Genomic and transcriptomic analyses identify a prognostic gene signature and predict response to therapy in pleural and peritoneal mesothelioma

[1]  Ash A. Alizadeh,et al.  Atlas of clinically distinct cell states and ecosystems across human solid tumors , 2021, Cell.

[2]  Anna L. Brown,et al.  Notch signaling and efficacy of PD-1/PD-L1 blockade in relapsed small cell lung cancer , 2021, Nature Communications.

[3]  A. Maconi,et al.  Tumor Immune Microenvironment and Genetic Alterations in Mesothelioma , 2021, Frontiers in Oncology.

[4]  E. Ruppin,et al.  Synthetic lethality-mediated precision oncology via the tumor transcriptome , 2021, Cell.

[5]  A. Mansfield,et al.  First-line nivolumab plus ipilimumab in unresectable malignant pleural mesothelioma (CheckMate 743): a multicentre, randomised, open-label, phase 3 trial , 2021, The Lancet.

[6]  G. Frampton,et al.  Prevalence of High Tumor Mutational Burden and Association With Survival in Patients With Less Common Solid Tumors , 2020, JAMA network open.

[7]  J. Brugarolas,et al.  Biological Mechanisms and Clinical Significance of BAP1 Mutations in Human Cancer. , 2020, Cancer discovery.

[8]  C. Svendsen,et al.  Immunosuppressive Functions of M2 Macrophages Derived from iPSCs of Patients with ALS and Healthy Controls , 2020, iScience.

[9]  Angela N. Brooks,et al.  Visualizing and interpreting cancer genomics data via the Xena platform , 2020, Nature Biotechnology.

[10]  Anna L. Brown,et al.  Clonal Evolution and Heterogeneity of Osimertinib Acquired Resistance Mechanisms in EGFR Mutant Lung Cancer , 2020, Cell reports medicine.

[11]  A. Greenbaum,et al.  Peritoneal mesothelioma , 2020, Translational lung cancer research.

[12]  E. Ruppin,et al.  Multiomics Prediction of Response Rates to Therapies to Inhibit Programmed Cell Death 1 and Programmed Cell Death 1 Ligand 1. , 2019, JAMA oncology.

[13]  G. Wainrib,et al.  Deep learning-based classification of mesothelioma improves prediction of patient outcome , 2019, Nature Medicine.

[14]  F. Galateau-Sallé,et al.  Mesothelioma: Scientific clues for prevention, diagnosis, and therapy , 2019, CA: a cancer journal for clinicians.

[15]  T. Walsh,et al.  Inherited predisposition to malignant mesothelioma and overall survival following platinum chemotherapy , 2019, Proceedings of the National Academy of Sciences.

[16]  M. Ladanyi,et al.  Loss of BAP1 as a candidate predictive biomarker for immunotherapy of mesothelioma , 2019, Genome Medicine.

[17]  Adam A. Friedman,et al.  Genome‐wide prediction of synthetic rescue mediators of resistance to targeted and immunotherapy , 2018, bioRxiv.

[18]  Damian Szklarczyk,et al.  STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets , 2018, Nucleic Acids Res..

[19]  Andreas Ruepp,et al.  CORUM: the comprehensive resource of mammalian protein complexes—2019 , 2018, Nucleic Acids Res..

[20]  Xi Zhang,et al.  Nucleolar and Spindle Associated Protein 1 (NUSAP1) Inhibits Cell Proliferation and Enhances Susceptibility to Epirubicin In Invasive Breast Cancer Cells by Regulating Cyclin D Kinase (CDK1) and DLGAP5 Expression , 2018, Medical science monitor : international medical journal of experimental and clinical research.

[21]  David L. Gibbs,et al.  Integrative Molecular Characterization of Malignant Pleural Mesothelioma. , 2018, Cancer discovery.

[22]  Xiaonan Wei,et al.  NUSAP1 gene silencing inhibits cell proliferation, migration and invasion through inhibiting DNMT1 gene expression in human colorectal cancer , 2018, Experimental cell research.

[23]  David S. Wishart,et al.  DrugBank 5.0: a major update to the DrugBank database for 2018 , 2017, Nucleic Acids Res..

[24]  Hyojin Kim,et al.  TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions , 2017, Nucleic Acids Res..

[25]  James T. Robinson,et al.  Variant Review with the Integrative Genomics Viewer. , 2017, Cancer research.

[26]  F. Mowat,et al.  Therapeutic radiation for lymphoma and risk of second primary malignant mesothelioma , 2017, Cancer Causes & Control.

[27]  L. Staudt,et al.  The NCI Genomic Data Commons as an engine for precision medicine. , 2017, Blood.

[28]  Ann E. Sizemore,et al.  Computational correction of copy-number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells , 2017, Nature Genetics.

[29]  P. Hieter,et al.  Synthetic lethality and cancer , 2017, Nature Reviews Genetics.

[30]  A. Santoro,et al.  Clinical safety and activity of pembrolizumab in patients with malignant pleural mesothelioma (KEYNOTE-028): preliminary results from a non-randomised, open-label, phase 1b trial. , 2017, The Lancet. Oncology.

[31]  J. Brooks,et al.  NUSAP1 promotes invasion and metastasis of prostate cancer , 2017, Oncotarget.

[32]  Ying Chai,et al.  Prognostic role of cyclin B1 in solid tumors: a meta-analysis , 2016, Oncotarget.

[33]  M. Carbone,et al.  Environmental risk of mesothelioma in the United States: An emerging concern—epidemiological issues , 2016, Journal of toxicology and environmental health. Part B, Critical reviews.

[34]  G. Matullo,et al.  CDKN2A and BAP1 germline mutations predispose to melanoma and mesothelioma. , 2016, Cancer letters.

[35]  Thomas D. Wu,et al.  Comprehensive genomic analysis of malignant pleural mesothelioma identifies recurrent mutations, gene fusions and splicing alterations , 2016, Nature Genetics.

[36]  A. Farioli,et al.  Radiation‐induced mesothelioma among long‐term solid cancer survivors: a longitudinal analysis of SEER database , 2016, Cancer medicine.

[37]  Meagan E. Sullender,et al.  Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9 , 2015, Nature Biotechnology.

[38]  Wei Zhou,et al.  MTBP Promotes the Invasion and Metastasis of Hepatocellular Carcinoma by Enhancing the MDM2-Mediated Degradation of E-Cadherin , 2015, Digestive Diseases and Sciences.

[39]  M. Maio,et al.  Efficacy and safety of an intensified schedule of tremelimumab for chemotherapy-resistant malignant mesothelioma: an open-label, single-arm, phase 2 study. , 2015, The Lancet. Respiratory medicine.

[40]  Ash A. Alizadeh,et al.  Robust enumeration of cell subsets from tissue expression profiles , 2015, Nature Methods.

[41]  N. Agarwal,et al.  MTBP inhibits migration and metastasis of hepatocellular carcinoma , 2015, Clinical & Experimental Metastasis.

[42]  Bale,et al.  Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology , 2015, Genetics in Medicine.

[43]  M. Lucchi,et al.  Expression status of candidate genes in mesothelioma tissues and cell lines. , 2015, Mutation research.

[44]  T. Nakajima,et al.  Identification of actionable mutations in malignant pleural mesothelioma. , 2014, Lung cancer.

[45]  Jeffrey W Pollard,et al.  Tumor-associated macrophages: from mechanisms to therapy. , 2014, Immunity.

[46]  G. Ceresoli,et al.  Vinorelbine in pemetrexed-pretreated patients with malignant pleural mesothelioma. , 2014, Lung cancer.

[47]  M. Maio,et al.  Tremelimumab for patients with chemotherapy-resistant advanced malignant mesothelioma: an open-label, single-arm, phase 2 trial. , 2013, The Lancet. Oncology.

[48]  D. Landau,et al.  Phase 2 Study of Sorafenib in Malignant Mesothelioma Previously Treated with Platinum-Containing Chemotherapy , 2013, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[49]  M. Pagano,et al.  A cyclin without cyclin-dependent kinases: cyclin F controls genome stability through ubiquitin-mediated proteolysis. , 2013, Trends in cell biology.

[50]  N. Agarwal,et al.  MTBP suppresses cell migration and filopodia formation by inhibiting ACTN4 , 2012, Oncogene.

[51]  A. Musk,et al.  A Phase II Study of Intermittent Sunitinib Malate as Second-Line Therapy in Progressive Malignant Pleural Mesothelioma , 2012, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[52]  L. Seymour,et al.  Brief Report: A Phase II Study of Sunitinib in Malignant Pleural Mesothelioma. The NCIC Clinical Trials Group , 2011, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[53]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[54]  R. Labianca,et al.  Single-Agent Pemetrexed for Chemonaïve and Pretreated Patients with Malignant Pleural Mesothelioma: Results of an International Expanded Access Program , 2008, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[55]  Q. Zhan,et al.  Overexpression of cyclin B1 in human esophageal squamous cell carcinoma cells induces tumor cell invasive growth and metastasis. , 2008, Carcinogenesis.

[56]  A. Olshen,et al.  Global gene expression profiling of pleural mesotheliomas: overexpression of aurora kinases and P16/CDKN2A deletion as prognostic factors and critical evaluation of microarray-based prognostic prediction. , 2006, Cancer research.

[57]  R. Govindan,et al.  Gefitinib in Patients with Malignant Mesothelioma: A Phase II Study by the Cancer and Leukemia Group B , 2005, Clinical Cancer Research.

[58]  Sorin Draghici,et al.  Gene Expression Profiles Predict Survival and Progression of Pleural Mesothelioma , 2004, Clinical Cancer Research.

[59]  J. Ellenberg,et al.  NuSAP, a novel microtubule-associated protein involved in mitotic spindle organization , 2003, The Journal of cell biology.

[60]  Claude Denham,et al.  Phase III study of pemetrexed in combination with cisplatin versus cisplatin alone in patients with malignant pleural mesothelioma. , 2003, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[61]  J. Blumenstock,et al.  Using gene expression ratios to predict outcome among patients with mesothelioma. , 2003, Journal of the National Cancer Institute.

[62]  G. Scagliotti,et al.  Phase II study of pemetrexed with and without folic acid and vitamin B12 as front-line therapy in malignant pleural mesothelioma. , 2003, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[63]  J. Shamash,et al.  Phase II study of vinorelbine in patients with malignant pleural mesothelioma. , 2000, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[64]  F. Khuri,et al.  Overexpression of cyclin B1 in early-stage non-small cell lung cancer and its clinical implication. , 2000, Cancer research.

[65]  F. Liddell,et al.  The mortality of amphibole miners in South Africa, 1946-80. , 1992, British journal of industrial medicine.

[66]  E. Kaplan,et al.  Nonparametric Estimation from Incomplete Observations , 1958 .

[67]  H. Ehrhart,et al.  [Cancer and leukemia]. , 1957, Medizinische Klinik.