Biology subjects

Zheng, Y.

Publications and source records attributed to Zheng, Y..

At least 397 records · Page 22Linked to original sources

bioRxiv2020

Regional radiomics similarity networks (R2SNs) in the human brain: reproducibility, small-world properties and a biological basis

BackgroundStructural covariance network (SCN) has been applied successfully to structural magnetic resonance imaging (MRI) study. However, most SCNs were constructed by the unitary marker, which was insensitive for the different disease phases. The aim of this study is to devise a novel regional radiomics similarity network (R2SN) that could provide more comprehensive information in morphological network analysis. MethodsRegional radiomics similarity network (R2SN) was constructed by computing the Pearson correlations between the radiomics features extracted from any pair of regions for each subject. We further assessed the small-world property of R2SN using the graph theory method, as well as the reproducibility in the different datasets and the reliability with test-retest analysis. The relationship between the R2SN and inter-regional co-expression of gene enriched was also explored, as well as the relationship with general intelligence. ResultsThe R2SN can be replicated in different datasets, also regardless of using different feature subsets. The R2SN showed high reliability with the test-retest analysis (ICC>0.7). Besides, the small-word property ({sigma}>2) and the high correlation with the gene expression (R=0.24, P<0.001) and the general intelligence was found by R2SN. ConclusionR2SN provides a novel, reliable, and biologically plausible method to understand human morphological covariance based on structural MRI. Impact StatementImaging biomarkers are the cornerstone of modern radiology, and the development of valid biomarkers is crucial for optimizing individualized prediction in neurological disorders like AD. Thus, the development of the data mining method from neuroimaging is crucial for adding the biomarkers of disease. This study confirmed that R2SN provides a novel, robust and biologically plausible model and a new perspective for understanding the human brain, therefore. Thus, the R2SN has great promise in further study.

neuroscience↗

bioRxiv2020

Phytochrome contributes to blue-light-mediated stem elongation and associated shade-avoidance response in mature Arabidopsis plants

Our recent studies on ornamental plants and microgreens indicate that blue-light-mediated stem elongation is related to phytochrome activity, which was based on the calculated phytochrome photoequilibrium. To examine whether phytochromes really contribute to the blue lights effect, plant phenotypic responses were investigated in wild type Arabidopsis (Col-0), and its quintuple phytochrome (phyA phyB phyC phyD phyE) mutant plants under the following light treatments: (1) R, a pure red light from 660-nm LED; (2) B, a pure blue light from 455-nm LED; (3) BR, a impure blue light from LED combination of 94% B and 6% R; and (4) BRF, another impure blue light from LED combination of BR and 6 {micro}mol m-2 s-1 of FR (735 nm). For all the light treatments, a photosynthetic photon flux density of {approx}100 mol m-2 s-1 were provided by 24-h lighting daily inside a walk-in growth chamber, which had an air temperature of {approx} 23 {degrees}C. The calculated phytochrome photoequilibrium was 0.89, 0.50, 0.69, and 0.60 for R, B, BR, and BRF, respectively, indicating a higher phytochrome activity under R and BR than B and BRF. After 18 days of light treatment, B or BRF increased main stem length in wild-type plants compared with R, but BR had an inhibition effect similar to R. Also, B and BRF relative to R or BR induced earlier flowering and reduced leaf size in wild type plants, showing typical shade-avoidance responses. In phytochrome-deficient mutant plants, the above shade-avoidance responses were inhibited under B or BRF, and induced under BR. However, as an exception, hypocotyl length, a growth trait during the de-etiolation stage, was reduced under B, BR and BRF vs. R regardless of phytochrome absence. It suggests that for mature Arabidopsis plants, phytochrome plays an active role in blue-light-mediated stem elongation and associated shade-avoidance response.

plant biology↗

bioRxiv2020

Accelerating Drug Discovery and Repurposingby Combining Transcriptional Signature Connectivity with Docking

The development of targeted treatment options for precision medicine is hampered by a slow and costly process of drug screening. While small molecule docking simulations are often applied in conjunction with cheminformatic methods to reduce the number of candidate molecules to be tested experimentally, the current approaches suffer from high false positive rates and are computationally expensive. Here, we present a novel in silico approach for drug discovery and repurposing, dubbed connectivity enhanced Structure Activity Relationship (ceSAR) that improves on current methods by combining docking and virtual screening approaches with pharmacogenomics and transcriptional signature connectivity analysis. ceSAR builds on the landmark LINCS library of transcriptional signatures of over 20,000 drug-like molecules and ~5,000 gene knock-downs (KDs) to connect small molecules and their potential targets. For a set of candidate molecules and specific target gene, candidate molecules are first ranked by chemical similarity to their concordant LINCS analogs that share signature similarity with a knock-down of the target gene. An efficient method for chemical similarity search, optimized for sparse binary fingerprints of chemical moieties, is used to enable fast searches for large libraries of small molecules. A small subset of candidate compounds identified in the first step is then re-scored by combining signature connectivity with docking simulations. On a set of 20 DUD-E benchmark targets with LINCS KDs, the consensus approach reduces significantly false positive rates, improving the median precision 3-fold over docking methods at the extreme library reduction. We conclude that signature connectivity and docking provide complementary signals, offering an avenue to improve the accuracy of virtual screening while reducing run times by multiple orders of magnitude.

bioinformatics↗

bioRxiv2020

Early Dietary Exposures Epigenetically Program Mammary Cancer Susceptibility through IGF1-mediated Expansion of Mammary Stem Cells

Dietary exposures at early developmental stages have been shown to program lifetime breast cancer susceptibility. We previously reported that manipulation of gestational and postweaning diets leads to different mammary tumor outcomes in carcinogen-treated mice. The high tumor incidence (HT) groups (average 61.5% tumor incidence) received a low-fat, low-sugar, mildly restricted (12%v/v) (DR) diet during gestation, followed by a high-fat, high-sugar (HF) diet postweaning. Conversely, the low tumor incidence (LT) groups (average 20% tumor incidence) received the HF diet during gestation, followed by the DR diet postweaning. Herein, we extended these findings by demonstrating that HT animals had an expanded mammary stem cell (MaSC) population compared to LT animals before puberty, and this expansion persisted into adulthood. IGF1 expression was increased in mammary stromal cells from HT animals, which promoted the self-renewal capacity of MaSCs in a paracrine fashion. This increased IGF1 expression was programmed prepubertally through DNA hypomethylation of the IGF1 promoter 1, mediated by decreased DNMT3b levels. IGFBP5 mRNA and protein levels were also reduced in mammary tissues from HT animals, indicating an increased bioavailability of tissue IGF1. In association with these changes, mammary tissues from carcinogen-treated HT animals developed an increased proportion of mammary adenosquamous carcinomas compared to carcinogen-treated LT animals. This study provides novel mechanistic insights into how early dietary exposures program mammary cancer risk and tumor phenotypes by increasing IGF1 expression through epigenetic alterations, thereby expanding the MaSC population, resulting in a higher number of carcinogen targets susceptible to transformation in adulthood. SignificanceEarly high-fat dietary exposure programs lifetime mammary cancer susceptibility before puberty through epigenetic alterations of IGF1 promoters and IGF1-mediated paracrine regulation of mammary stem cell homeostasis.

cancer biology↗

bioRxiv2020

NyuWa Genome Resource: Deep Whole Genome Sequencing Based Chinese Population Variation Profile and Reference Panel

The lack of Chinese population specific haplotype reference panel and whole genome sequencing resources has greatly hindered the genetics studies in the worlds largest population. Here we presented the NyuWa genome resource based on deep (26.2X) sequencing of 2,999 Chinese individuals, and constructed NyuWa reference panel of 5,804 haplotypes and 19.3M variants, which is the first publicly available Chinese population specific reference panel with thousands of samples. Compared with other panels, NyuWa reference panel reduces the Han Chinese imputation error rate by the range of 30% to 51%. Population structure and imputation simulation tests supported the applicability of one integrated reference panel for both northern and southern Chinese. In addition, a total of 22,504 loss-of-function variants in coding and noncoding genes were identified, including 11,493 novel variants. These results highlight the value of NyuWa genome resource to facilitate genetics research in Chinese and Asian populations.

genomics↗

bioRxiv2020

Role and Dynamics of Vacuolar pH during Cell-in-Cell mediated Death

The non-autonomous cell death by entosis was mediated by the so-called cell-in-cell structures, which were believed to kill the internalized cells by a mechanism dependent on acidified lysosomes. However, the precise values and roles of pH critical for the death of the internalized cells remained undetermined yet. We creatively employed keima, a fluorescent protein that displays different excitation spectra in responding to pH changes, to monitor the pH dynamics of the entotic vacuoles during cell-in-cell mediated death. We found that different cells varied in their basal intracellular pH, and the pH was relatively stable for entotic vacuoles containing live cells, but sharply dropped to a narrow range along with the inner cell death. In contrast, the lipidation of entotic vacuoles by LC3 displayed previously underappreciated complex patterns associated with entotic and apoptotic death, respectively. The pH decline seemed to play distinct roles in the two types of inner cell deaths, where apoptosis is preceded with moderate pH decline while a profound pH decline is likely to be determinate for entotic death. Whereas the cancer cells seemed to be lesser tolerant to acidified environments than non-cancerous cells, manipulating vacuolar pH could effectively control inner cell fates and switch the ways whereby inner cell die. Together, this study demonstrated for the first time the pH dynamics of entotic vacuoles that dictate the fates of internalized cells, providing a rationale for tuning cellular pH as a potential way to treat cell-in-cell associated diseases such as cancer.

cell biology↗

bioRxiv2020

Flower Power: Floral reversion as a viable alternative to nodal micropropagation in Cannabis sativa.

The legalization of Cannabis sativa L. for recreational and medical purposes has been gaining global momentum, leading to a rise in interest in Cannabis tissue culture as growers look for large-scale solutions to germplasm storage and clean plant propagation. Mother plants used in commercial propagation are susceptible to insect pests and disease and require considerable space. While micropropagation can produce disease free starting material in less space, current published in vitro micropropagation methods are not robust and few report high multiplication rates. Further, these micropropagation methods rely on photoperiod-sensitive plants which can be maintained in a perpetual vegetative state. Current methods are not adaptable to long-term tissue culture of day-neutral cultivars, which cannot be maintained in perpetual vegetative growth. In this study, we chose to develop a micropropagation system which uses C. sativa inflorescences as starting materials. This study used two cannabis cultivars, two plant growth regulators (PGR; 6-benzylaminopurine and meta-topolin) at different concentrations, and two different numbers of florets. Here we show that floral reversion occurs from meristematic tissue in C. sativa florets and that it can be used to enhance multiplication rates compared to existing in vitro methods. Floret number was shown to have a significant impact on percent reversion, with pairs of florets reverting more frequently and producing healthier explants than single florets, while cultivar and PGR had no significant effect on percent reversion. Compared with our previously published nodal culture studies, the current floral reversion method produced up to eight times more explants per tissue culture cycle. Floral reversion provides a foundation for effective inflorescence-based micropropagation systems in C. sativa.

plant biology↗

bioRxiv2020

Whole-genome analysis of Nigerian patients with breast cancer reveals ethnic-driven somatic evolution and distinct genomic subtypes

Black women of African ancestry experience more aggressive breast cancer with higher mortality rates than White women of European ancestry. Although inter-ethnic germline variation is known, differential somatic evolution has not been investigated in detail. Analysis of deep whole genomes of 97 breast tumors, with RNA-seq in a subset, from indigenous African patients in Nigeria in comparison to The Cancer Genome Atlas (n=76) revealed a higher rate of genomic instability and increased intra-tumoral heterogeneity as well as a unique genomic subtype defined by early clonal GATA3 mutations and a 10.5-year younger age at diagnosis. We also found evidence for non-coding mutations in two novel drivers (ZNF217 and SYPL1) and a novel INDEL signature strongly associated with African ancestry proportion. This comprehensive analysis of an understudied population underscores the need to incorporate diversity of genomes as a key parameter in fundamental research with potential to tailor clinical intervention and promote equity in precision oncology care.

genomics↗

bioRxiv2020

Large-scale Gradient Dysfunction of the Functional Connectome in Major Depression

BackgroundPatients with major depressive disorder (MDD) exhibit concurrent deficits in sensory processing and high-order cognitive functions such as self-awareness and rumination. Connectome mapping studies have suggested a principal primary-to-transmodal gradient in functional brain networks, supporting the spectrum from sensation to cognition. However, whether this principal connectome gradient is disrupted in patients with MDD and how this disruption is associated with gene expression profiles remain unclear. MethodsUsing a large cohort of resting-state functional magnetic resonance imaging data from 2,234 participants (1,150 patients with MDD and 1,084 healthy controls) recruited at 10 sites, we investigated MDD-related alterations in the principal connectome gradient. We further used Neurosynth and postmortem gene expression data to assess the cognitive functions and transcriptional profiles related to the gradient alterations in MDD, respectively. ResultsRelative to controls, patients with MDD exhibited abnormal global topography of the principal primary-to-transmodal gradient, as indicated by reduced explanation ratio, gradient range, and gradient variation (Cohens d = -0.16[~]-0.21). Focal alterations of gradient scores were mostly in the primary systems involved in sensory processing and in the transmodal systems implicated in high-order cognition. The transcriptional profiles explained 53.9% of the spatial variance in the altered gradient patterns, with the most correlated genes enriched in transsynaptic signaling and calcium ion binding. ConclusionsThese results highlight the dysfunction of the core connectome hierarchy in MDD and its linkage with gene expression profiles, providing insights into the neurobiological and molecular genetic underpinnings of sensory-cognitive deficits in this disorder.

neuroscience↗

bioRxiv2020

Deciphering the mechanism underlying circRNA-mediated immune responses of western honeybees to Nosema ceranae infection

Nosema ceranae is a widespread fungal parasite for adult honeybees, severely damaging bee health and sustainable development of apiculture. Circular RNAs (circRNAs) are a class of newly discovered noncoding RNAs (ncRNAs) that regulate a number of biological processes such as immune defense and development. In this current work, based on previously obtained whole transcriptome data, 8 199 and 8 711 circRNAs were predicted from the midguts of Apis mellifera ligustica workers at 7 days (AmT1) and 10 days (AmT2) post inoculation (dpi) with N. ceranae using bioinformatics. Additionally, in combination with transcriptome data from uninfected midguts (AmCK1 and AmCK2) (Xiong et al., 2018), 4 464 circRNAs were found to be shared by the aforementioned four groups, whereas the numbers of specifically transcribed circRNAs in each group were 1 389, 1 696, 1 019 and 1 871, respectively. Furthermore, 10 226 circRNAs were homologous to Apis cerana cerana circRNAs, while 20 circRNAs had homology with Homo sapiens circRNAs; in addition, 16 circRNAs were highly conserved in these three species. Differential expression analysis showed that 168 (306) differentially expressed circRNAs (DEcircRNAs) were identified in AmCK1 vs AmT1 (AmCK2 vs AmT2) comparison group, including 61 (143) upregulated circRNAs and 107 (163) downregulated circRNAs. Moreover, RT-qPCR results showed that the expression trend of eight DEcircRNAs was consistent with that of the transcriptome dataset. Based on GO database annotation, we observed that source genes of DEcircRNAs in AmCK1 vs AmT1 (AmCK2 vs AmT2) were engaged in 27 (35) functional terms, including two (two) cell renewal-associated terms, seven (seven) cell structure-associated terms, and one (one) immunity-associated terms. Additionally, DEcircRNA source genes in AmCK1 vs AmT1 were involved in two cell renewal-related pathways, Hippo and Wnt signaling pathways, and three carbohydrate metabolism-related pathways, galactose metabolism, starch and sucrose metabolism, fructose and mannose metabolism, only one energy metabolism-related pathway (oxidative phosphorylation pathway), three cellular immune-related pathways, endocytosis, phagosome, and lysosome, and a humoral immune-related pathway (FoxO signaling pathway). In AmCK2 vs AmT2 comparison group, more source genes of DEcircRNAs were associated with the abovementioned pathways relative to cell renewal, carbohydrate metabolism, and cellular and humoral immune pathways. In addition, 122 (234) DEcircRNAs in the host midgut at 7 dpi (10 dpi) with N. ceranae targeted 82 (106) miRNAs. Furthermore, 75 (103) miRNAs targeted by 86 (178) DEcircRNAs in AmCK1 vs AmT1 (AmCK2 vs AmT2) further bound to 215 (305) mRNAs. These targets could be annotated as an array of functional terms and pathways related to cellular renewal, cellular structure, carbohydrate and energy metabolism, and cellular and humoral immunity. In a word, we for the first time explored immune responses mediated by DEcircRNAs in the midguts of A. m. ligustica workers to N. ceranae infection. Our data provide a foundation for clarifying the molecular mechanism underlying immune response of western honeybee to N. ceranae invasion, but also a new insight into further understanding the host-pathogen interaction during bee microsporidiosis.

genomics↗

bioRxiv2020

Apical-root apoplastic acidification affects cell-wall extensibility in wheat under salinity stress

Plant salt tolerance is closely associated with a high rate of root growth. Although root growth is governed by cell-wall and apoplastic pH, the relationship between these factors in the root elongation zone under salinity stress remains unclear. Here, we assess apoplastic pH, pH- and expansin-dependent cell-wall extensibility, and expansin expression in the root elongation zone of salt-sensitive (Yongliang-15) and -tolerant (JS-7) cultivars under salinity stress. A six-day 80 mM NaCl treatment significantly reduced apical-root apoplastic pH, from 6.2 to 5.3, in both cultivars. Using a pH-dependent cell-wall extensibility experiment, we found that, under 0 mM NaCl treatment, the optimal pH for cell-wall loosening was 6.0 in the salinity-tolerant cultivar and 4.6 in the salinity-sensitive cultivar. Under 80 mM treatment, a pH of 5.0 mitigated the cell-wall stiffness caused by salinity stress in the salinity-tolerant cultivar, but promoted cell-wall stiffening in the salinity-sensitive cultivar. These changes in pH-dependent cell-wall extensibility are consistent with differences in the root growth of two cultivars under salinity stress. Exogenous expansin application, and expansin expression experiments, we found that salinity stress altered expansin expression, differentially affecting cell-wall extensibility under pH 5.0 and 6.0. TaEXPA7 and TaEXPA8 induced cell-wall loosening at pH 5.0, whereas TaEXPA5 induced cell-wall loosening at pH 6.0. These results elucidate the relationship between expansin and cell-wall extensibility in the root elongation zone, with important implications for enhancing plant growth under salinity stress.

plant biology↗

bioRxiv2020

The wheat 55K SNP-based exploration of loci for spikelet number per spike from a tetraploid wheat (Triticum turgidum L.) recombinant inbred line population derived from a Chinese landrace Ailanmai and a wild emmer accession

The spikelet number per spike (SNS) is a primary factor determining wheat yield. Common wheat breeding reduces the genetic diversity among elite germplasm resources, leading to a detrimental effect on future wheat production. It is, therefore, necessary to explore new genetic resources for SNS to increase wheat yield. A tetraploid landrace Ailanmai x wild emmer wheat recombinant inbred line (RIL) population was used to construct a genetic map using the wheat 55K single nucleotide polymorphism (SNP) array. The linkage map containing 1150 bin markers with a total genetic distance of 2411.8 cM was obtained. Based on phenotypic data from eight environments and best linear unbiased prediction (BLUP) values, five quantitative trait loci (QTL) for SNS were identified, explaining 6.71-29.40% of the phenotypic variation. Two of them, QSns.sau-AM-2B.3 and QSns.sau-AM-3B.2, were detected as the major and novel QTL. Their effects were further validated in two additional F2 populations using tightly linked Kompetitive Allele-Specific PCR (KASP) markers. Potential candidate genes within the physical intervals of corresponding QTL were predicted to participate in inflorescence development and spikelet formation. Genetic associations between SNS and other agronomic traits were also detected and analyzed. This study demonstrates the feasibility of wheat 55K SNP array developed for common wheat in genetic mapping of tetraploid population and shows the potential application of wheat related species in wheat improvement programs.

genetics↗

bioRxiv2020

Auxin guides germ cell specification in Arabidopsis anthers

Germ cells (GCs) transmit genetic information from one generation to the next. Unlike animal GCs, plant GCs are induced post-embryonically, forming locally from somatic cells. This induction is coordinated with organogenesis and might be guided by positional cues. In angiosperms, male GCs initiate from the internal layers at the four corners of the anther primordia and are gradually enclosed by parietal cell (PC) layers, leading to a concentric GC-PC pattern.1,2 However, the underlying mechanism of GC initiation and GC-PC pattern formation is unclear. Auxin affects pattern formation3 and anther development.4-11 However, whether GC formation involves auxin remains unknown. We report that the auxin distribution in pre-meiotic anthers parallels GC initiation, forming a centripetal gradient between the outer primordial cells and the inner GCs. The auxin biosynthesis genes TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS 1 (TAA1) and TRYPTOPHAN AMINOTRANSFERASE RELATED 2 (TAR2)5,12 are responsible for this patterning and essential for GC specification. SPOROCYTELESS/NOZZLE (SPL/NZZ, a determinant for GC specification)13-15 mediates the effect of auxin on GC specification, modulates auxin homeostasis, and maintains centripetal auxin patterning. Our results reveal that auxin is a key factor guiding GC specification in Arabidopsis anthers.

plant biology↗

bioRxiv2020

Co-infection of influenza A virus enhances SARS-CoV-2 infectivity

The upcoming flu season in the northern hemisphere merging with the current COVID-19 pandemic raises a potentially severe threat to public health. Through experimental co-infection of IAV with either pseudotyped or SARS-CoV-2 live virus, we found that IAV pre-infection significantly promoted the infectivity of SARS-CoV-2 in a broad range of cell types. Remarkably, increased SARS-CoV-2 viral load and more severe lung damage were observed in mice co-infected with IAV in vivo. Moreover, such enhancement of SARS-CoV-2 infectivity was not seen with several other viruses probably due to a unique IAV segment as an inducer to elevate ACE2 expression. This study illustrates that IAV has a special nature to aggravate SARS-CoV-2 infection, and prevention of IAV is of great significance during the COVID-19 pandemic.

microbiology↗

bioRxiv2020

Cevipabulin-tubulin complex reveals a novel agent binding site on α-tubulin and provides insights into microtubule dynamic instability

Microtubule, composed of {beta}-tubulin heterodimers, remains as one of the most popular anticancer targets for decades. To date, anti-microtubule drugs are mainly functionally divided into microtubule-destabilizing and microtubule-stabilizing agents while microtubule- or tubulin-degradation agents are rarely reported. Six known binding sites on tubulin dimer are identified with five sites on {beta}-tubulin and only one site on -tubulin (pironetin site), hinting compounds binding to -tubulin are less well characterized. Cevipabulin, a microtubule-active antitumor clinical candidate, is widely accepted as a microtubule-stabilizing agent by binding to the vinblastine site. Our X-ray crystallography study reveals that, in addition binding to the vinblastine site, cevipabulin also binds to a novel site on -tubulin (named the seventh site) which located near the nonexchangeable GTP. Interestingly, we find the binding of cevipabulin to the seventh site induces tubulin degradation. As the non-exchangeable GTP has structural role and is important for the stability of tubulin dimers, we propose and confirm the tubulin degradation mechanism as: Cevipabulin at the seventh site puts the T5 loop outward to make the non-exchangeable GTP exchangeable, which reduces the stability of tubulin and results in its destabilization and degradation. Our results confirm a novel agent binding site on -tubulin and shed light on the development of tubulin degraders as a new generation of anti-microtubule drugs targeting this novel site.

cell biology↗

bioRxiv2020

Single-cell analysis of chromatin silencing programs in developmental and tumor progression

Single-cell analysis has become a powerful approach for the molecular characterization of complex tissues. Methods for quantifying gene expression1 and chromatin accessibility2 of single cells are now well-established, but analysis of chromatin regions with specific histone modifications has been technically challenging. Here, we adapt the recently published CUT&Tag method3 to scalable single-cell platforms to profile chromatin landscapes in single cells (scCUT&Tag) from complex tissues. We focus on profiling Polycomb Group (PcG) silenced regions marked by H3K27 trimethylation (H3K27me3) in single cells as an orthogonal approach to chromatin accessibility for identifying cell states. We show that scCUT&Tag profiling of H3K27me3 distinguishes cell types in human blood and allows the generation of cell-type-specific PcG landscapes from heterogeneous tissues. Furthermore, we use scCUT&Tag to profile H3K27me3 in a brain tumor patient before and after treatment, identifying cell types in the tumor microenvironment and heterogeneity in PcG activity in the primary sample and after treatment.

genomics↗

bioRxiv2020

Modeling SARS-CoV-2 infection in vitro with a human intestine-on-chip device

Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2) has given rise to a global pandemic. The gastrointestinal symptoms of some COVID-19 patients are underestimated. There is an urgent need to develop physiologically relevant model that can accurately reflect human response to viral infection. Here, we report the creation of a biomimetic human intestine infection model on a chip system that allows to recapitulate the intestinal injury and immune response induced by SARS-CoV-2, for the first time. The microengineered intestine-on-chip device contains human intestinal epithelium (co-cultured human intestinal epithelial Caco-2 cells and mucin secreting HT-29 cells) lined in upper channel and vascular endothelium (human umbilical vein endothelial cells, HUVECs) in a parallel lower channel under fluidic flow condition, sandwiched by a porous PDMS membrane coated with extracellular matrix (ECM). At day 3 post-infection of SARS-CoV-2, the intestine epithelium showed high susceptibility to viral infection and obvious morphological changes with destruction of intestinal villus, dispersed distribution of mucus secreting cells and reduced expression of tight junction (E-cadherin), indicating the destruction of mucous layer and the integrity of intestinal barrier caused by virus. Moreover, the endothelium exhibited abnormal cell morphology with disrupted expression of adherent junction protein (VE-cadherin). Transcriptional analysis revealed the abnormal RNA and protein metabolism, as well as activated immune responses in both epithelial and endothelial cells after viral infection (e.g., up-regulated cytokine genes, TNF signaling and NF-kappa B signaling-related genes). This bioengineered in vitro model system can mirror the human relevant pathophysiology and response to viral infection at the organ level, which is not possible in existing in vitro culture systems. It may provide a promising tool to accelerate our understanding of COVID-19 and devising novel therapies.

bioengineering↗

bioRxiv2020

COSI for label-free multiparameter quantitative imaging of intra-thrombus stability in vitro.

Although existing microfluidics in vitro assays recapitulate blood vessel microenvironment using surface-immobilized agonists under biofluidic flows, these assays do not quantify intra-thrombus mass and activities of adhesive platelets at agonist margin and uses fluorescence labeling, therefore limiting clinical translation potential. Here, we describe a real time label-free in vitro quantitative imaging flow assay called Coherent Optical Scattering and phase Interferometry (COSI) that evaluates both intra-thrombus and adhesive-only platelet dynamics using only changes in refractive index. By combining coherent optical scattering and optical interferometry, we evaluated and quantified both intra-thrombus mass with picogram accuracy and adhesive platelet-only events/dynamics with high spatial-temporal resolution (400 nm/s) under fluid shear stress using only changes in refractive index. Using oblique illumination, COSI provide a [~] 4 {micro}m thin axial slice that quantifies the magnitude of physical of surface adhesive platelets (spreading, adhesion and consolidation) in a developing thrombus without labelling under fluid shear stress. We achieve real time visualization of recruitment of single platelet into thrombus and further correlate it to the developing mass of a thrombus. The adhesive platelet activity exhibit stabilized surface activity of around 2 {micro}m/s and intra-thrombus mass exchange were balanced at around 1 picogram after treatment of a broad range metalloproteinase inhibitor (250 {micro}M GM6001). SignificanceThe combination of phase imaging with transmitted light and backscattering imaging via oblique illumination in COSI unpicked intra-thrombus mass and adhesive platelet-only activity events at picogram and sub-micrometer precision with millisecond time resolution under fluid shear stress. COSI maps the longitudinal time dynamics of adhesive platelets along changing thrombus mass under metalloproteinase inhibition, and demonstrates potential for real-time correlative microfluidic label-free imaging for flow-dependent biological adhesive events.

bioengineering↗