Biology subjects

Jia, Q.

Publications and source records attributed to Jia, Q..

At least 19 recordsLinked to original sources

bioRxiv2026

Dietary vitamin B5 positively regulates intestinal neuropeptide secretion in C. elegans

Vitamin B5 is an essential vitamin that must be acquired via diet or by the gut microbiota, and vitamin B5 deficiency or altered vitamin B5 metabolism leads to a variety of physiological and neuronal disorders. We conducted a genetic analysis of the effects of exogenous vitamin B5 in C. elegans, and we found that vitamin B5 confers protection to toxicity caused by oxidative stress and acute exposure to vitamin B5 positively regulates neuropeptide secretion. We identified a sodium-dependent multivitamin transporter family member, smvt-1 that is required for B5 uptake into cells and for protection conferred by vitamin B5. Vitamin B5 positively regulates the intestinal secretion of FLP-2, a neuropeptide-like protein whose release activates the antioxidant response. Vitamin B5 promotes FLP-2 secretion rapidly, specifically, and in a manner that is dependent upon uptake into intestinal cells by smvt-1. Vitamin B5-induced neuropeptide secretion is strictly dependent upon the SNARE protein aex-4/SNAP-25 and on the calcium dependent protein kinase C family member, pkc-2/PKCa in the intestine. These results reveal a previously uncharacterized function for dietary vitamin B5 in positively regulating intestinal neuropeptide secretion from dense core vesicles and in shaping the antioxidant response.

neuroscience↗

bioRxiv2026

Ara h 2 and FcϵRIα binding elicit state-dependent allostery in IgE

Background: Peanuts are among the most prevalent food allergens responsible for anaphylaxis, particularly in children. Allergic responses may be mitigated by disrupting molecular interactions between immunoglobulin-E (IgE) and its binding partners: peanut allergen (Ara h 2) and IgE receptors (Fc{epsilon}RI). However, the structural dynamics of IgE upon engaging these factors are not yet fully elucidated. Objective: To characterize how Ara h 2 and/or Fc{epsilon}RI binding influence IgE flexibility and its interdomain communications. Methods: The structural dynamics of full-length IgE in various unbound and bound states were examined by combining molecular dynamics (MD) simulations with cross linking mass spectrometry (XLMS). Causal relationship between IgE domains were characterized to infer allosteric communication pathways, which were assessed through hydrogen-deuterium exchange mass spectrometry (HDX-MS). Results: Non canonical bent IgE conformations were identified. We demonstrate that Fc{epsilon}RI binding immobilizes IgE predominantly by stabilizing and restricting Fc flexibility, whereas Ara h 2 binding induces specific conformational changes within the Fc{epsilon}RI-binding region. Our results further suggest that the C{epsilon} domains retain sufficient freedom to enable causal dynamics by the Fabs in a binding-dependent manner, thereby modulating the receptor engagement potential of IgE. Notably, concurrent binding of Ara h 2 and Fc{varepsilon}RI to IgE shifts the allosteric communication between the Fabs and Fc regions from the C{epsilon}3 to C{epsilon}4 domain. Conclusion: Our findings provide new insights into the dynamic regulation of IgE and its role in allergic responses. This could serve as a structural framework for understanding IgE signaling in peanut allergy and suggest potential targets for therapeutic interventions

immunology↗

bioRxiv2026

RNA Quality Control Enables Antibiotic Tolerance

The mechanisms underlying adaptation to antibiotic pressure within complex host environments remain incompletely understood. By experimentally evolving Streptococcus pneumoniae subjected to various antibiotics and immune states, we demonstrate populations adopting distinct adaptive strategies depending on specific selective context. General antibiotic stress drives convergent mutations in rny, encoding the RNA degradosome scaffold RNase Y, that exhibit broad-spectrum antibiotic tolerance and accelerated recovery. Single-cell transcriptomics revealed antibiotic-induced death is driven by transcriptional collapse, a catastrophic loss of RNA quantity and integrity. In contrast, rny mutants avert this via a bet-hedging strategy: a resilient minority maintains a baseline transcriptional profile, while a quiescent majority undergoes selective RNA degradation to preserve transcript fidelity. Upon stress removal, these populations execute a prioritized transcriptional ribosomal reboot, facilitating accelerated recovery. These findings identify RNA turnover as a tunable master regulator to survive combined pressures of antibiotics and immunity.

microbiology↗

bioRxiv2025

Distinct Mechanisms for Inhibition of SARS-CoV-2 Main Protease: Dimerization Promoted by Peptidomimetic Inhibitors and Disrupted by Ebselen

The SARS-CoV-2 main protease (Mpro) is a key antiviral target that equilibrates between an active dimer and inactive monomer, making the dimerization interface a promising therapeutic vulnerability. This study investigates Mpro monomer-dimer equilibrium and conformational changes induced by inhibitor binding using 13C labeling with native mass spectrometry and hydrogen/deuterium exchange mass spectrometry (HDX-MS). We evaluated how peptidomimetic inhibitors (PF-07321332, PF-00835231, GC376, boceprevir) and non-peptidomimetic inhibitors (carmofur, ebselen, MR6-31-2, AT7519, pelitinib) influence Mpro dimerization and subunit exchange. Key findings revealed divergent mechanisms: peptidomimetic inhibitors significantly shifted the equilibrium towards the dimeric state, suppressing subunit exchange dynamics and rigidifying the dimer interface; in contrast, ebselen impaired dimer form and increased interface flexibility. Notably, tandem mass spectrometry identified a novel covalent binding site for ebselen at C300. Molecular dynamics simulations and mutational analyses demonstrated that this C300 modification allosterically alters the hydrogen bond network of the dimer interface, directly contributing to ebselen-mediated dimer disruption and enzymatic inhibition. Overall, this study clarifies distinct inhibitory modes between peptidomimetics and ebselen, highlighting the therapeutic potential of targeting allosteric sites at the dimer interface for designing next-generation Mpro inhibitors.

molecular biology↗

bioRxiv2025

Clustering of Omic Data Using Semi-Supervised Transfer Learning for Gaussian Mixture Models via Natural-Gradient Variational Inference: Method and Applications to Bulk and Single-Cell Transcriptomics

MotivationHigh-dimensional omics data are typically measured on limited sample sizes, which challenges model-based clustering methods such as Gaussian mixture models, often leading to instability and poor generalization under complex mixture structures. To address these limitations, we developed Praxis-BGM, a natural-gradient variational inference framework for Gaussian mixture models that enables semi-supervised transfer learning by incorporating an informative prior Gaussian mixture model derived from large-scale reference data with robust cluster structures. This prior can encode cluster-specific means, covariance structures, and structural connectivity patterns, and is updated using the target data with variational inference to improve clustering in small-sample settings. ResultsWe derived natural-gradient updates for standard parameters and assess feature-level contributions to posterior clustering via Bayes Factors. Implemented in Python library JAX for accelerator-oriented computation, Praxis-BGM is computationally efficient and scalable. Across extensive simulations and two real-world applications--breast cancer bulk transcriptomics for subtype recovery and single-cell transcriptomics for cross-platform label transfer--Praxis-BGM improves posterior clustering performance, stability, and biological interpretability, even when priors are partially mismatched. Availability and ImplementationPraxis-BGM is freely available at https://github.com/ContiLab-usc/Praxis-BGM, and an archival version is available on Zenodo at https://doi.org/10.5281/zenodo.19657680. Contactqiranjia@usc.edu Supplementary InformationSupplementary materials are available with the manuscript submission.

bioinformatics↗

bioRxiv2025

AlphaGEM Enables Precise Genome-Scale Metabolic Modelling by Integrating Protein Structure Alignment with deep-learning-based Dark Metabolism Mining

Constructing high-quality genome-scale metabolic models (GEMs) for less-studied species remains challenging. To address this, we developed AlphaGEM, a versatile toolbox leveraging proteome-scale structural alignment and deep-learning-based predictions for efficient genomic mining to generate GEMs ready for applications. Our findings show that the structural alignment or protein-language-model-based prediction (i.e., PLMSearch), could identify more homologous protein relationships than sequence-blast-based alignment, contributing to the accurate profiling of metabolism from target organisms. Additionally, AlphaGEM encompasses an ensemble procedure empowered by multiple deep learning toolboxes to effectively mine the dark metabolic functions encoded by nonhomologous proteins, significantly expanding species-specific metabolic networks. We demonstrate AlphaGEMs accuracy by building GEMs for eukaryotes (e.g., S. pombe, C. albicans) and prokaryotes (e.g., K. pneumoniae, B. subtilis), achieving predictions comparable to manually curated models while outperforming existing tools. AlphaGEM also successfully reconstructs GEMs for M. musculus and C. griseus, showcasing its great potential for uncovering dark metabolism in complex mammals. Lastly, we demonstrate that AlphaGEM could facilitate the automatic GEMs reconstruction for 332 distinct yeast species with high prediction fidelity. In conclusion, AlphaGEM provides unprecedented opportunities for the precise, rapid construction of GEMs across diverse domains, which sets a solid foundation for universal functional analysis of non-model organisms having genome sequences available.

bioinformatics↗

bioRxiv2025

A Complete Telomere-to-Telomere Diploid Reference Genome for Indian Population

Human reference genomes have been instrumental in advancing genomic and biomedical research, but South and Southeast Asian populations are underrepresented, despite accounting for a large proportion of world population. As a part of effort on generating reference genomes for these populations, we present the first gapless, telomere-to-telomere (T2T) diploid genome assembly created by using a trio sample set of Indian ancestry (I002C), with NG50 of 154.89 Mb and 146.27 Mb for the maternal and paternal haplotypes, including the fully assembled rDNA array for the maternal chromosome 21 and Y chromosome. With the Merqury QVs of 82.05, 83.08 and 82.64 for the maternal, paternal and haploid assemblies respectively, I002C represents the highest-quality human genome assembled in both diploid and haploid forms to date. Compared to CHM13, the I002C genome displays substantial sequence diversity, resulting in 14,943 structural variants, including 3,236 novel variants absent from public databases. Analysis of trio-phased haplotypes further revealed elevated inter-haplotype divergence within centromeric and subtelomeric regions, along with identification of differentially methylated regions (DMRs) as candidates for novel imprinting loci. As a result of substantial SVs between them, I002C is a more suitable reference than CHM13 for the genomic analysis of South Asian samples with less reference bias and better performance in mapping and variant calling, particularly for long read sequencing data. As the first high-quality T2T diploid reference genome for Indian, the largest worlds population, I002C contributes to the growing set of population-specific reference genomes and helps to overcome a significant gap in human genome diversity.

genomics↗

bioRxiv2025

Mechanisms of 10-Hydroxyoctadecanoic acid resistance in Streptococcus pneumoniae

Profiles of human nasal colonization consistently demonstrate that Staphylococcus aureus and Streptococcus pneumoniae can co-exist in the nasopharynx. Several studies have demonstrated the antagonist relationship between the two organisms via several molecular mechanisms including competition for nutrients as well as via direct killing by hydrogen peroxide. During nasal colonization, the pneumococcus is in direct contact with the fatty acid h18:0, which is released into the extracellular environment by S. aureus. We report that h18:0 is specifically toxic to the pneumococcus amongst the pathogenic streptococci, providing a unique mechanism for interspecies competition during colonization. Exposure of cells to h18:0 revealed that S. pneumoniae could rapidly adapt to and overcome the observed toxicity. Whole genome analysis revealed the mechanism underlying this resistance being linked to a truncation of a glycosyltransferase in the capsule biosynthesis locus and a genomic inversion in the phase variation locus, leading to altered cell surface charge and membrane lipid composition. These physiological differences in the resistant isolates may aid in repelling toxic, charged fatty acids such as h18:0 from the cell membrane. IMPORTANCEThe pneumococcus and S. aureus are two of the most well-characterized residents of the human nasopharynx; yet much remains unknown regarding how the two bacteria interact. Here, we describe the potential of S. aureus-produced h18:0, whose function and biological impact are still being described, to act as an inter-species competition molecule against S. pneumoniae, and how the pneumococcus can adapt to overcome its toxicity.

microbiology↗

bioRxiv2025

A class of COPI adaptors regulates processing of transmembrane receptors by reinforcing their Golgi retention

Many transmembrane (TM) receptors undergo essential post-translational modification in the Golgi prior to their delivery to the plasma membrane. Whether and how the passage and accompanied modification of these receptors across the Golgi is controlled remains unclear. Here, we show that leptin receptor overlapping transcript (LEPROT) and LEPROT-like 1 (LEPROTL1) regulate receptor activation by securing their sufficient Golgi retention. LEPROTs localize to cis and medial Golgi in a COPI-dependent manner. Deletion of LEPROTs in cells causes expedited release of receptors transiting through the Golgi, and leakage of some Golgi-enriched proteins into the endomembrane compartments. LEPROTs interact directly with COPI coats and simultaneously engage a variety of integral membrane proteins with relatively long TM domains at acidic pH. Loss of LEPROTs dysregulates receptor activity, including that of EGFR and TFRC, due to defective modification. Collectively, LEPROTs serve as a class of COPI adaptors for TM receptors, ensuring adequate preparation, which is vital for subsequent action on the plasma membrane.

cell biology↗

bioRxiv2024

Endogenous hydrogen peroxide positively regulates secretion of a gut-derived peptide in neuroendocrine potentiation of the oxidative stress response in C. elegans

The gut-brain axis mediates bidirectional signaling between the intestine and the nervous system and is critical for organism-wide homeostasis. Here we report the identification of a peptidergic endocrine circuit in which bidirectional signaling between neurons and the intestine potentiates the activation of the antioxidant response in C. elegans in the intestine. We identify a FMRF-amide-like peptide, FLP-2, whose release from the intestine is necessary and sufficient to activate the intestinal oxidative stress response by promoting the release of the antioxidant FLP-1 neuropeptide from neurons. FLP-2 secretion from the intestine is positively regulated by endogenous hydrogen peroxide (H2O2) produced in the mitochondrial matrix by sod-3/superoxide dismutase, and is negatively regulated by prdx-2/peroxiredoxin, which depletes H2O2 in both the mitochondria and cytosol. H2O2 promotes FLP-2 secretion through the DAG and calcium-dependent protein kinase C family member pkc-2 and by the SNAP25 family member aex-4 in the intestine. Together, our data demonstrate a role for intestinal H2O2 in promoting inter-tissue antioxidant signaling through regulated neuropeptide-like protein exocytosis in a gut-brain axis to activate the oxidative stress response.

neuroscience↗

bioRxiv2024

Engineering oncogenic hotspot mutations on SF3B1 via CRISPR-directed PRECIS mutagenesis

SF3B1 is the most recurrently mutated RNA splicing factor in cancer; However, its study has been hindered by a lack of disease-relevant cell line models. Here, we compared four genome engineering platforms to establish SF3B1mutant cell lines: CRISPR-Cas9 editing, AAV HDR editing, base editing (ABEmax, ABE8e), and prime editing (PE2, PE3, PE5Max). We showed that prime editing via PE5max achieved the most efficient SF3B1 K700E editing across a wide range of cell lines. We further refined our approach by coupling prime editing with a with a fluorescent reporter that leverages a SF3B1 mutation-responsive synthetic intron to mark prime edited cells. Calling this approach prime editing coupled intron-assisted selection (PRECIS), we then introduced the K700E hotspot mutation into two chronic lymphocytic leukemia (CLL) cell lines, HG-3 and MEC-1, and demonstrated that our PRECIS-engineered cells faithfully recapitulate the altered splicing and copy number variation (CNV) events frequently found in CLL patients with SF3B1 mutation. Our results showcase PRECIS as an efficient and generalizable method for engineering genetically faithful SF3B1 mutant models, shed new light on the role of SF3B1 mutation in cancer biology, and enables generation of novel SF3B1 mutant cell lines in any cellular context.

cancer biology↗

bioRxiv2023

CDCA7 is a hemimethylated DNA adaptor for the nucleosome remodeler HELLS

Mutations of the SNF2 family ATPase HELLS and its activator CDCA7 cause immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome, characterized by hypomethylation at heterochromatin. The unique zinc-finger domain, zf-4CXXC_R1, of CDCA7 is widely conserved across eukaryotes but is absent from species that lack HELLS and DNA methyltransferases, implying its specialized relation with methylated DNA. Here we demonstrate that zf-4CXXC_R1 acts as a hemimethylated DNA sensor. The zf-4CXXC_R1 domain of CDCA7 selectively binds to DNA with a hemimethylated CpG, but not unmethylated or fully methylated CpG, and ICF disease mutations eliminated this binding. CDCA7 and HELLS interact via their N-terminal alpha helices, through which HELLS is recruited to hemimethylated DNA. While placement of a hemimethylated CpG within the nucleosome core particle can hinder its recognition by CDCA7, cryo-EM structure analysis of the CDCA7-nucleosome complex suggests that zf-4CXXC_R1 recognizes a hemimethylated CpG in the major groove at linker DNA. Our study provides insights into how the CDCA7-HELLS nucleosome remodeling complex uniquely assists maintenance DNA methylation.

molecular biology↗

bioRxiv2023

Evidence for impaired hippocampal circuitry in schizophrenia and its link to memory dysfunction

Pattern separation and pattern completion are opposing yet complementary components of mnemonic processing that heavily rely on the hippocampus. It has been shown that processing within the dentate gyrus (DG) subfield promotes pattern separation while operations within the CA3 subfield are important for pattern completion. Schizophrenia has been associated with anatomical and functional hippocampal abnormalities, including within the DG and CA3. We hypothesized that an impairment in hippocampal circuitry in individuals with first-episode schizophrenia leads to deficits in pattern separation (mnemonic discrimination) and pattern completion (recognition memory), that these deficits contribute to delusions, and that antipsychotic treatment improves circuit functioning. We measured behavioral and neural responses during the identification of new, repeated, and similar stimuli using high-resolution fMRI in 45 medication-free or minimally-treated patients with first-episode schizophrenia and 49 matched controls. We found recognition memory and pattern separation deficits in patients and a negative association between memory performance and the severity of delusions. Neural analyses revealed deficits in both univariate BOLD responses and multivariate patterns in the hippocampus during mnemonic discrimination in patients compared to controls. Importantly, by investigating the association between trial-level neural activity and behavior before and after treatment, we found that antipsychotics normalized DG activity during pattern separation and CA3 activity during pattern completion. Lastly, trial-level cortical responses during mnemonic discrimination predicted performance in patients at baseline, suggesting a compensatory role. This study provides new insight into the impact of schizophrenia and antipsychotic treatment on memory systems and uncovers systems-level contributions to pattern separation and pattern completion.

neuroscience↗

bioRxiv2023

NaV1.6 inhibition drives the efficacy of voltage-gated sodium channel inhibitors to prevent electrically induced seizures in both wild type and Scn8aN1768D/+ gain-of-function mice

Inhibitors of voltage-gated sodium channels (NaVs) are important anti-epileptic drugs, but the contribution of specific channel isoforms is unknown since available inhibitors are nonselective. We created a series of compounds with diverse selectivity profiles enabling block of NaV1.6 alone or together with NaV1.2. Mice with a heterozygous gain-of-function mutation (N1768D/+) in Scn8a (encoding NaV1.6) responded with a tonic-clonic seizure to a mild 6 Hz stimulus that was innocuous to wild-type mice. Pharmacologic inhibition of NaV1.6 in Scn8aN1768D/+ mice prevented seizures. Inhibitors were also effective in a direct current maximal electroshock seizure assay in wild-type mice. NaV1.6 inhibition correlated with efficacy in both models, even without inhibition of other CNS NaV isoforms. Our data suggest NaV1.6 inhibition is a driver of efficacy for NaV inhibitor anti-seizure medicines. Selective NaV1.6 inhibitors may provide targeted therapies for human Scn8a developmental and epileptic encephalopathies and better tolerated treatments for idiopathic epilepsies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/551823v2_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@39c09borg.highwire.dtl.DTLVardef@19413b8org.highwire.dtl.DTLVardef@9aa226org.highwire.dtl.DTLVardef@b9207_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2023

Coevolution of the CDCA7-HELLS ICF-related nucleosome remodeling complex and DNA methyltransferases

5-Methylcytosine (5mC) and DNA methyltransferases (DNMTs) are broadly conserved in eukaryotes but are also frequently lost during evolution. The mammalian SNF2 family ATPase HELLS and its plant ortholog DDM1 are critical for maintaining 5mC. Mutations in HELLS, its activator CDCA7, and the de novo DNA methyltransferase DNMT3B, cause immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome, a genetic disorder associated with the loss of DNA methylation. We here examine the coevolution of CDCA7, HELLS and DNMTs. While DNMT3, the maintenance DNA methyltransferase DNMT1, HELLS, and CDCA7 are all highly conserved in vertebrates and green plants, they are frequently co-lost in other evolutionary clades. The presence-absence patterns of these genes are not random; almost all CDCA7 harboring eukaryote species also have HELLS and DNMT1 (or another maintenance methyltransferase, DNMT5). Coevolution of presence-absence patterns (CoPAP) analysis in Ecdysozoa further indicates coevolutionary linkages among CDCA7, HELLS, DNMT1 and its activator UHRF1. We hypothesize that CDCA7 becomes dispensable in species that lost HELLS or DNA methylation, and/or the loss of CDCA7 triggers the replacement of DNA methylation by other chromatin regulation mechanisms. Our study suggests that a unique specialized role of CDCA7 in HELLS-dependent DNA methylation maintenance is broadly inherited from the last eukaryotic common ancestor.

evolutionary biology↗

bioRxiv2022

Pneumococcal Evasion of Antibiotics via Metabolic Adaptation During Infection

Streptococcus pneumoniae is a major human pathogen of global health concern, causing a range of mild to severe infections, including acute otitis media, pneumonia, sepsis, and meningitis. The rapid emergence of antibiotic resistance among S. pneumoniae isolates poses a serious public health problem worldwide. Resistant pneumococcal strains have rendered the mainstay treatment with beta-lactams, fluoroquinolones, and macrolides, ineffective. Antibiotic resistance in S. pneumoniae has spread globally via the emergence of de novo mutations and horizontal transfer of resistance. Fluoroquinolone resistance in S. pneumoniae is an intriguing case because the prevalence of fluoroquinolone resistance does not correlate with increasing usage, as is often the case with other classes of antibiotics. In this study, we demonstrated that deleterious fitness costs constrain the emergence of individual fluoroquinolone resistance mutations in either topoisomerase IV or gyrase A in S. pneumoniae. Generation of double point mutations in the target enzymes in topoisomerase IV and gyrase A conferred high-level fluoroquinolone resistance while restoring fitness comparable to the sensitive wild-type. During an in vivo model of antibiotic resistance evolution, S. pneumoniae was able to circumvent deleterious fitness costs imposed by resistance determinants through development of antibiotic tolerance through metabolic adaptation that reduced the production of reactive oxygen species, an effect that could be recapitulated pharmacologically. The metabolic mutants conferring tolerance resulted in a fitness benefit during infection following antibiotic treatment with fluroquinolones. These data suggest that emergence of fluoroquinolone resistance is tightly constrained in S. pneumoniae by host fitness tradeoffs and that mutational pathways involving metabolic networks to enable tolerance phenotypes may be an important contributor to the evasion of antibiotic mediated killing.

microbiology↗

bioRxiv2022

Harringtonine has the effects of double blocking SARS-CoV-2 membrane fusion

Fusion with host cell membrane is the main mechanism of infection of SARS-CoV-2. Here, we propose a new strategy to double block SARS-CoV-2 membrane fusion by using Harringtonine (HT), a small-molecule antagonist. By using cell membrane chromatography (CMC), we found that HT specifically targeted the SARS-CoV-2 S protein and host cell TMPRSS2, and then confirmed that HT can inhibit pseudotyped virus membrane fusion. Furthermore, HT successfully blocked SARS-CoV-2 infection, especially in the delta and Omicron mutant. Since HT is a small-molecule antagonist, it is minimally affected by the continuous variation of SARS-CoV-2. Our findings show that HT is a potential small-molecule antagonist with a new mechanism of action against SARS-CoV-2 infection, and thus HT mainly targets the S protein, and thus, greatly reduces the damage of the S proteins autotoxicity to the organ system, has promising advantages in the clinical treatment of COVID-19.

pharmacology and toxicology↗

bioRxiv2021

Competition Between Cell-Cell and Cell-Substrate Adhesion Determines Epithelial Monolayer Architecture in Culture

Organ surfaces are lined by epithelial monolayers - sheets of cells that are one-cell thick. This architecture underlies tissue function, and its loss is associated with disease, including cancer. Studies of in-plane epithelial cell behaviors show that a developing epithelium behaves as a fluid in respect to the tissue plane, and can therefore readily adapt to varying mechanical influences during morphogenesis. We asked the question of how monolayer architecture is achieved, and whether it demonstrates the same fluid behavior. To address this problem, we cultured MDCK (Madin-Darby Canine Kidney) cell layers at different densities and timepoints and analyzed their architectures using a novel tool, Automated Layer Analysis (ALAn), which we introduce here. Our experimental and theoretical results lead us to propose that epithelial monolayer architecture is governed by a balance of counteracting forces due to cell-cell and cell-substrate adhesion, and that this balance is influenced by cell density. MDCK cells do not undergo obvious rearrangement along the apical-basal axis; instead, cells that do not contact the substrate aggregate on top of the monolayer. Our findings therefore imply that monolayered architecture is under more rigid control than planar tissue shape in epithelia.

cell biology↗