-
BMC Medical Genomics Jun 2022Hepatitis B virus (HBV) related hepatocellular carcinoma (HCC) is heterogeneous and frequently contains multifocal tumors, but how the multifocal tumors relate to each...
BACKGROUND
Hepatitis B virus (HBV) related hepatocellular carcinoma (HCC) is heterogeneous and frequently contains multifocal tumors, but how the multifocal tumors relate to each other in terms of HBV integration and other genomic patterns is not clear.
METHODS
To interrogate heterogeneity of HBV-HCC, we developed a HBV genome enriched single cell sequencing (HGE-scSeq) procedure and a computational method to identify HBV integration sites and infer DNA copy number variations (CNVs).
RESULTS
We performed HGE-scSeq on 269 cells from four tumor sites and two tumor thrombi of a HBV-HCC patient. HBV integrations were identified in 142 out of 269 (53%) cells sequenced, and were enriched in two HBV integration hotspots chr1:34,397,059 (CSMD2) and chr8:118,557,327 (MED30/EXT1). There were also 162 rare integration sites. HBV integration sites were enriched in DNA fragile sites and sequences around HBV integration sites were enriched for microhomologous sequences between human and HBV genomes. CNVs were inferred for each individual cell and cells were grouped into four clonal groups based on their CNVs. Cells in different clonal groups had different degrees of HBV integration heterogeneity. All of 269 cells carried chromosome 1q amplification, a recurrent feature of HCC tumors, suggesting that 1q amplification occurred before HBV integration events in this case study. Further, we performed simulation studies to demonstrate that the sequential events (HBV infecting transformed cells) could result in the observed phenotype with biologically reasonable parameters.
CONCLUSION
Our HGE-scSeq data reveals high heterogeneity of HCC tumor cells in terms of both HBV integrations and CNVs. There were two HBV integration hotspots across cells, and cells from multiple tumor sites shared some HBV integration and CNV patterns.
Topics: Carcinoma, Hepatocellular; DNA Copy Number Variations; DNA, Viral; Hepatitis B virus; Humans; Liver Neoplasms; Virus Integration
PubMed: 35710421
DOI: 10.1186/s12920-022-01264-2 -
Nature Communications May 2022A multimer of retroviral integrase (IN) synapses viral DNA ends within a stable intasome nucleoprotein complex for integration into a host cell genome. Reconstitution of...
A multimer of retroviral integrase (IN) synapses viral DNA ends within a stable intasome nucleoprotein complex for integration into a host cell genome. Reconstitution of the intasome from the maedi-visna virus (MVV), an ovine lentivirus, revealed a large assembly containing sixteen IN subunits. Herein, we report cryo-EM structures of the lentiviral intasome prior to engagement of target DNA and following strand transfer, refined at 3.4 and 3.5 Å resolution, respectively. The structures elucidate details of the protein-protein and protein-DNA interfaces involved in lentiviral intasome formation. We show that the homomeric interfaces involved in IN hexadecamer formation and the α-helical configuration of the linker connecting the C-terminal and catalytic core domains are critical for MVV IN strand transfer activity in vitro and for virus infectivity. Single-molecule microscopy in conjunction with photobleaching reveals that the MVV intasome can bind a variable number, up to sixteen molecules, of the lentivirus-specific host factor LEDGF/p75. Concordantly, ablation of endogenous LEDGF/p75 results in gross redistribution of MVV integration sites in human and ovine cells. Our data confirm the importance of the expanded architecture observed in cryo-EM studies of lentiviral intasomes and suggest that this organization underlies multivalent interactions with chromatin for integration targeting to active genes.
Topics: Animals; Humans; Catalytic Domain; DNA, Viral; Integrases; Lentivirus; Models, Molecular; Retroviridae; Sheep; Virus Integration
PubMed: 35504909
DOI: 10.1038/s41467-022-29928-8 -
Cells Feb 2022HIV-1 integrase and capsid proteins interact with host proteins to direct preintegration complexes to active transcription units within gene-dense regions of chromosomes...
HIV-1 integrase and capsid proteins interact with host proteins to direct preintegration complexes to active transcription units within gene-dense regions of chromosomes for viral DNA integration. Analyses of spatially-derived genomic DNA coordinates, such as nuclear speckle-associated domains, lamina-associated domains, super enhancers, and Spatial Position Inference of the Nuclear (SPIN) genome states, have further informed the mechanisms of HIV-1 integration targeting. Critically, however, these different types of genomic coordinates have not been systematically analyzed to synthesize a concise description of the regions of chromatin that HIV-1 prefers for integration. To address this informational gap, we have extensively correlated genomic DNA coordinates of HIV-1 integration targeting preferences. We demonstrate that nuclear speckle-associated and speckle-proximal chromatin are highly predictive markers of integration and that these regions account for known HIV biases for gene-dense regions, highly transcribed genes, as well as the mid-regions of gene bodies. In contrast to a prior report that intronless genes were poorly targeted for integration, we find that intronless genes in proximity to nuclear speckles are more highly targeted than are spatially-matched intron-containing genes. Our results additionally highlight the contributions of capsid and integrase interactions with respective CPSF6 and LEDGF/p75 host factors in these HIV-1 integration targeting preferences.
Topics: Capsid; Capsid Proteins; Chromatin; HIV-1; Host-Pathogen Interactions; Virus Integration
PubMed: 35203306
DOI: 10.3390/cells11040655 -
Viruses May 2022Bacteriophages are obligatory parasites propagating in bacterial hosts in a lytic or lysogenic/pseudolysogenic cycle [...].
Bacteriophages are obligatory parasites propagating in bacterial hosts in a lytic or lysogenic/pseudolysogenic cycle [...].
Topics: Bacteria; Bacteriophages; Lysogeny
PubMed: 35632795
DOI: 10.3390/v14051054 -
Virologie (Montrouge, France) Aug 2019Human immunodeficiency virus (HIV-1) latency is clinically highlighting via the persistence of a residual viral load in cART-treated patients due to the reactivation of... (Review)
Review
Human immunodeficiency virus (HIV-1) latency is clinically highlighting via the persistence of a residual viral load in cART-treated patients due to the reactivation of cellular reservoirs. Two forms of latency coexist but the contribution of the pre-integrationnal latency clearly plays a minor role in viral persistence. In contrast, the post-integrationnal latency significantly contributes to the evasion of the immune system by the HIV-1 cellular reservoir and consequently to HIV-1 pathogenesis. Although post-transcriptional mechanisms can contribute to the maintenance of viral latency, HIV-1 transcriptional inhibition is critical for the establishment and maintenance of post-integrational latency. This inhibition is a multifactorial phenomenon, making the development of anti-latency therapeutic strategies complex. These different notions will be described throughout this review.
Topics: CD4-Positive T-Lymphocytes; Chromatin Assembly and Disassembly; DNA Methylation; Disease Reservoirs; HIV Infections; HIV-1; Histone Code; Humans; Immune Evasion; Immunologic Memory; Macrophages; Monocytes; Nucleosomes; Proviruses; Signal Transduction; Transcription Factors; Transcription, Genetic; Viral Load; Virus Activation; Virus Integration; Virus Latency; tat Gene Products, Human Immunodeficiency Virus
PubMed: 31414658
DOI: 10.1684/vir.2019.0782 -
Biochemical and Biophysical Research... May 2021Hepatitis B virus (HBV) DNA integration is closely related to the occurrence of liver cancer. However, current studies mostly focus on the detection of the viral...
Hepatitis B virus (HBV) DNA integration is closely related to the occurrence of liver cancer. However, current studies mostly focus on the detection of the viral integration sites, ignoring the relationship between the frequency of viral integration and liver cancer. Thus, this study uses previous data to distinguish the breakpoints according to the integration frequency and analyzes the characteristics of different groups. This analysis revealed that three sets of breakpoints were characterized by its own integrated sample frequency, breakpoint distribution, and affected gene pathways. This result indicated an evolution in the virus integration sites in the process of tumor formation and development. Therefore, our research clarified the characteristics and differences in the sites of viral integration in tumors and adjacent tissues, and clarified the key signaling pathways affected by viral integration. Hence, these findings might be of great significance in the understanding of the role of viral integration frequency in hepatocellular carcinoma.
Topics: Carcinogenesis; Carcinoma, Hepatocellular; Case-Control Studies; Chromosome Breakpoints; Gene Frequency; Hepatitis B virus; Humans; Liver Neoplasms; Signal Transduction; Virus Integration
PubMed: 33773138
DOI: 10.1016/j.bbrc.2021.03.056 -
Viruses May 2020Three decades of extensive work in the HIV field have revealed key viral and host cell factors controlling proviral transcription. Various models of transcriptional... (Review)
Review
Three decades of extensive work in the HIV field have revealed key viral and host cell factors controlling proviral transcription. Various models of transcriptional regulation have emerged based on the collective information from in vitro assays and work in both immortalized and primary cell-based models. Here, we provide a recount of the past and current literature, highlight key regulatory aspects, and further describe potential limitations of previous studies. We particularly delve into critical steps of HIV gene expression including the role of the integration site, nucleosome positioning and epigenomics, and the transition from initiation to pausing and pause release. We also discuss open questions in the field concerning the generality of previous regulatory models to the control of HIV transcription in patients under suppressive therapy, including the role of the heterogeneous integration landscape, clonal expansion, and bottlenecks to eradicate viral persistence. Finally, we propose that building upon previous discoveries and improved or yet-to-be discovered technologies will unravel molecular mechanisms of latency establishment and reactivation in a "new era".
Topics: Anti-Retroviral Agents; Epigenesis, Genetic; Gene Expression Regulation, Viral; HIV Infections; HIV-1; Humans; Proviruses; Transcription, Genetic; Virus Integration; Virus Latency
PubMed: 32443452
DOI: 10.3390/v12050555 -
Med (New York, N.Y.) Jun 2023The majority of oncogenic viruses are capable of integrating into the host genome, posing significant challenges to clinical control. Recent conceptual and technological...
The majority of oncogenic viruses are capable of integrating into the host genome, posing significant challenges to clinical control. Recent conceptual and technological advances, however, offer promising clinical applications. Here, we summarize the advances in our understanding of oncogenic viral integration, their clinical relevance, and the future perspectives.
Topics: Oncogenic Viruses; Genome; Virus Integration
PubMed: 37301195
DOI: 10.1016/j.medj.2023.04.007 -
Nucleic Acids Research Jan 2021The integration of retroviral reverse transcripts into the chromatin of the cells that they infect is required for virus replication. Retroviral integration has... (Review)
Review
The integration of retroviral reverse transcripts into the chromatin of the cells that they infect is required for virus replication. Retroviral integration has far-reaching consequences, from perpetuating deadly human diseases to molding metazoan evolution. The lentivirus human immunodeficiency virus 1 (HIV-1), which is the causative agent of the AIDS pandemic, efficiently infects interphase cells due to the active nuclear import of its preintegration complex (PIC). To enable integration, the PIC must navigate the densely-packed nuclear environment where the genome is organized into different chromatin states of varying accessibility in accordance with cellular needs. The HIV-1 capsid protein interacts with specific host factors to facilitate PIC nuclear import, while additional interactions of viral integrase, the enzyme responsible for viral DNA integration, with cellular nuclear proteins and nucleobases guide integration to specific chromosomal sites. HIV-1 integration favors transcriptionally active chromatin such as speckle-associated domains and disfavors heterochromatin including lamina-associated domains. In this review, we describe virus-host interactions that facilitate HIV-1 PIC nuclear import and integration site targeting, highlighting commonalities among factors that participate in both of these steps. We moreover discuss how the nuclear landscape influences HIV-1 integration site selection as well as the establishment of active versus latent virus infection.
Topics: Active Transport, Cell Nucleus; Adaptor Proteins, Signal Transducing; Capsid Proteins; Cell Nucleus; Chromatin; Cytoplasm; Cytoskeletal Proteins; HIV Reverse Transcriptase; HIV-1; Host-Pathogen Interactions; Human Immunodeficiency Virus Proteins; Humans; Interphase; Models, Molecular; Multiprotein Complexes; Nuclear Pore; Nuclear Proteins; Protein Conformation; Protein Domains; Transcription Factors; Virus Integration; Virus Latency; Virus Replication; mRNA Cleavage and Polyadenylation Factors
PubMed: 33337475
DOI: 10.1093/nar/gkaa1207 -
MSphere Feb 2022Modern sequencing technologies have provided insight into the genetic diversity of numerous species, including the human pathogen Pseudomonas aeruginosa. Bacterial...
Modern sequencing technologies have provided insight into the genetic diversity of numerous species, including the human pathogen Pseudomonas aeruginosa. Bacterial genomes often harbor bacteriophage genomes (prophages), which can account for upwards of 20% of the genome. Prior studies have found P. aeruginosa prophages that contribute to their host's pathogenicity and fitness. These advantages come in many different forms, including the production of toxins, promotion of biofilm formation, and displacement of other P. aeruginosa strains. While several different genera and species of P. aeruginosa prophages have been studied, there has not been a comprehensive study of the overall diversity of P. aeruginosa-infecting prophages. Here, we present the results of just such an analysis. A total of 6,852 high-confidence prophages were identified from 5,383 P. aeruginosa genomes from strains isolated from the human body and other environments. In total, 3,201 unique prophage sequences were identified. While 53.1% of these prophage sequences displayed sequence similarity to publicly available phage genomes, novel and highly mosaic prophages were discovered. Among these prophages, there is extensive diversity, including diversity within the functionally conserved integrase and C repressor coding regions, two genes responsible for prophage entering and persisting through the lysogenic life cycle. Analysis of integrase, C repressor, and terminase coding regions revealed extensive reassortment among P. aeruginosa prophages. This catalog of P. aeruginosa prophages provides a resource for future studies into the evolution of the species. Prophages play a critical role in the evolution of their host species and can also contribute to the virulence and fitness of pathogenic species. Here, we conducted a comprehensive investigation of prophage sequences from 5,383 publicly available Pseudomonas aeruginosa genomes from human as well as environmental isolates. We identified a diverse population of prophages, including tailed phages, inoviruses, and microviruses; 46.9% of the prophage sequences found share no significant sequence similarity with characterized phages, representing a vast array of novel P. aeruginosa-infecting phages. Our investigation into these prophages found substantial evidence of reassortment. In producing this, the first catalog of P. aeruginosa prophages, we uncovered both novel prophages as well as genetic content that have yet to be explored.
Topics: Bacteriophages; Integrases; Lysogeny; Prophages; Pseudomonas aeruginosa
PubMed: 35196122
DOI: 10.1128/msphere.01015-21