Cellular Factors Targeting HIV-1 Transcription and Viral RNA Transcripts

Friends and Foes: The Ambivalent Role of Autophagy in HIV-1 Infection

Autophagy has emerged as an integral part of the antiviral innate immune defenses, targeting viruses or their components for lysosomal degradation. Thus, successful viruses, like pandemic human immunodeficiency virus 1 (HIV-1), evolved strategies to counteract or even exploit autophagy for efficient replication. Here, we provide an overview of the intricate interplay between autophagy and HIV-1. We discuss the impact of autophagy on HIV-1 replication and report in detail how HIV-1 manipulates autophagy in infected cells and beyond. We also highlight tissue and cell-type specifics in the interplay between autophagy and HIV-1. In addition, we weigh exogenous modulation of autophagy as a putative double-edged sword against HIV-1 and discuss potential implications for future antiretroviral therapy and curative approaches. Taken together, we consider both antiviral and proviral roles of autophagy to illustrate the ambivalent role of autophagy in HIV-1 pathogenesis and therapy.

Cellular proteins as potential targets for antiretroviral therapy

The review article conducts an in-depth analysis of information gleaned from a comprehensive literature search across Scopus, Web of Science, and MedLine databases. The focal point of this search revolves around the identification and exploration of the mechanisms orchestrated by host cell factors in the replication cycle of the human immunodeficiency virus (HIV-1, Retroviridae: Orthoretrovirinae: Lentivirus: Human immunodeficiency virus-1). The article delves into two primary categories of proteins, namely HIV dependence factors (such as CypA, LEDGF, TSG101) and restriction factors (including SERINС5, TRIM5α, APOBEC3G), providing illustrative examples. The current understanding of the functioning mechanisms of these proteins is elucidated, and an evaluation is presented on the potential development of drugs for treating HIV infection. These drugs aim to either inhibit or stimulate the activity of host factors, offering insights into promising avenues for future research and therapeutic advancements.

Genetic polymorphisms in the C19orf66 gene influenced HIV-1 infection in a Yunnan population

Background

Due to the deficiencies of vaccines and effective medicine, the human immunodeficiency virus (HIV) infection mechanism should be studied. The C19orf66 gene, one of the interferon-stimulated genes (ISGs), expresses broad-spectra anti-viral activity, including inhibiting HIV replication.

Methods

In this study, we collect 421 HIV-1 infected patients and 448 controls to genotype three SNPs in the C19orf66 gene. Then, the association between SNPs and biochemical indices/ HIV-1 subtypes are analyzed.

Results

Genotypes CC and CT of rs12611087 show statistically lower and higher frequencies in HIV-1 infected patients than in controls, respectively. Alleles C and T of rs12611087 play protective and risk roles in Yunnan HIV population, respectively. Biochemical indices analysis shows that HIV-1 infected persons carried genotype TT of rs77076061 express significantly lower CD3+/CD45+ ratio level and higher IBIL level. The epidemic subtypes of HIV-1 patients in this study are CRF 07_BC and CRF 08_BC. Moreover, subtype CRF 08_BC tends to infect persons with genotype CC of rs12611087.

Conclusion

The genetic polymorphisms of the C19orf66 gene are firstly studied and reported to associate with HIV-1 infection and biochemical indices of patients in Yunnan. Furthermore, subtype CRF 08_BC infection could be influenced by genotypes of SNP in the C19orf66 gene.

TRIM5α recruits HDAC1 to p50 and Sp1 and promotes H3K9 deacetylation at the HIV-1 LTR

Tripartite motif-containing protein 5α (TRIM5α) is generally known to block the postentry events of HIV-1. Here, we report an uncharacterized role for TRIM5α in the maintenance of viral latency. Knockdown of TRIM5α potentiates the transcription of HIV-1 in multiple latency models, which is reversed by shRNA-resistant TRIM5α. TRIM5α suppresses TNFα-activated HIV-1 LTR-driven as well as NF-κB- and Sp1-driven gene expression, with the RING and B-box 2 domains being the essential determinants. Mechanistically, TRIM5α binds to and enhances the recruitment of histone deacetylase 1 (HDAC1) to NF-κB p50 and Sp1. ChIP‒qPCR analyses further reveal that the association of TRIM5α with HIV-1 LTR induces HDAC1 recruitment and local H3K9 deacetylation. Conserved suppression effects of TRIM5α orthologs from multiple species on both HIV-1 and endo-retroelement HERV-K LTR activities have also been demonstrated. These findings provide new insights into the molecular mechanisms by which proviral latency is initially established and activatable proviruses are resilenced by histone deacetylase recruitment.

Genetic Ethnic Differences in Human 2'-5'-Oligoadenylate Synthetase and Disease Associations: A Systematic Review

Recently, several studies have highlighted a skewed prevalence of infectious diseases within the African continent. Furthermore, a growing number of studies have demonstrated unique genetic variants found within the African genome are one of the contributing factors to the disease severity of infectious diseases within Africa. Understanding the host genetic mechanisms that offer protection against infectious diseases provides an opportunity to develop unique therapeutic interventions. Over the past two decades, several studies have linked the 2'-5'-oligoadenylate synthetase (OAS) family with a range of infectious diseases. More recently, the OAS-1 gene has also been associated with disease severity caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which led to a global pandemic. The OAS family serves as an antiviral factor through the interaction with Ribonuclease-Latent (RNase-L). This review explores the genetic variants observed within the OAS genes and the associations with various viral infections and how previously reported ethnic-specific polymorphisms drive clinical significance. This review provides an overview of OAS genetic association studies with a particular focus on viral diseases affecting individuals of African descent.

Inflammasomes as mediators of inflammation in HIV-1 infection

Human immunodeficiency virus type 1 (HIV-1) infection is a chronic disease without a known cure. The advent of effective antiretroviral therapy (ART) has enabled people with HIV (PWH) to have significantly prolonged life expectancies. As a result, morbidity and mortality associated with HIV-1 infection have declined considerably. However, these individuals experience chronic systemic inflammation whose multifaceted etiology is associated with other numerous comorbidities. Inflammasomes are vital mediators that contribute to inflammatory signaling in HIV-1 infection. Here, we provide an overview of the inflammatory pathway that underlies HIV-1 infection, explicitly highlighting the role of the NLRP3 inflammasome. We also delineate the current literature on inflammasomes and the therapeutic targeting strategies aimed at the NLRP3 inflammasome to moderate HIV-1 infection-associated inflammation. Here we describe the NLRP3 inflammasome as a key pathway in developing novel therapeutic targets to block HIV-1 replication and HIV-1-associated inflammatory signaling. Controlling the inflammatory pathways is critical in alleviating the morbidities and mortality associated with chronic HIV-1 infection in PWH.

MIR-29A-3P, MIR-29C-3P, MIR-146B-5P AND MIR-150-5P, Their Target Genes and lncrnas in HIV Infection: A Bioinformatic Study

INTRODUCTION

Increasing evidence suggests that microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) have emerged as attractive targets in viral infections, including Human immunodeficiency virus (HIV).

OBJECTIVE

To deepen the understanding of the molecular mechanisms that lead to HIV and provide potential targets for the future development of molecular therapies for its treatment.

METHODS

Four miRNAs were selected as candidates based on a previous systematic review. A combination of bioinformatic analyses was performed to identify their target genes, lncRNAs and biological processes that regulate them.

RESULTS

In the constructed miRNA-mRNA network, 193 gene targets are identified. These miRNAs potentially control genes from several important processes, including signal transduction and cancer. LncRNA-XIST, lncRNA-NEAT1 and lncRNA-HCG18 interact with all four miRNAs.

CONCLUSION

This preliminary result forms the basis for improving reliability in future studies to fully understand the role these molecules and their interactions play in HIV.

Strategies to overcome HIV drug resistance-current and future perspectives

The availability of combined antiretroviral therapy (cART) has revolutionized the course of HIV infection, suppressing HIV viremia, restoring the immune system, and improving the quality of life of HIV infected patients. However, the emergence of drug resistant and multidrug resistant strains remains an important contributor to cART failure, associated with a higher risk of HIV-disease progression and mortality. According to the latest WHO HIV Drug Resistance Report, the prevalence of acquired and transmitted HIV drug resistance in ART naive individuals has exponentially increased in the recent years, being an important obstacle in ending HIV-1 epidemic as a public health threat by 2030. The prevalence of three and four-class resistance is estimated to range from 5 to 10% in Europe and less than 3% in North America. The new drug development strategies are focused on improved safety and resistance profile within the existing antiretroviral classes, discovery of drugs with novel mechanisms of action (e.g., attachment/post-attachment inhibitors, capsid inhibitors, maturation inhibitors, nucleoside reverse transcriptase translocation inhibitors), combination therapies with improved adherence, and treatment simplification with infrequent dosing. This review highlight the current progress in the management of salvage therapy for patients with multidrug-resistant HIV-1 infection, discussing the recently approved and under development antiretroviral agents, as well as the new drug targets that are providing a new avenue for the development of therapeutic interventions in HIV infection.

Deep RNA sequencing of intensive care unit patients with COVID-19

COVID-19 has impacted millions of patients across the world. Molecular testing occurring now identifies the presence of the virus at the sampling site: nasopharynx, nares, or oral cavity. RNA sequencing has the potential to establish both the presence of the virus and define the host's response in COVID-19. Single center, prospective study of patients with COVID-19 admitted to the intensive care unit where deep RNA sequencing (> 100 million reads) of peripheral blood with computational biology analysis was done. All patients had positive SARS-CoV-2 PCR. Clinical data was prospectively collected. We enrolled fifteen patients at a single hospital. Patients were critically ill with a mortality of 47% and 67% were on a ventilator. All the patients had the SARS-CoV-2 RNA identified in the blood in addition to RNA from other viruses, bacteria, and archaea. The expression of many immune modulating genes, including PD-L1 and PD-L2, were significantly different in patients who died from COVID-19. Some proteins were influenced by alternative transcription and splicing events, as seen in HLA-C, HLA-E, NRP1 and NRP2. Entropy calculated from alternative RNA splicing and transcription start/end predicted mortality in these patients. Current upper respiratory tract testing for COVID-19 only determines if the virus is present. Deep RNA sequencing with appropriate computational biology may provide important prognostic information and point to therapeutic foci to be precisely targeted in future studies.

Forging a Functional Cure for HIV: Transcription Regulators and Inhibitors

Current antiretroviral therapy (ART) increases the survival of HIV-infected individuals, yet it is not curative. The major barrier to finding a definitive cure for HIV is our inability to identify and eliminate long-lived cells containing the dormant provirus, termed viral reservoir. When ART is interrupted, the viral reservoir ensures heterogenous and stochastic HIV viral gene expression, which can reseed infection back to pre-ART levels. While strategies to permanently eradicate the virus have not yet provided significant success, recent work has focused on the management of this residual viral reservoir to effectively limit comorbidities associated with the ongoing viral transcription still observed during suppressive ART, as well as limit the need for daily ART. Our group has been at the forefront of exploring the viability of the block-and-lock remission approach, focused on the long-lasting epigenetic block of viral transcription such that without daily ART, there is no risk of viral rebound, transmission, or progression to AIDS. Numerous studies have reported inhibitors of both viral and host factors required for HIV transcriptional activation. Here, we highlight and review some of the latest HIV transcriptional inhibitor discoveries that may be leveraged for the clinical exploration of block-and-lock and revolutionize the way we treat HIV infections.

Innate immune regulation in HIV latency models

BACKGROUND

Innate immunity and type 1 interferon (IFN) defenses are critical for early control of HIV infection within CD4 + T cells. Despite these defenses, some acutely infected cells silence viral transcription to become latently infected and form the HIV reservoir in vivo. Latently infected cells persist through antiretroviral therapy (ART) and are a major barrier to HIV cure. Here, we evaluated innate immunity and IFN responses in multiple T cell models of HIV latency, including established latent cell lines, Jurkat cells latently infected with a reporter virus, and a primary CD4 + T cell model of virologic suppression.

RESULTS

We found that while latently infected T cell lines have functional RNA sensing and IFN signaling pathways, they fail to induce specific interferon-stimulated genes (ISGs) in response to innate immune activation or type 1 IFN treatment. Jurkat cells latently infected with a fluorescent reporter HIV similarly demonstrate attenuated responses to type 1 IFN. Using bulk and single-cell RNA sequencing we applied a functional genomics approach and define ISG expression dynamics in latent HIV infection, including HIV-infected ART-suppressed primary CD4 + T cells.

CONCLUSIONS

Our observations indicate that HIV latency and viral suppression each link with cell-intrinsic defects in specific ISG induction. We identify a set of ISGs for consideration as latency restriction factors whose expression and function could possibly mitigate establishing latent HIV infection.

Role of inflammasomes in HIV-1 infection and treatment

Although combined antiretroviral therapy (cART) is effective in inhibiting human immunodeficiency virus type 1 (HIV-1) replication, it does not eradicate the virus because small amounts of latent HIV-1 provirus persist in quiescent memory CD4⁺ T cells. Therefore, strategies for eradicating latent HIV-1 are urgently needed. Recently, several studies have reported that the inflammatory response and lymphocyte death induced by HIV-1 depend on inflammasomes and pyroptosis, suggesting that inflammasomes and pyroptosis have a vital role in HIV-1 infection and contribute to the eradication of latent HIV-1. In this review, we summarize current knowledge of the role of inflammasomes, including NLR family pyrin domain-containing protein 3 (NLRP3), caspase recruitment domain-containing protein 8 (CARD8), interferon-inducible protein 16 (IFI16), NLRP1, NLR family CARD domain-containing 4 (NLRC4), and absent in melanoma 2 (AIM2), in HIV-1 infection and discuss promising therapeutic strategies for HIV-1-associated diseases by targeting inflammasomes.

Reducing HIV-1 env gene CpG frequency increases the replication capacity of the HXB2 virus strain

Synonymous replacement of CpG dinucleotides in the HIV-1 envelope (env) coding region has been correlated with evasion of the antiviral activity of the zinc-finger antiviral protein (ZAP). We aimed to explore the effect of depleting HIV-1 env CpG dinucleotides by synonymous substitution on ex vivo viral replication capacity. To this end, we eliminated 11 env CpG dinucleotides through synonymous substitutions in the CXCR4-tropic HXB2 strain. The replication kinetics in MT-4 cells and peripheral blood mononuclear cells (PBMCs) of the WT and synonymously recoded mutant viruses were indistinguishable. However, virus competition assays in MT4 cells between the WT and recoded viruses showed that the mutant with fewer CpG dinucleotides quickly overgrew the WT virus. These results demonstrate that a reduction in HIV-1 env CpG dinucleotide frequency can improve viral replication capacity in cell culture. Our results support the previous observation that the frequency of CpGs in the HIV-1 env region correlates with differences in clinical progression rates in infected individuals.

When good turns bad: how viruses exploit innate immunity factors

Humans evolved numerous cell-intrinsic restriction factors as a first line of defense against viral pathogens. Typically, they inhibit efficient viral replication and thus prevent viral zoonoses and pandemics. However, viruses show enormous adaptability and are well known for their ability to counteract antiviral mechanisms. Accumulating evidence shows that some viruses are even capable of exploiting antiviral factors for efficient infection. In addition, antiviral factors may exert enhancing effects under specific circumstances. While much progress has been made in understanding the antiviral mechanisms of restriction factors, their proviral effects are poorly defined. Here, we summarize current knowledge on how viral pathogens may exploit otherwise antiviral cellular factors for efficient infection and replication.

Inhibition of miR-155 Promotes TGF-β Mediated Suppression of HIV Release in the Cervical Epithelial Cells

TGF-β has been shown to play a differential role in either restricting or aiding HIV infection in different cell types, however its role in the cervical cells is hitherto undefined. Among females, more than 80% of infections occur through heterosexual contact where cervicovaginal mucosa plays a critical role, however the early events during the establishment of infection at female genital mucosa are poorly understood. We earlier showed that increased TGF-β level has been associated with cervical viral shedding in the HIV infected women, however a causal relationship could not be examined. Therefore, here we first established an in vitro cell-associated model of HIV infection in the cervical epithelial cells (ME-180) and demonstrated that TGF-β plays an important role as a negative regulator of HIV release in the infected cervical epithelial cells. Inhibition of miR-155 upregulated TGF-β signaling and mRNA expression of host restriction factors such as APOBEC-3G, IFI-16 and IFITM-3, while decreased the HIV release in ME-180 cells. To conclude, this is the first study to decipher the complex interplay between TGF-β, miR-155 and HIV release in the cervical epithelial cells. Collectively, our data suggest the plausible role of TGF-β in promoting HIV latency in cervical epithelial cells which needs further investigations.

Less is more: Biased loss of CpG dinucleotides strengthens antiviral immunity

Viruses may not only affect our daily lives but also shape our genome evolution. A recent study shows that the zinc-finger antiviral protein (ZAP) drives CpG suppression in a biased manner. Genes involved in the defense against viral invaders are particularly CpG suppressed to avoid self-targeting and to promote an effective immune response.

TRIM22. A Multitasking Antiviral Factor

Viral invasion of target cells triggers an immediate intracellular host defense system aimed at preventing further propagation of the virus. Viral genomes or early products of viral replication are sensed by a number of pattern recognition receptors, leading to the synthesis and production of type I interferons (IFNs) that, in turn, activate a cascade of IFN-stimulated genes (ISGs) with antiviral functions. Among these, several members of the tripartite motif (TRIM) family are antiviral executors. This article will focus, in particular, on TRIM22 as an example of a multitarget antiviral member of the TRIM family. The antiviral activities of TRIM22 against different DNA and RNA viruses, particularly human immunodeficiency virus type 1 (HIV-1) and influenza A virus (IAV), will be discussed. TRIM22 restriction of virus replication can involve either direct interaction of TRIM22 E3 ubiquitin ligase activity with viral proteins, or indirect protein–protein interactions resulting in control of viral gene transcription, but also epigenetic effects exerted at the chromatin level.

Differential Inhibition of HIV Replication by the 12 Interferon Alpha Subtypes

Type I interferons (IFNs) are a family of cytokines that represent a first line of defense against virus infections. The 12 different IFN-α subtypes share a receptor on target cells and trigger similar signaling cascades. Several studies have collectively shown that this apparent redundancy conceals qualitatively different responses induced by individual subtypes, which display different efficacies of inhibition of HIV replication. Some studies, however, provided evidence that the disparities are quantitative rather than qualitative. Since RNA expression analyses show a large but incomplete overlap of the genes induced, they may support both models. To explore if the IFN-α subtypes induce functionally relevant different anti-HIV activities, we have compared the efficacies of inhibition of all 12 subtypes on HIV spread and on specific steps of the viral replication cycle, including viral entry, reverse transcription, protein synthesis, and virus release. Finding different hierarchies of inhibition would validate the induction of qualitatively different responses. We found that while most subtypes similarly inhibit virus entry, they display distinctive potencies on other early steps of HIV replication. In addition, only some subtypes were able to target effectively the late steps. The extent of induction of known anti-HIV factors helps to explain some, but not all differences observed, confirming the participation of additional IFN-induced anti-HIV effectors. Our findings support the notion that different IFN-α subtypes can induce the expression of qualitatively different antiviral activities. IMPORTANCE The initial response against viruses relies in large part on type I interferons, which include 12 subtypes of IFN-α. These cytokines bind to a common receptor on the cell surface and trigger the expression of incompletely overlapping sets of genes. Whether the anti-HIV responses induced by IFN-α subtypes differ in the extent of expression or in the nature of the genes involved remains debated. Also, RNA expression profiles led to opposite conclusions, depending on the importance attributed to the induction of common or distinctive genes. To explore if relevant anti-HIV activities can be differently induced by the IFN-α subtypes, we compared their relative efficacies on specific steps of the replication cycle. We show that the hierarchy of IFN potencies depends on the step analyzed, supporting qualitatively different responses. This work will also prompt the search for novel IFN-induced anti-HIV factors acting on specific steps of the replication cycle.

Evolutionary conflicts and adverse effects of antiviral factors

Human cells are equipped with a plethora of antiviral proteins protecting them against invading viral pathogens. In contrast to apoptotic or pyroptotic cell death, which serves as ultima ratio to combat viral infections, these cell-intrinsic restriction factors may prevent or at least slow down viral spread while allowing the host cell to survive. Nevertheless, their antiviral activity may also have detrimental effects on the host. While the molecular mechanisms underlying the antiviral activity of restriction factors are frequently well investigated, potential undesired effects of their antiviral functions on the host cell are hardly explored. With a focus on antiretroviral proteins, we summarize in this review how individual restriction factors may exert adverse effects as trade-off for efficient defense against attacking pathogens.