1
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Shen CI, Chang JC, Jain S, Olsen S, Wu CE. Afatinib Plus Bevacizumab Treatment for a Patient With EGFR S645C-Mutant Non-Small Cell Lung Cancer: A Case Report. JCO Precis Oncol 2024; 8:e2400007. [PMID: 38838275 DOI: 10.1200/po.24.00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/21/2024] [Accepted: 04/11/2024] [Indexed: 06/07/2024] Open
Affiliation(s)
- Chia-I Shen
- Department of Chest Medicine, Taipei Veterans General Hospital, Taipei, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ju-Chen Chang
- Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Suyog Jain
- Medical Affairs, Guardant Health AMEA, Singapore
| | - Steve Olsen
- Medical Affairs, Guardant Health AMEA, Singapore
| | - Chiao-En Wu
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital at Linkou, Chang Gung University College of Medicine, Taoyuan, Taiwan
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2
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Soleymani S, Gravel N, Huang LC, Yeung W, Bozorgi E, Bendzunas NG, Kochut KJ, Kannan N. Dark kinase annotation, mining, and visualization using the Protein Kinase Ontology. PeerJ 2023; 11:e16087. [PMID: 38077442 PMCID: PMC10704995 DOI: 10.7717/peerj.16087] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 08/22/2023] [Indexed: 12/18/2023] Open
Abstract
The Protein Kinase Ontology (ProKinO) is an integrated knowledge graph that conceptualizes the complex relationships among protein kinase sequence, structure, function, and disease in a human and machine-readable format. In this study, we have significantly expanded ProKinO by incorporating additional data on expression patterns and drug interactions. Furthermore, we have developed a completely new browser from the ground up to render the knowledge graph visible and interactive on the web. We have enriched ProKinO with new classes and relationships that capture information on kinase ligand binding sites, expression patterns, and functional features. These additions extend ProKinO's capabilities as a discovery tool, enabling it to uncover novel insights about understudied members of the protein kinase family. We next demonstrate the application of ProKinO. Specifically, through graph mining and aggregate SPARQL queries, we identify the p21-activated protein kinase 5 (PAK5) as one of the most frequently mutated dark kinases in human cancers with abnormal expression in multiple cancers, including a previously unappreciated role in acute myeloid leukemia. We have identified recurrent oncogenic mutations in the PAK5 activation loop predicted to alter substrate binding and phosphorylation. Additionally, we have identified common ligand/drug binding residues in PAK family kinases, underscoring ProKinO's potential application in drug discovery. The updated ontology browser and the addition of a web component, ProtVista, which enables interactive mining of kinase sequence annotations in 3D structures and Alphafold models, provide a valuable resource for the signaling community. The updated ProKinO database is accessible at https://prokino.uga.edu.
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Affiliation(s)
- Saber Soleymani
- Department of Computer Science, University of Georgia, Athens, GA, United States
| | - Nathan Gravel
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Liang-Chin Huang
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Wayland Yeung
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
| | - Elika Bozorgi
- Department of Computer Science, University of Georgia, Athens, GA, United States
| | - Nathaniel G. Bendzunas
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Krzysztof J. Kochut
- Department of Computer Science, University of Georgia, Athens, GA, United States
| | - Natarajan Kannan
- Institute of Bioinformatics, University of Georgia, Athens, GA, United States
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
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3
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Isolation of TTF-1 Positive Circulating Tumor Cells for Single-Cell Sequencing by Using an Automatic Platform Based on Microfluidic Devices. Int J Mol Sci 2022; 23:ijms232315139. [PMID: 36499466 PMCID: PMC9736518 DOI: 10.3390/ijms232315139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/23/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
Single-cell sequencing provides promising information in tumor evolution and heterogeneity. Even with the recent advances in circulating tumor cell (CTC) technologies, it remains a big challenge to precisely and effectively isolate CTCs for downstream analysis. The Cell RevealTM system integrates an automatic CTC enrichment and staining machine, an AI-assisted automatic CTC scanning and identification system, and an automatic cell picking machine for CTC isolation. H1975 cell line was used for the spiking test. The identification of CTCs and the isolation of target CTCs for genetic sequencing were performed from the peripheral blood of three cancer patients, including two with lung cancer and one with both lung cancer and thyroid cancer. The spiking test revealed a mean recovery rate of 81.81% even with extremely low spiking cell counts with a linear relationship between the spiked cell counts and the recovered cell counts (Y = 0.7241 × X + 19.76, R2 = 0.9984). The three cancer patients had significantly higher TTF-1+ CTCs than healthy volunteers. All target CTCs were successfully isolated by the Cell Picker machine for a subsequent genetic analysis. Six tumor-associated mutations in four genes were detected. The present study reveals the Cell RevealTM platform can precisely identify and isolate target CTCs and then successfully perform single-cell sequencing by using commercially available genetic devices.
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4
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Esfahani MS, Hamilton EG, Mehrmohamadi M, Nabet BY, Alig SK, King DA, Steen CB, Macaulay CW, Schultz A, Nesselbush MC, Soo J, Schroers-Martin JG, Chen B, Binkley MS, Stehr H, Chabon JJ, Sworder BJ, Hui ABY, Frank MJ, Moding EJ, Liu CL, Newman AM, Isbell JM, Rudin CM, Li BT, Kurtz DM, Diehn M, Alizadeh AA. Inferring gene expression from cell-free DNA fragmentation profiles. Nat Biotechnol 2022; 40:585-597. [PMID: 35361996 PMCID: PMC9337986 DOI: 10.1038/s41587-022-01222-4] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 01/14/2022] [Indexed: 02/07/2023]
Abstract
Profiling of circulating tumor DNA (ctDNA) in the bloodstream shows promise for noninvasive cancer detection. Chromatin fragmentation features have previously been explored to infer gene expression profiles from cell-free DNA (cfDNA), but current fragmentomic methods require high concentrations of tumor-derived DNA and provide limited resolution. Here we describe promoter fragmentation entropy as an epigenomic cfDNA feature that predicts RNA expression levels at individual genes. We developed 'epigenetic expression inference from cell-free DNA-sequencing' (EPIC-seq), a method that uses targeted sequencing of promoters of genes of interest. Profiling 329 blood samples from 201 patients with cancer and 87 healthy adults, we demonstrate classification of subtypes of lung carcinoma and diffuse large B cell lymphoma. Applying EPIC-seq to serial blood samples from patients treated with PD-(L)1 immune-checkpoint inhibitors, we show that gene expression profiles inferred by EPIC-seq are correlated with clinical response. Our results indicate that EPIC-seq could enable noninvasive, high-throughput tissue-of-origin characterization with diagnostic, prognostic and therapeutic potential.
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Affiliation(s)
- Mohammad Shahrokh Esfahani
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Emily G. Hamilton
- Program in Cancer Biology, Stanford School of Medicine, Stanford, CA, USA
| | - Mahya Mehrmohamadi
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Barzin Y. Nabet
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Stefan K. Alig
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Daniel A. King
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Chloé B. Steen
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Biomedical Informatics, Stanford School of Medicine, Stanford, CA, USA
| | - Charles W. Macaulay
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Andre Schultz
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | | | - Joanne Soo
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Joseph G. Schroers-Martin
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Binbin Chen
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Michael S. Binkley
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Henning Stehr
- Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Jacob J. Chabon
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Brian J. Sworder
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Angela B-Y Hui
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Matthew J. Frank
- Division of Blood and Marrow Transplantation and Cellular Therapy, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Everett J. Moding
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA
| | - Chih Long Liu
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA
| | - Aaron M. Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Department of Biomedical Informatics, Stanford School of Medicine, Stanford, CA, USA
| | - James M. Isbell
- Thoracic Surgery Service, Memorial Sloan Kettering Cancer Center and Weill Cornell Medicine, New York, NY, USA
| | - Charles M. Rudin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bob T. Li
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - David M. Kurtz
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Correspondence and requests for materials should be addressed to Maximilian Diehn or Ash A. Alizadeh, ;
| | - Ash A. Alizadeh
- Divisions of Oncology and of Hematology, Department of Medicine, Stanford School of Medicine, Stanford, CA, USA.,Stanford Cancer Institute, Stanford School of Medicine, Stanford, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford School of Medicine, Stanford, CA, USA.,Correspondence and requests for materials should be addressed to Maximilian Diehn or Ash A. Alizadeh, ;
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5
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Sahasrabuddhe NA, Korlimarla A, Kulkarni M, Kusuma V, Prabhu JS, Dixit S, Deshmukh C, Sridhar TS, Phatak A, Koppiker C. NGS-based profiling of key cancer genes in Indian triple-negative breast cancer patients reinforces molecular heterogeneity of the disease. Indian J Cancer 2022; 58:598-602. [PMID: 34975100 DOI: 10.4103/ijc.ijc_432_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Triple-negative breast cancers (TNBC) are one of the most aggressive forms of breast cancers. With poor patient outcomes, it presents a great burden on the healthcare systems. There have been some efforts to explore the genomic changes that occur in TNBCs. However, there is not enough data on Indian TNBCs. We sought to understand the mutational landscape of key cancer-associated genes in Indian TNBC patients using TruSeq Cancer Amplicon Panel. We sequenced 51 TNBC patient samples and found great heterogeneity amongst samples with respect to the genomic variants. Several previously reported including alterations in PI3K-AKT pathway genes were also identified. Likewise, we identified several novel high-frequency variants, for example, GNAQ F341S (17%), the functional role of which remains unclear. Our study lays the foundation of larger efforts needed to understand the genomic landscape of Indian TNBCs which can aid in classification and better therapeutic management of patients.
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Affiliation(s)
| | | | - Madhura Kulkarni
- Prashanti Cancer Care Mission (PCCM); Center for Translational Cancer Research - a joint initiative of PCCM and Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, India
| | - Vinay Kusuma
- PierianDx India Pvt. Ltd. Pune, Maharashtra, India
| | | | - Santosh Dixit
- Prashanti Cancer Care Mission (PCCM); Center for Translational Cancer Research - a joint initiative of PCCM and Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, India
| | - Chetan Deshmukh
- Prashanti Cancer Care Mission (PCCM), Pune, Maharashtra, India
| | - T S Sridhar
- St. John's Research Institute, Bengaluru, Karnataka, India
| | | | - Chaitanyananda Koppiker
- Prashanti Cancer Care Mission (PCCM); Center for Translational Cancer Research - a joint initiative of PCCM and Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, India
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6
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Zhu Z, Li J, Zhang S, Geng N, Xu L, Greenwald SE. Quality evaluation of signals collected by portable ECG devices using dimensionality reduction and flexible model integration. Physiol Meas 2020; 41:105001. [PMID: 32947264 DOI: 10.1088/1361-6579/abba0b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
OBJECTIVE Portable devices for collecting electrocardiograms (ECGs) and telemedicine systems for diagnosis are available to residents in deprived areas, but ECGs collected by non-professionals are not necessarily reliable and may impair the accuracy of diagnosis. We propose an algorithm for accurate ECG quality assessment, which can help improve the reliability of ECGs collected by portable devices. APPROACH Using challenge data from CinC (2019), signals were classified as 'acceptable' and 'unacceptable' by annotators. The training set contained 998 12-lead ECGs and the test set contained 500. A 998 × 84 feature matrix, S, was formed by feature extraction and three basic models were obtained through training SVM, DT and NBC on S. The feature subsets S1, S2 and S3 were obtained by dimensionality reduction on S using SVM, DT and NBC, respectively. Three other basic models were obtained through training SVM on S1, DT on S2 and NBC on S3. By combining these six basic models, several integrated models were formed. An iterative method was proposed to select the integrated model with the highest accuracy on the training set. Having compared differences between the output labels and the original data labels, evaluation criteria were calculated. MAIN RESULTS An accuracy of 98.70% and 98.60% was achieved on the training and test datasets, respectively. High F1 score and Kappa values were also obtained. SIGNIFICANCE The proposed algorithm has advantages over previously reported approaches during automatic assessment of ECG quality and can thus help to reduce reliance on highly trained professionals when assessing the quality of ECGs.
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Affiliation(s)
- Zeyang Zhu
- Collage of Medicine and Biological Information Engineering, Northeastern University, Shenyang 110819, Liaoning, People's Republic of China
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7
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Mateo J, Seed G, Bertan C, Rescigno P, Dolling D, Figueiredo I, Miranda S, Nava Rodrigues D, Gurel B, Clarke M, Atkin M, Chandler R, Messina C, Sumanasuriya S, Bianchini D, Barrero M, Petermolo A, Zafeiriou Z, Fontes M, Perez-Lopez R, Tunariu N, Fulton B, Jones R, McGovern U, Ralph C, Varughese M, Parikh O, Jain S, Elliott T, Sandhu S, Porta N, Hall E, Yuan W, Carreira S, de Bono JS. Genomics of lethal prostate cancer at diagnosis and castration resistance. J Clin Invest 2020; 130:1743-1751. [PMID: 31874108 PMCID: PMC7108902 DOI: 10.1172/jci132031] [Citation(s) in RCA: 180] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/18/2019] [Indexed: 12/11/2022] Open
Abstract
The genomics of primary prostate cancer differ from those of metastatic castration-resistant prostate cancer (mCRPC). We studied genomic aberrations in primary prostate cancer biopsies from patients who developed mCRPC, also studying matching, same-patient, diagnostic, and mCRPC biopsies following treatment. We profiled 470 treatment-naive prostate cancer diagnostic biopsies and, for 61 cases, mCRPC biopsies, using targeted and low-pass whole-genome sequencing (n = 52). Descriptive statistics were used to summarize mutation and copy number profile. Prevalence was compared using Fisher's exact test. Survival correlations were studied using log-rank test. TP53 (27%) and PTEN (12%) and DDR gene defects (BRCA2 7%; CDK12 5%; ATM 4%) were commonly detected. TP53, BRCA2, and CDK12 mutations were markedly more common than described in the TCGA cohort. Patients with RB1 loss in the primary tumor had a worse prognosis. Among 61 men with matched hormone-naive and mCRPC biopsies, differences were identified in AR, TP53, RB1, and PI3K/AKT mutational status between same-patient samples. In conclusion, the genomics of diagnostic prostatic biopsies acquired from men who develop mCRPC differ from those of the nonlethal primary prostatic cancers. RB1/TP53/AR aberrations are enriched in later stages, but the prevalence of DDR defects in diagnostic samples is similar to mCRPC.
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Affiliation(s)
- Joaquin Mateo
- Vall d’Hebron Institute of Oncology (VHIO) and Vall d’Hebron University Hospital, Barcelona, Spain
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - George Seed
- The Institute of Cancer Research, London, United Kingdom
| | - Claudia Bertan
- The Institute of Cancer Research, London, United Kingdom
| | - Pasquale Rescigno
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - David Dolling
- The Institute of Cancer Research, London, United Kingdom
| | | | - Susana Miranda
- The Institute of Cancer Research, London, United Kingdom
| | | | - Bora Gurel
- The Institute of Cancer Research, London, United Kingdom
| | - Matthew Clarke
- The Institute of Cancer Research, London, United Kingdom
| | - Mark Atkin
- The Institute of Cancer Research, London, United Kingdom
| | - Rob Chandler
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Carlo Messina
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Semini Sumanasuriya
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Diletta Bianchini
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Maialen Barrero
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Antonella Petermolo
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Zafeiris Zafeiriou
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Mariane Fontes
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
- Instituto Oncoclinicas-Grupo Oncoclinicas, Rio de Janeiro, Brazil
| | - Raquel Perez-Lopez
- Vall d’Hebron Institute of Oncology (VHIO) and Vall d’Hebron University Hospital, Barcelona, Spain
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Nina Tunariu
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Ben Fulton
- The Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | - Robert Jones
- The Beatson West of Scotland Cancer Centre, Glasgow, United Kingdom
| | | | - Christy Ralph
- St James’s University Hospital, Leeds, United Kingdom
| | | | - Omi Parikh
- Royal Blackburn Hospital, Blackburn, United Kingdom
| | - Suneil Jain
- Belfast City Hospital, Belfast, United Kingdom
| | - Tony Elliott
- The Christie Hospital, Manchester, United Kingdom
| | | | - Nuria Porta
- The Institute of Cancer Research, London, United Kingdom
| | - Emma Hall
- The Institute of Cancer Research, London, United Kingdom
| | - Wei Yuan
- The Institute of Cancer Research, London, United Kingdom
| | | | - Johann S. de Bono
- The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
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8
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Li M, Shang Z, Yang Z, Zhang Y, Wan H. Machine learning methods for MRI biomarkers analysis of pediatric posterior fossa tumors. Biocybern Biomed Eng 2019. [DOI: 10.1016/j.bbe.2019.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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9
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Martin J, Lehmann A, Klauschen F, Hummel M, Lenze D, Grohé C, Tessmer A, Gottschalk J, Schmidt B, Pau HW, Witt C, Moegling S, Kromminga R, Jöhrens K. Clinical Impact of Rare and Compound Mutations of Epidermal Growth Factor Receptor in Patients With Non-Small-Cell Lung Cancer. Clin Lung Cancer 2019; 20:350-362.e4. [PMID: 31175009 DOI: 10.1016/j.cllc.2019.04.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/29/2019] [Accepted: 04/20/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND Standard therapy of advanced non-small-cell lung cancer harboring an activating mutation in the epidermal growth factor receptor (EGFR) gene is treatment with tyrosine kinase inhibitors (TKI). However, for rare and compound mutations of the EGFR gene, the clinical evidence of TKI therapy is still unclear. PATIENTS AND METHODS A total of 2906 lung cancer samples were analyzed for EGFR mutations during routine analysis between 2010 and 2017. The samples have been investigated by Sanger sequencing and since 2014 by next-generation sequencing. RESULTS We detected EGFR mutations in 408 specimens (14%). Among these, we found 41 samples with rare and 22 with compound mutations. In these 63 samples, 56 different rare EGFR mutations occurred. Information about the clinical outcome was available for 37. Among those with rare mutations, only one patient harboring the mutation p.G874D had disease that responded to first-generation TKI therapy. In contrast, the disease of all patients with compound mutations responded to first- or second-generation TKI therapy. Furthermore, we collected data on clinical relevance regarding TKI therapy from different databases and from an additional literature search, and only found data for 36 of the 56 detected rare mutations. CONCLUSION Information about the clinical outcome of patients with rare and compound EGFR mutations remains limited. At present, second- and third-generation TKIs are available, which may represent new treatment strategies for these patients. Therefore, it is becoming increasingly important to maintain databases concerning rare EGFR mutations.
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Affiliation(s)
- Juliane Martin
- Institute of Pathology, Charité, University Medicine Berlin, Berlin, Germany; Provitro AG, Berlin, Germany.
| | - Annika Lehmann
- Institute of Pathology, Charité, University Medicine Berlin, Berlin, Germany
| | - Frederick Klauschen
- Institute of Pathology, Charité, University Medicine Berlin, Berlin, Germany
| | - Michael Hummel
- Institute of Pathology, Charité, University Medicine Berlin, Berlin, Germany
| | - Dido Lenze
- Institute of Pathology, Charité, University Medicine Berlin, Berlin, Germany
| | | | | | - Joachim Gottschalk
- Department of Pathology and Neuropathology, Asklepios Klinik Nord, Hamburg, Germany
| | - Berndt Schmidt
- Lung Cancer Centrum, DRK-Kliniken Berlin Mitte, Berlin, Germany
| | - Hans-Wilhelm Pau
- Department of Otorhinolaryngology, Head and Neck Surgery, University Medical Center, Rostock, Germany
| | - Christian Witt
- Department of Pneumonology and Immunology, Charité, University Medicine Berlin, Berlin, Germany
| | | | | | - Korinna Jöhrens
- Institute of Pathology, University Hospital Carl Gustav Carus, TU Dresden, Germany
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10
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Ashford P, Pang CSM, Moya-García AA, Adeyelu T, Orengo CA. A CATH domain functional family based approach to identify putative cancer driver genes and driver mutations. Sci Rep 2019; 9:263. [PMID: 30670742 PMCID: PMC6343001 DOI: 10.1038/s41598-018-36401-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 11/13/2018] [Indexed: 12/31/2022] Open
Abstract
Tumour sequencing identifies highly recurrent point mutations in cancer driver genes, but rare functional mutations are hard to distinguish from large numbers of passengers. We developed a novel computational platform applying a multi-modal approach to filter out passengers and more robustly identify putative driver genes. The primary filter identifies enrichment of cancer mutations in CATH functional families (CATH-FunFams) – structurally and functionally coherent sets of evolutionary related domains. Using structural representatives from CATH-FunFams, we subsequently seek enrichment of mutations in 3D and show that these mutation clusters have a very significant tendency to lie close to known functional sites or conserved sites predicted using CATH-FunFams. Our third filter identifies enrichment of putative driver genes in functionally coherent protein network modules confirmed by literature analysis to be cancer associated. Our approach is complementary to other domain enrichment approaches exploiting Pfam families, but benefits from more functionally coherent groupings of domains. Using a set of mutations from 22 cancers we detect 151 putative cancer drivers, of which 79 are not listed in cancer resources and include recently validated cancer associated genes EPHA7, DCC netrin-1 receptor and zinc-finger protein ZNF479.
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Affiliation(s)
- Paul Ashford
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Camilla S M Pang
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Aurelio A Moya-García
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK.,Laboratorio de Biología Molecular del Cáncer, Centro de Investigaciones Médico-Sanitarias (CIMES), Universidad de Málaga, Málaga, Spain
| | - Tolulope Adeyelu
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Christine A Orengo
- Institute of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT, UK.
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11
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Zhang Y, He B, Zhou D, Li M, Hu C. Newly emergent acquired EGFR exon 18 G724S mutation after resistance of a T790M specific EGFR inhibitor osimertinib in non-small-cell lung cancer: a case report. Onco Targets Ther 2018; 12:51-56. [PMID: 30588029 PMCID: PMC6302808 DOI: 10.2147/ott.s188612] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background T790M mutation is well known as the most common mechanism for resistance to the first- and second-generation tyrosine kinase inhibitors (TKIs) for EGFR mutation in non-small-cell lung cancer. Several third-generation EGFR TKIs, such as osimertinib, have been explored and approved for conquering this resistance; however, acquired resistance to osimertinib is evident and the resistance mechanisms remain complex and incompletely explored. Case presentation A non-smoking 58-year-old female patient was initially diagnosed with lung adenocarcinoma harboring EGFR exon 19 deletion and clinically responded to initial gefitinib treatment. The patient progressed on gefitinib after >1 year and a T790M mutation was detected in tissue biopsy by next-generation sequencing (NGS). Osimertinib treatment was administrated for several months and an acquired rare EGFR G724S mutation was detected via NGS blood sample after osimertinib resistance. Conclusion The specific mechanisms of acquiring drug resistance for EGFR-TKIs have not been fully explored. EGFR G724S mutation might be associated with osimertinib resistance but more studies about the mechanism should be explored.
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Affiliation(s)
- Yan Zhang
- Department of Respiratory Medicine, Xiangya Hospital (Key Cite of National Clinical Research Center for Respiratory Disease), Central South University, Changsha, Hunan, P.R. China, ;
| | - Bixiu He
- Department of Gerontology, Xiangya Hospital, Central South University, Changsha, Hunan, P.R. China
| | - Dongbo Zhou
- Department of Gerontology, Xiangya Hospital, Central South University, Changsha, Hunan, P.R. China
| | - Min Li
- Department of Respiratory Medicine, Xiangya Hospital (Key Cite of National Clinical Research Center for Respiratory Disease), Central South University, Changsha, Hunan, P.R. China, ;
| | - Chengping Hu
- Department of Respiratory Medicine, Xiangya Hospital (Key Cite of National Clinical Research Center for Respiratory Disease), Central South University, Changsha, Hunan, P.R. China, ;
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12
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Quigley D, Alumkal JJ, Wyatt AW, Kothari V, Foye A, Lloyd P, Aggarwal R, Kim W, Lu E, Schwartzman J, Beja K, Annala M, Das R, Diolaiti M, Pritchard C, Thomas G, Tomlins S, Knudsen K, Lord CJ, Ryan C, Youngren J, Beer TM, Ashworth A, Small EJ, Feng FY. Analysis of Circulating Cell-Free DNA Identifies Multiclonal Heterogeneity of BRCA2 Reversion Mutations Associated with Resistance to PARP Inhibitors. Cancer Discov 2017; 7:999-1005. [PMID: 28450426 PMCID: PMC5581695 DOI: 10.1158/2159-8290.cd-17-0146] [Citation(s) in RCA: 205] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 03/22/2017] [Accepted: 04/26/2017] [Indexed: 12/12/2022]
Abstract
Approximately 20% of metastatic prostate cancers harbor mutations in genes required for DNA repair by homologous recombination repair (HRR) such as BRCA2 HRR defects confer synthetic lethality to PARP inhibitors (PARPi) such as olaparib and talazoparib. In ovarian or breast cancers, olaparib resistance has been associated with HRR restoration, including by BRCA2 mutation reversion. Whether similar mechanisms operate in prostate cancer, and could be detected in liquid biopsies, is unclear. Here, we identify BRCA2 reversion mutations associated with olaparib and talazoparib resistance in patients with prostate cancer. Analysis of circulating cell-free DNA (cfDNA) reveals reversion mutation heterogeneity not discernable from a single solid-tumor biopsy and potentially allows monitoring for the emergence of PARPi resistance.Significance: The mechanisms of clinical resistance to PARPi in DNA repair-deficient prostate cancer have not been described. Here, we show BRCA2 reversion mutations in patients with prostate cancer with metastatic disease who developed resistance to talazoparib and olaparib. Furthermore, we show that PARPi resistance is highly multiclonal and that cfDNA allows monitoring for PARPi resistance. Cancer Discov; 7(9); 999-1005. ©2017 AACR.See related commentary by Domchek, p. 937See related article by Kondrashova et al., p. 984See related article by Goodall et al., p. 1006This article is highlighted in the In This Issue feature, p. 920.
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Affiliation(s)
- David Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California
- Department of Epidemiology and Biostatistics, UCSF, San Francisco, California
| | - Joshi J Alumkal
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, British Columbia, Canada
| | - Vishal Kothari
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California
- Department of Radiation Oncology, UCSF, San Francisco, California
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California
- Division of Hematology and Oncology, UCSF, San Francisco, California
| | - Paul Lloyd
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California
- Division of Hematology and Oncology, UCSF, San Francisco, California
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California
- Division of Hematology and Oncology, UCSF, San Francisco, California
| | - Won Kim
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California
- Division of Hematology and Oncology, UCSF, San Francisco, California
| | - Eric Lu
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Jacob Schwartzman
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Kevin Beja
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, British Columbia, Canada
| | - Matti Annala
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, British Columbia, Canada
- Institute of Biosciences and Medical Technology, University of Tampere, Tampere, Finland
| | - Rajdeep Das
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California
- Department of Radiation Oncology, UCSF, San Francisco, California
| | - Morgan Diolaiti
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California
| | - Colin Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - George Thomas
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
- Department of Pathology, Oregon Health & Science University, Portland, Oregon
| | - Scott Tomlins
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Karen Knudsen
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Christopher J Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Charles Ryan
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California
- Division of Hematology and Oncology, UCSF, San Francisco, California
| | - Jack Youngren
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California
- Division of Hematology and Oncology, UCSF, San Francisco, California
| | - Tomasz M Beer
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California.
- Department of Medicine, UCSF, San Francisco, California
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California.
- Division of Hematology and Oncology, UCSF, San Francisco, California
| | - Felix Y Feng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California.
- Department of Radiation Oncology, UCSF, San Francisco, California
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13
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Analysis of somatic mutations across the kinome reveals loss-of-function mutations in multiple cancer types. Sci Rep 2017; 7:6418. [PMID: 28743916 PMCID: PMC5527104 DOI: 10.1038/s41598-017-06366-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 06/13/2017] [Indexed: 12/17/2022] Open
Abstract
In this study we use somatic cancer mutations to identify important functional residues within sets of related genes. We focus on protein kinases, a superfamily of phosphotransferases that share homologous sequences and structural motifs and have many connections to cancer. We develop several statistical tests for identifying Significantly Mutated Positions (SMPs), which are positions in an alignment with mutations that show signs of selection. We apply our methods to 21,917 mutations that map to the alignment of human kinases and identify 23 SMPs. SMPs occur throughout the alignment, with many in the important A-loop region, and others spread between the N and C lobes of the kinase domain. Since mutations are pooled across the superfamily, these positions may be important to many protein kinases. We select eleven mutations from these positions for functional validation. All eleven mutations cause a reduction or loss of function in the affected kinase. The tested mutations are from four genes, including two tumor suppressors (TGFBR1 and CHEK2) and two oncogenes (KDR and ERBB2). They also represent multiple cancer types, and include both recurrent and non-recurrent events. Many of these mutations warrant further investigation as potential cancer drivers.
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14
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Deihimi S, Lev A, Slifker M, Shagisultanova E, Xu Q, Jung K, Vijayvergia N, Ross EA, Xiu J, Swensen J, Gatalica Z, Andrake M, Dunbrack RL, El-Deiry WS. BRCA2, EGFR, and NTRK mutations in mismatch repair-deficient colorectal cancers with MSH2 or MLH1 mutations. Oncotarget 2017; 8:39945-39962. [PMID: 28591715 PMCID: PMC5522275 DOI: 10.18632/oncotarget.18098] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 04/26/2017] [Indexed: 02/07/2023] Open
Abstract
Deficient mismatch repair (MMR) and microsatellite instability (MSI) contribute to ~15% of colorectal cancer (CRCs). We hypothesized MSI leads to mutations in DNA repair proteins including BRCA2 and cancer drivers including EGFR. We analyzed mutations among a discovery cohort of 26 MSI-High (MSI-H) and 558 non-MSI-H CRCs profiled at Caris Life Sciences. Caris-profiled MSI-H CRCs had high mutation rates (50% vs 14% in non-MSI-H, P < 0.0001) in BRCA2. Of 1104 profiled CRCs from a second cohort (COSMIC), MSH2/MLH1-mutant CRCs showed higher mutation rates in BRCA2 compared to non-MSH2/MLH1-mutant tumors (38% vs 6%, P < 0.0000001). BRCA2 mutations in MSH2/MLH1-mutant CRCs included 75 unique mutations not known to occur in breast or pancreatic cancer per COSMIC v73. Only 5 deleterious BRCA2 mutations in CRC were previously reported in the BIC database as germ-line mutations in breast cancer. Some BRCA2 mutations were predicted to disrupt interactions with partner proteins DSS1 and RAD51. Some CRCs harbored multiple BRCA2 mutations. EGFR was mutated in 45.5% of MSH2/MLH1-mutant and 6.5% of non-MSH2/MLH1-mutant tumors (P < 0.0000001). Approximately 15% of EGFR mutations found may be actionable through TKI therapy, including N700D, G719D, T725M, T790M, and E884K. NTRK gene mutations were identified in MSH2/MLH1-mutant CRC including NTRK1 I699V, NTRK2 P716S, and NTRK3 R745L. Our findings have clinical relevance regarding therapeutic targeting of BRCA2 vulnerabilities, EGFR mutations or other identified oncogenic drivers such as NTRK in MSH2/MLH1-mutant CRCs or other tumors with mismatch repair deficiency.
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Affiliation(s)
- Safoora Deihimi
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, USA
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Avital Lev
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, USA
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Michael Slifker
- Biostatistics and Bioinformatics Department, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Elena Shagisultanova
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
- University of Colorado Denver Cancer Center, Denver, CO, USA
| | - Qifang Xu
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Kyungsuk Jung
- Department of Medicine, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Namrata Vijayvergia
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Eric A. Ross
- Biostatistics and Bioinformatics Department, Fox Chase Cancer Center, Philadelphia, PA, USA
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | | | | | | | - Mark Andrake
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Roland L. Dunbrack
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Wafik S. El-Deiry
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, USA
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA, USA
- Department of Hematology/Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
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15
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Quigley D, Alumkal JJ, Wyatt AW, Kothari V, Foye A, Lloyd P, Aggarwal R, Kim W, Lu E, Schwartzman J, Beja K, Annala M, Das R, Diolaiti M, Pritchard C, Thomas G, Tomlins S, Knudsen K, Lord CJ, Ryan C, Youngren J, Beer TM, Ashworth A, Small EJ, Feng FY. Analysis of Circulating Cell-Free DNA Identifies Multiclonal Heterogeneity of BRCA2 Reversion Mutations Associated with Resistance to PARP Inhibitors. Cancer Discov 2017. [PMID: 28450426 DOI: 10.1158/2159-8290.cd-17-0146] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Approximately 20% of metastatic prostate cancers harbor mutations in genes required for DNA repair by homologous recombination repair (HRR) such as BRCA2 HRR defects confer synthetic lethality to PARP inhibitors (PARPi) such as olaparib and talazoparib. In ovarian or breast cancers, olaparib resistance has been associated with HRR restoration, including by BRCA2 mutation reversion. Whether similar mechanisms operate in prostate cancer, and could be detected in liquid biopsies, is unclear. Here, we identify BRCA2 reversion mutations associated with olaparib and talazoparib resistance in patients with prostate cancer. Analysis of circulating cell-free DNA (cfDNA) reveals reversion mutation heterogeneity not discernable from a single solid-tumor biopsy and potentially allows monitoring for the emergence of PARPi resistance.Significance: The mechanisms of clinical resistance to PARPi in DNA repair-deficient prostate cancer have not been described. Here, we show BRCA2 reversion mutations in patients with prostate cancer with metastatic disease who developed resistance to talazoparib and olaparib. Furthermore, we show that PARPi resistance is highly multiclonal and that cfDNA allows monitoring for PARPi resistance. Cancer Discov; 7(9); 999-1005. ©2017 AACR.See related commentary by Domchek, p. 937See related article by Kondrashova et al., p. 984See related article by Goodall et al., p. 1006This article is highlighted in the In This Issue feature, p. 920.
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Affiliation(s)
- David Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California.,Department of Epidemiology and Biostatistics, UCSF, San Francisco, California
| | - Joshi J Alumkal
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon.,Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, British Columbia, Canada
| | - Vishal Kothari
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California.,Department of Radiation Oncology, UCSF, San Francisco, California
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California.,Division of Hematology and Oncology, UCSF, San Francisco, California
| | - Paul Lloyd
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California.,Division of Hematology and Oncology, UCSF, San Francisco, California
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California.,Division of Hematology and Oncology, UCSF, San Francisco, California
| | - Won Kim
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California.,Division of Hematology and Oncology, UCSF, San Francisco, California
| | - Eric Lu
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Jacob Schwartzman
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Kevin Beja
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, British Columbia, Canada
| | - Matti Annala
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, British Columbia, Canada.,Institute of Biosciences and Medical Technology, University of Tampere, Tampere, Finland
| | - Rajdeep Das
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California.,Department of Radiation Oncology, UCSF, San Francisco, California
| | - Morgan Diolaiti
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California
| | - Colin Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, Washington
| | - George Thomas
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon.,Department of Pathology, Oregon Health & Science University, Portland, Oregon
| | - Scott Tomlins
- Department of Pathology, University of Michigan School of Medicine, Ann Arbor, Michigan
| | - Karen Knudsen
- Department of Cancer Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Christopher J Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Charles Ryan
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California.,Division of Hematology and Oncology, UCSF, San Francisco, California
| | - Jack Youngren
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California.,Division of Hematology and Oncology, UCSF, San Francisco, California
| | - Tomasz M Beer
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California. .,Department of Medicine, UCSF, San Francisco, California
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California. .,Division of Hematology and Oncology, UCSF, San Francisco, California
| | - Felix Y Feng
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, California. .,Department of Radiation Oncology, UCSF, San Francisco, California
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16
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Gallion J, Koire A, Katsonis P, Schoenegge A, Bouvier M, Lichtarge O. Predicting phenotype from genotype: Improving accuracy through more robust experimental and computational modeling. Hum Mutat 2017; 38:569-580. [PMID: 28230923 PMCID: PMC5516182 DOI: 10.1002/humu.23193] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 01/25/2017] [Accepted: 02/04/2017] [Indexed: 11/11/2022]
Abstract
Computational prediction yields efficient and scalable initial assessments of how variants of unknown significance may affect human health. However, when discrepancies between these predictions and direct experimental measurements of functional impact arise, inaccurate computational predictions are frequently assumed as the source. Here, we present a methodological analysis indicating that shortcomings in both computational and biological data can contribute to these disagreements. We demonstrate that incomplete assaying of multifunctional proteins can affect the strength of correlations between prediction and experiments; a variant's full impact on function is better quantified by considering multiple assays that probe an ensemble of protein functions. Additionally, many variants predictions are sensitive to protein alignment construction and can be customized to maximize relevance of predictions to a specific experimental question. We conclude that inconsistencies between computation and experiment can often be attributed to the fact that they do not test identical hypotheses. Aligning the design of the computational input with the design of the experimental output will require cooperation between computational and biological scientists, but will also lead to improved estimations of computational prediction accuracy and a better understanding of the genotype–phenotype relationship.
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Affiliation(s)
- Jonathan Gallion
- Program in Structural and Computational Biology and Molecular BiophysicsBaylor College of MedicineHoustonTexas
| | - Amanda Koire
- Program in Structural and Computational Biology and Molecular BiophysicsBaylor College of MedicineHoustonTexas
| | - Panagiotis Katsonis
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| | - Anne‐Marie Schoenegge
- Department of BiochemistryInstitute for Research in Immunology and CancerUniversité de MontrealQuebecCanada
| | - Michel Bouvier
- Department of BiochemistryInstitute for Research in Immunology and CancerUniversité de MontrealQuebecCanada
| | - Olivier Lichtarge
- Program in Structural and Computational Biology and Molecular BiophysicsBaylor College of MedicineHoustonTexas
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
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17
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Desmedt C, Zoppoli G, Gundem G, Pruneri G, Larsimont D, Fornili M, Fumagalli D, Brown D, Rothé F, Vincent D, Kheddoumi N, Rouas G, Majjaj S, Brohée S, Van Loo P, Maisonneuve P, Salgado R, Van Brussel T, Lambrechts D, Bose R, Metzger O, Galant C, Bertucci F, Piccart-Gebhart M, Viale G, Biganzoli E, Campbell PJ, Sotiriou C. Genomic Characterization of Primary Invasive Lobular Breast Cancer. J Clin Oncol 2016; 34:1872-81. [DOI: 10.1200/jco.2015.64.0334] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Purpose Invasive lobular breast cancer (ILBC) is the second most common histologic subtype after invasive ductal breast cancer (IDBC). Despite clinical and pathologic differences, ILBC is still treated as IDBC. We aimed to identify genomic alterations in ILBC with potential clinical implications. Methods From an initial 630 ILBC primary tumors, we interrogated oncogenic substitutions and insertions and deletions of 360 cancer genes and genome-wide copy number aberrations in 413 and 170 ILBC samples, respectively, and correlated those findings with clinicopathologic and outcome features. Results Besides the high mutation frequency of CDH1 in 65% of tumors, alterations in one of the three key genes of the phosphatidylinositol 3-kinase pathway, PIK3CA, PTEN, and AKT1, were present in more than one-half of the cases. HER2 and HER3 were mutated in 5.1% and 3.6% of the tumors, with most of these mutations having a proven role in activating the human epidermal growth factor receptor/ERBB pathway. Mutations in FOXA1 and ESR1 copy number gains were detected in 9% and 25% of the samples. All these alterations were more frequent in ILBC than in IDBC. The histologic diversity of ILBC was associated with specific alterations, such as enrichment for HER2 mutations in the mixed, nonclassic, and ESR1 gains in the solid subtype. Survival analyses revealed that chromosome 1q and 11p gains showed independent prognostic value in ILBC and that HER2 and AKT1 mutations were associated with increased risk of early relapse. Conclusion This study demonstrates that we can now begin to individualize the treatment of ILBC, with HER2, HER3, and AKT1 mutations representing high-prevalence therapeutic targets and FOXA1 mutations and ESR1 gains deserving urgent dedicated clinical investigation, especially in the context of endocrine treatment.
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Affiliation(s)
- Christine Desmedt
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - Gabriele Zoppoli
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - Gunes Gundem
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - Giancarlo Pruneri
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - Denis Larsimont
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - Marco Fornili
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - Debora Fumagalli
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - David Brown
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - Françoise Rothé
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - Delphine Vincent
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - Naima Kheddoumi
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - Ghizlane Rouas
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - Samira Majjaj
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - Sylvain Brohée
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - Peter Van Loo
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - Patrick Maisonneuve
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - Roberto Salgado
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - Thomas Van Brussel
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - Diether Lambrechts
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - Ron Bose
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - Otto Metzger
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - Christine Galant
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - François Bertucci
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - Martine Piccart-Gebhart
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - Giuseppe Viale
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - Elia Biganzoli
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - Peter J. Campbell
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
| | - Christos Sotiriou
- Christine Desmedt, Gabriele Zoppoli, Denis Larsimont, Debora Fumagalli, David Brown, Françoise Rothé, Delphine Vincent, Naima Kheddoumi, Ghizlane Rouas, Samira Majjaj, Sylvain Brohée, Roberto Salgado, Martine Piccart-Gebhart, and Christos Sotiriou, Institut Jules Bordet; Christine Galant, Cliniques Universitaires Saint Luc, Brussels; Peter Van Loo, University of Leuven; Thomas Van Brussel and Diether Lambrechts, VIB Vesalius Research Center, Leuven, Belgium; Gabriele Zoppoli, University of Genoa and
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Fernandez-Lozano C, Cuiñas RF, Seoane JA, Fernández-Blanco E, Dorado J, Munteanu CR. Classification of signaling proteins based on molecular star graph descriptors using Machine Learning models. J Theor Biol 2015; 384:50-8. [DOI: 10.1016/j.jtbi.2015.07.038] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 07/20/2015] [Accepted: 07/27/2015] [Indexed: 12/11/2022]
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Verleyen W, Ballouz S, Gillis J. Measuring the wisdom of the crowds in network-based gene function inference. Bioinformatics 2014; 31:745-52. [DOI: 10.1093/bioinformatics/btu715] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Abstract
A new model of kinase regulation based on the assembly of hydrophobic spines has been proposed. Changes in their positions can explain the mechanism of kinase activation. Here, we examined mutations in human cancer for clues about the regulation of the hydrophobic spines by focusing initially on mutations to Phe. We identified a selected number of Phe mutations in a small group of kinases that included BRAF, ABL1, and the epidermal growth factor receptor. Testing some of these mutations in BRAF, we found that one of the mutations impaired ATP binding and catalytic activity but promoted noncatalytic allosteric functions. Other Phe mutations functioned to promote constitutive catalytic activity. One of these mutations revealed a previously underappreciated hydrophobic surface that functions to position the dynamic regulatory αC-helix. This supports the key role of the C-helix as a signal integration motif for coordinating multiple elements of the kinase to create an active conformation. The importance of the hydrophobic space around the αC-helix was further tested by studying a V600F mutant, which was constitutively active in the absence of the negative charge that is associated with the common V600E mutation. Many hydrophobic mutations strategically localized along the C-helix can thus drive kinase activation.
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