Biology subjects

Ahmed, Z.

Publications and source records attributed to Ahmed, Z..

At least 19 recordsLinked to original sources

bioRxiv2026

Autophagy activator AA-20 engages CDK5 to promote lipophagy and improve neurodegeneration-associated phenotypes

Lipophagy, the selective degradation of lipid droplets (LDs) by autophagy, has the potential to ameliorate neurodegenerative diseases such as Parkinson's (PD) and Alzheimer's (AD), wherein LD accumulation has been linked to the exacerbation of the proteinopathy component of neurodegeneration. Pharmacological lipophagy inducers remain scarce. We previously identified AA-20 as a novel autophagy activator that acts independently of mTORC1 inhibition, thereby providing a means of stimulating autophagy while avoiding the immunosuppressive side effects associated with direct mTORC1 inhibition. Prior work also showed that AA-20 treatment reduces PolyQ aggregate levels in several C. elegans tissues. Here, we demonstrate that AA-20 enhances LD recruitment to autophagosomes and promotes LD degradation via lysosomal acid lipase activation in murine hippocampal neuronal cells, consistent with lipophagy activation. In human Swedish Amyloid Precursor Protein mutated cerebral organoids, two weeks of AA-20 treatment normalized aberrant lipidomic profiles by selectively reducing various disease-associated lipids, while also correcting the AD-associated electrical hyperexcitability phenotype. Moreover, we identified cyclin-dependent kinase 5 (CDK5), a neuronal kinase linked to AD hyperexcitability and PD pathology, as a target of AA-20. AA-20-induced autophagy and lipid clearance in HT22 cells require CDK5. In a neuronal seeding model of -synuclein pathology, AA-20 reduced pS129--synuclein levels. Collectively, these findings indicate AA-20 can promote lipophagic clearance of LDs and mitigate multiple cellular phenotypes associated with lipidopathy and proteinopathy in neurodegenerative disease models.

molecular biology↗

bioRxiv2026

Single-molecule nanophotonic resolution of binding dynamics from apo to fully liganded for a cyclic nucleotide-gated ion channel in cell-derived vesicles

Many biological macromolecules are activated upon ligand binding at multiple specific binding domains. However, how these domains interact and the transient intermediate conformations that connect binding events to protein activity are typically unknown. Ensemble-averaged measures over stochastic binding events are challenged to resolve the underlying asynchronous dynamics. Single-molecule resolution of these dynamics offers an attractive approach to investigate the ligand-activation process. Optical methods using fluorescently labeled ligands enable observation of individual binding events that report on the energetics of early ligand-bound conformational changes. However, diffraction-limited microscopy limits these methods to low ligand concentrations, often below what is required for physiologically relevant activation. Here, we overcome this limitation using nanophotonic zero-mode waveguides to observe the sequential binding of a fluorescent cyclic nucleotide to each of four subunits in TAX-4 cyclic nucleotide-gated ion channels in cell-derived vesicles. Our observations suggest that binding at one domain positively promotes binding at other domains, and that binding induces an isomerization of the binding domain in individual subunits which we attribute to a sequence of pre-activated intermediate states. This approach provides a broadly applicable tool to dissect the energetic landscape of ligand-binding at macromolecules in native cell membranes.

biophysics↗

bioRxiv2026

Minoxidil hydrochloride impedes NLRP3 inflammasome activation via upregulation of AMPK-mediated autophagy

NLRP3 inflammasome is a cytosolic multi-protein complex that plays a crucial role in the immune system, responding to various exogenous and endogenous stimuli by triggering protective inflammatory responses. However, aberrant NLRP3 inflammasome activation is implicated in numerous inflammatory diseases. Therefore, the NLRP3 inflammasome is an important pharmacological target for the treatment of multiple diseases. In this context, we screened various US-FDA-approved drugs for NLRP3 inflammasome inhibition. We found that among various drugs, minoxidil hydrochloride (MXL) effectively inhibits NLRP3 inflammasome, evidenced by reduced secretion of IL-1{beta} and IL-18 in J774A.1 cells treated with MXL. The IC50 values of MXL for inhibition of IL-1{beta} and IL-18 were calculated to be 1.2 and 1.06 {micro}M, respectively. MXL was found to prevent ASC oligomerization, thereby inhibiting the NLRP3 inflammasome and leading to CASP1 cleavage. Further investigation revealed that MXL also utilizes AMPK-mediated autophagy to modulate NLRP3 inflammasome activity. Using siAMPK and bafilomycin A1, an end-stage autophagy inhibitor, we elucidated crosstalk between the NLRP3 inflammasome and autophagic pathways, which was modulated by MXL. Furthermore, we demonstrated the efficacy of MXL in two different mouse models of inflammation, involving the NLRP3 inflammasome. MXL at doses of 10 and 20 mg/kg effectively inhibited the activation of NLRP3 inflammasome by monosodium urate in the air pouch model and by ATP in the peritoneal inflammation model, as evidenced by reduced secretion of 1{beta} and IL-18 in the lavage. Our study identifies MXL as a potent NLRP3 inflammasome inhibitor, warranting further investigation as a potential therapeutic agent for inflammatory diseases.

immunology↗

bioRxiv2026

The multifaceted role of acetamide derivative of Chalcone: Anti-inflammatory Action and Impact on Osteoclastogenesis, insights on NF-kB and MAPK pathways.

Inflammation serves as a vital physiological process essential for preserving health and countering illness. Yet, persistent inflammation drives osteoclastogenesis and ongoing bone erosion in rheumatoid arthritis (RA), mainly via macrophage activation and overproduction of pro-inflammatory cytokines like TNF-, IL-1{beta}, and IL-6. Limitations of prolonged conventional treatments underscore the need for safer small-molecule inhibitors that address both inflammation and osteoclast formation. Chalcones, natural plant defense compounds, exhibit diverse pharmacological properties including anti-inflammatory, anticancer, antibacterial, antifungal, and antiparasitic actions, owing to their characteristic reactive , {beta}- unsaturated carbonyl moiety. This study assessed chalcone derivative 7a for its anti-inflammatory effects in vitro and in vivo, alongside its capacity to modulate osteoclast differentiation, offering the inaugural demonstration of its dual anti-inflammatory and anti-osteoclastogenic properties. In LPS-stimulated macrophages, 7a substantially curtailed nitric oxide production, curbed pro-inflammatory cytokines (TNF-, IL-1{beta}, IL-6), and concentration-dependently diminished iNOS and COX-2 expression while inhibiting reactive oxygen species levels. In vivo, oral 7a dosing potently alleviated carrageenan-evoked paw swelling and restored serum lactate dehydrogenase and C-reactive protein to normalcy. In LPS-exposed mice, it further lowered systemic cytokines and rectified dysregulated biomarkers such as LDH, ALP, ALT, AST, creatinine, and urea. Moreover, in RANKL-stimulated osteoclast cultures, 7a markedly suppressed osteoclastogenesis by downregulating pivotal markers like tartrate-resistant acid phosphatase (TRAP) and matrix metalloproteinase-9 (MMP-9). Derivative 7a also enhances antioxidant defense--superoxide dismutase and catalase--via blockade of NF-{kappa}B and MAPK pathways. Overall, chalcone derivative 7a displays robust anti-inflammatory and anti-osteoclastogenic activity, positioning it as a compelling candidate for RA therapy.

immunology↗

bioRxiv2026

Hepatic Ketogenesis Attenuates Cardiac Hypertrophy via Metabolic Reprogramming

BackgroundHeart failure with preserved ejection fraction (HfpEF) is increasingly recognized as a multisystem disorder linked to the cardiovascular-kidney-metabolic (CKM) syndrome. While the falling heart undergoes metabolic reprogramming, the interorgan crosstalk regulating myocardial substrate preference in HFpEF remains elusive. We aimed to clarify the role of systemic and local ketogenesis in the pathogenesis of cardiac hypertrophy and HFpEF. MethodsA mouse model of HFpEF was employed using a high-fat diet combined with NG-Nitro-L-arginine methyl ester hydrochloride (L-NAME). Cardiac hypertrophy and systemic metabolic profiling including ketogenesis were evaluated. To dissect the role of site-specific ketogenesis, we generated inducible cardiomyocyte-specific (Hmgcs2{Delta}iCM) and hepatocyte-specific (Hmgcs2{Delta}Hep) knockout mice of HMG-CoA synthase 2 (Hmgcs2), deficient in the rate-limiting enzyme for ketogenesis. Cardiomyocyte -specific nuclei were isolated for transcriptomic (RNA-seq) and in vitro assays in H9C2 cells were used to elucidate molecular mechanisms. ResultsThe HFpEF model successfully exhibited diastolic dysfunction, impaired exercise capacity and cardiac hypertrophy with elevated circulating ketone body concentration. Myocardial metabolomics and snRNA-seq identified a profound metabolic shift characterized by the accumulation of long-chain fatty acids and Krebs cycle intermediates, coupled with the transcriptional downregulation of insulin signaling and fatty acid degradation pathways. Although circulating ketone body level was upregulated, Hmgcs2{Delta}iCM mice showed no exacerbation of the HFpEF phenotype. In contrast, Hmgcs2{Delta}Hep mice exhibited significantly aggravated cardiac hypertrophy (HW/TL; Hmgcs2flox: 7.41 {+/-} 0.87: Hmgcs2{Delta}Hep: 8.29 {+/-} 0.73; p = 0.0154). Mechanistically, hepatic ketogenesis was required to maintain circulating beta-hydroxybutyrate (BHB) levels, which directly modulated cardiomyocyte metabolism. BHB acted as a metabolic signal to dampen fatty acid overload and facilitate glucose utilization. ConclusionsOur study identifies a critical "liver-heart axis" where hepatic ketogenesis serves as an essential regulator of myocardial metabolic resilience. Impaired hepatic ketogenesis creates a metabolic mismatch that drives pathological cardiac remodeling. These findings highlight the liver as a therapeutic target within the CKM syndrome framework, suggesting that restoring the hepato-cardiac metabolic bridge may ameliorate HFpEF progression. What is New?O_LIThis study identifies a novel liver-adipose-heart axis that governs myocardial metabolic resilience during the development of heart failure with preserved ejection fraction (HFpEF). C_LIO_LIWe demonstrate that while both the liver and heart upregulate ketogenesis under metabolic stress, only hepatic ketogenesis--and not cardiac-intrinsic ketogenesis--is essential for mitigating pathological cardiac remodeling. C_LIO_LIMechanistically, liver-derived {beta} -hydroxybutyrate acts as a critical C_LIO_LIendocrine signal that dampens fatty acid oxidation and facilitates myocardial glucose utilization. C_LI What Are the Clinical Implications?O_LIOur findings highlight the liver as a central therapeutic target within the cardiovascular-kidney-metabolic (CKM) syndrome framework, where hepatic metabolic failure directly drives cardiac dysfunction. C_LIO_LIRestoring the hepato-cardiac metabolic bridge, through either hepatic-targeted therapies or ketone body supplementation, represents a promising strategy to enhance myocardial metabolic flexibility and ameliorate HfpEF in patients with multi-organ metabolic disorders. C_LI

biochemistry↗

bioRxiv2025

Prioritizing Combinational Drug Screening: A Ranking System for In Vitro Drug Combinations in Neurofibromatosis Type 1

Neurofibromatosis type 1 (NF1) is a genetic disorder characterized by benign tumors, including plexiform neurofibromas, which can be difficult to treat. Currently, only two FDA-approved therapies exist: selumetinib, approved for pediatric patients with inoperable tumors, and mirdametinib, approved for patients aged two and older with symptomatic peripheral neuropathy where surgical resection is not possible. These limited options highlight the urgent need for novel therapeutic strategies, including combination therapies and therapies applicable to adult populations. In this study, we introduce the Composite Matrix Reduction Score (CMRS), a novel algorithm designed to evaluate the in vitro efficacy of drug combinations for NF1-related plexiform neurofibromas. Using a high-throughput 6x6 combinatorial matrix, we screened three cell lines: ipnNF95.11c (NF1+/-, non-tumor reference), and two NF1-/- tumor lines: ipNF05.5mc and ipNF95.6. Cell viability responses to drug combinations were normalized to vehicle controls, and combination effects were compared to single-agent responses. Tumor-to-non-tumor response ratios were aggregated to generate a composite ranking for each drug pair. Our results show that certain drug combinations outperformed single agents in reducing tumor cell viability, consistent with findings in other cancers. A focused analysis on selumetinib combinations supported the CMRS algorithm and identified potential synergistic partners that may surpass a single-agent therapy, highlighting candidates for continued investigation. CMRS provides a scalable, standardized framework for prioritizing drug combinations in NF1 and potentially other cancers. By integrating multi-cell line analysis, this approach enhances the identification of promising therapeutic candidates and mechanisms of action for further preclinical development.

cancer biology↗

bioRxiv2025

Methylomic signatures of tau and amyloid-beta in transgenic mouse models of Alzheimer's disease neuropathology

Alzheimers disease (AD) is characterized by progressive neurodegeneration driven by tau and amyloid-{beta} (A{beta}) pathology. Emerging evidence implicates a role for epigenetic modifications, particularly altered DNA methylation (DNAm), in AD pathogenesis. However, few studies have comprehensively investigated DNAm in experimental models. Here, we profile DNAm dynamics in two widely used transgenic mouse models of tau (rTg4510) and A{beta} (J20) neuropathology, focusing on variation in the entorhinal cortex and hippocampus. Using reduced representation bisulfite sequencing (RRBS) and methylation arrays across multiple disease stages, we identified widespread DNAm alterations associated with genotype and neuropathological burden. In rTg4510 mice, tau accumulation was linked to extensive DNAm remodeling at genes involved in neuronal plasticity and apoptosis (including Dcaf5, Creb3l4, and As3mt). J20 mice exhibited more modest changes annotated to immune-related genes, notably at Grk2, Ncam2, and Prmt8. Of note, tau-associated DNAm changes were more consistent across brain areas than those associated with A{beta} pathology. Comparison with DNAm data from human studies revealed that a subset of DNAm sites mirrored those observed in the human AD cortex, including hypermethylation at Ank1 and Prdm16. These findings provide evidence for pathology-associated epigenetic alterations in AD, highlight shared and distinct DNAm signatures of tau and A{beta}, and offer insight into molecular mechanisms that may precede overt neurodegeneration. Our work underscores the utility of epigenomic profiling in transgenic models and provides a foundation for identifying novel targets for early intervention in AD.

neuroscience↗

bioRxiv2025

Morphology-Aware Profiling of Highly Multiplexed Tissue Images using Variational Autoencoders

Spatial proteomics (highly multiplexed tissue imaging) provides unprecedented insight into the types, states, and spatial organization of cells within preserved tissue environments. To enable single-cell analysis, high-plex images are typically segmented using algorithms that assign marker signals to individual cells. However, conventional segmentation is often imprecise and susceptible to signal spillover between adjacent cells, interfering with accurate cell type identification. Segmentation-based methods also fail to capture the morphological detail that histopathologists rely on for disease diagnosis and staging. Here, we present a method that combines unsupervised, pixel-level machine learning using autoencoders with traditional segmentation to generate single-cell data that captures information on protein abundance, morphology, and local neighborhood in a manner analogous to human experts while overcoming signal spillover. We demonstrate the generality of this approach by applying it to CyCIF, Lunaphore COMET, and CODEX data, and show that it can learn histological features across multiple spatial scales.

pathology↗

bioRxiv2025

Bisdemethoxycurcumin mitigates Alzheimer disease pathology through autophagy-mediated reduction of senescence and amyloid beta

AD pathology is accompanied by increased senescence and reduced levels of autophagy in the brain. We investigated whether pharmacologically inducing autophagy could alter the senescent phenotype and help ameliorate AD pathology. We discovered that Bisdemethoxycurcumin (BDMC), a natural compound found in Curcuma longa, stimulates autophagy in primary astrocytes. We found that autophagy and senescence exhibit an inverse relationship in aging astrocytes, with increased expression of senescent proteins and downregulation of autophagic proteins. However, treatment of aged astrocytes with BDMC reversed the senescent phenotype by ameliorating the impaired autophagy. Interestingly, the senescent phenotype persisted when autophagy was downregulated by knockdown of AMPK. Additionally, BDMC-induced autophagy aided in the removal of amyloid beta that was administered externally to the astrocytes. Further, to validate these results in a mouse model of AD, we confirmed that BDMC can significantly penetrate the blood-brain barrier (BBB) in mice. Therefore, we administered 50 and 100 mg/kg b.w. of BDMC to transgenic 3xTg-AD mice for two months. In their hippocampus, the Control 3xTg-AD animals showed more senescent cells and lower autophagy levels. In contrast, autophagic proteins were significantly upregulated while senescence indicators, such as senescence-associated secretory phenotype (SASP) proteins, were sharply downregulated in the brain of treated animals. Additionally, we discovered that the treated mices hippocampus had a significantly lower amyloid beta load. These molecular changes in the brain were ultimately reflected in the improved working memory and neuromuscular coordination behavior of mice treated with BDMC. This study warrants further evaluation of BDMC for the management of AD. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/654834v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@1176bbforg.highwire.dtl.DTLVardef@a2e2cdorg.highwire.dtl.DTLVardef@1d824f5org.highwire.dtl.DTLVardef@1628a30_HPS_FORMAT_FIGEXP M_FIG This illustration was created by using biorender.com C_FIG

pharmacology and toxicology↗

bioRxiv2025

Smart Dura: a functional artificial dura for multimodal neural recording and modulation

A multi-modal neural interface capable of long-term recording and stimulation is essential for advancing brain monitoring and developing targeted therapeutics. Among the traditional electrophysiological methods, micro-electrocorticography (ECoG) is appealing for chronic applications because it provides a good compromise between invasiveness and high-resolution neural recording. When combining ECoG with optical technologies, such as calcium imaging and optogenetics, this multi-modal approach enables the simultaneous collection of neural activity from individual neurons and the ability to perform cell-specific manipulation. While previous efforts have focused on multi-modal interfaces for small animal models, scaling these technologies to larger brains, of primates, remains challenging. In this paper, we present a multi-modal neural interface, named Smart Dura, a functional version of the commonly used artificial dura with integrated electrophysiological electrodes for large cortical area coverage for the NHP brain. The Smart Dura is fabricated using a thin-film microfabrication process to monolithically integrate a micron-scale electrode array into a soft, flexible, and transparent substrate with high-density electrodes (up to 256 electrodes) while providing matched mechanical compliance with the native tissue and achieving high optical transparency (exceeding 97%). Our in vivo experiments demonstrate electrophysiological recording capabilities combined with neuromodulation, as well as optical transparency via multiphoton imaging. This work paves the way toward a chronic neural interface that can provide large-scale, bidirectional interfacing for multimodal and closed-loop neuromodulation capabilities to study cortical brain activity in non-human primates, with the potential for translation to humans.

neuroscience↗

bioRxiv2024

Freely foraging macaques value information in ambiguous terrains

Among non-human primates, macaques are recognized for thriving in a wide range of novel environments. Previous studies show macaques affinity for new information. However, little is known about how information-seeking manifests in their spatial navigation pattern in ambiguous foraging terrains, where the location and distribution of the food are unknown. We investigated the spatial pattern of foraging in free-moving macaques in an ambiguous terrain, lacking sensory cues about the reward distribution. Rewards were hidden in a uniform grid of woodchip piles spread over a 15 sqm open terrain and spatially distributed according to different patchy distributions. We observed Levy-like random walks in macaques spatial search pattern, balancing relocation effort with exploration. Encountering rewards altered the foraging path to favor the vicinity of discovered rewards temporarily, without preventing longer-distance travels. These results point toward continuous exploration, suggesting that explicit information-seeking is a part of macaques foraging strategy. We further quantified the role of information seeking using a kernel-based model, combining a map of ambiguity, promoting information seeking, with a map of discovered rewards and a map of proximity. Fitting this model to the foraging paths of our macaques revealed individual differences in their relative preference for information, reward, or proximity. The model predicted that a balanced contribution of all three factors performs and adapts to an ambiguous terrain with semi-scattered rewards, a prediction we confirmed using further experimental evidence. We postulate an explicit role for seeking information as a valuable entity to reduce ambiguity in macaques foraging strategies, suggesting an ecologically valid way of foraging ambiguous terrains. Author SummaryIn a novel and ambiguous terrain lacking sensory information about the location or distribution of food, foragers obtain information by sampling. This process is crucial for animals thriving in a new habitat. We allowed free-roaming macaques to forage at their own pace in a controlled terrain to which they had limited prior exposure. Based on their foraging paths, we developed a computational model representing an individuals drive for reward-seeking, information-seeking, or energy preservation. These drives were represented as superimposing maps from the foragers perspective. We found that information-seeking, continuous exploration of unknown areas, is crucial for foraging under ambiguity. This finding is consistent with a theory suggesting that animals, specifically humans and other primates, seek information to reduce their uncertainty about the environment. Our study suggests that the statistical properties of primates random foraging patterns reveal their complex decision-making process, including adaptation to novel environments.

animal behavior and cognition↗

bioRxiv2024

S1PR1 Regulates Lymphatic Valve Development And Prevents Ileitis-Independent Tertiary Lymphoid Organ Formation

Lymphatic vessels function throughout the body to drain interstitial fluids. Efficient lymph flow is ensured by lymphatic valves (LVs). However, the mechanisms that regulate LV development are incompletely understood. Here, we show that the deletion of the GPCR sphingosine 1-phosphate receptor-1 (S1PR1) from lymphatic endothelial cells (LECs) results in fewer LVs. Interestingly, LVs that remained in the terminal-ileum draining lymphatic vessels were specifically dysfunctional, and tertiary lymphoid organs (TLOs) formed in this location. TLOs in the terminal ileum are associated with ileitis in humans and mice. However, mice lacking S1PR1 did not develop obvious characteristics of ileitis. Sphingosine kinases 1 and 2 (SPHK1/2) are required for the synthesis of S1P, the ligand of S1PR1. Mice that lack Sphk1/2 in LECs recapitulate the LV and TLO phenotypes of mice that lack S1PR1. Mechanistically, S1PR1 regulates shear stress signaling and the expression of the valve-regulatory molecules FOXC2 and connexin-37. Importantly, Foxc2+/- mice, a model for lymphedema-distichiasis syndrome, also develop TLOs in the terminal ileum. Thus, we have discovered S1PR1 as a previously unknown regulator of LV and TLO development. We also suggest that TLOs are a sign of subclinical inflammation that can form due to lymphatic disorders in the absence of ileitis.

developmental biology↗

bioRxiv2024

PriMAT: A robust multi-animal tracking model for primates in the wild

O_LIDetection and tracking of animals is an important first step for automated behavioral studies using videos. Animal tracking is currently done mostly using deep learning frameworks based on keypoints, which show remarkable results in lab settings with fixed cameras, backgrounds, and lighting. However, multi-animal tracking in the wild presents several challenges such as high variability in background and lighting conditions, complex motion, and occlusion. C_LIO_LIWe propose a multi-animal tracking model, PriMAT, for nonhuman primates in the wild. The model learns to detect and track primates and other objects of interest from labeled videos or single images using bounding boxes instead of keypoints. Using bounding boxes significantly facilitates data annotation and robustness. Our one-stage model is conceptually simple but highly flexible, and we add a classification branch that allows us to train individual identification. C_LIO_LITo evaluate the performance of our model, we applied it in two case studies with Assamese macaques (Macaca assamensis) and redfronted lemurs (Eulemur rufifrons) in the wild. We show that with only a few hundred frames labeled with bounding boxes, we can achieve robust tracking results. Combining these results with the classification branch for the lemur videos, our model shows an accuracy of 84% in predicting lemur identities. C_LIO_LIOur approach presents a promising solution for accurately tracking and identifying animals in the wild, offering researchers a tool to study animal behavior in their natural habitats. Our code, models, training images, and evaluation video sequences are publicly available1, facilitating their use for animal behavior analyses and future research in this field. C_LI

animal behavior and cognition↗

bioRxiv2024

Multimodal AI/ML for discovering novel biomarkers and predicting disease using multi-omics profiles of patients with cardiovascular diseases

Cardiovascular diseases (CVDs) are multifactorial diseases, requiring personalized assessment and treatment. The advancements in multi-omics technologies, namely RNA-seq and whole genome sequencing, have offered translational researchers a comprehensive view of the human genome; utilizing this data, we can reveal novel biomarkers and segment patient populations based on personalized risk factors. Limitations in these technologies in failing to capture disease complexity can be accounted for by using an integrated approach, characterizing variants alongside expression related to emerging phenotypes. Designed and implemented data analytics methodology is based on a nexus of orthodox bioinformatics, classical statistics, and multimodal artificial intelligence and machine learning techniques. Our approach has the potential to reveal the intricate mechanisms of CVD that can facilitate patient-specific disease risk and response profiling. We sourced transcriptomic expression and variants from CVD and control subjects. By integrating these multi-omics datasets with clinical demographics, we generated patient-specific profiles. Utilizing a robust feature selection approach, we reported a signature of 27 transcripts and variants efficient at predicting CVD. Here, differential expression analysis and minimum redundancy maximum relevance feature selection elucidated biomarkers explanatory of the disease phenotype. We used Combination Annotation Dependent Depletion and allele frequencies to identify variants with pathogenic characteristics in CVD patients. Classification models trained on this signature demonstrated high-accuracy predictions for CVDs. Overall, we observed an XGBoost model hyperparameterized using Bayesian optimization perform the best (AUC 1.0). Using SHapley Additive exPlanations, we compiled risk assessments for patients capable of further contextualizing these predictions in a clinical setting. We discovered a 27-component signature explanatory of phenotypic differences in CVD patients and healthy controls using a feature selection approach prioritizing both biological relevance and efficiency in machine learning. Literature review revealed previous CVD associations in a majority of these diagnostic biomarkers. Classification models trained on this signature were able to predict CVD in patients with high accuracy. Here, we propose a framework generalizable to other diseases and disorders.

genomics↗

bioRxiv2024

Volumetric mesoscopic electrophysiology: a new imaging modality for the non-human primate

The primate brain is a densely interconnected organ whose function is best understood by recording from the entire structure in parallel, rather than parts of it in sequence. However, available methods either have limited temporal resolution (functional magnetic resonance imaging), limited spatial resolution (macroscopic electroencephalography), or a limited field of view (microscopic electrophysiology). To address this need, we developed a volumetric, mesoscopic recording approach (MePhys) by tessellating the volume of a monkey hemisphere with 992 electrode contacts that were distributed across 62 chronically implanted multi-electrode shafts. We showcase the scientific promise of MePhys by describing the functional interactions of local field potentials between the more than 300,000 simultaneously recorded pairs of electrodes. We find that a subanesthetic dose of ketamine -believed to mimic certain aspects of psychosis- can create a pronounced state of functional disconnection and prevent the formation of stable large-scale intrinsic states. We conclude that MePhys provides a new and fundamentally distinct window into brain function whose unique profile of strengths and weaknesses complements existing approaches in synergistic ways.

neuroscience↗

bioRxiv2024

How clinically relevant are prostate cancer cell lines? A comprehensive characterisation and multiomics comparison.

Cell line experiments arguably remain the most used tool in preclinical cancer research, despite their limitations. With almost 95% drugs entering human trials failing, and up to 90% preclinical research failing before even being tested in humans, we must shift the pre-clinical paradigm. A range of in silico, in vitro, in vivo and ex vivo approaches are gaining popularity, with the aim of potentially replacing cell line use. However, we cannot ignore the plethora of historical data from cell lines, nor write off their future use- especially within advanced bioengineered models. Therefore, we must question if and how cell lines hold clinical relevance. This study evaluates the clinical characteristics of 46 prostate cancer cell lines against worldwide data and investigates the biological features of seven cell lines in depth, comparing them to over 10,000 well characterised human cases from 24 studies in nine countries. Clinical features compared included age, ethnicity, Gleason grade, cancer type, treatment history and multiomics variables included mutations, copy number alterations, structural variants, microsatellite instability, mRNA and protein expression, and tumour mutational burden. We found that the most used cell lines accurately represent a minute proportion of prostate cancer patients. Furthermore, we recommend a pipeline for tailoring selection of clinically relevant cell lines with the ultimate aim of increasing the scientific methodology behind choosing a cell line.

cancer biology↗

bioRxiv2023

Fluvoxamine maleate ameliorates Alzheimer disease pathology by mitigating amyloid-beta load and neuroinflammation in 5XFAD mice

BackgroundAlzheimer pathology (AD) is accompanied by the deposition of amyloid beta (A{beta}) and chronic neuroinflammation, where NLRP3 inflammasome is particularly involved. In this study, we found that the OCD drug fluvoxamine maleate (FXN) can potently ameliorate AD pathology in 5XFAD mice by autophagy-mediated clearance of A{beta} and inhibition of NLRP3 inflammasome. MethodsWe used mice primary astrocytes to establish the mechanism of action of FXN against NLRP3 inflammasome by using various techniques like ELISA, Western blotting, confocal microscopy, Immunofluorescence, etc. The validation of the anti-AD activity of FXN was done in transgenic 5XFAD mice after two months of treatment followed by behavior analysis and studying inflammatory and autophagy proteins along with immunohistochemistry analysis for A{beta} load in the hippocampi. ResultsOur data showed that FXN induces autophagy to inhibit NF-{kappa}B and NLRP3 inflammasome at a low concentration of 78 nM apart from directly inhibiting NLRP3 inflammasome in primary astrocytes. FXN activated the PRKAA2 pathway through CAMKK2 signaling, which led to the induction of autophagy in primary astrocytes. FXN inhibited the ATP-mediated NLRP3 inflammasome through autophagic degradation of NF-{kappa}B and thus caused the downregulation of pro-IL-1{beta} and NLRP3. The anti-NLRP3 inflammasome effect of FXN was reversed when autophagy was inhibited either by genetic knockdown of the PRKAA2 pathway or by bafilomycin A1. Furthermore, FXN treatment led to improved AD pathology in 5XFAD mice, which displayed a significant improvement in multiple behavior parameters like working memory and neuromuscular coordination and they behaved more like wild-type animals. We found that FXN improved behavior in 5XFAD mice by clearing the A{beta} deposits from the hippocampi along with a significant reduction in multiple inflammatory proteins, including NF-{kappa}B, GFAP, IBA1, IL-1{beta}, TNF-, and IL-6 associated with NF-{kappa}B and NLRP3 inflammasome in the brain. Moreover, these changes were accompanied by increased expression of autophagic proteins. ConclusionOur data suggest that to ameliorate AD pathology, FXN simultaneously targets two key pathological features of AD that is A{beta} deposits and neuroinflammation. Being an approved drug, FXN can be pushed as a potential drug candidate for human studies against AD.

neuroscience↗

bioRxiv2023

Long-read transcript sequencing identifies differential isoform expression in the entorhinal cortex in a transgenic model of tau pathology

Increasing evidence suggests that alternative splicing plays an important role in Alzheimers disease (AD), a devastating neurodegenerative disorder involving the intracellular aggregation of hyperphosphorylated tau. We used long-read cDNA sequencing to profile transcript diversity in the entorhinal cortex of wild-type (WT) and transgenic (TG) mice harboring a mutant form of human tau. Whole transcriptome profiling showed that previously reported gene-level expression differences between WT and TG mice reflect changes in the abundance of specific transcripts. Ultradeep targeted long-read cDNA sequencing of genes implicated in AD revealed hundreds of novel isoforms and identified specific transcripts associated with the development of tau pathology. Our results highlight the importance of differential transcript usage, even in the absence of gene-level expression alterations, as a mechanism underpinning gene regulation in the development of neuropathology. Our transcript annotations and a novel informatics pipeline for the analysis of long-read transcript sequencing data are provided as a resource to the community.

neuroscience↗