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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2018

Towards Improving Embryo Selection: Simultaneous Next Generation Sequencing Of DNA And RNA From A Single Trophectoderm Biopsy

Improved embryo selection is crucial in optimizing the results from assisted reproduction. Preimplantation genetic screening reduces time to pregnancy and miscarriages. Correlating the transcriptome of an embryo, with fertility treatments and outcomes, holds promise in improving the overall results. We developed a novel method for embryo selection in fertility treatments that integrates embryonic genomic and transcriptomic data and evaluated it in this pilot study.\n\nA total of 21 embryos donated for research were included. Three were used for the initial development and optimization of sample processing and sequencing. Thereafter, 18 embryos were used to demonstrate the clinical safety and reproducibility of our method. Two trophectoderm biopsies were taken from each embryo: one was processed as a clinical sample for genomic profiling (control, n=18), while the other biopsy (n=18) was split and utilized for independent, simultaneous genomic and transcriptomic analysis, here termed Preimplantation Genetic and Transcriptomic Testing (PGT2).\n\nHigh quality genomic and transcriptomic data were obtained from all analyzed samples. The concordance between genomic data obtained with PGT2 and control samples was 100% with clinical grade quality metrics. Euploid embryos showed downregulation of genes involved in anaerobic metabolism, oxidative phosphorylation, and fatty-acid oxidation. This is the first study to provide full genomic and transcriptomic profiles from a single TE biopsy from human embryos in a clinical setting unleashing the potential of improving embryo selection and outcomes in infertility treatments. Clinical trials are needed to correlate transcriptomic data with outcomes.\n\nSUMMARYDespite advances in assisted reproductive technologies, the success rate has remained relatively constant. Under the age of 35, there is a 40% chance of delivering a child per embryo transfer, which decreases with increasing maternal age. Prioritizing embryos for transfer is based on morphological assessment and, in some cases, incorporates genetic testing as well. Selection of euploid embryos for transfer shortens the time to pregnancy and reduces the risk for miscarriages. Adding the mRNA analysis to the genomic assessment of an embryo has the potential of improving the outcomes of fertility treatments.

developmental biology↗

bioRxiv2018

A systematic study of repetitive transcranial magnetic stimulation to enhance working memory manipulation abilities

A core element of human working memory (WM) is the ability to perform mental operations on information that is stored in a flexible, limited capacity buffer. Given the profound importance of such WM manipulation (WM-M) abilities, there is a concerted effort aimed at developing approaches to improve them. Past research has identified neural substrates of WM-M centered in the dorsolateral prefrontal cortex (DLPFC), thereby providing a plausible and accessible target for noninvasive neuromodulatory stimulation that can be used to alter cortical excitability and potentially lead to facilitation of WM-M. In the current study, 5Hz online repetitive transcranial magnetic stimulation (rTMS), applied over the left DLPFC, was used to test the hypothesis that active rTMS would lead to significant improvements in memory recall accuracy compared to sham stimulation, and that these effects would be most pronounced in the WM-M conditions with the highest cognitive demand (registered Clinical Trial: #NCT02767323). Participants performed a delayed response alphabetization task with three individually-titrated levels of difficulty during active and sham rTMS. Analyses revealed that active rTMS led to numerically greater accuracy relative to sham stimulation for the hardest condition; however, this effect did not survive Bonferroni correction over all task conditions. Despite the lack of robust, study-wise significant effects, when considered in isolation, the magnitude of behavioral improvement in the hardest condition was negatively correlated with parametric difficulty-related fMRI activity in the targeted brain region, suggesting that individuals with less activation benefit more from rTMS. The present findings therefore suggest evidence towards the hypothesis that active rTMS can enhance performance during difficult memory manipulation conditions; however, firm conclusions cannot be drawn given the lack of overall significant effects. These findings are discussed in the context of individualized targeting and other factors that might moderate rTMS effects.

neuroscience↗

bioRxiv2018

Expectations may Influence the Effects of Transcranial Direct-Current Stimulation

Growing interest surrounds transcranial direct current stimulation (tDCS) as a safe and inexpensive method for improving cognitive functions and mood. Nevertheless, tDCS studies rarely examine psychological factors such as expectations of outcomes, which may influence tDCS responsiveness through placebo-like effects. Here we sought to evaluate the potential influence of expectations on tDCS intervention outcomes. We assessed expectations of tDCS outcomes in 88 healthy young adults on three occasions: i) at baseline; ii) after reading information implying either high or low effectiveness of stimulation; and iii) after a single-session of sham-controlled anodal tDCS applied to the left dorsolateral prefrontal cortex, during working memory (WM) training. Participants were largely uncertain about the effectiveness of stimulation in improving cognitive function at baseline. High or low expectation priming using simple positive or cautionary messages significantly increased or decreased expectation ratings, respectively, but ratings significantly decreased following stimulation in all groups. We found greater improvement in participants who received high compared to low expectation priming. Participants who received active stimulation and low expectation priming exhibited the lowest performance, suggesting that expectation priming and stimulation may have interacted. We did not find a significant effect of baseline expectations, belief of group assignment, or individual characteristics on measures of WM and verbal fluency. However, controlling for baseline expectations revealed greater post-intervention improvement on the executive function measures in participants who received high (compared to low) expectation priming. People randomly assigned to receive high expectation priming reported having a more pleasant experience overall, including greater satisfaction. Our findings suggest that expectations of outcomes should be taken into account in tDCS-based experimental studies and clinical trials.\n\nHighlights- Based on prior knowledge, healthy subjects are uncertain about NIBS effectiveness.\n\n- Expectations of NIBS can change after a single exposure to simple written messages.\n\n- Expectations of outcomes may influence cognitive performance.\n\n- High expectations may lead to a more positive experience and motivation to perform.\n\n- Low expectations may be counterproductive to NIBS.

neuroscience↗

bioRxiv2018

Mavacamten stabilizes the auto-inhibited state of two-headed cardiac myosin

We used transient biochemical and structural kinetics to elucidate the molecular mechanism of mavacamten, an allosteric cardiac myosin inhibitor and prospective treatment for hypertrophic cardiomyopathy. We find that mavacamten stabilizes an auto-inhibited state of two-headed cardiac myosin, not found in the isolated S1 myosin motor fragment. We determined this by measuring cardiac myosin actin-activated and actin-independent ATPase and single ATP turnover kinetics. A two-headed myosin fragment exhibits distinct auto-inhibited ATP turnover kinetics compared to a single-headed fragment. Mavacamten enhanced this auto-inhibition. It also enhanced auto-inhibition of ADP release. Furthermore, actin changes the structure of the auto-inhibited state by forcing myosin lever-arm rotation. Mavacamten slows this rotation in two-headed myosin but does not prevent it. We conclude that cardiac myosin is regulated in solution by an interaction between its two heads and propose that mavacamten stabilizes this state.\n\nSignificance StatementSmall-molecule allosteric effectors designed to target and modulate striated and smooth myosin isoforms for the treatment of disease show promise in preclinical and clinical trials. Beta-cardiac myosin is an especially important target, as heart disease remains a primary cause of death in the U.S. One prevalent type of heart disease is hypertrophic cardiomyopathy (HCM), which is hypothesized to result from dysregulated force generation by cardiac myosin. Mavacamten is a potent cardiac myosin ATPase activity inhibitor that improves cardiac output in HCM animal models. Our results show that mavacamten selectively stabilizes a two-head dependent, auto-inhibited state of cardiac myosin in solution. The kinetics and energetics of this state are consistent with the auto-inhibited super-relaxed state, previously only observed in intact sarcomeres.

biophysics↗

bioRxiv2018

P. falciparum PfATP4 Multi-Drug Resistance to KAE609 (Cipargamin) is Present in Africa

The PfATP4 (PF3D7 1211900) multi-drug resistance mutation G223R is found in Africa by genetically analyzing 2640 worldwide Plasmodium falciparum blood stage isolates (the MalariaGen Pf3k resource). This mutation confers an approximate 8 fold [4] increase in the PfATP4 IC50 of Spiroindolones (KAE609 & KAE678) [14],[16],[4],[10] and Aminopyrazoles (GNF-Pf4492) [4]. It is postulated that the G223R mutation may be a consequence of the drug resistant Southeast Asian Dd2 genotype becoming more dominant in Africa [3]. The presence of this mutation has important policy implications for the eventual general deployment of the Spiroindolone KAE609 (Cipargamin) which is currently undergoing stage 2 clinical trials.

bioinformatics↗

bioRxiv2018

Reactivation of latent HIV-1 in vitro using an alcoholic extract from Euphorbia umbellata (Euphorbiaceae) latex.

Euphorbia umbellata (E. umbellata) belongs to Euphorbiaceae family, popularly known as Janauba, and contains in its latex a combination of phorbol esters with biological activities described to different cellular protein kinase C (PKC) isoforms. Here, we identified deoxi-phorbol esters present in E. umbellata latex alcoholic extract able to increase HIV transcription and reactivate HIV from latency models. This activity was mediated by NF-kB activation followed by nuclear translocation and binding to HIV LTR promoter. In addition, E. umbellate latex extract induced the production of pro inflammatory cytokines together with IL21 in in vitro human PBMC cultures. Our latex extract activates latent HIV in human PBMCs isolated from HIV positive patients as well as latent SIV in non-human primate primary CD4+ T lymphocytes. These results strongly indicate that the phorbol esters present in E. umbellata latex are promising candidate compounds for future clinical trials for shock and kill therapy to promote HIV cure and eradication.

microbiology↗

bioRxiv2018

Stratification of amyotrophic lateral sclerosis patients: a crowdsourcing approach

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with substantial heterogeneity in clinical presentation with an urgent need for better stratification tools for clinical development and care. In this study we used a crowdsourcing approach to address the problem of ALS patient stratification. The DREAM Prize4Life ALS Stratification Challenge was a crowdsourcing initiative using data from >10,000 patients from completed ALS clinical trials and 1479 patients from community-based patient registers. Challenge participants used machine learning and clustering techniques to predict ALS progression and survival. By developing new approaches, the best performing teams were able to predict disease outcomes better than currently available methods. At the same time, the integration of clustering components across methods led to the emergence of distinct consensus clusters, separating patients into four consistent groups, each with its unique predictors for classification. This analysis reveals for the first time the potential of a crowdsourcing approach to uncover covert patient sub-populations, and to accelerate disease understanding and therapeutic development.

bioinformatics↗

bioRxiv2018

The trypanocidal benzoxaborole AN7973 inhibits trypanosome mRNA processing

Kinetoplastid parasites - trypanosomes and leishmanias - infect millions of humans and cause economically devastating diseases of livestock, and the few existing drugs have serious deficiencies. Benzoxaborole-based compounds are very promising potential novel anti-trypanosomal therapies, with candidates already in human and animal clinical trials. Their targets in trypanosomes were hitherto unknown. We investigated the mechanism of action of several benzoxaboroles, including AN7973, an early candidate for veterinary trypanosomosis.\n\nIn all kinetoplastids, transcription is polycistronic. Individual mRNA 5-ends are created by trans splicing of a short leader sequence, with coupled polyadenylation of the preceding mRNA. Treatment of Trypanosoma brucei with AN7973 inhibited trans splicing within 1h, as judged by loss of the Y-structure splicing intermediate and reduced levels of mRNA, and accumulation of peri-nuclear granules which are typical for splicing inhibition. Methylation of the spliced leader precursor RNA was not affected, but more prolonged AN7973 treatment caused an increase in S-adenosyl methionine and methylated lysine. Together, these results indicate that mRNA processing is the primary target of AN7973. Polyadenylation is required for kinetoplastid trans splicing. The EC50 for AN7973 in T. brucei was increased three-fold by over-expression of the T. brucei cleavage and polyadenylation factor CPSF3, identifying CPSF3 as a potential molecular target. Our results thus chemically validate mRNA processing as a viable drug target in trypanosomes.\n\nSeveral other benzoxaboroles showed metabolomic and splicing effects that were similar to those of AN7973, identifying splicing inhibition as a common mode of action, and suggesting that it might be linked to subsequent changes in methylated metabolites. Granule formation, splicing inhibition, and resistance after CPSF3 expression did not, however, always correlate, and prolonged selection of trypanosomes in AN7973 resulted in only 1.5-fold resistance. This suggests that the modes of action of oxaboroles that target trypanosome mRNA processing may extend beyond CPSF3 inhibition.\n\nAuthor summaryTrypanosomes and leishmanias infect millions of humans and cause economically devastating diseases of livestock; the few existing drugs have serious deficiencies. Trypanosomosis of cattle, caused mainly by Trypanosoma congolense and Trypanosoma vivax, is a serious problem in Africa, because bovids are used not only for meat and milk, but also for traction. Only two drugs are in routine use for chemotherapy and chemoprophylaxis of bovine trypanosomosis. A single injection of the benzoxaborole compound AN7973 was sufficient to cure T. congolense infection in cattle and goats, but AN7973 was less effective against T. vivax. This precluded development of AN7973 as a commercially viable treatment against cattle trypanosomosis, but it could still have potential for diseases caused by other salivarian trypanosomes.\n\nWe used a large range of methods to find out how AN7973 kills trypanosomes, and compared it with several other benzoxaboroles. AN7973 and some of the other compounds had effects on parasite metabolism that resembled those previously seen for a benzoxaborole that is being tested for human sleeping sickness. The most rapid effect of AN7973, however, was on processing of trypanosome mRNA. As a consequence, amounts of mRNA decreased and synthesis of proteins stopped. We conclude that AN7973 and some other benzoxaboroles kill trypanosomes by stopping gene expression.

microbiology↗

bioRxiv2018

Positive Cardiac Inotrope, Omecamtiv Mecarbil, Activates Muscle Despite Suppressing the Myosin Working Stroke

Omecamtiv mecarbil (OM) is a positive cardiac inotrope in phase-3 clinical trials for treatment of heart failure. Although initially described as a direct myosin activator, subsequent studies are at odds with this description and do not explain OM-mediated increases in cardiac output. Single-molecule, biophysical experiments on cardiac myosin show that OM suppresses myosins working stroke and prolongs actomyosin attachment 5-fold, which explain inhibitory actions of the drug observed in vitro. Surprisingly, the increased myocardial force output in the presence of OM can be explained by cooperative thin filament activation by OM-inhibited myosin molecules. Selective suppression of myosin is an unanticipated route to muscle activation that may guide future development of therapeutic drugs.

biophysics↗

bioRxiv2018

Profound perturbation of the human metabolome by obesity

Obesity is a heterogeneous phenotype that is crudely measured by body mass index (BMI). More precise phenotyping and categorization of risk in large numbers of people with obesity is needed to advance clinical care and drug development. Here, we used non-targeted metabolome analysis and whole genome sequencing to identify metabolic and genetic signatures of obesity. We collected anthropomorphic and metabolic measurements at three timepoints over a median of 13 years in 1,969 adult twins of European ancestry and at a single timepoint in 427 unrelated volunteers. We observe that obesity results in a profound perturbation of the metabolome; nearly a third of the assayed metabolites are associated with changes in BMI. A metabolome signature identifies the healthy obese and also identifies lean individuals with abnormal metabolomes - these groups differ in health outcomes and underlying genetic risk. Because metabolome profiling identifies clinically meaningful heterogeneity in obesity, this approach could help select patients for clinical trials.

genetics↗

bioRxiv2018

Repurposing cytarabine for treating primary effusion lymphoma by targeting KSHV latent and lytic replications

Oncogenic Kaposis sarcoma-associated herpesvirus (KSHV) is etiologically linked to primary effusion lymphoma (PEL), an aggressive and non-treatable malignancy commonly found in AIDS patients. In this study, we performed a high throughput screening of 3,731 characterized compounds, and identified cytarabine approved by FDA for treating numerous types of cancer as a potent inhibitor of KSHV-induced PEL. We showed the high efficacy of cytarabine in the growth inhibition of various PEL cells by inducing cell cycle arrest and apoptosis. Cytarabine inhibited host DNA and RNA syntheses and therefore induced cellular cytotoxicity. Furthermore, cytarabine inhibited viral DNA and RNA syntheses and induced the the rapid degradation of KSHV major latent protein LANA, leading to the suppression of KSHV latent replication. Importantly, cytarabine effectively inhibited active KSHV replication and virion production in PEL cells. Finally, cytarabine treatments not only effectively inhibited the initiation and progression of PEL tumors, but also induced regression of grown PEL tumors in a xenograft mouse model. Together, our study has identified cytarabine as novel therapeutic agent for treating PEL as well as eliminating KSHV persistent infection.\n\nImportancePrimary effusion lymphoma is an aggressive malignancy caused by Kaposis sarcoma-associated herpesvirus. The outcome of primary effusion lymphoma is dismal without specific treatment. Through a high throughput screening of characterized compounds, we identified a FDA-approved compound cytarabine as a potent inhibitor of primary effusion lymphoma. We showed that cytarabine induced regression of PEL tumors in a xenograft mouse model. Cytarabine inhibited host and viral DNA and RNA syntheses, resulting in the induction of cytotoxicity. Of interest, cytarabine induced the degradation of KSHV major latent protein LANA, hence suppressing KSHV latent replication, which is required for PEL survival. Furthermore, cytarabine inhibited KSHV lytic replication program, preventing virion production. Our findings identified cytarabine as novel therapeutic agent for treating PEL as well as for eliminating KSHV persistent infection. Since cytarabine is already approved by the FDA, it might be an ideal candidate for repurposing for PEL therapy and for further evaluation in advanced clinical trials.

microbiology↗

bioRxiv2018

A population-based human enCYCLOPedia for circadian medicine

The discovery that half of the mammalian protein-coding genome is clock-regulated has clear implications for medicine. Indeed, recent studies demonstrate time-of-day impact on therapeutic outcomes in human heart disease and cancer. Yet biological time is rarely given clinical consideration. A key barrier is the absence of information on the what and where of molecular rhythms in the human body. Here, we have applied CYCLOPS, an algorithm designed to reconstruct sample order in the absence of time-of-day information, to the GTEx collection of 632 human donors contributing 4,292 RNA-seq samples from 13 distinct human tissue types. We identify rhythms in expression across the body that persist at the population-level. This includes a set of ubiquitous cyclers comprised of well-established circadian clock factors but also many genes without prior circadian context. Among thousands of tissue-divergent rhythms, we discover a set of genes robustly oscillating in cardiovascular tissue, including key drug targets relevant to heart disease. These results also have implications for genetic studies where circadian variability may have masked genetic influence. It is our hope that the human enCYCLOPedia helps drive the translation of circadian biology into prospective clinical trials in cardiology and many other therapeutic areas.\n\nOne Sentence SummaryBioinformatic analyses on thousands of human tissue samples reveals an enCYCLOPedia of rhythmic gene expression across the body and identifies key translational opportunities for circadian medicine in cardiovascular disease.

bioinformatics↗

bioRxiv2018

Association Between Colonic Level of microRNA 31 and Subtypes of Adult and Pediatric Crohn’s Disease

Crohns disease (CD) is highly heterogeneous, due in large part to variability in cellular processes that underlie the natural history of CD, thereby confounding effective therapy. There is a critical need to advance understanding of the cellular mechanisms that drive CD heterogeneity. In this study, small RNA-sequencing and microRNA profiling in the colon revealed two distinct molecular subtypes, each with different clinical associations, in both adult and treatment-naive pediatric CD patients. Notably, we found that microRNA-31 (miR-31) expression by itself can stratify patients into these two subtypes. Through detailed analysis of several colonic mucosa cell types from adult patients, we found that differential levels of miR-31 are particularly pronounced in epithelial cells. We generated patient crypt-derived epithelial colonoids and showed that miR-31 expression differences preserved in this ex-vivo system. In adult patients, low colonic miR-31 expression levels at the time of surgery are associated with post-operative recurrence of ileal disease. In pediatric patients, lower miR-31 expression at the time of diagnosis is associated with the future development of fibrostenotic ileal CD requiring surgery. These findings represent an important step forward in designing more effective clinical trials and developing personalized therapies for CD.

genomics↗

bioRxiv2018

Enhanced context reveals the scope of somatic missense mutations driving human cancers

Large-scale cancer sequencing studies of patient cohorts have statistically implicated many genes driving cancer growth and progression, and their identification has yielded substantial translational impact. However, a remaining challenge is to increase the resolution of driver prediction from the gene level to the mutation level, because mutation-level predictions are more closely aligned with the goal of precision cancer medicine. Here we present CHASMplus, a computational method, that is uniquely capable of identifying driver missense mutations, including those specific to a cancer type, as evidenced by significantly superior performance on diverse benchmarks. Applied to 8,657 tumor samples across 32 cancer types in The Cancer Genome Atlas, CHASMplus identifies over 4,000 unique driver missense mutations in 240 genes, supporting a prominent role for rare driver mutations. We show which TCGA cancer types are likely to yield discovery of new driver missense mutations by additional sequencing, which has important implications for public policy. SignificanceMissense mutations are the most frequent mutation type in cancers and the most difficult to interpret. While many computational methods have been developed to predict whether genes are cancer drivers or whether missense mutations are generally deleterious or pathogenic, there has not previously been a method to score the oncogenic impact of a missense mutation specifically by cancer type, limiting adoption of computational missense mutation predictors in the clinic. Cancer patients are routinely sequenced with targeted panels of cancer driver genes, but such genes contain a mixture of driver and passenger missense mutations which differ by cancer type. A patients therapeutic response to drugs and optimal assignment to a clinical trial depends on both the specific mutation in the gene of interest and cancer type. We present a new machine learning method honed for each TCGA cancer type, and a resource for fast lookup of the cancer-specific driver propensity of every possible missense mutation in the human exome.

bioinformatics↗

bioRxiv2018

Human Als3p Antibodies are Surrogate Markers of NDV-3A Vaccine Efficacy Against Recurrent Vulvovaginal Candidiasis

A Phase 1b/2a clinical trial of NDV-3A vaccine containing a Candida albicans recombinant Als3 protein protected women <40 years old from recurrent vulvovaginal candidiasis (RVVC). We investigated the potential use of anti-Als3p sera as surrogate marker of NDV-3A efficacy. Pre- and post-vaccination sera from subjects who experienced recurrence of VVC (R) versus those who were recurrence-free (non-recurrent, NR) were evaluated. Anti-Als3p antisera obtained were evaluated for; 1) titer and subclass profile; 2) their ability to influence C. albicans virulence traits including hyphal elongation, adherence to plastic, invasion of vaginal epithelial cells, biofilm formation on plastic and catheter material, and susceptibility to neutrophil killing in vitro. Serum IgG titers in NR patients were consistently higher than in R patients, particularly for anti-Als3 subclass IgG2. Sera from vaccinated NR patients reduced hyphal elongation, adhesion to plastic, invasion of vaginal epithelial cells and biofilm formation significantly more than pre-immune sera, or sera from R- or placebo-group subjects. Pre-adsorption of sera with C. albicans germ tubes eliminated these effects, while heat inactivation did not. Finally, sera from NR subjects enhanced neutrophil-mediated killing of C. albicans relative to pre-immune sera or sera from R patients. Our results suggest that higher Als3p antibody titers are associated with protection from RVVC, attenuate C. albicans virulence and augment immune clearance of the fungus in vitro. Thus, Als3p serum IgG antibodies are likely useful markers of efficacy in RVVC patients vaccinated with NDV-3A.\n\nAbbreviations

immunology↗

bioRxiv2018

Oncogenic Wnt/STOP signaling regulates ribosome biogenesis in vivo

Activating mutations in the Wnt pathway drive a variety of cancers, but the specific targets and pathways activated by Wnt ligands are not fully understood. To bridge this knowledge gap, we performed a comprehensive time-course analysis of Wnt-dependent signaling pathways in an orthotopic model of Wnt-addicted pancreatic cancer, using a PORCN inhibitor currently in clinical trials, and validated key results in additional Wnt-addicted models. The analysis of temporal changes following Wnt withdrawal demonstrated direct and indirect regulation of >3,500 Wnt activated genes (23% of the transcriptome). Regulation was both transcriptional via Wnt/{beta}-catenin, and through the modulation of protein abundance of important transcription factors including MYC via Wnt/STOP. Our study identifies a central role of Wnt /{beta}-catenin and Wnt/STOP signaling in controlling ribosomal biogenesis, a key driver of cancer proliferation.

cancer biology↗

bioRxiv2018

Assessing intra-lab precision and inter-lab repeatability of outgrowth assays of HIV-1 latent reservoir size

Quantitative viral outgrowth assays (QVOA) use limiting dilutions of CD4+ T cells to measure the size of the latent HIV-1 reservoir, a major obstacle to curing HIV-1. Efforts to reduce the reservoir require assays that can reliably quantify its size in blood and tissues. Although QVOA is regarded as a \"gold standard\" for reservoir measurement, little is known about its accuracy and precision or about how cell storage conditions or laboratory-specific practices affect results. Owing to this lack of knowledge, confidence intervals around reservoir size estimates - as well as judgments of the ability of therapeutic interventions to alter the size of the replication-competent but transcriptionally inactive latent reservoir - rely on theoretical statistical assumptions about dilution assays. To address this gap, we have carried out a Bayesian statistical analysis of QVOA reliability on 75 split samples of peripheral blood mononuclear cells (PBMC) from 5 antiretroviral therapy (ART)-suppressed participants, measured using four different QVOAs at separate labs, estimating assay precision and the effect of frozen cell storage on estimated reservoir size. We found that typical assay results are expected to differ from the true value by a factor of 1.6 to 1.9 up or down. Systematic assay differences comprised a 24-fold range between the assays with highest and lowest scales, likely reflecting differences in viral outgrowth readout and input cell stimulation protocols. We also found that controlled-rate freezing and storage of samples did not cause substantial differences in QVOA compared to use of fresh cells (95% probability of < 2-fold change), supporting continued use of frozen storage to allow transport and batched analysis of samples. Finally, we simulated an early-phase clinical trial to demonstrate that batched analysis of pre- and post-therapy samples may increase power to detect a three-fold reservoir reduction by 15 to 24 percentage points.\n\nAuthor summaryThe latent reservoir of resting CD4+ T cells is a major, if not the primary, obstacle to curing HIV. Quantitative viral outgrowth assays (QVOAs) are used to measure the latent reservoir in ART-suppressed HIV-infected people. Using QVOA is difficult, however, as the fraction of cells constituting the latent reservoir is typically about one in one million, far lower than other infectious disease biomarkers. To study reliability of these assays, we distributed 75 PBMC samples from five ART-suppressed HIV-infected participants among four labs, each conducting QVOA and following prespecified sample batching procedures. Using a Bayesian statistical method, we analyzed detailed assay output to understand how results varied within batches, between batches, and between labs. We found that, if batch variation can be controlled (i.e., a lab assays all samples in one batch), typical assay results are expected to differ from the true value by a factor of 1.6 to 1.9 up or down. We also found that freezing, storing, and thawing samples for later analysis caused no more than a 2-fold change in results. These outcomes, and the statistical methods developed to obtain them, should lead towards more precise and powerful assessments of HIV cure strategies.

microbiology↗

bioRxiv2018

Susceptibility to Neutralization by Broadly Neutralizing Antibodies Correlates with Infected Cell Binding for a Panel of Clade B HIV Reactivated from Latent Reservoirs

Efforts to HIV cure are obstructed by reservoirs of latently infected CD4+ T-cells that can re-establish viremia. Broadly neutralizing HIV-specific antibodies (bNAbs), defined by unusually high neutralization breadths against globally diverse viruses, may contribute to the elimination of these reservoirs by binding to reactivated cells, targeting them for immune clearance. However, the relationship between neutralization of reservoir isolates and binding to corresponding infected primary CD4+ T-cells has not been determined. Thus, the extent to which neutralization breadths and potencies can be used to infer the corresponding parameters of infected-cell binding is currently unknown. We assessed the breadths and potencies of bNAbs against 36 viruses reactivated from peripheral blood CD4+ T-cells of ARV-treated HIV-infected individuals, using paired neutralization and infected-cell binding assays. Single antibody breadths ranged from 0-64% for neutralization (IC80[≤]10g/ml) and 0-89% for binding, with two-antibody combinations reaching 0-83% and 50-100%, respectively. Infected-cell binding correlated with virus neutralization for 10 out of 14 antibodies (e.g. 3BNC117, r=0.87, p<0.0001). Heterogeneity was observed, however, with a lack of significant correlations for 2G12, CAP256.VRC26.25, 2F5, and 4E10. Our results provide guidance on the selection of bNAbs for interventional cure studies; both by providing a direct assessment of intra-and inter-individual variability in neutralization and infected cell binding in a novel cohort, and by defining the relationships between these parameters for a panel of bNAbs.\n\nImportanceAlthough anti-retroviral therapies have improved the lives of people who are living with HIV, they do not cure infection. Efforts are being directed towards harnessing the immune system to eliminate the virus that persists, potentially resulting in virus-free remission without medication. HIV-specific antibodies hold promise for such therapies owing to their abilities to both prevent the infection of new cells (neutralization), and also to direct the killing of infected cells. We isolated 36 HIV strains from individuals whose virus was suppressed by medication, and tested 14 different antibodies for neutralization of these viruses and for binding to cells infected with the same viruses (critical for engaging natural killer cells). For both neutralization and infected-cell binding, we observed variation both between individuals, and amongst different viruses within an individual. For most antibodies, neutralization activity correlated with infected cell binding. These data provide guidance on the selection of antibodies for clinical trials.

immunology↗