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bioRxiv2017

ITHANET: Information and database community portal for haemoglobinopathies

Haemoglobinopathies are the commonest monogenic diseases, with millions of carriers and patients worldwide. Online resources for haemoglobinopathies are largely divided into specialised sites catering for patients, researchers and clinicians separately. However, the severity, ubiquity and surprising genetic complexity of the haemoglobinopathies call for an integrated website to serve as a free and comprehensive repository and tool for patients, scientists and health professionals alike. This paper presents the ITHANET community portal, an expanding resource for clinicians and researchers dealing with haemoglobinopathies. It integrates information on news, events, publications, clinical trials and haemoglobinopathy-related organisations and experts and, most importantly, databases of variations, epidemiology and diagnostic and clinical data. Specifically, ITHANET provides annotation for 2690 haemoglobinopathy-related variations, epidemiological data for more than 180 countries and information for more than 600 HPLC diagnostic reports. The ITHANET portal accepts and incorporates contributions to its content by local experts from any country in the world and is freely available for the public at http://www.ithanet.eu.

bioinformatics↗

bioRxiv2022

Characterization of Three Variants of SARS-CoV-2 in vivo Shows Host-Dependent Pathogenicity in Hamsters

Animal models are used in preclinical trials to test vaccines, antivirals, monoclonal antibodies, and immunomodulatory drug therapies against SARS-CoV-2. However, these drugs often do not produce equivalent results in human clinical trials. Here, we show how different animal models infected with some of the most clinically relevant SARS-CoV-2 variants, WA1/2020, B.1.617.2/Delta, B.1.1.529/Omicron and BA5.2/Omicron, have independent outcomes. We show that in mice, B.1.617.2 is more pathogenic, followed by WA1, while B.1.1.529 showed an absence of clinical signs. Only B.1.1.529 was able to infect C57BL/6J mice, which lack the human ACE2 receptor. B.1.1.529-infected ACE2 mice had different T cell profiles compared to infected K18-hACE2 mice, while viral shedding profiles and viral titers in lungs were similar between the ACE2 and the C57BL/6J mice. These data suggest B.1.1.529 virus adaptation to a new host and shows that asymptomatic carriers can accumulate and shed virus. Next, we show how B.1.617.2, WA1 and BA5.2/Omicron have similar viral replication kinetics, pathogenicity, and viral shedding profiles in hamsters, demonstrating that the increased pathogenicity of B.1.617.2 observed in mice is host-dependent. Overall, these findings suggest that small animal models are useful to parallel human clinical data, but the experimental design places an important role in interpreting the data. IMPORTANCEThere is a need to investigate SARS-CoV-2 variants phenotypes in different animal models due to the lack of reproducible outcomes when translating experiments to the human population. Our findings highlight the correlation of clinically relevant SARS-CoV-2 variants in animal models with human infections. Experimental design and understanding of correct animal models are essential to interpreting data to develop antivirals, vaccines, and other therapeutic compounds against COVID-19.

microbiology↗

bioRxiv2021

Finding the right fit: A comprehensive evaluation of short-read and long-read sequencing approaches to maximize the utility of clinical microbiome data

A longstanding challenge in human microbiome research is achieving the taxonomic and functional resolution needed to generate testable hypotheses about the gut microbiomes impact on health and disease. More recently, this challenge has extended to a need for in-depth understanding of the pharmacokinetics and pharmacodynamics of clinical microbiome-based interventions. Whole genome metagenomic sequencing provides high taxonomic resolution and information on metagenome functional capacity, but the required deep sequencing is costly. For this reason, short-read sequencing of the bacterial 16S ribosomal RNA (rRNA) gene is the standard for microbiota profiling, despite its poor taxonomic resolution. The recent falling costs and improved fidelity of long-read sequencing warrant an evaluation of this approach for clinical microbiome analysis. We used samples from participants enrolled in a Phase 1b clinical trial of a novel live biotherapeutic product to perform a comparative analysis of short-read and long-read amplicon and metagenomic sequencing approaches to assess their value for generating informative and actionable clinical microbiome data. Comparison of ubiquitous short-read 16S rRNA amplicon profiling to long-read profiling of the 16S-ITS-23S rRNA amplicon showed that only the latter provided strain-level community resolution and insight into novel taxa. Across all methods, overall community taxonomic profiles were comparable and relationships between samples were conserved, highlighting the accuracy of modern microbiome analysis pipelines. All methods identified an active ingredient strain in treated study participants, though detection confidence was higher for long-read methods. Read coverage from both metagenomic methods provided evidence of active ingredient strain replication in some treated participants. Compared to short-read metagenomics, approximately twice the proportion of long reads were assigned functional annotations (63% vs. 34%). Finally, similar bacterial metagenome-assembled genomes (MAGs) were recovered across short-read and long-read metagenomic methods, although MAGs recovered from long reads were more complete. Overall, despite higher costs, long-read microbiome characterization provides added scientific value for clinical microbiome research in the form of higher taxonomic and functional resolution and improved recovery of microbial genomes compared to traditional short-read methodologies. Data SummaryAll supporting data, code and protocols have been provided within the article or as supplementary data files. Two supplementary figures and four supplementary tables are available with the online version of this article. Sequencing data are accessible in the National Center for Biotechnology Information (NCBI) database under BioProject accession number PRJNA754443. The R code and additional data files used for analysis and figure generation are accessible in a GitHub repository (https://github.com/jeanette-gehrig/Gehrig_et_al_sequencing_comparison). Impact StatementAccurate sequencing and analysis are essential for informative microbiome profiling, which is critical for the development of novel microbiome-targeted therapeutics. Recent improvements in long-read sequencing technology provide a promising, but more costly, alternative to ubiquitous short-read sequencing. To our knowledge, a direct comparison of the informational value of short-read and HiFi long-read sequencing approaches has not been reported for clinical microbiome samples. Using samples from participants in a Phase 1b trial of a live biotherapeutic product, we compare microbiome profiles generated from short-read and long-read sequencing for both amplicon-based 16S ribosomal RNA profiling and metagenomic sequencing. Though overall taxonomic profiles were similar across methods, only long-read amplicon sequencing provided strain-level resolution, and long-read metagenomic sequencing resulted in a significantly greater proportion of functionally annotated genes. Detection of a live biotherapeutic active ingredient strain in treated participants was achieved with all methods, and both metagenomic methods provided evidence of active replication of this strain in some participants. Similar taxonomies were recovered through metagenomic assemblies of short and long reads, although assemblies were more complete with long reads. Overall, we show the utility of long-read microbiome sequencing in direct comparison to commonly used short-read methods for clinically relevant microbiome profiling.

genomics↗

bioRxiv2025

Multi-center Translational Trial of Remote Ischemic Conditioning in Acute Ischemic Stroke (TRICS BASIC)

BackgroundBasic science studies have reported remote ischemic conditioning (RIC) as neuroprotective in acute ischemic stroke, while clinical evidence remains conflicting. The TRICS BASIC study investigated the efficacy and safety of RIC in experimental ischemic stroke using a rigorous clinical trial methodology. MethodsMulti-center, multi-species, parallel group, randomized, controlled, preclinical trial of transient femoral artery clipping to induce RIC in female and male rats and mice subjected to transient endovascular occlusion of the middle cerebral artery. Animals were randomized to receive RIC, or sham surgery, after reperfusion. The primary endpoint was good functional outcome at 48 hours, assessed using a composite functional neuroscore. Secondary endpoints was infarct volume at 48 hours and safety, assessed using a standardized health report at 24 and 48 hours. Pre-enrollment harmonization, centralized monitoring, allocation concealment, blinded outcome assessment and intention-to-treat analysis were applied. ResultsThe trial enrolled 164 rodents (82 mice and 82 rats) of both sexes (53% females), across seven laboratories. A greater proportion of RIC-treated rodents achieved a favorable functional outcome compared to controls, at 48 hours post-ischemia (55% versus 36%; OR 2.2, 95% CI [1.23-4.4], p=0.009). RIC was associated with a small reduction in infarct volume (standardized mean difference -0.38, 95% CI [-0.70, -0.05], p=0.024). Health monitoring indicated no major safety concerns, and post-operative analgesia requirements were lower in RIC-treated mice. ConclusionsSurgically-induced RIC provided a modest but evident neuroprotective effect in experimental ischemic stroke, underscoring the potential of this strategy as an adjunctive treatment in stroke care. The findings of the TRICS BASIC study highlighted the importance of multicenter preclinical trials in addressing variability and enhancing translational validity. Registrationregistered at preclinicaltrials.eu, identifier PCTE0000177.

neuroscience↗

bioRxiv2020

Spike mutation D614G alters SARS-CoV-2 fitness and neutralization susceptibility

A spike protein mutation D614G became dominant in SARS-CoV-2 during the COVID-19 pandemic. However, the mutational impact on viral spread and vaccine efficacy remains to be defined. Here we engineer the D614G mutation in the SARS-CoV-2 USA-WA1/2020 strain and characterize its effect on viral replication, pathogenesis, and antibody neutralization. The D614G mutation significantly enhances SARS-CoV-2 replication on human lung epithelial cells and primary human airway tissues, through an improved infectivity of virions with the spike receptor-binding domain in an "up" conformation for binding to ACE2 receptor. Hamsters infected with D614 or G614 variants developed similar levels of weight loss. However, the G614 virus produced higher infectious titers in the nasal washes and trachea, but not lungs, than the D614 virus. The hamster results confirm clinical evidence that the D614G mutation enhances viral loads in the upper respiratory tract of COVID-19 patients and may increases transmission. For antibody neutralization, sera from D614 virus-infected hamsters consistently exhibit higher neutralization titers against G614 virus than those against D614 virus, indicating that (i) the mutation may not reduce the ability of vaccines in clinical trials to protect against COVID-19 and (ii) therapeutic antibodies should be tested against the circulating G614 virus before clinical development. ImportanceUnderstanding the evolution of SARS-CoV-2 during the COVID-19 pandemic is essential for disease control and prevention. A spike protein mutation D614G emerged and became dominant soon after the pandemic started. By engineering the D614G mutation into an authentic wild-type SARS-CoV-2 strain, we demonstrate the importance of this mutation to (i) enhanced viral replication on human lung epithelial cells and primary human airway tissues, (ii) improved viral fitness in the upper airway of infected hamsters, and (iii) increased susceptibility to neutralization. Together with clinical findings, our work underscores the importance of this mutation in viral spread, vaccine efficacy, and antibody therapy.

microbiology↗

bioRxiv2021

N4-hydroxycytidine and inhibitors of dihydroorotate dehydrogenase synergistically suppress SARS-CoV-2 replication

Effective therapeutics to inhibit the replication of SARS-CoV-2 in infected individuals are still under development. The nucleoside analogue N4-hydroxycytidine (NHC), also known as EIDD-1931, interferes with SARS-CoV-2 replication in cell culture. It is the active metabolite of the prodrug Molnupiravir (MK-4482), which is currently being evaluated for the treatment of COVID-19 in advanced clinical studies. Meanwhile, inhibitors of dihydroorotate dehydrogenase (DHODH), by reducing the cellular synthesis of pyrimidines, counteract virus replication and are also being clinically evaluated for COVID-19 therapy. Here we show that the combination of NHC and DHODH inhibitors such as teriflunomide, IMU-838/vidofludimus, and BAY2402234, strongly synergizes to inhibit SARS-CoV-2 replication. While single drug treatment only mildly impaired virus replication, combination treatments reduced virus yields by at least two orders of magnitude. We determined this by RT-PCR, TCID50, immunoblot and immunofluorescence assays in Vero E6 and Calu-3 cells infected with wildtype and the Alpha and Beta variants of SARS-CoV-2. We propose that the lack of available pyrimidine nucleotides upon DHODH inhibition increases the incorporation of NHC in nascent viral RNA, thus precluding the correct synthesis of the viral genome in subsequent rounds of replication, thereby inhibiting the production of replication competent virus particles. This concept was further supported by the rescue of replicating virus after addition of pyrimidine nucleosides to the media. Based on our results, we suggest combining these drug candidates, which are currently both tested in clinical studies, to counteract the replication of SARS-CoV-2, the progression of COVID-19, and the transmission of the disease within the population. SIGNIFICANCEO_LIThe strong synergy displayed by DHODH inhibitors and the active compound of Molnupiravir might enable lower concentrations of each drug to antagonize virus replication, with less toxicity. C_LIO_LIBoth Molnupiravir and DHODH inhibitors are currently being tested in advanced clinical trials or are FDA-approved for different purposes, raising the perspective of rapidly testing their combinatory efficacy in clinical studies. C_LIO_LIMolnupiravir is currently a promising candidate for treating early stages of COVID-19, under phase II/III clinical evaluation. However, like Remdesivir, it appears only moderately useful in treating severe COVID-19. Since the combination inhibits virus replication far more strongly, and since DHODH inhibitors may also suppress excessive immune responses, the combined clinical application bears the potential of alleviating the disease burden even at later stages. C_LI

molecular biology↗

bioRxiv2021

Epithelial Immunomodulation by Aerosolized Toll-like Receptor Agonists Attenuates Allergic Responsiveness in Mice

Allergic asthma is a chronic inflammatory respiratory disease associated with eosinophilic infiltration, increased mucus production, airway hyperresponsiveness (AHR), and airway remodeling. Epidemiologic data has revealed that the prevalence of allergic sensitization and associated diseases has increased in the twentieth century. This has been hypothesized to be partly due to reduced contact with microbial organisms (the hygiene hypothesis) in industrialized society. Airway epithelial cells, once considered a static physical barrier between the body and the external world, are now widely recognized as immunologically active cells that can initiate, maintain, and restrain inflammatory responses, such as those that mediate allergic disease. Airway epithelial cells can sense allergens via myriad expression of Toll-like receptors (TLRs) and other pattern-recognition receptors (PRRs). We sought to determine whether the innate immune response stimulated by a combination of Pam2CSK4 ("Pam2", TLR2/6 ligand) and a class C oligodeoxynucleotide ODN362 ("ODN", TLR9 ligand) when delivered together by aerosol ("Pam2ODN"), can modulate the allergic immune response to allergens. Treatment with Pam2ODN 7 days before sensitization to House Dust Mite (HDM) extract resulted in a strong reduction in eosinophilic and lymphocytic inflammation. This Pam2ODN immunomodulatory effect was also seen using Ovalbumin (OVA) and A. oryzae (Ao) mouse models. The immunomodulatory effect was observed as much as 30 days before sensitization to HDM, but ineffective just 2 days after sensitization, suggesting that Pam2ODN immunomodulation lowers the allergic responsiveness of airway epithelial cells. Furthermore, Pam2 and ODN cooperated synergistically suggesting that this treatment is superior to any single agonist in the setting of allergen immunotherapy. One Sentence SummaryA synergistic combination of Toll-like Receptor agonists, delivered directly into the lung mucosa, can attenuate allergic responsiveness of airway epithelial cells and prevent host sensitization to aeroallergens. What is already knownO_LIAllergic sensitization has increased in the 20th century due to reduced contact with microbial organisms in industrialized society (ie. hygiene hypothesis) C_LIO_LIWe have previously identified a pharmacological means to stimulate innate immunity of lung epithelial cells. C_LI What this study addsO_LIActivation of innate immunity in lung epithelial cells attenuates the allergic responsiveness of mice. C_LIO_LISynergistic cooperation of pattern recognition receptors induces stronger immunomodulatory responses C_LI What is the clinical significanceO_LIAerosolized Toll-like Receptor agonists have been demonstrated as safe in human clinical trials C_LIO_LIThis study provides proof-of-principle that aerosolized toll-like receptor agonists could have clinical efficacy in the setting of the allergen immunotherapy C_LI

immunology↗

bioRxiv2022

Integrated Autolysis, DNA Hydrolysis and Precipitation Enables an Improved Bioprocess for Q-Griffithsin, a Broad-Spectrum Antiviral and Clinical-Stage anti-COVID-19 Candidate

Across the biomanufacturing industry, innovations are needed to improve efficiency and flexibility, especially in the face of challenges such as the COVID-19 pandemic. Here we report an improved bioprocess for Q-Griffithsin, a broad-spectrum antiviral currently in clinical trials for COVID-19. Q-Griffithsin is produced at high titer in E. coli and purified to anticipated clinical grade without conventional chromatography or the need for any fixed downstream equipment. The process is thus both low-cost and highly flexible, facilitating low sales prices and agile modifications of production capacity, two key features for pandemic response. The simplicity of this process is enabled by a novel unit operation that integrates cellular autolysis, autohydrolysis of nucleic acids, and contaminant precipitation, giving essentially complete removal of host cell DNA as well as reducing host cell proteins and endotoxin by 3.6 and 2.4 log10 units, respectively. This unit operation can be performed rapidly and in the fermentation vessel, such that Q-GRFT is obtained with 100% yield and >99.9% purity immediately after fermentation and requires only a flow-through membrane chromatography step for further contaminant removal. Using this operation or variations of it may enable improved bioprocesses for a range of other high-value proteins in E. coli. HighlightsO_LIIntegrating autolysis, DNA hydrolysis and precipitation enables process simplification C_LIO_LIAutolysis reduces endotoxin release and burden to purification C_LIO_LIQ-Griffithsin recovered from fermentation vessel at >99.9% purity and 100% yield C_LIO_LIQ-Griffithsin purified to anticipated clinical grade without conventional chromatography C_LIO_LIThe resulting bioprocess is 100% disposables-compatible, scalable, and low-cost C_LI

synthetic biology↗

bioRxiv2022

Angelman syndrome patient neuron screen identifies a potent and selective clinical ASO targeting UBE3A-ATS with long lasting effect in cynomolgus monkey

Angelman syndrome (AS) is a severe neurodevelopmental disorder caused by the loss of neuronal E3 ligase UBE3A with no available treatment. Restoring UBE3A levels via downregulation of the paternally cis-acting long non-coding antisense transcript (UBE3A-ATS) is a potential disease modifying. Developing molecules targeting human UBE3A-ATS is challenging because it is expressed only in neurons and lacks animal species sequence conservation. To overcome this, we performed a library screen of locked-nucleic acid (LNA)-modified antisense oligonucleotides (ASOs) on AS patient-derived neurons, identifying initial sequences. Further optimization led to the identification of the ASO, RO7248824, which selectively and potently reduces UBE3A-ATS, while concomitantly upregulating the UBE3A mRNA and protein. These properties held true in both human AS patient- and neurotypical-, as well as cynomolgus monkey-derived neurons. In vivo use of tool molecules in wild-type (WT) and AS Ube3am-/p+ mice, revealed a steep relationship between UBE3A-ATS knock-down and UBE3A mRNA/protein upregulation, whereby an almost 90% downregulation was needed to achieve a 50% upregulation, respectively. This relationship was confirmed in cynomolgus monkeys. Whereby, repeated lumbar intrathecal administrations of RO7248824 was well tolerated without adverse in-life effects or tissue pathology and produced a robust, long lasting (up to 3 months) paternal reactivation of UBE3A mRNA/protein across key monkey brain regions. Our results demonstrate that AS human pluripotent stem cell neurons serve as an excellent translational tool and furthermore LNA-modified ASOs exhibit excellent drug-like properties. Sustained efficacy translated to infrequent, intrathecal dosing and serves as the basis for the ongoing clinical development of RO7248824 for AS. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=131 SRC="FIGDIR/small/495066v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1c2a97eorg.highwire.dtl.DTLVardef@1059954org.highwire.dtl.DTLVardef@95835aorg.highwire.dtl.DTLVardef@1e2adea_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstract.C_FLOATNO From AS patient blood to a neuronal screen, identifies clinical ASO with excellent in vivo properties. (1) Patients were recruited. (2) Whereby blood was reprogrammed into hIPSC and subsequently differentiated into neurons. (3) ASOs were designed and screened on human neurons to downregulate the UBE3A-ATS likely via directed RNase H Cleavage of Nascent Transcripts. (4a) RO7248824 was identified that potently and selective reduces UBE3A-ATS, concomitantly with upregulating the UBE3A sense transcript and protein which was used for in vitro pk/pd. (4b) In parallel tool murine ASO were used demonstrate in vivo POC.(5) Pivotal nonhuman primate studies to monitor safety and predict the human dose. (6) RO7248824 is in AS clinical trial. C_FIG One Sentence SummaryFrom angelman syndrome human neuron screen to cynomolgus monkey proof of concept identifies the clinical molecule RO7248824

neuroscience↗

bioRxiv2023

The impact of extracellular matrix on the precision medicine utility of pancreatic cancer patient-derived organoids

The use of patient-derived organoids (PDOs) to characterize therapeutic sensitivity and resistance (pharmacotyping) is a promising precision medicine approach. The potential of this approach to inform clinical decisions is now being tested in several large multi-institutional clinical trials. PDOs are cultivated in extracellular matrix from basement membrane extracts (BMEs) that are most commonly acquired commercially. Each clinical site utilizes distinct BME lots and may be restricted due to the availability of commercial BME sources. However, the impact of different sources and lots of BMEs on organoid drug response is unknown. Here, we tested the impact of BME source and lot on proliferation, chemotherapy and targeted therapy drug response, and gene expression in mouse and human pancreatic ductal adenocarcinoma (PDA) organoids. Both human and mouse organoids displayed increased proliferation in Matrigel (Corning) compared to Cultrex (RnD) and UltiMatrix (RnD). However, we observed no substantial impact on drug response when oragnoids were cultured in Matrigel, Cultrex, or UltiMatrix. We also did not observe major shifts in gene expression across the different BME sources, and PDOs maintained their Classical or Basal-like designation. Overall, we find that BME source (Matrigel, Cultrex, UltiMatrix) does not shift PDO dose-response curves and drug testing results, indicating that PDO pharmacotyping is a robust approach for precision medicine.

cancer biology↗

bioRxiv2024

Armored Bicistronic CAR T Cells with Dominant-negative TGF-β Receptor II to Overcome Resistance in Glioblastoma.

Chimeric antigen receptor (CAR) T cells have shown significant efficacy in hematological diseases. However, CAR T therapy has demonstrated limited efficacy in solid tumors, including glioblastoma (GBM). One of the most important reasons is the immunosuppressive tumor microenvironment (TME), which promotes tumor growth and suppresses immune cells to eliminate tumor cells. The human transforming growth factor-beta (TGF-{beta}) plays a crucial role in forming the suppressive GBM TME and driving the suppression of the anti-GBM response. In order to mitigate TGF-{beta} mediated suppressive activity, we combined a dominant-negative TGF-{beta} receptor II (dnTGF{beta}RII) with our previous bicistronic CART-EGFR-IL13R2 construct, currently being evaluated in a clinical trial, to generate CART-EGFR-IL13R2-dnTGF{beta}RII, a tri-modular construct we are developing for clinical application. We hypothesized that this approach would more effectively subvert resistance mechanisms observed with GBM. Our data suggests that CART-EGFR-IL13R2-dnTGF{beta}RII significantly augmented T cell proliferation and enhanced functional responses, particularly in a TGF{beta}-rich tumor environment. Additionally, in vivo studies validated the safety and efficacy of the dnTGF{beta}RII cooperating with CARs in targeting and eradicating GBM in a NSG mouse model.

cancer biology↗

bioRxiv2024

Targeting of PTP4A3 overexpression sensitises HGSOC cells towards chemotherapeutic drugs.

Of all the gynecologic malignancies, Ovarian cancer (OC) has the highest mortality rate, partly attributable to its propensity for chemotherapy resistance. The most common sub-type of OC is serous, of which High-Grade Serous Ovarian Cancer (HGSOC) is the most lethal sub-type. Elevated expression of Protein Tyrosine Phosphatase 4 A3 (PTP4A3) is implicated in tumour cell invasion and metastasis, by upregulating the PI3K/Akt/mTORC1 axis. Previously we reported PTP4A3 increased the survival of non-serous OC cells in vitro by activating the autophagy pathway. The present study focused on understanding the impact of PTP4A3 on cell growth, proliferation, and autophagy in HGSOC cells. In particular, we sought to understand whether targeting PTP4A3 in cancer cells that overexpress this phosphatase would sensitise HGSOC cells to existing chemotherapeutic drugs. We report that shRNA-mediated gene silencing of PTP4A3 resulted in the upregulation of compensatory mechanisms that may render PTP4A3 targeting redundant as a monotherapy. However, pan-PTP4A inhibition with JMS-053 overcame this. Finally, silencing of PTP4A3 expression sensitized HGSOC cells to clinically relevant chemotherapeutic drugs. Since mAb therapies targeting PTP4A3 are already in clinical trials, therapeutic targeting of PTP4A3 may have significant value in improving outcomes for those patients with HGSOC, in the clinical setting.

cancer biology↗

bioRxiv2025

Multi-omics dissection of Parkinson's patient subgroups associated with motor and cognitive severity

Heterogeneity in the severity of Parkinsons disease (PD) inhibits the effective interpretation of clinical trial outcomes. Multi-omics analysis may help explain the pathological mechanisms underlying disease progression and reveal biomarkers of clinical severity. We performed Multi-Omics Factor Analysis (MOFA) on whole blood RNA, miRNA and Cerebrospinal fluid (CSF) and blood plasma proteomics from the Parkinsons Progression Marker Initiative (PPMI), to identify molecular factors correlated with motor (MDS-UPDRS3) and cognitive (Semantic Fluency Test, SFT) function. Three molecular factors significantly correlated with the MDS-UPDRS3 score and two with SFT, which remained significant after adjusting for age, sex, and medication dose. We used the identified factors to stratify patients into subgroups with distinct motor and cognitive severity. The severe motor clusters showed deregulation of cytotoxic natural killer cell mechanisms in peripheral blood, and changes to proteins associated with the endoplasmic reticulum in CSF. The severe cognitive clusters showed changes in complement and synaptic dysfunction. Our analysis capitalizes on multi-omics data integration to enrich our understanding of the mechanisms driving motor and cognitive decline in PD, to support precision medicine.

bioinformatics↗

bioRxiv2026

Synergistic anti-tumor activity of EGFR inhibition and C/EBPβ antagonism in GBM.

Glioblastoma (GBM) is the most prevalent primary brain cancer, with poor prognosis and limited therapeutic options available. The genetic and cellular heterogeneity characteristic of GBM contributes to poor response rates. Activating mutations of the epidermal growth factor receptor (EGFR) gene are among the most frequent alterations in GBM, occurring in roughly half of cases. Despite the prevalence of EGFR mutations, EGFR inhibition has shown limited success in GBM. The transcription factor C/EBP{beta} is a master regulator of the mesenchymal transformation in GBM, an aggressive state characterized by increased invasiveness and resistance to chemotherapy. Lucicebtide is a C/EBP{beta} antagonist peptide with demonstrated single agent activity in patients with recurrent GBM that is currently being evaluated in a clinical trial in combination with radiation and temozolomide in patients with newly-diagnosed GBM (NCT04478279), with emerging data supporting clinical activity in that setting. Here we show that in the TCGA-GBM dataset, patients with EGFR mutations display significant enrichment of a high C/EBP{beta} activity signature. Functionally, genetic inactivation of EGFR by CRISPR results in synthetic lethality in the presence of lucicebtide in GBM cell lines, and synergistic in vitro cytotoxicity and suppression of C/EBP{beta} target gene expression was observed in combination experiments with lucicebtide and EGFR inhibitors. Finally, enhanced anti-tumor activity was demonstrated in vivo in the combination setting, as combined subpharmacologic dose levels of lucicebtide and the EGFR inhibitor osimertinib potently suppressed GBM xenograft growth. These data identify EGFR and C/EBP{beta} dependencies in GBM and support lucicebtide combination with EGFR inhibitors as a potential therapeutic option for a sizable fraction of GBM patients.

cancer biology↗

bioRxiv2026

Causally-inspired meta-representation learning framework for predicting patient-specific clinical responses to drug combinations

Large-scale prediction and assessment of clinical patient responses (i.e., RECIST class) to drug combinations remains challenging due to scarce patient-derived data. The existing prediction methods mainly rely on cancer cell line models. However, substantial biological heterogeneity between cancer cell lines and cancer patients within same tissues, as well as the heterogeneity between one tissue and another, often limit the generalizability of these methods in clinical patients. To overcome these limitations, here we present CaMeRe, a Causally-inspired Meta-representation learning framework designed to predict patient-specific clinical Response to drug combinations. In situations where stable causal factors and domain-specific response-modulating factors are unobservable, explicit discrete domain labels are unavailable, and data is scarce, CaMeRe designed a domain-invariant causal representation learning (DICRL) model guided by the invariant information bottleneck theory and causal intervention invariance principle, and also built a meta-learning framework with bi-level domain generalization to optimize DICRL model for achieving multi-domain generalization within and across tissues. By integrating the causal representation learning and meta learning framework, CaMeRe not only exhibited robust multi-domain generalization performance across multiple clinical drug combination response datasets and PDXs drug combination response datasets and generalization scenarios, but also had better interpretability. We applied CaMeRe to predict drug-combination response scores for 3,423 patients across 542,080 drug combinations. The predicted scores were significantly associated with biomarkers of known drug combinations and enabled the prioritization of candidate drug combinations across 11 cancer types, with stronger support from literature and clinical trial evidences than random baselines. We believe that CaMeRe can be a useful tool for predicting large-scale clinical individual drug combination responses and it has broad clinical applications.

bioinformatics↗

bioRxiv2020

Understanding the Human Brain using Brain Organoids and a Structure-Function Theory

A basic neurobiology-clinical trial paradigm motivates our use of constrained mathematical models and analysis of personalized human-derived brain organoids toward predicting clinical outcomes and safely developing new therapeutics. Physical constraints imposed on the brain can guide the analyses an interpretation of experimental data and the construction of mathematical models that attempt to make sense of how the brain works and how cognitive functions emerge. Development of these mathematical models for human-derived brain organoids offer an opportunity for testing new hypotheses about the human brain. When it comes to testing ideas about the brain that require a careful balance between experimental accessibility, manipulation, and complexity, in order to connect neurobiological details with higher level cognitive properties and clinical considerations, we argue that fundamental structure-function constraints applied to models of brain organoids offer a path forward. Moreover, we show these constraints appear in canonical and novel math models of neural activity and learning, and we make the case that constraint-based modeling and use of representations can bridge to machine learning for powerful mutual benefit.

neuroscience↗

bioRxiv2021

Pre-clinical evaluation of antiviral activity of nitazoxanide against Sars-CoV-2

To address the emergence of SARS-CoV-2, multiple clinical trials in humans were rapidly started, including those involving an oral treatment by nitazoxanide, despite no or limited pre-clinical evidence of antiviral efficacy. In this work, we present a complete pre-clinical evaluation of the antiviral activity of nitazoxanide against SARS-CoV-2. First, we confirmed the in vitro efficacy of nitazoxanide and tizoxanide (its active metabolite) against SARS-CoV-2. Then, we demonstrated nitazoxanide activity in a reconstructed bronchial human airway epithelium model. In a SARS-CoV-2 virus challenge model in hamsters, oral and intranasal treatment with nitazoxanide failed to impair viral replication in commonly affected organs. We hypothesized that this could be due to insufficient diffusion of the drug into organs of interest. Indeed, our pharmacokinetic study confirmed that concentrations of tizoxanide in organs of interest were always below the in vitro EC50. These preclinical results suggest, if directly applicable to humans, that the standard formulation and dosage of nitazoxanide is not effective in providing antiviral therapy for Covid-19.

pathology↗

bioRxiv2024

Individual Patient Data Analysis of Liver Lesion Dynamics: A Pan Cancer Analysis

There are now several databases available that enable the exploration of individual patient data from past Oncology clinical trials. These databases provide researchers with the opportunity to investigate the dynamics of individual lesions across various tumour sites within a patient and compare them across different patients. In this report, we specifically focus on liver metastases and examine the dynamics of individual lesions across different treatment and tumour types. Our findings reveal that when a lesion progresses early on, the rate of growth is significantly higher for liver lesions compared to other types of lesions, regardless of the treatment modality (chemotherapy, targeted therapy, or combination of both). These results indicate the need for further basic research on tumours and their microenvironment specifically within liver metastases. This analysis demonstrates how analysing open trial data can uncover new research prospects at the fundamental science level, thereby bridging the gap between laboratory research and clinical applications.

cancer biology↗