Biology subjects

Chen, R.

Publications and source records attributed to Chen, R..

At least 127 records · Page 7Linked to original sources

bioRxiv2025

Development of a novel murine model of in-stent neoatherosclerosis

ObjectiveIn-stent neoatherosclerosis is a phenomenon of percutaneous coronary intervention with stenting. Whilst similar to de novo atherosclerosis, it develops rapidly over 1-5 years rather than over a lifetime. No preclinical small animal models exist that allow full elucidation of neoatherosclerosis biology and future treatments. The aim of this study was to establish and validate a novel murine model of in-stent neoatherosclerosis. Approach and ResultsMurine stainless-steel stents (2.5 x 0.7 mm) were deployed into donor descending aortas of atherosclerosis-prone apolipoprotein (Apo)e-/- mice, then carotid-interposition grafted into Apoe-/- recipients. Mice (n=6-8/group) received chow or a high cholesterol diet (HCD) for 7- or 28-days post-surgery. Multimodal intravascular imaging, simultaneously combining optical coherence tomography (OCT, plaque burden) and fluorescence for indocyanine green (ICG, plaque instability), visualized in-stent neoatherosclerosis across the entire length of the stented site. Histological analyses revealed that stented vessels from mice fed HCD had neointimas with prominent lipid cores and an elevated CD68+ macrophage content, similar to human neoatherosclerosis. Mice fed chow post-stenting had distinctly different neointimas that were smooth muscle cell rich, resembling neointimal hyperplasia. Consistent with this, flow cytometry revealed a higher content of monocytes/macrophages and dendritic cells in stented aortas from mice fed HCD than in non-stented aortas. ConclusionWe have developed and validated the first murine model that replicates the unique characteristics of human in-stent neoatherosclerosis. This project has implications for exploring the mechanisms that promote neoatherosclerosis and testing targeted new therapies. RESEARCH PERSPECTIVEO_ST_ABSWhat Is New?C_ST_ABSO_LIWe have developed and validated a novel murine model of in-stent neoatherosclerosis, presenting a new platform that will facilitate the discovery of novel mechanistic targets of in-stent neoatherosclerosis and preventative therapies. C_LIO_LIThis model develops lesions with a similar morphology to human in-stent neoatherosclerosis and distinct to in-stent neointimal hyperplasia, with higher extracellular lipid and macrophage content and proportionately less smooth muscle cells. C_LIO_LIWe show a first-time visualization of murine in-stent neoatherosclerosis using bimodal intravascular imaging with simultaneous capture of structural information (optical coherence tomography, plaque burden) and the distribution of areas of plaque instability (high-sensitivity fluorescence, indocyanine green) within the plaque. C_LI What new question does this study raise?O_LIHow can the utility of this novel model be maximized as a platform for discovering novel agents that prevent in-stent neoatherosclerosis? C_LI What question should be addressed next?O_LIAre there unique mechanisms of in-stent neoatherosclerosis, distinct to de novo atherosclerosis, that can be specifically targeted to prevent disease and ultimately increase stent performance? C_LI

cell biology↗

bioRxiv2025

Neuronal LAG3 facilitates pathogenic α-synuclein neuron-to-neuron propagation

Lymphocyte activation gene 3 (LAG3) is a key receptor involved in the propagation of pathological proteins in Parkinsons disease (PD). This study investigates the role of neuronal LAG3 in mediating the binding, uptake, and propagation of -synuclein (Syn) preformed fibrils (PFFs). Using neuronal LAG3 conditional knockout mice and human induced pluripotent stem cells-derived dopaminergic (DA) neurons, we demonstrate that LAG3 expression is critical for pathogenic Syn propagation. Our results show that the absence of neuronal LAG3 significantly reduces Syn pathology, alleviates motor dysfunction, and inhibits neurodegeneration in vivo. Electrophysiological recordings revealed that Syn PFFs induce pronounced neuronal hyperactivity in wild-type (WT) neurons, increasing firing rates in cell-attached and whole-cell configurations, and reducing miniature excitatory postsynaptic currents. In contrast, neurons lacking LAG3 resisted these electrophysiological effects. Moreover, treatment with an anti-human LAG3 antibody in human DA neurons inhibited Syn PFFs binding and uptake, preventing pathology propagation. These findings confirm the essential function of neuronal LAG3 in mediating Syn propagation and associated disruptions, identifying LAG3 as a potential therapeutic target for PD and related -synucleinopathies.

neuroscience↗

bioRxiv2024

Learning the Language of Phylogeny with MSA Transformer

Classical phylogenetics assumes site independence, potentially overlooking epistasis. Protein language models capture dependencies in conserved structural and functional domains across the protein universe. Here, we ask whether MSA Transformer, which takes a multiple sequence alignment (MSA) as input, captures evolutionary distance and to what extent its representations reflect epistasis in protein sequence evolution, neither of which are explicitly available during training. Systematic shuffling of natural and simulated MSAs demonstrates the model exploits column-wise conservation to distinguish phylogenetic relationships. Using internal embeddings, we reconstruct trees that are markedly consistent with trees generated by maximum likelihood inference. Applying this approach to both the RNA-dependent RNA polymerase of RNA viruses and the nucleo-cytoplasmic large DNA virus domain, we recover both established and novel evolutionary relationships. We conclude that MSA Transformer complements, rather than replaces, classical inference for more accurate histories of protein families.

bioinformatics↗

bioRxiv2024

Evolution of Salmonella Chromosomes and Its Influence on Gene Expression and Chromosomal Conformation

Salmonella is one of the most important bacterial pathogens in the world, causing an estimated 120 million infections each year. There is considerable diversity, with [~]2,600 serovars, but it remains unclear how the genomes have evolved as the species and subspecies of Salmonella differentiate. Here, we have reconstructed the ancient orthologous chromosomes of each major Salmonella lineage and traced their evolutionary process. In total, 911 rearrangement events were identified, with 64% of events occurring in a locus-specific way. Using RNA sequencing and multi-strain association analysis, we demonstrate that genetic rearrangements have a significant effect on gene expression across Salmonella lineages. Moreover, we perform chromosome conformation capture (3C) sequencing analysis, which demonstrates large variations for the organization of ter chromosomal interaction domains among Salmonella lineages. In conclusion, our work delineates the evolutionary trajectory of Salmonella chromosomes, and demonstrates the influence of rearrangements on gene expression profiles and chromosomal conformation. ImportanceThis study reconstructed the ancient orthologous chromosomes of the Salmonella genus, species and well-recognized subspecies, by which the trajectory of gene flow caused by genetic rearrangements was delineated chronologically. The rearrangements show apparent hotspot distribution property and are enriched with genes important for bacterial fitness. Correlation analysis further disclosed the general influence of the rearrangements on gene expression and the organization and conformation of chromosome interaction domains. The results provide new insights on the evolution of Salmonella chromosomes, especially the genetic rearrangements and their epigenetic consequences.

microbiology↗

bioRxiv2024

Cell types associated with human brain functional connectomes and their implications in psychiatric diseases

Cell types are fundamental to the functional organization of the human brain, yet the specific cell clusters contributing to functional connectomes remain unclear. Using human whole-brain single-cell RNA sequencing data, we investigated the relationship between cortical cell cluster distribution and functional connectomes. Our analysis identified dozens of cell clusters significantly associated with resting-state network connectivity, with excitatory neurons predominantly driving positive correlations and inhibitory neurons driving negative correlations. Many of these cell clusters are also conserved in macaques. Notably, functional network connectivity is predicted by cellular communication among these clusters. We further identified cell clusters linked to various neuropsychiatric disorders, with several clusters implicated in multiple conditions. Comparative analysis of schizophrenia and autism spectrum disorder revealed distinct expression patterns, highlighting disease-specific cellular mechanisms. These findings underscore the critical role of specific cell clusters in shaping functional connectomes and their implications for neuropsychiatric diseases.

neuroscience↗

bioRxiv2024

Cryo-EM Structure of AAA + ATPase Thorase Reveals Novel Helical Filament Formation

The AAA+ (ATPases associated with a variety of cellular activities) ATPase, Thorase, also known as ATAD1, plays multiple roles in synaptic plasticity, mitochondrial quality control and mTOR signaling through disassembling protein complexes like AMPAR and mTORC1 in an ATP-dependent manner. The Oligomerization of Thorase is crucial for its disassembly and remodeling functions. We show that wild-type Thorase forms long helical filaments in vitro, dependent on ATP binding but not hydrolysis. We report the Cryogenic Electron Microscopy (cryo-EM) structure of the Thorase filament at a resolution of 4 [A], revealing the dimeric arrangement of the basic repeating unit that is formed through a distinct interface compared to the hexameric MSP1/ATAD1E193Q assembly. Structure-guided mutagenesis confirms the role of critical amino acid residues required for filament formation, oligomerization and disassembly of mTORC1 protein complex. Together, our data reveals a novel filament structure of Thorase and provides critical information that elucidates the mechanism underlying Thorase filament formation and Thorase-mediated disassembly of the mTORC1 complex.

biochemistry↗

bioRxiv2024

Comparative spatiotemporal single cell transcriptomes reveal rewiring of pre-existing regulations during emergence of Kranz anatomy in C4 grasses

Many of the worlds most productive food and bioenergy crops use C4 photosynthesis, which have high photosynthetic efficiency due to a Kranz anatomy-based CO2 concentrating mechanism. Here, we took a comparative transcriptomics approach using single cell spatial transcriptomes of leaf primordia for maize (Zea mays) and single cell RNA-seq (scRNA-seq) atlases of corresponding leaf tissues for three C4 species (Zea mays, Sorghum bicolor, Setaria viridis) and one C3 rice (Oryza sativa) to study regulatory networks involved in the development and evolution of Kranz anatomy. We show that the formation of Kranz anatomy involves extensive recruitment and modification of pre-existing regulatory modules, especially the SHR-SCR module and the auxin signaling pathway. Members of the INDETERMINATE DOMAIN (IDD) family transcription factors, including IDD7 and IDDP1, contribute to the modification of the involved modules. These extensive recruitment and modification of existing genetic regulatory programs underlie the repeated emergence of C4 photosynthesis during evolution.

plant biology↗

bioRxiv2024

SLB-msSIM: a spectral library-based multiplex segmented SIM platform for single-cell proteomic analysis

Mass spectrometry (MS)-based single-cell proteomics, while highly challenging, offers unique potential for a wide range of applications to interrogate cellular heterogeneity, trajectories, and phenotypes at a functional level. We report here the development of the spectral library-based multiplex segmented selected ion monitoring (SLB-msSIM) method, a conceptually unique approach with significantly enhanced sensitivity and robustness for single-cell analysis. The single-cell MS data is acquired by multiplex segmented selected ion monitoring (msSIM) technique, which sequentially applies multiple isolation cycles with the quadrupole using a wide isolation window in each cycle to accumulate and store precursor ions in the C-trap for a single scan in the Orbitrap. Proteomic identification is achieved through spectral matching using a well-defined spectral library. We applied the SLB-msSIM method to interrogate cellular heterogeneity in various pancreatic cancer cell lines, revealing common and distinct functional traits among PANC-1, MIA-PaCa2, AsPc-1, HPAF, and normal HPDE cells. Furthermore, for the first time, our novel data revealed the diverse cell trajectories of individual PANC-1 cells during the induction and reversal of epithelial-mesenchymal transition (EMT). Collectively, our results demonstrate that SLB-msSIM is a highly sensitive and robust platform, applicable to a wide range of instruments for single-cell proteomic studies.

systems biology↗

bioRxiv2024

The E3 ligase NEDD4L prevents colorectal cancer liver metastasis via degradation of PRMT5 to inhibit the AKT/mTOR signaling pathway

Colorectal cancer is the second most common cause of cancer mortality worldwide, and liver metastasis is the major cause of death in patients with colorectal cancer. Dysfunctional E3 ligase activity has recently been shown to be associated with colorectal cancer. However, the key E3 ligase affecting colorectal cancer liver metastasis remains unknown. Therefore, we used an shRNA library targeting 156 E3 ubiquitin ligases to perform an in vivo loss-of-function screen of a human colorectal cancer cell line in a mouse model of colorectal cancer liver metastasis. The screen revealed that NEDD4L knockdown promoted colorectal cancer liver metastasis. Moreover, overexpression of NEDD4L prevented colorectal cancer liver metastasis. Mechanistic studies revealed that NEDD4L bound to the PPNAY motif in PRMT5 and ubiquitinated PRMT5 to promote its degradation. PRMT5 degradation attenuated the methylation of an arginine residue in AKT1 to inhibit the AKT/mTOR signaling pathway, consequently decreasing colorectal cancer cell proliferation. We are the first to show that PRMT5 is a substrate protein of the E3 ligase NEDD4L and reveals not only the metastasis-inhibiting function of NEDD4L but also a novel mechanism by which NEDD4L suppresses colorectal cancer liver metastasis. These findings may provide a new preventive strategy for liver metastasis.

cancer biology↗

bioRxiv2024

α-Synuclein Strain Dynamics Correlate with Cognitive Shifts in Parkinson's Disease

-Synuclein (-syn) strains can serve as discriminators between Parkinsons disease (PD) and related -synucleinopathies. The relationship between -syn strain dynamics and clinical performance as patients transition from normal cognition (NC) to cognitive impairment (CI) is not known. Here, we show that the biophysical properties and neurotoxicity of -syn strains change as PD cognitive status transitions from NC to mild cognitive impairment (PD-MCI) and dementia (PD-D). Both cross-sectional and longitudinal analyses reveal distinct -syn strains in PD patients correlating to their level of cognitive impairment. Machine learning (ML) was employed to achieve high classification accuracy. The combination of thioflavin T (ThT) maximal fluorescence intensity (mfi), max slope of rise curve (forming rate), lag time (tlag), 20% time (t20), and half-time (t50), dynamic light scattering (DLS) (peak number, [1/2] peak size, [1/2] peak intensity) and neurotoxicity together with demographic variables for model training yielded superior performance (89[~]99% accuracy in the 4- and 2- classification schema) compared to individual features alone in classifying cognitive status. For the longitudinal study, DLS peak number emerged as the strongest predictor of cognitive transition (HR = 0.12, P = 0.002), with the optimal predictive model combining DLS peak number, sex, education, DLS peak 1 size, and DLS peak 2 polydispersity achieving high accuracy (C-index of [~]93%). This study presents evidence that individuals with PD have different -syn strains correlating to their cognitive status and highlights the potential of -syn strain dynamics to guide future diagnosis, management, and stratification of PD patients. One Sentence SummaryDistinct features of -syn strains change with cognitive decline in Parkinsons disease and AI-based analysis incorporating these combined characteristics serves as a powerful tool for PD clinical stratification.

neuroscience↗

bioRxiv2024

Stereotype of mouse social competency and status revealed by a novel competition paradigm in combination with available paradigms

Psychological, behavioral and biological studies on social organization and competition with animal models are boosting. The mouse has been recognized as a valuable and economic model animal for biomedical research in social behaviors, however, currently available food competition paradigms for mice remain limited. Discrepant paradigms involving different competitive factors, such as physical strength vs psychological features, muscular confrontation vs threat perception, and boldness vs timidity, may produce task-specific win-or-lose outcomes and lead to inconsistent ranking results. Here, we developed a food competition apparatus for mouse, in which contenders were a pair of mice eager to take over the same food pellet placed under a movable block in the middle of a narrow chamber where they were separated to the either right or left side. This Food Pellet Competition Test (FPCT) was designed to (1) provide researchers with a choice of new food competition paradigm and (2) expose psychological factors influencing the establishment and/or expression social status in mice by avoiding direct physical competition between contenders. Meanwhile, we wanted to evaluate the consistency of social ranking results between FPCT and typically available space competition paradigms--tube test and warm spot test (WST). We hypothesized inconsistency of rankings of mice tested by FPCT, tube test and WST as they possess different targets for mice to compete and different factors determining competitiveness. Interestingly, application of FPCT in combination with tube test and WST discovered unexpected consistency of mouse social competitivity and rankings in a grouped male or female mice that were housed in an either 2-or 3-member cage, most likely indicating that the status sense of animals is part of a comprehensive identify of self-recognition of individuals in an established social colony. Furthermore, the FPCT may facilitate researches on social organization and competition, given its reliability, validity, and ease of use.

neuroscience↗

bioRxiv2024

Longitudinal multi-omics reveals pathogenic TSC2 variants disrupt developmental trajectories of human cortical organoids derived from Tuberous Sclerosis Complex

Tuberous Sclerosis Complex (TSC), an autosomal dominant condition, is caused by heterozygous mutations in either the TSC1 or TSC2 genes, manifesting in systemic growth of benign tumors. In addition to brain lesions, neurologic sequelae represent the greatest morbidity in TSC patients. Investigations utilizing TSC1/2-knockout animal or human stem cell models suggest that TSC deficiency-causing hyper-activation of mTOR signaling might precipitate anomalous neurodevelopmental processes. However, how the pathogenic variants of TSC1/2 genes affect the longitudinal trajectory of human brain development remains largely unexplored. Here, we employed 3-dimensional cortical organoids derived from induced pluripotent stem cells (iPSCs) from TSC patients harboring TSC2 variants, alongside organoids from age- and sex-matched healthy individuals as controls. Through comprehensively longitudinal molecular and cellular analyses of TSC organoids, we found that TSC2 pathogenic variants dysregulate neurogenesis, synaptogenesis, and gliogenesis, particularly for reactive astrogliosis. The altered developmental trajectory of TSC organoids significantly resembles the molecular signatures of neuropsychiatric disorders, including autism spectrum disorders, epilepsy, and intellectual disability. Intriguingly, single cell transcriptomic analyses on TSC organoids revealed that TSC2 pathogenic variants disrupt the neuron/reactive astrocyte crosstalk within the NLGN-NRXN signaling network. Furthermore, cellular and electrophysiological assessments of TSC cortical organoids, along with proteomic analyses of synaptosomes, demonstrated that the TSC2 variants precipitate perturbations in synaptic transmission, neuronal network activity, mitochondrial translational integrity, and neurofilament formation. Notably, similar perturbations were observed in surgically resected cortical specimens from TSC patients. Collectively, our study illustrates that disease-associated TSC2 variants disrupt the neurodevelopmental trajectories through perturbations of gene regulatory networks during early cortical development, leading to mitochondrial dysfunction, aberrant neurofilament formation, impaired synaptic formation and neuronal network activity.

neuroscience↗

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

Traumatic Brain Injury Exacerbates Alcohol Consumption and Neuroinflammation with Decline in Cognition and Cholinergic Activity

Traumatic brain injury (TBI) is a global health challenge, responsible for 30% of injury-related deaths and significantly contributing to disability. Annually, over 50 million TBIs occur worldwide, with most adult patients at emergency departments showing alcohol in their system. TBI is also a known risk factor for alcohol abuse, yet its interaction with alcohol consumption remains poorly understood. In this study, we demonstrate that the fluid percussion injury (FPI) model of TBI in mice significantly increases alcohol consumption and impairs cognitive function. At cellular levels, FPI markedly reduced the number and activity of striatal cholinergic interneurons (CINs) while increasing microglial cells. Notably, depleting microglial cells provided neuroprotection, mitigating cholinergic loss and enhancing cholinergic activity. These findings suggest that TBI may promote alcohol consumption and impair cognitive abilities through microglia activation and consequently reduced cholinergic function. Our research provides critical insights into the mechanisms linking TBI with increased alcohol use and cognitive deficits, potentially guiding future therapeutic strategies.

neuroscience↗

bioRxiv2024

Loss of Diurnal Oscillatory Rhythms in Gut Microbiota Correlates with Progression of Atherosclerosis

Circadian rhythms in gut microbiota composition are crucial for metabolic function and disease progression, yet the diurnal oscillation patterns of gut microbiota in atherosclerotic cardiovascular disease (ASCVD) and their role in disease progression remain unknown. Here, we investigate gut bacterial dynamics in ApoE-/- mice within a day, and elucidated the dynamic changes in fecal microbiota composition and function differences among C57BL/6 and ApoE-/- mice with standard chow diet or high-fat, high-cholesterol diet under ad libitum conditions. Compared with C57BL/6 mice, ApoE-/- mice exhibit significant differences in fecal microbial composition. Rhythmic analysis showed that the dynamic changes in the composition and function of fecal microbiota in ApoE-/- mice were significantly different from those in C57BL/6 mice. We further found that the rhythmic strains (Blautia Coccoides) inhibit the progression of ASCVD by improving the intestinal and endothelial barrier function. Our findings demonstrate that diurnal oscillations in gut microbiota are closely related to the progression of ASCVD, and provide a new insight for microbial-targeted therapies for ASCVD.

microbiology↗

bioRxiv2024

Contrasting patterns of specificity and transfer in human odor discrimination learning

Practice enhances olfactory performance. However, laboratory studies to date suggest that olfactory learning is largely restricted to the trained odors, posing a significant challenge for training-based rehabilitation therapies for olfactory loss. In this study, we introduce various types of odors to olfactory discrimination training, conducted unilaterally. We demonstrate contrasting patterns of specificity and transfer of learning, independent of adaptation and task difficulty. Individuals trained with odor mixtures of different ratios show long-term perceptual gains that completely transfer to the untrained nostril and effectively generalize to untrained mixtures dissimilar in structure and odor quality from the trained ones. Conversely, those trained with odor enantiomers show no transfer of learning across nostrils or to unrelated enantiomers, replicating our earlier findings (Feng & Zhou, 2019). Our observations indicate that concentration ratio and chirality represent distinct olfactory attributes. Furthermore, discrimination learning occurs at different stages of olfactory processing, depending on which attribute is task-relevant. These findings open up new avenues to enhance the effectiveness of olfactory training.

neuroscience↗

bioRxiv2024

Informing biologically relevant signal from spatial transcriptomic data

Visium is a spatial sequencing technology that utilizes messenger RNA (mRNA) to spatially map gene expression within tissues. Despite its potential, research utilizing deconvolution tools and exploring microenvironment dynamics remains challenging. We address this gap by benchmarking deconvolution tools across diverse biological contexts, identifying optimal methodologies. Subsequently, we introduce a novel pipeline integrating advanced deconvolution techniques and novel tools for reproducible tissue microenvironment analysis. Through this approach, we uncover intricate immune aggregate biology, highlighting the power of our methodology in unraveling complex biological phenomena.

bioinformatics↗

bioRxiv2024

A wheat tandem kinase sensor activates an NLR helper to trigger immunity

Most plant resistance genes encode membrane-anchored receptor-like proteins or intracellular nucleotide-binding and leucine-rich repeat (NLR) receptors. In wheat and barley, tandem kinases (TKs) have emerged as a new class of resistance determinants. To understand the modus operandi of the wheat stem rust resistance protein Sr62TK, we identified two genetic interactors-- a host gene required for Sr62TK function and the corresponding fungal AvrSr62 effector. We discovered that the SR62 locus consists of a digenic module encoding Sr62TK and an NLR (Sr62NLR). AvrSr62 binds to the N-terminal kinase of Sr62TK. This triggers displacement of the C-terminal kinase allowing it to recruit Sr62NLR for activation of immune responses. Understanding the mechanism of this two-component resistance complex will help engineering and breeding for durable resistance.

plant biology↗