Biology subjects

Li, T.

Publications and source records attributed to Li, T..

At least 271 records · Page 15Linked to original sources

bioRxiv2024

Molecular and Cellular Mechanisms of Teneurin Signaling in Synaptic Partner Matching

In developing brains, axons exhibit remarkable precision in selecting synaptic partners among many non-partner cells. Evolutionally conserved teneurins were the first identified transmembrane proteins that instruct synaptic partner matching. However, how intracellular signaling pathways execute teneurins functions is unclear. Here, we use in situ proximity labeling to obtain the intracellular interactome of teneurin (Ten-m) in the Drosophila brain. Genetic interaction studies using quantitative partner matching assays in both olfactory receptor neurons (ORNs) and projection neurons (PNs) reveal a common pathway: Ten-m binds to and negatively regulates a RhoGAP, thus activating the Rac1 small GTPases to promote synaptic partner matching. Developmental analyses with single-axon resolution identify the cellular mechanism of synaptic partner matching: Ten-m signaling promotes local F-actin levels and stabilizes ORN axon branches that contact partner PN dendrites. Combining spatial proteomics and high-resolution phenotypic analyses, this study advanced our understanding of both cellular and molecular mechanisms of synaptic partner matching. HIGHLIGHTSO_LIIn situ spatial proteomics reveal the first intracellular interactome of teneurins C_LIO_LITen-m signals via a RhoGAP and Rac1 GTPase to regulate synaptic partner matching C_LIO_LISingle-axon analyses reveal a stabilization-upon-contact model for partner matching C_LIO_LITen-m signaling promotes F-actin in axon branches contacting partner dendrites C_LI

neuroscience↗

bioRxiv2024

The Drosophila histone methyl-transferase SET1 coordinates multiple signaling pathways in regulating male germline stem cell maintenance and differentiation

Many cell types come from tissue-specific adult stem cells that maintain the balance between proliferation and differentiation. Here, we study how the H3K4me3 methyltransferase, Set1, regulates early-stage male germ cell proliferation and differentiation in Drosophila. Early-stage germline-specific knockdown of set1 results in a temporally progressed defects, arising as germ cell loss and developing to overpopulated early-stage germ cells. These germline defects also impact the niche architecture and cyst stem cell lineage in a non-cell-autonomous manner. Additionally, wild-type Set1, but not the catalytically inactive Set1, could rescue the set1 knockdown phenotypes, highlighting the functional importance of the methyl-transferase activity of the Set1 enzyme. Further, RNA-seq experiments reveal key signaling pathway components, such as the JAK-STAT pathway gene stat92E and the BMP pathway gene mad, that are upregulated upon set1 knockdown. Genetic interaction assays support the functional relationships between set1 and JAK-STAT or BMP pathways, as mutations of both the stat92E and mad genes suppress the set1 knockdown phenotypes. These findings enhance our understanding of the balance between proliferation and differentiation in an adult stem cell lineage. The germ cell loss followed by over-proliferation phenotypes when inhibiting a histone methyl-transferase raise concerns about using their inhibitors in cancer therapy.

developmental biology↗

bioRxiv2024

Infer metabolic directions and magnitudes from moment differences of mass-weighted intensity distributions

Metabolic pathways are fundamental maps in biochemistry that detail how molecules are transformed through various reactions. The complexity of metabolic network, where a single compound can play a part in multiple pathways, poses a challenge in inferring metabolic balance changes over time or after different treatments. Isotopic labeling experiment is the standard method to infer metabolic flux, which is currently defined as the flow of a single metabolite through a given pathway over time. However, there is still no way to accurately infer the metabolic balance changes after different treatments in an experiment. This study introduces a different concept: molecular weight distribution, which is the empirical distribution of the molecular weights of all metabolites of interest. By estimating the differences of the location and scale estimates of these distributions, it becomes possible to quantitatively infer the metabolic balance changes even without requiring knowledge of the exact chemical structures of these compounds and their related pathways. This research article provides a mathematical framing for a classic biological concept.

bioinformatics↗

bioRxiv2024

ATP13A1 engages GET3 to facilitate substrate-specific translocation

Proper localization of proteins to their final destinations is crucial for preserving cellular structure and functions. The interpretation and sorting of highly variable targeting sequences in secreted and membrane proteins, however, pose a challenge in achieving precise localization within specific secretory apparatus. In this study, we demonstrate that atypical signal sequences characterized by high hydrophobicity and/or the absence of characteristic charges undergo targeting to the endoplasmic reticulum (ER) in a reverse orientation, followed by partial cleavage. The P5A- ATPase ATP13A1 recognizes the cleaved signal sequence and dislocates it to the targeting factor GET3, subsequently engaging SEC61 for further translocation. Our findings unveil a comprehensive translocation pathway that operates in a substrate- specific manner, ensuring both high efficiency and fidelity in the protein subcellular localization.

biochemistry↗

bioRxiv2024

Huntingtin is an RNA-binding protein and participates in NEAT1-mediated paraspeckles

AbstractHuntingtin protein, mutated in Huntington disease, is implicated in nucleic acid- mediated processes, yet evidence for direct huntingtin-nucleic acid interaction is limited. Here we show wildtype and mutant huntingtin co-purify with nucleic acids, primarily RNA, and interact directly with G-rich RNAs in in vitro assays. Huntingtin RNA immunoprecipitation sequencing from patient-derived fibroblasts and neuronal progenitor cells expressing wildtype and mutant huntingtin revealed NEAT1 as a significantly enriched transcript. Altered NEAT1 levels were evident in Huntingtons disease cells and postmortem brain tissues, and huntingtin knockdown decreased NEAT1 levels. Huntingtin co-localized with NEAT1 in paraspeckles, and we identified a high-affinity RNA motif preferred by huntingtin. This study highlights NEAT1 as a novel huntingtin interactor, demonstrating huntingtins involvement in RNA-mediated functions and paraspeckle regulation. One-Sentence SummaryHTT is an RNA-binding protein that interacts with G-rich sequences, including those in the paraspeckle lncRNA NEAT1.

cell biology↗

bioRxiv2024

The Origin and Evolution of Orphan Genes: A Case Study in Tea Plant Family

Orphan genes and transcription factor genes (TFs) are pervasive across genomes, play pivotal roles as regulators in a myriad of biological processes. Despite their ubiquity, the evolutionary trajectories and functional divergence of these genes remain largely unexplored. Theaceae family, encompassing the economically and culturally significant tea plant, presents a unique opportunity to study these dynamics. Here, we decoded a nearly complete, chromosome-scale reference genome of Stewartia gemmata spanning 2.95 Gb. This study is enhanced by integrating the genome of S. gemmata, an early-diverging species within Theaceae, crucial for phylogenomic analyses and understanding the functional dynamics of orphan genes in this family. Our analysis confirmed the absence of a recent specific whole-genome duplication (WGD) event, with tandem duplications emerging as the predominant mechanism for gene duplication at ancestral nodes within Theaceae. By conducting an extensive comparative genomics analysis across 13 Theaceae and comparing these with a wide array of eukaryotic and prokaryotic proteins, we identified 37,618 orphan genes and 25,884 TFs in Theaceae. Interestingly, some orphan genes appear to have ancient origins in tea plant ancestors, suggesting relatively early origins with frequent gains and losses, conversely, many others seem more specific and recent. Notably, the orphan genes are characterized by shorter lengths, fewer exons and functional domains than TFs, implying relatively simpler functional roles. These orphan genes demonstrate diverse cellular localization and functions as predicted by GO/KEGG analysis, and are implicated in environmental response and flavor formation in tea plants. This study not only sheds light on the distinct evolutionary histories and functional divergences between orphan genes and TFs in Theaceae, but also contributes to our understanding of the genetic complexity and adaptability of this economically and culturally valuable plant family. Short summary: The nearly complete genome of an early-diverging species Stewartia gemmata and phylogenomic studies provide insights into new gene evolution in Theaceae.

bioinformatics↗

bioRxiv2024

Transcriptomic and epigenetic responses shed light on soybean resistance to Phytophthora sansomeana

Phytophthora root rot caused by oomycete pathogens in the Phytophthora genus poses a significant threat to soybean productivity. While resistance mechanisms against Phytophthora sojae have been extensively studied in soybean, the molecular basis underlying immune responses to Phytophthora sansomeana remains unclear. We investigated transcriptomic and epigenetic responses of two resistant (Colfax and NE2701) and two susceptible (Williams 82 and Senaki) soybean lines at four time points (2, 4, 8, and 16 hours post inoculation, hpi) after P. sansomeana inoculation. Comparative transcriptomic analyses revealed a greater number of differentially expressed genes (DEGs) upon pathogen inoculation in resistant lines, particularly at 8 and 16 hpi, predominantly associated with ethylene and reactive oxygen species-mediated defense pathways. Moreover, DE transposons were predominantly up-regulated after inoculation and enriched near genes in Colfax. A long non-coding RNA (lncRNA) within the mapped region of the resistance gene exhibited exclusive up-regulation in the resistant lines after inoculation, potentially regulating two flanking LURP-one-related genes. Furthermore, DNA methylation analysis revealed increased CHH methylation levels in lncRNAs after inoculation, with delayed responses in Colfax compared to Williams 82. Overall, our results provide comprehensive insights into soybean responses to P. sansomeana, highlighting potential roles of lncRNAs and epigenetic regulation in plant defense.

plant biology↗

bioRxiv2024

Discovery of the 1-naphthylamine biodegradation pathway reveals an enzyme that catalyzes 1-naphthylamine glutamylation

1-Naphthylamine (1NA), which is harmful to human and aquatic animals, has been used widely in the manufacturing of dyes, pesticides, and rubber antioxidants. Nevertheless, little is known about its environmental behavior and no bacteria have been reported to use it as the growth substrate. Herein, we describe a pathway for 1NA degradation in isolate Pseudomonas sp. strain JS3066, determine the structure and mechanism of the enzyme NpaA1 that catalyzes the initial reaction, and reveal how the pathway evolved. From genetic and enzymatic analysis, a cluster of 5 genes encoding a dioxygenase system was determined to be responsible for the initial steps in 1NA degradation through glutamylation of 1NA. The {gamma}-glutamylated 1NA was subsequently oxidized to 1,2-dihydroxynaphthalene which was further degraded by the well-established pathway of naphthalene degradation via catechol. Enzymatic analysis showed that NpaA1 catalyzed conversion of various anilines and naphthylamine derivatives. Structural and biochemical studies of NpaA1 revealed that the broad substrate specificity of NpaA1 is due to a large hydrophobic pocket, which is different from type I glutamine synthetase (GSI). The findings enhance understanding of degrading polycyclic aromatic amines, and will also enable the application of bioremediation at naphthylamine contaminated sites.

microbiology↗

bioRxiv2024

High-content phenotypic analysis of a C. elegans recombinant inbred population identifies genetic and molecular regulators of lifespan

Lifespan is influenced by complex interactions between genetic and environmental factors. Studying those factors in model organisms of a single genetic background limits their translational value for humans. Here, we mapped lifespan determinants in 85 genetically diverse C. elegans recombinant intercross advanced inbred lines (RIAILs). We assessed molecular profiles - transcriptome, proteome, and lipidome - and life-history traits, including lifespan, development, growth dynamics, and reproduction. RIAILs exhibited large variations in lifespan, which positively correlated with developmental time. Among the top candidates obtained from multi-omics data integration and QTL mapping, we validated known and novel longevity modulators, including rict-1, gfm-1 and mltn-1. We translated their relevance to humans using UK Biobank data and showed that variants in RICTOR and GFM1 are associated with an elevated risk of age-related heart disease, dementia, diabetes, kidney, and liver diseases. We organized our dataset as a resource (https://lisp-lms.shinyapps.io/RIAILs/) that allows interactive explorations for new longevity targets.

systems biology↗

bioRxiv2024

Gating of Memory to Behavior by the Locus Coeruleus

An essential function of memory is to guide behavior for survival and adaptation. While considerable knowledge has been accumulated on memory formation, much less is understood about how retrieved memories direct behavior/action. In the auditory Pavolovian threat conditioning paradigm, retrieval of conditioned threat memory activates dorsomedial prefrontal (dmPFC) neurons exhibiting transient responses (T-neurons), which activate both dmPFC neurons exhibiting sustained responses (S-neurons) and locus coeruleus (LC) neurons. Auditory inputs to S-neurons enable the conversion from transient to sustained responses so that the freezing durations match those of the auditory cues. Activation of LC neurons is required for the conversion by enhancing S-neuron responses, which, interestingly, opens a short time window during which non-conditioned cues also lead to freezing. The transition from memory to behavior thus hinges on the integration of retrieved memory, sensory inputs, and emotional/body state cues to generate a selective, adequate, and finely tuned behavior. Significance statementThis study provides new insights into the neural circuitry and mechanisms of how retrieved memories direct the execution of behavior in response to conditioned threatening stimuli. It reveals how different neuron types in the dmPFC interact with LC neurons to determine and modulate the duration and intensity of defensive responses. It also shows that activation of LC neurons can induce the generalization of freezing to non-threatening cues, which may have implications for understanding anxiety disorders. This study contributes to the field of neuroscience by advancing the understanding of memory-behavior conversion and role of the dmPFC and LC in conditioned threat/fear behavior.

neuroscience↗

bioRxiv2024

Blocker-SELEX: A Structure-guided Strategy for Developing Inhibitory Aptamers Disrupting Undruggable Transcription Factor Interactions

Despite the well-established significance of transcription factors (TFs) in pathogenesis, their utilization as pharmacological targets has been limited by the inherent challenges associated with modulating their protein-protein and protein-DNA interactions. The lack of defined small-molecule binding pockets and the nuclear localization of TFs do not favor the use of small-molecule inhibitors, or neutral antibodies, in blocking TF interactions. Aptamers are short oligonucleotides exhibiting high affinity and specificity for a diverse range of targets. Large molecular weights, expansive blocking surfaces and efficient cellular internalization make aptamers a compelling molecular tool for use as traditional TF interaction modulators. Here, we report a structure-guided design strategy called Blocker-SELEX to develop inhibitory aptamers (iAptamer) that selectively block TF interactions. Our approach led to the discovery of iAptamers that cooperatively disrupts SCAF4/SCAF8-RNA Polymerase II (RNAP2) interactions, thereby dysregulating RNAP2-dependent gene expression and splicing and, in turn, leading to the impairment of cell proliferation. This approach was further applied to develop iAptamers to efficiently block WDR5-MYC interaction with a nexus in cancer. Taken together, our study highlights the potential of Blocker-SELEX in developing iAptamers that effectively disrupt potentially pathogenic TF interactions with attendant implications for iAptamers as chemical tools for use in the study of biological functions of TF interactions, but also for potential use in nucleic acids drug discovery.

biochemistry↗

bioRxiv2024

The sea urchin Paracentrotus lividus orients to visual stimuli

Though lacking eyes, some sea urchins can see: Several species exhibit resolving vision, as distinct from mere light detection. How and where light is captured in the eyeless sea urchins, and how this information is integrated to elicit visual behaviour, remains a fascinating enigma. We assessed the spatial resolution of the sea urchin Paracentrotus lividus in laboratory experiments using fifty adults from the Bay of Naples. This keystone species is an important grazer of the NE Atlantic and Mediterranean and a model system to study development. We carried out behavioural trials in which individuals were placed in a submerged cylindrical arena to determine if they orient towards a visual stimulus on the arena wall, under diffuse, downwelling light. We adopted a novel isoluminant stimulus, necessitating vision of a given resolving power around the horizon to be detected. We tested individuals at five stimulus widths, including a uniform control. Animals oriented (upon clearing an obstacle) only to the widest stimuli (45 deg and above). This acuity may suffice for tasks such as finding nearby shelters or distant patches of habitat. We modelled the visual and neuronal processes to recapitulate these responses in P. lividus, by fine-tuning the model of Li et al. (2022), as applied to the sea urchin Diadema africanum. While these species differ morphologically, the model robustly predicts angular sensitivity in keeping with the behavioural experiments. We find that P. lividus (and likely many Echinacea) possesses coarse spatial vision and that the neurosensory model applies broadly to sea urchins.

zoology↗

bioRxiv2024

Neu5Gc binding loss of subtype H7 influenza A virus facilitates adaptation to gallinaceous poultry following transmission from waterbirds but restricts spillback

Migratory waterfowl, gulls, and shorebirds serve as natural reservoirs for influenza A viruses, with potential spillovers to domestic poultry and humans. The intricacies of interspecies adaptation among avian species, particularly from wild birds to domestic poultry, are not fully elucidated. In this study, we investigated the molecular mechanisms underlying avian species barriers in H7 transmission, particularly the factors responsible for the disproportionate distribution of poultry infected with A/Anhui/1/2013 (AH/13)-lineage H7N9 viruses. We hypothesized that the differential expression of N-glycolylneuraminic acid (Neu5Gc) among avian species exerts selective pressure on H7 viruses, shaping their evolution and enabling them to replicate and transmit efficiently among gallinaceous poultry, particularly chickens. Our glycan microarray and biolayer interferometry experiments showed that AH/13-lineage H7N9 viruses exclusively bind to Neu5Ac, in contrast to wild waterbird H7 viruses that bind both Neu5Ac and Neu5Gc. Significantly, reverting the V179 amino acid in AH/13-lineage back to the I179, predominantly found in wild waterbirds, expanded the binding affinity of AH/13-lineage H7 viruses from exclusively Neu5Ac to both Neu5Ac and Neu5Gc. When cultivating H7 viruses in cell lines with varied Neu5Gc levels, we observed that Neu5Gc expression impairs the replication of Neu5Ac-specific H7 viruses and facilitates adaptive mutations. Conversely, Neu5Gc deficiency triggers adaptive changes in H7 viruses capable of binding to both Neu5Ac and Neu5Gc. Additionally, we assessed Neu5Gc expression in the respiratory and gastrointestinal tissues of seven avian species, including chickens, Canada geese, and various dabbling ducks. Neu5Gc was absent in chicken and Canada goose, but its expression varied in the duck species. In summary, our findings reveal the crucial role of Neu5Gc in shaping the host range and interspecies transmission of H7 viruses. This understanding of virus-host interactions is crucial for developing strategies to manage and prevent influenza virus outbreaks in diverse avian populations. Author SummaryMigratory waterfowl, gulls, and shorebirds are natural reservoirs for influenza A viruses that can occasionally spill over to domestic poultry, and ultimately humans. The molecular mechanisms underlying interspecies transmission and adaptation, particularly between wild birds and domestic poultry, remain poorly understood. This study showed wild-type H7 influenza A viruses from waterbirds initially bind to glycan receptors terminated with N-Acetylneuraminic acid (Neu5Ac) or N-Glycolylneuraminic acid (Neu5Gc). However, after enzootic transmission in chickens, the viruses exclusively bind to Neu5Ac. The absence of Neu5Gc expression in gallinaceous poultry, particularly chickens, exerts selective pressure, shaping influenza virus populations, and promoting the acquisition of adaptive amino acid substitutions in the hemagglutinin protein of H7 influenza A viruses. This results in the loss of Neu5Gc binding and an increase in virus transmissibility in gallinaceous poultry, particularly chickens. Consequently, the transmission capability of these poultry-adapted H7 viruses in wild water birds decreases. Timely intervention, such as stamping out, may help reduce virus adaptation to domestic chicken populations and lower the risk of enzootic outbreaks, including those caused by influenza A viruses exhibiting high pathogenicity.

microbiology↗

bioRxiv2024

MobiChIP: a compatible library construction method of single-cell ChIP-seq based droplets

In order to illustrate the epigenetic heterogeneity, versatile tools of single-cell ChIP-seq (scChIP-seq) are necessary to meet the convenience and accuracy. Here, we develop MobiChIP, a compatible ChIP-seq library construction method based current sequencing platform with single cell level. As a novel capture strategy, MobiChIP is efficient to capture the fragments from tagmented nuclei of numerous species and execute the mixing of samples from different tissues or species. Especially, this strategy enables the flexible sequencing manipulation and sufficient nucleosome amplification without customized sequencing primers. MobiChIP reveals the landscape of chromatin regulation regions with active(H3K27ac) and repressive(H3K27me3) histone modification markers in peripheral blood mononuclear cells (PBMCs), and accurately unveiled the epigenetic repression of hox gene cluster in PBMCs than ATAC-seq. Meanwhile, we complete the bioinformatics pipeline to integrates the scChIP-seq data and scRNA-seq to illustrate the cellular epigenetic and genetic heterogeneity. One-Sentence SummaryA high-throughput single-cell ChIP-seq based droplet reveals the integration of scRNA-seq data and scChIP-seq data.

molecular biology↗

bioRxiv2023

Discrimination of Isomeric Glycans via High-sensitive Engineered Nanopore

Glycan isomers are the basis for forming the spatial structure of glycans, which poses great challenges to glycan structural analysis and hinders the study of the relationship between structure and function. An economical and convenient analytical method with high resolution is still in demand. Here, we designed an engineered -hemolysin nanopore with double-mutants (-HL M113R/T115A) to achieve sensing of glycans with different glycosidic linkages. By extracting three parameters to depict a 3D scatter plot, four glycans with different degrees of polymerization and glycosidic bonds could be distinguished. Through molecular dynamics (MD), we further elucidated the motion trajectories of two different glycosidic bonds in the pore region. In addition, the sensing ability was also applied in the direct identification of glycans in mixture systems. The obtained nanopore data permitted us to achieve a separation accuracy of over 90% independent of the assistance of machine learning algorithms. Designing biological nanopores with high discrimination and sensitivity for glycans with different lineages paves the way for nanopore glycan profiling and potentially sequencing.

bioengineering↗

bioRxiv2023

FGF12 Modulates Cardiomyocyte Hypertrophy by Inhibiting GATA4-ERK1/2 Phosphorylation Through Altered Intracellular Localization

BackgroundHypertrophic cardiomyopathy (HCM) is a heritable pathological condition resulting from mutations in sarcomere-related proteins, leading to severe structural abnormalities without effective treatment options. Although reduced fibroblast growth factor 12(FGF12) expression is observed in HCM patients, its functional role remains unclear. MethodsEmploying immunoprecipitation (IP)-mass spectrometry (MS) and CUT&Tag sequencing, we investigated FGF12-interacting proteins in myocardial samples from healthy volunteers and HCM patients. CRISPR-Cas9 was utilized to explore the function and interaction partners of FGF12 in cardiomyocytes induced from human pluripotent stem cells (hiPSCs-CMs), other cell lines, and mouse models (MYH7R403Q and MYBPC3c.790G>A, transverse aortic constriction (TAC)). During hypertrophy, FGF12 localizes intranuclearly, prompting investigations into its binding to gene promoter regions through CUT&Tag sequencing and dual-luciferase experiments using myocardial tissues from patients. The beating frequency of hiPS-CMs was assessed using the CardioExcyte 96 real-time label-free cardiomyocyte functional analysis system. ResultsFGF12 was found to associate with proteins involved in energy metabolism, predominantly localizing to the perinuclear space under physiological conditions but shifting into the nucleus of hypertrophic cardiomyocytes. Co-IP-MS revealed significant interactions between FGF12 and metabolism-associated proteins, particularly GATA binding protein 4 (GATA4) and mitogen-activated protein kinase 1/3 (MAPK1/3) in the perinuclear space. In a hypertrophic state, FGF12 bound to the GATA4 promoter region, increasing its expression upon nuclear translocation. Both in vitro and in vivo models demonstrated that FGF12 interaction with GATA4 inhibited GATA4 and MAPK1/3 phosphorylation, inducing the expression of hypertrophy-associated genes. Overexpression of FGF12-NLS-del (nuclear localization signal deletion) resulted in decreased GATA4 phosphorylation, suggesting inhibition in the perinuclear region. ConclusionsThis study elucidates a pathological mechanism of HCM involving FGF12, where its nuclear localization enhances phosphorylation, GATA4 expression, and activation of the ERK1/2-pGATA4 pathway genes associated with hypertrophy. Beyond advancing our understanding of HCM, these findings propose FGF12 as a potential therapeutic target for HCM, warranting further exploration to potentially alleviate this condition affecting millions of individuals.

molecular biology↗

bioRxiv2023

Single cell transcriptomics reveals chondrocyte differentiation dynamics in vivo and in vitro

The consistent production of in vitro chondrocytes that faithfully recapitulate in vivo development would be of great benefit for musculoskeletal disease modelling and regenerative medicine. Current efforts are often limited by off-target differentiation, resulting in a heterogeneous product. Furthermore, the lack of comparison to human embryonic tissue, precludes detailed evaluation of in vitro cells. Here, we perform single-cell RNA sequencing of embryonic long bones dissected from first trimester hind limbs from a range of gestational ages. We combine this with publicly available data to form a detailed atlas of endochondral ossification, which we then use to evaluate a series of published in vitro chondrogenesis protocols, finding substantial variability in cell states produced by each. We apply single-nuclear RNA sequencing to one protocol to enable direct comparison between in vitro and in vivo, and perform trajectory alignment between the two to reveal differentiation dynamics at the single-cell level, shedding new light on off-target differentiation in vitro. Using this information, we inhibit the activity of FOXO1, a transcription factor predicted to be active in embryonic bone development and in chondrogenic cells in vitro, and increase chondrocyte transcripts in vitro. This study therefore presents a new framework for evaluating tissue engineering protocols, using single-cell data from human development to drive improvement and bring the prospect of true engineered cartilage closer to reality.

bioengineering↗

bioRxiv2023

Integrated histopathology, spatial and single cell transcriptomics resolve cellular drivers of early and late alveolar damage in COVID-19

The most common cause of death due to COVID-19 remains respiratory failure. Yet, our understanding of the precise cellular and molecular changes underlying lung alveolar damage is limited. Here, we integrate single cell transcriptomic data of COVID-19 donor lungs with spatial transcriptomic data stratifying histopathological stages of diffuse alveolar damage (DAD). We identify changes in cellular composition across progressive DAD, including waves of molecularly distinct macrophages and depleted epithelial and endothelial populations throughout different types of tissue damage. Predicted markers of pathological states identify immunoregulatory signatures, including IFN-alpha and metallothionein signatures in early DAD, and fibrosis-related collagens in organised DAD. Furthermore, we predict a fibrinolytic shutdown via endothelial upregulation of SERPINE1/PAI-1. Cell-cell interaction analysis revealed macrophage-derived SPP1/osteopontin signalling as a key regulator during early DAD. These results provide the first comprehensive, spatially resolved atlas of DAD stages, highlighting the cellular mechanisms underlying pro-inflammatory and pro-fibrotic pathways across alveolar damage progression.

pathology↗