Biology subjects

Zuo, S.

Publications and source records attributed to Zuo, S..

12 recordsLinked to original sources

bioRxiv2026

Beyond Generic Signal Peptides: ApexSP Enables Cargo-Specific Secretion Design

Recombinant proteins are widely used in biopharmaceuticals, industrial manufacturing, and molecular diagnostics; however, efficient secretion remains a major bottleneck limiting their large scale production. As core elements controlling protein entry into secretion pathways, signal peptides do not function solely based on their own sequences, but rather depend on coordinated compatibility among cargo protein properties, secretion pathways, and host backgrounds. Current signal peptide engineering mainly relies on a limited number of commonly used signal peptides, empirical selection, and individual experimental screening, making it difficult to design efficient secretion elements tailored to specific expression systems. Here, we present ApexSP, a signal peptide design framework for secretion engineering tailored to individual cargo proteins. ApexSP is built upon a large scale, high quality signal peptide knowledge base and integrates a discrete diffusion generative model constrained by evolutionary information, a multitask biological filter incorporating topology information, and a signal peptide and mature protein compatibility ranking model to enable integrated design of signal peptides for specific expression systems. ApexSP achieved high accuracy in multiple attribute prediction tasks, including pathway classification and cleavage site prediction, reaching or exceeding the performance of existing signal peptide prediction tools. Moreover, the cargo protein aware ranking module improved the enrichment of candidates with high secretion performance. Experimental validation across multiple eukaryotic and prokaryotic expression systems demonstrated that screening only 10 candidate sequences generated by ApexSP yielded multiple designed signal peptides outperforming reference signal peptides, with the best performing design in the ApGA expressed Pichia pastoris system achieving a 1.71 fold increase in secretion performance compared with the factor signal peptide. Overall, ApexSP advances signal peptide research from sequence prediction toward secretion element design, demonstrating that a single round of designed signal peptides can achieve high secretion performance suitable for further engineering optimization.

synthetic biology↗

bioRxiv2025

Ferrapoptosis: Discovery of a Hybrid Programmed Cell Death

Traditional taxonomies classify ferroptosis and apoptosis as distinct forms of regulated cell death. Here, we challenge this view by defining and validating a previously unrecognized neuronal death entity in traumatic brain injury (TBI), which we term "Ferrapoptosis". This hybrid mode of death is characterized by the coexistence of ferroptotic and apoptotic molecular and ultrastructural features within the same neuron-- ultrastructural alterations that cannot be fully characterized by any known cell death modalities. By integrating single-cell transcriptomics with multi-layered functional assays, we show that Ferrapoptosis dominates in severe injury and the acute phase, and is critically driven by mitochondrial oxidative stress. Over time, its predominance is gradually replaced by death modes in which either ferroptosis or apoptosis alone becomes the major pathway. Genome-wide CRISPR screening further identifies Smg7 as a key regulator that synchronously activates both death programs to drive the hybrid phenotype, whereas genetic or viral inhibition of Smg7 reduces Ferrapoptosis and promotes neurological recovery after TBI in mice. Our work systematically delineates a previously unrecognized form of cell death and its pathogenetic mechanisms, providing experimental evidence to refine cell death classification, and suggesting a conceptual strategy for treating complex diseases such as TBI by targeting shared regulatory nodes. HIGHLIGHTSO_LIDefined and validated a previously unrecognized cell death modality, termed "Ferrapoptosis". C_LIO_LIElucidated the ordered pattern of Ferrapoptosis across key stages of TBI pathogenesis. C_LIO_LIRevealed mitochondrial oxidative stress as the pivotal hub integrating ferroptosis and apoptosis. C_LIO_LIIdentify Smg7 as a core driver of Ferrapoptosis and a promising neuroprotective target. C_LI

cell biology↗

bioRxiv2025

Pooled screening identifies combinatorial CAR signaling domains for next-generation CAR-M immunotherapies

Chimeric antigen receptor-engineered macrophages (CAR-Ms) hold great promise for solid tumor immunotherapy. The intracellular domains (ICDs) of CARs determine the phenotypic output of therapeutic macrophages but remain largely unexplored. Here, we constructed a CAR library containing 131 unique signaling domains derived from native immune receptors and identified 17 ICDs that enhance macrophage phagocytosis, inflammatory responses, or tumor infiltration in vitro and in vivo. We further developed a scalable 3 barcode technology, CARode, to uniquely label and trace ICD variants within large-scale combinatorial CAR library and applied it to single-cell RNA sequencing and single-cell CAR analysis to assess the synergetic effects of ICD combinations on macrophage activation. Our approach uncovered a novel CD40-LY9-FCRL1 chimeric receptor that modulates the tumor microenvironment and improves solid tumor clearance. In conclusion, our findings demonstrate that pooled screening can accelerate the discovery of complex ICD constructs, providing a powerful platform for engineering macrophage-based immunotherapies.

bioengineering↗

bioRxiv2024

Chromosome-level genome assembly of autotetraploid Selenicereus megalanthus and gaining genomic insights into the evolution of trait patterning in diploid and polyploid pitaya species

Yellow pitaya (Selenicereus megalanthus, 2n=4x=44) breeding remains severely hindered due to lacking a reference genome. Here we report yellow pitayas high-quality chromosome-level genome assembly and link the phenotypic trait with genomic data, based on Hi-C, ATAC, and RNA-seq data of specific tissues. We declared yellow pitaya as an autotetraploid with a 7.16 Gb genome size (harboring 27,246 high confidence genes) and majorly evolved from diploid ancestors, which remains unknown. Beyond generating the genome assembly, we explored the 3D chromatin organization which revealed insights into the genome, compartments A (648 and 519), compartments B (728 and 1064), topologically associated domains-TADs (3376 and 2031), and varying numbers of structural variations (SVs) in diploid and polyploid pitaya species, respectively. Overall, TAD boundaries were enriched with the motifs of AP2, WRKY18/60/75, MYB63/116, PHL2, and GATA8 in both pitaya species. By linking the open chromatin genomic structure to function, we identified the major changes in betalains biosynthesis pathway in diploid and polyploid pitaya. Moreover, the higher genetic expression of SmeADH1 [Chr11, Compartment A (135400000 - 135500000), genes inside the TAD region (135480000 - 135520000)], and lower expression of HuDOPA [Chr11, Compartment A (87100000 - 87200000), genes inside the TAD region (87160000-87200000)] acts as a key regulator of yellow and red color on the pericarp of polyploid and diploid pitaya, respectively. In addition, higher expression of HuCYP76AD1 genes in diploid pitaya and lower expression of SmeCYP76AD1 in polyploid pitaya potentially created the difference in the oxidase process that led to the production of betacyanin and betaxanthin, respectively. Furthermore, our results revealed not only the type of motifs that play a potential role in trait patterning but we also further uncovered that motif count in TAD-boundaries may impact the gene expression within the TAD regions of diploid and polyploid pitaya. Our valuable genomic resource and comparison of 3D euchromatin architecture of diploid and polyploid pitaya species will not only aid in the advancement of molecular breeding efforts but also offer insights into the organization of genomes, SVs, compartmentalization (A and B), and TADs, which have the potential to strengthen the idea of TADs-based trait improvement to achieve global food security.

plant biology↗

bioRxiv2024

Centromeric localization of KNL2 and CENP-C proteins in plants depends on their centromere-targeting domain and DNA-binding regions

In eukaryotic organisms, proper chromosome segregation during cell division depends on the centromeric histone H3 (CENH3) variant. Our previous studies identified a plant CENH3 assembly factor, Kinetochore Null2 (KNL2), that possesses a centromere-targeting motif, CENPC-k, similar to the CENPC motif in CENP-C. Additionally, we have demonstrated that KNL2 can bind DNA in vitro, independent of its CENPC-k motif. Thus, the mechanism underlying the binding of KNL2 to centromeric DNA remains elusive. Our study shows that the CENPC-k and CENPC motifs alone are not sufficient to target the centromere in N. benthamiana and A. thaliana. In-silico analysis revealed flanking DNA-binding regions near the CENPC-k and CENPC motifs, suggesting their importance in interacting with centromeric DNA. Fusion of protein fragments containing these motifs to EYFP facilitated targeting to the centromere. Deletion of DNA-binding domains reduced the centromeric localization of KNL2-C, whereas fusion of CENPC-k to the H-NS protein from E. coli targeted it to centromeres. We conclude that targeting of KNL2 and CENP-C proteins to centromeres is dependent on the CENPC-k/CENPC motifs, and their sequence-independent DNA-binding promotes anchoring at the centromere. Understanding the targeting mechanisms of KNL2 and CENP-C may help to engineer kinetochore structure by targeting chromatin modifying proteins to centromeres.

plant biology↗

bioRxiv2023

Neural signatures for temporal-order memory in the medial posterior parietal cortex

Episodic memory involves encoding and remembering the order of events experienced over time. Previous work examining the mechanisms of temporal-order memories has focused on the hippocampus and prefrontal cortices but has largely ignored the memory ensembles in the medial posterior parietal cortex (mPPC). Combining in vivo multi-unit electrophysiology and a temporal-order judgment task with cinematic material in the macaque, we find that mPPC neuronal activity reflects temporal context both during encoding and recall. During learning, mPPC neuronal ensembles encode the temporal information as well as contextual information embedded in the videos, whereas at retrieval these neurons fire in synchrony prior to memory-guided decisions. Moreover, the similarity between encoding and retrieval correlates with the animals performance. A control experiment further ruled out eye saccades, fixation, and scan path for their confounding roles in the neural results. Together, these data suggest that neurons in mPPC track the passage of time and contextual changes, thereby orchestrating for successful temporal-order memories at retrieval. SIGNIFICANCERemembering the temporal order of events is a vital function of the brain. This study provides the first evidence for the retrieval of temporal order of episodes at both single neuron and ensemble levels in the primate parietal cortex. The studys key breakthrough is the revelation that ensembles of time perceptive neurons, acting as "temporal context cells", can encode a spectrum of time constants and contexts for the experienced past and subsequently utilize this temporal record to discriminate the chronological order of past experiences. These results enhance theoretical frameworks for how encoded temporal past is maintained and reconstructed during memory retrieval.

neuroscience↗

bioRxiv2023

Depletion-assisted multiplexing cell-free RNA sequencing reveals distinct human and microbial signatures in plasma versus extracellular vesicle

Cell-free long RNAs in human plasma and extracellular vesicles (EVs) have shown promise as biomarkers in liquid biopsy, despite their fragmented nature. To investigate these fragmented cell-free RNAs (cfRNAs), we developed a cost-effective cfRNA sequencing method called DETECTOR-seq (depletion-assisted multiplexed cell-free total RNA sequencing). DETECTOR-seq utilized a meticulously tailored set of customized guide RNAs to remove large amounts of unwanted RNAs (i.e., fragmented ribosomal and mitochondrial RNAs) in human plasma. Early barcoding strategy was implemented to reduce costs and minimize plasma requirements. Using DETECTOR-seq, we conducted a comprehensive analysis of cell-free transcriptomes in both whole human plasma and EVs. Our analysis revealed discernible distributions of RNA types in plasma and EVs. Plasma exhibited pronounced enrichment in structured circular RNAs, tRNAs, Y RNAs, and viral RNAs, while EVs showed enrichment in mRNAs and srpRNAs. Functional pathway analysis highlighted RNA splicing-related ribonucleoproteins (RNPs) and antimicrobial humoral response genes in plasma, while EVs demonstrated enrichment in transcriptional activity, cell migration, and antigen receptor-mediated immune signals. Our study indicates the comparable potential of cfRNAs from whole plasma and EVs in distinguishing cancer patients (i.e., colorectal and lung cancer) from healthy donors. And microbial cfRNAs in plasma showed potential in classifying specific cancer types. Our comprehensive analysis of total and EV cfRNAs in paired plasma samples provides valuable insights for determining the need for EV purification in cfRNA-based studies. We envision the cost-effectiveness and efficiency of DETECTOR-seq will empower transcriptome-wide investigations in the fields of extracellular vesicles and liquid biopsy.

molecular biology↗

bioRxiv2023

Cell-free multi-omics analysis reveals tumor status-informative signatures in gastrointestinal cancer patients' plasma

During cancer development, hosts tumorigenesis and immune signals are released to and informed by circulating molecules, like cell-free DNA (cfDNA) and RNA (cfRNA) in blood. However, these two kinds of molecules are still not systematically compared in gastrointestinal cancer. Here, we profiled 4 types of cell-free omics data from colorectal and stomach cancer patients, and assayed 15 types of genomic, epi-genomic, and transcriptomic variations. First, we demonstrated that the multi-omics data were more capable of detecting cancer genes than the single-omics data, where cfRNAs were more sensitive and informative than cfDNAs in terms of detection ratio, variation type, altered number, and enriched functional pathway. Moreover, we revealed several peripheral immune signatures that were suppressed in cancer patients and originated from specific circulating and tumor-microenvironment cells. Particularly, we defined a {gamma}{delta}-T-cell score and a cancer-associated-fibroblast (CAF) score using the cfRNA-seq data of 143 cancer patients. They were informative of clinical status like cancer stage, tumor size, and survival. In summary, our work reveals the cell-free multi-molecular landscape of colorectal and stomach cancer, and provides a potential monitoring utility in blood for the personalized cancer treatment.

systems biology↗

bioRxiv2022

Mixed selectivity coding of content-temporal detail by dorsomedial posterior parietal neurons

The dorsomedial posterior parietal cortex is part of a higher-cognition network implicated in elaborate processes underpinning memory formation, recollection, episodes reconstruction, and temporal information processing. Neural coding for complex episodic processing is however under-documented. Here we revealed a set of neural codes of neuroethogram in the primate parietal cortex. Analyzing neural responses in macaque dmPPC to naturalistic videos, we discovered several groups of neurons that are sensitive to different categories of ethogram-items and to low-level sensory features, and saccadic eye movement. We also discovered that the processing of category and feature information by these neurons is sustained by accumulation of temporal information over a long timescale up to 30 s, corroborating its reported long temporal receptive windows. We performed an additional behavioral experiment and found that saccade-related activities could not account for the mixed neuronal responses elicited by the video stimuli. We further observed monkeys scan-paths and gaze consistency are modulated by video content. Taken altogether, these neural findings explain how dorsomedial PPC weaves fabrics of ongoing experiences together in real-time. The high dimensionality of neural representations should motivate us to shift the focus of attention from pure selectivity neurons to mixed selectivity neurons, especially in increasingly complex naturalistic task designs. HIGHLIGHTSO_LINeural codes for "neuroethogram" in macaque dorsomedial parietal cortex C_LIO_LIParietal neural codes exhibit mixed selectivity of event features C_LIO_LIDorsomedial PPC neurons support a long temporal receptive window for episodes C_LIO_LISaccadic movement could not explain away mixed neuronal responses C_LIO_LIConsistency in scan-path and gaze shown across viewing repetitions C_LI

neuroscience↗

bioRxiv2022

High temperature increases centromere-mediated genome elimination frequency in Arabidopsis deficient in cenH3 or its assembly factor KNL2

Double haploid production is the most effective way of creating true-breeding lines in a single generation. In Arabidopsis, haploid induction via mutation of the centromere-specific histone H3 (cenH3) has been shown when outcrossed to wild-type. Here we report that a mutant of the cenH3 assembly factor KNL2 can be used as a haploid inducer. We elucidated that short temperature stress of the knl2 mutant increased the efficiency of haploid induction from 1 to 10%. Moreover, we have demonstrated that a point mutation in the CENPC-k motif of KNL2 is sufficient to generate haploid inducing lines, suggesting that haploid inducing lines in crops can be identified in a naturally occurring or chemically induced mutant population, avoiding the GMO approach at any stage. In addition, we have shown that the cenh3-4 mutant, which does not induce haploids under standard growth conditions, functions as a haploid inducer after exposure to short temperature stress.

plant biology↗

bioRxiv2020

Behavioral evidence for memory replay of video episodes in macaque monkeys

Humans recall the past by replaying fragments of events temporally. Here, we demonstrate a similar effect in macaques. We trained six rhesus monkeys with a temporal-order judgement (TOJ) task and collected 5000 TOJ trials. In each trial, they watched a naturalistic video of about 10 s comprising two across-context clips, and after a 2-s delay, performed TOJ between two frames from the video. The monkeys apply a non-linear forward, time-compressed replay mechanism during the temporal-order judgement. In contrast with humans, such compression of replay is however not sophisticated enough to allow them to skip over irrelevant information by compressing the encoded video globally. We also reveal that the monkeys detect event contextual boundaries and such detection facilitates recall by an increased rate of information accumulation. Demonstration of a time-compressed, forward replay like pattern in the macaque monkeys provides insights into the evolution of episodic memory in our lineage. Impact StatementMacaque monkeys temporally compress past experiences and use a forward-replay mechanism during judgment of temporal-order between episodes.

neuroscience↗

bioRxiv2019

Epidemic foci of hemorrhagic fever with renal syndrome in Shandong Province, China, based on patients, rodents and molecular epidemiology characteristics, 2012-2015

BackgroundHemorrhagic fever with renal syndrome (HFRS), an infectious disease caused by hantaviruses, is endemic in China and remains a serious public health problem. Historically, Shandong Province has had the largest HFRS burden in China. However, we do not have a comprehensive and clear understanding of the current epidemic foci of HFRS in Shandong Province.\n\nMethodology/Principal FindingsThe incidence and mortality rates were calculated, and a phylogenetic analysis was performed after laboratory testing of the virus in rodents. Spatial epidemiology analysis was applied to investigate the epidemic foci, including their sources. A total of 6,206 HFRS cases and 59 related deaths were reported in Shandong Province. The virus carriage rates of the rodents Rattus norvegicus, Apodemus agrarius and Mus musculus were 10.24%, 6.31% and 0.27%, respectively. The phylogenetic analysis indicated that two novel viruses isolated from R. norvegicus in Anqiu City and Qingzhou City were dissimilar to the other isolated strains, but closely related to strains previously isolated in northeastern China. Three epidemic foci were defined, two of which were derived from the Jining and Linyi epidemic foci, respectively, while the other was the residue of the Jining epidemic focus.\n\nConclusions/SignificanceThe southeastern and central Shandong Province are current key HFRS epidemic foci dominated by A. agrarius and R. norvegicus, respectively. Our study could help local departments to strengthen prevention and control measures in key areas to reduce the hazards of HFRS.\n\nAuthor summaryHemorrhagic fever with renal syndrome (HFRS) is a global infectious disease, which is still a serious public health threat in China today. The reported HFRS cases in Shandong Province accounted for approximate one third of total cases in the whole country. HFRS is a zoonosis mainly caused by Hantaan virus (HTNV) and Seoul virus (SEOV), which natural rodent hosts are A. agrarius and R. norvegicus, respectively. To explore the current HFRS epidemic foci based on patients, rodents and molecular epidemiology characteristics in Shandong Province, we collected the records of HFRS cases from whole province and the rodents captured in 14 surveillance sites. We found that the epidemic situation of HFRS is quiet different in temporal and spatial distribution. Three epidemic foci were defined based on patients, rodents and molecular epidemiology characteristics. The situation of HFRS epidemic foci in Shandong Province was clear. Our study provides a reference for relevant departments to develop key prevention strategies.

epidemiology↗