RNAseq expression patterns of canine invasive urothelial carcinoma reveal two distinct tumor clusters and shared regions of dysregulation with human bladder tumors

[1]  F. Feng,et al.  Impact of Immune and Stromal Infiltration on Outcomes Following Bladder-Sparing Trimodality Therapy for Muscle-Invasive Bladder Cancer. , 2019, European urology.

[2]  Jianjun Gao,et al.  Targeting advanced urothelial carcinoma-developing strategies , 2019, Current opinion in oncology.

[3]  L. Paz-Ares,et al.  FGFR1 Cooperates with EGFR in Lung Cancer Oncogenesis, and Their Combined Inhibition Shows Improved Efficacy , 2019, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[4]  J. Bartlett,et al.  Molecular profiling in muscle‐invasive bladder cancer: more than the sum of its parts , 2019, The Journal of pathology.

[5]  P. Low,et al.  Phase I/II clinical trial of the targeted chemotherapeutic drug, folate-tubulysin, in dogs with naturally-occurring invasive urothelial carcinoma , 2018, Oncotarget.

[6]  S. Mahmood,et al.  CCR5 blockage by maraviroc: a potential therapeutic option for metastatic breast cancer , 2018, Cellular Oncology.

[7]  Wei Li,et al.  Overexpression of Epidermal Growth Factor Receptor (EGFR) and HER-2 in Bladder Carcinoma and Its Association with Patients’ Clinical Features , 2018, Medical science monitor : international medical journal of experimental and clinical research.

[8]  D. Dhawan,et al.  Naturally-occurring canine invasive urothelial carcinoma harbors luminal and basal transcriptional subtypes found in human muscle invasive bladder cancer , 2018, PLoS genetics.

[9]  G. Lubas,et al.  Overexpression of HER-2 via immunohistochemistry in canine urinary bladder transitional cell carcinoma - A marker of malignancy and possible therapeutic target. , 2018, Veterinary and comparative oncology.

[10]  Genki Ishihara,et al.  Comprehensive gene expression analysis of canine invasive urothelial bladder carcinoma by RNA-Seq , 2018, BMC cancer.

[11]  T. Ratliff,et al.  Naturally-Occurring Canine Invasive Urothelial Carcinoma: A Model for Emerging Therapies , 2018, Bladder cancer.

[12]  P. Choyke,et al.  Near infrared photoimmunotherapy targeting bladder cancer with a canine anti-epidermal growth factor receptor (EGFR) antibody , 2018, Oncotarget.

[13]  A. Hartmann,et al.  Urothelial Bladder Cancer: An Update on Molecular Pathology with Clinical Implications , 2017 .

[14]  Steven J. M. Jones,et al.  Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer , 2017, Cell.

[15]  K. Hoadley,et al.  Impact of Molecular Subtypes in Muscle-invasive Bladder Cancer on Predicting Response and Survival after Neoadjuvant Chemotherapy. , 2017, European urology.

[16]  C. Lindskog,et al.  A pathology atlas of the human cancer transcriptome , 2017, Science.

[17]  Dong-qing Zhang,et al.  Identification of hub genes and pathways associated with bladder cancer based on co-expression network analysis. , 2017, Oncology letters.

[18]  M. Miller,et al.  Skeletal Metastasis of Canine Urothelial Carcinoma: Pathologic and Computed Tomographic Features , 2017, Veterinary pathology.

[19]  T. Ratliff,et al.  Naturally Occurring Canine Invasive Urinary Bladder Cancer: A Complementary Animal Model to Improve the Success Rate in Human Clinical Trials of New Cancer Drugs , 2017, International journal of genomics.

[20]  Adelaide C. Rhodes,et al.  Cross‐species analysis of the canine and human bladder cancer transcriptome and exome , 2017, Genes, chromosomes & cancer.

[21]  M. Höglund,et al.  Molecular classification of urothelial carcinoma: global mRNA classification versus tumour‐cell phenotype classification , 2017, The Journal of pathology.

[22]  Frédéric Baribaud,et al.  Integrating personalized gene expression profiles into predictive disease-associated gene pools , 2017, npj Systems Biology and Applications.

[23]  N. James,et al.  Gene expression profiling in bladder cancer identifies potential therapeutic targets , 2017, International journal of oncology.

[24]  K. Lindblad-Toh,et al.  FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome , 2017, Nucleic acids research.

[25]  D. Stover,et al.  Enfortumab Vedotin Antibody-Drug Conjugate Targeting Nectin-4 Is a Highly Potent Therapeutic Agent in Multiple Preclinical Cancer Models. , 2016, Cancer research.

[26]  R. Bourgon,et al.  Atezolizumab in patients with locally advanced and metastatic urothelial carcinoma who have progressed following treatment with platinum-based chemotherapy: a single-arm, multicentre, phase 2 trial , 2016, The Lancet.

[27]  M. Koch,et al.  Tumoral Immune Cell Exploitation in Colorectal Cancer Metastases Can Be Targeted Effectively by Anti-CCR5 Therapy in Cancer Patients. , 2016, Cancer cell.

[28]  B. Craig,et al.  Comparative Gene Expression Analyses Identify Luminal and Basal Subtypes of Canine Invasive Urothelial Carcinoma That Mimic Patterns in Human Invasive Bladder Cancer , 2015, PloS one.

[29]  D. Knapp,et al.  Management of transitional cell carcinoma of the urinary bladder in dogs: a review. , 2015, Veterinary journal.

[30]  M. Höglund,et al.  Biological determinants of bladder cancer gene expression subtypes , 2015, Scientific Reports.

[31]  M. Breen,et al.  BRAF Mutations in Canine Cancers , 2015, PloS one.

[32]  M. Höglund,et al.  Molecular subtypes of urothelial carcinoma are defined by specific gene regulatory systems , 2015, BMC Medical Genomics.

[33]  Frank Emmert-Streib,et al.  Urothelial cancer gene regulatory networks inferred from large-scale RNAseq, Bead and Oligo gene expression data , 2015, BMC Systems Biology.

[34]  A. Motsinger-Reif,et al.  Canine urothelial carcinoma: genomically aberrant and comparatively relevant , 2015, Chromosome Research.

[35]  E. Ostrander,et al.  Homologous Mutation to Human BRAF V600E Is Common in Naturally Occurring Canine Bladder Cancer—Evidence for a Relevant Model System and Urine-Based Diagnostic Test , 2015, Molecular Cancer Research.

[36]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[37]  Paul Theodor Pyl,et al.  HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[38]  Katherine A. Hoadley,et al.  Intrinsic subtypes of high-grade bladder cancer reflect the hallmarks of breast cancer biology , 2014, Proceedings of the National Academy of Sciences.

[39]  K. Baggerly,et al.  Identification of distinct basal and luminal subtypes of muscle-invasive bladder cancer with different sensitivities to frontline chemotherapy. , 2014, Cancer cell.

[40]  J. Lubin,et al.  The increase in thyroid cancer incidence during the last four decades is accompanied by a high frequency of BRAF mutations and a sharp increase in RAS mutations. , 2014, The Journal of clinical endocrinology and metabolism.

[41]  W. Hahn,et al.  Integrative Analysis of 1q23.3 Copy-Number Gain in Metastatic Urothelial Carcinoma , 2014, Clinical Cancer Research.

[42]  Steven J. M. Jones,et al.  Comprehensive molecular characterization of urothelial bladder carcinoma , 2014, Nature.

[43]  Andreas Krämer,et al.  Causal analysis approaches in Ingenuity Pathway Analysis , 2013, Bioinform..

[44]  N. Rosen,et al.  Tumor adaptation and resistance to RAF inhibitors , 2013, Nature Medicine.

[45]  S. Gabriel,et al.  Pan-cancer patterns of somatic copy-number alteration , 2013, Nature Genetics.

[46]  Joaquim Bellmunt,et al.  Identification of prefoldin amplification (1q23.3-q24.1) in bladder cancer using comparative genomic hybridization (CGH) arrays of urinary DNA , 2013, Journal of Translational Medicine.

[47]  P. Low,et al.  Targeting folate receptors to treat invasive urinary bladder cancer. , 2013, Cancer research.

[48]  Günter P. Wagner,et al.  Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples , 2012, Theory in Biosciences.

[49]  M. Lisanti,et al.  CCR5 antagonist blocks metastasis of basal breast cancer cells. , 2012, Cancer research.

[50]  Mårten Fernö,et al.  A Molecular Taxonomy for Urothelial Carcinoma , 2012, Clinical Cancer Research.

[51]  E. Ostrander,et al.  Subcutaneous 5-azacitidine treatment of naturally occurring canine urothelial carcinoma: a novel epigenetic approach to human urothelial carcinoma drug development. , 2011, The Journal of urology.

[52]  Helga Thorvaldsdóttir,et al.  Molecular signatures database (MSigDB) 3.0 , 2011, Bioinform..

[53]  Xuejiang Guo,et al.  RGS22, a novel cancer/testis antigen, inhibits epithelial cell invasion and metastasis , 2011, Clinical & Experimental Metastasis.

[54]  N. Seki,et al.  LY6K is a novel molecular target in bladder cancer on basis of integrate genome-wide profiling , 2010, British Journal of Cancer.

[55]  Matthew D. Wilkerson,et al.  ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking , 2010, Bioinform..

[56]  D. Spandidos,et al.  Mutational analysis of the BRAF gene in transitional cell carcinoma of the bladder. , 2009, The International journal of biological markers.

[57]  D. Spandidos,et al.  Mutational Analysis of the BRAF Gene in Transitional Cell Carcinoma of the Bladder , 2009 .

[58]  M. D'urso,et al.  MRX87 family with Aristaless X dup24bp mutation and implication for polyAlanine expansions , 2007, BMC Medical Genetics.

[59]  Tapio Visakorpi,et al.  Genetic aberrations in prostate cancer by microarray analysis , 2006, International journal of cancer.

[60]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[61]  Mathew J Garnett,et al.  Guilty as charged: B-RAF is a human oncogene. , 2004, Cancer cell.

[62]  S. Lima,et al.  Total bladder replacement with de-epithelialized ileum. Experimental study in dogs. , 2004, International braz j urol : official journal of the Brazilian Society of Urology.

[63]  Wen-Lin Kuo,et al.  Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors. , 2003, Cancer research.

[64]  A. Nicholson,et al.  Mutations of the BRAF gene in human cancer , 2002, Nature.

[65]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[66]  L. Glickman,et al.  Naturally-occurring canine transitional cell carcinoma of the urinary bladder A relevant model of human invasive bladder cancer. , 2000, Urologic oncology.

[67]  W. Rutter,et al.  Polymorphic DNA region adjacent to the 5' end of the human insulin gene. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[68]  M. A. Weinberger Tumors in Domestic Animals , 1962 .

[69]  Targeting Nectin-4 in Bladder Cancer. , 2017, Cancer discovery.

[70]  D. Dhawan,et al.  Urinary bladder cancer in dogs, a naturally occurring model for cancer biology and drug development. , 2014, ILAR journal.

[71]  The Cancer Genome Atlas Research Network,et al.  Comprehensive molecular characterization of urothelial bladder carcinoma , 2014, Nature.

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

[73]  Hilde van der Togt,et al.  Publisher's Note , 2003, J. Netw. Comput. Appl..

[74]  D. Meuten Tumors in Domestic Animals: Meuten/Tumors , 2002 .

[75]  Josef Korinek,et al.  Proceedings of the American Society of Clinical Oncology , 1982 .