Biology subjects

Bi, L.

Publications and source records attributed to Bi, L..

At least 19 recordsLinked to original sources

bioRxiv2026

Brain and kidney Extracellular Vesicle Morphology and Complementary Brain proteomics after Inflammatory Challenge

Shape, size variation, and protein composition describe different properties of tissue extracellular vesicle (EV) preparations. We compared brain and kidney EV shape and size using transmission electron microscopy (TEM). We also assessed repeated protein detection and reanalyzed a deposited brain proteomics cohort, with attribution to its original source. The study used intracerebroventricular lipopolysaccharide (LPS) and an intravenous miRNA-associated EV formulation. Each group contained three biological samples, as labelled in the source data. Source morphometry summaries included 385 brain and 101 kidney profiles. Kidney circularity was 0.9225, 0.8977, and 0.9288 in the control, LPS, and treatment groups, respectively. The corresponding values for diameter quartile dispersion, a measure of size variation, were 0.2603, 0.5334, and 0.6018. Thus, near-control outline shape coexisted with persistent size variation. None of the six primary morphology tests remained significant after Holm correction. Independent recalculation confirmed 1,527 eligible rat protein accessions across individual searches. The complete quantitative matrix contained 953 features. The main peptide filter combined unique and razor peptides. A stricter analysis retained 916 features. PTGFRN and LAMB2 remained the only significant treatment-versus-LPS findings. In the main analysis, PTGFRN increased 14.71-fold (q = 0.0365), and LAMB2 increased 6.23-fold (q = 0.00585). Their LPS levels were already close to control values. Exploratory normalization used the geometric mean of four measured EV-associated markers. The resulting treatment-versus-LPS increases were 16.43-fold and 6.96-fold, respectively. These ratios support selective changes in relative protein representation within the recovered mixture. They do not establish protein copies per EV. Analysis of the full protein profile and calibration of the complete selection process did not support an overall return to control. This study compares morphology and composition as separate outcomes. It identifies membrane and matrix associations as priorities for validation. Original TEM measurements were unavailable, sample matching remained unresolved, and kidney proteomics were absent. These limitations prevent causal conclusions and individual-sample comparisons between morphology and protein composition.

neuroscience↗

bioRxiv2026

Exploratory Proteomics of Brain Extracellular Vesicle Enriched Preparations After LPS Challenge and miRNA Associated Vesicle Administration

We used brain extracellular vesicle (EV) proteomics to identify protein responses to acute neuroinflammation and an EV-based microRNA intervention. Rats received vehicle, intracerebroventricular lipopolysaccharide (LPS), or LPS followed by an intravenous EV formulation containing anti-inflammatory microRNAs (miRNAs). Brains were collected 24 h after LPS or vehicle administration, and three independently processed animal-derived EV-enriched preparations per group were analyzed by label-free proteomics. Across all nine samples, 953 protein groups had complete normalized abundance measurements. Compared with vehicle controls, LPS exposure was associated with 227 exploratory protein changes, comprising 95 increases and 132 decreases at nominal P < 0.05 and an absolute log2 fold change >= log2(1.5). Increased proteins were enriched for translation-related annotations, whereas decreased proteins were enriched for plasma-membrane annotations. These LPS-associated changes did not remain significant after Benjamini-Hochberg correction at a false discovery rate (FDR) threshold of q < 0.05. Following treatment, 119 of the 227 candidates were closer to control abundance on the log2 scale; 23 candidates also showed nominal treatment-versus-LPS differences. Lamb2 and Ptgfrn were the two proteins that differed significantly between treated and LPS-only animals after FDR correction, identifying them as priorities for further validation. Nevertheless, 174 proteins differed significantly between treated animals and vehicle controls, and analysis across the measured proteins did not demonstrate an overall shift toward control values. Thus, the intervention was associated with specific protein responses, but treated animals retained substantial differences from controls. This study identifies candidate markers for investigating treatment responses in brain EV-enriched preparations and demonstrates the value of examining individual proteins alongside broader proteomic changes. Independent validation is needed to determine their functional relevance and distinguish miRNA-specific effects from contributions of the administered EV carrier.

neuroscience↗

bioRxiv2026

Spatial MALDI-MSI Reveals a Coordinated Vicious Cycle of Oxidative Membrane Damage and Ceramide-Driven Sphingolipid Dysregulation in the Chronically Neuroinflamed Brain

BackgroundChronic neuroinflammation is a major driver of cognitive decline, vascular cognitive impairment, and Alzheimers disease. However, the spatial lipidomic alterations underlying neuroinflammatory brain injury remain poorly defined. Oxidative stress and sphingolipid dysregulation have been implicated, but their regional distribution and interplay in the brain are not well characterized. MethodsWe performed positive-ion mode matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) on coronal brain sections from middle-aged spontaneously hypertensive rats (SHR), a model of chronic neuroinflammation, and normotensive Wistar-Kyoto (WKY) controls. Spatial distributions and relative abundances of multiple lipid classes, including phosphatidylcholines (PCs), sphingomyelins (SMs), hexosylceramides (HexCers), ceramides, phosphatidylserines (PSs), phosphatidylinositols (PIs), phosphatidylethanolamines (PEs), phosphatidic acids (PAs), and sulfatides, were mapped and compared between genotypes. Region-of-interest analysis was used to quantify changes across cortex, hippocampus, and white-matter tracts. ResultsSHR brains exhibited a coordinated lipidomic signature characterized by pronounced oxidative stress and membrane remodeling. Oxidized and short-chain PCs were markedly upregulated (up to 11.6-fold), while major structural diacyl PCs were broadly downregulated. Concurrently, sphingolipids were significantly altered, with robust upregulation of SM(d36:1) (7.5-fold) and multiple HexCer species (1.5-1.9-fold), accompanied by accumulation of ceramides. These changes were accompanied by heterogeneous redistribution of PS, PI, and PE species, particularly within the hippocampus. Sulfatide patterns in white-matter tracts were also altered, suggesting myelin remodeling. Region-of-interest analysis confirmed that the most pronounced lipid alterations were concentrated in the hippocampus and white-matter regions. ConclusionsChronic neuroinflammation induces a spatially organized, multi-class lipid remodeling response in the brain, driven by advanced oxidative membrane damage and a shift toward a pro-apoptotic sphingolipid profile. The convergence of these pathways creates a vicious cycle of membrane injury, mitochondrial dysfunction, and sustained neuroinflammation that is especially prominent in the hippocampus and white matter. These spatially resolved findings provide direct evidence that oxidative stress and sphingolipid dysregulation are central, interrelated mechanisms contributing to neurovascular injury and increased risk of cognitive impairment. The study highlights the power of MALDI-MSI to uncover region-specific lipid pathology and identifies potential lipid-based targets for therapeutic intervention in neuroinflammatory brain disease. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/738110v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@853af9org.highwire.dtl.DTLVardef@e2d079org.highwire.dtl.DTLVardef@e4e065org.highwire.dtl.DTLVardef@480d80_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

Age-Dependent Spatiotemporal Remodeling of Brain Sphingolipids During LPS-Induced Neuroinflammation: MALDI-MSI Reveals Accelerated Sphingomyelin Depletion and Sulfatide Accumulation Linked to Mitochondrial Oxidative Stress

Aging is a major risk factor for exacerbated neuroinflammation and neurodegenerative diseases, yet the underlying lipid metabolic mechanisms remain incompletely understood. Here, we employed high-resolution matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) combined with quantitative peak-area analysis and conceptual kinetic modeling to investigate age-dependent sphingolipid remodeling in the rat brain following intracerebro-ventricular (ICV) LPS challenge. In old rats, MALDI-MSI revealed pronounced and progressive sphingolipid dysregulation compared with young animals. Quantitative analysis showed a dramatic [~]10-fold reduction in SM(d36:1) and [~]4-fold reduction in SM(d42:2), accompanied by significant accumulation of long-chain sulfatides (2.12-fold increase in C24:1-sulfatide and 1.45-fold increase in C24(OH)-sulfatide) at both 24 h and 72 h post-LPS. Spatial imaging demonstrated that these changes were markedly amplified in white matter regions and became more widespread and intense at 72 h. A simplified Michaelis-Menten kinetic model successfully recapitulated the experimental data, identifying increased nSMase2 activity (higher Vmax) as the primary driver of accelerated sphingomyelin hydrolysis and subsequent ceramide rerouting into sulfatide synthesis. This metabolic shift generates excess ceramide that promotes Drp1-mediated mitochondrial fission, elevates mitochondrial ROS production, and disrupts bioenergetics, establishing a feed-forward loop linking sphingolipid remodeling to mitochondrial oxidative stress and white matter vulnerability in the aged brain. These findings provide the first spatially and temporally resolved demonstration of age-dependent sphingolipid metabolic reprogramming during neuroinflammation. By integrating multimodal MALDI-MSI, quantitative lipidomics, and kinetic modeling, this study reveals a previously underappreciated nSMase2-ceramide-mitochondrial axis in neuroinflammaging. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=179 SRC="FIGDIR/small/734865v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@be7a9eorg.highwire.dtl.DTLVardef@164499dorg.highwire.dtl.DTLVardef@11cea50org.highwire.dtl.DTLVardef@15b2ac2_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

Discovery of Tcf7 regulators with clonally-resolved CRISPR screens identifies Trim28 as a mediator of CD8 T cell differentiation in tumors

Stem-like TCF7+ CD8 T cells sustain anti-tumor responses and support immune checkpoint blockade. We systematically identified regulators of this cell state using genome-wide CRISPR screens in primary T cells in vitro. Using random barcodes to link clonal relationships with guide identity and transcriptional states in single cells, we inferred differentiation trajectories and differentiation rates of CD8 T cells in tumors, while mitigating confounding clonal bias. We found that Trim28-deficient T cells in tumors were enriched in the TCF7+ cell state, depleted in cycling and terminal effector states, and uniquely generated a tissue-resident memory (TRM)-like state with increased chromatin accessibility at known TRM loci as well as repeat elements. Despite the increase in TCF7+ CD8 T cells, loss of Trim28 did not improve tumor control, likely because of reduced effector differentiation, highlighting the need for tuning the balance and dynamics of stem-like versus effector states for effective tumor clearance.

immunology↗

bioRxiv2026

Chronic Paraventricular OX1R Overexpression Induces Oxidative Stress and Hypertension in Rats

BackgroundHyperactivity of the orexin system has been implicated in hypertension, yet the long-term impact of orexin 1 receptor (OX1R) overexpression in the paraventricular nucleus (PVN), a key brain region involved in arterial blood pressure (ABP) regulation, remains unclear. This study examined whether chronic OX1R overexpression in the PVN alters cardiovascular, neuroendocrine, and oxidative functions. MethodsAdult male Sprague-Dawley rats received bilateral PVN injections of AAV2-OX1R or control virus AAV2-GFP. Their ABP and heart rate (HR) were monitored for eight weeks via radiotelemetry. Renal sympathetic nerve activity (RSNA) and ABP responses to PVN orexin A administration were assessed using in vivo recordings. Reactive oxygen species (ROS) were quantified using MitoProbe, and gene expression was analyzed by qPCR. Primary neuronal cultures were used to explore underlying mechanism involved in increased ROS production and neuronal activity. ResultsPVN OX1R overexpression increased mean ABP ([~]10 mmHg), water intake, and ROS levels in both the PVN and peripheral organs. In addition, orexin A evoked exaggerated RSNA (155% vs. 73%) and pressor responses (27 vs. 16 mmHg) in PVN OX1R overexpression rats compared to control rats, these effects were attenuated by the OX1R antagonist SB408124. Plasma vasopressin levels were elevated, and brain sections confirmed increased ROS in OX1R-positive neurons. In vitro experiments further demonstrated that orexin A upregulated ROS-generating enzymes, suppressed antioxidant genes, and enhanced neuronal excitability. ConclusionChronic PVN OX1R overexpression induces oxidative stress, sympathetic overactivity, and increased plasma vasopressin, contributing to hypertension development. Targeting PVN OX1R signaling may provide therapeutic benefit for hypertension.

physiology↗

bioRxiv2025

Copper-Free Click Chemistry Enables High-Fidelity Engineering of Mitochondria Targeted Brain-Derived Exosomes

Mitochondrial dysfunction is a hallmark of neurodegenerative and neuroinflammatory disorders, including hypertension and cardiovascular disease, yet strategies for safe and precise mitochondrial-targeted delivery remain limited. Here, we establish strain-promoted azide-alkyne cycloaddition (SPAAC) as a biocompatible, high-fidelity chemical platform for engineering mitochondria-targeted brain-derived exosomes (BR-EVs). Copper-free click conjugation of a mitochondrial-targeting ligand (e.g. Cy5-DBCO) under mild aqueous conditions preserved vesicle morphology (30-150 nm core; 120-200 nm hydrodynamic), proteomic composition, and uptake dynamics. Time-course imaging and fluorescence recovery after photobleaching (FRAP) revealed unaltered endocytic kinetics, >75 % mitochondrial colocalization, and intact organelle architecture. In vivo neuroinflammation and biodistribution analyses demonstrated immunological neutrality, strong central nervous system retention, and minimal peripheral dispersion following intracerebroventricular administration. Proteomic profiling of unlabeled Sprague-Dawley (SD) and hypertensive Dahl salt-sensitive (DSS) BR-EVs uncovered hypertension-driven enrichment of oxidative and complement pathways correlating with mitochondrial fragmentation and reactive oxygen species generation in neuronal cultures. These findings establish SPAAC-mediated ligand conjugation as a biocompatible and chemically precise approach for generating mitochondria-targeted exosomes that preserve exosomal identity, biodistribution, and signaling fidelity--advancing a foundational platform for organelle-specific delivery and mechanistic imaging in the central nervous system.

neuroscience↗

bioRxiv2025

A Reversible Mitochondrial ROS Probe for Monitoring Mitophagy Dynamics: Development and Application of MitoFlare

Mitochondrial dysfunction and defective mitophagy are defining features of numerous neurodegenerative and metabolic disorders, yet existing tools provide limited ability to quantify mitophagy dynamics in real time within living, post-mitotic cells. Here we present MitoFlare, a mitochondria-targeted, reversible mtROS-responsive fluorogenic probe that enables continuous, non-genetic visualization of mitochondrial oxidative activation and turnover. MitoFlare incorporates dual TEMPO nitroxide quenchers into a long-wavelength rhodamine scaffold, producing >95% basal quenching and rapid, fully reversible fluorescence activation in response to mitochondrial superoxide, hydroxyl radicals, lipid-derived peroxyl species, and peroxynitrite. When combined with LysoTracker Green, MitoFlare forms a dual-probe imaging platform that resolves the entire mitophagy cascade with high spatial and temporal fidelity in intact PC12 neuronal cells. Using this platform, we established a quantitative framework comprising three mechanistically distinct metrics: (i) a proximity index that reports early mitochondrial engagement with lysosomes, (ii) Manders M1 coefficient that captures mid-stage mitochondria-lysosome fusion and mitophagosome formation, and (iii) a quenching/swelling index that resolves terminal lysosomal degradation. Nutrient deprivation induced a complete, temporally ordered mitophagy program, including mtROS priming, Parkin-OPTN-associated fusion, and efficient acidification-dependent cargo degradation. In contrast, inhibition of v-ATPase with bafilomycin A1 arrested mitophagy at the fusion stage, resulting in persistent redox-active mitochondrial cargo that failed to undergo lysosomal digestion. Importantly, MitoFlares reversible redox chemistry uniquely revealed accumulation of undegraded, oxidatively active mitochondrial remnants within non-acidified vesicles--pathological intermediates that are undetectable using irreversible ROS dyes or genetically encoded reporters. These findings demonstrate that mitophagy proceeds through discrete, redox-regulated and lysosome-dependent phases that can be quantitatively mapped in real time. By enabling synchronized measurement of oxidative activation, organelle trafficking, fusion, and degradation, the MitoFlare-LysoTracker system establishes a new benchmark for dynamic mitophagy analysis in physiologically relevant models. This platform provides a powerful foundation for mechanistic interrogation of mitochondrial quality control and for accelerating the discovery of therapeutic strategies aimed at restoring mitophagic fidelity in neurodegenerative, cardiovascular, and metabolic diseases.

neuroscience↗

bioRxiv2025

Genomic and Epigenetic Interplay Drives Adaptive Fusion via Reproduction Trade-Off

Investment in sexual reproduction has long been seen as a fitness cost for asexual proliferation, raising the question of how cells evolve to accommodate cyclical demands of sexual and asexual cycles. We addressed this question by evolving Schizosaccharomyces pombe lacking the critical fusion gene Prm1 through 18 cycles of alternating meiosis and mitosis. Initially, transcriptional tweaks offered a fragile means to fuse despite Prm1s absence. However, a telomeric 1% genome deletion that epigenetically silenced Clr5 ultimately locked in a latent, Prm1-independent fusion pathway involving the mating regulator Ste11 and the pheromone-MAPK scaffold Sms1. This adaptation, though efficient at restoring sexual reproduction, came at the cost of mitotic growth. By contrast, rationally constructing mutations in a "synthetic evolution" approach bypassed the trade-off, enabling simultaneous high fusion efficiency and near-wild-type proliferation. Our findings illustrate how epigenetic de-repression and genetic assimilation converge to create innovative solutions under cyclical selection pressures with trade-offs.

evolutionary biology↗

bioRxiv2024

A Novel Cyanine-Based Fluorescent Dye for Targeted Mitochondrial Imaging in Neurotoxic Conditions and In Vivo Brain Studies

Mitochondrial dysfunction is a key feature of neurodegenerative diseases, often preceding symptoms and influencing disease progression. However, real-time in vivo imaging of mitochondria in the brain is limited by existing dyes like MitoTrackers, which struggle with poor tissue penetration, phototoxicity, and inability to cross the blood-brain barrier (BBB). This study introduces Cy5-PEG4, a novel mitochondrial-targeting dye that overcomes these limitations, enabling high-resolution, non-invasive imaging of mitochondrial dynamics. Cy5-PEG4 effectively labels mitochondria in primary neuronal cells exposed to the SARS-CoV-2 RNYIAQVD peptide, revealing dose-dependent alterations in mitochondrial function that may contribute to COVID-19-related neurodegeneration. Importantly, Cy5-PEG4 crosses the BBB without causing neuroinflammation or toxicity, making it a safe tool for in vivo brain imaging and detailed studies of mitochondrial responses. In 3D cultured cells, Cy5-PEG4 captures dynamic changes in mitochondrial distribution and morphology as cell structures mature, highlighting its potential in neurobiological research, diagnostics, and therapeutic development. These findings support Cy5-PEG4 as a powerful tool for studying disease progression, identifying early biomarkers, and evaluating therapeutic strategies in neurodegenerative disorders and COVID-19.

neuroscience↗

bioRxiv2024

Increased regional P2X7R expression detected by GSK1482160 PET in a tauopathy mouse model

Neuroinflammation plays an important role in Alzheimers disease and primary tauopathies. The aim of the current study was to map [18F]GSK1482160 for imaging of purinergic P2X7R in Alzheimers disease and primary tauopathy mouse models. MicroPET was performed using [18F]GSK1482160 in widely used mouse models of Alzheimers disease (APP/PS1, 5xFAD and 3xTg), 4-repeat tauopathy (rTg4510) mice and age-matched wild-type mice. Increased uptake of [18F]GSK1482160 was observed in the cortex and basal forebrain of 7-month-old rTg4510 mice compared to age-matched wild-type mice and compared to 3-month-old rTg4510 mice. Nonparametric Spearmans rank analysis revealed a positive correlation between tau [18F]APN-1607 uptake and [18F]GSK1482160 in the hippocampus of rTg4510 mice. No significant differences in the uptake of [18F]GSK1482160 were observed between wild-type mice and APP/PS1 mice (5, 10 months), 5xFAD mice (3, 7 months) or 3xTg mice (10 months). Immunofluorescence staining further indicated the distribution of P2X7Rs in the brains of 7-month-old rTg4510 mice with accumulation of tau inclusion compared to wild-type mice. These findings provide in vivo imaging evidence for increased P2X7R in the brains of tauopathy model mice.

neuroscience↗

bioRxiv2023

A Novel Fluorogenic Spin Probe for Real-time Monitoring of Mitochondrial Reactive Oxygen Species (mROS) Generation in an in vitro Stroke Model

The extent of oxidative damage caused by a stroke can be assessed by monitoring mitochondrial reactive oxygen species (mROS), which can further aid in early diagnosis and evaluation of treatment efficacy. Mitochondrial ROS have been identified as a potential biomarker for stroke, as they are known to cause oxidative stress and mitochondrial dysfunction in brain tissue. However, monitoring reversible mROS levels has been challenging due to the lack of appropriate probes. In this study, we developed a fluorogenic spin probe, Mito-RT-ROS, based on the rhodamine skeleton, which demonstrated good sensitivity for reversible monitoring of mROS in a physiological environment such as starvation and recovery. We also evaluated the probes efficacy in an in vitro stroke model for real-time tracking of mROS generation in a pathological setting.

neuroscience↗

bioRxiv2023

Targeting and Imaging Mitochondria with a Novel Cyanine-based Fluorescent Dye and Its Application to Whole Brain Imaging

In vivo, brain imaging poses several challenges due to the complexity of brain tissue and the requirements for effective and safe imaging. In this manuscript, we reported on developing a new fluorescent dye, Cy5-PEG2, that can selectively accumulate in mitochondria, allowing us to visualize these organelles in different cell lines. Its versatility makes it broadly applicable in various experimental conditions, including monitoring mitochondrial dynamics in living cells. Moreover, we demonstrated that the Cy5-PEG2 dye could penetrate the blood-brain barrier (BBB), making it a promising tool for in vivo brain imaging. We further examined the response of glial cells in the hippocampus and neocortex regions of the brain through biomarkers GFAP and Iba1 but found no significant increase in their expression levels. This indicates that Cy5-PEG2 dye had no noticeable adverse effects on the brains immune response or neuronal health. We anticipate such a mitochondria-targeting fluorescent dye can be used to facilitate the study of mitochondrial dynamics and function in the context of whole-brain physiology and disease progression. Further research into the safety and efficacy of this dye may be necessary.

neuroscience↗

bioRxiv2023

Design, Synthesis, and Biological Evaluation of Novel Mitochondria-targeting Exosomes

Mitochondrial dysfunction is implicated in both brain tumors and neurodegenerative diseases, leading to various cellular abnormalities that can promote tumor growth and resistance to thera-pies, as well as impaired energy production and compromised neuronal function. Developing targeted therapies aimed at restoring mitochondrial function and improving overall cellular health could potentially be a promising approach to treating these conditions. Brain-derived exosomes (BR-EVs) have emerged as potential drug delivery vessels for neurological conditions. Herein, we report a new method for creating mitochondria-targeting exosomes and test its application in vitro and in vivo.

neuroscience↗

bioRxiv2022

Induction of Autophagy Prevents Mutant SOD1G93A Related Neurotoxicity in Experimental Models of Amyotrophic Lateral Sclerosis (ALS)

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder resulting from the progressive loss of both upper and lower motor neurons in the cerebral cortex, brainstem, and spinal cord. Currently, there are only two drugs, Riluzole (Rilutek) and Edaravone (Radicava), approved by FDA for ALS treatment. These two drugs are very expensive with only a few months of life extension. So far, there is no cure for ALS. Aberrant protein aggregation in motor neurons is an intracellular hallmark of ALS. The disturbance in protein homeostasis may contribute to the onset and progression of ALS. Autophagy plays an important role in degrading misfolded proteins, thereby preventing their aggregation. Pharmacological manipulation of autophagy has been proposed as a new therapeutic approach for treating ALS. IADB, a novel indole alkaloid derivative, has been reported to exert mitochondrial protection and cardioprotection through its autophagy-modulating potential. Our present study attempted to examine whether IADB has therapeutic potential in SOD1G93A-associated experimental models of ALS. We found that IADB could promote the clearance of SOD1G93A aggregates and reduce the overproduction of mitochondrial reactive oxygen species (mtROS) in motor neuron-like NSC-34 cells transfected with SOD1G93A. We further examined the IADB in a SOD1-G93A mouse model of ALS. Administration of IADB started at the age of 55 days until the end stage of the disease. IADB treatment significantly increased LC3-II levels and decreased human SOD1 levels and p62 expression in the spinal cords of SOD1G93A mice, suggesting that IADB treatment could induce autophagy activation and promote clearance of mutant SOD1 aggregates in this mouse model of ALS. Moreover, IADB treatment could alleviate the activation of microglia and astrocytes and reduce mitochondrial oxidative damage in the spinal cord of SOD1G93A mice. Finally, we demonstrated that IADB treatment could improve motor performance and delay the onset and progression of the disease in a mouse model of ALS. The neuroprotective effects of IADB may mainly originate from its autophagy-promoting property.

neuroscience↗

bioRxiv2022

Plasma proteomic biomarkers identify non-responders and reveal biological insights about the tumor microenvironment in melanoma patients after PD1 blockade

Most patients treated with immune checkpoint blockade (ICB) do not have durable treatment responses. Therefore, there is a critical need to identify early non-invasive biomarkers of response. We performed plasma proteomic analysis (>700 proteins) at three timepoints on 174 metastatic melanoma patients treated with ICB. We leverage independent training and testing cohorts to build a predictor of immunotherapy response that outperforms several tissue-based approaches. We found 217 differentially expressed proteins between ICB responders (R) and non-responders (NR), including a co-regulated module of proteins enriched in certain NR patients. By analyzing single-cell RNA-sequencing data of tumor biopsies from 32 patients, we dissected the relative contribution of cells in the tumor to proteins in circulation. The majority of proteins in the co-regulated NR module derived from tumor and myeloid cells. Amongst myeloid cells, we identified a subset of tumor-associated macrophages (TAMs) with a suppressive phenotype that expressed high levels of the co-regulated NR module, thus suggesting they are key drivers of non-response signatures. Together, our data demonstrates the utility of plasma proteomics in biomarker discovery and in understanding the biology of host response to tumors.

cancer biology↗

bioRxiv2021

Nephronectin-Integrin α8 signaling is required for proper migration of periocular neural crest cells during chick corneal development

During development, cells aggregate at tissue boundaries to form normal tissue architecture of organs. However, how cells are segregated into tissue precursors remains largely unknown. Cornea development is a perfect example of this process whereby neural crest cells aggregate in the periocular region prior to their migration and differentiation into corneal cells. Our recent RNA-Seq analysis identified upregulation of Nephronectin (Npnt) transcripts during early stages of corneal development where its function has not been investigated. We found that Npnt mRNA and protein are expressed by various ocular tissues including the migratory periocular neural crest (pNC), which also express the integrin alpha 8 (Itg8) receptor. Knockdown of either Npnt or Itg8 attenuated cornea development, whereas overexpression of Npnt resulted in cornea thickening. Moreover, overexpression of Npnt variants lacking RGD binding sites did not affect corneal thickness. Neither the knockdown or augmentation of Npnt caused significant changes in cell proliferation, suggesting that Npnt directs pNC migration into the cornea. In vitro analyses showed that Npnt promotes pNC migration from explanted periocular mesenchyme, which requires Itg8. Combined, these findings show that Npnt specifies and tunes cell migration into the presumptive cornea ECM by providing a substrate for Itg8-positive pNC cells.

developmental biology↗

bioRxiv2020

Genetic composition and evolution of the prevalent Mycobacterium tuberculosis lineages 2 and 4 in the Chinese and Zhejiang Province populations

The causative agent of tuberculosis (TB) comprises seven human-adapted lineages. Human movements and host genetics are crucial to TB dissemination. We analyzed whole-genome sequencing data for a countrywide collection of 1154 isolates and a provincial collection of 1296 isolates, constructed the best-scoring maximum likelihood phylogenetic tree, conducted Bayesian evolutionary analysis to compute the most recent common ancestors of lineages 2 and 4, and assessed the antigenic diversity in human T cell epitopes by calculating pairwise dN/dS ratios. Of the 1296 Zhejiang isolates, 964 (74.38%) belonged to lineage 2 and 332 (25.62%) belonged to lineage 4. L2.2 is the most ancient sub-lineage in Zhejiang, first appearing approximately 6897 years ago (95% HDI: 6513-7298). L4.4 is the most modern sub-lineage, first appearing approximately 2217 years ago (95% HDI: 1864-2581). The dN/dS ratios revealed that the epitope and non-epitope regions of lineage 2 strains were significantly (P<0.001) more conserved than those of lineage 4. An increase in the frequency of lineage 4 may reflect its successful transmission over the last 20 years. The recent common ancestors and transmission routes of the sub-lineages are related to the entry of humans into China and Zhejiang Province.

molecular biology↗