Multiple shRNA combinations for near-complete coverage of all HIV-1 strains

Intergenerational spillover effects of antiretroviral therapy in sub-Saharan Africa: a scoping review and future directions for research

BACKGROUND

Antiretroviral therapy (ART) may influence individuals who do not receive the intervention but who are connected in some way to the person who does. Relatively little is known, however, about the size and scope of, what we term, spillover effects of ART. We explored intergenerational spillover effects of ART in sub-Saharan Africa (SSA) and identified several directions for future research.

METHODS

We conducted a scoping review between March and April 2022. We systematically searched PubMed, PsycINFO, EconLit, OTseeker, AIDSInfo, Web of Science, CINHAL, Google Scholar and African Index Medicus. We analysed the distribution of included studies over time and summarised their findings. We examined the intergenerational impact of ART provision to working-age adults living with HIV on children ('downward' spillover effects) and older adults ('upward' spillover effects). We categorised types of intergenerational spillover effects according to broad themes which emerged from our analysis of included studies.

FINDINGS

We identified 26 studies published between 2005 and 2022 with 16 studies assessing spillover effects from adults to children (downward), and 1 study explicitly assessing spillover effects from working-age adults to older adults (upward). The remaining studies did not fully specify the direction of spillover effects. Most spillover effects of ART to household and family members were beneficial and included improvements in wealth, labour market outcomes, health outcomes and health services utilisation, schooling, and household composition. Both children and older adults benefited from ART availability among adults. Detrimental spillover effects were only reported in three studies and included financial and opportunity costs associated with health services utilisation and food insecurity in the first year after ART.

CONCLUSIONS

ART may lead to substantial spillover effects across generations and sectors in SSA. Further research is needed to capitalise on positive spillover effects while mitigating potential negative spillover effects. The returns to investments in large-scale health interventions such as ART may be underestimated without considering these societal benefits.

Multiplexed shRNA-miRs as a candidate for anti HIV-1 therapy: strategies, challenges, and future potential

The spread of HIV is on the rise and has become a global issue, especially for underdeveloped and developing countries. This is due to the fact that HIV majorly occurs asymptomatically and is implausible for early diagnosis. Recent advances in research and science have enabled the investigation of a new potential treatment involving gene-based therapy, known as RNA interference (RNAi) that will direct gene silencing and further compensate for natural variants and viral mutants. Several types of small regulatory RNA are discussed in this present study, including microRNA (miRNA), small interfering RNA (siRNA), and short hairpin RNA (shRNA).This paper examines the mechanism of RNAi as a viable HIV therapy, using a minimum of four shRNAs to target both dispensable host components (CCR5) and viral genes (Gag, Env, Tat, Pol I, Pol II and Vif). Moreover, a multiplexed mechanism of shRNAs and miRNA is known to be effective in preventing viral escape due to mutation as the miRNA develops a general polycistronic platform for the expression of a large amount of shRNA-miRs. Several administration methods as well as the advantages of this RNAi treatment are also discussed in this study. The administration methods include (1) ex vivo delivery with the help of viral vectors, nanoparticles, and electroporation, (2) nonspecific in vivo delivery using non-viral carriers including liposomes, dendrimers and aptamers, as well as (3) targeted delivery that uses antibodies, modified nanoparticles, nucleic acid aptamers, and tissue-specific serotypes of AAV. Moreover, the advantages of this treatment are related to the effectiveness in silencing the HIV gene, which is more compatible compared to other gene therapy treatments, such as ZFN, TALEN, and CRISPR/Cas9.

Predictors of first-line antiretroviral treatment failure among children on antiretroviral therapy at the University of Gondar comprehensive specialised hospital, North-west, Ethiopia: a 14-year long-term follow-up study

OBJECTIVE

To determine the incidence and predictors of first-line human immune deficiency virus treatment failure among human immune deficiency virus-infected children at the University of Gondar comprehensive specialised hospital in Ethiopia.

DESIGN

A retrospective follow-up study.

SETTING

University of Gondar comprehensive specialised hospital, North-west, Ethiopia.

PARTICIPANTS

Children were among the HIV infected from January 2005 to December 2018. There were 336 children included in the study. The data were entered into EPi Info V.7.2 and then exported to STATA V.14.0 Software for analysis. Both bivariable and multivariable analyses with Cox proportional hazards models were used to identify the predictors of treatment failure.

PRIMARY OUTCOME MEASURES

Predictors of first-line antiretroviral treatment failure among children on antiretroviral therapy (ART) during 14 years long-term follow-up study.

RESULT

A total of 336 human immunodeficiency virus-infected children participated in this study with 27 058 child years of observation. The overall incidence rate was 2.1 (95% CI 1.57 to 2.78) per 100 child years. Poor adherence (adjusted HR (AHR); 6.5 (95% CI 2.03 to 21.39)), fair adherence (AHR; 6.55 (95% CI 2.64 to 16.53), the presence of opportunistic infection (AHR; 4.22 (95% CI 1.44 to 12.30), clinical staging of III/IV (AHR; 3.08 (95% CI 1.17 to 8.08) and a baseline CD4 count less than 200 cells/mm³ (AHR; 3.61 (95% CI 1.12 to 11.54)).

CONCLUSION

The incidence of first-line ART failure was found to be high. Baseline opportunistic infection, poor and fair adherence, advanced WHO clinical staging III/IV and a CD4 count less than 200 cells/mm³ were all predictors of first-line treatment failure. Early identification of associated factors and monitoring treatment failure has to be important for the optimal management of HIV-infected children who are receiving ART and to prevent further complications.

Factors associated with anti-retroviral therapy (ART) adherence among adult people living with HIV (PLWH): A 5-year retrospective multi-centre study in Kumasi, Ghana

Background

Combined antiretroviral therapy (cART) is the recommended treatment regimen for people living with HIV (PLWH). Long-term HIV treatment of over 95% adherence inhibits increase in viral load and boosts immune system performance. On the contrary, non-adherence results in treatment failure, accelerated development of HIV drug-resistance and increased mortality. However, there is paucity of data on the prevalence of antiretroviral therapy (ART) adherence and its associated factors in Ghana. We assessed the prevalence, sociodemographic and clinical factors associated with ART adherence among registered PLWH.

Methods

In a multi-centre hospital-based retrospective study, we collected data on 720 registered PLWH 18 years and above, who attend the HIV clinic at the University Hospital (KNUST), Komfo Anokye Teaching Hospital (KATH), and the Bomso Clinic, on ART and with up-to-date medical records. They were enrolled using a multistage sampling technique. Adherence was assessed retrospectively using missed doses and prescriptions renewal. All analysis were done using SPSS Version 26.0 and GraphPad prism version 8.0.

Results

Of 720 registered PLWH, 51.8% had good ART adherence, 35.3% had fair ART adherence and 12.9% had poor ART adherence. Those diagnosed at WHO stage II (aOR = 0.45, 95% CI: (0.30-0.68); p < 0.0001) and stage III (aOR = 0.40, 95% CI: (0.27-0.59) < 0.0001) were independently associated with lower chances of good adherence to ART. Moreover, those treated with AZT/3TC/EFV (aOR = 0.33, 95% CI: (0.16-0.68); p = 0.0030), and AZT/3TC/NVP (aOR = 0.50, 95% CI: (0.26-0.98); p = 0.0410) were independently associated with lower likelihood of good ART adherence. On the contrary, PLWH who have been on treatment for 4 years (aOR = 3.56, 95% CI: (1.10-11.54); p = 0.0340) was an independent predictor of good ART adherence.

Conclusion

About half of PLWH on treatment have good adherence to ART. Being diagnosed at WHO stage II and stage III, being treated with AZT/3TC/EFV, and AZT/3TC/NVP ART combination are associated with lesser chances of good ART adherence. However, increased duration of ART among PLWH influence good ART adherence. PLWH on ART should be monitored to achieve over 95% ART adherence for effective management of HIV/AIDS.

Dyslipidemia and Associated Factors Among Adult Patients on Antiretroviral Therapy in Armed Force Comprehensive and Specialized Hospital, Addis Ababa, Ethiopia

Background

The development of antiretroviral drugs and subsequent access to combined antiretroviral therapy contributed to the decline in morbidity and mortality rates associated with acquired immune deficiency syndrome, resulting in an increased life expectancy and improved quality of life for people living with human immunodeficiency virus. However, a cluster of metabolic derangements such as dyslipidemia is increasing, especially for those on antiretroviral therapy. Limited studies were done on the prevalence of dyslipidemia and its associated factors among adult patients on antiretroviral therapy in Ethiopia which demand the conduct of the present investigation entitled on the prevalence of dyslipidemia and its associated factors among adult patients on antiretroviral therapy in Armed Force Comprehensive and Specialized Hospital Addis Ababa, Ethiopia, 2018.

Methods

Institution-based cross-sectional study design was employed between March and April 2018. Systematic sampling method was used to select 353 study participants. Pretested stepwise approach of the World Health Organization questionnaire (WHO Stepwise), document review, anthropometric measurements, and laboratory analysis were used to collect data on different variables under the study. Collected data were entered in Epidata version 3 and analyzed by SPSS version 21.

Results

The prevalence of dyslipidemia among study participants was 74.8%. Female participants were twice and half at risk of developing dyslipidemia compared to males (AOR= 2.38; 95% CI: 1.15, 3.66). Similarly, compared to those attended college level of education, not attended formal education (AOR=0.19; 95% CI: 0.05, 0.66), and having primary/secondary educational level (AOR= 0.33; 95% CI: 0.16, 0.66) showed lower odds to develop dyslipidemia. Furthermore, WHO clinical stage II (AOR= 0.35; 95% CI: 0.14,0.92), stage III (AOR=0.25; 95% CI:0.10,0.64), duration on ART (AOR= 1.01; 95% CI: 1.001,1.02), and BMI (AOR =1.13; 95% CI: 1.06,1.23) were significantly associated with dyslipidemia.

Conclusion

There exists a high prevalence of dyslipidemia among study participants. Sex, educational status, WHO clinical stage, duration on ART, and BMI were significantly associated factors for dyslipidemia. Intervention strategies including the identified factors are demanded in the setting.

CRISPR-Cas13a Inhibits HIV-1 Infection

CRISPR-Cas provides bacteria and archaea with immunity against invading phages and foreign plasmid DNA and has been successfully adapted for gene editing in a variety of species. The class 2 type VI CRISPR-Cas effector Cas13a targets and cleaves RNA, providing protection against RNA phages. Here we report the repurposing of CRISPR-Cas13a to inhibit human immunodeficiency virus type 1 (HIV-1) infection through targeting HIV-1 RNA and diminishing viral gene expression. We observed strong inhibition of HIV-1 infection by CRISPR-Cas13a in human cells. We showed that CRISPR-Cas13a not only diminishes the level of newly synthesized viral RNA, either from the transfected plasmid DNA or from the viral DNA, which is integrated into cellular DNA, but it also targets and destroys the viral RNA that enters cells within viral capsid, leading to strong inhibition of HIV-1 infection. Together, our results suggest that CRISPR-Cas13a provides a potential novel tool to treat viral diseases in humans.

Novel AgoshRNA molecules for silencing of the CCR5 co-receptor for HIV-1 infection

Allogeneic transplantation of blood stem cells from a CCR5-Δ32 homozygous donor to an HIV-infected individual, the “Berlin patient”, led to a cure. Since then there has been a search for approaches that mimic this intervention in a gene therapy setting. RNA interference (RNAi) has evolved as a powerful tool to regulate gene expression in a sequence-specific manner and can be used to inactivate the CCR5 mRNA. Short hairpin RNA (shRNA) molecules can impair CCR5 expression, but these molecules may cause unintended side effects and they will not be processed in cells that lack Dicer, such as monocytes. Dicer-independent RNAi pathways have opened opportunities for new AgoshRNA designs that rely exclusively on Ago2 for maturation. Furthermore, AgoshRNA processing yields a single active guide RNA, thus reducing off-target effects. In this study, we tested different AgoshRNA designs against CCR5. We selected AgoshRNAs that potently downregulated CCR5 expression on human T cells and peripheral blood mononuclear cells (PBMC) and that had no apparent adverse effect on T cell development as assessed in a competitive cell growth assay. CCR5 knockdown significantly protected T cells from CCR5 tropic HIV-1 infection.

Recent advances in RNAi-based strategies for therapy and prevention of HIV-1/AIDS

RNA interference (RNAi) provides a powerful tool to silence specific gene expression and has been widely used to suppress host factors such as CCR5 and/or viral genes involved in HIV-1 replication. Newer nuclease-based gene-editing technologies, such as zinc finger nucleases (ZFN), transcription activator-like effector nucleases (TALEN) and the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system, also provide powerful tools to ablate specific genes. Because of differences in co-receptor usage and the high mutability of the HIV-1 genome, a combination of host factors and viral genes needs to be suppressed for effective prevention and treatment of HIV-1 infection. Whereas the continued presence of small interfering/short hairpin RNA (si/shRNA) mediators is needed for RNAi to be effective, the continued expression of nucleases in the gene-editing systems is undesirable. Thus, RNAi provides the only practical way for expression of multiple silencers in infected and uninfected cells, which is needed for effective prevention/treatment of infection. There have been several advances in the RNAi field in terms of si/shRNA design, targeted delivery to HIV-1 susceptible cells, and testing for efficacy in preclinical humanized mouse models. Here, we comprehensively review the latest advances in RNAi technology towards prevention and treatment of HIV-1.

RNA interference approaches for treatment of HIV-1 infection

HIV/AIDS is a chronic and debilitating disease that cannot be cured with current antiretroviral drugs. While combinatorial antiretroviral therapy (cART) can potently suppress HIV-1 replication and delay the onset of AIDS, viral mutagenesis often leads to viral escape from multiple drugs. In addition to the pharmacological agents that comprise cART drug cocktails, new biological therapeutics are reaching the clinic. These include gene-based therapies that utilize RNA interference (RNAi) to silence the expression of viral or host mRNA targets that are required for HIV-1 infection and/or replication. RNAi allows sequence-specific design to compensate for viral mutants and natural variants, thereby drastically expanding the number of therapeutic targets beyond the capabilities of cART. Recent advances in clinical and preclinical studies have demonstrated the promise of RNAi therapeutics, reinforcing the concept that RNAi-based agents might offer a safe, effective, and more durable approach for the treatment of HIV/AIDS. Nevertheless, there are challenges that must be overcome in order for RNAi therapeutics to reach their clinical potential. These include the refinement of strategies for delivery and to reduce the risk of mutational escape. In this review, we provide an overview of RNAi-based therapies for HIV-1, examine a variety of combinatorial RNAi strategies, and discuss approaches for ex vivo delivery and in vivo delivery.

Who wants to adopt and who wants to be adopted: a sample of American families and sub-Saharan African orphans

The debate between pro- and anti-international adoption advocates relies heavily on rhetoric and little on data analysis. To better understand the state of orphans and potential adopters in this debate, we utilize the National Survey of Family Growth (NSFG) and the Demographic and Health Surveys (DHS) to study who adopts internationally and the status of orphaned children in sub-Saharan Africa. According to NSFG data adopters are church going, highly educated, stable families aware of the challenges faced by international adoption, with high rates of infertility and rates of child abuse half the population average. According to the DHS data, orphans in sub-Saharan Africa suffer from significantly higher deprivation, reduced schooling and increased levels of stunting and underweight reported than their cohort. Using this data, we estimate conservatively that that 1 50 000 orphans from our sample of sub-Saharan African countries died from their 5-year birth cohort. Given the large number of families seeking to adopt and the high number of orphan deaths, it seems counterproductive to restrict international adoptions given the significantly lower risks faced by children in adopted families compared with remaining orphaned.

Multiplexing seven miRNA-Based shRNAs to suppress HIV replication

Multiplexed miRNA-based shRNAs (shRNA-miRs) could have wide potential to simultaneously suppress multiple genes. Here, we describe a simple strategy to express a large number of shRNA-miRs using minimal flanking sequences from multiple endogenous miRNAs. We found that a sequence of 30 nucleotides flanking the miRNA duplex was sufficient for efficient processing of shRNA-miRs. We inserted multiple shRNAs in tandem, each containing minimal flanking sequence from a different miRNA. Deep sequencing of transfected cells showed accurate processing of individual shRNA-miRs and that their expression did not decrease with the distance from the promoter. Moreover, each shRNA was as functionally competent as its singly expressed counterpart. We used this system to express one shRNA-miR targeting CCR5 and six shRNA-miRs targeting the HIV-1 genome. The lentiviral construct was pseudotyped with HIV-1 envelope to allow transduction of both resting and activated primary CD4 T cells. Unlike one shRNA-miR, the seven shRNA-miR transduced T cells nearly abrogated HIV-1 infection in vitro. Additionally, when PBMCs from HIV-1 seropositive individuals were transduced and transplanted into NOD/SCID/IL-2R γc(-/-) mice (Hu-PBL model) efficient suppression of endogenous HIV-1 replication with restoration of CD4 T cell counts was observed. Thus, our multiplexed shRNA appears to provide a promising gene therapeutic approach for HIV-1 infection.

Safe, long-term hepatic expression of anti-HCV shRNA in a nonhuman primate model. Mol Ther. 2012;20:1737-1749. [PMID: 22735378 PMCID: PMC3437581 DOI: 10.1038/mt.2012.119]

The hepatitis C virus (HCV) chronically infects 2% of the world population and effective treatment is limited by long duration and significant side-effects. Here, we describe a novel drug, intended as a “single-shot ” therapy, which expresses three short hairpin RNAs (shRNAs) that simultaneously target multiple conserved regions of the HCV genome as confirmed in vitro by knockdown of an HCV replicon system. Using a recombinant adeno-associated virus (AAV) serotype 8 vector for delivery, comprehensive transduction of hepatocytes was achieved in vivo in a nonhuman primate (NHP) model following a single intravenous injection. However, dose ranging studies performed in 13 NHP resulted in high-expression levels of shRNA from wild-type (wt) Pol III promoters and dose-dependent hepatocellular toxicity, the first demonstration of shRNA-related toxicity in primates, establishing that the hepatotoxicity arises from highly conserved features of the RNA interference (RNAi) pathway. In the second generation drug, each promoter was re-engineered to reduce shRNA transcription to levels that circumvent toxicity but still inhibit replicon activity. In vivo testing of this modified construct in 18 NHPs showed conservation of hepatocyte transduction but complete elimination of hepatotoxicity, even with sustained shRNA expression for 50 days. These data support progression to a clinical study for treatment of HCV infection.

HIV develops indirect cross-resistance to combinatorial RNAi targeting two distinct and spatially distant sites

Resistance to existing HIV therapies is an increasing problem, and alternative treatments are urgently needed. RNA interference (RNAi), an innate mechanism for sequence-specific gene silencing, can be harnessed therapeutically to treat viral infections, yet viral resistance can still emerge. Here, we demonstrate that HIV can develop indirect resistance to individual and combinatorial RNAi-targeting protein-coding regions up to 5,500 nucleotides (nt) downstream of the viral promoter. We identify several variants harboring mutations in the HIV promoter, and not within the RNAi targets, that produce more fully elongated transcripts. Furthermore, these variants are resistant to the RNAi, potentially by stoichiometrically overwhelming this cellular mechanism. Alarmingly, virus resistant to one short hairpin RNA (shRNA) also exhibits cross-resistance to a different shRNA, which targets a distinct and spatially distant region to which the virus has not been previously exposed. To our knowledge, this is the first example of HIV "cross-resistance" to viral inhibitors targeting different loci. Finally, combining anti-HIV RNAi with a small molecule enhancer of RNAi can inhibit the replication of an indirectly resistant mutant. These results suggest that indirect resistance to RNAi is a general mechanism that should be considered when investigating viral resistance and designing combinatorial RNAi therapies.

In vitro characterization of the activity of PF-05095808, a novel biological agent for hepatitis C virus therapy. Antimicrob Agents Chemother. 2012;56:1364-1375. [PMID: 22203606 DOI: 10.1128/aac.05357-11]

PF-05095808 is a novel biological agent for chronic hepatitis C virus (HCV) therapy. It comprises a recombinant adeno-associated virus (AAV) DNA vector packaged into an AAV serotype 8 capsid. The vector directs expression of three short hairpin RNAs (shRNAs) targeted to conserved regions of the HCV genome. These shRNAs are processed by the host cell into the small interfering RNAs which mediate sequence-specific cleavage of target regions. For small-molecule inhibitors the key screens needed to assess in vitro activity are well defined; we developed new assays to assess this RNA interference agent and so to understand its therapeutic potential. Following administration of PF-05095808 or corresponding synthetic shRNAs, sequence-specific antiviral activity was observed in HCV replicon and infectious virus systems. To quantify the numbers of shRNA molecules required for antiviral activity in vitro and potentially also in vivo, a universal quantitative PCR (qPCR) assay was developed. The number of shRNA molecules needed to drive antiviral activity proved to be independent of the vector delivery system used for PF-05095808 administration. The emergence of resistant variants at the target site of one shRNA was characterized. A novel RNA cleavage assay was developed to confirm the spectrum of activity of PF-05095808 against common HCV clinical isolates. In summary, our data both support antiviral activity consistent with an RNA interference mechanism and demonstrate the potential of PF-05095808 as a therapeutic agent for chronic HCV infection.

HIVsirDB: a database of HIV inhibiting siRNAs

BACKGROUND

Human immunodeficiency virus (HIV) is responsible for millions of deaths every year. The current treatment involves the use of multiple antiretroviral agents that may harm patients due to their toxic nature. RNA interference (RNAi) is a potent candidate for the future treatment of HIV, uses short interfering RNA (siRNA/shRNA) for silencing HIV genes. In this study, attempts have been made to create a database HIVsirDB of siRNAs responsible for silencing HIV genes.

DESCRIPTIONS

HIVsirDB is a manually curated database of HIV inhibiting siRNAs that provides comprehensive information about each siRNA or shRNA. Information was collected and compiled from literature and public resources. This database contains around 750 siRNAs that includes 75 partially complementary siRNAs differing by one or more bases with the target sites and over 100 escape mutant sequences. HIVsirDB structure contains sixteen fields including siRNA sequence, HIV strain, targeted genome region, efficacy and conservation of target sequences. In order to facilitate user, many tools have been integrated in this database that includes; i) siRNAmap for mapping siRNAs on target sequence, ii) HIVsirblast for BLAST search against database, iii) siRNAalign for aligning siRNAs.

CONCLUSION

HIVsirDB is a freely accessible database of siRNAs which can silence or degrade HIV genes. It covers 26 types of HIV strains and 28 cell types. This database will be very useful for developing models for predicting efficacy of HIV inhibiting siRNAs. In summary this is a useful resource for researchers working in the field of siRNA based HIV therapy. HIVsirDB database is accessible at http://crdd.osdd.net/raghava/hivsir/.

Antiviral RNAi: translating science towards therapeutic success

Viruses continuously evolve to contend with an ever-changing environment that involves transmission between hosts and sometimes species, immune responses, and in some cases therapeutic interventions. Given the high mutation rate of viruses relative to the timescales of host evolution and drug development, novel drug classes that are readily screened and translated to the clinic are needed. RNA interference (RNAi)—a natural mechanism for specific degradation of target RNAs that is conserved from plants to invertebrates and vertebrates—can potentially be harnessed to yield therapies with extensive specificity, ease of design, and broad application. In this review, we discuss basic mechanisms of action and therapeutic applications of RNAi, including design considerations and areas for future development in the field.