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      MmuPV1 E6 induces cell proliferation and other hallmarks of cancer

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          ABSTRACT

          The E6 protein encoded by the murine papillomavirus (MmuPV1) is essential for MmuPV1-induced skin disease. Our previous work has identified a number of cellular interacting partners of MmuPV1 E6 and E7 through affinity purification/mass spectrometry analysis. These studies revealed that MmuPV1 E6 potently inhibits keratinocyte differentiation through multiple molecular mechanisms including inhibition of NOTCH and TGF-β signaling. Here, we report that MmuPV1 E6 has additional important oncogenic activities when expressed in its natural host cells, mouse keratinocytes, including increasing proliferation, overcoming density-mediated growth arrest, and proliferation under conditions of limited supply of growth factors. Unbiased proteomic/transcriptomic analyses of mouse keratinocytes expressing MmuPV1 E6 substantiated its effect on these cellular processes and divulged that some of these effects may be mediated in part through it upregulating E2F activity. Our analyses also revealed that MmuPV1 E6 may alter other cancer hallmarks including evasion of growth suppressors, inhibition of immune response, resistance to cell death, and alterations in DNA damage response. Collectively, our results suggest that MmuPV1 E6 is a major driver of multiple hallmarks of cancer in MmuPV1’s natural host cells, mouse keratinocytes.

          IMPORTANCE

          The Mus musculus papillomavirus 1 (MmuPV1) E6 and E7 proteins are required for MmuPV1-induced disease. Our understanding of the activities of MmuPV1 E6 has been based on affinity purification/mass spectrometry studies where cellular interacting partners of MmuPV1 E6 were identified, and these studies revealed that MmuPV1 E6 can inhibit keratinocyte differentiation through multiple mechanisms. We report that MmuPV1 E6 encodes additional activities including the induction of proliferation, resistance to density-mediated growth arrest, and decreased dependence on exogenous growth factors. Proteomic and transcriptomic analyses provided evidence that MmuPV1 E6 increases the expression and steady state levels of a number of cellular proteins that promote cellular proliferation and other hallmarks of cancer. These results indicate that MmuPV1 E6 is a major driver of MmuPV1-induced pathogenesis.

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          STAR: ultrafast universal RNA-seq aligner.

          Accurate alignment of high-throughput RNA-seq data is a challenging and yet unsolved problem because of the non-contiguous transcript structure, relatively short read lengths and constantly increasing throughput of the sequencing technologies. Currently available RNA-seq aligners suffer from high mapping error rates, low mapping speed, read length limitation and mapping biases. To align our large (>80 billon reads) ENCODE Transcriptome RNA-seq dataset, we developed the Spliced Transcripts Alignment to a Reference (STAR) software based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure. STAR outperforms other aligners by a factor of >50 in mapping speed, aligning to the human genome 550 million 2 × 76 bp paired-end reads per hour on a modest 12-core server, while at the same time improving alignment sensitivity and precision. In addition to unbiased de novo detection of canonical junctions, STAR can discover non-canonical splices and chimeric (fusion) transcripts, and is also capable of mapping full-length RNA sequences. Using Roche 454 sequencing of reverse transcription polymerase chain reaction amplicons, we experimentally validated 1960 novel intergenic splice junctions with an 80-90% success rate, corroborating the high precision of the STAR mapping strategy. STAR is implemented as a standalone C++ code. STAR is free open source software distributed under GPLv3 license and can be downloaded from http://code.google.com/p/rna-star/.
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            Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles

            Although genomewide RNA expression analysis has become a routine tool in biomedical research, extracting biological insight from such information remains a major challenge. Here, we describe a powerful analytical method called Gene Set Enrichment Analysis (GSEA) for interpreting gene expression data. The method derives its power by focusing on gene sets, that is, groups of genes that share common biological function, chromosomal location, or regulation. We demonstrate how GSEA yields insights into several cancer-related data sets, including leukemia and lung cancer. Notably, where single-gene analysis finds little similarity between two independent studies of patient survival in lung cancer, GSEA reveals many biological pathways in common. The GSEA method is embodied in a freely available software package, together with an initial database of 1,325 biologically defined gene sets.
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              Hallmarks of Cancer: The Next Generation

              The hallmarks of cancer comprise six biological capabilities acquired during the multistep development of human tumors. The hallmarks constitute an organizing principle for rationalizing the complexities of neoplastic disease. They include sustaining proliferative signaling, evading growth suppressors, resisting cell death, enabling replicative immortality, inducing angiogenesis, and activating invasion and metastasis. Underlying these hallmarks are genome instability, which generates the genetic diversity that expedites their acquisition, and inflammation, which fosters multiple hallmark functions. Conceptual progress in the last decade has added two emerging hallmarks of potential generality to this list-reprogramming of energy metabolism and evading immune destruction. In addition to cancer cells, tumors exhibit another dimension of complexity: they contain a repertoire of recruited, ostensibly normal cells that contribute to the acquisition of hallmark traits by creating the "tumor microenvironment." Recognition of the widespread applicability of these concepts will increasingly affect the development of new means to treat human cancer. Copyright © 2011 Elsevier Inc. All rights reserved.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: Writing – original draftRole: Writing – review and editing
                Role: Data curationRole: InvestigationRole: Writing – original draftRole: Writing – review and editing
                Role: Formal analysisRole: Writing – review and editing
                Role: InvestigationRole: Writing – original draftRole: Writing – review and editing
                Role: Project administrationRole: Writing – review and editing
                Role: Project administrationRole: Writing – review and editing
                Role: ConceptualizationRole: Funding acquisitionRole: Project administrationRole: SupervisionRole: Writing – original draftRole: Writing – review and editing
                Role: ConceptualizationRole: Funding acquisitionRole: Project administrationRole: Writing – original draftRole: Writing – review and editing
                Role: Editor
                Journal
                mBio
                mBio
                mbio
                mBio
                American Society for Microbiology (1752 N St., N.W., Washington, DC )
                2150-7511
                Nov-Dec 2023
                31 October 2023
                31 October 2023
                : 14
                : 6
                : e02458-23
                Affiliations
                [1 ]McArdle Laboratory for Cancer Research, University of Wisconsin School of Medicine and Public Health; , Madison, Wisconsin, USA
                [2 ]Departments of Chemistry and Biomolecular Chemistry, University of Wisconsin-Madison; , Madison, Wisconsin, USA
                [3 ]Department of Developmental, Molecular and Chemical Biology, Tufts University School of Medicine; , Boston, Massachusetts, USA
                [4 ]Morgridge Institute for Research; , Madison, Wisconsin, USA
                Johns Hopkins University School of Medicine; , Baltimore, Maryland, USA
                Author notes
                Address correspondence to Paul F. Lambert, plambert@ 123456wisc.edu
                Address correspondence to Karl Munger, Karl.Munger@ 123456tufts.edu

                Present address: Virginia Tech, Blacksburg, Virginia, USA

                The authors declare no conflict of interest.

                Author information
                https://orcid.org/0000-0001-6871-0568
                https://orcid.org/0000-0003-3288-9935
                https://orcid.org/0000-0001-7983-2755
                Article
                02458-23 mbio.02458-23
                10.1128/mbio.02458-23
                10746199
                37905801
                e77c6f78-dcf1-43cc-9063-ed92093ad88c
                Copyright © 2023 Romero-Masters et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license.

                History
                : 13 September 2023
                : 22 September 2023
                Page count
                supplementary-material: 3, authors: 8, Figures: 14, Tables: 2, References: 99, Pages: 28, Words: 13597
                Funding
                Funded by: HHS | NIH | National Cancer Institute (NCI);
                Award ID: F32 CA254019
                Award Recipient :
                Funded by: HHS | NIH | National Cancer Institute (NCI);
                Award ID: R01 CA228543
                Award Recipient :
                Funded by: HHS | NIH | National Cancer Institute (NCI);
                Award ID: R35 CA210807
                Award Recipient :
                Funded by: HHS | NIH | National Cancer Institute (NCI);
                Award ID: P01 CA022443
                Award Recipient :
                Funded by: HHS | National Institutes of Health (NIH);
                Award ID: P41 GM108538
                Award Recipient :
                Categories
                Research Article
                virology, Virology
                Custom metadata
                November/December 2023

                Life sciences
                papillomavirus,cell proliferation,e6
                Life sciences
                papillomavirus, cell proliferation, e6

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