Biology subjects

Tian, X.

Publications and source records attributed to Tian, X..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

METTL1/WDR4-mediated m7G Hypermethylation of SCLT1 mRNA Promotes Gefitinib Resistance in Non-small Cell Lung Cancer

Epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) have produced durable complete responses, but the eventual development of acquired resistance presents a huge challenge in the treatment of non-small cell lung cancer (NSCLC). N7-methylguanosine (m7G), a prevalent post-transcriptional modification within RNA, play regulatory roles in RNA stability, expression dynamics, and functional diversity. Despite these insights, the contribution of m7G methylation to EGFR-TKIs resistance remains poorly characterized. Here, we identified substantial upregulation of mRNA internal m7G modifications and their associated methyltransferase complex composed of methyltransferase-like 1 (METTL1) /WD repeat domain 4 (WDR4) were significantly elevated in NSCLC specimens, correlating with therapeutic resistance. Functional assays confirmed that METTL1/WDR4 enhances gefitinib resistance in both cellular and animal models via the internal RNA m7G methyltransferase activity in NSCLC. Mechanistically, m7G MeRIP-seq coupled with RNA-seq identified sodium channel and clathrin linker 1 (SCLT1) as the m7G target of METTL1/WDR4. METTL1/WDR4 knockdown may result in a decrease in both the demethylation level and mRNA stability of the SCLT1 transcript, while overexpression of wild-type METTL1, but not its catalytically inactive mutant, rescues mRNA stability. METTL1/WDR4-mediated m7G modification of SCLT1 regulates gefitinib resistance by activating the NF-{kappa}B signaling. These results establish aberrant mRNA internal m7G modification as a novel resistance mechanism and propose therapeutic targeting of the METTL1/WDR4-SCLT1-NF-{kappa}B axis cascade to overcome EGFR-TKIs resistance.

molecular biology↗

bioRxiv2025

A transcriptional atlas of the pubertal human growth plate reveals direct stimulation of cartilage stem cells by growth hormone.

The cartilaginous growth plate is a critical organ responsible for longitudinal bone growth. It remains open throughout life in mice but closes in humans after puberty. Growth hormone (GH) is a widely used therapy for children with growth retardation and open growth plates. However, it remains unclear whether GH directly targets human growth plates. Furthermore, while cartilage stem cells have recently been identified in mouse growth plates, their presence and GH responsiveness in human growth plates are unknown. To address these gaps, we characterized the cellular and molecular organization of early pubertal human growth plates using unique tissue samples obtained during growth-restricting surgeries. Our analysis identified two distinct populations of stem cells differing in cycling activity, molecular profiles, and regulatory factors. Quiescent stem cells were localized within a niche characterized by low Wnt and TGF{beta} signaling. To investigate the direct effects of GH, we developed a human growth plate explant culture system. GH directly stimulated explant growth and promoted stem cell proliferation by activating the JAK/STAT, TGF{beta}, and ERK pathways while inhibiting the AKT pathway. Notably, activation of the TGF{beta} pathway occurred in an autocrine manner. These findings provide critical new insights into human longitudinal growth and the mechanisms of GH action, with potential implications for optimizing treatments for growth disorders. One Sentence SummaryThis study reveals that growth hormone (GH) directly promotes proliferation within the human growth plate and activates TGF{beta} and ERK signaling pathways in cartilage stem cells, providing critical insights into human longitudinal growth and potential improvements in treatments for growth disorders.

cell biology↗

bioRxiv2025

Comparative Transcriptomic Analysis of Embryonic Stem Cells (ESCs) across Mammalian Species

Pluripotency, the ability of cells to self-renew and differentiate into all the cell types in an animals body, is vital for mammalian early development. This study presented a comprehensive comparative transcriptomic analysis of embryonic stem cells across multiple mammalian species, defining their progression through expanded/extended, naive, formative, and primed pluripotency states. Our findings revealed both conserved and species-specific mechanisms underlying pluripotency regulation. We also emphasized the limitations of existing state-specific markers and their limited cross-species applicability, while identifying de novo pluripotency markers that can inform future research. Despite variability in gene expression dynamics, gene co-expression networks showed remarkable conservation across species. Among pluripotency states, the primed state demonstrated the highest conservation, evidenced by shared markers, preserved gene networks, and stronger selective pressures acting on its genes. These findings provide critical insights into the evolution and regulation of pluripotency, laying a foundation for refining stem cell models to enhance their translational potential in regenerative medicine, agriculture, and conservation biology.

genomics↗

bioRxiv2025

The stress response factor SigH mediates intrinsic resistance to multiple antibiotics in Mycobacterium abscessus

Mycobacterium abscessus (Mab) causes pulmonary diseases with limited treatment options due to its high level of intrinsic resistance to available drugs. Mab possesses complex and poorly understood drug resistance mechanisms. Identifying new drug targets and gaining a deeper understanding of drug resistance mechanisms are essential for discovering novel therapeutic alternatives. Here, we investigated the role of a putative sigma factor SigH in intrinsic multi-drug resistance in Mab. Mab SigH shares an 84% peptide sequence identity with Mycobacterium tuberculosis (Mtb) SigH, a well-known stress response protein and global transcriptional regulator. We constructed a sigH gene deletion strain of Mab ({Delta}sigH) and complemented strains by expressing either Mab sigH (CPMabsigH) or Mtb sigH (CPMtbsigH) in {Delta}sigH. The {Delta}sigH strain exhibited hypersensitivity to a broad range of antibiotics, including levofloxacin, moxifloxacin, tigecycline, tetracycline, amikacin, vancomycin, and rifabutin and all complemented strains restored the drug resistance phenotype. Additionally, {Delta}sigH showed increased sensitivity to oxidative and heat stress compared to the wild-type Mab and complemented strains. Transcriptomic analysis revealed that deletion of sigH disrupted the balance of gene expression, primarily elevating the expression of genes encoding YrbE and MCE family proteins and downregulating genes expressing ABC-type transporters, sigma and anti-sigma factors and other genes associated with antimicrobial resistance. Collectively, our findings indicate that SigH is a key regulator of global gene expression in response to environmental stresses, including antimicrobial treatment, and is crucial for the intrinsic drug resistance of Mab. SigH represents a promising target for the development of novel therapeutic strategies against Mab infections.

molecular biology↗

bioRxiv2025

Identification of a new inhibitor of Ran GTPase with therapeutic value in epithelial ovarian cancer

Compiled research studies suggest that the small GTPase Ran is critical in cancer initiation and progression. Compounds that block Ran activity would be valuable for cancer treatment. Yet, to date, there is no inhibitor proven to be efficient and specific to Ran. Here, by learning lessons from the discovery of KRAS G12C inhibitors, we generated a structural model of the switch II pocket of GDP-bound Ran to identify potential inhibitors of Ran by virtual screening. After in vitro verification, compound M26 was detected. Subsequent hit optimization lead us to identify compound M36 as an inhibitor of Ran with a promising therapeutic value. Binding of M36 to Ran was confirmed by cellular thermal shift assay. The specificity of M36 towards Ran was demonstrated by the evaluation of the active GTP-bound forms of a range of GTPases including Ran, RhoA, Cdc42 and Rac1; and by the expression of a dominant active mutant of Ran. Remarkably, similar to depletion of Ran by siRNA, M36 exhibits a specific toxicity in aneuploid ovarian cancer cells and represses DNA repair systems. In accordance with this, we demonstrated a synergistic relationship between M36 and the FDA approved PARP inhibitor Olaparib. In vivo, M36 presents acceptable pharmacokinetic properties and, more importantly, inhibits the tumor growth of an aggressive epithelial ovarian cancer xenograft model. Clinically relevant, M36 was able to induce cell death in ex vivo EOC patient derived micro-dissected tumor. Overall, our study is the first to provide a small-molecule compound inhibitor of Ran with a promising therapeutic potential.

cancer biology↗

bioRxiv2025

QWENDY: Gene Regulatory Network Inference Enhanced by Large Language Model and Transformer

Knowing gene regulatory networks (GRNs) is important for understanding various biological mechanisms. In this paper, we present a method, QWENDY, that uses single-cell gene expression data measured at four time points to infer GRNs. Based on a linear gene expression model, it solves the transformation of the covariance matrices. Unlike its predecessor WENDY, QWENDY avoids solving a non-convex optimization problem and produces a unique solution. We test the performance of QWENDY on three experimental data sets and two synthetic data sets. Compared to previously tested methods on the same data sets, QWENDY ranks the first on experimental data, although it does not perform well on synthetic data.

genetics↗

bioRxiv2025

Synergistic MAPT mutations as a platform to uncover modifiers of tau pathogenesis

The natively unfolded tau (MAPT) protein is extremely soluble, which poses challenges when modeling neurofibrillary tangle (NFT) pathology in Alzheimers disease (AD). To overcome this hurdle, we combined P301L and S320F mutations (PL-SF) to generate a rapid and reliable tau pathology platform to expedite the discovery of factors that modify tau aggregation. Using this model, we evaluated heat-shock proteins (Hsp), which have been linked to tau pathology, but whose role in AD remains enigmatic and controversial. In primary neurons, expression of Hsp70, but not Hsc70 or Hsp90, exacerbated tau aggregation. Conversely, lowering Hsp70 or employing a chaperone-deficient tau mutant (PL-SF-4{Delta}) reduced tau phosphorylation and abrogated tau aggregation, highlighting Hsp70 as a key driver of tau aggregation. Hsp70 foci clustered within and surrounding neuritic plaques and NFTs in post-mortem AD brain. Functionally, mature aggregate-bearing neurons showed deficits in neuronal firing and network communication, which were restored by chaperone-binding deficient tau variants that abrogated tau pathology. This study provides a powerful cell-intrinsic model for accelerated tau aggregation, which can be harnessed to identify potent regulators of tau aggregation as promising therapeutic targets.

neuroscience↗

bioRxiv2025

TLR4 Modulates Simvastatin's Impact on HDL Cholesterol and Glycemic Control

Statins lower cardiovascular risk by inhibiting HMG-CoA reductase, with their efficacy and adverse effects linked to SREBP-regulated cholesterol metabolism. Nutritional states-- particularly the alternating fasting and feeding cycles, rather than intrinsic circadian rhythms-- exert tight control over hepatic lipid metabolism via SREBP-mediated regulation of cholesterol and fatty acid synthesis. We exploited the natural diurnal oscillations in food intake in mice to determine how nutritional state modulates simvastatins metabolic actions. When administered during fasting, simvastatin impaired glucose homeostasis through SREBP-2-driven autophagy that enhanced PPAR activity, whereas simvastatin given during feeding reduced HDL cholesterol and improved glucose metabolism. Mechanistically, a feeding-induced surge in lipopolysaccharide (LPS) suppressed hepatic oxysterol synthesis, thereby enabling simvastatin to further deplete oxysterols and inhibit activation of LXR and SREBP-1c--key regulators of PPAR signaling under both postprandial and fasting conditions. This cascade resulted in decreased HDL cholesterol levels and improved glycemic control. Moreover, TLR4 deficiency disrupted the LPS-simvastatin interplay on LXR/SREBP-1c/PPAR signaling, reversing the HDL-lowering and glucose-improving effects seen during feeding. Together, these results identify feeding-induced LPS-TLR4 signaling as a critical determinant of simvastatins metabolic effects and suggest strategies to optimize statin therapy based on nutritional state.

pharmacology and toxicology↗

bioRxiv2025

Lethal streptococcal infection is associated with widened lymph node bottlenecks

Streptococcus suis serotype 2 (SS2) infection causes streptococcal toxic shock-like syndrome (STSLS), which can be lethal in both pigs and humans. In mouse models, relatively subtle differences in the inoculum size result in drastically different infection outcomes, from clearance to acute death. Here, we leveraged barcoded SS2 in a murine model to define the bacterial population dynamics associated with death. Barcode sequencing analysis demonstrated that a 10-fold increase in inoculum size led to a 100-1,000-fold increase in the number of bacteria that initiated infection in certain lymph nodes, ultimately driving lethality. This lethal dose threshold was in part driven by suilysin (SLY), the major SS2 virulence factor. At higher doses, the clearance and replication kinetics of bacteria lacking SLY mimicked WT SS2 at sub-lethal doses. Our findings suggest that acute death in SS2 infection is caused by a wholesale failure of the immune system, enabling a large number of bacteria to initiate infection. These results demonstrate how subtle changes in inoculum size can have dramatic consequences for infection outcome and how lethal infection is driven by widened infection bottlenecks. Author SummaryLethal infections are often associated with a specific dose threshold, where increasing inoculum size is associated with an increased likelihood of death. However, a quantitative explanation how this numeric threshold is established is lacking. For example, lethal dose thresholds may reflect a dose where at least one microbe can pass through host-imposed barriers to infection. Alternatively, lethal dose thresholds may reflect a failure of the host immune system, leading to numerous microbes initiating infection. Here, using barcoded Streptococcus suis serotype 2 (SS2), we compare the within-host population dynamics associated between lethal and non-lethal infections. We find that lethal doses are associated with dramatic widening of infection bottlenecks, leading to a large number of bacteria that initiate infection. Lethal infection is also driven by suilysin, the major SS2 virulence factor. These observations demonstrate how lethal doses are quantitatively established by the relationship between host bottlenecks and bacterial virulence factors.

microbiology↗

bioRxiv2025

TransBrain: A computational framework for translating brain-wide phenotypes between humans and mice

Despite remarkable advances in whole-brain imaging technologies, the lack of quantitative approaches to bridge rodent preclinical and human studies remains a critical challenge. Here we present TransBrain, a computational framework enabling bidirectional translation of brain-wide phenotypes between humans and mice. TransBrain improves human-mouse homology mapping accuracy through: (1) a novel detached region-specific deep neural network trained on integrated multi-modal human transcriptomics to improve cortical correspondence (89.5% improvement over the original transcriptome), which revealed two evolutionarily conserved gradients explaining >50% of cortical organizational variance, and (2) random walk-based graph representation learning to construct a unified cross-species latent space incorporating anatomical hierarchies and structural connectivity. We demonstrated TransBrains utility through three cross-species applications: quantitative assessment of resting-state brain organizational features, inferring human cognitive functions from mouse optogenetic circuits, and translating molecular insights from mouse models to individual-level mechanisms in autism. TransBrain enables quantitative cross-species comparison and mechanistic investigation of both normal and pathological brain functions.

neuroscience↗

bioRxiv2025

Protective mechanisms against Alzheimer's Disease in APOE3-Christchurch homozygous astrocytes

The APOE3-Christchurch (APOE3-Ch) variant has been linked to reduced Alzheimers Disease (AD) risk, but its protective mechanisms remain unclear. This study explores the neuroprotective phenotype of APOE3-Ch astrocytes, focusing on lipid metabolism and tau processing. APOE3-Ch astrocytes demonstrate enhanced tau oligomer uptake via HSPG- and LRP1-mediated pathways, facilitated by elevated HSPG expression, and achieve superior tau degradation through lysosomal pathways and proteasomal pathways, in contrast to wild-type astrocytes, which primarily use proteasomal mechanisms. Transcriptomic analysis reveals upregulation of genes involved in endocytosis and cell projection assembly, explaining enhanced tau uptake and clearance in APOE3-Ch astrocytes. Lipidomic profiling identifies reduced levels of pathological lipids such as ceramides and gamma-linolenic acid (GLA), potentially mitigating neuroinflammation. These findings provide insight into the protective mechanisms of APOE3-Ch astrocytes and underscore their potential as therapeutic targets for tauopathy and neurodegeneration in AD. TeaserAPOE3-Christchurch astrocytes enhance tau clearance and mitigate neurotoxic lipid accumulation, unveiling protective mechanisms against Alzheimers.

neuroscience↗

bioRxiv2025

7-ketocholesterol contributes to microglia-driven increases in astrocyte reactive oxygen species in Alzheimer's disease

Oxidative stress is a prominent feature of Alzheimers disease. Within this context, cholesterol undergoes oxidation, producing the pro-inflammatory product 7-ketocholesterol (7-KC). In this study, we observe elevated levels of 7-KC in the brains of the 3xTg mouse model of AD. To further understand the contribution of 7-KC on the oxidative environment, we developed a method to express a genetically encoded fluorescent hydrogen peroxide (H2O2) sensor in astrocytes, the primary source of cholesterol in the brain. With this sensor, we discovered that 7-KC increases H2O2 levels in astrocytes in vivo, but not when directly applied to astrocytes in vitro. Interestingly, when 7-KC was applied to a microglia cell line alone or mixed astrocyte and microglia cultures, it resulted in microglia activation and increased oxidative stress in astrocytes. Depletion of microglia from 3xTg mice resulted in reduced 7-KC in the brains of these mice. Taken together, these findings suggest that 7-KC, acting through microglia, contributes to increased astrocyte oxidative stress in AD. This study sheds light on the complex interplay between cholesterol oxidation, microglia activation, and astrocyte oxidative stress in the pathogenesis of AD.

neuroscience↗

bioRxiv2024

Bovine Formative Embryonic Stem Cell Plasticity in Embryonic and Extraembryonic Differentiation

Bovine embryonic stem cells (bESCs) can greatly enhance understanding of bovine embryonic development and applications for disease-resistance, biomedical and zoonotic pre-clinical models. However, formative bESCs with distinct morphology and complete differentiation capacity are still unreported. We document here the generation of bESCs which are pluripotent both in vitro and in vivo, and efficiently converted into neural progenitor cells (NPCs) and primordial germ cell-like cells (PGCLCs) by direct differentiation. These cells exhibited distinct metabolic features from human and mouse ESCs and early embryos. Formative bESCs contributed to a wide range of cell types within embryonic and extraembryonic tissues after aggregating with mouse and bovine embryos. The establishment of bovine formative ESCs with dual developmental plasticity represents a milestone for agricultural biotechnology and decoding the underlying mechanism of bona fide bovine pluripotency. Summary statementGenerating bovine ESCs would greatly enhance understanding of bovine embryonic development and bioengineering of cattle for disease-resistance, biomedical and zoonotic pre-clinical models.

developmental biology↗

bioRxiv2024

Foveal action for the control of extrafoveal vision

Microsaccades have been convincingly linked to extrafoveal covert attention shifts for more than two decades. However, the direction of causality between individual microsaccade generation and an alteration in both extrafoveal visual sensitivity and behavior remains debated: do microsaccades merely reflect, perhaps probabilistically, an altered extrafoveal sensitivity, or is the act of generating microsaccades sufficient, on its own, to modify such sensitivity? Using a novel exploitation of real-time retinal image stabilization, behavior, and neurophysiology in the superior colliculus of rhesus macaque monkeys, we show that exclusive experimental control over foveal oculomotor state is entirely sufficient to influence extrafoveal sensitivity. This happens for eccentricities as large as [~]50 times those associated with microsaccades, and it also takes place in the absence of any differential attentional demands. Most importantly, such influence is mediated through well-known, classic pre- and post-saccadic visual processing changes. Thus, seemingly-innocuous subliminal eye movements do constitute an integral component of cognitive processes like attention.

neuroscience↗

bioRxiv2024

Expanding the Landscape of Aging via Orbitrap Astral Mass Spectrometry and Tandem Mass Tag (TMT) Integration

Aging results in a progressive decline in physiological function due to the deterioration of essential biological processes, such as transcription and RNA splicing, ultimately increasing mortality risk. Although proteomics is emerging as a powerful tool for elucidating the molecular mechanisms of aging, existing studies are constrained by limited proteome coverage and only observe a narrow range of lifespan. To overcome these limitations, we integrated the Orbitrap Astral Mass Spectrometer with the multiplex tandem mass tag (TMT) technology to profile the proteomes of three brain tissues (cortex, hippocampus, striatum) and kidney in the C57BL/6JN mouse model, achieving quantification of 8,954 to 9,376 proteins per tissue (cumulatively 12,749 across all tissues). Our sample population represents balanced sampling across both sexes and three age groups (3, 12, and 20 months), comprising young adulthood to early late life (approximately 20-60 years of age for human lifespan). To enhance quantitative accuracy, we developed a peptide filtering strategy based on resolution and signal-to-noise thresholds. Our analysis uncovered distinct tissue-specific patterns of protein abundance, with age and sex differences in the kidney, while brain tissues exhibit notable age changes and limited sex differences. In addition, we identified both proteomic changes that are linear with age (i.e., continuous) and that have a non-linear pattern (i.e., non-continuous), revealing complex protein dynamics over the adult lifespan. Integrating our findings with early developmental proteomic data from brain tissues highlighted further divergent age-related trajectories, particularly in synaptic proteins. This study not only provides a robust data analysis workflow for TMT datasets generated using the Orbitrap Astral mass spectrometer but also expands the proteomic landscape of aging, capturing proteins with age and sex effects with unprecedented depth.

systems biology↗

bioRxiv2024

Vaginal Microbiome and Inflammation Among Chinese Women.

Human papillomavirus (HPV) infection, cervical intraepithelial neoplasia (CIN), pelvic organ prolapse (POP), cervical polyps (CP), abnormal uterine bleeding (AUB), and vaginitis are common conditions encountered in gynecological practice. In this study, we collected vaginal secretions from patients diagnosed with these diseases (n = 310) and from healthy donors (n = 112) to analyze their vaginal microbiome using 16S rRNA sequencing and cytokine expression using a cytometric bead array (CBA). Our findings revealed that the vaginal microbiome in POP patients exhibited higher complexity compared to other groups. Regarding cytokine expression, levels of IL-1, IL-1{beta}, IL-6, IL-8, MCP-1, and MIG were significantly elevated in HPV and CIN patients. Analysis of microbial associations showed that Lactobacillus crispatus and Lactobacillus iners were significantly negatively correlated with IL-1 and IL-1{beta} expression. In contrast, non-Lactobacillus bacteria, including Bifidobacterium breve, Prevotella bivia, Gardnerella vaginalis, Sneathia amnii, Sneathia sanguinegens, Prevotella amnii, Escherichia coli, and Chlamydia trachomatis, were positively correlated with IL-1, IL-1{beta}, IL-6, IL-8, MCP-1, and MIG levels. Furthermore, Lactobacillus iners exhibited a significant negative effect in the HPV and CIN patient groups.

microbiology↗

bioRxiv2024

Age-associated modulation of TREM1/2- expressing macrophages promotes melanoma progression and metastasis

Aging is a known risk factor for melanoma, yet mechanisms underlying melanoma progression and metastasis in older populations remain largely unexplored. Among the current knowledge gaps is how aging alters phenotypes of cells in the melanoma microenvironment. Here we demonstrate that age enriches the immunosuppressor tumor microenvironment, which is linked to phenotypes associated with melanoma metastasis. Among cellular populations enriched by aging were macrophages with a tolerogenic phenotype expressing TREM2 and dysfunctional CD8-positive cells with an exhausted phenotype, while macrophages with profibrotic phenotype expressing TREM1 were depleted. Notably, TREM1 inhibition decreased melanoma growth in young but not old mice, whereas TREM2 inhibition prevented lung metastasis in aged mice. These data identify novel targets associated with melanoma metastasis and may guide aged-dependent immunotherapies.

cancer biology↗

bioRxiv2024

Spatially Resolved in vivo CRISPR Screen Sequencing via Perturb-DBiT

Perturb-seq enabled the profiling of transcriptional effects of genetic perturbations in single cells but lacks the ability to examine the impact on tissue environments. We present Perturb-DBiT for simultaneous co- sequencing of spatial transcriptome and guide RNAs (gRNAs) on the same tissue section for in vivo CRISPR screen with genome-scale gRNA libraries, offering a comprehensive understanding of how genetic modifications affect cellular behavior and tissue architecture. This platform supports a variety of delivery vectors, gRNA library sizes, and tissue preparations, along with two distinct gRNA capture methods, making it adaptable to a wide range of experimental setups. In applying Perturb-DBiT, we conducted un-biased knockouts of tens of genes or at genome-wide scale across three cancer models. We mapped all gRNAs in individual colonies and corresponding transcriptomes in a human cancer metastatic colonization model, revealing clonal dynamics and cooperation. We also examined the effect of genetic perturbation on the tumor immune microenvironment in an immune-competent syngeneic model, uncovering differential and synergistic perturbations in promoting immune infiltration or suppression in tumors. Perturb-DBiT allows for simultaneously evaluating the impact of each knockout on tumor initiation, development, metastasis, histopathology, and immune landscape. Ultimately, it not only broadens the scope of genetic inquiry, but also lays the groundwork for developing targeted therapeutic strategies.

genomics↗