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bioRxiv2018

Comparative efficacy and acceptability of non-surgical brain stimulation for the acute treatment of adult major depressive episodes: A systematic review and network meta-analysis of 113 randomised clinical trials

Background: Non-surgical brain stimulation techniques have been applied as tertiary treatments in major depression. However, the relative efficacy and acceptability of individual protocols is uncertain. Our aim was to estimate the comparative clinical efficacy and acceptability of non-surgical brain stimulation for the acute treatment of major depressive episodes in adults.\n\nMethods: Embase, PubMed/MEDLINE and PsycINFO were searched up until May 8, 2018, supplemented by manual searches of bibliographies of recent reviews and included trials. We included clinical trials with random allocation to electroconvulsive therapy (ECT), repetitive transcranial magnetic stimulation (rTMS), accelerated TMS (aTMS), priming TMS (pTMS), deep TMS (dTMS), theta burst stimulation (TBS), synchronised TMS (sTMS), magnetic seizure therapy (MST) or transcranial direct current stimulation (tDCS) protocols or sham. Data were extracted from published reports and outcomes were synthesised using pairwise and network random-effects meta-analysis. Primary outcomes were response (efficacy) and all-cause discontinuation (acceptability). We computed odds ratios (OR) with 95% confidence intervals (CI). Remission and continuous post-treatment depression severity scores were also examined.\n\nResults: 113 trials (262 treatment arms) randomising 6,750 patients (mean age = 47.9 years; 59% female) with major depressive disorder or bipolar depression met our inclusion criteria. In terms of efficacy, 10 out of 18 treatment protocols were associated with higher response relative to sham in network meta-analysis: bitemporal ECT (OR=8.91, 95%CI 2.57-30.91), high-dose right-unilateral ECT (OR=7.27, 1.90-27.78), pTMS (OR=6.02, 2.21-16.38), MST (OR=5.55, 1.06-28.99), bilateral rTMS (OR=4.92, 2.93-8.25), bilateral TBS (OR=4.44, 1.47-13.41), low-frequency right rTMS (OR=3.65, 2.13-6.24), intermittent TBS (OR=3.20, 1.45-7.08), high-frequency left rTMS (OR=3.17, 2.29-4.37) and tDCS (OR=2.65, 1.55-4.55). Comparing active treatments, bitemporal ECT and high-dose right-unilateral ECT were associated with increased response. All treatment protocols were at least as acceptable as sham treatment.\n\nConclusion: We found that non-surgical brain stimulation techniques constitute viable alternative or add-on treatments for adult patients with major depressive episodes. Our findings also highlight the need to consider other patient and treatment-related factors in addition to antidepressant efficacy and acceptability when making clinical decisions; and emphasize important research priorities in the field of brain stimulation.\n\nO_LSTTreatment abbreviationsC_LSTECT = Electroconvulsive Therapy O_LIBF ECT = bifrontal ECT (1)\nC_LIO_LIBT ECT = bitemporal ECT (2)\nC_LIO_LIRUL ECT= right unilateral ECT O_LIH-RUL = high-dose RUL ECT (3)\nC_LIO_LILM-RUL = low to moderate-dose RUL ECT (4)\nC_LI\nC_LI\nrTMS = repetitive Transcranial Magnetic Stimulation O_LIHF-L rTMS = high-frequency rTMS of the left DLPFC (5)\nC_LIO_LIHF-R rTMS = high-frequency rTMS of the right DLPFC (6)\nC_LIO_LILF-R rTMS = low-frequency rTMS of the right DLPFC (7)\nC_LIO_LILF-L rTMS = low-frequency rTMS of the left DLPFC (8)\nC_LIO_LIBL rTMS = bilateral rTMS of the DLPFC (9)\nC_LI\ndTMS = deep Transcranial Magnetic Stimulation (10)\npTMS = priming Transcranial Magnetic Stimulation (11)\naTMS = accelerated Transcranial Magnetic Stimulation (12)\nsTMS = synchronised Transcranial Magnetic Stimulation (13)\nTBS = Theta Burst Stimulation O_LIiTBS = intermittent TBS of the left DLPFC (14)\nC_LIO_LIcTBS = continuous TBS of the right DLPFC (15)\nC_LIO_LIblTBS = bilateral TBS of the DLPFC (16)\nC_LI\nMST = Magnetic Seizure Therapy (17)\ntDCS = transcranial Direct Current Stimulation (18)\n\n\nKey points\n\nQuestion: What is the clinical efficacy and acceptability of non-surgical brain stimulation protocols for the acute treatment of major depressive episodes in adults?\n\nFindings: In this network meta-analysis, 10 out of 18 treatment protocols were associated with higher response rates relative to sham, most notably bitemporal and high-dose right unilateral electroconvulsive therapy. All treatment protocols were at least as acceptable as sham treatment.\n\nMeaning: Non-surgical brain stimulation techniques constitute viable alternative or add-on treatment strategies for adult patients with major depressive episodes.

neuroscience↗

bioRxiv2019

Efficacy and safety of a novel vaginal medical device in Recurrent Bacterial Vaginosis: an international multicentre clinical trial

Several risk factors have been identified but the etiology and pathogenesis of Bacterial vaginosis (BV) are still not completely understood, and the recurrence rate of BV remains high despite adequate chemotherapy treatment. The primary objective of the study was to assess the effectiveness of a new vaginal medical device, which contains polycarbophil, 0.04 % lauryl glucoside, and glycerides (Polybactum(R) - Effik Italia), in reducing BV recurrence rate. This was a multicenter, open label, not comparative study performed in Italy and Romania. Female subjects over 18-years-old affected by recurrent BV were included. The latest episode was diagnosed by Amsel criteria 6-9 days before the start of the study and treated with vaginal metronidazole (gel 0.75% mg for 5 days or ovules 500 mg for 7 days). The recurrence was defined by at least 2 episodes in the previous 12 months. Polybactum(R) vaginal ovules, day 1-4-7, were started within the 12th and the 24th hr after the end of metronidazole therapy and repeated monthly for 3 cycles. The first 41 patients enrolled were evaluated for an interim analysis 6 months after the study started; 2 patients interrupted the trial, leaving 39 evaluable subjects. The recurrence rate was significantly reduced compared to previous published data (10.26% vs 40% p<0.001). In 35 patients without recurrence, the assessment of Lactobacillus vaginal flora performed by phase contrast microscopy evidenced a significant improvement form baseline (p=0.022) The Investigator global assessment of tolerability was excellent in 38 out of 39 cases. IMPORTANCEBacterial vaginosis (BV) is the most common vaginal disorder in women of childbearing age. In BV, Lactobacillus species, which are predominant in a healthy vaginal flora, are replaced by anaerobes, mainly Gardnerella vaginalis. BV is responsible for more than 60% of vulvovaginal infections and has been linked to serious, potentially life-threatening conditions, including: pelvic inflammatory disease, postoperative infections, acquisition and transmission of the human immunodeficiency virus, preterm birth, and several adverse pregnancy outcomes. Our research showed that 3 monthly cycles of Polybactum(R) ovules administered after one course of metronidazole vaginal therapy can reduce the rate of Bacterial vaginosis recurrence and improve the vaginal milieu, favouring the growth of vaginal lactobacillus species. Taken together our results confirm that Polibactum(R) is a safe and effective treatment to reduce BV recurrence rate after a first line therapy with metronidazole.

clinical trials↗

bioRxiv2019

Rice bran supplementation modulates growth, microbiome and metabolome in weaning infants: a clinical trial in Nicaragua and Mali

Rice bran supplementation provides nutrients, prebiotics and phytochemicals that enhance gut immunity, reduce enteric pathogens in mice and diarrhea in neonatal pigs, and warranted attention for improvement of environmental enteric dysfunction (EED) in children at risk. EED is a condition that drives childhood stunting via intestinal dysbiosis and impaired nutrient metabolism. This study investigated effects of rice bran supplementation on growth, EED biomarkers, gut microbiome and metabolome in weaning infants from 6 to 12 months old in Nicaragua and Mali. Healthy infants were randomized to a control group or rice bran group that received daily supplementation at increasing doses each month. Stool microbiomes were characterized using 16S rDNA amplicon sequencing. Stool metabolomes were analyzed using ultra-high-performance liquid-chromatography tandem mass-spectrometry. Statistical comparisons were completed at 6, 8, and 12 months of age. Daily consumption of rice bran was safe and feasible for infant growth, decreasing alpha-1 antitrypsin levels, and modulating gut microbiome and metabolome when compared to control. Rice bran merits investigation as a practical intervention strategy that could decrease EED prevalence and risk for children from low- and middle-income countries where rice is grown as a staple food, and bran is used as animal feed or wasted. One Sentence SummaryDietary rice bran supplementation during infant weaning from 6-12 months of age improved growth outcomes, modulated environmental enteric dysfunction biomarkers, and supported metabolism by the gut microbiome. The authors declare no competing financial or non financial interests to disclose as defined by Nature Research. There are also no other interests that might be perceived to influence the results and/or discussion reported in this paper. Correspondence and requests for materials should be addressed to Dr. Elizabeth Ryan (e.p.ryan@colostate.edu).

clinical trials↗

bioRxiv2018

Long-Term Effects of a Novel Continuous Remote Care Intervention Including Nutritional Ketosis for the Management of Type 2 Diabetes: A 2-year Non-randomized Clinical Trial.

OBJECTIVEStudies on long-term sustainability of low-carbohydrate approaches to treat diabetes are limited. We aim to assess the effects of a continuous care intervention (CCI) on retention, glycemic control, weight, body composition, cardiovascular, liver, kidney, thyroid, inflammatory markers, diabetes medication usage and disease outcomes at 2 years in adults with type 2 diabetes (T2D). RESEARCH DESIGN AND METHODSAn open label, non-randomized, controlled study with 262 and 87 participants with T2D were enrolled in the CCI and usual care (UC) groups, respectively. RESULTSSignificant changes from baseline to 2 years in the CCI group included: HbA1c (-12% from 7.7{+/-}0.1%); fasting glucose (-18% from 163.67{+/-}3.90 mg/dL); fasting insulin (-42% from 27.73{+/-}1.26 pmol L-1); weight (-10% from 114.56{+/-}0.60 kg); systolic blood pressure (-4% from 131.7{+/-}0.9 mmHg); diastolic blood pressure (-4% from 81.8{+/-}0.5 mmHg); triglycerides (-22% from 197.2{+/-}9.1 mg/dL); HDL-C (+19% from 41.8{+/-}0.9 mg/dL), and liver alanine transaminase (-21% from 29.16{+/-}0.97 U/L). Spine bone mineral density in the CCI group was unchanged. Glycemic control medication use (excluding metformin) among CCI participants declined (from 56.9% to 26.8%, P=1.3x10-11) including prescribed insulin (-62%) and sulfonylureas (-100%). The UC group had no significant changes in these parameters (except uric acid and anion gap) or diabetes medication use. There was also significant resolution of diabetes (reversal, 53.5%; remission, 17.6%) in the CCI group but not in UC. All the reported improvements had p-values <0.00012. CONCLUSIONSThe CCI sustained long-term beneficial effects on multiple clinical markers of diabetes and cardiometabolic health at 2 years while utilizing less medication. The intervention was also effective in the resolution of diabetes and visceral obesity, with no adverse effect on bone health. TRIAL REGISTRATIONClinicaltrials.gov NCT02519309 DATA SHARINGThe complete data and statistical codes are available upon reasonable request. Conflicts of InterestsSJA, RNA, SJH, ALM, NHB, SDP and JPM are employed by Virta Health Corp and were offered stock options. SDP and JSV are founders of Virta Health Corp. WWC has no conflict of interest to declare. Financial supportVirta Health Corp. is the study sponsor. Author contributionsS.J.A, R.N.A, and J.P.M drafted the manuscript. S.J.A, R.N.A, A.L.M, N.H.B, and S.J.H participated in data acquisition and compiling. R.N.A and S.J.A analyzed the data. J.P.M, A.L.M, N.H.B, W.W.C, R.N.A, S.J.A, S.J.H, S.D.P and J.S.V edited the manuscript. All authors approved the final version of the manuscript. Abbreviations

clinical trials↗

bioRxiv2026

Reliable extraction of clinical-trial evidence with provenance, verification, and targeted review

Reliable extraction of trial characteristics and outcomes is essential for systematic reviews, yet incorrect values can alter evidence synthesis and are difficult to detect without clear source evidence. We evaluate EviSearch, a clinical evidence-curation system that links extracted values to source passages, independently verifies cited evidence, and prioritizes higher-risk cells for review. Using ten trial publications, a 133-column schema, reference annotations, and consistent scoring across model families, we assess answer quality, inter-reading agreement, evidence reproduction, targeted review, and evidence modality. In the Qwen evaluation, EviSearch achieved 91.70% accuracy, cited 100.0% of admitted values, and reproduced 98.9% independently. Reviewing 15.6% of cells increased accuracy to 95.22%.

bioinformatics↗

bioRxiv2026

An in vivo model of Amyloid-Related Imaging Abnormalities (ARIA) predicts ARIA incidence of anti-Aβ antibodies seen in clinical trials

Amyloid-related imaging abnormality (ARIA) is the most common adverse event associated with amyloid-beta (A{beta}) immunotherapy. The neuropathology underlying active ARIA lesions has been studied in only a few rare fatal cases. A faithful translational model of ARIA should allow a better understanding of pathogenic mechanisms and enable development of mitigation strategies. Since bapineuzumab induced the most frequent and severe forms of ARIA in humans, we assessed the ability of its murine precursor, 3D6, to induce ARIA-like lesions by applying clinically-validated MRI sequences in a mouse model with extensive amyloid deposition. Using this paradigm we documented ARIA-like changes based on their imaging features, location, and temporal evolution and established postmortem histopathologic correlates. We observed that ARIA-like lesions were ubiquitously induced with 3D6, including T2-hyperintense leptomeningeal effusions, T2-hyperintense parenchymal lesions and T2* hypointense parenchymal lesions. Histological assays demonstrated meningovascular inflammation as well as vascular mural permeation and microvascular lesions, including microhemorrhages and microinfarcts. Compared to 3D6-treated mice, animals treated with mouse analogues of aducanumab and gantenerumab showed less frequent radiologic and histopathologic ARIA-like lesions with delayed onset. Our results align well with the differential incidence of ARIA observed in humans treated with different anti-A{beta} antibodies. Collectively, our studies demonstrate that: i) anti-A{beta} antibodies chronically administered to 5xFAD mice can induce MRI lesions reminiscent of human ARIA; ii) this paradigm allows identification of transient lesions other than microhemorrhages, and (iii) the incidence and severity of ARIA-like lesions induced with three clinically tested antibodies faithfully recapitulates that seen in humans. One Sentence SummaryMRI and histological correlation in a preclinical ARIA mouse model treated with anti-A{beta} antibodies that recapitulates results seen in humans.

neuroscience↗

bioRxiv2020

Contemplative mental training reduces hair glucocorticoid levels in a randomized clinical trial

ObjectiveThis study had the objective to investigate the effect of regular contemplative mental training on endocrine indices of long-term stress. MethodsAn open-label efficacy trial comprising three distinct 3-month modules targeting attention and interoception, socio-affective or socio-cognitive abilities through dyadic exercises and secularised meditation practices was designed and carried out in 332 healthy meditation-naive adults. Participants underwent the training for up to 9 months or were assigned to a retest control cohort. Chronic stress indices were assayed at four timepoints, i.e., pre-training and following each module. The main outcome measures were cortisol and cortisone concentration in hair and self-reported chronic stress ResultsN=362 initial individuals were randomized, of whom n=30 dropped out before study initiation, n=4 before first sampling and n=2 were excluded. N=99 participants did not provide hair samples. Data from three separate training cohorts revealed consistent decreases in hair cortisol and cortisone levels over the training period. This effect increased with practice frequency, was independent of training content and not associated with change in self-reported chronic stress. ConclusionsOur results point to the reduction of long-term cortisol exposure as a mechanism via which contemplative mental training may exert positive effects on practitioners health. Trial registrationClinicalTrials.gov identifier: NCT01833104

molecular biology↗

bioRxiv2024

A Randomized, Controlled Clinical Trial Demonstrates Improved Cognitive Function in Senior Dogs Supplemented with a Senolytic and NAD+ Precursor Combination.

Age-related decline in mobility and cognition are associated with cellular senescence and NAD+ depletion in dogs and people. A combination of a novel NAD+ precursor and senolytic, LY-D6/2 was examined in this randomized controlled trial. Seventy dogs were enrolled and allocated into placebo, low or full dose groups. Primary outcomes were change in cognitive impairment measured with the owner-reported Canine Cognitive Dysfunction Rating (CCDR) scale and change in activity measured with physical activity monitors. Fifty-nine dogs completed evaluations at the three-month primary endpoint, and 51 reached the six-month secondary endpoint. There was a significant difference in CCDR score across treatment groups from baseline to the primary endpoint (p=0.02) with the largest decrease in the full dose group. There were no significant differences between groups in changes in measured activity. However, the proportion of dogs that improved in frailty and owner-reported activity levels and happiness was higher in the full dose group than other groups. Adverse events occurred equally across groups. All groups showed improvement in cognition, frailty, and activity suggesting placebo effect and benefits of trial participation. We conclude that LY-D6/2 significantly improves owner-assessed cognitive function and may have broader effects on frailty, activity and happiness as reported by owners.

animal behavior and cognition↗

bioRxiv2018

Rapamycin, an Immunosuppressant and mTORC1 Inhibitor, Triples the antidepressant Response Rate of Ketamine at 2 Weeks Following Treatment: A double-blind, placebo-controlled, cross-over, randomized clinical trial

BACKGROUNDKetamine exerts rapid and robust antidepressant effects thought to be mediated by activation of the mechanistic target of rapamycin complex 1 (mTORC1). To test this hypothesis, depressed patients were pretreated with rapamycin, an mTORC1 inhibitor, prior to receiving ketamine.\n\nMETHODSTwenty-three patients suffering a major depressive episode were randomized to oral rapamycin (6 mg) or placebo, each was followed 2 hours later by ketamine 0.5 mg/kg in a double-blind cross-over design with treatment days separated by at least 2 weeks. Depression severity was assessed using Montgomery-[A]sberg Depression Rating Scale (MADRS). Antidepressant response was defined as a MADRS improvement of 50% or more.\n\nRESULTSOver the two-week follow-up, we found a significant treatment by time interaction (F(8,245) = 2.02, p = 0.04), reflecting prolonged antidepressant effects post rapamycin+ketamine treatment. At 2 weeks, we found a significantly higher response rate following rapamycin+ketamine (41%) compared to placebo+ketamine (13%, p = 0.04). However, rapamycin pretreatment did not alter the acute effects of ketamine.\n\nCONCLUSIONUnexpectedly, pretreatment with rapamycin prolonged rather than blocked the acute antidepressant effects of ketamine. This observation raises questions about the role of mTORC1 in the antidepressant effects of keta-mine, raises the possibility that rapamycin may extend the benefits of ketamine, and thereby potentially sheds light on mechanisms that limit the duration of ketamine effects. The supplementing of ketamine with rapamycin may be a treat-ment strategy for reducing the frequency of ketamine infusions during maintenance treatment.

neuroscience↗

bioRxiv2019

Adaptive Deep Brain Stimulation as an Advanced Parkinson’s disease Treatment (ADAPT): a pseudorandomised clinical trial

BackgroundBeta-based adaptive Deep Brain Stimulation (aDBS) is effective in Parkinsons disease (PD), when assessed in the immediate post-implantation phase. However, the potential benefits of aDBS in patients with electrodes chronically implanted, in whom the benefits of the microlesion effect have disappeared, are yet to be assessed. MethodsTo determine the acute effectiveness and side-effect profile of aDBS in PD compared to conventional continuous DBS (cDBS) and no stimulation (NoStim), years after DBS implantation. 13 PD patients undergoing battery replacement were pseudo-randomised in a crossover fashion, in- to three conditions (NoStim, aDBS or cDBS). Patient videos were blindly evaluated using a short version of the Unified Parkinsons Disease Rating Scale (subUPDRS) and the Speech Intelligibility Test (SIT). ResultsPatients had a mean disease duration of 16 years, and the mean time since DBS implantation was 6.9 years. subUPDRS scores (11 patients tested) were significantly lower both in aDBS (p=<.001), and cDBS (p=.001), when compared to NoStim. Bradykinesia subscores were significantly lower in aDBS (p=.002), but not in cDBS (p=.08), when compared to NoStim. Two patients presented re-emerging tremor during NoStim. SIT scores of patients with stimulation-induced dysarthria (11 patients tested) significantly worsened in cDBS (p=.009), but not in aDBS (p=.407), when compared to NoStim. Overall, stimulation was applied 48.8% of the time during aDBS. ConclusionBeta oscillations is effective in PD patients with bradykinetic phenotypes, delivers less stimulation than cDBS, and potentially has a more favourable speech side-effect profile. Patients with prominent tremor may require a modified adaptive control strategy.

neuroscience↗

bioRxiv2020

Extracellular vesicles as predictors of individual response to exercise training in youth living with obesity

Exercise is associated with various health benefits, including the prevention and management of obesity and cardiometabolic risk factors. However, a strong heterogeneity in the adaptive response to exercise training exists. The objective of this study was to evaluate if changes in extracellular vesicles (EVs) after acute aerobic exercise (AE) were associated with the responder phenotype following 6-weeks of resistance exercise training. This is a secondary analysis of plasma samples from the EXIT trial (clinical trial #02204670). Eleven sedentary youth with obesity (15.7{+/-}0.5 years, BMI [≥] 95th percentile) underwent an acute bout of AE (60% heart rate reserve, 45 min). Blood was collected before exercise [at time (AT) 0 min], during [AT15, 30, 45 min], and 75 min after exercise [AT120]. Afterward, youth participated in 6-week resistance training program, and were categorized into responders (RE) or non-responders (NRE) based on changes in insulin sensitivity as measured by the Matsuda Index. EVs were isolated using size exclusion chromatography (Izon(R)). The primary outcome variable was EV biophysical profile, which includes size, zeta potential, protein yield and expression of markers associated with EV subtypes. The variables were analyzed in a single-blind fashion. Overall, there was a general increase in EV production in both groups. Average EV size was larger in RE (~147 nm) vs. NRE (~124 nm; p<0.05). Average EV size at AT0 was associated with absolute change in Matsuda index following 6-weeks of resistance training (r=0.44, p=0.08). EV size distribution revealed RE preferentially expressed EVs between 150 - 250 nm in size, whereas NRE expressed EVs between 50 - 100 nm (p<0.05). At baseline, RE-EVs contained ~25% lower Tsg101 protein, ~85% higher MMP2 content, while CD63 levels remained unchanged between the groups. Total protein yield in RE-EVs was higher than NRE at AT15 (p<0.05). Our data suggest that youth with obesity that respond to exercise training produce larger EVs, with lower exosome- and higher microvesicle-specific protein expression. RE-EVs also had higher EV protein yield during AE. The relationship between larger EV subtypes and/or cargo, and the individual response to exercise has yet to be fully elucidated.

physiology↗

bioRxiv2015

Sequential Multiple Assignment Randomized Trials: An Opportunity for Improved Design of Stroke Reperfusion Trials

Background: Modern clinical trials in stroke reperfusion fall into two categories: alternative systemic pharmacological regimens to alteplase and \"rescue\" endovascular approaches using targeted thrombectomy devices and/or medications delivered directly for persistently vessel occlusions. Clinical trials in stroke have not evaluated how initial pharmacological thrombolytic management might influence subsequent rescue strategy. A sequential multiple assignment randomized trial (SMART) is a novel trial design that can test these dynamic treatment regimens and lead to treatment guidelines which more closely mimic practice.\n\nAim: To characterize a SMART design in comparison to traditional approaches for stroke reperfusion trials.\n\nMethods: We conducted a numerical simulation study that evaluated the performance of contrasting acute stroke clinical trial designs of both initial reperfusion and rescue therapy. We compare a SMART design where the same patients are followed through initial reperfusion and rescue therapy within one trial to a standard phase III design comparing two reperfusion treatments and a separate phase II futility design of rescue therapy in terms of sample size, power, and ability to address particular research questions.\n\nResults: Traditional trial designs can be well powered and have optimal design characteristics for independent treatment effects. When treatments, such as the reperfusion and rescue therapies, may interact, commonly used designs fail to detect this. A SMART design, with similar sample size to standard designs, can detect treatment interactions.\n\nConclusions: The use of SMART designs to investigate effective and realistic dynamic treatment regimens is a promising way to accelerate the discovery of new, effective treatments for stroke.

Scientific Communication and Education↗

bioRxiv2022

p38 MAPK Signaling Enhances Reovirus Replication by Facilitating Efficient Virus Entry, Virus Capsid Uncoating and Post-Uncoating Steps.

Mammalian orthoreovirus serotype 3 Dearing an orphan human virus currently being pursued as an oncolytic virus in multiple phase I/II clinical trials. Previous clinical trials have emphasized the importance of patient pre-screening for prognostic markers to improve therapeutic success. However, currently, only generic cancer markers such as EGFR, Hras, Kras, Nras, Braf and/or p53 are utilized and have exhibited limited benefit in predicting therapeutic efficacy. Utilization of more specific markers that influence specific steps during reovirus replication could prove beneficial as prognostic markers. This study delineated the role of p38 MAPK signaling during reovirus infection and illustrated a connection between specific p38 MAPK isoforms and reovirus infection. Using a panel of specific p38 MAPK inhibitors and an inactive inhibitor analogue, we demonstrated that p38 MAPK signaling is essential for establishment of reovirus infection by enhancing reovirus endocytosis, facilitating efficient reovirus uncoating at the endo-lysosomal stage, and augmenting post uncoating replication steps. Using a broad panel of human breast cancer cell lines, we observed susceptibility of reovirus infection corresponded with virus binding and uncoating efficiency, which was strongly correlated with status of the p38{beta} isoform. Together, our study proposes p38{beta} as a potential prognostic marker for early stages of reovirus infection that are crucial to establishment of successful reovirus infection.

cell biology↗

bioRxiv2026

Type 1-polarized DC immunotherapeutic contains heterogeneous populations with IL-12p70 production restricted to a rare subset

Monocyte-derived DC therapies programmed for robust IL-12p70 production have been associated with favorable outcomes in cancer clinical trials. However, clinical responses remain inconsistent even under standardized protocols, and the cellular basis for this variability is unknown. We leveraged single-cell multiomics to characterize two widely used DC platforms, the high-IL-12p70-producing alpha-Type-1-polarized DC (DC1) and the IL-12p70-deficient DC induced in the presence of PGE2 (PGE2-DC), at baseline and following rhCD40L activation. DC generated from 7 healthy participants representing the spectrum of rhCD40L-induced IL-12p70 production were profiled by transcriptome analysis with concurrent 42-plex surface proteomics, multiplex ELISA, and ELISpot quantification of IL-12p70-producing cells. While DC1 and PGE2-DC distinctly responded to rhCD40L, DC1 alone unexpectedly comprised 3 transcriptionally and phenotypically distinct subpopulations in resting and stimulated states. Only a limited fraction of DC1 coexpressed IL12A and IL12B (IL-12p70 producers), which was confirmed by ELISpot at the protein level. The distribution of DC1 subclusters varied markedly between individuals and correlated with bulk cytokine and chemokine secretion profiles. Heterogeneity within DC1 preparations may underlie inconsistent clinical trial outcomes, and identification of associated surface proteins provides a prospective strategy for subcluster enrichment to enhance DC release criteria and patient stratification for optimized therapeutic efficacy.

immunology↗

bioRxiv2015

Phase i trials in melanoma: A framework to translate preclinical findings to the clinic

AbstractWe present a, mathematical model driven, framework to implement virtual or imaginary clinical trials (phase i trials) that can be used to bridge the gap between preclinical studies and the clinic. The trial implementation process includes the development of an experimentally validated mathematical model, generation of a cohort of heterogeneous virtual patients, an assessment of stratification factors, and optimization of treatment strategy. We show the detailed process through application to melanoma treatment, using a combination therapy of chemotherapy and an AKT inhibitor, which was recently tested in a phase 1 clinical trial. We developed a mathematical model, composed of ordinary differential equations, based on experimental data showing that such therapies differentially induce autophagy in melanoma cells. Model parameters were estimated using an optimization algorithm that minimizes differences between predicted cell populations and experimentally measured cell numbers. The calibrated model was validated by comparing predicted cell populations with experimentally measured melanoma cell populations in twelve different treatment scheduling conditions. By using this validated model as the foundation for a genetic algorithm, we generated a cohort of virtual patients that mimics the heterogeneous combination therapy responses observed in a companion clinical trial. Sensitivity analysis of this cohort defined parameters that discriminated virtual patients having more favorable versus less favorable outcomes. Finally, the model predicts optimal therapeutic approaches across all virtual patients.\n\nOne Sentence SummaryWe propose a computational framework to implement phase i trials (virtual/imaginary yet informed clinical trials) in cancer, using an experimentally calibrated mathematical model of melanoma combination therapy, that can readily capture observed heterogeneous clinical outcomes and be used to optimize future clinical trial design.

Cancer Biology↗

bioRxiv2018

Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis

BackgroundThere are multiple existing and emerging therapeutic avenues for metastatic prostate cancer, with a common denominator, which is the need for predictive biomarkers. Circulating tumor DNA (ctDNA) has the potential to cost-efficiently accelerate precision medicine trials to improve clinical efficacy and diminish costs and toxicity. However, comprehensive ctDNA profiling in metastatic prostate cancer to date has been limited.\n\nMethodsA combination of targeted- and low-pass whole genome sequencing was performed on plasma cell-free DNA and matched white blood cell germline DNA in 364 blood samples from 217 metastatic prostate cancer patients.\n\nResultsctDNA was detected in 85.9% of baseline samples, correlated to line of therapy and was mirrored by circulating tumor cell enumeration of synchronous blood samples. Comprehensive profiling of the androgen receptor (AR) revealed a continuous increase in the fraction of patients with intra-AR structural variation, from 15.4% during first line mCRPC therapy to 45.2% in fourth line, indicating a continuous evolution of AR during the course of the disease. Patients displayed frequent alterations in DNA repair deficiency genes (18.0%). Additionally, the microsatellite instability phenotype was identified in 3.81% of eligible samples ([≥]0.1 ctDNA fraction). Sequencing of non-repetitive intronic- and exonic regions of PTEN, RB1 and TP53 detected biallelic inactivation in 47.5%, 20.3% and 44.1% of samples with [≥]0.2 ctDNA fraction, respectively. Only one patient carried a clonal high-impact variant without a detectable second hit. Intronic high-impact structural variation was twice as common as exonic mutations in PTEN and RB1. Finally, 14.6% of patients presented false positive variants due to clonal hematopoiesis, commonly ignored in commercially available assays.\n\nConclusionsctDNA profiles appear to mirror the genomic landscape of metastatic prostate cancer tissue and may cost-efficiently provide somatic information in clinical trials designed to identify predictive biomarkers. However, intronic sequencing of the interrogated tumor suppressors challenge the ubiquitous focus on coding regions and is vital, together with profiling of synchronous white blood cells, to minimize erroneous assignments which in turn may confound results and impede true associations in clinical trials.

genomics↗

bioRxiv2022

Predicting FDA approvability of small-molecule drugs

A high rate of compound attrition makes drug discovery via conventional methods time-consuming and expensive. Here, we showed that machine learning models can be trained to classify compounds into distinctive groups according to their status in the drug development process, which can significantly reduce the compound attrition rate. Using molecular structure fingerprints and physicochemical properties as input, our models accurately predicted which drug compounds would proceed to trial, with an area under the receiver operating curve (AUC) of 0.94 {+/-} 0.01 (mean {+/-} standard deviation). Our models also identified which drugs in clinical trials would be approved by the US Food and Drug Administration (FDA) to go on the market, with an AUC of 0.73 {+/-} 0.02. The predictive power of our models could reduce the attrition rate of preclinical compounds to enter clinical trials from 65%, as with conventional methods, to 12% (with 92% sensitivity) and the clinical trial failure rate from 80-90% to 29% (with 83% sensitivity). The results largely held in additional tests on new clinical trial compounds and new FDA-approved drugs, as well as on drugs uniquely approved for use in Europe and Japan. SIGNIFICANCE STATEMENTThe odds of developing a drug approved by the US Food and Drug Administration (FDA) are slim, meaning that the vast majority of drug candidates would fail tests for safety and efficacy in the drug discovery process, rendering it highly inefficient and costly. Here, we have developed machine learning models to predict drug compounds worthy of clinical trials with high accuracy, and clinical-trial compounds to receive FDA approval with a much higher success rate than that achieved by the traditional approach. Our computational prediction requires input of only the drug compounds chemical structure and physicochemical properties. It can help mitigate the long-standing problem of drug discovery.

bioinformatics↗

bioRxiv2019

Comparison of three different eye-tracking tasks for distinguishing autistic from typically developing children and autistic symptom severity

Altered patterns of visual social attention preference detected using eye-tracking and a variety of different paradigms are increasingly proposed as sensitive biomarkers for autism spectrum disorder. However, few eye tracking studies have compared the relative efficacy of different paradigms to discriminate between autistic compared with typically developing children and their sensitivity to specific symptoms. To target this issue, the current study used three common eye tracking protocols contrasting social versus non-social stimuli in young (2-7 years old) Chinese autistic (n = 35) and typically developing (n = 34) children matched for age and gender. Protocols included dancing people vs. dynamic geometrical images, biological motion (dynamic light point walking human or cat) vs. non-biological motion (scrambled controls) and child playing with toy vs. toy alone. Although all three paradigms differentiated autistic and typically developing children, the dancing people versus dynamic geometry pattern paradigm was the most effective, with autistic children showing marked reductions in visual preference for dancing people and correspondingly increased one for geometric patterns. Furthermore, this altered visual preference in autistic children was correlated with the ADOS social affect score and had the highest discrimination accuracy. Our results therefore indicate that decreased visual preference for dynamic social stimuli may be the most effective visual attention-based paradigm for use as a biomarker for autism in Chinese children. Clinical trial ID: NCT03286621 (clinicaltrials.gov); Clinical trial name: Development of Eye-tracking Based Markers for Autism in Young Children. Lay summaryEye-tracking measures may be useful in aiding diagnosis and treatment of autism, although it is unclear which specific tasks are optimal. Here we compare the ability of three different social eye-gaze tasks to discriminate between autistic and typically developing young Chinese children and their sensitivity to specific autistic symptoms. Our results show that a dynamic task comparing visual preference for social (individuals dancing) versus geometric patterns is the most effective both for diagnosing autism and sensitivity to its social affect symptoms.

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