Biology subjects

Zeng, Y.

Publications and source records attributed to Zeng, Y..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

Quantitative phosphoproteomic analysis of testes from Iqcn-deficient mice highlights the significance of calmodulin signaling in spermiogenesis

Calmodulin (CaM) plays a crucial role in sperm function. Studies have reported that proteins containing IQ motif interact with CaM, subsequently engaging with downstream target proteins known as calmodulin-binding proteins (CaMBPs). It is reported that the loss of interaction between IQCN and CaM is mainly manifested as decreased motility, leading to fertilization failure and male infertility. However, no relevant reports have been published detailing which CaMBPs exist and the mechanisms by which they are regulated. In this study, we conducted a comprehensive quantitative proteomic and phosphoproteomic analysis of mouse testes from wild-type (WT) and Iqcn knockout (Iqcn-/-) mice. The results indicated that Iqcn deficiency substantially rewires the downstream phosphorylation signaling pathway, while not causing equivalent changes in protein levels. Among the total 577 differentially regulated phosphorylated sites in our results, most of them (494/577) belong to calmodulin-binding proteins (CaMBPs). Gene ontology analysis of these differentially phosphorylated CaMBPs showed enrichment in male gamete generation, actin cytoskeleton organization and microtubule cytoskeleton organization process, demonstrating IQCN regulates sperm function by interacting with CaM, which in turn affects the phosphorylation level of CaMBPs. Further kinase substrate network analysis revealed that most kinases with substrates phosphorylation sites up-regulated were tyrosine kinases, and the inhibition assay showed that FGFR4 and SYK tyrosine kinases are important for sperm motility and progressive motility. In summary, this study reveals the interaction between IQ motif-containing protein IQCN and CaM, which regulates the phosphorylation of downstream CaMBPs and is involved in the related processes of spermiogenesis and sperm function.

developmental biology↗

bioRxiv2025

Acute chromatin decompaction stiffens the nucleus as revealed by nanopillar-induced nuclear deformation in cells

Chromatin architecture is critical in determining nuclear mechanics. Most studies focus on the mechanical rigidity conferred by chromatin compaction from densely packed heterochromatin, but less is known on how transient changes in chromatin decompaction state impinge on nucleus stiffness. Here, we used an array of vertically aligned nanopillars to study nuclear deformability in situ after chromatin decompaction in cells. The nucleus significantly stiffened within 4 hours of chromatin decompaction but softened at longer timescales. This acute nucleus stiffening was predominantly underlied by an increase in nucleus volume, nuclear import and partially enhanced by lamin protein recruitment to the nuclear periphery. The coupling between nucleus stiffening and acute chromatin decompaction was observed in cancer cell lines with lower malignancy (e.g. MCF7, PEO1, A549) but weakened in those with higher metastatic potential (e.g. MDA-MB-231, HEYA8, HT1080), which was found to be associated with the capacity to efficiently compact heterochromatin into foci that sustains nucleus deformability required for confined migration. Our work signals how a rapid chromatin remodeling is a physiologically relevant pathway to modulate nucleus mechanics and cell migration behavior. STATEMENT OF SIGNIFICANCEMany cell processes such as wound healing, immune activation and DNA damage repair require a decompact and accessible chromatin structure. Whether such short-term remodeling of the chromatin impacts nucleus mechanics and function is poorly defined. Using nanopillars that allow interrogation of nucleus rigidity within intact cells, we showed that contrary to conventional knowledge the nucleus becomes less deformable and more rigid when chromatin is acutely decompacted due to enhanced nuclear import and swelling of the nucleus. In cancer cells, the coupling of transient chromatin decompaction to nucleus rigidity is weakened and appears to be countered by heterochromatin formation and compaction. We demonstrate here how short-term chromatin remodeling can impact nucleus and cellular properties in a time-dependent and non-genetic manner.

bioengineering↗

bioRxiv2025

Macroscopic cerebral energy efficiency corresponds to neuron reorganization in awake and anesthetized mice

Non-invasive imaging of brain function and energy supply is crucial for diagnosing and treating brain disorders. Conventional imaging struggles to capture altered relationships between energy supply and utilization caused by brain diseases. A novel method, which can be translated to human patients, is to calculate relative power (rPWR) and relative cost (rCST) to assess cerebral energy efficiency. However, whether rPWR/rCST can track individual changes and neural activity remains unproven. Our study compared these non-invasive measures with invasive two-photon microscopy in awake and anesthetized mice. We found that rPWR/rCST distributions were similar between awake mice and humans, but changed in anesthetized mice, indicating a shift in the brains economic balance. Furthermore, changes in rPWR/rCST were linked to the reorganization of microscopic neural networks, observed with two-photon microscopy. Our work highlights the potential of rPWR/rCST for medical applications, and that neural network reorganization is linked to the brains economic balance.

neuroscience↗

bioRxiv2025

Isolated Configuration: Holistic Processing Beyond the Realm of Faces

Holistic processing of visual stimuli has long been regarded as unique to faces, or otherwise extended to other object categories given sufficient expertise. We designed novel abstract stimuli that are recognizable strictly by configural information, and matched control stimuli that require the use of only featural information. We then tested four classic markers of holistic perception: inversion, misalignment, part-whole, and composite effects. We found that second-order configuration stimuli elicited robust holistic effects, while featural stimuli do not, showing that such effects emerge specifically when recognition depends on configural information, but not when it relies on featural cues. We further observed that first-order configuration stimuli were also sufficient to induce holistic effects, indicating that holistic processing can emerge from multiple levels of configural information. We also found a significant correlation between individual differences in face recognition ability and holistic processing effects with the second-order configuration stimuli, but not with the first order configuration stimuli, nor the featural stimuli. Lastly, convolutional neural networks trained on the same stimuli reproduced these patterns, strengthening the interpretation that holistic processing arises when configural information must be used to recognize a stimulus. Together, these findings demonstrate that holistic processing is fundamentally rooted in the representation of spatial configuration, with second-order relations providing the critical link to face recognition ability.

neuroscience↗

bioRxiv2025

Generalization but not strengthening of negative memories drives the development of depression-like behaviors

Individuals with depression exhibit intensified and generalized negative memories. However, how prior memories actually influence onset and/or progression of depression, particularly whether the strengthening or the generalization of prior memories play a key role, is poorly understood. Here, we introduced behavioral paradigms to differentiate between memory strengthening and generalization, and found that negative experiences that produced memory overgeneralization, but not strengthening, induced depression-like behaviors. Furthermore, we identified that the medial prefrontal cortex (mPFC) to the bed nucleus of the stria terminals (BNST) projection functionally linked memory generalization to depression, together with single-cell calcium imaging which revealed a significant overlap in the mPFCBNST neuronal ensemble encoding depression-like behaviors with that encoding generalized memory, but not memory strength. Circuit-based transcriptomic analysis and chromophore-assisted light inactivation demonstrated that triggering actin remodeling in the mPFCBNST neurons, a memory consolidation mechanism enhanced generalization while reducing memory strength, also induced depression-like behaviors. Collectively, these findings suggest generalization of negative memories as a primary factor that drives depression-like behaviors, highlighting the importance of early identification of individuals at risk for depression who exhibit overgeneralized negative memories, and targeting overgeneralized negative memories in the treatment of depression.

animal behavior and cognition↗

bioRxiv2025

Increased maize chromosome number by engineered chromosome fission

Activation of synthetic centromeres on chromosome 4 in maize leads to its breakage and formation of trisomic fragments called neochromosomes. A limitation of neochromosomes is their low and unpredictable transmission rates due to trisomy. Here we report that selecting for dicentric recombinants through male crosses uncovers stabilized chromosome 4 fission events which split it into 4a-4b complementary chromosome pairs, where 4a carries a native centromere and 4b a synthetic one. The cells rapidly stabilized chromosome ends by de novo telomere formation and the new centromeres spread among genes without altering their expression. When both 4a and 4b chromosomes were present in a homozygous state, they segregated through meiosis indistinguishably from wild-type, and gave rise to healthy plants with normal seed set. This work leverages synthetic centromeres to engineer chromosome fission, effectively raising the diploid chromosome number of maize from 20 to 22. TEASERUsing synthetic centromeres, we divide one maize chromosome into two chromosomes, and show that both chromosomes are fully functional.

synthetic biology↗

bioRxiv2024

Phages-bacteria interactions underlying the dynamics of polyhydroxyalkanoates-producing mixed microbial cultures via meta-omics study

The dynamics of the structure of polyhydroxyalkanoates-producing mixed microbial cultures (PHA-MMCs) during enrichment and maintenance is an unsolved problem. The effect of phages has been proposed as a cause of dynamic changes in community structure, but evidence is lacking. To address this question, we enriched five PHA-MMCs and sampled temporally to study the interactions between phage and prokaryotic members by combining metagenomics and metatranscriptomics. 963 metagenome-assemble genomes and 4294 phage operational taxonomic units were assembled from bulk metagenomic data. There were complex interactions between the phages in Casadabanvirus and Unclassified Hendrixvirinae and the dominant species in Azomonas, Paracoccus, Thauera and Breundimonas. The dynamic change of the structure of phage and prokaryotic communities were remarkably consistent. Further structural equation modeling analysis showed that phage communities could significantly affect the activity and community structure of prokaryotic microorganisms. In addition, seven key auxiliary metabolic genes (phaC, fadJ, acs, ackA, phbB, acdAB and fadD) in the PHA synthesis pathway were identified from phage sequences. Importantly, these auxiliary metabolic genes were expressed at the transcriptional level, indicating that they were in an active functional state. This meta-analysis provides the first catalog of phages in PHA-MMCs and the auxiliary metabolic genes they carry, as well as how they play a role in the dynamic changes of prokaryotic communities. This study provides a reference for subsequent studies on understanding and regulating the microbial community structure of artificial open microbial systems. ImportanceThe synthesis of biodegradable plastic PHA from organic waste through mixed microbial cultures (MMCs), with extremely low cost, has the potential for expanded production. However, there is a gap of understanding of the dynamics of dominant species in MMCs to better control community structure. Our results demonstrate for the first time the impact of phages on the structure of prokaryotic communities in the MMCs. There are complex interactions between the PHA producers (Azomonas, Paracoccus, Thauera) and phages (Casadabanvirus and Unclassified Hendrixvirinae). Phage communities can negatively regulate the activity and structure of prokaryotic communities. In addition, the auxiliary metabolic genes in the PHA synthesis pathways carried by phages may promote the PHA synthesis ability of prokaryotic members. This study highlights the impact of phages on prokaryotic community structure, suggesting that phages have the potential to become a tool for better controlling the microbial community structure of PHA-MMCs.

microbiology↗

bioRxiv2024

The RING-finger domain of Arabidopsis RMR functions as an E3 ligase essential for post-Golgi trafficking

Receptor-homology-transmembrane-RING-H2 (RMR) sorting receptors are essential for directing soluble cargo proteins to protein storage vacuoles in plants. These type I integral membrane proteins comprise a single transmembrane domain, an N-terminal lumenal region containing a protease-associated domain for cargo recognition, and a C-terminal cytoplasmic region (CT) with a Really-Interesting-New-Gene-H2 (RING-H2) domain. Here, we determined the crystal structure of the RING-H2 domain of Arabidopsis RMR isoform-1 (AtRMR1-RING), where the conserved C3H2C3 motif coordinates two Zn ions, a feature typical of RING-type E3 ligases. AtRMR1-RING was shown to interact with Arabidopsis E2 ubiquitin-conjugating enzyme, and exhibits E3 ligase activity in an in vitro ubiquitination assay. Biochemical analysis reveals that I234Y substitution disrupted the E2/E3 interaction and greatly reduced E3 ligase activity. Furthermore, we showed that the conserved RING-H2 domains of AtRMR isoform 2, 3 and 4 are also E3 ligases. Inactivation of E3 ligase activity by the I234Y mutation resulted in Golgi retention of AtRMR1-CT and AtRMR2. These findings suggest that the E3 ligase activity is essential for post-Golgi trafficking of RMR receptors, providing new insights into receptor-mediated protein sorting in plants.

plant biology↗

bioRxiv2024

Diverse and Location-Specific Roles of PlexinA2, PlexinA4, and NCAM in Developing Hippocampal Mossy Fibers

Mossy fibers (MFs) originate from dentate granule cells and innervate area CA3 of the hippocampus. Upon entry of CA3, MFs partition into two prominent axon bundles, the suprapyramidal tract (SPT) and infrapyramidal tract (IPT) and form lamina specific synaptic contacts in the stratum lucidum (SL) and stratum oriens (SO), respectively. Here we employed new mouse lines to dissect the function of Sema6A and its receptors, PlexinA2 (PlxnA2) and PlxnA4, in developing MFs. In Sema6a-/- mice, MF partitioning into SPT and IPT bundles is incomplete and IPT axons in the SO are overextended, while the SPT correctly innervates the SL. Loss of neuronal Sema6a results in defective MF patterning and we show that this involves Sema6A reverse signaling. Plxna4 controls MF partitioning, SPT axon bundling and laminar targeting to the SL, as well as IPT length. Many of these defects are replicated in mice deficient for PlxnA4 GAP catalytic activity, underscoring the importance of this GAP domain. MFs are tightly fasciculated in Plxna2-/- mice and fail to separate into SPT and IPT bundles, and defects are significantly reduced in PlxnA2 GAP mutants, highlighting the involvement of GAP-independent signaling events. To further explore the molecular basis of aberrant axon fasciculation, we employed anti-PlxnA2 dependent proximity biotinylation and identified several PlxnA2-associated Ig-CAM family members. We observed a genetic interaction between Plxna2 and Ncam1, but not Plxna4 and Ncam1, for SPT and IPT formation and positioning in CA3. Together, our studies provide insights into the multifaceted and overlapping, yet distinct, functions of PlxnA family members in orchestrating specific guidance decisions in developing MFs.

developmental biology↗

bioRxiv2024

Cardiac Reprogramming with Drug Resistance Alleviates Doxorubicin-induced Cardiotoxicity in Mice and Pigs

Doxorubicin (Dox)-induced cardiotoxicity represents a significant clinical adverse effect associated with cancer chemotherapy treatment. The systematic toxicity associated with the currently available drug dexrazoxane has limited its clinical utility. Inspired by cancer drug resistance mechanisms, we propose a novel strategy termed Transient overexpression of p-glycoprotein (P-gp) for Cardiac reprogramming (TopCare) to induce cardiac drug resistance as a treatment for cardiotoxicity. This approach involves reprogramming cardiomyocytes by delivering lipid nanoparticles (LNPs)-based mRNA therapeutics to induce temporary P-gp overexpression, which in turn reduces intracellular Dox levels and suppresses cytotoxic effects. Our results demonstrated that LNPs with P-gp mRNAs (P-gp LNPs) enhance P-gp expression in H9c2 cells, significantly lowering the cytotoxicity of both Dox and paclitaxel (PTX). In a mouse model with Dox-induced cardiotoxicity, it was observed that P-gp LNPs effectively promoted P-gp overexpression in cardiomyocytes, with a time-dependent decline in P-gp protein levels. This TopCare strategy resulted in improved survival rates, restored cardiac function, and reduced myocardial fibrosis and structural cardiac alterations. Furthermore, studies in large animals have shown that intrapericardial (iPC) injection of P-gp LNPs effectively mitigates adverse effects and restores cardiac function in pig models of Dox-induced cardiotoxicity. The significant cardioprotective effects achieved through cardiac drug resistance highlight the safety, efficacy, and clinical potential of the TopCare strategy for alleviating doxorubicin-induced cardiotoxicity.

bioengineering↗

bioRxiv2024

A generative artificial intelligence approach for antibiotic optimization

Antimicrobial resistance (AMR) poses a critical global health threat, underscoring the urgent need for innovative antibiotic discovery strategies. While recent advances in peptide design have yielded numerous antimicrobial agents, optimizing these molecules experimentally remains challenging due to unpredictable and resource-intensive trial-and-error approaches. Here, we introduce APEX Generative Optimization (APEXGO), a generative artificial intelligence (AI) framework that integrates a transformer-based variational autoencoder with Bayesian optimization to design and optimize antimicrobial peptides. Unlike traditional supervised learning approaches that screen fixed databases of existing molecules, APEXGO generates entirely novel peptide sequences through arbitrary modifications of template peptides, representing a paradigm shift in peptide design and antibiotic discovery. Our framework introduces a new peptide variational autoencoder with design and diversity constraints to maintain similarity to specific templates while enabling sequence innovation. This work represents the first in vitro and in vivo experimental validation of generative Bayesian optimization in any setting. Using ten de-extinct peptides as templates, APEXGO generated optimized derivatives with enhanced antimicrobial properties. We synthesized 100 of these optimized peptides and conducted comprehensive in vitro characterizations, including assessments of antimicrobial activity, mechanism of action, secondary structure, and cytotoxicity. Notably, APEXGO achieved an outstanding 85% ground-truth experimental hit rate and a 72% success rate in enhancing antimicrobial activity against clinically relevant Gram-negative pathogens, outperforming previously reported methods for antibiotic discovery and optimization. In preclinical mouse models of Acinetobacter baumannii infection, several AI-optimized molecules--most notably derivatives of mammuthusin-3 and mylodonin-2--exhibited potent anti-infective activity comparable to or exceeding that of polymyxin B, a widely used last-resort antibiotic. These findings highlight the potential of APEXGO as a novel generative AI approach for peptide design and antibiotic optimization, offering a powerful tool to accelerate antibiotic discovery and address the escalating challenge of AMR.

microbiology↗

bioRxiv2024

Stacked Human Arterial Endothelial Cells Generate Atherosclerotic Fatty Streaks and Release Proinflammatory Cytokines

Fatty streaks are the first sign of atherosclerosis. They consist of lipid-containing foam cells, which were believed to be derived from the monocytes in the blood through the leaky endothelium, and from the vascular smooth muscle cells migrating into the intima from the media. Here, we showed that fatty streaks can also be formed by the stacked human arterial endothelial cells (HAECs) cultured in vitro. Via SEM we revealed a novel cell phenotype (coralthelial) that forms a streak/coral-like structure. We observed accumulation of lipids in the coralthelial cell and increased Golgi and coat protein II markers in its nucleus. Additionally, proinflammatory cytokines were upregulated in these cells, likely due to Golgi nuclear translocation and subsequently increased expression of the ribosomal protein RPL23 in the nucleus. We demonstrated, for the first time, that the atherosclerotic fatty streak-like structure can be generated from the stacked HAECs, which also create a proinflammatory microenvironment. Significance StatementOur work presents a novel perspective on atherosclerotic fatty streak formation, a critical early event in atherosclerosis development. We demonstrate, for the first time, that human arterial endothelial cells (HAECs) can transform into a novel phenotype, termed "coralthelial cells". These cells contribute to fatty streak formation, and produce proinflammatory cytokines through the relocation of RPL23 with the Golgi apparatus to the nucleus. This finding provides a new cellular mechanism by which endothelial cells initiate atherosclerosis, independent of traditional monocyte-derived foam cells. By enriching established paradigms, our research not only opens new avenues for therapeutic intervention targeting endothelial cells but also enhances understanding of vascular diseases and provides potential diagnostic and prognostic markers for atherosclerosis.

cell biology↗

bioRxiv2024

Mechanism of N-Myc Downstream Regulated Gene-1 regulating Integrin expression to inhibit gastric cancer metastasis

BackgroundN-myc downstream regulated gene-1 (NDRG1), the first member of the NDRG family, is widely distributed in various tissues and organs. In gastric cancer, the hypo-expression of NDRG1 has been positively associated with malignant biological behavior and poor prognosis. In-depth investigation of the potential regulatory mechanism of NDRG1 on gastric cancer is crucial for understanding the pathogenesis of this disease, identifying new therapeutic targets, and developing personalized treatment strategies. This study aims to explore the significance of NDRG1 in regulating the expression of integrins during the progression of gastric cancer. MethodsThe expression of NDRG1 in gastric cancer was analyzed using R software v4.0.3, Boxplot, and the Kaplan-Meier Plotter. Stable cell lines with NDRG1 knockdown and overexpression were subjected to wound healing assays, transwell migration assays, CCK8 assays, and colony formation assays, in order to determine the effects of NDRG1 on the migration and proliferation of gastric cancer cells. Western blotting was employed to examine the impact of NDRG1 on the expression of integrin-related proteins. Immunostaining was used to comprehensively analyze the in vitro experimental results. ResultsThe mRNA and protein levels of NDRG1 were downregulated substantially in gastric cancer, which was inversely correlated with the malignancy of pathological behavior and poor prognosis in gastric cancer. Knockdown of the NDRG1 gene significantly enhanced the proliferation and migration capabilities of gastric cancer cells, whereas overexpression of NDRG1 reduced their metastatic potential and inhibited both migration and proliferation. NDRG1 was found to regulate the expression of fibronectin 1, which in turn influenced the expression of a series of integrins, including v, 5, {beta}1, and {beta}3. This regulatory mechanism may play a crucial role in the early distant metastasis observed in gastric cancer. ConclusionsThis study demonstrated that NDRG1 could regulate the expression levels of integrins through specific signaling pathways, thereby interfering the adhesive and migratory capacities of gastric cancer cells. NDRG1 could serve as a valuable biomarker for the diagnosis and prognosis of gastric cancer, offering new potential targets for its treatment.

cancer biology↗

bioRxiv2024

Foamy microglia link oxylipins to disease progression in multiple sclerosis

Multiple sclerosis (MS) is a neuroinflammatory disease characterized by expanding demyelinating lesions, leading to severe and irreversible disability. The mechanisms driving lesion expansion, however, remain poorly understood. Here, using a multi-omics approach, we identified foamy microglia as primary contributors to the molecular profile of lesions and disease progression in secondary progressive MS. Lesions with foamy microglia are marked by the accumulation of cholesterol esters, bismonoacylglycerolphosphates (BMP), and oxylipins, along with high B-cell infiltration, increased levels of immunoglobulin G1, and elevated expression of Fc{gamma}- and complement receptors. Lesions with foamy GPNMB+-microglia display markers of enhanced phagocytosis, lipid metabolism, lysosomal dysfunction, and antigen presentation, but lack classical pro-inflammatory markers. Our data suggest that sustained phagocytosis of myelin overwhelms microglial endo-lysosomal capacity, leading to lipid droplet and oxylipin formation. This microglial phenotype may induce further recruitment of adaptive immune cells, axonal damage, drive lesion expansion and prevent remyelination. Monoacylglycerol lipase, involved in producing oxylipin precursors, was identified as a potential therapeutic target to disrupt this cycle and prevent chronic lesion expansion.

neuroscience↗

bioRxiv2024

A CXCR4 partial agonist improves immunotherapy by targeting polymorphonuclear myeloid-derived suppressor cells and cancer-driven granulopoiesis

Polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs) are pathologically activated neutrophils that potently impair immunotherapy responses. The chemokine receptor CXCR4, a central regulator of hematopoiesis, represents an attractive PMN-MDSC target1. Here, we fused a secreted CXCR4 partial agonist TFF2 to mouse serum albumin (MSA) and demonstrated that TFF2-MSA peptide synergized with anti-PD-1 to induce tumor regression or eradication, inhibited distant metastases, and prolonged survival in multiple gastric cancer (GC) models. Using histidine decarboxylase (Hdc)-GFP transgenic mice to track PMN-MDSC in vivo, we found TFF2-MSA selectively reduced the immunosuppressive Hdc-GFP+ CXCR4hi tumor PMN-MDSCs while preserving proinflammatory neutrophils, thereby boosting CD8+ T cell-mediated anti-tumor response together with anti-PD-1. Furthermore, TFF2-MSA systemically reduced PMN-MDSCs and bone marrow granulopoiesis. In contrast, CXCR4 antagonism plus anti-PD-1 failed to provide a similar therapeutic benefit. In GC patients, expanded PMN-MDSCs containing a prominent CXCR4+LOX-1+ subset are inversely correlated with the TFF2 level and CD8+ T cells in circulation. Collectively, our studies introduce a strategy of using CXCR4 partial agonism to restore anti-PD-1 sensitivity in GC by targeting PMN-MDSCs and granulopoiesis.

cancer biology↗

bioRxiv2024

CXXC-finger protein 1 associates with FOXP3 to stabilize homeostasis and suppressive functions of regulatory T cells

FOXP3-expressing regulatory T (Treg) cells play a pivotal role in maintaining immune homeostasis and tolerance, with their activation being crucial for preventing various inflammatory responses. However, the mechanisms governing the epigenetic program in Treg cells during their dynamic activation remain unclear. In this study, we demonstrate that CXXC finger protein 1 (CXXC1) interacts with the transcription factor FOXP3 and facilitates the regulation of target genes by modulating H3K4me3 deposition. Cxxc1 deletion in Treg cells leads to severe inflammatory disease and spontaneous T-cell activation, with impaired immunosuppressive function. As a transcriptional regulator, CXXC1 promotes the expression of key Treg functional markers under steady-state conditions, which are essential for the maintenance of Treg cell homeostasis and their suppressive functions. Epigenetically, CXXC1 binds to the genomic regulatory regions of Treg program genes in mouse Treg cells, overlapping with FOXP3 binding sites. Given its critical role in Treg cell homeostasis, CXXC1 presents itself as a promising therapeutic target for autoimmune diseases.

immunology↗

bioRxiv2024

Tumor Priming by Ultrasound Mechanogenetics for with SynNotch CAR T Therapy

Cell-based cancer immunotherapy holds potential as a therapeutic approach, yet its application for solid tumor treatment remains challenging. We created a system where focused ultrasound (FUS) is able to remotely stimulate gene expressions in a specific tissue area through mechanical induction, gated by a chemical inducer to minimize the background noise. This system, known as CaDox, integrates FUS-triggered mechanical and calcium stimulation with doxycycline-responsive genetic circuits, which allows the localized expression of the clinically validated and specific antigen CD19 within a subpopulation of cancer cells upon FUS stimulation. These CD19-expressing cells can then function as "training centers" that activate synNotch chimeric antigen receptor (CAR) T cells to generate CARs that recognize a less specific but widespread antigen in cancer cells, thereby attacking and suppress the whole cancer cell population nearby at the tumor site. We validated the functionality of this CaDox system in vitro, in organoids, and in vivo, demonstrating its potential for various cell types and as a versatile platform for precisely controllable immunotherapy. Our combinatorial approach thus offers a FUS-controlled remote and non-invasive priming of solid tumors for effective and safe CAR T immunotherapy via the induced production of clinically validated antigens.

synthetic biology↗

bioRxiv2024

Proteomic responses of oat (Avena sativa L.) to drought stress

Drought is a major abiotic factor limiting the growth and development of the oat industry, and understanding its drought tolerance mechanisms is vital to oat production. In this study, we measured the phenotypic and physiological indices of drought-resistant (Grain King [G]) and water-sensitive (XiYue [X]) oat varieties and performed comparative proteomic analysis under drought stress and normal water supply (soil water content of 75% {+/-} 5% of field water holding capacity) conditions. The results indicated that plant height, aboveground biomass, and underground biomass of variety X were 7.9%, 9.5%, and 14.6% lower than those under normal water supply, respectively, and the difference in plant height was significant (p < 0.05), whereas the decrease in all these indicators of variety G was small. Drought stress significantly increased malondialdehyde (MDA) content, soluble sugar (SS) content, superoxide dismutase (SOD) activity, and peroxidase (POD) activity of variety G by 48.6%, 68.5%, 81.3%, and 101.7%, respectively (p < 0.05). Variety X also showed increases up to various extents, but the increases were smaller than those of variety G. Additionally, 151 and 792 differentially expressed proteins (DEPs) identified in varieties G and X, respectively. Weighted Gene Co-expression Network Analysis(WGCNA), Gene Ontology(GO) and Kyoto Encyclopedia of Genes and Genome(KEGG) analyses demonstrated that the DEPs who were highly correlated with POD and SOD activity and SS content in variety G, were majorly involved in energy metabolism, protein translation, RNA processing, amino acid metabolism, and protein folding, whereas those with high correlation with the above three physiological indicators in variety X were primarily involved in RNA processing, protein stabilization, plant photosynthesis, intracellular signal transduction, and protein folding. Overall, the study elucidated the drought resistance mechanisms of different types of oats at the protein level

molecular biology↗