Biology subjects

Chen, N.

Publications and source records attributed to Chen, N..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

RIF1 orchestrates a multi-step restoration of post-replicative H3K9me3

DNA replication causes the dilution of parental histones along with their specific post-translational modifications. The kinetics of restoring these marks on newly incorporated histones dictate how quickly genomic domains regain their epigenetic identity after replication. H3K9me3 is restored extremely slowly; the process of reconstitution, to achieve the pre-replication levels, continues throughout the following G1 phase. The molecular mechanisms behind this slow reconstitution are unknown. We show here that RIF1s reassociation with heterochromatin during mitotic exit is required to set up a chromatin environment permissive for histone methyltransferases to resume H3K9me3 deposition. RIF1 facilitates the recruitment of SUV39H1, HP1 and HP1{beta} and is required for the increased tri-methylation of H3K9 that occurs during G1 phase. RIF1 is also indispensable for recruiting Protein Phosphatase 1 (PP1) to heterochromatin, and the interaction between RIF1 and PP1 is essential for the maintenance of H3K9me3 levels. In addition, RIF1-PP1 complex temporally restrains the activity of Aurora kinase at heterochromatin, ensuring that phosphorylation of H3S10 does not precede replication. This creates a time- window permissive for SUV39Hs to initiate the reinstatement of H3K9me3.

cell biology↗

bioRxiv2025

Targeting PI3K Signaling for Broad Inhibition of β-Coronavirus Infection

The phosphatidylinositol 3-kinase (PI3K) signaling pathway plays a central role in regulating key cellular processes such as survival, metabolism, and immune responses. Aberrant activation of this pathway is associated with tumorigenesis, and several PI3K inhibitors have been developed as anticancer agents. Emerging evidence suggests that viruses, including {beta}-coronaviruses, have evolved mechanisms to exploit host PI3K signaling for their replication and immune evasion. In this study, we evaluated the antiviral efficacy of a panel of PI3K inhibitors against {beta}-coronaviruses, including mouse hepatitis virus (MHV), human OC43 (HuCoV-OC43) and four major SARS-CoV-2 variants using both cell line and organoid models. Our findings reveal that these compounds exhibit low micromolar potency in inhibiting viral replication. Notably, the inhibitor C20 (PWT33597) demonstrated broad-spectrum activity against multiple {beta}-coronaviruses, including SARS-CoV-2, MHV, and HuCoV-OC43, in conventional cell lines as well as in air-liquid interface (ALI)-cultured, differentiated primary human nasal and bronchial epithelial cells. Given that cytokine storm is a major contributor to SARS-CoV-2-related multiorgan failure and mortality, we further explored the impact of PI3K inhibition on host inflammatory responses. We found that MHV infection markedly increased cytokine expression in 17CL-1 fibroblasts and RAW264.7 macrophages. Interestingly, treatment with C20 further amplified cytokine production in this context, suggesting complex immunomodulatory effects that warrant further investigation. Together, our findings support the therapeutic potential of repurposing PI3K inhibitors as broad-spectrum antivirals. These compounds not only suppress viral replication but may also influence host immune responses, providing a promising avenue for intervention against current and emerging coronavirus threats.

microbiology↗

bioRxiv2025

Q1020R in the spike proteins of MERS-CoV from Arabian camels and recent human cases confers resistance against soluble human DPP4

The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is a pre-pandemic coronavirus that is transmitted from camels, the natural reservoir, to humans and can cause severe disease. MERS cases have been documented in Arabia but not Africa, although the virus is circulating in both Arabian and African camels. Further, evidence has been provided that viruses in African camels might have a reduced capacity to cause disease. However, the underlying determinants are incompletely understood. Here, employing pseudotyped particles as model systems for MERS-CoV entry into cells, we compared cell entry of viruses from African and Arabian camels and its inhibition. We show that viruses found in Arabian camels and recent human cases are less susceptible to inhibition by human soluble DPP4 (sDPP4) than viruses from African camels, although both enter human cells efficiently and are comparably sensitive to inhibition by IFITM proteins and neutralizing antibodies. Furthermore, relative resistance to soluble DPP4 was linked to mutation Q1020R, present in the spike proteins of recent Arabian but not African viruses. These results support the concept that soluble DPP4 might constitute a natural barrier against human infection that is more efficiently overcome by viruses currently circulating in Arabian camels than those in African camels. IMPORTANCEMERS-CoV is an emerging virus that can cause severe lung disease, MERS, and is transmitted from camels to humans. Although MERS-CoV infects camels in both Africa and Arabia, MERS cases have only been documented in Arabia for reasons that remain incompletely understood. Here, we provide evidence that viruses recently circulating in Arabian camels and causing human infections are less susceptible to inhibition by human sDPP4 - a secreted version of the viral receptor that is present in various bodily fluids. Furthermore, we link sDPP4 resistance to mutation Q1020R in the spike protein of these viruses. These results suggest that viruses currently circulating in Arabian camels are better equipped to overcome a natural barrier to infection, sDPP4, than those circulating in African camels.

microbiology↗

bioRxiv2025

Spatial and temporal scale-dependent feedbacks govern dynamics of biocrusts in drylands

Biota could be ecosystem engineers in generating an intrinsic heterogeneous landscape through scale-dependent feedbacks. Thereby, they can form resource enriched patchiness or islands of fertility, comprising of self-organizing spatial patterns. Research so far has largely focused on the self-organized spatial patterns of plant communities in drylands. It, however, remains unclear whether and how biocrusts having distinct morphology and life history from plant communities could self-organize themselves and form unique spatial patterns. Here we conducted field observations of biocrusts across successional stages and employed a probabilistic Cellular Automaton (CA) model to investigate the distinct self-organized spatial patterns exhibited by mosaic patches of mosses and lichens with different patch size distributions (PSDs). Our study demonstrates that short-range positive feedbacks initially promote the development of patches, featured with a heavy-tailed PSD, while long-range negative feedbacks subsequently curtail further expansion of big patches, thereby establishing a characteristic patch scale with regular PSDs. Strikingly, only lichens reverted back to the heavy-tailed PSD in the late succession stage, presumably implying self-organized critical fragmentation of lichen patches. Field measurements of biocrust performance at the center and edge of patches of varying sizes along succession stages further support the classic scale-dependent feedback mechanism for Turing pattern formation. Collectively, our results clearly demonstrate the capability of the biocrust communities to self-organize themselves to form distinct spatial patterns governed by the spatial and temporal scale-dependent feedbacks, potentially impacting dryland ecosystem functions and resilience. Significance StatementAn intriguing phenomenon is the capability of biota to form striking self-organized spatial patterns. Biocrusts serve as the soils skin and have different morphology and life history as compared to plant communities. We investigated these distinct self-organized spatial patterns exhibited by mosaic patches of mosses and lichens across succession stages through field surveys and a probabilistic Cellular Automaton (CA) model. Our results provide empirical evidence that biocrusts act as ecosystem engineers, forming self-organized spatial patterns. Simulations and field measurements of biocrust performance elucidate the mechanism of spatial and temporal scale-dependent feedbacks in governing biocrust spatial pattern formation. This self-organizing ability of biocrusts holds significant implications for ecosystem functions and the resilience of dryland ecosystems.

ecology↗

bioRxiv2025

Contrastive Learning-Enhanced Drug Metabolite Prediction Drives the Discovery of an Orally Bioavailable RSK4 Inhibitor for Esophageal Cancer

Drug metabolism liabilities are a major bottleneck in drug development, necessitating accurate metabolite prediction tools. While AI-driven methods have advanced, challenges remain in achieving high-precision, robustness, broad reaction coverage and seamless integration into the drug development workflow. To address this, we first constructed the most comprehensive human-specific drug metabolism database to date, encompassing 11,665 human metabolic reactions and 2,497 high-quality rules. Leveraging this resource, we developed ConMeter (Contrastive learning and feature interaction based Metabolic Reaction prediction), a novel model integrating chemical feature interaction and contrastive learning. ConMeter demonstrates significant improvements, achieving [~]80% accuracy in identifying at least one metabolite within the top 5 predictions and showing an average 25% relative enhancement in ranking true positives compared to state-of-the-art methods. The comprehensive database also expands the range of predictable metabolic reactions. To demonstrate the utility of ConMeter, we integrated it into a metabolite prediction-guided drug design strategy aimed at addressing the low oral bioavailability of a metabolically vulnerable RSK4 lead compound -- a pervasive issue among known RSK inhibitors. This strategy successfully yielded R636, a novel RSK4 inhibitor exhibiting remarkably improved bioavailability (a 63-fold increase, reaching 63% absolute bioavailability) while maintaining its potent activity. Notably, R636 showed favorable safety profile and significant anti-tumor efficacy against esophageal squamous cell carcinoma (ESCC) in vitro and in two distinct patient-derived xenograft (PDX) mouse models. This work introduces ConMeter as a powerful and practical tool for high-accuracy metabolite prediction, demonstrating its potential to accelerate lead optimization, exemplified by the discovery of R636 as a promising orally bioavailable candidate for ESCC.

cancer biology↗

bioRxiv2025

Electroacupuncture promotes post-stroke motor recovery through miR-124-3p-mediated regulation of NRG1/ErbB4 signaling pathway

ObjectiveElectroacupuncture has demonstrated beneficial effects in post-stroke motor dysfunction, yet the molecular mechanisms underlying its therapeutic efficacy remain incompletely understood. This study aims to investigate whether electroacupuncture promotes post-stroke motor function recovery by modulating the interaction between miR-124-3p and the NRG1/ErbB4 signaling pathway, specifically exploring whether miR-124-3p directly targets NRG1 to regulate neural plasticity in a focal cerebral ischemia rat model. MethodsThe ischemic stroke model was established by middle cerebral artery occlusion/reperfusion (MCAO/R) in adult rats. These rats were randomly divided into sham, model, electroacupuncture and model plus miR-124-3p inhibitor groups. The model group, electroacupuncture group and model plus miR-124-3p inhibitor group received EA intervention 24 h after modelling for 7 consecutive days. Behavioural function was assessed by Zea Longa score and mechanical pain rating. Hippocampal damage was detected by HE staining and neuronal apoptosis was observed by TUNEL staining. IL-1{beta} and IL-18 levels were measured by ELISA. PCR and Western blotting were used to detect the expression of miR-124-3p and inflammatory pathway proteins. The interaction between miR-124-3p and TLR4 was verified by dual-luciferase reporter assay. ResultsElectroacupuncture improved motor function in rat model of MCAO/R, as evidenced by improved Zea Longa scores and decreased mechanical withdrawal thresholds. Electroacupuncture significantly attenuated neuronal damage and also inhibited the inflammatory response by decreasing IL-18 and IL-1{beta} levels (P < 0.001). Notably, electroacupuncture upregulated miR-124-3p expression (P < 0.0001) and activated the NRG1/ErbB4 signaling pathway in the hippocampus. When miR-124-3p was inhibited, NRG1 protein expression decreased while GABA expression tended to increase. Dual-luciferase reporter assays confirmed that miR-124-3p directly targets the 3UTR of NRG1 mRNA and regulates its expression at the translational level. These findings suggest that electroacupuncture may alleviate neuronal and axonal damage by modulating miR-124-3p/NRG1/ErbB4 signalling and regulating GABA release. ConclusionElectroacupuncture can ameliorate motor dysfunction induced after brain I/R injury by targeting and modulating the NRG1-ErbB4 signaling pathway via miR-124-3p. These data are expected to provide new insights into the mechanisms of electroacupuncture for the prevention of potential targets for the recovery of motor dysfunction after stroke.

animal behavior and cognition↗

bioRxiv2025

The Rationalization of Carbon Monoxide and Hemoglobin Association

Carbon monoxide is a colorless, odorless, and poisonous gas, responsible for approximately 100,000 emergency room visits and over 420 deaths in the U.S. each year. Both carbon monoxide and oxygen bind to the ferrous ions in hemoglobin, but carbon monoxide has a significantly higher affinity. Extensive research has been conducted on the interaction between carbon monoxide and hemoglobin. However, a straightforward and practically applicable equation describing the relationship between carbon monoxide saturation and pressure is not found in the existing literature. In this paper, we establish an equation and confirm that the plot of CO saturation against CO pressure follows a hyperbolic shape, characterized by a continuous decrease in slope. In contrast, the oxygen-hemoglobin association curve is sigmoidal. These distinct curve shapes have different physiological implications. Our equation enables the determination of one variable--either saturation or pressure--if the other is known. Further analysis reveals the distribution of all five species of carboxyhemoglobin, showing that the triply bound form is abundant--a notable contrast to the distribution of oxyhemoglobin species. Additionally, our equation confirms that carbon monoxides affinity for hemoglobin is approximately 230 times higher than that of oxygen. Lastly, we propose a new general equation that may generate all carbon monoxide-hemoglobin association curves under various oxygen pressures. New and NoteworthyIn this paper, we introduce the first known set of equations that model the Carbon Monoxide Hemoglobin association curve and the Carbon Monoxide Hemoglobin Fractional association curves. These novel equations represent a noteworthy advancement in the ability to quantitatively model CO binding to hemoglobin. We present the methodology utilized that explains the derivation of precise coefficients for these equations, along with the data points used to calculate the coefficients. Unlike existing models, our equations allow the direct computation of the CO saturation from the CO association equation and the CO fraction association equations from the partial pressure of carbon monoxide. This approach simplifies the mathematical modeling process while preserving a high degree of biological significance. Furthermore, the equations are built upon a complex and precise methodological foundation, enabling a deeper understanding of the binding behavior of hemoglobin in response to varying CO levels. This quantitative model has the potential to be applied to clinical practices in medicine. It provides insight into the complex relationship between CO and hemoglobin that is critical to many biological processes.

physiology↗

bioRxiv2025

Structure of the conjugation surface exclusion protein TraT

Conjugal transfer of plasmids between bacteria is a major route for the spread of antimicrobial resistance. Many conjugative plasmids encode exclusion systems that inhibit redundant conjugation. In incompatibility group F (IncF) plasmids surface exclusion is mediated by the outer membrane protein TraT. Here we report the cryoEM structure of the TraT exclusion protein complex from the canonical F plasmid of Escherichia coli. TraT is a hollow homodecamer shaped like a chefs hat. In contrast to most outer membrane proteins, TraT spans the outer membrane using transmembrane helices. We use a novel microscopy-based conjugation assay to probe the effects of directed mutagenesis on TraT. Our analysis provides no support for the idea that TraT has specific interactions with partner proteins. Instead, we infer that TraT is most likely to function by physical interference with conjugation.

microbiology↗

bioRxiv2025

Integrated Classification of Cortical Cells and Quantitative Projectomic Mapping Unveil Organizational Principles of Brain-Wide Connectomes at Single Cell Level

Molecularly defined cortical cell types have recently been linked to whole neuronal morphology (WNM), particularly those characterized by whole-brain-wide projections, such as intratelencephalic (IT), extratelencephalic (ET), and corticothalamic (CT) neurons. In contrast, classical morphological classifications (e.g., tufted TPC, small tufted SPC, and stellate SSC) are based primarily on local dendrosomatic and axonal structures, especially apical dendrites. This study bridges these perspectives by establishing a new neuronal taxonomy, analyzing the connectomes of defined cortical cell types, and comparing them with those obtained from bulk anterograde injections. Neurons were sparsely labeled via tamoxifen-inducible Cre lines with GFP reporters, and 1,419 WNM cells were comprehensively reconstructed with Vaa3D-TeraVR from [~]15 areas across six functional regions of molecularly labeled brains imaged with 2p-fMOST. These cells were newly classified by integrating current molecular-WNM and classical morphological perspectives, with sample size augmented by 1,455 publicly available WNM cells reconstructed from the Mouse-Light project and CEBSIT. This effort defined ten combined molecular-WNM-classical morphological cell types: L5ET_TPC, L6CT_NPC, L6b_HPC, and seven IT types--L2/3IT_TPC, L4IT_SSC, L4IT_UPC, L4IT_TPC, L5IT_SPC, L6IT_IPC, and L6IT_car3PC. Clustering, quantitative analyses and random Forest classifier objectively validated these types and revealed their distinct connectomes, along with convergent, topographic, and hierarchical organizations across their projection brain regions. At the single-cell level, multiple organizational principles governing cortico-cortical (C-C) and cortico-subcortical (C-subC) connectomes emerged with unprecedented detail, offering a precise GPS-like tool for in vivo recordings and robust datasets for neuronal network modeling. Comparisons with bulk anterograde injection data underscored the limitations of traditional methods in identifying projection targets. Overall, our approach provides significant insights into cortical circuitry and elucidates the complex interplay between neuronal molecular identity, whole morphology, and classical morphological classification.

neuroscience↗

bioRxiv2025

PRRSV evades innate immune cGAS-STING antiviral function via its Nsp5 to deter STING translocation and activation

Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) is an important pathogen that seriously endangers pig breeding, causing significant economic losses to the global swine industry. Our previous study found that the DNA sensing innate cGAS-STING signaling pathway plays an important role in inducing interferon (IFN) upon PRRSV infection and inhibition of PRRSV replication. However, the immune evasion and its mechanism by PRRSV is still unclear. In current study, we found that PRRSV Non-structural protein 5 (Nsp5) strongly inhibits the cGAS-STING-IFN antiviral response. Further, we found that Nsp5 interacts with STING, blocking STING transport from ER to Golgi apparatus and interfering with STING recruitment of TBK1/IKK{varepsilon}/IRF3. Finally, we demonstrated that the Nsp5 36-47 and 58-67 amino acid regions are critical regions for inhibiting STING activity and PRRSV replication. The study describes a novel mechanism by PRRSV for suppression of the host innate antiviral response and have implications for our understanding of PRRSV pathogenesis. Author summaryThe innate immune system is the first line of host defense against infections. PRRSV is an immunosuppressive pathogen that has developed different strategies to evade the host innate immune responses. Here, we demonstrate for the first time that PRRSV utilizes its non-structural protein Nsp5 to inhibit the innate immune cGAS-STING-IFN signaling pathway, promoting the viral replication. Nsp5 can inhibit the cGAS-STING pathway by interacting with STING, blocking STING transport from ER to Golgi apparatus and interfering with STING recruitment of TBK1/IKK{varepsilon}/IRF3. In particular, the 36-47 and 58-67 amino acid regions of the Nsp5 is indispensable. This information will help us understand PRRSV-host interactions and provides new insights into the prevention and control of PRRSV.

immunology↗

bioRxiv2025

Kidney cortex macrophages prevent the formation of mineral stones by reabsorbing phosphate from the urine

Resident macrophages are important in maintaining tissue homeostasis by meeting specialized physiological demands and mitigating the unique stresses each tissue endures. In the kidney, urine is formed in a process of glomerular filtration and tubular reabsorption. Supersaturation of mineral solutes such as calcium phosphate poses a persistent challenge to the kidney; if left unchecked, kidneys stones form, which will cause tubular obstruction and even kidney failure. However, cellular mechanisms of preventing kidney stone formation remain incompletely understood. In this study, we found that resident macrophages in kidney cortex distinguishably expressed phosphate transporter SLC34A1. These cells extend transtubular protrusions and were capable of reabsorbing phosphate from the urine through the SLC34A1, a function previously only attributed to tubular epithelial cells. Depletion of Slc34a1 from kidney cortex macrophages led to increased urinary phosphate excretion, disrupting body phosphorus balance. More importantly, loss of macrophage-mediated phosphate reabsorption from the urine resulted in a drastic over-deposition of calcium phosphate microcrystals in kidney tubules, particularly in the late proximal tubules of inner cortex where intratubular calcium concentration is high. This also accelerated mineral stone formation. Exposure to mineral crystals stimulated cortex macrophages to upregulate SLC34A1 expression, a response mechanistically driven by lysosomal disruption. As such, cortex macrophages employed phosphate reabsorption as a proactive strategy to prevent mineral stone formation.

immunology↗

bioRxiv2025

Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants

Structural variants (SVs) are widespread in vertebrate genomes, yet their evolutionary dynamics remain poorly understood. Using 45 long-read de novo genome assemblies and pangenome tools, we analyze SVs within three closely related species of North American jays (Aphelocoma, scrub-jays) displaying a 60-fold range in effective population size. We find rapid evolution of genome architecture, including [~]100 Mb variation in genome size driven by dynamic satellite landscapes with unexpectedly long (> 10 kb) repeat units and widespread variation in gene content, influencing gene expression. SVs exhibit slightly deleterious dynamics modulated by variant length and population size, with strong evidence of adaptive fixation only in large populations. Our results demonstrate how population size shapes the distribution of SVs and the importance of pangenomes to characterizing genomic diversity.

evolutionary biology↗

bioRxiv2024

Base-modified nucleotides mediate immune signaling in bacteria

Signaling from pathogen sensing to effector activation is a fundamental principle of cellular immunity. While cyclic (oligo)nucleotides have emerged as key signaling molecules, the existence of other messengers remains largely unexplored. Here, we reveal a bacterial anti-phage system that mediates immune signaling through nucleobase modification. Immunity is triggered by phage nucleotide kinases, which, combined with the system-encoded adenosine deaminase, produce deoxyinosine 5-triphosphate (dITP) as immune messengers. The dITP signal activates downstream effector to mediate cellular NAD+ depletion, resulting in population-level defense through the death of infected cells. To counteract immune signaling, phages deploy specialized enzymes that deplete cellular dAMP, the precursor of dITP messengers. Our findings uncover a nucleobase modification-based anti-phage signaling pathway, establishing noncanonical nucleotides as a new type of immune messengers in bacteria.

microbiology↗

bioRxiv2024

Substrate Stiffness Dictates Unique Doxorubicin-induced Senescence-associated Secretory Phenotypes and Transcriptomic Signatures in Human Pulmonary Fibroblasts

Cells are subjected to dynamic mechanical environments which impart forces and induce cellular responses. In age-related conditions like pulmonary fibrosis, there is both an increase in tissue stiffness and an accumulation of senescent cells. While senescent cells produce a senescence-associated secretory phenotype (SASP), the impact of physical stimuli on both cellular senescence and the SASP is not well understood. Here, we show that mechanical tension, modeled using cell culture substrate rigidity, influences senescent cell markers like SA-{beta}-gal and secretory phenotypes. Comparing human primary pulmonary fibroblasts (IMR-90) cultured on physiological (2 kPa), fibrotic (50 kPa), and plastic (approximately 3 GPa) substrates, followed by senescence induction using doxorubicin, we identified unique high-stiffness-driven secretory protein profiles using mass spectrometry and transcriptomic signatures, both showing an enrichment in collagen proteins. Consistently, clusters of p21+ cells are seen in fibrotic regions of bleomycin induced pulmonary fibrosis in mice. Computational meta-analysis of single-cell RNA sequencing datasets from human interstitial lung disease confirmed these stiffness SASP genes are highly expressed in disease fibroblasts and strongly correlate with mechanotransduction and senescence-related pathways. Thus, mechanical forces shape cell senescence and their secretory phenotypes.

cell biology↗

bioRxiv2024

Whole-genome sequencing across space and time reveals impact of population decline and reduced gene flow in Florida Scrub-Jays

Whole-genome sequence data is proving to be highly informative about the past demography of free-living populations, and in the context of endangered species, it can provide a quantification of the genetic risk posed by reduced genetic diversity and inbreeding. Prior to 1920, the Florida scrub-jay (Aphelocoma coerulescens) had been widespread across Florida, but with the expansion of agriculture and human habitation, its population has declined by 95%, resulting in fragmentation into semi-isolated subpopulations. By sequencing 241 individuals sampled from five different regions and across two time points, this study quantifies a greater magnitude of loss of genetic diversity and greater levels of inbreeding in smaller and more isolated subpopulations. Consistent with population genetics theory, reduction in population size results in a dramatic loss of rare alleles, skewing the site frequency spectrum far from the expected equilibrium. Increased inbreeding in the smaller, more remote subpopulations is especially evident in the increased size and number of runs of homozygosity. The Florida scrub-jay displays limited dispersal, and habitat fragmentation has greatly reduced the magnitude of gene flow in the past 30 years, resulting in further decline of genetic diversity, especially in the peripheral populations. Analysis of these data is informative in guiding conservation efforts to retain genetic diversity and minimize the consequences of inbreeding in the Florida scrub-jay. HighlightsO_LIFive regional populations show distinct degrees of population isolation and decline. C_LIO_LIThere has been commensurate loss of genetic diversity, skewed site frequency spectra, reduced migration, and increased inbreeding (FROH). C_LIO_LIAs many state-wide populations decline, the smaller, more remote populations provide a glimpse into the future and a testbed for remediation approaches. C_LI

genomics↗

bioRxiv2024

Revolutionizing large-scale DNA synthesis with microchip-based massive in parallel synthesis system

DNA synthesis serves as the fundamental enabling technology of engineering biology, aiming to provide DNA molecules of designed composition, length, and complexity at scale and low cost. Current high-throughput DNA synthesis technologies rely on intricate chip manufacturing and microfluidic systems to provide large-scale synthetic oligonucleotides, at the expense of low concentration and limited compatibility in the processing of longer DNA constructs assembly. Here, we report a microchip-based massive in parallel synthesis (mMPS), pioneering an "identification-sorting-synthesis-recycling" iteration mechanism to microchips for high throughput DNA synthesis. In comparison to microarray-based methods, we demonstrate that our method can increase the DNA product concentration by 4 magnitudes (to picomole-scale per sequence) and greatly simplifies the downstream processes for large-scale gene synthesis construction. By the construction of 1.97 million-diversity variant libraries that cover 1,254 human protein domains, we demonstrated the uniformity of the constructed variant libraries using mMPS-derived oligos is greatly improved, with amino acid distribution highly consistent as designed. In addition, by synthesizing 285 1kb-to-3kb genes with varying degrees of sequence complexity from previously reported strains A501 and 3DAC, potential ancestor of early archaea and bacteria, our result shows that the overall gene assembly success rate using mMPS-derived oligos is increased by 10-fold in comparison to other methods. Our mMPS technology holds the potential to close the gap between the quality and cost of writing DNA in increasing demand across many sectors of research and industrial activities.

synthetic biology↗

bioRxiv2024

Tumor-specific antibodies elicited by engineered bacteria promote bladder cancer immunotherapy

The intratumoral microbiome has recently emerged as a new hallmark of cancer, with implications for response or resistance to therapy. While bacteria can either promote or inhibit cancer growth, intratumoral bacteria can also be engineered using synthetic biology to remodel the tumor microenvironment. Here, we engineered the probiotic bacterium E. coli Nissle 1917 (EcN) to express the human chemokine CXCL13, a critical component of germinal center (GC) formation. The GC reaction is a fundamental aspect of adaptive immunity by which antibody affinity develops in secondary lymphoid organs for defense against pathogens. Using orthotopic models of bladder cancer, engineered CXCL13-expressing EcN colonized bladder tumors and elicited GC responses in bladder tumor-draining lymph nodes after intravesical delivery. Furthermore, when combined with PD-1 blockade, engineered EcN amplified the antitumor antibody response and promoted long-term survival and protective immunity upon tumor rechallenge. Thus, we demonstrate that synthetically engineered CXCL13-expressing EcN can enhance the efficacy of PD-1 checkpoint blockade immunotherapy by amplifying tumor-specific humoral immunity.

immunology↗

bioRxiv2024

Cell type-specific driver lines targeting the Drosophila central complex and their use to investigate neuropeptide expression and sleep regulation

The central complex (CX) plays a key role in many higher-order functions of the insect brain including navigation and activity regulation. Genetic tools for manipulating individual cell types, and knowledge of what neurotransmitters and neuromodulators they express, will be required to gain mechanistic understanding of how these functions are implemented. We generated and characterized split-GAL4 driver lines that express in individual or small subsets of about half of CX cell types. We surveyed neuropeptide and neuropeptide receptor expression in the central brain using fluorescent in situ hybridization. About half of the neuropeptides we examined were expressed in only a few cells, while the rest were expressed in dozens to hundreds of cells. Neuropeptide receptors were expressed more broadly and at lower levels. Using our GAL4 drivers to mark individual cell types, we found that 51 of the 85 CX cell types we examined expressed at least one neuropeptide and 21 expressed multiple neuropeptides. Surprisingly, all co-expressed a small neurotransmitter. Finally, we used our driver lines to identify CX cell types whose activation a)ects sleep, and identified other central brain cell types that link the circadian clock to the CX. The well-characterized genetic tools and information on neuropeptide and neurotransmitter expression we provide should enhance studies of the CX.

neuroscience↗