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Results for “Clinical Trials”

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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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At least 1,045 records · Page 58Linked to original sources

bioRxiv2023

Micromagnetic Stimulation (μMS) Controls Dopamine Release: An in vivo Study Using WINCS Harmoni

ObjectiveResearch into the role of neurotransmitters in regulating normal and pathologic brain functions has made significant progress. Yet, clinical trials that aim to improve therapeutic interventions do not take advantage of the in vivo changes in the neurochemistry that occur in real time during disease progression, drug interactions or response to pharmacological, cognitive, behavioral, and neuromodulation therapies. In this work, we used the WINCS Harmoni tool to study the real time in vivo changes in dopamine release in rodent brains for the micromagnetic neuromodulation therapy. ApproachAlthough still in its infancy, micromagnetic stimulation (MS) using micro-meter sized coils or microcoils (coils) has shown incredible promise in spatially selective, galvanic contact free and highly focal neuromodulation. These coils are powered by a time-varying current which generates a magnetic field. As per Faradays Laws of Electromagnetic Induction, this magnetic field induces an electric field in a conducting medium (here, the brain tissues). We used a solenoidal-shaped coil to stimulate the medial forebrain bundle (MFB) of the rodent brain in vivo. The evoked in vivo dopamine releases in the striatum were tracked in real time by carbon fiber microelectrodes (CFM) using fast scan cyclic voltammetry (FSCV). ResultsOur experiments report that coils can successfully activate the MFB in rodent brains, triggering dopamine release in vivo. We further show that the successful release of dopamine upon micromagnetic stimulation is dependent on the orientation of the coil. Furthermore, varied intensities of MS can control the concentration of dopamine releases in the striatum. SignificanceThis work helps us better understand the brain and its conditions arising from a new therapeutic intervention, like MS, at the level of neurotransmitter release. Despite its early stage, this study potentially paves the path for MS to enter the clinical world as a precisely controlled and optimized neuromodulation therapy.

neuroscience↗

bioRxiv2024

Striking Long Term Beneficial Effects of Single Dose Psilocybin and Psychedelic Mushroom Extract in the SAPAP3 Rodent Model of OCD-Like Excessive Self-Grooming

Obsessive compulsive disorder (OCD) is a highly prevalent disorder that causes serious disability. Available treatments leave 40% or more of people with OCD significantly symptomatic. There is an urgent need for novel therapeutic approaches. Mice that carry a homozygous deletion of the SAPAP3 gene (SAPAP3 KO) manifest a phenotype of excessive self-grooming, tic-like head-body twitches and anxiety. These behaviors closely resemble pathological self-grooming behaviors observed in humans in conditions that overlap with OCD. Following a preliminary report that the tryptaminergic psychedelic, psilocybin, may reduce symptoms in patients with OCD, we undertook a randomized controlled trial of psilocybin in 50 SAPAP3 KO mice (28 male, 22 female). Mice that fulfilled inclusion criteria were randomly assigned to a single intraperitoneal injection of psilocybin (4.4 mg/kg), psychedelic mushroom extract (encompassing the same psilocybin dose) or vehicle control and were evaluated after 2, 4 and 21 days by a rater blind to treatment allocation for grooming characteristics, head-body twitches, anxiety and other behavioral features. Mice treated with vehicle (n=18) manifested a 118.71+95.96 % increase in total self-grooming (the primary outcome measure) over the 21-day observation period. In contrast, total self-grooming decreased by 14.60%+17.90% in mice treated with psilocybin (n=16) and by 19.20+20.05% in mice treated with psychedelic mushroom extract (n=16) (p=.001 for effect of time; p=.0001 for time X treatment interaction). 5 mice were dropped from the vehicle group because they developed skin lesions; 4 from the psilocybin group and none from the psychedelic mushroom extract group. Secondary outcome measures such as head-body twitches and anxiety all showed a significant improvement over 21 days. Notably, in mice that responded to psilocybin (n=12) and psychedelic mushroom extract (n=13), the beneficial effect of a single treatment persisted up to 7 weeks. Mice initially treated with vehicle and non-responsive, showed a clear and lasting therapeutic response when treated with a single dose of psilocybin or psychedelic mushroom extract and followed for a further 3 weeks. While equivalent to psilocybin in overall effect on self-grooming, psychedelic mushroom extract showed superior effects in alleviating head-body twitches and anxiety. These findings strongly justify clinical trials of psilocybin in the treatment of OCD and further studies aimed at elucidating mechanisms that underlie the long-term effects to alleviate excessive self-grooming observed in this study. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=157 SRC="FIGDIR/small/600634v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@1205a77org.highwire.dtl.DTLVardef@11355e0org.highwire.dtl.DTLVardef@6b15e3org.highwire.dtl.DTLVardef@6a22b7_HPS_FORMAT_FIGEXP M_FIG C_FIG Prepared with BioRender (https://www.biorender.com/)

pharmacology and toxicology↗

bioRxiv2024

Psilocybin causes sex, time, and dose dependent alterations in brain signaling pathways

Psilocybin is a psychedelic tryptamine that has emerged as a potential candidate for the treatment of a variety of conditions, including treatment resistant depression and post-traumatic stress disorder. Clinical trials which have assessed the efficacy of psilocybin for these conditions report a rapid and sustained improvement in patient- and clinician-rated depression scores. The established mechanism of action for psychedelics such as psilocybin is agonism of the serotonin 2A receptor (5HT2AR), however, the downstream events that mediate their therapeutic effects remain uncertain. As high doses of psychedelics are known to induce strong perceptual alterations, an additional outstanding question is whether subperceptual doses induce similar molecular effects as psychoactive dosages. Here, we report the first analysis of dose- and sex-dependent transcriptional changes in forebrains of female and male mice at 3 timepoints (8 hours, 24 hours, and 7 days) following a single administration of psilocybin at low (0.25 mg/kg) or high (1 mg/kg) doses. Grouped analysis of both sexes reveals dose- and time-dependent transcriptomic alterations. We report more rapid transcriptional changes and attenuation of such changes in females following a single low-dose relative to males treated identically. Females also responded more robustly to high-dose administration relative to males at 8 and 24 hours, with signal attenuation in both sexes by 7 days. A notable observation was the persistent transcriptional effect of low-dose psilocybin at 7 days, which outlasted high-dose changes, and which suggests that low doses may have prolonged biological effects. A myriad of pathways were altered depending on sex and timepoint, but common features included functions related to neuronal differentiation, neurogenesis, and changes in receptor signaling. These data reveal dose- and sex-dependent molecular effects of psilocybin and support previous studies demonstrating its effect on dendritogenesis. Given ongoing clinical interest in psilocybin for treating mental health disorders, our results suggest that these sexually divergent changes should be considered when weighing treatment strategies. Additional consideration should be given to temporal effects of low vs high dosages on gene transcription, especially when timing psilocybin with adjuvant cognitive behavioral therapy.

neuroscience↗

bioRxiv2021

Platelet HMGB1 in Platelet-Rich Plasma Promotes Tendon Wound Healing

Platelet-rich plasma (PRP) is a widely used autologous treatment for tendon injuries in clinics, but clinical trials often produce conflicting results. Platelets (PLTs) are a major source of high mobility group box1 (HMGB1) that is gaining attention as a chemoattractant that can recruit stem cells to the wound area to enhance healing; however, the contribution of PLT HMGB1 in wounded tendon healing remains unexplored. This study investigated the effect of PLT HMGB1 within PRP to enhance healing in an acute patellar tendon injury model in PLT HMGB1 knockout (KO) mice and GFP mice. A window defect was created in the patellar tendons of both groups of mice, and wounds were treated with either saline, PRP isolated from PLT HMGB1 KO mice, or PRP isolated from GFP mice. Seven days post-treatment, animals were sacrificed and analyzed by gross inspection, histology, and immunostaining for characteristic signs of tendon healing and repair. Our results showed that in comparison to mice treated with PRP from PLT HMGB1-KO mice, wounds treated with PRP from GFP mice healed faster and exhibited a better organization in tendon structure. Mice treated with PRP from PLT HMGB1-KO mice produced tendon tissue with large premature wound areas and low cell densities. However, wounds of PLT HMGB1 KO mice showed better healing with PRP from HMGB1 KO mice compared to saline treatment. Moreover, wounds treated with PRP from GFP mice had increased extracellular HMGB1, decreased CD68, increased stem cell markers CD146 and CD73, and increased collagen III protein expression levels compared to those treated with PRP from PLT HMGB1 KO mice. Thus, PLT HMGB1 within PRP plays an important role in the healing of wounded tendon. Our findings also suggest that the efficacy of PRP treatment for tendon injuries in clinics may be affected by PLT HMGB1 within PRP preparations.

cell biology↗

bioRxiv2025

Deep Learning for Predicting Stem Cell Efficiency for use in Beta Cell Differentiation

Recent clinical trial data have shown that cell therapy holds curative potential for type-1 diabetes, however the large amounts of lab-grown cells required is a substantial bottleneck. The necessary cell differentiation process exhibits substantial variability, even among clones of induced pluripotent stem cells generated from the same patient. In contrast to many established data sets in medical imaging, human experts struggle to see the difference between highly- and lowly-efficient cell clones. We therefore propose an image-based deep learning model to guide the selection of the most efficient stem cell clones. We apply different deep learning model architectures to learn the morphological differences between good and bad stem cell clones and classify them based on only phase-contrast imaging. To gain critical insight into the learned features and enhance trust in our model, we use layer-wise relevance propagation (LRP), and Fourier-based frequency analysis. Using an EfficientNet-V2-S model, we obtain a novel early prediction for the outcome of the differentiation process from patient-derived stem cell to {beta}-cells using only phase-contrast images. Clone level accuracy is 76.7 % at 24 hours and 96.7 % at 53 hours after start of differentiation. The LRP-generated attribution maps and structure factor analysis show that the structure of the cell population is an important predictive feature. All in all, we present a highly predictive model for successful stem cell differentiation from phase-contrast images, which learns biologically relevant features. This study is a proof-of-concept that deep learning combined with label-free imaging can guide selection of induced pluripotent stem cell clones, thereby reduce cost of {beta}-cell production, and bring curative treatments one step closer to the clinic.

bioinformatics↗

bioRxiv2023

Participant-derived cell line transcriptomic analyses and mouse studies reveal a role for ZNF335 in plasma cholesterol statin response

BackgroundStatins lower circulating low-density lipoprotein cholesterol (LDLC) levels and reduce cardiovascular disease risk. Though highly efficacious in general, there is considerable inter-individual variation in statin efficacy that remains largely unexplained. MethodsTo identify novel genes that may modulate statin-induced LDLC lowering, we used RNA-sequencing data from 426 control- and 2 M simvastatin-treated lymphoblastoid cell lines (LCLs) derived from European and African American ancestry participants of the Cholesterol and Pharmacogenetics (CAP) 40 mg/day 6-week simvastatin clinical trial (ClinicalTrials.gov Identifier: NCT00451828). We correlated statin-induced changes in LCL gene expression with plasma LDLC statin response in the corresponding CAP participants. For the most correlated gene identified (ZNF335), we followed up in vivo by comparing plasma cholesterol levels, lipoprotein profiles, and lipid statin response between wild-type mice and carriers of a hypomorphic (partial loss of function) missense mutation in Zfp335 (the mouse homolog of ZNF335). ResultsThe statin-induced expression changes of 147 human LCL genes were significantly correlated to the plasma LDLC statin responses of the corresponding CAP participants in vivo (FDR=5%). The two genes with the strongest correlations were zinc finger protein 335 (ZNF335 aka NIF-1, rho=0.237, FDR-adj p=0.0085) and CCR4-NOT transcription complex subunit 3 (CNOT3, rho=0.233, FDR-adj p=0.0085). Chow-fed mice carrying a hypomorphic missense (R1092W; aka bloto) mutation in Zfp335 had significantly lower non-HDL cholesterol levels than wild type C57BL/6J mice in a sex combined model (p=0.04). Furthermore, male (but not female) mice carrying the Zfp335R1092W allele had significantly lower total and HDL cholesterol levels than wild-type mice. In a separate experiment, wild-type mice fed a control diet for 4 weeks and a matched simvastatin diet for an additional 4 weeks had significant statin-induced reductions in non-HDLC (-43{+/-}18% and -23{+/-}19% for males and females, respectively). Wild-type male (but not female) mice experienced significant reductions in plasma LDL particle concentrations, while male mice carrying Zfp335R1092W allele(s) exhibited a significantly blunted LDL statin response. ConclusionsOur in vitro and in vivo studies identified ZNF335 as a novel modulator of plasma cholesterol levels and statin response, suggesting that variation in ZNF335 activity could contribute to inter-individual differences in statin clinical efficacy.

genomics↗

bioRxiv2026

Efficacy of a long lasting ivermectin formulation against malaria vectors in a semi-field trial in Bapla, Southwest of Burkina Faso

BackgroundIvermectin, a widely used endectocide with activity against Anopheles (An) mosquitoes, has emerged as a promising complementary tool for malaria vector control. However, currently approved oral formulations provide only short-lived plasma concentrations at mosquitocidal levels, thereby limiting their operational impact. To overcome this limitation, a long-acting injectable formulation based on ivermectin and BEPO technology (mdc-STM-001) was selected through laboratory screening using mosquito colonies. This formulation demonstrated mosquitocidal efficacy meeting WHO criteria, with a hazard ratio (HR) >4 maintained for at least two months. The present study aims to further characterize the efficacy of ivermectin under robust field conditions and to expand susceptibility assessments to wild Anopheles populations representing different species and vectorial status. Ivermectin was tested in cattle at two doses under field conditions using experimental huts and tent traps. Plasma drug levels were also monitored to characterize the pharmacokinetic profile of ivermectin. MethodsThirty-six calves were involved in the study and allocated to three groups (n = 12 per group). The mdc-STM-1.0 group received a single subcutaneous injection of the long-acting ivermectin formulation mdc-STM-001 at a dose of 1.0 mg/kg; the mdc-STM-1.5 group received the same formulation at 1.5 mg/kg and the third group served as controls. Using a three-arm design, cattle from each treatment group were simultaneously exposed to mosquitoes in experimental huts and tent traps, following a Greco-Latin Square rotation to minimize positional confounding factors. Pharmacokinetic data were collected to assess ivermectin release from the subcutaneous depot. Correlations between plasma ivermectin concentrations and mosquito mortality were explored, and survival analysis including Kaplan-Meier and cox proportional hazards models were performed to assess the effect of treatment on mosquito survival. ResultsThe mdc-STM-001 formulation was well tolerated and produced sustained, dose-dependent plasma ivermectin concentrations, with detectable levels maintained for more than 90 days after a single administration. Both doses induced strong mosquitocidal activity against wild Anopheles, with hazard ratios reaching 8.03 and 16.47 for the 1.0 and 1.5 mg/kg doses, respectively. An. funestus and An. rufipes were the most susceptible species (LC50: 5.1-6.9 ng/mL) exhibiting prolonged LC50 coverage (>75 days), whereas An. coustani was less susceptible (LC50: 12.4-19.2 ng/mL) resulting in a shorter duration of effective coverage (17-41 days). ConclusionsTaken together, our results revealed the potential of the mdc-STM-001 long-acting ivermectin formulation as an effective endectocide against residual malaria transmission by primary and secondary vectors and establish evidence basis to support its progression to early-phase clinical trials in humans.

ecology↗

bioRxiv2022

Introduced chemokine gradients guide transplanted and regenerated retinal neurons toward their natural position in the retina

Ongoing cell replacement studies and clinical trials have demonstrated the need to control donor and newborn cell behavior within their target tissue. Here we present a methodology to guide stem cell-derived and endogenously regenerated neurons by engineering the microenvironment. Being an "approachable part of the brain," the eye provides a unique opportunity to study donor neuron fate, migration, and integration within the central nervous system. Glaucoma and other optic neuropathies lead to the permanent loss of retinal ganglion cells (RGCs) - the neurons in the retina that transfer all visual information from the eye to the brain. Cell transplantation and transdifferentiation strategies have been proposed to restore RGCs, and one of the significant barriers to successful RGC integration into the existing retinal circuitry is cell migration towards their natural position in the retina. Here we describe a framework for identifying, selecting, and applying chemokines to direct cell migration in vivo within the retina. We have performed an in silico analysis of the single-cell transcriptome of the developing human retina and identified six receptor-ligand candidates to guide stem cell-derived or newborn neurons. The lead candidates were then tested in functional in vitro assays for their ability to guide stem cell-derived RGCs. For the in vivo studies, donor and newborn neurons were differentiated in human and mouse retinal organoids or endogenously reprogrammed with proneuronal transcription factors, respectively. An exogenous stromal cell-derived factor-1 (SDF1) gradient led to a 2.7-fold increase in donor RGC migration into the ganglion cell layer and a 3.3-fold increase in the displacement of newborn RGCs out of the inner nuclear layer. Furthermore, by altering the migratory profile of donor RGCs toward multipolar migration, overall migration was improved in mature retinal tissues. Together, these results highlight the ability and importance of engineering the tissue microenvironment and the individual cells for research and clinical applications in gene and cell therapies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=175 SRC="FIGDIR/small/510158v1_ufig1.gif" ALT="Figure 1"> View larger version (62K): org.highwire.dtl.DTLVardef@1856140org.highwire.dtl.DTLVardef@1b3ca26org.highwire.dtl.DTLVardef@9c9b34org.highwire.dtl.DTLVardef@19187c0_HPS_FORMAT_FIGEXP M_FIG C_FIG In brief, the "in silico - in vitro - in vivo" funnel holds significant potential for identifying targets to control cellular processes in research and clinical applications. In this report, Soucy et al. describes a framework for identifying, selecting, and applying chemokines to direct retinal ganglion cell migration in vivo within the adult mouse retina.

bioengineering↗

bioRxiv2023

Fibroblast growth factor-21 induces skeletal muscle atrophy and increases plasma amino acids in female mice: a potential role for glucocorticoids

BackgroundFibroblast growth factor-21 (FGF21) is an intercellular signaling molecule secreted by metabolic organs, including skeletal muscle, in response to intracellular stress. FGF21 crosses the blood brain barrier and acts via the nervous system to coordinate aspects of the adaptive starvation response, including increased lipolysis, gluconeogenesis, hepatic fatty acid oxidation, and activation of the hypothalamic-pituitary-adrenocortical (HPA) axis. Given its beneficial effects for hepatic lipid metabolism, pharmaceutical FGF21 analogues are in clinical trials treatment of fatty liver disease. We predicted pharmacologic treatment with FGF21 in-creases HPA axis activity and skeletal muscle glucocorticoid signaling and induces skeletal muscle atrophy in mice. MethodsWe treated male and female mice with FGF21 or saline, delivered either pe-ripherally or directly to the brain, to determine its effect on skeletal muscle. To identify metabolic pathways affected by FGF21, we analyzed untargeted primary metabolites measured in plasma by GCTOF-MS. To determine mechanisms underlying sex-and FGF21-dependent changes in muscle mass, we measured hormonal and molecular mediators of muscle protein synthesis and degradation. We performed stable isotope labeling with deuterium oxide to directly measure muscle protein synthesis. ResultsA short course of systemic FGF21 treatment decreased muscle protein synthe-sis (P < 0.001) and reduced tibialis anterior weight (P < 0.05); this was driven primarily by its effect in female mice (P < 0.05). Similarly, intracerebroventricular FGF21 reduced TA muscle fiber cross sectional area (P < 0.01); this was more apparent among female mice compared to male littermates (P < 0.05). In agreement with the reduced muscle mass, the topmost enriched meta-bolic pathways in FGF21-treated females were related to amino acid metabolism, and the relative abundance of plasma proteinogenic amino acids were increased up to three-fold (P < 0.05). FGF21 treatment increased hypothalamic Crh mRNA (P < 0.01), plasma corticosterone (P < 0.01), and adrenal weight (P < 0.05), and increased expression of glucocorticoid receptor target genes known to reduce muscle protein synthesis and/or promote degradation including Foxo1, Redd1, and Klf15 (P < 0.05). Again, these changes were driven primarily by effects of FGF21 in females (P < 0.05). ConclusionsFGF21 increased plasma amino acids and decreased skeletal muscle mass, together with activation of the HPA axis and glucocorticoid receptor target genes in skeletal muscle--and female mice were more sensitive to all these outcomes. Given the proposed use of FGF21 analogues for the treatment of metabolic disease, the study is both physiologically relevant and may have important clinical implications.

physiology↗

bioRxiv2025

Insulin-Like Growth Factor 1 Receptor Regulates Breast Cancer Cell Adhesion through Beta-1 Integrin

IntroductionThe insulin-like growth factor (IGF-1/IGF1R) pathway has been implicated in breast cancer aggressiveness; however, inhibition of this pathway has not been successful in clinical trials, indicating a lack of understanding about its role in TNBC metastasis. Recent studies have explored IGF1R involvement in integrin function and cancer cell adhesion dynamics. The goal of this study was to test the hypothesis that IGF1R itself regulates cancer cell adhesion. MethodsWe use MDA-MB-231 and Hs578T TNBC cell lines, siRNA-mediated knockdown, and adhesion assays to assess how IGF1R and integrin knockdowns impact cancer cell adhesion. Using xCELLigence E-plates, we quantify the effect of IGF-1 ligand stimulation versus IGF1R knockdown on functional cell adhesion. We also use HUVEC human endothelial cells to determine how IGF1R regulates adhesion to the endothelium. ResultsWe found that IGF-1 stimulation increased MDA-MB-231 TNBC adhesion, which was reversed by the IGF1R tyrosine kinase inhibitor BMS-754807 and the ligand-dependent receptor internalization inhibitor dansylcadaverine. Unexpectedly, IGF1R knockdown also potently stimulated cell adhesion. Concomitant {beta}1 integrin knockdown reversed the increased cell adhesion after both IGF-1 stimulation or IGF1R knockdown, indicating that the increased adhesion is {beta}1 integrin dependent. This was also seen via immunocytochemistry when cells were seeded on fibronectin. Finally, inhibiting IGF1R signaling also reduced MDA-MB-231 cell adhesion to HUVEC endothelial cells. DiscussionBoth IGF-1 stimulation and IGF1R knockdown in TNBC cells promote cell adhesion, which seems paradoxical. However, the commonality of both interventions is removal of IGF1R from the cell surface, since IGF-1 stimulation causes IGF1R internalization and intracellular trafficking. Blocking IGF1R signaling using a tyrosine kinase IGF1R inhibitor preserves IGF1R on the cell surface. Thus, we propose a model whereby surface-bound IGF1R inhibits {beta}1 integrin function and blocks cell adhesion. This model is supported further by our finding that treatment of MDA-MB-231 cells with dansylcadaverine, which inhibits ligand-mediated receptor internalization, blocked the effect of IGF-1 on adhesion. These findings may explain why selective IGF1R receptor antagonists, which downregulate IGF1R protein upon chronic administration, were unsuccessful in the clinical setting.

cancer biology↗

bioRxiv2018

A framework for translation of genomic responses from mouse models to human inflammatory disease contexts

The high failure rate of therapeutics showing promise in mouse disease models to translate to patients is a pressing challenge in biomedical science. However, mouse models are a useful tool for evaluating mechanisms of disease and prioritizing novel therapeutic agents for clinical trials. Though retrospective studies have examined the fidelity of mouse models of inflammatory disease to their respective human in vivo conditions, approaches for prospective translation of insights from mouse models to patients remain relatively unexplored. Here, we develop a semi-supervised learning approach for prospective inference of disease-associated human in vivo differentially expressed genes and pathways from mouse model experiments. We examined 36 transcriptomic case studies where comparable phenotypes were available for mouse and human inflammatory diseases and assessed multiple computational approaches for inferring human in vivo biology from mouse model datasets. We found that a semi-supervised artificial neural network identified significantly more true human in vivo associations than interpreting mouse experiments directly (95% CI on F-score for mouse experiments [0.090, 0.175], neural network [0.278, 0.375], p = 0.00013). Our study shows that when prospectively evaluating biological associations in mouse studies, semi-supervised learning approaches combining mouse and human data for biological inference provides the most accurate assessment of human in vivo disease and therapeutic mechanisms. The task of translating insights from model systems to human disease contexts may therefore be better accomplished by the use of systems modeling driven approaches.\n\nAuthor SummaryComparison of genomic responses in mouse models and human disease contexts is not sufficient for addressing the challenge of prospective translation from mouse models to human disease contexts. Here, we address this challenge by developing a semi-supervised machine learning approach that combines supervised modeling of mouse experiment datasets with unsupervised modeling of human disease-context datasets to predict human in vivo differentially expressed genes and pathways as if the model system experiment had been run in the human cohort. A semi-supervised version of a feed forward artificial neural network was the most efficacious model for translating experimentally derived mouse molecule-phenotype associations to the human in vivo disease context. We find that computational generalization of signaling insights from mouse to human contexts substantially improves upon direct generalization of mouse experimental insights and argue that such approaches can facilitate more clinically impactful translation of insights from preclinical studies in model systems to patients.

systems biology↗

bioRxiv2024

Cancer Interception During Treatment: Using Growth Kinetics to Create a Continuous Variable for Assessing Disease Response

BackgroundWe applied 11 mathematical models of tumor growth to clinical trial data available from public and private sources. We have previously described the remarkable capacity for a simple biexponential model of tumor growth to fit thousands of datasets, and to correlate with overall survival. The goal of this study was to extend our analysis to additional tumor types and to evaluate whether alternate growth models could describe the time course of disease burden in the small subset of patients in whom the biexponential model failed. MethodsFor this analysis, we obtained data for tumor burden from 17,140 patients with six different tumor types. Imaging data and serum levels of tumor markers were available for 3,346 and 13,794 patients, respectively. Data from patients were first analyzed using the biexponential model to determine rates of tumor growth (g) and regression (d); for those whose data could not be described by this model, fit of their data was assessed using seven alternative models. The model that minimized the Akaike Information Criterion was selected as the best fit. Using the model that best fit an individual patients data, we estimated the rates of growth (g) and regression (d) of disease burden over time. The rates of tumor growth (g) were examined for association with a traditional endpoint (overall survival). FindingsFor each model, the number of patient datasets that fit the model were obtained. As we have previously reported, data from most patients fit a simple model of exponential growth and exponential regression (86%). Data from another 7% of patients fit an alternative model, including 3% fitting to a model of constant or linear regression and exponential growth of tumor on the surface and 3% fitting to model of exponential decay on tumor surface with asymmetric growth. As previously reported, we found that growth rate correlates well with overall survival, remarkably even when data from various histologies are considered together. For patients with multiple timepoints of tumor measurement, the growth rate could often be estimated even during the phase when only net regression of tumor quantity could be discerned. InterpretationThe validation of a simple mathematical model across different cancers and its application to existing clinical data allowed estimation of the rate of growth of a treatment resistant subpopulation of cancer cells. The quantification of available clinical data using the growth rate of tumors in individual patients and its strong correlation with overall survival makes the growth rate an excellent marker of the efficacy of therapy specific to the individual patient.

cancer biology↗

bioRxiv2023

Long non-coding RNA TUG1 is down-regulated in Friedreich's ataxia.

Friedreichs Ataxia (FRDA) is a neurodegenerative disorder caused by reduced frataxin (FXN) levels. It leads to motor and sensory impairments and has a median life expectancy of around 35 years. As the most common inherited form of ataxia with no cure, FRDA lacks reliable, non-invasive biomarkers, prolonging and inflating the cost of clinical trials. This study identifies long non-coding RNA Tug1 as a potential blood-based FRDA biomarker. In a previous study using a frataxin knockdown mouse model (FRDAkd), we observed several hallmark FRDA symptoms and abnormalities in various tissues. Building on this, we hypothesized that a dual-source approach--comparing the data from peripheral blood samples from FRDA patients with tissue samples from affected areas in FRDAkd mice, tissues usually unattainable from patients--would effectively identify robust biomarkers. A comprehensive reanalysis was conducted on gene expression data from 183 age- and sex-matched peripheral blood samples of FRDA patients, carriers, and controls, as well as 192 tissue datasets from FRDAkd mice. Blood and tissue samples underwent RNA isolation and qRT-PCR, and frataxin knockdown was confirmed through ELISA. Tug1 RNA interaction was explored via RNA pull-down assays. Validation was performed in serum and blood samples on an independent set of 45 healthy controls, 45 FRDA patients; 66 heterozygous carriers, and 72 FRDA patients. Tug1 and Slc40a1 emerged as potential blood-based biomarkers, confirmed in the FRDAkd mouse model (One-way ANOVA, p [≤] 0.05). Tug1 was consistently downregulated after Fxn knockdown and correlated strongly with Fxn levels (R2 = 0.71 during depletion, R2 = 0.74 during rescue). Slc40a1 showed a similar but tissue-specific pattern. Further validation of Tug1s downstream targets strengthened its biomarker candidacy. In additional human samples, TUG1 levels were significantly downregulated in both whole blood and serum of FRDA patients compared to controls (Wilcoxon signed-rank test, p < 0.05). Regression analyses revealed a negative correlation between TUG1 levels and disease onset (p < 0.0037), and positive correlations with disease duration and Functional Disability Stage score (p < 0.04). This suggests that elevated TUG1 levels correlate with earlier onset and more severe cases. In summary, this study highlights Tug1 as a crucial blood-based biomarker for FRDA. Tug1s consistent expression variance across human and mouse tissues is closely associated to disease severity and key FRDA pathways. It also correlates strongly with Fxn levels, making it a promising early, non-invasive marker. TUG1 offers potential for FRDA monitoring and therapeutic development, warranting further clinical research.

neuroscience↗

bioRxiv2021

Suppression of B-Cell Activation by Human Cord Blood-Derived Stem Cells (CB-SC) through the Galectin-9-Dependent Cell Contact Mechanism

BackgroundWe developed the Stem Cell Educator therapy among multiple clinical trials based on the immune modulations of multipotent cord blood-derived stem cells (CB-SC) on different compartments of immune cells such as T cells and monocytes/macrophages in diabetes and other autoimmune diseases. However, the effects of CB-SC on the B cells remained unclear. To better understand the molecular mechanisms underlying the immune education of CB-SC, we explored the modulations of CB-SC on human B cells. MethodsCB-SC were isolated from human cord blood units and confirmed by flow cytometry with different markers for their purity. B cells were purified by using anti-CD19 immunomagnetic beads from human peripheral blood mononuclear cells (PBMC). Next, the activated B cells were treated in the presence or absence of coculture with CB-SC for 7 days before undergoing flow cytometry analysis of phenotypic change with different markers. RT-PCR was utilized to evaluate the levels of galectin expressions with or without treatment of activated B cells in order to find the key galectin contributing to the B-cell modulation. ResultsFlow cytometry demonstrated that the proliferation of activated B cells was markedly suppressed in the presence of CB-SC, leading to the down-regulation of immunoglobulin productions from the activated B cells. Phenotypic analysis revealed that treatment with CB-SC increased the percentage of IgD+CD27- naive B cells, but decreased the percentage of IgD-CD27+ switched B cells. Transwell assay showed that the immune suppression of CB-SC on B cells was dependent on the manner of cell-cell contact via Gal-9 molecule, as confirmed by the blocking experiment with the anti-Gal-9 monoclonal antibody. Mechanistic studies demonstrated that both calcium levels of cytoplasm and mitochondria were down-regulated after the treatment with CB-SC, causing the decline of mitochondrial membrane potential in the activated B cells. Western blot exhibited that the levels of phosphorylated Akt and Erk1/2 signaling proteins in the activated B cells were also markedly reduced in the presence of CB-SC. ConclusionsCB-SC displayed multiple immune modulations on B cells through the Gal-9-mediated cell-cell contact mechanism and calcium flux/Akt/Erk1/2 signaling pathways. The data advances current understanding about the molecular mechanisms underlying the Stem Cell Educator therapy to treat autoimmune diseases in clinics.

immunology↗

bioRxiv2019

HIV-1 co-receptor usage and variable loop contact impacts V3 loop bnAb susceptibility

In clinical trials, HIV-1 broadly neutralizing antibodies (bnAbs) effectively lower plasma viremia and delay virus reemergence after antiretroviral treatment is stopped among infected individuals that have undetectable virus levels. Presence of less neutralization susceptible strains prior to treatment, however, decreases the efficacy of these antibody-based treatments. The HIV-1 envelope glycoprotein harbors extensive genetic variation, and thus, neutralization sensitivity often cannot be predicted by sequence analysis alone. Sequence-based prediction methods are needed because phenotypic-based assays are labor intensive and not sensitive. Based on the finding that phenotypically confirmed CXCR4- as compared to exclusive CCR5-utilizing strains are less neutralization sensitive, especially to variable loop 1 and 2 (V1-V2) and V3 loop bnAbs, we show that an algorithm that predicts receptor usage identifies envelopes with decreased V3 loop bnAb susceptibility. Homology modeling suggests that the primary V3 loop bnAb epitope is equally accessible among CCR5- and CXCR4-using strains although variants that exclusively use CXCR4 have V3 loop protrusions that interfere with CCR5 receptor interactions. On the other hand, homology modeling also shows that envelope V1 loop orientation interferes with V3 loop directed bnAb binding, and this accounts for decreased neutralization sensitivity in some but not all cases. Thus, there are likely different structural reasons for the co-receptor usage restriction and the differential bnAb susceptibility. Algorithms that use sequence data to predict receptor usage and antibody-envelope homology models can be used to identify variants with decreased sensitivity to V3 loop and potentially other bnAbs.\n\nAUTHOR SUMMARYHIV-1 broadly neutralizing antibody (bnAb) therapies are effective, but the pre-existence of less susceptible variants may lead to therapeutic failure. Sequence-based methods are needed to predict pre-treatment variants neutralization sensitivity. HIV-1 strains that use the CXCR4 as compared to the CCR5 receptor are less neutralization susceptible, especially to V1-V2 and V3 loop bnAbs. A sequence-based algorithm that predicts receptor usage can identify envelope variants with decreased V3 loop bnAb susceptibility. While the inability to utilize the CCR5 receptor maps to a predicted protrusion in the envelope V3 loop, this viral determinant does not directly influence V3 loop bnAb sensitivity. Furthermore, homology modeling predicted contact between the envelope V1 loop and an antibody also impact V3 loop bnAb susceptibility in some but not all cases. An algorithm that predicts receptor usage and homology modeling can be used to predict sensitivity to bnAbs that target the V3 loop and potentially other envelope domains. These sequence-based methods will be useful as HIV-1 bnAbs enter the clinical arena.

microbiology↗

bioRxiv2018

Estimating the probable cause of recurrence in Plasmodium vivax malaria: relapse, reinfection or recrudescence?

BackgroundRelapse of Plasmodium vivax infection is the main cause of vivax malaria in many parts of Asia. However at the individual patient level, recurrence of a blood stage infection following treatment within the endemic area can be either a relapse (from dormant liver-stage parasites), a recrudescence (blood-stage treatment failure), or a reinfection (following a new mosquito inoculation). Each requires a different prevention strategy, but previously they could not be distinguished reliably. Time-of-event and genetic data provide complimentary information about the cause of P. vivax recurrence, but the optimum approach to genotyping and analysis remains uncertain.\n\nMethodsIndividual-level data from two large drug trials in acute vivax malaria patients (Vivax History: VHX; Best Primaquine Dose: BPD) conducted on the Thailand-Myanmar border with follow-up of one year were pooled (n=1299). A total of 710 isolates from both acute and recurrent P. vivax episodes were genotyped using 3-9 highly polymorphic microsatellite markers. These pooled data were analyzed using a novel population statistical model incorporating an assessment of genetic relatedness, treatment drug administered, and the time-to-recurrence.\n\nResults99% of genotyped recurrences in individuals who did not receive primaquine (n=365) were estimated to be relapses. In comparison, 14% of genotyped recurrences (n=121) were estimated to be relapses following high-dose supervised primaquine. By comparing episodes across individuals (90194 comparisons), the false-positive rate of relapse identification using genetic data alone was estimated to be 2.2%. We estimated the true failure rate after high-dose primaquine (7mg/kg total dose) to be 2.6% in this epidemiological context, substantially lower the reinfection unadjusted estimate of 12%. Simulation studies show that 9 highly polymorphic microsatellite markers suffice to discriminate between recurrence states. Drug exposures reflected by plasma carboxy-primaquine concentrations were not predictive of treatment failure, but did identify non-adherence.\n\nConclusionUsing this novel statistical model, relapse of P. vivax malaria could be distinguished reliably from reinfection. This showed that in this population supervised high-dose primaquine could avert up to 99% of relapses. In low transmission settings, microsatellite genotyping combined with time-to-event data can accurately discriminate between the different causes of recurrent P. vivax malaria.\n\nAuthor summaryOne hundred years ago, Plasmodium vivax, the most globally diverse cause of human malaria, was present across most of the old-world, throughout tropical and temperate climes. Its main evolutionary advantage over Plasmodium falciparum, responsible for the most deadly type of human malaria, is its ability to stay dormant in the liver, emerging weeks to years later causing recurring illness and continuing transmission. The dormant liver-stage parasites are called hypnozoites. A recurrent infection can either be hypnozoite-derived (a relapse), a blood-stage treatment failure (recrudescence), or from a new mosquito bite (a reinfection). At a population level, each requires a different preventative strategy but no widely applicable methodology existed to discriminate between the three possible states: relapse, recrudescence and reinfection. Parasite genetic data alone cannot resolve the different possibilities. We developed a novel probabilistic framework which uses both epidemiological and genetic data to determine the most likely cause of vivax recurrence at the individual level. We applied this method to the largest available pooled clinical trial data from Southeast Asia incorporating information from highly polymorphic microsatellite markers, drug treatments received and time-to-recurrent illness. This analysis provides a tool for estimating probabilities of relapse, recrudescence and reinfection and, importantly, shows that hypnozoiticidal high-dose primaquine radical cure is much more effective than previously thought.

epidemiology↗

bioRxiv2014

High Bacterial Load Predicts Poor Outcomes in Patients with Idiopathic Pulmonary Fibrosis

BackgroundRepetitive alveolar damage and aberrant repair may be important in the development of the fatal condition Idiopathic Pulmonary Fibrosis (IPF). The role played by microorganisms in this cycle is unknown.\n\nMethodsWe consecutively enrolled patients diagnosed with IPF according to international criteria together with healthy smokers, non-smokers and subjects with moderate Chronic Obstructive Pulmonary Disease (COPD) as controls. Subjects underwent bronchoalveolar lavage (BAL) from which genomic DNA was isolated. The V3-V5 region of the bacterial 16S rRNA gene was amplified, allowing quantification of bacterial load and identification of communities by 16S rRNA qPCR and pyrosequencing.\n\nResultsOur 65 IPF patients had 3.9x109 copies of the 16S rRNA gene per ml of BAL, two-fold more than the 1.8x109 copies in 44 sex- and smoking-matched controls (P<0.0001). Baseline BAL bacterial burden predicted Forced Vital Capacity (FVC) decline (P=0.02). Patients in the highest tertile of bacterial burden were at a higher risk of mortality compared to subjects in the lowest tertile (hazard ratio 4.59 (95% CI, 1.05-20); P=0.04).\n\nSequencing yielded 912,883 high quality reads from all subjects. Operational Taxonomic Units (OTUs) representing Haemophilus, Streptococcus, Neisseria and Veillonella were 1.5 to 3.5 fold more abundant in cases than controls (P<0.05). Regression analyses indicated that these specific OTUs as well as bacterial burden associated independently with IPF.\n\nConclusionsIPF is characterised by an increased bacterial burden in BAL that predicts decline in lung function and death. Clinical trials of antimicrobial therapy may determine if microbial burden is causal or not in IPF progression.

Microbiology↗

bioRxiv2014

Online Self-Report Data for Duchenne Muscular Dystrophy confirms natural history and can be used to assess for therapeutic benefits

To assess the utility of online patient self-report outcomes in a rare disease, we attempted to observe the effects of corticosteroids in delaying age at fulltime wheelchair use in Duchenne muscular dystrophy (DMD) using data from 1,057 males from DuchenneConnect, an online registry. Data collected were compared to prior natural history data in regard to age at diagnosis, mutation spectrum, and age at loss of ambulation. Because registrants reported differences in steroid and other medication usage, as well as age and ambulation status, we could explore these data for correlations with age at loss of ambulation. Using multivariate analysis, current steroid usage was the most significant and largest independent predictor of improved wheelchair-free survival. Thus, these online self-report data were sufficient to retrospectively observe that current steroid use by patients with DMD is associated with a delay in loss of ambulation. Comparing commonly used steroid drugs, deflazacort prolonged ambulation longer than prednisone (median 14 years and 13 years, respectively). Further, use of Vitamin D and Coenzyme Q10, insurance status, and age at diagnosis after 4 years were also significant, but smaller, independent predictors of longer wheelchair-free survival. Nine other common supplements were also individually tested but had lower study power. This study demonstrates the utility of DuchenneConnect data to observe therapeutic differences, and highlights needs for improvement in quality and quantity of patient-report data, which may allow exploration of drug/therapeutic practice combinations impractical to study in clinical trial settings. Further, with the low barrier to participation, we anticipate substantial growth in the dataset in the coming years.

Physiology↗