Biology subjects

Song, W.

Publications and source records attributed to Song, W..

At least 73 records · Page 4Linked to original sources

bioRxiv2024

Non-Invasive dsRNA Delivery via Feeding for Effective Gene Silencing in Teleost Fish: A Novel Approach in the Study of Gene Function Analysis

RNA interference is a powerful technique for gene silencing, involving post-transcriptional regulation of gene expression. Successful application of RNAi has been demonstrated in various organisms like nematodes, insects, and oysters by ingesting dsRNA-expressing bacteria. In this study, we attempted a non-invasive feeding method in the marine economy teleost fish, Sebastes schlegelii. To validate the feasibility of this approach in S. schlegelii, we utilized rotifers (Brachionus plicatilis), Artemia nauplii, and commercial pellet feed as vectors to deliver Escherichia coli strain HT115 engineered to express double-stranded RNA (dsRNA), targeting dead end (dnd) gene, known to be important for primordial germ cells (PGCs) migration and proliferation in fish. Our experimental results consistently showed that knockdown of the dnd gene effectively inhibited the development of PGCs in S. schlegelii, resulting in gonadal dysplasia and even sex reversal. This study marks a significant advancement in understanding gene function in teleost fish, laying the groundwork for future large-scale research in this field.

genetics↗

bioRxiv2023

EMO: Predicting Non-coding Mutation-induced Up- and Down-regulation of Risk Gene Expression using Deep Learning

The challenge of understanding how alterations in non-coding DNA regulate gene expression is substantial, with far-reaching consequences for the advancement of human genetics and disease research. Accurately predicting the up- and down-regulation of gene expression quantitative trait loci (eQTLs) offers a potential avenue to accelerate the identification of associations between non-coding variants and phenotypic traits. However, current methods for predicting the impact of non-coding mutations on gene expression changes fail to predict the sign of eQTLs accurately. Additionally, the requirement for tissue-specific training models within these methods restricts their applicability, especially when extending predictive abilities to single-cell resolution. In this study, we present EMO, an innovative transformer-based pre-trained method, designed to predict the up- and down-regulation of gene expression caused by single non-coding mutations using DNA sequences and ATAC-seq data. EMO extends the effective prediction range up to 1Mbp between the non-coding mutation and the transcription start site (TSS) of the target gene. It demonstrates competitive prediction performance across various variant TSS distances and surpasses the state-of-the-art structure. To assess its effectiveness, EMO was fine-tuned using eQTLs from two brain tissues for external validation. We also evaluated EMOs transferability to single-cell resolution by fine-tuning it on eQTLs from six types of immune cells, achieving satisfactory results in each cell type (AUC > 0.860). Furthermore, EMO displayed promising potential in analyzing disease-associated eQTLs.

bioinformatics↗

bioRxiv2023

Spatial and temporal profiling of the complement system uncovered novel functions of the alternative complement pathway in brain development

Mounting evidence implicated the classical complement pathway (CP) in normal brain development, and the pathogenesis of neuropsychiatric and neurodegenerative diseases. However the source and regulation of complement in the brain remain unclear. Using MERFISH, a spatial transcriptomic method with single-cell resolution, we established a developmental brain atlas of the complement system. We showed that the brain synthesizes essential building blocks of the complement system locally with remarkable cellular and spatial heterogeneity. We provided transcriptional evidence supporting the presence of the alternative pathway (AP), but lack of lectin pathway (LP) activity in postnatal brain development. Cell type, temporal and spatial expression patterns of genes involved indicate non-redundant functions of the CP and AP. In addition, deficiency in Masp3-driven AP resulted in developmental and cognitive defects, indicating essential functions of the AP, an observation that highlights the necessity to disentangle differential involvement of the three complement activation pathways in development and diseases.

neuroscience↗

bioRxiv2023

Fast evolution of SARS-CoV-2 BA.2.86 to JN.1 under heavy immune pressure

While the BA.2.86 variant demonstrated significant antigenic drift and enhanced ACE2 binding affinity, its ability to evade humoral immunity was relatively moderate compared to dominant strains like EG.5 and HK.3. However, the emergence of a new subvariant, JN.1 (BA.2.86.1.1), which possesses an additional spike mutation, L455S, compared to BA.2.86, showed a markedly increased prevalence in Europe and North America, especially in France. Here, we found that L455S of JN.1 significantly enhances immune evasion capabilities at the expense of reduced ACE2 binding affinity. This mutation enables JN.1 to effectively evade Class 1 neutralizing antibodies, offsetting BA.2.86s susceptibility and thus allowing it to outcompete both its precursor BA.2.86 and the prevailing variants HV.1 (XBB.1.5+L452R+F456L) and JD.1.1 (XBB.1.5+L455F+F456L+A475V) in terms of humoral immune evasion. The rapid evolution from BA.2.86 to JN.1, similar to the earlier transition from BA.2.75 to CH.1.1, highlights the importance of closely monitoring strains with high ACE2 binding affinity and distinct antigenicity, despite their temporarily unremarkable immune evasion capabilities. Such strains could survive and transmit at low levels, since their large antigenic distance to dominant strains allow them to target distinct populations and accumulate immune-evasive mutations rapidly, often at the cost of receptor binding affinity.

immunology↗

bioRxiv2023

Single-cell bisulfite-free 5mC and 5hmC sequencing with high sensitivity and scalability

Existing single cell bisulfite-based DNA methylation analysis is limited by low DNA recovery, and the measurement of 5hmC at single-base resolution remains challenging. Here we present a bisulfite-free single-cell whole-genome 5mC and 5hmC profiling technique, named Cabernet, which can characterize 5mC and 5hmC at single-base resolution with high genomic coverage. Cabernet utilizes Tn5 transposome for DNA fragmentation, which enables the discrimination between different alleles for measuring hemi-methylation status. Using Cabernet, we revealed the 5mC, hemi-5mC and 5hmC dynamics during early mouse embryo development, uncovering genomic regions exclusively governed by active or passive demethylation. We show that hemi-methylation status can be used to distinguish between pre- and post-replication cells, enabling more efficient cell grouping when integrated with 5mC profile. The property of Tn5 naturally enables Cabernet to achieve high-throughput single-cell methylome profiling, where we probed mouse cortical neurons and embryonic day 7.5 (E7.5) embryos, and constructed the library for thousands of single cells at high efficiency, demonstrating its potential for analyzing complex tissues at substantially low cost. Together, we present a new way of high-throughput methylome and hydroxymethylome detection at single-cell resolution, enabling efficient analysis of epigenetic status of biological systems with complicated nature such as neurons and cancer cells. Significance StatementMost of current methylation profiling techniques rely on bisulfite treatment, which suffers low DNA recovery. The technique proposed in this study, named Cabernet, can be used to measure 5mC and 5hmC at single-base resolution with high genomic coverage. By using Tn5 transposome, hemi-methylation status can be measured and high-throughput methylome profiling can be achieved. Together, it provides an efficient way to analyze the epigenetic landscape of complicated biological systems.

genomics↗

bioRxiv2023

Guided Diffusion for molecular generation with interaction prompt

Molecular generative models have demonstrated their potential in designing molecules from scratch with high binding affinities in a pre-determined protein pocket and could be combined with traditional structural based drug design strategy. However, the generative processes of such models are random and the atomic interaction information between ligand and protein are ignored. On the other hand, the ligand has high propensity to bind with residues called hotspots. Hotspot residues contribute to the majority of the binding free energies and have been recognized as appealing targets for designed molecules. In this work, we develop an interaction prompt guided diffusion model-InterDiff to deal with the challenges. Four kinds of atomic interactions are involved in our model and represented as learnable vector embeddings. These embeddings serve as conditions for each residue to guide the molecular generative process. Comprehensive in-silico experiments evince that our model could generate molecules with desired ligand-protein interactions in a guidable way. Furthermore, we validate InterDiff on two realistic protein-based therapeutic agents. Results show that InterDiff could generate molecules with better or similar binding mode compared to known targeted drugs.

bioinformatics↗

bioRxiv2023

Antigenicity and infectivity characterization of SARS-CoV-2 BA.2.86

The recently identified SARS-CoV-2 variant, BA.2.86, which carries a substantial number of Spike mutations, has raised a global alarm. An immediate assessment of its antigenic properties and infectivity is necessary. Here, we reveal the distinct antigenicity of BA.2.86 compared with previous variants including XBB.1.5. BA.2.86 significantly evades convalescent plasma from XBB breakthrough infection (BTI) and reinfections. Key mutations that mediate the enhanced resistance include N450D, K356T, L452W, A484K, V483del, and V445H on the RBD, while BA.2.86s NTD mutations and E554K on SD1 also largely contribute. However, we found that BA.2.86 pseudovirus exhibits compromised efficiency of infecting HEK293T-hACE2 cells compared to XBB.1.5 and EG.5, which may be caused by K356T, V483del, and E554K, and could potentially limit BA.2.86s transmissibility. In sum, it appears that BA.2.86 has traded its infectivity for higher immune evasion during long-term host-viral evolution. Close attention should be paid to monitoring additional mutations that could improve BA.2.86s infectivity.

immunology↗

bioRxiv2023

Convergent evolution of SARS-CoV-2 XBB lineages on receptor-binding domain 455-456 enhances antibody evasion and ACE2 binding

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) XBB lineages have achieved dominance worldwide and keep on evolving. Convergent evolution of XBB lineages on the receptor-binding domain (RBD) L455F and F456L is observed, resulting in variants like EG.5, FL.1.5.1, XBB.1.5.70, and HK.3. Here, we show that neutralizing antibody (NAb) evasion drives the convergent evolution of F456L, while the epistatic shift caused by F456L enables the subsequent convergence of L455F through ACE2 binding enhancement and further immune evasion. L455F and F456L evade Class 1 NAbs, reducing the neutralization efficacy of XBB breakthrough infection (BTI) and reinfection convalescent plasma. Importantly, L455F single substitution significantly dampens receptor binding; however, the combination of L455F and F456L forms an adjacent residue flipping, which leads to enhanced NAbs resistance and ACE2 binding affinity. The perturbed receptor-binding mode leads to the exceptional ACE2 binding and NAb evasion, as revealed by structural analyses. Our results indicate the evolution flexibility contributed by epistasis cannot be underestimated, and the evolution potential of SARS-CoV-2 RBD remains high.

immunology↗

bioRxiv2023

Haplotype Function Score improves biological interpretation and cross-ancestry polygenic prediction of human complex traits

We propose a new framework for human genetic association studies: at each locus, a deep learning model (in this study, Sei) is used to calculate the functional genomic activity score for two haplotypes per individual. This score, defined as the Haplotype Function Score (HFS), replaces the original genotype in association studies. Applying the HFS framework to 14 complex traits in the UK Biobank, we identified 3,619 independent HFS-trait associations with a significance of p<5x10-8. Fine-mapping revealed 2,699 causal associations, corresponding to a median increase of 63 causal findings per trait compared with SNP-based analysis. HFS-based enrichment analysis uncovered 727 pathway-trait associations and 153 tissue-trait associations with strong biological interpretability, including "circadian pathway-chronotype" and "arachidonic acid-intelligence". Lastly, we applied LASSO regression to integrate HFS prediction score with SNP-based polygenic risk scores, which showed an improvement of 16.1% to 39.8% in cross-ancestry polygenic prediction. We concluded that HFS is a promising strategy for understanding the genetic basis of human complex traits.

genetics↗

bioRxiv2023

Large-scale lensless microscopy with fast acquisition and region-wise focusing

The imaging field of view (FOV) of lensless microscope is consistent with the size of image sensor in use, enabling the observation of sample areas larger than 20 mm2. Combined with high-performance and even super-resolution phase retrieval algorithms, micron and sub-micron resolution can be achieved, ultimately realizing wide-field and high-resolution imaging performance simultaneously. However, high-throughput lensless imaging poses significant challenges in terms of rapid data acquisition and large-scale phase retrieval. Additionally, when observing biological samples over a large FOV, the focus plane often exhibits inconsistency among different regions, necessitating further parameter calibration. In this study, we propose a fast acquisition and efficient reconstruction strategy for coherent lensless imaging based on a multi-height imaging model. Multiple measurements are manually modulated using an axial translation stage and continuously captured by an image sensor, facilitating rapid data acquisition within seconds and requiring no hardware synchronization. The efficiency and accuracy of phase retrieval are enhanced through precise parameter calibration algorithms, as well as techniques such as region-wise parallel computing and region-wise auto-focusing. Experimental results demonstrate 7.4x5.5 mm2 FOV and 1.55 m half-pitch resolution imaging of human skin and lung tumor sections with region-wise focusing, requiring only an approximate 0.5-s acquisition time and 44-s reconstruction time. Furthermore, by incorporating the pixel super-resolution principle, the 1.10 m half-pitch imaging resolution is demonstrated in full-FOV peripheral blood smears without additional data required, beneficial to the identification of hollow shape and segmentation of blood cells.

bioengineering↗

bioRxiv2023

KoNA: Korean Nucleotide Archive as a New Data Repository for Nucleotide Sequence Data

During the last decade, generation and accumulation of petabase-scale high-throughput sequencing data have resulted in ethical and technical challenges, including access to human data, and transfer, storage, and sharing of enormous amount of data. To promote data-driven research in biology, the Korean government announced that all the biological data generated from government-funded research projects should be deposited in the Korea BioData Station (K-BDS), which consists of multiple databases for individual data types. We introduce the Korean Nucleotide Archive (KoNA), a repository for nucleotide sequence data. As of July 2022, the Korean Read Archive in KoNA has collected over 477 TB of raw next generation sequencing data from several national genome projects. To ensure data quality and prepare for international alignment, a standard operating procedure (SOP) was adopted, which is similar to the International Nucleotide Sequence Database Collaboration. The SOP includes quality control processes for submitted data and metadata using an automated pipeline followed by manual examination. To ensure fast and stable data transfer, a high-speed transmission system called GBox is used in KoNA. Furthermore, the data uploaded to or downloaded from KoNA through GBox can be readily processed in a cloud-computing service for genomic data analysis called Bio-Express. This seamless coupling of KoNA, GBox, and Bio-Express enhances data experience including submission, access, and analysis of raw nucleotide sequences. KoNA not only satisfies the unmet needs for a national sequence repository in Korea, but also provides datasets to researchers globally and contribute to advances in genomics. KoNA is available at https://www.kobic.re.kr/kona/.

genomics↗

bioRxiv2023

Aster-dependent non-vesicular transport facilitates dietary cholesterol uptake

Intestinal cholesterol absorption is an important contributor to systemic cholesterol homeostasis. Niemann-Pick C1 Like 1 (NPC1L1), the target of the drug ezetimibe (EZ), assists in the initial step of dietary cholesterol uptake. However, how cholesterol moves downstream of NPC1L1 is unknown. Here we show that Aster-B and Aster-C are critical for non-vesicular cholesterol movement in enterocytes, bridging NPC1L1 at the plasma membrane (PM) and ACAT2 in the endoplasmic reticulum (ER). Loss of NPC1L1 diminishes accessible PM cholesterol in enterocytes and abolishes Aster recruitment to the intestinal brush border. Enterocytes lacking Asters accumulate cholesterol at the PM and display evidence of ER cholesterol depletion, including decreased cholesterol ester stores and activation of the SREBP-2 transcriptional pathway. Aster-deficient mice have impaired cholesterol absorption and are protected against diet-induced hypercholesterolemia. Finally, we show that the Aster pathway can be targeted with a small molecule inhibitor to manipulate dietary cholesterol uptake. These findings identify the Aster pathway as a physiologically important and pharmacologically tractable node in dietary lipid absorption. One-Sentence SummaryIdentification of a targetable pathway for regulation of dietary cholesterol absorption

physiology↗

bioRxiv2023

Detection of new pioneer transcription factors as cell-type specific nucleosome binders

Wrapping of DNA into nucleosomes restricts accessibility to the DNA and may affect the recognition of binding motifs by transcription factors. A certain class of transcription factors, the pioneer transcription factors, can specifically recognize their DNA binding sites on nucleosomes, may initiate local chromatin opening and facilitate the binding of co-factors in a cell-type-specific manner. For the majority of human pioneer transcription factors, the locations of their binding sites, mechanisms of binding and regulation remain unknown. We have developed a computational method to predict the cell-type-specific ability of transcription factors to bind nucleosomes by integrating ChIP-seq, MNase-seq and DNase-seq data with details of nucleosome structure. We have demonstrated the ability of our approach in discriminating pioneer from canonical transcription factors and predicted new potential pioneer transcription factors in H1, K562, HepG2 and HeLa cell lines. Lastly, we systemically analyzed the interaction modes between various pioneer transcription factors and detected several clusters of distinctive binding sites on nucleosomal DNA.

bioinformatics↗

bioRxiv2023

Genetic basis of expression and splicing underlying spike architecture in wheat (Triticum aestivum L.)

IntroductionWheat is one of the most important staple crops worldwide, and an important source of human protein and mineral element intake. Continuously increasing stable production of wheat is critical for global food security under the challenge of population growth and limited resource input. ObjectiveSpike architecture determines the potential grain yield of wheat. However, the mechanisms of transcriptional regulation of spike architecture in wheat remain largely unknown, limiting further genetic improvement of wheat yield. In this study we explored the genetic basis of spike architecture in wheat. MethodsPopulation RNA-seq methods were used to identify the eQTLs and sQTLs associated with spike architecture and applied this to dissection of the genetic basis of gene expression and splicing controlling these complex yield-related traits. ResultsIn total, 4,143 expression quantitative trait loci (eQTLs) and 12,933 splice QTLs (sQTLs) were identified in wheat based on 178 RNA-seq samples, revealing 774 cis-eQTLs and 321 cis-sQTLs for 86 eGenes and 73 sGenes, respectively. Integration of eQTLs and sQTLs with genome-wide association study (GWAS) identified dozens of additional novel candidate genes that may contribute to spike-related traits. Gene network analysis showed that eQTLs and sQTLs were widely involved in the co-expression modules that regulate wheat spike architecture. Notably, the eQTL locus AX-108754757 regulated the expression of 5 eGenes that negatively controled grain number per spike. AX-111592099 regulated both the splicing and expression of TraesCS7B02G442100, encoding an E3 ubiquitin ligase, and playing a central role in regulating spike length. ConclusionThis study provides new insights into the genetic basis of spike architecture. This improved understanding of spike-related traits in wheat will contribute to more rapid genetic improvement.

plant biology↗

bioRxiv2023

Repeated Omicron infection alleviates SARS-CoV-2 immune imprinting

The continuous emergence of highly immune evasive SARS-CoV-2 variants, like XBB.1.51,2 and XBB.1.163,4, highlights the need to update COVID-19 vaccine compositions. However, immune imprinting induced by wildtype (WT)-based vaccination would compromise the antibody response to Omicron-based boosters5-9. Vaccination strategies that can counter immune imprinting are critically needed. In this study, we investigated the degree and dynamics of immune imprinting in mouse models and human cohorts, especially focusing on the role of repeated Omicron stimulation. Our results show that in mice, the efficacy of single Omicron-boosting is heavily limited by immune imprinting, especially when using variants antigenically distinct from WT, like XBB, while the concerning situation could be largely mitigated by a second Omicron booster. Similarly, in humans, we found that repeated Omicron infections could also alleviate WT-vaccination-induced immune imprinting and generate high neutralizing titers against XBB.1.5 and XBB.1.16 in both plasma and nasal mucosa. By isolating 781 RBD-targeting mAbs from repeated Omicron infection cohorts, we revealed that double Omicron exposure alleviates immune imprinting by generating a large proportion of highly matured and potent Omicron-specific antibodies. Importantly, epitope characterization using deep mutational scanning (DMS) showed that these Omicron-specific antibodies target distinct RBD epitopes compared to WT-induced antibodies, and the bias towards non-neutralizing epitopes observed in single Omicron exposures due to imprinting was largely restored after repeated Omicron stimulation, together leading to a substantial neutralizing epitope shift. Based on the DMS profiles, we identified evolution hotspots of XBB.1.5 RBD and demonstrated the combinations of these mutations could further boost XBB.1.5s immune-evasion capability while maintaining high ACE2 binding affinity. Our findings suggest the WT component should be abandoned when updating COVID-19 vaccine antigen compositions to XBB lineages, and those who havent been exposed to Omicron yet should receive two updated vaccine boosters.

immunology↗

bioRxiv2023

A small number of human lineage mutations regulated RNA-protein binding of conserved genes and promoted human evolution

Whether human lineage mutations (HLM) have contributed to human evolution via post-transcriptional modification remained unknown. We applied deep learning models Seqweaver to predict how HLM impacts RNA-binding protein affinity (RBP). At the threshold of the top 1% of human common variation, only 0.27% of HLM had large impacts on RBP. These HLMs enriched in a set of conserved genes that are highly expressed in adult excitatory neurons and prenatal Purkinje neurons, and involved in synapse organization and the GTPase pathway. These genes also carried excess damaging coding mutations that caused neurodevelopmental disorders, ataxia, and Schizophrenia. Among these genes, NTRK2 and ITPR1 had the most aggregated evidence of functional importance, pointing to an essential role in cognition and bipedalism. We concluded that a very small number of human-specific mutations have contributed to human speciation via impacts on post-transcriptional modification of critical brain-related genes. Author summaryPost-transcriptional modification has important functions in biological systems, but its role in evolution has long been a mystery due to the difficulty in predicting how a mutation could impact this process. Here we applied the newly developed deep learning model Seqweaver on human lineage mutations (HLM) to predict their effect on RNA-protein binding affinity profile (RBP). We found that only a very small number HLM are influential to RBP. Influential HLMs enriched in a set of conserved genes that are enriched in cells and functions critical for cognition and bipedal walking, and severe mutations on these genes cause the disruption of cognition (neurodevelopmental disorders) and bipedalism (ataxia). NTRK2 and ITPR1 had the most aggregated pieces of evidence of functional importance, pointing to an important role in cognition and bipedal walking. Taken together, our result demonstrated that there is a small number of human lineage mutations that modified the post-transcriptional modifications of conserved neuronal genes, which contributed to human speciation.

evolutionary biology↗

bioRxiv2023

Identification of RNA-Binding Protein Targets with HyperTRIBE in Saccharomyces cerevisiae

As a mater regulator in cells, RNA-binding protein (RBP) plays critical roles in organismal development, metabolism and various diseases. It controls gene expression at multiple levels mostly by specific recognition of target RNA. The traditional CLIP-seq method to detect transcriptome-wide RNA targets of RBP is less efficient in yeasts due to their cell walls. Here, we established an efficient HyperTRIBE (Targets of RNA-binding proteins Identified By Editing) in yeast, by fusing a RBP to the hyper active catalytic domain of human RNA editing enzyme ADAR2 and expressing the fusion protein in yeast cells. The target transcripts of RBP were marked with new RNA editing events and identified by high-throughput sequencing. We successfully applied TRIBE to identifying the RNA targets of two yeast RBPs, KHD1 and BFR1. The antibody-free HyperTRIBE has competitive advantages including low background, high sensitivity and reproducibility, and a simple library preparation procedure, which provides a reliable strategy for RBP target identification in Saccharomyces cerevisiae.

molecular biology↗

bioRxiv2023

N-WASP-dependent branched actin polymerization attenuates B-cell receptor signaling by increasing the molecular density of receptor clusters

Antigen-induced B-cell receptor (BCR) signaling is critical for initiating and regulating B-cell activation. The actin cytoskeleton plays essential roles in BCR signaling. Upon encountering cell-surface antigens, actin-driven B-cell spreading amplifies signaling, while B-cell contraction following spreading leads to signal attenuation. However, the mechanism by which actin dynamics switch BCR signaling from amplification to attenuation is unknown. Here, we show that Arp2/3-mediated branched actin polymerization is required for B-cell contraction. Contracting B-cells generate centripetally moving actin foci from lamellipodial F-actin networks in the B-cell plasma membrane region contacting antigen-presenting surfaces. Actin polymerization driven by N-WASP, but not WASP, initiates these actin foci and facilitates non-muscle myosin II recruitment to the contact zone, creating actomyosin ring-like structures. Furthermore, B-cell contraction increases BCR molecular density in individual clusters, leading to decreased BCR phosphorylation. Increased BCR molecular density reduced levels of the stimulatory kinase Syk, the inhibitory phosphatase SHIP-1, and their phosphorylated forms in individual BCR clusters. These results suggest that N-WASP-activated Arp2/3, coordinating with myosin, generates centripetally moving foci and contractile actomyosin ring-like structures from lamellipodial networks, enabling contraction. B-cell contraction attenuates BCR signaling by pushing out both stimulatory kinases and inhibitory phosphatases from BCR clusters, providing novel insights into actin-facilitated signal attenuation.

cell biology↗