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Evidence for virus-mediated oncogenesis in bladder cancers arising in solid organ transplant recipients

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Nuclear factor I X is a recurrent target for HPV16 insertions in anal carcinomas

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Cancer incidence and risk factors after solid organ transplantation

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The region of the HPV E7 oncoprotein homologous to adenovirus E1a and Sv40 large T antigen contains separate domains for Rb binding and casein kinase II phosphorylation.

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The oncogenic potential of BK ‐polyomavirus is linked to viral integration into the human genome

inferredcites →https://doi.org/10.1002/path.5012openalex-snapshot

Donor‐derived, metastatic urothelial cancer after kidney transplantation associated with a potentially oncogenic BK polyomavirus

inferredcites →https://doi.org/10.1002/path.5127openalex-snapshot

The two‐faced nature of BK polyomavirus: lytic infection or non‐lytic large‐T‐positive carcinoma

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Degradation of p53 can be targeted by HPV E6 sequences distinct from those required for p53 binding and trans-activation

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APOBEC3A and 3C decrease human papillomavirus 16 pseudovirion infectivity

inferredcites →https://doi.org/10.1016/j.cell.2013.10.034openalex-snapshot

Temporal Response of the Human Virome to Immunosuppression and Antiviral Therapy

inferredcites →https://doi.org/10.1016/j.cell.2017.08.001openalex-snapshot

HPV16 E7 Genetic Conservation Is Critical to Carcinogenesis

inferredcites →https://doi.org/10.1016/j.cell.2017.09.007openalex-snapshot

Comprehensive Molecular Characterization of Muscle-Invasive Bladder Cancer

inferredcites →https://doi.org/10.1016/j.chom.2018.04.005openalex-snapshot

Characterization of BK Polyomaviruses from Kidney Transplant Recipients Suggests a Role for APOBEC3 in Driving In-Host Virus Evolution

inferredcites →https://doi.org/10.1016/j.humpath.2012.09.019openalex-snapshot

BK virus–associated urinary bladder carcinoma in transplant recipients: report of 2 cases, review of the literature, and proposed pathogenetic model

inferredcites →https://doi.org/10.1016/j.jcv.2020.104283openalex-snapshot

Novel 3D organotypic urothelial cell culture model for identification of new therapeutic approaches in urological infections

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A fork in the road: Where homologous recombination and stalled replication fork protection part ways

inferredcites →https://doi.org/10.1016/j.stem.2021.07.012openalex-snapshot

Antiviral treatment causes a unique mutational signature in cancers of transplantation recipients

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Resolution of a High Grade and Metastatic BK Polyomavirus-Associated Urothelial Cell Carcinoma Following Radical Allograft Nephroureterectomy and Immune Checkpoint Treatment: A Case Report

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Human polyomaviruses in disease and cancer

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Viral sequences in human cancer

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Global burden of cancer attributable to infections in 2018: a worldwide incidence analysis

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The ubiquitin ligase LIN41/TRIM71 targets p53 to antagonize cell death and differentiation pathways during stem cell differentiation

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Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project

inferredcites →https://doi.org/10.1038/jid.2008.317openalex-snapshot

High β-HPV DNA Loads and Strong Seroreactivity Are Present in Epidermodysplasia Verruciformis

inferredcites →https://doi.org/10.1038/ng.2701openalex-snapshot

Evidence for APOBEC3B mutagenesis in multiple human cancers

inferredcites →https://doi.org/10.1038/ng.2702openalex-snapshot

An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/onc.2013.449openalex-snapshot

Human papillomavirus type 16 E7 perturbs DREAM to promote cellular proliferation and mitotic gene expression

inferredcites →https://doi.org/10.1038/s41379-018-0065-zopenalex-snapshot

Polyoma virus-associated carcinomas of the urologic tract: a clinicopathologic and molecular study

inferredcites →https://doi.org/10.1038/s41388-019-0767-9openalex-snapshot

Cyclin D–CDK4 relieves cooperative repression of proliferation and cell cycle gene expression by DREAM and RB

inferredcites →https://doi.org/10.1038/s41388-020-01398-6openalex-snapshot

Viral integration in BK polyomavirus-associated urothelial carcinoma in renal transplant recipients: multistage carcinogenesis revealed by next-generation virome capture sequencing

inferredcites →https://doi.org/10.1038/s41388-020-01502-wopenalex-snapshot

Genome-wide profiling of BK polyomavirus integration in bladder cancer of kidney transplant recipients reveals mechanisms of the integration at the nucleotide level

inferredcites →https://doi.org/10.1038/s41388-022-02235-8openalex-snapshot

Induction of APOBEC3-mediated genomic damage in urothelium implicates BK polyomavirus (BKPyV) as a hit-and-run driver for bladder cancer

inferredcites →https://doi.org/10.1038/s41467-019-08886-8openalex-snapshot

Overexpression of Claspin and Timeless protects cancer cells from replication stress in a checkpoint-independent manner

inferredcites →https://doi.org/10.1038/s41588-019-0558-9openalex-snapshot

The landscape of viral associations in human cancers

inferredcites →https://doi.org/10.1038/s41598-018-29438-yopenalex-snapshot

Defining the frequency of human papillomavirus and polyomavirus infection in urothelial bladder tumours

inferredcites →https://doi.org/10.1038/sj.onc.1208854openalex-snapshot

Identification of a proliferation gene cluster associated with HPV E6/E7 expression level and viral DNA load in invasive cervical carcinoma

inferredcites →https://doi.org/10.1042/cs20160786openalex-snapshot

The human papillomavirus replication cycle, and its links to cancer progression: a comprehensive review

inferredcites →https://doi.org/10.1042/cs20180443openalex-snapshot

Occurrence and regression of BK polyomavirus associated carcinoma: a clinical and next-generation sequencing study

inferredcites →https://doi.org/10.1073/pnas.0806526105openalex-snapshot

T antigen mutations are a human tumor-specific signature for Merkel cell polyomavirus

inferredcites →https://doi.org/10.1073/pnas.1904024116openalex-snapshot

The deaminase APOBEC3B triggers the death of cells lacking uracil DNA glycosylase

inferredcites →https://doi.org/10.1074/jbc.m113.541839openalex-snapshot

Association of the Breast Cancer Antiestrogen Resistance Protein 1 (BCAR1) and BCAR3 Scaffolding Proteins in Cell Signaling and Antiestrogen Resistance

inferredcites →https://doi.org/10.1080/10409238.2017.1360836openalex-snapshot

Cell cycle transcription control: DREAM/MuvB and RB-E2F complexes

inferredcites →https://doi.org/10.1089/cmb.2012.0021openalex-snapshot

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

inferredcites →https://doi.org/10.1093/bioinformatics/bts635openalex-snapshot

STAR: ultrafast universal RNA-seq aligner

inferredcites →https://doi.org/10.1093/bioinformatics/btv033openalex-snapshot

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

inferredcites →https://doi.org/10.1093/gigascience/giz100openalex-snapshot

rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data

inferredcites →https://doi.org/10.1093/jnci/djaa078openalex-snapshot

Risk of Rare Cancers Among Solid Organ Transplant Recipients

inferredcites →https://doi.org/10.1093/nar/gks918openalex-snapshot

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

inferredcites →https://doi.org/10.1093/nar/gkw377openalex-snapshot

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

inferredcites →https://doi.org/10.1093/nar/gkw879openalex-snapshot

The Papillomavirus Episteme: a major update to the papillomavirus sequence database

inferredcites →https://doi.org/10.1093/ve/veaa100openalex-snapshot

Cenote-Taker 2 democratizes virus discovery and sequence annotation

inferredcites →https://doi.org/10.1093/ve/vev015openalex-snapshot

Role of the host restriction factor APOBEC3 on papillomavirus evolution

inferredcites →https://doi.org/10.1097/tp.0000000000003193openalex-snapshot

Immunologic Clearance of a BK Virus-associated Metastatic Renal Allograft Carcinoma

inferredcites →https://doi.org/10.1101/gad.181933.111openalex-snapshot

The MuvB complex sequentially recruits B-Myb and FoxM1 to promote mitotic gene expression

inferredcites →https://doi.org/10.1101/gr.129684.111openalex-snapshot

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

inferredcites →https://doi.org/10.1101/gr.164806.113openalex-snapshot

Genome-wide analysis of HPV integration in human cancers reveals recurrent, focal genomic instability

inferredcites →https://doi.org/10.1111/ajt.13550openalex-snapshot

BK Polyomavirus Infection and Renourinary Tumorigenesis

inferredcites →https://doi.org/10.1111/ajt.14191openalex-snapshot

BK Polyomavirus Genomic Integration and Large T Antigen Expression: Evolving Paradigms in Human Oncogenesis

inferredcites →https://doi.org/10.1111/ajt.14530openalex-snapshot

Treatment for presumed BK polyomavirus nephropathy and risk of urinary tract cancers among kidney transplant recipients in the United States

inferredcites →https://doi.org/10.1111/ajt.15663openalex-snapshot

High-grade urothelial carcinoma in a kidney transplant recipient after JC virus nephropathy: The first evidence of JC virus as a potential oncovirus in bladder cancer

inferredcites →https://doi.org/10.1111/petr.13069openalex-snapshot

Anellovirus loads are associated with outcomes in pediatric lung transplantation

inferredcites →https://doi.org/10.1126/science.1152586openalex-snapshot

Clonal Integration of a Polyomavirus in Human Merkel Cell Carcinoma

inferredcites →https://doi.org/10.1126/science.1256930openalex-snapshot

Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing

inferredcites →https://doi.org/10.1126/science.7997879openalex-snapshot

Identification of Herpesvirus-Like DNA Sequences in AIDS-Sssociated Kaposi's Sarcoma

inferredcites →https://doi.org/10.1128/jvi.00595-19openalex-snapshot

Temporal Proteomic Analysis of BK Polyomavirus Infection Reveals Virus-Induced G 2 Arrest and Highly Effective Evasion of Innate Immune Sensing

inferredcites →https://doi.org/10.1128/jvi.00771-16openalex-snapshot

Functional Upregulation of the DNA Cytosine Deaminase APOBEC3B by Polyomaviruses

inferredcites →https://doi.org/10.1128/jvi.00954-06openalex-snapshot

E6/E7 Expression of Human Papillomavirus Type 20 (HPV-20) and HPV-27 Influences Proliferation and Differentiation of the Skin in UV-Irradiated SKH-hr1 Transgenic Mice

inferredcites →https://doi.org/10.1128/jvi.02383-14openalex-snapshot

APOBEC3A Functions as a Restriction Factor of Human Papillomavirus

inferredcites →https://doi.org/10.1128/jvi.02413-16openalex-snapshot

Human Papillomavirus 16 E6 Upregulates APOBEC3B via the TEAD Transcription Factor

inferredcites →https://doi.org/10.1128/jvi.70.4.2378-2386.1996openalex-snapshot

BK virus large T antigen: interactions with the retinoblastoma family of tumor suppressor proteins and effects on cellular growth control

inferredcites →https://doi.org/10.1128/mbio.01446-16openalex-snapshot

Tandemly Integrated HPV16 Can Form a Brd4-Dependent Super-Enhancer-Like Element That Drives Transcription of Viral Oncogenes

inferredcites →https://doi.org/10.1128/mbio.02079-16openalex-snapshot

Merkel Cell Polyomavirus Exhibits Dominant Control of the Tumor Genome and Transcriptome in Virus-Associated Merkel Cell Carcinoma

inferredcites →https://doi.org/10.1128/mbio.02234-14openalex-snapshot

Human Papillomavirus E6 Triggers Upregulation of the Antiviral and Cancer Genomic DNA Deaminase APOBEC3B

inferredcites →https://doi.org/10.1128/mbio.02690-18openalex-snapshot

Polyomavirus T Antigen Induces APOBEC3B Expression Using an LXCXE-Dependent and TP53-Independent Mechanism

inferredcites →https://doi.org/10.1158/0008-5472.can-08-0949openalex-snapshot

Frequent Detection of Merkel Cell Polyomavirus in Human Merkel Cell Carcinomas and Identification of a Unique Deletion in the VP1 Gene

inferredcites →https://doi.org/10.1158/0008-5472.can-16-0370openalex-snapshot

Novel ß-HPV49 Transgenic Mouse Model of Upper Digestive Tract Cancer

inferredcites →https://doi.org/10.1158/1078-0432.ccr-18-3147openalex-snapshot

Mutational Analysis of 472 Urothelial Carcinoma Across Grades and Anatomic Sites

inferredcites →https://doi.org/10.1158/2159-8290.cd-15-0344openalex-snapshot

APOBEC Enzymes: Mutagenic Fuel for Cancer Evolution and Heterogeneity

inferredcites →https://doi.org/10.1172/jci.insight.85562openalex-snapshot

Survey for human polyomaviruses in cancer

inferredcites →https://doi.org/10.1186/1471-2105-14-128openalex-snapshot

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

inferredcites →https://doi.org/10.1186/gb-2014-15-1-r1openalex-snapshot

Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis

inferredcites →https://doi.org/10.1186/s12920-019-0579-3openalex-snapshot

Integrative genomic analyses of APOBEC-mutational signature, expression and germline deletion of APOBEC3 genes, and immunogenicity in multiple cancer types

inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

inferredcites →https://doi.org/10.1186/s13059-015-0758-2openalex-snapshot

An ensemble approach to accurately detect somatic mutations using SomaticSeq

inferredcites →https://doi.org/10.1186/s13059-020-02230-wopenalex-snapshot

Comprehensive integrative profiling of upper tract urothelial carcinomas

inferredcites →https://doi.org/10.1186/s13073-015-0161-3openalex-snapshot

Mutation signatures implicate aristolochic acid in bladder cancer development

inferredcites →https://doi.org/10.1186/s13073-020-00727-4openalex-snapshot

Clinical and molecular characterization of virus-positive and virus-negative Merkel cell carcinoma

inferredcites →https://doi.org/10.1371/journal.pgen.1007179openalex-snapshot

HPV integration hijacks and multimerizes a cellular enhancer to generate a viral-cellular super-enhancer that drives high viral oncogene expression

inferredcites →https://doi.org/10.1371/journal.pone.0065678openalex-snapshot

Breast Cancer Antiestrogen Resistance 3 (BCAR3) Promotes Cell Motility by Regulating Actin Cytoskeletal and Adhesion Remodeling in Invasive Breast Cancer Cells

inferredcites →https://doi.org/10.1371/journal.ppat.1006783openalex-snapshot

Beta HPV38 oncoproteins act with a hit-and-run mechanism in ultraviolet radiation-induced skin carcinogenesis in mice

inferredcites →https://doi.org/10.1371/journal.ppat.1008562openalex-snapshot

High-resolution analysis of Merkel Cell Polyomavirus in Merkel Cell Carcinoma reveals distinct integration patterns and suggests NHEJ and MMBIR as underlying mechanisms

inferredcites →https://doi.org/10.1371/journal.ppat.1008718openalex-snapshot

Footprint of the host restriction factors APOBEC3 on the genome of human viruses

inferredcites →https://doi.org/10.1681/asn.2017050532openalex-snapshot

Neutralizing Antibody–Mediated Response and Risk of BK Virus–Associated Nephropathy

inferredcites →https://doi.org/10.17615/za09-dk57openalex-snapshot

Comprehensive molecular characterization of urothelial bladder carcinoma

inferredcites →https://doi.org/10.3390/ijms20163914openalex-snapshot

Effect of the Large and Small T-Antigens of Human Polyomaviruses on Signaling Pathways

inferredcites →https://doi.org/10.3390/v12080837openalex-snapshot

BKTyper: Free Online Tool for Polyoma BK Virus VP1 and NCCR Typing

inferredcites →https://doi.org/10.3390/v13030476openalex-snapshot

High Incidence and Early Onset of Urinary Tract Cancers in Patients with BK Polyomavirus Associated Nephropathy

inferredcites →https://doi.org/10.3390/v9080233openalex-snapshot

Roles of APOBEC3A and APOBEC3B in Human Papillomavirus Infection and Disease Progression

inferredcites →https://doi.org/10.3391/mbi.2014.5.1.01openalex-snapshot

Tackling Invasive Alien Species in Europe: the top 20 issues

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Discovery of several thousand highly diverse circular DNA viruses

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Dynamic viral integration patterns actively participate in the progression of BK polyomavirus-associated diseases after renal transplantation

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Long‐Term Outcomes of BK Viremia in Kidney Transplant Recipients

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Virus-induced APOBEC3 transmutagenesis in bladder cancer initiation

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Analysis of Several Common APOBEC-type Mutations in Bladder Tumors Suggests Links to Viral Infection

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