Publications by authors named "Maria Teresa Sáenz-Robles"

16 Publications

  • Page 1 of 1

Single-Cell Transcriptomics Reveals a Heterogeneous Cellular Response to BK Virus Infection.

J Virol 2021 Feb 24;95(6). Epub 2021 Feb 24.

Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA

BK virus (BKV) is a human polyomavirus that is generally harmless but can cause devastating disease in immunosuppressed individuals. BKV infection of renal cells is a common problem for kidney transplant patients undergoing immunosuppressive therapy. In cultured primary human renal proximal tubule epithelial (RPTE) cells, BKV undergoes a productive infection. The BKV-encoded large T antigen (LT) induces cell cycle entry, resulting in the upregulation of numerous genes associated with cell proliferation. Consistently, microarray and transcriptome sequencing (RNA-seq) experiments performed on bulk infected cell populations identified several proliferation-related pathways that are upregulated by BKV. These studies revealed few genes that are downregulated. In this study, we analyzed viral and cellular transcripts in single mock- or BKV-infected cells. We found that the levels of viral mRNAs vary widely among infected cells, resulting in different levels of LT and viral capsid protein expression. Cells expressing the highest levels of viral transcripts account for approximately 20% of the culture and have a gene expression pattern that is distinct from that of cells expressing lower levels of viral mRNAs. Surprisingly, cells expressing low levels of viral mRNA do not progress with time to high expression, suggesting that the two cellular responses are determined prior to or shortly following infection. Finally, comparison of cellular gene expression patterns of cells expressing high levels of viral mRNA with those of mock-infected cells or cells expressing low levels of viral mRNA revealed previously unidentified pathways that are downregulated by BKV. Among these are pathways associated with drug metabolism and detoxification, tumor necrosis factor (TNF) signaling, energy metabolism, and translation. The outcome of viral infection is determined by the ability of the virus to redirect cellular systems toward progeny production countered by the ability of the cell to block these viral actions. Thus, an infected culture consists of thousands of cells, each fighting its own individual battle. Bulk measurements, such as PCR or RNA-seq, measure the average of these individual responses to infection. Single-cell transcriptomics provides a window to the one-on-one battle between BKV and each cell. Our studies reveal that only a minority of infected cells are overwhelmed by the virus and produce large amounts of BKV mRNAs and proteins, while the infection appears to be restricted in the remaining cells. Correlation of viral transcript levels with cellular gene expression patterns reveals pathways manipulated by BKV that may play a role in limiting infection.
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http://dx.doi.org/10.1128/JVI.02237-20DOI Listing
February 2021

Stability and detection of nucleic acid from viruses and hosts in controlled mosquito blood feeds.

PLoS One 2020 11;15(6):e0231061. Epub 2020 Jun 11.

Health Futures, Microsoft Research, Redmond, Washington, United States of America.

Monitoring the presence and spread of pathogens in the environment is of critical importance. Rapid detection of infectious disease outbreaks and prediction of their spread can facilitate early responses of health agencies and reduce the severity of outbreaks. Current sampling methods are sorely limited by available personnel and throughput. For instance, xenosurveillance utilizes captured arthropod vectors, such as mosquitoes, as sampling tools to access blood from a wide variety of vertebrate hosts. Next generation sequencing (NGS) of nucleic acid from individual blooded mosquitoes can be used to identify mosquito and host species, and microorganisms including pathogens circulating within either host. However, there are practical challenges to collecting and processing mosquitoes for xenosurveillance, such as the rapid metabolization or decay of microorganisms within the mosquito midgut. This particularly affects pathogens that do not replicate in mosquitoes, preventing their detection by NGS or other methods. Accordingly, we performed a series of experiments to establish the windows of detection for DNA or RNA from human blood and/or viruses present in mosquito blood meals. Our results will contribute to the development of xenosurveillance techniques with respect to optimal timing of sample collection and NGS processing and will also aid trap design by demonstrating the stabilizing effect of temperature control on viral genome recovery from blood-fed mosquitoes.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0231061PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7289426PMC
August 2020

Analysis of viruses present in urine from patients with interstitial cystitis.

Virus Genes 2020 Aug 23;56(4):430-438. Epub 2020 May 23.

Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.

The question of whether some cases of interstitial cystitis may have an infectious etiology has been debated for some time. Previous studies have looked for the presence of certain specific viruses, but generally did not use the types of sensitive and unbiased approaches that are currently available. As part of the MAPP (Multidisciplinary Approach to the Study of Chronic Pelvic Pain) Research Network, we examined urine specimens from interstitial cystitis patients who provided specimens over time and also reported various symptoms at the time of urine collection. We first performed next-generation sequencing to look for the presence of viruses in urines, and detected two human polyomaviruses that are known to be excreted into urine, BKPyV and JCPyV. We were especially interested in BKPyV because it is a known cause of another bladder disease, hemorrhagic cystitis, in bone marrow transplant recipients. Further analysis of individual samples indicates a trend toward higher excretion of polyomaviruses in patients experiencing increased symptoms.
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http://dx.doi.org/10.1007/s11262-020-01767-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7339973PMC
August 2020

Human polyomavirus BKV infection of endothelial cells results in interferon pathway induction and persistence.

PLoS Pathog 2019 01 8;15(1):e1007505. Epub 2019 Jan 8.

Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America.

Polyomavirus BKV is highly prevalent among humans. The virus establishes an asymptomatic persistent infection in the urinary system in healthy people, but uncontrolled productive infection of the virus in immunocompromised patients can lead to serious diseases. In spite of its high prevalence, our knowledge regarding key aspects of BKV polyomavirus infection remains incomplete. To determine tissue and cell type tropism of the virus, primary human epithelial cells, endothelial cells and fibroblasts isolated from the respiratory and urinary systems were tested. Results from this study demonstrated that all 9 different types of human cells were infectable by BKV polyomavirus but showed differential cellular responses. In microvascular endothelial cells from the lung and the bladder, BKV persistent infection led to prolonged viral protein expression, low yield of infectious progeny and delayed cell death, in contrast with infection in renal proximal tubular epithelial cells, a widely used cell culture model for studying productive infection of this virus. Transcriptomic profiling revealed the activation of interferon signaling and induction of multiple interferon stimulated genes in infected microvascular endothelial cells. Further investigation demonstrated production of IFNβ and secretion of chemokine CXCL10 by infected endothelial cells. Activation of IRF3 and STAT1 in infected endothelial cells was also confirmed. In contrast, renal proximal tubular epithelial cells failed to mount an interferon response and underwent progressive cell death. These results demonstrated that microvascular endothelial cells are able to activate interferon signaling in response to polyomavirus BKV infection. This raises the possibility that endothelial cells might provide initial immune defense against BKV infection. Our results shed light on the persistence of and immunity against infection by BKV polyomavirus.
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http://dx.doi.org/10.1371/journal.ppat.1007505DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6338385PMC
January 2019

Draft Genome Sequence of a Novel Rhabdovirus Isolated from Deinocerites Mosquitoes.

Genome Announc 2018 May 10;6(19). Epub 2018 May 10.

Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA

We present a draft genome of a novel rhabdovirus, called Grenada mosquito rhabdovirus 1 (GMRV1), with homology to Wuhan mosquito virus 9 (WMV9) (NCBI reference sequence NC_031303), isolated from mosquitoes. The genome has a length of 14,420 nucleotides and encodes five open reading frames.
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http://dx.doi.org/10.1128/genomeA.01438-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5946037PMC
May 2018

Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice.

Sci Data 2016 Feb 16;3:160008. Epub 2016 Feb 16.

Department of Molecular Virology, Immunology and Medical Genetics, College of Medicine, Columbus, Ohio 43210, USA.

E2F3 and MYC are transcription factors that control cellular proliferation. To study their mechanism of action in the context of a regenerating tissue, we isolated both proliferating (crypts) and non-dividing (villi) cells from wild-type and Rb depleted small intestines of mice and performed ChIP-exo-seq (chromatin immunoprecipitation combined with lambda exonuclease digestion followed by high-throughput sequencing). The genome-wide chromatin occupancy of E2F3 and MYC was determined by mapping sequence reads to the genome and predicting preferred binding sites (peaks). Binding sites could be accurately identified within small regions of only 24 bp-28 bp long, highlighting the precision to which binding peaks can be identified by ChIP-exo-seq. Forty randomly selected E2F3- and MYC-specific binding sites were validated by ChIP-PCR. In addition, we also presented gene expression data sets from wild type, Rb-, E2f3- and Myc-depleted crypts and villi within this manuscript. These represent comprehensive and validated datasets that can be integrated to identify putative direct targets of E2F3 and MYC involved in the control of cellular proliferation in normal and Rb-deficient small intestines.
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http://dx.doi.org/10.1038/sdata.2016.8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4755127PMC
February 2016

Expression of the small T antigen of Lymphotropic Papovavirus is sufficient to transform primary mouse embryo fibroblasts.

Virology 2016 Jan 27;487:112-20. Epub 2015 Oct 27.

Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA. Electronic address:

Polyomaviruses induce cell proliferation and transformation through different oncoproteins encoded within the early region (ER): large T antigen (LT), small T antigen (sT) and, in some cases, additional components. Each virus utilizes different mechanisms to achieve transformation. For instance, the LTs of Simian virus 40 (SV40), BK and/or JC virus can induce transformation; but Merkel Cell Polyomavirus (MCPyV) requires expression of sT. Lymphotropic Papovavirus (LPV) is closely related to Human Polyomavirus 9 (HuPyV9) and, under similar conditions, mice expressing LPV.ER exhibit higher rates of tumor formation than mice expressing SV40.ER. We have investigated the contributions of individual LPV.ER components to cell transformation. In contrast to SV40, LPV.ER transforms mouse embryonic fibroblasts (MEFs), but expression of LPV LT is insufficient to transform MEFs. Furthermore, LPV sT induces immortalization and transformation of MEFs. Thus, in the case of LPV, sT is the main mediator of oncogenesis.
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http://dx.doi.org/10.1016/j.virol.2015.10.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4679568PMC
January 2016

Redeployment of Myc and E2f1-3 drives Rb-deficient cell cycles.

Nat Cell Biol 2015 Aug 20;17(8):1036-48. Epub 2015 Jul 20.

1] Department of Molecular Virology, Immunology and Medical Genetics, College of Medicine, The Ohio State University, Columbus, Ohio 43210, USA [2] Department of Molecular Genetics, College of Biological Sciences, The Ohio State University, Columbus, Ohio 43210, USA [3] Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA.

Robust mechanisms to control cell proliferation have evolved to maintain the integrity of organ architecture. Here, we investigated how two critical proliferative pathways, Myc and E2f, are integrated to control cell cycles in normal and Rb-deficient cells using a murine intestinal model. We show that Myc and E2f1-3 have little impact on normal G1-S transitions. Instead, they synergistically control an S-G2 transcriptional program required for normal cell divisions and maintaining crypt-villus integrity. Surprisingly, Rb deficiency results in the Myc-dependent accumulation of E2f3 protein and chromatin repositioning of both Myc and E2f3, leading to the 'super activation' of a G1-S transcriptional program, ectopic S phase entry and rampant cell proliferation. These findings reveal that Rb-deficient cells hijack and redeploy Myc and E2f3 from an S-G2 program essential for normal cell cycles to a G1-S program that re-engages ectopic cell cycles, exposing an unanticipated addiction of Rb-null cells on Myc.
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http://dx.doi.org/10.1038/ncb3210DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4526313PMC
August 2015

Cellular transformation of mouse embryo fibroblasts in the absence of activator E2Fs.

J Virol 2015 May 25;89(9):5124-33. Epub 2015 Feb 25.

Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA

Unlabelled: The E2F family of transcription factors, broadly divided into activator and repressor E2Fs, regulates cell cycle genes. Current models indicate that activator E2Fs are necessary for cell cycle progression and tumorigenesis and are also required to mediate transformation induced by DNA tumor viruses. E2Fs are negatively regulated by the retinoblastoma (RB) family of tumor suppressor proteins, and virus-encoded oncogenes disrupt the RB-E2F repressor complexes. This results in the release of activator E2Fs and induction of E2F-dependent genes. In agreement, expression of large tumor T antigens (TAg) encoded by polyomaviruses in mammalian cells results in increased transcriptional levels of E2F target genes. In addition, tumorigenesis induced by transgenic expression of simian virus 40 (SV40) TAg in choroid plexus or intestinal villi requires at least one activator E2F. In contrast, we show that SV40 TAg-induced transformation in mouse embryonic fibroblasts is independent of activator E2Fs. This work, coupled with recent studies showing that proliferation in stem and progenitor cells is independent of activator E2Fs, suggests the presence of parallel pathways governing cell proliferation and tumorigenesis.

Importance: The RB-E2F pathway is altered in many cancers and is also targeted by DNA tumor viruses. Viral oncoprotein action on RBs results in the release of activator E2Fs and upregulation of E2F target genes; thus, activator E2Fs are considered essential for normal and tumorigenic cell proliferation. However, we have observed that SV40 large T antigen can induce cell proliferation and transformation in the absence of activator E2Fs. Our results also suggest that TAg action on pRBs regulates both E2F-dependent and -independent pathways that govern proliferation. Thus, specific cell proliferation pathways affected by RB alterations in cancer may be a factor in tumor behavior and response to therapy.
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http://dx.doi.org/10.1128/JVI.03578-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4403490PMC
May 2015

Removal of a small C-terminal region of JCV and SV40 large T antigens has differential effects on transformation.

Virology 2014 Nov 16;468-470:47-56. Epub 2014 Aug 16.

Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA. Electronic address:

The large T antigen (LT) protein of JCV and SV40 polyomaviruses is required to induce tumors in rodents and transform cells in culture. When both LTs are compared side-by-side in cell culture assays, SV40 shows a more robust transformation phenotype even though the LT sequences are highly conserved. A complete understanding of SV40׳s enhanced transforming capabilities relative to JCV is lacking. When the least conserved region of the LT proteins, the variable linker and host range region (VHR), was removed, changes in T antigen expression and cellular p53 post-translational modifications occurred, but interaction with the pRB pathway was unaffected. Transformation assessed by growth in low serum was reduced after VHR truncation of the SV40, but not the JCV, T antigen. Conversely, anchorage independent transformation was enhanced only by truncation of the JCV VHR. This is the first report to link the SV40 or JCV VHR region to transformation potential.
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http://dx.doi.org/10.1016/j.virol.2014.07.038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4253650PMC
November 2014

Viral oncogene expression in the stem/progenitor cell compartment of the mouse intestine induces adenomatous polyps.

Mol Cancer Res 2014 Oct 3;12(10):1355-64. Epub 2014 Jul 3.

Department of Biological Sciences, University of Pittsburgh. Pittsburgh, Pennsylvania.

Unlabelled: Genetic and epigenetic events that alter gene expression and/or protein function or localization are thought to be the primary mechanism that drives tumorigenesis and governs the clinical behavior of cancers. Yet, a number of studies have shown that the effects of oncogene expression or tumor suppressor ablation are highly dependent on cell type. The molecular basis for this cell-type specificity and how it contributes to tumorigenesis are unknown. Here, expression of a truncated SV40 large T antigen in murine intestinal crypts promoted the formation of numerous adenomatous polyps in the colon and small intestine. In contrast, when the same T-antigen construct is expressed in villous enterocytes, the consequences are limited to hyperplasia and dysplasia. The T-antigen-induced polyps show high levels of the proto-oncogene c-Myc protein even though there is no transport of β-catenin to the nucleus. Targeting the expression of viral oncogenes to intestinal crypts or villi provides a murine model system for studying cell-type specific effects in tumorigenesis, and is particularly relevant to the study of APC/β-catenin-independent pathways contributing to the generation of intestinal polyps.

Implications: This mouse model system describes the formation of colon polyps in the absence of Wnt/β-catenin signaling.
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http://dx.doi.org/10.1158/1541-7786.MCR-14-0166DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4201981PMC
October 2014

Two independent regions of simian virus 40 T antigen increase CBP/p300 levels, alter patterns of cellular histone acetylation, and immortalize primary cells.

J Virol 2013 Dec 2;87(24):13499-509. Epub 2013 Oct 2.

Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.

Simian virus 40 (SV40) large T antigen (SVT) interferes with normal cell regulation and thus has been used to identify cellular components controlling proliferation and homeostasis. We have previously shown that SVT-mediated transformation requires interaction with the histone acetyltransferases (HATs) CBP/p300 and now report that the ectopic expression of SVT in several cell types in vivo and in vitro results in a significant increase in the steady-state levels of CBP/p300. Furthermore, SVT-expressing cells contain higher levels of acetylated CBP/p300, a modification that has been linked to increased HAT activity. Concomitantly, the acetylation levels of histone residues H3K56 and H4K12 are markedly increased in SVT-expressing cells. Other polyomavirus-encoded large T antigens also increase the levels of CBP/p300 and sustain a rise in the acetylation levels of H3K56 and H4K12. SVT does not affect the transcription of CBP/p300, but rather, alters their overall levels through increasing the loading of CBP/p300 mRNAs onto polysomes. Two distinct regions within SVT, one located in the amino terminus and one in the carboxy terminus, can independently alter both the levels of CBP/p300 and the loading of CBP/p300 transcripts onto polysomes. Within the amino-terminal fragment, a functional J domain is necessary for increasing CBP/p300 and specific histone acetylation levels, as well as for immortalizing primary cells. These studies uncover the action of polyomavirus T antigens on cellular CBP/p300 and suggest that additional mechanisms are used by T antigens to induce cell immortalization and transformation.
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http://dx.doi.org/10.1128/JVI.02658-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3838271PMC
December 2013

Large T antigens of polyomaviruses: amazing molecular machines.

Annu Rev Microbiol 2012 ;66:213-36

Department of Biological Sciences, University of Pittsburgh, Pennsylvania 15260, USA.

The large tumor antigen (T antigen) encoded by simian virus 40 is an amazing molecular machine because it orchestrates viral infection by modulating multiple fundamental viral and cellular processes. T antigen is required for viral DNA replication, transcription, and virion assembly. In addition, T antigen targets multiple cellular pathways, including those that regulate cell proliferation, cell death, and the inflammatory response. Ectopic T antigen expression results in the immortalization and transformation of many cell types in culture and T antigen induces neoplasia when expressed in rodents. The analysis of the mechanisms by which T antigen carries out its many functions has proved to be a powerful way of gaining insights into cell biology. The accelerating pace at which new polyomaviruses are being discovered provides a collection of novel T antigens that, like simian virus 40, can be used to discover and study key cellular regulatory systems.
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http://dx.doi.org/10.1146/annurev-micro-092611-150154DOI Listing
January 2013

The retinoblastoma tumor suppressor regulates a xenobiotic detoxification pathway.

PLoS One 2011 12;6(10):e26019. Epub 2011 Oct 12.

Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America.

The retinoblastoma tumor suppressor (pRb) regulates cell cycle entry, progression and exit by controlling the activity of the E2F-family of transcription factors. During cell cycle exit pRb acts as a transcriptional repressor by associating with E2F proteins and thereby inhibiting their ability to stimulate the expression of genes required for S phase. Indeed, many tumors harbor mutations in the RB gene and the pRb-E2F pathway is compromised in nearly all types of cancers. In this report we show that both pRb and its interacting partners, the transcriptional factors E2F1-2-3, act as positive modulators of detoxification pathways important for metabolizing and clearing xenobiotics--such as toxins and drugs--from the body. Using a combination of conventional molecular biology techniques and microarray analysis of specific cell populations, we have analyzed the detoxification pathway in murine samples in the presence or absence of pRb and/or E2F1-2-3. In this report, we show that both pRb and E2F1-2-3 act as positive modulators of detoxification pathways in mice, challenging the conventional view of E2F1-2-3 as transcriptional repressors negatively regulated by pRb. These results suggest that mutations altering the pRb-E2F axis may have consequences beyond loss of cell cycle control by altering the ability of tissues to remove toxins and to properly metabolize anticancer drugs, and might help to understand the formation and progression rates of different types of cancer, as well as to better design appropriate therapies based on the particular genetic composition of the tumors.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0026019PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192141PMC
February 2012

T antigen transgenic mouse models.

Semin Cancer Biol 2009 Aug 14;19(4):229-35. Epub 2009 Feb 14.

Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA.

The study of polyomavirus has benefited immensely from two scientific methodologies, cell culture and in vitro studies on one side and the use of transgenic mice as experimental models on the other. Both approaches allowed us to identify cellular products targeted by the viruses, the consequences of these interactions at the phenotypic and molecular level, and thus the potential roles of the targets within their normal cellular context. In particular, cell culture and in vitro reports suggest a model explaining partially how SV40 large T antigen contributes to oncogenic transformation. In most cases, T antigen induces cell cycle entry by inactivation of the Rb proteins (pRb, p130, and p107), thus activating E2F-dependent transcription and subsequent S-phase entry. Simultaneously, T antigen blocks p53 activity and therefore prevents the ensuing cell-cycle arrest and apoptosis. For the most part, studies of T antigen expression in transgenic mice support this model, but the use of T antigen mutants and their expression in different tissue and cell type settings have expanded our knowledge of the model system and raised important questions regarding tumorigenic mechanisms functioning in vivo.
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http://dx.doi.org/10.1016/j.semcancer.2009.02.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2737746PMC
August 2009

Cell-type specific regulation of gene expression by simian virus 40 T antigens.

Virology 2009 Mar 8;386(1):183-91. Epub 2009 Feb 8.

Department of Biological Sciences, 559 Crawford Hall, University of Pittsburgh Pittsburgh, Pennsylvania 15260, USA.

SV40 transforms cells through the action of two oncoproteins, large T antigen and small t antigen. Small t antigen targets phosphatase PP2A, while large T antigen stimulates cell proliferation and survival by action on multiple proteins, including the tumor suppressors Rb and p53. Large T antigen also binds components of the transcription initiation complex and several transcription factors. We examined global gene expression in SV40-transformed mouse embryo fibroblasts, and in enterocytes obtained from transgenic mice. SV40 transformation alters the expression of approximately 800 cellular genes in both systems. Much of this regulation is observed in both MEFs and enterocytes and is consistent with T antigen action on the Rb-E2F pathway. However, the regulation of many genes is cell-type specific, suggesting that unique signaling pathways are activated in different cell types upon transformation, and that the consequences of SV40 transformation depends on the type of cell targeted.
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http://dx.doi.org/10.1016/j.virol.2008.12.038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2737743PMC
March 2009