Biology subjects

Zhang, L.

Publications and source records attributed to Zhang, L..

At least 721 records · Page 40Linked to original sources

bioRxiv2023

Harnessing light-activated gallium porphyrins to combat intracellular Staphylococcus aureus in dermatitis: Insights from a simplified model.

Staphylococcus aureus can survive inside nonprofessional phagocytes such as keratinocytes, demonstrating a novel strategy for evading antibiotic pressure. When antibiotic treatment ends, reinfection with staphylococci begins from the intracellular inoculum. This phenomenon is responsible for recurrent infections. The development of new antibacterial methods that can eliminate intracellular bacteria, including those with a multidrug-resistant phenotype, is necessary. In this study, we characterized and used a model of keratinocytes (both wild type and mutants with reduced filaggrin expression) infected with methicillin-resistant S. aureus (MRSA) to verify the possibility of using light-activated compounds, exemplified here by heme-mimetic gallium (III) porphyrin (Ga3+CHP) and visible light, an approach known as antimicrobial photodynamic inactivation (aPDI), to eliminate intracellular MRSA. We observed that Ga3+CHP accumulated more in infected cells than in uninfected cells. Moreover, Ga3+CHP accumulated in cells that harbored intracellular S. aureus. Using flow cytometry and fluorescence microscopy, we found that intracellular MRSA and Ga3+CHP mainly colocalized in lysosomal structures, and we showed that under the influence of aPDI, MRSA exhibited reduced adhesion to host cells and a significantly reduced (by 70%) GFP signal originating from intracellular bacteria. Moreover, the use of light-activated Ga3+CHP resulted in a significant reduction in the number of extracellular bacteria in the infection system, lowering the potential for further infection of host cells. For the first time, we used the infectious model to analyze the toxicity of aPDI in real time, showing that this approach is not significantly cyto-or phototoxic. Author SummaryStaphylococcus aureus is a highly virulent pathogen that is responsible for approximately 80% of all skin infections. During antibiotic treatment, one of the defense mechanisms of S. aureus is the invasion of keratinocytes. Intracellular bacteria are not accessible to antibiotics, which poorly penetrate the interior of host cells. Consequently, such bacteria contribute to recurrent infections. In our study, we proposed using a combination of a light-activated porphyrin compound loaded with gallium ions, Ga3+CHP, and visible light as a strategy to eliminate intracellular staphylococci. We demonstrated that the tested compound colocalized with the pathogen in the infected cells, which was an essential condition for the effective elimination of intracellular bacteria. We showed that the proposed approach effectively reduced the infection of keratinocytes with methicillin-resistant S. aureus (MRSA), as well as its adhesion to host cells, while maintaining host cells. The results presented here provide a basis for developing an effective therapy against staphylococci.

microbiology↗

bioRxiv2023

Divergence in herbivore resistance during the invasion of a global plant invader

O_LISuccessful plant invasions are often explained with adaptation to novel environments. However, invasive species often occupy broad niches within their native and introduced ranges, and a true understanding of microevolution during invasion therefore requires broad sampling of ranges, ideally with a knowledge of introduction history. C_LIO_LIWe tested for genetic differentiation in herbivore resistance among 128 introduced (Europe, North America) and native (China, Japan) populations of the invasive Japanese knotweed (Reynoutria japonica) in two common gardens in the native range. C_LIO_LIIn both common gardens we found that resistance traits of introduced populations differed from most Chinese native populations, but not from populations in Japan, the putative sources of introduction. Compared to Chinese populations, introduced European populations had thicker leaves with a lower C:N ratio but higher flavonoids contents. In the native range, variation in herbivore resistance was much more strongly associated with climate of origin than in introduced populations. C_LIO_LIOur results support the idea that founder effects played a key role in the invasion of knotweed into Europe and North America, with introduction of particular resistance phenotypes from Japan. Our study also demonstrates how knowledge of introduction history can avoid drawing wrong conclusions from observed biogeographic divergence. C_LI

ecology↗

bioRxiv2023

Single cell discovery of m6A RNA modifications in the hippocampus

N6-methyladenosine (m6A) is a prevalent and highly regulated RNA modification essential for RNA metabolism and normal brain function. It is particularly important in the hippocampus, where m6A is implicated in neurogenesis and learning. Although extensively studied, its presence in specific cell types remain poorly understood. We investigated m6A in the hippocampus at the single cell level, revealing a comprehensive landscape of m6A modifications within individual cells. Our data also identifies transcripts which have high m6A density and are associated with brain diseases. Our data suggests that m6A containing transcripts might be of particular importance for Camk2a neurons. Overall, this work provides new insights into the molecular mechanisms underlying hippocampal physiology and lays the foundation for future studies investigating the dynamic nature of m6A RNA methylation in the healthy and diseased brain.

neuroscience↗

bioRxiv2023

Differential developmental blueprints of organ-intrinsic nervous systems

The organ-intrinsic nervous system is a major interface between visceral organs and the brain, mediating important sensory and regulatory functions in the body-brain axis and serving as critical local processors for organ homeostasis. Molecularly, anatomically, and functionally, organ-intrinsic neurons are highly specialized for their host organs. However, the underlying mechanism that drives this specialization is largely unknown. Here, we describe the differential strategies utilized to achieve organ-specific organization between the enteric nervous system (ENS)1 and the intrinsic cardiac nervous system (ICNS)2, a neuronal network essential for heart performance but poorly characterized. Integrating high-resolution whole-embryo imaging, single-cell genomics, spatial transcriptomics, proteomics, and bioinformatics, we uncover that unlike the ENS which is highly mobile and colonizes the entire gastrointestinal (GI) tract, the ICNS uses a rich set of extracellular matrix (ECM) genes that match with surrounding heart cells and an intermediate dedicated neuronal progenitor state to stabilize itself for a beads-on-the-necklace organization on heart atria. While ICNS- and ENS-precursors are genetically similar, their differentiation paths are influenced by their host-organs, leading to distinct mature neuron types. Co-culturing ENS-precursors with heart cells shifts their identity towards the ICNS and induces the expression of heart-matching ECM genes. Our cross-organ study thus reveals fundamental principles for the maturation and specialization of organ-intrinsic neurons.

neuroscience↗

bioRxiv2023

Proximity labeling reveals dynamic changes in the SQSTM1 protein network

Sequestosome1 (SQSTM1) is an autophagy receptor that mediates degradation of intracellular cargo, including protein aggregates, through multiple protein interactions. These interactions form the SQSTM1 protein network, and these interactions are mediated by SQSTM1 functional interaction domains, which include LIR, PB1, UBA and KIR. Technological advances in cell biology continue to expand our knowledge of the SQSTM1 protein network and of the relationship of the actions of the SQSTM1 protein network in cellular physiology and disease states. Here we apply proximity profile labeling to investigate the SQSTM1 protein interaction network by fusing TurboID with the human protein SQSTM1 (TurboID::SQSTM1). This chimeric protein displayed well-established SQSTM1 features including production of SQSTM1 intracellular bodies, binding to known SQSTM1 interacting partners, and capture of novel SQSTM1 protein interactors. Strikingly, aggregated tau protein altered the protein interaction network of SQSTM1 to include many stress-associated proteins. We demonstrate the importance of the PB1 and/or UBA domains for binding network members, including the K18 domain of tau. Overall, our work reveals the dynamic landscape of the SQSTM1 protein network and offers a resource to study SQSTM1 function in cellular physiology and disease state.

cell biology↗

bioRxiv2023

Molecular Characterization of the Sea Lamprey Retina Illuminates the Evolutionary Origin of Retinal Cell Types

The lamprey, a primitive jawless vertebrate whose ancestors diverged from all other vertebrates over 500 million years ago, offers a unique window into the primordial formation of the retina. Using single-cell RNA-sequencing, we characterized retinal cell types in lamprey and compared their molecular differentiation and regulatory networks with those in mouse and other jawed vertebrates. Our analysis revealed six cell classes and 74 distinct cell types. We discovered multiple conserved cell types shared between jawless and jawed lineages, including notably rods and cones, ON and OFF bipolar cells, and starburst amacrine cells. The conservation of these cell types indicates their emergence early in vertebrate evolution, highlighting the primal designs of retinal circuits for the rod pathway, ON-OFF discrimination, and direction selectivity. In contrast to this evidence for conservation, the pathways of diversification for amacrine cells and retinal ganglion cells appear to have distinctly diverged between the two lineages. Furthermore, we inferred master regulators in specifying retinal cell classes in both lamprey and macaque and identified common regulatory elements across species, underscoring the ancestral nature of the molecular origins governing retinal cell classes. Altogether, our characterization of the lamprey retina illuminates the evolutionary origin of visual processing in the retina.

evolutionary biology↗

bioRxiv2023

Modulating social learning-induced evaluation updating during human sleep

People often change their evaluations upon learning about their peers evaluations, i.e., social learning. Given sleeps vital role in consolidating daytime experiences, sleep may facilitate social learning and thereby further changing peoples evaluations. Combining a social learning task and the sleep-based targeted memory reactivation technique, we asked whether social learning-induced evaluation changes can be modulated during sleep. After participants indicated their initial evaluation for snacks, they learned about their peers evaluation while hearing the snacks spoken names. During the post-learning non-rapid-eye-movement sleep, we re-played half of the snack names (i.e., cued snack) to reactivate the associated peers evaluations. Upon waking up, we found that the social learning-induced evaluation changes further enlarged for both cued and uncued snacks. Examining sleep electroencephalogram (EEG) activity revealed that cue-elicited delta-theta EEG power and the overnight N2 sleep spindle density predicted post-sleep evaluation changes for cued but not for uncued snacks. Our findings suggested that sleep-mediated memory reactivation processes could strengthen social learning-induced evaluation changes.

neuroscience↗

bioRxiv2023

Vitamin D attenuates diabetic myocardial injury via the Erbb4/ferroptosis axis

BackgroundHyperglycemia and hyperlipidemia lead to the ferroptosis, well as the phosphorylation of Erbb4, and thereby increase the risk of cardiac hypertrophy. Thus, our investigation aims to explore whether vitamin D could mitigate diabetic cardiac injury through modulation of the Erbb4/ferroptosis axis. Methods and resultsKKAy mice fed on a high-fat diet were utilized to construct the prediabetic model, which showed an up-regulated phosphorylation of Erbb4, with concurrent ferroptosis in cardiac tissues. Following the intervention with vitamin D for 16 weeks, the activity of Erbb4/YAP signaling was suppressed and the severeness of ferroptosis was improved. Meanwhile disturbances in glucose-lipid metabolism and insulin secretion induced by high fat were alleviated, along with improvements in cardiac hypertrophy and myocardial function. Moreover, we established an in vitro damage model by introducing H9c2 myocardial cells to high glucose (HG, 33.3 mM) and palmitic acid (PA, 0.25 mM). Unsurprisingly, similar results have been acquired after vitamin D supplementation. Subsequently, selective inhibitors of Erbb4 (Dacomitinib) and ferroptosis (Ferrostatin-1) were applied to evaluate the efficiency of Erbb4 signaling on modulating ferroptosis in vitro, and conclusively confirming that inhibiting of Erbb4 indeed reduce ferroptosis under HG and PA stimulus. Additionally, treatment of vitamin D was found to reduce cardiomyocyte hypertrophy and prevent cell death by inhibiting Erbb4 activity. Interestingly, the combined intervention of Vitamin D and Dacomitinib exerted a synergistic effect on ameliorating the abnormal conditions. ConclusionsOur study unveils, the correlation between Erbb4 and ferroptosis in diabetic heart. Providing evidences that vitamin D supplementation can improve ferroptosis related diabetic cardiac injury through inactivation of Erbb4. Proposing that the combination treatment of vitamin D and Erbb4 inhibitors may emerge as a highly feasible clinical strategy for diabetic myocardial injury.

pharmacology and toxicology↗

bioRxiv2023

ST-GEARS: Advancing 3D Downstream Research through Accurate Spatial Information Recovery

Three-dimensional Spatial Transcriptomics has revolutionized our understanding of tissue regionalization, organogenesis, and development. However, to reconstruct single sections back to their in situ three-dimensional morphology, existing approaches either only adopt gene expression information to guide reconstruction or overlook shape correction against experiment-induced section distortions. This leads to significant discrepancies between reconstruction results and the actual in vivo locations of cells, imposing unreliable spatial profiles to downstream analysis. To address these challenges, we propose ST-GEARS (Spatial Transcriptomics GEospatial profile recovery system through AnchoRS), which solves optimized anchors between in situ closest spots utilizing expression and structural similarity across sections and recovers in vivo spatial information under the guidance of anchors. By employing innovative Distributive Constraints into the Optimization scheme, it retrieves anchors with higher precision compared to existing methods. Taking these anchors as reference points, ST-GEARS first rigidly aligns sections, then introduces and infers Elastic Fields to counteract distortions. ST-GEARS denoises the fields using context information by Gaussian Denoising. Utilizing the denoised fields, it eliminates distortions and eventually recovers original spatial profile through innovative and mathematically proved Bi-sectional Fields Application. Studying ST-GEARS on both bi-sectional registration and complete tissue reconstruction across sectional distances and sequencing platforms, we observed its outstanding performance in spatial information recovery across tissue, cell, and gene levels compared to current approaches. Through this recovery, ST-GEARS provides precise and well-explainable gears between in vivo situations and 3D in vitro analysis, powerfully fueling the potential of biological discoveries.

bioinformatics↗

bioRxiv2023

Neurogenesis and neuronal migration in hypothalamic vasopressinergic magnocellular nuclei of the adult rat

Arginine vasopressin (AVP)-magnocellular neurosecretory system (AVPMNS) in the hypothalamus plays a critical role in homeostatic regulation as well as in allostatic motivational behaviors. However, it remains unclear whether adult neurogenesis exists in the AVPMNS. By using immunoreaction against AVP, neurophysin II, glial fibrillar acidic protein (GFAP), cell division marker (Ki67), migrating neuroblast markers (doublecortin, DCX), microglial marker Iba1, and 5'-bromo-2'-deoxyuridine (BrdU), we report morphological evidence that low rate neurogenesis and migration occur in adult AVPMNS in rat hypothalamus. Tangential AVP/GFAP migration routes and AVP/DCX neuronal chains as well as ascending AVP axonal scaffolds were observed. Chronic water deprivation significantly increased the BrdU+ nuclei within both the SON and PVN. These findings raise new questions about AVPMNSs potential hormonal role for brain physiological adaptation across the lifespan, with possible involvement in coping with homeostatic adversities.

neuroscience↗

bioRxiv2023

Evolutionary and Developmental Specialization of Foveal Cell Types in the Marmoset

In primates, high-acuity vision is mediated by the fovea, a small specialized central region of the retina. The fovea, unique to the anthropoid lineage among mammals, undergoes notable neuronal morphological changes during postnatal maturation. However, the extent of cellular similarity across anthropoid foveas and the molecular underpinnings of foveal maturation remain unclear. Here, we used high throughput single cell RNA sequencing to profile retinal cells of the common marmoset (Callithrix jacchus), an early divergent in anthropoid evolution from humans, apes, and macaques. We generated atlases of the marmoset fovea and peripheral retina for both neonates and adults. Our comparative analysis revealed that marmosets share almost all its foveal types with both humans and macaques, highlighting a conserved cellular structure among primate foveas. Furthermore, by tracing the developmental trajectory of cell types in the foveal and peripheral retina, we found distinct maturation paths for each. In-depth analysis of gene expression differences demonstrated that cone photoreceptors and Muller glia, among others, show the greatest molecular divergence between these two regions. Utilizing single-cell ATAC-seq and gene-regulatory network inference, we uncovered distinct transcriptional regulations differentiating foveal cones from their peripheral counterparts. Further analysis of predicted ligand-receptor interactions suggested a potential role for Muller glia in supporting the maturation of foveal cones. Together, these results provide valuable insights into foveal development, structure, and evolution. Significance statementThe sharpness of our eyesight hinges on a tiny retinal region known as the fovea. The fovea is pivotal for primate vision and is susceptible to diseases like age-related macular degeneration. We studied the fovea in the marmoset-a primate with ancient evolutionary ties. Our data illustrated the cellular and molecular composition of its fovea across different developmental ages. Our findings highlighted a profound cellular consistency among marmosets, humans, and macaques, emphasizing the value of marmosets in visual research and the study of visual diseases.

neuroscience↗

bioRxiv2023

Early-stage idiopathic pulmonary fibrosis is characterized by bronchoalveolar accumulation of SPP1+ macrophages

Patients affected by idiopathic pulmonary fibrosis (IPF), a progressive chronic and eventually fatal lung disease with unknown cause, suffer from delayed diagnosis and limited personalized treatment options due to the lack of predictive and staging relevant disease markers. Prior studies focused on the cellular and transcriptomic changes found in lung tissue during terminal IPF-associated lung fibrosis. In clinical routine, bronchoscopy is applied for diagnosis and staging of suspected IPF affected individuals, thus providing us with a clinically applicable window, to study the cellular and transcriptional changes within affected individuals at the time of diagnosis. Here we study a cohort consisting of 11 IPF affected individuals and 11 healthy controls. We investigate their single cell transcriptomic profile alongside the surface phenotype of alveolar-resident immune cells. Single cell transcriptional analysis reveals accumulation of SPP1+ macrophages (SPP1+M{varphi}) within the alveolar space during early stage diagnosed IPF, in the absence of a decline in lung function. SPP1+M{varphi} were characterized by high expression of lipid storage and handling genes, accumulation of intracellular cholesterol and expression of proinflammatory cytokine expression. In silico developmental trajectory analysis revealed that SPP1+M{varphi} are likely derived from classical monocytes. Finally, to confirm the clinical diagnostic value of SPP1+ M{varphi}, we developed a flow cytometry panel to rapidly identify and test for the presence of SPP1+ M{varphi} in bronchoalveolar lavage samples. The new panel has confirmed the increased frequency of SPP1+ M{varphi} in early-IPF in an independent validation cohort. Taken together, we show that SPP1+ M{varphi} are associated with early IPF pathogenesis in the absence of a decline in lung function, thus providing a clinically valuable markers for diagnosis of early IPF in clinical practice. HighlightsO_LIIPF patients can be stratified into early and advanced disease groups based on clinical features. C_LIO_LISingle cell transcriptomic and high dimensional flow cytometry enabled mapping of the myeloid compartment across the continuum of idiopathic pulmonary fibrosis associated disease states. C_LIO_LISPP1+M{varphi} accumulated during early clinical stage of IPF. C_LIO_LIDevelopment of a clinically applicable SPP1M{varphi} identification panel. C_LI

immunology↗

bioRxiv2023

The Arabidopsis PPR protein EMB1006 interacts with both EMB1270 and CFM2 to facilitate plastid clpP1 intron2 splicing

Plastid intron splicing is an essential step for gene expression. Although many nucleus-encoded splicing factors have been identified for plastid intron splicing, how these proteins coordinately regulate intron splicing is unclear. Here we found that EMB1006, an Arabidopsis P-type PPR protein, is required for splicing several plastid introns including clpP1 intron 2 by analyzing the level of intron retention in its knockdown lines and RIP-qPCR (RNA immunoprecipitation and quantitative PCR) assay. In addition, RNA electrophoretic mobility shift assay (REMSA) showed that EMB1006 specifically binds to the sequence UUACCAAACGU close to the 3 end of clpP1 exon 2 in vitro. Furthermore, yeast two hybrid (Y2H), split luciferase complementation (Split-LUC) and semi-in vivo pull-down assays showed that EMB1006 interacts with both EMB1270 and CFM2, which also interact each other. Taken together, our data indicate that EMB1006 forms a complex with EMB1270 and CFM2 to facilitate clpP1 intron 2 splicing in chloroplasts.

plant biology↗

bioRxiv2023

Altered Orbitofrontal Cortex Activation and Gaze Patterns to Happy Faces in Autistic Children Predict Adaptive Difficulties but Challenge the Social Motivation Hypothesis

Individuals diagnosed with Autism Spectrum Disorder (ASD) generally have altered responses to social reward, which the "social motivation" hypothesis posits as the primary contributor to their social deficits. Aberrant perception of rewarding faces is considered to be one of the most significant markers of this hypothesis. The orbitofrontal cortex (OFC) plays an important role in modulating reward and arousal responses to happy faces but few studies have investigated whether young autistic children with limited cognitive or language ability have altered neural and behavioral responses to reward related tasks. We therefore conducted an eye-tracking task where autistic (n = 36) and typically developing (n = 36) young children (aged 2.5-6 years) viewed the faces of happy children or of simplified faces (emoticons), combined with OFC activation measurement using functional near infrared spectroscopy (fNIRS), to compare ASD and typically developing (TD) children. Results revealed no differences between the two groups for time spent viewing happy faces although TD children spent more time looking at the eyes of real faces and at the mouths of emoticons whereas children with ASD did not. Children with ASD showed a greater pupil diameter (PD) and OFC activation compared to TD children during presentation of happy faces. Indeed, greater PD and OFC responses were predictive of greater adaptive behavior difficulties and severity of symptoms. Our results therefore demonstrate different gaze patterns and greater arousal and brain reward system responses to happy faces in young children with ASD which are incongruent with social motivation hypothesis. Availability of dataOur ethics approval does not permit public archiving of individual anonymized raw data. Those who wish to access the raw data should contact the corresponding author. Access will be granted to named individuals who adhere to the ethical procedures governing the reuse of sensitive data. They must complete a formal data sharing agreement to obtain the data. The data that support the main group different finding figures related anonymized data of this study are openly available via the Open Science Framework (OSF) Repository https://osf.io/sxkhc/?view_only=6eb51e64a9b54fce909b5ff6eacdc668 Ethics approval statementThe study was conducted in accordance with the principles of the Declaration of Helsinki. It was approved by the Local Ethics Committee (number 202165). Research Highlights[bullet] The present study examined whether altered social reward processing in ASD is caused by reduced behavioral and neural responses to rewarding stimuli. [bullet]Typically developing children showed a preference for viewing specific informative facial features (such as child eyes or emoticon mouths), children with autism did not. [bullet]Children with autism enhanced arousal (pupil dilation) and brain reward (orbitofrontal cortex) responses to happy child faces. [bullet]Altered, gaze patterns, arousal and brain reward responses were highly predictive of adaptive behavior abilities and autistic symptom severity.

neuroscience↗

bioRxiv2023

Yeast9: A Consensus Yeast Metabolic Model Enables Quantitative Analysis of Cellular Metabolism By Incorporating Big Data

Genome-scale metabolic models (GEMs) can facilitate metabolism-focused multi-omics integrative analysis. Since Yeast8, the yeast-GEM of Saccharomyces cerevisiae, published in 2019, has been continuously updated by the community. This have increased the quality and scope of this model, culminating now in Yeast9. To evaluate its predictive performance, we generated 163 condition-specific GEMs constrained by single-cell transcriptomics from osmotic pressure or normal conditions. Comparative flux analysis showed that yeast adapting to high osmotic pressure benefits from upregulating fluxes through the central carbon metabolism. Furthermore, combining Yeast9 with proteomics revealed metabolic rewiring underlying its preference in nitrogen sources. Lastly, we created strain-specific GEMs (ssGEMs) constrained by transcriptomics for 1229 mutant strains. Well able to predict the strains growth rates, fluxomics from those large-scale ssGEMs outperformed transcriptomics in predicting functional categories for all studied genes in machine-learning models. Based on those findings we anticipate that Yeast9 will empower systems biology studies of yeast metabolism.

systems biology↗

bioRxiv2023

Strong cascading impacts of micropollutants on planktonic food web in urban river

Urban rivers rely on intricate multitrophic interactions in food webs, which are vital for ecological functions. Human-induced pollutant discharge, notably micropollutants, poses a threat to these interactions. To study the impact of micropollutants on the microbial food web, we sampled downstream areas of the Jiulong Rivers north tributary (lower urbanization, [~]25% built land) and west tributary (higher urbanization, [~]65% built land) for eleven consecutive days in both dry and wet seasons in Fujian, China. We constructed a conceptualized planktonic food web model by employing DNA metabarcoding targeting bacteria, micro-eukaryotes (algae and protozoa), and microzooplankton. Our results revealed that the more urbanized west tributary exhibited significantly higher micropollutant concentrations. Structural equation modeling (SEM) incorporating micropollutants and all food web elements indicated a significantly stronger impact of micropollutants on the planktonic food web in the west tributary than in the north tributary. Micropollutants exhibited both direct and indirect (cascade) effects on high trophic levels (protozoa and microzooplankton), with algal communities mediating the cascade effects instead of bacterial communities, likely due to the increased eutrophication in the urbanized tributary. Overall, our study underscores the potential ecological disruptions caused by micropollutants in shaping planktonic food web interactions in urban rivers. SynopsisUrban rivers face ecological threats from micropollutants. This study shows elevated micropollutants significantly affected the planktonic food webs. Algal, rather than bacterial, food web pathway mediated micropollutants cascading effects on high trophic levels, emphasizing micropollutant-induced disruptions in urban rivers.

ecology↗

bioRxiv2023

DNA origami assembled spheroid for evaluating cytotoxicity and infiltration of chimeric antigen receptor macrophage (CAR-M)

Chimeric antigen receptor (CAR) T-cell therapies have shown remarkable results in patients with hematological malignancies. However, their success in treating solid tumors has been limited. As an alternative candidate for the CAR approach, CAR-macrophages (CAR-M) have demonstrated activation and phagocytosis directed by tumor antigens, showing promise in the treatment of solid tumors. Nevertheless, the mechanisms by which CARs direct tumor chemotaxis and invasion of CAR-M remain poorly understood. In this study, we aim to investigate the role of CARs in CAR-M attachment and infiltration using 3D tumor micro-spheroids, which were created by utilizing a novel nucleic acid nanostructures decorated living cells (NACs) based origami assembly technique. First, the effectiveness of phagocytosis and killing conducted by CAR-M was validated in the conventional 2D well/plate-surface culture models. Then,peripheral blood mononuclear cell (PBMC) invasion assay confirmed that the 3D tumor micro-spheroids were feasible for cell invasion. Finally, our results demonstrated that CAR-M exhibited higher invasion and killing capacity in 3D tumor micro-spheroids. In summary, the 3D NACs-origami assembled tumor spheroid model provides a suitable platform for target screening and pharmacodynamic evaluation of CAR-M.

bioengineering↗

bioRxiv2023

CpG Island Definition and Methylation Mapping of the T2T-YAO Genome

Precisely defining and mapping all cytosine positions and their clusters, known as CpG islands (CGIs), as well as their methylation status are pivotal for genome-wide epigenetic studies, especially when population-centric reference genomes are ready for timely application. Here we first align the two high-quality reference genomes, T2T-YAO and T2T-CHM13, from different ethnic backgrounds in a base-by-base fashion and compute their genome-wide density-defined and position-defined CGIs. Second, mapping some representative genome-wide methylation data from selected organs onto the two genomes, we find that there are about 4.7-5.8% sequence divergency of variable categories depending on quality cutoffs. Genes among the divergent sequences are mostly associated with neurological functions. Moreover, CGIs associated with the divergent sequences are significantly different with respect to CpG density and observed CpG/expected CpG (O/E) ratio between the two genomes. Finally, we find that the T2T-YAO genome not only has a greater CpG site coverage than that of the T2T-CHM13 genome when whole-genome bisulfite sequencing (WGBS) data from the European and American populations are mapped to each reference, but also show more hyper-methylated CpG sites as compared to the T2T-CHM13 genome. Our study suggests that future genome-wide epigenetic studies of the Chinese populations rely on both acquisition of high-quality methylation data and subsequent precision CGI mapping based on the Chinese T2T reference.

bioinformatics↗