Search bioRxiv⌕ Search

Biology subjects

Li, T.

Publications and source records attributed to Li, T..

At least 163 records · Page 9Linked to original sources

Genetic mapping of lifespan and mitochondrial stress response in C. elegans

The mitochondrial unfolded protein response (UPRmt) is one of the mito-nuclear regulatory circuits that restores mitochondrial function upon stress conditions, promoting metabolic health and longevity. However, the complex gene interactions that govern this pathway and its role in aging and healthspan remain to be fully elucidated. Here, we activated the UPRmt using doxycycline (Dox) in a genetically diverse C. elegans population comprising 85 strains and observed large variation in Dox-induced lifespan extension across these strains. Through multi-omic data integration, we identified an aging-related molecular signature that was partially reversed by Dox. To identify the mechanisms underlying Dox-induced lifespan extension, we applied quantitative trait locus (QTL) mapping analyses and found one UPRmt modulator, fipp-1/FIP1L1, which was functionally validated in C. elegans and humans. In the human UK Biobank, FIP1L1 was associated with metabolic homeostasis, underscoring its translational relevance. Overall, our findings demonstrate a novel UPRmt modulator across species and provide insights into potential translational research.

genetics↗

ASC contributes to sustained glial reactivity and mild cognitive impairment after closed-head injury

Mild brain traumatic brain injury (mTBI) from closed-head injuries (CHI) can lead to prevalent neuropsychiatric disorders, including an increased risk for neurodegenerative diseases and dementia. Inflammasomes are molecular complexes crucial for neuroinflammation and secondary damage after trauma, however their role in mild CHI is poorly understood. In this study, we investigate the cellular expression of inflammasome-related genes and their functional significance in CHI models. Single-cell RNA sequencing of cortical tissue revealed selective expression of Pycard (PYD and CARD domain containing), also known as Asc (apoptosis-associated speck-like protein containing a caspase recruitment domain), which encodes the inflammasome adaptor ASC, predominantly in microglial clusters. Sustained upregulation of inflammasome-related proteins persisted up to 21 days in a model for mTBI, with this pattern significantly reduced in Asc-/- mice. Importantly, mild cognitive impairment induced after mild CHI was largely abrogated in Asc-/- mice. These findings suggest that ASC, as the primary inflammasome adaptor, plays a critical role in sustaining neuroinflammation and contributes to cognitive deficits after mild CHI. This study provides insights into the molecular neuroinflammatory mechanisms underlying CHI, potentially informing future therapeutic strategies.

neuroscience↗

Simple 3D-Printed Stirred Bioreactor Enhances Retinal Organoid Production Via Improved Oxygenation

Retinal organoids (ROs), derived from human pluripotent stem cells (hPSCs), simulate in vivo development and retinal morphology, providing a platform to study retinal development and diseases. However, current differentiation protocols often yield inconsistent results with substantial cell line and batch variability. These protocols utilize static culture methods that rely on passive oxygen diffusion to reach the vessel bottom, where adherent hPSCs initially differentiate. Static culture is standard for adherent monolayer cells and is presumed suitable for RO differentiation. We questioned this assumption given that, during differentiation, the monolayer hPSCs become highly structured and multi-layered, first as neural rosettes and then as optic vesicles (OVs). We hypothesized that the cellular oxygen consumption rate would exceed the rate of delivery via passive diffusion, particularly to inner regions of emerging OVs. To test this hypothesis, we measured dissolved oxygen concentrations at the vessel bottom and found that within hours of media change, oxygen dropped to < 1 %, a level considered non-physiologically hypoxic, which imperils cell viability. This non-physiological hypoxia caused OV degeneration, hypoxic marker expression, and necrosis. To address this problem, we developed a novel 3D-printed stirred bioreactor (SBR) that maintains physiological oxygen levels between [~]4-6%. This approach significantly improved organoid yield, quality, and reproducibility while being easily adaptable to typical laboratory cell culture workflows. We conclude that non-physiological hypoxia, a previously unappreciated condition, is a limiting factor underlying inconsistent yield and quality in RO production. Physiological oxygenation levels can be restored by the SBR platform, resulting in greater consistency and improved production outcomes.

bioengineering↗

Heme drives cardiac endothelial senescence in sepsis via STING activation

Sepsis-induced cardiac dysfunction is a major contributor to sepsis-related mortality, and many patients continue to experience long-term cardiac complications after recovery. Here, we demonstrate that cardiac senescence is a key feature of sepsis-associated cardiac dysfunction, with endothelial cells identified as the predominant senescent population in septic cardiac tissue. Yet, the pathogenic drivers of endothelial senescence in sepsis remain poorly characterized. Among potential mediators, we found that elevated levels of heme, a byproduct of hemolysis, strongly correlate with increased endothelial senescence and impaired cardiac function. Mechanistic studies revealed that heme acts as a novel ligand for STING, exacerbating bacterial infection induced STING polymerization and activation, thereby promoting endothelial senescence. Notably, either STING inhibition or enhanced heme clearance via increased hemopexin expression significantly alleviated cardiac endothelial senescence and facilitated cardiac functional recovery in septic mice. These findings identify heme as a critical pathogenic driver of endothelial senescence and highlight heme clearance as a promising therapeutic strategy for mitigating sepsis induced cardiac dysfunction.

cell biology↗

A Multimodal Adaptive Optical Microscope For In Vivo Imaging from Molecules to Organisms

Understanding biological systems requires observing features and processes across vast spatial and temporal scales, spanning nanometers to centimeters and milliseconds to days, often using multiple imaging modalities within complex native microenvironments. Yet, achieving this comprehensive view is challenging because microscopes optimized for specific tasks typically lack versatility due to inherent optical and sample handling trade-offs, and frequently suffer performance degradation from sample-induced optical aberrations in multicellular contexts. Here, we present MOSAIC, a reconfigurable microscope that integrates multiple advanced imaging techniques including light-sheet, label-free, super-resolution, and multi-photon, all equipped with adaptive optics. MOSAIC enables non-invasive imaging of subcellular dynamics in both cultured cells and live multicellular organisms, nanoscale mapping of molecular architectures across millimeter-scale expanded tissues, and structural/functional neural imaging within live mice. MOSAIC facilitates correlative studies across biological scales within the same specimen, providing an integrated platform for broad biological investigation.

cell biology↗

Mitochondrial calcium influx-driven bioenergetics in the dopaminergic system selectively enable drug reward

Drugs of abuse hijack the brains reward system, driving pathological dopamine surges that underlie compulsive behavior and addiction. However, directly targeting dopamine signaling for treatment risks disrupting natural reward processes. Here, we identify a bioenergetic mechanism that selectively promotes addiction-related dopamine release and behaviors. Opioids and methamphetamine, but not natural rewards, induce mitochondrial calcium (Ca2+) influx via the mitochondrial calcium uniporter (MCU) in dopaminergic terminals of the nucleus accumbens. Optogenetic stimulation reveals that this mitochondrial Ca2+ influx occurs exclusively during high-intensity dopaminergic neuronal activation. This Ca2+ influx drives rapid ATP production, compensating for energy deficits caused by neuronal hyperactivity and enabling sustained dopamine release. Genetic deletion or pharmacological inhibition of MCU in dopaminergic neurons selectively reduces drug-induced dopamine release and prevents addictive behaviors while sparing natural reward processing in mice. These findings uncover a distinct mitochondrial bioenergetic mechanism underlying drug reward and propose MCU as a promising therapeutic target for addiction treatment.

neuroscience↗

Ultra-wide-field, deep, adaptive two-photon microscopy

Observing the activity patterns of large neural populations throughout the brain is essential for understanding brain function. However, capturing neural interactions across widely distributed brain regions from both superficial and deep cortical layers remains challenging with existing microscopy technologies. Here, we introduce a state-of-the-art two-photon microscopy system, ULTRA, capable of single-cell resolution imaging across an ultra-large field of view (FOV) exceeding 50 mm{superscript 2}, enabling deep and very wide field in vivo imaging. To demonstrate its capabilities, we conducted a series of experiments under multiple imaging conditions, successfully visualizing brain structures and neuronal activities spanning a spatial range of over 7 mm from superficial layers to depths of up to 900 m, while covering a volume of 45.24 mm3 in the mouse brain. This versatile imaging platform overcomes traditional spatial constraints, providing a powerful tool for comprehensive exploration of neuronal circuitry over extensive spatial scales with cellular resolution.

neuroscience↗

Proliferation of Early and Mature Osteoblasts Is Required for Bone Fracture Healing in Mice

Fractures heal by rapid formation of mineralized callus. Essential to this process is proliferation of periosteal cells to supply bone-forming osteoblasts. To better understand the role of cell proliferation in fracture healing, we asked: How is callus composition altered when osteolineage cells proliferation is blocked? Do mature osteoblasts proliferate to contribute to callus formation? First, mice expressing herpes simplex virus-thymidine kinase (HSV-TK) driven by the 3.6Col1a1 promoter were treated with ganciclovir (GCV) to ablate proliferating osteolineage cells for 5 or 10 days. Analysis of callus cells using single-cell RNA-seq revealed that GCV-treated Col1-TK mice had fewer osteoblasts and chondrocytes than control mice, with more myofibroblasts and immune cells, consistent with fibrous nonunion. In controls, 15-30% of callus cells that expressed the early osteoblast markers osterix (OSX) and the late marker osteocalcin (OCN) were in the cell cycle. Next, we targeted proliferating osteoblasts at different stages of differentiation by crossing Osx-CreERT2, Ocn-Cre and Dmp1-CreERT2 mice with novel ROSA-TK mice. Following fracture, each Cre;ROSA-TK mouse line exhibited poorer radiographic healing, decreased callus bone volume and a shift from callus bone to fibrous tissue. We conclude that osteoblasts, often considered post-mitotic, proliferate after fracture to contribute to formation of mineralized callus essential to healing.

physiology↗

Xcr1+ type 1 conventional dendritic cells are essential mediators for atherosclerosis progression

BackgroundAtherosclerosis is characterized by lipid accumulation within plaques, leading to foam cell formation and an inflammatory response within the aortic lesions. Lipid disorders have been extensively investigated, however the cellular and molecular mechanisms that trigger the inflammatory response in atherosclerotic plaques remain far from being fully understood. Xcr1+ cDC1 cells are newly identified antigen-presenting cells in activating immune cells. However, the role of cDC1 cells in the development of atherosclerosis remains highly controversial. ResultsWe first confirmed the presence of cDC1 within human atherosclerotic plaques and discovered a significant association between the increasing cDC1 numbers and atherosclerosis progression in mice. Subsequently, we established Xcr1Cre-Gfp Rosa26LSL-DTA ApoE-/- mice, a novel and complex genetic model, in which cDC1 was constitutively depleted in vivo during atherosclerosis development. Intriguingly, we observed a notable reduction in atherosclerotic lesions in hyperlipidemic mice, alongside suppressed T cell activation of both CD4+ and CD8+ subsets in the aortic plaques. Notably, aortic macrophages and serum lipid levels were not significantly changed in the cDC1-depleted mice. Single-cell RNA sequencing revealed heterogeneity of Xcr1+ cDC1 cells across the aorta and lymphoid organs under hyperlipidemic conditions. As Xcr1 is the sole receptor for Xcl1, we next explored to target Xcr1+ cDC1 cells via Xcl1 by establishing Xcl1 and ApoE deficient mice. Xcl1 knockout mice exhibited decreased atherosclerotic plaque formation and reduced aortic cDC1 accumulation, indicating that Xcl1 contributes to cDC1-mediated atherosclerotic lesion development. ConclusionsOur results reveal crucial roles of cDC1 in atherosclerosis progression and provide insights into the development of immunotherapies by targeting cDC1 through Xcl1.

immunology↗

Cryo-EM structure of plant urea transporter DUR3 reveals essential role of C-terminal domain in tetramer assembly and insights into proton-coupled transport

Nitrogen pollution, caused by the overuse of nitrogen-fertilizers such as urea in agricultural production, has become a serious problem that threatens both the environment and human health. Improving the nitrogen use efficiency of crops is an important approach to reduce fertilizer use. DUR3, a high-affinity urea transporter, enables plants to acquire urea from natural or agricultural soils with low urea concentrations and has been proposed as a promising target for engineering crops to improve nitrogen-fertilizer use efficiency. Despite extensive studies for more than 20 years, the structure, substrate recognition and transport mechanism of DUR3 have remained unknown. Here we report the cryo-EM structure of maize DUR3 (ZmDUR3) at 3.41 [A] resolution. ZmDUR3 adopts an amino acid-polyamine-organocation (APC) superfamily fold and is structurally distinct from animal facilitative urea transporters. Our structure provides important insights into urea recognition by DUR3 and suggests that a pair of acidic residues is potentially involved in proton coupling during urea transport. Furthermore, our structural and functional studies indicate that DUR3 assembles into a tetramer and tetramer formation is important for its function. Our results pave the way for engineering plant DUR3 protein for applications in sustainable agricultural production.

plant biology↗

Single-Cell RNA Sequencing and Inferred Protein Activity Analysis Reveal a Distinct Tumor Phenotype in Early-Onset Colorectal Cancer Patients

Colorectal cancer (CRC) diagnosed before age 50 years (early-onset CRC, EO-CRC) is rising at an alarming rate, yet its molecular and microenvironmental drivers remain poorly understood. EO-CRC is highly heterogeneous, and while subtle differences from late-onset CRC (LO-CRC) have been reported, their full extent remains unresolved due to the limited scope of previous studies. Here, we integrate public data with in-house clinical samples profiled by single-cell RNA sequencing (scRNA-seq) and multiplex immunofluorescence (mIF) to compare EO-CRC and LO-CRC. Additionally, we employ gene regulatory network-based protein activity inference (VIPER), enabling a more precise characterization of key regulatory proteins driving tumor-stroma interactions. Our analysis reveals that EO-CRC and LO-CRC have a largely similar immune composition, challenging previous reports of an "immune-cold" phenotype in EO-CRC. However, we identify distinct stromal differences, including a significant enrichment of fibroblasts in EO-CRC. Notably, we define a previously unrecognized epithelial subpopulation in EO-CRC, marked by high expression of toll-like receptor 4 (TLR4) and C-C chemokine receptor type 5 (CCR5)--key mediators of inflammation-driven tumor progression and fibroblast recruitment. These findings suggest that EO-CRC may be driven by a tumor-intrinsic inflammatory phenotype with enhanced stromagenesis, providing new insights into potential mechanisms underlying its increasing incidence in young adults.

cancer biology↗

Lactate metabolism antagonizes antiviral innate immunity bypromoting VDAC1-lactylation-mediated mtDNA release

Foot-and-mouth disease (FMD) is an acute, highly contagious disease caused by the foot-and-mouth disease virus (FMDV). Due to its zoonotic nature, this disease not only significantly impacts livestock productivity but also poses a serious threat to human health. FMDV exhibits distinct host specificity, mainly infecting cloven-hoofed animals such as cattle, sheep, pigs, and deer, while perissodactyl animals like horses and donkeys show natural resistance. Elucidating the interspecies differences in response to FMDV infection is essential for understanding the pathogenesis of the virus. In this study, we report that FMDV infection in horse epithelial cells induces the production of lactate, which modulates the function of VDAC1 protein through lactylation, facilitating the release of mtDNA from mitochondria into the cytoplasm. This process activates the cGAS-STING signaling pathway, which stimulates interferon-{beta} expression and suppresses FMDV replication. Our findings provide new insights into the mechanism behind horse resistance to FMDV and lay a theoretical foundation for further research concerning the differential pathogenesis of FMDV infection across species.

cell biology↗

Regulation of the Yolk Microtubule and Actin Cytoskeleton by Dachsous Cadherins during Zebrafish Epiboly

Epiboly is a crucial morphogenetic process during early animal embryogenesis that expands surface area of embryonic tissues while thinning them. During zebrafish development, epiboly spreads the superficial enveloping layer (EVL), germ layers, and yolk syncytial layer to cover the yolk cell. Here we investigated functions of the three zebrafish dchs genes, dchs1a, dchs1b and dchs2 that encode large atypical cadherins and report that they have partially overlapping functions in epiboly progression. We have inserted GFP at the C-terminal Dchs1b intracellular domain of the endogenous dchs1b locus using homologous recombination. We observed the resulting Dchs1b-GFP fusion protein localized in both the cell membrane and the cytoplasm of EVL and embryonic cells during gastrulation. The dynamic microtubule and actin cytoskeleton of the yolk cell are essential for epiboly. Our studies of the yolk microtubule network demonstrate that these microtubules are more bundled and show faster polymerization during epiboly in dchs triple loss-of-function mutant embryos than in wild-type embryos, indicating that dchs genes are required for limiting microtubule polymerization and promoting dynamics during epiboly. The epiboly progression defects of dchs1b deficient mutants were suppressed by mutations in the tetratricopeptide repeat protein 28 (ttc28) gene encoding a cytoplasmic protein previously shown to bind to Dchs1b intracellular domain and alter microtubule dynamics during early cleavages. We further demonstrate that MZdchs1b mutants exhibit abnormal organization and dynamics of yolk cell actin cytoskeleton during epiboly. Together, these lines of evidence as well as our transcriptomic analyses support the notion that like during early embryonic cleavages, Dchs1b plays a major role, while Dchs1a and Dchs2 proteins have supporting roles in regulating microtubule dynamics and organization of both microtubule and actin cytoskeleton to ensure normal epiboly.

developmental biology↗

Locus coeruleus-related insula activation supports implicit learning

The noradrenergic locus coeruleus and its neuromodulatory cortical projections are critical for adaptive behavior, however how they contribute to human implicit learning in novel environments is not yet well understood, due to the challenges of assessing this system non-invasively. Here, we combined multimodal neuroimaging--including locus-coeruleus-sensitive structural MRI, concurrent pupillometry-EEG, pupillometry-fMRI, and PET-derived noradrenergic transporter maps--with repeated behavioral assessments to investigate noradrenergic contributions to implicit learning across younger and older adults (n = 77). Salient expectation-violating stimuli elicited pupil dilation, indicating enhanced neuromodulation, activated the action-mode network and deactivated the default-mode network. Pupil-linked BOLD responses suggested a functional coupling between the locus coeruleus and action-mode network, further supported by spatial overlap of activation patterns with PET-derived noradrenergic transporter maps. Locus coeruleus MRI-guided functional connectivity analyses demonstrated coupled locus coeruleus and anterior insula activity, suggesting a noradrenergic role in shifting cortical dynamics toward action-oriented processing. Behaviorally, participants implicitly learned the statistical task structure over time, shifting their response times based on stimulus probabilities. Critically, stronger locus coeruleus integrity, greater task-related anterior insula activation, and more pronounced pupil dilation were associated with enhanced implicit learning, highlighting the behavioral relevance of noradrenergic neuromodulation. Notably, noradrenergic responses and their link to learning were preserved across age groups, suggesting a robust noradrenergic role in supporting adaptive behavior throughout adulthood. Complementary electrophysiological analyses revealed pupil-linked increases in cortical excitability that were coupled with shifts from default-mode to action-mode network activation. Together, these findings provide novel insights into the neuromodulatory mechanisms underlying learning and cognitive flexibility, emphasizing the pivotal role of locus coeruleus-action-mode network interactions in behavioral adaptation.

neuroscience↗

CLONEID: A Framework for Monitoring and Steering Subclonal Dynamics

Molecular assays can resolve clonal structure, but they are expensive and typically sparse in time, whereas phenotypic observations such as imaging can be collected frequently but often are not preserved in the context needed for later interpretation. We present CLONEID, an event-based framework for organizing clone-resolved phenotypic, molecular, and specimen-context records so that genotype-to-phenotype interpretation can be maintained across time. CLONEID links time-stamped Events, assay-specific Perspectives, and reconciled Identities through structured ingestion, provenance-aware retrieval, and reproducible export, complementing upstream clone-calling methods. In a long-term gastric cancer density-selection experiment, CLONEID linked repeated culture events, growth measurements, and late karyotypic profiling within a shared record, supporting longitudinal interpretation of phenotypic adaptation together with underlying chromosomal state.

bioinformatics↗

Computational Assessment of Circularization Impact on Saxitoxin G-quadruplex Aptamer Performance

Although high-affinity and high-specificity aptamers can be obtained by SELEX (Systematic Evolution of Ligands by Exponential Enrichment), and have good activity in vitro, their performance in vivo is poor. This is mainly because of the degradation of linear nucleic acids by nucleases in body fluids and the difficulty of maintaining stable 3D structures in complex body fluid environments, which seriously hinders the clinical application of aptamers. This makes circular aptamers, which can resist degradation and are more stable in complex body fluid environments, an attractive option. However, the cyclization process may have a considerable impact on the structure of the original linear aptamer, and blind cyclization may lead to a decrease in its affinity. Here, we developed a new method to guide the cyclization of saxitoxin (STX) aptamers based on molecular computation, and verified the activity of circular aptamers through bioactivity experiments to further verify the authenticity and reliability of our methods. Consistent with the computational analysis, although circularization disrupts the G4 structure, circular aptamer not only has a higher affinity than the linear one but also provides certain protection to mice and greatly prolongs their survival, which proves the accuracy and reliability of the circular structure designed by our computational method. Our findings provide important ideas for better guidance in the design of circular aptamers and demonstrate their great potential in therapeutic applications.

biochemistry↗

A Non-canonical Role for Hepatocyte MLKL in Promoting Mitochondrial Dysfunction and Senescence in the Aging Liver

Liver aging is characterized by chronic inflammation and metabolic dysfunction that contributes to the progression of metabolic dysfunction-associated steatotic liver disease (MASLD). Necroptosis, a form of inflammatory cell death, is activated in aging livers, and genetic (Ripk3-/-or Mlkl-/- mice) or pharmacological (RIPK1 inhibitor necrostatin-1s) inhibition of necroptosis attenuates liver inflammation and pathology. However, the cell type-specific role of necroptosis in liver aging remains unclear. Given that MLKL is expressed in hepatocytes, and its expression increases with age, we generated hepatocyte-specific MLKL-overexpressing mice (MLKLHepOE) to determine its role in liver aging. Unexpectedly, MLKL overexpression in hepatocytes did not induce necroptosis, but instead upregulated markers of cellular senescence (cell cycle arrest genes and SASP factors), increased macrophage infiltration, and elevated M1 macrophage marker expression. Electron microscopy and mitochondrial analyses revealed abnormal mitochondrial morphology, elevated oxidative stress, and disrupted mitochondrial dynamics, while lipidomics demonstrated alterations in hepatic lipid metabolites. In agreement with our observations in MLKLHepOE mice, MLKL overexpression in AML12 hepatocytes impaired mitochondrial respiration, increased proinflammatory extracellular vesicle (EV) release, and induced senescence markers, without triggering cell death. Together, these findings reveal a non-lethal, non-necroptotic role for MLKL in promoting hepatocyte senescence and metabolic dysfunction via mitochondrial impairment and EV-mediated inflammation. Our study highlights MLKL as a novel driver of liver inflammaging and a potential therapeutic target for age-related liver disease.

cell biology↗

Oncogene SETDB1s Dual Role in Endometrial Cancer: Driving Tumor Progression and Immune Escape

Oncogene SETDB1, an H3K9 methyltransferase, drives tumorigenesis in various cancers. Using endometrial cancer (EC) as a model, we discovered SETDB1s dual mechanisms in driving EC tumorigenesis and mediating immune evasion. SETDB1 knockout (SETDB1-/-) tumor-bearing mice exhibited prolonged survival of up to 100 days. Transcriptomic profiling of SETDB1-/- EC cells revealed decreased expression of oncogenes (POLR2A, MSH6, FLNA) and increased expression of tumor suppressor genes (PGR, RERG, ZNF582), which indicates that SETDB1 intrinsically promotes EC tumor proliferation by regulating these downstream genes. SETDB1 repressed repeat elements and the interferon pathway, mediating immune evasion extrinsically by inhibiting anti-tumor macrophage infiltration. ChIP-seq analysis showed SETDB1 binding at pericentromeric regions on many chromosomes and numerous ZNFs. Loss of SETDB1 resulted in abnormal cell division. SETDB1-/- tumors displayed reduced proliferation markers (Ki67, pHH3) and increased macrophage infiltration. Mechanistically, SETDB1 promotes CD47 (a dont-eat-me signal) and represses CCL5 and CXCL9 (macrophage and T-cell recruiting chemokines), contributing to immune evasion. M1-like macrophages killed more SETDB1-/- cells in co-culture. Additionally, SETDB1 knockout in mouse EC cells reduced tumor growth in C57BL/6 mice, with increased macrophage and CD4+ T-cell infiltration. Our results indicates that elevated SETDB1 and its target genes can predict higher tumor grade and worse survival, suggesting that targeting SETDB1 could be a promising therapeutic strategy for EC.

cancer biology↗