Inhibition Of Reverse Transcription Research Articles

Ayurvedic and Chinese Herbs against Coronaviruses.

Coronavirus disease 2019 (COVID-19) is a viral disease that infects the lower airways, causing severe acute respiratory syndrome (SARS) and fatal pneumonia. The ripple effect of the COVID-19 outbreak has created serious problems in the healthcare systems of many countries and had far-reaching consequences for the global economy. Thus, effective control measures should be implemented for this coronavirus infection in the future. The ongoing episode of the SARS-CoV-2 sickness, COVID-19, in China, and the subsequent irregular spread of contamination to different nations, has alarmed the clinical and academic community primarily due to the deadly nature of this disease. Being a newly identified virus in the viral classification and having the highest mutation rate, rapid therapeutics are not readily available for treating this ailment, leading to the widespread of the disease and causing social issues for affected individuals. Evidence of Ayurveda and traditional Chinese medicine (TCM) has been found in ancient civilizations, such as those of the Hindus, Babylonians, Hebrews, and Arabs. Although TCM and Ayurvedic herbs do not promise to be very effective treatments for this pandemic, they can reduce infectivity and virulence by enhancing immunity and showing effectiveness in rehabilitation after COVID-19 disease. Thus, they could be used as sources of inhibitor molecules for certain phenomena, such as viral replication, attachment to the host, 3CL protease inhibition, 3a ion channel inhibitors, and reverse transcription inhibition. Medicinal plants from TCM and Ayurveda and their biologically active phytoconstituents can effectively modulate the targets and pathways relevant to inflammation and immune responses in human bodies. The present review analyzes the role of certain TCM and Ayurvedic medicinal plants in healing COVID-19 infection. Medicinal plants such as Glycyrrhiza glabra (licorice), Curcuma longa (turmeric), and Zingiber officinale (ginger) are regarded as the main antiviral herbs. Their extracts and individual bioactive compounds could be used as potential substances for developing remedies to prevent or cure the coronavirus disease. Generally, antiviral phytochemicals obtained from natural sources are considered potent candidates for fighting COVID-19 infection and rehabilitation after it.

Abstract 1417: IRF8 driven reprogramming of the immune microenvironment enhances anti-tumor adaptive immunity and reduces immunosuppression in murine glioblastoma

Abstract Glioblastoma (GBM) has an extremely immunosuppressive microenvironment, primarily mediated by the recruitment of immature myeloid cells (IMCs) to the tumor. IMCs suppress T cell function and dampen the anti-tumor response. In this study, we sought to “reprogram” IMCs into antigen-presenting cells (APCs) to enhance anti-tumor T cell responses. To induce IMC differentiation into APCs, we utilized a retroviral replicating vector (RRV) expressing IRF8, a master regulator of type 1 conventional dendritic cell (cDC1) development. We evaluated the impact of IRF8 RRV on in vivo tumor growth kinetics, survival, immunosuppression, and immune microenvironment. Because RRV transduction requires the proliferation of target cells, we assessed the proliferative capacity of myeloid cells in murine and human GBM samples. We utilized the SB28 cell line, a poorly immunogenic murine GBM model. We pre-transduced SB28 cells with IRF8 RRV and implanted them intracranially into syngeneic C57BL/6 mice; controls expressed an empty vector. Intratumoral myeloid cells were proliferative in both murine and human samples. In vivo, tumor and myeloid cells are infected proportionately to their respective levels of proliferation. Mice with IRF8 RRV pre-transduced intracranial tumors had significantly longer survival (median 28 days) compared to controls (median 19 days) (p <0.0001). Additionally, tumor growth was delayed in IRF8 RRV mice. IRF8 RRV mice had significant enrichment of dendritic cells (p = 0.0145), cDC1s (p < 0.0001), T cells (p = 0.0025) and CD8+ T cells (p < 0.0001). Both monocytic and granulocytic IMCs had decreased expression of the immunosuppressive markers Arginase 1 and IDO1. Further, ex vivo co-culture of intra-tumoral myeloid cells with naïve T cells showed a functional decrease in immunosuppression in IRF8 RRV tumors compared to controls (p < 0.0001). To study the mechanism of action, we assessed whether IRF8 transduction of tumor cells alone or both tumor and immune cells, was necessary for the observed survival benefit. To inhibit RRV spread from infected cells to other cells, we treated mice with azidothymidine, a reverse transcription inhibitor. A robust survival benefit and tumor growth inhibition were seen only in mice where the RRV could spread freely (p = 0.0005). This finding shows that both tumor and immune cells must be infected to cause the phenotype and suggests that reprogramming immune cells is required for therapeutic efficacy. Our novel approach used RRV to deliver a myeloid transcriptional regulator in intracerebral GBM. This therapy achieved significant survival benefits and increased intratumoral cytotoxic T cells and APCs, while decreasing myeloid immunosuppression. Further studies will expand upon the mechanism of action and test combination therapies. Citation Format: Megan Montoya, Sara A. Collins, Pavlina Chuntova, Noriyuki Kasahara, Hideho Okada. IRF8 driven reprogramming of the immune microenvironment enhances anti-tumor adaptive immunity and reduces immunosuppression in murine glioblastoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1417.

G4-binding drugs, chlorpromazine and prochlorperazine, repurposed against COVID-19 infection in hamsters.

The COVID-19 pandemic caused by SARS-CoV-2 has caused millions of infections and deaths worldwide. Limited treatment options and the threat from emerging variants underline the need for novel and widely accessible therapeutics. G-quadruplexes (G4s) are nucleic acid secondary structures known to affect many cellular processes including viral replication and transcription. We identified heretofore not reported G4s with remarkably low mutation frequency across >5 million SARS-CoV-2 genomes. The G4 structure was targeted using FDA-approved drugs that can bind G4s - Chlorpromazine (CPZ) and Prochlorperazine (PCZ). We found significant inhibition in lung pathology and lung viral load of SARS-CoV-2 challenged hamsters when treated with CPZ or PCZ that was comparable to the widely used antiviral drug Remdesivir. In support, in vitro G4 binding, inhibition of reverse transcription from RNA isolated from COVID-infected humans, and attenuated viral replication and infectivity in Vero cell cultures were clear in case of both CPZ and PCZ. Apart from the wide accessibility of CPZ/PCZ, targeting relatively invariant nucleic acid structures poses an attractive strategy against viruses like SARS-CoV-2, which spread fast and accumulate mutations quickly.

Evaluation of Advantages of Lithium Chloride as a Precipitating Agent in RNA Isolation from Frozen Vein Segments.

Contamination of the sample with DNA is a problem when isolating RNA by phenol-chloroform extraction, and DNase treatment introduces an additional error in the analysis of gene expression. Bearing in mind the ability of LiCl to precipitate RNA selectively, we studied the possibility and advantage of using LiCl as a precipitation agent in the protocol for RNA precipitation [3] from frozen segments of large vessels. Combined use of LiCl with isopropanol as precipitating agents (optimal ratio 2.5 M and 40%, respectively) significantly eliminates negative effects of using this salt (inhibition of reverse transcription and low RNA yield).

Investigation of Drug-resistance substitutions in HIV-1 RT Protein in Iranian HIV Infected Patients

Abstract: 
 Background:
 Currently, more than 37 million people are living with human immunodeficiency virus type 1. Reverse transcription (RT) is a main part in the life cycle of retroviruses which is responsible for synthesis of DNA complementary to an RNA or DNA template. Recently several inhibitors have been introduced to target RT protein; however, drug resistance is one of the greatest challenges in the improvement of effective treatment for human immunodeficiency virus (HIV) infection. Here, we determined the resistance mutations in the RT gene in treatment failure patients and searched for the dominant subtype among them. 
 Methods:
 HIV viral load and a reverse transcriptase nested polymerase chain (RT-nested PCR) reactions were performed in 15 patients with treatment failure to amplify the RT gene. Drug resistance mutations, as well as the viral subtypes, were analyzed using by using several bioinformatics software and online tools.
 Results: 
 The frequency of RT related drug-resistance mutations in patients was 33.3%, among which the major mutation consisted of 20% of all those occurring in codon 184. Moreover, the results showed 6.6% and 26.6% of patients were resistant to Non-Nucleoside RT Inhibitor (NNRTIs) and Nucleoside RT Inhibitors (NRTIs), respectively. In addition, the vast majority of samples (12 patients of 15) belonged to subtype CRF35-AD.
 Conclusions:
 The present study reports updates on the mutations related to RT resistance in Iranian HIV patients receiving treatment, show that 20% of the samples had a high-level of resistance to Lamivudine, and Emtricitabine which should be confirmed for further antiretroviral (AVR) regimens for HIV infected patients. Also, two new mutations related to resistance to Nevirapine, Doravirine, Zidovudine, and Stavudine were introduced in this investigation.
 The present results could be used as predictive information on the response to anti-RT, and also highlight the importance of considering the periodic monitoring of HIV resistance test in HIV infected patients.

A Novel Mouse Model Harboring Hepatitis B Virus Covalently Closed Circular DNA

Background and AimsThe persistence of viral covalently closed circular DNA (cccDNA) is the major obstacle for antiviral treatment against hepatitis B virus (HBV). Basic and translational studies are largely hampered due to the lack of feasible small animal models to support HBV cccDNA formation. The aim of this study is to establish a novel mouse model harboring cccDNA.MethodsAn adeno-associated virus (AAV) vector carrying a replication-deficient HBV1.04-fold genome (AAV-HBV1.04) was constructed. The linear HBV genome starts from nucleotide 403 and ends at 538, which results in the splitting of HBV surface and polymerase genes. Different HBV replication markers were evaluated for AAV-HBV1.04 plasmid–transfected cells, the AAV-HBV1.04 viral vector–transduced cells, and mice injected with the AAV-HBV1.04 viral vector.ResultsCompared with the previously reported AAV-HBV1.2 construct, direct transfection of AAV-HBV1.04 plasmid failed to produce hepatitis B surface antigen and progeny virus. Interestingly, AAV-HBV1.04 viral vector transduction could result in the formation of cccDNA and the production of all HBV replication markers in vitro and in vivo. The formation of cccDNA could be blocked by ATR (ataxia-telangiectasia and Rad3-related protein) inhibitors but not HBV reverse transcription inhibitor or capsid inhibitors. The AAV-HBV1.04 mouse supported long-term HBV replication and responded to antiviral treatments.ConclusionsThis AAV-HBV1.04 mouse model can support HBV cccDNA formation through ATR-mediated DNA damage response. The de novo formed cccDNA but not the parental AAV vector can lead to the production of hepatitis B surface antigen and HBV progeny. This model will provide a unique platform for studying HBV cccDNA and developing novel antivirals against HBV infection.

Dynamic analysis of humoral immunity HIV for both virus-to-cell and cell-to-cell transmissions with RTI

In this paper, we have fabricated an HIV RTI model accompanied with humoral immunity. Positivity solution for the model and boundedness of the model were derived. Stability analysis of the constructed model about its steady states has been deliberated. Sensitivity analysis is performed on a delay differential equation model for human immunodeficiency virus (HIV) with reverse transcription inhibitors (RTI) model.

Differential Activity of APOBEC3F, APOBEC3G, and APOBEC3H in the Restriction of HIV-2

Human immunodeficiency virus (HIV) mutagenesis is driven by a variety of internal and external sources, including the host APOBEC3 (apolipoprotein B mRNA editing enzyme catalytic polypetide-like 3; A3) family of mutagenesis factors, which catalyze G-to-A transition mutations during virus replication. HIV-2 replication is characterized by a relative lack of G-to-A mutations, suggesting infrequent mutagenesis by A3 proteins. To date, the activity of the A3 repertoire against HIV-2 has remained largely uncharacterized, and the mutagenic activity of these proteins against HIV-2 remains to be elucidated. In this study, we provide the first comprehensive characterization of the restrictive capacity of A3 proteins against HIV-2 in cell culture using a dual fluorescent reporter HIV-2 vector virus. We found that A3F, A3G, and A3H restricted HIV-2 infectivity in the absence of Vif and were associated with significant increases in the frequency of viral mutants. These proteins increased the frequency of G-to-A mutations within the proviruses of infected cells as well. A3G and A3H also reduced HIV-2 infectivity via inhibition of reverse transcription and the accumulation of DNA products during replication. In contrast, A3D did not exhibit any restrictive activity against HIV-2, even at higher expression levels. Taken together, these results provide evidence that A3F, A3G, and A3H, but not A3D, are capable of HIV-2 restriction. Differences in A3-mediated restriction of HIV-1 and HIV-2 may serve to provide new insights in the observed mutation profiles of these viruses.

Evolution of HIV-1 Surveillance Drug Resistance Mutations Over 10 Years in New South Wales, Australia.

New South Wales has the greatest burden of HIV in Australia, with 2012 and 2013 recording the highest rates of new diagnoses in 20 years. Concurrently, there has been significant changes in antiretroviral treatments and testing paradigms. We compiled a statewide resistance database to characterize changes in HIV-1 resistance mutations over time. Genotypic antiretroviral resistance testing (GART) was performed on request at three reference laboratories using commercial and in-house methods. In total, 7629 HIV-1 polymerase sequences obtained from GART from 2004 to 2013 were retrospectively collated, reformatted, de-identified, and analyzed using Stanford HIVdb program 7.0 and the 2009 World Health Organization (WHO) surveillance drug resistance mutations (SDRMs). Analyses were performed on subgroups of known treatment naives, treatment experienced, and seroconverters. There has been a decrease in overall rates of prevalent drug resistance mutations from 57.8% in 2004 to 21% in 2013. Dual and triple class resistance mutations have decreased from 32.7% in 2004 to 5.8% in 2013 and 16.4% to 1.2%, respectively. In treatment-naive individuals (n = 450), the frequency of protease inhibitor (PI) mutations remains low at 2.7%. In seroconverters, rates of transmitted drug resistance (TDR) are 6.6%, 3%, 3%, and 1.5% for overall, PI, non-nucleoside reverse transcription inhibitor (NNRTI), and NRTI, respectively. In treatment experienced, rates remain stable with 36.0%, 18.9%, 29.1%, and 6.4% for overall, NNRTI, NRTI, and PI mutations. The most common mutations in treatment experienced occurred at position M184, T215 (NRTI); K103 (NNRTI); I54 (PI). Apparent decreases in prevalent SDRMs can be attributed to changes in GART testing indications over time. In treatment-naive and -experienced subgroups, rates have been stable with low rates of TDR in seroconverters.

Sequence-specific inhibition of reverse transcription by recombinant CRISPR/dCas13a ribonucleoprotein complexes in vitro.

The clustered regularly interspaced short palindromic repeats (CRISPR) system is widely used for genome editing because of its ability to cleave specific DNA sequences. Recently, RNA-specific CRISPR systems have been reported. CRISPR systems, consisting of a guide RNA (gRNA) and a nuclease-dead form of Cas13a (dCas13a), can be used for RNA editing and visualization of target RNA. In this study, we examined whether a recombinant CRISPR/dCas13a ribonucleoprotein (RNP) complex could be used to inhibit reverse transcription (RT) in a sequence-specific manner in vitro. Recombinant Leptotrichia wadei dCas13a was expressed using the silkworm-baculovirus expression system and affinity-purified. We found that the CRISPR/dCas13a RNP complex, combined with a chemically synthesized gRNA sequence, could specifically inhibit RT of EGFR and NEAT1, but not nonspecific RNA. Thus, the CRISPR/dCas13a RNP complex can inhibit RT reactions in a sequence-specific manner. RT inhibition by the CRISPR/dCas13a system may be useful to assess target binding activity, to discriminate RNA species retaining target sequences of gRNA, or to suppress RT from undesirable RNA species.

937. Factors Associated with Metabolic Syndrome in People with HIV under 40 Years in Guatemala

BackgroundHIV infection and antiretroviral therapy (ART) can lead to metabolic abnormalities associated with increased cardiovascular disease risk, some of these abnormalities (central obesity, elevated fasting glucose, triglycerides, and blood pressure and low HDL cholesterol) are in metabolic syndrome (MetS). The prevalence of MetS increases with age. Currently, the status of MetS in people with HIV (PWH) Guatemala is unknown. We assessed the prevalence of MetS and potential predictors in PWH participating in prospective cohort study at Hospital Roosevelt in Guatemala City.MethodsWe performed a cross-sectional analysis of PWH under 40 years old receiving ART for at least 6 months from July 2019 to March 2020. The harmonized criteria for MetS and the cut-off for waist circumference recommended by the Latin American Diabetes Association were used. Association between MetS and gender, place of residency, ethnicity, educational level, baseline and current CD4 count, smoking, alcohol consumption, physical activity, viral load, body mass index (BMI) and ART exposure was assessed in bivariate analysis. Potential predictors (p-value < 0.1) were included in a multivariate binary logistic regression model.ResultsOf total cohort of 757 participants enrolled390 (51.5%) were younger than 40 years. Of those under < 40 years, 150 (38.5%) were women, 59 (15.1%) Mayan, median age was 32 years (IQR 27, 37). 93 (23.8%) had MetS. Between group differences in Table 1. Of those with Met, 51 (54.8%) had elevated waist circumference, 87 (93.5%) elevated triglycerides, 83 (89.2%) low HDL-c, 56 (60.2%) elevated blood pressure and 35 (37.6%) elevated fasting glucose. Body mass index (BMI) ≥ 25 kg/m2 or higher and 2 years or more of cumulative non-nucleoside reverse transcription inhibitors (NNRTI) where more common in those < 40 years with MetS compared to those without MetS. On multivariable regression, MetS was associated with current CD4 count < 200 (OR 3.1; IC 1.51, 6.34; p-value < 0.01) and BMI ≥ 25 kg/m2 (OR; 6.53; IC 3.64, 11.73; p-value < 0.01).Table1. Between group differences (No MetS vs MetS) ConclusionNearly one in every four PWH under 40 years old in our cohort was affected by MetS. Dyslipidemia (elevated triglycerides and low HDL-c) was the main driver of MetS. Lower CD4 count and overweight were predictors for MetS in PWH under 40.Disclosures Andrej Spec, MD, MSCI, Astellas (Grant/Research Support)Mayne (Consultant)Scynexis (Consultant)

Nuclear Import of the HIV-1 Core Precedes Reverse Transcription and Uncoating

SUMMARYHIV-1 reverse transcription (RT) occurs before or during uncoating, but the cellular compartment where RT and uncoating occurs is unknown. Using imaging and biochemical assays to track HIV-1 capsids in the nucleus during infection, we demonstrated that higher-order capsid complexes and/or complete cores containing the viral genome are imported into the nucleus. Inhibition of RT does not prevent capsid nuclear import; thus, RT may occur in nuclear compartments. Cytosolic and nuclear fractions of infected cells reveal that most RT intermediates are enriched in nuclear fractions, suggesting that HIV-1 RT occurs in the nucleus alongside uncoating. In agreement, we find that capsid in the nucleus induces recruitment of cleavage and polyadenylation specific factor 6 (CPSF6) to SC35 nuclear speckles, which are highly active transcription sites, suggesting that CPSF6 through capsid is recruiting viral complexes to SC35 speckles for the occurrence of RT. Thus, nuclear import precedes RT and uncoating, which fundamentally changes our understanding of HIV-1 infection.

Chiral Separation of Non-Nucleoside Reverse Transcription Inhibitor Efavirenz by HPLC on Cellulose-Based Chiral Stationary Phase

A stereospecific HPLC method for the separation of efavirenz (EFZ) enantiomers in bulk drug and formulations was developed and validated on a normal-phase cellulose derivatized chiral column. The effect of organic modifiers, namely, 2-propanol, ethanol and trifluoroacetic acid in mobile phase was optimized to obtain the best enantiomeric separation. The retention times of (R)-EFZ and (S)-EFZ were observed to be 7.5 and 9.2 min, respectively. The calibration curve was found to be linear over the concentration range of 200 - 6210 ng/mL with a determination coefficient (R 2 ) of 0.9999 for the (R)-isomer. The limit of detection (LOD) and limit of quantification (LOQ) were calculated to be 66 ng/mL and 200 ng/mL, respectively. The proposed method was found to be accurate, precise and suitable for the separation and quantification of unwanted (R)-EFZ in active pharmaceutical ingredients (API). The analytical results were supported by statistical parameters. The proposed method could be successfully applied to the enantiomeric purity analysis of EFZ in bulk drug samples and formulations.

Treatment Experience and Repeat Pregnancy Impact the Effectiveness of Non-Nucleoside Reverse Transcription Inhibitor-Highly Active Antiretroviral Therapy for the Prevention of Mother to Child Transmission of Human Immunodeficiency Virus.

Non-nucleoside reverse transcription inhibitor (NNRTI)-containing antiretroviral therapy (ART) for the prevention of mother to child transmission (PMTCT) of human immunodeficiency virus (HIV) has led to dramatic reductions in perinatal HIV infection in resource-constrained settings. Nonetheless, PMTCT programs are complicated by repeat pregnancies, in which long-term or repeat exposures to PMTCT regimens over time may lead to the acquisition of HIV drug resistance mutations, and consequent treatment failure. In this study, we retrospectively assessed the effectiveness of the NNRTI-based PMTCT protocol from 2008 to 2010 in The Bahamas National HIV/AIDS Program. We show that women who had been in repeat pregnancies and those who were already prescribed ART at conception were at increased risk of virologic failure, relative to treatment-inexperienced women and primigravida, respectively (AOR 3.1, 95% CI: 1.3-7.1, p = .008 and AOR 5.0, 95% CI: 1.8-14.1, p = .002). In addition, women undergoing treatment at conception were more likely to possess HIVDR mutations relative to treatment-naive women (AOR 447.1, 95% CI: 17.9-11,173.5, p = .001). Therefore, individual treatment history is a key metric determining the effectiveness of current and future PMTCT interventions. The implications of this to PMTCT programmatic success in light of the most recent WHO guidelines are discussed.

Regorafenib therapy for hepatocellular carcinoma in a HIV‐1‐infected patient: A case report

Regorafenib therapy for hepatocellular carcinoma in a HIV‐1‐infected patient: A case report

A High-Throughput HIV-1 Drug Screening Platform, Based on Lentiviral Vectors and Compatible with Biosafety Level-1.

HIV-1 infection is a complex, multi-step process involving not only viral, but also multiple cellular factors. To date, drug discovery methods have primarily focused on the inhibition of single viral proteins. We present an efficient and unbiased approach, compatible with biosafety level 1 (BSL-1) conditions, to identify inhibitors of HIV-1 reverse transcription, intracellular trafficking, nuclear entry and genome integration. Starting with a fluorescent assay setup, we systematically improved the screening methodology in terms of stability, efficiency and pharmacological relevance. Stability and throughput were optimized by switching to a luciferase-based readout. BSL-1 compliance was achieved without sacrificing pharmacological relevance by using lentiviral particles pseudo-typed with the mouse ecotropic envelope protein to transduce human PM1 T cells gene-modified to express the corresponding murine receptor. The cellular assay was used to screen 26,048 compounds selected for maximum diversity from a 200,640-compound in-house library. This yielded z’ values greater than 0.8 with a hit rate of 3.3% and a confirmation rate of 50%. We selected 93 hits and enriched the collection with 279 similar compounds from the in-house library to identify promising structural features. The most active compounds were validated using orthogonal assay formats. The similarity of the compound profiles across the different platforms demonstrated that the reported lentiviral assay system is a robust and versatile tool for the identification of novel HIV-1 inhibitors.

Flexibility in Nucleic Acid Binding Is Central to APOBEC3H Antiviral Activity.

APOBEC3 proteins APOBEC3F (A3F), APOBEC3G (A3G), and APOBEC3H (A3H) are host restriction factors that inhibit HIV-1 through DNA cytidine deaminase-dependent and -independent mechanisms and have either one (A3H) or two (A3F and A3G) zinc-binding domains. A3H antiviral activity encompasses multiple molecular functions, all of which depend on recognition of RNA or DNA. A3H crystal structures revealed an unusual interaction with RNA wherein an RNA duplex mediates dimerization of two A3H proteins. In this study, we sought to determine the importance of RNA-binding amino acids in the antiviral and biochemical properties of A3H. We show that the wild-type A3H-RNA interaction is essential for A3H antiviral activity and for two deaminase-independent processes: encapsidation into viral particles and inhibition of reverse transcription. Furthermore, an extensive mutagenesis campaign revealed distinct roles for two groups of amino acids at the RNA binding interface. C-terminal helix residues exclusively bind RNA, and loop 1 residues play a dual role in recognition of DNA substrates and in RNA binding. Weakening the interface between A3H and RNA allows DNA substrates to bind with greater affinity and enhances deamination rates, suggesting that RNA binding must be disrupted to accommodate DNA. Intriguingly, we demonstrate that A3H can deaminate overhanging DNA strands of RNA/DNA heteroduplexes, which are early intermediates during reverse transcription and may represent natural A3H substrates. Overall, we present a mechanistic model of A3H restriction and a step-by-step elucidation of the roles of RNA-binding residues in A3H activity, particle incorporation, inhibition of reverse transcriptase inhibition, and DNA cytidine deamination.IMPORTANCE APOBEC3 proteins are host factors that protect the integrity of the host genome by inhibiting retroelements as well as retroviruses, such as HIV-1. To do this, the APOBEC3H protein has evolved unique interactions with structured RNAs. Here, we studied the importance of these interactions in driving antiviral activity of APOBEC3H. Our results provide a clear picture of how RNA binding drives the ability of APOBEC3H to infiltrate new viruses and prevent synthesis of viral DNA. We also explore how RNA binding by APOBEC3H influences recognition and deamination of viral DNA and describe two possible routes by which APOBEC3H might hypermutate the HIV-1 genome. These results highlight how one protein can sense many nucleic acid species for a variety of antiviral activities.

Insights into Innate Sensing of Prototype Foamy Viruses in Myeloid Cells.

Foamy viruses (FVs) belong to the Spumaretrovirinae subfamily of retroviruses and are characterized by unique features in their replication strategy. This includes a reverse transcription (RTr) step of the packaged RNA genome late in replication, resulting in the release of particles with a fraction of them already containing an infectious viral DNA (vDNA) genome. Little is known about the immune responses against FVs in their hosts, which control infection and may be responsible for their apparent apathogenic nature. We studied the interaction of FVs with the innate immune system in myeloid cells, and characterized the viral pathogen-associated molecular patterns (PAMPs) and the cellular pattern recognition receptors and sensing pathways involved. Upon cytoplasmic access, full-length but not minimal vector genome containing FVs with active reverse transcriptase, induced an efficient innate immune response in various myeloid cells. It was dependent on cellular cGAS and STING and largely unaffected by RTr inhibition during viral entry. This suggests that RTr products, which are generated during FV morphogenesis in infected cells, and are therefore already present in FV particles taken up by immune cells, are the main PAMPs of FVs with full-length genomes sensed in a cGAS and STING-dependent manner by the innate immune system in host cells of the myeloid lineage.

Development of Lentiviral Vectors for HIV-1 Gene Therapy with Vif-Resistant APOBEC3G

Strategies to control HIV-1 replication without antiviral therapy are needed to achieve a functional cure. To exploit the innate antiviral function of restriction factor cytidine deaminase APOBEC3G (A3G), we developed self-activating lentiviral vectors that efficiently deliver HIV-1 Vif-resistant mutant A3G-D128K to target cells. To circumvent APOBEC3 expression in virus-producing cells, which diminishes virus infectivity, a vector containing two overlapping fragments of A3G-D128K was designed that maintained the gene in an inactive form in the virus-producer cells. However, during transduction of target cells, retroviral recombination between the direct repeats reconstituted an active A3G-D128K in 89%–98% of transduced cells. Lentiviral vectors that expressed A3G-D128K transduced CD34+ hematopoietic stem and progenitor cells with a high efficiency (>30%). A3G-D128K expression in T cell lines CEM, CEMSS, and PM1 potently inhibited spreading infection of several HIV-1 subtypes by C-to-U deamination leading to lethal G-to-A hypermutation and inhibition of reverse transcription. SIVmac239 and HIV-2 were not inhibited, since their Vifs degraded A3G-D128K. A3G-D128K expression in CEM cells potently suppressed HIV-1 replication for >3.5 months without detectable resistant virus, suggesting a high genetic barrier for the emergence of A3G-D128K resistance. Because of this, A3G-D128K expression in HIV-1 target cells is a potential anti-HIV gene therapy approach that could be combined with other therapies for the treatment and functional cure of HIV-1 infection.

LINE-1 Retrotransposition Promotes the Development and Progression of Lung Squamous Cell Carcinoma by Disrupting the Tumor-Suppressor Gene FGGY.

Somatic long interspersed element-1 (LINE-1) retrotransposition is a genomic process that relates to gene disruption and tumor occurrence. However, the expression and function of LINE-1 retrotransposition in lung squamous cell carcinoma (LUSC) remain unclear. We analyzed the transcriptomes of LUSC samples in The Cancer Genome Atlas and observed LINE-1 retrotransposition in 90% of tumor samples. Thirteen LINE-1 retrotranspositions of high occurrence were identified and further validated from an independent Chinese LUSC cohort. Among them, LINE-1-FGGY (L1-FGGY) was identified as the most frequent LINE-1 retrotransposition in the Chinese cohort and significantly correlated with poor clinical outcome. L1-FGGY occurred with smoke-induced hypomethylation of the LINE-1 promoter and contributed to the development of local immune evasion and dysfunctional metabolism. Overexpression of L1-FGGY or knockdown of FGGY promoted cell proliferation and invasion in vitro, facilitated tumorigenesis in vivo, and dysregulated cell energy metabolism and cytokine/chemotaxin transcription. Importantly, specific reverse transcription inhibitors, nevirapine and efavirenz, dramatically countered L1-FGGY abundance, inhibited tumor growth, recovered metabolism dysfunction, and improved the local immune evasion. In conclusion, hypomethylation-induced L1-FGGY expression is a frequent genomic event that promotes the development and progression of LUSC and represents a promising predictive biomarker and therapeutic target in LUSC. SIGNIFICANCE: LINE-1-FGGY is a prognosis predictive biomarker and potential therapeutic target to overcome local immune evasion in lung squamous cell carcinoma.