Truncated FGFR2 is a clinically actionable oncogene in multiple cancers

[1]  D. Smith,et al.  FIGHT-101, a first-in-human study of potent and selective FGFR 1-3 inhibitor pemigatinib in pan-cancer patients with FGF/FGFR alterations and advanced malignancies. , 2022, Annals of oncology : official journal of the European Society for Medical Oncology.

[2]  Howard Y. Chang,et al.  ecDNA hubs drive cooperative intermolecular oncogene expression , 2021, Nature.

[3]  Toshio Shimizu,et al.  Comprehensive functional evaluation of variants of fibroblast growth factor receptor genes in cancer , 2021, npj Precision Oncology.

[4]  Seyed Ziaeddin Alborzi,et al.  PPIDomainMiner: Inferring domain-domain interactions from multiple sources of protein-protein interactions , 2021, bioRxiv.

[5]  J. Wesche,et al.  Negative Regulation of FGFR (Fibroblast Growth Factor Receptor) Signaling , 2021, Cells.

[6]  J. Jonkers,et al.  Feasibility of Phosphoproteomics on Leftover Samples After RNA Extraction With Guanidinium Thiocyanate , 2020, bioRxiv.

[7]  Mehmet Koyutürk,et al.  Robust inference of kinase activity using functional networks , 2020, bioRxiv.

[8]  R. Wynn,et al.  INCB054828 (pemigatinib), a potent and selective inhibitor of fibroblast growth factor receptors 1, 2, and 3, displays activity against genetically defined tumor models , 2020, PloS one.

[9]  Nuno A. Fonseca,et al.  Patterns of somatic structural variation in human cancer genomes , 2020, Nature.

[10]  B. Haas,et al.  Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods , 2019, Genome Biology.

[11]  A. Sonnenberg,et al.  Rebalancing of actomyosin contractility enables mammary tumor formation upon loss of E-cadherin , 2019, Nature Communications.

[12]  A. Berns,et al.  Tumor Heterogeneity Underlies Differential Cisplatin Sensitivity in Mouse Models of Small-Cell Lung Cancer , 2019, Cell reports.

[13]  J. Wesche,et al.  Cancer Mutations in FGFR2 Prevent a Negative Feedback Loop Mediated by the ERK1/2 Pathway , 2019, Cells.

[14]  Andrea Bertotti,et al.  INKA, an integrative data analysis pipeline for phosphoproteomic inference of active kinases , 2019, Molecular systems biology.

[15]  Yan Guo,et al.  Aberrant FGFR signaling mediates resistance to CDK4/6 inhibitors in ER+ breast cancer , 2019, Nature Communications.

[16]  I. Huijbers,et al.  Comparative oncogenomics identifies combinations of driver genes and drug targets in BRCA1-mutated breast cancer , 2019, Nature Communications.

[17]  V. Miller,et al.  Detection of Known and Novel FGFR Fusions in Non–Small Cell Lung Cancer by Comprehensive Genomic Profiling , 2019, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[18]  Martin Eisenacher,et al.  The PRIDE database and related tools and resources in 2019: improving support for quantification data , 2018, Nucleic Acids Res..

[19]  Joshua M. Korn,et al.  Next-generation characterization of the Cancer Cell Line Encyclopedia , 2019, Nature.

[20]  M. Katoh.  Fibroblast growth factor receptors as treatment targets in clinical oncology , 2018, Nature Reviews Clinical Oncology.

[21]  S. Sleijfer,et al.  Pan-cancer whole-genome analyses of metastatic solid tumours , 2018, bioRxiv.

[22]  Doron Lipson,et al.  Analytical Validation of a Hybrid Capture–Based Next-Generation Sequencing Clinical Assay for Genomic Profiling of Cell-Free Circulating Tumor DNA , 2018, The Journal of molecular diagnostics : JMD.

[23]  Kwok-Kin Wong,et al.  EZH2-Mediated Primary Cilium Deconstruction Drives Metastatic Melanoma Formation. , 2018, Cancer cell.

[24]  M. Lopes,et al.  Selective Loss of PARG Restores PARylation and Counteracts PARP Inhibitor-Mediated Synthetic Lethality. , 2018, Cancer cell.

[25]  Li Ding,et al.  Driver Fusions and Their Implications in the Development and Treatment of Human Cancers , 2018, Cell reports.

[26]  D. Constam,et al.  Crystal Structure of Bicc1 SAM Polymer and Mapping of Interactions between the Ciliopathy-Associated Proteins Bicc1, ANKS3, and ANKS6. , 2017, Structure.

[27]  Zhaleh Safikhani,et al.  PharmacoDB: an integrative database for mining in vitro anticancer drug screening studies , 2017, bioRxiv.

[28]  David A. Knowles,et al.  Annotation-free quantification of RNA splicing using LeafCutter , 2017, Nature Genetics.

[29]  T. Speed,et al.  GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly. , 2017, Genome research.

[30]  D. Adams,et al.  Insertional mutagenesis identifies drivers of a novel oncogenic pathway in invasive lobular breast carcinoma , 2017, Nature Genetics.

[31]  L. Wessels,et al.  Identifying transposon insertions and their effects from RNA-sequencing data , 2017, Nucleic acids research.

[32]  Y. Bang,et al.  A randomized, open-label study of the efficacy and safety of AZD4547 monotherapy versus paclitaxel for the treatment of advanced gastric adenocarcinoma with FGFR2 polysomy or gene amplification , 2017, Annals of oncology : official journal of the European Society for Medical Oncology.

[33]  M. Eldridge,et al.  Disambiguate: An open-source application for disambiguating two species in next generation sequencing data from grafted , 2018 .

[34]  Jüergen Cox,et al.  The MaxQuant computational platform for mass spectrometry-based shotgun proteomics , 2016, Nature Protocols.

[35]  L. Wessels,et al.  PTEN Loss in E-Cadherin-Deficient Mouse Mammary Epithelial Cells Rescues Apoptosis and Results in Development of Classical Invasive Lobular Carcinoma , 2016, Cell reports.

[36]  Emanuel J. V. Gonçalves,et al.  A Landscape of Pharmacogenomic Interactions in Cancer , 2016, Cell.

[37]  B. Cho,et al.  Activation of the Met kinase confers acquired drug resistance in FGFR-targeted lung cancer therapy , 2016, Oncogenesis.

[38]  Alex M. Fichtenholtz,et al.  Integrated genomic DNA/RNA profiling of hematologic malignancies in the clinical setting. , 2016, Blood.

[39]  Jos Jonkers,et al.  Modeling invasive lobular breast carcinoma by CRISPR/Cas9-mediated somatic genome editing of the mammary gland , 2016, Genes & development.

[40]  Gianluca Bontempi,et al.  TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data , 2015, Nucleic acids research.

[41]  J. Mesirov,et al.  The Molecular Signatures Database Hallmark Gene Set Collection , 2015 .

[42]  I. Huijbers,et al.  Using the GEMM-ESC strategy to study gene function in mouse models , 2015, Nature Protocols.

[43]  Steven J. M. Jones,et al.  Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer , 2015, Cell.

[44]  I. Huijbers,et al.  Selective resistance to the PARP inhibitor olaparib in a mouse model for BRCA1-deficient metaplastic breast cancer , 2015, Proceedings of the National Academy of Sciences.

[45]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

[46]  Pieter Wesseling,et al.  DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly , 2014, Genome research.

[47]  J. Wesche,et al.  RSK2 regulates endocytosis of FGF receptor 1 by phosphorylation on serine 789 , 2014, Oncogene.

[48]  B. Pan,et al.  FGFR2 Is Amplified in the NCI-H716 Colorectal Cancer Cell Line and Is Required for Growth and Survival , 2014, PloS one.

[49]  M. Kadakia,et al.  Pten loss induces autocrine FGF signaling to promote skin tumorigenesis. , 2014, Cell reports.

[50]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[51]  Alex M. Fichtenholtz,et al.  Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing , 2013, Nature Biotechnology.

[52]  Joshua M. Stuart,et al.  The Cancer Genome Atlas Pan-Cancer analysis project , 2013, Nature Genetics.

[53]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[54]  Johannes E. Schindelin,et al.  Fiji: an open-source platform for biological-image analysis , 2012, Nature Methods.

[55]  S. Arold,et al.  Inhibition of Basal FGF Receptor Signaling by Dimeric Grb2 , 2012, Cell.

[56]  Jian Ye,et al.  Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction , 2012, BMC Bioinformatics.

[57]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[58]  J. Wesseling,et al.  Mammary-specific inactivation of E-cadherin and p53 impairs functional gland development and leads to pleomorphic invasive lobular carcinoma in mice , 2011, Disease Models & Mechanisms.

[59]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[60]  Hugo M. Horlings,et al.  Integrative molecular profiling of triple negative breast cancers identifies amplicon drivers and potential therapeutic targets , 2009, Oncogene.

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

[62]  M. Robinson,et al.  A scaling normalization method for differential expression analysis of RNA-seq data , 2010, Genome Biology.

[63]  Ben S. Wittner,et al.  Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1 , 2009, Nature.

[64]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[65]  P. Hurlin,et al.  The role of senescence and prosurvival signaling in controlling the oncogenic activity of FGFR2 mutants associated with cancer and birth defects , 2009, Human molecular genetics.

[66]  M. Mann,et al.  MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.

[67]  Brad T. Sherman,et al.  Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources , 2008, Nature Protocols.

[68]  M. Mann,et al.  Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks , 2006, Cell.

[69]  Jos Jonkers,et al.  Somatic inactivation of E-cadherin and p53 in mice leads to metastatic lobular mammary carcinoma through induction of anoikis resistance and angiogenesis. , 2006, Cancer cell.

[70]  J. Mesirov,et al.  GenePattern 2.0 , 2006, Nature Genetics.

[71]  Robert B. Russell,et al.  3did: interacting protein domains of known three-dimensional structure , 2004, Nucleic Acids Res..

[72]  S. Ethier,et al.  Transforming potential of alternatively spliced variants of fibroblast growth factor receptor 2 in human mammary epithelial cells. , 2004, Molecular cancer research : MCR.

[73]  N. Hynes,et al.  Blocking of FGFR signaling inhibits breast cancer cell proliferation through downregulation of D-type cyclins , 2004, Oncogene.

[74]  S C Robertson,et al.  Identification of tyrosine residues in constitutively activated fibroblast growth factor receptor 3 involved in mitogenesis, Stat activation, and phosphatidylinositol 3-kinase activation. , 2001, Molecular biology of the cell.

[75]  L. Ailles,et al.  Gene transfer by lentiviral vectors is limited by nuclear translocation and rescued by HIV-1 pol sequences , 2000, Nature Genetics.

[76]  R. Cardiff,et al.  The mammary pathology of genetically engineered mice: the consensus report and recommendations from the Annapolis meeting‡ , 2000, Oncogene.

[77]  A. Rehemtulla,et al.  Characterization of fibroblast growth factor receptor 2 overexpression in the human breast cancer cell line SUM-52PE , 2000, Breast Cancer Research.

[78]  K. Sakaguchi,et al.  Identification of a novel activated form of the keratinocyte growth factor receptor by expression cloning from parathyroid adenoma tissue , 1999, Oncogene.

[79]  T. Miki,et al.  Ligand-independent activation of fibroblast growth factor receptor-2 by carboxyl terminal alterations , 1997, Oncogene.

[80]  K. Sakaguchi,et al.  FRAG1, a gene that potently activates fibroblast growth factor receptor by C-terminal fusion through chromosomal rearrangement. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[81]  L. Rohrschneider,et al.  Activation of the feline c-fms proto-oncogene: Multiple alterations are required to generate a fully transformed phenotype , 1988, Cell.

[82]  A. Ullrich,et al.  Truncation of the human EGF receptor leads to differential transforming potentials in primary avian fibroblasts and erythroblasts. , 1988, The EMBO journal.