Biology subjects

Kong, W.

Publications and source records attributed to Kong, W..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

CENP-C-Mis12 complex establishes a regulatory loop through Aurora B for chromosome segregation

Establishing the correct kinetochore-microtubule attachment is crucial for faithful chromosome segregation. The kinetochore has various regulatory mechanisms for establishing correct bipolar attachment. However, how the regulations are coupled is not fully understood. Here, we demonstrate a regulatory loop between the kinetochore protein CENP-C and Aurora B kinase, which is critical for the error correction of kinetochore-microtubule attachment. This regulatory loop is mediated through the binding of CENP-C to the outer kinetochore Mis12 complex (Mis12C). Although the Mis12C binding region of CENP-C is dispensable for mouse development and proliferation in human RPE-1 cells, those cells lacking this region display increased mitotic defects. The CENP-C-Mis12C interaction facilitates the centromeric recruitment of Aurora B and the mitotic error correction in human cells. Given that Aurora B reinforces the CENP-C-Mis12C interaction, our findings reveal a positive regulatory loop between Aurora B recruitment and the CENP-C-Mis12C interaction, which ensures chromosome bi-orientation for accurate chromosome segregation.

cell biology↗

bioRxiv2024

TET2 regulates early and late transitions in exhausted CD8+ T-cell differentiation and limits CAR T-cell function

CD8+ T-cell exhaustion hampers disease control in cancer and chronic infections and limits efficacy of T-cell-based therapies, such as CAR T-cells. Epigenetic reprogramming of CAR T-cells by targeting TET2, a methylcytosine dioxygenase that mediates active DNA demethylation, has shown therapeutic potential; however, the role of TET2 in exhausted T-cell (TEX) development is unclear. In CAR T-cell exhaustion models and chronic LCMV infection, TET2 drove the conversion from stem cell-like, self-renewing TEX progenitors towards terminally differentiated and effector (TEFF)-like TEX. In mouse T-cells, TET2-deficient terminally differentiated TEX retained aspects of TEX progenitor biology, alongside decreased expression of the transcription factor TOX, suggesting that TET2 potentiates terminal exhaustion. TET2 also enforced a TEFF-like terminally differentiated CD8+ T-cell state in the early bifurcation between TEFF and TEX, indicating a broad role for TET2 in mediating the acquisition of an effector biology program that could be exploited therapeutically. Finally, we developed a clinically actionable strategy for TET2- targeted CAR T-cells, using CRISPR/Cas9 editing and site-specific adeno-associated virus transduction to simultaneously knock-in a CAR at the TRAC locus and a functional safety switch within TET2. Disruption of TET2 with this safety switch in CAR T-cells restrained terminal TEX differentiation in vitro and enhanced anti-tumor responses in vivo. Thus, TET2 regulates pivotal fate transitions in TEX differentiation and can be targeted with a safety mechanism in CAR T-cells for improved tumor control and risk mitigation. One Sentence SummaryModulation of exhausted CD8+ T-cell differentiation by targeting TET2 improves therapeutic potential of CAR T-cells in cancer.

immunology↗

bioRxiv2024

ELO-6 expression predicts longevity in isogenic populations of Caenorhabditis elegans

Variations of individual lifespans within genetically identical populations in homogenous environments are remarkable, with the cause largely unknown. Gene expression changes with age, and the transcriptome changes correlate with chronological aging. Here, we show that in Caenorhabditis elegans, the expression dynamic of the fatty acid elongase ELO-6 during aging predicts individual longevity in isogenic populations. The expression of elo-6 is reduced with age. From adult day 5, ELO-6 expression level exhibits variation between individuals, and the expression level is positively correlated with adult lifespan and health span. Interventions that prolong longevity enhance the expression stability of ELO-6 during aging from adult day 4 to adult day 8, indicating ELO-6 is also a populational lifespan predictor. We performed transcriptome analysis in short-lived and long-lived isogenic worms and identified differentially expressed genes, which are enriched for PQM-1 binding sites. Decreasing pqm-1 expression in young adults improved the homogeneity of ELO-6 levels between individuals and enhanced health span. Furthermore, we found reducing the expression of genes that are highly expressed in short-lived individuals, including PQM-1 target genes, enhanced ELO-6 expression stability with age and extended lifespan. Thus, our study identified ELO-6 as a predictor of individual and populational lifespan and revealed the role of pqm-1 in restricting health span and possibly causing individual lifespan variation.

physiology↗

bioRxiv2024

Intermittent energy restriction inhibits tumor growth and enhances paclitaxel response in a transgenic mouse model of endometrial cancer

ObjectiveOverweight/obesity is the strongest risk factor for endometrial cancer (EC), and weight management can reduce that risk and improve survival. We aimed to establish the differential abilities of intermittent energy restriction (IER) and low-fat diet (LFD), alone and in combination with paclitaxel, to reverse the procancer effects of high-fat diet (HFD)-induced obesity in a mouse model of EC. MethodsLkb1fl/flp53fl/fl mice were fed high-fat diet (HFD) or LFD to generate obese and lean phenotypes, respectively. Obese mice were maintained on HFD or switched to LFD (HFD-LFD) or IER (HFD-IER). Ten weeks after induction of endometrial tumor, mice in each group received paclitaxel or placebo for 4 weeks. Body and tumor weights; tumoral transcriptomic, metabolomic and oxylipin profiles; and serum metabolic hormones and chemocytokines were assessed. ResultsHFD-IER and HFD-LFD, relative to HFD, reduced body weight; reversed obesity-induced alterations in serum insulin, leptin and inflammatory factors; and decreased tumor incidence and mass, often to levels emulating those associated with continuous LFD. Concurrent paclitaxel, versus placebo, enhanced tumor suppression in each group, with greatest benefit in HFD-IER. The diets produced distinct tumoral gene expression and metabolic profiles, with HFD-IER associated with a more favorable (antitumor) metabolic and inflammatory environment. ConclusionIn Lkb1fl/flp53fl/fl mice, IER is generally more effective than LFD in promoting weight loss, inhibiting obesity-related endometrial tumor growth (particularly in combination with paclitaxel), and reversing detrimental obesity-related metabolic effects. These findings lay the foundation for further investigations of IER as a EC prevention strategy in women with overweight/obesity.

cancer biology↗

bioRxiv2024

Systemic Dosing of Virus-derived Serpin Improves Survival and Immunothrombotic Damage in Murine Colitis

Inflammatory bowel disease (IBD) is potentially life-threatening, with risk of bleeding, clotting, infection, sepsis, cancer and toxic megacolon. Systemic and local immune and coagulation dysfunction increase IBD severity. Current treatments are partially effective, but there is no definitive cure. Serine protease cascades activate thrombotic, thrombolytic and complement pathways and are regulated by inhibitors, serpins. Viruses encode proteins evolved from endogenous central regulatory pathways. A purified secreted Myxomavirus-derived serpin, Serp-1, dosed as a systemic anti-inflammatory drug, has proven efficacy in vascular and inflammatory disorders. PEGylated Serp-1 protein (PEGSerp-1) has improved efficacy in lupus and SARS-CoV-2 models. We examined PEGSerp-1 treatment in a mouse Dextran Sodium Sulfate (DSS) colitis model. Prophylactic PEGSerp-1 significantly improved survival in acute severe 4-5% DSS colitis, reducing inflammation and crypt damage in acute 4-5% DSS induced colitis and when dosed as a chronic delayed treatment for recurrent 2% DSS colitis. PEGSerp-1 reduced iNOS+ M1 macrophage invasion, damage to crypt architecture and vascular inflammation with decreased uPAR, fXa, fibrinogen and complement activation. This work supports PEGSerp-1 as a tissue targeting serpin therapeutic.

molecular biology↗

bioRxiv2023

Optimizing Proteomics Data Differential Expression Analysis via High-Performing Rules and Ensemble Inference

In the process of identifying phenotype-specific or differentially expressed proteins from proteomic data, a standard workflow consists of five key steps: raw data quantification, expression matrix construction, matrix normalization, missing data imputation, and differential expression analysis. However, due to the availability of multiple options at each step, selecting ad hoc combinations of options can result in suboptimal analysis. To address this, we conducted an extensive study involving 10,808 experiments to compare the performance of exhaustive option combinations for each step across 12 gold standard spike-in datasets and three quantification platforms: FragPipe, MaxQuant, and DIA-NN. By employing frequent pattern mining techniques on the data from these experiments, we discovered high-performing rules for selecting optimal workflows. These rules included avoiding normalization, utilizing MinProb for missing value imputation, and employing limma for differential expression analysis. We found that workflow performances were predictable and could be accurately categorized using average F1 scores and Matthews correlation coefficients, both exceeding 0.79 in 10-fold cross-validations. Furthermore, by integrating the top-ranked workflows through ensemble inference, we not only improved the accuracy of differential expression analysis (e.g., achieving a 1-5% gain under five performance metrics for FragPipe), but also enhanced the workflows ability to aggregate proteomic information across various levels, including peptide and protein level intensities and spectral counts, providing a comprehensive perspective on the data. Overall, our study highlights the importance of selecting optimal workflow combinations and demonstrates the benefits of ensemble inference in improving both the accuracy and comprehensiveness of proteomic data analysis.

bioinformatics↗

bioRxiv2023

Single-cell lineage tracing reveals hierarchy and mechanism of adipocyte precursor maturation

White adipose tissue is crucial in various physiological processes. In response to high caloric intake, adipose tissue may expand by generating new adipocytes. Adipocyte precursor cells (progenitors and preadipocytes) are essential for generating mature adipocytes, and single-cell RNA sequencing provides new means to identify these populations. Here, we characterized adipocyte precursor populations in the skin, an adipose depot with rapid and robust generation of mature adipocytes. We identified a new population of immature preadipocytes, revealed a biased differentiation potential of progenitor cells, and identified Sox9 as a critical factor in driving progenitors toward adipose commitment, the first known mechanism of progenitor differentiation. These findings shed light on the specific dynamics and molecular mechanisms underlying rapid adipogenesis in the skin.

developmental biology↗

bioRxiv2023

Population genomics reveals extensive inbreeding and purging of mutational load in wild Amur tigers

The inbreeding is a big threat for the persistence of genetic diversity in small and isolated populations of endangered species. The homozygous genome could exacerbate inbreeding depression by introducing homozygous deleterious alleles in the population. However, purging of inbreeding loads as they become homozygotes in small populations could alleviate the depression. The Amur tiger (Panthera tigris altaica) is typically exists in small population living in forests in Northeast Asia and is among the most endangered animals on the planet with great symbolic significance of conservation. By comparing with captive individuals, we revealed substantially higher and more extensive inbreeding in the wild Amur tiger population (FROH=0.51) than in captive Amur tigers (FROH=0.26). We further found much less mutational loads in wild populations when compared with captive Amur tigers. However, the frequency of loss of function and deleterious nonsynonymous mutations inside ROH regions are much lower than that in non-ROH regions in both wild and captive Amur tigers, indicating the purging may had occurred in both populations but much effective in the wild population. In addition, we found the average frequency of deleterious alleles was much lower than that of neutral alleles in the wild population, indicating that the purifying selection contributed to the purging of mutational loads in the wild Amur tigers. These findings provide valuable genome-wide evidence to support the making of future conservation plans of wild Amur tigers.

genomics↗

bioRxiv2023

Development of membrane-like pre-stem cells after released from tube-shaped niches

We previously identified three distinct pre-stem cell lineages that further develop into blood CD34-positive stem cells, and mesenchymal stem cells. The pre-CD34-positive stem cells are spore-like, while the pre-mesenchymal stem cells are fusiform-shaped. All of them originate or released from tube-shaped tissue structures, or niches. In the current study, we present two membrane-like pre-stem progenitors. One of them had red thin membrane structures that were from disconnection of bamboo-like tissues and developed into thin membrane-like multi-nucleated cells. The other membrane-like structure had geometric-shape and was the place of developing numerous c-kit-positive stem cell progenitors. One geometric-shaped membrane could produce dozens to hundreds of progenitors in a synchronized pattern. Our findings provide more evidence that postnatal stem cells are unipotent and self-renewed in sealed tube-shaped structures. The tube-shaped structures released their inclusions that have distinct morphological differences among the cellular lineages. Thus, the self-renewal of each lineage-distinct stem cell has its unique pattern. Further, our data suggests that postnatal stem cells are renewed via a recurrent pattern. Our findings again challenged the old concepts of stem cell niche components, the origins of stem cell lineages and the self-renewal of stem cells.

cell biology↗

bioRxiv2023

The self-renewal procedures of mesenchymal stem cells in the blood

BackgroundAlthough mesenchymal stem cells (MSCs) are most commonly used in cell therapy and stem cell research, the mechanism and the locations of their self-renewal are still unknown. MethodMouse blood was collected, and examined under microscopy. The results were compared with the data of human umbilical cord blood (hUCB) collected 10 years ago. ResultsWe found that the procedure of self-renewal for the mesenchymal stem cells in mouse blood and hUCB needs at least 5 steps. First, tube-shaped stem cell niches release long segmented materials composed of sand-like particles and semitransparent granules. Second, the sand-like particles and semitransparent granules separate from the segmented materials. Third, each of the individual semitransparent granules releases groups of fusiform-shaped structures that do not stain to H&E. The sizes of the fusiform-shaped structures range from 1 to 100 m in length in mouse blood, but can be 200 m in hUCB. Fourth, the large-sized fusiform structures can directly transform into lineage-restricted cellular structures; the medium-sized fusiform structures fuse or engulf each other to form cellular structures. The cellular structures further acquire membranes from the adjacent nucleated cells. Fifth, the nucleolus appears in the new cellular structures before the nucleus. During all the procedures, the adjacent nucleated mesenchymal cells are must needed. Thus, these newly formed cellular structures will further differentiate into nucleated mesenchymal stem cells. ConclusionOur findings again provide new evidence that, in physiological conditions, mesenchymal stem cell self-renewal needs several steps to complete, which, however, does not occur by mitotic division. The tube-shaped structures are the niches of the stem cells.

cell biology↗

bioRxiv2022

DNA looping mediates cooperative transcription activation

Transcription factors respond to multi-level stimuli and co-occupy promoter regions of target genes to activate RNA polymerase (RNAP) in a cooperative manner. To decipher the molecular mechanism, here we report two cryo-electron microscopy structures of Anabaena transcription activation complexes (TACs): NtcA-TAC composed of RNAP holoenzyme, promoter and a global activator NtcA, and NtcA-NtcB-TAC comprising an extra context-specific regulator NtcB. Structural analysis showed that NtcA binding makes the promoter DNA bend by [~]50{o}, which facilitates RNAP to contact NtcB at the distal upstream NtcB box. The sequential binding of NtcA and NtcB induces looping back of promoter DNA towards RNAP, enabling the assembly of a fully activated TAC bound with two activators. Together with biochemical assays, we propose a DNA looping mechanism of cooperative transcription activation in bacteria.

molecular biology↗

bioRxiv2022

Gene Regulatory Network Reconfiguration in Direct Lineage Reprogramming

In direct lineage reprogramming, transcription factor (TF) overexpression reconfigures Gene Regulatory Networks (GRNs) to convert cell identities between fully differentiated cell types. We previously developed CellOracle, a computational pipeline that integrates single-cell transcriptome and epigenome profiles to infer GRNs. CellOracle leverages these inferred GRNs to simulate gene expression changes in response to TF perturbation, enabling network re-configuration during reprogramming to be interrogated in silico. Here, we integrate CellOracle analysis with lineage tracing of fibroblast to induced endoderm progenitor (iEP) conversion, a prototypical direct lineage reprogramming paradigm. By linking early network state to reprogramming success or failure, we reveal distinct network configurations underlying different reprogramming outcomes. Using these network analyses and in silico simulation of TF perturbation, we identify new factors to coax cells into successfully converting cell identity, uncovering a central role for the AP-1 subunit Fos with the Hippo signaling effector, Yap1. Together, these results demonstrate the efficacy of CellOracle to infer and interpret cell-type-specific GRN configurations at high resolution, providing new mechanistic insights into the regulation and reprogramming of cell identity.

genomics↗

bioRxiv2022

In situ architecture and membrane fusion of SARS-CoV-2 Delta variant

Among the current five Variants of Concern, infections caused by the SARS-CoV-2 B.1.617.2 (Delta) variant are often associated with the greatest severity. Despite recent advances on the molecular basis of elevated pathogenicity using recombinant proteins, architecture of intact Delta virions remains veiled. Moreover, molecular evidences for the detailed mechanism of S-mediated membrane fusion are missing. Here we reported the in situ structure and distribution of S on the authentic Delta variant, and discovered invagination in the distinctive Delta architecture. We also captured fusion snapshots from the virus-virus fusion events, provided structural evidences for Deltas attenuated dependency on cellular factors for fusion activation, and proposed a model of S-mediated membrane fusion. Site-specific glycan analysis revealed increased oligomannose-type glycosylation of native Delta S over that of the Wuhan-Hu-1 S. Together, these results disclose distinctive factors of Delta being the most virulent SARS-CoV-2 variant. In BriefCryo-ET of intact SARS-CoV-2 Delta variant revealed its distinctive architecture and captured snapshots of its membrane fusion in action.

biophysics↗

bioRxiv2022

Soil nitrogen impacts the rhizosphere microbial community owing to microbial hitchhiking

Microbial hitchhiking demonstrates that some nonmotile microbes utilize trans-species motility to traverse their environment; however, whether driving forces, such as plants and nitrogen, affect microbial hitchhiking is not clear. In our study, we explored the effects of plants and nitrogen fertilizer on Bacillus-hitchhiking by setting filter membranes and different nitrogen fertilizer concentration gradients. In the experimental treatment, we added a filter membrane to the soil to prevent hitchhiking. In the absence of plants, nitrogen alone had little influence on motile bacteria and hitchhiking. However, Bacillus contents were significantly impacted by the nitrogen concentration when the plants were rooted, leading to a great variation in cell motility function according to the functional analysis in the soil microbial community. After applying the filter membrane, there were no significant differences in Bacillus contents, microbial community structure or cell motility functional abundance, which illustrated that hitchhiking impacted the microbial community. Our analysis of co-occurrence between bulk soil motile bacteria (Bacillus) and rhizosphere bacteria also confirmed this. The correlation between bulk soil motile bacteria and the rhizosphere microbial community was strong in the groups with suitable nitrogen concentrations without filter membranes and was weak at all nitrogen levels in the no-membrane treatments. Thus, we concluded that plants and different nitrogen doses synergistically altered the soil microbiome by hitchhiking, whose effect depends on nitrogen.

microbiology↗

bioRxiv2022

HMGN5 escorts oncogenic STAT3 signaling by regulating chromatin landscape in tumorigenesis of breast cancer

Epigenetic alterations are widely linked with carcinogenesis, therefore becoming emerging therapeutic targets in the treatment of cancers, including breast cancer. HMGNs are nucleosome binding proteins, which regulate chromatin structures in a cell type- and disease-specific manner. However, the roles of HMGNs in the tumorigenesis of breast cancer are less known. In this study, we report that HMGNs are highly expressed in 3D-cultured breast cancer cells. HMGN5, a member of HMGNs, controls the proliferation, invasion and metastasis of breast cancer cells in vitro and in vivo. Clinically, HMGN5 is an unfavorable prognostic marker in patients. Mechanistically, HMGN5 is governed by active STAT3 transcriptionally and further escorts STAT3 to shape oncogenic chromatin landscape and transcriptional program. Lastly, we provide evidence that interference of HMGN5 by nanoparticle-packaged siRNA is potentially an effective approach in breast cancer treatment. Taken together, our findings reveal a novel feed-forward circuit between HMGN5 and STAT3 in promoting breast cancer tumorigenesis and suggest HMGN5 as a novel epigenetic therapeutic-target in STAT3- hyperactive breast cancer.

cancer biology↗

bioRxiv2021

Modeling of microRNA-derived disease network repurposes methotrexate for the prevention and therapy of abdominal aortic aneurysm in mice

Abdominal aortic aneurysm (AAA) is a highly lethal vascular disease characterized by permanent dilatation of the abdominal aorta. The main purpose of the current study is to search for noninvasive medical therapies for abdominal aortic aneurysm (AAA), for which there is currently no effective drug therapy. Network medicine represents a cutting-edge technology, as analysis and modeling of disease networks can provide critical clues regarding the etiology of specific diseases and which therapeutics may be effective. Here, we proposed a novel algorithm to quantify disease relations based on a large accumulated microRNA-disease association dataset and then built a disease network that covered 15 disease classes and included 304 diseases. Analysis revealed a number of patterns for these diseases; for example, diseases tended to be clustered and coherent in the network. Surprisingly, we found that AAA showed the strongest similarity with rheumatoid arthritis and systemic lupus erythematosus, both of which are autoimmune diseases, suggesting that AAA could be one type of autoimmune disease in etiology. Based on this observation, we further hypothesized that drugs for autoimmune disease could be repurposed for the prevention and therapy of AAA. Finally, animal experiments confirmed that methotrexate, a drug for autoimmune disease, was able to prevent the formation and inhibit the development of AAA.

bioinformatics↗

bioRxiv2021

Single-sample proteome enrichment enables missing protein recovery and phenotype association

Proteomic studies characterize the protein composition of complex biological samples. Despite recent developments in mass spectrometry instrumentation and computational tools, low proteome coverage remains a challenge. To address this, we present Proteome Support Vector Enrichment (PROSE), a fast, scalable, and effective pipeline for scoring protein identifications based on gene co-expression matrices. Using a simple set of observed proteins as input, PROSE gauges the relative importance of proteins in the phenotype. The resultant enrichment scores are interpretable and stable, corresponding well to the source phenotype, thus enabling reproducible recovery of missing proteins. We further demonstrate its utility via reanalysis of the Cancer Cell Line Encyclopedia (CCLE) proteomic data, with prediction of oncogenic dependencies and identification of well-defined regulatory modules. PROSE is available as a user-friendly Python module from https://github.com/bwbio/PROSE.

bioinformatics↗

bioRxiv2021

The PELOTA-HBS1 Complex Orchestrates mRNA Translation Surveillance and PDK1-mediated Plant Growth and Development

The quality control system for messenger RNA is fundamental for cellular activities in eukaryotes. To elucidate the molecular mechanism of 3-Phosphoinositide-Dependent Protein Kinase1 (PDK1), an essential regulator throughout growth and development of eukaryotes, a forward genetic approach was employed to screen for suppressors of the loss-of-function T-DNA insertional pdk1.1 pdk1.2 double mutant in Arabidopsis. Notably, the severe growth attenuation of pdk1.1 pdk1.2 is rescued by sop21 (suppressor of pdk1.1 pdk1.2) that harbours a loss-of-function mutation in PELOTA1 (PEL1). PEL1 is a homologue of mammalian PELOTA and yeast DOM34, which form a heterodimeric complex with the GTPase HBS1, responsible for ribosome rescue to assure the quality and fidelity of mRNA molecules. Genetic analysis further reveals that the dysfunction of PEL1-HBS complex fails to degrade the T-DNA-disrupted, truncated but functional PDK1 transcripts, thus rescuing pdk1.1 pdk1.2. Our studies demonstrate the functionality and identify the essential functions of a homologous PELOTA-HBS1 complex in higher plant, and provide novel insights into the mRNA quality control mechanism.

plant biology↗