | - W. Jochum
- Institute of Pathology; Kantonsspital St. Gallen; St. Gallen Switzerland
| | - M. Früh
- Department of Internal Medicine; Division Medical Oncology; Kantonsspital St. Gallen; St. Gallen Switzerland
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11
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Malapelle U, Sirera R, Jantus-Lewintre E, Reclusa P, Calabuig-Fariñas S, Blasco A, Pisapia P, Rolfo C, Camps C. Profile of the Roche cobas® EGFR mutation test v2 for non-small cell lung cancer. Expert Rev Mol Diagn 2017; 17:209-215. [PMID: 28129709 DOI: 10.1080/14737159.2017.1288568] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
INTRODUCTION The discovery of driver mutations in non-small cell lung cancer (NSCLC) has led to the development of genome-based personalized medicine. Fifteen to 20% of adenocarcinomas harbor an epidermal growth factor receptor (EGFR) activating mutation associated with responses to EGFR tyrosine kinase inhibitors (TKIs). Individual laboratories' expertise and the availability of appropriate equipment are valuable assets in predictive molecular pathology, although the choice of methods should be determined by the nature of the samples to be tested and whether the detection of only well-characterized EGFR mutations or rather, of all detectable mutations, is required. Areas covered: The EGFR mutation testing landscape is manifold and includes both screening and targeted methods, each with their own pros and cons. Here we review one of these companion tests, the Roche cobas® EGFR mutation test v2, from a methodological point of view, also exploring its liquid-biopsy applications. Expert commentary: The Roche cobas® EGFR mutation test v2, based on real time RT-PCR, is a reliable option for testing EGFR mutations in clinical practice, either using tissue-derived DNA or plasma-derived cfDNA. This application will be valuable for laboratories with whose purpose is purely diagnostic and lacking high-throughput technologies.
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Affiliation(s)
- Umberto Malapelle
- a Department of Public Health , University of Naples Federico II , Naples , Italy
| | - Rafael Sirera
- b Department of Biotechnology , Universitat Politècnica de València , Valencia , Spain.,c Department of Medical Oncology , Hospital General Universitario de Valencia , Valencia , Spain.,d Molecular Oncology Laboratory , Fundación Hospital General Universitario de Valencia , Valencia , Spain
| | - Eloísa Jantus-Lewintre
- b Department of Biotechnology , Universitat Politècnica de València , Valencia , Spain.,c Department of Medical Oncology , Hospital General Universitario de Valencia , Valencia , Spain.,d Molecular Oncology Laboratory , Fundación Hospital General Universitario de Valencia , Valencia , Spain
| | - Pablo Reclusa
- e Phase I-Early Clinical Trials Unit, Oncology Department , Antwerp University Hospital , Antwerp , Belgium.,f Center for Oncological Research (CORE) , Antwerp University , Antwerp , Belgium
| | - Silvia Calabuig-Fariñas
- c Department of Medical Oncology , Hospital General Universitario de Valencia , Valencia , Spain.,d Molecular Oncology Laboratory , Fundación Hospital General Universitario de Valencia , Valencia , Spain.,g Department of Pathology , Universitat de València , Valencia , Spain
| | - Ana Blasco
- c Department of Medical Oncology , Hospital General Universitario de Valencia , Valencia , Spain
| | - Pasquale Pisapia
- a Department of Public Health , University of Naples Federico II , Naples , Italy
| | - Christian Rolfo
- e Phase I-Early Clinical Trials Unit, Oncology Department , Antwerp University Hospital , Antwerp , Belgium.,f Center for Oncological Research (CORE) , Antwerp University , Antwerp , Belgium
| | - Carlos Camps
- c Department of Medical Oncology , Hospital General Universitario de Valencia , Valencia , Spain.,d Molecular Oncology Laboratory , Fundación Hospital General Universitario de Valencia , Valencia , Spain.,h Department of Medicine , Universitat de València , Valencia , Spain.,i CIBERONC , Valencia , Spain
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12
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Akizuki R, Shimobaba S, Matsunaga T, Endo S, Ikari A. Claudin-5, -7, and -18 suppress proliferation mediated by inhibition of phosphorylation of Akt in human lung squamous cell carcinoma. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1864:293-302. [PMID: 27884700 DOI: 10.1016/j.bbamcr.2016.11.018] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/26/2016] [Accepted: 11/18/2016] [Indexed: 12/11/2022]
Abstract
Abnormal expression of claudin (CLDN) subtypes has been reported in various solid cancers. However, it is unknown which subtype plays a key role in the regulation of proliferation in cancer cells. The expression of CLDN3-5, 7, and 18 in human lung squamous carcinoma tissues was lower than that in normal tissue. Here, we examined which combination of exogenous CLDNs expression inhibits proliferation and the molecular mechanism using human lung squamous RERF-LC-AI cells. Real-time polymerase chain reaction and western blotting showed that CLDN3-5, 7, and 18 are little expressed in RERF-LC-AI cells. In the exogenously transfected cells, CLDN5, 7, and 18 were distributed in the cell-cell contact areas concomitant with ZO-1, a tight junctional scaffolding protein, whereas CLDN3 and 4 were not. Cell proliferation was individually and additively suppressed by CLDN5, 7, and 18. The expression of these CLDNs showed no cytotoxicity compared with mock cells. CLDN5, 7, and 18 increased p21 and decreased cyclin D1, resulting in the suppression of cell cycle G1-S transition. The expression of these CLDNs inhibited phosphorylation of Akt without affecting phosphorylated ERK1/2. Furthermore, these CLDNs inhibited the nuclear localization of Akt and its association with 3-phosphoinositide-dependent protein kinase-1 (PDK1). The suppression of G1-S transition caused by CLDN5, 7, and 18 was rescued by the expression of constitutively active-Akt. We suggest that the reduction of CLDN5, 7, and 18 expression loses the suppressive ability of interaction between PDK1 and Akt and causes sustained phosphorylation of Akt, resulting in the disordered proliferation in lung squamous carcinoma cells.
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Affiliation(s)
- Risa Akizuki
- Laboratory of Biochemistry, Department of Biopharmaceutical Sciences, Gifu Pharmaceutical University
| | - Shun Shimobaba
- Laboratory of Biochemistry, Department of Biopharmaceutical Sciences, Gifu Pharmaceutical University
| | - Toshiyuki Matsunaga
- Laboratory of Biochemistry, Department of Biopharmaceutical Sciences, Gifu Pharmaceutical University
| | - Satoshi Endo
- Laboratory of Biochemistry, Department of Biopharmaceutical Sciences, Gifu Pharmaceutical University
| | - Akira Ikari
- Laboratory of Biochemistry, Department of Biopharmaceutical Sciences, Gifu Pharmaceutical University.
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13
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Pérez-Ramírez C, Cañadas-Garre M, Robles AI, Molina MÁ, Faus-Dáder MJ, Calleja-Hernández MÁ. Liquid biopsy in early stage lung cancer. Transl Lung Cancer Res 2016; 5:517-524. [PMID: 27826533 DOI: 10.21037/tlcr.2016.10.15] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Lung cancer is the leading cause of cancer-associated deaths worldwide. Surgery is the standard treatment for early-stage non-small cell lung cancer (NSCLC). However, 30% to 80% of these patients will die within 5 yearS of diagnosis. Circulating cell-free DNA (cfDNA) harbors pathologic characteristics of the original tumor, such as gene mutations or epigenetic alterations. Analysis of cfDNA has revolutionized the clinical care of advanced lung cancer patients undergoing targeted therapies. However, the low concentration of cfDNA in the blood of early-stage NSCLC patients has hampered its use for management of early disease. Continuing development of more specific and sensitive techniques for detection and analysis of cfDNA will soon enable its leverage in early stage and, perhaps, even screening settings. Therefore, cfDNA analysis may become a tool used for routine NSCLC diagnosis and for monitoring tumor burden, as well as for identifying hidden residual disease. In this review, we will focus on the current evidence of cfDNA in patients with early-stage NSCLC, new and upcoming approaches to identify circulating-tumor biomarkers, their clinical applications and future directions.
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Affiliation(s)
- Cristina Pérez-Ramírez
- Pharmacogenetics Unit, UGC Provincial de Farmacia de Granada, Instituto de Investigación Biosanitaria de Granada, Complejo Hospitalario Universitario de Granada, Avda. Fuerzas Armadas, 2, 18014 Granada, Spain;; Department of Biochemistry, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, s/n 18071 Granada, Spain
| | - Marisa Cañadas-Garre
- Pharmacogenetics Unit, UGC Provincial de Farmacia de Granada, Instituto de Investigación Biosanitaria de Granada, Complejo Hospitalario Universitario de Granada, Avda. Fuerzas Armadas, 2, 18014 Granada, Spain
| | - Ana I Robles
- Laboratory of Human Carcinogenesis, National Cancer Institute, 37 Convent Dr, Bethesda, MD 20892, USA
| | - Miguel Ángel Molina
- Pangaea Biotech, S.L., Hospital Universitario Quirón Dexeus, C/ Sabino Arana, 5-19. 08028 Barcelona, Spain
| | - María José Faus-Dáder
- Department of Biochemistry, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, s/n 18071 Granada, Spain
| | - Miguel Ángel Calleja-Hernández
- Pharmacogenetics Unit, UGC Provincial de Farmacia de Granada, Instituto de Investigación Biosanitaria de Granada, Complejo Hospitalario Universitario de Granada, Avda. Fuerzas Armadas, 2, 18014 Granada, Spain;; Department of Pharmacology, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, s/n, 18071 Granada, Spain
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