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Rallis KS, George AM, Wozniak AM, Bigogno CM, Chow B, Hanrahan JG, Sideris M. Molecular Genetics and Targeted Therapies for Paediatric High-grade Glioma. Cancer Genomics Proteomics 2022; 19:390-414. [PMID: 35732328 PMCID: PMC9247880 DOI: 10.21873/cgp.20328] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 04/30/2022] [Accepted: 05/09/2022] [Indexed: 11/10/2022] Open
Abstract
Brain tumours are the leading cause of paediatric cancer-associated death worldwide. High-grade glioma (HGG) represents a main cause of paediatric brain tumours and is associated with poor prognosis despite surgical and chemoradiotherapeutic advances. The molecular genetics of paediatric HGG (pHGG) are distinct from those in adults, and therefore, adult clinical trial data cannot be extrapolated to children. Compared to adult HGG, pHGG is characterised by more frequent mutations in PDGFRA, TP53 and recurrent K27M and G34R/V mutations on histone H3. Ongoing trials are investigating novel targeted therapies in pHGG. Promising results have been achieved with BRAF/MEK and PI3K/mTOR inhibitors. Combination of PI3K/mTOR, EGFR, CDK4/6, and HDAC inhibitors are potentially viable options. Inhibitors targeting the UPS proteosome, ADAM10/17, IDO, and XPO1 are more novel and are being investigated in early-phase trials. Despite preclinical and clinical trials holding promise for the discovery of effective pHGG treatments, several issues persist. Inadequate blood-brain barrier penetration, unfavourable pharmacokinetics, dose-limiting toxicities, long-term adverse effects in the developing child, and short-lived duration of response due to relapse and resistance highlight the need for further improvement. Future pHGG management will largely depend on selecting combination therapies which work synergistically based on a sound knowledge of the underlying molecular target pathways. A systematic investigation of multimodal therapy with chemoradiotherapy, surgery, target agents and immunotherapy is paramount. This review provides a comprehensive overview of pHGG focusing on molecular genetics and novel targeted therapies. The diagnostics, genetic discrepancies with adults and their clinical implications, as well as conventional treatment approaches are discussed.
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Affiliation(s)
- Kathrine S Rallis
- Barts Cancer Institute, Queen Mary University of London, London, U.K.;
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, U.K
| | - Alan Mathew George
- Liverpool School of Medicine, University of Liverpool, Liverpool, U.K
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, U.K
| | - Anna Maria Wozniak
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, U.K
| | - Carola Maria Bigogno
- Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, U.K
| | - Barbara Chow
- UCL Cancer Institute, University College London, London, U.K
- GKT School of Medicine, King's College London, London, U.K
| | | | - Michail Sideris
- Women's Health Research Unit, Queen Mary University of London, London, U.K
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Finkle JD, Boulos H, Driessen TM, Lo C, Blidner RA, Hafez A, Khan AA, Lozac'hmeur A, McKinnon KE, Perera J, Zhu W, Dowlati A, White KP, Tell R, Beaubier N. Validation of a liquid biopsy assay with molecular and clinical profiling of circulating tumor DNA. NPJ Precis Oncol 2021; 5:63. [PMID: 34215841 PMCID: PMC8253837 DOI: 10.1038/s41698-021-00202-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 05/28/2021] [Indexed: 11/09/2022] Open
Abstract
Liquid biopsy is a valuable precision oncology tool that is increasingly used as a non-invasive approach to identify biomarkers, detect resistance mutations, monitor disease burden, and identify early recurrence. The Tempus xF liquid biopsy assay is a 105-gene, hybrid-capture, next-generation sequencing (NGS) assay that detects single-nucleotide variants, insertions/deletions, copy number variants, and chromosomal rearrangements. Here, we present extensive validation studies of the xF assay using reference standards, cell lines, and patient samples that establish high sensitivity, specificity, and accuracy in variant detection. The Tempus xF assay is highly concordant with orthogonal methods, including ddPCR, tumor tissue-based NGS assays, and another commercial plasma-based NGS assay. Using matched samples, we developed a dynamic filtering method to account for germline mutations and clonal hematopoiesis, while significantly decreasing the number of false-positive variants reported. Additionally, we calculated accurate circulating tumor fraction estimates (ctFEs) using the Off-Target Tumor Estimation Routine (OTTER) algorithm for targeted-panel sequencing. In a cohort of 1,000 randomly selected cancer patients who underwent xF testing, we found that ctFEs correlated with disease burden and clinical outcomes. These results highlight the potential of serial testing to monitor treatment efficacy and disease course, providing strong support for incorporating liquid biopsy in the management of patients with advanced disease.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Wei Zhu
- Tempus Labs, Chicago, IL, USA
| | - Afshin Dowlati
- University Hospitals Seidman Cancer Center, Cleveland, OH, USA
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Obradovic J, Todosijevic J, Jurisic V. Application of the conventional and novel methods in testing EGFR variants for NSCLC patients in the last 10 years through different regions: a systematic review. Mol Biol Rep 2021; 48:3593-3604. [PMID: 33973139 DOI: 10.1007/s11033-021-06379-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 04/24/2021] [Indexed: 12/12/2022]
Abstract
Variants in the epidermal growth factor receptor (EGFR) gene are recognized as predictors of therapy response and are correlated with progression-free and overall survival in non-small cell lung cancer (NSCLC) patients. Molecularly guided therapy needs precise and cost-effective molecular tests. This review focused primarily on screening or target methods for the EGFR variants detection with diagnostic and prognostic potential in the clinical research published papers. Concerning the inclusion and exclusion criteria, the search interval comprised available articles published from 2010 until 2020 in three electronic databases, ISI Web of Science, Pub Med, and Scopus. The analysis of eligible studies started with 5647 and obtained the final 987 full-text articles analyzed as clinical research. The regions comprised were Africa, America, Australia, Asia, Euro-Asia, Europe, or a consortium of different countries. All of the tested methods were applied prevalently in Asia. In clinical research, the polymerase chain reaction (PCR), followed by sequencing methods have been involved mostly over the years. The identified high-through output approaches evolved to improve the survival and quality of the NSCLC patient's life becoming more sensitive, specific, and cost-effective.
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Affiliation(s)
- Jasmina Obradovic
- Department of Sciences, Institute for Information Technologies Kragujevac, University of Kragujevac, Kragujevac, Serbia
| | - Jovana Todosijevic
- Faculty of Science, Institute of Biology and Ecology, University of Kragujevac, Kragujevac, Serbia
| | - Vladimir Jurisic
- Faculty of Medical Sciences, University of Kragujevac, 34000, Kragujevac, Serbia.
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González de Aledo-Castillo JM, Arcocha A, Victoria I, Martinez-Puchol AI, Sánchez C, Jares P, Rodríguez GF, Viñolas N, Reyes R, Reguart N, Puig-Butillé JA. Molecular characterization of advanced non-small cell lung cancer patients by cfDNA analysis: experience from routine laboratory practice. J Thorac Dis 2021; 13:1658-1670. [PMID: 33841957 PMCID: PMC8024825 DOI: 10.21037/jtd-20-3142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 01/20/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Analysis of circulating free DNA (cfDNA) by the real-time PCR cobas® EGFR Mutation Test v2 (cobas® EGFR Test) is a diagnostic approach used in clinical practice for the characterization of advanced non-small cell lung cancer (NSCLC) patients. The test additionally outputs a semiquantitative index (SQI) which reflects the proportion of mutated versus wild-type copies of the EGFR gene in cfDNA with potential use as a biomarker. CfDNA concentration and cfDNA fragmentation pattern have also shown potential utility as biomarkers for cancer patients. We evaluated the implementation of EGFR testing and cfDNA related parameters in NSCLC patients in routine clinical setting as biomarkers for disease stage and diagnosis. METHODS A prospective cohort of 173 locally advanced or metastatic NSCLC TKI-naïve patients analyzed by the cobas® EGFR Test were included in the study. Reproducibility of the test was assessed in 56 patients. The concentration of cfDNA and fragment size pattern was measured using fluorometry and microchip electrophoresis respectively. RESULTS The test showed high diagnostic accuracy when compared to the gold standard of biopsy tumor tissue testing. The SQI value showed a moderate reproducibility (r2=0.70) and did not correlate with cfDNA concentration (r2=0.17, P=0.28) or disease stage (stage III patients SQI =9.1±3.1 and stage IV patients SQI =11.5±4.8, P=0.41). We found differences in SQI values according to the type of EGFR mutation (Ex19Del mutations, SQI =13.6; p.L858R, SQI =8.88; P=0.001). Stage IV patients had higher concentrations of cfDNA (P<0.0001) and higher fractions of cfDNA 100-250 base pairs (bp) fragments (P=0.01) compared to stage III patients. From the ROC curve analysis, cfDNA concentration showed higher AUC compared to cfDNA 100-250 bp fragments (0.86 vs. 0.71). We obtained a cut-off value for cfDNA concentration of 20.3 ng/mL with 72.3% sensitivity and 95% specificity for predicting disease stage in TKI-naïve advanced NSCLC patients. CONCLUSIONS The study indicates that cfDNA analysis in plasma for EGFR testing by RT-PCR is an accurate and fast method to initially stratify NSCLC patients in a real-world clinical setting. However, the SQI has limited clinical value. The cfDNA concentration and fragmentation pattern have clear potential clinical utility for tumor staging in NSCLC patients.
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Affiliation(s)
| | - Ainara Arcocha
- Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain
- Medical Oncology Department, Hospital Clínic, Barcelona, Spain
| | - Iván Victoria
- Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain
- Medical Oncology Department, Hospital Clínic, Barcelona, Spain
| | | | | | - Pedro Jares
- Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain
- Molecular Biology CORE, Hospital Clínic, Barcelona, Spain
- Pathology Department, Hospital Clínic, Barcelona, Spain
| | | | - Núria Viñolas
- Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain
- Medical Oncology Department, Hospital Clínic, Barcelona, Spain
| | - Roxana Reyes
- Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain
- Medical Oncology Department, Hospital Clínic, Barcelona, Spain
| | - Noemí Reguart
- Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain
- Medical Oncology Department, Hospital Clínic, Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
| | - Joan Antón Puig-Butillé
- Thoracic Oncology Unit, Hospital Clínic, Barcelona, Spain
- Molecular Biology CORE, Hospital Clínic, Barcelona, Spain
- August Pi i Sunyer Biomedical Research Institute (IDIBAPS), Barcelona, Spain
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Li J, Li X, Wang W, Shao Y, Zhang Y, Song Z. Gene Alterations in Paired Supernatants and Precipitates from Malignant Pleural Effusions of Non-Squamous Non-Small Cell Lung Cancer. Transl Oncol 2020; 13:100784. [PMID: 32428850 PMCID: PMC7236047 DOI: 10.1016/j.tranon.2020.100784] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/10/2020] [Accepted: 04/13/2020] [Indexed: 02/06/2023] Open
Abstract
OBJECTIVE: This study investigated the feasibility of using malignant pleural effusion (MPE) supernatant and paired cell blocks (precipitate) for gene profiling in patients with non-small cell lung cancer (NSCLC) using next-generation sequencing (NGS) technique. METHODS: Stage IV non-squamous NSCLC patients with MPE were eligible in this prospective study and recruited from Zhejiang Cancer Hospital between May 2014 and October 2015. MPE supernatant and paired precipitate sample gene alterations were determined with NGS containing 14 cancer-related genes. Progression free survival (PFS) was evaluated using Kaplan–Meier method and compared using log-rank test. RESULTS: A total of 102 patients were enrolled in the present study. All pleural effusions were confirmed as malignant with cytological smears. A total of 77 paired MPE supernatant and precipitate samples were acquired from the 102 patients. The results revealed that there were no statistically significant differences in the detection rate and maximum allelic fraction between supernatant and precipitate samples (P = 1.0 and P = .6). Collectively, 172 and 158 genomic alterations with 112 shared mutations were identified in supernatant and precipitate samples, respectively. Comparable PFS was found in EGFR mutation patients according to the supernatant and precipitate sample results (14.0 vs.13.9 months, P = .90). CONCLUSIONS: These results demonstrated that MPE supernatants were comparable to precipitate samples for detection of genetic alterations. However, gene mutation heterogeneity was found between these two media types.
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Affiliation(s)
- Jianqiang Li
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Hangzhou 310022, China; Department of Thoracic Oncology Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, China; Department of Thoracic Oncology Surgery, Zhejiang Cancer Hospital, Hangzhou 310022, China
| | - Xingliang Li
- Department of Thoracic Disease Diagnosis and Treatment Center, Zhejiang Rongjun Hospital, Jiaxing, Zhejiang 314000, China
| | - Wenxian Wang
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Hangzhou 310022, China; Department of Thoracic Oncology Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, China; Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou 310022, China
| | - Yang Shao
- Translational Medicine Research Centre, Geneseeq Technology Inc., Toronto, Ontario, Canada
| | - Yiping Zhang
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Hangzhou 310022, China; Department of Thoracic Oncology Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, China; Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou 310022, China
| | - Zhengbo Song
- Institute of Cancer and Basic Medicine, Chinese Academy of Sciences, Hangzhou 310022, China; Department of Thoracic Oncology Surgery, Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou 310022, China; Department of Medical Oncology, Zhejiang Cancer Hospital, Hangzhou 310022, China.
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