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Hou TC, Wu PS, Huang WY, Yang YT, Tan KT, Liu SH, Chen YJ, Chen SJ, Su YW. Over expression of CDK4 and MDM2 in a patient with recurrent ALK-negative mediastinal inflammatory myofibroblastic tumor: A case report. Medicine (Baltimore) 2020; 99:e19577. [PMID: 32195970 PMCID: PMC7220190 DOI: 10.1097/md.0000000000019577] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
RATIONALE The diagnosis of anaplastic lymphoma kinase (ALK)-negative inflammatory myofibroblastic tumors (IMT) remains challenging because of their morphological resemblance with spindle cell sarcoma with myofibroblastic characteristics. PATIENT CONCERNS A 69-year-old female patient presented with loco-regional recurrent IMT several times within 8 years after primary treatment and neck lymph node metastasis 3.5 years after last recurrence. DIAGNOSIS The primary, recurrence, and lymph node metastasis lesions were diagnosed as ALK-negative IMTs based on the histopathological features. INTERVENTIONS Biopsy samples were obtained during repeated surgeries and evaluated for genomic alterations during first and recurrent presentations. The evaluation was done using pathway-driven massive parallel sequencing, and genomic alterations between primary and recurrent tumors were compared. OUTCOMES Copy number gains and overexpression of mouse double minute 2 homolog (MDM2) and cyclin dependent kinase 4 (CDK4) were observed in the primary lesion, and additional gene amplification of Discoidin Domain Receptor Tyrosine Kinase 2 (DDR2), Succinate Dehydrogenase Complex II subunit C (SDHC), and thyroid stimulating hormone receptor (TSHR) Q720H were found in the recurrent tumors. Metastases to the neck lymph node were observed 3.5 years after recurrence. LESSONS Our results indicated genetic evolution in a microscopically benign condition and highlighted the importance of molecular characterization of fibro-inflammatory lesions of uncertain malignant potential.
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Affiliation(s)
| | | | - Wen-Yu Huang
- Laboratory of Good Clinical Research Center, Mackay Memorial Hospital, Tamsui Branch, New Taipei City
| | | | | | | | | | | | - Ying-Wen Su
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Mackay Memorial Hospital, Taipei, Taiwan
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Derouault P, Chauzeix J, Rizzo D, Miressi F, Magdelaine C, Bourthoumieu S, Durand K, Dzugan H, Feuillard J, Sturtz F, Mérillou S, Lia AS. CovCopCan: An efficient tool to detect Copy Number Variation from amplicon sequencing data in inherited diseases and cancer. PLoS Comput Biol 2020; 16:e1007503. [PMID: 32049956 PMCID: PMC7041855 DOI: 10.1371/journal.pcbi.1007503] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 02/25/2020] [Accepted: 10/23/2019] [Indexed: 02/07/2023] Open
Abstract
Molecular diagnosis is an essential step of patient care. An increasing number of Copy Number Variations (CNVs) have been identified that are involved in inherited and somatic diseases. However, there are few existing tools to identify them among amplicon sequencing data generated by Next Generation Sequencing (NGS). We present here a new tool, CovCopCan, that allows the rapid and easy detection of CNVs in inherited diseases, as well as somatic data of patients with cancer, even with a low ratio of cancer cells to healthy cells. This tool could be very useful for molecular geneticists to rapidly identify CNVs in an interactive and user-friendly way.
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Affiliation(s)
| | - Jasmine Chauzeix
- CHU Limoges, Service Hématologie Biologique, Limoges, France
- Univ. Limoges, UMR CNRS 7276 CRIBL, Limoges, France
| | - David Rizzo
- CHU Limoges, Service Hématologie Biologique, Limoges, France
- Univ. Limoges, UMR CNRS 7276 CRIBL, Limoges, France
| | | | - Corinne Magdelaine
- Univ. Limoges, MMNP, EA 6309, Limoges, France
- CHU Limoges, Service Biochimie et Génétique Moléculaire, Limoges France
| | - Sylvie Bourthoumieu
- Univ. Limoges, MMNP, EA 6309, Limoges, France
- CHU Limoges, Service de Cytogénétique, Limoges, France
| | - Karine Durand
- CHU Limoges, Service Anatomie Pathologie, Limoges, France
- Univ. Limoges, EA CAPTur, Limoges, France
| | - Hélène Dzugan
- Univ. Limoges, MMNP, EA 6309, Limoges, France
- CHU Limoges, Service Biochimie et Génétique Moléculaire, Limoges France
| | - Jean Feuillard
- CHU Limoges, Service Hématologie Biologique, Limoges, France
- Univ. Limoges, UMR CNRS 7276 CRIBL, Limoges, France
| | - Franck Sturtz
- Univ. Limoges, MMNP, EA 6309, Limoges, France
- CHU Limoges, Service Biochimie et Génétique Moléculaire, Limoges France
| | | | - Anne-Sophie Lia
- CHU Limoges, UF de Bioinformatique, Limoges France
- Univ. Limoges, MMNP, EA 6309, Limoges, France
- CHU Limoges, Service Biochimie et Génétique Moléculaire, Limoges France
- * E-mail:
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53
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Olbryt M, Pigłowski W, Rajczykowski M, Pfeifer A, Student S, Fiszer-Kierzkowska A. Genetic Profiling of Advanced Melanoma: Candidate Mutations for Predicting Sensitivity and Resistance to Targeted Therapy. Target Oncol 2020; 15:101-113. [PMID: 31980996 PMCID: PMC7028806 DOI: 10.1007/s11523-020-00695-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BACKGROUND Molecularly targeted therapy has revolutionized the treatment of advanced melanoma. However, despite its high efficiency, a majority of patients experience relapse within 1 year of treatment because of acquired resistance, and approximately 10-25% patients gain no benefit from these agents owing to intrinsic resistance. This is mainly caused by the genetic heterogeneity of melanoma cells. OBJECTIVE We aimed to validate the predictive significance of selected genes in advanced melanoma patients before treatment with BRAF/MEK inhibitors. PATIENTS AND METHODS Archival DNA derived from 37 formalin-fixed paraffin-embedded pre-treatment advanced melanoma samples of patients treated with targeted therapy was used for next-generation sequencing analysis using the Ion Torrent platform. The AmpliSeq Custom Panel comprised coding sequences or hot spots of 23 melanoma genes: ATM, BRAF, CDK4, CDKN2A, CTNNB1, EGFR, HOXD8, HRAS, IDH1, KIT, KRAS, MAP3K8, MAP2K1, MAP2K2, MITF, MYC, NF1, NRAS, PAX5, PIK3R1, PTEN, RAC1, and RB1. The sequences were evaluated for genomic alterations and further validated using Sanger sequencing. RESULTS Our analysis revealed non-BRAF genetic alterations in 28 out of 37 samples (75.7%). Genetic changes were identified in PTEN, CDK4, CDKN2A, CTNNB1, EGFR, HOXD8, HRAS, KIT, MAP2K1, MAP2K2, MITF, MYC, NF1, PAX5, RAC1, and RB1. Fifteen known pathogenic mutations (single nucleotide variants or indels) and 11 variants of unknown significance were detected. Statistical analysis revealed an association between the presence of pathogenic mutations and time to progression during treatment with combination therapy. CONCLUSIONS Pathogenic mutations identified by gene panel sequencing have potential predictive value for targeted therapy of melanoma and are worth further validation in a larger series of cases. The role of some known mutations (e.g. CDK4R24, PTEN c.801 + 1G > A, CTNNB1S45F) as well as variants of unknown significance identified in this study (e.g. MITFR316K, KITG498S) in the generation of resistance to BRAF/MEK inhibitors should be further investigated.
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Affiliation(s)
- Magdalena Olbryt
- Center for Translational Research and Molecular Biology of Cancer, Maria Sklodowska-Curie Institute, Oncology Center Gliwice Branch, Wybrzeze Armii Krajowej 15, Gliwice, Poland.
| | - Wojciech Pigłowski
- Center for Translational Research and Molecular Biology of Cancer, Maria Sklodowska-Curie Institute, Oncology Center Gliwice Branch, Wybrzeze Armii Krajowej 15, Gliwice, Poland
- Tumor Pathology Department, Maria Sklodowska-Curie Institute, Oncology Center Gliwice Branch, Gliwice, Poland
| | - Marcin Rajczykowski
- II Clinic of Radiotherapy and Chemotherapy, Maria Sklodowska-Curie Institute, Oncology Center Gliwice Branch, Gliwice, Poland
| | - Aleksandra Pfeifer
- Department of Nuclear Medicine and Endocrine Oncology, Maria Sklodowska-Curie Institute, Oncology Center Gliwice Branch, Gliwice, Poland
| | - Sebastian Student
- Department of Systems Biology and Engineering, Silesian University of Technology, Akademicka 16, Gliwice, Poland
- Biotechnology Centre, Silesian University of Technology, Krzywoustego 8, Gliwice, Poland
| | - Anna Fiszer-Kierzkowska
- Center for Translational Research and Molecular Biology of Cancer, Maria Sklodowska-Curie Institute, Oncology Center Gliwice Branch, Wybrzeze Armii Krajowej 15, Gliwice, Poland
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Tan TZ, Ye J, Yee CV, Lim D, Ngoi NYL, Tan DSP, Huang RYJ. Analysis of gene expression signatures identifies prognostic and functionally distinct ovarian clear cell carcinoma subtypes. EBioMedicine 2019; 50:203-210. [PMID: 31761620 PMCID: PMC6921362 DOI: 10.1016/j.ebiom.2019.11.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 11/06/2019] [Accepted: 11/08/2019] [Indexed: 12/17/2022] Open
Abstract
Background Ovarian clear cell carcinoma (OCCC) is a histological subtype of epithelial ovarian cancer (EOC) with distinct pathological, biological, and molecular features. OCCCs are more resistant to conventional treatment regimen of EOC and have the worst stage-adjusted prognosis amongst EOC subtypes. As the OCCC incidence rate in Asian populations has significantly increased in recent decades, it is critical to elucidate its molecular features that could lead to OCCC-tailored therapeutic strategies. Methods Gene expression profiles of 222 OCCC were analyzed by hierarchical clustering and statistical analyses. Findings We identified two OCCC gene expression subtypes: EpiCC—epithelial-like, which is associated with early-stage disease, with a relatively higher rate of gene mutations in the SWI/SNF complex; and MesCC—mesenchymal-like, associated with late-stage and higher enrichment of immune-related pathway activity. Genetic, copy number and transcriptomic analyses showed that both EpiCC and MesCC carried OCCC-associated aberrations. The EpiCC/MesCC classification was reproducible in validation cohorts and OCCC cell lines. MesCC tumors had a poorer progression-free survival (PFS) than EpiCC tumors (HR: 3·0, p = 0·0006). Functional assays in cell lines showed that the MesCC subtype was more proliferative and more anoikis-resistant than the EpiCC. By applying the EpiCC/MesCC classification to the TCGA renal clear cell carcinoma cohort, our results indicated interoperability of the subtyping scheme, and revealed preferential drug response of MesCC to bevacizumab. Interpretation The EpiCC/MesCC classification shows promise for prognostic and therapeutic stratification in OCCC patients and warrants further investigation in the context of OCCC gene expression subtype-tailored treatment strategies.
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Affiliation(s)
- Tuan Zea Tan
- Center for Translational Medicine, Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, #12-01, Singapore 117599, Singapore
| | - Jieru Ye
- School of Medicine, College of Medicine, National Taiwan University, No. 1 Ren Ai Road Sec. 1, Taipei 100, Taiwan
| | - Chung Vin Yee
- Center for Translational Medicine, Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, #12-01, Singapore 117599, Singapore
| | - Diana Lim
- Department of Pathology, National University Health System, 1E Kent Ridge Road Singapore 119228, Singapore
| | - Natalie Yan Li Ngoi
- Department of Haematology-Oncology, National University Cancer Institute Singapore, Level 7 NUHS Tower Block, 1E Lower Kent Ridge Road, Singapore 119228, Singapore
| | - David Shao Peng Tan
- Center for Translational Medicine, Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, #12-01, Singapore 117599, Singapore; Department of Haematology-Oncology, National University Cancer Institute Singapore, Level 7 NUHS Tower Block, 1E Lower Kent Ridge Road, Singapore 119228, Singapore; Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore. 1E Kent Ridge Road, NUHS Tower Block, Level 10, Singapore 119228, Singapore
| | - Ruby Yun-Ju Huang
- Center for Translational Medicine, Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, #12-01, Singapore 117599, Singapore; School of Medicine, College of Medicine, National Taiwan University, No. 1 Ren Ai Road Sec. 1, Taipei 100, Taiwan.
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55
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Sheen Y, Tan K, Tse K, Liao Y, Lin M, Chen J, Liau J, Tseng Y, Lee C, Hong C, Liao J, Chang H, Chu C. Genetic alterations in primary melanoma in Taiwan. Br J Dermatol 2019; 182:1205-1213. [DOI: 10.1111/bjd.18425] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2019] [Indexed: 12/27/2022]
Affiliation(s)
- Y.‐S. Sheen
- Department of Dermatology National Taiwan University Hospital and National Taiwan University College of Medicine Taipei Taiwan
| | | | | | - Y.‐H. Liao
- Department of Dermatology National Taiwan University Hospital and National Taiwan University College of Medicine Taipei Taiwan
| | - M.‐H. Lin
- Graduate Institute of Clinical Medicine College of Medicine National Taiwan University Taipei Taiwan
- Department of Surgery National Taiwan University Hospital Hsin‐Chu Branch Hsin‐Chu Taiwan
| | - J.‐S. Chen
- Department of Dermatology National Taiwan University Hospital and National Taiwan University College of Medicine Taipei Taiwan
| | - J.‐Y. Liau
- Department of Pathology National Taiwan University Hospital and National Taiwan University College of Medicine Taipei Taiwan
| | - Y.‐J. Tseng
- Department of Dermatology Kaohsiung Chang Gung Memorial Hospital Kaohsiung Taiwan
| | - C.‐H. Lee
- Department of Dermatology Kaohsiung Chang Gung Memorial Hospital Kaohsiung Taiwan
- Department of Dermatology Chang Gung University College of Medicine Taoyuan Taiwan
| | - C.‐H. Hong
- Department of Dermatology Faculty of Medicine School of Medicine National Yang‐Ming University Taipei Taiwan
- Department of Dermatology Kaohsiung Veterans General Hospital Kaohsiung Taiwan
| | - J.‐B. Liao
- Department of Pathology and Laboratory Medicine Kaohsiung Veterans General Hospital Kaohsiung Taiwan
| | - H.‐T. Chang
- Department of Surgery Kaohsiung Municipal United Hospital Kaohsiung Taiwan
- College of Management National Sun Yet‐sen University Kaohsiung Taiwan
| | - C.‐Y. Chu
- Department of Dermatology National Taiwan University Hospital and National Taiwan University College of Medicine Taipei Taiwan
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56
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Simbolo M, Barbi S, Fassan M, Mafficini A, Ali G, Vicentini C, Sperandio N, Corbo V, Rusev B, Mastracci L, Grillo F, Pilotto S, Pelosi G, Pelliccioni S, Lawlor RT, Tortora G, Fontanini G, Volante M, Scarpa A, Bria E. Gene Expression Profiling of Lung Atypical Carcinoids and Large Cell Neuroendocrine Carcinomas Identifies Three Transcriptomic Subtypes with Specific Genomic Alterations. J Thorac Oncol 2019; 14:1651-1661. [PMID: 31085341 DOI: 10.1016/j.jtho.2019.05.003] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/25/2019] [Accepted: 05/06/2019] [Indexed: 12/12/2022]
Abstract
INTRODUCTION DNA mutational profiling showed that atypical carcinoids (ACs) share alterations with large cell neuroendocrine carcinomas (LCNECs). Transcriptomic studies suggested that LCNECs are composed of two subtypes, one of which shares molecular anomalies with SCLC. The missing piece of information is the transcriptomic relationship between ACs and LCNECs, as a direct comparison is lacking in the literature. METHODS Transcriptomic and genomic alterations were investigated by next-generation sequencing in a discovery set of 14 ACs and 14 LCNECs and validated on 21 ACs and 18 LCNECs by using custom gene panels and immunohistochemistry for Men1 and Rb1. RESULTS A 58-gene signature distinguished three transcriptional clusters. Cluster 1 comprised 20 LCNECs and one AC harboring concurrent inactivation of tumor protein p53 gene (TP53) and retinoblastoma 1 gene (RB1) in the absence of menin 1 gene (MEN1) mutations; all cases lacked Rb1 nuclear immunostaining. Cluster 3 included 20 ACs and four LCNECs lacking RB1 alterations and having frequent MEN1 (37.5%) and TP53 mutations (16.7%); menin nuclear immunostaining was lost in 75% of cases. Cluster 2 included 14 ACs and eight LCNECs showing intermediate features: TP53, 40.9%; MEN1, 22.7%; and RB1, 18.2%. Patients in cluster C1 had a shorter cancer-specific survival than did patients in C2 or C3. CONCLUSIONS ACs and LCNECs comprise three different and clinically relevant molecular diseases, one AC-enriched group in which MEN1 inactivation plays a major role, one LCNEC-enriched group whose hallmark is RB1 inactivation, and one mixed group with intermediate molecular features. These data support a progression of malignancy that may be traced by using combined molecular and immunohistochemical analysis.
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Affiliation(s)
- Michele Simbolo
- Department of Diagnostics and Public Health, Section of Anatomical Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Stefano Barbi
- Department of Diagnostics and Public Health, Section of Anatomical Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Matteo Fassan
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Andrea Mafficini
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Greta Ali
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, AOU Pisana, Pisa, Italy
| | - Caterina Vicentini
- Department of Diagnostics and Public Health, Section of Anatomical Pathology, University and Hospital Trust of Verona, Verona, Italy; ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Nicola Sperandio
- Department of Diagnostics and Public Health, Section of Anatomical Pathology, University and Hospital Trust of Verona, Verona, Italy; ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Vincenzo Corbo
- Department of Diagnostics and Public Health, Section of Anatomical Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Borislav Rusev
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Luca Mastracci
- Department of Surgical and Diagnostic Sciences, University of Genoa and IRCCS S. Martino-IST University Hospital, Genoa, Italy
| | - Federica Grillo
- Department of Surgical and Diagnostic Sciences, University of Genoa and IRCCS S. Martino-IST University Hospital, Genoa, Italy
| | - Sara Pilotto
- Department of Medicine, Section of Medical Oncology, University and Hospital Trust of Verona, Verona, Italy
| | - Giuseppe Pelosi
- Department of Oncology and Hemato-Oncology, University of Milan, and Inter-Hospital Pathology Division, IRCCS MultiMedica, Milan, Italy
| | - Serena Pelliccioni
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, AOU Pisana, Pisa, Italy
| | - Rita T Lawlor
- ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy
| | - Giampaolo Tortora
- Department of Medicine, Section of Medical Oncology, University and Hospital Trust of Verona, Verona, Italy; Comprehensive Cancer Center, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy; Sacred Hearth Catholic University, Rome, Italy
| | - Gabriella Fontanini
- Department of Surgical, Medical, Molecular Pathology and Critical Area, University of Pisa, AOU Pisana, Pisa, Italy
| | - Marco Volante
- Department of Oncology, University of Turin at San Luigi Hospital, Orbassano, Turin, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Anatomical Pathology, University and Hospital Trust of Verona, Verona, Italy; ARC-Net Research Centre, University and Hospital Trust of Verona, Verona, Italy.
| | - Emilio Bria
- Comprehensive Cancer Center, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy; Sacred Hearth Catholic University, Rome, Italy
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Barresi V, Simbolo M, Mafficini A, Piredda ML, Caffo M, Cardali SM, Germanò A, Cingarlini S, Ghimenton C, Scarpa A. Ultra-Mutation in IDH Wild-Type Glioblastomas of Patients Younger than 55 Years is Associated with Defective Mismatch Repair, Microsatellite Instability, and Giant Cell Enrichment. Cancers (Basel) 2019; 11:cancers11091279. [PMID: 31480372 PMCID: PMC6770353 DOI: 10.3390/cancers11091279] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 08/27/2019] [Accepted: 08/27/2019] [Indexed: 12/16/2022] Open
Abstract
Background: Glioblastomas (GBMs) are classified into isocitrate dehydrogenase (IDH) mutants and IDH wild-types (IDH-wt). This study aimed at identifying the mutational assets of IDH-wt GBMs in patients aged 18–54 years for which limited data are available. Methods: Sixteen IDH-wt GBMs from adults < 55 years old were explored for mutations, copy number variations, tumour mutational load (TML), and mutational spectrum by a 409 genes TML panel. Results: Eight (50%) IDH-wt GBMs were hypermutated (TML > 9 mutations/Mb) and two (12.5%) were ultra-mutated (TML > 100 mutations/Mb). One ultra-mutated GBM had microsatellite instability (MSI), a somatic MSH6 mutation, and a germline POLE mutation. The other ultra-mutated GBMs had MSI and two somatic mutations in MSH2. Both ultra-mutated GBMs featured at least 25% giant cells. The overall survival of eight patients with hypermutated GBMs was significantly longer than that of patients with non-hypermutated GBMs (p = 0.04). Conclusions: We identified a hyper-mutated subgroup among IDH-wt GBMs in adults < 55 years that had improved prognosis. Two cases were ultra-mutated and characterized by the presence of at least 25% giant cells, MMR mutations, and MSI. Since high TML has been associated with response to immune checkpoint inhibition in paediatric gliomas, the identification of a subtype of ultra-mutated IDH-wt GBM may have implications for immunotherapy.
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Affiliation(s)
- Valeria Barresi
- Department of Diagnostics and Public Health, Section of Anatomical Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy.
| | - Michele Simbolo
- Department of Diagnostics and Public Health, Section of Anatomical Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Andrea Mafficini
- ARC-Net Research Centre, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Maria Liliana Piredda
- Department of Diagnostics and Public Health, Section of Anatomical Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy
| | - Maria Caffo
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Section of Neurosurgery, University of Messina, 98125 Messina, Italy
| | - Salvatore Massimiliano Cardali
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Section of Neurosurgery, University of Messina, 98125 Messina, Italy
| | - Antonino Germanò
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, Section of Neurosurgery, University of Messina, 98125 Messina, Italy
| | - Sara Cingarlini
- Department of Medicine, Section of Medical Oncology, University and Hospital Trust Verona, 37134 Verona, Italy
| | - Claudio Ghimenton
- Department of Pathology and Diagnostics, Section of Pathology, Hospital Trust Verona, 37134 Verona, Italy
| | - Aldo Scarpa
- Department of Diagnostics and Public Health, Section of Anatomical Pathology, University and Hospital Trust of Verona, 37134 Verona, Italy
- ARC-Net Research Centre, University and Hospital Trust of Verona, 37134 Verona, Italy
- Department of Pathology and Diagnostics, Section of Pathology, Hospital Trust Verona, 37134 Verona, Italy
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58
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Datta KK, Patil S, Patel K, Babu N, Raja R, Nanjappa V, Mangalaparthi KK, Dhaka B, Rajagopalan P, Deolankar SC, Kannan R, Kumar P, Prasad TSK, Mathur PP, Kumari A, Manoharan M, Coral K, Murugan S, Sidransky D, Gupta R, Gupta R, Khanna-Gupta A, Chatterjee A, Gowda H. Chronic Exposure to Chewing Tobacco Induces Metabolic Reprogramming and Cancer Stem Cell-Like Properties in Esophageal Epithelial Cells. Cells 2019; 8:cells8090949. [PMID: 31438645 PMCID: PMC6770059 DOI: 10.3390/cells8090949] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/10/2019] [Accepted: 08/17/2019] [Indexed: 12/14/2022] Open
Abstract
Tobacco in its smoke and smokeless form are major risk factors for esophageal squamous cell carcinoma (ESCC). However, molecular alterations associated with smokeless tobacco exposure are poorly understood. In the Indian subcontinent, tobacco is predominantly consumed in chewing form. An understanding of molecular alterations associated with chewing tobacco exposure is vital for identifying molecular markers and potential targets. We developed an in vitro cellular model by exposing non-transformed esophageal epithelial cells to chewing tobacco over an eight-month period. Chronic exposure to chewing tobacco led to increase in cell proliferation, invasive ability and anchorage independent growth, indicating cell transformation. Molecular alterations associated with chewing tobacco exposure were characterized by carrying out exome sequencing and quantitative proteomic profiling of parental cells and chewing tobacco exposed cells. Quantitative proteomic analysis revealed increased expression of cancer stem cell markers in tobacco treated cells. In addition, tobacco exposed cells showed the Oxidative Phosphorylation (OXPHOS) phenotype with decreased expression of enzymes associated with glycolytic pathway and increased expression of a large number of mitochondrial proteins involved in electron transport chain as well as enzymes of the tricarboxylic acid (TCA) cycle. Electron micrographs revealed increase in number and size of mitochondria. Based on these observations, we propose that chronic exposure of esophageal epithelial cells to tobacco leads to cancer stem cell-like phenotype. These cells show the characteristic OXPHOS phenotype, which can be potentially targeted as a therapeutic strategy.
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Affiliation(s)
- Keshava K Datta
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
| | - Shankargouda Patil
- Department of Maxillofacial Surgery and Diagnostic Sciences, Division of Oral Pathology, College of Dentistry, Jazan University, Jazan 45142, Saudi Arabia
- Department of Medical Biotechnologies, School of Dental Medicine, University of Siena, 53100 Siena, Italy
| | - Krishna Patel
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India
| | - Niraj Babu
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
- Manipal Academy of Higher Education (MAHE), Madhav Nagar, Manipal 576104, India
| | - Remya Raja
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
| | | | - Kiran Kumar Mangalaparthi
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Kollam 690525, India
| | - Bharti Dhaka
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
| | | | - Sayali Chandrashekhar Deolankar
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore 575018, India
- National Institute of Mental Health and Neuro Sciences (NIMHANS), Hosur Road, Bangalore 560029, India
| | - Ramakrishnan Kannan
- National Institute of Mental Health and Neuro Sciences (NIMHANS), Hosur Road, Bangalore 560029, India
| | - Prashant Kumar
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India
| | - T S Keshava Prasad
- Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Premendu P Mathur
- School of Biotechnology, KIIT (Deemed to be University), Bhubaneswar 751024, India
- Department of Biochemistry and Molecular Biology, School of Life Sciences, Pondicherry University, Pondicherry 605014, India
| | | | | | | | | | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Ravi Gupta
- Medgenome Labs Pvt. Ltd., Bangalore 560099, India
| | - Rohit Gupta
- Medgenome Labs Pvt. Ltd., Bangalore 560099, India
| | | | - Aditi Chatterjee
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India.
- Manipal Academy of Higher Education (MAHE), Madhav Nagar, Manipal 576104, India.
| | - Harsha Gowda
- Institute of Bioinformatics, International Tech Park, Bangalore 560066, India.
- Manipal Academy of Higher Education (MAHE), Madhav Nagar, Manipal 576104, India.
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59
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Chang SC, Lai YC, Chang CY, Huang LK, Chen SJ, Tan KT, Yu PN, Lai JI. Concomitant Genetic Alterations are Associated with Worse Clinical Outcome in EGFR Mutant NSCLC Patients Treated with Tyrosine Kinase Inhibitors. Transl Oncol 2019; 12:1425-1431. [PMID: 31401335 PMCID: PMC6700434 DOI: 10.1016/j.tranon.2019.07.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/08/2019] [Accepted: 07/10/2019] [Indexed: 01/17/2023] Open
Abstract
Epidermal growth factor receptor- tyrosine kinase inhibitors (EGFR-TKI) are recommended first-line therapy for advanced non-small cell lung cancer (NSCLC) with sensitizing EGFR mutations. It is of clinical interest to identify concurrent genetic mutations in NSCLC patients with EGFR mutations in the hopes of discovering predictive biomarkers towards EGFR-TKI treatment. We retrospectively analyzed a cohort of patients with advanced EGFR mutant NSCLC who underwent treatment with first generation TKIs at our hospital by a multi-gene panel via next generation sequencing. A total of 33 patients with mutant EGFR were enrolled. Up to 26 (78.8%) patients had at least one concomitant genetic alteration coexisting with mutant EGFR. Among the concomitant genetic alterations discovered, TP53 mutation was most common (n = 10,30.3%), followed by CDK4 (n = 8, 24.2%) and CDKN2A (n = 7, 21.2%)copy number variation (CNV). Progression-free survival was shorter in patients with concomitant FGFR3 mutation (1.6 vs. 12.6 months, P = .003) and CDKN2A CNV loss (6.5 vs. 13.4months, P = .019). Patients with any concomitant genetic alterations also had significant worse overall survival (24.1 vs. 40.8 months, P = .029). In summary, our study revealed an unfavorable association between concomitant genetic mutations and treatment response towards EGFR-TKI. FGFR3 mutation and CDKN2A CNV loss may be potential predictive markers for treatment outcome and warrant further investigation.
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Affiliation(s)
- Shih-Chieh Chang
- Division of Chest Medicine, Department of Internal Medicine, National Yang-Ming, University Hospital, Yi-Lan, Taiwan; Department of Critical Care Medicine, National Yang-Ming University Hospital, Yi-Lan, Taiwan
| | - Yi-Chun Lai
- Division of Chest Medicine, Department of Internal Medicine, National Yang-Ming, University Hospital, Yi-Lan, Taiwan
| | - Cheng-Yu Chang
- Division of Chest Medicine, Department of Internal Medicine, Far Eastern Memorial Hospital, New Taipei City, Taiwan
| | - Li-Kuo Huang
- Department of Radiology, National Yang-Ming University Hospital, Yi-Lan, Taiwan
| | | | | | | | - Jiun-I Lai
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan; Division of Medical Oncology, Department of Oncology, Taipei Veterans General, Hospital, Taipei, Taiwan.
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60
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Liao Y, Ma Z, Zhang Y, Li D, Lv D, Chen Z, Li P, Ai-Dherasi A, Zheng F, Tian J, Zou K, Wang Y, Wang D, Cordova M, Zhou H, Li X, Liu D, Yu R, Zhang Q, Zhang X, Zhang J, Zhang X, Zhang X, Li Y, Shao Y, Song L, Liu R, Wang Y, Sufiyan S, Liu Q, Owen GI, Li Z, Chen J. Targeted deep sequencing from multiple sources demonstrates increased NOTCH1 alterations in lung cancer patient plasma. Cancer Med 2019; 8:5673-5686. [PMID: 31369215 PMCID: PMC6745866 DOI: 10.1002/cam4.2458] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 07/13/2019] [Accepted: 07/18/2019] [Indexed: 12/19/2022] Open
Abstract
Introduction Targeted therapies are based on specific gene alterations. Various specimen types have been used to determine gene alterations, however, no systemic comparisons have yet been made. Herein, we assessed alterations in selected cancer‐associated genes across varying sample sites in lung cancer patients. Materials and Methods Targeted deep sequencing for 48 tumor‐related genes was applied to 153 samples from 55 lung cancer patients obtained from six sources: Formalin‐fixed paraffin‐embedded (FFPE) tumor tissues, pleural effusion supernatant (PES) and pleural effusion cell sediments (PEC), white blood cells (WBCs), oral epithelial cells (OECs), and plasma. Results Mutations were detected in 96% (53/55) of the patients and in 83% (40/48) of the selected genes. Each sample type exhibited a characteristic mutational pattern. As anticipated, TP53 was the most affected sequence (54.5% patients), however this was followed by NOTCH1 (36%, across all sample types). EGFR was altered in patient samples at a frequency of 32.7% and KRAS 10.9%. This high EGFR/ low KRAS frequency is in accordance with other TCGA cohorts of Asian origin but differs from the Caucasian population where KRAS is the more dominant mutation. Additionally, 66% (31/47) of PEC samples had copy number variants (CNVs) in at least one gene. Unlike the concurrent loss and gain in most genes, herein NOTCH1 loss was identified in 21% patients, with no gain observed. Based on the relative prevalence of mutations and CNVs, we divided lung cancer patients into SNV‐dominated, CNV‐dominated, and codominated groups. Conclusions Our results confirm previous reports that EGFR mutations are more prevalent than KRAS in Chinese lung cancer patients. NOTCH1 gene alterations are more common than previously reported and reveals a role of NOTCH1 modifications in tumor metastasis. Furthermore, genetic material from malignant pleural effusion cell sediments may be a noninvasive manner to identify CNV and participate in treatment decisions.
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Affiliation(s)
- Yuwei Liao
- The Second Hospital of Dalian Medical University, Dalian, China.,Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Zhaokui Ma
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Yu Zhang
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Dan Li
- The Second Hospital of Dalian Medical University, Dalian, China
| | - Dekang Lv
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Zhisheng Chen
- The Second Hospital of Dalian Medical University, Dalian, China
| | - Peiying Li
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Aisha Ai-Dherasi
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Feng Zheng
- Advanced Institute for Medical Sciences, Dalian Medical University, Dalian, China
| | - Jichao Tian
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Kun Zou
- The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yue Wang
- The Second Hospital of Dalian Medical University, Dalian, China
| | - Dongxia Wang
- The Second Hospital of Dalian Medical University, Dalian, China
| | - Miguel Cordova
- Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Huan Zhou
- The Second Hospital of Dalian Medical University, Dalian, China
| | - Xiuhua Li
- The Second Hospital of Dalian Medical University, Dalian, China
| | - Dan Liu
- The Second Hospital of Dalian Medical University, Dalian, China
| | - Ruofei Yu
- The Second Hospital of Dalian Medical University, Dalian, China
| | - Qingzheng Zhang
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Xiaolong Zhang
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Jian Zhang
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Xuehong Zhang
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Xia Zhang
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Yulong Li
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Yanyan Shao
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Luyao Song
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Ruimei Liu
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Yichen Wang
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Sufiyan Sufiyan
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Quentin Liu
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China
| | - Gareth I Owen
- Faculty of Biological Sciences, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Zhiguang Li
- Center of Genome and Personalized Medicine, Institute of Cancer Stem Cell, Dalian Medical University, Dalian, China.,The Second Affiliated Hospital, School of Medicine, Zhengzhou University, Zhengzhou, China
| | - Jun Chen
- The Second Hospital of Dalian Medical University, Dalian, China
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61
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Chung AK, OuYang CN, Liu H, Chao M, Luo JD, Lee CY, Lu YJ, Chung IC, Chen LC, Wu SM, Tsang NM, Chang KP, Hsu CL, Li HP, Chang YS. Targeted sequencing of cancer-related genes in nasopharyngeal carcinoma identifies mutations in the TGF-β pathway. Cancer Med 2019; 8:5116-5127. [PMID: 31328403 PMCID: PMC6718742 DOI: 10.1002/cam4.2429] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/28/2019] [Accepted: 07/03/2019] [Indexed: 12/18/2022] Open
Abstract
Approximately, 25% of nasopharyngeal carcinoma (NPC) patients develop recurrent disease. NPC may involve relatively few genomic alterations compared to other cancers due to its association with Epstein‐Barr virus (EBV). We envisioned that in‐depth sequencing of tumor tissues might provide new insights into the genetic alterations of this cancer. Thirty‐three NPC paired tumor/adjacent normal or peripheral blood mononuclear cell samples were deep‐sequenced (>1000×) with respect to a panel of 409 cancer‐related genes. Newly identified mutations and its correlation with clinical outcomes were evaluated. Profiling of somatic mutations and copy number variations (CNV) in NPC tumors identified alterations in RTK/RAS/PI3K, NOTCH, DNA repair, chromatin remodeling, cell cycle, NF‐κB, and TGF‐β pathways. In addition, patients harbored CNV among 409 cancer‐related genes and missense mutations in TGF‐β/SMAD signaling were associated with poor overall survival and poor recurrence‐free survival, respectively. The CNV events were correlated with plasma EBV copies, while mutations in TGFBR2 and SMAD4 abrogate SMAD‐dependent TGF‐β signaling. Functional analysis revealed that the new TGFBR2 kinase domain mutants were incapable of transducing the signal, leading to failure of phosphorylation of SMAD2/3 and activation of downstream TGF‐β‐mediated cell growth arrest. This study provides evidence supporting CNV and dysregulated TGF‐β signaling contributes to exacerbating the NPC pathogenesis.
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Affiliation(s)
- An-Ko Chung
- Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan City, Taiwan, Republic of China
| | - Chun-Nan OuYang
- Molecular Medicine Research Center, Chang Gung University, Taoyuan City, Taiwan, Republic of China
| | - Hsuan Liu
- Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan City, Taiwan, Republic of China.,Molecular Medicine Research Center, Chang Gung University, Taoyuan City, Taiwan, Republic of China.,Department of Biochemistry, Chang Gung University, Taoyuan City, Taiwan, Republic of China.,Division of Colon and Rectal Surgery, Chang Gung Memorial Hospital, Taoyuan City, Taiwan, Republic of China
| | - Mei Chao
- Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan City, Taiwan, Republic of China.,Department of Microbiology and Immunology, Chang Gung University, Taoyuan City, Taiwan, Republic of China.,Liver Research Center, Department of Hepato-Gastroenterology, Chang Gung Memorial Hospital, Taoyuan City, Taiwan, Republic of China
| | - Ji-Dung Luo
- Molecular Medicine Research Center, Chang Gung University, Taoyuan City, Taiwan, Republic of China.,Bioinformatics Center, Chang Gung University, Taoyuan City, Taiwan, Republic of China
| | - Cheng-Yang Lee
- Research Information Session, Office of Information Technology, Taipei Medical University, Taipei City, Taiwan, Republic of China
| | - Yen-Jung Lu
- ACT Genomics, Co. Ltd., Taipei City, Taiwan, Republic of China
| | - I-Che Chung
- Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan City, Taiwan, Republic of China.,Molecular Medicine Research Center, Chang Gung University, Taoyuan City, Taiwan, Republic of China
| | - Lih-Chyang Chen
- Department of Medicine, Mackay Medical College, New Taipei City, Taiwan, Republic of China
| | - Shao-Min Wu
- Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan City, Taiwan, Republic of China
| | - Ngan-Ming Tsang
- Department of Radiation, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan City, Taiwan, Republic of China
| | - Kai-Ping Chang
- Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan City, Taiwan, Republic of China
| | - Cheng-Lung Hsu
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan City, Taiwan, Republic of China
| | - Hsin-Pai Li
- Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan City, Taiwan, Republic of China.,Molecular Medicine Research Center, Chang Gung University, Taoyuan City, Taiwan, Republic of China.,Department of Microbiology and Immunology, Chang Gung University, Taoyuan City, Taiwan, Republic of China.,Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan City, Taiwan, Republic of China
| | - Yu-Sun Chang
- Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan City, Taiwan, Republic of China.,Molecular Medicine Research Center, Chang Gung University, Taoyuan City, Taiwan, Republic of China.,Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan City, Taiwan, Republic of China
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62
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Nie D, Cao P, Wang F, Zhang J, Liu M, Zhang W, Liu L, Zhao H, Teng W, Tian W, Chen X, Zhang Y, Nan H, Wei Z, Wang T, Liu H. Analysis of overlapping heterozygous novel submicroscopic CNVs and FANCA-VPS9D1 fusion transcripts in a Fanconi anemia patient. J Hum Genet 2019; 64:899-909. [PMID: 31239491 DOI: 10.1038/s10038-019-0629-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 05/28/2019] [Accepted: 06/03/2019] [Indexed: 12/19/2022]
Abstract
Fanconi anemia (FA) is the most common inherited bone marrow failure syndrome with 22 FA-related genes identified to date. Fragment deletions are frequently occurring aberrances accounting for ~30% of pathogenic variants in them, especially in FANCA, most of which are the results of genomic rearrangement events mediated by the highly concentrated Alu elements interspersing in it. Owing to the capability to detect genome-wide copy number variations (CNVs) with the resolution of 400 kb or larger, cytogenomic microarray is the most widely used method in the clinic currently. However, thereis still a technical gap in the detection of CNVs ranging from hundreds of bp to hundreds of kb between microarray, Sanger sequencing, and direct targeted high-throughput sequencing (THS). Here, we report the analysis of overlapping heterozygous novel submicroscopic deletions of FANCA gene in a FA patient, and discuss the mechanism of the deletions and the formation of FANCA-VPS9D1 fusion transcripts. Our results support that both low-coverage whole-genome sequencing and bioinformatics analysis of THS data for submicroscopic CNVs surpass SNP array in efficacy and accuracy.
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Affiliation(s)
- Daijing Nie
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 065201, Langfang, China
| | - Panxiang Cao
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 065201, Langfang, China
| | - Fang Wang
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 065201, Langfang, China
| | - Jing Zhang
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 065201, Langfang, China
| | - Mingyue Liu
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 065201, Langfang, China
| | - Wei Zhang
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 065201, Langfang, China
| | - Lili Liu
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 065201, Langfang, China
| | - Huizheng Zhao
- Division of Pathology & Laboratory Medicine, Beijing Lu Daopei Hospital, 100176, Beijing, China
| | - Wen Teng
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 065201, Langfang, China
| | - Wenjun Tian
- Department of Clinical Laboratory Medicine, Shandong Provincial Hospital Affiliated to Shandong University, 250000, Jinan, China
| | - Xue Chen
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 065201, Langfang, China
| | - Yang Zhang
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 065201, Langfang, China
| | - Hua Nan
- Department of Hematology, Hebei Yanda Lu Daopei Hospital, 065201, Langfang, China
| | - Zhijie Wei
- Department of Hematology, Hebei Yanda Lu Daopei Hospital, 065201, Langfang, China
| | - Tong Wang
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 065201, Langfang, China
| | - Hongxing Liu
- Division of Pathology & Laboratory Medicine, Hebei Yanda Lu Daopei Hospital, 065201, Langfang, China. .,Division of Pathology & Laboratory Medicine, Beijing Lu Daopei Hospital, 100176, Beijing, China. .,Beijing Lu Daopei Hospital Institute of Hematology, 100176, Beijing, China.
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63
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Bellini A, Bessoltane-Bentahar N, Bhalshankar J, Clement N, Raynal V, Baulande S, Bernard V, Danzon A, Chicard M, Colmet-Daage L, Pierron G, Le Roux L, Planchon JM, Combaret V, Lapouble E, Corradini N, Thebaud E, Gambart M, Valteau-Couanet D, Michon J, Louis-Brennetot C, Janoueix-Lerosey I, Defachelles AS, Bourdeaut F, Delattre O, Schleiermacher G. Study of chromatin remodeling genes implicates SMARCA4 as a putative player in oncogenesis in neuroblastoma. Int J Cancer 2019; 145:2781-2791. [PMID: 31018240 PMCID: PMC6771805 DOI: 10.1002/ijc.32361] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 02/21/2019] [Accepted: 03/14/2019] [Indexed: 12/21/2022]
Abstract
In neuroblastoma (NB), genetic alterations in chromatin remodeling (CRGs) and epigenetic modifier genes (EMGs) have been described. We sought to determine their frequency and clinical impact. Whole exome (WES)/whole genome sequencing (WGS) data and targeted sequencing (TSCA®) of exonic regions of 33 CRGs/EMGs were analyzed in tumor samples from 283 NB patients, with constitutional material available for 55 patients. The frequency of CRG/EMG variations in NB cases was then compared to the Genome Aggregation Database (gnomAD). The sequencing revealed SNVs/small InDels or focal CNAs of CRGs/EMGs in 20% (56/283) of all cases, occurring at a somatic level in 4 (7.2%), at a germline level in 12 (22%) cases, whereas for the remaining cases, only tumor material could be analyzed. The most frequently altered genes were ATRX (5%), SMARCA4 (2.5%), MLL3 (2.5%) and ARID1B (2.5%). Double events (SNVs/small InDels/CNAs associated with LOH) were observed in SMARCA4 (n = 3), ATRX (n = 1) and PBRM1 (n = 1). Among the 60 variations, 24 (8.4%) targeted domains of functional importance for chromatin remodeling or highly conserved domains but of unknown function. Variations in SMARCA4 and ATRX occurred more frequently in the NB as compared to the gnomAD control cohort (OR = 4.49, 95%CI: 1.63-9.97, p = 0.038; OR 3.44, 95%CI: 1.46-6.91, p = 0.043, respectively). Cases with CRG/EMG variations showed a poorer overall survival compared to cases without variations. Genetic variations of CRGs/EMGs with likely functional impact were observed in 8.4% (24/283) of NB. Our case-control approach suggests a role of SMARCA4 as a player of NB oncogenesis.
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Affiliation(s)
- Angela Bellini
- Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, Institut Curie, Paris, France.,INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Nadia Bessoltane-Bentahar
- Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, Institut Curie, Paris, France.,INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Jaydutt Bhalshankar
- Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, Institut Curie, Paris, France.,INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Nathalie Clement
- Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, Institut Curie, Paris, France.,INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Virginie Raynal
- Institut Curie, PSL Research University, Inserm U830, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Plateforme de Séquençage ICGex, Institut Curie, Paris, France
| | - Sylvain Baulande
- Institut Curie, PSL Research University, NGS Platform, Paris, France
| | - Virginie Bernard
- Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Adrien Danzon
- Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, Institut Curie, Paris, France.,INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Mathieu Chicard
- Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, Institut Curie, Paris, France.,INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Léo Colmet-Daage
- Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, Institut Curie, Paris, France.,INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Gaelle Pierron
- Unité de Génétique Somatique, Institut Curie, Paris, France
| | - Laura Le Roux
- Unité de Génétique Somatique, Institut Curie, Paris, France
| | - Julien M Planchon
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France.,Department of Biopathology, Institut Curie, PSL Research University, Paris, France
| | - Valérie Combaret
- Laboratoire de Recherche Translationnelle, Centre Léon-Bérard, Lyon, France
| | - Eve Lapouble
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France.,Unité de Génétique Somatique, Institut Curie, Paris, France
| | | | - Estelle Thebaud
- Service d'Oncologie Pédiatrique, Hôpital de la Mère et l'enfant, Nantes, France
| | - Marion Gambart
- Unite d'Hemato-Oncologie, Hôpital des Enfants, Toulouse, France
| | | | - Jean Michon
- SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Caroline Louis-Brennetot
- INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France.,Institut Curie, PSL Research University, Inserm U830, Equipe Labellisée Ligue contre le Cancer, Paris, France
| | - Isabelle Janoueix-Lerosey
- INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France.,Institut Curie, PSL Research University, Inserm U830, Equipe Labellisée Ligue contre le Cancer, Paris, France
| | | | - Franck Bourdeaut
- Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, Institut Curie, Paris, France.,INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Olivier Delattre
- INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France.,Institut Curie, PSL Research University, Inserm U830, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Unité de Génétique Somatique, Institut Curie, Paris, France
| | - Gudrun Schleiermacher
- Equipe SiRIC RTOP Recherche Translationelle en Oncologie Pédiatrique, Institut Curie, Paris, France.,INSERM U830, Laboratoire de Génétique et Biologie des Cancers, Institut Curie, Paris, France.,SIREDO: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
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64
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Ducharme O, Beylot-Barry M, Pham-Ledard A, Bohers E, Viailly PJ, Bandres T, Faur N, Frison E, Vergier B, Jardin F, Merlio JP, Gros A. Mutations of the B-Cell Receptor Pathway Confer Chemoresistance in Primary Cutaneous Diffuse Large B-Cell Lymphoma Leg Type. J Invest Dermatol 2019; 139:2334-2342.e8. [PMID: 31150604 DOI: 10.1016/j.jid.2019.05.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 04/16/2019] [Accepted: 05/10/2019] [Indexed: 11/25/2022]
Abstract
Primary cutaneous diffuse large B-cell lymphoma, leg type (PCLBCL-LT) preferentially involves the lower limb in elderly subjects. A combination of polychemotherapy and rituximab has improved prognosis. However, about 50% of patients will experience progression or relapse without any predictive biologic marker of therapeutic response. The mutational profile of PCLBCL-LT has highlighted mutations contributing to constitutive NF-κB and B-cell receptor (BCR) signaling pathways but has not demonstrated clinical utility. Therefore, the mutational status of 32 patients with PCLBCL-LT (14 patients with complete durable response and 18 patients with relapsing or refractory disease) was determined with a dedicated lymphopanel. Tumor pairs at diagnosis and relapse or progression were analyzed in 14 relapsing or refractory patients. Patients with PCLBCL-LT harboring one mutation that targets one of the BCR signaling genes, CD79A/B or CARD11, displayed a reduced progression-free survival and specific survival (median 18 months, P = 0.002 and 51 months, P = 0.03, respectively, whereas median duration in the wild-type group was not reached) and were associated with therapeutic resistance (P = 0.0006). Longitudinal analyses revealed that MYD88 and CD79B were the earliest and among the most mutated genes. Our data suggest that evaluating BCR mutations in patients with PCLBCL-LT may help to predict first-line therapeutic response and to select targeted therapies.
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Affiliation(s)
- Océane Ducharme
- Service de Dermatologie, CHU de Bordeaux, Bordeaux, France; INSERM U1053, Equipe Oncogenèse des lymphomes cutanés, Université de Bordeaux
| | - Marie Beylot-Barry
- Service de Dermatologie, CHU de Bordeaux, Bordeaux, France; INSERM U1053, Equipe Oncogenèse des lymphomes cutanés, Université de Bordeaux
| | - Anne Pham-Ledard
- Service de Dermatologie, CHU de Bordeaux, Bordeaux, France; INSERM U1053, Equipe Oncogenèse des lymphomes cutanés, Université de Bordeaux
| | - Elodie Bohers
- INSERM U1245 and Centre Henri Becquerel, Rouen, France
| | | | - Thomas Bandres
- Service de Biologie des tumeurs, CHU de Bordeaux, Pessac, France
| | - Nicolas Faur
- Service de Biologie des tumeurs, CHU de Bordeaux, Pessac, France
| | - Eric Frison
- Service d'information médicale, CHU Bordeaux, Bordeaux, France
| | - Béatrice Vergier
- INSERM U1053, Equipe Oncogenèse des lymphomes cutanés, Université de Bordeaux; Service d'Anatomie pathologique, CHU de Bordeaux, Pessac, France
| | | | - Jean-Philippe Merlio
- INSERM U1053, Equipe Oncogenèse des lymphomes cutanés, Université de Bordeaux; Service de Biologie des tumeurs, CHU de Bordeaux, Pessac, France
| | - Audrey Gros
- INSERM U1053, Equipe Oncogenèse des lymphomes cutanés, Université de Bordeaux; Service de Biologie des tumeurs, CHU de Bordeaux, Pessac, France.
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Petridis C, Arora I, Shah V, Megalios A, Moss C, Mera A, Clifford A, Gillett C, Pinder SE, Tomlinson I, Roylance R, Simpson MA, Sawyer EJ. Frequency of pathogenic germline variants in BRCA1, BRCA2, PALB2, CHEK2 and TP53 in ductal carcinoma in situ diagnosed in women under the age of 50 years. Breast Cancer Res 2019; 21:58. [PMID: 31060593 PMCID: PMC6501320 DOI: 10.1186/s13058-019-1143-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 04/17/2019] [Indexed: 11/10/2022] Open
Abstract
INTRODUCTION Ductal carcinoma in situ (DCIS) is a non-obligate precursor of invasive ductal breast cancer, and approximately 20% of screen-detected tumours are pure DCIS. Most risk factors for breast cancer have similar associations with DCIS and IDC; however, there is limited data on the prevalence of the known high and moderate penetrance breast cancer predisposition genes in DCIS and which women with DCIS should be referred for genetic screening. The aim of this study was to assess the frequency of germline variants in BRCA2, BRCA1, CHEK2, PALB2 and TP53 in DCIS in women aged less than 50 years of age. METHODS After DNA extraction from the peripheral blood, Access Array technology (Fluidigm) was used to amplify all exons of these five known breast cancer predisposition genes using a custom made targeted sequencing panel in 655 cases of pure DCIS presenting in women under the age of 50 years together with 1611 controls. RESULTS Case-control analysis revealed an excess of pathogenic variants in BRCA2 (OR = 27.96, 95%CI 6.56-119.26, P = 2.0 × 10-10) and CHEK2 (OR = 8.04, 95%CI 2.93-22.05, P = 9.0 × 10-6), with weaker associations with PALB2 (P = 0.003), BRCA1 (P = 0.007) and TP53 (P = 0.02). For oestrogen receptor (ER)-positive DCIS the frequency of pathogenic variants was 9% under the age of 50 (14% with a family history of breast cancer) and 29% under the age of 40 (42% with a family history of breast cancer). For ER-negative DCIS, the frequency was 9% (16% with a family history of breast cancer) and 8% (11% with a family history of breast cancer) under the ages of 50 and 40, respectively. CONCLUSIONS This study has shown that breast tumourigenesis in women with pathogenic variants in BRCA2, CHEK2, PALB2, BRCA1 and TP53 can involve a DCIS precursor stage and that the focus of genetic testing in DCIS should be on women under the age of 40 with ER-positive DCIS.
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Affiliation(s)
- Christos Petridis
- School of Cancer and Pharmaceutical Sciences, Guy's Hospital, King's College London, London, SE1 9RT, UK.,Medical and Molecular Genetics, Guy's Hospital, King's College London, London, SE1 9RT, UK
| | - Iteeka Arora
- School of Cancer and Pharmaceutical Sciences, Guy's Hospital, King's College London, London, SE1 9RT, UK
| | - Vandna Shah
- School of Cancer and Pharmaceutical Sciences, Guy's Hospital, King's College London, London, SE1 9RT, UK
| | - Anargyros Megalios
- School of Cancer and Pharmaceutical Sciences, Guy's Hospital, King's College London, London, SE1 9RT, UK
| | - Charlotte Moss
- School of Cancer and Pharmaceutical Sciences, Guy's Hospital, King's College London, London, SE1 9RT, UK
| | - Anca Mera
- School of Cancer and Pharmaceutical Sciences, Guy's Hospital, King's College London, London, SE1 9RT, UK
| | - Angela Clifford
- School of Cancer and Pharmaceutical Sciences, Guy's Hospital, King's College London, London, SE1 9RT, UK
| | - Cheryl Gillett
- School of Cancer and Pharmaceutical Sciences, Guy's Hospital, King's College London, London, SE1 9RT, UK
| | - Sarah E Pinder
- School of Cancer and Pharmaceutical Sciences, Guy's Hospital, King's College London, London, SE1 9RT, UK
| | - Ian Tomlinson
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Rebecca Roylance
- Department of Oncology, UCLH Foundation Trust, London, NW1 2PG, UK
| | - Michael A Simpson
- Medical and Molecular Genetics, Guy's Hospital, King's College London, London, SE1 9RT, UK
| | - Elinor J Sawyer
- School of Cancer and Pharmaceutical Sciences, Guy's Hospital, King's College London, London, SE1 9RT, UK. .,Innovation Hub, Guy's Cancer Centre, Guy's Hospital, London, SE1 9RT, UK.
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Cho WCS, Tan KT, Ma VWS, Li JYC, Ngan RKC, Cheuk W, Yip TTC, Yang YT, Chen SJ. Targeted next-generation sequencing reveals recurrence-associated genomic alterations in early-stage non-small cell lung cancer. Oncotarget 2018; 9:36344-36357. [PMID: 30555633 PMCID: PMC6284742 DOI: 10.18632/oncotarget.26349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 11/01/2018] [Indexed: 12/14/2022] Open
Abstract
Purpose The identification of genomic alterations related to recurrence in early-stage non-small cell lung cancer (NSCLC) patients may help better stratify high-risk individuals and guide treatment strategies. This study aimed to identify the molecular biomarkers of recurrence in early-stage NSCLC. Results Of the 42 tumors evaluable for genomic alterations, TP53 and EGFR were the most frequent alterations with population frequency 52.4% and 50.0%, respectively. Fusion genes were detected in four patients, which had lower mutational burden and relatively better genomic stability. EGFR mutation and fusion gene were mutually exclusive in this study. CDKN2A, FAS, SUFU and SMARCA4 genomic alterations were only observed in the relapsed patients. Increased copy number alteration index was observed in early relapsed patients. Among these genomic alterations, early-stage NSCLCs harboring CDKN2A, FAS, SUFU and SMARCA4 genomic alterations were found to be significantly associated with recurrence. Some of these new findings were validated using The Cancer Genome Atlas (TCGA) dataset. Conclusions The genomic alterations of CDKN2A, FAS, SUFU and SMARCA4 in early-stage NSCLC are found to be associated with recurrence, but confirmation in a larger independent cohort is required to define the clinical impact. Materials and Methods Paired primary tumor and normal lung tissue samples were collected for targeted next-generation sequencing analysis. A panel targets exons for 440 genes was used to assess the mutational and copy number status of selected genes in three clinically relevant groups of stage I/II NSCLC patients: 1) Early relapse; 2) Late relapse; and 3) No relapse.
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Affiliation(s)
- William C S Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | | | - Victor W S Ma
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - Jacky Y C Li
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
| | - Roger K C Ngan
- Department of Clinical Oncology, The University of Hong Kong, Gleneagles Hong Kong Hospital, Wong Chuk Hang, Hong Kong
| | - Wah Cheuk
- Department of Pathology, Queen Elizabeth Hospital, Kowloon, Hong Kong
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O'Leary B, Cutts RJ, Liu Y, Hrebien S, Huang X, Fenwick K, André F, Loibl S, Loi S, Garcia-Murillas I, Cristofanilli M, Huang Bartlett C, Turner NC. The Genetic Landscape and Clonal Evolution of Breast Cancer Resistance to Palbociclib plus Fulvestrant in the PALOMA-3 Trial. Cancer Discov 2018; 8:1390-1403. [PMID: 30206110 PMCID: PMC6368247 DOI: 10.1158/2159-8290.cd-18-0264] [Citation(s) in RCA: 435] [Impact Index Per Article: 62.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 07/09/2018] [Accepted: 09/06/2018] [Indexed: 12/20/2022]
Abstract
CDK4/6 inhibition with endocrine therapy is now a standard of care for advanced estrogen receptor-positive breast cancer. Mechanisms of CDK4/6 inhibitor resistance have been described preclinically, with limited evidence from clinical samples. We conducted paired baseline and end-of-treatment circulating tumor DNA sequencing from 195 patients in the PALOMA-3 randomized phase III trial of palbociclib plus fulvestrant versus placebo plus fulvestrant. We show that clonal evolution occurs frequently during treatment, reflecting substantial subclonal complexity in breast cancer that has progressed after prior endocrine therapy. RB1 mutations emerged only in the palbociclib plus fulvestrant arm and in a minority of patients (6/127, 4.7%, P = 0.041). New driver mutations emerged in PIK3CA (P = 0.00069) and ESR1 after treatment in both arms, in particular ESR1 Y537S (P = 0.0037). Evolution of driver gene mutations was uncommon in patients progressing early on palbociclib plus fulvestrant but common in patients progressing later on treatment. These findings inform future treatment strategies to address resistance to palbociclib plus fulvestrant.Significance: Acquired mutations from fulvestrant are a major driver of resistance to fulvestrant and palbociclib combination therapy. ESR1 Y537S mutation promotes resistance to fulvestrant. Clonal evolution results in frequent acquisition of driver mutations in patients progressing late on therapy, which suggests that early and late progression have distinct mechanisms of resistance. Cancer Discov; 8(11); 1390-403. ©2018 AACR. See related commentary by Schiff and Jeselsohn, p. 1352 This article is highlighted in the In This Issue feature, p. 1333.
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Affiliation(s)
- Ben O'Leary
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
- Breast Unit, Royal Marsden Hospital, London, United Kingdom
| | - Rosalind J Cutts
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | | | - Sarah Hrebien
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | | | - Kerry Fenwick
- Tumour Profiling Unit, The Institute of Cancer Research, London, United Kingdom
| | - Fabrice André
- Department of Medical Oncology, Institut Gustave Roussy, Villejuif, France
| | | | - Sherene Loi
- Division of Research and Cancer Medicine, University of Melbourne, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Isaac Garcia-Murillas
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Massimo Cristofanilli
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Chicago, Illinois
| | | | - Nicholas C Turner
- Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom.
- Breast Unit, Royal Marsden Hospital, London, United Kingdom
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Kang Y, Nam SH, Park KS, Kim Y, Kim JW, Lee E, Ko JM, Lee KA, Park I. DeviCNV: detection and visualization of exon-level copy number variants in targeted next-generation sequencing data. BMC Bioinformatics 2018; 19:381. [PMID: 30326846 PMCID: PMC6192323 DOI: 10.1186/s12859-018-2409-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 10/04/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Targeted next-generation sequencing (NGS) is increasingly being adopted in clinical laboratories for genomic diagnostic tests. RESULTS We developed a new computational method, DeviCNV, intended for the detection of exon-level copy number variants (CNVs) in targeted NGS data. DeviCNV builds linear regression models with bootstrapping for every probe to capture the relationship between read depth of an individual probe and the median of read depth values of all probes in the sample. From the regression models, it estimates the read depth ratio of the observed and predicted read depth with confidence interval for each probe which is applied to a circular binary segmentation (CBS) algorithm to obtain CNV candidates. Then, it assigns confidence scores to those candidates based on the reliability and strength of the CNV signals inferred from the read depth ratios of the probes within them. Finally, it also provides gene-centric plots with confidence levels of CNV candidates for visual inspection. We applied DeviCNV to targeted NGS data generated for newborn screening and demonstrated its ability to detect novel pathogenic CNVs from clinical samples. CONCLUSIONS We propose a new pragmatic method for detecting CNVs in targeted NGS data with an intuitive visualization and a systematic method to assign confidence scores for candidate CNVs. Since DeviCNV was developed for use in clinical diagnosis, sensitivity is increased by the detection of exon-level CNVs.
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Affiliation(s)
- Yeeok Kang
- SD Genomics Co., Ltd., 11F, Seoul Gangnam Post Office, 619 Gaepo-ro, Gangnam-gu, Seoul, 06336 Republic of Korea
- Department of Bio and Brain Engineering, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon, Republic of Korea
| | - Seong-Hyeuk Nam
- SD Genomics Co., Ltd., 11F, Seoul Gangnam Post Office, 619 Gaepo-ro, Gangnam-gu, Seoul, 06336 Republic of Korea
| | - Kyung Sun Park
- SD Genomics Co., Ltd., 11F, Seoul Gangnam Post Office, 619 Gaepo-ro, Gangnam-gu, Seoul, 06336 Republic of Korea
| | - Yoonjung Kim
- Department of Laboratory Medicine, Yonsei University College of Medicine, 211 Eonjuro, Gangnam-gu, Seoul, 06273 Republic of Korea
| | - Jong-Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Eunjung Lee
- Division of Genetics and Genomics, Boston Children’s Hospital and Harvard Medical School, Boston, USA
| | - Jung Min Ko
- Department of Pediatrics, Seoul National University Children’s Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyung-A Lee
- Department of Laboratory Medicine, Yonsei University College of Medicine, 211 Eonjuro, Gangnam-gu, Seoul, 06273 Republic of Korea
| | - Inho Park
- SD Genomics Co., Ltd., 11F, Seoul Gangnam Post Office, 619 Gaepo-ro, Gangnam-gu, Seoul, 06336 Republic of Korea
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Hsu CL, Lui KW, Chi LM, Kuo YC, Chao YK, Yeh CN, Lee LY, Huang Y, Lin TL, Huang MY, Lai YR, Yeh YM, Fan HC, Lin AC, Lu YJ, Hsieh CH, Chang KP, Tsang NM, Wang HM, Chang AY, Chang YS, Li HP. Integrated genomic analyses in PDX model reveal a cyclin-dependent kinase inhibitor Palbociclib as a novel candidate drug for nasopharyngeal carcinoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:233. [PMID: 30236142 PMCID: PMC6149192 DOI: 10.1186/s13046-018-0873-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 08/13/2018] [Indexed: 02/07/2023]
Abstract
Background Patient-derived xenograft (PDX) tumor model has become a new approach in identifying druggable tumor mutations, screening and evaluating personalized cancer drugs based on the mutated targets. Methods We established five nasopharyngeal carcinoma (NPC) PDXs in mouse model. Subsequently, whole-exome sequencing (WES) and genomic mutation analyses were performed to search for genetic alterations for new drug targets. Potential drugs were applied in two NPC PDX mice model to assess their anti-cancer activities. RNA sequencing and transcriptomic analysis were performed in one NPC PDX mice to correlate with the efficacy of the anti-cancer drugs. Results A relative high incident rate of copy number variations (CNVs) of cell cycle-associated genes. Among the five NPC-PDXs, three had cyclin D1 (CCND1) amplification while four had cyclin-dependent kinase inhibitor CDKN2A deletion. Furthermore, CCND1 overexpression was observed in > 90% FFPE clinical metastatic NPC tumors (87/91) and was associated with poor outcomes. CNV analysis disclosed that plasma CCND1/CDKN2A ratio is correlated with EBV DNA load in NPC patients’ plasma and could serve as a screening test to select potential CDK4/6 inhibitor treatment candidates. Based on our NPC PDX model and RNA sequencing, Palbociclib, a cyclin-dependent kinase inhibitor, proved to have anti-tumor effects by inducing G1 arrest. One NPC patient with liver metastatic was treated with Palbociclib, had stable disease response and a drop in Epstein Barr virus (EBV) EBV titer. Conclusions Our integrated information of sequencing-based genomic studies and tumor transcriptomes with drug treatment in NPC-PDX models provided guidelines for personalized precision treatments and revealed a cyclin-dependent kinase inhibitor Palbociclib as a novel candidate drug for NPC. Electronic supplementary material The online version of this article (10.1186/s13046-018-0873-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cheng-Lung Hsu
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Kar-Wai Lui
- Department of Medical Imaging and Intervention, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Lang-Ming Chi
- Clinical Proteomics Core Laboratory, Chang Gung Memorial Hospital, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Yung-Chia Kuo
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Yin-Kai Chao
- Division of Thoracic and Cardiovascular Surgery, Department of Surgery, Chang Gung Memorial Hospital, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Chun-Nan Yeh
- Department of General Surgery, Liver Research Center, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Li-Yu Lee
- Department of Pathology, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Yenlin Huang
- Department of Pathology, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Tung-Liang Lin
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Mei-Yuan Huang
- Department of Microbiology and Immunology, Molecular Medicine Research Center, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist., Lin-Kou, Taoyuan, 333, Taiwan, Republic of China
| | - Yi-Ru Lai
- Department of Microbiology and Immunology, Molecular Medicine Research Center, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist., Lin-Kou, Taoyuan, 333, Taiwan, Republic of China
| | - Yuan-Ming Yeh
- Molecular Medicine Research Center, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist, Taoyuan City, 333, Taiwan, Republic of China
| | - Hsien-Chi Fan
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - An-Chi Lin
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Yen-Jung Lu
- ACT Genomics, Co. Ltd., 1F., No.280, Xinhu 2nd Rd., Neihu Dist, Taipei City, 114, Taiwan, Republic of China
| | - Chia-Hsun Hsieh
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Kai-Ping Chang
- Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Ngan-Ming Tsang
- Department of Radiation, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Hung-Ming Wang
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Alex Y Chang
- Johns Hopkins Singapore International Medical Centre, 11 Jalan Tan Tock Seng, Singapore City, 308433, Singapore
| | - Yu-Sun Chang
- Department of Microbiology and Immunology, Molecular Medicine Research Center, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist., Lin-Kou, Taoyuan, 333, Taiwan, Republic of China.,Molecular Medicine Research Center, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist, Taoyuan City, 333, Taiwan, Republic of China.,Department of Otolaryngology-Head and Neck Surgery, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China
| | - Hsin-Pai Li
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, No.5, Fuxing St., Guishan Dist, Taoyuan City, 333, Lin-Kou, Taiwan, Republic of China. .,Department of Microbiology and Immunology, Molecular Medicine Research Center, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist., Lin-Kou, Taoyuan, 333, Taiwan, Republic of China. .,Molecular Medicine Research Center, Chang Gung University, No.259, Wenhua 1st Rd., Guishan Dist, Taoyuan City, 333, Taiwan, Republic of China.
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Hsu HC, Lapke N, Chen SJ, Lu YJ, Jhou RS, Yeh CY, Tsai WS, Hung HY, Hsieh JCH, Yang TS, Thiam TK, You JF. PTPRT and PTPRD Deleterious Mutations and Deletion Predict Bevacizumab Resistance in Metastatic Colorectal Cancer Patients. Cancers (Basel) 2018; 10:cancers10090314. [PMID: 30200630 PMCID: PMC6162606 DOI: 10.3390/cancers10090314] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 08/25/2018] [Accepted: 09/03/2018] [Indexed: 12/22/2022] Open
Abstract
Background: Bevacizumab-based regimens are used as standard treatments for colorectal cancer. Unfortunately, there are no established predictive markers for bevacizumab response. Methods: Tumor samples from 36 metastatic colorectal cancer patients treated with bevacizumab plus chemotherapy were analyzed by next-generation sequencing of all coding exons of more than 400 genes. Single gene and signaling pathway analyses were performed to correlate genomic data with response. Results: Among the genes most frequently mutated in our cohort, only mutations in PTPRT, a phosphatase involved in JAK/STAT signaling, were associated with response status, with deleterious mutations being enriched in non-responders. Pathway analysis revealed that deleterious mutations in genes of the JAK/STAT pathway, namely in PTPRT and the related gene PTPRD, correlated with resistance. Mutations in RTK/PI3K/RAS, Wnt and TGFβ pathways did not associate with response. Lack of response was observed in all patients with deleterious mutations or copy number loss of PTPRT/PTPRD (n = 10), compared to only 30.8% (n = 8) of patients without such alterations (relative risk, 3.25; 95% CI, 1.83–5.79, p = 0.0003). Similarly, PTPRT/PTPRD deleterious alterations were associated with shorter progression-free survival, an association that was retained in multivariate analysis (HR, 3.33; 95% CI, 1.47–7.54; p = 0.0038). Conclusion: Deleterious alterations in PTPRT/PTPRD are potential biomarkers for bevacizumab resistance.
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Affiliation(s)
- Hung-Chih Hsu
- Division of Hematology/Oncology, Chang Gung Memorial Hospital at Linkou, Taoyuan City 333, Taiwan.
- College of Medicine, Chang Gung University, Taoyuan City 33302, Taiwan.
| | - Nina Lapke
- ACT Genomics, Neihu Dist., Taipei City 114, Taiwan.
| | - Shu-Jen Chen
- ACT Genomics, Neihu Dist., Taipei City 114, Taiwan.
| | - Yen-Jung Lu
- ACT Genomics, Neihu Dist., Taipei City 114, Taiwan.
| | | | - Chien-Yuh Yeh
- College of Medicine, Chang Gung University, Taoyuan City 33302, Taiwan.
- ACT Genomics, Neihu Dist., Taipei City 114, Taiwan.
| | - Wen-Sy Tsai
- College of Medicine, Chang Gung University, Taoyuan City 33302, Taiwan.
- Division of Colon and Rectal Surgery, Chang Gung Memorial Hospital at Linkou, Taoyuan City 333, Taiwan.
| | - Hsin-Yuan Hung
- College of Medicine, Chang Gung University, Taoyuan City 33302, Taiwan.
- Division of Colon and Rectal Surgery, Chang Gung Memorial Hospital at Linkou, Taoyuan City 333, Taiwan.
| | - Jason Chia-Hsun Hsieh
- Division of Hematology/Oncology, Chang Gung Memorial Hospital at Linkou, Taoyuan City 333, Taiwan.
- College of Medicine, Chang Gung University, Taoyuan City 33302, Taiwan.
| | - Tsai-Sheng Yang
- Division of Hematology/Oncology, Chang Gung Memorial Hospital at Linkou, Taoyuan City 333, Taiwan.
- College of Medicine, Chang Gung University, Taoyuan City 33302, Taiwan.
| | | | - Jeng-Fu You
- College of Medicine, Chang Gung University, Taoyuan City 33302, Taiwan.
- Division of Colon and Rectal Surgery, Chang Gung Memorial Hospital at Linkou, Taoyuan City 333, Taiwan.
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71
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Liang X, Vacher S, Boulai A, Bernard V, Baulande S, Bohec M, Bièche I, Lerebours F, Callens C. Targeted next-generation sequencing identifies clinically relevant somatic mutations in a large cohort of inflammatory breast cancer. Breast Cancer Res 2018; 20:88. [PMID: 30086764 PMCID: PMC6081877 DOI: 10.1186/s13058-018-1007-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 06/18/2018] [Indexed: 11/10/2022] Open
Abstract
Background Inflammatory breast cancer (IBC) is the most aggressive form of primary breast cancer. Using a custom-made breast cancer gene sequencing panel, we investigated somatic mutations in IBC to better understand the genomic differences compared with non-IBC and to consider new targeted therapy in IBC patients. Methods Targeted next-generation sequencing (NGS) of 91 candidate breast cancer-associated genes was performed on 156 fresh-frozen breast tumor tissues from IBC patients. Mutational profiles from 197 primary breast tumors from The Cancer Genome Atlas (TCGA) were used as non-IBC controls for comparison analysis. The mutational landscape of IBC was correlated with clinicopathological data and outcomes. Results After genotype calling and algorithmic annotations, we identified 392 deleterious variants in IBC and 320 variants in non-IBC cohorts, respectively. IBC tumors harbored more mutations than non-IBC (2.5 per sample vs. 1.6 per sample, p < 0.0001). Eighteen mutated genes were significantly different between the two cohorts, namely TP53, CDH1, NOTCH2, MYH9, BRCA2, ERBB4, POLE, FGFR3, ROS1, NOTCH4, LAMA2, EGFR, BRCA1, TP53BP1, ESR1, THBS1, CASP8, and NOTCH1. In IBC, the most frequently mutated genes were TP53 (43.0%), PIK3CA (29.5%), MYH9 (8.3%), NOTCH2 (8.3%), BRCA2 (7.7%), ERBB4 (7.1%), FGFR3 (6.4%), POLE (6.4%), LAMA2 (5.8%), ARID1A (5.1%), NOTCH4 (5.1%), and ROS1 (5.1%). After grouping 91 genes on 10 signaling pathways, we found that the DNA repair pathway for the triple-negative breast cancer (TNBC) subgroup, the RTK/RAS/MAPK and cell cycle pathways for the HR–/HER2+ subgroup, the DNA repair, RTK/RAS/MAPK, and NOTCH pathways for the HR+/HER2– subgroup, and the DNA repair, epigenome, and diverse pathways for the HR+/HER2+ subgroup were all significantly differently altered between IBC and non-IBC. PIK3CA mutation was independently associated with worse metastasis-free survival (MFS) in IBC since the median MFS for the PIK3CA mutant type was 26.0 months and for the PIK3CA wild type was 101.1 months (p = 0.002). This association was observed in TNBC (p = 0.04) and the HR–/HER2+ subgroups (p = 0.0003), but not in the HR+/HER2– subgroup of IBC. Conclusions Breast cancer-specific targeted NGS uncovered a high frequency of deleterious somatic mutations in IBC, some of which may be relevant for clinical management. Electronic supplementary material The online version of this article (10.1186/s13058-018-1007-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xu Liang
- Department of Breast Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital & Institute, Beijing, China.,Pharmacogenomic Unit, Department of Genetics, Curie Institute, PSL Research University, 26 rue d'Ulm, 75005, Paris, France
| | - Sophie Vacher
- Pharmacogenomic Unit, Department of Genetics, Curie Institute, PSL Research University, 26 rue d'Ulm, 75005, Paris, France
| | - Anais Boulai
- Pharmacogenomic Unit, Department of Genetics, Curie Institute, PSL Research University, 26 rue d'Ulm, 75005, Paris, France
| | - Virginie Bernard
- Clinic bioinformatic Unit, Department of Biopathology, Curie Institute, PSL Research University, Paris, France
| | - Sylvain Baulande
- Institut Curie Genomics of Excellence (ICGex) Platform, Curie Institute, PSL Research University, Paris, France
| | - Mylene Bohec
- Institut Curie Genomics of Excellence (ICGex) Platform, Curie Institute, PSL Research University, Paris, France
| | - Ivan Bièche
- Pharmacogenomic Unit, Department of Genetics, Curie Institute, PSL Research University, 26 rue d'Ulm, 75005, Paris, France.,EA7331, Paris Descartes University, Sorbonne Paris Cité, Faculty of Pharmaceutical and Biological Sciences, Paris, France
| | - Florence Lerebours
- Department of Medical Oncology, Curie Institute, René Huguenin Hospital, Saint-Cloud, France
| | - Céline Callens
- Pharmacogenomic Unit, Department of Genetics, Curie Institute, PSL Research University, 26 rue d'Ulm, 75005, Paris, France.
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72
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Bohers E, Viailly PJ, Becker S, Marchand V, Ruminy P, Maingonnat C, Bertrand P, Etancelin P, Picquenot JM, Camus V, Menard AL, Lemasle E, Contentin N, Leprêtre S, Lenain P, Stamatoullas A, Lanic H, Libraire J, Vaudaux S, Pepin LF, Vera P, Tilly H, Jardin F. Non-invasive monitoring of diffuse large B-cell lymphoma by cell-free DNA high-throughput targeted sequencing: analysis of a prospective cohort. Blood Cancer J 2018; 8:74. [PMID: 30069017 PMCID: PMC6070497 DOI: 10.1038/s41408-018-0111-6] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/28/2018] [Accepted: 06/08/2018] [Indexed: 12/15/2022] Open
Abstract
From a liquid biopsy, cell-free DNA (cfDNA) can provide information regarding basal tumoral genetic patterns and changes upon treatment. In a prospective cohort of 30 diffuse large B-cell lymphomas (DLBCL), we determined the clinical relevance of cfDNA using targeted next-generation sequencing and its correlation with PET scan imaging at the time of diagnosis and during treatment. Using a dedicated DLBCL panel, mutations were identified at baseline for 19 cfDNAs and profiles were consistent with expected DLBCL patterns. Tumor burden-related clinical and PET scan features (LDH, IPI, and metabolic tumor volume) were significantly correlated with the quantity of tumoral cfDNA. Among the four patients presenting additional mutations in their cfDNAs, three had high metabolic tumor volumes, suggesting that cfDNA more accurately reflects tumor heterogeneity than tissues biopsy itself. Mid-treatment, four patients still had basal mutations in their cfDNAs, including three in partial response according to their Deauville scores. Our study highlights the major interests in liquid biopsy, in particular in the context of bulky tumors where cfDNA allows capturing the entire tumoral mutation profile. Therefore, cfDNA analysis in DLBCL represents a complementary approach to PET scan imaging.
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Affiliation(s)
- Elodie Bohers
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | | | - Stéphanie Becker
- Department of Nuclear Medicine, Centre Henri Becquerel, University of Rouen, Rouen, France
- QuantIF-LITIS (EA 4108-FR CNRS 3638), Faculty of Medicine, University of Rouen, Rouen, France
| | - Vinciane Marchand
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | - Philippe Ruminy
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | | | - Philippe Bertrand
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
| | | | | | - Vincent Camus
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | - Anne-Lise Menard
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | - Emilie Lemasle
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | - Nathalie Contentin
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | - Stéphane Leprêtre
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | - Pascal Lenain
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | | | - Hélène Lanic
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
| | - Julie Libraire
- Clinical Research Unit, Centre Henri Becquerel, Rouen, France
| | | | | | - Pierre Vera
- Department of Nuclear Medicine, Centre Henri Becquerel, University of Rouen, Rouen, France
- QuantIF-LITIS (EA 4108-FR CNRS 3638), Faculty of Medicine, University of Rouen, Rouen, France
| | - Hervé Tilly
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France
- Clinical Research Unit, Centre Henri Becquerel, Rouen, France
| | - Fabrice Jardin
- INSERM U1245, Centre Henri Becquerel, University of Rouen, Rouen, France.
- Department of Clinical Haematology, Centre Henri Becquerel, Rouen, France.
- Clinical Research Unit, Centre Henri Becquerel, Rouen, France.
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73
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Her NG, Oh JW, Oh YJ, Han S, Cho HJ, Lee Y, Ryu GH, Nam DH. Potent effect of the MDM2 inhibitor AMG232 on suppression of glioblastoma stem cells. Cell Death Dis 2018; 9:792. [PMID: 30022047 PMCID: PMC6052082 DOI: 10.1038/s41419-018-0825-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 06/08/2018] [Accepted: 06/20/2018] [Indexed: 02/07/2023]
Abstract
Testing new ways to identify untapped opportunities for glioblastoma therapies remains highly significant. Amplification and overexpression of MDM2 gene is frequent in glioblastoma and disrupting the MDM2-p53 interaction is a promising strategy to treat the cancer. RG7112 is the first-in class inhibitor and recently discovered AMG232 is the most potent MDM2 inhibitor known to date. Here, we compared the effects of these two clinical MDM2 inhibitors in six glioblastoma cell lines and ten patient-derived glioblastoma stem cells. Targeted sequencing of the TP53, MDM2 genes and whole transcriptome analysis were conducted to verify genetic status associated with sensitivity and resistance to the drugs. Although TP53 wild-type glioblastoma cell lines are similarly sensitive to AMG232 and RG7112, we found that four TP53 wild-type out of ten patient-derived glioblastoma cells are much more sensitive to AMG232 than RG7112 (average IC50 of 76 nM vs. 720 nM). Among these, 464T stem cells containing MDM2 gene amplification were most sensitive to AMG232 with IC50 of 5.3 nM. Moreover, AMG232 exhibited higher selectivity against p53 wild-type cells over p53 mutant stem cells compared to RG7112 (average selectivity of 512-fold vs. 16.5-fold). Importantly, we also found that AMG232 is highly efficacious in three-dimensional (3D) tumor spheroids growth and effectively inhibits the stemness-related factors, Nestin and ZEB1. Our data provide new evidence that glioblastoma stem cells have high susceptibility to AMG232 suggesting the potential clinical implications of MDM2 inhibition for glioblastoma treatment. These will facilitate additional preclinical and clinical studies evaluating MDM2 inhibitors in glioblastoma and direct further efforts towards developing better MDM2-targeted therapeutics.
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Affiliation(s)
- Nam-Gu Her
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, 06351, Korea
| | - Jeong-Woo Oh
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, 06351, Korea.,Department of Health Sciences & Technology, Samsung Advanced Institute for Health Science & Technology, Sungkyunkwan University, Seoul, 06351, Korea
| | - Yun Jeong Oh
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, 06351, Korea
| | - Suji Han
- Department of Health Sciences & Technology, Samsung Advanced Institute for Health Science & Technology, Sungkyunkwan University, Seoul, 06351, Korea
| | - Hee Jin Cho
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, 06351, Korea
| | - Yeri Lee
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, 06351, Korea
| | - Gyu Ha Ryu
- Office of R&D Strategy & Planning, Samsung Medical Center, Seoul, 06351, Korea.
| | - Do-Hyun Nam
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, 06351, Korea. .,Department of Health Sciences & Technology, Samsung Advanced Institute for Health Science & Technology, Sungkyunkwan University, Seoul, 06351, Korea. .,Department of Neurosurgery, Samsung Medical Center, Sungkyunkwan University, Seoul, 06351, Korea.
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74
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Maitre E, Bertrand P, Maingonnat C, Viailly PJ, Wiber M, Naguib D, Salaün V, Cornet E, Damaj G, Sola B, Jardin F, Troussard X. New generation sequencing of targeted genes in the classical and the variant form of hairy cell leukemia highlights mutations in epigenetic regulation genes. Oncotarget 2018; 9:28866-28876. [PMID: 29989027 PMCID: PMC6034755 DOI: 10.18632/oncotarget.25601] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 05/24/2018] [Indexed: 11/25/2022] Open
Abstract
Classical hairy cell leukemia (HCL-c) is a rare lymphoid neoplasm. BRAFV600E mutation, detected in more than 80% of the cases, is described as a driver mutation, but additional genetic abnormalities appear to be necessary for the disease progression. For cases of HCL-c harboring a wild-type BRAF gene, the differential diagnosis of the variant form of HCL (HCL-v) or splenic diffuse red pulp lymphoma (SDRPL) is complex. We selected a panel of 21 relevant genes based on a literature review of whole exome sequencing studies (BRAF, MAP2K1, DUSP2, MAPK15, ARID1A, ARID1B, EZH2, KDM6A, CREBBP, TP53, CDKN1B, XPO1, KLF2, CXCR4, NOTH1, NOTCH2, MYD88, ANXA1, U2AF1, BCOR, and ABCA8). We analyzed 20 HCL-c and 4 HCL-v patients. The analysis of diagnostic samples mutations in BRAF (n = 18), KLF2 (n = 4), MAP2K1 (n = 3), KDM6A (n = 2), CDKN1B (n = 2), ARID1A (n = 2), CREBBP (n = 2) NOTCH1 (n = 1) and ARID1B (n = 1). BRAFV600E was found in 90% (18/20) of HCL-c patients. In HCL-c patients with BRAFV600E, other mutations were found in 33% (6/18) of cases. All 4 HCL-v patients had mutations in epigenetic regulatory genes: KDM6A (n = 2), CREBBP (n = 1) or ARID1A (n = 1). The analysis of sequential samples (at diagnosis and relapse) from 5 patients (2 HCL-c and 3 HCL-v), showed the presence of 2 new subclonal mutations (BCORE1430X and XPO1E571K) in one patient and variations of the mutated allele frequency in 2 other cases. In the HCL-v disease, we described new mutations targeting KDM6A that encode a lysine demethylase protein. This opens new perspectives for personalized medicine for this group of patients.
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Affiliation(s)
- Elsa Maitre
- Normandie Univ, INSERM U1245, Université de Caen, Caen, France
| | | | | | | | | | - Dina Naguib
- Laboratoire d'hématologie, CHU Caen, Caen, France
| | | | - Edouard Cornet
- Normandie Univ, INSERM U1245, Université de Caen, Caen, France.,Laboratoire d'hématologie, CHU Caen, Caen, France
| | - Gandhi Damaj
- Normandie Univ, INSERM U1245, Université de Caen, Caen, France.,Institut d'Hématologie de Basse-Normandie, CHU Caen, Caen, France
| | - Brigitte Sola
- Normandie Univ, INSERM U1245, Université de Caen, Caen, France
| | - Fabrice Jardin
- Normandie Univ, INSERM U1245, Université de Rouen, Rouen, France.,Service d'hématologie, Centre Henri Becquerel, Rouen, France
| | - Xavier Troussard
- Normandie Univ, INSERM U1245, Université de Caen, Caen, France.,Laboratoire d'hématologie, CHU Caen, Caen, France.,Institut d'Hématologie de Basse-Normandie, CHU Caen, Caen, France
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75
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Rieber N, Bohnert R, Ziehm U, Jansen G. Reliability of algorithmic somatic copy number alteration detection from targeted capture data. Bioinformatics 2018; 33:2791-2798. [PMID: 28472276 PMCID: PMC5870863 DOI: 10.1093/bioinformatics/btx284] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 05/03/2017] [Indexed: 01/11/2023] Open
Abstract
Motivation Whole exome and gene panel sequencing are increasingly used for oncological diagnostics. To investigate the accuracy of SCNA detection algorithms on simulated and clinical tumor samples, the precision and sensitivity of four SCNA callers were measured using 50 simulated whole exome and 50 simulated targeted gene panel datasets, and using 119 TCGA tumor samples for which SNP array data were available. Results On synthetic exome and panel data, VarScan2 mostly called false positives, whereas Control-FREEC was precise (>90% correct calls) at the cost of low sensitivity (<40% detected). ONCOCNV was slightly less precise on gene panel data, with similarly low sensitivity. This could be explained by low sensitivity for amplifications and high precision for deletions. Surprisingly, these results were not strongly affected by moderate tumor impurities; only contaminations with more than 60% non-cancerous cells resulted in strongly declining precision and sensitivity. On the 119 clinical samples, both Control-FREEC and CNVkit called 71.8% and 94%, respectively, of the SCNAs found by the SNP arrays, but with a considerable amount of false positives (precision 29% and 4.9%). Discussion Whole exome and targeted gene panel methods by design limit the precision of SCNA callers, making them prone to false positives. SCNA calls cannot easily be integrated in clinical pipelines that use data from targeted capture-based sequencing. If used at all, they need to be cross-validated using orthogonal methods. Availability and implementation Scripts are provided as supplementary information. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Nora Rieber
- Molecular Health GmbH, Kurfürsten-Anlage 21, 69115 Heidelberg, Germany
| | - Regina Bohnert
- Molecular Health GmbH, Kurfürsten-Anlage 21, 69115 Heidelberg, Germany
| | - Ulrike Ziehm
- Molecular Health GmbH, Kurfürsten-Anlage 21, 69115 Heidelberg, Germany
| | - Gunther Jansen
- Molecular Health GmbH, Kurfürsten-Anlage 21, 69115 Heidelberg, Germany
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76
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Fontanilles M, Marguet F, Bohers É, Viailly PJ, Dubois S, Bertrand P, Camus V, Mareschal S, Ruminy P, Maingonnat C, Lepretre S, Veresezan EL, Derrey S, Tilly H, Picquenot JM, Laquerrière A, Jardin F. Non-invasive detection of somatic mutations using next-generation sequencing in primary central nervous system lymphoma. Oncotarget 2018. [PMID: 28636991 PMCID: PMC5564634 DOI: 10.18632/oncotarget.18325] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Purpose Primary central nervous system lymphomas (PCNSL) have recurrent genomic alterations. The main objective of our study was to demonstrate that targeted sequencing of circulating cell-free DNA (cfDNA) released by PCNSL at the time of diagnosis could identify somatic mutations by next-generation sequencing (NGS). Patients and Methods PlasmacfDNA and matched tumor DNA (tDNA) from 25 PCNSL patients were sequenced using an Ion Torrent Personal Genome Machine (Life Technologies®). First, patient-specific targeted sequencing of identified somatic mutations in tDNA was performed. Then, a second sequencing targeting MYD88 c.T778C was performed and compared to plasma samples from 25 age-matched control patients suffering from other types of cancer. Results According to the patient-specific targeted sequencing, eight patients (32% [95% CI 15-54%]) had detectable somatic mutations in cfDNA. Considering MYD88 sequencing, six patients had the specific c.T778C alteration detected in plasma. Using a control group, the sensitivity was 24% [9-45%] and the specificity was 100%. Tumor volume or deep brain structure involvement did not influence the detection of somatic mutations in plasma. Conclusion This pilot study provided evidence that somatic mutations can be detected by NGS in the cfDNA of a subset of patients suffering from PCNSL.
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Affiliation(s)
- Maxime Fontanilles
- Department of Hematology, Cancer Center Henri Becquerel, 76000 Rouen, France.,INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, 76000 Rouen, France
| | - Florent Marguet
- INSERM U1245 and Hôpital Charles Nicolle, NeoVasc Team, University of Normandy, UNIVROUEN, CHU-Hôpitaux de Rouen, 76031 Rouen, France.,Department of Neuropathology, Hôpital Charles Nicolle, Normandy Center for Genomic and Personalized Medicine, CHU-Hôpitaux de Rouen, 76031 Rouen, France
| | - Élodie Bohers
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, 76000 Rouen, France
| | - Pierre-Julien Viailly
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, 76000 Rouen, France
| | - Sydney Dubois
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, 76000 Rouen, France
| | - Philippe Bertrand
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, 76000 Rouen, France
| | - Vincent Camus
- Department of Hematology, Cancer Center Henri Becquerel, 76000 Rouen, France.,INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, 76000 Rouen, France
| | - Sylvain Mareschal
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, 76000 Rouen, France
| | - Philippe Ruminy
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, 76000 Rouen, France
| | - Catherine Maingonnat
- INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, 76000 Rouen, France
| | - Stéphane Lepretre
- Department of Hematology, Cancer Center Henri Becquerel, 76000 Rouen, France
| | | | - Stéphane Derrey
- Department of Neurosurgery, Hôpital Charles Nicolle, CHU-Hôpitaux de Rouen, 76031 Rouen, France
| | - Hervé Tilly
- Department of Hematology, Cancer Center Henri Becquerel, 76000 Rouen, France.,INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, 76000 Rouen, France
| | | | - Annie Laquerrière
- INSERM U1245 and Hôpital Charles Nicolle, NeoVasc Team, University of Normandy, UNIVROUEN, CHU-Hôpitaux de Rouen, 76031 Rouen, France.,Department of Neuropathology, Hôpital Charles Nicolle, Normandy Center for Genomic and Personalized Medicine, CHU-Hôpitaux de Rouen, 76031 Rouen, France
| | - Fabrice Jardin
- Department of Hematology, Cancer Center Henri Becquerel, 76000 Rouen, France.,INSERM U1245, Cancer Center Henri Becquerel, Institute of Research and Innovation in Biomedicine (IRIB), University of Normandy, UNIVROUEN, 76000 Rouen, France
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77
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Nishio S, Moteki H, Usami S. Simple and efficient germline copy number variant visualization method for the Ion AmpliSeq™ custom panel. Mol Genet Genomic Med 2018; 6:678-686. [PMID: 29633566 PMCID: PMC6081219 DOI: 10.1002/mgg3.399] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 03/02/2018] [Accepted: 03/06/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Recent advances in molecular genetic analysis using next-generation sequencing (NGS) have drastically accelerated the identification of disease-causing gene mutations. Most next-generation sequencing analyses of inherited diseases have mainly focused on single-nucleotide variants and short indels, although, recently, structure variations including copy number variations have come to be considered an important cause of many different diseases. However, only a limited number of tools are available for multiplex PCR-based target genome enrichment. METHODS In this paper, we reported a simple and efficient copy number variation visualization method for Ion AmpliSeq™ target resequencing data. Unlike the hybridization capture-based target genome enrichment system, Ion AmpliSeq™ reads are multiplex PCR products, and each read generated by the same amplicon is quite uniform in length and position. Based on this feature, the depth of coverage information for each amplicon included in the barcode/amplicon coverage matrix file was used for copy number detection analysis. We also performed copy number analysis to investigate the utility of this method through the use of positive controls and a large Japanese hearing loss cohort. RESULTS Using this method, we successfully confirmed previously reported copy number loss cases involving the STRC gene and copy number gain in trisomy 21 cases. We also performed copy number analysis of a large Japanese hearing loss cohort (2,475 patients) and identified many gene copy number variants. The most prevalent copy number variation was STRC gene copy number loss, with 129 patients carrying this copy number variation. CONCLUSION Our copy number visualization method for Ion AmpliSeq™ data can be utilized in efficient copy number analysis for the comparison of a large number of samples. This method is simple and requires only easy calculations using standard spread sheet software.
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Affiliation(s)
- Shin‐ya Nishio
- Department of OtorhinolaryngologyShinshu University School of MedicineMatsumoto CityJapan
| | - Hideaki Moteki
- Department of OtorhinolaryngologyShinshu University School of MedicineMatsumoto CityJapan
| | - Shin‐ichi Usami
- Department of OtorhinolaryngologyShinshu University School of MedicineMatsumoto CityJapan
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78
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Wang YA, Jian JW, Hung CF, Peng HP, Yang CF, Cheng HCS, Yang AS. Germline breast cancer susceptibility gene mutations and breast cancer outcomes. BMC Cancer 2018; 18:315. [PMID: 29566657 PMCID: PMC5863855 DOI: 10.1186/s12885-018-4229-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 03/15/2018] [Indexed: 01/07/2023] Open
Abstract
Background It is unclear whether germline breast cancer susceptibility gene mutations affect breast cancer related outcomes. We wanted to evaluate mutation patterns in 20 breast cancer susceptibility genes and correlate the mutations with clinical characteristics to determine the effects of these germline mutations on breast cancer prognosis. Methods The study cohort included 480 ethnic Chinese individuals in Taiwan with at least one of the six clinical risk factors for hereditary breast cancer: family history of breast or ovarian cancer, young age of onset for breast cancer, bilateral breast cancer, triple negative breast cancer, both breast and ovarian cancer, and male breast cancer. PCR-enriched amplicon-sequencing on a next generation sequencing platform was used to determine the germline DNA sequences of all exons and exon-flanking regions of the 20 genes. Protein-truncating variants were identified as pathogenic. Results We detected a 13.5% carrier rate of pathogenic germline mutations, with BRCA2 being the most prevalent and the non-BRCA genes accounting for 38.5% of the mutation carriers. BRCA mutation carriers were more likely to be diagnosed of breast cancer with lymph node involvement (66.7% vs 42.6%; P = 0.011), and had significantly worse breast cancer specific outcomes. The 5-year disease-free survival was 73.3% for BRCA mutation carriers and 91.1% for non-carriers (hazard ratio for recurrence or death 2.42, 95% CI 1.29–4.53; P = 0.013). After adjusting for clinical prognostic factors, BRCA mutation remained an independent poor prognostic factor for cancer recurrence or death (adjusted hazard ratio 3.04, 95% CI 1.40–6.58; P = 0.005). Non-BRCA gene mutation carriers did not exhibit any significant difference in cancer characteristics or outcomes compared to those without detected mutations. Among the risk factors for hereditary breast cancer, the odds of detecting a germline mutation increased significantly with having bilateral breast cancer (adjusted odds ratio 3.27, 95% CI 1.64–6.51; P = 0.0008) or having more than one risk factor (odds ratio 2.07, 95% CI 1.22–3.51; P = 0.007). Conclusions Without prior knowledge of the mutation status, BRCA mutation carriers had more advanced breast cancer on initial diagnosis and worse cancer-related outcomes. Optimal approach to breast cancer treatment for BRCA mutation carriers warrants further investigation. Electronic supplementary material The online version of this article (10.1186/s12885-018-4229-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yong Alison Wang
- Department of Internal Medicine, Koo Foundation Sun-Yat Sen Cancer Center, Taipei, Taiwan.
| | - Jhih-Wei Jian
- Genomic Research Center, Academia Sinica, Taipei, Taiwan.,Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan.,Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Science, Academia Sinica, Taipei, Taiwan
| | - Chen-Fang Hung
- Department of Research, Koo Foundation Sun-Yat Sen Cancer Center, Taipei, Taiwan
| | - Hung-Pin Peng
- Genomic Research Center, Academia Sinica, Taipei, Taiwan
| | - Chi-Fan Yang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hung-Chun Skye Cheng
- Department of Research, Koo Foundation Sun-Yat Sen Cancer Center, Taipei, Taiwan.,Department of Radiation Oncology, Koo Foundation Sun-Yat Sen Cancer Center, Taipei, Taiwan
| | - An-Suei Yang
- Genomic Research Center, Academia Sinica, Taipei, Taiwan.
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Lesueur P, Chevalier F, El-Habr EA, Junier MP, Chneiweiss H, Castera L, Müller E, Stefan D, Saintigny Y. Radiosensitization Effect of Talazoparib, a Parp Inhibitor, on Glioblastoma Stem Cells Exposed to Low and High Linear Energy Transfer Radiation. Sci Rep 2018; 8:3664. [PMID: 29483558 PMCID: PMC5826933 DOI: 10.1038/s41598-018-22022-4] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 02/15/2018] [Indexed: 11/09/2022] Open
Abstract
Despite continuous improvements in treatment of glioblastoma, tumor recurrence and therapy resistance still occur in a high proportion of patients. One underlying reason for this radioresistance might be the presence of glioblastoma cancer stem cells (GSCs), which feature high DNA repair capability. PARP protein plays an important cellular role by detecting the presence of damaged DNA and then activating signaling pathways that promote appropriate cellular responses. Thus, PARP inhibitors (PARPi) have recently emerged as potential radiosensitizing agents. In this study, we investigated the preclinical efficacy of talazoparib, a new PARPi, in association with low and high linear energy transfer (LET) irradiation in two GSC cell lines. Reduction of GSC fraction, impact on cell proliferation, and cell cycle arrest were evaluated for each condition. All combinations were compared with a reference schedule: photonic irradiation combined with temozolomide. The use of PARPi combined with photon beam and even more carbon beam irradiation drastically reduced the GSC frequency of GBM cell lines in vitro. Furthermore, talazoparib combined with irradiation induced a marked and prolonged G2/M block, and decreased proliferation. These results show that talazoparib is a new candidate that effects radiosensitization in radioresistant GSCs, and its combination with high LET irradiation, is promising.
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Affiliation(s)
- Paul Lesueur
- LARIA, iRCM, François Jacob Institute, DRF-CEA, Caen, France.
- UMR6252 CIMAP, CEA - CNRS - ENSICAEN - Université de Caen Normandie, Caen, France.
- Radiotherapy Department, Centre François Baclesse, Caen, France.
| | - François Chevalier
- LARIA, iRCM, François Jacob Institute, DRF-CEA, Caen, France
- UMR6252 CIMAP, CEA - CNRS - ENSICAEN - Université de Caen Normandie, Caen, France
| | - Elias A El-Habr
- CNRS UMR8246, Inserm U1130, UPMC, Neuroscience Seine-IBPS, Sorbonne Universities, 75005, Paris, France
| | - Marie-Pierre Junier
- CNRS UMR8246, Inserm U1130, UPMC, Neuroscience Seine-IBPS, Sorbonne Universities, 75005, Paris, France
| | - Hervé Chneiweiss
- CNRS UMR8246, Inserm U1130, UPMC, Neuroscience Seine-IBPS, Sorbonne Universities, 75005, Paris, France
| | - Laurent Castera
- Plateforme de sequencage haut debit, Centre François Baclesse, Caen, France
| | - Etienne Müller
- Plateforme de sequencage haut debit, Centre François Baclesse, Caen, France
| | - Dinu Stefan
- Radiotherapy Department, Centre François Baclesse, Caen, France
| | - Yannick Saintigny
- LARIA, iRCM, François Jacob Institute, DRF-CEA, Caen, France
- UMR6252 CIMAP, CEA - CNRS - ENSICAEN - Université de Caen Normandie, Caen, France
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80
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Luo Z, Fan X, Su Y, Huang YS. Accurity: accurate tumor purity and ploidy inference from tumor-normal WGS data by jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants. Bioinformatics 2018; 34:2004-2011. [PMID: 29385401 PMCID: PMC9881684 DOI: 10.1093/bioinformatics/bty043] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Accepted: 01/26/2018] [Indexed: 02/02/2023] Open
Abstract
Motivation Tumor purity and ploidy have a substantial impact on next-gen sequence analyses of tumor samples and may alter the biological and clinical interpretation of results. Despite the existence of several computational methods that are dedicated to estimate tumor purity and/or ploidy from The Cancer Genome Atlas (TCGA) tumor-normal whole-genome-sequencing (WGS) data, an accurate, fast and fully-automated method that works in a wide range of sequencing coverage, level of tumor purity and level of intra-tumor heterogeneity, is still missing. Results We describe a computational method called Accurity that infers tumor purity, tumor cell ploidy and absolute allelic copy numbers for somatic copy number alterations (SCNAs) from tumor-normal WGS data by jointly modelling SCNAs and heterozygous germline single-nucleotide-variants (HGSNVs). Results from both in silico and real sequencing data demonstrated that Accurity is highly accurate and robust, even in low-purity, high-ploidy and low-coverage settings in which several existing methods perform poorly. Accounting for tumor purity and ploidy, Accurity significantly increased signal/noise gaps between different copy numbers. We are hopeful that Accurity is of clinical use for identifying cancer diagnostic biomarkers. Availability and implementation Accurity is implemented in C++/Rust, available at http://www.yfish.org/software/. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Yao Su
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yu S Huang
- To whom correspondence should be addressed.
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81
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Dubot C, Bernard V, Sablin MP, Vacher S, Chemlali W, Schnitzler A, Pierron G, Ait Rais K, Bessoltane N, Jeannot E, Klijanienko J, Mariani O, Jouffroy T, Calugaru V, Hoffmann C, Lesnik M, Badois N, Berger F, Le Tourneau C, Kamal M, Bieche I. Comprehensive genomic profiling of head and neck squamous cell carcinoma reveals FGFR1 amplifications and tumour genomic alterations burden as prognostic biomarkers of survival. Eur J Cancer 2018; 91:47-55. [PMID: 29331751 DOI: 10.1016/j.ejca.2017.12.016] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/25/2017] [Accepted: 12/09/2017] [Indexed: 12/20/2022]
Abstract
BACKGROUND We aimed at identifying deleterious genomic alterations from untreated head and neck squamous cell carcinoma (HNSCC) patients, and assessing their prognostic value. PATIENTS AND METHODS We retrieved 122 HNSCC patients who underwent primary surgery. Targeted NGS was used to analyse a panel of 100 genes selected among the most frequently altered genes in HNSCC and potential therapeutic targets. We selected only deleterious (activating or inactivating) single nucleotide variations, and copy number variations for analysis. Univariate and multivariate analyses were performed to assess the prognostic value of altered genes. RESULTS A median of 2 (range: 0-10) genomic alterations per sample was observed. Most frequently altered genes involved the cell cycle pathway (TP53 [60%], CCND1 [30%], CDKN2A [25%]), the PI3K/AKT/MTOR pathway (PIK3CA [12%]), tyrosine kinase receptors (EGFR [9%], FGFR1 [5%]) and cell differentiation (FAT1 [7%], NOTCH1 [4%]). TP53 mutations (p = 0.003), CCND1 amplifications (p = 0.04), CDKN2A alterations (p = 0.02) and FGFR1 amplifications (p = 0.003), correlated with shorter overall survival (OS). The number of genomic alterations was significantly higher in the HPV-negative population (p = 0.029) and correlated with a shorter OS (p < 0.0001). Only TP53 mutation and FGFR1 amplification status remained statistically significant in the multivariate analysis. CONCLUSION These results suggest that genomic alterations involving the cell cycle (TP53, CCND1, CDKN2A), as well as FGFR1 amplifications and tumour genomic alterations burden are prognostic biomarkers and might be therapeutic targets for patients with HNSCC.
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Affiliation(s)
- C Dubot
- Department of Medical Oncology, Institut Curie, Paris, Saint-Cloud, France; Unit of Pharmacogenomics, Department of Genetics, Institut Curie, Paris, France.
| | - V Bernard
- Unit of Bioinformatics, Next Generation Sequencing Platform-ICGex, Institut Curie, Paris, France
| | - M P Sablin
- Department of Medical Oncology, Institut Curie, Paris, Saint-Cloud, France
| | - S Vacher
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, Paris, France
| | - W Chemlali
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, Paris, France
| | - A Schnitzler
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, Paris, France
| | - G Pierron
- Unit of Somatic Genomics, Department of Genetics, Institut Curie, Paris, France
| | - K Ait Rais
- Unit of Somatic Genomics, Department of Genetics, Institut Curie, Paris, France
| | - N Bessoltane
- Unit of Bioinformatics, Next Generation Sequencing Platform-ICGex, Institut Curie, Paris, France
| | - E Jeannot
- Department of Biopathology, Institut Curie, Paris, France
| | - J Klijanienko
- Department of Biopathology, Institut Curie, Paris, France
| | - O Mariani
- Department of Biopathology, Institut Curie, Paris, France
| | - T Jouffroy
- Department of Surgery, Institut Curie, Paris, France
| | - V Calugaru
- Department of Radiotherapy, Institut Curie, Paris, France
| | - C Hoffmann
- Department of Surgery, Institut Curie, Paris, France
| | - M Lesnik
- Department of Surgery, Institut Curie, Paris, France
| | - N Badois
- Department of Surgery, Institut Curie, Paris, France
| | - F Berger
- Department of Biostatistics, Institut Curie, Paris, France
| | - C Le Tourneau
- Department of Medical Oncology, Institut Curie, Paris, Saint-Cloud, France; INSERM U900 Research Unit, Saint-Cloud, France
| | - M Kamal
- Department of Medical Oncology, Institut Curie, Paris, Saint-Cloud, France
| | - I Bieche
- Unit of Pharmacogenomics, Department of Genetics, Institut Curie, Paris, France; EA7331, Paris Descartes University, Faculty of Pharmaceutical and Biological Sciences, Paris, France
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82
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van Riet J, Krol NMG, Atmodimedjo PN, Brosens E, van IJcken WFJ, Jansen MPHM, Martens JWM, Looijenga LH, Jenster G, Dubbink HJ, Dinjens WNM, van de Werken HJG. SNPitty: An Intuitive Web Application for Interactive B-Allele Frequency and Copy Number Visualization of Next-Generation Sequencing Data. J Mol Diagn 2018; 20:166-176. [PMID: 29305224 DOI: 10.1016/j.jmoldx.2017.11.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 11/16/2017] [Accepted: 11/27/2017] [Indexed: 01/19/2023] Open
Abstract
Exploration and visualization of next-generation sequencing data are crucial for clinical diagnostics. Software allowing simultaneous visualization of multiple regions of interest coupled with dynamic heuristic filtering of genetic aberrations is, however, lacking. Therefore, the authors developed the web application SNPitty that allows interactive visualization and interrogation of variant call format files by using B-allele frequencies of single-nucleotide polymorphisms and single-nucleotide variants, coverage metrics, and copy numbers analysis results. SNPitty displays variant alleles and allelic imbalances with a focus on loss of heterozygosity and copy number variation using genome-wide heterozygous markers and somatic mutations. In addition, SNPitty is capable of generating predefined reports that summarize and highlight disease-specific targets of interest. SNPitty was validated for diagnostic interpretation of somatic events by showcasing a serial dilution series of glioma tissue. Additionally, SNPitty is demonstrated in four cancer-related scenarios encountered in daily clinical practice and on whole-exome sequencing data of peripheral blood from a Down syndrome patient. SNPitty allows detection of loss of heterozygosity, chromosomal and gene amplifications, homozygous or heterozygous deletions, somatic mutations, or any combination thereof in regions or genes of interest. Furthermore, SNPitty can be used to distinguish molecular relationships between multiple tumors from a single patient. On the basis of these data, the authors demonstrate that SNPitty is robust and user friendly in a wide range of diagnostic scenarios.
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Affiliation(s)
- Job van Riet
- Cancer Computational Biology Center, Erasmus MC, University Medical Center, Rotterdam, the Netherlands; Department of Urology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Niels M G Krol
- Cancer Computational Biology Center, Erasmus MC, University Medical Center, Rotterdam, the Netherlands; Department of Pathology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Peggy N Atmodimedjo
- Department of Pathology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Erwin Brosens
- Department of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | | | - Maurice P H M Jansen
- Department of Medical Oncology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Leendert H Looijenga
- Department of Pathology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Guido Jenster
- Department of Urology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Hendrikus J Dubbink
- Department of Pathology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Harmen J G van de Werken
- Cancer Computational Biology Center, Erasmus MC, University Medical Center, Rotterdam, the Netherlands; Department of Urology, Erasmus MC, University Medical Center, Rotterdam, the Netherlands.
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83
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Calling Chromosome Alterations, DNA Methylation Statuses, and Mutations in Tumors by Simple Targeted Next-Generation Sequencing. J Mol Diagn 2017; 19:776-787. [DOI: 10.1016/j.jmoldx.2017.06.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 06/01/2017] [Indexed: 12/16/2022] Open
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Russo M, Broach J, Sheldon K, Houser KR, Liu DJ, Kesterson J, Phaeton R, Hossler C, Hempel N, Baker M, Newell JM, Zaino R, Warrick JI. Clonal evolution in paired endometrial intraepithelial neoplasia/atypical hyperplasia and endometrioid adenocarcinoma. Hum Pathol 2017; 67:69-77. [PMID: 28712776 DOI: 10.1016/j.humpath.2017.07.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 06/18/2017] [Accepted: 07/05/2017] [Indexed: 12/01/2022]
Abstract
Endometrial intraepithelial neoplasia (EIN) and atypical endometrial hyperplasia (AH) are histomorphologically defined precursors to endometrioid adenocarcinoma, which are unified as EIN/AH by the World Health Organization. EIN/AH harbors a constellation of molecular alterations similar to those found in endometrioid adenocarcinoma. However, the process of clonal evolution from EIN/AH to carcinoma is poorly characterized. To investigate, we performed next-generation sequencing, copy number alteration (CNA) analysis, and immunohistochemistry for mismatch repair protein expression on EIN/AH and endometrioid adenocarcinoma samples from 6 hysterectomy cases with spatially distinct EIN/AH and carcinoma. In evaluating all samples, EIN/AH and carcinoma did not differ in mutational burden, CNA burden, or specific genes mutated (all P>.1). All paired EIN/AH and carcinoma samples shared at least one identical somatic mutation, frequently in PI(3)K pathway members. Large CNAs (>10 genes in length) were identified in 83% of cases; paired EIN/AH and carcinoma samples shared at least one identical CNA in these cases. Mismatch repair protein expression matched in all paired EIN/AH and carcinoma samples. All paired EIN/AH and carcinoma samples had identical The Cancer Genome Atlas subtype, with 3 classified as "copy number low endometrioid" and 3 classified as "microsatellite instability hypermutated." Although paired EIN/AH and carcinoma samples were clonal, private mutations (ie, present in only one sample) were identified in EIN/AH and carcinoma in all cases, frequently in established cancer-driving genes. These findings indicate that EIN/AH gives rise to endometrioid adenocarcinoma by a complex process of subclone evolution, not a linear accumulation of molecular events.
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Affiliation(s)
- Mariano Russo
- Department of Biochemistry, Penn State College of Medicine and Milton S. Hershey Medical Center, Hershey, PA 17033; Institute for Personalized Medicine, Penn State College of Medicine and Milton S. Hershey Medical Center, Hershey, PA 17033
| | - James Broach
- Department of Biochemistry, Penn State College of Medicine and Milton S. Hershey Medical Center, Hershey, PA 17033; Institute for Personalized Medicine, Penn State College of Medicine and Milton S. Hershey Medical Center, Hershey, PA 17033
| | - Kathryn Sheldon
- Department of Biochemistry, Penn State College of Medicine and Milton S. Hershey Medical Center, Hershey, PA 17033; Institute for Personalized Medicine, Penn State College of Medicine and Milton S. Hershey Medical Center, Hershey, PA 17033
| | - Kenneth R Houser
- Department of Biochemistry, Penn State College of Medicine and Milton S. Hershey Medical Center, Hershey, PA 17033; Institute for Personalized Medicine, Penn State College of Medicine and Milton S. Hershey Medical Center, Hershey, PA 17033
| | - Dajiang J Liu
- Institute for Personalized Medicine, Penn State College of Medicine and Milton S. Hershey Medical Center, Hershey, PA 17033; Public Health Sciences, Penn State College of Medicine, Hershey, PA 17033
| | - Joshua Kesterson
- Department of Obstetrics and Gynecology, Penn State College of Medicine and Milton S. Hershey Medical Center, Hershey, PA 17033
| | - Rebecca Phaeton
- Department of Obstetrics and Gynecology, Penn State College of Medicine and Milton S. Hershey Medical Center, Hershey, PA 17033
| | - Carrie Hossler
- Department of Obstetrics and Gynecology, Penn State College of Medicine and Milton S. Hershey Medical Center, Hershey, PA 17033
| | - Nadine Hempel
- Department of Pharmacology, Penn State College of Medicine and Milton S. Hershey Medical Center, Hershey, PA 17033
| | - Maria Baker
- Department of Medicine, Penn State College of Medicine and Milton S. Hershey Medical Center, Penn State Cancer Institute, Hershey, PA 17033
| | - Jordan M Newell
- Department of Pathology, Penn State College of Medicine and Milton S. Hershey Medical Center, Hershey, PA 17033
| | - Richard Zaino
- Department of Pathology, Penn State College of Medicine and Milton S. Hershey Medical Center, Hershey, PA 17033
| | - Joshua I Warrick
- Department of Pathology, Penn State College of Medicine and Milton S. Hershey Medical Center, Hershey, PA 17033.
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The AURORA pilot study for molecular screening of patients with advanced breast cancer-a study of the breast international group. NPJ Breast Cancer 2017; 3:23. [PMID: 28685159 PMCID: PMC5491498 DOI: 10.1038/s41523-017-0026-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 05/04/2017] [Accepted: 06/01/2017] [Indexed: 12/24/2022] Open
Abstract
Several studies have demonstrated the feasibility of molecular screening of tumour samples for matching patients with cancer to targeted therapies. However, most of them have been carried out at institutional or national level. Herein, we report on the pilot phase of AURORA (NCT02102165), a European multinational collaborative molecular screening initiative for advanced breast cancer patients. Forty-one patients were prospectively enroled at four participating centres across Europe. Metastatic tumours were biopsied and profiled using an Ion Torrent sequencing platform at a central facility. Sequencing results were obtained for 63% of the patients in real-time with variable turnaround time stemming from delays between patient consent and biopsy. At least one clinically actionable mutation was identified in 73% of patients. We used the Illumina sequencing technology for orthogonal validation and achieved an average of 66% concordance of substitution calls per patient. Additionally, copy number aberrations inferred from the Ion Torrent sequencing were compared to single nucleotide polymorphism arrays and found to be 59% concordant on average. Although this study demonstrates that powerful next generation genomic techniques are logistically ready for international molecular screening programs in routine clinical settings, technical challenges remain to be addressed in order to ensure the accuracy and clinical utility of the genomic data. A pilot study demonstrated that a large-scale, international screening programme for women with metastatic breast cancer is feasible. The study, coordinated by the Institut Jules Bordet and the Breast International Group, aimed to determine whether biopsies and blood could be collected from women with metastatic breast cancer across Europe and sent to a central laboratory for targeted gene sequencing. Genetic information was successfully obtained for 26 of the 41 participants, 19 of whom had mutations that could be targeted with a known drug, potentially influencing treatment decision-making. They concluded that genomic testing is logistically ready for international molecular screening in routine clinical settings laying the groundwork for the parent European AURORA molecular screening programme which aims at recruiting 1300 metastatic breast cancer patients. However, technical challenges remain to be addressed to ensure the accuracy and robustness across different sequencing platforms.
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86
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Goldenberg D, Russo M, Houser K, Crist H, Derr JB, Walter V, Warrick JI, Sheldon KE, Broach J, Bann DV. Altered molecular profile in thyroid cancers from patients affected by the Three Mile Island nuclear accident. Laryngoscope 2017; 127 Suppl 3:S1-S9. [PMID: 28555940 DOI: 10.1002/lary.26687] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/20/2017] [Indexed: 01/02/2023]
Abstract
OBJECTIVES/HYPOTHESIS In 1979, Three Mile Island (TMI) nuclear power plant experienced a partial meltdown with release of radioactive material. The effects of the accident on thyroid cancer (TC) in the surrounding population remain unclear. Radiation-induced TCs have a lower incidence of single nucleotide oncogenic driver mutations and higher incidence of gene fusions. We used next generation sequencing (NGS) to identify molecular signatures of radiation-induced TC in a cohort of TC patients residing near TMI during the time of the accident. STUDY DESIGN Case series. METHODS We identified 44 patients who developed papillary thyroid carcinoma between 1974 and 2014. Patients who developed TC between 1984 and 1996 were at risk for radiation-induced TC, patients who developed TC before 1984 or after 1996 were the control group. We used targeted NGS of paired tumor and normal tissue from each patient to identify single nucleotide oncogenic driver mutations. Oncogenic gene fusions were identified using quantitative reverse transcription polymerase chain reaction. RESULTS We identified 15 patients in the at-risk group and 29 patients in the control group. BRAFV600E mutations were identified in 53% patients in the at-risk group and 83% patients in the control group. The proportion of patients with BRAF mutations in the at-risk group was significantly lower than predicted by the The Cancer Genome Atlas cohort. Gene fusion or somatic copy number alteration drivers were identified in 33% tumors in the at-risk group and 14% of tumors in the control group. CONCLUSIONS Findings were consistent with observations from other radiation-exposed populations. These data raise the possibility that radiation released from TMI may have altered the molecular profile of TC in the population surrounding TMI. LEVEL OF EVIDENCE 4 Laryngoscope, 127:S1-S9, 2017.
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Affiliation(s)
- David Goldenberg
- Department of Surgery, Pennsylvania State University, College of Medicine, Hershey, Pennsylvania, U.S.A
| | - Mariano Russo
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, College of Medicine, Hershey, Pennsylvania, U.S.A
| | - Kenneth Houser
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, College of Medicine, Hershey, Pennsylvania, U.S.A
| | - Henry Crist
- Department of Pathology, Pennsylvania State University, College of Medicine, Hershey, Pennsylvania, U.S.A
| | - Jonathan B Derr
- Department of Surgery, Pennsylvania State University, College of Medicine, Hershey, Pennsylvania, U.S.A
| | - Vonn Walter
- Institute for Personalized Medicine, Pennsylvania State University, College of Medicine, Hershey, Pennsylvania, U.S.A
| | - Joshua I Warrick
- Department of Pathology, Pennsylvania State University, College of Medicine, Hershey, Pennsylvania, U.S.A
| | - Kathryn E Sheldon
- Department of Biochemistry and Public Health Sciences, Pennsylvania State University, College of Medicine, Hershey, Pennsylvania, U.S.A
| | - James Broach
- Department of Biochemistry and Public Health Sciences, Pennsylvania State University, College of Medicine, Hershey, Pennsylvania, U.S.A
| | - Darrin V Bann
- Department of Surgery, Pennsylvania State University, College of Medicine, Hershey, Pennsylvania, U.S.A.,Department of Biochemistry and Public Health Sciences, Pennsylvania State University, College of Medicine, Hershey, Pennsylvania, U.S.A
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Page K, Guttery DS, Fernandez-Garcia D, Hills A, Hastings RK, Luo J, Goddard K, Shahin V, Woodley-Barker L, Rosales BM, Coombes RC, Stebbing J, Shaw JA. Next Generation Sequencing of Circulating Cell-Free DNA for Evaluating Mutations and Gene Amplification in Metastatic Breast Cancer. Clin Chem 2017; 63:532-541. [PMID: 27940449 PMCID: PMC6241835 DOI: 10.1373/clinchem.2016.261834] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 09/19/2016] [Indexed: 12/21/2022]
Abstract
BACKGROUND Breast cancer tissues are heterogeneous and show diverse somatic mutations and somatic copy number alterations (CNAs). We used a novel targeted next generation sequencing (NGS) panel to examine cell-free DNA (cfDNA) to detect somatic mutations and gene amplification in women with metastatic breast cancer (MBC). METHODS cfDNA from pretreated patients (n = 42) and 9 healthy controls were compared with matched lymphocyte DNA by NGS, using a custom 158 amplicon panel covering hot-spot mutations and CNAs in 16 genes, with further validation of results by droplet digital PCR. RESULTS No mutations were identified in cfDNA of healthy controls, whereas exactly half the patients with metastatic breast cancer had at least one mutation or amplification in cfDNA (mean 2, range 1-6) across a total of 13 genes. Longitudinal follow up showed dynamic changes to mutations and gene amplification in cfDNA indicating clonal and subclonal response to treatment that was more dynamic than cancer antigen 15-3 (CA15-3). Interestingly, at the time of blood sampling disease progression was occurring in 7 patients with erb-b2 receptor tyrosine kinase 2 (ERBB2) gene amplification in their cfDNA and 3 of these patients were human epidermal growth factor receptor 2 (HER2) negative at diagnosis, suggesting clonal evolution to a more aggressive phenotype. Lastly, 6 patients harbored estrogen receptor 1 (ESR1) mutations in cfDNA, suggesting resistance to endocrine therapy. Overall 9 of 42 patients (21%) had alterations in cfDNA that could herald a change in treatment. CONCLUSIONS Targeted NGS of cfDNA has potential for monitoring response to targeted therapies through both mutations and gene amplification, for analysis of dynamic tumor heterogeneity and stratification to targeted therapy.
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Affiliation(s)
- Karen Page
- Department of Cancer Studies and Cancer Research UK Leicester Centre, University of Leicester, Leicester, UK
| | - David S Guttery
- Department of Cancer Studies and Cancer Research UK Leicester Centre, University of Leicester, Leicester, UK
| | - Daniel Fernandez-Garcia
- Department of Cancer Studies and Cancer Research UK Leicester Centre, University of Leicester, Leicester, UK
| | - Allison Hills
- Department of Surgery and Cancer, Division of Cancer, and
| | - Robert K Hastings
- Department of Cancer Studies and Cancer Research UK Leicester Centre, University of Leicester, Leicester, UK
| | - Jinli Luo
- Department of Cancer Studies and Cancer Research UK Leicester Centre, University of Leicester, Leicester, UK
| | - Kate Goddard
- Department of Medical Oncology, Imperial College London, Charing Cross Hospital, London, UK
| | - Vedia Shahin
- Department of Medical Oncology, Imperial College London, Charing Cross Hospital, London, UK
| | - Laura Woodley-Barker
- Department of Medical Oncology, Imperial College London, Charing Cross Hospital, London, UK
| | | | | | | | - Jacqueline A Shaw
- Department of Cancer Studies and Cancer Research UK Leicester Centre, University of Leicester, Leicester, UK;
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88
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Rizzo D, Viailly PJ, Mareschal S, Bohers E, Picquenot JM, Penther D, Dubois S, Marchand V, Bertrand P, Maingonnat C, Etancelin P, Feuillard J, Bastard C, Tilly H, Jardin F, Ruminy P. Oncogenic events rather than antigen selection pressure may be the main driving forces for relapse in diffuse large B-cell lymphomas. Am J Hematol 2017; 92:68-76. [PMID: 27737507 DOI: 10.1002/ajh.24584] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Revised: 09/29/2016] [Accepted: 10/11/2016] [Indexed: 01/07/2023]
Abstract
Little is known on the phylogenetic relationship between diagnostic and relapse clones of diffuse large B-cell lymphoma (DLBCL). We applied high throughput sequencing (HTS) of the VDJ locus of Immunoglobulin heavy chain (IGHV) on 14 DLBCL patients with serial samples, including tumor biopsies and/or peripheral blood mononuclear cells (PBMC). Phylogenetic data were consolidated with targeted sequencing and cytogenetics. Phylogeny clearly showed that DLBCL relapse could occur according either an early or a late divergent mode. These two modes of divergence were independent from the elapsed time between diagnosis and relapse. We found no significant features for antigen selection pressure in complementary determining region both at diagnosis and relapse for 9/12 pairs and a conserved negative selection pressure for the three remaining cases. Targeted HTS and conventional cytogenetics revealed a branched vs. linear evolution for 5/5 IGHV early divergent cases, but unexpected such "oncogenetic" branched evolution could be found in at least 2/7 IGHV late divergent cases. Thus, if BCR signaling is mandatory for DLBCL emergence, oncogenetic events under chemotherapy selection pressure may be the main driving forces at relapse. Finally, circulating subclones with divergent IGHV somatic hypermutations patterns from initial biopsy could be detected in PBMC at diagnosis for 4/6 patients and, for two of them, at least one was similar to the ones found at relapse. This study highlights that oncogenetic intraclonal diversity of DLBCL should be evaluated beyond the scope a single biopsy and represents a rationale for future investigations using peripheral blood for lymphoid malignancies genotyping. Am. J. Hematol. 92:68-76, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- David Rizzo
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
- Department of biological hematology; Centre Hospitalier Universitaire Dupuytren; Limoges France
| | - Pierre-Julien Viailly
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
| | - Sylvain Mareschal
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
| | - Elodie Bohers
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
| | - Jean-Michel Picquenot
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
- Department of pathology; Centre Henri Becquerel; Rouen France
| | - Dominique Penther
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
- Department of oncology genetics; Centre Henri Becquerel; Rouen France
| | - Sydney Dubois
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
| | - Vinciane Marchand
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
| | - Philippe Bertrand
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
| | - Catherine Maingonnat
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
| | - Pascaline Etancelin
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
- Department of oncology genetics; Centre Henri Becquerel; Rouen France
| | - Jean Feuillard
- Department of biological hematology; Centre Hospitalier Universitaire Dupuytren; Limoges France
- UMR CNRS 7276, University of Limoges; Limoges France
| | - Christian Bastard
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
- Department of oncology genetics; Centre Henri Becquerel; Rouen France
| | - Hervé Tilly
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
- Department of clinical hematology; Centre Henri Becquerel; Rouen France
| | - Fabrice Jardin
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
- Department of clinical hematology; Centre Henri Becquerel; Rouen France
| | - Philippe Ruminy
- INSERM U918, Centre Henri Becquerel, Institute for Research and Innovation in Biomedicine, University of Rouen; Rouen France
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89
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Dubois S, Viailly PJ, Bohers E, Bertrand P, Ruminy P, Marchand V, Maingonnat C, Mareschal S, Picquenot JM, Penther D, Jais JP, Tesson B, Peyrouze P, Figeac M, Desmots F, Fest T, Haioun C, Lamy T, Copie-Bergman C, Fabiani B, Delarue R, Peyrade F, André M, Ketterer N, Leroy K, Salles G, Molina TJ, Tilly H, Jardin F. Biological and Clinical Relevance of Associated Genomic Alterations in MYD88 L265P and non-L265P-Mutated Diffuse Large B-Cell Lymphoma: Analysis of 361 Cases. Clin Cancer Res 2016; 23:2232-2244. [PMID: 27923841 DOI: 10.1158/1078-0432.ccr-16-1922] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 11/01/2016] [Accepted: 11/17/2016] [Indexed: 01/01/2023]
Abstract
Purpose:MYD88 mutations, notably the recurrent gain-of-function L265P variant, are a distinguishing feature of activated B-cell like (ABC) diffuse large B-cell lymphoma (DLBCL), leading to constitutive NFκB pathway activation. The aim of this study was to examine the distinct genomic profiles of MYD88-mutant DLBCL, notably according to the presence of the L265P or other non-L265P MYD88 variants.Experimental Design: A cohort of 361 DLBCL cases (94 MYD88 mutant and 267 MYD88 wild-type) was submitted to next-generation sequencing (NGS) focusing on 34 genes to analyze associated mutations and copy number variations, as well as gene expression profiling, and clinical and prognostic analyses.Results: Importantly, we highlighted different genomic profiles for MYD88 L265P and MYD88 non-L265P-mutant DLBCL, shedding light on their divergent backgrounds. Clustering analysis also segregated subgroups according to associated genetic alterations among patients with the same MYD88 mutation. We showed that associated CD79B and MYD88 L265P mutations act synergistically to increase NFκB pathway activation, although the majority of MYD88 L265P-mutant cases harbors downstream NFκB alterations, which can predict BTK inhibitor resistance. Finally, although the MYD88 L265P variant was not an independent prognostic factor in ABC DLBCL, associated CD79B mutations significantly improved the survival of MYD88 L265P-mutant ABC DLBCL in our cohort.Conclusions: This study highlights the relative heterogeneity of MYD88-mutant DLBCL, adding to the field's knowledge of the theranostic importance of MYD88 mutations, but also of associated alterations, emphasizing the usefulness of genomic profiling to best stratify patients for targeted therapy. Clin Cancer Res; 23(9); 2232-44. ©2016 AACR.
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Affiliation(s)
- Sydney Dubois
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Pierre-Julien Viailly
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France.,LITIS EA 4108, Normandie Université, Rouen, France
| | - Elodie Bohers
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Philippe Bertrand
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Philippe Ruminy
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Vinciane Marchand
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | | | - Sylvain Mareschal
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | | | - Dominique Penther
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | | | | | | | | | | | | | - Corinne Haioun
- Unité Hémopathies Lymphoïdes, AP-HP Hôpital Henri Mondor, Créteil, France
| | | | | | - Bettina Fabiani
- Laboratoire de Pathologie, AP-HP Hôpital Saint Antoine, Paris, France
| | - Richard Delarue
- Department of Hematology, AP-HP Hôpital Necker, Paris, France
| | | | - Marc André
- CHU Dinant Godinne, UcL Namur, Yvoir, Belgium
| | | | - Karen Leroy
- Inserm U955 Team 09, AP-HP Hôpital Henri Mondor, Créteil, France
| | | | - Thierry J Molina
- Pathology, AP-HP Hôpital Necker, Université Paris Descartes, Paris, France
| | - Hervé Tilly
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France
| | - Fabrice Jardin
- Inserm U918, Centre Henri Becquerel, Université de Rouen, IRIB, Rouen, France.
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90
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Demidov G, Simakova T, Vnuchkova J, Bragin A. A statistical approach to detection of copy number variations in PCR-enriched targeted sequencing data. BMC Bioinformatics 2016; 17:429. [PMID: 27770783 PMCID: PMC5075217 DOI: 10.1186/s12859-016-1272-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 09/21/2016] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Multiplex polymerase chain reaction (PCR) is a common enrichment technique for targeted massive parallel sequencing (MPS) protocols. MPS is widely used in biomedical research and clinical diagnostics as the fast and accurate tool for the detection of short genetic variations. However, identification of larger variations such as structure variants and copy number variations (CNV) is still being a challenge for targeted MPS. Some approaches and tools for structural variants detection were proposed, but they have limitations and often require datasets of certain type, size and expected number of amplicons affected by CNVs. In the paper, we describe novel algorithm for high-resolution germinal CNV detection in the PCR-enriched targeted sequencing data and present accompanying tool. RESULTS We have developed a machine learning algorithm for the detection of large duplications and deletions in the targeted sequencing data generated with PCR-based enrichment step. We have performed verification studies and established the algorithm's sensitivity and specificity. We have compared developed tool with other available methods applicable for the described data and revealed its higher performance. CONCLUSION We showed that our method has high specificity and sensitivity for high-resolution copy number detection in targeted sequencing data using large cohort of samples.
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Affiliation(s)
- German Demidov
- Parseq Lab, Birzhevaya, 16, Saint-Petersburg, 199053 Russia
- Department of Mathematics and Information Technology in SPbAU RAS, Khlopina, 8/3, Saint-Petersburg, 194021 Russia
- Genomic and Epigenomic Variation in Disease Group, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003 Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | | | | | - Anton Bragin
- Parseq Lab, Birzhevaya, 16, Saint-Petersburg, 199053 Russia
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91
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Macintyre G, Ylstra B, Brenton JD. Sequencing Structural Variants in Cancer for Precision Therapeutics. Trends Genet 2016; 32:530-542. [PMID: 27478068 DOI: 10.1016/j.tig.2016.07.002] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 07/11/2016] [Accepted: 07/12/2016] [Indexed: 12/18/2022]
Abstract
The identification of mutations that guide therapy selection for patients with cancer is now routine in many clinical centres. The majority of assays used for solid tumour profiling use DNA sequencing to interrogate somatic point mutations because they are relatively easy to identify and interpret. Many cancers, however, including high-grade serous ovarian, oesophageal, and small-cell lung cancer, are driven by somatic structural variants that are not measured by these assays. Therefore, there is currently an unmet need for clinical assays that can cheaply and rapidly profile structural variants in solid tumours. In this review we survey the landscape of 'actionable' structural variants in cancer and identify promising detection strategies based on massively-parallel sequencing.
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Affiliation(s)
- Geoff Macintyre
- Cancer Research UK Cambridge Institute, University of Cambridge, UK
| | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, PO Box 7057, 1007 MB Amsterdam, The Netherlands
| | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, UK.
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92
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Dubbink HJ, Atmodimedjo PN, van Marion R, Krol NMG, Riegman PHJ, Kros JM, van den Bent MJ, Dinjens WNM. Diagnostic Detection of Allelic Losses and Imbalances by Next-Generation Sequencing: 1p/19q Co-Deletion Analysis of Gliomas. J Mol Diagn 2016; 18:775-786. [PMID: 27461031 DOI: 10.1016/j.jmoldx.2016.06.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 05/06/2016] [Accepted: 06/01/2016] [Indexed: 02/05/2023] Open
Abstract
Cancer cells are genomically unstable and accumulate tumor type-specific molecular aberrations, which may represent hallmarks for predicting prognosis and targets for therapy. Co-deletion of chromosomes 1p and 19q marks gliomas with an oligodendroglioma component and predicts a better prognosis and response to chemotherapy. In the current study, we present a novel method to detect chromosome 1p/19q co-deletion or loss of heterozygosity (LOH) in a diagnostic setting, based on single-nucleotide polymorphism (SNP) analysis and next-generation sequencing (NGS). We selected highly polymorphic SNPs distributed evenly over both chromosome arms. To experimentally determine the sensitivity and specificity of targeted SNP analysis, we used DNAs extracted from 49 routine formalin-fixed, paraffin-embedded glioma tissues and compared the outcome with diagnostic microsatellite-based LOH analysis and calculated estimates. We show that targeted SNP analysis by NGS allows reliable detection of 1p and/or 19q deletion in a background of 70% of normal cells according to calculated outcomes, is more sensitive than microsatellite-based LOH analysis, and requires much less DNA. This specific and sensitive SNP assay is broadly applicable for simultaneous allelic imbalance analysis of multiple genomic regions and can be incorporated easily into NGS mutation analyses. The combined mutation and chromosomal imbalance analysis in a single NGS assay is suited perfectly for routine glioma diagnostics and other diagnostic molecular pathology applications.
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Affiliation(s)
- Hendrikus J Dubbink
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands.
| | - Peggy N Atmodimedjo
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ronald van Marion
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Niels M G Krol
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Peter H J Riegman
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Johan M Kros
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Martin J van den Bent
- Department of Neuro-Oncology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute, University Medical Center Rotterdam, Rotterdam, The Netherlands
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93
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Mason-Suares H, Landry L, S. Lebo M. Detecting Copy Number Variation via Next Generation Technology. CURRENT GENETIC MEDICINE REPORTS 2016. [DOI: 10.1007/s40142-016-0091-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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94
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Peng CH, Liao CT, Ng KP, Tai AS, Peng SC, Yeh JP, Chen SJ, Tsao KC, Yen TC, Hsieh WP. Somatic copy number alterations detected by ultra-deep targeted sequencing predict prognosis in oral cavity squamous cell carcinoma. Oncotarget 2016; 6:19891-906. [PMID: 26087196 PMCID: PMC4637328 DOI: 10.18632/oncotarget.4336] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 05/23/2015] [Indexed: 12/20/2022] Open
Abstract
Background Ultra-deep targeted sequencing (UDT-Seq) has advanced our knowledge on the incidence and functional significance of somatic mutations. However, the utility of UDT-Seq in detecting copy number alterations (CNAs) remains unclear. With the goal of improving molecular prognostication and identifying new therapeutic targets, we designed this study to assess whether UDT-Seq may be useful for detecting CNA in oral cavity squamous cell carcinoma (OSCC). Methods We sequenced a panel of clinically actionable cancer mutations in 310 formalin-fixed paraffin-embedded OSCC specimens. A linear model was developed to overcome uneven coverage across target regions and multiple samples. The 5-year rates of secondary primary tumors, local recurrence, neck recurrence, distant metastases, and survival served as the outcome measures. We confirmed the prognostic significance of the CNA signatures in an independent sample of 105 primary OSCC specimens. Results The CNA burden across 10 targeted genes was found to predict prognosis in two independent cohorts. FGFR1 and PIK3CAamplifications were associated with prognosis independent of clinical risk factors. Genes exhibiting CNA were clustered in the proteoglycan metabolism, the FOXO signaling, and the PI3K-AKT signaling pathways, for which targeted drugs are already available or currently under development. Conclusions UDT-Seq is clinically useful to identify CNA, which significantly improve the prognostic information provided by traditional clinicopathological risk factors in OSCC patients.
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Affiliation(s)
- Chien-Hua Peng
- Departments of Resource Center for Clinical Research, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C
| | - Chun-Ta Liao
- Otorhinolaryngology, Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C.,Head and Neck Oncology Group, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C
| | - Ka-Pou Ng
- Institute of Statistics, National Tsing Hua University, Hsinchu, Taiwan, R.O.C
| | - An-Shun Tai
- Institute of Statistics, National Tsing Hua University, Hsinchu, Taiwan, R.O.C
| | - Shih-Chi Peng
- Department of Nuclear Medicine and Molecular Imaging Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C
| | - Jen-Pao Yeh
- Institute of Statistics, National Tsing Hua University, Hsinchu, Taiwan, R.O.C
| | - Shu-Jen Chen
- Department of Biomedical Sciences, School of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C
| | - Kuo-Chien Tsao
- Medical Biotechnology and Laboratory Science, Research Center for Emerging Viral Infections, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C.,Laboratory Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C
| | - Tzu-Chen Yen
- Department of Nuclear Medicine and Molecular Imaging Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C
| | - Wen-Ping Hsieh
- Otorhinolaryngology, Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C
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95
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Talevich E, Shain AH, Botton T, Bastian BC. CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing. PLoS Comput Biol 2016; 12:e1004873. [PMID: 27100738 PMCID: PMC4839673 DOI: 10.1371/journal.pcbi.1004873] [Citation(s) in RCA: 1341] [Impact Index Per Article: 149.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 03/16/2016] [Indexed: 01/19/2023] Open
Abstract
Germline copy number variants (CNVs) and somatic copy number alterations (SCNAs) are of significant importance in syndromic conditions and cancer. Massively parallel sequencing is increasingly used to infer copy number information from variations in the read depth in sequencing data. However, this approach has limitations in the case of targeted re-sequencing, which leaves gaps in coverage between the regions chosen for enrichment and introduces biases related to the efficiency of target capture and library preparation. We present a method for copy number detection, implemented in the software package CNVkit, that uses both the targeted reads and the nonspecifically captured off-target reads to infer copy number evenly across the genome. This combination achieves both exon-level resolution in targeted regions and sufficient resolution in the larger intronic and intergenic regions to identify copy number changes. In particular, we successfully inferred copy number at equivalent to 100-kilobase resolution genome-wide from a platform targeting as few as 293 genes. After normalizing read counts to a pooled reference, we evaluated and corrected for three sources of bias that explain most of the extraneous variability in the sequencing read depth: GC content, target footprint size and spacing, and repetitive sequences. We compared the performance of CNVkit to copy number changes identified by array comparative genomic hybridization. We packaged the components of CNVkit so that it is straightforward to use and provides visualizations, detailed reporting of significant features, and export options for integration into existing analysis pipelines. CNVkit is freely available from https://github.com/etal/cnvkit.
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Affiliation(s)
- Eric Talevich
- Department of Dermatology, University of California, San Francisco, San Francisco, California, United States of America
- Department of Pathology, University of California, San Francisco, San Francisco, California, United States of America
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, United States of America
| | - A. Hunter Shain
- Department of Dermatology, University of California, San Francisco, San Francisco, California, United States of America
- Department of Pathology, University of California, San Francisco, San Francisco, California, United States of America
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, United States of America
| | - Thomas Botton
- Department of Dermatology, University of California, San Francisco, San Francisco, California, United States of America
- Department of Pathology, University of California, San Francisco, San Francisco, California, United States of America
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, United States of America
| | - Boris C. Bastian
- Department of Dermatology, University of California, San Francisco, San Francisco, California, United States of America
- Department of Pathology, University of California, San Francisco, San Francisco, California, United States of America
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail:
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96
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Dubois S, Jardin F. The role of next-generation sequencing in understanding the genomic basis of diffuse large B cell lymphoma and advancing targeted therapies. Expert Rev Hematol 2016; 9:255-69. [PMID: 26652775 DOI: 10.1586/17474086.2016.1130616] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Next Generation Sequencing (NGS) has redefined the genetic landscape of Diffuse Large B-Cell Lymphoma (DLBCL) by identifying recurrent somatic mutations. Importantly, in some cases these mutations impact potentially actionable targets, thus affording novel personalized therapy opportunities. At the forefront of today's precision therapy era, how to best incorporate NGS into daily clinical practice is of primordial concern, in order to tailor patient's treatment regimens according to their individual mutational profiles. With the advent of cell-free DNA sequencing, which provides a sensitive and less invasive means of monitoring DLBCL patients, the clinical feasibility of NGS has been greatly improved. This article reviews the current landscape of DLBCL mutations, as well as the targeted therapies developed to counter their effects, and discusses how best to utilize NGS data for treatment decision-making.
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Affiliation(s)
- Sydney Dubois
- a Inserm U918, Centre Henri Becquerel , Université de Rouen, IRIB , Rouen , France
| | - Fabrice Jardin
- a Inserm U918, Centre Henri Becquerel , Université de Rouen, IRIB , Rouen , France.,b Department of Hematology , Centre Henri Becquerel , Rouen , France
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Le Tourneau C, Kamal M, Tsimberidou AM, Bedard P, Pierron G, Callens C, Rouleau E, Vincent-Salomon A, Servant N, Alt M, Rouzier R, Paoletti X, Delattre O, Bièche I. Treatment Algorithms Based on Tumor Molecular Profiling: The Essence of Precision Medicine Trials. J Natl Cancer Inst 2015; 108:djv362. [PMID: 26598514 PMCID: PMC4830395 DOI: 10.1093/jnci/djv362] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/26/2015] [Indexed: 12/13/2022] Open
Abstract
With the advent of high-throughput molecular technologies, several precision medicine (PM) studies are currently ongoing that include molecular screening programs and PM clinical trials. Molecular profiling programs establish the molecular profile of patients' tumors with the aim to guide therapy based on identified molecular alterations. The aim of prospective PM clinical trials is to assess the clinical utility of tumor molecular profiling and to determine whether treatment selection based on molecular alterations produces superior outcomes compared with unselected treatment. These trials use treatment algorithms to assign patients to specific targeted therapies based on tumor molecular alterations. These algorithms should be governed by fixed rules to ensure standardization and reproducibility. Here, we summarize key molecular, biological, and technical criteria that, in our view, should be addressed when establishing treatment algorithms based on tumor molecular profiling for PM trials.
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Affiliation(s)
- Christophe Le Tourneau
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
| | - Maud Kamal
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
| | - Apostolia-Maria Tsimberidou
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
| | - Philippe Bedard
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
| | - Gaëlle Pierron
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
| | - Céline Callens
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
| | - Etienne Rouleau
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
| | - Anne Vincent-Salomon
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
| | - Nicolas Servant
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
| | - Marie Alt
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
| | - Roman Rouzier
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
| | - Xavier Paoletti
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
| | - Olivier Delattre
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
| | - Ivan Bièche
- Affiliations of authors:Department of Medical Oncology, Institut Curie , Paris & Saint-Cloud , France (CLT, MK, MA); EA7285 Versailles-St-Quentin-en-Yvelines University , France (CLT, RR); Investigational Cancer Therapeutics, M. D. Anderson Cancer Center , Houston, TX (AMT); Drug Development Program, Department of Medical Oncology and Hematology, Princess Margaret Hospital , Toronto , Canada (PB); Department of Genetics, Institut Curie , Paris , France (GP, CC, ER, IB); Department of Pathology, Institut Curie , Paris , France (AVS); Institut Curie / INSERM U900 , Paris , France (NS, XP); Department of Surgery, Institut Curie , Paris & Saint-Cloud , France (RR); Institut Curie, INSERM U830 , Paris , France (OD); EA7331, University of Paris-Descartes , Paris , France (IB)
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98
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Genomic landscapes of breast fibroepithelial tumors. Nat Genet 2015; 47:1341-5. [PMID: 26437033 DOI: 10.1038/ng.3409] [Citation(s) in RCA: 165] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 08/31/2015] [Indexed: 12/13/2022]
Abstract
Breast fibroepithelial tumors comprise a heterogeneous spectrum of pathological entities, from benign fibroadenomas to malignant phyllodes tumors. Although MED12 mutations have been frequently found in fibroadenomas and phyllodes tumors, the landscapes of genetic alterations across the fibroepithelial tumor spectrum remain unclear. Here, by performing exome sequencing of 22 phyllodes tumors followed by targeted sequencing of 100 breast fibroepithelial tumors, we observed three distinct somatic mutation patterns. First, we frequently observed MED12 and RARA mutations in both fibroadenomas and phyllodes tumors, emphasizing the importance of these mutations in fibroepithelial tumorigenesis. Second, phyllodes tumors exhibited mutations in FLNA, SETD2 and KMT2D, suggesting a role in driving phyllodes tumor development. Third, borderline and malignant phyllodes tumors harbored additional mutations in cancer-associated genes. RARA mutations exhibited clustering in the portion of the gene encoding the ligand-binding domain, functionally suppressed RARA-mediated transcriptional activation and enhanced RARA interactions with transcriptional co-repressors. This study provides insights into the molecular pathogenesis of breast fibroepithelial tumors, with potential clinical implications.
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Walker CJ, Miranda MA, O'Hern MJ, McElroy JP, Coombes KR, Bundschuh R, Cohn DE, Mutch DG, Goodfellow PJ. Patterns of CTCF and ZFHX3 Mutation and Associated Outcomes in Endometrial Cancer. J Natl Cancer Inst 2015; 107:djv249. [PMID: 26330387 DOI: 10.1093/jnci/djv249] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 08/05/2015] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The genetic events responsible for tumor aggressiveness in endometrioid endometrial cancer (EEC) remain poorly understood. The chromosome 16q22 tumor suppressor genes CTCF and ZFHX3 are both frequently mutated in EEC, but their respective roles in outcome have not been determined. METHODS Targeted deep sequencing of CTCF and ZFHX3 was performed for 542 EEC samples. Copy number loss (CNL) was determined using microsatellite typing of paired tumor and normal DNA and a novel Bayesian method based on variant allele frequencies of germline polymorphisms. All statistical tests were two-sided. RESULTS Mutation rates for CTCF and ZFHX3 were 25.3% and 20.4%, respectively, and there was a statistically significant excess of tumors with mutation in both genes (P = .003). CNL rates were 17.4% for CTCF and 17.2% for ZFHX3, and the majority of CNLs included both CTCF and ZFHX3. Mutations were more frequent in tumors with microsatellite instability, and CNLs were more common in microsatellite-stable tumors (P < .001). Patients with ZFHX3 mutation and/or CNL had higher-grade tumors (P = .001), were older (P < .001), and tended to have more frequent lymphovascular space invasion (P = .07). These patients had reduced recurrence-free and overall survival (RFS: hazard ratio [HR] = 2.35, 95% confidence interval [CI] = 1.38 to 3.99, P = .007; OS: HR = 1.51, 95% CI = 1.11 to 2.07, P = .04). CONCLUSIONS Our data demonstrate there is strong selection for inactivation of both CTCF and ZFHX3 in EEC. Mutation occurs at high frequency in microsatellite-unstable tumors, whereas CNLs are common in microsatellite-stable cancers. Loss of these two tumor suppressors is a frequent event in endometrial tumorigenesis, and ZFHX3 defects are associated with poor outcome.
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Affiliation(s)
- Christopher J Walker
- Department of Obstetrics and Gynecology, Division of Gynecology Oncology (CJW, MAM, MJO, DEC, PJG), Department of Biomedical Informatics, Center for Biostatistics, College of Medicine (JPM, KRC), The Ohio State University Comprehensive Cancer Center - James Cancer Hospital and Solove Research Institute (CJW, MAM, MJO, JPM, KRC, DEC, PJG), Department of Physics, Department of Chemistry & Biochemistry, Department of Internal Medicine, Division of Hematology, Center for RNA Biology (RB), The Ohio State University, Columbus, OH; Department of Obstetrics and Gynecology, Division of Gynecology Oncology, Washington University, St. Louis, MO (DGM)
| | - Mario A Miranda
- Department of Obstetrics and Gynecology, Division of Gynecology Oncology (CJW, MAM, MJO, DEC, PJG), Department of Biomedical Informatics, Center for Biostatistics, College of Medicine (JPM, KRC), The Ohio State University Comprehensive Cancer Center - James Cancer Hospital and Solove Research Institute (CJW, MAM, MJO, JPM, KRC, DEC, PJG), Department of Physics, Department of Chemistry & Biochemistry, Department of Internal Medicine, Division of Hematology, Center for RNA Biology (RB), The Ohio State University, Columbus, OH; Department of Obstetrics and Gynecology, Division of Gynecology Oncology, Washington University, St. Louis, MO (DGM)
| | - Matthew J O'Hern
- Department of Obstetrics and Gynecology, Division of Gynecology Oncology (CJW, MAM, MJO, DEC, PJG), Department of Biomedical Informatics, Center for Biostatistics, College of Medicine (JPM, KRC), The Ohio State University Comprehensive Cancer Center - James Cancer Hospital and Solove Research Institute (CJW, MAM, MJO, JPM, KRC, DEC, PJG), Department of Physics, Department of Chemistry & Biochemistry, Department of Internal Medicine, Division of Hematology, Center for RNA Biology (RB), The Ohio State University, Columbus, OH; Department of Obstetrics and Gynecology, Division of Gynecology Oncology, Washington University, St. Louis, MO (DGM)
| | - Joseph P McElroy
- Department of Obstetrics and Gynecology, Division of Gynecology Oncology (CJW, MAM, MJO, DEC, PJG), Department of Biomedical Informatics, Center for Biostatistics, College of Medicine (JPM, KRC), The Ohio State University Comprehensive Cancer Center - James Cancer Hospital and Solove Research Institute (CJW, MAM, MJO, JPM, KRC, DEC, PJG), Department of Physics, Department of Chemistry & Biochemistry, Department of Internal Medicine, Division of Hematology, Center for RNA Biology (RB), The Ohio State University, Columbus, OH; Department of Obstetrics and Gynecology, Division of Gynecology Oncology, Washington University, St. Louis, MO (DGM)
| | - Kevin R Coombes
- Department of Obstetrics and Gynecology, Division of Gynecology Oncology (CJW, MAM, MJO, DEC, PJG), Department of Biomedical Informatics, Center for Biostatistics, College of Medicine (JPM, KRC), The Ohio State University Comprehensive Cancer Center - James Cancer Hospital and Solove Research Institute (CJW, MAM, MJO, JPM, KRC, DEC, PJG), Department of Physics, Department of Chemistry & Biochemistry, Department of Internal Medicine, Division of Hematology, Center for RNA Biology (RB), The Ohio State University, Columbus, OH; Department of Obstetrics and Gynecology, Division of Gynecology Oncology, Washington University, St. Louis, MO (DGM)
| | - Ralf Bundschuh
- Department of Obstetrics and Gynecology, Division of Gynecology Oncology (CJW, MAM, MJO, DEC, PJG), Department of Biomedical Informatics, Center for Biostatistics, College of Medicine (JPM, KRC), The Ohio State University Comprehensive Cancer Center - James Cancer Hospital and Solove Research Institute (CJW, MAM, MJO, JPM, KRC, DEC, PJG), Department of Physics, Department of Chemistry & Biochemistry, Department of Internal Medicine, Division of Hematology, Center for RNA Biology (RB), The Ohio State University, Columbus, OH; Department of Obstetrics and Gynecology, Division of Gynecology Oncology, Washington University, St. Louis, MO (DGM)
| | - David E Cohn
- Department of Obstetrics and Gynecology, Division of Gynecology Oncology (CJW, MAM, MJO, DEC, PJG), Department of Biomedical Informatics, Center for Biostatistics, College of Medicine (JPM, KRC), The Ohio State University Comprehensive Cancer Center - James Cancer Hospital and Solove Research Institute (CJW, MAM, MJO, JPM, KRC, DEC, PJG), Department of Physics, Department of Chemistry & Biochemistry, Department of Internal Medicine, Division of Hematology, Center for RNA Biology (RB), The Ohio State University, Columbus, OH; Department of Obstetrics and Gynecology, Division of Gynecology Oncology, Washington University, St. Louis, MO (DGM)
| | - David G Mutch
- Department of Obstetrics and Gynecology, Division of Gynecology Oncology (CJW, MAM, MJO, DEC, PJG), Department of Biomedical Informatics, Center for Biostatistics, College of Medicine (JPM, KRC), The Ohio State University Comprehensive Cancer Center - James Cancer Hospital and Solove Research Institute (CJW, MAM, MJO, JPM, KRC, DEC, PJG), Department of Physics, Department of Chemistry & Biochemistry, Department of Internal Medicine, Division of Hematology, Center for RNA Biology (RB), The Ohio State University, Columbus, OH; Department of Obstetrics and Gynecology, Division of Gynecology Oncology, Washington University, St. Louis, MO (DGM)
| | - Paul J Goodfellow
- Department of Obstetrics and Gynecology, Division of Gynecology Oncology (CJW, MAM, MJO, DEC, PJG), Department of Biomedical Informatics, Center for Biostatistics, College of Medicine (JPM, KRC), The Ohio State University Comprehensive Cancer Center - James Cancer Hospital and Solove Research Institute (CJW, MAM, MJO, JPM, KRC, DEC, PJG), Department of Physics, Department of Chemistry & Biochemistry, Department of Internal Medicine, Division of Hematology, Center for RNA Biology (RB), The Ohio State University, Columbus, OH; Department of Obstetrics and Gynecology, Division of Gynecology Oncology, Washington University, St. Louis, MO (DGM).
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Tattini L, D'Aurizio R, Magi A. Detection of Genomic Structural Variants from Next-Generation Sequencing Data. Front Bioeng Biotechnol 2015; 3:92. [PMID: 26161383 PMCID: PMC4479793 DOI: 10.3389/fbioe.2015.00092] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 06/10/2015] [Indexed: 01/16/2023] Open
Abstract
Structural variants are genomic rearrangements larger than 50 bp accounting for around 1% of the variation among human genomes. They impact on phenotypic diversity and play a role in various diseases including neurological/neurocognitive disorders and cancer development and progression. Dissecting structural variants from next-generation sequencing data presents several challenges and a number of approaches have been proposed in the literature. In this mini review, we describe and summarize the latest tools – and their underlying algorithms – designed for the analysis of whole-genome sequencing, whole-exome sequencing, custom captures, and amplicon sequencing data, pointing out the major advantages/drawbacks. We also report a summary of the most recent applications of third-generation sequencing platforms. This assessment provides a guided indication – with particular emphasis on human genetics and copy number variants – for researchers involved in the investigation of these genomic events.
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Affiliation(s)
- Lorenzo Tattini
- Department of Neurosciences, Psychology, Pharmacology and Child Health, University of Florence , Florence , Italy
| | - Romina D'Aurizio
- Laboratory of Integrative Systems Medicine (LISM), Institute of Informatics and Telematics and Institute of Clinical Physiology, National Research Council , Pisa , Italy
| | - Alberto Magi
- Department of Clinical and Experimental Medicine, University of Florence , Florence , Italy
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