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Nikolaidi A, Kotoula V, Koliou GA, Giannoulatou E, Papadopoulou K, Zagouri F, Pentheroudakis G, Gogas H, Bobos M, Chatzopoulos K, Oikonomopoulos G, Pectasides D, Saloustros E, Arnogiannaki N, Nicolaou I, Papakostas P, Bompolaki I, Aravantinos G, Athanasiadis I, Fountzilas G. Tumor Mutational Patterns and Infiltrating Lymphocyte Density in Young and Elderly Patients With Breast Cancer. Cancer Genomics Proteomics 2020; 17:181-193. [PMID: 32108041 DOI: 10.21873/cgp.20179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND/AIM Age may pertain to different tumor genotype characteristics which may interfere with treatment efficacy and prognosis. We investigated the distribution and prognostic effect of mutations and tumor infiltrating lymphocyte (stromal TIL density) in young (≤35 years) and elderly (>65 years) early breast cancer patients. MATERIALS AND METHODS Paraffin tumor genotypes of all clinical subtypes from 345 patients were examined. RESULTS A total of 638 mutations were detected in 221 patients (64.1%). Compared to young, elderly patients presented with lower TIL density (p<0.001) but more TILs in TP53 mutated tumors (p=0.042). Mutation in one, rather than in 2 or more genes, conferred better outcome (DFS: HR=0.51, p=0.016; OS: HR=0.47, p=0.015) but the effect was age-independent. CONCLUSION There are fewer TILs and different mutations patterns in tumors from elderly patients compared to young. Age and TIL-independent gene agnostic co-mutations affect patient outcome.
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Affiliation(s)
| | - Vassiliki Kotoula
- Department of Pathology, School of Health Sciences, Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece.,Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Eleni Giannoulatou
- Bioinformatics and Systems Medicine Laboratory, Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.,The University of New South Wales, Kensington, NSW, Australia
| | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Flora Zagouri
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - George Pentheroudakis
- Department of Medical Oncology, Medical School, University of Ioannina, Ioannina, Greece.,Society for Study of Clonal Heterogeneity of Neoplasia (EMEKEN), Ioannina, Greece
| | - Helen Gogas
- First Department of Medicine, Laiko General Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Mattheos Bobos
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Kyriakos Chatzopoulos
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Dimitrios Pectasides
- Oncology Section, Second Department of Internal Medicine, Hippokration Hospital, Athens, Greece
| | | | - Niki Arnogiannaki
- Department of Surgical Pathology, Saint Savvas Anticancer Hospital, Athens, Greece
| | - Irene Nicolaou
- Department of Histopathology, Agii Anagriri Hospital, Athens, Greece
| | | | | | - Gerasimos Aravantinos
- Second Department of Medical Oncology, Agii Anargiri Cancer Hospital, Athens, Greece
| | | | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.,Aristotle University of Thessaloniki, Thessaloniki, Greece.,German Oncology Center, Limassol, Cyprus
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2
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Lazaridis G, Kotoula V, Vrettou E, Kostopoulos I, Manousou K, Papadopoulou K, Giannoulatou E, Bobos M, Sotiropoulou M, Pentheroudakis G, Efstratiou I, Papoudou-Bai A, Psyrri A, Christodoulou C, Gogas H, Koutras A, Timotheadou E, Pectasides D, Zagouri F, Fountzilas G. Opposite Prognostic Impact of Single PTEN-loss and PIK3CA Mutations in Early High-risk Breast Cancer. Cancer Genomics Proteomics 2019; 16:195-206. [PMID: 31018950 DOI: 10.21873/cgp.20125] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND/AIM PTEN-loss and PIK3CA mutations have been addressed as markers of PI3K activation in breast cancer. We evaluated these markers in early high-risk breast cancer (EBC) focusing on PTEN immunohistochemistry (IHC) issues, particularly in HER2-positive disease. MATERIALS AND METHODS We examined PTEN-loss and PIK3CA mutations in 1265 EBC patients treated with adjuvant chemotherapy within two clinical trials. Two different methods for the evaluation of PTEN IHC were used, one upfront binary (loss; no-loss) and the other initially multi-scale allowing for the classification of "grey zone" tumors with low and very low PTEN protein expression. RESULTS PTEN-loss (33.4% and 22.1%, depending on the IHC method) and PIK3CA mutations (29.6%) were associated with ER/PgR/HER2-negative and ER/PgR-positive disease, respectively. Concordance of the two IHC methods was moderate (Cohen's kappa 0.624). PTEN-loss discrepancy and intra-tumor heterogeneity concerned "grey zone" tumors that were prevalent among HER2-positive cancers. PTEN-loss independently conferred higher risk for relapse and death. Compared to single PIK3CA mutations,single PTEN-loss was independently associated with increased risk for relapse and death. Depending on the evaluation method, in HER2-positive cancer, PTEN-loss was without- or of marginal unfavorable prognostic significance. CONCLUSION In EBC, PTEN-loss is an independent predictor of poor outcome. When occurring singly, PTEN-loss and PIK3CA mutations have opposite prognostic impact. In HER2-positive disease, assessment of PTEN-loss by IHC appears unreliable and the marker is without clear prognostic significance.
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Affiliation(s)
- Georgios Lazaridis
- Department of Medical Oncology, Faculty of Medicine Papageorgiou Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Thessaloniki, Greece
| | - Vassiliki Kotoula
- Department of Pathology, School of Health Sciences, Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece.,Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eleni Vrettou
- Department of Pathology, School of Health Sciences, Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ioannis Kostopoulos
- Department of Pathology, School of Health Sciences, Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Kyriaki Manousou
- Section of Biostatistics, Hellenic Cooperative Oncology Group, Data Office, Athens, Greece
| | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.,The University of New South Wales, Kensington, NSW, Australia
| | - Mattheos Bobos
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | | | - Ioannis Efstratiou
- Department of Pathology, School of Health Sciences, Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Amanda Psyrri
- Division of Oncology, Second Department of Internal Medicine, Attikon University Hospital, Athens, Greece
| | | | - Helen Gogas
- First Department of Medicine, Laiko General Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Angelos Koutras
- Division of Oncology, Department of Medicine, University Hospital, University of Patras Medical School, Patras, Greece
| | - Eleni Timotheadou
- Department of Medical Oncology, Faculty of Medicine Papageorgiou Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Thessaloniki, Greece
| | - Dimitrios Pectasides
- Oncology Section, Second Department of Internal Medicine, Hippokration Hospital, Athens, Greece
| | - Flora Zagouri
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki, Thessaloniki, Greece.,Aristotle University of Thessaloniki, Thessaloniki, Greece
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3
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Kotoula V, Tsakiri K, Koliou GA, Lazaridis G, Papadopoulou K, Giannoulatou E, Tikas I, Christodoulou C, Chatzopoulos K, Bobos M, Pentheroudakis G, Tsolaki E, Batistatou A, Kotsakis A, Koutras A, Linardou H, Razis E, Res E, Pectasides D, Fountzilas G. Relapsed and De Novo Metastatic HER2-positive Breast Cancer Treated With Trastuzumab: Tumor Genotypes and Clinical Measures Associated With Patient Outcome. Clin Breast Cancer 2018; 19:113-125.e4. [PMID: 30545790 DOI: 10.1016/j.clbc.2018.10.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 08/22/2018] [Accepted: 10/29/2018] [Indexed: 01/28/2023]
Abstract
BACKGROUND We examined tumor genotype characteristics of human epidermal growth factor receptor 2 (HER2)-positive relapsed (R-) and de novo (dn-) metastatic breast cancer (MBC) in trastuzumab-treated patients who were previously not exposed to this agent. MATERIALS AND METHODS We analyzed genotypes obtained upon deep sequencing from 113 HER2-positive primary tumors from 69 patients with R-MBC and 44 patients with dn-MBC. RESULTS Mutations were observed in 90 (79.6%) tumors, 56 R-MBC and 34 dn-MBC (median number per tumor: 2; mean: 11.2; range: 0-150). The top mutated gene was TP53 (63.7%) followed by PIK3CA (24.8%) and others that were mostly co-mutated with TP53 (eg, 22 of 28 PIK3CA mutated tumors were co-mutated in TP53, 17 of these were R-MBC [P = .041]). dn-MBC had higher CEN17 average copies (P = .048). Tumor mutational burden inversely correlated with average HER2 copies (rho -0.32; P < .001). In all patients, PIK3CA mutations and higher proliferation rate were independent unfavorable prognosticators. In R-MBC, longer disease-free interval between initial diagnosis and relapse conferred lower risk for time-to-progression (P < .001) and death (P = .009); PIK3CA mutations conferred higher risk for death (P = .035). In dn-MBC, surgical removal of the primary tumor before any other therapy was favorable for time-to-progression (P = .002); higher tumor mutational burden was unfavorable for survival (P = .026). CONCLUSIONS Except for the overall unfavorable prognostic effect of PIK3CA mutations in trastuzumab-treated MBC, our exploratory findings indicate that the outcome of patients with R-MBC is related to patient benefit from the preceding adjuvant chemotherapy and provide initial evidence that tumor mutational burden may be related to prognosis in dn-MBC, which is of potential clinical relevance and merits further investigation.
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Affiliation(s)
- Vassiliki Kotoula
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece; Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.
| | - Kalliopi Tsakiri
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Georgios Lazaridis
- Department of Medical Oncology, Papageorgiou Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece
| | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia; The University of New South Wales, Kensington, NSW, Australia
| | - Ioannis Tikas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Kyriakos Chatzopoulos
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Mattheos Bobos
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Eleftheria Tsolaki
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anna Batistatou
- Department of Pathology, Ioannina University Hospital, Ioannina, Greece
| | - Athanassios Kotsakis
- University Hospital of Heraklion, University of Crete, School of Medicine, Heraklion, Crete, Greece
| | - Angelos Koutras
- Division of Oncology, Department of Medicine, University Hospital, University of Patras Medical School, Patras, Greece
| | - Helena Linardou
- First Department of Medical Oncology, Metropolitan Hospital, Piraeus, Greece
| | - Evangelia Razis
- Third Department of Medical Oncology, Hygeia Hospital, Athens, Greece
| | - Eleni Res
- Third Department of Medical Oncology, Agii Anargiri Cancer Hospital, Athens, Greece
| | - Dimitrios Pectasides
- Oncology Section, Second Department of Internal Medicine, Hippokration Hospital, Athens, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece; Aristotle University of Thessaloniki, Thessaloniki, Greece
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4
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Cravero K, Medford A, Pallavajjala A, Canzoniero J, Hunter N, Chu D, Cochran RL, Waters I, Christenson ES, Kyker-Snowman K, Button B, Cole AJ, Park BH. Biotinylated amplicon sequencing: A method for preserving DNA samples of limited quantity. Pract Lab Med 2018; 12:e00108. [PMID: 30140723 PMCID: PMC6104457 DOI: 10.1016/j.plabm.2018.e00108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Revised: 07/06/2018] [Accepted: 08/08/2018] [Indexed: 11/24/2022] Open
Abstract
Background Genomic testing is often limited by the exhaustible nature of human tissue and blood samples. Here we describe biotinylated amplicon sequencing (BAmSeq), a method that allows for the creation of PCR amplicon based next-generation sequencing (NGS) libraries while retaining the original source DNA. Design and methods Biotinylated primers for different loci were designed to create NGS libraries using human genomic DNA from cell lines, plasma, and formalin-fixed paraffin embedded (FFPE) tissues using the BAmSeq protocol. DNA from the original template used for each BAmSeq library was recovered after separation with streptavidin magnetic beads. The recovered DNA was then used for end-point, quantitative and droplet digital PCR (ddPCR) as well as NGS using a cancer gene panel. Results Recovered DNA was analyzed and compared to the original DNA after one or two rounds of BAmSeq. Recovered DNA revealed comparable genomic distributions and mutational allelic frequencies when compared to original source DNA. Sufficient quantities of recovered DNA after BAmSeq were obtained, allowing for additional downstream applications. Conclusions We demonstrate that BAmSeq allows original DNA template to be recovered with comparable quality and quantity to the source DNA. This recovered DNA is suitable for many downstream applications and may prevent sample exhaustion, especially when DNA quantity or source material is limiting. Modification of targeted panel sequencing allows for recovery of original DNA template. Protocol provides value in the setting of scarce DNA template. Recovered DNA is suitable for NGS, ddPCR and qPCR. Recovered DNA shows no loss of genomic regions.
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Affiliation(s)
- Karen Cravero
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Arielle Medford
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Aparna Pallavajjala
- The Sidney Kimmel Comprehensive Cancer Center, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jenna Canzoniero
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Natasha Hunter
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - David Chu
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Rory L Cochran
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Ian Waters
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Eric S Christenson
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Kelly Kyker-Snowman
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Berry Button
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Alex J Cole
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Ben Ho Park
- The Sidney Kimmel Comprehensive Cancer Center, Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, MD, United States.,The Whiting School of Engineering, Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States
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5
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Levva S, Kotoula V, Kostopoulos I, Manousou K, Papadimitriou C, Papadopoulou K, Lakis S, Koukoulias K, Karavasilis V, Pentheroudakis G, Balassi E, Zagouri F, Kaklamanos IG, Pectasides D, Razis E, Aravantinos G, Papakostas P, Bafaloukos D, Rallis G, Gogas H, Fountzilas G. Prognostic Evaluation of Epidermal Growth Factor Receptor (EGFR) Genotype and Phenotype Parameters in Triple-negative Breast Cancers. Cancer Genomics Proteomics 2018; 14:181-195. [PMID: 28446533 DOI: 10.21873/cgp.20030] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/23/2017] [Accepted: 03/27/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Epidermal growth factor receptor (EGFR) aberrations have been implicated in the pathogenesis of triple-negative breast cancer (TNBC) but their impact on prognosis and, therefore, druggability, remain controversial. Herein, we studied EGFR aberrations at different molecular levels and assessed their prognostic impact in patients with operable TNBC treated with adjuvant anthracycline-based chemotherapy. MATERIALS AND METHODS We evaluated the prognostic impact of EGFR gene status by fluorescent in situ hybridization (FISH), EGFR coding mutations by Sanger and next-generation sequencing, relative EGFR messenger RNA (mRNA) levels by qPCR (upper quartile) and EGFR and p53 protein expression by immunohistochemistry (IHC), in 352 centrally-assessed tumors from an equal number of TNBC patients. RESULTS Approximately 53.5% of the tumors expressed EGFR, 59.3% p53 and 35.9% both EGFR and p53 proteins; 4.1% showed EGFR gene amplification and 4.4% carried EGFR mutations. The latter were located outside the druggable kinase domain region and presented at low frequencies. Amplification and mutations overlapped only in one case of glycogen-rich carcinoma. EGFR and CEN7 copies were higher in tumors from older patients (p=0.002 and p=0.003, respectively). Patients with amplified tumors (n=11) had excellent prognosis (0 relapses and deaths). Upon multivariate analysis, high EGFR copies conferred significantly favorable disease-free survival (HR=0.57, 95% CI 0.36-0.90, Wald's p=0.017) and high CEN7 copies favorable overall survival (HR=0.49, 95% CI=0.29-0.83, Wald's p=0.008). Patients with EGFR-/p53+ and EGFR+/p53- tumors had significantly higher risk for relapse than those with EGFR-/p53- and EGFR+/p53+ tumors (HR=1.73, 95% CI=1.12-2.67, Wald's p=0.013). CONCLUSION EGFR gene amplification and mutations are rare in TNBC, the latter of no apparent clinical relevance. Surrogate markers of EGFR-related chromosomal aberrations and combined EGFR/p53 IHC phenotypes appear to be associated with favorable prognosis in patients with operable TNBC receiving conventional adjuvant chemotherapy.
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Affiliation(s)
- Sofia Levva
- Department of Medical Oncology, Papageorgiou Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece
| | - Vassiliki Kotoula
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece.,Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ioannis Kostopoulos
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Kyriaki Manousou
- Section of Biostatistics, Hellenic Cooperative Oncology Group, Data Office, Athens, Greece
| | - Christos Papadimitriou
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sotiris Lakis
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Kyriakos Koukoulias
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Vasilios Karavasilis
- Department of Medical Oncology, Papageorgiou Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece
| | | | - Eufemia Balassi
- Department of Pathology, Hatzikosta Hospital, Ioannina, Greece
| | - Flora Zagouri
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Ioannis G Kaklamanos
- Department of Surgery, Agii Anargiri Hospital, University of Athens, School of Health Sciences, Athens, Greece
| | - Dimitrios Pectasides
- Oncology Section, Second Department of Internal Medicine, Hippokration Hospital, Athens, Greece
| | - Evangelia Razis
- Third Department of Medical Oncology, Hygeia Hospital, Athens, Greece
| | - Gerasimos Aravantinos
- Second Department of Medical Oncology, Agii Anargiri Cancer Hospital, Athens, Greece
| | | | | | - Grigorios Rallis
- Department of Medical Oncology, Papageorgiou Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece
| | - Helen Gogas
- First Department of Medicine, Laiko General Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.,Aristotle University of Thessaloniki, Thessaloniki, Greece
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6
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Fountzilas G, Giannoulatou E, Alexopoulou Z, Zagouri F, Timotheadou E, Papadopoulou K, Lakis S, Bobos M, Poulios C, Sotiropoulou M, Lyberopoulou A, Gogas H, Pentheroudakis G, Pectasides D, Koutras A, Christodoulou C, Papandreou C, Samantas E, Papakostas P, Kosmidis P, Bafaloukos D, Karanikiotis C, Dimopoulos MA, Kotoula V. TP53 mutations and protein immunopositivity may predict for poor outcome but also for trastuzumab benefit in patients with early breast cancer treated in the adjuvant setting. Oncotarget 2017; 7:32731-53. [PMID: 27129168 PMCID: PMC5078047 DOI: 10.18632/oncotarget.9022] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/28/2016] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND We investigated the impact of PIK3CA and TP53 mutations and p53 protein status on the outcome of patients who had been treated with adjuvant anthracycline-taxane chemotherapy within clinical trials in the pre- and post-trastuzumab era. RESULTS TP53 and PIK3CA mutations were found in 380 (21.5%) and 458 (25.9%) cases, respectively, including 104 (5.9%) co-mutated tumors; p53 immunopositivity was observed in 848 tumors (53.5%). TP53 mutations (p < 0.001) and p53 protein positivity (p = 0.001) were more frequent in HER2-positive and triple negative (TNBC) tumors, while PIK3CA mutations were more frequent in Luminal A/B tumors (p < 0.001). TP53 mutation status and p53 protein expression but not PIK3CA mutation status interacted with trastuzumab treatment for disease-free survival; patients with tumors bearing TP53 mutations or immunopositive for p53 protein fared better when treated with trastuzumab, while among patients treated with trastuzumab those with the above characteristics fared best (interaction p = 0.017 for mutations; p = 0.015 for IHC). Upon multivariate analysis the above interactions remained significant in HER2-positive patients; in the entire cohort, TP53 mutations were unfavorable in patients with Luminal A/B (p = 0.003) and TNBC (p = 0.025); p53 immunopositivity was strongly favorable in patients treated with trastuzumab (p = 0.009). MATERIALS AND METHODS TP53 and PIK3CA mutation status was examined in 1766 paraffin tumor DNA samples with informative semiconductor sequencing results. Among these, 1585 cases were also informative for p53 protein status assessed by immunohistochemistry (IHC; 10% positivity cut-off). CONCLUSIONS TP53 mutations confer unfavorable prognosis in patients with Luminal A/B and TNBC tumors, while p53 immunopositivity may predict for trastuzumab benefit in the adjuvant setting.
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Affiliation(s)
- George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.,Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.,The University of New South Wales, NSW, Australia
| | - Zoi Alexopoulou
- Department of Biostatistics, Health Data Specialists Ltd, Athens, Greece
| | - Flora Zagouri
- Department of Clinical Therapeutics, "Alexandra" Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Eleni Timotheadou
- Department of Medical Oncology, "Papageorgiou" Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece
| | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sotiris Lakis
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Mattheos Bobos
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Christos Poulios
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece
| | | | - Aggeliki Lyberopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Helen Gogas
- First Department of Medicine, "Laiko" General Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | | | - Dimitrios Pectasides
- Oncology Section, Second Department of Internal Medicine, "Hippokration" Hospital, Athens, Greece
| | - Angelos Koutras
- Division of Oncology, Department of Medicine, University Hospital, University of Patras Medical School, Patras, Greece
| | | | - Christos Papandreou
- Department of Medical Oncology, University Hospital of Larissa, University of Thessaly School of Medicine, Larissa, Greece
| | - Epaminontas Samantas
- Third Department of Medical Oncology, "Agii Anargiri" Cancer Hospital, Athens, Greece
| | | | - Paris Kosmidis
- Second Department of Medical Oncology, Hygeia Hospital, Athens, Greece
| | | | | | | | - Vassiliki Kotoula
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.,Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece
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Kamps R, Brandão RD, Bosch BJVD, Paulussen ADC, Xanthoulea S, Blok MJ, Romano A. Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification. Int J Mol Sci 2017; 18:ijms18020308. [PMID: 28146134 PMCID: PMC5343844 DOI: 10.3390/ijms18020308] [Citation(s) in RCA: 284] [Impact Index Per Article: 40.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 01/19/2017] [Indexed: 12/17/2022] Open
Abstract
Next-generation sequencing (NGS) technology has expanded in the last decades with significant improvements in the reliability, sequencing chemistry, pipeline analyses, data interpretation and costs. Such advances make the use of NGS feasible in clinical practice today. This review describes the recent technological developments in NGS applied to the field of oncology. A number of clinical applications are reviewed, i.e., mutation detection in inherited cancer syndromes based on DNA-sequencing, detection of spliceogenic variants based on RNA-sequencing, DNA-sequencing to identify risk modifiers and application for pre-implantation genetic diagnosis, cancer somatic mutation analysis, pharmacogenetics and liquid biopsy. Conclusive remarks, clinical limitations, implications and ethical considerations that relate to the different applications are provided.
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Affiliation(s)
- Rick Kamps
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Rita D Brandão
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Bianca J van den Bosch
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Aimee D C Paulussen
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Sofia Xanthoulea
- Department of Gynaecology and Obstetrics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Marinus J Blok
- Department of Clinical Genetics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
| | - Andrea Romano
- Department of Gynaecology and Obstetrics: GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, 6229HX Maastricht, The Netherlands.
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8
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Kotoula V, Fostira F, Papadopoulou K, Apostolou P, Tsolaki E, Lazaridis G, Manoussou K, Zagouri F, Pectasides D, Vlachos I, Tikas I, Lakis S, Konstantopoulou I, Pentheroudakis G, Gogas H, Papakostas P, Christodoulou C, Bafaloukos D, Razis E, Karavasilis V, Bamias C, Yannoukakos D, Fountzilas G. The fate of BRCA1-related germline mutations in triple-negative breast tumors. Am J Cancer Res 2017; 7:98-114. [PMID: 28123851 PMCID: PMC5250684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 12/13/2016] [Indexed: 06/06/2023] Open
Abstract
The preservation of pathogenic BRCA1/2 germline mutations in tumor tissues is usually not questioned, while it remains unknown whether these interact with somatic genotypes for patient outcome. Herein we compared germline and tumor genotypes in operable triple-negative breast cancer (TNBC) and evaluated their combined effects on prognosis. We analyzed baseline germline and primary tumor genotype data obtained by Sanger and Next Generation Sequencing in 194 TNBC patients. We also performed multiple tests interrogating the preservation of germline mutations in matched tumors and breast tissue from carriers with available material. Patients had been treated within clinical trials with adjuvant anthracyclines-taxanes based chemotherapy. We identified 50 (26%) germline mutation carriers (78% in BRCA1) and 136 (71%) tumors with somatic mutations (83% in TP53). Tumor mutation patterns differed between carriers and non-carriers (P<0.001); PIK3CA mutations were exclusively present in non-carriers (P=0.007). Germline BRCA1/2 mutations were not detected in matched tumors and breast tissues from 14 out of 33 (42%) evaluable carriers. Microsatellite markers revealed tumor loss of the germline mutant allele in one case only. Tumors that had lost the germline mutation demonstrated a higher incidence of somatic TP53 mutations as compared to tumors with preserved germline mutations (P=0.036). Germline mutation status significantly interacted with tumor TP53 mutations for patient disease-free survival (interaction P=0.026): In non-carriers, tumor TP53 mutations did not affect outcome; In carriers, those with mutated TP53 tumors experienced more relapses compared to those with wild-type TP53 tumors (36% vs. 9% relapse rate, respectively). In conclusion, we show that loss of germline BRCA1/2 mutations is not a rare event in TNBC. This finding, the observed differences in tumor genotypes with respect to germline status and the prognostic interaction between germline BRCA1-related and tumor TP53 mutation status prompt for combined germline and tumor genotyping for the classification of TNBC, particularly in the context of clinical trials evaluating synthetic lethality drugs.
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Affiliation(s)
- Vassiliki Kotoula
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of MedicineThessaloniki, Greece
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of ThessalonikiThessaloniki, Greece
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, INRASTES, National Center for Scientific Research NCSR DemokritosAthens, Greece
| | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of ThessalonikiThessaloniki, Greece
| | - Paraskevi Apostolou
- Molecular Diagnostics Laboratory, INRASTES, National Center for Scientific Research NCSR DemokritosAthens, Greece
| | - Eleftheria Tsolaki
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of ThessalonikiThessaloniki, Greece
| | - Georgios Lazaridis
- Department of Medical Oncology, Papageorgiou Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of MedicineThessaloniki, Greece
| | - Kyriaki Manoussou
- Section of Biostatistics, Hellenic Cooperative Oncology Group, Data OfficeAthens, Greece
| | - Flora Zagouri
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of MedicineAthens, Greece
| | - Dimitrios Pectasides
- Oncology Section, Second Department of Internal Medicine, Hippokration HospitalAthens, Greece
| | - Ioannis Vlachos
- Molecular Diagnostics Laboratory, INRASTES, National Center for Scientific Research NCSR DemokritosAthens, Greece
- DIANA-Lab, Department of Computer and Communication Engineering, University of ThessalyVolos, Greece
| | - Ioannis Tikas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of ThessalonikiThessaloniki, Greece
| | - Sotiris Lakis
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of ThessalonikiThessaloniki, Greece
| | - Irene Konstantopoulou
- Molecular Diagnostics Laboratory, INRASTES, National Center for Scientific Research NCSR DemokritosAthens, Greece
| | | | - Helen Gogas
- First Department of Medicine, Laiko General Hospital, National and Kapodistrian University of Athens School of MedicineAthens, Greece
| | | | | | | | - Evangelia Razis
- Third Department of Medical Oncology, Hygeia HospitalAthens, Greece
| | - Vasilios Karavasilis
- Department of Medical Oncology, Papageorgiou Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of MedicineThessaloniki, Greece
| | - Christina Bamias
- National and Kapodistrian University of Athens, Medical School, Department of Hygiene, Epidemiology and Medical StatisticsAthens, Greece
| | - Drakoulis Yannoukakos
- Molecular Diagnostics Laboratory, INRASTES, National Center for Scientific Research NCSR DemokritosAthens, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of ThessalonikiThessaloniki, Greece
- Aristotle University of ThessalonikiThessaloniki, Greece
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Considerations when using next-generation sequencing for genetic diagnosis of long-QT syndrome in the clinical testing laboratory. Clin Chim Acta 2017; 464:128-135. [DOI: 10.1016/j.cca.2016.11.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 11/08/2016] [Accepted: 11/08/2016] [Indexed: 11/23/2022]
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10
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Fountzilas E, Kotoula V, Zagouri F, Giannoulatou E, Kouvatseas G, Pentheroudakis G, Koletsa T, Bobos M, Papadopoulou K, Samantas E, Demiri E, Miliaras S, Christodoulou C, Chrisafi S, Razis E, Fostira F, Pectasides D, Zografos G, Fountzilas G. Disease evolution and heterogeneity in bilateral breast cancer. Am J Cancer Res 2016; 6:2611-2630. [PMID: 27904775 PMCID: PMC5126277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 09/29/2016] [Indexed: 06/06/2023] Open
Abstract
Bilateral breast cancers (BBC) are currently treated as independent tumors arising in the same patient. Herein, we investigated whether BBC indeed evolve independently at the genomic level. We examined paired targeted next generation sequencing genotypes from 155 paraffin tumors corresponding to 76 BBC patients (75 women and one man; 52 concurrent and 24 metachronous), for coding mutations (amino acid changing, minor allele frequency <0.1%) and single nucleotide polymorphism (SNP) zygosity. Germline genotypes were available for 29 patients. Mutations were present in 80 tumors (54/76 patients; 71%), were mostly tumor-private (90%), more frequent in TP53 (19%), PIK3CA (14%), CDH1, GATA3, MLL3. TP53 mutations were more frequent in metachronous tumors (P<0.001); hormone receptor negative (P<0.001); with higher Ki-67 (P=0.002); and, in younger patients (P=0.01). Hypermutated tumors, all TP53 mutated, were diagnosed as the first incidence in 5 patients; their metachronous counterparts were mutation poor without TP53 involvement. Paired tumors shared common mutations at intratumoral frequency >20% in 10/54 comparable BBC (18.5%), 8/10 concurrent. SNP zygosity status was less preserved in metachronous, compared to concurrent disease. Pathogenic germline mutations were present in 10/29 patients, 9 in BRCA1 and one in TP53 (p.Phe341Val, first report in the germline). BBC demonstrated extensive inter- and intra-patient heterogeneity in the present thus far largest series of corresponding paired genotypes. The majority evolve independently and unpredictably, supporting current clinical practice. A considerable minority though, retains clonal origin and may be regarded as a distinct group for therapeutic interventions among concurrent BBC.
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Affiliation(s)
- Elena Fountzilas
- Department of Medical Oncology, Papageorgiou Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of MedicineThessaloniki, Greece
| | - Vassiliki Kotoula
- Department of Pathology, Aristotle University of Thessaloniki School of Health Sciences, Faculty of MedicineThessaloniki, Greece
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of ThessalonikiThessaloniki, Greece
| | - Flora Zagouri
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of MedicineAthens, Greece
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research InstituteDarlinghurst, NSW, Australia
- The University of New South WalesKensington, NSW, Australia
| | | | | | - Triantafyllia Koletsa
- Department of Pathology, Aristotle University of Thessaloniki School of Health Sciences, Faculty of MedicineThessaloniki, Greece
| | - Mattheos Bobos
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of ThessalonikiThessaloniki, Greece
| | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of ThessalonikiThessaloniki, Greece
| | - Epaminontas Samantas
- Third Department of Medical Oncology, Agii Anargiri Cancer HospitalAthens, Greece
| | - Efterpi Demiri
- Department of Plastic Surgery, Papageorgiou Hospital, Aristotle University of Thessaloniki School of MedineThessaloniki, Greece
| | - Spyros Miliaras
- First Department of Surgery, Papageorgiou Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of MedicineThessaloniki, Greece
| | | | - Sofia Chrisafi
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of ThessalonikiThessaloniki, Greece
| | - Evangelia Razis
- Third Department of Medical Oncology, Hygeia HospitalAthens, Greece
| | - Florentia Fostira
- Molecular Diagnostics Laboratory, INRaSTES, National Centre for Scientific Research DemokritosAthens, Greece
| | - Dimitrios Pectasides
- Oncology Section, Second Department of Internal Medicine, Hippokration HospitalAthens, Greece
| | - George Zografos
- Breast Unit, National and Kapodistrian University of Athens School of MedicineAthens, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of ThessalonikiThessaloniki, Greece
- Aristotle University of ThessalonikiThessaloniki, Greece
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11
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Kotoula V, Lakis S, Vlachos IS, Giannoulatou E, Zagouri F, Alexopoulou Z, Gogas H, Pectasides D, Aravantinos G, Efstratiou I, Pentheroudakis G, Papadopoulou K, Chatzopoulos K, Papakostas P, Sotiropoulou M, Nicolaou I, Razis E, Psyrri A, Kosmidis P, Papadimitriou C, Fountzilas G. Tumor Infiltrating Lymphocytes Affect the Outcome of Patients with Operable Triple-Negative Breast Cancer in Combination with Mutated Amino Acid Classes. PLoS One 2016; 11:e0163138. [PMID: 27685159 PMCID: PMC5042538 DOI: 10.1371/journal.pone.0163138] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 09/02/2016] [Indexed: 12/26/2022] Open
Abstract
Background Stromal tumor infiltrating lymphocytes (TILs) density is an outcome predictor in triple-negative breast cancer (TNBC). Herein we asked whether TILs are related to coding mutation load and to the chemical class of the resulting mutated amino acids, i.e., charged, polar, and hydrophobic mutations. Methods We examined paraffin tumors from TNBC patients who had been treated with adjuvant chemotherapy mostly within clinical trials (training cohort, N = 133; validation, N = 190) for phenotype concordance; TILs density; mutation load and types. Results Concordance of TNBC phenotypes was 42.1% upon local / central, and 72% upon central / central pathology assessment. TILs were not associated with mutation load, type and class of mutated amino acids. Polar and charged mutation patterns differed between TP53 and PIK3CA (p<0.001). Hydrophobic mutations predicted for early relapse in patients with high nodal burden and <50% TILs tumors (training: HR 3.03, 95%CI 1.11–8.29, p = 0.031; validation: HR 2.90, 95%CI 0.97–8.70, p = 0.057), especially if compared to patients with >50% TILs tumors (training p = 0.003; validation p = 0.015). Conclusions TILs density is unrelated to mutation load in TNBC, which may be regarded as an unstable phenotype. If further validated, hydrophobic mutations along with TILs density may help identifying TNBC patients in higher risk for relapse.
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Affiliation(s)
- Vassiliki Kotoula
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
- * E-mail:
| | - Sotiris Lakis
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ioannis S. Vlachos
- Molecular Diagnostics Laboratory, INRASTES, NCSR 'Demokritos', Athens, Greece
- DIANA-Lab, Department of Computer and Communication Engineering, University of Thessaly, Volos, Greece
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
- The University of New South Wales, New South Wales, Australia
| | - Flora Zagouri
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Zoi Alexopoulou
- Department of Biostatistics, Health Data Specialists Ltd, Athens, Greece
| | - Helen Gogas
- First Department of Medicine, Laiko General Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Dimitrios Pectasides
- Oncology Section, Second Department of Internal Medicine, Hippokration Hospital, Athens, Greece
| | - Gerasimos Aravantinos
- Second Department of Medical Oncology, Agii Anargiri Cancer Hospital, Athens, Greece
| | | | | | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Kyriakos Chatzopoulos
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | | | - Irene Nicolaou
- Department of Histopathology, Agii Anagriri Cancer Hospital, Athens, Greece
| | - Evangelia Razis
- Third Department of Medical Oncology, Hygeia Hospital, Athens, Greece
| | - Amanda Psyrri
- Division of Oncology, Second Department of Internal Medicine, Attikon University Hospital, Athens, Greece
| | - Paris Kosmidis
- Second Department of Medical Oncology, Hygeia Hospital, Athens, Greece
| | - Christos Papadimitriou
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
- Aristotle University of Thessaloniki, Thessaloniki, Greece
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12
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Kotoula V, Karavasilis V, Zagouri F, Kouvatseas G, Giannoulatou E, Gogas H, Lakis S, Pentheroudakis G, Bobos M, Papadopoulou K, Tsolaki E, Pectasides D, Lazaridis G, Koutras A, Aravantinos G, Christodoulou C, Papakostas P, Markopoulos C, Zografos G, Papandreou C, Fountzilas G. Effects of TP53 and PIK3CA mutations in early breast cancer: a matter of co-mutation and tumor-infiltrating lymphocytes. Breast Cancer Res Treat 2016; 158:307-21. [PMID: 27369359 DOI: 10.1007/s10549-016-3883-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 06/21/2016] [Indexed: 10/21/2022]
Abstract
The purpose of this study is to investigate whether the outcome of breast cancer (BC) patients treated with adjuvant chemotherapy is affected by co-mutated TP53 and PIK3CA according to stromal tumor-infiltrating lymphocytes (TILs). Paraffin tumors of all clinical subtypes from 1661 patients with operable breast cancer who were treated within 4 adjuvant trials with anthracycline-taxanes chemotherapy were informative for TP53 and PIK3CA mutation status (semiconductor sequencing genotyping) and for stromal TILs density. Disease-free survival (DFS) was examined. TP53 mutations were associated with higher (p < 0.001) and PIK3CA with lower (p = 0.004) TILs in an ER /PgR-specific manner (p < 0.001). Mutations did not affect the favorable DFS of patients with lymphocyte-predominant (LP) BC. Within non-LPBC, PIK3CA-only mutations conferred best, while TP53-PIK3CA co-mutations (6 % of all tumors) conferred worst DFS (HR 0.59; 95 % CI 0.44-0.79; p = 0.001 for PIK3CA-only). TP53-only mutations were unfavorable in patients with lower TILs, while patients with lower TILs performed worse if their tumors carried TP53-only mutations (interaction p = 0.046). Multivariate analysis revealed favorable PIK3CA-only mutations in non-LPBC (HR 0.64; 95 % CI 0.47-0.88; p = 0.007), and unfavorable TP53 mutations in ER/PgRpos/HER2neg (HR 1.55; 95 % CI 1.07-2.24; p = 0.021). Mutations did not interact with TILs in non-LP triple-negative and HER2-positive patients. TP53 and PIK3CA mutations appear to have diverse effects on the outcome of early BC patients, according to whether these genes are co-mutated or not, and for TP53 according to TILs density and ER/PgR-status. These findings need to be considered when evaluating the effect of these two most frequently mutated genes in the context of large clinical trials.
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Affiliation(s)
- Vassiliki Kotoula
- Department of Pathology, School of Health Sciences, School of Medicine, Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece. .,Faculty of Medicine, Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.
| | - Vasilios Karavasilis
- Department of Medical Oncology, Papageorgiou Hospital, Faculty of Medicine, School of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Flora Zagouri
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - George Kouvatseas
- Department of Biostatistics, Health Data Specialists Ltd, Athens, Greece
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.,The University of New South Wales, Kensington, NSW, Australia
| | - Helen Gogas
- First Department of Medicine, Laiko General Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Sotiris Lakis
- Faculty of Medicine, Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Mattheos Bobos
- Faculty of Medicine, Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Kyriaki Papadopoulou
- Faculty of Medicine, Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eleftheria Tsolaki
- Faculty of Medicine, Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitrios Pectasides
- Oncology Section, Second Department of Internal Medicine, Hippokration Hospital, Athens, Greece
| | - Georgios Lazaridis
- Department of Medical Oncology, Papageorgiou Hospital, Faculty of Medicine, School of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Angelos Koutras
- Division of Oncology, Department of Medicine, University Hospital, University of Patras Medical School, Patras, Greece
| | - Gerasimos Aravantinos
- Second Department of Medical Oncology, Agii Anargiri Cancer Hospital, Athens, Greece
| | | | | | - Christos Markopoulos
- Second Department of Prop. Surgery, Laiko General Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - George Zografos
- Breast Unit, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Christos Papandreou
- Department of Medical Oncology, University Hospital of Larissa, University of Thessaly School of Medicine, Larissa, Greece
| | - George Fountzilas
- Faculty of Medicine, Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.,Aristotle University of Thessaloniki, Thessaloniki, Greece
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13
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Papaxoinis G, Kotoula V, Alexopoulou Z, Kalogeras KT, Zagouri F, Timotheadou E, Gogas H, Pentheroudakis G, Christodoulou C, Koutras A, Bafaloukos D, Aravantinos G, Papakostas P, Charalambous E, Papadopoulou K, Varthalitis I, Efstratiou I, Zaramboukas T, Patsea H, Scopa CD, Skondra M, Kosmidis P, Pectasides D, Fountzilas G. Significance of PIK3CA Mutations in Patients with Early Breast Cancer Treated with Adjuvant Chemotherapy: A Hellenic Cooperative Oncology Group (HeCOG) Study. PLoS One 2015; 10:e0140293. [PMID: 26452060 PMCID: PMC4599795 DOI: 10.1371/journal.pone.0140293] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 09/23/2015] [Indexed: 11/28/2022] Open
Abstract
Background The PI3K-AKT pathway is frequently activated in breast cancer. PIK3CA mutations are most frequently found in the helical (exon 9) and kinase (exon 20) domains of this protein. The aim of the present study was to examine the role of different types of PIK3CA mutations in combination with molecular biomarkers related to PI3K-AKT signaling in patients with early breast cancer. Methods Tumor tissue samples from 1008 early breast cancer patients treated with adjuvant chemotherapy in two similar randomized trials of HeCOG were examined. Tumors were subtyped with immunohistochemistry (IHC) and FISH for ER, PgR, Ki67, HER2 and androgen receptor (AR). PIK3CA mutations were analyzed by Sanger sequencing (exon 20) and qPCR (exon 9) (Sanger/qPCR mutations). In 610 cases, next generation sequencing (NGS) PIK3CA mutation data were also available. PIK3CA mutations and PTEN protein expression (IHC) were analyzed in luminal tumors (ER and/or PgR positive), molecular apocrine carcinomas (MAC; ER/PgR negative / AR positive) and hormone receptor (ER/PgR/AR) negative tumors. Results PIK3CA mutations were detected in 235/1008 tumors (23%) with Sanger/qPCR and in 149/610 tumors (24%) with NGS. Concordance between the two methods was good with a Kappa coefficient of 0.76 (95% CI 0.69–0.82). Lobular histology, low tumor grade and luminal A tumors were associated with helical domain mutations (PIK3CAhel), while luminal B with kinase domain mutations (PIK3CAkin). The overall incidence of PIK3CA mutations was higher in luminal as compared to MAC and hormone receptor negative tumors (p = 0.004). Disease-free and overall survival did not significantly differ with respect to PIK3CA mutation presence and type. However, a statistically significant interaction between PIK3CA mutation status and PTEN low protein expression with regard to prognosis was identified. Conclusions The present study did not show any prognostic significance of specific PIK3CA mutations in a large group of predominantly lymph-node positive breast cancer women treated with adjuvant chemotherapy. Further analyses in larger cohorts are warranted to investigate possible differential effect of distinct PIK3CA mutations in small subgroups of patients.
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Affiliation(s)
- George Papaxoinis
- Oncology Section, Second Department of Internal Medicine, “Hippokration” Hospital, Athens, Greece
- * E-mail:
| | - Vassiliki Kotoula
- Department of Pathology, Aristotle University of Thessaloniki, Faculty of Medicine, Thessaloniki, Greece
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki, Faculty of Medicine, Thessaloniki, Greece
| | - Zoi Alexopoulou
- Health Data Specialists Ltd, Dept of Biostatistics, Athens, Greece
| | - Konstantine T. Kalogeras
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki, Faculty of Medicine, Thessaloniki, Greece
- Translational Research Section, Hellenic Cooperative Oncology Group, Data Office, Athens, Greece
| | - Flora Zagouri
- Department of Clinical Therapeutics, “Alexandra” Hospital, University of Athens School of Medicine, Athens, Greece
| | - Eleni Timotheadou
- Department of Medical Oncology, “Papageorgiou” Hospital, Aristotle University of Thessaloniki, Faculty of Medicine, Thessaloniki, Greece
| | - Helen Gogas
- First Department of Medicine, “Laiko” General Hospital, University of Athens School of Medicine, Athens, Greece
| | | | | | - Angelos Koutras
- Division of Oncology, Department of Medicine, University Hospital, University of Patras Medical School, Patras, Greece
| | | | - Gerasimos Aravantinos
- Second Department of Medical Oncology, “Agii Anargiri” Cancer Hospital, Athens, Greece
| | | | - Elpida Charalambous
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki, Faculty of Medicine, Thessaloniki, Greece
| | - Kyriaki Papadopoulou
- Department of Pathology, Aristotle University of Thessaloniki, Faculty of Medicine, Thessaloniki, Greece
| | | | | | - Thomas Zaramboukas
- Department of Pathology, Aristotle University of Thessaloniki, Faculty of Medicine, Thessaloniki, Greece
| | - Helen Patsea
- Department of Pathology, IASSO General Hospital, Athens, Greece
| | - Chrisoula D. Scopa
- Department of Pathology, University Hospital, University of Patras Medical School, Patras, Greece
| | - Maria Skondra
- Oncology Section, Second Department of Internal Medicine, “Hippokration” Hospital, Athens, Greece
| | - Paris Kosmidis
- Second Department of Medical Oncology, Hygeia Hospital, Athens, Greece
| | - Dimitrios Pectasides
- Oncology Section, Second Department of Internal Medicine, “Hippokration” Hospital, Athens, Greece
| | - George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research, Aristotle University of Thessaloniki, Faculty of Medicine, Thessaloniki, Greece
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