Biology subjects

Hao, X.

Publications and source records attributed to Hao, X..

At least 73 records · Page 4Linked to original sources

bioRxiv2021

B.1.1.529 escapes the majority of SARS-CoV-2 neutralizing antibodies of diverse epitopes

The SARS-CoV-2 B.1.1.529 variant (Omicron) contains 15 mutations on the receptor-binding domain (RBD). How Omicron would evade RBD neutralizing antibodies (NAbs) requires immediate investigation. Here, we used high-throughput yeast display screening1,2 to determine the RBD escaping mutation profiles for 247 human anti-RBD NAbs and showed that the NAbs could be unsupervised clustered into six epitope groups (A-F), which is highly concordant with knowledge-based structural classifications3-5. Strikingly, various single mutations of Omicron could impair NAbs of different epitope groups. Specifically, NAbs in Group A-D, whose epitope overlap with ACE2-binding motif, are largely escaped by K417N, G446S, E484A, and Q493R. Group E (S309 site)6 and F (CR3022 site)7 NAbs, which often exhibit broad sarbecovirus neutralizing activity, are less affected by Omicron, but still, a subset of NAbs are escaped by G339D, N440K, and S371L. Furthermore, Omicron pseudovirus neutralization showed that single mutation tolerating NAbs could also be escaped due to multiple synergetic mutations on their epitopes. In total, over 85% of the tested NAbs are escaped by Omicron. Regarding NAb drugs, the neutralization potency of LY-CoV016/LY-CoV555, REGN10933/REGN10987, AZD1061/AZD8895, and BRII-196 were greatly reduced by Omicron, while VIR-7831 and DXP-604 still function at reduced efficacy. Together, data suggest Omicron would cause significant humoral immune evasion, while NAbs targeting the sarbecovirus conserved region remain most effective. Our results offer instructions for developing NAb drugs and vaccines against Omicron and future variants.

immunology↗

bioRxiv2021

Consistent predictors of microbial community composition across scales in grasslands reveal low context-dependency

Environmental circumstances shaping soil microbial communities have been studied extensively, but due to disparate study designs it has been difficult to resolve whether a globally consistent set of predictors exists, or context-dependency prevails. Here, we used a network of 18 grassland sites (11 sampled across regional plant productivity gradients) to examine i) if the same abiotic or biotic factors predict both large- and regional-scale patterns in bacterial and fungal community composition, and ii) if microbial community composition differs consistently with regional plant productivity (low vs high) across different sites. We found that there is high congruence between predictors of microbial community composition across spatial scales; bacteria were predominantly associated with soil properties and fungi with plant community composition. Moreover, there was a microbial community signal that clearly distinguished high and low productivity soils that was shared across worldwide distributed grasslands suggesting that microbial assemblages vary predictably depending on grassland productivity.

ecology↗

bioRxiv2021

Ameliorating Emotional Attention through Modulation of Neural Oscillations with Transcranial Alternating Current Stimulation

BackgroundNumerous clinical reports suggest that psychopathy like schizophrenia, anxiety and depressive disorder is accompanied by early attentional abnormalities in emotional information processing. In the past decade, the efficacy of transcranial alternating current stimulation (tACS) in changing emotional functioning has been repeatedly observed and has demonstrated a causal relationship between endogenous oscillations and emotional processing. However, tACS effects on emotional attention have not yet been tested. MethodsA total of 53 healthy participants were randomized to 2 groups, and they were subjected to active or sham tACS at individual alpha frequency (IAF) in the bilaterally dorsolateral prefrontal cortex (dlPFC). Participants and received this treatment for 20 min durations daily for 7 consecutive days. On days 1 and 7, electroencephalogram (EEG) recording of 8 minute resting with eyes open and closed. Responses to a facial emotion identification task were also recorded to measure alpha changes and event-related potential (ERP) alterations. ResultsOn day 7 after tACS, the active group showed a more clear elevation in alpha power at rest, especially in open state around stimulation area, compared to the sham group. ERPs revealed a significant larger P200 amplitude after active stimulation (p < 0.05), indicating attentional improvement in facial emotion processing. Additionally, a notable positive correlation (p < 0.05) between alpha power and P200 amplitude was found, providing an electrophysiological interpretation regarding the role of tACS in emotional attention modulation. In addition, the IAF-tACS showed an obvious advantage in alpha entrainment compared to an additional 10 Hz-tACS. ConclusionsThese results support a seminal outcome for the effect of IAF-tACS on emotional attention modulation, demonstrating a feasible and individual-specific therapy for neuropsychiatric disorders related to emotion processing, especially regarding oscillatory disturbances.

bioengineering↗

bioRxiv2021

IRGM/Irgm1 Aggravates Progression of Atherosclerosis by Inducing Macrophage Apoptosis

AimsAtherosclerosis underlies most cardiovascular diseases, among which acute coronary syndrome (ACS) caused by plaque rupture (PR) often leads to death. Immune-related GTPases (IRGM/Irgm1) have been extensively studied in inflammatory diseases, but their role in atherosclerosis is unclear. Determining how IRGM/Irgm1 promotes atherosclerotic plaque vulnerability will provide information for new biomarkers and/or therapeutic targets. Methods and resultsWe identified ruptured and unruptured plaques by optical coherence tomography, and found that serum IRGM was highly expressed in patients with ST-segment elevation myocardial infarction in PR. We used ApoE-/-Irgm1+/+, ApoE-/-Irgm1+/- mice and chimeric mice to establish a model of advanced atherosclerosis. The results of pathological experiments showed that Irgm1 caused plaque necrosis. The ratio of neutral lipids and cholesterol crystals increases, while the content of collagen fibers decreases, aggravating the destabilization of atherosclerotic plaques. In vitro, we used multiple approaches to confirm that Irgm1 promotes macrophage apoptosis by promoting the production of reactive oxygen species and activating the MAPK signaling pathway. ConclusionsIRGM may be a potential risk factor for PR. Mechanistic studies have shown that IRGM/Irgm1 contributes to the formation and rupture of fragile plaques. This is partly mediated by the induction of macrophage apoptosis via the MAPK signaling pathway. IRGM may offer new strategies for early treatment of ACS. Translation viewOur findings indicate that IRGM/Irgm1 contributes to formation and rupture of vulnerable plaques. It suggests that IRGM may provide a new target for the early treatment of ACS.

pathology↗

bioRxiv2020

Genome-wide imaging screen uncovers molecular determinants of arsenite-induced protein aggregation and toxicity and an important role for transcriptional and translational control

Exposure to toxic metals and metalloids such as cadmium and arsenic results in widespread misfolding and aggregation of cellular proteins. How these protein aggregates are formed in vivo, the mechanisms by which they affect cells, and how cells prevent their accumulation during environmental stress is not fully understood. To find components involved in these processes, we performed a genome-wide imaging screen and identified yeast deletion mutants with either enhanced or reduced protein aggregation levels during arsenite exposure. Mutants with reduced aggregation levels were enriched for functions related to protein biosynthesis and transcription, whilst functions related to cellular signalling, metabolism, and protein folding and degradation were overrepresented among mutants with enhanced aggregation levels. On a genome-wide scale, protein aggregation correlated with arsenite resistance and sensitivity, indicating that many of the identified factors are crucial to safeguard protein homeostasis (proteostasis) and to protect against arsenite toxicity. Dedicated follow-up experiments indicated that intracellular arsenic is a direct cause of protein aggregation and that accurate transcriptional and translational control are crucial for proteostasis during arsenite stress. Specifically, we provide evidence that global transcription affects protein aggregation levels, that loss of transcriptional control impacts proteostasis through distinct mechanisms, and that translational repression is central to control protein aggregation and cell viability. Some of the identified factors are associated with pathological conditions suggesting that arsenite-induced protein aggregation may impact disease processes. The broad network of cellular systems that impinge on proteostasis during arsenic stress provides a valuable resource and a framework for further elucidation of the mechanistic details of metalloid toxicity and pathogenesis. AUTHOR SUMMARYHuman exposure to poisonous metals is increasing in many parts of the world and chronic exposure is associated with certain protein folding-associated disorders such as Alzheimers disease and Parkinsons disease. While the toxicity of many metals is undisputed, their molecular modes of action have remained unclear. Recent studies revealed that toxic metals such as arsenic and cadmium profoundly affect the correct folding of proteins, resulting in the accumulation of toxic protein aggregates. In this study, we used high-content microscopy to identify a broad network of cellular systems that impinge on protein homeostasis and cell viability during arsenite stress. Follow-up experiments highlight the importance of accurate transcriptional and translational control for mitigating arsenite-induced protein aggregation and toxicity. Some of the identified factors are associated with pathological conditions suggesting that arsenite-induced protein aggregation may impact disease processes. The broad network of cellular systems that impinge on proteostasis during arsenic stress provides a valuable resource and a framework for further elucidation of the mechanistic details of metal toxicity and pathogenesis.

cell biology↗

bioRxiv2020

3D Adaptive Optical Nanoscopy for Thick Specimen Imaging at sub-50 nm Resolution

Understanding cellular organization demands the best possible spatial resolution in all three dimensions (3D). In fluorescence microscopy, this is achieved by 4Pi nanoscopy methods that combine the concepts of using two opposing objectives for optimal diffraction-limited 3D resolution with switching fluorescent molecules between bright and dark states to break the diffraction limit. However, optical aberrations have limited these nanoscopes to thin samples and prevented their application in thick specimens. Here, we have developed a nanoscope that, by utilizing an advanced adaptive optics strategy, achieves sub-50 nm isotropic resolution of structures such as neuronal synapses and ring canals previously inaccessible in tissue.

biophysics↗

bioRxiv2020

The bone microenvironment invigorates metastatic seeds for further dissemination

Metastasis has been considered as the terminal step of tumor progression. However, recent clinical studies suggest that many metastases are seeded from other metastases, rather than primary tumors. Thus, some metastases can further spread, but the corresponding pre-clinical models are lacking. By using several approaches including parabiosis and an evolving barcode system, we demonstrated that the bone microenvironment facilitates breast and prostate cancer cells to further metastasize and establish multi-organ secondary metastases. Importantly, dissemination from the bone microenvironment appears to be more aggressive compared to that from mammary tumors and lung metastases. We further uncovered that this metastasis-promoting effect is independent from genetic selection, as single cell-derived cancer cell populations (SCPs) exhibited enhanced metastasis capacity after being extracted from the bone microenvironment. Taken together, our work revealed a previously unappreciated effect of the bone microenvironment on metastasis evolution, and suggested a stable reprogramming process that engenders cancer cells more metastatic.

cancer biology↗

bioRxiv2020

Calcitriol, the active form of vitamin D, is a promising candidate for COVID-19 prophylaxis

COVID-19, the disease caused by SARS-CoV-2 (1), was declared a pandemic by the World Health Organization (WHO) in March 2020 (2). While awaiting a vaccine, several antivirals are being used to manage the disease with limited success (3, 4). To expand this arsenal, we screened 4 compound libraries: a United States Food and Drug Administration (FDA) approved drug library, an angiotensin converting enzyme-2 (ACE2) targeted compound library, a flavonoid compound library as well as a natural product library. Of the 121 compounds identified with activity against SARS-CoV-2, 7 were shortlisted for validation. We show for the first time that the active form of Vitamin D, calcitriol, exhibits significant potent activity against SARS-CoV-2. This finding paves the way for consideration of host-directed therapies for ring prophylaxis of contacts of SARS-CoV-2 patients.

microbiology↗

bioRxiv2020

Labeling subcellular structures in living specimens using live-cell incompatible dyes with excellent optical properties

Despite the urgent needs of imaging living specimens for cutting-edge biological research, most of the existing fluorescent labeling methods suffer from either poor optical properties or complicated operations to realize cell-permeability and specificity. Here, we introduce a method to overcome this tradeoff by incubating living cells and tissues with fluorescent dyes, no matter if they are cell-permeable or not, at particular conditions (concentration and temperature) without physical cell-penetration or chemical modifications. Based on this method, the mitochondrial labeling capability of Atto dyes, especially Atto 647N with extraordinary optical properties, together with interesting interactions between organelles is revealed. These results indicate the great potential of using dyes, which are normally considered "live-cell incompatible", to capture the morphology and dynamics of subcellular structures in living specimens.

cell biology↗

bioRxiv2020

The Coevolution of Promoters and Transcription Factors in Animal and Plant Cells

Coevolution has been acknowledged to play a significant role in driving the evolution of molecules and species. Promoters and transcription factors (TFs), especially their interactions, are key determinants for the regulation of gene expression. However, the evolutionary processes and mechanisms of promoter and TF interactions are still poorly understood. Here we conduct extensive physicochemical analyses of multi-omics sequences in 440 animal species and 223 plant species which span nearly one billion years of phylogeny. We demonstrate that promoters and TFs obey antagonistic coevolution in the animal kingdom while follow mutualistic coevolution in the plant kingdom. Furthermore, we reveal that such two coevolutionary strategies result in different evolutionary transitions of transcriptional networks in the two kingdoms. These results suggest that the two distinct coevolutionary mechanisms are likely to be major drivers of far greater genetic divergence between animals and plants, and open a new door to understanding the roles of promoters and TFs in tumor initiation and progression, and human ageing as well in molecular interactions and evolution.

evolutionary biology↗

bioRxiv2020

A newly-identified inactive starch synthase simultaneously regulates starch synthesis and carbon allocation in storage roots of cassava (Manihot esculenta Crantz)

Starch is a glucose polymer synthesized by green plants for energy storage, and is crucial for plant growth and reproduction. The biosynthesis of starch polysaccharides is mediated by members of the large starch synthase (SS) protein superfamily. Here, we showed that in cassava storage roots, soluble starch synthase II (MeSSII) plays an important role in starch biosynthesis via forming protein complexes with other starch biosynthetic enzymes by directly interacting with MeSSI, MeSBEII and MeISAII. The MeSSII-RNAi cassava lines showed increased amylose content and reduced intermediate chain of amylopectin (B1 type) biosynthesis in their storage roots, leading to altered starch physico-chemical properties. Further gel permeation chromatography analysis of starch biosynthetic enzymes between the wild type and MeSSII-RNAi lines confirmed the key rule of MeSSII in the organization of heteromeric starch synthetic protein complexes, including the MeSSII-MeSSI-MeGBSSI and MeSBEII-MeSSI-MeSSII-MeISAII-MeISAI complexes. The lack of MeSSII in cassava also reduced the binding capacity of the MeSSI, MeSBEII, MeISAI, and MeISAII to starch granules. Our results show a close coordination between granule-bound starch synthase and amylopectin biosynthetic enzymes, which implies that the processes of amylose synthesis and amylopectin synthesis are directly interrelated. These findings shed light on the key components of the starch biosynthesis machinery in root crops. One Sentence SummaryHere, by focusing on cassava SSII, we elucidated its function and the molecular mechanism by which it chaperones the starch synthase complex to regulate starch biosynthesis in cassava storage roots.

plant biology↗

bioRxiv2020

Population sequencing enhances understanding of tea plant evolution

Tea is an economically important plant characterized by a large genome size and high heterozygosity and species diversity. In this study, we assembled a 3.26 Gb high-quality chromosome-scale genome for tea using the Longjing 43 cultivar of Camellia sinensis var. sinensis. Population resequencing of 139 tea accessions from around the world was used to investigate the evolution of tea and to reveal the phylogenetic relationships among tea accessions. With the spread of tea cultivation, hybridization has increased the heterozygosity and wide-ranging gene flow among tea populations. Population genetics and transcriptomics analyses revealed that during domestication, the selection for disease resistance and flavor in C. sinensis var. sinensis populations has been stronger than that in C. sinensis var. assamica populations. The data compiled in this study provide new resources for the marker assisted breeding of tea and are a basis for further research on the genetics and evolution of tea.

genomics↗

bioRxiv2019

Single-cell whole-genome sequencing reveals mutational landscapes of DNA mismatch repair deficiency in mouse primary fibroblasts

DNA Mismatch repair (MMR) deficiency is a major cause of hereditary non-polyposis colorectal cancer, and is also associated with increased risk of several other cancers. This is generally ascribed to the role of MMR in avoiding mutations by correcting DNA replication errors. In MMR knockout mice very high frequencies of somatic mutations, up until 100-fold of background, have been reported. However, these results have been obtained using bacterial reporter transgenes, which are not representative for the genome overall, and mutational patterns of MMR deficiency remain largely unknown. To fill this knowledge gap, we performed single-cell whole-genome sequencing of lung fibroblasts of Msh2-/- and wild-type mice. We observed a 4-fold increase of somatic single nucleotide variants (SNVs) in the fibroblasts of Msh2-/- mice compared to those of wild-type mice. The SNV signature of Msh2 deficiency was found to be driven by C>T and T>C transitions. By comparing it to human cancer signatures, we not only confirmed the inferred MMR-deficiency-related etiology of several cancer signatures but also suggested that MMR deficiency is likely the cause of a cancer signature with its etiology previously unknown. We also observed a 7-fold increase of somatic small insertions and deletions (INDELs) in the Msh2-/- mice. An elevated INDEL frequency has also been found in human MMR-related cancers. INDELs and SNVs distributed differently across genomic features in the Msh2-/- and control cells, with evidence of selection pressure and repair preference. These results provide insights into the landscape of somatic mutations in normal somatic cells caused by MMR deficiency.\n\nSignificanceOur results show that MMR deficiency in the mouse is associated with a much lower elevation of somatic mutation rates than previously reported and provides the first MMR whole-genome mutational landscapes in normal somatic cells in vivo.

genomics↗

bioRxiv2019

SCCNV: a software tool for identifying copy number variation from single-cell whole-genome sequencing

BackgroundIdentification of de novo mutations from cell populations requires single-cell whole-genome sequencing (SCWGS). Although many experimental protocols of SCWGS have been developed, few computational tools are available for downstream analysis of different types of somatic mutations, including copy number variation (CNV). ResultsWe developed SCCNV, a software tool for detecting CNVs from whole genome-amplified single cells. SCCNV is a read-depth based approach with adjustment for the whole-genome amplification bias. ConclusionsWe demonstrate its performance by analyzing data collected from most of the single-cell amplification methods, including DOP-PCR, MDA, MALBAC and LIANTI. SCCNV is freely available at https://github.com/biosinodx/SCCNV.

bioinformatics↗

bioRxiv2019

Spontaneous retrotranspositions in normal tissues are rare and associated with cell-type-specific differentiation

Activation of retrotransposons and their insertions into new genomic locations, i.e., retrotranspositions (RTs), have been identified in about 50% of tumors. However, the landscape of RTs in different, normal somatic cell types in humans remains largely unknown. Using single-cell whole-genome sequencing we identified 528 RT events, including LINE-1 (L1), and Alu, in 164 single cells and clones of fibroblasts, neurons, B lymphocytes, hepatocytes and liver stem cells, of 29 healthy human subjects aged from 0 to 106 years. The frequency of RTs was found to vary from <1 on average per cell in primary fibroblasts to 7.8 per cell in hepatocytes. Somewhat surprisingly, RT frequency does not increase with age, which is in contrast to other types of spontaneous mutation. RTs were found significantly more likely to insert in or close to target genes of the Polycomb Repressive Complex 2 (PRC2), which represses most of the genes encoding developmental regulators through H3K27me3 histone modification in embryonic stem cells. Indeed, when directly comparing RT frequency between differentiated liver hepatocytes with liver stem cells, the latter were almost devoid of RTs. These results indicate that spontaneous RTs are associated with cellular differentiation and occur, possibly, as a consequence of the transient chromatin transition of differentiation-specific genes from a transcriptionally repressed to activated state during the differentiation process.

genomics↗

bioRxiv2018

Production of very-high-amylose cassava by post-transcriptional silencing of branching enzyme genes

High amylose starch, a desired raw material in the starch industry, can be produced by plants deficient in the function of branching enzymes (BEs). Here we report the production of transgenic cassava plants with starches containing up to 50% amylose due to the constitutive expression of hair-pin dsRNAs targeting the BE1 or BE2 genes. A significant decrease in BE transcripts was confirmed in these transgenic plants by quantitative real-time RT-PCR. The absence of BE1 protein in the BE1-RNAi plant lines (BE1i) and a dramatically lower level of BE2 protein in the BE2-RNAi plant lines (BE2i) were further confirmed by Western blot assays. All transgenic plant lines were grown up in the field, but with reduced biomass production of the above-ground parts and storage roots compared to wild type (WT). Considerably high amylose content in the storage roots of BE2i plant lines was achieved, though not in BE1i plant lines. Storage starch granules of BE1i and BE2i plants had similar morphology as WT, however, the size of BE1i starch granules were bigger than that of WT. Comparisons of amylograms and thermograms of all three sources of storage starches revealed dramatic changes to the pasting properties and a higher melting temperature for BE2i starches. Glucan chain length distribution analysis showed a slight increase in chains of DP>36 in BE1i lines and a dramatic increase in glucan chains between DP 10-20 and DP>40 in BE2i lines, compared to that of WT starch. Furthermore, BE2i starches displayed a B-type X-ray diffraction pattern instead of the A-type pattern found in BE1i and WT starches. Therefore, cassava BE1 and BE2 function differently in storage root starch biosynthesis; silencing of cassava BE1 or BE2 caused various changes to starch physico-chemical properties and amylopectin structure. We also report that remarkably high amylose content in cassava starch has been first obtained in transgenic cassava by silencing of BE2 expression, thus showing a high potential for future industrial utilization.

bioengineering↗

bioRxiv2018

The functional genomic circuitry of human glioblastoma stem cells

SummarySuccessful glioblastoma (GBM) therapies have remained elusive due to limitations in understanding mechanisms of growth and survival of the tumorigenic population. Using CRISPR-Cas9 approaches in patient-derived GBM stem cells to interrogate function of the coding genome, we identify diverse actionable pathways responsible for growth that reveal the gene-essential circuitry of GBM stemness. In particular, we describe the Sox developmental transcription factor family; H3K79 methylation by DOT1L; and ufmylation stress responsiveness programs as essential for GBM stemness. Additionally, we find mechanisms of temozolomide resistance and sensitivity that could lead to combination strategies with this standard of care treatment. By reaching beyond static genome analysis of bulk tumors, with a genome wide functional approach, we dive deep into a broad range of biological processes to provide new understanding of GBM growth and treatment resistance.\n\nSignificanceGlioblastoma (GBM) remains an incurable disease despite an increasingly thorough depth of knowledge of the genomic and epigenomic alterations of bulk tumors. Evidence from multiple approaches support that GBM reflects an aberrant developmental hierarchy, with GBM stem cells (GSCs), fueling tumor growth and invasion. The properties of this tumor subpopulation may also in part explain treatment resistance and disease recurrence. Unfortunately, we still have a limited knowledge of the molecular circuitry of these cells and progress has been slow as we have not been able, until recently, to interrogate function at the genome-wide scale. Here, using parallel genome-wide CRISPR-Cas9 screens, we identify the essential genes for GSC growth. Further, by screening in the presence of low and high dose temozolomide, we identify mechanisms of drug resistance and sensitivity. These functional screens in patient derived cells reveal new aspects of GBM biology and identify a diversity of actionable targets such as genes governing stem cell traits, epigenome regulation and the response to stress stimuli.

cancer biology↗

bioRxiv2018

Pleiotropic Mapping and Annotation Selection in Genome-wide Association Studies with Pe-nalized Gaussian Mixture Models

MotivationGenome-wide association studies (GWASs) have identified many genetic loci associated with complex traits. A substantial fraction of these identified loci are associated with multiple traits - a phenomena known as pleiotropy. Identification of pleiotropic associations can help characterize the genetic relationship among complex traits and can facilitate our understanding of disease etiology. Effective pleiotropic association mapping requires the development of statistical methods that can jointly model multiple traits with genome-wide SNPs together.\n\nResultsWe develop a joint modeling method, which we refer to as the integrative MApping of Pleiotropic association (iMAP). iMAP models summary statistics from GWASs, uses a multivariate Gaussian distribution to account for phenotypic correlation, simultaneously infers genome-wide SNP association pattern using mixture modeling, and has the potential to reveal causal relationship between traits. Importantly, iMAP integrates a large number of SNP functional annotations to substantially improve association mapping power, and, with a sparsity-inducing penalty, is capable of selecting informative annotations from a large, potentially noninformative set. To enable scalable inference of iMAP to association studies with hundreds of thousands of individuals and millions of SNPs, we develop an efficient expectation maximization algorithm based on an approximate penalized regression algorithm. With simulations and comparisons to existing methods, we illustrate the benefits of iMAP both in terms of high association mapping power and in terms of accurate estimation of genome-wide SNP association patterns. Finally, we apply iMAP to perform a joint analysis of 48 traits from 31 GWAS consortia together with 40 tissue-specific SNP annotations generated from the Roadmap Project. iMAP is freely available at www.xzlab.org/software.html.

bioinformatics↗