Biology subjects

Qu, T.

Publications and source records attributed to Qu, T..

8 recordsLinked to original sources

bioRxiv2025

Cell Cycle Arrest of a "Zippering" Epithelial Cell Cluster Shapes the Face and is Disrupted in Craniofacial Disorders

Facial features identify individuals, but the mechanisms shaping the human face remain elusive. Orofacial clefting (OFC), the most common craniofacial abnormality, results from failed fusion of the facial prominences that is in part caused by persistence of the cephalic epithelium. Here we uncover the identity, behaviors, and molecular blueprints of a novel craniofacial epithelial population, the Zippering Lambda (ZL), which mediates prominence fusion and is characterized by cell cycle arrest in mouse and human embryos. Remarkably, cell cycle is unleashed in the ZL of Pbx1/2 and p63 mutant mice with OFC. Intersection of ZL-enriched genes with human OFC whole-genome sequencing datasets identifies ZFHX3 variants in affected individuals and cephalic epithelial Zfhx3 deletion causes murine OFC. ZFHX3 and PBX1 genetically interact and synergistically regulate cell cycle inhibitor genes within a complex in embryonic faces. Collectively, we deconstruct new mechanisms that pattern the face, connecting cell cycle arrest to developmental tissue fusion.

developmental biology↗

bioRxiv2025

High-resolution taxonomic profiling and metatranscriptomics identify microbial, biochemical, host and ecological factors in peri-implant disease

Biofilm-associated diseases like peri-implant mucositis (PIM) and peri-implantitis (PI) are significant clinical challenges affecting millions of dental implant patients globally. Although studies have described the role of microbial, host, or environmental factors in disease development, their complex interplay, particularly during dysbiosis remains poorly understood. This cross-sectional study characterized the microbiome composition and metatranscriptomes of 125 peri-implant biofilms from 48 individuals uncovering molecular signatures linked to peri-implant health (PIH), PIM, and PI. Distinct variations were observed in biofilm amount, composition, activity, phage populations and host response. Biofilms were categorized into four community types (CTs) based on the bacterial transcriptional activity: one linked to PIH, one to PI, and two to PIM. PIH and PIM were primarily characterized by aerotolerant taxa with increased anabolic processes, while PI was dominated by obligate anaerobes with complex biofilm morphology, and heightened catabolic activity and virulence. PIM samples, relative to PIH were characterized by biofilm expansion with minimal functional changes, except for the Neisseria-rich PIM subtype showing higher pyruvate and lipoic acid metabolism. The phagome mirrored the bacterial compositional variations across disease states. Furthermore, human transcriptome responses varied indicating increased keratinization in PIH, enhanced expression of ribosome components in PIM, and inflammatory signaling and hypoxia in PI. Additionally, we identified complex species-enzyme, phage-bacteria, and host-microbe associations within the peri-implant ecosystem. Our integrative multi-omics approach provides a comprehensive view of microbial, biochemical, host, and ecological factors associated with dysbiosis, offering novel insights into peri-implant disease dynamics. ImportancePeri-implant mucositis and peri-implantitis are highly prevalent inflammatory conditions that compromise the long-term survival and success of dental implants, yet their underlying biological mechanisms are largely unresolved. While next-generation sequencing has advanced our understanding of microbial composition across health and peri-implant diseases, it falls short of capturing microbial activity and the broader molecular context of peri-implant dysbiosis. Metatranscriptomics overcomes this limitation by profiling actively transcribed genes within the biofilm, offering direct insights into microbial community functions. In this study, we integrated full-length 16S rRNA gene amplicon sequencing with metatranscriptomic profiling to simultaneously assess microbial taxonomy, functional activity, phage dynamics, and host gene expression in peri-implant biofilms. Importantly, we provide a systems-level view and report previously undescribed associations between different molecular signatures in peri-implant ecosystem.

microbiology↗

bioRxiv2025

Invasive species drive polymicrobial resistance to amoxicillin in oral biofilms through beta-lactamase release

Since bacterial biofilms often cause refractory infections, antimicrobial susceptibility testing (AST) is highly desirable even for oral peri-implant biofilms. However, characterization of polymicrobial drug resistance is challenging due to high diversity and complexity of these biofilms. In this work, we developed laser-assisted AST and detected polymicrobial amoxicillin resistance in peri-implantitis. TEM-1 {beta}-lactamase production enabled an Enterobacter sp. strain SPS_532 to protect its otherwise susceptible biofilm cohabitants. To understand the {beta}-lactamase driven cross-protection in the human microbiome we aggregated genomic (n = 200,000) and patient microbial data (n = 27,000), developed a cross-protection assay, studied a representative strain collection (n = 118) and established a complex biofilm in vitro model (with an average of 133 species from 164 found in dental plaque). Multiple oral allochthonous species, e.g., Enterobacter, Klebsiella, Escherichia, Staphylococcus, and only a single typical oral microorganism, Haemophilus, were able to cross-protect. Diverse bla genes conferred activity, via a high expression of chromosomal gene, e.g., blaAmpC gene or by the presence of plasmidic gene, e.g., blaTEM-1 gene. Invaders not only cross-protected the biofilm from the antibiotic, but also supported expansion of opportunistic pathogens like Fusobacterium species. Cross-protection in complex biofilms depended on the diffusion rate and population size of the invader, which could be bio-controlled with a phage. Deciphering polymicrobial resistance might support the development of diagnostic and therapeutic approaches to combat implant-associated biofilm infections in the human mouth.

microbiology↗

bioRxiv2025

Integrative microbiome- and metatranscriptome-based analyses reveal diagnostic biomarkers for peri-implantitis

Peri-implantitis is a severe biofilm-associated infection of the tissues around dental implants that increases the risk of implant failure. The prognosis of peri-implantitis treatment is compromised by the resistance of well-organized and mature bacterial biofilms. Thus, early diagnosis of a pathogenic biofilm would enable treatment at a prognostically favourable stage. However, relatively little is known about how the microbial constitution of the biofilm changes during disease development. The aim of this cross-sectional study was therefore to identify peri-implant taxonomic and functional biomarkers that reliably indicate peri-implantitis using paired data from full length 16S rRNA gene amplicon sequencing (full-16S) and metatranscriptomics (RNAseq). Disease signatures were identified using 24 healthy and 24 peri-implantitis-associated biofilm samples from 32 patients. The taxonomic measurements were validated with 68 additional full-16S samples from another 40 patients. Both full-16S and RNAseq revealed significant differences between healthy and peri-implantitis samples, with respect to both the microbiome and functional profiles. A shift from aerotolerant Gram-positive bacteria to anaerobic Gram-negative bacteria was observed in peri-implantitis. Distinct metabolic pathways were expressed in healthy and peri-implantitis samples. Our results, based on paired taxonomic and functional profiles, provide for the first time important insights into the complex peri-implant biofilm ecology related to amino acid metabolism. Integrating taxonomic and functional information improved the predictive ability (AUC = 0.85) of the machine learning models and revealed diagnostic biomarkers with large effect sizes (Cohens d > 0.8). Primary biomarkers included health-associated Streptococcus, Rothia species and enzymes associated with peri-implantitis (urocanate hydratase, tripeptide aminopeptidase, NADH:ubiquinone reductase, phosphoenolpyruvate carboxykinase and polyribonucleotide nucleotidyltransferase - mostly expressed by Fusobacteriia and Bacteroidia). Thus, biofilm profiling at these two molecular levels reveals highly predictive disease biomarkers and provide the basis for developing early diagnostics and individualized therapy approaches for peri-implant diseases.

microbiology↗

bioRxiv2022

Administration of amniotic fluid stem cell extracellular vesicles promotes development of fetal hypoplastic lungs by immunomodulating lung macrophages

Congenital diaphragmatic hernia (CDH) is a devastating condition characterized by incomplete closure of the diaphragm and herniation of abdominal organs into the chest. As a result, fetuses have pulmonary hypoplasia, whose severity is the main determinant of poor outcome. The pathogenesis of pulmonary hypoplasia secondary to CDH is at least in part explained by lack or dysregulation of miRNAs that are known to regulate lung developmental processes. Herein, we report that intra-amniotic administration of extracellular vesicles derived from amniotic fluid stem cells (AFSC-EVs) rescues lung growth and maturation in a fetal rat model of CDH. To understand which fetal lung cells and biological pathways are affected by AFSC-EVs, we conducted whole lung single nucleus RNA-sequencing. We discovered that CDH lungs have a multilineage inflammatory signature with macrophage enrichment, and confirmed these findings in autopsy samples of lungs from human fetuses with CDH. Transcriptomic analysis of CDH fetal rat lungs also showed that AFSC-EV treatment reduced macrophage density and inflammation to normal levels. Analyzing the miRNAs contained in the AFSC-EV cargo with validated mRNA targets, we found that the downregulated genes in AFSC-EV treated CDH lungs were involved in inflammatory response and immune system processes. This study reports a single cell atlas of normal and hypoplastic CDH fetal rat lungs and provides evidence that AFSC-EVs restore lung development by addressing multiple pathophysiological aspects of CDH. One Sentence SummaryAmniotic fluid stem cell extracellular vesicle treatment for fetal lung macrophage modulation

developmental biology↗

bioRxiv2021

Species-specific deployment of Runx2 isoforms and differential regulation of target genes during avian jaw development and evolution

Developmental regulation of bone formation in the jaw skeleton is essential to species-specific adaptation. The jaws are derived from neural crest mesenchyme (NCM), a progenitor population that directs skeletal patterning by exerting temporal and spatial control over molecular and cellular programs for osteogenesis. One important NCM-mediated gene is Runx2, which is a transcription factor required for osteoblast differentiation. RUNX2 protein binds many target genes involved in the deposition and resorption of bone. To determine the extent to which changes in Runx2 structure, function, and expression underlie the evolution of the jaw skeleton, we compare Runx2 across vertebrates and within birds. Runx2 contains two alternative promoters, tandem repeats of glutamine and alanine with variable lengths in different species, a conserved DNA-binding domain, an exon that is alternatively spliced, as well as two possible C-termini. Such alternative splicing produces eight potential isoforms that show distinct stage- and species-specific patterns in the jaw primordia of chick, quail and duck embryos. We also find that certain isoforms are strongly induced by TGF{beta} signaling whereas others are not. Overexpressing Runx2 isoforms in NCM reveals that some are transcriptionally activating, while others are repressive. But context appears to be relevant since species-specific polymorphisms in the promoter of target genes like Mmp13, can modulate the effects of different isoforms. Overall, our study indicates that the structure and species-specific deployment of Runx2 isoforms affect the transcriptional activity of target genes in ways that may have played a generative and regulatory role in the evolution of the avian jaw skeleton.

developmental biology↗

bioRxiv2021

Phenotypic analysis of catastrophic childhood epilepsy genes: The Epilepsy Zebrafish Project

Genetic engineering techniques have contributed to the now widespread use of zebrafish to investigate gene function, but zebrafish-based human disease studies, and particularly for neurological disorders, are limited. Here we used CRISPR-Cas9 to generate 40 single-gene mutant zebrafish lines representing catastrophic childhood epilepsies. We evaluated larval phenotypes using electrophysiological, behavioral, neuro-anatomical, survival and pharmacological assays. Phenotypes with unprovoked electrographic seizure activity (i.e., epilepsy) were identified in zebrafish lines for 8 genes; ARX, EEF1A, GABRB3, GRIN1, PNPO, SCN1A, STRADA and STXBP1. A unifying epilepsy classification scheme was developed based on local field potential recordings and blinded scoring from ~3300 larvae. We also created an open-source database containing sequencing information, survival curves, behavioral profiles and representative electrophysiology data. We offer all zebrafish lines as a resource to the neuroscience community and envision them as a starting point for further functional analysis and/or identification of new therapies.

neuroscience↗

bioRxiv2020

Species-specific sensitivity to TGFβ signaling and changes to the Mmp13 promoter underlie avian jaw development and evolution

Developmental control of jaw length is critical for survival. The jaw skeleton arises from neural crest mesenchyme and previously we demonstrated that these progenitors upregulate bone-resorbing enzymes including Matrix metalloproteinase 13 (Mmp13) when generating short quail beaks versus long duck bills. Inhibiting bone resorption or Mmp13 increases jaw length. Here, we uncover mechanisms establishing species-specific levels of Mmp13 and bone resorption. Quail show greater activation of, and sensitivity to Transforming Growth Factor-Beta (TGF{beta}) signaling than duck; where mediators like SMADs and targets like Runx2, which bind Mmp13, become elevated. Inhibiting TGF{beta} signaling decreases bone resorption. We discover a SMAD binding element in the quail Mmp13 promoter not found in duck and single nucleotide polymorphisms (SNPs) near a RUNX2 binding element that affect expression. Switching the SNPs and SMAD site abolishes TGF{beta}-sensitivity in the quail Mmp13 promoter but makes duck responsive. Thus, differential regulation of TGF{beta} signaling and Mmp13 promoter structure underlie avian jaw development and evolution.

developmental biology↗