Biology subjects

Tu, H.

Publications and source records attributed to Tu, H..

15 recordsLinked to original sources

bioRxiv2026

Dysregulation of miR-103a-3p/AGFG1 axis links endocytic trafficking dysfunction to ER stress in Parkinson's disease

Background: Parkinson's disease is defined by progressive dopaminergic neurodegeneration and -synuclein pathology. Endoplasmic reticulum (ER) stress and clathrin-mediated endocytosis dysfunction are implicated in disease pathogenesis, but the molecular mechanisms connecting these processes remain poorly understood. Here, we investigate a miR-103a-3p/AGFG1 axis as a regulator link between endocytic trafficking and ER stress in Parkinson's disease. Methods: MiR-103a-3p and AGFG1 were examined in plasma and postmortem substantia nigra from patients with Parkinson's disease and controls. Gain- and loss-of-function studies, target validation and live-cell imaging were used to define the role of the miR-103a-3p/AGFG1 axis in ER stress and endocytic trafficking. The pathway was further investigated in SNCA A53T and LRRK2 G2019S hiPSC-derived neurons. Therapeutic targeting of AGFG1 was evaluated using antisense oligonucleotides (ASOs) in vitro and in a 6-hydroxydopamine mouse model. Results: MiR-103a-3p was significantly reduced in Parkinson's disease plasma and substantia nigra, whereas AGFG1 was increased in nigral tissue. MiR-103a-3p directly repressed AGFG1 and attenuated thapsigargin-induced ER stress, while miR-103a-3p inhibition or AGFG1 overexpression exacerbated stress signalling. AGFG1 knockdown reversed the effects of miR-103a-3p inhibition, establishing AGFG1 as a functional downstream effector. Mechanistically, AGFG1 associated and co-trafficked with clathrin-positive vesicles, whereas ER stress progressively disrupted AGFG1-clathrin vesicle dynamics, revealing an association between endocytic trafficking and stress signalling. In genetic Parkinson's disease models, SNCA A53T and LRRK2 G2019S neurons showed mutation-dependent differences in AGFG1 expression and stress regulation. eIF2 phosphorylation increased in both SNCA A53T and LRRK2 G2019S neurons, whereas AGFG1 and GADD34 upregulation was selective to SNCA A53T neurons. Importantly, ASO-mediated AGFG1 suppression attenuated ER stress in vitro and preserved nigral dopaminergic neurons with improved motor performance in vivo. Conclusion: Our findings identify the miR-103a-3p/AGFG1 axis as a previously unrecognised molecular link between endocytic trafficking dysfunction and ER stress in Parkinson's disease, and support AGFG1 as a mechanistically potential therapeutic target.

neuroscience↗

bioRxiv2026

Site-specific integration of transposon via engineered piggyBac transposase

The precise integration of large DNA fragments into the human genome holds significant therapeutic potential. Here, we demonstrate that combining engineered piggyBac (PB) transposase with CRISPR/Cas9 enables targeted integration of PB transposons into specified genomic loci. Our engineered PB transposase (PBase) retains high excision activity while substantially reducing endogenous integration activity. In the developed Cas9-PBase fusion system, PBase excises the transposon to generate linear DNA fragments, while Cas9 introduces site-specific double-strand breaks (DSBs), facilitating insertion of the excised fragment at the target locus. The optimized tool achieves 6.1-7.3 kb transposon integration at multiple genomic sites with 10-15% efficiency, demonstrating 60-80% targeted integration specificity. As a proof of concept, we inserted a 7.1 kb transposon encoding three genes into the {beta}2M locus of human induced pluripotent stem cells (iPSCs), conferring protection against allogeneic natural killer (NK) cell-mediated cytotoxicity in derived iNK cells. These results establish Cas9-PBase as a precise and programmable platform for large DNA sequence insertion with potential clinical applications.

genetics↗

bioRxiv2025

Mitoxantrone Hydrochloride Targets APP and LRRK2 to Improve Neurodegeneration in Parkinson's Models

BackgroundParkinsons disease (PD) is the second common neurodegenerative disorder, driven by the loss of dopaminergic neurons and pathological -synuclein protein accumulation. Currently, there is no disease-modifying therapy that can halt PD progression. Our previous study uncovered a critical pathogenic feed-forward loop between amyloid precursor protein (APP) and leucine-rich repeat kinase 2 (LRRK2), in which the two proteins mutually enhance each others expression, ultimately leading to mitochondrial dysfunction and neurotoxicity. Targeting this vicious cycle represents a promising therapeutic strategy for PD. MethodsTo discover novel inhibitors targeting this axis, we performed high-throughput screening of an FDA-approved drug library using a fluorescence-based biosensor system. We identified Mitoxantrone hydrochloride (MH), an antineoplastic agent, as a lead compound that inhibits both APP and LRRK2 expression. Its efficacy was validated in cellular models, including patient induced pluripotent stem cell (iPSC)-derived dopaminergic neurons and human peripheral blood mononuclear cells (PBMCs). Motor behavioural and safety assessments were subsequently conducted in PD mouse models. ResultsWe demonstrated that MH suppresses both APP and LRRK2 expression in various cell types in a dosage-dependent manner. In addition, MH also inhibits phosphorylation of LRRK2 and its downstream substrate Rab10. We further showed MH inhibits LRRK2 activity through direct binding to its kinase domain. Critically, MH treatment rescued dopaminergic neuron loss and reversed motor deficits in both 6-Hydroxydopamine (6-OHDA)-induced and LRRK2G2019S genetic PD mouse models. Moreover, we found that oral administration of MH is therapeutically effective, providing superior neuroprotection and behavioral recovery without detectable cardiotoxicity or gastrointestinal damage. ConclusionsOur findings demonstrate MH as a compelling, repurposable therapeutic candidate capable of disrupting a core pathogenic mechanism in PD.

neuroscience↗

bioRxiv2025

Programming cellular condensates for living materials using an intrinsically disordered protein display platform

Self-organization of multicellular systems is vital for building structure in living system but remains underexplored in engineered living materials. We developed iDP2, a platform enabling high-density display of intrinsically disordered proteins on the surface of E. coli using CsgF as a surface-bound anchor protein to which other protein domains can be fused. Display depends on a lack of intrinsic structure and enable multivalent weak interactions that drive environmental responsiveness and sequence-programmable self-segregation. iDP2 allow the programming of material properties like viscoelasticity, stability, offering a method to rationally control cell-cell interactions. This approach could be applied to engineer self-organizing tissues or materials with customized properties.

synthetic biology↗

bioRxiv2024

Supercontinuum intrinsic fluorescence imaging heralds free view of living systems

Optimal imaging strategies remain underdeveloped to maximize information for fluorescence microscopy while minimizing the harm to fragile living systems. Taking hint from the supercontinuum generation in ultrafast laser physics, we generated supercontinuum fluorescence from untreated unlabeled live samples before nonlinear photodamage onset. Our imaging achieved high-content cell phenotyping and tissue histology, identified bovine embryo polarization, quantified aging-related stress across cell types and species, demystified embryogenesis before and after implantation, sensed drug cytotoxicity in real-time, scanned brain area for targeted patching, optimized machine learning to track small moving organisms, induced two-photon phototropism of leaf chloroplasts under two-photon photosynthesis, unraveled microscopic origin of autumn colors, and interrogated intestinal microbiome. The results enable a facility-type microscope to freely explore vital molecular biology across life sciences.

bioengineering↗

bioRxiv2023

Gentle label-free nonlinear optical imaging relaxes linear-absorption-mediated triplet

Sample health is critical for live-cell fluorescence microscopy and has promoted light-sheet microscopy that restricts its ultraviolet-visible excitation to one plane inside a three-dimensional sample. It is thus intriguing that laser-scanning nonlinear optical microscopy, which similarly restricts its near-infrared excitation, has not broadly enabled gentle label-free molecular imaging. We hypothesize that intense near-infrared excitation induces phototoxicity via linear absorption of intrinsic biomolecules with subsequent triplet buildup, rather than the commonly assumed mechanism of nonlinear absorption. Using a reproducible phototoxicity assay based on the time-lapse elevation of auto-fluorescence (hyper-fluorescence) from a homogeneous tissue model (chicken breast), we provide strong evidence supporting this hypothesis. Our study justifies a simple imaging technique, e.g., rapidly scanned sub-80-fs excitation with full triplet-relaxation, to mitigate this ubiquitous linear-absorption-mediated phototoxicity independent of sample types. The corresponding label-free imaging can track freely moving C. elegans in real-time at an irradiance up to one-half of water optical breakdown.

bioengineering↗

bioRxiv2023

A parabrachial-hypothalamic parallel circuit governs cold defense in mice

Thermal homeostasis is vital for mammals and is controlled by brain neurocircuits. Remarkable advances have been made in understanding how neurocircuits centered in the hypothalamic preoptic area (POA), the brains thermoregulation center, control warm defense, whereas mechanisms by which the POA regulates cold defense remain unclear. Here, we confirmed that the pathway from the lateral parabrachial nucleus (LPB) to the POA, is critical for cold defense. Parallel to this pathway, we uncovered that a pathway from the LPB to the dorsomedial hypothalamus (DMH), namely the LPB[->]DMH pathway, is also essential for cold defense. Projection-specific blockings revealed that both pathways provide an equivalent and cumulative contribution to cold defense, forming a parallel circuit. Specifically, activation of the LPB[->]DMH pathway induced strong cold-defense responses, including increases in thermogenesis of brown adipose tissue (BAT), muscle shivering, heart rate, and physical activity. Further, we identified a subpopulation of somatostatin+ neurons in the LPB that target the DMH to promote BAT thermogenesis. Therefore, we reveal a parabrachial-hypothalamic parallel circuit in governing cold defense in mice. This not only enables resilience to hypothermia but also provides a scalable and robust network in heat production, reshaping our understanding of how neural circuits regulate essential homeostatic behaviors.

neuroscience↗

bioRxiv2023

A deep learning-based stripe self-correction method for stitched microscopic images

The stitched fluorescence microscope images inevitably exist in various types of stripes or artifacts caused by uncertain factors such as optical devices or specimens, which severely affects the image quality and downstream quantitative analysis. In this paper, we present a deep learning-based Stripe Self-Correction method, so-called SSCOR. Specifically, we propose a proximity sampling scheme and adversarial reciprocal self-training paradigm that enable SSCOR to utilize stripe-free patches sampled from the stitched microscope image itself to correct their adjacent stripe patches. Comparing to off-the-shelf approaches, SSCOR can not only adaptively correct non-uniform, oblique, and grid stripes, but also remove scanning, bubble, and out-of-focus artifacts, achieving the state-of-the-art performance across different imaging conditions and modalities. Moreover, SSCOR does not require any physical parameter estimation, patch-wise manual annotation, and raw stitched information in the correction process, which provides an intelligent image quality optimization solution for microscopist or even microscope company, and facilitates more precise biomedical applications for researchers.

bioinformatics↗

bioRxiv2022

Pneumatic Controlled Nano-Sieve for Efficient Capture and Release of Nanoparticles

A pneumatic controlled nano-sieve device is demonstrated for the efficient capture and release of 15 nm quantum dots. This device consists of a 200 nm deep glass channel and a PDMS-based pneumatic pressure layer to enhance target capture. The fluid motion inside the nano-sieve is studied by computational fluidic dynamics (CFD) and microfluidic experiments, enabling efficient target capture with a flow rate as high as 100 L/min. In addition, micro-grooves are fabricated inside the nano-sieve to create low flow rate regions, which further improves the target capture efficiency. A velocity contour plot is constructed with CFD, revealing the flow rate is lowest at the top and bottom of the micro-grooves. This phenomenon is supported by the observed nanoparticle clusters surrounding the micro-grooves. By changing the morphology and pneumatic pressure, this device will also facilitate rapid capture and release of various biomolecules.

bioengineering↗

bioRxiv2022

Weakly supervised deep learning for human breast cancer-related optical biomarker discovery in label-free virtual histopathology

With the latest advancements in optical bioimaging, rich structural and functional information has been generated from biological samples, which calls for capable computational tools to identify patterns and uncover relationships between optical characteristics and various biomedical conditions. Constrained by the existing knowledge of the novel signals obtained by those bioimaging techniques, precise and accurate ground truth annotations can be difficult to obtain. Here we present a weakly supervised Deep Learning framework for optical signature discovery based on inexact and incomplete supervision. The framework consists of a Multiple Instance Learning-based classifier for the identification of regions of interest in coarsely labeled images, and model interpretation techniques for optical signature discovery. We applied this framework to investigate human breast cancer-related optical signatures based on virtual histopathology enabled by simultaneous label-free autofluorescence multiharmonic microscopy (SLAM), with the goal to explore unconventional cancer-related optical signatures from normal-appearing breast tissues. The framework has achieved an average area under the curve (AUC) of 0.975 on the cancer diagnosis task. In addition to well-known cancer biomarkers, non-obvious cancer-related patterns were revealed by the framework, including NAD(P)H-rich extracellular vesicles observed in normal-appearing breast cancer tissue, which facilitate new insights into the tumor microenvironment and field cancerization. This framework can be further extended to diverse imaging modalities and optical signature discovery tasks.

bioinformatics↗

bioRxiv2021

Wound-like tumor periphery in human breast cancer predicts a convergent drug nonresponse

A significant portion of breast cancer patients are nonresponsive to well-established drugs and destined for a poor outcome regardless of molecular subtype. Although several (multiparameter) molecular markers have predicted their resistance to some of these drugs, profound uniparameter markers predictive of a convergent nonresponse to all these drugs remain elusive. We employ co-registered standard-multiphoton histology to representatively sample a few peripheral niches of the primary tumor, so that hundreds of patients can be stratified with either a wound-like or non-wound tumor periphery. With no fitting variable, this simple uniparameter morphological marker is: (a) highly sensitive and specific to predict a multidrug-nonresponsive phenotype that accounts for the majority of recurrence or death, independent of the molecular subtype or related adjuvant drug selection, clinical endpoint (disease-free versus overall survival), and hosting medical center; (b) robust against intratumor heterogeneity and valid at the earliest clinicopathological stage; and (c) dominant in predicting prognosis in the context of routine clinicopathological markers. Considering the mechanistic link between a wound-like extracellular matrix and a microenvironment supporting migratory or mesenchymal tumor cells, we attribute these unusual capabilities to an epithelial-mesenchymal transition nature of the morphological marker long sought after by pathologists.

pathology↗

bioRxiv2021

Distinct Patterns of Emergence of SARS-CoV-2 Spike Variants including N501Y in Clinical Samples in Columbus Ohio

Following the worldwide emergence of the p.Asp614Gly shift in the Spike (S) gene of SARS-CoV-2, there have been few recurring pathogenic shifts occurring during 2020, as assessed by genomic sequencing. This situation has evolved in the last several months with the emergence of several distinct variants (first identified in the United Kingdom and South Africa) that manifest multiple changes in the S gene, particularly p.Asn501Tyr (N501Y), that likely have clinical impact. We report here the emergence in Columbus, Ohio in December 2020 of two novel SARS-CoV-2 clade 20G variants. One variant, that has become the predominant virus found in nasopharyngeal swabs in the December 2020-January 2021 period, harbors S p.Gln677His (Q677H), affecting a consensus QTQTN domain near the S1/S2 furin cleavage site, nucleocapsid (N) p.Asp377Tyr (D377Y) and membrane glycoprotein (M) p.Ala85Ser (A85S) mutations, with additional S mutations in subsets. The other variant present in two samples, contains S N501Y, which is a marker of the UK-B.1.1.7 (clade 20I/501Y.V1) strain, but lacks all other mutations from that virus. The Ohio variant is from a different clade and shares multiple mutations with the clade 20G viruses circulating in the area prior to December 2020. These two SARS-CoV-2 viruses, which we show are also present and evolving currently in several other parts of North America, add to the diversity of S gene shifts occurring worldwide. These and other shifts in this period of the pandemic support multiple independent acquisition of functionally significant and potentially complementing mutations affecting the S QTQTN site (Q675H or Q677H) and certain receptor binding domain mutations (e.g., E484K and N501Y).

genomics↗

bioRxiv2021

Correlation of Computerized Tomography (CT) Severity Score for COVID-19 pneumonia with Clinical Outcomes

IntroductionVarious CT severity scores have already been described in literature since the start of this pandemic. One pertinent issue with all of the previously described severity scores is their relative challenging calculation and variance in inter-observer agreement. The severity score proposed in our study is relatively simpler, easier to calculate and apart from a trained radiologist, can easily be calculated even by physicians with good inter-observer agreement. Therefore, a rapid CT severity score calculation can give a clue to physician about possible clinical outcome without being dependent on radiologist who may not be readily available especially in third world countries. ObjectiveThe objective of this study is to develop a simple CT severity score (CT-SS) with good inter-observer agreement and access its correlation with clinical outcome. MethodsThis retrospective study was conducted by the Department of Radiology and Internal Medicine, at the Aga Khan University Hospital Karachi, from April 2020 to August 2020. Non-probability consecutive sampling was used to include all patients who were positive for COVID-19 on PCR, and underwent CT chest examination at AKUH. Severity of disease was calculated in each lobe on the basis of following proposed CT severity scoring system (CT-SS). For each lobe the percentage of involvement by disease was scored - 0% involvement was scored 0, <50% involvement was scored 1 and >50% involvement was scored 2. Maximum score for one lobe was 2 and hence total maximum overall score for all lobes was 10. Continuous data was represented using mean and standard deviation, and compared using independent sample t-tests. Categorical data was represented using frequencies and percentages, and compared using Chi-squared tests. Inter-observer reliability between radiologist and COVID intensivist for the 10 point CT-SS rated on 0-10 was assessed using the Kappa statistic. A p-value < 0.05 was considered significant for all analyses. ResultsA total of 73 patients were included, the majority male (58.9%) with mean age 55.8 {+/-} 13.93 years. The CT-SS rated on 0-10 showed substantial inter-observer reliability between radiologist and intensivist with a Kappa statistic of 0.78. Patients with CT-SS 8-10 had a significantly higher ICU admission & intubation rate (53.8% vs. 23.5%) and mortality rate (35.9% vs. 11.8%; p = 0.017), as compared to those with CT-SS 0-7. ConclusionWe conclude that the described CT severity score (CT-SS) is a quick, effective and easily reproducible tool for prediction of adverse clinical outcome in patients with COVID 19 pneumonia. The tool shows good inter-observer agreement when calculated by radiologist and physician independently.

pathology↗

bioRxiv2020

Large-scale geographic survey provides insights into the colonization history of a major aphid pest on its cultivated apple host in Europe, North America and North Africa

AO_SCPLOWBSTRACTC_SCPLOWWith frequent host shifts involving the colonization of new hosts across large geographical ranges, crop pests are good models for examining the mechanisms of rapid colonization. The microbial partners of pest insects may also be involved in or affected by colonization processes, which has been little studied so far. We investigated the demographic history of the rosy apple aphid, Dysaphis plantaginea, a major pest of the cultivated apple (Malus domestica) in Europe, North Africa and North America, as well as the diversity of its microbiota. We genotyped a comprehensive sample of 714 colonies from Europe, Morocco and the US using mitochondrial (CytB and CO1), bacterial (16s rRNA and TrnpB), and 30 microsatellite markers. We detected five populations spread across the US, Morocco, Western and Eastern Europe and Spain. Populations showed weak genetic differentiation and high genetic diversity, except the ones from Morocco and North America that are likely the result of recent colonization events. Coalescent-based inferences revealed high levels of gene flow among populations during the colonization but did not allow determining the sequence of colonization of Europe, North America and Morroco by D. plantaginea, likely because of the weak genetic differentiation and the occurrence of gene flow among populations. We found that D. plantaginea rarely hosts other endosymbiotic bacteria than its obligate nutritional symbiont Buchnera aphidicola. This suggests that secondary endosymbionts did not play an important role in the rapid spread of the rosy apple aphid. These findings have fundamental importance for understanding pest colonization processes and implications for sustainable pest control programs.

evolutionary biology↗

bioRxiv2020

Parabrachial neuron types categorically encode thermoregulation variables during heat defense

Heat defense is crucial for survival and fitness, and its dysregulation may result in deaths due to poor management. Transmission of thermosensory signals into hypothalamic thermoregulation centers represent a key layer of regulation in heat defense. However, the mechanism by which these signals are transmitted into the hypothalamus remains poorly understood. Here, we reveal that glutamatergic prodynorphin and cholecystokinin neuron populations in the lateral parabrachial (LPB) are progressively recruited to defend elevated body temperature. These two nonoverlapping neuron types form circuitries with downstream preoptic hypothalamic neurons to inhibit BAT thermogenesis and activate tail vasodilation, respectively. Both circuitries are selectively activated by warm temperatures and are required for fever limiting. The prodynorphin circuitry is further required for regulation of energy expenditure and weight homeostasis. Thus, these findings establish that the genetic and functional specificity of heat defense neurons occurs as early as in the LPB and uncover categorical neuron types for encoding two heat defense variables, which may provide targets for treating thermoregulation disorders.

neuroscience↗