Publications

Cancer Virus Discovery

Giacobbi NS, Gupta T, Coxon AT, Pipas JM. Polyomavirus T antigens activate an antiviral state. Virology. 2015 Feb;476377-385. doi: 10.1016/j.virol.2014.12.032. PubMed PMID: 25589241; PMCID: PMC4323618.
Kwun HJ, Shuda M, Camacho CJ, Gamper AM, Thant M, Chang Y, Moore PS. Restricted protein phosphatase 2A targeting by Merkel cell polyomavirus small T antigen. J Virol. 2015 Apr;89(8):4191-200. doi: 10.1128/JVI.00157-15. PubMed PMID: 25631078; PMCID: PMC4442354.
Cantalupo PG, Katz JP, Pipas JM. HeLa nucleic acid contamination in the cancer genome atlas leads to the misidentification of human papillomavirus 18. J Virol. 2015 Apr;89(8):4051-7. doi: 10.1128/JVI.03365-14. PubMed PMID: 25631090; PMCID: PMC4442357.
Wendzicki JA, Moore PS, Chang Y. Large T and small T antigens of Merkel cell polyomavirus. Curr Opin Virol. 2015 Apr;1138-43. doi: 10.1016/j.coviro.2015.01.009. PubMed PMID: 25681708; PMCID: PMC4456251.
Gupta T, Sáenz Robles MT, Pipas JM. Cellular transformation of mouse embryo fibroblasts in the absence of activator E2Fs. J Virol. 2015 May;89(9):5124-33. doi: 10.1128/JVI.03578-14. PubMed PMID: 25717106; PMCID: PMC4403490.
An P, Brodsky JL, Pipas JM. The conserved core enzymatic activities and the distinct dynamics of polyomavirus large T antigens. Arch Biochem Biophys. 2015 May 1;57323-31. doi: 10.1016/j.abb.2015.02.033. PubMed PMID: 25752954; PMCID: PMC4865250.
Shuda M, Velásquez C, Cheng E, Cordek DG, Kwun HJ, Chang Y, Moore PS. CDK1 substitutes for mTOR kinase to activate mitotic cap-dependent protein translation. Proc Natl Acad Sci U S A. 2015 May 12;112(19):5875-82. doi: 10.1073/pnas.1505787112. PubMed PMID: 25883264; PMCID: PMC4434708.
Zhang H, Cockrell SK, Kolawole AO, Rotem A, Serohijos AW, Chang CB, Tao Y, Mehoke TS, Han Y, Lin JS, Giacobbi NS, Feldman AB, Shakhnovich E, Weitz DA, Wobus CE, Pipas JM. Isolation and Analysis of Rare Norovirus Recombinants from Coinfected Mice Using Drop-Based Microfluidics. J Virol. 2015 Aug;89(15):7722-34. doi: 10.1128/JVI.01137-15. PubMed PMID: 25972549; PMCID: PMC4505660.
Liu H, Tang X, Srivastava A, Pécot T, Daniel P, Hemmelgarn B, Reyes S, Fackler N, Bajwa A, Kladney R, Koivisto C, Chen Z, Wang Q, Huang K, Machiraju R, Sáenz-Robles MT, Cantalupo P, Pipas JM, Leone G. Redeployment of Myc and E2f1-3 drives Rb-deficient cell cycles. Nat Cell Biol. 2015 Aug;17(8):1036-48. doi: 10.1038/ncb3210. PubMed PMID: 26192440; PMCID: PMC4526313.
Tao Y, Rotem A, Zhang H, Cockrell SK, Koehler SA, Chang CB, Ung LW, Cantalupo PG, Ren Y, Lin JS, Feldman AB, Wobus CE, Pipas JM, Weitz DA. Artifact-Free Quantification and Sequencing of Rare Recombinant Viruses by Using Drop-Based Microfluidics. Chembiochem. 2015 Oct 12;16(15):2167-71. doi: 10.1002/cbic.201500384. PubMed PMID: 26247541.
Han HS, Cantalupo PG, Rotem A, Cockrell SK, Carbonnaux M, Pipas JM, Weitz DA. Whole-Genome Sequencing of a Single Viral Species from a Highly Heterogeneous Sample. Angew Chem Int Ed Engl. 2015 Nov 16;54(47):13985-8. doi: 10.1002/anie.201507047. PubMed PMID: 26316088; PMCID: PMC4715630.
Hu M, Wang C, Li W, Lu W, Bai Z, Qin D, Yan Q, Zhu J, Krueger BJ, Renne R, Gao SJ, Lu C. A KSHV microRNA Directly Targets G Protein-Coupled Receptor Kinase 2 to Promote the Migration and Invasion of Endothelial Cells by Inducing CXCR2 and Activating AKT Signaling. PLoS Pathog. 2015 Sep;11(9):e1005171. doi: 10.1371/journal.ppat.1005171. PubMed PMID: 26402907; PMCID: PMC4581863.
Yao S, Hu M, Hao T, Li W, Xue X, Xue M, Zhu X, Zhou F, Qin D, Yan Q, Zhu J, Gao SJ, Lu C. MiRNA-891a-5p mediates HIV-1 Tat and KSHV Orf-K1 synergistic induction of angiogenesis by activating NF-κB signaling. Nucleic Acids Res. 2015 Oct 30;43(19):9362-78. doi: 10.1093/nar/gkv988. PubMed PMID: 26446987; PMCID: PMC4627096.
Gupta T, Robles MT, Schowalter RM, Buck CB, Pipas JM. Expression of the small T antigen of Lymphotropic Papovavirus is sufficient to transform primary mouse embryo fibroblasts. Virology. 2016 Jan;487112-20. doi: 10.1016/j.virol.2015.10.003. PubMed PMID: 26517398; PMCID: PMC4679568.
Shuda M, Guastafierro A, Geng X, Shuda Y, Ostrowski SM, Lukianov S, Jenkins FJ, Honda K, Maricich SM, Moore PS, Chang Y. Merkel Cell Polyomavirus Small T Antigen Induces Cancer and Embryonic Merkel Cell Proliferation in a Transgenic Mouse Model. PLoS One. 2015;10(11):e0142329. doi: 10.1371/journal.pone.0142329. PubMed PMID: 26544690; PMCID: PMC4636375.
Tang X, Liu H, Srivastava A, Pécot T, Chen Z, Wang Q, Huang K, Sáenz-Robles MT, Cantalupo P, Pipas J, Leone G. Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice. Sci Data. 2016 Feb 16;3160008. doi: 10.1038/sdata.2016.8. PubMed PMID: 26881867; PMCID: PMC4755127.
Toptan T, Yousem SA, Ho J, Matsushima Y, Stabile LP, Fernández-Figueras MT, Bhargava R, Ryo A, Moore PS, Chang Y. Survey for human polyomaviruses in cancer. JCI Insight. 2016 Feb;1(2): doi: 10.1172/jci.insight.85562. PubMed PMID: 27034991; PMCID: PMC4811373.
Li W, Jia X, Shen C, Zhang M, Xu J, Shang Y, Zhu K, Hu M, Yan Q, Qin D, Lee MS, Zhu J, Lu H, Krueger BJ, Renne R, Gao SJ, Lu C. A KSHV microRNA enhances viral latency and induces angiogenesis by targeting GRK2 to activate the CXCR2/AKT pathway. Oncotarget. 2016 May 31;7(22):32286-305. doi: 10.18632/oncotarget.8591. PubMed PMID: 27058419; PMCID: PMC5078013.
Buck CB, Van Doorslaer K, Peretti A, Geoghegan EM, Tisza MJ, An P, Katz JP, Pipas JM, McBride AA, Camus AC, McDermott AJ, Dill JA, Delwart E, Ng TF, Farkas K, Austin C, Kraberger S, Davison W, Pastrana DV, Varsani A. The Ancient Evolutionary History of Polyomaviruses. PLoS Pathog. 2016 Apr;12(4):e1005574. doi: 10.1371/journal.ppat.1005574. PubMed PMID: 27093155; PMCID: PMC4836724.
Mirvish ED, Shuda M. Strategies for Human Tumor Virus Discoveries: From Microscopic Observation to Digital Transcriptome Subtraction. Front Microbiol. 2016;7676. doi: 10.3389/fmicb.2016.00676. PubMed PMID: 27242703; PMCID: PMC4865503.
Velásquez C, Cheng E, Shuda M, Lee-Oesterreich PJ, Pogge von Strandmann L, Gritsenko MA, Jacobs JM, Moore PS, Chang Y. Mitotic protein kinase CDK1 phosphorylation of mRNA translation regulator 4E-BP1 Ser83 may contribute to cell transformation. Proc Natl Acad Sci U S A. 2016 Jul 26;113(30):8466-71. doi: 10.1073/pnas.1607768113. PubMed PMID: 27402756; PMCID: PMC4968757.
Rigatti LH, Toptan T, Newsome JT, Moore PS, Chang Y. Identification and Characterization of Novel Rat Polyomavirus 2 in a Colony of X-SCID Rats by P-PIT assay. mSphere. 2016 Nov-Dec;1(6): doi: 10.1128/mSphere.00334-16. PubMed PMID: 28028546; PMCID: PMC5177731.
Starrett GJ, Marcelus C, Cantalupo PG, Katz JP, Cheng J, Akagi K, Thakuria M, Rabinowits G, Wang LC, Symer DE, Pipas JM, Harris RS, DeCaprio JA. Merkel Cell Polyomavirus Exhibits Dominant Control of the Tumor Genome and Transcriptome in Virus-Associated Merkel Cell Carcinoma. MBio. 2017 Jan 3;8(1): doi: 10.1128/mBio.02079-16. PubMed PMID: 28049147; PMCID: PMC5210499.
Cantalupo PG, Buck CB, Pipas JM. Complete Genome Sequence of a Polyomavirus Recovered from a Pomona Leaf-Nosed Bat (Hipposideros pomona) Metagenome Data Set. Genome Announc. 2017 Jan 19;5(3): doi: 10.1128/genomeA.01053-16. PubMed PMID: 28104645; PMCID: PMC5255915.
Kwun HJ, Chang Y, Moore PS. Protein-mediated viral latency is a novel mechanism for Merkel cell polyomavirus persistence. Proc Natl Acad Sci U S A. 2017 May 16;114(20):E4040-E4047. doi: 10.1073/pnas.1703879114. PubMed PMID: 28461484; PMCID: PMC5441811.
Yates CC, Rodrigues M, Nuschke A, Johnson ZI, Whaley D, Stolz D, Newsome J, Wells A. Multipotent stromal cells/mesenchymal stem cells and fibroblasts combine to minimize skin hypertrophic scarring. Stem Cell Res Ther. 2017 Sep 5;8(1):193. doi: 10.1186/s13287-017-0644-9. PubMed PMID: 28874184; PMCID: PMC5585998.
Chang Y, Moore PS, Weiss RA. Human oncogenic viruses: nature and discovery. Philos Trans R Soc Lond B Biol Sci. 2017 Oct 19;372(1732): doi: 10.1098/rstb.2016.0264. PubMed PMID: 28893931; PMCID: PMC5597731.
Cantalupo PG, Katz JP, Pipas JM. Viral sequences in human cancer. Virology. 2018 Jan 1;513208-216. doi: 10.1016/j.virol.2017.10.017. PubMed PMID: 29107929; PMCID: PMC5828528.
Johnson ME, Cantalupo PG, Pipas JM. Identification of Head and Neck Cancer Subtypes Based on Human Papillomavirus Presence and E2F-Regulated Gene Expression. mSphere. 2018 Jan-Feb;3(1): doi: 10.1128/mSphere.00580-17. PubMed PMID: 29359188; PMCID: PMC5760753.
Cantalupo PG, Pipas JM. Complete Genome Sequence of Pittsburgh Sewage-Associated Virus 1. Genome Announc. 2018 Mar 15;6(11): doi: 10.1128/genomeA.01460-17. PubMed PMID: 29545305; PMCID: PMC5854781.
Velásquez C, Amako Y, Harold A, Toptan T, Chang Y, Shuda M. Characterization of a Merkel Cell Polyomavirus-Positive Merkel Cell Carcinoma Cell Line CVG-1. Front Microbiol. 2018;9713. doi: 10.3389/fmicb.2018.00713. PubMed PMID: 29696010; PMCID: PMC5905237.
Xu CL, Cantalupo PG, Sáenz-Robles MT, Baldwin A, Fitzpatrick D, Norris DE, Jackson E, Pipas JM. Draft Genome Sequence of a Novel Rhabdovirus Isolated from Deinocerites Mosquitoes. Genome Announc. 2018 May 10;6(19): doi: 10.1128/genomeA.01438-17. PubMed PMID: 29748415; PMCID: PMC5946037.
Rotem A, Serohijos AWR, Chang CB, Wolfe JT, Fischer AE, Mehoke TS, Zhang H, Tao Y, Lloyd Ung W, Choi JM, Rodrigues JV, Kolawole AO, Koehler SA, Wu S, Thielen PM, Cui N, Demirev PA, Giacobbi NS, Julian TR, Schwab K, Lin JS, Smith TJ, Pipas JM, Wobus CE, Feldman AB, Weitz DA, Shakhnovich EI. Evolution on the Biophysical Fitness Landscape of an RNA Virus. Mol Biol Evol. 2018 Oct 1;35(10):2390-2400. doi: 10.1093/molbev/msy131. PubMed PMID: 29955873; PMCID: PMC6188569.
Yan Q, Zhao R, Shen C, Wang F, Li W, Gao SJ, Lu C. Upregulation of MicroRNA 711 Mediates HIV-1 Vpr Promotion of Kaposi's Sarcoma-Associated Herpesvirus Latency and Induction of Pro-proliferation and Pro-survival Cytokines by Targeting the Notch/NF-κB-Signaling Axis. J Virol. 2018 Sep 15;92(18): doi: 10.1128/JVI.00580-18. PubMed PMID: 29976660; PMCID: PMC6146700.
Toptan T, Abere B, Nalesnik MA, Swerdlow SH, Ranganathan S, Lee N, Shair KH, Moore PS, Chang Y. Circular DNA tumor viruses make circular RNAs. Proc Natl Acad Sci U S A. 2018 Sep 11;115(37):E8737-E8745. doi: 10.1073/pnas.1811728115. PubMed PMID: 30150410; PMCID: PMC6140489.
Tan B, Gao SJ. The RNA Epitranscriptome of DNA Viruses. J Virol. 2018 Nov 15;92(22): doi: 10.1128/JVI.00696-18. PubMed PMID: 30185592; PMCID: PMC6206477.
Ramos da Silva S, Cheng F, Huang IC, Jung JU, Gao SJ. Efficiencies and kinetics of infection in different cell types/lines by African and Asian strains of Zika virus. J Med Virol. 2019 Feb;91(2):179-189. doi: 10.1002/jmv.25306. PubMed PMID: 30192399; PMCID: PMC6294704.
Harms PW, Harms KL, Moore PS, DeCaprio JA, Nghiem P, Wong MKK, Brownell I, International Workshop on Merkel Cell Carcinoma Research (IWMCC) Working Group.. The biology and treatment of Merkel cell carcinoma: current understanding and research priorities. Nat Rev Clin Oncol. 2018 Dec;15(12):763-776. doi: 10.1038/s41571-018-0103-2. PubMed PMID: 30287935; PMCID: PMC6319370.
Gao R, Li T, Tan B, Ramos da Silva S, Jung JU, Feng P, Gao SJ. FoxO1 Suppresses Kaposi's Sarcoma-Associated Herpesvirus Lytic Replication and Controls Viral Latency. J Virol. 2019 Feb 1;93(3): doi: 10.1128/JVI.01681-18. PubMed PMID: 30404794; PMCID: PMC6340022.
Li T, Zhu Y, Cheng F, Lu C, Jung JU, Gao SJ. Oncogenic Kaposi's Sarcoma-Associated Herpesvirus Upregulates Argininosuccinate Synthase 1, a Rate-Limiting Enzyme of the Citrulline-Nitric Oxide Cycle, To Activate the STAT3 Pathway and Promote Growth Transformation. J Virol. 2019 Feb 15;93(4): doi: 10.1128/JVI.01599-18. PubMed PMID: 30463977; PMCID: PMC6364034.
Ding X, Jia X, Wang C, Xu J, Gao SJ, Lu C. A DHX9-lncRNA-MDM2 interaction regulates cell invasion and angiogenesis of cervical cancer. Cell Death Differ. 2018 Dec 5; doi: 10.1038/s41418-018-0242-0. PubMed PMID: 30518908.
Khatun H, Yamaoka Y, Matsushima Y, Matsunaga S, Kimura H, Ho J, Shuda M, Ryo A. Production and characterization of monoclonal antibodies specific for major capsid VP1 protein of trichodysplasia spinulosa-associated polyomavirus. Microbiol Immunol. 2018 Dec;62(12):763-773. doi: 10.1111/1348-0421.12662. PubMed PMID: 30537287.
Toptan T, Brusadelli MG, Turpin B, Witte DP, Surrallés J, Velleuer E, Schramm M, Dietrich R, Brakenhoff RH, Moore PS, Chang Y, Wells SI. Limited detection of human polyomaviruses in Fanconi anemia related squamous cell carcinoma. PLoS One. 2018;13(12):e0209235. doi: 10.1371/journal.pone.0209235. PubMed PMID: 30589865; PMCID: PMC6307729.
Zhang SY, Zhang SW, Fan XN, Meng J, Chen Y, Gao SJ, Huang Y. Global analysis of N6-methyladenosine functions and its disease association using deep learning and network-based methods. PLoS Comput Biol. 2019 Jan;15(1):e1006663. doi: 10.1371/journal.pcbi.1006663. PubMed PMID: 30601803; PMCID: PMC6331136.
An P, Sáenz Robles MT, Duray AM, Cantalupo PG, Pipas JM. Human polyomavirus BKV infection of endothelial cells results in interferon pathway induction and persistence. PLoS Pathog. 2019 Jan;15(1):e1007505. doi: 10.1371/journal.ppat.1007505. PubMed PMID: 30620752; PMCID: PMC6338385.
Ding X, Xu J, Wang C, Feng Q, Wang Q, Yang Y, Lu H, Wang F, Zhu K, Li W, Yan Q, Gao SJ, Lu C. Suppression of the SAP18/HDAC1 complex by targeting TRIM56 and Nanog is essential for oncogenic viral FLICE-inhibitory protein-induced acetylation of p65/RelA, NF-κB activation, and promotion of cell invasion and angiogenesis. Cell Death Differ. 2019 Jan 22; doi: 10.1038/s41418-018-0268-3. PubMed PMID: 30670829.
Li W, Wang Q, Feng Q, Wang F, Yan Q, Gao SJ, Lu C. Oncogenic KSHV-encoded interferon regulatory factor upregulates HMGB2 and CMPK1 expression to promote cell invasion by disrupting a complex lncRNA-OIP5-AS1/miR-218-5p network. PLoS Pathog. 2019 Jan;15(1):e1007578. doi: 10.1371/journal.ppat.1007578. PubMed PMID: 30699189; PMCID: PMC6370251.
Ding X, Jia X, Wang C, Xu J, Gao SJ, Lu C. Correction to: A DHX9-lncRNA-MDM2 interaction regulates cell invasion and angiogenesis of cervical cancer. Cell Death Differ. 2019 Feb 25; doi: 10.1038/s41418-019-0273-1. PubMed PMID: 30804472.
Pipas JM. DNA Tumor Viruses and Their Contributions to Molecular Biology. J Virol. 2019 May 1;93(9): doi: 10.1128/JVI.01524-18. PubMed PMID: 30814278; PMCID: PMC6475781.
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