Whole-Organ Genomic Characterization of Mucosal Field Effects Initiating Bladder Carcinogenesis.

[1]  A. G. Murachelli,et al.  The structure of the ASAP core complex reveals the existence of a Pinin-containing PSAP complex , 2012, Nature Structural &Molecular Biology.

[2]  A. Behrens,et al.  ATM signalling and cancer , 2014, Oncogene.

[3]  J. Stein,et al.  EphB4 receptor tyrosine kinase is expressed in bladder cancer and provides signals for cell survival , 2006, Oncogene.

[4]  L. Kluth,et al.  The contemporary role and impact of urine-based biomarkers in bladder cancer , 2017, Translational andrology and urology.

[5]  Yang Zhao,et al.  The RNA Pol II sub-complex hsRpb4/7 is required for viability of multiple human cell lines , 2012, Protein & Cell.

[6]  K. Burridge,et al.  The on-off relationship of Rho and Rac during integrin-mediated adhesion and cell migration , 2014, Small GTPases.

[7]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[8]  J. Catto,et al.  Occupation and Bladder Cancer Phenotype: Identification of Workplace Patterns That Increase the Risk of Advanced Disease Beyond Overall Incidence. , 2016, European urology focus.

[9]  Adam B. Olshen,et al.  Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis , 2009, Bioinform..

[10]  D. Barbie,et al.  Inflammation as a driver and vulnerability of KRAS mediated oncogenesis. , 2016, Seminars in cell & developmental biology.

[11]  G. Sonpavde,et al.  Current Preclinical Models for the Advancement of Translational Bladder Cancer Research , 2012, Molecular Cancer Therapeutics.

[12]  Ming-Ming Zhou,et al.  Chemical modulators for epigenome reader domains as emerging epigenetic therapies for cancer and inflammation. , 2017, Current opinion in chemical biology.

[13]  D. Angelis,et al.  Septin Mutations in Human Cancers , 2016, Front. Cell Dev. Biol..

[14]  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.

[15]  T. Angata.  Associations of genetic polymorphisms of Siglecs with human diseases. , 2014, Glycobiology.

[16]  J. Weinstein,et al.  Meta-Analysis of the Luminal and Basal Subtypes of Bladder Cancer and the Identification of Signature Immunohistochemical Markers for Clinical Use , 2016, EBioMedicine.

[17]  S. Slovin.  The need for immune biomarkers for treatment prognosis and response in genitourinary malignancies. , 2017, Biomarkers in medicine.

[18]  X. Mu,et al.  Isl1 and Pou4f2 Form a Complex to Regulate Target Genes in Developing Retinal Ganglion Cells , 2014, PloS one.

[19]  L. Kiemeney,et al.  Epidemiology and risk factors of urothelial bladder cancer. , 2013, European urology.

[20]  M. Osaki,et al.  Chemopreventive Strategies for Inflammation-Related Carcinogenesis: Current Status and Future Direction , 2017, International journal of molecular sciences.

[21]  A. Moris,et al.  AID and APOBECs span the gap between innate and adaptive immunity , 2014, Front. Microbiol..

[22]  Masaaki Ito,et al.  Characterization of the human hair keratin-associated protein 2 (KRTAP2) gene family. , 2012, The Journal of investigative dermatology.

[23]  J. Melamed,et al.  Mini-review: perspective of the microbiome in the pathogenesis of urothelial carcinoma. , 2014, American journal of clinical and experimental urology.

[24]  Mauricio O. Carneiro,et al.  From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline , 2013, Current protocols in bioinformatics.

[25]  F. Martinon,et al.  Inflammasome Components NALP 1 and 3 Show Distinct but Separate Expression Profiles in Human Tissues Suggesting a Site-specific Role in the Inflammatory Response , 2007, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.

[26]  A. Nepveu,et al.  CUX1, a haploinsufficient tumour suppressor gene overexpressed in advanced cancers , 2014, Nature Reviews Cancer.

[27]  R. Salgia,et al.  Critical role for the receptor tyrosine kinase EPHB4 in esophageal cancers. , 2013, Cancer research.

[28]  Feng-jun Liu,et al.  TUSC3: a novel tumour suppressor gene and its functional implications , 2017, Journal of cellular and molecular medicine.

[29]  Finn Werner,et al.  Crystal structure and RNA binding of the Rpb4/Rpb7 subunits of human RNA polymerase II , 2005, Nucleic acids research.

[30]  S. Ihara,et al.  Cooperation of DEF6 with Activated Rac in Regulating Cell Morphology* , 2007, Journal of Biological Chemistry.

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

[32]  J. Cui,et al.  Mechanisms and pathways of innate immune activation and regulation in health and cancer , 2014, Human vaccines & immunotherapeutics.

[33]  Xiaojiang S. Chen,et al.  APOBEC deaminases-mutases with defensive roles for immunity , 2009, Science in China Series C: Life Sciences.

[34]  D. Zwijnenburg,et al.  Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes , 2012, Nature.

[35]  U. Sinha,et al.  EphB4 provides survival advantage to squamous cell carcinoma of the head and neck , 2006, International journal of cancer.

[36]  David T. W. Jones,et al.  Signatures of mutational processes in human cancer , 2013, Nature.

[37]  Alice T. Loo,et al.  PTEN-deficient cancers depend on PIK3CB , 2008, Proceedings of the National Academy of Sciences.

[38]  I. Inoue,et al.  High Order Formation and Evolution of Hornerin in Primates , 2018, Genome biology and evolution.

[39]  D. Reinberg,et al.  ASAP, a Novel Protein Complex Involved in RNA Processing and Apoptosis , 2003, Molecular and Cellular Biology.

[40]  E. Messing,et al.  Smoking and Bladder Cancer: A Systematic Review of Risk and Outcomes. , 2015, European urology focus.

[41]  Stephen C. J. Parker,et al.  DNA sequence and analysis of human chromosome 8 , 2006, Nature.

[42]  A. Leiblich.  Recent Developments in the Search for Urinary Biomarkers in Bladder Cancer , 2017, Current Urology Reports.

[43]  Sara Al-Khawaga,et al.  Enhanced differentiation of human pluripotent stem cells into pancreatic progenitors co-expressing PDX1 and NKX6.1 , 2018, Stem Cell Research & Therapy.

[44]  C. Arce,et al.  Biological pathway analysis by ArrayUnlock and Ingenuity Pathway Analysis , 2009, BMC proceedings.

[45]  R. Froissart,et al.  Electron transfer flavoprotein deficiency: functional and molecular aspects. , 2006, Molecular genetics and metabolism.

[46]  E. Paradis.  Analysis of Phylogenetics and Evolution with R , 2006 .

[47]  Ann M. Janowski,et al.  Inflammasomes in cancer: a double-edged sword , 2014, Protein & Cell.

[48]  I. Dunham,et al.  DNA sequence and analysis of human chromosome 9 , 2003, Nature.

[49]  S. Nimmagadda,et al.  The intricate role of CXCR4 in cancer. , 2014, Advances in cancer research.

[50]  Davide Prandi,et al.  Clonal evolution of chemotherapy-resistant urothelial carcinoma , 2016, Nature Genetics.

[51]  Wuyuan Lu,et al.  Defensins in innate immunity , 2014, Current opinion in hematology.

[52]  J. Martin-Serrano,et al.  Multiple Interactions between the ESCRT Machinery and Arrestin-Related Proteins: Implications for PPXY-Dependent Budding , 2010, Journal of Virology.

[53]  J. McKiernan,et al.  Modelling bladder cancer in mice: opportunities and challenges , 2014, Nature Reviews Cancer.

[54]  Lin He,et al.  In-depth comparison of somatic point mutation callers based on different tumor next-generation sequencing depth data , 2016, Scientific Reports.

[55]  L. Gan,et al.  Comparative expression analysis of POU4F1, POU4F2 and ISL1 in developing mouse cochleovestibular ganglion neurons. , 2014, Gene expression patterns : GEP.

[56]  R. Horvath.  Update on clinical aspects and treatment of selected vitamin-responsive disorders II (riboflavin and CoQ10) , 2012, Journal of Inherited Metabolic Disease.

[57]  K. Baggerly,et al.  Forerunner genes contiguous to RB1 contribute to the development of in situ neoplasia , 2007, Proceedings of the National Academy of Sciences.

[58]  O. Gokcumen,et al.  Atopic Dermatitis Susceptibility Variants in Filaggrin Hitchhike Hornerin Selective Sweep , 2016, Genome biology and evolution.

[59]  Peter A. Jones,et al.  Targeting the cancer epigenome for therapy , 2016, Nature Reviews Genetics.

[60]  S. Shen,et al.  Hornerin promotes tumor progression and is associated with poor prognosis in hepatocellular carcinoma , 2018, BMC Cancer.

[61]  L. Maquat,et al.  Staufen‐mediated mRNA decay , 2013, Wiley interdisciplinary reviews. RNA.

[62]  B. Czerniak,et al.  Genetic modeling of human urinary bladder carcinogenesis , 2000, Genes, chromosomes & cancer.

[63]  K. Nixon.  The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis , 1999 .

[64]  I. Sesterhenn,et al.  World health organization classifications of tumours. pathology and genetics of tumours of the urinary system and male genital organs , 2005 .

[65]  Trevor J Pugh,et al.  Oncotator: Cancer Variant Annotation Tool , 2015, Human mutation.

[66]  Hong‐yu Li,et al.  Targeting mutant KRAS for anticancer therapeutics: a review of novel small molecule modulators. , 2013, Journal of medicinal chemistry.

[67]  J. Livny,et al.  A mucosal imprint left by prior Escherichia coli bladder infection sensitizes to recurrent disease , 2016, Nature Microbiology.

[68]  H. Weng,et al.  CXCR4 over-expression and survival in cancer: A system review and meta-analysis , 2014, Oncotarget.

[69]  B. Czerniak,et al.  Origins of Bladder Cancer. , 2016, Annual review of pathology.

[70]  L. Sobin,et al.  TNM Classification of Malignant Tumours , 1987, UICC International Union Against Cancer.

[71]  Y. Shih,et al.  NKX6.1 hypermethylation predicts the outcome of stage II colorectal cancer patients undergoing chemotherapy , 2018, Genes, chromosomes & cancer.

[72]  Gang Ma,et al.  Roles of ZIC family genes in human gastric cancer. , 2016, International journal of molecular medicine.

[73]  Roberto Piñeiro,et al.  Molecules in medicine mini-review: isoforms of PI3K in biology and disease , 2015, Journal of Molecular Medicine.

[74]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[75]  R. Millikan,et al.  Focus on bladder cancer. , 2004, Cancer cell.

[76]  M. Qadir,et al.  Cdc42: Role in Cancer Management , 2015, Chemical biology & drug design.

[77]  Peter W. Laird,et al.  Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer , 2018, Cell.

[78]  Y. Zhang,et al.  Over-Expression of Ephb4 Is Associated with Carcinogenesis of Gastric Cancer , 2011, Digestive Diseases and Sciences.

[79]  Emily C. McGaugh,et al.  Efficient Differentiation of Pluripotent Stem Cells to NKX6-1+ Pancreatic Progenitors. , 2017, Journal of visualized experiments : JoVE.

[80]  Marc J. Williams,et al.  Identification of neutral tumor evolution across cancer types , 2016, Nature Genetics.

[81]  A. Takaori-Kondo.  APOBEC Family Proteins: Novel Antiviral Innate Immunity , 2006, International journal of hematology.

[82]  Staufen1-mediated mRNA decay induces Requiem mRNA decay through binding of Staufen1 to the Requiem 3′UTR , 2014, Nucleic acids research.

[83]  T. Gajewski,et al.  Innate immune recognition of cancer. , 2015, Annual review of immunology.

[84]  V. Korzh,et al.  Changing Faces of Transcriptional Regulation Reflected by Zic3 , 2015, Current genomics.

[85]  D. Raoult.  Is there a link between urinary microbiota and bladder cancer? , 2017, European Journal of Epidemiology.

[86]  L. Xiaoyan,et al.  FBXW10 is negatively regulated in transcription and expression level by protein O-GlcNAcylation. , 2013, Biochemical and biophysical research communications.

[87]  J. Schröder,et al.  Skin-Derived C-Terminal Filaggrin-2 Fragments Are Pseudomonas aeruginosa-Directed Antimicrobials Targeting Bacterial Replication , 2015, PLoS pathogens.

[88]  Hassan Razvi,et al.  The microbiome of the urinary tract—a role beyond infection , 2015, Nature Reviews Urology.

[89]  H. B. Pearson,et al.  Keratin 76 Is Required for Tight Junction Function and Maintenance of the Skin Barrier , 2014, PLoS genetics.

[90]  Carlos Caldas,et al.  Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers , 2017, Genome Medicine.

[91]  C. James,et al.  GBAS, a novel gene encoding a protein with tyrosine phosphorylation sites and a transmembrane domain, is co-amplified with EGFR. , 1998, Genomics.

[92]  T. Ørntoft,et al.  Comprehensive multiregional analysis of molecular heterogeneity in bladder cancer , 2017, Scientific Reports.

[93]  P. Delvenne,et al.  Defensins: "Simple" antimicrobial peptides or broad-spectrum molecules? , 2015, Cytokine & growth factor reviews.

[94]  K. Baggerly,et al.  Understanding the development of human bladder cancer by using a whole-organ genomic mapping strategy , 2008, Laboratory Investigation.

[95]  Maha Almanan,et al.  Mechanism of Siglec-8-mediated cell death in IL-5-activated eosinophils: role for reactive oxygen species-enhanced MEK/ERK activation. , 2013, The Journal of allergy and clinical immunology.

[96]  Youngdoo Kim,et al.  Role of S5b/PSMD5 in proteasome inhibition caused by TNF-α/NFκB in higher eukaryotes. , 2012, Cell reports.

[97]  M. Simon,et al.  Hornerin is a component of the epidermal cornified cell envelopes , 2011, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[98]  M. Noguchi,et al.  The ACIN1 Gene is Hypermethylated in Early Stage Lung Adenocarcinoma , 2006, Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer.

[99]  C. Der,et al.  Ras and Rho regulation of the cell cycle and oncogenesis. , 2001, Cancer letters.

[100]  Daniel MacLean,et al.  bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby , 2015, Bioinform..

[101]  A. Børresen-Dale,et al.  Mutational Processes Molding the Genomes of 21 Breast Cancers , 2012, Cell.