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Frezzetti D, Caridi V, Marra L, Camerlingo R, D’Alessio A, Russo F, Dotolo S, Rachiglio AM, Esposito Abate R, Gallo M, Maiello MR, Morabito A, Normanno N, De Luca A. The Impact of Inadequate Exposure to Epidermal Growth Factor Receptor-Tyrosine Kinase Inhibitors on the Development of Resistance in Non-Small-Cell Lung Cancer Cells. Int J Mol Sci 2024; 25:4844. [PMID: 38732063 PMCID: PMC11084975 DOI: 10.3390/ijms25094844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 05/13/2024] Open
Abstract
Epidermal growth factor receptor (EGFR)-mutant non-small-cell lung cancer (NSCLC) patients treated with EGFR-tyrosine kinase inhibitors (TKIs) inevitably develop resistance through several biological mechanisms. However, little is known on the molecular mechanisms underlying acquired resistance to suboptimal EGFR-TKI doses, due to pharmacodynamics leading to inadequate drug exposure. To evaluate the effects of suboptimal EGFR-TKI exposure on resistance in NSCLC, we obtained HCC827 and PC9 cell lines resistant to suboptimal fixed and intermittent doses of gefitinib and compared them to cells exposed to higher doses of the drug. We analyzed the differences in terms of EGFR signaling activation and the expression of epithelial-mesenchymal transition (EMT) markers, whole transcriptomes byRNA sequencing, and cell motility. We observed that the exposure to low doses of gefitinib more frequently induced a partial EMT associated with an induced migratory ability, and an enhanced transcription of cancer stem cell markers, particularly in the HCC827 gefitinib-resistant cells. Finally, the HCC827 gefitinib-resistant cells showed increased secretion of the EMT inducer transforming growth factor (TGF)-β1, whose inhibition was able to partially restore gefitinib sensitivity. These data provide evidence that different levels of exposure to EGFR-TKIs in tumor masses might promote different mechanisms of acquired resistance.
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Affiliation(s)
- Daniela Frezzetti
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (D.F.); (V.C.); (L.M.); (R.C.); (S.D.); (A.M.R.); (R.E.A.); (M.G.); (M.R.M.); (A.D.L.)
| | - Vincenza Caridi
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (D.F.); (V.C.); (L.M.); (R.C.); (S.D.); (A.M.R.); (R.E.A.); (M.G.); (M.R.M.); (A.D.L.)
| | - Laura Marra
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (D.F.); (V.C.); (L.M.); (R.C.); (S.D.); (A.M.R.); (R.E.A.); (M.G.); (M.R.M.); (A.D.L.)
| | - Rosa Camerlingo
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (D.F.); (V.C.); (L.M.); (R.C.); (S.D.); (A.M.R.); (R.E.A.); (M.G.); (M.R.M.); (A.D.L.)
| | - Amelia D’Alessio
- Laboratory of Toxicology Analysis, Department for the Treatment of Addictions, ASL Salerno, 84124 Salerno, Italy;
| | - Francesco Russo
- Institute of Endocrinology and Experimental Oncology, National Research Council of Italy, 80131 Naples, Italy;
| | - Serena Dotolo
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (D.F.); (V.C.); (L.M.); (R.C.); (S.D.); (A.M.R.); (R.E.A.); (M.G.); (M.R.M.); (A.D.L.)
| | - Anna Maria Rachiglio
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (D.F.); (V.C.); (L.M.); (R.C.); (S.D.); (A.M.R.); (R.E.A.); (M.G.); (M.R.M.); (A.D.L.)
| | - Riziero Esposito Abate
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (D.F.); (V.C.); (L.M.); (R.C.); (S.D.); (A.M.R.); (R.E.A.); (M.G.); (M.R.M.); (A.D.L.)
| | - Marianna Gallo
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (D.F.); (V.C.); (L.M.); (R.C.); (S.D.); (A.M.R.); (R.E.A.); (M.G.); (M.R.M.); (A.D.L.)
| | - Monica Rosaria Maiello
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (D.F.); (V.C.); (L.M.); (R.C.); (S.D.); (A.M.R.); (R.E.A.); (M.G.); (M.R.M.); (A.D.L.)
| | - Alessandro Morabito
- Thoracic Department, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy;
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (D.F.); (V.C.); (L.M.); (R.C.); (S.D.); (A.M.R.); (R.E.A.); (M.G.); (M.R.M.); (A.D.L.)
| | - Antonella De Luca
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (D.F.); (V.C.); (L.M.); (R.C.); (S.D.); (A.M.R.); (R.E.A.); (M.G.); (M.R.M.); (A.D.L.)
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Esposito Abate R, Pasquale R, Sacco A, Simeon V, Maiello MR, Frezzetti D, Chiodini P, Normanno N. Harmonization of tumor mutation burden testing with comprehensive genomic profiling assays: an IQN Path initiative. J Immunother Cancer 2024; 12:e007800. [PMID: 38309725 PMCID: PMC10840060 DOI: 10.1136/jitc-2023-007800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2023] [Indexed: 02/05/2024] Open
Abstract
BACKGROUND Although conflicting results emerged from different studies, the tumor mutational burden (TMB) appears as one of most reliable biomarkers of sensitivity to immune checkpoint inhibitors. Several laboratories are reporting TMB values when performing comprehensive genomic profiling (CGP) without providing a clinical interpretation, due to the lack of validated cut-off values. The International Quality Network for Pathology launched an initiative to harmonize TMB testing with CGP assay and favor the clinical implementation of this biomarker. METHODS TMB evaluation was performed with three commercially available CGP panels, TruSight Oncology 500 (TSO500), Oncomine Comprehensive Plus Assay (OCA) and QIAseq Multimodal Panel (QIA), versus the reference assay FoundationOne CDx (F1CDx). Archived clinical samples derived from 60 patients with non-small cell lung cancer were used for TMB assessment. Adjusted cut-off values for each panel were calculated. RESULTS Testing was successful for 91.7%, 100%, 96.7% and 100% of cases using F1CDx, TSO500, OCA and QIA, respectively. The matrix comparison analysis, between the F1CDx and CGP assays, showed a linear correlation for all three panels, with a higher correlation between F1CDx and TSO500 (rho=0.88) than in the other two comparisons (rho=0.77 for QIA; 0.72 for OCA). The TSO500 showed the best area under the curve (AUC, value 0.96), with a statistically significant difference when compared with the AUC of OCA (0.83, p value=0.01) and QIA (0.88, p value=0.028). The Youden Index calculation allowed us to extrapolate TMB cut-offs of the different panels corresponding to the 10 mutations/megabase (muts/Mb) cut-off of F1CDx: 10.19, 10.4 and 12.37 muts/Mb for TSO500, OCA and QIA, respectively. Using these values, we calculated the relative accuracy measures for the three panels. TSO500 showed 86% specificity and 96% sensitivity, while OCA and QIA had lower yet similar values of specificity and sensitivity (73% and 88%, respectively). CONCLUSION This study estimated TMB cut-off values for commercially available CGP panels. The results showed a good performance of all panels on clinical samples and the calculated cut-offs support better accuracy measures for TSO500. The validated cut-off values can drive clinical interpretation of TMB testing in clinical research and clinical practice.
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Affiliation(s)
- Riziero Esposito Abate
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori IRCCS Fondazione G.Pascale, Napoli, Italy
| | | | - Alessandra Sacco
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori IRCCS Fondazione G.Pascale, Napoli, Italy
| | - Vittorio Simeon
- Medical Statistics Unit, Department of Mental Health and Public Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Italy
| | - Monica Rosaria Maiello
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori IRCCS Fondazione G.Pascale, Napoli, Italy
| | - Daniela Frezzetti
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori IRCCS Fondazione G.Pascale, Napoli, Italy
| | - Paolo Chiodini
- Medical Statistics Unit, Department of Mental Health and Public Medicine, Università degli Studi della Campania Luigi Vanvitelli, Napoli, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori IRCCS Fondazione G.Pascale, Napoli, Italy
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Normanno N, Machado JC, Pescarmona E, Buglioni S, Navarro L, Esposito Abate R, Ferro A, Mensink R, Lambiase M, Lespinet-Fabre V, Calgua B, Jermann PM, Ilié M, Hofman P. European Real-World Assessment of the Clinical Validity of a CE-IVD Panel for Ultra-Fast Next-Generation Sequencing in Solid Tumors. Int J Mol Sci 2023; 24:13788. [PMID: 37762091 PMCID: PMC10531166 DOI: 10.3390/ijms241813788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/02/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Molecular profiling of solid tumors facilitates personalized, targeted therapeutic interventions. The ability to perform next-generation sequencing (NGS), especially from small tissue samples, in a short turnaround time (TAT) is essential to providing results that enable rapid clinical decisions. This multicenter study evaluated the performance of a CE in vitro diagnostic (IVD) assay, the Oncomine Dx Express Test, on the Ion Torrent Genexus System for detecting DNA and RNA variants in solid tumors. Eighty-two archived formalin-fixed paraffin embedded (FFPE) tissue samples from lung, colorectal, central nervous system, melanoma, breast, gastric, thyroid, and soft tissue cancers were used to assess the presence of single nucleotide variants (SNVs), insertions and deletions (indels), copy number variations (CNVs), gene fusions, and splice variants. These clinical samples were previously characterized at the various academic centers using orthogonal methods. The Oncomine Dx Express Test showed high performance with 100% concordance with previous characterization for SNVs, indels, CNVs, gene fusions, and splice variants. SNVs and indels with allele frequencies as low as 5% were correctly identified. The test detected all the expected ALK, RET, NTRK1, and ROS1 fusion isoforms and MET exon 14-skipping splice variants. The average TAT from extracted nucleic acids to the final variant report was 18.3 h. The Oncomine Dx Express Test in combination with the Ion Torrent Genexus System is a CE-IVD-compliant, performant, and multicenter reproducible method for NGS detection of actionable biomarkers from a range of tumor samples, providing results in a short TAT that could support timely decision- making for targeted therapeutic interventions.
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Affiliation(s)
- Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (N.N.); (R.E.A.)
| | - José Carlos Machado
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal; (J.C.M.); (A.F.); (R.M.)
- Institute of Molecular Pathology and Immunology, University of Porto (Ipatimup), 4200-135 Porto, Portugal
- Department of Pathology, Faculty of Medicine, University of Porto (FMUP), 4200-319 Porto, Portugal
| | - Edoardo Pescarmona
- I.R.C.C.S. Regina Elena National Cancer Institute, 00144 Rome, Italy; (E.P.); (S.B.)
| | - Simonetta Buglioni
- I.R.C.C.S. Regina Elena National Cancer Institute, 00144 Rome, Italy; (E.P.); (S.B.)
| | - Lara Navarro
- Consorcio Hospital General de Valencia, 46014 Valencia, Spain;
| | - Riziero Esposito Abate
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (N.N.); (R.E.A.)
| | - Anabela Ferro
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal; (J.C.M.); (A.F.); (R.M.)
- Institute of Molecular Pathology and Immunology, University of Porto (Ipatimup), 4200-135 Porto, Portugal
| | - Rob Mensink
- Instituto de Investigação e Inovação em Saúde (i3S), University of Porto, 4200-135 Porto, Portugal; (J.C.M.); (A.F.); (R.M.)
- Institute of Molecular Pathology and Immunology, University of Porto (Ipatimup), 4200-135 Porto, Portugal
| | - Matilde Lambiase
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (N.N.); (R.E.A.)
| | - Virginie Lespinet-Fabre
- Laboratory of Clinical and Experimental Pathology, Biobank BB-0033-00025, FHU OncoAge, IHU RespirERA, CHU de Nice, Université Côte d’Azur, 06000 Nice, France; (V.L.-F.); (M.I.)
| | - Byron Calgua
- Institute of Pathology, University Hospital Basel, 4031 Basel, Switzerland; (B.C.); (P.M.J.)
| | - Philip M. Jermann
- Institute of Pathology, University Hospital Basel, 4031 Basel, Switzerland; (B.C.); (P.M.J.)
| | - Marius Ilié
- Laboratory of Clinical and Experimental Pathology, Biobank BB-0033-00025, FHU OncoAge, IHU RespirERA, CHU de Nice, Université Côte d’Azur, 06000 Nice, France; (V.L.-F.); (M.I.)
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Biobank BB-0033-00025, FHU OncoAge, IHU RespirERA, CHU de Nice, Université Côte d’Azur, 06000 Nice, France; (V.L.-F.); (M.I.)
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Normanno N, De Luca A, Abate RE, Morabito A, Milella M, Tabbò F, Curigliano G, Masini C, Marchetti P, Pruneri G, Guarneri V, Frassineti GL, Fasola G, Adamo V, Daniele B, Berardi R, Feroce F, Maiello E, Pinto C. Current practice of genomic profiling of patients with advanced solid tumours in Italy: the Italian Register of Actionable Mutations (RATIONAL) study. Eur J Cancer 2023; 187:174-184. [PMID: 37167765 DOI: 10.1016/j.ejca.2023.03.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/23/2023] [Accepted: 03/23/2023] [Indexed: 04/03/2023]
Abstract
BACKGROUND The Italian Register of Actionable Mutations (RATIONAL) is a multicentric, observational study collecting next-generation sequencing (NGS)-based tumour profiling data of patients with advanced solid tumours. METHODS The study enrols patients who had available an NGS-based tumour profiling (Pathway-A) or undergo comprehensive genomic profiling (CGP) with FoundationOne CDx assays within the trial (Pathway-B). The primary endpoint was the rate of actionable mutations identified. RESULTS Sequencing data were available for 738 patients in Pathway-A (218) and -B (520). In Pathway-A, 154/218 (70.6%) tests were performed using NGS panels ≤52 genes, and genomic alterations (GAs) were found in 164/218 (75.2%) patients. In Pathway-B, CGP revealed GAs in 512/520 (98.5%) patients. Levels I/II/III actionable GAs according to the European Society of Medical Oncology Scale for Clinical Actionability of molecular Targets (ESCAT) were identified in 254/554 (45.8%) patients with non-small-cell lung cancer, cholangiocarcinoma, colorectal, gastric, pancreatic and breast cancer. The rate of patients with level I GAs was similar in Pathways A and B (69 versus 102). CGP in Pathway-B revealed a higher number of patients with level II/III GAs (99 versus 20) and potentially germline pathogenic/likely pathogenic variants (58 versus 15) as compared with standard testing in Pathway-A. In patients with cancer of unknown primary, CGP detected OncoKB levels 3B/4 GAs in 31/58 (53.4%) cases. Overall, 67/573 (11.7%) of patients received targeted therapy based on genomic testing. CONCLUSION The Italian Register of Actionable Mutations represents the first overview of genomic profiling in Italian current clinical practice and highlights the utility of CGP for identifying therapeutic targets in selected cancer patients.
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Affiliation(s)
- Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy.
| | - Antonella De Luca
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Riziero Esposito Abate
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Alessandro Morabito
- Thoracic Department, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Michele Milella
- U.O.C. Oncology, Azienda Ospedaliera Universitaria Integrata, University and Hospital Trust of Verona, Verona, Italy
| | - Fabrizio Tabbò
- Department of Oncology, Università degli Studi di Torino, AOU San Luigi, Orbassano, Italy
| | - Giuseppe Curigliano
- Department of Oncology and Hemato-Oncology, University of Milano, Milano, Italy; Division of Early Drug Development, European Institute of Oncology IRCCS, Milano, Italy
| | - Cristina Masini
- Medical Oncology, Comprehensive Cancer Centre IRCCS - AUSL Reggio Emilia, Reggio Emilia, Italy
| | - Paolo Marchetti
- Istituto Dermopatico dell'Immacolata (IDI-IRCCS), Roma, Italy
| | - Giancarlo Pruneri
- Department of Pathology, Fondazione IRCCS Istituto Nazionale dei Tumori di Milano, Milano, Italy
| | - Valentina Guarneri
- Department of Surgery, Oncology and Gastroenterology, University of Padova, Padova, Italy; Oncology 2, Istituto Oncologico Veneto (IOV) IRCCS, Padova, Italy
| | - Giovanni L Frassineti
- Department of Medical Oncology-IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", Meldola, Italy
| | - Gianpiero Fasola
- Department of Medical Oncology, University Hospital of Udine, Udine, Italy
| | - Vincenzo Adamo
- Scientific Direction Oncology Department, Papardo Hospital, Messina, Italy
| | | | | | - Florinda Feroce
- Surgical Pathology Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Evaristo Maiello
- Oncology Unit, Fondazione Casa Sollievo della Sofferenza IRCCS, San Giovanni Rotondo, Italy
| | - Carmine Pinto
- Medical Oncology, Comprehensive Cancer Centre IRCCS - AUSL Reggio Emilia, Reggio Emilia, Italy
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Esposito Abate R, Cheetham MH, Fairley JA, Pasquale R, Sacco A, Nicola W, Deans ZC, Patton SJ, Normanno N. External quality assessment (EQA) for tumor mutational burden: results of an international IQN path feasibility pilot scheme. Virchows Arch 2023; 482:347-355. [PMID: 36355212 PMCID: PMC9931778 DOI: 10.1007/s00428-022-03444-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 10/12/2022] [Accepted: 10/25/2022] [Indexed: 11/11/2022]
Abstract
Tumor mutational burden (TMB) has recently been approved as an agnostic biomarker for immune checkpoint inhibitors. However, methods for TMB testing have not yet been standardized. The International Quality Network for Pathology (IQNPath) organized a pilot external quality assessment (EQA) scheme for TMB testing. The aim of this program was the validation of the materials and the procedures for the EQA of this complex biomarker. Five formalin-fixed paraffin-embedded (FFPE) cell lines were selected to mimic the various TMB values observed in clinical practice. The FFPE samples were tested with the FoundationOne CDx (F1CDx) assay as the reference test and three commercially available targeted sequencing panels. Following this internal validation, the five cell lines were sent to 29 laboratories selected on the basis of a previous survey. Nineteen of the 23 laboratories that submitted results (82.6%) used targeted sequencing for TMB estimation. Only two laboratories performed whole exome sequencing (WES) and two assessed TMB by clinical exome. A high variability in the reported TMB values was observed. The variability was higher for samples with the highest TMB value according to the F1CDx test. However, good reproducibility of the TMB score was shown by laboratories using the same panel. The majority of laboratories did not indicate a TMB cut-off value for clinical interpretation. In conclusion, this pilot EQA scheme suggests that it is feasible to run such an EQA program for TMB assessment. However, the results of our pilot highlight the numerous challenges for the standardization of this test.
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Affiliation(s)
- Riziero Esposito Abate
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Melanie H Cheetham
- European Molecular Genetics Quality Network (EMQN), Unit 4, Enterprise House, Pencroft Way, Manchester Science Park, Manchester, M15 6SE, UK
| | - Jennifer A Fairley
- GenQA, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Little France Crescent, Edinburgh, EH16 4SA, UK
| | - Raffaella Pasquale
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Alessandra Sacco
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Wolstenholme Nicola
- European Molecular Genetics Quality Network (EMQN), Unit 4, Enterprise House, Pencroft Way, Manchester Science Park, Manchester, M15 6SE, UK
| | - Zandra C Deans
- GenQA, Department of Laboratory Medicine, Royal Infirmary of Edinburgh, Little France Crescent, Edinburgh, EH16 4SA, UK
| | - Simon J Patton
- European Molecular Genetics Quality Network (EMQN), Unit 4, Enterprise House, Pencroft Way, Manchester Science Park, Manchester, M15 6SE, UK
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy.
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Dotolo S, Esposito Abate R, Roma C, Guido D, Preziosi A, Tropea B, Palluzzi F, Giacò L, Normanno N. Bioinformatics: From NGS Data to Biological Complexity in Variant Detection and Oncological Clinical Practice. Biomedicines 2022; 10:biomedicines10092074. [PMID: 36140175 PMCID: PMC9495893 DOI: 10.3390/biomedicines10092074] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/12/2022] [Accepted: 08/22/2022] [Indexed: 11/22/2022] Open
Abstract
The use of next-generation sequencing (NGS) techniques for variant detection has become increasingly important in clinical research and in clinical practice in oncology. Many cancer patients are currently being treated in clinical practice or in clinical trials with drugs directed against specific genomic alterations. In this scenario, the development of reliable and reproducible bioinformatics tools is essential to derive information on the molecular characteristics of each patient’s tumor from the NGS data. The development of bioinformatics pipelines based on the use of machine learning and statistical methods is even more relevant for the determination of complex biomarkers. In this review, we describe some important technologies, computational algorithms and models that can be applied to NGS data from Whole Genome to Targeted Sequencing, to address the problem of finding complex cancer-associated biomarkers. In addition, we explore the future perspectives and challenges faced by bioinformatics for precision medicine both at a molecular and clinical level, with a focus on an emerging complex biomarker such as homologous recombination deficiency (HRD).
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Affiliation(s)
- Serena Dotolo
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori—IRCCS—Fondazione G. Pascale, 80131 Naples, Italy
| | - Riziero Esposito Abate
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori—IRCCS—Fondazione G. Pascale, 80131 Naples, Italy
| | - Cristin Roma
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori—IRCCS—Fondazione G. Pascale, 80131 Naples, Italy
| | - Davide Guido
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo A. Gemelli, 8, 00168 Rome, Italy
| | - Alessia Preziosi
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo A. Gemelli, 8, 00168 Rome, Italy
| | - Beatrice Tropea
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo A. Gemelli, 8, 00168 Rome, Italy
| | - Fernando Palluzzi
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo A. Gemelli, 8, 00168 Rome, Italy
| | - Luciano Giacò
- Bioinformatics Research Core Facility, Gemelli Science and Technology Park (GSTeP), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Largo A. Gemelli, 8, 00168 Rome, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori—IRCCS—Fondazione G. Pascale, 80131 Naples, Italy
- Correspondence:
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Roma C, Sacco A, Forgione L, Esposito Abate R, Lambiase M, Dotolo S, Maiello MR, Frezzetti D, Nasti G, Morabito A, De Luca A, Normanno N. Low Impact of Clonal Hematopoiesis on the Determination of RAS Mutations by Cell-Free DNA Testing in Routine Clinical Diagnostics. Diagnostics (Basel) 2022; 12:diagnostics12081956. [PMID: 36010306 PMCID: PMC9406879 DOI: 10.3390/diagnostics12081956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 11/23/2022] Open
Abstract
Targeted sequencing of circulating cell-free DNA (cfDNA) is used in routine clinical diagnostics for the identification of predictive biomarkers in cancer patients in an advanced stage. The presence of KRAS mutations associated with clonal hematopoiesis of indeterminate potential (CHIP) might represent a confounding factor. We used an amplicon-based targeted sequencing panel, covering selected regions of 52 genes, for circulating cell-free total nucleic acid (cfTNA) analysis of 495 plasma samples from cancer patients. The cfDNA test failed in 4 cases, while circulating cell-free RNA (cfRNA) sequencing was invalid in 48 cases. In the 491 samples successfully tested on cfDNA, at least one genomic alteration was found in 222 cases (45.21%). We identified 316 single nucleotide variants (SNVs) in 21 genes. The most frequently mutated gene was TP53 (74 variants), followed by KRAS (71), EGFR (56), PIK3CA (33) and BRAF (19). Copy number variations (CNVs) were detected in 36 cases, while sequencing of cfRNA revealed 6 alterations. Analysis with droplet digital PCR (ddPCR) of peripheral blood leukocyte (PBL)-derived genomic DNA did not identify any KRAS mutations in 39 cases that showed KRAS mutations at cfDNA analysis. These findings suggest that the incidence of CHIP-associated KRAS mutations is relatively rare in routine clinical diagnostics.
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Affiliation(s)
- Cristin Roma
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Alessandra Sacco
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Laura Forgione
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Riziero Esposito Abate
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Matilde Lambiase
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Serena Dotolo
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Monica Rosaria Maiello
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Daniela Frezzetti
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Guglielmo Nasti
- SSD Innovative Therapies for Abdominal Metastases, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Alessandro Morabito
- Thoracic Medical Oncology, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Antonella De Luca
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy
- Correspondence:
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8
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Ieranò C, Righelli D, D'Alterio C, Napolitano M, Portella L, Rea G, Auletta F, Santagata S, Trotta AM, Guardascione G, Liotti F, Prevete N, Maiolino P, Luciano A, Barbieri A, Di Mauro A, Roma C, Esposito Abate R, Tatangelo F, Pacelli R, Normanno N, Melillo RM, Scala S. In PD-1+ human colon cancer cells NIVOLUMAB promotes survival and could protect tumor cells from conventional therapies. J Immunother Cancer 2022; 10:jitc-2021-004032. [PMID: 35246475 PMCID: PMC8900051 DOI: 10.1136/jitc-2021-004032] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [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] [Accepted: 01/18/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most prevalent and deadly tumors worldwide. The majority of CRC is resistant to anti-programmed cell death-1 (PD-1)-based cancer immunotherapy, with approximately 15% with high-microsatellite instability, high tumor mutation burden, and intratumoral lymphocytic infiltration. Programmed death-ligand 1 (PD-L1)/PD-1 signaling was described in solid tumor cells. In melanoma, liver, and thyroid cancer cells, intrinsic PD-1 signaling activates oncogenic functions, while in lung cancer cells, it has a tumor suppressor effect. Our work aimed to evaluate the effects of the anti-PD-1 nivolumab (NIVO) on CRC cells. METHODS In vitro NIVO-treated human colon cancer cells (HT29, HCT116, and LoVo) were evaluated for cell growth, chemo/radiotherapeutic sensitivity, apoptosis, and spheroid growth. Total RNA-seq was assessed in 6-24 hours NIVO-treated human colon cancer cells HT29 and HCT116 as compared with NIVO-treated PES43 human melanoma cells. In vivo mice carrying HT29 xenograft were intraperitoneally treated with NIVO, OXA (oxaliplatin), and NIVO+OXA, and the tumors were characterized for growth, apoptosis, and pERK1/2/pP38. Forty-eight human primary colon cancers were evaluated for PD-1 expression through immunohistochemistry. RESULTS In PD-1+ human colon cancer cells, intrinsic PD-1 signaling significantly decreased proliferation and promoted apoptosis. On the contrary, NIVO promoted proliferation, reduced apoptosis, and protected PD-1+ cells from chemo/radiotherapy. Transcriptional profile of NIVO-treated HT29 and HCT116 human colon cancer cells revealed downregulation of BATF2, DRAM1, FXYD3, IFIT3, MT-TN, and TNFRSF11A, and upregulation of CLK1, DCAF13, DNAJC2, MTHFD1L, PRPF3, PSMD7, and SCFD1; the opposite regulation was described in NIVO-treated human melanoma PES43 cells. Differentially expressed genes (DEGs) were significantly enriched for interferon pathway, innate immune, cytokine-mediated signaling pathways. In vivo, NIVO promoted HT29 tumor growth, thus reducing OXA efficacy as revealed through significant Ki-67 increase, pERK1/2 and pP38 increase, and apoptotic cell reduction. Eleven out of 48 primary human colon cancer biopsies expressed PD-1 (22.9%). PD-1 expression is significantly associated with lower pT stage. CONCLUSIONS In PD-1+ human colon cancer cells, NIVO activates tumor survival pathways and could protect tumor cells from conventional therapies.
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Affiliation(s)
- Caterina Ieranò
- Microenvironment Molecular Targets, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | | | - Crescenzo D'Alterio
- Microenvironment Molecular Targets, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Maria Napolitano
- Microenvironment Molecular Targets, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Luigi Portella
- Microenvironment Molecular Targets, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Giuseppina Rea
- Microenvironment Molecular Targets, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Federica Auletta
- Microenvironment Molecular Targets, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Sara Santagata
- Microenvironment Molecular Targets, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Anna Maria Trotta
- Microenvironment Molecular Targets, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Giuseppe Guardascione
- Microenvironment Molecular Targets, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Federica Liotti
- Institute of Endocrinology and Experimental Oncology (IEOS), CNR-NA1, Napoli, Italy
| | - Nella Prevete
- Institute of Endocrinology and Experimental Oncology (IEOS), CNR-NA1, Napoli, Italy.,Traslational Medical Sciences, University of Naples Federico II, Napoli, Italy
| | - Piera Maiolino
- Pharmacy, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Antonio Luciano
- Animal Facility, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Antonio Barbieri
- Animal Facility, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Annabella Di Mauro
- Pathology, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Cristin Roma
- Cell Biology and Biotherapy, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Riziero Esposito Abate
- Cell Biology and Biotherapy, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Fabiana Tatangelo
- Pathology, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Roberto Pacelli
- Advanced Biomedical Sciences, University of Naples Federico II, Napoli, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
| | - Rosa Marina Melillo
- Institute of Endocrinology and Experimental Oncology (IEOS), CNR-NA1, Napoli, Italy.,Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Napoli, Italy
| | - Stefania Scala
- Microenvironment Molecular Targets, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Napoli, Italy
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9
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Dotolo S, Marabotti A, Rachiglio AM, Esposito Abate R, Benedetto M, Ciardiello F, De Luca A, Normanno N, Facchiano A, Tagliaferri R. A multiple network-based bioinformatics pipeline for the study of molecular mechanisms in oncological diseases for personalized medicine. Brief Bioinform 2021; 22:6287337. [PMID: 34050359 PMCID: PMC8574709 DOI: 10.1093/bib/bbab180] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 03/17/2021] [Accepted: 04/20/2021] [Indexed: 01/03/2023] Open
Abstract
Motivation Assessment of genetic mutations is an essential element in the modern era of personalized cancer treatment. Our strategy is focused on ‘multiple network analysis’ in which we try to improve cancer diagnostics by using biological networks. Genetic alterations in some important hubs or in driver genes such as BRAF and TP53 play a critical role in regulating many important molecular processes. Most of the studies are focused on the analysis of the effects of single mutations, while tumors often carry mutations of multiple driver genes. The aim of this work is to define an innovative bioinformatics pipeline focused on the design and analysis of networks (such as biomedical and molecular networks), in order to: (1) improve the disease diagnosis; (2) identify the patients that could better respond to a given drug treatment; and (3) predict what are the primary and secondary effects of gene mutations involved in human diseases. Results By using our pipeline based on a multiple network approach, it has been possible to demonstrate and validate what are the joint effects and changes of the molecular profile that occur in patients with metastatic colorectal carcinoma (mCRC) carrying mutations in multiple genes. In this way, we can identify the most suitable drugs for the therapy for the individual patient. This information is useful to improve precision medicine in cancer patients. As an application of our pipeline, the clinically significant case studies of a cohort of mCRC patients with the BRAF V600E-TP53 I195N missense combined mutation were considered. Availability The procedures used in this paper are part of the Cytoscape Core, available at (www.cytoscape.org). Data used here on mCRC patients have been published in [55]. Supplementary Information A supplementary file containing a more detailed discussion of this case study and other cases is available at the journal site as Supplementary Data.
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Affiliation(s)
- Serena Dotolo
- Dipartimento di Scienze Aziendali, Management & Innovation Systems, Università degli Studi di Salerno, Fisciano (SA), Italy
| | - Anna Marabotti
- Dipartimento di Chimica e Biologia "A. Zambelli", Università degli Studi di Salerno, Fisciano (SA), Italy
| | - Anna Maria Rachiglio
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Naples, Italy
| | - Riziero Esposito Abate
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori -IRCCS - Fondazione G. Pascale, Naples, Italy
| | | | - Fortunato Ciardiello
- Dipartimento di Medicina di Precisione, Università degli Studi della Campania "Luigi Vanvitelli", Naples, Italy
| | - Antonella De Luca
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Naples, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori - IRCCS - Fondazione G. Pascale, Naples, Italy
| | - Angelo Facchiano
- Institute of Food Sciences, Italian National Research Council (CNR), Avellino, Italy
| | - Roberto Tagliaferri
- Dipartimento di Scienze Aziendali, Management & Innovation Systems, Università degli Studi di Salerno, Fisciano (SA), Italy
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10
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Fenizia F, Pasquale R, Abate RE, Lambiase M, Roma C, Bergantino F, Chaudhury R, Hyland F, Allen C, Normanno N. Challenges in bioinformatics approaches to tumor mutation burden analysis. Oncol Lett 2021; 22:555. [PMID: 34084222 PMCID: PMC8161416 DOI: 10.3892/ol.2021.12816] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 03/19/2020] [Accepted: 01/12/2021] [Indexed: 12/28/2022] Open
Abstract
Several immune checkpoint inhibitors (ICIs) have already been introduced into clinical practice or are in advanced phases of clinical experimentation. Extensive efforts are being made to identify robust biomarkers to select patients who may benefit from treatment with ICIs. Tumor mutation burden (TMB) may be a relevant biomarker of response to ICIs in different tumor types; however, its clinical use is challenged by the analytical methods required for its evaluation. The possibility of using targeted next-generation sequencing panels has been investigated as an alternative to the standard whole exome sequencing approach. However, no standardization exists in terms of genes covered, types of mutations included in the estimation of TMB, bioinformatics pipelines for data analysis, and cut-offs used to discriminate samples with high, intermediate or low TMB. Bioinformatics serve a relevant role in the analysis of targeted sequencing data and its standardization is essential to deliver a reliable test in clinical practice. In the present study, cultured and formalin-fixed, paraffin-embedded cell lines were analyzed using a commercial panel for TMB testing; the results were compared with data from the literature and public databases, demonstrating a good correlation. Additionally, the correlation between high tumor mutation burden and microsatellite instability was confirmed. The bioinformatics analyses were conducted using two different pipelines to highlight the challenges associated with the development of an appropriate analytical workflow.
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Affiliation(s)
- Francesca Fenizia
- Cell Biology and Biotherapy Unit, Department of Research, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, I-80131 Naples, Italy
| | - Raffaella Pasquale
- Cell Biology and Biotherapy Unit, Department of Research, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, I-80131 Naples, Italy
| | - Riziero Esposito Abate
- Cell Biology and Biotherapy Unit, Department of Research, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, I-80131 Naples, Italy
| | - Matilde Lambiase
- Department of Molecular Medicine and Medical Biotechnology, Federico II University, I-80131 Naples, Italy
| | - Cristin Roma
- Cell Biology and Biotherapy Unit, Department of Research, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, I-80131 Naples, Italy
| | - Francesca Bergantino
- Cell Biology and Biotherapy Unit, Department of Research, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, I-80131 Naples, Italy
| | - Ruchi Chaudhury
- Thermo Fisher Scientific, Inc., South San Francisco, CA 94080, USA
| | - Fiona Hyland
- Thermo Fisher Scientific, Inc., South San Francisco, CA 94080, USA
| | | | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Department of Research, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, I-80131 Naples, Italy
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11
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Esposito Abate R, Frezzetti D, Maiello MR, Gallo M, Camerlingo R, De Luca A, De Cecio R, Morabito A, Normanno N. Next Generation Sequencing-Based Profiling of Cell Free DNA in Patients with Advanced Non-Small Cell Lung Cancer: Advantages and Pitfalls. Cancers (Basel) 2020; 12:E3804. [PMID: 33348595 PMCID: PMC7766403 DOI: 10.3390/cancers12123804] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 12/12/2022] Open
Abstract
Lung cancer (LC) is the main cause of death for cancer worldwide and non-small cell lung cancer (NSCLC) represents the most common histology. The discovery of genomic alterations in driver genes that offer the possibility of therapeutic intervention has completely changed the approach to the diagnosis and therapy of advanced NSCLC patients, and tumor molecular profiling has become mandatory for the choice of the most appropriate therapeutic strategy. However, in approximately 30% of NSCLC patients tumor tissue is inadequate for biomarker analysis. The development of highly sensitive next generation sequencing (NGS) technologies for the analysis of circulating cell-free DNA (cfDNA) is emerging as a valuable alternative to assess tumor molecular landscape in case of tissue unavailability. Additionally, cfDNA NGS testing can better recapitulate NSCLC heterogeneity as compared with tissue testing. In this review we describe the main advantages and limits of using NGS-based cfDNA analysis to guide the therapeutic decision-making process in advanced NSCLC patients, to monitor the response to therapy and to identify mechanisms of resistance early. Therefore, we provide evidence that the implementation of cfDNA NGS testing in clinical research and in the clinical practice can significantly improve precision medicine approaches in patients with advanced NSCLC.
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Affiliation(s)
- Riziero Esposito Abate
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (R.E.A.); (D.F.); (M.R.M.); (M.G.); (R.C.); (A.D.L.)
| | - Daniela Frezzetti
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (R.E.A.); (D.F.); (M.R.M.); (M.G.); (R.C.); (A.D.L.)
| | - Monica Rosaria Maiello
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (R.E.A.); (D.F.); (M.R.M.); (M.G.); (R.C.); (A.D.L.)
| | - Marianna Gallo
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (R.E.A.); (D.F.); (M.R.M.); (M.G.); (R.C.); (A.D.L.)
| | - Rosa Camerlingo
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (R.E.A.); (D.F.); (M.R.M.); (M.G.); (R.C.); (A.D.L.)
| | - Antonella De Luca
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (R.E.A.); (D.F.); (M.R.M.); (M.G.); (R.C.); (A.D.L.)
| | - Rossella De Cecio
- Department of Pathology, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy;
| | - Alessandro Morabito
- Department of Thoracic Medical Oncology, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy;
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (R.E.A.); (D.F.); (M.R.M.); (M.G.); (R.C.); (A.D.L.)
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12
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De Luca A, Esposito Abate R, Rachiglio AM, Maiello MR, Esposito C, Schettino C, Izzo F, Nasti G, Normanno N. FGFR Fusions in Cancer: From Diagnostic Approaches to Therapeutic Intervention. Int J Mol Sci 2020; 21:E6856. [PMID: 32962091 PMCID: PMC7555921 DOI: 10.3390/ijms21186856] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/15/2020] [Accepted: 09/15/2020] [Indexed: 12/11/2022] Open
Abstract
Fibroblast growth factor receptors (FGFRs) are tyrosine kinase receptors involved in many biological processes. Deregulated FGFR signaling plays an important role in tumor development and progression in different cancer types. FGFR genomic alterations, including FGFR gene fusions that originate by chromosomal rearrangements, represent a promising therapeutic target. Next-generation-sequencing (NGS) approaches have significantly improved the discovery of FGFR gene fusions and their detection in clinical samples. A variety of FGFR inhibitors have been developed, and several studies are trying to evaluate the efficacy of these agents in molecularly selected patients carrying FGFR genomic alterations. In this review, we describe the most frequent FGFR aberrations in human cancer. We also discuss the different approaches employed for the detection of FGFR fusions and the potential role of these genomic alterations as prognostic/predictive biomarkers.
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Affiliation(s)
- Antonella De Luca
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.D.L.); (R.E.A.); (A.M.R.); (M.R.M.); (C.E.)
| | - Riziero Esposito Abate
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.D.L.); (R.E.A.); (A.M.R.); (M.R.M.); (C.E.)
| | - Anna Maria Rachiglio
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.D.L.); (R.E.A.); (A.M.R.); (M.R.M.); (C.E.)
| | - Monica Rosaria Maiello
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.D.L.); (R.E.A.); (A.M.R.); (M.R.M.); (C.E.)
| | - Claudia Esposito
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.D.L.); (R.E.A.); (A.M.R.); (M.R.M.); (C.E.)
| | - Clorinda Schettino
- Clinical Trials Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy;
| | - Francesco Izzo
- Division of Surgical Oncology, Hepatobiliary Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy;
| | - Guglielmo Nasti
- SSD Innovative Therapies for Abdominal Cancers, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy;
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.D.L.); (R.E.A.); (A.M.R.); (M.R.M.); (C.E.)
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13
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Elez E, Chianese C, Sanz-García E, Martinelli E, Noguerido A, Mancuso FM, Caratù G, Matito J, Grasselli J, Cardone C, Esposito Abate R, Martini G, Santos C, Macarulla T, Argilés G, Capdevila J, Garcia A, Mulet N, Maiello E, Normanno N, Jones F, Tabernero J, Ciardello F, Salazar R, Vivancos A. Impact of circulating tumor DNA mutant allele fraction on prognosis in RAS-mutant metastatic colorectal cancer. Mol Oncol 2019; 13:1827-1835. [PMID: 31322322 PMCID: PMC6717744 DOI: 10.1002/1878-0261.12547] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [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: 10/21/2018] [Revised: 05/11/2019] [Accepted: 07/15/2019] [Indexed: 12/21/2022] Open
Abstract
Despite major advances in the treatment of metastatic colorectal cancer (mCRC), the survival rate remains very poor. This study aims at exploring the prognostic value of RAS-mutant allele fraction (MAF) in plasma in mCRC. Forty-seven plasma samples from 37 RAS-mutated patients with nonresectable metastases were tested for RAS in circulating tumor DNA using BEAMing before first- and/or second-line treatment. RAS MAF was correlated with several clinical parameters (number of metastatic sites, hepatic volume, carcinoembryonic antigen, CA19-9 levels, primary site location, and treatment line) and clinical outcome [progression-free survival (PFS) and overall survival (OS)]. An independent cohort of 32 patients from the CAPRI-GOIM trial was assessed for clinical outcome based on plasma baseline MAF. RAS MAF analysis at baseline revealed a significant correlation with longer OS [Hazard ratios (HR) = 3.514; P = 0.00066]. Patients with lower MAF also showed a tendency to longer PFS, although not statistically significant. Multivariate analysis showed RAS MAFs as an independent prognostic factor in both OS (HR = 2.73; P = 0.006) and first-line PFS (HR = 3.74; P = 0.049). Tumor response to treatment in patients with higher MAF was progression disease (P = 0.007). Patients with low MAFs at baseline in the CAPRI-GOIM group also showed better OS [HR = 3.84; 95% confidence intervals (CI) 1.5-9.6; P = 0.004] and better PFS (HR = 2.5; 95% CI: 1.07-5.62; P = 0.033). This minimally invasive test may help in adding an independent factor to better estimate outcomes before initiating treatment. Further prospective studies using MAF as a stratification factor could further validate its utility in clinical practice.
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Affiliation(s)
- Elena Elez
- Department of Medical Oncology, Vall d'Hebron Institute of Oncology, Barcelona, Spain.,Department of Medical Oncology, Vall d' Hebron University Hospital, Universitat Autònoma de Barcelona, Spain
| | - Chiara Chianese
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Enrique Sanz-García
- Department of Medical Oncology, Vall d'Hebron Institute of Oncology, Barcelona, Spain.,Department of Medical Oncology, Vall d' Hebron University Hospital, Universitat Autònoma de Barcelona, Spain
| | - Erica Martinelli
- Medical Oncology, Department of Clinical and Experimental Medicine 'F. Magrassi', Università della Campania 'L. Vanvitelli', Napoli, Italy
| | - Alba Noguerido
- Department of Medical Oncology, Vall d'Hebron Institute of Oncology, Barcelona, Spain.,Department of Medical Oncology, Vall d' Hebron University Hospital, Universitat Autònoma de Barcelona, Spain
| | | | - Ginevra Caratù
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Judit Matito
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Julieta Grasselli
- Department of Medical Oncology, Vall d'Hebron Institute of Oncology, Barcelona, Spain.,Department of Medical Oncology, Catalan Institute of Oncology, Universitat de Barcelona, L'Hospitalet, Spain
| | - Claudia Cardone
- Medical Oncology, Department of Clinical and Experimental Medicine 'F. Magrassi', Università della Campania 'L. Vanvitelli', Napoli, Italy
| | - Riziero Esposito Abate
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori 'Fondazione Giovanni Pascale' IRCCS, Napoli, Italy
| | - Giulia Martini
- Department of Medical Oncology, Vall d'Hebron Institute of Oncology, Barcelona, Spain.,Department of Medical Oncology, Vall d' Hebron University Hospital, Universitat Autònoma de Barcelona, Spain
| | - Cristina Santos
- Department of Medical Oncology, Catalan Institute of Oncology, Universitat de Barcelona, L'Hospitalet, Spain
| | - Teresa Macarulla
- Department of Medical Oncology, Vall d'Hebron Institute of Oncology, Barcelona, Spain.,Department of Medical Oncology, Vall d' Hebron University Hospital, Universitat Autònoma de Barcelona, Spain
| | - Guillem Argilés
- Department of Medical Oncology, Vall d'Hebron Institute of Oncology, Barcelona, Spain.,Department of Medical Oncology, Vall d' Hebron University Hospital, Universitat Autònoma de Barcelona, Spain
| | - Jaume Capdevila
- Department of Medical Oncology, Vall d'Hebron Institute of Oncology, Barcelona, Spain.,Department of Medical Oncology, Vall d' Hebron University Hospital, Universitat Autònoma de Barcelona, Spain
| | - Ariadna Garcia
- Department of Medical Oncology, Vall d'Hebron Institute of Oncology, Barcelona, Spain.,Department of Medical Oncology, Vall d' Hebron University Hospital, Universitat Autònoma de Barcelona, Spain
| | - Nuria Mulet
- Department of Medical Oncology, Vall d'Hebron Institute of Oncology, Barcelona, Spain.,Department of Medical Oncology, Vall d' Hebron University Hospital, Universitat Autònoma de Barcelona, Spain.,Department of Medical Oncology, Catalan Institute of Oncology, Universitat de Barcelona, L'Hospitalet, Spain
| | - Evaristo Maiello
- Medical Oncology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (Foggia), Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori 'Fondazione Giovanni Pascale' IRCCS, Napoli, Italy
| | | | - Josep Tabernero
- Department of Medical Oncology, Vall d'Hebron Institute of Oncology, Barcelona, Spain.,Department of Medical Oncology, Vall d' Hebron University Hospital, Universitat Autònoma de Barcelona, Spain
| | - Fortunato Ciardello
- Medical Oncology, Department of Clinical and Experimental Medicine 'F. Magrassi', Università della Campania 'L. Vanvitelli', Napoli, Italy
| | - Ramon Salazar
- Department of Medical Oncology, Catalan Institute of Oncology, Universitat de Barcelona, L'Hospitalet, Spain
| | - Ana Vivancos
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, Barcelona, Spain
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14
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Falcone F, Normanno N, Losito NS, Scognamiglio G, Esposito Abate R, Chicchinelli N, Casella G, Laurelli G, Scaffa C, Greggi S. Application of the Proactive Molecular Risk Classifier for Endometrial Cancer (ProMisE) to patients conservatively treated: Outcomes from an institutional series. Eur J Obstet Gynecol Reprod Biol 2019; 240:220-225. [PMID: 31326637 DOI: 10.1016/j.ejogrb.2019.07.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 07/04/2019] [Accepted: 07/12/2019] [Indexed: 10/26/2022]
Abstract
OBJECTIVE To test the Proactive Molecular Risk Classifier for Endometrial Cancer (ProMisE) and determine the frequency of specific/prognostic molecular alterations within a cohort of endometrial cancer (EC) women conservatively treated by combined hysteroscopic resection and progestin therapy. STUDY DESIGN We used blocks of formalin-fixed paraffin-embedded tissue from the primary tumors of patients enrolled into the ECCo trial (EudraCT 2010-018581-23) between 2007 and 2016. In order to assign EC resectoscopic specimens to one of four ProMisE subgroups, testing involved sequential assessment of i) immunohistochemistry (IHC) for mismatch repair (MMR) proteins MLH1, MSH2, MSH6 and PMS2; ii) sequencing for POLE/POLD1 exonuclease domain mutations (EDMs); iii) p53 IHC. RESULTS Molecular analysis methods were used in 25 patients (stage IA, G1-2 endometrioid EC), of whom 15 (60%) represented fully evaluable cases. Seven cases (46.7%) had abnormal MMR IHC, POLE/POLD1 EDMs were found in 3 cases (20%), and abnormal p53 IHC in 1 case (6.6%). Three patients (20%) had more than one molecular feature. Among 10 (40%) 'unclassifiable' patients, six failures in achieving complete molecular categorization were due to the low tumor volume. Molecular classification of the 15 fully evaluable cases yielded the following ProMisE subtypes: 7 (46.7%) MMR IHC abnormal, 1 (6.6%) POLE EDM, 0 (0%) p53 IHC abnormal, 7 (46.7%) p53 IHC wild-type. CONCLUSIONS Although larger series are needed to further assess the feasibility of a molecular categorization in a fertility-sparing setting, data presented are promising. In women with early stage low-volume disease, operative hysteroscopy could be advantageous to provide samples allowing complete genetic risk assessment.
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Affiliation(s)
- Francesca Falcone
- Department of Gynecologic Oncology Surgery, Istituto Nazionale Tumori, IRCSS, "Fondazione G. Pascale", Naples, Italy.
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori, IRCSS, "Fondazione G. Pascale", Naples, Italy
| | - Nunzia S Losito
- Pathology Unit, Istituto Nazionale Tumori, IRCSS, "Fondazione G. Pascale", Naples, Italy
| | - Giosuè Scognamiglio
- Pathology Unit, Istituto Nazionale Tumori, IRCSS, "Fondazione G. Pascale", Naples, Italy
| | - Riziero Esposito Abate
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori, IRCSS, "Fondazione G. Pascale", Naples, Italy
| | - Nicoletta Chicchinelli
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori, IRCSS, "Fondazione G. Pascale", Naples, Italy
| | - Gennaro Casella
- Department of Gynecologic Oncology Surgery, Istituto Nazionale Tumori, IRCSS, "Fondazione G. Pascale", Naples, Italy
| | - Giuseppe Laurelli
- Department of Gynecologic Oncology Surgery, Istituto Nazionale Tumori, IRCSS, "Fondazione G. Pascale", Naples, Italy
| | - Cono Scaffa
- Department of Gynecologic Oncology Surgery, Istituto Nazionale Tumori, IRCSS, "Fondazione G. Pascale", Naples, Italy
| | - Stefano Greggi
- Department of Gynecologic Oncology Surgery, Istituto Nazionale Tumori, IRCSS, "Fondazione G. Pascale", Naples, Italy
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15
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Esposito Abate R, Pasquale R, Fenizia F, Rachiglio AM, Roma C, Bergantino F, Forgione L, Lambiase M, Sacco A, Piccirillo MC, Morabito A, Normanno N. The role of circulating free DNA in the management of NSCLC. Expert Rev Anticancer Ther 2018; 19:19-28. [PMID: 30462523 DOI: 10.1080/14737140.2019.1548938] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
INTRODUCTION Circulating cell-free DNA (cfDNA) testing has emerged as an alternative to tumor tissue analyses for the management of metastatic non-small-cell lung cancer (NSCLC) patients. Analysis of cfDNA is a minimally invasive procedure that might better reflect tumor heterogeneity and allows repeated testing over the time. Areas covered: This review article covers the different applications of cfDNA testing in NSCLC: early diagnosis of the disease; detection of minimal residual disease in early lung cancer; identification of predictive and prognostic markers in advanced NSCLC patients; monitoring the response to therapy; assessment of tumor mutation burden. Expert commentary: The use of liquid biopsy is rapidly expanding to different applications. The combination of different circulating biomarkers (cfDNA, protein, miRNA) might improve the sensitivity and specificity of this approach in patients with low tumor burden. cfDNA testing is representing a valid source for molecular profiling in management of metastatic NSCLC patients and is providing important knowledge on tumor heterogeneity. Clinical trials are needed in order to transfer the information deriving from liquid biopsy testing in new therapeutic strategies.
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Affiliation(s)
- Riziero Esposito Abate
- a Cell Biology and Biotherapy Unit , Istituto Nazionale Tumori, IRCSS, Fondazione G. Pascale , Napoli , Italy
| | - Raffaella Pasquale
- a Cell Biology and Biotherapy Unit , Istituto Nazionale Tumori, IRCSS, Fondazione G. Pascale , Napoli , Italy
| | - Francesca Fenizia
- a Cell Biology and Biotherapy Unit , Istituto Nazionale Tumori, IRCSS, Fondazione G. Pascale , Napoli , Italy
| | - Anna Maria Rachiglio
- a Cell Biology and Biotherapy Unit , Istituto Nazionale Tumori, IRCSS, Fondazione G. Pascale , Napoli , Italy
| | - Cristin Roma
- a Cell Biology and Biotherapy Unit , Istituto Nazionale Tumori, IRCSS, Fondazione G. Pascale , Napoli , Italy
| | - Francesca Bergantino
- a Cell Biology and Biotherapy Unit , Istituto Nazionale Tumori, IRCSS, Fondazione G. Pascale , Napoli , Italy
| | - Laura Forgione
- a Cell Biology and Biotherapy Unit , Istituto Nazionale Tumori, IRCSS, Fondazione G. Pascale , Napoli , Italy
| | - Matilde Lambiase
- a Cell Biology and Biotherapy Unit , Istituto Nazionale Tumori, IRCSS, Fondazione G. Pascale , Napoli , Italy
| | - Alessandra Sacco
- a Cell Biology and Biotherapy Unit , Istituto Nazionale Tumori, IRCSS, Fondazione G. Pascale , Napoli , Italy
| | - Maria Carmela Piccirillo
- b Clinical Trials Unit , Istituto Nazionale Tumori - IRCSS - Fondazione G. Pascale , Napoli , Italy
| | - Alessandro Morabito
- c Department of Thoracic Medical Oncology , Istituto Nazionale Tumori - IRCSS - Fondazione G. Pascale , Napoli , Italy
| | - Nicola Normanno
- a Cell Biology and Biotherapy Unit , Istituto Nazionale Tumori, IRCSS, Fondazione G. Pascale , Napoli , Italy
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16
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Rachiglio AM, Esposito Abate R, Sacco A, Pasquale R, Fenizia F, Lambiase M, Morabito A, Montanino A, Rocco G, Romano C, Nappi A, Iaffaioli RV, Tatangelo F, Botti G, Ciardiello F, Maiello MR, De Luca A, Normanno N. Limits and potential of targeted sequencing analysis of liquid biopsy in patients with lung and colon carcinoma. Oncotarget 2018; 7:66595-66605. [PMID: 27448974 PMCID: PMC5341823 DOI: 10.18632/oncotarget.10704] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 05/29/2016] [Indexed: 12/12/2022] Open
Abstract
The circulating free tumor DNA (ctDNA) represents an alternative, minimally invasive source of tumor DNA for molecular profiling. Targeted sequencing with next generation sequencing (NGS) can assess hundred mutations starting from a low DNA input. We performed NGS analysis of ctDNA from 44 patients with metastatic non-small-cell lung carcinoma (NSCLC) and 35 patients with metastatic colorectal carcinoma (CRC). NGS detected EGFR mutations in 17/22 plasma samples from EGFR-mutant NSCLC patients (sensitivity 77.3%). The concordance rate between tissue and plasma in NSCLC was much lower for other mutations such as KRAS that, based on the allelic frequency and the fraction of neoplastic cells, were likely to be sub-clonal. NGS also identified EGFR mutations in plasma samples from two patients with EGFR wild type tumor tissue. Both mutations were confirmed by droplet digital PCR (ddPCR) in both plasma and tissue samples. In CRC, the sensitivity of the NGS plasma analysis for RAS mutations was 100% (6/6) in patients that had not resection of the primary tumor before blood drawing, and 46.2% (6/13) in patients with primary tumor resected before enrollment. Our study showed that NGS is a suitable method for plasma testing. However, its clinical sensitivity is significantly affected by the presence of the primary tumor and by the heterogeneity of driver mutations.
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Affiliation(s)
- Anna Maria Rachiglio
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Riziero Esposito Abate
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Alessandra Sacco
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Raffaella Pasquale
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Francesca Fenizia
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Matilde Lambiase
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Alessandro Morabito
- Thoraco-Pulmonary, Medical Oncology, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Agnese Montanino
- Thoraco-Pulmonary, Medical Oncology, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Gaetano Rocco
- Thoracic Surgery, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Carmen Romano
- Gastro-Intestinal Medical Oncology, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Anna Nappi
- Gastro-Intestinal Medical Oncology, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Rosario Vincenzo Iaffaioli
- Gastro-Intestinal Medical Oncology, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Fabiana Tatangelo
- Surgical Pathology Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Gerardo Botti
- Surgical Pathology Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Fortunato Ciardiello
- Department of Clinical and Experimental Medicine 'F. Magrassi' - Medical Oncology, Seconda Università degli Studi di Napoli, Napoli, Italy
| | - Monica R Maiello
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Antonella De Luca
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Nicola Normanno
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy.,Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
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17
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Pasquale R, Fenizia F, Esposito Abate R, Sacco A, Esposito C, Forgione L, Rachiglio AM, Bevilacqua S, Montanino A, Franco R, Rocco G, Botti G, Denis MG, Morabito A, De Luca A, Normanno N. Assessment of high-sensitive methods for the detection of EGFR mutations in circulating free tumor DNA from NSCLC patients. Pharmacogenomics 2015; 16:1135-48. [PMID: 26249748 DOI: 10.2217/pgs.15.45] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
AIM We assessed the ability of the Therascreen(®) kit (plasma-Therascreen) and of a peptide nucleic acids (PNA)-clamp approach to detect EGFR mutations in plasma-derived circulating-free tumor DNA (cftDNA) from non-small-cell lung cancer patients. MATERIALS & METHODS cftDNA from 96 patients was analyzed for exon 19 deletions and the p.L858R mutation, using both plasma-Therascreen and PNA-clamp-based assays. RESULTS None of the 70 EGFR wild-type patients showed EGFR mutations in cftDNA with both techniques (specificity: 100%). In 17/26 EGFR-mutant patients, plasma-Therascreen analysis confirmed the mutation identified in the primary tumor (analytical sensitivity: 65.4%). Similar results were obtained with the PNA-clamp method. CONCLUSION Both approaches were specific and sensitive for EGFR mutational analysis of cftDNA in non-small-cell lung cancer patients.
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Affiliation(s)
- Raffaella Pasquale
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Francesca Fenizia
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Riziero Esposito Abate
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Alessandra Sacco
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Claudia Esposito
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Laura Forgione
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Anna Maria Rachiglio
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy
| | - Simona Bevilacqua
- Cell Biology & Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G Pascale"-IRCCS, Naples, Italy
| | - Agnese Montanino
- Thoraco-Pulmonary Medical Oncology, Istituto Nazionale Tumori "Fondazione G Pascale"-IRCCS, Naples, Italy
| | - Renato Franco
- Surgical Pathology Unit, Istituto Nazionale Tumori "Fondazione G Pascale"-IRCCS, Naples, Italy
| | - Gaetano Rocco
- Thoracic Surgery, Istituto Nazionale Tumori "Fondazione G Pascale"-IRCCS, Naples, Italy
| | - Gerardo Botti
- Surgical Pathology Unit, Istituto Nazionale Tumori "Fondazione G Pascale"-IRCCS, Naples, Italy
| | - Marc G Denis
- Department of Biochemistry, Nantes University Hospital, Nantes, France
| | - Alessandro Morabito
- Thoraco-Pulmonary Medical Oncology, Istituto Nazionale Tumori "Fondazione G Pascale"-IRCCS, Naples, Italy
| | - Antonella De Luca
- Cell Biology & Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G Pascale"-IRCCS, Naples, Italy
| | - Nicola Normanno
- Laboratory of Pharmacogenomics, CROM-Istituto Nazionale Tumori "Fondazione G. Pascale"-IRCCS, Naples, Italy.,Cell Biology & Biotherapy Unit, Istituto Nazionale Tumori "Fondazione G Pascale"-IRCCS, Naples, Italy
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