A count-based model for delineating cell-cell interactions in spatial transcriptomics data.

MOTIVATION: Cell-cell interactions (CCIs) consist of cells exchanging signals with themselves and neighboring cells by expressing ligand and receptor molecules and play a key role in cellular development, tissue homeostasis, and other critical biological functions. Since direct measurement of CCIs is challenging, multiple methods have been developed to infer CCIs by quantifying correlations between the gene expression of the ligands and receptors that mediate CCIs, originally from bulk RNA-sequencing data and more recently from single-cell or spatially resolved transcriptomics (SRT) data. SRT has a particular advantage over single-cell approaches, since ligand-receptor correlations can be computed between cells or spots that are physically close in the tissue. However, the transcript counts of individual ligands and receptors in SRT data are generally low, complicating the inference of CCIs from expression correlations. RESULTS: We introduce Copulacci, a count-based model for inferring CCIs from SRT data. Copulacci uses a Gaussian copula to model dependencies between the expression of ligands and receptors from nearby spatial locations even when the transcript counts are low. On simulated data, Copulacci outperforms existing CCI inference methods based on the standard Spearman and Pearson correlation coefficients. Using several real SRT datasets, we show that Copulacci discovers biologically meaningful ligand-receptor interactions that are lowly expressed and undiscoverable by existing CCI inference methods. AVAILABILITY AND IMPLEMENTATION: Copulacci is implemented in Python and available at https://github.com/raphael-group/copulacci.

DeST-OT: Alignment of Spatiotemporal Transcriptomics Data.

Spatially resolved transcriptomics (SRT) measures mRNA transcripts at thousands of locations within a tissue slice, revealing spatial variations in gene expression and distribution of cell types. In recent studies, SRT has been applied to tissue slices from multiple timepoints during the development of an organism. Alignment of this spatiotemporal transcriptomics data can provide insights into the gene expression programs governing the growth and differentiation of cells over space and time. We introduce DeST-OT (Developmental SpatioTemporal Optimal Transport), a method to align SRT slices from pairs of developmental timepoints using the framework of optimal transport (OT). DeST-OT uses semi-relaxed optimal transport to precisely model cellular growth, death, and differentiation processes that are not well-modeled by existing alignment methods. We demonstrate the advantage of DeST-OT on simulated slices. We further introduce two metrics to quantify the plausibility of a spatiotemporal alignment: a growth distortion metric which quantifies the discrepancy between the inferred and the true cell type growth rates, and a migration metric which quantifies the distance traveled between ancestor and descendant cells. DeST-OT outperforms existing methods on these metrics in the alignment of spatiotemporal transcriptomics data from the development of axolotl brain.

A phase 2a open-label clinical trial to determine the effect of famciclovir on EBV activity as measured by EBV shedding in the saliva of patients with multiple sclerosis.

BACKGROUND: Despite increasing evidence that Epstein-Barr virus (EBV) plays a causal role in MS, no treatments have been shown to reduce EBV turnover. We studied the effect of famciclovir on salivary EBV shedding in people with MS (NCT05283551) in a pilot, proof-of-concept study. METHODS: People with MS receiving natalizumab provided weekly saliva samples for 12 weeks before starting famciclovir 500 mg twice daily for 12 weeks. Twelve saliva samples were provided on treatment and 12 following treatment. A real-time qPCR Taqman assay was used to detect EBV DNA in saliva. The proportion of saliva samples containing EBV DNA was compared using the Friedman test. RESULTS: Of 30 participants (19 F; mean age 41 years; median EDSS 3.5), 29 received famciclovir, and 24 completed the 12-week course. Twenty-one participants provided at least one usable saliva sample in all epochs. Ten of the 21 had shedding in at least one sample pre-drug; 7/21 when taking famciclovir (not significant). No difference in EBV DNA copy number was seen. There were no drug-related serious adverse events. CONCLUSION: No significant effect of famciclovir on EBV shedding was seen in this small pilot study. Given the low numbers, a small effect of famciclovir cannot be excluded. Salivary EBV shedding in this natalizumab-treated cohort was lower than in previous studies, which requires replication.

Effect of teriflunomide on Epstein-Barr virus shedding in relapsing-remitting multiple sclerosis patients: Outcomes from a real-world pilot cohort study.

BACKGROUND: Given its potential antiviral activity, we investigated the effect of teriflunomide on EBV in patients with relapsing-remitting MS (RRMS). METHODS: Saliva samples were collected at home and analysed for EBV DNA presence in patients with RRMS treated with teriflunomide for ≥3 months. RESULTS: The proportion of patients with detectable EBV in the teriflunomide cohort was lower than in the reference cohorts. The proportion of samples with EBV DNA or shedding from teriflunomide-treated patients was reduced relative to each reference cohort (P<0.0001; >5.8 virus copies/µL cut-off). CONCLUSION: This pilot study demonstrated the feasibility of at-home saliva sample collection and revealed a possible effect of teriflunomide on EBV shedding.

Pathological manifestation of human endogenous retrovirus K in frontotemporal dementia.

BACKGROUND: Behavioral variant frontotemporal dementia (bvFTD) is a common form of younger-onset dementia with a proportion of cases overlapping pathologically and genetically with amyotrophic lateral sclerosis (ALS). Previous studies have identified that the human endogenous retrovirus K (HERV-K) is elevated in ALS serum and is associated with ALS TDP-43 pathology. In contrast, little is known about HERV-K changes in bvFTD. Here, we investigated the possible role of HERV-K in bvFTD. METHODS: We measured the HERV-K env gene in sporadic bvFTD (N=63), sporadic ALS (N=89) and control (N=21) serum by ddPCR. We also analyzed HERV-K env, by qPCR, and the HERV-K reverse transcriptase protein, by confocal immunofluorescence microscopy, in the disease-affected superior frontal cortex of bvFTD with TDP-43 pathology. RESULTS: Here, we show that HERV-K env levels are significantly elevated (P=3.5×10-6) in bvFTD compared to control serum, differentiating cases with an AUC value of 0.867. HERV-K env levels are also specifically elevated in the superior frontal cortex of bvFTD with TDP-43 pathology, with the HERV-K reverse transcriptase protein and TDP-43 deposit localized to the neuronal cytoplasm. Furthermore, in a neuronal cell line overexpression of TDP-43 induces HERV-K env transcription. CONCLUSIONS: These results suggest that manifestation of HERV-K is associated with bvFTD TDP-43 pathology. Analysis of HERV-K in bvFTD may provide insight into an unrecognized but targetable perturbed pathology.

Safety and tolerability of Triumeq in amyotrophic lateral sclerosis: the Lighthouse trial.

Background: Neuroinflammation and human endogenous retroviruses (HERV) are thought to have a role in the pathophysiology of amyotrophic lateral sclerosis (ALS). Therapy directed against endogenous retroviruses has demonstrated positive effects during in vitro and biomarker studies. Consequently, the present study was undertaken to assess the safety and tolerability of long-term antiretroviral therapy (ART), Triumeq (abacavir, lamivudine, and dolutegravir) exposure in patients with ALS, and efficacy against biomarkers of disease progression. Methods: Patients were observed during a 10-week lead-in period before receiving Triumeq treatment for 24 weeks at four specialist ALS centers. The primary outcomes were safety and tolerability. Secondary outcomes included HERV-K expression levels, urinary p75ECD levels, neurophysiological parameters, and clinical indicators. The ENCALS prediction model was applied to provide an estimate of the cohort survival. The trial was registered (NCT02868580). Findings: 40 patients with ALS received Triumeq and 35 (88%) completed treatment. There were no drug-related serious adverse events; one patient was withdrawn from the study due to a drug-associated increase in liver enzymes. A favorable response on HERV-K expression levels was observed, accompanied by a decline in ALSFRS-R progression rate of 21.8% (95% CI -4.8%-48.6%) and the amount of urinary p75ECD measured. One patient died five months after stopping treatment, while five were expected to have died during the treatment period (interquartile range 2-8). Interpretation: Long-term Triumeq exposure was safe and well tolerated in this cohort. There was suggestive indication for a possible biological response in some pharmacodynamic and clinical biomarkers. A larger international phase 3 trial will be deployed to assess the effect of Triumeq on overall survival and disease progression. Funding: Funding was provided by the FightMND Foundation; MND Research Institute of Australia; MND Association, United Kingdom, and GSK. ViiV Healthcare provided the Triumeq.

Epstein Barr virus shedding in multiple sclerosis: Similar frequencies of EBV in saliva across separate patient cohorts.

BACKGROUND: Epstein Barr Virus (EBV) infection is closely associated with multiple sclerosis (MS), but the relationship between viral load and disease activity is unclear. This study tested the observed levels of salivary EBV in MS, as a first step in investigating this relationship. METHODS: Real-time quantitative PCR (qPCR) was used to measure EBV DNA levels in saliva samples from three separate Multiple Sclerosis (MS) patient cohorts. RESULTS: The qPCR assay was used to delineate EBV shedding, defined here as a reliably detectable level of extracellular EBV DNA in saliva. Frequency of EBV shedding was found to be similar across the groups, with 20-25% of subjects releasing virus on any given sampling date. Diurnal variation in EBV count was tested in one of the cohorts, in which 26% of subjects showed more than a 10-fold difference between the highest and lowest EBV levels on a single day. In the same cohort, elevated viral levels at one time point did not predict elevated viral levels at a subsequent time point. CONCLUSIONS: These results indicate that EBV lytic activity in a subject cannot be inferred from a single measure of EBV in saliva. Also, subjects do not appear to be behave constantly as "EBV shedders" or "non-shedders". The assay is useful in giving a clear indication of salivary gland EBV lytic activity across a patient cohort - for example, in testing anti-viral drugs in MS.

A phase II baseline versus treatment study to determine the efficacy of raltegravir (Isentress) in preventing progression of relapsing remitting multiple sclerosis as determined by gadolinium-enhanced MRI: The INSPIRE study.

BACKGROUND: Although the aetiology of multiple sclerosis (MS) remains elusive, it is clear that Epstein Barr virus (EBV) and possibly other viruses play a role in the pathogenesis of MS. Laboratory evidence suggests that human endogenous retroviruses (HERVs) could also have a role, but no interventional therapy has determined what will happen if HERVs are suppressed. Recent epidemiological evidence indicates patients with HIV infection have a significantly lower risk of developing MS and that HIV antiretroviral therapies may be coincidentally inhibiting HERVs, or other retroelements, that could be implicated in MS. OBJECTIVES: To systematically investigate the effects of an HIV integrase strand inhibitor, raltegravir, on the number of gadolinium (Gd)-enhanced MRI lesions in people with active relapsing MS. METHODS: This is a Phase 2a clinical trial where twenty participants were enrolled in a 3 month baseline phase followed by 3 months of treatment with raltegravir 400 mg twice a day. Patients had monthly Gd-enhanced MRI, saliva collection to test for EBV shedding, blood sampling for safety monitoring, virology (including HERVs), measurement of immunological and inflammatory markers; and physical, neurological and quality-of-life assessments. RESULTS: All patients completed the six months trial period.The primary outcome measure of MS disease activity was the number of Gd-enhancing lesions observed, and raltegravir had no significant effect on the rate of development of Gd-enhancing lesions during the treatment phase compared with the baseline phase. Additionally, there was no change in secondary outcomes of either disability or quality-of-life measures that could reasonably be attributed to the intervention. There was a significant positive between HERV-W/MSRV (multiple sclerosis related virus) Gag Flix (Fluorescence index) B cells and the number of Gd-enhanced lesions at any visit (p = 0.029), which was independent of any potential influence of the trial drug administration. Regarding EBV shedding, there was no significant correlation between the amount of EBV shedding and the number of lesions. No change was detected in inflammatory markers (IL-8, IL-1ß, IL-6, IL-10, TNF, IL-12p70 and HCRP), which were all within normal limits both before and after the intervention. Serum CD163 expression was also unchanged by raltegravir. CONCLUSIONS: Raltegravir did not have any impact on MS disease activity. This could be due to the choice of antiretroviral agent used in this study, the need for a combination of agents, as used in treating HIV infection, the short treatment period or dosing regimen, or the lack of a role of HERV expression in MS once the disease is established. Borderline significance for the association between EBV shedding and the total number of lesions, probably driven by new lesion development, may indicate EBV shedding as a marker of inflammatory disease activity. In conclusion, interesting correlations between HERV-W markers, EBV shedding and new MRI lesions, independent from treatment effects, were found.

Human Endogenous Retroviruses in Neurological Diseases.

The causes of multiple sclerosis and amyotrophic lateral sclerosis have long remained elusive. A new category of pathogenic components, normally dormant within human genomes, has been identified: human endogenous retroviruses (HERVs). These represent ∼8% of the human genome, and environmental factors have reproducibly been shown to trigger their expression. The resulting production of envelope (Env) proteins from HERV-W and HERV-K appears to engage pathophysiological pathways leading to the pathognomonic features of MS and ALS, respectively. Pathogenic HERV elements may thus provide a missing link in understanding these complex diseases. Moreover, their neutralization may represent a promising strategy to establish novel and more powerful therapeutic approaches.

Using eHealth to engage and retain priority populations in the HIV treatment and care cascade in the Asia-Pacific region: a systematic review of literature.

BACKGROUND: The exponential growth in the reach and development of new technologies over the past decade means that mobile technologies and social media play an increasingly important role in service delivery models to maximise HIV testing and access to treatment and care. This systematic review examines the impact of electronic and mobile technologies in medical care (eHealth) in the linkage to and retention of priority populations in the HIV treatment and care cascade, focussing on the Asia-Pacific region. METHODS: The review was informed by the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement from the Cochrane Collaboration guidelines. Both grey and published scientific literature from five different databases were searched for all original articles in English published from 2010 to 2017. Studies conducted outside the Asia-Pacific region or not including HIV priority populations were excluded. The methodological quality of studies included in the review was assessed using the Quality Assessment Tool for Quantitative Studies. RESULTS: The database search identified 7309 records. Of the 224 peer-reviewed articles identified for full text review, 16 studies from seven countries met inclusion criteria. Six cross sectional studies found evidence to support the use of eHealth, via text messages, instant messaging, social media and health promotion websites, to increase rates of HIV testing and re-testing among men who have sex with men (MSM). Evidence regarding the efficacy of eHealth interventions to improve antiretroviral treatment (ART) adherence was mixed, where one randomised controlled trial (RCT) showed significant benefit of weekly phone call reminders on improving ART adherence. Three further RCTs found that biofeedback eHealth interventions that provided estimated ART plasma concentration levels, showed promising results for ART adherence. CONCLUSIONS: This review found encouraging evidence about how eHealth can be used across the HIV treatment and care cascade in the Asia-Pacific region, including increasing HIV testing and re-testing in priority populations as well as ART adherence. eHealth interventions have an important role to play in the movement towards the end of AIDS, particularly to target harder-to-reach HIV priority populations, such as MSM.

Prehistoric enemies within: The contribution of human endogenous retroviruses to neurological diseases. Meeting report: "Second International Workshop on Human Endogenous Retroviruses and Disease", Washington DC, March 13th and 14th 2017.

The Second International Workshop on Human Endogenous Retroviruses and Disease, Washington DC, March 13-14 2017 brought together international basic and clinical scientists investigating the involvement of human endogenous retroviruses (HERVs) in complex human diseases.

HIV and lower risk of multiple sclerosis: beginning to unravel a mystery using a record-linked database study.

OBJECTIVES: Even though multiple sclerosis (MS) and HIV infection are well-documented conditions in clinical medicine, there is only a single case report of a patient with MS and HIV treated with HIV antiretroviral therapies. In this report, the patient's MS symptoms resolved completely after starting combination antiretroviral therapy and remain subsided for more than 12 years. Authors hypothesised that because the pathogenesis of MS has been linked to human endogenous retroviruses, antiretroviral therapy for HIV may be coincidentally treating or preventing progression of MS. This led researchers from Denmark to conduct an epidemiological study on the incidence of MS in a newly diagnosed HIV population (5018 HIV cases compared with 50,149 controls followed for 31,875 and 393,871 person-years, respectively). The incidence rate ratio for an HIV patient acquiring MS was low at 0.3 (95% CI 0.04 to 2.20) but did not reach statistical significance possibly due to the relatively small numbers in both groups. Our study was designed to further investigate the possible association between HIV and MS. METHODS: We conducted a comparative cohort study accessing one of the world's largest linked medical data sets with a cohort of 21,207 HIV-positive patients and 5,298,496 controls stratified by age, sex, year of first hospital admission, region of residence and socioeconomic status and 'followed up' by record linkage. RESULTS: Overall, the rate ratio of developing MS in people with HIV, relative to those without HIV, was 0.38 (95% CI 0.15 to 0.79). CONCLUSIONS: HIV infection is associated with a significantly decreased risk of developing MS. Mechanisms of this observed possibly protective association may include immunosuppression induced by chronic HIV infection and antiretroviral medications.

Look-back investigation of a health care worker infected with human immunodeficiency virus.

We report the referral of an HIV-infected surgeon and a subsequent first-ever recommended look-back investigation in Hong Kong. Efficient coordination and effective implementation of the look-back investigation yielded a high response rate of 92.3% of priority patients, with none tested HIV positive. Our experience reconfirmed the very small risk of provider-to-patient HIV transmission and the crucial importance of infection control.

The economics of effective AIDS treatment in Thailand.

INTRODUCTION: The speed with which Thailand has scaled up public provision of antiretroviral therapy (ART) has been unprecedented, with more than 80 000 individuals on treatment at the end of 2006 through Thailand's National Access to Antiretroviral Program for People Living with HIV/AIDS (NAPHA). This paper projects the cost effectiveness, the affordability and the future fiscal burden of NAPHA to the government of Thailand under several different policy scenarios until the year 2025. METHODS: An economic/epidemiological model of access to ART was constructed, and this composite model was calibrated to economic and epidemiological data from Thailand and other countries. The economic model adopts the conditional logit specification of demand allocation across multiple treatment modes, and the epidemiological model is a deterministic difference-equation model fitted to the cumulated data on HIV incidence in each risk group. RESULTS: The paper estimates that under 2005 prices NAPHA will save life-years at approximately US$736 per life-year saved with first-line drugs alone and for approximately US$2145 per life-year if second-line drugs are included. Enhancing NAPHA with policies to recruit patients soon after they are first eligible for ART or to enhance their adherence would raise the cost per life-year saved, but the cost would be small per additional life-year saved, and is therefore justifiable. The fiscal burden of a policy including second as well as first-line drugs would be substantial, rising to 23% of the total health budget by 2014, but the authors judge this cost to be affordable given Thailand's strong overall economic performance. The paper estimates that a 90% reduction in the future cost of second-line therapy by the exercise of Thailand's World Trade Organization authority to issue compulsory licences would save the government approximately US$3.2 billion to 2025 and reduce the cost of NAPHA per life-year saved from US$2145 to approximately US$940.

Antiretroviral therapy and HIV prevention in India: modeling costs and consequences of policy options.

OBJECTIVES: The objective of this study is to assess the costs, cost-effectiveness, and HIV epidemic impact of 3 antiretroviral therapy (ART) policy options. STUDY DESIGN: We constructed an epidemiologic model to predict the course of the HIV epidemic in the absence of expanded ART availability. Based on background studies of the willingness to pay for ART among patients with AIDS, of the costs to the government of the alternative treatment interventions, and of ART's likely effects on HIV transmission, we simulated the consequences of 3 possible alternative government ART policies. RESULTS: A program to reduce the negative consequences of the currently unstructured private-sector provision of ART is the most cost-effective of the 3 options at a 10% discount rate and least cost-effective at a 3% rate. The costs and cost-effectiveness of all options are highly sensitive to the effect of ART on condom use. CONCLUSION: The design of ART policy should capitalize on the potential of ART to decrease HIV transmission through institutional arrangements that reward effective prevention programs, thereby raising the likelihood that treatment has beneficial rather than negative external effects.

Early clinical experience with atazanavir in treatment-experienced patients.

BACKGROUND: Atazanavir (ATV) is a newly approved protease inhibitor following successful clinical trials in naive and treatment-experienced patients. We describe early experience with ATV in treatment-experienced patients attending a single ambulatory care clinic in Sydney. METHODS: Patients commencing ATV between February 2003 and May 2004 in an expanded access program were identified from the clinic pharmacy's database. Data were retrospectively collected from patients' medical records. RESULTS: Data from 30 patients were analysed. Reasons for commencing ATV were: virological failure in six patients (20%); toxicity to previous regimen in 13 patients (43%); simplification strategy in two patients (7%); and recommencing therapy in nine patients (30%) following treatment interruption. Six patients (20%) discontinued ATV. One patient discontinued ATV due to virological failure, two patients discontinued due to toxicity to concomitant antiretrovirals, two as a result of the patient's choice and one as a result of the physician's decision. Eighteen patients commenced ATV in combination therapy with a detectable viral load (VL). From a baseline VL of 4.3 +/- 1.1 log10 copies mL(-1), 15 (83%) had > 1.0 log decrease in VL with 11 (61%) achieving viral suppression (<50 copies mL(-1)). Three (16%) failures were recorded in this group. Twelve subjects commenced ATV with an undetectable VL. One failure was recorded in this group. Bilirubin increased by 22.7 micromol L(-1) (P < 0.001), with significant decreases in cholesterol (1.4 mmol L(-1), P = 0.01) and triglycerides (1.5 mmol L(-1), P = 0.01) in 12 patients on ritonavir-boosted ATV. CONCLUSION: This audit found ATV to be safe, well tolerated and had good potency in treatment-experienced patients. However caution should be exercised in switching to ATV in heavily pre-treated patients.

Altered lymphocyte heat shock protein 70 expression in patients with HIV disease.

Heat shock protein (HSP) expression in lymphocytes isolated from 20 patients with HIV disease and 15 age-matched controls was determined. Fold increases in lymphocyte hsp70 expression after heat shock were 4.52 +/- 2.97 in HIV-positive individuals compared with 2.60 +/- 1.29 for HIV-negative controls (P= 0.001). Given clear roles for HSP in the cross-presentation of antigens, alpha-defensin internalization and pro-inflammatory cytokine production, a further investigation of HSP in HIV patients is merited.