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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 Read source abstracts and check manuscript versions; preprints are not peer reviewed.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 919 records · Page 51Linked to original sources

bioRxiv2018

AAV-mediated gene transfer restores a normal muscle transcriptome in a canine model of X-linked myotubular myopathy

Multiple clinical trials employing recombinant adeno-associated viral (rAAV) vectors have been initiated for neuromuscular disorders, including Duchenne and limb-girdle muscular dystrophies, spinal muscular atrophy, and recently X-linked myotubular myopathy (XLMTM). Previous work from our laboratory on a canine model of XLMTM showed that a single rAAV8-cMTM1 systemic infusion corrects structural abnormalities within the muscle and restores contractile function, with affected dogs surviving more than four years post injection. This exceptional therapeutic efficacy presents a unique opportunity to identify the downstream molecular drivers of XLMTM pathology, and to what extent the whole muscle transcriptome is restored to normal after gene transfer. Herein, RNA-sequencing was used to examine the transcriptomes of the Biceps femoris and Vastus lateralis in a previously-described canine cohort showing dose-dependent clinical improvements after rAAV8-cMTM1 gene transfer. Our analysis confirmed several dysregulated genes previously observed in XLMTM mice, but also identified new transcripts linked to XLMTM pathology. We demonstrated XLMTM transcriptome remodeling and dose-dependent normalization of gene expression after gene transfer and created new metrics to pinpoint potential biomarkers of disease progression and correction.

pathology↗

bioRxiv2020

Tumor genotype dictates radiosensitization after Atm deletion in brainstem gliomas

Diffuse intrinsic pontine glioma (DIPG) kills more children than any other type of brain tumor. Despite clinical trials testing many chemotherapeutic agents, radiotherapy remains the standard treatment. Here, we utilized Cre/loxP technology to show that deleting Ataxia telangiectasia mutated (Atm) in primary mouse models of DIPG can enhance tumor radiosensitivity. Genetic deletion of Atm improved survival of mice with p53 deficient but not p53 wild-type gliomas following radiotherapy. Similar to patients with DIPG, mice with p53 wild-type tumors had improved survival after radiotherapy independent of Atm deletion. p53 wild-type tumor cell lines induced proapoptotic genes after radiation and repressed the NRF2 target, Nqo1. Tumors lacking p53 and Ink4a/Arf expressed the highest level of Nqo1 and were most resistant to radiation, but deletion of Atm enhanced the radiation response. These results suggest that tumor genotype may determine whether inhibition of ATM during radiotherapy will be an effective clinical approach to treat DIPGs.

cancer biology↗

bioRxiv2025

A Novel In Vitro Potency Assay Demonstrating the Anti-Fibrotic Mechanism of Action of CDCs in Deramiocel

Duchenne muscular dystrophy (DMD) is characterized by progressive skeletal and cardiac muscle degeneration driven by inflammation and fibrosis, ultimately leading to cardiomyopathy and premature death. Deramiocel, an allogeneic cell therapy composed of cardiosphere-derived cells (CDCs), has demonstrated potent anti-fibrotic and immunomodulatory effects in preclinical models and clinical trials, including HOPE-2 and its open-label extension (HOPE-2 OLE), where Deramiocel treatment significantly attenuated progression of skeletal and cardiac muscle dysfunction. Here, we describe the development of a novel in vitro potency assay to quantify the anti-fibrotic activity of Deramiocel. Conditioned media (CM) from multiple Deramiocel manufacturing lots significantly suppressed expression of collagen type I alpha 1 (COL1A1) and collagen type III alpha 1 (COL3A1) in primary human dermal fibroblasts compared with non-conditioned media controls, establishing a robust, reproducible readout of anti-fibrotic activity. The effect was dose-dependent and abrogated by sequential depletion of exosomes and soluble proteins, implicating both as critical mediators of Deramiocels mechanism of action. Importantly, CDCs in deramiocel lots classified as potent by this assay were shown to exert a clinically meaningful benefit in DMD patients in the HOPE-2 and HOPE-2 OLE studies. This assay represents a mechanistically informative, therapeutically relevant, reproducible, scalable, and regulatory-compliant approach for assessing Deramiocel potency, enabling consistent manufacturing and facilitating the continued development of Deramiocel as a disease-modifying therapy for DMD.

cell biology↗

bioRxiv2025

Single Cell Analysis of pBMCs of Psoriasis patients reveals distinct CD4+ T cell phenotypes associated with response to IL-23 blockade.

The use of IL-23 inhibitors (IL-23i) for psoriatic diseases has resulted in significant improvement in disease symptoms for many patients. The extent of disease improvement following IL-23 blockade varies across patients with psoriasis; however, the immunologic factors associated with a good or poor response to IL-23 blockade remain unclear. Here, we utilized peripheral blood mononuclear cells (pBMCs) collected through the MINIMA clinical trial (NCT04271540) and applied single-cell RNA sequencing to profile circulating immune populations from 27 patients with psoriasis or psoriatic arthritis, aiming to identify cellular features associated with a response to IL-23 blockade. We identified populations of CD4+ T cells whose abundance in circulation before treatment was associated with improved skin disease following IL-23i treatment. Circulating CD4+ T cells that demonstrate transcriptomic features of Th1-like cells were associated with better psoriasis skin improvement and had transcriptomic signatures resembling T cells identified in psoriasis lesional skin. Further, decrease in levels of IL-17A and IFN{gamma} in serum each correlated with improvement in PASI levels. These results suggest that immune cell features detectable in blood may be informative in identifying patients with psoriasis who are likely to have a robust clinical response to IL-23 blockade.

immunology↗

bioRxiv2026

STING agonists in combination with epigenetic drugs potentiate ZNFX1-driven inflammatory necroptosis in TP53-mutated AML

TP53-mutated acute myeloid leukemia (AML) has dismal outcomes with current treatments and represents a critical unmet need. TP53-mutated AML is proposed to be susceptible to immunotherapeutic approaches but, to date, there is no established immunotherapy for this sub-group. Expression of stimulator of interferon genes (STING), a key innate immune driver that activates interferon (IFN) signaling, is decreased by epigenetic silencing or mutation in many cancers, including those with TP53 mutations. Here, we report that response to the next-generation synthetic STING agonist C92 is potentiated in AML cell lines and primary cells with TP53-mutated versus wild-type (WT) cells, representing a previously undescribed vulnerability of these leukemia cells to STING small molecule therapies. Moreover, combining treatment with the DNA methyltransferase inhibitor (DNMTi) decitabine (DAC), significantly increases STING activation, with marked transcriptome-wide increase in repetitive elements (REs) and upregulation of a critical set of interferon-related genes. Cell death in TP53 KO versus WT AML is specifically dependent on innate immune zinc finger NFX1-type containing 1 (ZNFX1) and Z-DNA-binding protein 1 (ZBP1) driving increased cleavage and activation of Receptor-Interacting-Serine/Threonine-Protein Kinase 3 (RIPK3) and mixed lineage kinase domain-like protein (MLKL), suggesting mechanisms of necroptosis. Finally, C92 and DAC combination significantly reduces leukemia burden in humanized AML mouse models, accompanied by increased immune responses, including cytokines and cytotoxic T lymphocytes in the leukemia microenvironment. These results support development of clinical trial strategies combining STING agonists with DNMTis for patients with TP53-mutated AML. SummaryO_LITP53-mutated AML potentiates effects of novel next-generation STING agonist C92, with unique allosteric and non-cyclic dinucleotide (non-CD) mechanism of action, inducing increased STING activation and cytokine release C_LIO_LISTING agonists and DNMTis, synergistically increase STING activation with marked transcriptome-wide increase in repetitive elements (REs) and upregulation of a critical set of interferon-related genes in TP53-mutated AML C_LIO_LISTING agonists induce necroptosis via a STING-ZNFX1-ZBP1-necroptosis axis in TP53-mutated AML. C_LIO_LIThis drug combination reduces leukemia burden, activates immune responses in AML models and supports translation for high-risk AML patients. C_LI Statement of Translational RelevanceThis pre-clinical study identifies a novel therapeutic vulnerability in (TP53)-mutated acute myeloid leukemia (AML), a poor prognosis subtype with a critical unmet need. Novel next-generation STING agonist C92, with unique allosteric and non-cyclic dinucleotide (non-CD) mechanism of action, induces increased STING activation and cytokine release, compared with WT TP53 in AML cell lines and primary cells, and has superior STING activity with respect to several STING agonists currently in clinical studies. Combining C92 treatment with the DNA methyltransferase inhibitor (DNMTi) decitabine (DAC) synergistically increases STING activation, with marked transcriptome-wide increase in repetitive elements (REs) and upregulation of a critical set of interferon-related genes, driving ZNFX1-driven inflammatory necroptotic cell death. Utilizing humanized mouse models, C92 in combination with DAC significantly reduces leukemia burden and enhances cytotoxic T-cell responses in the tumor microenvironment, supporting clinical translation for high-risk AML patients.

cancer biology↗

bioRxiv2024

The kinetics of bedaquiline diffusion in tuberculous cavities opens a window for emergence of resistance.

Cavitary tuberculosis (TB) is difficult to cure and a site of relapse. Bedaquiline has been a wonder drug in the treatment of multidrug resistant TB, but emergence of resistance threatens its sustained success. To investigate the role of drug distribution in resistance development, we designed a novel laser-capture microdissection scheme to spatially resolve the penetration of bedaquiline in the necrotic center (caseum) of cavities, a recalcitrant site of disease. Working with preclinical models that form large necrotic lesions, we profiled bedaquiline and two next generation diarylquinolines TBAJ-587 and TBAJ-876. Drug concentrations were measured in laser-captured areas of cavity caseum as a function of time and distance from blood supply. To simulate drug coverage in patient cavities, the data were modeled, and drug penetration parameter estimates were linked to clinical plasma pharmacokinetics for bedaquiline and the new diarylquinolines. Pharmacokinetic-pharmacodynamic (PK-PD) simulations revealed that bedaquiline reaches efficacious concentrations in outer and deep caseum after several weeks to months and lingers at subtherapeutic concentrations up to 3 years after therapy ends. TBAJ-587 and TBAJ-876, currently in clinical development, achieve bactericidal concentrations in caseum more rapidly and shorten the window of suboptimal concentrations post treatment compared to bedaquiline. Simulations of clinically plausible dosing schemes were conducted to guide the design of clinical trials for cavitary TB and help mitigate resistance development. In summary, the slow kinetics of diffusion of bedaquiline into and out of cavity caseum creates spatio-temporal windows of subtherapeutic concentrations. Site-of-disease simulations of TBAJ-587 and TBAJ-876 predict reduced opportunities for resistance development. SIGNIFICANCEClinical resistance to bedaquiline has emerged faster than anticipated. Understanding potential contributing factors could help curb further resistance development, not only for bedaquiline but also for the next generation diarylquinolines currently in phase 2, TBAJ-587 and TBAJ-876. Here we hypothesized and confirmed that the extended time to reach steady state and slow clearance of bedaquiline leads to extremely slow diffusion into and out of cavity caseum, a recalcitrant site of TB disease and relapse. Through modeling of experimental data in a preclinical model of cavitary TB and clinical simulations, we show that the next generation diarylquinolines may reduce spatio-temporal windows of resistance development compared to bedaquiline. Our results can inform dosing schemes of diarylquinoline-based therapies that limit resistance development.

pharmacology and toxicology↗

bioRxiv2019

Predicting the Frequency of Drug Side effects

Drug side effects are a leading cause of morbidity and mortality. Currently, the frequency of drug side effects is determined experimentally during human clinical trials through placebo-controlled studies. Here we present a novel framework to computationally predict the frequency of drug side effects. Our algorithm is based on learning a latent variable model for drugs and side effects by matrix decomposition. Extensive evaluations on held out test sets show that the frequency class is predicted with 67.8% to 94% accuracy in the neighborhood of the correct class. Evaluations on prospective data confirm the commonly held hypothesis that most post-marketing side effects are very rare in the population, with occurrences of less than 1 in a 10,000. Importantly, our model provides explanations of the biology underlying drug side effect relationships. We show that the drug latent representations in our model are related to distinct anatomical drug activities and that the similarity between these representations are predictive of the drug clinical activity as well as drug targets.\n\nOne summary sentencenovel explainable machine learning algorithm predicts the frequency of drug side effects in the population

bioinformatics↗

bioRxiv2025

Meditation as a Bioactive Intervention: Molecular and Neurophysiological Mechanisms Revealed by Connectivity Mapping

Meditation practices are often used as non-pharmacological adjunct therapy for managing stress and well-being benefits. We propose that beneath their non-pharmacological facade, meditation practices might operate via drug target modulation having profound neurophysiological effects. Firstly, we leverage the Connectivity Map (CMap) to investigate (a) the overlap between meditation-induced molecular signatures and established drug responses, and (b) the pathways and mechanisms contributing to meditation potential therapeutic effects. This was studied in a comprehensive temporal RNAseq dataset comprising premeditation, meditation, and follow-up stages from a clinical trial involving 106 participants practising inner engineering meditation. Meditation signatures overlapped with over 438 drugs, but predominantly with drugs targeting the neuroactive ligand receptor pathways, capable of modulating the brains excitation-inhibition (E/I) balance. Next, to bridge the meditation-induced molecular changes to measurable neurophysiological effects, we performed a comprehensive meta-analysis of drugs affecting E/I balance through the lens of non-invasive brain stimulation, i.e., transcranial magnetic stimulation (TMS-EMG and TMS-EEG). Using multiple correspondence analysis, we then clustered the CMap informed neuroactive drugs and their E/I effects on the same latent space. We found that meditations effects mimic drugs targeting the GABAergic, Glutametergic and other neuromodulatory system pathways. Our findings lead to a working model to objectively test neurophysiological changes resulting from meditation that can lead to evidence-based clinical applications. Overall, these findings support the view that meditation acts as a biologically active intervention capable of modulating molecular pathways and cortical excitability, rather than functioning solely as a psychological or contemplative practice.

systems biology↗

bioRxiv2026

Microfluidic Osteoarthritis-on-a-Chip for Evaluating Joint-Cell Responses to Tanezumab, a Humanized Anti-NGF Monoclonal Antibody

Osteoarthritis (OA) drug development remains constrained by preclinical models that fail to recapitulate the multicellular interactions that regulate human joint inflammation and extracellular matrix degeneration in response to investigational drugs. Tanezumab, a humanized anti-nerve growth factor monoclonal antibody developed for non-opioid pain relief, advanced to late-stage clinical trials but was discontinued due to unresolved joint-localized safety concerns, including rapidly progressive OA. This study evaluated whether a human microfluidic joint-on-a-chip co-culture system could detect early biomarker responses to tanezumab exposure that were not apparent in conventional chondrocyte monoculture. Tanezumab was first tested in human chondrocyte monoculture under untreated and disease-like (i.e., IL-1{beta}-treated) conditions. Across a 20-analyte panel of inflammatory and matrix-remodeling biomarkers, statistically significant monoculture responses to tanezumab were limited to decreased IL-1{beta} from 335 to 132 pg/mL ([~]0.39-fold) and increased IL-8 from 575 to 675 pg/mL ([~]1.17-fold). Major OA-associated matrix-remodeling markers, including MMP-1, MMP-3, and MMP-13, remained largely unchanged, indicating that monoculture conditions are insufficiently sensitive to detect clinically predictive drug-related molecular changes. Tanezumab was then evaluated in co-cultures containing chondrocytes, osteoblasts, fibroblast-like cells, and macrophages under low-inflammation (i.e., M0 macrophage-based) and high-inflammation (i.e., M1 macrophage-based) conditions. In the M0-based co-culture, tanezumab increased MMP-1 from [~]4.20 x 104 to [~]6.20 x 104 pg/mL ([~]1.48-fold), MMP-3 from [~]8.00 x 104 to [~]1.20 x 105 pg/mL ([~]1.50-fold), and MCP-1 from 2.85 x 103 to 4.31 x 103 pg/mL ([~]1.51-fold). In contrast, the M1-based co-culture showed decreases in MMP-13 from [~]1.66 x 104 to [~]1.17 x 104 pg/mL ([~]0.70-fold) and IFN-{gamma} from [~]1.95 x 104 to [~]1.56 x 104 pg/mL ([~]0.80-fold), changes that may appear beneficial despite the drugs known clinical risks. Collectively, these findings show that low-inflammation multicellular co-culture revealed coordinated matrix remodeling and inflammatory responses to NGF blockade that were missed in monoculture and were partly obscured in highly stimulated disease-like conditions. This platform may provide a useful, human-relevant approach for safety signal assessment and early evaluation of OA therapeutics within a defined context of use focused on joint-specific, tissue-level drug-response testing.

bioengineering↗

bioRxiv2026

Reappraisal of GPR40/FFAR1 as a Therapeutic Target for Type 2 Diabetes Mellitus: Systematic Cheminformatic Analysis of 2,637 Compounds in ChEMBL 36 Identifies Superior Candidates to Fasiglifam

BackgroundThe discontinuation of Fasiglifam (TAK-875), a GPR40/FFAR1 full agonist, during Phase 3 clinical trials due to hepatotoxicity led to widespread abandonment of GPR40 as a viable therapeutic target for type 2 diabetes mellitus (T2DM). However, mechanistic evidence suggests that Fasiglifams hepatotoxicity arises from mitochondrial liability driven by high lipophilicity (aLogP = 5.31), rather than from on-target GPR40 signaling. We hypothesized that target-level failure was incorrectly inferred from compound-level safety concerns, and that superior candidates exist within publicly available databases. MethodsWe queried ChEMBL Release 36 (28 GB SQLite, 74 tables) for all compounds with documented GPR40/FFAR1 activity (UniProt: O14842). Compounds were filtered by EC50 [≤] 10 nM in nM units with standard relation "=". Drug-likeness was assessed using Lipinskis Rule of Five (Ro5), aLogP, molecular weight (MW), hydrogen bond donors/acceptors (HBD/HBA), and polar surface area (PSA). A parallel analysis of Therapeutic Target Database (TTD v10.1.01, 4,298 targets) provided clinical context. A real-world evidence (RWE) patient stratification framework was constructed using EMR data from tens of millions of patients with >10 years of longitudinal follow-up. ResultsOf 2,637 GPR40-active compounds in ChEMBL 36, 526 (19.9%) demonstrated EC50 < 100 nM and 102 (3.9%) demonstrated EC50 < 10 nM. Eight compounds met stringent drug-likeness criteria (Ro5 violations = 0, aLogP < 5.0, EC50 [≤] 1 nM). The lead compound (CHEMBL4859651) exhibited EC50 = 0.04 nM (8.75-fold more potent than Fasiglifam), MW = 297 Da (43% lower), and aLogP = 4.30 (19% lower), with zero Ro5 violations. Mean MW of the eight candidates was 317 {+/-} 28 Da versus 524 Da for Fasiglifam. A parallel GCK analysis identified a protein-protein interaction target (CHEMBL3885579, GCK-GKRP interface) harboring 40 exclusive compounds as an orthogonal strategy for partial GCK activation. ConclusionsSystematic cheminformatic analysis reveals that compounds with substantially superior activity and drug-likeness profiles relative to Fasiglifam exist within ChEMBL 36. Fasiglifams hepatotoxicity is attributable to compound-specific physicochemical properties, not GPR40-mediated toxicity. RWE patient stratification may further mitigate hepatotoxicity risk for next-generation GPR40 agonists. These findings argue for systematic reappraisal of GPR40 as a viable therapeutic target for T2DM.

pharmacology and toxicology↗

bioRxiv2025

Wee1 opposes APC/C(Cdh1) activity to promote S-phase entry

Wee1 phosphorylates and inhibits CDK activity to inhibit mitotic entry and establish a G2 DNA damage checkpoint. Consequently, Wee1 inhibitors are in clinical trials, developed to be synthetically lethal in TP53 mutant tumours that become reliant on a Wee1-mediated DNA damage checkpoint. However, Wee1 inhibitors have efficacy in TP53 wild-type tumours and many trials have been terminated due to high levels of toxic side-effects, suggesting that Wee1 has unknown functions. Here, we show that Wee1 promotes cell cycle re-entry from quiescence (G0) by opposing the activity of the E3 ubiquitin ligase, APC/CCdh1. Wee1 phosphorylates Cdh1 (FZR1) at key residues that mediate the interaction between Cdh1 and APC/C. Cells with loss-of-function of Wee1 during G0/G1 have delayed S-phase entry, an impaired G1/S transition, abnormal S-phase accumulation of the CDK inhibitor p21 and enter a p21-dependent G2 arrest. Reduced expression of APC/CCdh1 or p21 renders cells more sensitive to acute Wee1 inhibition and both pathways are downregulated in acquired Wee1 inhibitor resistance. Our study reveals a new cell cycle control mechanism that has implications for how Wee1 inhibitors should be used in the clinic.

cell biology↗

bioRxiv2026

Pharmaceutical assessment of low global warming potential alternatives to HFA-134a in a budesonide, glycopyrrolate, and formoterol fumarate pressurized metered dose inhaler

Manufacturers are adopting propellants for use in pressurized metered-dose inhalers (pMDIs) that have lower global warming potentials (GWPs) than the propellants traditionally used in pMDIs. Hydrofluoroalkane (HFA)-134a has been used as the propellant in the pMDI used to deliver the fixed-dose triple combination of budesonide, glycopyrrolate and formoterol fumarate (BGF); following successful clinical evaluation, the BGF pMDI is now being transitioned to the next generation propellant hydrofluoroolefin (HFO)-1234ze(E), which has near-zero GWP. We describe formulation development efforts that led to selection of HFO-1234ze(E) over another propellant, HFA-152a, for reformulation. Propellant-specific studies evaluated active pharmaceutical ingredient (API) stability and aerodynamic particle size distribution (aPSD). Those analyses have been complemented by in silico regional lung deposition modeling conducted after the clinical evaluation of the reformulated BGF pMDI. HFO-1234ze(E) supported favorable stability and aPSD characteristics for BGF pMDI reformulation, compared with HFA-152a, and modeling predicted regional deposition consistent with therapeutic intent. Given that each pMDI is a unique combination of APIs, device, propellant, and excipients, propellant substitution requires product-specific evidence and regulatory approval, and typically takes several years. Targeted analyses, such as those described here, helped to identify the most suitable candidate propellant for successful substitution in the BGF pMDI. HighlightsO_LIFormulation development efforts that led to evaluation of a budesonide-glycopyrrolate-formoterol fumarate pressurized metered-dose inhaler (BGF pMDI) reformulated with the next generation propellant HFO-1234ze(E) in a clinical trial program are described; the suitability of another propellant, HFA-152a, was also assessed C_LIO_LIOver 6 months under accelerated storage conditions (40{degrees}C/75% relative humidity [RH]), the HFA-152a formulation approached and, in one replicate, fell below the 90% of formulation label claim threshold of evaluation, whereas the original HFA-134a product and the HFO-1234ze(E) formulation remained above that threshold C_LIO_LIOver 6 months under accelerated storage conditions (40{degrees}C/75% RH) and 18 months under long-term stability storage conditions (25{degrees}C/60% RH), the fine particle mass and fine particle fraction for all active pharmaceutical ingredients (APIs) showed that the HFO-1234ze(E) formulation tracked more closely than the HFA-152a formulation to the original HFA-134a product C_LIO_LILater in silico modeling, conducted after clinical testing, predicted a trend for greater deposition of APIs in early airway generations with HFA-152a, whereas HFO-1234ze(E) was predicted to more closely match HFA-134a, indicating a greater likelihood of achieving equivalence to the original HFA-134a product with HFO-1234ze(E) than with HFA-152a C_LIO_LIBased on these analyses and other formulation development efforts, HFO-1234ze(E) was identified as the most suitable propellant for reformulation of the BGF pMDI; for HFA-152a, analyses raised concerns about storage stability, and differences in aerosol characteristics that can impact API deposition in the lungs and, in turn, efficacy C_LI

pharmacology and toxicology↗

bioRxiv2023

Targeted mutations in IFNα2 improve its antiviral activity against various viruses

During viral infections, type I interferons (IFN) are induced and play a key role in counteracting initial viral spread. Twelve different human IFN subtypes exist that bind the same receptor; however, they elicit unique host responses and display distinct potencies of antiviral activities. Our previous studies on HIV and HBV demonstrated that the clinically used IFN2 is not the most effective one among the IFN subtypes. By sequence modeling, we identified a region in helix B with mainly conserved residues at the outside facing IFNAR1, but variable residues at the inside facing the core of IFN, potentially representing a putative tunable anchor to tune pleiotropic IFN responses. Using site-directed mutagenesis various mutations were introduced into the IFN2b backbone targeting sites which are important for binding to IFNAR1 and IFNAR2, the putative tunable anchor, or outside these three regions. Selected mutations were based on sequence differences to high antiviral subtypes IFN6 and IFN14. Treatment assays against HBV and HIV identified several critical residues for the antiviral activity of IFN mainly in the IFNAR1 binding region. Combined mutations of the IFN2 IFNAR1/2 binding sites or the IFNAR1 binding region plus the putative tunable anchor by those of IFN14 further augmented activation of different downstream signaling cascades providing a molecular correlate for the enhanced antiviral activity. We describe here important functional residues within IFN subtype molecules, which enabled us to design novel and innovative drugs that may have the potential to be used in clinical trials against a variety of different viral infections. ImportanceThe potency of IFN to restrict viruses was already discovered in 1957. However, until today only IFN2 out of the 12 distinct human IFN subtypes has been therapeutically used against chronic viral infections. There is convincing evidence that other IFN subtypes are far more efficient than IFN2 against many viruses. In order to identify critical antiviral residues within the IFN subtype sequence, we designed hybrid molecules based on the IFN2 backbone with individual sequence motifs from the more potent subtypes IFN6 and IFN14. In different antiviral assays with HIV or HBV, residues binding to IFNAR1 as well as combinations of residues in the IFNAR1 binding region, the putative tunable anchor, and residues outside these regions were identified to be crucial for the antiviral activity of IFN. Thus, we designed artificial IFN molecules, based on the clinically approved IFN2 backbone, but with highly improved antiviral activity against several viruses.

immunology↗

bioRxiv2025

Clinical cure of chronic hepatitis B is dependent on activation and perpetuation of robust CD4+ T cell responses

Chronic infection with hepatitis B virus (HBV), a major global pathogen, often leads to immune-mediated progressive liver injury and liver cancer. While seroclearance of the surface antigen (HBsAg) defines clinical cure and reduces disease-associated risks, HBsAg clearance is rarely observed and remains therapeutically elusive. Here we overcome some of the challenges to studying immune mechanisms of HBsAg clearance in chronic hepatitis B (CHB) using our mouse model of age-dependent HBsAg clearance and persistence, and samples from our BeNEG-DO clinical trial that provided longitudinal PBMCs from patients who either cleared HBsAg or retained stable HBsAg levels after stopping nucleos(t)ide analog therapy. We show that young mice fail to clear HBsAg and have impaired ability to efficiently initiate and sustain HBV-specific CD4+ T cell responses. We also demonstrate a role for CD4+ T cells in hepatic leukocyte organization and cytotoxicity, and in HBV-specific CD8+ T cell cytotoxicity and HBsAg clearance. Upstream of the CD4+ T cell response, we reveal that hepatic dendritic cells, particularly cDC2s, direct effective CD4+ T cell activation and differentiation. Studies in CHB patients identified immune features of HBsAg clearance that overlap with the mouse model, including TH1 and cytotoxic CD4+ T cell activation and CD8+ T cell cytotoxic effector function. These findings identify an essential role for potent CD4+ T cell activation in the clinical cure of CHB and illuminate potential immunotherapeutic targets for enhancing CD4+ T cell responses to achieve greater HBsAg clearance rates. One Sentence SummaryUsing a mouse model of hepatitis B and longitudinal PBMCs from patients with chronic hepatitis B, we identify shared mechanisms of HBsAg seroclearance.

immunology↗

bioRxiv2020

Screening predictors of weight loss: an Integromics Approach

Obesity has reached epidemic proportions in the United States but little is known about the mechanisms of weight gain and weight loss. Integration of “omics” data is becoming a popular tool to increase understanding in such complex phenotypes. Biomarkers come in abundance from high-throughput experiments, but small sample size is still is a serious limitation in clinical trials. It makes assessment of more realistic assumptions for complex relationships such as nonlinearity, interaction and normality more difficult. In the present study, we developed a strategy to screen predictors of weight loss from a multi-omics, high-dimensional and longitudinal dataset from a small cohort of subjects. Our proposal explores the combinatorial space of candidate biomarkers from different data sources with the use of first-order Spearman partial correlation coefficients. Statistics derived from the sample correlations are used to rank and select biomarkers, and to evaluate the relative importance of each data source. We tackle the small sample size problem by combining nonparametric statistics and dimensionality reduction techniques useful for omics data. We applied the proposed strategy to assess the relative importance of biomarkers from 6 different data sources: RNA-seq, RT-qPCR, metabolomics, fecal microbiome, fecal bile acid, and clinical data used to predict the rate of weight loss in 10 obese subjects provided an identical low-calorie diet in a hospital metabolic facility. The strategy has reduced an initial set of more than 40K biomarkers to a set of 61 informative ones across 3 time points: pre-study, post-study and changes from pre- to post-study. Our study sheds light on the relative importance of different omics to predict rates of weight loss. We showed that baseline fecal bile acids, and changes in RT-qPCR biomarkers from pre- to post-study are the most predictive data sources for the rate of weight loss.Competing Interest StatementThe authors have declared no competing interest.AbbreviationsBPSBiomarker Predictive ScoreGSEAGene Set Enrichment AnalysisGSVAGene Set Variation AnalysisRT-qPCRReal Time quantitative Polymerase Chain ReactionSATSubcutaneous Adipose TissueVLCDVery Low Calorie DietWLWeight LossView Full Text

bioinformatics↗

bioRxiv2022

High-frequency longitudinal white matter diffusion- & myelin-based MRI database: reliability and variability

Assessing the consistency of quantitative MRI measurements is critical for inclusion in longitudinal studies and clinical trials. Intraclass coefficient correlation and coefficient of variation were used to evaluate the different consistency aspects of diffusion- and myelinbased MRI measures. Multi-shell diffusion and inhomogeneous magnetization transfer datasets were collected from twenty healthy adults at a high-frequency of five MRI sessions. The consistency was evaluated across whole bundles and the track-profile along the bundles. The impact of the fiber populations on the consistency was also evaluated using the number of fiber orientations map. For whole and profile bundles, moderate to high reliability of diffusion and myelin measures were observed. We report higher reliability of measures for multiple fiber populations than single. The overall portrait of the most consistent measurements and bundles drawn from a wide range of MRI techniques presented here will be particularly useful for identifying reliable biomarkers capable of detecting, monitoring and predicting white matter changes in clinical applications and has the potential to inform patient-specific treatment strategies. Key pointsO_LIReliability and variability are excellent to good for DWI measurements, and good to moderate for MT measures for whole bundles and along the bundles. C_LIO_LIThe number of fiber populations affects the reliability and variability of the MRI measurements. C_LIO_LIThe reliability and variability of MRI measurements are also bundle dependent. C_LI

neuroscience↗

bioRxiv2025

Artemether and Euphorbia Factor L9 suppress kynurenine production through distinct effects on Tryptophan metabolism.

L-Tryptophan (Trp) is an essential amino acid, catabolised through the kynurenine pathway, which is mediated by the enzymes indoleamine-2,3-dioxygenase 1 (IDO1), IDO2, or Trp-2,3-deoxygenase (TDO). Therapeutic targeting of Trp metabolism could be relevant to several pathologies. In cancer, IDO1 acts as an immune checkpoint suppressing effector T cell function. Yet, direct inhibition of IDO1 has had limited success in clinical trials. Therefore, alternative approaches to Trp metabolism therapeutic targeting are needed. We screened a library of 597 natural products (NPs) or NP derivatives for their effect on kynurenine production in triple negative breast cancer cells. This revealed 24 candidate inhibitors of kynurenine production. Amongst them, artemether, a member of the artemisinin family of anti-malarial drugs, suppressed kynurenine production, likely via an endoperoxide bridge-dependent mechanism. The Euphorbia factor L9 (EFL9) inhibited kynurenine production likely via a C7-benzoylation-dependent mechanism. Neither artemether nor EFL9 affected JAK/STAT signaling or IDO1 levels. Targeted metabolomics analyses demonstrated that artemether suppressed kynurenine production through heme sequestration, a mechanism that would affect all members of the IDO/TDO family of metalloenzymes. EFL9 affected purine and amino acid metabolism and the cellular redox balance. Comparisons to the effects of ouabain, a NP regulator of IDO1 levels, and Linrodostat, a clinically used small molecule IDO1 inhibitor, revealed distinct metabolic profiles, with ouabain and EFL9 showing the largest overlap. Importantly, the kynurenine-suppressing activity of artemether and EFL9 is not cancer cell-specific. Overall, our findings set the foundation for the use of derivatives of artemether or EFL9 as novel Trp metabolism-targeting therapeutics.

cancer biology↗

bioRxiv2023

Next-generation diarylquinolines improve sterilizing activity of regimens with pretomanid and the novel oxazolidinone TBI-223 in a mouse tuberculosis model

A regimen comprised of bedaquiline, pretomanid and linezolid (BPaL) is the first oral 6-month regimen approved by the US Food and Drug Administration and recommended by the World Health Organization for treatment of extensively drug-resistant tuberculosis. We used a well-established BALB/c mouse model of tuberculosis to evaluate the treatment-shortening potential of replacing bedaquiline with either of two new, more potent diarylquinolines in early clinical trials, TBAJ-587 and TBAJ-876. We also evaluated the effect of replacing linezolid with a new oxazolidinone, TBI-223, exhibiting a larger safety margin with respect to mitochondrial toxicity in preclinical studies. Replacing bedaquiline with TBAJ-587 at the same 25 mg/kg dose significantly reduced the proportion of mice relapsing after 2 months of treatment, while replacing linezolid with TBI-223 at the same 100 mg/kg dose did not significantly change the proportion of mice relapsing. Replacing linezolid or TBI-223 with sutezolid in combination with TBAJ-587 and pretomanid significantly reduced the proportion of mice relapsing. In combination with pretomanid and TBI-223, TBAJ-876 at 6.25 mg/kg was equipotent to TBAJ-587 at 25 mg/kg. We conclude that replacement of bedaquiline with these more efficacious and potentially safer diarylquinolines and replacement of linezolid with potentially safer and at least as efficacious oxazolidinones in the clinically successful BPaL regimen may lead to superior regimens capable of treating both drug-susceptible and drug-resistant TB more effectively and safely.

microbiology↗