Biology subjects

Chen, X.

Publications and source records attributed to Chen, X..

At least 901 records · Page 50Linked to original sources

bioRxiv2023

Unraveling codon usage of Escherichia coli using machine learning

Machine learning is used to investigate the codon usage of protein-encoding genes, which is one of the fundamental questions of molecular biology. The presentation, parameter learning, and decoding of the conditional random field (CRF) model are implemented and then utilized to analyze the codon usage of the genes of Escherichia coli and its phages. Most genes of E. coli use codons conforming to the weights of the model determined by all E. coli genes. Phages use the codons like their host E. coli. Finally, the study evaluates the codon usage of several example genes in the context of the model. These results help to understand the codon usage in E. coli.

systems biology↗

bioRxiv2023

Network-based molecular subtyping of acral melanoma

Acral melanoma is more biologically aggressive with a worse prognosis compared with other melanoma subtypes. However, the molecular basis underlying the biological and clinical behavior of this cancer is still unclear. Here, using the combination of multi-omics data analysis and network-based disease gene prediction algorithm, we first demonstrate the existence of two acral melanoma subtypes which greatly differed in clinical performance, cellular and molecular mechanisms, and discovered a biomarker panel (EREG, VSIG4, FCGR3A, RAB20) that accurately distinguished these two subtypes with the AUC of 0.946, which has been verified by clinical samples. Subtype I has thinner Breslow with a better prognosis. On the contrary, subtype II is a high-risk subtype that is easier to invade the dermis. We further analyzes the intrinsic biological mechanism of the two subtypes from the cellular level, and reveals the important role of macrophages subgroups in the molecular typing of acral melanoma. Feature genes of subtype I are enriched in FCN1+ macrophages that promote inflammatory and immune responses. In contrast, feature genes of subtype II are enriched in SPP1+ macrophages which ha the greatest impact on tumor cells. The identification of the two subtypes opens up important biological and clinical perspectives for acral melanoma.

bioinformatics↗

bioRxiv2023

Imaging Microglia Surveillance during Sleep-wake Cycles in Freely Behaving Mice

Microglia surveillance manifests itself as dynamic changes in cell morphology and functional remodeling. Whether and how microglia surveillance is coupled to brain state switches during natural sleep-wake cycles remain unclear. To address this question, we used miniature two-photon microscopy (mTPM) to acquire time-lapse high-resolution microglia images of the somatosensory cortex, along with EEG/EMG recordings and behavioral video, in freely-behaving mice. We uncovered fast and robust brain state-dependent changes in microglia surveillance, occurring in parallel with sleep dynamics and early-onset phagocytic microglial contraction during sleep deprivation stress. We also detected local norepinephrine fluctuation occurring in a sleep state-dependent manner. We showed that the locus coeruleus-norepinephrine system, which is crucial to sleep homeostasis, is required for both sleep state-dependent and stress-induced microglial responses and {beta}2-adrenergic receptor signaling plays a significant role in this process. These results provide direct evidence that microglial surveillance is exquisitely tuned to signals and stressors that regulate sleep dynamics and homeostasis so as to adjust its varied roles to complement those of neurons in the brain. In vivo imaging with mTPM in freely behaving animals, as demonstrated here, opens a new avenue for future investigation of microglia dynamics and sleep biology in freely behaving animals.

neuroscience↗

bioRxiv2023

PLANET: A Multi-Objective Graph Neural Network Model for Protein-Ligand Binding Affinity Prediction

Predicting protein-ligand binding affinity is a central issue in drug design. Various deep learning models have been developed in recent years to tackle this issue, but many of them merely focus on reproducing the binding affinity of known binders. In this study, we have developed a graph neural network model called PLANET (Protein-Ligand Affinity prediction NETwork). This model takes the graph-represented 3D structure of the binding pocket on the target protein and the 2D chemical structure of the ligand molecule as input, and it was trained through a multi-objective process with three related tasks, including deriving the protein-ligand binding affinity, protein-ligand contact map, and intra-ligand distance matrix. To serve those tasks, a large number of decoy non-binders were selected and added to the standard PDBbind data set. When tested on the CASF-2016 benchmark, PLANET exhibited a scoring power comparable to other deep learning models that rely on 3D protein-ligand complex structures as input. It also showed notably better performance in virtual screening trials on the DUD-E and LIT-PCBA benchmark. In particular, PLANET achieved comparable accuracy on LIT-PCBA as the conventional docking program Glide. However, it only took less than 1% of the computation time required by Glide to finish the same job because it did not perform exhaustive conformational sampling. In summary, PLANET exhibited a decent performance in binding affinity prediction as well as virtual screening, which makes it potentially useful for drug discovery in practice.

bioinformatics↗

bioRxiv2023

Homeostatic control of an iron repressor in a GI tract resident

The transition metal iron plays a crucial role in living cells. However, high level of iron is potentially toxic through the production of reactive oxygen species (ROS), serving as a deterrent to the commensal fungus Candida albicans for colonization in the iron-rich gastrointestinal (GI) tract. We observe that the mutant lacking an iron-responsive transcription factor Hap43 is hyper-fit for colonization in murine gut. We demonstrate that high iron specifically triggers multiple post-translational modifications (PTMs) and proteasomal degradation of Hap43, a vital process guaranteeing the precision of intestinal ROS detoxification. Reduced levels of Hap43 lead to de-repression of antioxidant genes and therefore alleviate the deleterious ROS derived from iron metabolism. Our data reveal that Hap43 functions as a negative regulator for oxidative stress-adaptation of C. albicans to gut colonization and thereby provide a new insight into understanding the interplay between iron homeostasis and fungal commensalism. ImportanceIron homeostasis is critical for creatures. Candida albicans is one of the major commensals in the GI tract where is iron-replete environment. Transcriptional factor Hap43 was believed to repress iron utilizations genes in iron-depleted conditions for decades. However, the mystery in iron-replete conditions of Hap43 has never been uncovered. We discovered that reduced levels of Hap43 via phosphorylation-dependent nuclear export, followed by proteosome-mediated protein degradation, leads to de-repression of downstream antioxidant genes and promote its colonization in GI tract. We propose that C. albicans has a strict detoxification process to ensure its survival, which has important implications for understanding how the fungi survives in the mammalian host.

microbiology↗

bioRxiv2023

Multi-omics Comparison among Populations of Three Plant Sources of Amomi Fructus

Amomi Fructus (Sharen, AF) is a traditional Chinese medicine (TCM) from three source species (or subspecies) including Wurfbainia villosa var. villosa (WVV), W. villosa var. xanthioides (WVX) or W. longiligularis (WL). Among them, WVV has been transplanted from its top-geoherb region Guangdong to its current main production area Yunnan for more than 50 years in China. However, the genetic and transcriptomic differentiation among multiple AF source (sub)species and between the origin and transplanted populations of WVV is unknown. In our study, the observed overall higher expression of terpenoid biosynthesis genes in WVV than that of WVX supplied possible evidence for the better pharmacological effect of WVV. We also screened ten candidate borneol dehydrogenase (BDH) genes that potentially catalyzed borneol into camphor in WVV. The BDH genes may experience independent evolution after acquiring the ancestral copies and the followed tandem duplications might account for the abundant camphor content in WVV. Furthermore, four populations of WVV, WVX and WL are genetically differentiated and the gene flow from WVX to WVV in Yunnan contributed to the increased genetic diversity in the introduced population (WVV-JH) compared to its top-geoherb region (WVV-YC), which showed the lowest genetic diversity and might undergo genetic degradation. In addition, TPS and BDH genes were selected among populations of multiple AF source (sub)species and between the top-geoherb and non-top-geoherb regions, which might explain the metabolite difference of these populations. Our findings provide important guidance for the conservation, genetic improvement, industrial development of the three source (sub)species, and identifying top-geoherbalism with molecular markers and proper clinical application of AF.

evolutionary biology↗

bioRxiv2023

rRNA intermediates coordinate the multilayered nucleolar phase transition in C. elegans

The nucleolus is the most prominent membraneless organelle within the nucleus and plays essential roles in rRNA transcription and processing and ribosome assembly. How the structure of the nucleolus is maintained and regulated is poorly understood. Here, we identified two types of nucleoli in C. elegans. Type I nucleoli are spherical, and rRNA transcription and processing factors are evenly distributed throughout the nucleolus. In type II nucleoli, rRNA transcription and processing factors exclusively accumulate in the periphery rim, which is named the nucleolar ring. The hollow vacuole inside the nucleolar ring contains proteins that usually localize in the nucleoplasm but are capable of exchanging contents across the ring. The high-order structure of the nucleolus is dynamically regulated in C. elegans. Faithful rRNA processing is important to maintain the spherical structure of the nucleoli. The depletion of a class of rRNA processing factors, for example, class I ribosomal proteins of the large subunit (RPL), which are involved in 27SA2 rRNA processing, reshaped spherical nucleoli to a ring-shaped nucleolar structure. The inhibition of RNAP I transcription and depletion of two conserved nucleolar factors, nucleolin and fibrillarin, prohibits the formation of the nucleolar ring. We concluded that the integrity of nucleoli is highly dependent on rRNA processing and maturation, which may provide a mechanism to coordinate structure maintenance and gene expression.

cell biology↗

bioRxiv2023

Elucidating the combined toxicity of aflatoxin B1 and fumonisin B1 on HepG2 cells based on respirometry and transcriptome analyses

Aflatoxin B1 (AFB1) and fumonisin B1 (FB1) are two toxic mycotoxins widely found in food contaminants, and known for their hepatotoxicity in human. However, their combined toxicity still needs to be deeply investigated especially for their harmful effect. Therefore, the current work aimed at investigating the (combined) effect of AFB1 and FB1 on mitochondrial and glycolytic activity of HepG2 cell line, a well-recognized in vitro model system to study liver cell function. In our previous work, we studied the impact of a short term exposure to different doses of AFB1, FB1, and their binary mixture (MIX) on the bioenergetic status of HepG2 cells. Seahorse respirometry analysis revealed that the co-exposure, especially at high doses (8 {micro}g/mL for AFB1 and 160 {micro}g/mL for FB1), is more toxic as a result of more inhibition of all parameters of mitochondrial respiration. RNA transcriptome sequencing showed that the p53 signaling pathway, which is a major orchestrator of mitochondrial apoptosis, was differentially expressed. Moreover, the co-exposure has significantly downregulated Cx I, Cx II, Cx III, and Cx IV genes, which represent the onset of the suppressed mitochondrial respiration in HepG2 cells. It was found that FB1 is contributed more to the MIX effects than AFB1. Environmental ImplicationAflatoxin B1 (AFB1) and fumonisin B1 (FB1) are two main mycotoxins that frequently (co-)contaminate maize and maize-based ingredients in several parts of the world. Both toxins are well-known for their hepatotoxicity in humans as the liver is their main target organ. However, the combined toxicity of AFB1 and FB1 still needs to be deeply investigated especially for their effect on cellular respiration. In this study, we proved that a binary mixture of AFB1 and FB1 is more toxic on mitochondrial respiration, and disrupted the p53 signaling pathway to induce apoptosis, which promised a novel insight of hazardous materials-induced hepatic damage.

pharmacology and toxicology↗

bioRxiv2023

Effect of oncolytic virotherapy on immune microenvironment in immune subtypes identified in gastric cancer and hepatocellular carcinoma

Tumor occurrence and progression are significantly influenced by immunity, and the immune infiltration and immune-related gene expression in solid tumors are closely correlated to the response of patients to immunotherapy. In this study, the level of tumor infiltrating immune cells in gastric cancer and hepatocellular carcinoma samples from the TCGA database were assessed using ssGSEA, and the tumor samples were divided into two subtypes (Imm_H and Imm_L) with different immune cell infiltration level. The differences in immune cell percentage and immune checkpoint gene expression between the two subtypes indicated that the Imm_H group had higher levels of immune infiltration, but also more infiltrated immunosuppressive cells and higher mRNA levels of immune checkpoint genes. Then the immune subtype-specific gene network was built and the main modules representing the genes and functions that differ between the two immune subtypes were identified. To explore the effect of oncolytic virus on tumor immune microenvironment, we constructed the previously developed synthetic adenovirus containing the synthetic sensory switch gene circuit, assessed the antitumor effect in mouse models, and measured the proportion of different cell types by single-cell RNA sequencing. The results showed that synthetic oncolytic virus inhibited tumor development and altered the proportion of infiltrating immune cells, suggesting that synthetic oncolytic virus may have different mechanism on the two immune subtypes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=168 HEIGHT=200 SRC="FIGDIR/small/524374v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@dffa9dorg.highwire.dtl.DTLVardef@be8e2eorg.highwire.dtl.DTLVardef@68acf6org.highwire.dtl.DTLVardef@33862f_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2023

RNA sequencing identifies lung cancer lineage and facilitates drug repositioning

Breakthrough therapies recently improve survival in lung adenocarcinoma (LUAD), yet we still lack a paradigm to support prospective confirmation. To classify three clusters including bronchioid, neuroendocrine, and squamoid, the non-negative matrix factorization (NMF) algorithm was first performed at The Cancer Genome Atlas (TCGA), Clinical Proteomic Tumor Analysis Consortium (CPTAC), Gene Expression Omnibus (GEO) and preclinical models. In terms of prognostic value, the squamoid cluster is of poor prognostic factor. The neuroendocrine cluster is characterized by STK11 mutations and 14q13.3 amplifications. From an immunological perspective, the bronchioid cluster is considered an immune activation because of the highest immune-related genetic perturbation. Further analysis is the estimation of the relative cell abundance of the tumor microenvironment (TME), specific cell types can be reflected among three clusters. Meanwhile, the higher portion of immune cell infiltration belonged to bronchioid and squamous, not neuroendocrine cluster. Taken together, the neuroendocrine cluster show resistance to PD-L1 blockade. While pemetrexed or platinum-based therapies are suitable for bronchioid and squamoid clusters, respectively. Our emphasis was on phenotype-based action to explore compounds. Large-scale drug sensitivity databases including ConnectivityMap (CMAP), Cancer Cell Line Encyclopedia (CCLE), and Genomics of Drug Sensitivity in Cancer (GDSC) were analyzed. MEK inhibitors exhibited resistance in the bronchioid, while sensitive to the squamous cluster. Dinaciclib and alvocidib showed similar activity and sensitivity in the neuroendocrine cluster. A lineage factor named KLF5 recognized by two networks could be suppressed by verteporfin. This work adds to the knowledge of the lung cancer lineage and facilitates drug repositioning.

cancer biology↗

bioRxiv2023

Activation-induced cytidine deaminase-based in vivo continuous evolution system enables rapid protein engineering

Directed evolution is a powerful tool to modify the properties of proteins. However, due to multi-round and stage combinations, directed evolution usually requires time- and labor-intensive manual intervention, which limits the efficiency of protein modification to some extent. Therefore, in vivo continuous evolution system is highly preferred because it can couple the multiple rounds and steps of direction evolution with the host growth cycle, leading to the advantages of effort-saving and accuracy. However, the existing types of this kind of systems can not meet the booming demand. Herein, this paper describes promoted Escherichia coli-assisted continuous evolution (PEACE) that allows for in vivo continuous evolution of target genes. This system polymorphisms the target gene by activation-induced cytidine deaminase-T7 RNA polymerase (AID-T7 PNAP) fusion protein, then it couples the enzymatic properties of desired variants with the expression of antitoxins to achieve efficient growth-coupled screen using the toxin-antitoxin system (TAS). In this study, T7 RNAP was finally employed for validation of PEACE system, and its specificity to the promoter was successfully altered. These results demonstrated the feasibility and further application potential of PEACE.

molecular biology↗

bioRxiv2023

APPRAISE: Fast, accurate ranking of engineered proteins by receptor binding propensity using structural modeling

Deep learning-based methods for protein structure prediction have achieved unprecedented accuracy. However, the power of these tools to guide the engineering of protein-based therapeutics remains limited due to a gap between the ability to predict the structures of candidate proteins and the ability to assess which of those proteins are most likely to bind to a target receptor. Here we bridge this gap by introducing Automated Pairwise Peptide-Receptor AnalysIs for Screening Engineered proteins (APPRAISE), a method for predicting the receptor binding propensity of engineered proteins. After generating models of engineered proteins competing for binding to a target using an established structure-prediction tool such as AlphaFold-Multimer or ESM-Fold, APPRAISE performs a rapid (under 1 CPU second per model) scoring analysis that takes into account biophysical and geometrical constraints. As a proof-of-concept, we demonstrate that APPRAISE can accurately classify receptor-dependent vs. receptor-independent adeno-associated viral vectors and diverse classes of engineered proteins such as miniproteins targeting the SARS-CoV-2 spike, nanobodies targeting a G-protein-coupled receptor, and peptides that specifically bind to transferrin receptor or PD-L1. APPRAISE is accessible through a web-based notebook interface using Google Colaboratory (https://tiny.cc/APPRAISE). With its accuracy, interpretability, and generalizability, APPRAISE promises to expand the utility of protein structure prediction and accelerate protein engineering for biomedical applications.

bioengineering↗

bioRxiv2023

Primate-conserved Carbonic Anhydrase IV and murine-restricted Ly6c1 are new targets for crossing the blood-brain barrier

The blood-brain barrier (BBB) presents a major challenge to delivering large molecules to study and treat the central nervous system (CNS). This is due in part to the scarcity of effective targets for BBB crossing, the identification of which is the crucial first step of drug development. Here, we leveraged a panel of adeno-associated viruses (AAVs) previously identified through directed evolution for improved BBB transport to reverse engineer protein targets for enhanced BBB crossing. We identify both murine-restricted Ly6c1 and primate-conserved carbonic anhydrase IV (Car4; CA4) as novel receptors for crossing the BBB. We demonstrate how these receptors can unlock new experimental and computational target-focused engineering strategies by creating the enhanced Ly6c1-binding vector AAV-PHP.eC and by applying AlphaFold2-enabled in silico methods to rank capsids against identified receptors and generate capsid-receptor binding models. Here, with Car4, we add a completely new receptor to the very short list currently available for crossing the BBB in humans and, with Ly6c1, we validate a pipeline for receptor-targeted engineering. The identification of Car4/CA4 and structural insights from computational modeling provide new paths toward human brain-penetrant chemicals (drugs) and biologicals (including gene delivery).

bioengineering↗

bioRxiv2023

Functional gene delivery to and across brain vasculature of systemic AAVs with endothelial-specific tropism in rodents and broad tropism in primates

Delivering genes to and across the brain vasculature efficiently and specifically across species remains a critical challenge for addressing neurological diseases. We have evolved adeno-associated virus (AAV9) capsids into vectors that transduce brain endothelial cells specifically and efficiently following systemic administration in wild-type mice with diverse genetic backgrounds and rats. These AAVs also exhibit superior transduction of the CNS across non-human primates (marmosets and rhesus macaques), and ex vivo human brain slices although the endothelial tropism is not conserved across species. The capsid modifications translate from AAV9 to other serotypes such as AAV1 and AAV-DJ, enabling serotype switching for sequential AAV administration in mice. We demonstrate that the endothelial specific mouse capsids can be used to genetically engineer the blood-brain barrier by transforming the mouse brain vasculature into a functional biofactory. Vasculature-secreted Hevin (a synaptogenic protein) rescued synaptic deficits in a mouse model.

bioengineering↗

bioRxiv2023

Heritable maize microbiomes contribute to local adaptation and host stress resilience

Beneficial interactions with microorganisms are pivotal for crop performance and resilience. However, it remains unclear how heritable the microbiome is with respect to the host plant genotype and to what extent host genetic mechanisms can modulate plant-microbe interactions in the face of environmental stress. Here, we surveyed the root and rhizosphere microbiome of 129 accessions of locally adapted Zea mays, sourced from diverse habitats and grown under control and different stress conditions. We quantified treatment and host genotype effects on the microbiome. Plant genotype and source environment were predictive of microbiome composition. Genome wide association analysis identified host genetic variants linked to both rhizosphere microbiome composition and source environment. We identified transposon insertions in a candidate gene linked to both the abundance of a keystone microbe Massilia and source total soil nitrogen, finding mutant plants to show a reduction in lateral root density. We conclude that locally adapted maize varieties exert patterns of genetic control on their root and rhizosphere microbiomes that follow variation in their home environments, consistent with a role in tolerance to prevailing stress.

genetics↗

bioRxiv2023

Activity Hierarchy Measurement to Establish Trace Memory-eligible "Primed" Neurons

While it is known that associative memory is preferentially encoded by memory-eligible primed neurons, in vivo neural activity hierarchy has not been quantified and little is known about how such a hierarchy is established. Leveraging in vivo calcium imaging of hippocampal neurons on freely behaving mice, we developed the first method to quantify real-time neural activity hierarchy in the CA1 region. Neurons on the top of activity hierarchy are identified as primed neurons. In cilia knockout mice that exhibit severe learning deficits, the percentage of primed neurons is drastically reduced. We developed a simplified neural network model that incorporates simulations of linear and non-linear weighted components, modeling the synaptic ionic conductance of AMPA and NMDA receptors, respectively. We found that moderate non-linear to linear conductance ratios naturally leads a small fraction of neurons to be primed in the simulated neural network. Removal of the non-linear component eliminates the existing activity hierarchy and reinstate it to the network stochastically primes a new pool of neurons. Blockade of NMDA receptors by ketamine not only decreases general neuronal activity causing learning impairments, but also disrupts neural activity hierarchy. Additionally, ketamine-induced super-synchronized slow oscillation during anesthesia can be simulated if the non-linear NMDAR component is removed to flatten activity hierarchy. Together, this study develops a unique method to measure neural activity hierarchy and identifies NMDA receptors as a key factor that controls the hierarchy. It presents the first evidence suggesting that hierarchy disruption by NMDAR blockade causes dissociation and psychosis.

neuroscience↗

bioRxiv2023

Accurate and Rapid Detection of Peritoneal Metastasis from Gastric Cancer by AI-assisted Stimulated Raman Cytology

Peritoneal metastasis (PM) is the most common form of distant metastasis and one of the leading causes of death in gastric cancer (GC). For locally advanced GC, clinical guidelines recommend peritoneal lavage cytology for intraoperative PM detection. Unfortunately, current peritoneal lavage cytology is limited by low sensitivity (<60%). Here we established the stimulated Raman cytology (SRC), a chemical microscopy-based intelligent cytology. By taking advantages of stimulated Raman scattering in label-free, high-speed, and high-resolution chemical imaging, we firstly imaged 53951 exfoliated cells in ascites obtained from 80 GC patients (27 PM positive, 53 PM negative), at the Raman bands corresponding to DNA, protein, and lipid, respectively. Then, we revealed 12 single cell features of morphology and composition that were significantly different between PM positive and negative specimens, including cellular area, lipid protein ratio, etc. Importantly, we developed a single cell phenotyping algorithm to further transform the above raw features to feature matrix. Such matrix was crucial to identify the significant marker cell cluster, the divergence of which was finally used to differentiate the PM positive and negative. Compared with histopathology, the gold standard of PM detection, our SRC method assisted by machine learning classifiers could reach 81.5% sensitivity, 84.9% specificity, and the area under receiver operating characteristic curve of 0.85, within 20 minutes for each patient. Such remarkable improvement in detection accuracy is largely owing to incorporation of the single-cell composition features in SRC. Together, our SRC method shows great potential for accurate and rapid detection of PM from GC.

biophysics↗

bioRxiv2023

Programmable Drug Control of Receptor Valency Modulates the Potency of Cell Therapeutics

Designer T cells offer a novel paradigm for treating diseases like cancer, yet they are often hindered by target recognition evasion and limited in vivo control. To overcome these challenges, we develop valency-controlled receptors (VCRs), a novel class of synthetic receptors engineered to enable precise modulation of immune cell activity. VCRs use custom-designed valency-control ligands (VCLs) to modulate T cell signaling via spatial molecular clustering. Using multivalent DNA origami as VCL, we first establish that valency is important for tuning the activity of CD3-mediated immune activation. We then generate multivalent formats of clinically relevant drugs as VCL and incorporate VCR into the architecture of chimeric antigen receptors (CARs). Our data demonstrate that VCL-mediated VCRs can significantly amplify CAR activities and improve suboptimal CARs. Finally, through medicinal chemistry, we synthesize programmable, bioavailable VCL drugs that potentiate targeted immune response against low-antigen tumors both in vitro and in vivo. Our findings establish receptor valency as a core mechanism for enhancing CAR functionality and offer a synthetic chemical biology platform for strengthening customizable, potent, and safer cell therapies.

synthetic biology↗