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Roy S, Sengupta S. The RNA-DNA world and the emergence of DNA-encoded heritable traits. RNA Biol 2024; 21:1-9. [PMID: 38785360 PMCID: PMC11135857 DOI: 10.1080/15476286.2024.2355391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/01/2024] [Indexed: 05/25/2024] Open
Abstract
The RNA world hypothesis confers a central role to RNA molecules in information encoding and catalysis. Even though evidence in support of this hypothesis has accumulated from both experiments and computational modelling, the transition from an RNA world to a world where heritable genetic information is encoded in DNA remains an open question. Recent experiments show that both RNA and DNA templates can extend complementary primers using free RNA/DNA nucleotides, either non-enzymatically or in the presence of a replicase ribozyme. Guided by these experiments, we analyse protocellular evolution with an expanded set of reaction pathways made possible through the presence of DNA nucleotides. By encapsulating these reactions inside three different types of protocellular compartments, each subject to distinct modes of selection, we show how protocells containing DNA-encoded replicases in low copy numbers and replicases in high copy numbers can dominate the population. This is facilitated by a reaction that leads to auto-catalytic synthesis of replicase ribozymes from DNA templates encoding the replicase after the chance emergence of a replicase through non-enzymatic reactions. Our work unveils a pathway for the transition from an RNA world to a mixed RNA-DNA world characterized by Darwinian evolution, where DNA sequences encode heritable phenotypes.
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Affiliation(s)
- Suvam Roy
- Department of Physical Sciences, Indian Institute of Science Education and ResearchKolkata, Mohanpur, West Bengal, India
| | - Supratim Sengupta
- Department of Physical Sciences, Indian Institute of Science Education and ResearchKolkata, Mohanpur, West Bengal, India
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Overton MS, Manuel RD, Lawrence CM, Snyder JC. Viruses of the Turriviridae: an emerging model system for studying archaeal virus-host interactions. Front Microbiol 2023; 14:1258997. [PMID: 37808280 PMCID: PMC10551542 DOI: 10.3389/fmicb.2023.1258997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Viruses have played a central role in the evolution and ecology of cellular life since it first arose. Investigations into viral molecular biology and ecological dynamics have propelled abundant progress in our understanding of living systems, including genetic inheritance, cellular signaling and trafficking, and organismal development. As well, the discovery of viral lineages that infect members of all three domains suggest that these lineages originated at the earliest stages of biological evolution. Research into these viruses is helping to elucidate the conditions under which life arose, and the dynamics that directed its early development. Archaeal viruses have only recently become a subject of intense study, but investigations have already produced intriguing and exciting results. STIV was originally discovered in Yellowstone National Park and has been the focus of concentrated research. Through this research, a viral genetic system was created, a novel lysis mechanism was discovered, and the interaction of the virus with cellular ESCRT machinery was revealed. This review will summarize the discoveries within this group of viruses and will also discuss future work.
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Affiliation(s)
- Michael S. Overton
- Department of Biological Sciences, Cal Poly Pomona, Pomona, CA, United States
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Robert D. Manuel
- Department of Biological Sciences, Cal Poly Pomona, Pomona, CA, United States
| | - C. Martin Lawrence
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT, United States
| | - Jamie C. Snyder
- Department of Biological Sciences, Cal Poly Pomona, Pomona, CA, United States
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Human Papillomavirus Genome Copy Number Is Maintained by S-Phase Amplification, Genome Loss to the Cytosol during Mitosis, and Degradation in G 1 Phase. J Virol 2023; 97:e0187922. [PMID: 36749071 PMCID: PMC9972943 DOI: 10.1128/jvi.01879-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The current model of human papillomavirus (HPV) replication is comprised of three modes of replication. Following infectious delivery, the viral genome is amplified during the establishment phase to reach up to some hundred copies per cell. The HPV genome copy number remains constant during the maintenance stage. The differentiation of infected cells induces HPV genome amplification. Using highly sensitive in situ hybridization (DNAscope) and freshly HPV16-infected as well as established HPV16-positive cell lines, we observed that the viral genome is amplified in each S phase of undifferentiated keratinocytes cultured as monolayers. The nuclear viral genome copy number is reset to pre-S-phase levels during mitosis. The majority of the viral genome fails to tether to host chromosomes and is lost to the cytosol. Cytosolic viral genomes gradually decrease during cell cycle progression. The loss of cytosolic genomes is blocked in the presence of NH4Cl or other drugs that interfere with lysosomal acidification, suggesting the involvement of autophagy in viral genome degradation. These observations were also made with HPV31 cell lines obtained from patient samples. Cytosolic viral genomes were not detected in UMSCC47 cells carrying integrated HPV16 DNA. Analyses of organotypic raft cultures derived from keratinocytes harboring episomal HPV16 revealed the presence of cytosolic viral genomes as well. We conclude that HPV maintains viral genome copy numbers by balancing viral genome amplification during S phase with the loss of viral genomes to the cytosol during mitosis. It seems plausible that restrictions to viral genome tethering to mitotic chromosomes reset genome copy numbers in each cell cycle. IMPORTANCE HPV genome maintenance is currently thought to be achieved by regulating the expression and activity of the viral replication factors E1 and E2. In addition, the E8^E2 repressor has been shown to be important for restricting genome copy numbers by competing with E1 and E2 for binding to the viral origin of replication and by recruiting repressor complexes. Here, we demonstrate that the HPV genome is amplified in each S phase. The nuclear genome copy number is reset during mitosis by a failure of the majority of the genomes to tether to mitotic chromosomes. Rather, HPV genomes accumulate in the cytoplasm of freshly divided cells. Cytosolic viral DNA is degraded in G1 in a lysosome-dependent manner, contributing to the genome copy reset. Our data imply that the mode of replication during establishment and maintenance is the same and further suggest that restrictions to genome tethering significantly contribute to viral genome maintenance.
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Sianga-Mete R, Hartnady P, Mandikumba WC, Rutherford K, Currin CB, Phelanyane F, Stefan S, Kosakovsky Pond SL, Martin DP. Viral genome sequence datasets display pervasive evidence of strand-specific substitution biases that are best described using non-reversible nucleotide substitution models. RESEARCH SQUARE 2022:rs.3.rs-2407778. [PMID: 36597548 PMCID: PMC9810213 DOI: 10.21203/rs.3.rs-2407778/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Background The vast majority of phylogenetic trees are inferred from molecular sequence data (nucleotides or amino acids) using time-reversible evolutionary models which assume that, for any pair of nucleotide or amino acid characters, the relative rate of X to Y substitution is the same as the relative rate of Y to X substitution. However, this reversibility assumption is unlikely to accurately reflect the actual underlying biochemical and/or evolutionary processes that lead to the fixation of substitutions. Here, we use empirical viral genome sequence data to reveal that evolutionary non-reversibility is pervasive among most groups of viruses. Specifically, we consider two non-reversible nucleotide substitution models: (1) a 6-rate non-reversible model (NREV6) in which Watson-Crick complementary substitutions occur at identical relative rates and which might therefor be most applicable to analyzing the evolution of genomes where both complementary strands are subject to the same mutational processes (such as might be expected for double-stranded (ds) RNA or dsDNA genomes); and (2) a 12-rate non-reversible model (NREV12) in which all relative substitution types are free to occur at different rates and which might therefore be applicable to analyzing the evolution of genomes where the complementary genome strands are subject to different mutational processes (such as might be expected for viruses with single-stranded (ss) RNA or ssDNA genomes). Results Using likelihood ratio and Akaike Information Criterion-based model tests, we show that, surprisingly, NREV12 provided a significantly better fit to 21/31 dsRNA and 20/30 dsDNA datasets than did the general time reversible (GTR) and NREV6 models with NREV6 providing a better fit than NREV12 and GTR in only 5/30 dsDNA and 2/31 dsRNA datasets. As expected, NREV12 provided a significantly better fit to 24/33 ssDNA and 40/47 ssRNA datasets. Next, we used simulations to show that increasing degrees of strand-specific substitution bias decrease the accuracy of phylogenetic inference irrespective of whether GTR or NREV12 is used to describe mutational processes. However, in cases where strand-specific substitution biases are extreme (such as in SARS-CoV-2 and Torque teno sus virus datasets) NREV12 tends to yield more accurate phylogenetic trees than those obtained using GTR. Conclusion We show that NREV12 should, be seriously considered during the model selection phase of phylogenetic analyses involving viral genomic sequences.
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Shirshikov FV, Bespyatykh JA. Loop-Mediated Isothermal Amplification: From Theory to Practice. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2022; 48:1159-1174. [PMID: 36590469 PMCID: PMC9788664 DOI: 10.1134/s106816202206022x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/01/2022] [Accepted: 06/17/2022] [Indexed: 12/24/2022]
Abstract
Increasing the accuracy of pathogen identification and reducing the duration of analysis remain relevant for modern molecular diagnostics up to this day. In laboratory and clinical practice, detection of pathogens mostly relies on methods of nucleic acid amplification, among which the polymerase chain reaction (PCR) is considered the "gold standard." Nevertheless, in some cases, isothermal amplification methods act as an alternative to PCR diagnostics. Upon more than thirty years of the development of isothermal DNA synthesis, the appearance of loop-mediated isothermal amplification (LAMP) has enabled new directions of in-field diagnostics of bacterial and viral infections. This review examines the key characteristics of the LAMP method and corresponding features in practice. We discuss the structure of LAMP amplicons with single-stranded loops, which have the sites for primer annealing under isothermal conditions. The latest achievements in the modification of the LAMP method are analyzed, which allow considering it as a unique platform for creating the next-generation diagnostic assays.
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Affiliation(s)
- F. V. Shirshikov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - J. A. Bespyatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
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Roy S, Sengupta S. The Effect of Environment on the Evolution and Proliferation of Protocells of Increasing Complexity. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081227. [PMID: 36013406 PMCID: PMC9410160 DOI: 10.3390/life12081227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/01/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022]
Abstract
The formation, growth, division and proliferation of protocells containing RNA strands is an important step in ensuring the viability of a mixed RNA-lipid world. Experiments and computer simulations indicate that RNA encapsulated inside protocells can favor the protocell, promoting its growth while protecting the system from being over-run by selfish RNA sequences. Recent work has also shown that the rolling-circle replication mechanism can be harnessed to ensure the rapid growth of RNA strands and the probabilistic emergence and proliferation of protocells with functionally diverse ribozymes. Despite these advances in our understanding of a primordial RNA-lipid world, key questions remain about the ideal environment for the formation of protocells and its role in regulating the proliferation of functionally complex protocells. The hot spring hypothesis suggests that mineral-rich regions near hot springs, subject to dry-wet cycles, provide an ideal environment for the origin of primitive protocells. We develop a computational model to study protocellular evolution in such environments that are distinguished by the occurrence of three distinct phases, a wet phase, followed by a gel phase, and subsequently by a dry phase. We determine the conditions under which protocells containing multiple types of ribozymes can evolve and proliferate in such regions. We find that diffusion in the gel phase can inhibit the proliferation of complex protocells with the extent of inhibition being most significant when a small fraction of protocells is eliminated during environmental cycling. Our work clarifies how the environment can shape the evolution and proliferation of complex protocells.
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Baral SK, Biswas P, Kaium MA, Islam MA, Dey D, Saber MA, Rahaman TI, M A, Emran TB, Hasan MN, Jeong MK, Han I, Rahman MA, Kim B. A Comprehensive Discussion in Vaginal Cancer Based on Mechanisms, Treatments, Risk Factors and Prevention. Front Oncol 2022; 12:883805. [PMID: 35924174 PMCID: PMC9341270 DOI: 10.3389/fonc.2022.883805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 06/23/2022] [Indexed: 12/27/2022] Open
Abstract
Vaginal cancer is a rare and uncommon disease that is rarely discussed. Although vaginal cancer traditionally occurs in older postmenopausal women, the incidence of high-risk human papillomavirus (HPV)-induced cancers is increasing in younger women. Cervical cancer cells contain high-risk human papillomavirus (HPV) E6 and E7 proteins and inhibiting HPV gene expression leads the cells to stop proliferating and enter senescence. As E6, and E7 protein promoted the carcinogenesis mechanism, and here not only regulate the cellular degradation of P53, and pRb but also enhances the cell proliferation along with E6 protein targets the p53 for breakdown and subsequently promote the apoptotic cell death, and DNA repair inhibition, that is indispensable to the continue the lifecycle of the HPV. As a synchronous or metachronous tumor, vaginal cancer is frequently found in combination with cervical cancer. It is uncertain what causes invasive female vaginal organ cancer. HPV type 16 is the most often isolated HPV type in female vaginal organ cancers. Due to cancer's rarity, case studies have provided the majority of etiologic findings. Many findings demonstrate that ring pessaries, chronic vaginitis, sexual behavior, birth trauma, obesity, vaginal chemical exposure, and viruses are all risk factors. Because of insufficient understanding and disease findings, we are trying to find the disease's mechanism with the available data. We also address different risk factors, therapy at various stages, diagnosis, and management of vaginal cancer in this review.
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Affiliation(s)
| | - Partha Biswas
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology (JUST), Jashore, Bangladesh
- ABEx Bio-Research Center, Dhaka, Bangladesh
| | - Md. Abu Kaium
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology (JUST), Jashore, Bangladesh
| | - Md. Aminul Islam
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology (JUST), Jashore, Bangladesh
| | - Dipta Dey
- Biochemistry and Molecular Biology department, Life Science faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalgonj, Bangladesh
| | - Md Al Saber
- Biotechnology, University of Pécs, Medical School, Pécs, Hungary
| | - Tanjim Ishraq Rahaman
- Department of Biotechnology and Genetic Engineering, Faculty of Life Science, Bangabandhu Sheikh Mujibur Rahman Science and Technology University, Gopalganj, Bangladesh
| | - A. M
- Department of Microbiology, Chittagong University, Chittagong, Bangladesh
| | - Talha Bin Emran
- Department of Pharmacy, Begum Gulchemonara (BGC) Trust University Bangladesh, Chittagong, Bangladesh
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Md. Nazmul Hasan
- Laboratory of Pharmaceutical Biotechnology and Bioinformatics, Department of Genetic Engineering and Biotechnology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Mi-Kyung Jeong
- Korean Medicine (KM) Convergence Research Division, Korea Institute of Oriental Medicine, Daejeon, South Korea
| | - Ihn Han
- Plasma Bioscience Research Center, Kwangwoon University, Seoul, South Korea
| | - Md. Ataur Rahman
- Global Biotechnology & Biomedical Research Network (GBBRN), Department of Biotechnology and Genetic Engineering, Faculty of Biological Sciences, Islamic University, Kushtia, Bangladesh
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Seoul, South Korea
- Korean Medicine-Based Drug Repositioning Cancer Research Center, College of Korean Medicine, Kyung Hee University, Seoul, South Korea
| | - Bonglee Kim
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Seoul, South Korea
- Korean Medicine-Based Drug Repositioning Cancer Research Center, College of Korean Medicine, Kyung Hee University, Seoul, South Korea
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Roy S, Sengupta S. Evolution towards increasing complexity through functional diversification in a protocell model of the RNA world. Proc Biol Sci 2021; 288:20212098. [PMID: 34784760 PMCID: PMC8596018 DOI: 10.1098/rspb.2021.2098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/21/2021] [Indexed: 11/12/2022] Open
Abstract
The encapsulation of genetic material inside compartments together with the creation and sustenance of functionally diverse internal components are likely to have been key steps in the formation of 'live', replicating protocells in an RNA world. Several experiments have shown that RNA encapsulated inside lipid vesicles can lead to vesicular growth and division through physical processes alone. Replication of RNA inside such vesicles can produce a large number of RNA strands. Yet, the impact of such replication processes on the emergence of the first ribozymes inside such protocells and on the subsequent evolution of the protocell population remains an open question. In this paper, we present a model for the evolution of protocells with functionally diverse ribozymes. Distinct ribozymes can be created with small probabilities during the error-prone RNA replication process via the rolling circle mechanism. We identify the conditions that can synergistically enhance the number of different ribozymes inside a protocell and allow functionally diverse protocells containing multiple ribozymes to dominate the population. Our work demonstrates the existence of an effective pathway towards increasing complexity of protocells that might have eventually led to the origin of life in an RNA world.
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Affiliation(s)
- Suvam Roy
- Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India
| | - Supratim Sengupta
- Department of Physical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India
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Jia W, Xu C, Li SC. Resolving complex structures at oncovirus integration loci with conjugate graph. Brief Bioinform 2021; 22:6359003. [PMID: 34463709 DOI: 10.1093/bib/bbab359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 01/10/2023] Open
Abstract
Oncovirus integrations cause copy number variations and complex structural variations (SVs) on host genomes. However, the understanding of how inserted viral DNA impacts the local genome remains limited. The linear structure of the oncovirus integrated local genomic map (LGM) will lay the foundations to understand how oncovirus integrations emerge and compromise the host genome's functioning. We propose a conjugate graph model to reconstruct the rearranged LGM at integrated loci. Simulation tests prove the reliability and credibility of the algorithm. Applications of the algorithm to whole-genome sequencing data of human papillomavirus (HPV) and hepatitis B virus (HBV)-infected cancer samples gained biological insights on oncovirus integrations. We observed four affection patterns of oncovirus integrations from the HPV and HBV-integrated cancer samples, including the coding-frame truncation, hyper-amplification of tumor gene, the viral cis-regulation inserted at the single intron and at the intergenic region. We found that the focal duplicates and host SVs are frequent in the HPV-integrated LGMs, while the focal deletions are prevalent in HBV-integrated LGMs. Furthermore, with the results yields from our method, we found the enhanced microhomology-mediated end joining might lead to both HPV and HBV integrations and conjectured that the HPV integrations might mainly occur during the DNA replication process. The conjugate graph algorithm code and LGM construction pipeline, available at https://github.com/deepomicslab/FuseSV.
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Affiliation(s)
- Wenlong Jia
- Department of Computer Science, City University of Hong Kong, Hong Kong
| | - Chang Xu
- Department of Computer Science, City University of Hong Kong, Hong Kong
| | - Shuai Cheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong
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Hirose Y, Yamaguchi-Naka M, Onuki M, Tenjimbayashi Y, Tasaka N, Satoh T, Tanaka K, Iwata T, Sekizawa A, Matsumoto K, Kukimoto I. High Levels of Within-Host Variations of Human Papillomavirus 16 E1/E2 Genes in Invasive Cervical Cancer. Front Microbiol 2020; 11:596334. [PMID: 33324377 PMCID: PMC7721666 DOI: 10.3389/fmicb.2020.596334] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/22/2020] [Indexed: 12/01/2022] Open
Abstract
Human papillomavirus type 16 (HPV16) is the most common HPV genotype found in invasive cervical cancer (ICC). Recent comprehensive genomics studies of HPV16 have revealed that a large number of minor nucleotide variations in the viral genome are present in each infected woman; however, it remains unclear whether such within-host variations of HPV16 are linked to cervical carcinogenesis. Here, by employing next-generation sequencing approaches, we explored the mutational profiles of the HPV16 genome within individual clinical specimens from ICC (n = 31) and normal cervix (n = 21) in greater detail. A total of 367 minor nucleotide variations (167 from ICC and 200 from the normal cervix) were detected throughout the viral genome in both groups, while nucleotide variations at high frequencies (>10% abundance in relative read counts in a single sample) were more prevalent in ICC (10 in ICC versus 1 in normal). Among the high-level variations found in ICC, six were located in the E1/E2 genes, and all of them were non-synonymous substitutions (Q142K, M207I, and L262V for E1; D153Y, R302T, and T357A for E2). In vitro functional analyses of these E1/E2 variants revealed that E1/M207I, E2/D153Y, and E2/R302T had reduced abilities to support viral replication, and that E2/D153Y and E2/R302T failed to suppress the viral early promoter. These results imply that some within-host variations of E1/E2 present at high levels in ICC may be positively selected for and contribute to cervical cancer development through dysfunction or de-stabilization of viral replication/transcription proteins.
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Affiliation(s)
- Yusuke Hirose
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan
| | - Mayuko Yamaguchi-Naka
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan
| | - Mamiko Onuki
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan
| | - Yuri Tenjimbayashi
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan
| | - Nobutaka Tasaka
- Department of Obstetrics and Gynecology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Toyomi Satoh
- Department of Obstetrics and Gynecology, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kohsei Tanaka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan.,Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Takashi Iwata
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo, Japan
| | - Akihiko Sekizawa
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan
| | - Koji Matsumoto
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo, Japan
| | - Iwao Kukimoto
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
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Czech-Sioli M, Günther T, Therre M, Spohn M, Indenbirken D, Theiss J, Riethdorf S, Qi M, Alawi M, Wülbeck C, Fernandez-Cuesta I, Esmek F, Becker JC, Grundhoff A, Fischer N. High-resolution analysis of Merkel Cell Polyomavirus in Merkel Cell Carcinoma reveals distinct integration patterns and suggests NHEJ and MMBIR as underlying mechanisms. PLoS Pathog 2020; 16:e1008562. [PMID: 32833988 PMCID: PMC7470373 DOI: 10.1371/journal.ppat.1008562] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 09/03/2020] [Accepted: 07/08/2020] [Indexed: 12/17/2022] Open
Abstract
Merkel Cell Polyomavirus (MCPyV) is the etiological agent of the majority of Merkel Cell Carcinomas (MCC). MCPyV positive MCCs harbor integrated, defective viral genomes that constitutively express viral oncogenes. Which molecular mechanisms promote viral integration, if distinct integration patterns exist, and if integration occurs preferentially at loci with specific chromatin states is unknown. We here combined short and long-read (nanopore) next-generation sequencing and present the first high-resolution analysis of integration site structure in MCC cell lines as well as primary tumor material. We find two main types of integration site structure: Linear patterns with chromosomal breakpoints that map closely together, and complex integration loci that exhibit local amplification of genomic sequences flanking the viral DNA. Sequence analysis suggests that linear patterns are produced during viral replication by integration of defective/linear genomes into host DNA double strand breaks via non-homologous end joining, NHEJ. In contrast, our data strongly suggest that complex integration patterns are mediated by microhomology-mediated break-induced replication, MMBIR. Furthermore, we show by ChIP-Seq and RNA-Seq analysis that MCPyV preferably integrates in open chromatin and provide evidence that viral oncogene expression is driven by the viral promoter region, rather than transcription from juxtaposed host promoters. Taken together, our data explain the characteristics of MCPyV integration and may also provide a model for integration of other oncogenic DNA viruses such as papillomaviruses.
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Affiliation(s)
- Manja Czech-Sioli
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Günther
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Marlin Therre
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Spohn
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Daniela Indenbirken
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Juliane Theiss
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
| | - Sabine Riethdorf
- Institute of Tumorbiology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Minyue Qi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Malik Alawi
- Bioinformatics Core, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Corinna Wülbeck
- Translational skin cancer research, German Cancer Consortium (DKTK), University Hospital Essen, Essen, Germany
| | - Irene Fernandez-Cuesta
- Institute of Nanostructure- and Solid State Physics (INF), Center for Hybrid Nanostructures (CHyN), University of Hamburg, Hamburg, Germany
| | - Franziska Esmek
- Institute of Nanostructure- and Solid State Physics (INF), Center for Hybrid Nanostructures (CHyN), University of Hamburg, Hamburg, Germany
| | - Jürgen C. Becker
- Translational skin cancer research, German Cancer Consortium (DKTK), University Hospital Essen, Essen, Germany
- Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | - Adam Grundhoff
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Hamburg, Germany
- * E-mail: (AG); (NF)
| | - Nicole Fischer
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- * E-mail: (AG); (NF)
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Xu X, Xing S, Xu M, Fu P, Gao T, Zhang X, Zhao Y, Zhao C. Highly sensitive and specific screening of EGFR mutation using a PNA microarray-based fluorometric assay based on rolling circle amplification and graphene oxide. RSC Adv 2019; 9:38298-38308. [PMID: 35540182 PMCID: PMC9075832 DOI: 10.1039/c9ra06758b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/16/2019] [Indexed: 01/23/2023] Open
Abstract
Screening epidermal growth factor receptor (EGFR) mutations, especially deletions, is essential for diagnosis of non-small cell lung cancer (NSCLC) and also critical to inform treatment decisions for NSCLC patients. Here, we demonstrated a facile peptide nucleic acid (PNA) microarray-based fluorometric method for sensitive and specific detection of EGFR mutation, using rolling circle amplification (RCA), graphene oxide (GO), and a fluorescently-labeled detection probe (F-DP). First, the EGFR gene sequence was efficiently captured by the label-free PNA probe which was attached on the surface of a 96-well plate. And then, the EGFR mutation sequence was specifically amplified by RCA using the circular DNA, which was formed by the ligation of the padlock probe when hybridizing with the EGFR mutation, as a template. The single-stranded RCA product (RCAP) was then sensitively detected with the F-DP and GO system. This method has a detection limit of 0.3 pM for EGFR mutation and a high discrimination capability to target EGFR mutation against EGFR wildtype. The use of a PNA microarray and a fluorescence quenching platform make this system quite suitable for high-throughput analysis of EGFR mutations in resource-limited settings without the need of costly and cumbersome equipment. Furthermore, this detection system provides a novel way for the diagnosis of other diseases that are caused by gene deletion mutations.
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Affiliation(s)
- Xiaojun Xu
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences Ningbo 315201 P. R. China
- Institute of Pharmaceutical Chemistry, Zhejiang Pharmaceutical College Ningbo 315100 P. R. China
| | - Shu Xing
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences Ningbo 315201 P. R. China
| | - Mengjia Xu
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences Ningbo 315201 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Pan Fu
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences Ningbo 315201 P. R. China
- University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Tingting Gao
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences Ningbo 315201 P. R. China
| | - Xiaokang Zhang
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences Ningbo 315201 P. R. China
| | - Yang Zhao
- College of Science and Technology, Ningbo University Ningbo 315212 P. R. China
| | - Chao Zhao
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences Ningbo 315201 P. R. China
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13
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Alkhilaiwi F, Paul S, Zhou D, Zhang X, Wang F, Palechor-Ceron N, Wilson K, Guha R, Ferrer M, Grant N, Thomas C, Schlegel R, Yuan H. High-throughput screening identifies candidate drugs for the treatment of recurrent respiratory papillomatosis. PAPILLOMAVIRUS RESEARCH 2019; 8:100181. [PMID: 31446060 PMCID: PMC6723410 DOI: 10.1016/j.pvr.2019.100181] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 07/23/2019] [Accepted: 08/21/2019] [Indexed: 12/29/2022]
Abstract
Recurrent respiratory papillomatosis (RRP) is a benign neoplasm of the larynx caused mainly by human papillomavirus type 6 or 11 and its standard treatment involves repeated surgical debulking of the laryngeal tumors. However, significant morbidity and occasional mortality due to multiple recurrences occur. Conditional reprogramming (CR) was used to establish a HPV-6 positive culture from an RRP patient, named GUMC-403. High-throughput screening was performed at the National Center for Advanced Technology (NCATS) to identify potential drugs to treat this rare but morbid disease. GUMC-403 cells were screened against the NPC library of >2800 approved drugs and the MIPE library of >1900 investigational drugs to identify new uses for FDA-approved drugs or drugs that have undergone significant research and development. From the two libraries, we identified a total of 13 drugs that induced significant cytotoxicity in RRP cells at IC50 values that were clinically achievable. We validated the efficacy of the drugs in vitro using CR 2D and 3D models and further refined our list of drugs to panobinostat, dinaciclib and forskolin as potential therapies for RRP patients.
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Affiliation(s)
- Faris Alkhilaiwi
- Department of Pathology, Georgetown University, Medical School, Washington DC, 20057, USA; Department of Oncology, Georgetown University, Medical School, Washington DC, 20057, USA; Department of Biochemistry and Molecular Biology, Georgetown University, Medical School, Washington DC, 20057, USA; College of Pharmacy, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Siddartha Paul
- Department of Pathology, Georgetown University, Medical School, Washington DC, 20057, USA
| | - Dan Zhou
- Department of Pathology, Georgetown University, Medical School, Washington DC, 20057, USA
| | - Xiaohu Zhang
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, USA
| | - Feibai Wang
- Department of Pathology, Georgetown University, Medical School, Washington DC, 20057, USA
| | - Nancy Palechor-Ceron
- Department of Pathology, Georgetown University, Medical School, Washington DC, 20057, USA
| | - Kelli Wilson
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, USA
| | - Rajarshi Guha
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, USA
| | - Marc Ferrer
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, USA
| | - Nazaneen Grant
- Department of Otolaryngology, Georgetown University, Medical School, Washington DC, 20057, USA
| | - Craig Thomas
- Division of Pre-Clinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, USA
| | - Richard Schlegel
- Department of Pathology, Georgetown University, Medical School, Washington DC, 20057, USA
| | - Hang Yuan
- Department of Pathology, Georgetown University, Medical School, Washington DC, 20057, USA.
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14
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Gupta SM, Mania-Pramanik J. Molecular mechanisms in progression of HPV-associated cervical carcinogenesis. J Biomed Sci 2019; 26:28. [PMID: 31014351 PMCID: PMC6477741 DOI: 10.1186/s12929-019-0520-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 04/11/2019] [Indexed: 12/13/2022] Open
Abstract
Cervical cancer is the fourth most frequent cancer in women worldwide and a major cause of mortality in developing countries. Persistent infection with high-risk human papillomavirus (HPV) is a necessary cause for the development of cervical cancer. In addition, genetic and epigenetic alterations in host cell genes are crucial for progression of cervical precancerous lesions to invasive cancer. Although much progress has been made in understanding the life cycle of HPV and it’s role in the development of cervical cancer, there is still a critical need for accurate surveillance strategies and targeted therapeutic options to eradicate these cancers in patients. Given the widespread nature of HPV infection and the type specificity of currently available HPV vaccines, it is crucial that molecular details of the natural history of HPV infection as well as the biological activities of viral oncoproteins be elucidated. A better understanding of the mechanisms involved in oncogenesis can provide novel insights and opportunities for designing effective therapeutic approaches against HPV-associated malignancies. In this review, we briefly summarize epigenetic alterations and events that cause alterations in host genomes inducing cell cycle deregulation, aberrant proliferation and genomic instability contributing to tumorigenesis.
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Affiliation(s)
- Sadhana M Gupta
- Department of Infectious Diseases Biology, National Institute for Research in Reproductive Health, J.M. Street, Parel, Mumbai, 400012, India.
| | - Jayanti Mania-Pramanik
- Department of Infectious Diseases Biology, National Institute for Research in Reproductive Health, J.M. Street, Parel, Mumbai, 400012, India
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15
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Schrama D, Sarosi EM, Adam C, Ritter C, Kaemmerer U, Klopocki E, König EM, Utikal J, Becker JC, Houben R. Characterization of six Merkel cell polyomavirus-positive Merkel cell carcinoma cell lines: Integration pattern suggest that large T antigen truncating events occur before or during integration. Int J Cancer 2019; 145:1020-1032. [PMID: 30873613 DOI: 10.1002/ijc.32280] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 02/06/2019] [Accepted: 03/11/2019] [Indexed: 12/16/2022]
Abstract
Merkel cell carcinoma (MCC), an aggressive neuroendocrine skin tumor, is a polyomavirus-induced human cancer. To study the causal relationship of MCC carcinogenesis with the integrated Merkel cell polyomavirus (MCPyV) in detail, well-characterized MCC cell lines are needed. Consequently, in the current study, we established and characterized six MCPyV-positive MCC cell lines. Microarray-based comparative genomic hybridization revealed a stable genome carrying only a limited number of chromosomal gains and deletions. All cell lines expressed MCC markers Keratin-20 and neuron-specific enolase as well as truncated MCPyV-encoded large T antigen (LT). For five cell lines, we were able to identify the MCPyV-integration sites in introns of different genes. The LT-truncating stop codon mutations and integration sites were affirmed in the respective clinical patient samples. Inverse PCR suggested that three of the cell lines contained MCPyV genomes as concatemers. This notion was confirmed for the two cell lines with known integration sites. Importantly, our observation of distinct stop codon mutations in cell lines with concatemeric MCPyV integration indicates that these LT-truncating mutations occur before integration. In summary, we provide the detailed characterization of six MCPyV-positive MCC cell lines, which are likely to serve as valuable tools in future MCC research.
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Affiliation(s)
- David Schrama
- Department of Dermatology, University Hospital Würzburg, Würzburg, Germany
| | - Eva-Maria Sarosi
- Department of Dermatology, University Hospital Würzburg, Würzburg, Germany
| | - Christian Adam
- Department of Dermatology, University Hospital Würzburg, Würzburg, Germany
| | - Cathrin Ritter
- Department of Translational Skin Cancer Research (tscr), University Hospital Essen, Essen, Germany.,German Cancer Consortium (DKTK/DKFZ), Heidelberg, Germany
| | - Ulrike Kaemmerer
- Department of Gynecology, University Hospital Würzburg, Würzburg, Germany
| | - Eva Klopocki
- Institute for Human Genetics, University of Würzburg, Würzburg, Germany
| | - Eva-Maria König
- Institute for Human Genetics, University of Würzburg, Würzburg, Germany
| | - Jochen Utikal
- Skin Cancer Unit, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Department of Dermatology, Venereology and Allergology, University Medical Center Mannheim, Ruprecht-Karl University of Heidelberg, Mannheim, Germany
| | - Jürgen C Becker
- Department of Translational Skin Cancer Research (tscr), University Hospital Essen, Essen, Germany.,German Cancer Consortium (DKTK/DKFZ), Heidelberg, Germany
| | - Roland Houben
- Department of Dermatology, University Hospital Würzburg, Würzburg, Germany
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16
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Helraiser intermediates provide insight into the mechanism of eukaryotic replicative transposition. Nat Commun 2018; 9:1278. [PMID: 29599430 PMCID: PMC5876387 DOI: 10.1038/s41467-018-03688-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 03/05/2018] [Indexed: 02/06/2023] Open
Abstract
Helitrons are eukaryotic DNA transposons that have profoundly affected genome variability via capture and mobilization of host genomic sequences. Defining their mode of action is therefore important for understanding how genome landscapes evolve. Sequence similarities with certain prokaryotic mobile elements suggest a “rolling circle” mode of transposition, involving only a single transposon strand. Using the reconstituted Helraiser transposon to study Helitron transposition in cells and in vitro, we show that the donor site must be double-stranded and that single-stranded donors will not suffice. Nevertheless, replication and integration assays demonstrate the use of only one of the transposon donor strands. Furthermore, repeated reuse of Helraiser donor sites occurs following DNA synthesis. In cells, circular double-stranded intermediates that serve as transposon donors are generated and replicated by Helraiser transposase. Cell-free experiments demonstrate strand-specific cleavage and strand transfer, supporting observations made in cells. Helitrons are eukaryotic DNA transposons that have profoundly affected genome variation due to their ability to capture and mobilize host genomic fragments. Here the authors provide insight into the mechanism of action of these transposons both in cells and in vitro.
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17
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Viral DNA Replication Orientation and hnRNPs Regulate Transcription of the Human Papillomavirus 18 Late Promoter. mBio 2017; 8:mBio.00713-17. [PMID: 28559488 PMCID: PMC5449659 DOI: 10.1128/mbio.00713-17] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The life cycle of human papillomaviruses (HPVs) is tightly linked to keratinocyte differentiation. Although expression of viral early genes is initiated immediately upon virus infection of undifferentiated basal cells, viral DNA amplification and late gene expression occur only in the mid to upper strata of the keratinocytes undergoing terminal differentiation. In this report, we show that the relative activity of HPV18 TATA-less late promoter P811 depends on its orientation relative to that of the origin (Ori) of viral DNA replication and is sensitive to the eukaryotic DNA polymerase inhibitor aphidicolin. Additionally, transfected 70-nucleotide (nt)-long single-strand DNA oligonucleotides that are homologous to the region near Ori induce late promoter activity. We also found that promoter activation in raft cultures leads to production of the late promoter-associated, sense-strand transcription initiation RNAs (tiRNAs) and splice-site small RNAs (spliRNAs). Finally, a cis-acting AAGTATGCA core element that functions as a repressor to the promoter was identified. This element interacts with hnRNP D0B and hnRNP A/B factors. Point mutations in the core prevented binding of hnRNPs and increased the promoter activity. Confirming this result, knocking down the expression of both hnRNPs in keratinocytes led to increased promoter activity. Taking the data together, our study revealed the mechanism of how the HPV18 late promoter is regulated by DNA replication and host factors. It has been known for decades that the activity of viral late promoters is associated with viral DNA replication among almost all DNA viruses. However, the mechanism of how DNA replication activates the viral late promoter and what components of the replication machinery are involved remain largely unknown. In this study, we characterized the P811 promoter region of HPV18 and demonstrated that its activation depends on the orientation of DNA replication. Using single-stranded oligonucleotides targeting the replication fork on either leading or lagging strands, we showed that viral lagging-strand replication activates the promoter. We also identified a transcriptional repressor element located upstream of the promoter transcription start site which interacts with cellular proteins hnRNP D0B and hnRNP A/B and modulates the late promoter activity. This is the first report on how DNA replication activates a viral late promoter.
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18
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Senapati R, Senapati NN, Dwibedi B. Molecular mechanisms of HPV mediated neoplastic progression. Infect Agent Cancer 2016; 11:59. [PMID: 27933097 PMCID: PMC5123406 DOI: 10.1186/s13027-016-0107-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 11/05/2016] [Indexed: 12/15/2022] Open
Abstract
Human Papillomavirus is the major etiological agent in the development of cervical cancer but not a sufficient cause. Despite significant research, the underlying mechanisms of progression from a low-grade squamous intraepithelial lesion to high grade squamous intraepithelial lesion are yet to be understood. Deregulation of viral gene expression and host genomic instability play a central role in virus-mediated carcinogenesis. Key events such as viral integration and epigenetic modifications may lead to the deregulation of viral and host gene expression. This review has summarized the available literature to describe the possible mechanism and role of viral integration in mediating carcinogenesis. HPV integration begins with DNA damage or double strand break induced either by oxidative stress or HPV proteins and the subsequent steps are driven by the DNA damage responses. Inflammation and oxidative stress could be considered as cofactors in stimulating viral integration and deregulation of cellular and viral oncogenes during the progression of cervical carcinoma. All these events together with the host and viral genetic and epigenetic modifications in neoplastic progression have also been reviewed which may be relevant in identifying a new preventive therapeutic strategy. In the absence of therapeutic intervention for HPV-infected individuals, future research focus should be directed towards preventing and reversing of HPV integration. DNA damage response, knocking out integrated HPV sequences, siRNA approach, modulating the selection mechanism of cells harboring integrated genomes and epigenetic modifiers are the possible therapeutic targets.
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Affiliation(s)
- Rashmirani Senapati
- Virology Division, Regional Medical Research centre (ICMR), Nalco square, Chandrasekharpur, Bhubaneswar, 751023 Odisha India
| | | | - Bhagirathi Dwibedi
- Virology Division, Regional Medical Research centre (ICMR), Nalco square, Chandrasekharpur, Bhubaneswar, 751023 Odisha India
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19
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Mori S, Kusumoto-Matsuo R, Ishii Y, Takeuchi T, Kukimoto I. Replication interference between human papillomavirus types 16 and 18 mediated by heterologous E1 helicases. Virol J 2014; 11:11. [PMID: 24456830 PMCID: PMC3904167 DOI: 10.1186/1743-422x-11-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 01/21/2014] [Indexed: 11/20/2022] Open
Abstract
Background Co-infection of multiple genotypes of human papillomavirus (HPV) is commonly observed among women with abnormal cervical cytology, but how different HPVs interact with each other in the same cell is not clearly understood. A previous study using cultured keratinocytes revealed that genome replication of one HPV type is inhibited by co-existence of the genome of another HPV type, suggesting that replication interference occurs between different HPV types when co-infected; however, molecular mechanisms underlying inter-type replication interference have not been fully explored. Methods Replication interference between two most prevalent HPV types, HPV16 and HPV18, was examined in HPV-negative C33A cervical carcinoma cells co-transfected with genomes of HPV16 and HPV18 together with expression plasmids for E1/E2 of both types. Levels of HPV16/18 genome replication were measured by quantitative real-time PCR. Physical interaction between HPV16/18 E1s was assessed by co-immunoprecipitation assays in the cell lysates. Results The replication of HPV16 and HPV18 genomes was suppressed by co-expression of E1/E2 of heterologous types. The interference was mediated by the heterologous E1, but not E2. The oligomerization domain of HPV16 E1 was essential for HPV18 replication inhibition, whereas the helicase domain was dispensable. HPV16 E1 co-precipitated with HPV18 E1 in the cell lysates, and an HPV16 E1 mutant Y379A, which bound to HPV18 E1 less efficiently, failed to inhibit HPV18 replication. Conclusions Co-infection of a single cell with both HPV16 and HPV18 results in replication interference between them, and physical interaction between the heterologous E1s is responsible for the interference. Heterooligomers composed of HPV16/18 E1s may lack the ability to support HPV genome replication.
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Affiliation(s)
- Seiichiro Mori
- Pathogen Genomics Center, National Institute of Infectious Diseases, 4-7-1 Gakuen, Musashi-murayama, Tokyo 208-0011, Japan.
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20
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Shin HJ, Joo J, Yoon JH, Yoo CW, Kim JY. Physical status of human papillomavirus integration in cervical cancer is associated with treatment outcome of the patients treated with radiotherapy. PLoS One 2014; 9:e78995. [PMID: 24427262 PMCID: PMC3888442 DOI: 10.1371/journal.pone.0078995] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 09/25/2013] [Indexed: 12/01/2022] Open
Abstract
Integration of human papillomavirus (HPV) DNA into the host genome is a critical aetiological event in the progression from normal cervix to intraepithelial neoplasm, and finally to invasive cervical cancer. However, there has been little work on how HPV integration status relates to treatment outcome for cervical carcinomas. In the current study, HPV E2 and E6 gene copy numbers were measured in 111 cervical cancer tissues using real-time QPCR. Integration patterns were divided into four groups: single copy-integrated with episomal components (group 1), single copy-integrated without episomal components (group 2), multicopy tandem repetition-integrated (group 3), and low HPV (group 4) groups. A relapse-predicting model was constructed using multivariable Cox proportional hazards model to classify patients into different risk groups for disease-free survival (DFS). The model was internally validated using bootstrap resampling. Oligonucleotide microarray analysis was performed to evaluate gene expression patterns in relation to the different integration groups. DFS rate was inferior in the order of the patients in group 4, group 2/3, and group 1. Multivariate analysis showed that histologic grade, clinical stage group, and integration pattern were significant prognostic factors for poor DFS. The current prognostic model accurately predicted the risk of relapse, with an area under the receiver operating characteristic curve (AUC) of 0.74 (bootstrap corrected, 0.71). In conclusion, these data suggest that HPV integration pattern is a potent prognostic factor for tailored treatment of cervical cancer.
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Affiliation(s)
- Hye-Jin Shin
- Radiation Medicine Branch, Research Institute and Hospital, National Cancer Center, Goyang, Korea
| | - Jungnam Joo
- Biometric Research Branch, Research Institute and Hospital, National Cancer Center, Goyang, Korea
| | - Ji Hyun Yoon
- Department of Microbiology & Immunology, McGill University, Montreal, Quebec, Canada
| | - Chong Woo Yoo
- Center for Uterine Cancer, Research Institute and Hospital, National Cancer Center, Goyang, Korea
| | - Joo-Young Kim
- Radiation Medicine Branch, Research Institute and Hospital, National Cancer Center, Goyang, Korea
- * E-mail:
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21
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Nakahara T, Kiyono T. [Regulation of human papillomavirus (HPV) genome replication in the viral life cycle and its association with the viral persistence and cancer development]. Uirusu 2014; 64:57-66. [PMID: 25765981 DOI: 10.2222/jsv.64.57] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
High-risk human papillomavirus (HR-HPV) infections account for more than 5% of all cancers (11% in women) such as cervical cancer worldwide. HPVs infect to basal cells of the stratified squamous epithelium and establish persistent infection within the basal compartment. HR-HPV infections can persist more than a decade, leading to development of cancers. The life cycle of HPVs is tightly associated with the differentiation processes of the stratified squamous epithelium; the replication of the viral genome and the expression of the viral genes are strictly regulated depending on differentiation of the host keratinocytes. The viral genome is transiently amplified immediately following infection and then maintained at constant copy numbers in the basal cells. In terminally differentiating keratinocytes, the viral genome is drastically amplified. However, molecular mechanisms underlying switching these three stages of viral genome replication in the viral life cycle are poorly understood. Recently, it has become evident that DNA damage response pathways are involved in the regulation of HPV genome replication. In this review, we would like to introduce recent findings describing the associations of DNA damage response with HPV genome replication.
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Affiliation(s)
- Tomomi Nakahara
- National Cancer Center Research Institute, Division of Virology
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22
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Polyomavirus large T antigen binds symmetrical repeats at the viral origin in an asymmetrical manner. J Virol 2013; 87:13751-9. [PMID: 24109229 DOI: 10.1128/jvi.01740-13] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Polyomaviruses have repeating sequences at their origins of replication that bind the origin-binding domain of virus-encoded large T antigen. In murine polyomavirus, the central region of the origin contains four copies (P1 to P4) of the sequence G(A/G)GGC. They are arranged as a pair of inverted repeats with a 2-bp overlap between the repeats at the center. In contrast to simian virus 40 (SV40), where the repeats are nonoverlapping and all four repeats can be simultaneously occupied, the crystal structure of the four central murine polyomavirus sequence repeats in complex with the polyomavirus origin-binding domain reveals that only three of the four repeats (P1, P2, and P4) are occupied. Isothermal titration calorimetry confirms that the stoichiometry is the same in solution as in the crystal structure. Consistent with these results, mutation of the third repeat has little effect on DNA replication in vivo. Thus, the apparent 2-fold symmetry within the DNA repeats is not carried over to the protein-DNA complex. Flanking sequences, such as the AT-rich region, are known to be important for DNA replication. When the orientation of the central region was reversed with respect to these flanking regions, the origin was still able to replicate and the P3 sequence (now located at the P2 position with respect to the flanking regions) was again dispensable. This highlights the critical importance of the precise sequence of the region containing the pentamers in replication.
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23
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Chen WG, Yang CM, Xu LH, Zhang N, Liu XY, Ma YG, Huo XL, Han YS, Tian DA, Zheng Y. Detection of human papilloma virus in esophageal cancer in Xinjiang Kazakh patients by general primer-mediated polymerase chain reaction. Shijie Huaren Xiaohua Zazhi 2012; 20:1049-1053. [DOI: 10.11569/wcjd.v20.i12.1049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To detect human papillomavirus (HPV) in esophageal squamous cell carcinoma (ESCC) in Xinjiang Kazakh patients by universal primer-mediated nested PCR to investigate the relationship between HPV infection and ESCC.
METHODS: DNA was isolated from ESCC and healthy esophageal mucosal specimens from Xinjiang Kazakh adults and used to amplify HPV using universal primers HPV MY09/11 and HPV-specific primers HPV G5+/6+ by nested PCR. The rate of HPV infection was then calculated.
RESULTS: The rate of HPV infection was 66.67% in the ESCC group and 12.12% in the healthy control group.
CONCLUSION: HPV infection may be involved in the development of ESCC in Xinjiang Kazakh adults. Universal primer-mediated nested PCR is a convenient and reliable method for detection of HPV-DNA.
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De-Castro Arce J, Göckel-Krzikalla E, Rösl F. Silencing of multi-copy HPV16 by viral self-methylation and chromatin occlusion: a model for epigenetic virus-host interaction. Hum Mol Genet 2011; 21:1693-705. [PMID: 22210627 DOI: 10.1093/hmg/ddr604] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
In the present study, we used the human papillomavirus type 16 (HPV16)-positive cervical carcinoma cell line CaSki as a paradigmatic model to understand epigenetic silencing of viral multi-copy genomes. We show that most of the hypermethylated HPV16 copies are kept as 'occluded' chromatin that defines a condition where genes were refractory in their response to trans-acting transcription factors and to external reactivation efforts. This provides the first example that viral genomes are silenced by such a host cell mechanism, hitherto only known for endogenous genes to preserve a stable and robust phenotype. Moreover, considering an adaptive cross-talk between viral proteins and the epigenetic modification machinery, we demonstrate that particularly E2-but also ectopically delivered E6/E7-can induce significant de novo methylation within the enhancer and, to a less extent, within the promoter region. These data suggest that under certain physiological conditions, HPV can down-regulate its own gene expression, regardless of the presence of transcriptional activators. We propose that self-methylation of multi-copy HPV could be the first event prior to heterochromatin formation. These processes favour an 'occluded' chromatin conformation, finally being unresponsive to transcriptional activation. The shift from potentially competent heterochromatin towards an occluded state is basically irreversible, possibly using the same mechanism described for lineage differentiation. Along this line, it is tempting to speculate that virus-cell interaction is able to 'sense' viral copy number and down-regulates excess of gene activity in order to guarantee cell viability.
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Affiliation(s)
- Johanna De-Castro Arce
- Division of Viral Transformation Mechanisms, Research Program: Infections and Cancer, Deutsches Krebsforschungszentrum, Heidelberg D-69120, Germany
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25
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Nikitin PA, Luftig MA. At a crossroads: human DNA tumor viruses and the host DNA damage response. Future Virol 2011; 6:813-830. [PMID: 21927617 DOI: 10.2217/fvl.11.55] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Human DNA tumor viruses induce host cell proliferation in order to establish the necessary cellular milieu to replicate viral DNA. The consequence of such viral-programmed induction of proliferation coupled with the introduction of foreign replicating DNA structures makes these viruses particularly sensitive to the host DNA damage response machinery. In fact, sensors of DNA damage are often activated and modulated by DNA tumor viruses in both latent and lytic infection. This article focuses on the role of the DNA damage response during the life cycle of human DNA tumor viruses, with a particular emphasis on recent advances in our understanding of the role of the DNA damage response in EBV, Kaposi's sarcoma-associated herpesvirus and human papillomavirus infection.
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Affiliation(s)
- Pavel A Nikitin
- Department of Molecular Genetics & Microbiology, Center for Virology, Duke University Medical Center, Durham, NC, 27708 USA
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