scholarly journals Use of Cap Analysis Gene Expression to detect human papillomavirus promoter activity patterns at different disease stages

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ayumi Taguchi ◽  
Kazunori Nagasaka ◽  
Charles Plessy ◽  
Hiroe Nakamura ◽  
Yoshiko Kawata ◽  
...  
Keyword(s):  
Gene Expression ◽  
Human Papillomavirus ◽  
Promoter Activity ◽  
Clinical Samples ◽  
Viral Gene ◽  
Type B ◽  
Dominant Type ◽  
Pattern Dynamics ◽  
Hpv Types ◽  
Cap Analysis

Abstract Transcription of human papillomavirus (HPV) genes proceeds unidirectionally from multiple promoters. Direct profiling of transcription start sites (TSSs) by Cap Analysis Gene Expression (CAGE) is a powerful strategy for examining individual HPV promoter activity. The objective of this study was to evaluate alterations of viral promoter activity during infection using CAGE technology. We used CAGE-based sequencing of 46 primary cervical samples, and quantitatively evaluated TSS patterns in the HPV transcriptome at a single-nucleotide resolution. TSS patterns were classified into two types: early promoter-dominant type (Type A) and late promoter-dominant type (Type B). The Type B pattern was more frequently found in CIN1 and CIN2 lesions than in CIN3 and cancer samples. We detected transcriptomes from multiple HPV types in five samples. Interestingly, in each sample, the TSS patterns of both HPV types were the same. The viral gene expression pattern was determined by the differentiation status of the epithelial cells, regardless of HPV type. We performed unbiased analyses of TSSs across the HPV genome in clinical samples. Visualising TSS pattern dynamics, including TSS shifts, provides new insights into how HPV infection status relates to disease state.

scholarly journals Differential early viral gene expression in two stages of human papillomavirus type 16 DNA-induced malignant transformation.

1987 ◽  
Vol 7 (6) ◽  
pp. 2165-2172 ◽  
Author(s):  
S Yasumoto ◽  
J Doniger ◽  
J A DiPaolo
Keyword(s):  
Gene Expression ◽  
Human Papillomavirus ◽  
Malignant Transformation ◽  
Cell Lines ◽  
Viral Gene Expression ◽  
Viral Gene ◽  
3T3 Cells ◽  
Hpv 16 ◽  
Nih 3T3 ◽  
Nih 3T3 Cells

Human papillomavirus (HPV) type 16 DNA induces progressive transformation in NIH 3T3 cells. Two types of cell lines, PM3T3G0 and PM3T3Fo, were isolated by G418 or focus selection, respectively, after transfection of cells by a recombinant HPV 16 DNA carrying the neo gene. These cell lines exhibited distinct phenotypes compared with controls. Saturation densities of PM3T3G0 and PM3T3Fo lines were two- to three- and five- to sevenfold greater than that of control NIH 3T3 cells, respectively. Neither cell type required high serum for growth, in contrast to NIH 3T3 cells. PM3T3G0 lines were premalignant, whereas PM3T3Fo lines manifested tumorigenicity within 2 weeks. Subpopulations of three PM3T3G0 lines underwent progressive transformation as reflected by focus formation. Analysis of HPV 16-specific mRNA species demonstrated that high levels of early and late gene expression were detected in premalignant PM3T3G0 lines, whereas relatively low quantities of selected gene messages were expressed in malignant transformants. Thus, high levels of viral gene expression are not crucial for malignant transformation.

scholarly journals Characterization of Novel Transcripts of Human Papillomavirus Type 16 Using Cap Analysis Gene Expression Technology

2014 ◽  
Vol 89 (4) ◽  
pp. 2448-2452 ◽  
Author(s):  
Ayumi Taguchi ◽  
Kazunori Nagasaka ◽  
Kei Kawana ◽  
Kosuke Hashimoto ◽  
Rika Kusumoto-Matsuo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Human Papillomavirus ◽  
Regulatory Networks ◽  
Intraepithelial Neoplasia ◽  
Cervical Intraepithelial Neoplasia Grade ◽  
Viral Transcript ◽  
Human Papillomavirus Type 16 ◽  
Cervical Cell ◽  
Transcriptome Expression ◽  
Cap Analysis

We have performed cap-analysis gene expression (CAGE) sequencing to identify the regulatory networks that orchestrate genome-wide transcription in human papillomavirus type 16 (HPV16)-positive cervical cell lines of different grades: W12E, SiHa, and CaSki. Additionally, a cervical intraepithelial neoplasia grade 1 (CIN1) lesion was assessed for identifying the transcriptome expression profile. Here we have precisely identified a novel antisense noncoding viral transcript in HPV16. In conclusion, CAGE sequencing should pave the way for understanding a diversity of viral transcript expression.

scholarly journals Human Papillomavirus Infectious Entry and Trafficking Is a Rapid Process

2015 ◽  
Vol 89 (17) ◽  
pp. 8727-8732 ◽  
Author(s):  
Justyna Broniarczyk ◽  
Paola Massimi ◽  
Martina Bergant ◽  
Lawrence Banks
Keyword(s):  
Gene Expression ◽  
Cell Cycle ◽  
Human Papillomavirus ◽  
Intracellular Transport ◽  
Nuclear Bodies ◽  
Viral Gene ◽  
Rapid Process ◽  
Pml Nuclear Bodies ◽  
Infectious Entry ◽  
In Cells

ABSTRACTPrevious studies have indicated that human papillomavirus (HPV) infectious entry is slow, requiring many hours after initial infection for the virus to gain entry into the nucleus. However, intracellular transport pathways typically are very rapid, and in the context of a natural HPV infection in a wounded epithelium, such slow intracellular transport would seem to be at odds with a normal viral infection. Using synchronized cell populations, we show that HPV trafficking can be a rapid process. In cells that are infected in the late S-early G2/M phase of the cell cycle, HPV16 pseudovirion (PsV) reporter DNA gene expression is detectable by 8 h postinfection. Likewise, reporter DNA can be visualized within the nucleus in conjunction with PML nuclear bodies 1 h to 2 h postinfection in cells that are infected with PsVs just prior to mitotic entry. This demonstrates that endosomal trafficking of HPV is rapid, with mitosis being the main restriction on nuclear entry.IMPORTANCEHPV infectious entry appears to be slow and requires mitosis to occur before the incoming viral DNA can access the nucleus. In this study, we show that HPV trafficking in the cell actually is very rapid. This demonstrates that in the context of a normal virus infection, the cell cycle state will have a major influence on the time it takes for an incoming virus to enter the nucleus and initiate viral gene expression.

scholarly journals Cyclooxygenase 2 Induced by Kaposi's Sarcoma-Associated Herpesvirus Early during In Vitro Infection of Target Cells Plays a Role in the Maintenance of Latent Viral Gene Expression

2006 ◽  
Vol 80 (13) ◽  
pp. 6534-6552 ◽  
Author(s):  
Neelam Sharma-Walia ◽  
Hari Raghu ◽  
Sathish Sadagopan ◽  
Ramu Sivakumar ◽  
Mohanan Valiya Veettil ◽  
...  
Keyword(s):  
Gene Expression ◽  
Kaposi's Sarcoma ◽  
Promoter Activity ◽  
Viral Gene Expression ◽  
Cyclooxygenase 2 ◽  
Viral Gene ◽  
Kshv Infection ◽  
Cox 2 ◽  
D Cells

ABSTRACT Infection of human dermal microvascular endothelial (HMVEC-d) cells and human foreskin fibroblast (HFF) cells in vitro by Kaposi's sarcoma-associated herpesvirus (KSHV) provides an excellent in vitro model system to study viral latency. KSHV infection is characterized by the induction of preexisting host signal cascades; sustained expression of the latency-associated open reading frame 73 (ORF73) (LANA-1), ORF72, and K13 genes; transient expression of a limited number of lytic genes, including the lytic cycle switch ORF50 (replication and transcription activator) gene; and reprogramming of host transcriptional machinery regulating a variety of cellular processes, including several proinflammatory responses. The cyclooxygenase 2 (COX-2) gene was one of the host cell genes that was highly up-regulated at 2 and 4 h postinfection (p.i.) of HMVEC-d and HFF cells (P. P. Naranatt, H. H. Krishnan, S. R. Svojanovsky, C. Bloomer, S. Mathur, and B. Chandran, Cancer Res. 64:72-84, 2004). Since COX-2 is an important mediator of inflammatory and angiogenic responses, here, using real-time PCR, Western blot, and immunofluorescence assays, we characterized the COX-2 stimulation and its role in KSHV infection. KSHV induced a robust COX-2 expression, which reached a maximum at 2 h p.i. in HMVEC-d cells and at 8 h p.i. in HFF cells, and significantly higher levels were continuously detected for up to 72 h p.i. Constitutive COX-1 protein levels were not modulated by KSHV infection. Moderate levels of COX-2 were also induced by UV-irradiated KSHV and by envelope glycoproteins gB and gpK8.1A; however, viral gene expression appears to be essential for the increased COX-2 induction. High levels of prostaglandin E2 (PGE2), a COX-2 product, were released in the culture supernatant medium of infected cells. PGE2 synthase, catalyzing the biosynthesis of PGE2, also increased upon infection and inhibition of COX-2 by NS-398, and indomethacin drastically reduced the levels of PGE2 and PGE2 synthase. COX-2 inhibition did not affect KSHV binding, internalization of virus, or the trafficking to the infected cell nuclei. However, latent ORF73 gene expression and ORF73 promoter activity were significantly reduced by COX-2 inhibitors, and this inhibition was relieved by exogenous supplementation with PGE2. In contrast, lytic ORF50 gene expression and ORF50 promoter activity were unaffected. These studies demonstrate that COX-2 and PGE2 play roles in facilitating latent viral gene expression and the establishment and maintenance of latency and suggest that KSHV has evolved to utilize the inflammatory responses induced during infection of endothelial cells for the maintenance of viral latent gene expression.

Molecular biology of human papillomavirus infection and cervical cancer

2006 ◽  
Vol 110 (5) ◽  
pp. 525-541 ◽  
Author(s):  
John Doorbar
Keyword(s):  
Gene Expression ◽  
High Risk ◽  
Viral Gene Expression ◽  
Cervical Neoplasia ◽  
Productive Infection ◽  
Viral Gene ◽  
Low Grade ◽  
Cervical Cancers ◽  
Hpv Types ◽  
High Risk Hpv

HPVs (human papillomaviruses) infect epithelial cells and cause a variety of lesions ranging from common warts/verrucas to cervical neoplasia and cancer. Over 100 different HPV types have been identified so far, with a subset of these being classified as high risk. High-risk HPV DNA is found in almost all cervical cancers (>99.7%), with HPV16 being the most prevalent type in both low-grade disease and cervical neoplasia. Productive infection by high-risk HPV types is manifest as cervical flat warts or condyloma that shed infectious virions from their surface. Viral genomes are maintained as episomes in the basal layer, with viral gene expression being tightly controlled as the infected cells move towards the epithelial surface. The pattern of viral gene expression in low-grade cervical lesions resembles that seen in productive warts caused by other HPV types. High-grade neoplasia represents an abortive infection in which viral gene expression becomes deregulated, and the normal life cycle of the virus cannot be completed. Most cervical cancers arise within the cervical transformation zone at the squamous/columnar junction, and it has been suggested that this is a site where productive infection may be inefficiently supported. The high-risk E6 and E7 proteins drive cell proliferation through their association with PDZ domain proteins and Rb (retinoblastoma), and contribute to neoplastic progression, whereas E6-mediated p53 degradation prevents the normal repair of chance mutations in the cellular genome. Cancers usually arise in individuals who fail to resolve their infection and who retain oncogene expression for years or decades. In most individuals, immune regression eventually leads to clearance of the virus, or to its maintenance in a latent or asymptomatic state in the basal cells.

Differential early viral gene expression in two stages of human papillomavirus type 16 DNA-induced malignant transformation

1987 ◽  
Vol 7 (6) ◽  
pp. 2165-2172
Author(s):  
S Yasumoto ◽  
J Doniger ◽  
J A DiPaolo
Keyword(s):  
Gene Expression ◽  
Human Papillomavirus ◽  
Malignant Transformation ◽  
Cell Lines ◽  
Viral Gene Expression ◽  
Viral Gene ◽  
3T3 Cells ◽  
Hpv 16 ◽  
Nih 3T3 ◽  
Nih 3T3 Cells

Human papillomavirus (HPV) type 16 DNA induces progressive transformation in NIH 3T3 cells. Two types of cell lines, PM3T3G0 and PM3T3Fo, were isolated by G418 or focus selection, respectively, after transfection of cells by a recombinant HPV 16 DNA carrying the neo gene. These cell lines exhibited distinct phenotypes compared with controls. Saturation densities of PM3T3G0 and PM3T3Fo lines were two- to three- and five- to sevenfold greater than that of control NIH 3T3 cells, respectively. Neither cell type required high serum for growth, in contrast to NIH 3T3 cells. PM3T3G0 lines were premalignant, whereas PM3T3Fo lines manifested tumorigenicity within 2 weeks. Subpopulations of three PM3T3G0 lines underwent progressive transformation as reflected by focus formation. Analysis of HPV 16-specific mRNA species demonstrated that high levels of early and late gene expression were detected in premalignant PM3T3G0 lines, whereas relatively low quantities of selected gene messages were expressed in malignant transformants. Thus, high levels of viral gene expression are not crucial for malignant transformation.

The Human Papillomavirus Type 16 E5 Gene Cooperates with the E7 Gene to Stimulate Proliferation of Primary Cells and Increases Viral Gene Expression

Virology ◽  
1994 ◽  
Vol 203 (1) ◽  
pp. 73-80 ◽  
Author(s):  
Veronique Bouvard ◽  
Greg Matlashewski ◽  
Zheng-Ming Gu ◽  
Alan Storey ◽  
Lawrence Banks
Keyword(s):  
Gene Expression ◽  
Human Papillomavirus ◽  
Viral Gene Expression ◽  
Viral Gene ◽  
Primary Cells ◽  
Human Papillomavirus Type 16 ◽  
E7 Gene

Human Papillomavirus-16 Is the Predominant Type Etiologically Involved in Penile Squamous Cell Carcinoma

2007 ◽  
Vol 25 (29) ◽  
pp. 4550-4556 ◽  
Author(s):  
Daniëlle A.M. Heideman ◽  
Tim Waterboer ◽  
Michael Pawlita ◽  
Pien Delis-van Diemen ◽  
Ingo Nindl ◽  
...  
Keyword(s):  
Squamous Cell Carcinoma ◽  
Human Papillomavirus ◽  
Viral Load ◽  
Cell Carcinoma ◽  
Squamous Cell ◽  
Broad Spectrum ◽  
Viral Gene ◽  
Predominant Type ◽  
Hpv Types ◽  
Penile Squamous Cell Carcinoma

PurposeHuman papillomavirus (HPV) infections are suggested to be involved in the development of penile squamous cell carcinoma (SCC), but comprehensive studies to define the association are limited. Therefore, we performed molecular and serologic analyses for a broad spectrum of HPV types on a large series of 83 penile SCCs, and we compared serological findings to those of age-matched male controls (N = 83).MethodsPenile SCCs were subjected to detection and typing assays for mucosal and cutaneous HPVs and to subsequent, type-specific viral load and viral gene expression assays. Sera of patients and of controls were analyzed for type-specific mucosal and cutaneous HPV L1, E6, and/or E7 antibodies using bead-based, multiplex serology.ResultsHPV DNA of mucosal and/or cutaneous types was found in 46 of 83 (55%) penile SCCs. HPV16 was the predominant type, appearing in 24 (52%) of 46 of penile SCCs. The majority of HPV16 DNA–positive SCCs (18 of 24; 75%) demonstrated E6 transcriptional activity and a high viral load. Additionally, HPV16 molecular findings were strongly associated with HPV16 L1-, E6-, and E7-antibody seropositivity. Furthermore, serologic case-control analyses demonstrated that, in addition to the association of HPV16 with penile SCC, seropositivity against any HPV type was significantly more common in patients compared with in controls. HPV18 and HPV6 seropositivity were associated with HPV16-negative SCCs but were not correlated to molecular findings.ConclusionHPV16 is the main HPV type etiologically involved in the development of penile SCC. Although individuals who develop penile SCC show a greater prior exposure to a broad spectrum of HPV types, insufficient evidence was found to claim a role for HPV types other than HPV16 in penile carcinogenesis.

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