Biology subjects

Wu, J.

Publications and source records attributed to Wu, J..

At least 271 records · Page 15Linked to original sources

bioRxiv2025

C-reactive protein and the menstrual cycle in females with sickle cell disease

There are notable sex disparities in the frequency and severity of vaso-occlusive pain episodes (VOEs) in sickle cell disease (SCD), with females experiencing more frequent and severe episodes during the reproductive years. Many individuals report a temporal link between VOEs and the menstrual cycle, suggesting that sex hormones may play a role in modulating inflammation and pain. This study explores the relationship between inflammatory markers and the menstrual cycle in females with SCD. Plasma samples from 13 female and 18 male individuals with confirmed SCD were analyzed for C-reactive protein (CRP) and other inflammatory biomarkers. In female patients, sex hormones were measured to determine the menstrual cycle phase. While no overall difference in CRP levels was observed between males and females, CRP levels fluctuated significantly across the menstrual cycle in females, with higher levels in the follicular phase compared to the luteal phase. Additionally, platelet counts were significantly elevated in females during the follicular phase compared to males. These findings suggest that cyclic inflammation may contribute to the increased frequency and severity of VOEs in females, particularly during the perimenstrual period. Further research is needed to explore whether hormonal interventions can reduce perimenstrual VOEs in SCD.

immunology↗

bioRxiv2025

Pluripotent stem cell-derived NK progenitor cell therapy prevents tumour occurrence and eradicates minimal residual disease

The lack of persistence and short-term efficacy presents a major challenge for CAR-NK cell therapy. Here, we addressed this issue by developing pluripotent stem cell-derived NK lineage-committed progenitor (iNKP) cell therapy. For the first time, we generated abundant iNKP cells via an organoid culture system. The iNKP cells, engineered to express CXCR4 and chimeric antigen receptors (CAR), efficiently migrated to the bone marrow and generated CAR-iNK cells persisting in peripheral blood (PB) for over 80 days. Notably, CAR-iNKP cell therapy durably protected animals from tumour occurrence. Furthermore, a single low-dose infusion of CAR-iNKP cells following conventional chemotherapy eradicated minimal residual disease (MRD), leading to long-term complete remission. Our findings present a novel strategy to overcome the limitations of traditional CAR-NK cell therapy and offer dural breakthroughs for the prevention of tumour occurrence and relapse.

cancer biology↗

bioRxiv2025

The miR156/SPL9 interaction mode regulates the anthocyanin accumulation in potato

Anthocyanins are an essential class of flavonoids that represent a large group of plant secondary metabolites. microRNAs (miRNAs) can target TFs related to anthocyanin synthesis and inhibit their expression, thereby affecting the expression level of key downstream structural genes and ultimately regulating the synthesis and accumulation of anthocyanins in plants. Nevertheless, the regulatory function of miR156a in anthocyanin synthesis, especially in potatoes, has yet to be investigated. In this study, the miR156a and its target gene StSPL9 were screened and analyzed from small RNA sequencing, degradome sequencing and transient expression assay. The function of miR156a in anthocyanin synthesis of potato tuber was investigated. Overexpression of miR156a (OE-miR156a) in potato tubers promoted anthocyanin synthesis while concurrently reducing flavonoid synthesis compared with wild-type (WT) potatoes. The miR156a-silenced tubers (STTM-miR156a) achieved using short tandem target mimics (STTM) contained significantly lower anthocyanin content and increased flavonoid accumulation compared to WT and OE-miR156a. Notably, overexpression of StSPL9 in potato yielded identical results. The relative expression levels of the anthocyanin-related structural genes PAL, 4CL, CHS, CHI, F3H, DFR, and UFGT in STTM-miR156a transgenic potato tubers showed the opposite trend to that observed in OE-miR156a potato tubers, as demonstrated by RNA sequencing and quantitative real-time PCR (qRT-PCR). The integrated analysis of the transcriptome and metabolome revealed that the accumulation of flavonoids and flavonols in STTM-miR156a was significantly increased than in the wild type, whereas the contents of anthocyanins and phenolic acids were notably reduced. Further analysis showed that the expression of CHS, FG2, BEATH, and CYP75A were up-regulated in STTM-miR156a, and HCT was downregulated, which resulted in a reduced accumulation of methyl 4-caffeoylquinate, a phenolic acid metabolite. Therefore, it is demonstrated that miR156a indirectly modulates the expression of CHS, BEATH, CYP75A, HCT, and FG2 by targeting and degrading its target gene StSPL9 and other SPL genes, thus influencing anthocyanin accumulation in potato tuber. This study provides valuable insights into the complex regulatory network governing anthocyanin biosynthesis in Solanum species.

molecular biology↗

bioRxiv2025

Improved Identification of Host Cell Proteins in Monoclonal Antibodies by Combining Filter Aided Sample Preparation and Native Digestion

Host cell proteins (HCPs) in biotherapeutics can present potential safety risks or compromise product stability at trace levels. Therefore, removal, testing, and characterization of HCPs are critical throughout biotherapeutic process development. While enzyme-linked immunosorbent assay (ELISA) is the gold standard for quantifying HCPs, it does not provide information on HCP identity. As a result, HCP analysis by liquid chromatography-mass spectrometry (LC-MS) has gained prominence for its ability to identifying HCPs. However, compared to ELISAs parts-per-billion sensitivity, LC-MS is limited by its dynamic range, often unable to cover magnitude difference between HCP and biotherapeutic concentrations. Thus, an effective HCP enrichment method is highly desirable. In this study, we propose a new strategy for HCP identification that combines filter-aided sample preparation (FASP) with native digestion, followed by shotgun proteomics analysis. This approach improves mAb removal compared to standard native digestion, enabling greater HCP enrichment and identification. Our method detects all spiked proteins at 1 ppm and most at 0.5 ppm, ranging from 12 to 470 kDa, demonstrating broad molecular weight coverage of HCPs. A proof-of-concept analysis using the NISTmAb standard demonstrates that our filter-aided native digestion identifies 155 more HCPs than the standard native digestion. When applying this strategy to an in-house antibody with low amounts of HCPs, we can quantify HCPs at levels as low as 0.03 ppm, demonstrating the high sensitivity in HCP characterization.

biochemistry↗

bioRxiv2025

ORP2 regulates free cholesterol accumulation in hepatocytes during MASH

BackgroundCholesterol crystals in hepatocytes are known to strongly associate with human Metabolic Dysfunction-Associated Steatohepatitis (MASH). However, it remains unclear which molecular pathway(s) regulates free cholesterol accumulation, and therefore the formation of cholesterol crystals in hepatocytes. In cultured cell lines, oxysterol-binding protein-related protein 2 (ORP2) functions to deliver cholesterol to the plasma membrane from internal organelles. MethodsHere, we generated liver-specific ORP2 knockout (ORP2-LKO) mice and characterized their metabolic phenotypes on chow and high fat diet. ResultsThe ORP2-LKO mice developed much more severe hepatic steatosis than wild type mice after high-fat diet feeding. They also demonstrated more severe liver inflammation and damage. Notably, free but not esterified cholesterol, as well as cholesterol crystals accumulated in ORP2-LKO liver. The expression of Cyp7a1 was significantly upregulated in ORP2-LKO liver, accompanied with accumulation of taurocholic acid. Our results thus unveil an important in vivo function of ORP2 in preventing free cholesterol from accumulating in mouse liver. Conclusionsour results suggest that impaired cholesterol trafficking may enhance the deposition of cholesterol crystals in hepatocytes, promoting the development of MASH.

cell biology↗

bioRxiv2025

Cortical responses to conflicting binocular stimuli in mouse primary visual cortex

Binocular vision requires that the brain integrate input from both eyes to form a unified percept. Small interocular differences support depth perception (stereopsis), while larger disparities can cause diplopia or binocular rivalry. The neural mechanisms by which early visual circuits process concordant versus conflicting binocular signals remain incompletely understood, particularly in the case of large disparities. Here, we used visually evoked potential (VEP) recordings, unit recordings, and 2-photon calcium imaging in the binocular region of mouse primary visual cortex (bV1) to examine how distinct forms of binocular disparity engage local circuits. Using a dichoptic display, we found that interocular phase disparities reduced VEP magnitude through decreased neuronal firing early in the response (40-80 ms after stimulus onset). In contrast, orientation disparities also decreased VEP magnitude, but via increased firing later in the response (100-200 ms). This late activity was enhanced in both regular-spiking (putative excitatory) and fast-spiking (putative parvalbumin-positive inhibitory) units. In contrast, calcium imaging revealed that somatostatin-positive interneurons were suppressed during orientation conflict. These findings suggest that phase differences suppress bV1 responses via feedforward mechanisms, while orientation disparities prolong activity through disinhibition mediated by somatostatin-positive interneurons. Our results identify distinct circuit pathways recruited by different forms of binocular conflict, clarify how early visual cortex contributes to binocular integration, and provide a foundation for investigating perceptual suppression and rivalry. IMPACT STATEMENTDistinct forms of binocular conflict engage separate circuit mechanisms in mouse primary visual cortex, revealing how interocular disparities shape population activity through feedforward and disinhibitory processes.

neuroscience↗

bioRxiv2024

Noninvasively real-time monitoring in-vivo immune cell and tumor cell interaction by NIR-II nanosensor

Immunocytotherapy holds significant promise as a novel cancer treatment, but its effectiveness is often hindered by delayed responses, requiring evaluations every two to three weeks based on current diagnostic methods. Early assessment of immune cell-tumor cell interactions could provide more timely insights into therapeutic efficacy, enabling adjustments to treatment plans. In this study, we report a noninvasive nanosensor (C8R-DSNP) for real-time monitoring of in vivo immune cell activities in the second near-infrared long-wavelength (NIR-II-L) window (1500-1900 nm), which offers deep tissue transparency. The C8R-DSNP responds rapidly to caspase-8, a key apoptotic signaling molecule generated during interactions between natural killer (NK-92) immune cells and tumor cells. Using ratiometric NIR-II-L fluorescence imaging, we captured dynamic in vivo observations of NK-92 cell engagement with tumor cells in a mouse model. These results demonstrated cancer cell apoptosis that happens as early as 4.5 hours after NK-92 cell infusion. Additionally, in vitro urine imaging confirmed the initiation of apoptosis via cleaved fluorescent small molecules, while single-cell tracking within blood vessels and tumors further elucidated immune cell dynamics. This real-time NIR-II-L monitoring approach offers valuable insights for optimizing immunocytotherapy strategies.

bioengineering↗

bioRxiv2024

AMPK acts to remove immune barriers to CD8+ T cell-mediated immunity against hepatocellular carcinoma

Dysregulated metabolism in tumor tissues, and para-tumor tissues alike, can lead to immunosuppression, which may underlie cancer development. However, metabolic intervention as a therapeutic strategy has been of no avail. In this study, we explored the anti-cancer therapeutic effect of aldometanib that specifically targets lysosome-associated aldolase to mimic glucose starvation and thereby activates the lysosomal AMP-activated protein kinase (AMPK), a master regulator of metabolic homeostasis. We show that aldometanib inhibits the growth of HCC in an AMPK-dependent manner, allowing hepatoma-bearing mice to survive to mature ages, although aldometanib does not possess cytotoxicity towards HCC or normal cells. Intriguingly, aldometanib exerts anti-cancer effects only in immune-competent host mice, but not in immune-defective mice. We have further found that the HCC tissues in aldometanib-treated mice are massively infiltrated with CD8+ T cells, which is not seen in mice with liver-specific knockout of AMPK. Our findings thus suggest that the metabolic regulator AMPK rebalances the tumor microenvironment to allow the cytotoxic immune cells inside the body to eliminate cancer cells and effectively contain the tumor tissues. The finding that metabolic intervention can make cancer a life-long manageable disease, may potentially usher in a new era of cancer therapy.

immunology↗

bioRxiv2024

Orthogonal RNA-regulated destabilization domains for three-color RNA imaging with minimal RNA perturbation

RNA-regulated destabilization domain allows live-cell imaging of single RNA. However, this method is limited to single-color RNA imaging and its long RNA tag induces destabilization of the tagged RNA. Here, we describe two orthogonal RNA-regulated destabilization domains that enable three-color mRNA imaging in living mammalian cells. One of these destabilizations can be combined with a short RNA tag (9XMS2) for single-molecule RNA imaging without perturbation of RNA stability.

bioengineering↗

bioRxiv2024

The Impact of Memory and Stress on Choice Consistency

Choice consistency is a fundamental aspect of rational decision-making, reflecting the stability and reliability of an individuals preferences. However, real-world decision-making often deviates from this ideal, as individuals frequently make irrational or inconsistent choices in value-based decision-making. This study combined computational modeling, neuroimaging, and behavioral assessments to elucidate the mechanisms by which stress and memory affect choice consistency. Remembered items exhibited higher choice consistency compared to forgotten items. Computational modeling further indicated that the drift rate was higher, and the decision threshold lower, for remembered food items compared to forgotten ones. Stress was found to impair both choice consistency and memory retrieval, with stress-induced declines in memory accuracy positively correlating with reductions in choice reaction times. Activation of the dorsolateral prefrontal cortex (DLPFC) during the pre-choice anticipation period was positively associated with choice consistency. Similarly, activation of the orbitofrontal cortex (OFC) during the memory retrieval of food stimuli correlated with improved memory accuracy. These findings suggest that stress may impair choice consistency by disrupting memory retrieval processes. Overall, our study provides novel insights into the role of stress and memory in decision-making, offering a more nuanced understanding of the neural and cognitive processes that govern choice behavior.

neuroscience↗

bioRxiv2024

Plant-induced transcriptional plasticity diverges between generalist and specialist herbivores

Most herbivores are specialized on particular host plants but some are generalists that can exploit distinct hosts. Generalists may have evolved adaptive transcriptional plasticity to cope with the defenses of the different hosts. However, the fundamental differences in plant-induced transcriptional plasticity between generalists and specialists remain poorly understood. Here, we investigated transcriptional plasticity of the generalist aphid Myzus persicae and two specialist aphids, Brevicoryne brassicae and Rhopalosiphum padi, by transferring them between Brassica napus (a host for B. brassicae but not for R. padi) and Zea mays (a host for R. padi but not for B. brassicae), both suitable hosts for M. persicae. Generalist and specialist aphids exhibited transcriptional plasticity coordinately in response to different plant species, but their gene expression patterns often diverged. Generalists suppressed plant-defense salicylic acid (SA) signaling in the host plants, while specialist aphids provoked it in nonhost plants. SA signaling had limited effects on gene expression in the generalist aphids, but significantly shaped transcriptional responses of the specialists. These findings underscore the fundamental differences in plant-induced transcriptional plasticity between generalists and specialists and highlight the critical role of plasticity directionality in insect adaptation. Significance statementMost insects specialize in feeding on just a few specific plants, but some generalists can thrive on many plant species. This study compares the gene expression of green peach aphid Myzus persicae, a generalist, with two specialist aphids in response to different types of plants. Generalists showed adaptive plasticity in their gene responses, while specialists often exhibited opposite gene expression changes. Interestingly, generalists appeared to suppress plant defense signals like salicylic acid, while specialists tended to trigger them. These findings highlight how gene expression plasticity enables generalists to adapt and survive, providing new insights into the evolution of insect-plant interactions.

plant biology↗

bioRxiv2024

HCN1 channels in GABAergic amygdalar neurons underpin male-biased aggressive behaviors

Aggression behaviors typically vary between sexes, but the molecular mechanisms driving these disparities in neural coding are unclear. We found that aggression selectively activates GABAergic neurons in the posterior substantia innominata (pSI), an extend amygdala region critical for aggressive behaviors in both sexes of mice, with males exhibiting higher neuronal activity during the attack. Utilizing single-nucleus RNA sequencing, we characterized the diverse molecular landscape of pSI neurons, revealing significant differences in ion channels and hormone regulator genes that may underpin sex-specific aggression. Male GABAergic pSI neurons exhibited remarkable hyperexcitability due to increased Ih currents. Strikingly, modulating HCN1 expression not only adjusted this hyperexcitability but also influenced sexual dimorphism in aggression: silencing HCN1 in the GABAergic pSI neurons reduced male aggression, while its overexpression markedly heightened aggression in females. Furthermore, testosterone was shown to intensify aggression by upregulating HCN1 and remodeling pSI circuits. These findings provide detailed sex-specific molecular mechanisms underlying social behaviors.

neuroscience↗

bioRxiv2024

Structural and functional interrelationship of histone H2A and its variants H2A.Z and H2A.W in Arabidopsis

Multiple histone H2A variants are known in eukaryotes. However, the functional relationship between H2A and its variants in plants remains largely obscure. Using CRISPR/Cas9 editing, we generated a mutant lacking four H2A isoforms in Arabidopsis and analyzed the functional and structural relationship between H2A and its variants H2A.Z and H2A.W. RNA-sequencing and phenotype analyses revealed mild changes in gene transcription and plant development in the mutants lacking H2A, H2A.Z, or H2A.W compared with the wild-type plants. Chromatin immunoprecipitation sequencing analysis showed that H2A is able to substitute for both H2A.Z and H2A.W across the genome, including in euchromatin and heterochromatin regions. However, H2A.Z replaced both H2A and H2A.W primarily within the euchromatin regions. By using DNA and histones derived from Arabidopsis, we constructed nucleosomes containing H2A, H2A.Z, or H2A.W and resolved their cryogenic electron microscopy structures at near-atomic resolution. Collectively, the results reveal the structural similarity and functional redundancy of H2A and H2A variants in Arabidopsis.

plant biology↗

bioRxiv2024

Multi-omics analysis of the mechanism of alfalfa and wheat-induced rumen flatulence in Xizang sheep

This study induced a rumen flatulence model in Xizang sheep using alfalfa (HRF) and wheat grass (MRF) to explore related mechanisms. The pH of HRF and MRF groups was lower than the natural grass group. SCFA concentrations varied in different groups. Microbial analysis showed HRF and MRF groups had lower alpha and beta diversity and different compositions. Transcriptome analysis found different numbers of differentially expressed genes in each group. Spearmans correlation analysis indicated Butyrivibrio was related to GLRX and DUOX2, and Quinella to several genes.

microbiology↗

bioRxiv2024

D-glucuronyl C5-epimerase binds to EGFR to suppress kidney fibrosis

Renal tubular cells may actively participate in fibrosis processes leading to end-stage renal failure. However, which molecule play pivotal role in the fibrogenesis is still vague. Glucuronyl C5-epimerase (Hsepi, gene name, Glce) is a key enzyme that catalyzes biosynthesis of Heparan sulfate (HS) chains attached to HS proteoglycan which are ubiquitously located on cell membrane. Homozygous Glce-/- mice may cause embryonic lethality and multi-organ defects. However, whether Glce plays a key role in kidney fibrosis is unknown. Here, we show that Glce expression is significant attenuated in kidneys of patients with renal fibrosis and the animal models. Further study shows that renal tubular-specific Glce deletion in mice exacerbate kidney fibrosis while AAV-mediated overexpressing of Glce in UUO-treated mice may ameliorate kidney fibrosis associated with epithelial-mesenchymal transition (EMT) progress via the TGF-{beta}/Smad2/3 signaling pathway. Mechanism study demonstrates that Glce protein may bind to EGFR to inactivate EGFR/ERK signaling and further impede TGF-{beta}/Smad-driven EMT and renal fibrosis in Glce-/- and the wild type mice. Interestingly, the anti-fibrosis function is independent of Glce enzymatic activation. These data uncover a novel function for Glce which plays a key role in kidney tissues against fibrosis.

pathology↗

bioRxiv2024

UniSPAC: A Unified Segmentation Framework for Proofreading and Annotation in Connectomics

Reconstructing dense neuronal connections from volume electron microscopy (vEM) images is a critical challenge in neuroscience, driving the development of various automatic neuron segmentation methods1. Although current state-of-the-art automated segmentation methods can achieve high segmentation accuracy, they still require substantial manual proofreading and rely heavily on labeled datasets, which are often scarce, particularly for non-model organisms. Here, we introduce a Unified Segmentation framework for Proofreading and Annotation in Connectomics (UniSPAC) by providing the interactive segmentation model in 2D-level and the neuron tracing model in 3D-level. UniSPAC-2D allows users to correct its segmentation errors through point-based prompts, combining segmentation and proofreading in a single framework. UniSPAC-3D automatically traces neurons segmented by UniSPAC-2D across image slices, significantly reducing human involvement. Furthermore, UniSPAC-2D and UniSPAC-3D models can facilitate the semi-automatic generation of labeled data for new species, eliminating the need for external annotation tools. The fresh annotated data generated during proofreading in turn optimizes the interactive model through an online learning strategy, reducing the labeling effort for novel species over time. UniSPAC outperforms the start-of-the-art Segment Anything Model (SAM) in Drosophila segmentation, achieving 47x higher efficiency, and surpasses ACRLSD in cross-species segmentation on zebra finch data.

neuroscience↗

bioRxiv2024

Ascitic fluid protects against ferroptosis and enables the peritoneal spread of ovarian cancer

One of the most common sites of metastasis in ovarian cancer (OVCA) is the peritoneum. Often, this spread is accompanied by the accumulation of a fluid called ascites in the peritoneal cavity. Despite its common occurrence in metastatic OVCA patients, ascites and its influence on the peritoneal spread of OVCA are poorly understood. Interestingly, OVCA cells are vulnerable to ferroptosis, a type of cell death caused by lipid peroxidation. Hence, how these ferroptosis-sensitive OVCA cells persist in their spread to the peritoneum remains unknown. Here, we show that ascites robustly protects OVCA cells and patient-derived organoids against ferroptosis and enhances the peritoneal spread of OVCA cells in mice. Mechanistically, ascites downregulates the mitochondrial enzyme, 3-hydroxy-3-methylglutaryl-CoA synthase 2 (HMGCS2), which contributes to an increase in lipid droplets. Additionally, upon ferroptosis induction, ascites represses the upregulation of the transferrin receptor, TFRC, thereby decreasing cellular labile iron levels. Furthermore, we show that lipid-lowering fibrates reverse cellular changes induced by ascites, and they attenuate the peritoneal spread of OVCA cells in mice. Our findings implicate the importance of ascites in ferroptosis protection and the peritoneal spread of OVCA, and they suggest that targeting the ferroptosis protection by ascites may present a novel therapeutic approach to limit OVCA metastasis.

cancer biology↗

bioRxiv2024

Three STEPs forward: A trio of unexpected structures of PTPN5

Protein tyrosine phosphatases (PTPs) play pivotal roles in myriad cellular processes by counteracting protein tyrosine kinases. Striatal-enriched protein tyrosine phosphatase (STEP, PTPN5) regulates synaptic function and neuronal plasticity in the brain and is a therapeutic target for several neurological disorders. Here, we present three new crystal structures of STEP, each with unexpected features. These include high-resolution conformational heterogeneity at multiple sites, and a highly coordinated citrate molecule in the active site, a previously unseen conformational change at an allosteric site, an intramolecular disulfide bond that was characterized biochemically but had never been visualized structurally, and two serendipitous covalent ligand binding events at surface-exposed cysteines that are nearly or entirely unique to STEP among human PTPs. Together, our results offer new views of the conformational landscape of STEP that may inform structure-based design of allosteric small molecules to specifically inhibit this biomedically important enzyme.

biophysics↗