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Zhao, Y.

Publications and source records attributed to Zhao, Y..

At least 721 records · Page 40Linked to original sources
bioRxiv2022

NFATc1 negatively determines chondrocyte differentiation in articular cartilage progenitors

The origin and differentiation mechanism of articular chondrocytes remain poorly understood. Broadly, the difference in developmental mechanisms of articular and growth-plate cartilage is still less elucidated. Here, we identified that the nuclear factor of activated T-cells cytoplasmic 1 (NFATc1) is a crucial regulator of articular, but not growth-plate, chondrocyte differentiation during development. At the early stage of mouse knee development (embryonic day 13.5), NFATc1-expressing cells were mainly located in the flanking region of the joint interzone. With development, NFATc1-expressing cells generated almost all articular chondrocytes, but not chondrocytes in limb growth-plate primordium. NFATc1-expressing cells displayed prominent capacities for colony formation and multipotent differentiation. Transcriptome analyses revealed a set of characteristic genes in NFATc1-enriched articular cartilage progenitors. Strikingly, the expression of NFATc1 was diminished with articular chondrocyte differentiation, and suppressing NFATc1 expression in articular cartilage progenitors was sufficient to induce spontaneous chondrogenesis while overexpressing NFATc1 suppresses chondrogenesis. Mechanistically, NFATc1 negatively regulated the transcriptional activity of the Col2a1 gene. Thus, our results reveal that NFATc1 characterizes articular, but not growth-plate, cartilage progenitors and negatively determines articular chondrocyte differentiation at least partly through regulating COL2A1 gene transcription.

developmental biology↗
bioRxiv2022

Gene expression as phenotype - Many small-step changes leading to little long-term phenotypic evolution

Unlike in genotypic evolution, there are few general rules governing phenotypic evolution with one of them being the small-step evolution. More specifically, natural selection tends to favor mutations of smaller phenotypic effects than of larger ones. This postulate can be viewed as a logical extension of Fishers Geometric Model (FGM). Testing this FGM postulate, however, is challenging as the test would require a large number of phenotypes, each with a clear genetic basis. For such a test, we treat the expression level of each gene as a phenotype. Furthermore, a mechanism of small-step expression evolution exists, namely via the control by microRNAs (miRNAs). Each miRNA in metazoans is known to weakly repress the expression of tens or hundreds of target genes. In our analysis of mammalian and Drosophila expression data, small step evolution via miRNA regulation happens frequently in long-term evolution. However, such small-step evolution does not lead to long-term phenotypic changes which would take too many such steps to accomplish. Furthermore, target site changes often cancel themselves out by continual gains and losses. The results suggest that the FGM postulate may be most appropriate for phenotypic fine-tuning near the expression optimum. In contrast, longterm expression evolution may occasionally take large steps (e.g., mutations in transcription factors) when big environmental shift happens. In another study (Lu et al. 2021), we further show how the small-step evolution of expression phenotypes is a manifestation of miRNAs role in developmental canalization. In conclusion, the rules of phenotypic evolution may depend crucially on the genetics of the phenotype, rather than its metric properties.

evolutionary biology↗
bioRxiv2022

Tissue specific LRRK2 interactomes reveal a distinct functional unit within the striatum

Mutations in LRRK2 are the most common genetic cause of Parkinsons disease. Despite substantial research efforts, the physiological and pathological role of this multidomain protein remains poorly defined. In this study, we used a systematic approach to construct the general protein-protein interactome around LRRK2, which was then differentiated into 15 tissue-specific interactomes taking into consideration the differential expression patterns and the co-expression behaviours of the LRRK2 interactors in different healthy tissues. The LRRK2 interactors exhibited distinct expression features in the brain as compared to the peripheral tissues analysed. Moreover, a high degree of similarity was found for the LRRK2 interactors in putamen, caudate and nucleus accumbens, thus defining a potential LRRK2 functional cluster within the striatum. We also explored the functions highlighted by the "core LRRK2 interactors" within each tissue and illustrated how the LRRK2 interactomes can be used as a tool to trace the relationship between LRRK2 and specific interactors of interest, here exemplified with a study focused on the LRRK2 interactors belonging to the Rab protein family.

neuroscience↗
bioRxiv2022

MrgprA3-expressing pruriceptors drive pruritogen-induced alloknesis through mechanosensitive Piezo2 channel

Although touch and itch are coded by distinct neuronal populations, light touch also provokes itch in the presence of exogenous pruritogens, resulting in a phenomenon called alloknesis. However, the cellular and molecular mechanisms underlying the initiation of pruritogen-induced mechanical itch sensitization are poorly understood. Here we show that intradermal injections of histamine or chloroquine (CQ) provoke alloknesis through activation of TRPV1- and MrgprA3- expressing prurioceptors, and functional ablation of these neurons reverses pruritogen-induced alloknesis. Moreover, genetic ablation of mechanosensitive Piezo2 channel function from MrgprA3-expressing prurioceptors also dampens pruritogen-induced alloknesis. Mechanistically, histamine and CQ sensitize Piezo2 channel function through activation of the PLC-PKC{delta} signaling. Collectively, our data uncovered a TRPV1+/MrgprA3+ prurioceptor-Piezo2 signaling axis in the initiation of pruritogen-induced mechanical itch sensitization in the skin.

neuroscience↗
bioRxiv2022

Episomal editing of synthetic constructs in yeast using CRISPR

Use of synthetic genomics to design and build "big" DNA has revolutionized our ability to answer fundamental biological questions by employing a bottom-up approach. S. cerevisiae, or budding yeast, has become the major platform to assemble large synthetic constructs thanks to its powerful homologous recombination machinery and the availability of well-established molecular biology techniques. However, efficiently and precisely introducing designer variations to episomal assemblies remains challenging. Here, we describe CRISPR Engineering of EPisomes in Yeast, or CREEPY, for rapid engineering of mammalian DNA constructs larger than 100 kb. We demonstrate that editing of circular episomes presents unique challenges compared to modifying native yeast chromosomes with CRISPR. After optimizing CREEPY for episomal editing, we achieve efficient simplex and multiplex editing as demonstrated by engineering a mouse Sox2-harboring episome.

synthetic biology↗
bioRxiv2022

Predicting neoadjuvant chemotherapy benefit using deep learning from stromal histology in breast cancer

Neoadjuvant chemotherapy (NAC) is a standard treatment option for locally advanced breast cancer. However, not all patients benefit from NAC; some even get worse outcomes after therapy. Hence, predictors for treatment benefit are crucial for guiding clinical decision-making. Here, we investigated the predictive potentials of breast cancer stromal histology via a deep learning (DL)-based approach and proposed the tumor-associated stroma score (TS-score) for predicting pathological complete response (pCR) to NAC with a multi-center dataset. The TS-score is demonstrated to to be an independent predictor of pCR as it not only outperformed the baseline variables and stromal tumor-infiltrating lymphocytes (sTILs) but also significantly improved the prediction performance of the baseline variable-based model. Further, we discovered that unlike lymphocyte, collagen and fibroblasts in stroma were likely associated with poor response to NAC. The TS-score has potentials to be a candidate for better stratification of breast cancer patients in NAC settings.

pathology↗
bioRxiv2022

Clean-PIE: a novel strategy for efficiently constructing precise circRNA with thoroughly minimized immunogenicity to direct potent and durable protein expression

Translatable circular RNAs (circRNAs) are emerging as a crucial molecular format for transient protein expression, with high potential to be an alternative for linear mRNA to reshape the landscape of mRNA pharmaceutical industry. Canonical Anabaena permuted intron-exon (Ana PIE) format that developed by ORNA is an efficient method for RNA circularization, and the engineered circRNAs direct supreme protein expression in eukaryotic cells. However, recent studies revealed that this method may unavoidably result in a remain of immunogenicity in the circRNA products, albeit after thorough RNA purification. In the current study, we develop a novel strategy for efficient generation of circRNA, via the permuted T4Td introns mediated autocatalytically ribozymatic reaction mediated ligation of the flanking segment sequences that concealing in ORF or translation initiation sequence (normally equal to IRES). This strategy universally realizes around 90% circularization effectivity, and the circRNA products can be purified to around 90% purity by our new purification method, and presented thoroughly minimized immunogenicity, thus is termed "Clean-PIE". The purified circRNAs are found to direct potent and durable expression of various proteins in vitro and in vivo. The partly purified Fluc circRNA by HPLC-SEC was found to direct Fluc expression in muscle for no less than 20 days. The highly purified circRNA exhibits much stronger protein expression in vitro and in vivo, and presumed a longer duration. Additionally, the scale-up of RNA circularization with the RNA precursors from 1 L transcription revealed high circularization effectivity (around 90%) and a high productivity of the final circRNA products. Collectively, Clean-PIE is a novel circRNA platform that possesses high circularization effectivity, enabled high RNA purity and thoroughly minimized immunogenicity, as well as scaling-up accessibility and directing extreme durability of protein expression, thus has the potential to develop advanced RNA vaccines and therapeutics in pharmaceutical industrial scale.

molecular biology↗
bioRxiv2022

Targeting Chromatin Effector Pygo2 to Enhance Immunotherapy in Prostate Cancer

The noninflamed microenvironment in prostate cancer represents a barrier to immunotherapy. Genetic alterations underlying cancer cell-intrinsic oncogenic signaling have emerging roles in shaping the immune landscape. Recently, we identified Pygopus 2 (PYGO2) as the driver oncogene for the amplicon at 1q21.3. Here, using transgenic mouse models of metastatic prostate adenocarcinoma, we found that Pygo2 deletion decelerated tumor progression, diminished metastases, and extended survival. Pygo2 loss augmented the infiltration of cytotoxic T lymphocytes (CTLs) and sensitized tumor cells to T cell killing. Mechanistically, Pygo2 orchestrated a p53/Sp1/Kit/Ido1 signaling network to foster a microenvironment hostile to CTLs. Genetic or pharmacological inhibition of Pygo2 enhanced the anti-tumor efficacy of immunotherapies using immune checkpoint blockade, adoptive cell transfer, or myeloid-derived suppressor cell inhibitors. In human prostate cancer samples, Pygo2 expression was inversely correlated with CD8+ T cells. Our results highlight a promising path to improving immunotherapy with targeted therapy for lethal prostate cancer.

cancer biology↗
bioRxiv2022

GM-CSF drives immune-mediated glomerular disease by licensing monocyte-derived cells to produce MMP12

Glomerulonephritis is a group of immune-mediated diseases that cause inflammation within the glomerulus and adjacent compartments of the kidney and is a major cause of end-stage renal disease. T cells are among the main drivers of glomerulonephritis. However, the T cell subsets, cytokine networks, and downstream effector mechanisms that lead to renal tissue injury are largely unknown, which has hindered the development of targeted therapies. Here we identify a population of GM-CSF-producing T cells that accumulates in the kidneys of patients with ANCA-associated glomerulonephritis, infiltrates the renal tissue in a mouse model of glomerulonephritis, and promotes tissue destruction and loss of renal function. Mechanistically, we show that GM-CSF producing T cells licence monocyte-derived cells to produce matrix metalloproteinase 12 (MMP12), which cleaves components of the glomerular basement membrane and exacerbates renal pathology. These findings provide a mechanistic rationale for the immunopathology of T cell-mediated diseases and identify the "GM-CSF - monocyte-derived cells - MMP12" pathway as a promising therapeutic target in treatment of glomerulonephritis.

immunology↗
bioRxiv2022

A Genome-scale Screen Reveals ANTXR1, Heparan Sulfate and Neu5Gc as Host Factors mediating Seneca Valley virus Entry into Porcine Cells

Seneca Valley virus (SVV) disease is a newly emerging infectious disease of pigs caused by SVV, which seriously endangers the pig industry. This study was set out to identify the essential host factors required for SVV entering porcine cells. Using a CRISPR/Cas9 library containing 93,859 sgRNAs that were designed to target approximately 22,707 porcine genes, we generated mutated porcine cell libraries, which were subjected to SVV challenge for enrichment of cells resistant to SVV infection. These resistant cells were subsequently analyzed to identify genes essential for SVV infection. We demonstrated that ANTXR1, a type I transmembrane protein encoded by ANTXR1, heparan sulfate (HS), glycosaminoglycans modified by acetylation and sulfation of HS2ST1, and Neu5Gc, a non-human sialic acid catalyzed by CMAH, were the essential host factors for SVV entry into porcine cells. These results will be helpful to elucidate the pathogenesis of SVV and the development of prevention and control measures.

pathology↗
bioRxiv2022

Endothelial TET2 Regulates Cardiac Remodeling by Modifying Endothelial-to-Mesenchymal Transition

DNA methylation modification has been proved to play an important role in heart diseases. In this study, the role of Ten-Eleven Translocation-2 (TET2), which is a key demethylation enzyme, is investigated in cardiac remodeling. TET2 is abundant in endothelial cells but decreased in hypertrophic hearts. TET2 knockdown in endothelial cells triggers endothelial-to-mesenchymal transition (EndMT), while overexpression of TET2 inhibits the EndMT. In vivo, Cdh5-CreERT2/TET2flox/flox; Rosa26-mTmG+/- mice are developed and undergo transverse aortic constriction (TAC) subsequently to induce pathological cardiac hypertrophy model. Hearts of Cdh5-CreERT2/TET2flox/flox mice show more severe hypertrophy and fibrosis than controls in the TAC model. Furthermore, EGLN3 is identified to participate in EndMT as the downstream target of TET2 by using RNA sequencing and whole-genome bisulfite sequencing (WGBS). Finally, vitamin C, which can mimic TET2 restoration, is found to partially improve cardiac function and inhibit myocardial fibrosis. These insights into how TET2 alleviates cardiac fibrosis may open new avenues for treating cardiac remodeling in the future.

genetics↗
bioRxiv2022

SARS-CoV-2 S protein antagonizes type I interferon downstream signal pathway through interacting and attenuating phosphorylation of STAT1/STAT2

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may keep patients in a clinically asymptomatic state by blocking cellular innate antiviral immunity, but the molecular mechanism remains unclear. Here, we screened the viral proteins of SARS-CoV-2 and found that the spike (S) protein inhibits the activation of interferon-stimulated genes (ISGs) and even reduces the expression of these genes to below background values. Mechanistically, the S protein interacted with STAT1, STAT2, and IRF9 and impedes the phosphorylation of STAT1/STAT2, thus preventing the formation of the interferon-stimulating gene factor 3 (ISGF3) complex and inhibiting the downstream production of Interferon-stimulated genes (ISGs). Remarkably, we also have found that the inhibitory mechanism of the S protein was conservative among SARS-CoV-2 variants and other human coronaviruses, including SARS-CoV, MERS-CoV, HCoV-229E, HCoV-NL63, and HCoV-HKU1. Truncation studies indicated that the most conserved S2 domain played a major inhibitory role. Altogether, our findings unveil a new mechanism by which SARS-CoV-2 S protein attenuated the hosts antiviral immune response and provide new insights into the pathogenic mechanism of coronavirus.

microbiology↗
bioRxiv2022

Root twisting drives halotropism via stress-induced microtubule reorientation

Plants have evolved signaling mechanisms that guide growth away from adverse environments that can cause yield losses. Root halotropism is a sodium-specific negative tropism that is crucial for surviving and thriving under high salinity. Although root halotropism was discovered some years ago, the underlying molecular and cellular mechanisms remain unknown. Here, we show that abscisic acid (ABA)-mediated root twisting determines halotropism in Arabidopsis. An ABA-activated SnRK2 protein kinase (SnRK2.6) phosphorylates the microtubule-associated protein SP2L at Ser406, which induces a change in the anisotropic cell expansion at the root transition zone that located between the apical meristem and basal elongation zone, and is required for root twisting during halotropsim. Salt stress triggers SP2L-mediated cortical microtubule reorientation in cells at the transition zone, which guides cellulose microfibril patterns. Our findings outline the cellular and molecular mechanisms of root halotropism and indicate that anisotropic cell expansion through MT-reorientation and microfibril deposition have a central role in mediating tropic responses.

plant biology↗
bioRxiv2022

Population Sequencing Reveals Rht-D1b Contributing the Bigger Seedling Root to Modern Wheat Cultivars

The Green Revolution (GR) has dramatically increased the yield of modern wheat cultivars; however, whether and how GR reshaped the wheat root system remains largely unknown. Here, a large-scale transcriptomic and phenotypical investigation was performed on seedling roots of 406 worldwide bread wheat accessions, showing differential transcriptomes and phenotypes between landrace and modern cultivars, and the GR allele Rht-D1b was the main genetic factor driving this phenotype differential, conferring a significantly larger seedling root to modern cultivars by increasing cell length and root meristem size. In this case, the translational reinitiation of TaRht-D1 underlies Rht-D1bs genetic effects. In contrast, another GR allele, Rht-B1b, has no significant effects on root-related traits, differing from the similar genetic effects of these two GR alleles on reducing plant height. This unexpected effect of Rht-D1b on root systems contributes to a substantially larger root-shoot ratio in modern wheat cultivars. These findings reveal previously overlooked benefits of GR alleles in modern wheat cultivars and provide clues for their future application to form a robust seminal root system.

plant biology↗
bioRxiv2022

Chemical genetic screening identifies nalacin as an inhibitor of GH3 amido synthetase for auxin conjugation

Root system is critical for plant growth and development. To develop plant growth regulators functioning in root development, we performed a phenotype-based chemical screen in Arabidopsis and identified a chemical, nalacin, that mimicked the effects of auxin on root development. Genetic, pharmacological and biochemical approaches demonstrated that nalacin exerts its auxin-like activities by inhibiting indole-3-acetic acid (IAA) conjugation that is mediated by Gretchen Hagen 3 (GH3) acyl acid amido synthetases. The crystal structure of Arabidopsis GH3.6 in complex with D4 (a derivative of nalacin) together with docking simulation analysis revealed the molecular basis of the inhibition of group II GH3 by nalacin. Sequence alignment analysis indicated broad bioactivities of nalacin and D4 as inhibitors of GH3s in vascular plants, which were confirmed, at least, in tomato and rice. In summary, our work identifies nalacin as a potent inhibitor of IAA conjugation mediated by group II GH3 that plays versatile roles in hormone-regulated plant development and has potential applications in both basic research and agriculture.

plant biology↗
bioRxiv2022

Improving Interdisciplinary Teaching through a Complexity Lens

In this article, we discuss the use of bipartite network analysis to understand and improve interdisciplinary teaching practice. We theorize mathematics and biology as part of a coevolving mutualistic ecosystem. As part of an interdisciplinary teaching initiative, we inventoried mathematics topics appearing in the marine biology classroom and their associated marine context. We then apply techniques of mutualistic bipartite networks analysis to this system to understand the use of mathematical concepts in a marine biology classroom. By analyzing the frequency and distribution of mathematics topics, we see that a variety of mathematical concepts are used across the course with most appearing only a few times. While this is an inherent trait of mutualistic coevolutionary networks, it can create a logistical challenge to supporting mathematics in the marine biology classroom. We find that marine biology topics containing the most mathematics are either close to the instructors research area or were introduced through externally developed educational resources. Finally, we analyze groups of topics that appear connected to each other more frequently to inform both interdisciplinary education development as well as disciplinary support. We also suggest ways to use network metrics to track interdisciplinary connections over time, helping us understand the impact of interventions on interdisciplinary teaching practice.

scientific communication and education↗
bioRxiv2022

The expression and function of 28s5-rtsRNA: an update

Our previous research identified an abundant 28s rRNA 5 terminal derived small RNA (named 28s5-rtsRNA), which could decrease multiple ribosomal protein mRNA levels. In the last several years, the development of novel high-throughput RNA sequencing methods, exampled as PANDORA-seq, has changed the repertoire of small RNAs. In the present study, we reanalyzed the PANDORA-seq data by using a sRNAbench bioinformatic tool and revealed that 28s5-rtsRNA was among the most abundant small RNAs, particularly after T4PNK treatment during sequencing library preparation. 28s5-rtsRNA pairing with 5.8s rRNA 3 terminal derived small RNA could also decrease multiple ribosomal mRNA levels. At last, we performed a mutational scan to identify the key nucleotides involved in the 28s5-rtsRNA duplex function.

biochemistry↗