Biology subjects

Liang, C.

Publications and source records attributed to Liang, C..

At least 91 records · Page 5Linked to original sources

bioRxiv2023

Epigenetically silenced DACT3 promotes tumor growth via affecting Wnt/beta-catenin signaling and supports chidamide plus azacitidine therapy in acute myeloid leukemia

BackgroundDACT gene is a potential Wnt antagonist and tumor suppressor gene. However, the expression of DACT gene in acute myeloid leukemia (AML) and its role are still unknown. MethodsIn this study, we first multidimensionally analyzed the expression of DACT gene in AML through RNA seq, qRT-PCR and Western blotting analysis as well as TCGA database analysis. Then DACT3 was identified as playing a critical role in AML, and its clinical significance was further explored. The molecular mechanism of DACT3 down-regulation in AML from aspects of DNA methylation and histone acetylation were inquired. Finally, the biological functions of DACT3 in AML were investigated by cell models in vitro and animal experiments in vivo. ResultsCompared with DACT1 and DACT2, DACT3 was the most differentially expressed DACT family member in AML, suggesting that DACT3 plays the major role. The mRNA and protein expression levels of DACT3 were significantly decreased and positively correlated in AML. Moreover, low expression of DACT3 is associated with no remission disease status and poor prognosis in AML patients. In addition, down-regulation of DACT3 in AML was not completely dependent on promoter methylation, but also affected by histone deacetylation. We found that loss of DACT3 in AML is related to activation of Wnt signaling pathway. Furthermore, DACT3 inhibits the growth of AML cells in vitro and in severe immunodeficiency (SCID) mice. Importantly, DACT3 improved the sensitivity of adriamycin in treating AML cells. Further research showed that co-treatment of chidamide and azacytidine up-regulates DACT3 expression and promotes cell apoptosis via inhibiting Wnt/{beta}-catenin signaling in AML, suggesting a promising therapeutic prospects in FLT3-mutant AML. ConclusionThis is the first study revealing the epigenetic regulatory molecular mechanism of the down regulated expression of DACT3 in AML. Our data also shows that DACT3 is a candidate gene for therapeutic target and targeting DACT3 has the potential to validate the combination therapy of DNMT inhibitors and HDAC inhibitors.

molecular biology↗

bioRxiv2022

Cx26 heterozygous mutations cause hyperacusis-like hearing sensitivity enhancement and increase susceptibility to noise

Gap junction gene GJB2 (Cx26) mutations cause >50% of nonsyndromic hearing loss. Its recessive hetero-mutation carriers, who have no deafness, occupy [~]10-20% of the general population. Here, we report an unexpected finding that these heterozygote carriers have hearing over-sensitivity and active cochlear amplification increased. Mouse models show that Cx26 hetero-deletion reduced endocochlear potential (EP) generation in the cochlear lateral wall and caused outer hair cell electromotor protein prestin compensatively upregulated to increase active cochlear amplification and hearing sensitivity. The increase of active cochlear amplification also increased sensitivity to noise; exposure of daily-level noise could cause Cx26+/- mice permanent hearing threshold shift leading to hearing loss. This study demonstrate that Cx26 recessive heterozygous mutations are not harmless for hearing as previously considered and can cause hyperacusis-like hearing over-sensitivity. The data also indicate that GJB2 hetero-mutation carriers are vulnerable to noise and should avoid noise exposure in daily-life. TeaserCx26 hetero-mutations are not harmless and can cause hearing over-sensitivity and increase susceptibility to noise.

neuroscience↗

bioRxiv2022

Biomimetic human lung alveolar interstitium chip with extended longevity

Determining the mechanistic causes of lung diseases, developing new treatments thereof, and assessing toxicity whether from chemical exposures or engineered nanomaterials would benefit significantly from a preclinical human lung alveolar interstitium model of physiological relevance. The existing preclinical models have limitations because they fail to replicate the key anatomical and physiological characteristics of human alveoli. Thus, a human lung alveolar interstitium chip was developed to imitate key alveolar microenvironmental factors including: an electrospun nanofibrous membrane as the analogue of the basement membrane for co-culture of epithelial cells with fibroblasts embedded in 3D collagenous gels; physiologically relevant interstitial matrix stiffness; interstitial fluid flow; and 3D breathing-like mechanical stretch. The biomimetic chip substantially improved epithelial barrier function compared to transwell models. Moreover, the chip having a gel made of a collagen I-fibrin blend as the interstitial matrix sustained the interstitium integrity and further enhanced the epithelial barrier resulting in a longevity that extended beyond eight weeks. The assessment of multiwalled carbon nanotube toxicity on the chip was in line with the animal study.

bioengineering↗

bioRxiv2022

Tissue- and sex-specific DNA damage tracks aging in rodents and humans

DNA damage causes genomic instability underlying many human diseases. Traditional approaches to DNA damage analysis provide minimal insights into the spectrum of disease-driving DNA lesions and the mechanisms causing imbalances in damage formation and repair. Here we used untargeted mass spectrometry-based adductomics1 to discover 114 putative DNA lesions and modifications consistently detected in humans and two independent analyses in rats, showing species-, tissue-, age-, and sex-biases. As evidence of methodologic rigor, 10 selected adductomic signals were structurally validated as epigenetic marks: 5-MdC, 5-HMdC, 5-FdC; DNA damage products: N2-CMdG, 1,N6 {varepsilon}-dA, 3,N4-{varepsilon}dC, M1dG, O6/N2-MdG, and 8-Oxo-dG; and established analytical artifacts: cyclobutane dimers of 2-deoxycytosine. With steady-state levels of putative DNA adducts integrating multiple cell types in each tissue, there was strong age-dependent variation for many putative adducts, including N2-CMdG, 5-HMdC, and 8-Oxo-dG in rats and 1,N6 {varepsilon}-dA in human heart, as well as sex biases for 67 putative adducts in rat tissues. These results demonstrate the potential of untargeted adductomic analysis for defining DNA adducts as disease determinants, assigning substrates to DNA repair pathways, discovering new metabolically-driven DNA lesions, and quantifying inter-individual variation in DNA damage and repair across populations.

biochemistry↗

bioRxiv2022

Integrated analysis of single-cell transcriptome of liver cancer and cirrhosis reveals cell lineage similarity and prognostic-associated subpopulations

Background & AimsLiver cancer is one of the most leading causes of cancer deaths. Cirrhosis is an important risk factor for liver cancer, which is the result of over-fibrosis caused by diffuse and long-term liver damage. Despite extensive research, a systematic study for characterizing similarity between liver cancer and cirrhosis at single cell resolution is still lacking. MethodsWe established a data analysis framework to elucidate cell lineage similarity between liver cancer and cirrhosis to discover prognostic-associated subpopulations. We integrated single-cell transcriptome data from liver samples at normal, cirrhotic and cancer conditions, which totally contained 78,000 cells. Gene regulation analysis, cellular interactions and trajectory analysis were performed to characterize cirrhosis-like cell subpopulations. Bulk transcriptomes were used to discover prognostic-associated subpopulations. ResultsBy aligning cellular subpopulations across different samples, we found remarkable similarity between KNG1+ hepatocytes in cirrhosis and PGA5+ hepatocytes in HCC. Furthermore, gene regulation analysis and cellular interactions implicated E2F1, FOXA2, EGF, CDH and ANGPTL signaling in maintaining cirrhosis-like ecosystem. Strikingly, subpopulations with higher expression of cirrhosis-like signatures were associated with patients worse survival. ConclusionsWe revealed a previously unexplored cirrhosis-like ecosystem of liver cancer, which could provide novel biomarkers for therapeutic interventions in HCC. Core analysis modules in this study were integrated into a user-friendly toolkit, SIMscRNA(https://github.com/xmuhuanglab/SIM-scRNA), which could facilitate the exploration of similarity and heterogeneity between precancerous diseases and solid tumors.

bioinformatics↗

bioRxiv2022

Mitoxantrone Targets Both Host and Bacteria to Overcome Vancomycin Resistance in Enterococcus faecalis

Among Enterococci, intrinsic and acquired resistance to antibiotics such as {beta}-lactams and vancomycin critically limit treatment options for infection with these opportunistic pathogens. Antimicrobials that enhance the host immune response are emerging as alternative approaches, with the potential to overcome bacterial resistance. Here, we investigate the antibiotic and immunological activity of the anticancer agent mitoxantrone (MTX) in vitro and in vivo against vancomycin resistant Enterococcus faecalis (VRE). We show that, in vitro, MTX is a potent antibiotic against Gram-positive bacteria with a minimal inhibitory concentration (MIC) of ~1 g/ml through induction of reactive oxygen species and DNA damage. MTX synergises with vancomycin and lowers the vancomycin concentration required to kill VRE by over 140-fold. This synergy is specific to vancomycin-resistant, but not susceptible strains because vancomycin rendered the resistant strains more permeable to MTX and thus MTX-mediated DNA damage. In a murine wound infection model, MTX treatment effectively reduced VRE bacterial numbers by 120-fold and with further reduction when combined with vancomycin. Wounds treated with MTX had significantly higher numbers of macrophages and higher pro-inflammatory cytokines compared to untreated wounds. In addition, MTX augmented intracellular bacterial killing by both murine and human macrophages by upregulating the expression of lysosomal hydrolases cathepsins D and H, and {beta}-Hexosaminidase. These results show that MTX is a potent antibiotic against Gram-positive bacteria, synergizes with vancomycin, enhances macrophage recruitment and intracellular bactericidal activity, and represents a promising dual bacterium- and host-targeted therapeutic for overcoming vancomycin resistance. One sentence summaryMitoxantrone synergizes with vancomycin against vancomycin resistant bacterial strains via direct antibiotic activity and by augmenting both host macrophage recruitment to the site of infection and macrophage bactericidal activity.

microbiology↗

bioRxiv2022

Born with intronless ERF transcriptional factors: C4 photosynthesis inherits a legacy dating back 450 million years

The genus Flaveria, containing species at different evolutionary stages of the progression from C3 to C4 photosynthesis, is used as a model system to study the evolution of C4 photosynthesis. Here, we report chromosome-scale genome sequences for five Flaveria species, including C3, C4, and intermediate species. Our analyses revealed that both acquiring additional gene copies and recruiting ethylene responsive factor (ERF) cis-regulatory elements (CREs) contributed to the emergence of C4 photosynthesis. ERF transcriptional factors (TFs), especially intronless ERF TFs, were co-opted in dicotyledonous C4 species and monocotyledonous C4 species in parallel. These C4 species co-opted intronless ERF TFs originated from the Late Ordovician mass extinction that occurred [~]450 million years ago in coping with environmental stress. Therefore, this study demonstrated that intronless ERF TFs were acquired during the early evolution of plants and provided the molecular toolbox facilitating multiple subsequent independent evolutions of C4 photosynthesis.

evolutionary biology↗

bioRxiv2022

Prioritizing prognostic-associated subpopulations and individualized recurrence risk signatures from single-cell transcriptomes of colorectal cancer

Colorectal cancer (CRC) is one of the most common gastrointestinal malignancies. There are few recurrence risk signatures for CRC patients. Single-cell RNA-sequencing (scRNA-seq) provides a high resolution platform for prognostic signature detection. However, scRNA-seq is not practical in large cohorts due to its high cost and most single-cell experiments lack clinical phenotype information. Few studies have been reported to use external bulk transcriptome with survival time to guide the detection of key cell subtypes in scRNA-seq data. We proposed a data analysis framework to prioritize prognostic-associated subpopulations based on relative expression orderings (REOs). Cell type specific gene pairs (C-GPs) were identified to evaluate prognostic value for each cell type. We found REOs-based signatures could accurately classify most cell subtypes. C-GPs achieves higher precision compared with four current methods. Moreover, we developed single-cell gene pair signatures to predict recurrence risk for patients individually. Fibro_SGK1 cells and IgA+ IGLC2+ B cells were novel prognostic-associated subpopulations. A user-friendly toolkit, scRankXMBD (https://github.com/xmuyulab/scRank-XMBD), was developed to enable implementation of this framework. Our work facilitate the application of the rank-based method in scRNA-seq data for prognostic biomarker discovery and precision oncology.

bioinformatics↗

bioRxiv2022

An RNA modification enzyme directly senses reactive oxygen species for translational regulation in Enterococcus faecalis

Bacteria possess elaborate systems to manage reactive oxygen and nitrogen species (ROS) arising from exposure to the mammalian immune system and environmental stresses. Here we report the discovery of an ROS-sensing RNA-modifying enzyme that regulates translation of stress-response proteins in the gut commensal and opportunistic pathogen Enterococcus faecalis. We analyzed the tRNA epitranscriptome of E. faecalis in response to reactive oxygen species (ROS) or sublethal doses of ROS-inducing antibiotics and identified large decreases in N2-methyladenosine (m2A) in both 23S ribosomal RNA and transfer RNA. This we determined to be due to ROS-mediated inactivation of the Fe-S cluster-containing methyltransferase, RlmN. Genetic knockout of RlmN gave rise to a proteome that mimicked the oxidative stress response, with increased levels of superoxide dismutase and decreased virulence proteins. While tRNA modifications are established to be dynamic for fine-tuning translation, here we report the first instance of a dynamically regulated, environmentally responsive rRNA modification. These studies lead to model in which RlmN serves as a redox-sensitive molecular switch, directly relaying oxidative stress to modulating translation through the rRNA and the tRNA epitranscriptome, revealing a new paradigm for understanding direct regulation of the proteome by RNA modifications.

microbiology↗

bioRxiv2022

Molecular and genetic mechanisms conferring dissolution of dioecy in Diospyros oleifera Cheng

Dioecy, a sexual system of single-sex (gynoecious/androecious) individuals, is rare in flowering plants. This rarity may be a result of the frequent transition from dioecy into systems with co-sex individuals. Here, we report potential molecular and genetic mechanisms that underlie the dissolution of dioecy to monoecy and andro(gyno)monoecy, based on multiscale genome-wide investigations of 150 accessions of Diospyros oleifera. All co-sex D. oleifera plants, including monoecious and andro(gyno)monoecious individuals, possessed the male determinant gene OGI, implying that genetic factors control gynoecia development in genetically male D. oleifera. In both single- and co-sex plants, female function was expressed in the presence of a genome-wide decrease in methylation levels, along with sexually distinct regulatory networks of smRNAs and their targets. Furthermore, a genome-wide association study (GWAS) identified a genomic region and a DUF247 gene cluster strongly associated with the monoecious phenotype, as well as several regions that may contribute to andromonoecy. Collectively, our findings imply stable breakdown of the dioecious system in D. oleifera, presumably a result of the genomic features of the sex-linked region.

plant biology↗

bioRxiv2022

Cross-amplified Barcodes on Slides for Spatial Transcriptomics Sequencing

Spatial transcriptomics can reveal molecular signatures of tissue at spatial scales, but current technologies cannot integrate excellent accessibility and easy data-decoding. Here, we use oligonucleotides whose number is the square root of the number of spots to generate cross-amplified spatial barcodes on slides using microfluidic technology. This method can obtain microarrays with well-defined barcodes easily and at low cost, without post-decoding, which contributes to the popularization of spatial transcriptomics.

genomics↗

bioRxiv2022

Human iPSC-derived neuron of 16p11.2 deletion reveals haplotype-specific expression of MAPK3 and its contribution to variable NDD phenotypes

Recurrent proximal 16p11.2 deletion (16p11.2del) is risk factor of diverse neurodevelopmental disorders (NDDs) with variable penetrance. Although previous human induced pluripotent stem cell (hiPSC) models of 16p11.2del confirmed disrupted neuron development, it is not known which gene(s) at this interval are mainly responsible for the abnormal cellular phenotypes and how the NDD penetrance is regulated. After haplotype phasing of 16p11.2 region, we generated hiPSCs for two 16p11.2del families with distinct residual haplotypes and variable NDD phenotypes. We also differentiated the hiPSCs to cortical neural cells and demonstrated MAPK3 as a driver signal of 16p11.2 region contributing to the dysfunctions in multiple pathways related to neuron development, which leads to altered morphological or electrophysiological properties in neuron cells. Furthermore, residual haplotype-specific MAPK3 expression was identified in 16p11.2del neuron cells, associating MAPK3 down-expression with the minor allele of the residual haplotype. Ten SNPs of the residual haplotype are mapped as enhancer SNPs (enSNPs) of MAPK3, eight enSNPs were functionally validated by luciferase assays, implying enSNPs contribute to residual haplotype-specific MAPK3 expression via cis-regulation. Finally, the analyses of three different patient cohorts showed that the residual haplotype of 16p11.2del is associated with variable NDD phenotypes.

genetics↗

bioRxiv2022

Underlying beneficial effects of Rhubarb on constipation-induced inflammation, disorder of gut microbiome and metabolism

BackgroundAlthough constipation is a common syndrome and a worldwide health problem. Constipation patients are becoming younger with a 29.6% overall prevalence in the children, which has captured great attention because of its epigenetic rejuvenation and recurrent episodes. Despite the usage of rhubarb to relieve constipation, novel targets and genes involved in target-relevant pathways with remarkable functionalities should still be sought after. Materials and methodsWe established a reliable constipation model in C57B/6N male mice using intragastric administration diphenoxylate and the eligible subjects received 600mg/25g rhubarb extraction to ameliorate constipation. Resultant constipation was morphological and genetically compared with the specimen from different groups. ResultsThe constipation mice exhibited thicker muscle layers, improved content of cytokines, including IL-17 and IL-23, and lower content of IL-22. The bacterial abundance and diversity varied tremendously. Notably, the alterations were reversed after rhubarb treatment. Additionally, SCFA and MLCFA were significantly influenced by constipation accompanied by enhanced expressions of SCFA receptors, GPR41 and GPR43. ConclusionThis thesis has provided an insight that rhubarb promoted the flexibility of collagen fiber, reduced pro-inflammatory cytokines and enhanced anti-inflammatory cytokines, and maintained intestinal microflora balance with potential effects on affecting the metabolism of fatty acids and polyamines.

pharmacology and toxicology↗

bioRxiv2022

A human embryonic limb cell atlas resolved in space and time

Human limbs emerge during the fourth post-conception week as mesenchymal buds which develop into fully-formed limbs over the subsequent months. Limb development is orchestrated by numerous temporally and spatially restricted gene expression programmes, making congenital alterations in phenotype common. Decades of work with model organisms has outlined the fundamental processes underlying vertebrate limb development, but an in-depth characterisation of this process in humans has yet to be performed. Here we detail the development of the human embryonic limb across space and time, using both single-cell and spatial transcriptomics. We demonstrate extensive diversification of cells, progressing from a restricted number of multipotent progenitors to myriad mature cell states, and identify several novel cell populations, including neural fibroblasts and multiple distinct mesenchymal states. We uncover two waves of human muscle development, each characterised by different cell states regulated by separate gene expression programmes. We identify musculin (MSC) as a key transcriptional repressor maintaining muscle stem cell identity and validate this by performing MSC knock down in human embryonic myoblasts, which results in significant upregulation of late myogenic genes. Through integration of multiple anatomically continuous spatial transcriptomic samples, we spatially map single-cell clusters across a sagittal section of a whole fetal hindlimb. We reveal a clear anatomical segregation between genes linked to brachydactyly and polysyndactyly, and uncover transcriptionally and spatially distinct populations of mesenchyme in the autopod. Finally, we perform scRNA-seq on murine embryonic limbs to facilitate cross-species developmental comparison at single-cell resolution, finding substantial homology between the two species.

developmental biology↗

bioRxiv2022

SARS-CoV-2 accessory protein ORF8 decreases antibody-dependent cellular cytotoxicity

SARS-CoV-2 Spike glycoprotein is the major target of host neutralizing antibodies and the most changing viral protein in the continuously emerging SARS-CoV-2 variants as a result of frequent viral evasion from host antibody responses. In addition, SARS-CoV-2 encodes multiple accessory proteins that modulate host antiviral immunity by different mechanisms. Among all SARS-CoV-2 accessory proteins, ORF8 is rapidly evolving and a deletion in this protein has been linked to milder disease. Here, we studied the effect of ORF8 on peripheral blood mononuclear cells (PBMC). Specifically, we found that ORF8 can bind monocytes as well as NK cells. Strikingly, ORF8 binds CD16a (Fc{gamma}RIIIA) with nanomolar affinity and decreases the overall level of CD16 at the surface of monocytes and, to a lesser extent, NK cells. Strikingly, this decrease significantly reduces the capacity of PBMCs and particularly monocytes to mediate antibody-dependent cellular cytotoxicity (ADCC). Overall, our data identifies a new immune-evasion activity used by SARS-CoV-2 to escape humoral responses.

immunology↗

bioRxiv2021

Identification and characterization of 19 predicted Myb-family DNA binding proteins in Magnaporthe oryzae concerning growth, conidiation, and pathogenicity

Proteins with DNA binding Myb domains have been suggested in regulating development and stress responses. Magnaporthe oryzae is considered the most destructive pathogen of rice. We screened the genome for genes with Myb domains encoding since these can be needed for pathogenesis. We found Myb1-19. Only MoMyb1 was previously shown to be involved in pathogenesis. We succeeded in deleting 12 of the other 18 genes. MoMyb2 deletion affected mainly growth, while MoMyb13 or MoMyb15 deletions gave additional defects in conidiation and plant infection. However, RT-qPCR showed that none of the 19 Myb genes are negligibly expressed. Instead, they have different expression profiles hours post-infection when infecting rice plants. Considering this, the unchanged infection phenotype for 9 gene deletions surprised us, and we extended the analysis to expression co-regulation of all 19 Myb proteins and found 5 co-regulated groups of predicted Myb-domain proteins. MoMyb13 or MoMyb15 are discussed and motivated as candidates for further, more detailed studies with aims also outside of plant pathology. Referring to what is found in other eukaryotes, we finally discuss possible redundancy or compensatory regulations for many of the other Myb genes hiding or compensating for the effect of many complete deletions. IMPORTANCEMagnaporthe oryzae is considered the most important rice pathogen limiting rice production. Our study attempts to find all genes encoding a DNA-binding gene family called Myb, and we found 19, many of which have not been studied before. The Myb gene family is suspected to regulate stress responses the pathogen needs to overcome plant defenses. Inhibiting or disturbing these genes, if they are indeed regulatory, can open new ways of controlling the pathogen and learning more about its physiology and ecology.

microbiology↗

bioRxiv2021

Dominant species determine ecosystem stability across scales in Inner Mongolian grassland

There is an urgent need to extend knowledge on ecosystem temporal stability to larger spatial scales because presently available local-scale studies generally do not provide effective guide for management and conservation decisions at the level of an entire region with diverse plant communities. We investigated temporal stability of plant biomass production across spatial scales and hierarchical levels of community organization and analyzed impacts of dominant species, species diversity and climatic factors using a multi-site survey of Inner Mongolian grassland. We found that temporal stability at a large spatial scale, i.e. a large area aggregating multiple local communities, was related to temporal stability of and asynchrony among spatially separated local communities and large-scale population dynamics of dominant species, yet not to species richness. Additionally, a lower mean and higher variation of yearly precipitation destabilized communities at local and large scales by destabilizing dominant species population dynamics. We argue that, for semi-arid temperate grassland, dynamics and precipitation responses of dominant species and asynchrony among local communities stabilize ecosystems at large spatial scales. Our results indicate that reduced amounts and increased variation of precipitation may present key threats to the sustainable provision of biological products and services to human well-being in this region.

ecology↗

bioRxiv2021

Clustering single cell CITE-seq data with a canonical correlation based deep learning method

Single cell sequencing examines the sequence information from individual cells with optimized next generation sequencing (NGS) technologies. It provides researchers a higher resolution of cellular differences and a better understanding of the function of an individual cell in the context of its microenvironment. CITE-seq, or Cellular Indexing of Transcriptomes and Epitopes by sequencing, is one of the latest innovations in the domain of single cell sequencing. It enables researchers to simultaneously capture RNA and surface protein expression on the same cells so that we can correlate the two data types, identify biomarkers and better characterize cell phenotypes. Although multi-omics sequencing technologies developed rapidly, data analyzing methods tailored for multiomics sequencing data are lacking. Several serious problems have to be faced. An important one is how to integrate the information from different modalities, namely scRNA and protein data, efficiently. In this paper, we introduce a canonical correlation based deep learning method called scCTClust for clustering analysis over CITE-seq data. We impute and extract the characteristics of the high dimensional RNA part of data with a ZINB model-based autoencoder. A t-kernel distance is introduced to measure the similarity between query cell and cluster centroids. And the protein data rectifies the feature extraction of scRNA data in a canonical correlation analysis(CCA) way. Extensive data experiments shows that scCTClust can precisely recover the dropout values for RNA sequencing data and extract authentic information from both modalities, getting a much better clustering result than state-of-the-art methods, no matter single-omic or multi-omics clustering algorithms.

bioinformatics↗