1
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Alontaga AY, Cano P, Ozakinci H, Puskas JA, Stewart PA, Welsh EA, Yoder SJ, Hicks JK, Saltos AN, Bossler AD, Haura EB, Koomen JM, Boyle TA. Implementation of a High-Accuracy Targeted Gene Expression Panel for Clinical Care. J Mol Diagn 2024:S1525-1578(24)00101-6. [PMID: 38777037 DOI: 10.1016/j.jmoldx.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 02/29/2024] [Accepted: 04/17/2024] [Indexed: 05/25/2024] Open
Abstract
This study describes the validation of a clinical RNA expression panel with evaluation of concordance between gene copy gain by a next-generation sequencing (NGS) assay and high gene expression by an RNA expression panel. The RNA Salah Targeted Expression Panel (RNA STEP) was designed with input from oncologists to include 204 genes with utility for clinical trial prescreening and therapy selection. RNA STEP was validated with the nanoString platform using remnant formalin-fixed, paraffin-embedded-derived RNA from 102 patients previously tested with a validated clinical NGS panel. The repeatability, reproducibility, and concordance of RNA STEP results with NGS results were evaluated. RNA STEP demonstrated high repeatability and reproducibility, with excellent correlation (r > 0.97, P < 0.0001) for all comparisons. Comparison of RNA STEP high gene expression (log2 ratio ≥ 2) versus NGS DNA-based gene copy number gain (copies ≥ 5) for 38 mutually covered genes revealed an accuracy of 93.0% with a positive percentage agreement of 69.4% and negative percentage agreement of 93.8%. Moderate correlation was observed between platforms (r = 0.53, P < 0.0001). Concordance between high gene expression and gene copy number gain varied by specific gene, and some genes had higher accuracy between assays. Clinical implementation of RNA STEP provides gene expression data complementary to NGS and offers a tool for prescreening patients for clinical trials.
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Affiliation(s)
- Aileen Y Alontaga
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Pedro Cano
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Hilal Ozakinci
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - John A Puskas
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Paul A Stewart
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Eric A Welsh
- Department of Biostatistics and Bioinformatics Shared Resource, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Sean J Yoder
- Molecular Genomics Core Facility, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - J Kevin Hicks
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Andreas N Saltos
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Aaron D Bossler
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Eric B Haura
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - John M Koomen
- Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida; Department of Molecular Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida
| | - Theresa A Boyle
- Department of Thoracic Oncology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida; Department of Pathology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, Florida.
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2
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Fassan M, Angerilli V, Normanno N, Pruneri G, Marchetti A, Grillo F, Tonini G, Scarpa A, Rimassa L. Practical guidelines for molecular testing of cholangiocarcinoma in clinical practice: Italian experts' position paper. Crit Rev Oncol Hematol 2024; 194:104224. [PMID: 38211900 DOI: 10.1016/j.critrevonc.2023.104224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/20/2023] [Accepted: 11/26/2023] [Indexed: 01/13/2024] Open
Abstract
Biliary tract cancers (BTCs) represent a spectrum of malignancies associated with a dismal prognosis. Recent genomic profiling studies have provided a deeper understanding of the complex and heterogenous molecular landscape of BTCs, identifying several actionable genetic alterations, and expanding treatment options. Due to the high number and complexity of genetic alterations which require testing, next-generation sequencing (NGS) is currently the preferred approach over conventional methods (i.e., immunohistochemistry, fluorescence in-situ hybridization and PCR) for molecular profiling of BTCs and should be performed upfront in all BTC patients. However, BTC sampling often yields low tumor cellularity tissue, hampering NGS analysis. Future perspectives to overcome this obstacle include liquid biopsy and optimization of biopsy protocols. In this position paper, the authors discuss the current histopathologic, molecular, and therapeutic landscape of BTCs, provide a critical overview of the available testing methods for molecular diagnostics, and propose a practical diagnostic algorithm for molecular testing of BTC samples.
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Affiliation(s)
- Matteo Fassan
- Department of Medicine (DIMED), University of Padua, Padua, Italy; Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy
| | | | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Naples, Italy
| | - Giancarlo Pruneri
- Pathology Unit 2, Department of Innovation Diagnostics, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy; University of Milan, School of Medicine, Milan, Italy
| | - Antonio Marchetti
- Department of Medical, Oral and Biotechnological Sciences, Centre for Advanced Studies and Technology (CAST), University of Chieti, Chieti, Italy
| | - Federica Grillo
- Pathology Unit, Department of Surgical Sciences and Integrated Diagnostics, University of Genoa, Italy; IRCCS-Ospedale Policlinico San Martino, Genoa, Italy.
| | - Giuseppe Tonini
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Roma, Italy; Department of Medicine and Surgery, Università Campus Bio-Medico di Roma, Roma, Italy
| | - Aldo Scarpa
- Section of Pathology, Department of Diagnostic and Public Health, University of Verona, Verona, Italy
| | - Lorenza Rimassa
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy; Medical Oncology and Hematology Unit, Humanitas Cancer Center, IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
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3
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Pepe F, Venetis K, Cursano G, Frascarelli C, Pisapia P, Vacirca D, Scimone C, Rappa A, Russo G, Mane E, Pagni F, Castellano I, Troncone G, Angelis CD, Curigliano G, Guerini-Rocco E, Malapelle U, Fusco N. PIK3CA testing in hormone receptor-positive/HER2-negative metastatic breast cancer: real-world data from Italian molecular pathology laboratories. Pharmacogenomics 2024; 25:161-169. [PMID: 38440825 DOI: 10.2217/pgs-2023-0238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024] Open
Abstract
Introduction: PIK3CA gene mutations occur in approximately 40% of hormone receptor-positive/HER2-negative (HR+/HER2-) metastatic breast cancers (MBCs), electing them to targeted therapy. Testing PIK3CA status is complex due to selection of biological specimen and testing method. Materials & methods: This work investigates real-life experience on PIK3CA testing in HR+/HER2- MBC. Clinical, technical and molecular data on PIK3CA testing were collected from two referral laboratories. Additionally, the results of a nationwide PIK3CA survey involving 116 institutions were assessed. Results: Overall, n = 35 MBCs were PIK3CA-mutated, with mutations mostly occurring in exons 9 (n = 19; 51.4%) and 20 (n = 15; 40.5%). The nationwide survey revealed significant variability across laboratories in terms of sampling methodology, technical assessment and clinical report signing healthcare figures for PIK3CA molecular testing in diagnostic routine practice. Conclusion: This study provides insights into the real-world routine of PIK3CA testing in HR+/HER2- MBC and highlights the need for standardization and networking in predictive pathology.
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Affiliation(s)
- Francesco Pepe
- Department of Public Health, Federico II University of Naples, 80131, Naples, Italy
| | - Konstantinos Venetis
- Division of Pathology, European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Giulia Cursano
- Division of Pathology, European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Chiara Frascarelli
- Division of Pathology, European Institute of Oncology IRCCS, 20141, Milan, Italy
- Department of Oncology & Hemato-Oncology, University of Milan, 20122, Milan, Italy
| | - Pasquale Pisapia
- Department of Public Health, Federico II University of Naples, 80131, Naples, Italy
| | - Davide Vacirca
- Division of Pathology, European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Claudia Scimone
- Department of Public Health, Federico II University of Naples, 80131, Naples, Italy
| | - Alessandra Rappa
- Division of Pathology, European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Gianluca Russo
- Department of Public Health, Federico II University of Naples, 80131, Naples, Italy
| | - Eltjona Mane
- Division of Pathology, European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Fabio Pagni
- Center for Digital Medicine, Department of Medicine & Surgery, University Milan Bicocca, Monza (MB), Italy
- Molecular Pathology & Predictive Medicine PMMP Group, Italian Society of Pathology, SIAPeC, Italy
| | - Isabella Castellano
- Pathology Unit, Department of Medical Sciences, City of Health and Science University Hospital, University of Turin, 10126, Turin, Italy
- Breast Pathology GIPaM Group, Italian Society of Pathology, SIAPeC, Italy
| | - Giancarlo Troncone
- Department of Public Health, Federico II University of Naples, 80131, Naples, Italy
| | - Carmine De Angelis
- Department of Clinical Medicine & Surgery, University Federico II, 80131, Naples, Italy
| | - Giuseppe Curigliano
- Department of Oncology & Hemato-Oncology, University of Milan, 20122, Milan, Italy
- Division of New Drugs & Early Drug Development, European Institute of Oncology, IRCCS, 20141, Milan, Italy
| | - Elena Guerini-Rocco
- Division of Pathology, European Institute of Oncology IRCCS, 20141, Milan, Italy
- Department of Oncology & Hemato-Oncology, University of Milan, 20122, Milan, Italy
- Molecular Pathology & Predictive Medicine PMMP Group, Italian Society of Pathology, SIAPeC, Italy
| | - Umberto Malapelle
- Department of Public Health, Federico II University of Naples, 80131, Naples, Italy
- Molecular Pathology & Predictive Medicine PMMP Group, Italian Society of Pathology, SIAPeC, Italy
| | - Nicola Fusco
- Division of Pathology, European Institute of Oncology IRCCS, 20141, Milan, Italy
- Department of Oncology & Hemato-Oncology, University of Milan, 20122, Milan, Italy
- Molecular Pathology & Predictive Medicine PMMP Group, Italian Society of Pathology, SIAPeC, Italy
- Breast Pathology GIPaM Group, Italian Society of Pathology, SIAPeC, Italy
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4
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Ivanova M, Porta FM, D'Ercole M, Pescia C, Sajjadi E, Cursano G, De Camilli E, Pala O, Mazzarol G, Venetis K, Guerini-Rocco E, Curigliano G, Viale G, Fusco N. Standardized pathology report for HER2 testing in compliance with 2023 ASCO/CAP updates and 2023 ESMO consensus statements on HER2-low breast cancer. Virchows Arch 2024; 484:3-14. [PMID: 37770765 PMCID: PMC10791807 DOI: 10.1007/s00428-023-03656-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/03/2023] [Accepted: 09/13/2023] [Indexed: 09/30/2023]
Abstract
Since the release of the DESTINY-Breast04 (DB-04) trial findings in June 2022, the field of pathology has seen a renaissance of HER2 as a predictive biomarker in breast cancer. The trial focused on patients with metastatic breast cancer who were classified as "HER2-low," i.e., those with immunohistochemistry (IHC) HER2 1 + or 2 + and negative in situ hybridization (ISH) results. The study revealed that treating these patients with trastuzumab deruxtecan (T-DXd) instead of the oncologist's chosen chemotherapy led to outstanding improvements in survival. This has challenged the existing binary HER2 pathological classification system, which categorized tumors as either positive (overexpression/amplification) or negative, as per the ASCO/CAP 2018 guideline reaffirmed by ASCO/CAP 2023 guideline update. Given that DB-04 excluded patients with HER2 IHC score 0 status, the results of the ongoing DB-06 trial may shed further light on the potential benefits of T-DXd therapy for these patients. Roughly half of all breast cancers are estimated to belong to the HER2-low category, which does not represent a distinct or specific subtype of cancer. Instead, it encompasses a diverse group of tumors that exhibit clinical, morphological, immunohistochemical, and molecular variations. However, HER2-low offers a distinctive biomarker status that identifies a specific therapeutic regimen (i.e., T-DXd) linked to a favorable prognosis in breast cancer. This unique association emphasizes the importance of accurately identifying these tumors. Differentiating between a HER2 IHC score 0 and score 1 + has not been clinically significant until now. To ensure accurate classification and avoid misdiagnosis, it is necessary to adopt standardized procedures, guidelines, and specialized training for pathologists in interpreting HER2 expression in the lower spectrum. Additionally, the utilization of artificial intelligence holds promise in supporting this endeavor. Here, we address the current state of the art and unresolved issues in assessing HER2-low status, with a particular emphasis on the score 0. We explore the dilemma surrounding the exclusion of HER2-zero patients from potentially beneficial therapy based on traditional HER2 testing. Additionally, we examine the clinical context, considering that DB-04 primarily involved heavily pretreated late-stage metastatic breast cancers. We also delve into emerging evidence suggesting that extrapolating HER2-low status from the original diagnosis may lead to misleading results. Finally, we provide recommendations for conducting high-quality testing and propose a standardized pathology report in compliance with 2023 ASCO/CAP updates and 2023 ESMO consensus statements on HER2-low breast cancer.
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Affiliation(s)
- Mariia Ivanova
- Division of Pathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Francesca Maria Porta
- Division of Pathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Marianna D'Ercole
- Division of Pathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Carlo Pescia
- Division of Pathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Elham Sajjadi
- Division of Pathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy
| | - Giulia Cursano
- Division of Pathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Elisa De Camilli
- Division of Pathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Oriana Pala
- Division of Pathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Giovanni Mazzarol
- Division of Pathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Konstantinos Venetis
- Division of Pathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Elena Guerini-Rocco
- Division of Pathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy
| | - Giuseppe Curigliano
- Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy
- Division of New Drugs and Early Drug Development for Innovative Therapies, IEO, European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Giuseppe Viale
- Division of Pathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy
| | - Nicola Fusco
- Division of Pathology, IEO European Institute of Oncology IRCCS, 20141, Milan, Italy.
- Department of Oncology and Hemato-Oncology, University of Milan, 20122, Milan, Italy.
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5
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Stenzinger A, Vogel A, Lehmann U, Lamarca A, Hofman P, Terracciano L, Normanno N. Molecular profiling in cholangiocarcinoma: A practical guide to next-generation sequencing. Cancer Treat Rev 2024; 122:102649. [PMID: 37984132 DOI: 10.1016/j.ctrv.2023.102649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/29/2023] [Indexed: 11/22/2023]
Abstract
Cholangiocarcinomas (CCA) are a heterogeneous group of tumors that are classified as intrahepatic, perihilar, or distal according to the anatomic location within the biliary tract. Each CCA subtype is associated with distinct genomic alterations, including single nucleotide variants, copy number variants, and chromosomal rearrangements or gene fusions, each of which can influence disease prognosis and/or treatment outcomes. Molecular profiling using next-generation sequencing (NGS) is a powerful technique for identifying unique gene variants carried by an individual tumor, which can facilitate their accurate diagnosis as well as promote the optimal selection of gene variant-matched targeted treatments. NGS is particularly useful in patients with CCA because between one-third and one-half of these patients have genomic alterations that can be targeted by drugs that are either approved or in clinical development. NGS can also provide information about disease evolution and secondary resistance alterations that can develop during targeted therapy, and thus facilitate assessment of prognosis and choice of alternative targeted treatments. Pathologists play a critical role in assessing the viability of biopsy samples for NGS, and advising treating clinicians whether NGS can be performed and which of the available platforms should be used to optimize testing outcomes. This review aims to provide clinical pathologists and other healthcare professionals with practical step-by-step guidance on the use of NGS for molecular profiling of patients with CCA, with respect to tumor biopsy techniques, pre-analytic sample preparation, selecting the appropriate NGS panel, and understanding and interpreting results of the NGS test.
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Affiliation(s)
- Albrecht Stenzinger
- Institute of Pathology Heidelberg (IPH), Center for Molecular Pathology, University Hospital Heidelberg, In Neuenheimer Feld 224, 69120 Heidelberg, Building 6224, Germany.
| | - Arndt Vogel
- Division of Gastroenterology and Hepatology, Toronto General Hospital Medical Oncology, Princess Margaret Cancer Centre, Schwartz Reisman Liver Research Centre, 200 Elizabeth Street, Office: 9 EB 236 Toronto, ON, M5G 2C4, Canada.
| | - Ulrich Lehmann
- Institute for Pathology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany.
| | - Angela Lamarca
- Department of Medical Oncology, Oncohealth Institute, Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Fundación Jiménez Díaz University Hospital, Av. de los Reyes Católicos, 2, 28040 Madrid, Spain; Department of Medical Oncology, The Christie NHS Foundation Trust, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PL, UK.
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, IHU RespirERA, Siège de l'Université: Grand Château, 28 Avenue de Valrose, 06103 Nice CEDEX 2, France.
| | - Luigi Terracciano
- Department of Biomedical Sciences, Humanitas University, Via Rita Levi Montalcini, 4, 20072 Pieve Emanuele, Milan, Italy; IRCCS Humanitas Research Hospital, Via Alessandro Manzoni, 56, 20089 Rozzano, Milan, Italy.
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy.
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Sztankovics D, Krencz I, Moldvai D, Dankó T, Nagy Á, Nagy N, Bedics G, Rókusz A, Papp G, Tőkés AM, Pápay J, Sápi Z, Dezső K, Bödör C, Sebestyén A. Novel RICTOR amplification harbouring entities: FISH validation of RICTOR amplification in tumour tissue after next-generation sequencing. Sci Rep 2023; 13:19610. [PMID: 37949943 PMCID: PMC10638425 DOI: 10.1038/s41598-023-46927-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023] Open
Abstract
Alterations in mTOR signalling molecules, including RICTOR amplification, have been previously described in many cancers, particularly associated with poor prognosis. In this study, RICTOR copy number variation (CNV) results of diagnostic next-generation sequencing (NGS) were analysed in 420 various human malignant tissues. RICTOR amplification was tested by Droplet Digital PCR (ddPCR) and validated using the "gold standard" fluorescence in situ hybridisation (FISH). Additionally, the consequences of Rictor protein expression were also studied by immunohistochemistry. RICTOR amplification was presumed in 37 cases with CNV ≥ 3 by NGS, among these, 16 cases (16/420; 3.8%) could be validated by FISH, however, ddPCR confirmed only 11 RICTOR-amplified cases with lower sensitivity. Based on these, neither NGS nor ddPCR could replace traditional FISH in proof of RICTOR amplification. However, NGS could be beneficial to highlight potential RICTOR-amplified cases. The obtained results of the 14 different tumour types with FISH-validated RICTOR amplification demonstrate the importance of RICTOR amplification in a broad spectrum of tumours. The newly described RICTOR-amplified entities could initiate further collaborative studies with larger cohorts to analyse the prevalence of RICTOR amplification in rare diseases. Finally, our and further work could help to improve and expand future therapeutic opportunities for mTOR-targeted therapies.
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Affiliation(s)
- Dániel Sztankovics
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Ildikó Krencz
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Dorottya Moldvai
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Titanilla Dankó
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Ákos Nagy
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Noémi Nagy
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Gábor Bedics
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - András Rókusz
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Gergő Papp
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Anna-Mária Tőkés
- Department of Pathology, Forensic and Insurance Medicine, Semmelweis University, Üllői út 93, 1091, Budapest, Hungary
| | - Judit Pápay
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Zoltán Sápi
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Katalin Dezső
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Csaba Bödör
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
- HCEMM-SE Molecular Oncohematology Research Group, Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary
| | - Anna Sebestyén
- Department of Pathology and Experimental Cancer Research, Semmelweis University, Üllői út 26, 1085, Budapest, Hungary.
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7
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Malapelle U, Angerilli V, Pepe F, Fontanini G, Lonardi S, Scartozzi M, Memeo L, Pruneri G, Marchetti A, Perrone G, Fassan M. The ideal reporting of RAS testing in colorectal adenocarcinoma: a pathologists' perspective. Pathologica 2023; 115:1-11. [PMID: 37314870 PMCID: PMC10462993 DOI: 10.32074/1591-951x-895] [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: 05/24/2023] [Accepted: 05/24/2023] [Indexed: 06/16/2023] Open
Abstract
RAS gene mutational status represents an imperative predictive biomarker to be tested in the clinical management of metastatic colorectal adenocarcinoma. Even if it is one of the most studied biomarkers in the era of precision medicine, several pre-analytical and analytical factors may still impasse an adequate reporting of RAS status in clinical practice, with significant therapeutic consequences. Thus, pathologists should be aware on the main topics related to this molecular evaluation: (i) adopt diagnostic limit of detections adequate to avoid the interference of sub-clonal cancer cell populations; (ii) choose the most adequate diagnostic strategy according to the available sample and its qualification for molecular testing; (iii) provide all the information regarding the mutation detected, since many RAS mutation-specific targeted therapeutic approaches are in development and will enter into routine clinical practice. In this review, we give a comprehensive description of the current scenario about RAS gene mutational testing in the clinic focusing on the pathologist's role in patient selection for targeted therapies.
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Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples (NA), Italy
| | | | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples (NA), Italy
| | - Gabriella Fontanini
- Department of Surgical, Medical and Molecular Pathology and Critical Care Medicine, University of Pisa, Pisa (PI), Italy
| | - Sara Lonardi
- Medical Oncology 3, Veneto Institute of Oncology IOV-IRCCS, Padua (PD), Italy
| | - Mario Scartozzi
- Medical Oncology, University Hospital and University of Cagliari, Cagliari (CA), Italy
| | - Lorenzo Memeo
- Department of Experimental Oncology, Mediterranean Institute of Oncology, Viagrande, Catania (CT), Italy
| | - Gianfranco Pruneri
- Department of Advanced Diagnostics, Fondazione IRCCS Istituto Nazionale Tumori and University of Milan, Milan (MI), Italy
| | - Antonio Marchetti
- Center for Advanced Studies and Technology (CAST), University Chieti-Pescara, Chieti (CH), Italy
- Diagnostic Molecular Pathology, Unit of Anatomic Pathology, SS Annunziata Hospital, Chieti (CH), Italy and Department of Medical, Oral, and Biotechnological Sciences University “G. D’Annunzio” of Chieti-Pescara, Chieti (CH), Italy
| | - Giuseppe Perrone
- Department of Medicine and Surgery, Research Unit of Anatomical Pathology, Università Campus Bio-Medico di Roma, Roma, Italy
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Roma, Italy
| | - Matteo Fassan
- Department of Medicine (DIMED), University of Padua, Padua (PD), Italy
- Veneto Institute of Oncology (IOV-IRCCS), Padua (PD), Italy
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8
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Oreper D, Klaeger S, Jhunjhunwala S, Delamarre L. The peptide woods are lovely, dark and deep: Hunting for novel cancer antigens. Semin Immunol 2023; 67:101758. [PMID: 37027981 DOI: 10.1016/j.smim.2023.101758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 04/08/2023]
Abstract
Harnessing the patient's immune system to control a tumor is a proven avenue for cancer therapy. T cell therapies as well as therapeutic vaccines, which target specific antigens of interest, are being explored as treatments in conjunction with immune checkpoint blockade. For these therapies, selecting the best suited antigens is crucial. Most of the focus has thus far been on neoantigens that arise from tumor-specific somatic mutations. Although there is clear evidence that T-cell responses against mutated neoantigens are protective, the large majority of these mutations are not immunogenic. In addition, most somatic mutations are unique to each individual patient and their targeting requires the development of individualized approaches. Therefore, novel antigen types are needed to broaden the scope of such treatments. We review high throughput approaches for discovering novel tumor antigens and some of the key challenges associated with their detection, and discuss considerations when selecting tumor antigens to target in the clinic.
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Affiliation(s)
- Daniel Oreper
- Genentech, 1 DNA way, South San Francisco, 94080 CA, USA.
| | - Susan Klaeger
- Genentech, 1 DNA way, South San Francisco, 94080 CA, USA.
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Angerilli V, Fornaro L, Pepe F, Rossi SM, Perrone G, Malapelle U, Fassan M. FGFR2 testing in cholangiocarcinoma: translating molecular studies into clinical practice. Pathologica 2023; 115:71-82. [PMID: 37017301 PMCID: PMC10462997 DOI: 10.32074/1591-951x-859] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 03/06/2023] [Indexed: 04/06/2023] Open
Abstract
Cholangiocarcinoma (CCA) is a heterogeneous group of neoplasms burdened by a dismal prognosis. Several studies have investigated the genomic profile of CCA and identified numerous druggable genetic alterations, including FGFR2 fusions/rearrangements. Approximately 5-7% of CCAs and 10-20% of intrahepatic iCCAs harbor FGFR2 fusions. With the recent advent of FGFR-targeting therapies into clinical practice, a standardization of molecular testing for FGFR2 alterations in CCA will be necessary. In this review, we describe the technical aspects and challenges related to FGFR2 testing in routine practice, focusing on the comparison between Next-Generation Sequencing (NGS) and FISH assays, the best timing to perform the test, and on the role of liquid biopsy.
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Affiliation(s)
- Valentina Angerilli
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, Padua (PD), Italy
| | - Lorenzo Fornaro
- Medical Oncology, Azienda Ospedaliero-Universitaria Pisana, Pisa (PI), Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples (NA), Italy
| | - Silvia Maria Rossi
- Department of Medicine and Surgery, Research Unit of Anatomical Pathology, Università Campus Bio-Medico di Roma, Roma, Italy
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Roma, Italy
| | - Giuseppe Perrone
- Department of Medicine and Surgery, Research Unit of Anatomical Pathology, Università Campus Bio-Medico di Roma, Roma, Italy
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Roma, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples (NA), Italy
| | - Matteo Fassan
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, Padua (PD), Italy
- Veneto Institute of Oncology, IOV - IRCCS, Padua (PD), Italy
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Analytical Performance of Next-Generation Sequencing and RT-PCR on Formalin-Fixed Paraffin-Embedded Tumor Tissues for PIK3CA Testing in HR+/HER2- Breast Cancer. Cells 2022; 11:cells11223545. [PMID: 36428975 PMCID: PMC9688837 DOI: 10.3390/cells11223545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/28/2022] [Accepted: 10/28/2022] [Indexed: 11/11/2022] Open
Abstract
Somatic mutations in PIK3CA are present in ~40% breast cancers (BC); their detection in hormone receptor (HR)+/HER2- tumors allows for selecting patients with advanced disease eligible for PIK3CA targeting with alpelisib. The choice of what type of PIK3CA testing approach to adopt and which tissue sample to analyze is a new task in breast pathology. In this methodological study, we sought to assess the performance of next-generation sequencing (NGS) and RT-PCR for PIK3CA testing on archival formalin-fixed paraffin-embedded (FFPE) primary tumors and corresponding metastases. Sixteen HR+/HER2- BC with known PIK3CA-mutated status (ex. 7, 9, and 20) on metastatic samples by means of amplicon-based targeted NGS were selected, and n = 13 of these samples were re-tested with a commercially available CE-IVD RT-PCR assay. All available primary tumors (n = 8) were tested with both methods. NGS detected mutations in all samples, while RT-PCR in n = 2 sample-pairs and overall, in n = 5/8 (62.5%) primary tumors and 7/13 (53.8%) metastases (κ = 0.09; 95% CI, -0.69-0.87). Slight agreement (κ = 0; 95% CI, -0.59-0.59) was observed between NGS and RT-PCR, with the former being generally more sensitive in cases with low DNA quality and quantity. Post hoc visual inspection of the RT-PCR data increased the concordance to 76.9%. Targeted NGS offers reliable and robust PIK3CA testing on both tumor and metastasis FFPE samples; the accuracy of RT-PCR depends on the DNA quantity and quality. In HR+/HER2- BC, both the selection of the PIK3CA testing strategy of FFPE tissues and which sample to analyze should consider several technical parameters and should be tailored for each case.
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Special Issue: Next-Generation Sequencing in Tumor Diagnosis and Treatment II. Diagnostics (Basel) 2022; 12:diagnostics12082017. [PMID: 36010367 PMCID: PMC9407571 DOI: 10.3390/diagnostics12082017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/17/2022] Open
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