Biology subjects

Liu, H.

Publications and source records attributed to Liu, H..

At least 685 records · Page 38Linked to original sources

bioRxiv2021

Comparative analysis of single cell lung atlas of bat, cat, tiger and pangolin

Horseshoe bats (Rhinolophus sinicus) might help maintain coronaviruses severely affecting human health, such as SARS-CoV and SARS-CoV-2. It has long been suggested that bats may be more tolerant of viral infection than other mammals due to their unique immune system, but the exact mechanism remains to be fully explored. During the COVID-19 pandemic, multiple animal species were diseased by SARS-CoV-2 infection, especially in the respiratory system. Herein, single-cell transcriptomic data of the lungs of a horseshoe bat, a cat, a tiger, and a pangolin were generated. The receptor distribution of twenty-eight respiratory viruses belonging to fourteen viral families were characterized for the four species. Comparison on the immune-related transcripts further revealed limited cytokine activations in bats, which might explain the reason why bats experienced only mild diseases or even no symptoms upon virus infection. Our findings might increase our understanding of the immune background of horseshoe bats and their insensitivity to virus infections.

bioinformatics↗

bioRxiv2021

A recurring YYDRxG pattern in broadly neutralizing antibodies to a conserved site on SARS-CoV-2, variants of concern, and related viruses

Studying the antibody response to SARS-CoV-2 informs on how the human immune system can respond to antigenic variants as well as other SARS-related viruses. Here, we structurally and functionally characterized a potent human antibody ADI-62113 that also neutralizes SARS-CoV- 2 variants of concern and cross-reacts with many other sarbecoviruses. A YYDRxG motif encoded by IGHD3-22 in CDR H3 facilitates targeting to a highly conserved epitope on the SARS-CoV-2 receptor binding domain. A computational search for a YYDRxG pattern in publicly available sequences identified many antibodies with broad neutralization activity against SARS-CoV-2 variants and SARS-CoV. Thus, the YYDRxG motif represents a common convergent solution for the human humoral immune system to counteract sarbecoviruses. These findings also suggest an epitope targeting strategy to identify potent and broadly neutralizing antibodies that can aid in the design of pan-sarbecovirus vaccines and antibody therapeutics. Short SummaryDecryption of a recurrent sequence feature in anti-SARS-CoV-2 antibodies identifies how potent pan-sarbecovirus antibodies target a conserved epitope on the receptor binding domain.

immunology↗

bioRxiv2021

Models for Evaluation of Biological Age Based on Multi-omics

Aging is a complex process of systemic degeneration at multiple cellular and tissue levels that has a complex mechanism. Individuals age at different rates, and there is a high degree of aging heterogeneity. Therefore, it is inaccurate to judge an individuals degree of aging by their chronological age. We performed transcriptome-focused multi-omics analyses (including transcriptomics, DNA methylation, proteomics, cytokine and telomere analysis, and single-cell transcriptome sequencing) on 139 healthy individuals aged 23 to 88 years. We systematically analyzed linear and non-linear changes in gene expression throughout aging. Genes with similar expression trajectories were enriched in similar biological pathways, including the PI3K-AKT signaling pathway and the inflammatory response. Through DNA methylation detection, we found that the expression of the top genes correlated with age was affected by methylation in the gene promoter region. These genes had no significant correlation with the expression of downstream proteins, but they were enriched in PI3K-AKT-associated proteins. Single-cell transcriptome sequencing showed that the expression of these genes did not significantly change in different cell subtypes, which proves that the gene expression changes were caused by internal age-related cellular changes rather than cell composition changes. We designed a transcriptome age clock and a methylation age clock using a set of 787 genes. Our models can accurately predict age with a mean absolute error (MAE) of 5.203 and 3.28, respectively, which is better than previously established aging models. The accuracy of our model was further verified by the detection of telomeres, which can identify accelerated aging of individuals.

genomics↗

bioRxiv2021

Mutations in RBD of SARS-CoV-2 Omicron variant result stronger binding to human ACE2 protein

The COVID-19 pandemic caused by the SARS-CoV-2 virus has led to more than 270 million infections and 5.3 million of deaths worldwide. Several major variants of SARS-CoV-2 have emerged and posed challenges in controlling the pandemic. The recently occurred Omicron variant raised serious concerns about reducing the efficacy of vaccines and neutralization antibodies due to its vast mutations. We have modelled the complex structure of the human ACE2 protein and the receptor binding domain (RBD) of Omicron Spike protein (S-protein), and conducted atomistic molecular dynamics simulations to study the binding interactions. The analysis shows that the Omicron RBD binds more strongly to the human ACE2 protein than the original strain. The mutations at the ACE2-RBD interface enhance the tight binding by increasing hydrogen bonding interaction and enlarging buried solvent accessible surface area.

bioinformatics↗

bioRxiv2021

High performance of a GPU-accelerated variant calling tool in genome data analysis

Rapid advances in next-generation sequencing (NGS) have facilitated ultralarge population and cohort studies that utilized whole-genome sequencing (WGS) to identify DNA variants that may impact gene function. Massive sequencing data require highly efficient bioinformatics tools to complete read alignment and variant calling as the fundamental analysis. Multiple software and hardware acceleration strategies have been developed to boost the analysis speed. This study comprehensively evaluated the germline variant calling of a GPU-based acceleration tool, BaseNumber, using WGS datasets from several sources, including gold-standard samples from the Genome in a Bottle (GIAB) project and the Golden Standard of China Genome (GSCG) project, resequenced GSCG samples, and 100 in-house samples from the China Deafness Genetics Consortium (CDGC) project. Sequencing data were analyzed on the GPU server using BaseNumber, the variant calling outputs of which were compared to the reference VCF or the results generated by the Burrows-Wheeler Aligner (BWA) + Genome Analysis Toolkit (GATK) pipeline on a generic CPU server. BaseNumber demonstrated high precision (99.32%) and recall (99.86%) rates in variant calls compared to the standard reference. The variant calling outputs of the BaseNumber and GATK pipelines were very similar, with a mean F1 of 99.69%. Additionally, BaseNumber took only 23 minutes on average to analyze a 48X WGS sample, which was 215.33 times shorter than the GATK workflow. The GPU-based BaseNumber provides a highly accurate and ultrafast variant calling capability, significantly improving the WGS analysis efficiency and facilitating time-sensitive tests, such as clinical WGS genetic diagnosis, and sheds light on the GPU-based acceleration of other omics data analyses.

bioinformatics↗

bioRxiv2021

Chronic AMPK inactivation slows SHH medulloblastoma progression by inhibiting mTORC1 signaling and depleting tumor stem cell populations

We show that inactivating AMPK in vivo in a genetic model of medulloblastoma depletes tumor stem cell populations and slows tumor progression. Medulloblastoma, the most common malignant pediatric brain tumor, grows as heterogenous communities comprising diverse types of tumor and stromal cells. Previously, we showed that different populations in medulloblastomas show different sensitivities to specific targeted therapies. To determine if specific populations depend on AMPK, we analyzed mice with AMPK-inactivated medulloblastomas. We engineered mice with conditional deletion of the AMPK catalytic subunits Prkaa1 and Prkaa2 and conditional expression SmoM2, an oncogenic Smo allele that hyperactivates Sonic Hedgehog (SHH) signaling. We compared these medulloblastomas to SmoM2-driven medulloblastomas in AMPK-intact mice. AMPK-inactivation slowed tumor growth and progression, allowing longer event-free survival (EFS). scRNA-seq showed that AMPK inactivation altered cellular heterogeneity, increasing differentiation, decreasing tumor stem cell populations and reducing glio-neuronal multipotency. Surprisingly, AMPK-inactivated tumors showed decreased mTORC1 activation and Hk2 expression. Genetic Hk2 deletion in SmoM2-medulloblastomas similarly decreased stem cell populations, implicating reduced aerobic glycolysis in the tumor-suppressive effect of AMPK inactivation. Our results show that AMPK inactivation impairs tumor growth through mechanisms that disproportionately affect tumor stem cell populations that have proved refractory to conventional therapies.

cancer biology↗

bioRxiv2021

PncA from bacteria improves diet-induced NAFLD by enabling the transition from NAM to NA in mice

Nicotinamide adenine dinucleotide (NAD+) is crucial for energy metabolism, oxidative stress, DNA damage repair, longevity regulation, and several signaling processes. To date, three NAD+ synthesis pathways have been found in microbiota and hosts, but the potential relationship between gut microbiota and their hosts in regulating NAD+ homeostasis remains unknown. Here, we show that an analog of the first-line tuberculosis drug pyrazinamide (a bacterial NAD+ synthesis inhibitor) affected NAD+ levels in the intestines and liver of mice and disrupted the intestinal microecological balance. Furthermore, using microbiota expressing the pyrazinamidase/nicotinamidase (PncA) gene, which is a target of pyrazinamide, hepatic NAD+ levels were greatly increased and significantly increased compared with other NAD+ precursors, and diet-induced non-alcoholic fatty liver disease (NAFLD) in mice was improved. Overall, the PncA gene in microbiota plays an important role in regulating NAD+ synthesis in the host, thereby providing a potential target for modulating the hosts NAD+ level. HighlightsO_LIPncA inhibitors disrupt gut microbiome homeostasis and reduce host NAD+ levels but do not affect NAD+ levels in cultured cells C_LIO_LIPncA gene in microbiota affects host liver NAD metabolism C_LIO_LIPncA affects lipid metabolism-related genes and metabolites in mice with NAFLD C_LIO_LIDiet-induced NAFLD is improved by PncA overexpression in the liver of mice C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=132 SRC="FIGDIR/small/471202v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@7279aeorg.highwire.dtl.DTLVardef@192a133org.highwire.dtl.DTLVardef@195482forg.highwire.dtl.DTLVardef@1b634a2_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

The SPICA Coarse-Grained Force Field for Proteins and Peptides

A coarse-grained (CG) model for peptides and proteins was developed as an extension of the SPICA (Surface Property fItting Coarse grAined) force field (FF). The model was designed to examine membrane proteins that are fully compatible with the lipid membranes of the SPICA FF. A preliminary version of this protein model was created using thermodynamic properties, including the surface tension and density in the SPICA (formerly called SDK) FF. In this study, we improved the CG protein model to facilitate molecular dynamics (MD) simulation with a reproduction of multiple properties from both experiments and all-atom (AA) simulations. The side chain analogs reproduced the transfer free energy profiles across the lipid membrane and demonstrated reasonable dimerization free energies in water compared to those from AA-MD. A series of peptides/proteins adsorbed or penetrated into the membrane simulated by the CG-MD correctly predicted the penetration depths and tilt angles of peripheral and transmembrane peptides/proteins comparable to those in the orientation of protein in membrane (OPM) database. In addition, the dimerization free energies of several transmembrane helices within a lipid bilayer were comparable to those from experimental estimation. Application studies on a series of membrane protein assemblies, scramblases, and poliovirus capsids demonstrated a good performance of the SPICA FF.

biophysics↗

bioRxiv2021

The role of indirect effects in coevolution as mutualism transitions into antagonism

Species interactions have evolved from antagonistic to mutualistic and back several times throughout lifes history. Yet, it is unclear how changes in the type of interaction between species alter the coevolutionary dynamics of entire communities. This is a pressing matter, as transitions from mutualisms to antagonisms may be becoming more common with human-induced global change. Here, we combine network and evolutionary theory to simulate how shifts in interaction types alter the coevolution of empirical communities. We show that as mutualistic networks shift to antagonistic, selection imposed by direct partners begins to outweigh that imposed by indirect partners. This weakening of indirect effects is associated with communities losing their tight integration of traits and increasing their rate of adaptation. The above changes are more pronounced when specialist consumers are the first species to switch to antagonism. A shift in the outcome of species interactions may therefore reverberate across communities and alter the direction and speed of coevolution.

evolutionary biology↗

bioRxiv2021

Zinc finger protein Zfp335 controls early T cell development and survival through beta-selection-dependent and -independent mechanisms

T cell development in the thymus undergoes the process of differentiation, selective proliferation and survival from CD4-CD8- double negative (DN) stage to CD4+CD8+ double positive (DP) stage prior to the formation of CD4+ helper and CD8+ cytolytic T cells ready for circulation. Each developmental stage is tightly regulated by sequentially-operating molecular networks, of which only limited numbers of transcription regulators have been deciphered. Here we identified Zfp335 transcription factor as a new player in the regulatory network controlling thymocyte development. We demonstrate that Zfp335 intrinsically controls DN to DP transition, as T cell-specific deficiency in Zfp335 leads to a substantial accumulation of DN3 along with reduction of DP, CD4+ and CD8+ thymocytes. This developmental blockade at DN stage results from the impaired intracellular TCR{beta} expression as well as increased susceptibility to apoptosis in thymocytes. Transcriptomic and ChIP-seq analyses revealed a direct regulation of transcription factors Bcl6 and Rorc by Zfp335. Importantly, enhanced expression of TCR{beta} and Bcl6/Ror{gamma}T restores the developmental defect during DN3 to DN4 transition and improves thymocytes survival, respectively. These findings identify a critical role of Zfp335 in controlling T cell development by maintaining intracellular TCR{beta} expression-mediated {beta}- selection and independently activating cell survival signaling.

immunology↗

bioRxiv2021

Atypical relationships between neurofunctional features of print-sound integration and reading abilities in Chinese children with dyslexia

Conquering print-sound mappings (e.g., grapheme-phoneme correspondence rules) is vital for developing fluent reading skills. In neuroimaging research, this ability can be indexed by activation differences between audiovisual congruent against incongruent conditions in brain areas such as the left superior temporal cortex. In line with it, individuals with dyslexia have difficulty in tasks requiring print-sound processing, accompanied by a reduced neural integration. However, existing evidence is almost restricted to alphabetic languages. Whether and how multisensory processing of print and sound is impaired in Chinese dyslexia remains underexplored. In this study, we applied a passive audiovisual integration paradigm with functional magnetic resonance imaging to investigate the possible dysfunctions in processing character-sound (opaque; semantics can be automatically accessed) and pinyin-sound associations (transparent; no particular meaning can be confirmed) in Chinese dyslexic children. Unexpectedly, the dyslexic group did not show reduced neural integration compared with typically developing readers in either character or pinyin experiment. However, the results revealed atypical correlations between neural integration and different reading abilities in dyslexia. Specifically, while the neural integration in the left inferior frontal cortex in processing character-sound pairs correlated with silent reading comprehension in both children with and without dyslexia, it was associated with morphological awareness (semantic-related) in controls but with rapid naming (phonological-related) in dyslexics. This result indicates Chinese dyslexic children may not use the same grapho-semantic processing strategy as their typical peers do. As for pinyin-sound processing, while a stronger neural integration in the direction of "congruent > incongruent" in the left occipito-temporal cortex and bilateral superior temporal cortices was associated with better oral reading fluency in the control group, an opposite pattern was found in dyslexia. This finding may reflect dyslexias dysfunctional recruitment of the regions in grapho-phonological processing, which further impedes character learning. HighlightsO_LINeurofunctional correlates of print-sound integration in Chinese children with and without dyslexia are investigated. C_LIO_LIDyslexic children show atypical relationships between neural audiovisual integration and reading abilities. C_LIO_LIChinese children with dyslexia are likely to use inefficient strategies to process characters and pinyin. C_LI

neuroscience↗

bioRxiv2021

HA and M2 sequences alter the replication of 2013-16 H1 Live Attenuated Influenza Vaccine Infection in Human Nasal Epithelial Cell cultures

From 2013-2016, the H1N1 component of live, attenuated influenza vaccine (LAIV) performed very poorly in contrast to the inactivated influenza vaccine. We utilized a primary, differentiated human nasal epithelial (hNEC) culture system to assess the replication differences between isogenic LAIVs containing the HA segment from either A/Bolivia/559/2013 (rBol), which showed poor vaccine efficacy, and A/Slovenia/2903/2015 (rSlov), which had restored reasonable vaccine efficacy. While there were minimal differences in infectious virus production in Madin-Darby Canine Kidney (MDCK) cells, the rSlov LAIV showed markedly improved replication in hNEC cultures at both 32{degrees}C and 37{degrees}C, demonstrating that the HA segment alone could impact LAIV replication. The rSlov-infected hNEC cultures showed stronger production of interferon and proinflammatory chemokines which might also be contributing to the increased overall vaccine effectiveness of the rSlov LAIV through enhanced recruitment and activation of immune cells. The introduction of an M2-S86A mutation had no positive effects on H1 LAIV replication in hNEC cultures, in contrast to the increased infectious virus production seen with that mutation in an H3 LAIV. No obvious defects in viral RNA packaging were detected, suggesting the HA function may be driving the differential infectious virus production in hNEC cultures. The use of physiologically relevant temperatures and primary cell cultures demonstrated that candidate LAIVs can replicate efficiently, which is a necessary property for effective vaccines.

microbiology↗

bioRxiv2021

Landscape, complexity and regulation of a filamentous fungal transcriptome

Alternative splicing (AS) and alternative polyadenylation (APA) of pre-mRNAs contribute greatly to transcriptome complexity and gene expression regulation in higher eukaryotes. Their biological impact in filamentous fungi, however, has been poorly studied. Here we combine PacBio Isoform Sequencing and strand-specific RNA-Seq of multiple tissues together with mutant characterization to reveal the landscape, complexity and regulation of AS and APA in the filamentous plant pathogenic fungus Fusarium graminearum. We updated the reference genome and generated a comprehensive annotation comprising 51,617 transcript isoforms from 17,189 genes. Majority of the transcripts represent novel isoforms, including 2,998 undiscovered protein-coding genes. In total, 42.7% of multi-exonic genes and 64.8% of genes have AS and APA isoforms, respectively, suggesting AS and APA increase previously unrecognized transcriptome complexity in fungi. Nonsense-mediated mRNA decay factor FgUPF1 may not degrade AS transcripts with premature-stop codons but regulate ribosome biogenesis. Distal polyadenylation sites have a strong signal but proximal polyadenylation isoforms are high expressed. The core 3-end processing factors FgRNA15, FgHRP1, and FgFIP1 play important roles in promoting proximal polyadenylation site usage and also intron splicing. Genome-wide increase in the abundance of transcripts with retained introns and long 3-UTRs and downregulation of the spliceosomal and 3-end processing factors are found in older tissues and quiescent conidia, indicating that intron retention and 3-UTR lengthening may be a transcriptional signature of aging and dormancy in fungi. Overall, our study generates a comprehensive full-length transcript annotation for F. graminearum and provides new insights into the complexity and regulation of transcriptome in filamentous fungi.

genomics↗

bioRxiv2021

Applications of AlphaFold beyond Protein Structure Prediction

Predicting structures accurately for natural protein sequences by DeepMinds AlphaFold is certainly one of the greatest breakthroughs in biology in the twenty-first century. For designed or engineered sequences, which can be unstable, predicting the stabilities together with their structures is essential since unstable structures will not function properly. We found that experimentally measured stability changes of point mutations correlate poorly with the confidence scores produced by AlphaFold. However, the stability changes can be accurately predicted using features extracted from the representations learned by AlphaFold, indicating greater generalizability of AlphaFold to designed or engineered sequences than previously thought. We then used AlphaFold to validate our previously developed protein design method, ProDCoNN, that designs sequences to fold to target protein structures given only the backbone structure information of the target proteins. We showed that ProDCoNN was able to design sequences that fold to structures very close to target structures. By combining a modified ProDCoNN, AlphaFold, and sequential Monte Carlo, we designed a novel framework to estimate the designability of protein structures. The designability of a protein structure is defined as the number of sequences, which encode the protein structure, and is an indicator of the functional robustness of proteins. For the first time, we estimated the designability of a real protein structure, chain A of FLT3 ligand (PDB ID: 1ETE) with 134 residues, as 3.12{+/-}2.14E85.

bioinformatics↗

bioRxiv2021

A Potential Novel COVID-19 Vaccine With RBD-HR1/HR2 Hexamer Structure

The COVID-19 pandemic and the continued spreading of the SARS-CoV-2 variants have brought a grave public health consequence and severely devastated the global economy with recessions. Vaccination is considered as one of the most promising and efficient methods to end the COVID-19 pandemic and mitigate the disease conditions if infected. Although a few vaccines have been developed with an unprecedented speed, scientists around the world are continuing pursuing the best possible vaccines with innovations. Comparing to the expensive mRNA vaccines and attenuated/inactivated SARS-CoV-2 vaccines, recombinant protein vaccines have certain advantages, including their safety (non-virus components), potential stronger immunogenicity, broader protection, ease of scaling-up production, reduced cost, etc. In this study, we reported a novel COVID-19 vaccine generated with RBD-HR1/HR2 hexamer that was creatively fused with the RBD domain and heptad repeat 1 (HR1) or heptad repeat 2 (HR2) to form a dumbbell-shaped hexamer to target the spike S1 subunit. The novel hexamer COVID-19 vaccine induced high titers of neutralizing antibody in mouse studies (>100,000), and further experiments also showed that the vaccine also induced an alternative antibody to the HR1 region, which probably alleviated the drop of immunogenicity from the frequent mutations of SARS-CoV-2.

biochemistry↗

bioRxiv2021

Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes

Integrating single-cell transcriptomes and epigenomes across diverse cell types can link genes with the cis-regulatory elements (CREs) that control expression. Gene co-expression across cell types confounds simple correlation-based analysis and results in high false prediction rates. We developed a procedure that controls for co-expression between genes and integrates multiple molecular modalities, and used it to identify >10,000 gene-CRE pairs that contribute to gene expression programs in different cell types in the mouse brain.

bioinformatics↗

bioRxiv2021

MiR-339-3p aggravates rat vascular inflammation induced by AT1R autoantibodies by down-regulating BKα protein expression

The abnormality of large-conductance calcium-activated potassium channels (BK channels) is an important factor in inducing vascular inflammation. BK channel agonists can readily recover BK channel function and improve vascular inflammation. However, it is not clear how to improve BK dysfunction caused by downregulation of BK channel protein expression. This study found that angiotensin II-1 receptor autoantibodies (AT1-AA), which are widely present in the body of various types of cardiovascular diseases, can down-regulate the expression of BK channel protein and induce vascular inflammation. Further research found that the elevated neural precursor cells expressed developmentally downregulated 4-like (NEDD4L) protein level is involved in the down-regulation of BK channel subunit (BK) protein level by AT1-AA. Bioinformatics analysis and experiments have confirmed that miR-339-3p plays an irreplaceable role in the high expression of NEDD4L and the low expression of BK, and aggravates the vascular inflammation induced by AT1-AA. Overall, AT1-AA increased miR-339-3p expression (targeting BK via the miR-339-3p/NEDD4L axis or miR-339-3p alone), reduced BK protein expression in VSMCs, and induced vascular inflammation. The results of the study indicate that miR-339-3p may become a new target for reversing vascular inflammation in AT1-AA-positive patients.

molecular biology↗

bioRxiv2021

Kernel-based genetic association analysis for microbiome phenotypes identifies host genetic drivers of beta-diversity

Understanding human genetic influences on the gut microbiota helps elucidate the mechanisms by which genetics affects health outcomes. We propose a novel approach, the covariate-adjusted kernel RV (KRV) framework, to map genetic variants associated with microbiome beta-diversity, which focuses on overall shifts in the microbiota. The proposed KRV framework improves statistical power by capturing intrinsic structure within the genetic and microbiome data while reducing the multiple-testing burden. We apply the covariate-adjusted KRV test to the Hispanic Community Health Study/Study of Latinos in a genome-wide association analysis (first gene-level, then variant-level) for microbiome beta-diversity. We have identified an immunity-related gene, IL23R, reported in previous association studies and discovered 3 other novel genes, 2 of which are involved in immune functions or autoimmune disorders. Our findings highlight the value of the KRV as a powerful microbiome GWAS approach and support an important role of immunity-related genes in shaping the gut microbiome composition.

genomics↗