Distribution and fate of HIV-1 unintegrated DNA species: a comprehensive update

Hamid, Faysal Bin; Kim, Jin-Sun; Shin, Cha‐Gyun

doi:10.1186/s12981-016-0127-6

Cited by 35 publications

(27 citation statements)

References 80 publications

(150 reference statements)

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“…Our observation of vRNA/vDNA clusters in cells infected by an integration-defective virus or upon inhibition of integration further suggests that most of the vDNA in nuclear clusters may be unintegrated. This dovetails with the common observation of large amounts of unintegrated viral DNA in the nucleus, which can act as viral reservoirs and constitute an important obstacle to successful treatment of HIV-1 infection (Bell et al, 2001;Hamid et al, 2017;Gelderblom et al, 2008). Thus, the unintegrated vDNA observed in our study may be relevant to understanding HIV reactivation in patients.…”

Section: Discussionsupporting

confidence: 76%

Clustering and reverse transcription of HIV-1 genomes in nuclear niches of macrophages

Rensen

Mueller

Scoca

et al. 2020

Preprint

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In order to replicate, the Human Immunodeficiency Virus (HIV-1) reverse transcribes its RNA genome into DNA, which subsequently integrates into host cell chromosomes.These two key events of the viral life cycle are commonly viewed as separate not only in time but also in cellular space, since reverse transcription (RT) is thought to be completed in the cytoplasm before nuclear import and integration. However, the spatiotemporal organization of the early replication cycle in macrophages, natural nondividing target cells that constitute reservoirs of HIV-1 and an obstacle to curing AIDS, remains unclear. Here, we demonstrate that infected macrophages display large nuclear foci of viral DNA and viral RNA, in which multiple genomes cluster together.These clusters form in the absence of chromosomal integration, sequester the paraspeckle protein CPSF6 and localize to nuclear speckles. Strikingly, we show that viral RNA clusters consist mostly of genomic, incoming RNA, both in cells where RT is pharmacologically suppressed and in untreated cells. We demonstrate that, after temporary inhibition of RT, RT can resume in the nucleus and lead to vDNA accumulation in these clusters. We further show that nuclear RT can result in transcription competent viral DNA. These findings change our understanding of the early HIV-1 replication cycle, and may have implications for understanding HIV-1 persistence.

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Section: Discussionsupporting

confidence: 76%

Clustering and reverse transcription of HIV-1 genomes in nuclear niches of macrophages

Rensen

Mueller

Scoca

et al. 2020

Preprint

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“…Similarly, higher levels of 2-LTR circles were reported in cells lacking LEDGF/p75 infected with a class I integrase mutant HIV-1 than with a wild type integrase virus in the presence of a strand transfer inhibitor, despite that integration was equivalently inhibited [ 15 ]. 3′ processing has also been shown to decrease the stability of unintegrated linear HIV cDNA in cells expressing LEDGF/p75 [ 39 , 40 ], indicating that this degradation mechanism is not the result of LEDGF/p75 deficiency and operates under normal circumstances. For example, in LEDGF/p75-expressing cells the junctions of 2-LTR circles formed in the presence of integrase inhibitors targeting the LEDGF/p75 binding site in integrase (LEDGINs), that affect both 3′ processing and strand transfer [ 41 ], contain significantly less deletions than the circles formed in the presence of strand transfer inhibitors [ 42 ].…”

Section: Discussionmentioning

confidence: 99%

LEDGF/p75 Deficiency Increases Deletions at the HIV-1 cDNA Ends

Bueno¹,

Reyes²,

Llano³

2017

Viruses

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Processing of unintegrated linear HIV-1 cDNA by the host DNA repair system results in its degradation and/or circularization. As a consequence, deficient viral cDNA integration generally leads to an increase in the levels of HIV-1 cDNA circles containing one or two long terminal repeats (LTRs). Intriguingly, impaired HIV-1 integration in LEDGF/p75-deficient cells does not result in a correspondent increase in viral cDNA circles. We postulate that increased degradation of unintegrated linear viral cDNA in cells lacking the lens epithelium-derived growth factor (LEDGF/p75) account for this inconsistency. To evaluate this hypothesis, we characterized the nucleotide sequence spanning 2-LTR junctions isolated from LEDGF/p75-deficient and control cells. LEDGF/p75 deficiency resulted in a significant increase in the frequency of 2-LTRs harboring large deletions. Of note, these deletions were dependent on the 3′ processing activity of integrase and were not originated by aberrant reverse transcription. Our findings suggest a novel role of LEDGF/p75 in protecting the unintegrated 3′ processed linear HIV-1 cDNA from exonucleolytic degradation.

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“…Reverse transcription is initiated within hours of infection by viral RT binding to host tRNA; HIV uses tRNA strand Lys3. Reverse transcription produces linear cDNA products with long-terminal repeats (LTR) on both ends of the DNA strand (Hamid et al, 2017) (Fig 1d).…”

Section: Hiv Reverse Transcriptionmentioning

confidence: 99%

“…As mentioned above, the linear cDNA produced by RT can integrate and be transcribed into viral mRNA. The circular cDNA can undergo an abortive integration process and accumulate within the infected cell, predominantly within the nucleus (Hamid et al, 2017) (Fig 1d). Circular cDNA can have multiple forms such as 2-LTR circles formed by nonhomologous end joining (NHEJ), or 1-LTR circles formed by defective RT, re-arrangement, or homologous recombination (Farnet and Haseltine, 1991;Hamid et al, 2017).…”

Section: Pre-integration Latencymentioning

confidence: 99%

“…The circular cDNA can undergo an abortive integration process and accumulate within the infected cell, predominantly within the nucleus (Hamid et al, 2017) (Fig 1d). Circular cDNA can have multiple forms such as 2-LTR circles formed by nonhomologous end joining (NHEJ), or 1-LTR circles formed by defective RT, re-arrangement, or homologous recombination (Farnet and Haseltine, 1991;Hamid et al, 2017). Integration is a key step in the viral pathogenesis of HIV; however, the presence of unintegrated viral DNA in macrophages may also contribute significantly to viral pathogenesis.…”

Section: Pre-integration Latencymentioning

confidence: 99%

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Current and Future Therapeutic Strategies for Lentiviral Eradication from Macrophage Reservoirs

Peterson

MacLean

2018

J Neuroimmune Pharmacol

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Macrophages, one of the most abundant populations of leukocytes in the body, function as the first line of defense against pathogen invaders. Human Immunodeficiency virus 1 (HIV-1) remains to date one of the most extensively studied viral infections. Naturally occurring lentiviruses in domestic and primate species serve as valuable models to investigate lentiviral pathogenesis and novel therapeutics. Better understanding of the role macrophages play in HIV pathogenesis will aid in the advancement towards a cure. Even with current efficacy of first-and second-line Antiretroviral Therapy (ART) guidelines and future efficacy of Long Acting Slow Effective Release-ART (LASER-ART); ART alone does not lead to a cure. The major challenge of HIV eradication is viral latency. Latency Reversal Agents (LRAs) show promise as a possible means to eradicate HIV-1 from the body. It has become evident that complete eradication will need to include combinations of various effective therapeutic strategies such as LASER-ART, LRAs, and gene editing. Review of the current literature indicates the most promising HIV eradication strategy appears to be LASER-ART in conjunction with viral and receptor gene modifications via the CRISPR/Cas9 system.

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Distribution and fate of HIV-1 unintegrated DNA species: a comprehensive update

Cited by 35 publications

References 80 publications

Clustering and reverse transcription of HIV-1 genomes in nuclear niches of macrophages

Clustering and reverse transcription of HIV-1 genomes in nuclear niches of macrophages

LEDGF/p75 Deficiency Increases Deletions at the HIV-1 cDNA Ends

Current and Future Therapeutic Strategies for Lentiviral Eradication from Macrophage Reservoirs

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