Biology subjects

Xu, J.

Publications and source records attributed to Xu, J..

At least 577 records · Page 32Linked to original sources

bioRxiv2022

The infiltration pattern of microenvironmental cells and different immune escape mechanisms in colorectal cancer

BackgroundThe tumour microenvironment (TME) plays a crucial role in tumour progression and metastasis. However, the infiltration pattern of TME cells in CRC samples and the immune escape mechanism underneath have not been studied sufficiently. MethodsTranscriptomic data from public datasets were retrieved online. In total, 1802 samples from the microarray dataset and 619 samples from the TCGA dataset were enrolled. The ssGSEA algorithm and unsupervised clustering were used for TME cells infiltration speculation and infiltration pattern recognition. ResultsCRC samples can be classified into three distinct TME cell subtypes. Subtype 1, the immune-active subtype, was characterised by high infiltration of activated adaptive immune cells. Subtype 2, the immune-desert subtype, featured high tumour purity and low infiltration of immune and stromal cells. And subtype 3, stroma-rich subtype, had high infiltration of stromal cells. The stroma-rich subtype conferred a significantly worse prognosis. Three subtypes had different immune escape mechanisms. The immune-active subtype has the highest immune checkpoint expression level. In comparison, the immune-desert subtype had the lowest immunogenicity and the defective antigen presentation. And the stroma-rich subtype lacked activated immune cells. ConclusionsDistinct TME cell subtypes and immune escape mechanisms may provide inspiration and direction for further researches on CRC immunotherapy.

cancer biology↗

bioRxiv2022

Factors that affected the qualification of standardized residency training of internal medicine: a prospective longitudinal study

IntroductionSince the standardized residency training (SRT) was launched in 2014, there were very few data on evaluation of the factors that could influence the residents competency in China. MethodsAll residents who started their SRT programme from September 2015 to September 2018 were enrolled in this study. During the following years, they finished the programme and took examinations. The demographic information and exam scores of each subject were collected and analyzed. ResultsWe found that the qualification rates of SRT programme differed significantly annually. Age, gender, the highest medical education degree, residents from different places, training duration and years of medical school study were also different significantly year by year. According to the scores of examinations, residents were divided into two groups: the qualified group and the non-qualified group. Age, the highest medical education degree, residents from different places, training duration, years of medical school study and prior medical work experience differed significantly between the two groups. Multivariate Logistic regression analysis showed the residents from different places and the training duration were factors that affected the qualification rate of SRT programme independently (P = 0.000 and 0.005, respectively). DiscussionThe "homogeneity" of SRT had been achieved regardless of the individual discrepancy, while the resident from different places and the training duration were obstacles we need to overcome further. Therefore, we should further advance the process of the transition from "Unit Persons" to "Society Persons". And extending training duration will facilitate their qualification and be benefit to improve their competency.

scientific communication and education↗

bioRxiv2022

The exchange rates of amide and arginine guanidinium CEST in the mouse brain

PurposeTo develop a pipeline for measuring the exchange rates and concentrations of in vivo excgangeable protons, and to demonstrate this for the amide and arginine (Arg) guanidinium (Guan) protons in mobile proteins in the mouse brain. MethodsAn ultra-short echo (UTE) CEST sequence with a continuous wave presaturation (preRadCEST) was applied to acquire Z-spectra with robustness to motion and physiological fluctuations. AmideCEST and Arginine guanCEST (ArgCEST) were extracted and their proton concentrations and exchange rates obtained using a two-step multi-B1 Bloch fitting approach that included the semisolid macromolecular background. To minimize contamination from the amine protons from creatine and phosphocreatine, ArgCEST measurements were performed on the Guanidinoacetate N-methyltransferase deficiency (GAMT-/-) mouse characterized by low creatine and phosphocreatine concentrations in the brain. ResultsFor the amideCEST proton pool, the exchange rate and concentrations were found to be 59.6 {+/-} 9.0 s-1 and 41.7 {+/-} 7.0 mM, respectively, with the maximum signal observed at B1 = 0.8 T. For the ArgCEST proton, the guanidinium exchange these were 70.1 {+/-} 5.5 s-1 and 10.1 {+/-} 1.3 mM, respectively, with the maximum effect observed at B1 = 0.9 T. The current study suggests that the inverse pH dependence in GuanCEST of brain is led by the CrCEST component, not ArgCEST. ConclusionThe current pipeline is expected to have general use for in vivo CEST quantitation and optimization of visible CEST resonances.

biophysics↗

bioRxiv2022

The Yeast Lifespan Machine: a microfluidic platform for automated replicative lifespan measurements

The budding yeast, Saccharomyces cerevisiae, has emerged as a model system for studying the aging processes in eukaryotic cells. However, the full complement of tools available in this organism has not been fully applied, in part because of limitations in throughput that restrict the ability to carry out detailed analyses. Recent advances in microfluidics have provided direct longitudinal observation of entire yeast lifespans, but have not yet achieved the normal scale of operation possible in this model system. Here we present a microfluidic platform, called the Yeast Lifespan Machine, where we combine improvements in microfluidics, image acquisition, and image analysis tools to increase robustness and throughput of lifespan measurements in aging yeast cells. We demonstrate the platforms ability to measure the lifespan of large populations of cells and distinguish long- and short-lived mutants, all with minimal involvement of the experimenter. We also show that environmental pH is capable of significantly modulating lifespan depending on the growth media, highlighting how microfluidic technologies reveal determinants of lifespan that are otherwise difficult to ascertain.

cell biology↗

bioRxiv2022

The chemokine receptor CXCR3 promotes CD8+ T cell-dependent lung pathology during influenza pathogenesis

While the role of CD8+ T cells in influenza clearance is established, their contribution to pathological lung injury is increasingly appreciated. To explore if protective versus pathological functions can be linked to CD8+ T cell subpopulations, we dissected their responses in influenza-infected murine lungs. Our single-cell RNASeq (scRNAseq) analysis revealed significant diversity in CD8+ T cell subpopulations during peak viral load vs. infection-resolved state. While enrichment of Cxcr3hi CD8+ T effector (Teff) subset was associated with a more robust cytotoxic response, both CD8+ Teff and CD8+ T central memory (TCM) exhibited equally potent effector potential. The scRNAseq analysis identified unique regulons regulating the cytotoxic response in CD8+ T cells. The neutralization of CXCR3 mitigated lung injury without affecting viral clearance. IFN-{gamma} was dispensable to regulate the cytotoxic response of Cxcr3hi CD8+ T cells. Collectively, our data imply that CXCR3 interception could have a therapeutic effect in preventing influenza-linked lung injury. TEASERThe CXCR3 expressing CD8+ T cell subset causes severe lung pathology and exacerbates disease severity without affecting viral clearance during influenza infection

immunology↗

bioRxiv2022

Cryomilling Tethered Chromatin Conformation Capture reveal new insights into inter-chromosomal interactions

Traditional methods used to map the three-dimensional organization of chromatin in-situ generally involve chromatin conformation capture by formaldehyde crosslinking, followed by detergent solubilization and enzymatic digestion of DNA. Ligation of proximal DNA fragments followed by next generation sequencing (NGS) generates contact information that enables a global view of the chromatin conformation. Here, we explore the use of cryomilling to physically fragmentize the cells under cryogenic conditions to probe chromatin interactions in the cryomilled cell fragments by the tethered chromatin conformation capture (TCC). Our results show that cryomilling TCC (CTCC) can generate a global contact map similar to that obtained with in-situ Hi-C. This result suggests that summation of chromatin interactions mapped in individual subcellular fragments can reconstitute the global contact map of intact cells in an ensemble manner, paving the way for chromatin conformation analyses of solid tissue by CTCC. Compared with the conventional in-situ methods such as Hi-C, CTCC shows more uniform access to different subcompartments of the folded genome. On the other hand, most inter-chromosomal (trans) contacts are diminished or lost in CTCC except for a group of unique trans contacts that remain intact throughout the cryomilling and in- vitro crosslinking steps. These apparently ultra-stable trans interactions have much enhanced signal in CTCC due to the elimination of signals of most, presumably weak and transient trans interactions. Systematic and comparative analyses between CTCC and in-situ Hi-C provide further insights into the chromatin structure organization and reveal a generally unentangled chromosome interface and the existence of stable inter-chromosomal contacts that may represent intermingled inter-chromosomal interfaces.

genomics↗

bioRxiv2022

ImmunoTyper-SR: A Novel Computational Approach for Genotyping Immunoglobulin Heavy Chain Variable Genes using Short Read Data

Human immunoglobulin heavy chain (IGH) locus on chromosome 14 includes more than 40 functional copies of the variable gene (IGHV), which, together with the joining genes (IGHJ), diversity genes (IGHD), constant genes (IGHC) and immunoglobulin light chains, code for antibodies that identify and neutralize pathogenic invaders as a part of the adaptive immune system. Because of its highly repetitive sequence composition, the IGH locus has been particularly difficult to assemble or genotype through the use of standard short read sequencing technologies. Here we introduce ImmunoTyper-SR, an algorithmic method for genotype and CNV analysis of the germline IGHV genes using Illumina whole genome sequencing (WGS) data. ImmunoTyper-SR is based on a novel combinatorial optimization formulation that aims to minimize the total edit distance between reads and their assigned IGHV alleles from a given database, with constraints on the number and distribution of reads across each called allele. We have validated ImmunoTyper-SR on 12 individuals with Illumina WGS data from the 1000 Genomes Project, whose IGHV allele composition have been studied extensively through the use of long read and targeted sequencing platforms, as well as nine individuals from the NIAID COVID Consortium who have been subjected to WGS twice. We have then applied ImmunoTyper-SR on 585 samples from the NIAID COVID Consortium to investigate associations between distinct IGHV alleles and anti-type I IFN autoantibodies which have been linked to COVID-19 severity.

bioinformatics↗

bioRxiv2022

3D Printable High Performance Conducting Polymer Hydrogel for All-Hydrogel Bioelectronics

Owing to the unique combination of electrical conductivity and tissue-like mechanical properties, conducting polymer hydrogels have emerged as a promising candidate for bioelectronic interfacing with biological systems. However, despite the recent advances, the development of hydrogels with both excellent electrical and mechanical properties in physiological environments remains a lingering challenge. Here, we report a bi-continuous conducting polymer hydrogel (BC-CPH) that simultaneously achieves high electrical conductivity (over 11 S cm-1), stretchability (over 400%) and fracture toughness (over 3,300 J m-2) in physiological environments, and is readily applicable to advanced fabrication methods including 3D printing. Enabled by the BC-CPH, we further demonstrate multi-material 3D printing of monolithic all-hydrogel bioelectronic interfaces for long-term electrophysiological recording and stimulation of various organs. This study may offer promising materials and a platform for future bioelectronic interfacing.

bioengineering↗

bioRxiv2022

Automated Human Habenula Segmentation from T1-weighted Magnetic Resonance Images using V-Net

The Habenula (Hb), a small bilateral midbrain structure, plays an important role in aversion and reward processing. Despite increasing interest in imaging human Hb structure and function, it is challenging to define the Hb in magnetic resonance imaging (MRI) due to its small size and low anatomical contrast to the surrounding thalamus. In this study, we developed a deep learning-based human Hb segmentation model. This model was trained and tested using about a thousand subjects 3T T1-weighted images with Hb labels from our previous myelin content-based Hb segmentation. The predicted Hb segmentation showed high similarity and small surface distance to the label; the average (across test subjects) dice similarity coefficient, mean distance, and Hausdorff distance were 0.79, 0.22 mm, and 1.63 mm, respectively. We also demonstrated out-of-sample robustness using other 7T and 3T MRI datasets. The proposed Hb segmentation method is automated, objective, fast, robust, and reliable, relieving the requirement of T2-weighted images in the established myelin content-based Hb segmentation to suite a broader range of MRI studies.

neuroscience↗

bioRxiv2022

DiSCs: Domains involving SETDB1 and Cohesin are critical regulators of genome topology and stem cell fate

SETDB1 is a key regulator of lineage-specific genes and endogenous retroviral elements (ERVs) through its deposition of repressive H3K9me3 mark. Apart from its H3K9me3 regulatory role, SETDB1 has seldom been studied in terms of its other potential regulatory roles. To investigate this, a genomic survey of SETDB1 binding in mouse embryonic stem cells across multiple libraries was conducted, leading to the unexpected discovery of regions bereft of common repressive histone marks (H3K9me3, H3K27me3). These regions were enriched with the CTCF motif that is often associated with the topological regulator Cohesin. Further profiling of these non-H3K9me3 regions led to the discovery of a cluster of non-repeat loci that were co-bound by SETDB1 and Cohesin. These regions, which we named DiSCs (Domains involving SETDB1 and Cohesin) were seen to be proximal to the gene promoters involved in embryonic stem cell pluripotency and lineage development. Importantly, it was found that SETDB1-Cohesin co-regulate target gene expression and genome topology at these DiSCs. Depletion of SETDB1 led to localized dysregulation of Cohesin binding thereby locally disrupting topological structures. Dysregulated gene expression trends revealed the importance of this cluster in ES cell maintenance as well as at gene islands that drive differentiation to other lineages. The unearthing of the DiSCs thus unravels a unique topological and transcriptional axis of control regulated chiefly by SETDB1.

genomics↗

bioRxiv2022

Impact of various vaccine boosters on neutralization against Omicron following prime vaccinations with inactivated or adenovirus-vectored vaccine

Since the first report on November 24, 2021, the Omicron SARS-CoV-2 variant is now overwhelmingly spreading across the world. Two SARS-CoV-2 inactivated vaccines (IAVs), one recombinant protein subunit vaccine (PRV), and one adenovirus-vectored vaccine (AdV) have been widely administrated in many countries including China to pursue herd immunity. Here we investigated cross-neutralizing activities in 341 human serum specimens elicited by full-course vaccinations with IAV, PRV and AdV, and by various vaccine boosters following prime IAV and AdV vaccinations. We found that all types of vaccines induced significantly lower neutralizing antibody titers against the Omicron variant than against the prototype strain. For prime vaccinations with IAV and AdV, heterologous boosters with AdV and PRV, respectively, elevated serum Omicron-neutralizing activities to the highest degrees. In a mouse model, we further demonstrated that among a series of variant-derived RBD-encoding mRNA vaccine boosters, it is only the Omicron booster that significantly enhanced Omicron neutralizing antibody titers compared with the prototype booster following a prime immunization with a prototype S-encoding mRNA vaccine candidate. In summary, our systematical investigations of various vaccine boosters inform potential booster administrations in the future to combat the Omicron variant.

immunology↗

bioRxiv2022

Enhanced anticipatory biasing of visuospatial attention in deaf native-signing adults indexed by alpha-band (8-14 Hz) oscillatory neural activity

Deaf people show increased visuospatial attention abilities, especially towards peripheral inputs, but the neural mechanisms of these heightened abilities are not yet understood. In hearing individuals, topographically-specific alpha-band oscillatory activity (8-14 Hz) over parieto-occipital regions has been associated with active suppression of irrelevant locations. Here, we asked whether increases in this spatially-specific anticipatory oscillatory mechanism might underpin enhanced visuospatial attention abilities in deaf individuals, on the premise that deaf people might be more adept at transiently engaging and disengaging attentional processes involved in processing peripheral inputs. An alternative hypothesis was that deaf individuals might not produce lateralized alpha-band activity, because of the need to continuously monitor the periphery due to the absence of an auxiliary auditory spatial alerting system. High-density electroencephalography was recorded from 20 deaf native signers and 20 hearing non-signers performing a cued covert visuospatial attention task. Deaf participants responded significantly more rapidly and accurately and showed highly typical alpha-band lateralization during the cue-target interval of the task. Topographic analysis showed a greater extent of alpha-band anticipatory activity over right parietal scalp, suggesting sequestration of extra-visual attentional circuits (i.e., unused auditory regions), and post-hoc analysis pointed to substantially earlier onset of this activity during the cue-target interval. The presence of cue-evoked anticipatory alpha lateralization in deaf participants suggests that they are rapidly engaging and disengaging attentional processes involved in orienting attention to the periphery. The earlier and more extensive engagement of these anticipatory oscillatory processes may contribute to the improved visuospatial performance observed in these individuals. Significance StatementPrior to this study, it was not known whether deaf people demonstrate lateralization of alpha-band oscillatory electroencephalographic (EEG) activity over the posterior region of the brain, which plays a role in the suppression of uncued regions of space during cued visuospatial attention tasks. We found that this lateralized pattern was observable in deaf participants and was not significantly different from that seen in hearing participants, except that alpha activity onsets earlier in deaf participants. However, when cue directions were collapsed, the scalp topographies of deaf participants showed a greater distribution of alpha activity, suggesting that they recruited a brain region typically reserved for audiospatial attentional control during the visuospatial attention task. Additionally, deaf participants responded significantly more quickly and accurately compared to hearing participants, demonstrating increased visuospatial attention abilities.

neuroscience↗

bioRxiv2022

Lineage-mosaic and mutation-patched spike proteins for broad-spectrum COVID-19 vaccine

The widespread SARS-CoV-2 in humans results in the continuous emergence of new variants. Recently emerged Omicron variant with multiple spike mutations sharply increases the risk of breakthrough infection or reinfection, highlighting the urgent need for new vaccines with broad-spectrum antigenic coverage. Using inter-lineage chimera and mutation patch strategies, we engineered a recombinant monomeric spike variant (STFK1628x), which showed high immunogenicity and mutually complementary antigenicity to its prototypic form (STFK). In hamsters, a bivalent vaccine comprised of STFK and STFK1628x elicited high titers of broad-spectrum antibodies to neutralize all 14 circulating SARS-CoV-2 variants, including Omicron; and fully protected vaccinees from intranasal SARS-CoV-2 challenges of either the ancestral strain or immune-evasive Beta variant. Strikingly, the vaccination of hamsters with the bivalent vaccine completely blocked the within-cage virus transmission to unvaccinated sentinels, for either the ancestral SARS-CoV-2 or Beta variant. Thus, our study provides new insights and antigen candidates for developing next-generation COVID-19 vaccines.

microbiology↗

bioRxiv2022

USH2A gene mutations in rabbits lead to progressive retinal degeneration and hearing loss

Mutations in USH2A gene are responsible for the greatest proportion of hearing and vision loss among individuals with Usher Syndrome (USH) and for autosomal recessive non-syndromic retinitis pigmentosa. Mutations on USH2A exon 13 account for more than 35% of the disease causing USH2A variants including the most prevalence point mutation, c.2299delG, a frameshift mutation. The lack of a clinically relevant animal model has been a bottleneck for the development of therapeutics for USH2A related vision loss. Using CRSPR/Cas9 technology, this study establishes a rabbit line carrying an USH2A frameshift mutation on exon12 (equivalent to human USH2A Exon 13) as a novel mammalian animal model of USH2A. The bi-allelic mutant rabbits exhibit hyper reflective signals in FAF indicating RPE damage and OCT changes indicating photoreceptor degeneration as early as 4 months of age. ERG signals of both rod and cone function were reduced in the USH2A mutant rabbits starting from 7 months old and further decreased at 15-22 months old, indicating progressive retinal photoreceptor degeneration, which is further confirmed by retinal histopathology examination. ABR examination showed moderate to server hearing loss in the USH2A mutant rabbits. These results indicated that disruption of USH2A gene in rabbits is sufficient to induce hearing loss and progressive photoreceptor degeneration. To our knowledge, this is the first mammalian animal model of USH2 which closely recapitulates the phenotype of retinitis pigmentosa in human patients. This study supports the use of rabbits as a clinically relevant animal model to understand the pathogenesis and to develop novel therapeutics for Usher Syndrome.

developmental biology↗

bioRxiv2022

The amyloid precursor protein modulates the position and length of the axon initial segment offering a new perspective on Alzheimer's disease genetics

The small A{beta} peptide has been hypothesized to be the main driver of Alzheimers disease (AD). A{beta} is a proteolytic cleavage product of a larger protein, the amyloid precursor protein (APP), whose normal functions remain largely unexplored. We report here activities of the full-length APP protein that relate directly to the etiology of AD. Increasing neuronal activity leads to a rapid increase in App gene expression. In both cultures of mouse cortical neurons and human iPSC-derived neurons, elevated APP protein changes the structure of the axon initial segment (AIS), the site of action potential initiation. In neurons with elevated APP, the AIS shortens in length and shifts in position away from the cell body. Both changes would be expected to reduce neuronal excitability. The AIS effects are due to the cell-autonomous actions of APP; exogenous A{beta} - either fibrillar or oligomeric - has no effect. The findings relate directly to AD in several ways. In culture, APP carrying the Swedish familial AD mutation (APPSwe) induces stronger AIS changes than wild type APP. Ankyrin G and {beta}IV-spectrin, scaffolding proteins of the AIS, both physically associate with APP, and APPSwe binds more avidly than wild type APP. Finally, neurons in the frontal cortex of humans with sporadic AD reveal histologically elevated levels of APP protein that invade the domain of the AIS, whose length is significantly shorter than that found in healthy control neurons. The findings offer an alternative explanation for the effects of at least some familial AD mutations. SignificanceIn familial Alzheimers disease (AD) the linkage between the genetics of APP, the neuropathology of the amyloid plaques and the symptoms of dementia are one of the strongest pieces of evidence supporting the amyloid cascade hypothesis - a conceptualization that marks the A{beta} peptide as the root cause of AD. Yet, formally, the genetics only point to APP, not its A{beta} breakdown product. We report here that the full-length APP protein affects the properties of the axon initial segment and through these changes serves as a dynamic regulator of neuronal activity. We propose that this newly discovered APP function offers a different, A{beta}-independent, view of the genetic evidence.

neuroscience↗

bioRxiv2022

Development and validation of Arc nanobodies: new tools for probing Arc dynamics and function

Activity-regulated cytoskeleton-associated (Arc) protein plays key roles in long-term synaptic plasticity, memory, and cognitive flexibility. However, an integral understanding of Arc mechanisms is lacking. Arc is proposed to function as an interaction hub in neuronal dendrites and the nucleus, yet Arc can also form retrovirus-like capsids with proposed roles in intercellular communication. Here, we sought to develop anti-Arc nanobodies (ArcNbs) as new tools for probing Arc dynamics and function. Six ArcNbs representing different clonal lines were selected from immunized alpaca. Immunoblotting with recombinant ArcNbs fused to a small ALFA-epitope tag demonstrated binding to recombinant Arc as well as endogenous Arc from rat cortical tissue. ALFA-ArcNb also provided efficient immunoprecipitation of stimulus-induced Arc after carbachol-treatment of SH-SY5Y neuroblastoma cells and induction of long-term potentiation in the rat dentate gyrus in vivo. Epitope mapping showed that all Nbs recognize the Arc C-terminal region containing the retroviral Gag capsid homology domain, comprised of tandem N-and C-lobes. ArcNbs E5 and H11 selectively bound the N-lobe, which harbors a peptide ligand binding pocket specific to mammals. Four additional ArcNbs bound the region containing the C-lobe and terminal tail. For use as genetically encoded fluorescent intrabodies, we show that ArcNbs fused to mScarlet-I are uniformly expressed, without aggregation, in the cytoplasm and nucleus of HEK293FT cells. Finally, mScarlet-I-ArcNb H11 expressed as intrabody selectively bound the N-lobe and enabled co-immunoprecipitation of full-length intracellular Arc. ArcNbs are versatile tools for live-cell labeling and purification of Arc and analysis of capsid domain specific functions.

neuroscience↗

bioRxiv2022

Unexpected growth of a classic yeast auxotroph

Organisms must either synthesize or assimilate essential organic compounds to survive. The homocysteine synthase Met15 has been considered essential for inorganic sulfur assimilation in yeast since its discovery in the 1970s. As a result, MET15 has served as a genetic marker for hundreds of experiments that play a foundational role in eukaryote genetics and systems biology. Nevertheless, we demonstrate here through structural and evolutionary modeling, in vitro kinetic assays, and genetic complementation, that an alternative homocysteine synthase encoded by the previously uncharacterized gene YLL058W enables cells lacking Met15 to assimilate enough inorganic sulfur for survival and proliferation. These cells however fail to grow in patches or liquid cultures unless provided with exogenous methionine or other organosulfurs. We show that this growth failure, which has historically justified the status of MET15 as a classic auxotrophic marker, is largely explained by toxic accumulation of the gas hydrogen sulfide due to a metabolic bottleneck. When patched or cultured with a hydrogen sulfide chelator, and when propagated as colony grids, cells without Met15 assimilate inorganic sulfur and grow, and cells with Met15 achieve even higher yields. Thus, Met15 is not essential for inorganic sulfur assimilation in yeast. Instead, MET15 is the first example of a yeast gene whose loss conditionally prevents growth in a manner that depends on local gas exchange. Our results have broad implications for investigations of sulfur metabolism, including studies of stress response, methionine restriction, and aging. More generally, our findings illustrate how unappreciated experimental variables can obfuscate biological discovery.

molecular biology↗

bioRxiv2022

Engineering Rotating Apical-Out Airway Organoid for Assessing Respiratory Cilia Motility

Motile cilia project from the airway apical surface and directly interface with inhaled external environment. Due to cilias nanoscale dimension and high beating frequency, quantitative assessment of their motility remains a sophisticated task. Here we described a robust approach for reproducible engineering of apical-out airway organoid (AOAO) of defined size. Propelled by exterior-facing cilia beating, the mature AOAO exhibited stable rotational motion when surrounded by Matrigel. We developed a computational framework leveraging computer vision algorithms to quantify AOAO rotation and validated its correlation with direct measurement of cilia motility. We further established the feasibility of using AOAO rotation to recapitulate and measure defective cilia motility caused by chemotherapy-induced toxicity and by CCDC39 mutations in cells from primary ciliary dyskinesia patient. We expect our rotating AOAO model and the associated computational pipeline to offer a generalizable framework to expediate modeling of and therapeutic development for genetic and environmental ciliopathies.

bioengineering↗