Biology subjects

Jiang, S.

Publications and source records attributed to Jiang, S..

At least 163 records · Page 9Linked to original sources

bioRxiv2022

Enhancer Reprogramming in Melanoma Immune Checkpoint Therapy Resistance

Immune checkpoint blockade (ICB) therapy has improved long-term survival for patients with advanced melanoma. However, there is critical need to identify potential biomarkers of response and actionable strategies to improve response rates. Through generation and analysis of 148 chromatin modification maps for 36 melanoma samples from patients treated with anti-PD- 1, we identified significant enrichment of active enhancer states in non-responders at baseline. Analysis of an independent cohort of 20 samples identified a set of 437 enhancers that predicted response to anti-PD-1 therapy (Area Under the Curve of 0.8417). The activated non-responder enhancers marked a group of key regulators of several pathways in melanoma cells (including c- MET, TGF{beta}, EMT and AKT) that are known to mediate resistance to ICB therapy and several checkpoint receptors in T cells. Epigenetic editing experiments implicated involvement of c-MET enhancers in the modulation of immune response. Finally, inhibition of enhancers and repression of these pathways using bromodomain inhibitors along with anti-PD-1 therapy significantly decreased melanoma tumor burden and increased T-cell infiltration. Together, these findings identify a potential enhancer-based biomarker of resistance to anti-PD-1 and suggest enhancer blockade in combination with ICB as a potential strategy to improve responses.

cancer biology↗

bioRxiv2022

Targeted degradation of microtubule-associated protein tau using an engineered nanobody-E3 ubiquitin ligase adapter fusion

Reducing the level of microtubule-associated protein tau has recently emerged as a promising therapeutic approach for a range of neurodegenerative diseases. Among the various approaches, targeted protein degradation provides a reversible means to rapidly reduce and specifically target disease-relevant forms of tau. However, in aging cells, the protein turnover activity is generally weakened, reducing the efficacy of protein degradation. A potential solution to this is to harness the nuclear proteasomal activity. The nucleus has a high proteasomal content and the degradation activity remains relatively unaffected even in aged cells. Here we show that an E3 ligase F-box domain from the nuclear protein human speckle type BTB/POZ protein (SPOP) is effective in degrading the microtubule-associated protein tau in primary mouse hippocampal neurons. Using EGFP-tagged tau and a GFP-binding nanobody fused to SPOP, we found that the native nuclear localization signal in SPOP causes nuclear sequestration of the target protein. However, degradation of the sequestered target proteins is incomplete, resulting in nuclear accumulation. Replacing the native SPOP nuclear localization signal (NLS) with variants having altered nuclear localization efficiency dramatically affects in the degree of nuclear accumulation of the target protein. Interestingly, nanobody-SPOP with no NLS was more efficient than that with a NLS in reducing overall tau level, causing an approximately 50% reduction in ectopically expressed human tau in mouse neurons. These results show the potential for harnessing the nuclear proteasomal activity for targeted tau degradation in cells and demonstrate a new modality of regulating intracellular protein degradation.

bioengineering↗

bioRxiv2022

Dissecting aneuploidy phenotypes by constructing Sc2.0 chromosome VII and SCRaMbLEing synthetic disomic yeast

Aneuploidy compromises genomic stability, often leading to embryo inviability, and is frequently associated with tumorigenesis and aging. Different aneuploid chromosome stoichiometries lead to distinct transcriptomic and phenotypic changes, making it helpful to study aneuploidy in tightly controlled genetic backgrounds. By deploying the engineered SCRaMbLE system to the newly synthesized Sc2.0 megabase chromosome VII (synVII), we constructed a synthetic disomic yeast and screened hundreds of SCRaMbLEd derivatives with diverse chromosomal rearrangements. Phenotypic characterization and multi-omics analysis revealed that fitness defects associated with aneuploidy could be restored by i) removing most of the chromosome content, or ii) modifying specific regions in the duplicated chromosome. These findings indicate that both chromosome copy number and chromosomal regions contribute to the aneuploidy-related phenotypes, and the synthetic yeast resource opens new paradigms in studying aneuploidy. In briefUse of SCRaMbLE and newly synthesized Mb-scale Sc2.0 chromosome VII enables insights into genotype/phenotype relationships associated with aneuploidy HighlightsO_LIDe novo design and synthesis of a Mb-scale synthetic yeast chromosome VII, carrying 11.8% sequence modifications and representing nearly 10% of the yeast genome. C_LIO_LIA disomic yeast (n + synVII) is constructed for dissecting the aneuploidy phenotype C_LIO_LISCRaMbLE enables systematic exploration of regions causing aneuploidy phenotypes C_LIO_LIChromosomal copy number and content both contribute to aneuploidy phenotypes C_LIO_LIA 20 Kb deletion on the right arm of synVII leads to fitness improvement linked to up-regulation of protein synthesis C_LI

synthetic biology↗

bioRxiv2022

The porcine cGAS-STING pathway exerts an unusual antiviral function independent of IFN and autophagy

The innate immune DNA sensing cGAS-STING pathway exerts strong antiviral activity through the downstream interferon (IFN) production; however, it has been recently recognized that IFN independent activity of STING also plays an important role in antiviral functions. Nevertheless, the IFN independent antiviral activity of STING is not fully understood. In this study, we showed that porcine STING (pSTING) played a critical role in anti-HSV1 and anti-VSV infections, and IFN defective mutants including pSTING pLxIS sub, S365A and {Delta}CTT all exhibited similar antiviral functions to wild type (WT) pSTING. Further, all these IFN defective pSTING mutants possessed a comparable autophagy activity relative to WT pSTING as expected. From pSTING WT, S365A and {Delta}CTT, the residues responsible for autophagy were mutated, which included L333A/R334A, Y167A/L170A and Y245A/L248A, respectively. Surprisingly, all these autophagy defective pSTING mutants still resisted from the two viral infections, demonstrating the pSTING antiviral function independent of IFN as well as autophagy. On the other hand, all the autophagy defective pSTING mutants triggered cell apoptosis, which was associated with the antiviral functions. Additionally, pSTING lost its antiviral activity in TBK1-/- and IRF3-/- porcine macrophages, indicating the involvement of TBK1 and IRF3 in other STING activity such as apoptosis. Collectively, our results revealed that STING exerts both IFN and autophagy independent antiviral activity, and also suggested that STING triggered cell apoptosis might resist from virus infections.

immunology↗

bioRxiv2022

The immunogenomic landscape of cattle

Here, we report the de novo assembly of a cattle genome using ultra-long-read nanopore sequencing in conjunction with other advanced technologies. The assembled genome contains only 145 contigs (N50 [~] 74.0 Mb). Compare to the current reference cattle genome ARS-UCD1.2, 154 gaps are closed, and 467 scaffolds are further placed in our assembly. Importantly, except two remained gaps in the T-cell receptor /{delta} (TRA/TRD) region, the gene loci of other TRs and immunoglobulins (IGs) are seamlessly assembled and exquisitely annotated. With the characterization of 258 IG genes and 626 TR genes that distributed in seven genomic loci, we illustrate the highest immune gene diversity in mammals to our knowledge. Moreover, the gene structures of major histocompatibility complex (MHC) are integrally depicted with properly phased haplotypes. Thus, our work not only reports a cattle genome with the most continuity and completeness, but also provide a comprehensive view of the complex immune- genome.

genomics↗

bioRxiv2022

Using NAMs to characterize chemical bioactivity at the transcriptomic, proteomic and phosphoproteomic levels

Omic-based technologies are of particular interest and importance for non-animal chemical hazard and risk characterization based on the premise that any apical endpoint change must be underpinned by some alterations measured at the omic levels. In this work we studied cellular responses to caffeine and coumarin by generating and integrating multi-omic data from transcriptomic, proteomic and phosphoproteomic experiments. We have shown that the methodology presented here is able to capture the complete chain of events from the first compound-induced changes at the phosphoproteome level to changes in gene expression induced by transcription factors and lastly to changes in protein abundance that further influence changes at the cellular level. In HepG2 cells we found the metabolism of lipids and general cellular stress to be dominant biological processes in response to caffeine and coumarin exposure, respectively. The phosphoproteomic changes were detected early in time, at very low concentrations and provided a fast adaptive cellular response to chemical exposure. Changes in protein abundance were found much less frequently than the transcriptomic changes and can be used, together with the transcriptomic changes, to facilitate a more complete understanding of pathway responses to chemical exposure. GRAPHIC ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=169 SRC="FIGDIR/small/492410v1_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@1e348c8org.highwire.dtl.DTLVardef@bf50c5org.highwire.dtl.DTLVardef@4fea36org.highwire.dtl.DTLVardef@998cb8_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2022

Cardiac patch treatment alleviates ischemic cardiomyopathy correlated with reverting Piezo1/2 expression by unloading left ventricular myocardium

Pathologically elevated mechanical load promotes the adverse remodeling of left ventricle (LV) post myocardial infarction, which results in the progression from ischemic cardiomyopathy to heart failure. Cardiac patches could attenuate adverse LV remodeling by providing mechanical support to infarcted myocardium and border zone tissue. However, the mechanism of the translation from mechanical effects to favorable therapeutic outcome is still not clear. By transcriptome analysis, we found that the myocardial transcription levels of mechanosensitive ion channel proteins Piezo1 and Piezo2 significantly increased in patients with ischemic cardiomyopathy. In vitro tensile tests with local tissue information revealed a significant decrease in local strain and mechanical load in rat infarct. Cardiac function and geometry were preserved compared to non-treated control. Further, in LV myocardium of the patch-treated group, MI induced expression levels of Piezo1/2 were significantly reverted to the similar levels of the Sham group, indicating that cardiac patch beneficial effects were correlated with suppressing mechanosensitive genes, particularly Piezo1/2. These findings demonstrated the potential of cardiac patches in treating ICM patients with remodeling risks, and could provide guidance for improvement in next generation of patch devices.

pathology↗

bioRxiv2022

Genome-wide identification of SINA gene family in sugarcane and functional analysis of SsSINA1a in drought response

Sugarcane (Saccharum spp. hybrid) is a crucial sugar and energy crop that provides majority of the raw material for sugar and ethanol production globally. Drought represents one of the most critical constraints of sugarcane production in the subtropical parts of China. SEVEN IN ABSENTIA (SINA) act as an important E3 ubiquitin ligase and play a significant role in plant stress responses. However, the characteristics of the sugarcane SINA gene family have not been previously studied currently. Here, we identified 15 SsSINA in Saccharum spontaneum, 5 ShSINA in Saccharum spp. hybrid and 6 SbSINA in Sorghum bicolor based on their conserved N{square}terminal RING and C-terminal SINA domains, and these genes were distributed into three phylogenetic groups (I, {square} and {square}). Collinearity analysis showed a close genetic relationship between the SINA genes of S. spontaneum and S. bicolor. The cis-regulatory elements in the promoter regions of the SINA genes were involved in a variety of plant physiological responses. Further, we identified a SINA gene SsSINA1a that significantly induced by drought stress. Overexpression of SsSINA1a enhanced drought tolerance in Arabidopsis through reducing leaf water loss rate. These finding indicate that SsSINA1a mediates plant drought tolerance and this study provides a new potential candidate gene for sugarcane drought-resistant breeding.

molecular biology↗

bioRxiv2022

Development of a Novel Peptide Aptamer that Interacts with the eIF4E Capped-mRNA Binding Site using Peptide Epitope Linker Evolution (PELE).

Identifying new binding sites and poses that modify biological function are an important step towards drug discovery. We have identified a novel disulphide constrained peptide that interacts with the cap-binding site of eIF4E, an attractive therapeutic target that is commonly overexpressed in many cancers and plays a significant role in initiating a cancer specific protein synthesis program though binding the 5cap (7methyl-guanoisine) moiety found on mammalian mRNAs. The use of disulphide constrained peptides to explore intracellular biological targets is limited by their lack of cell permeability and the instability of the disulphide bond in the reducing environment of the cell, loss of which results in abrogation of binding. To overcome these challenges, the cap-binding site interaction motif was placed in a hypervariable loop on an VH domain, and then selections performed to select a molecule that could recapitulate the interaction of the peptide with the target of interest in a process termed Peptide Epitope Linker Evolution (PELE). A novel VH domain was identified that interacted with the eIF4E cap binding site with a nanomolar affinity and that could be intracellularly expressed in mammalian cells. Additionally, it was demonstrated to specifically modulate eIF4E function by decreasing cap-dependent translation and cyclin D1 expression, common effects of eIF4F complex disruption.

biochemistry↗

bioRxiv2022

Binocular visual experience and sleep promote visual cortex plasticity and restore binocular vision in a mouse model of amblyopia

Amblyopia arises from an altered balance of input from the two eyes to the binocular zone of primary visual cortex (bV1) during childhood, causing long-lasting visual impairment. Amblyopia is commonly treated by patching the dominant eye, however, the relative impacts of monocular vs. binocular visual experiences on restoration of bV1 function remains unclear. Moreover, while sleep has been implicated in V1 plasticity in response to vision loss, its role in recovery from amblyopia is unknown. We used monocular deprivation (MD) in juvenile mice to model amblyopia in bV1. We compared recovery of visual responses for the two eyes among bV1 regular spiking (RS, putative principal) neurons and fast-spiking (FS, putative parvalbumin-expressing [PV+]) interneurons after identical-duration, identical-quality binocular recovery (BR) or monocular, reverse occlusion (RO) experiences. We find that BR is quantitatively superior to RO with respect to renormalizing both bV1 populations visual responses. However, this recovery was seen only in freely-sleeping mice; post-BR sleep deprivation prevented functional recovery. Thus, both binocular visual experience and subsequent sleep are required to optimally renormalize bV1 responses in a mouse model of amblyopia.

neuroscience↗

bioRxiv2022

Observing noncovalent interactions in experimental electron density for macromolecular systems: A novel perspective for protein-ligand interaction research

We report for the first time the use of experimental electron density (ED) in the Protein Data Bank for modeling non-covalent interactions (NCIs) for protein-ligand complexes. Our methodology is based on the reduced electron density gradient (RDG) theory describing intermolecular NCI by ED and its first derivative. We established a database called the Experimental NCI Database (ExptNCI; http://ncidatabase.stonewise.cn/#/nci) containing ED saddle points, indicating ~200,000 NCIs from over 12,000 protein-ligand complexes. We also demonstrated the use of the database for depicting amide-{pi} interactions in a protein-ligand binding system. In summary, the database provides details on experimentally observed NCIs for protein-ligand complexes and can support future studies, including studies on rarely documented NCIs and the development of artificial intelligent models for protein-ligand binding prediction.

biochemistry↗

bioRxiv2022

Metagenomics revealing molecular profiling of microbial community structure and metabolic capacity in Bamucuo, Tibet

We performed a survey of the microorganisms in Bamucuo, Tibet, resulting in 160,212 (soil) and 135,994 (water) contigs by shotgun metagenomic methods. We discovered 74 new bacterial species and reconstructed their draft genomes, which were obtained from the 75 reconstructed almost complete metagenomic assembly genomes (MAG) in the soil and water samples. Proteobacteria and Actinobacteria were found to be the most dominant bacterial phyla, while Euryarchaeota was the most dominant archaeal phylum. To our surprise, Pandoravirus salinus was found in the soil microbial community. We concluded that the microorganisms in Bamucuo fix carbon mainly through the 3-hydroxypropionic bi-cycle pathway. IMPORTANCEThe Qinghai-Tibet Plateau (QTP) is the highest plateau in the world, and the microorganisms there play vital ecological roles in the global biogeochemical cycle; however, detailed information on the microbial communities in QTP is still lacking, especially in high altitude areas above 4500 meters. This study, for the first time, characterized the microbial community composition and metabolic capacity in QTP high-altitude areas (with an altitude of 4,555 meters), confirmed that QTP is a huge and valuable resource bank in which more new non-resistant antibiotics and many other bioactive substances could be developed. In addition, the discovery of Pandoravirus salinus in the soil provides important information for further exploring this unique microorganism, and many draft genomes and the genome annotation information obtained in this study have laid the foundation for further in-depth study of the microbial ecology in Qinghai-Tibet Plateau.

microbiology↗

bioRxiv2021

Homologous or Heterologous Booster of Inactivated Vaccine Reduces SARS-CoV-2 Omicron Variant Escape from Neutralizing Antibodies

The massive and rapid transmission of SARS-CoV-2 has led to the emergence of several viral variants of concern (VOCs), with the most recent one, B.1.1.529 (Omicron), which accumulated a large number of spike mutations, raising the specter that this newly identified variant may escape from the currently available vaccines and therapeutic antibodies. Using VSV-based pseudovirus, we found that Omicron variant is markedly resistant to neutralization of sera form convalescents or individuals vaccinated by two doses of inactivated whole-virion vaccines (BBIBP-CorV). However, a homologous inactivated vaccine booster or a heterologous booster with protein subunit vaccine (ZF2001) significantly increased neutralization titers to both WT and Omicron variant. Moreover, at day 14 post the third dose, neutralizing antibody titer reduction for Omicron was less than that for convalescents or individuals who had only two doses of the vaccine, indicating that a homologous or heterologous booster can reduce the Omicron escape from neutralizing. In addition, we tested a panel of 17 SARS-CoV-2 monoclonal antibodies (mAbs). Omicron resists 7 of 8 authorized/approved mAbs, as well as most of the other mAbs targeting distinct epitopes on RBD and NTD. Taken together, our results suggest the urgency to push forward the booster vaccination to combat the emerging SARS-CoV-2 variants.

microbiology↗

bioRxiv2021

SoyFGB v2.0: a unique access to variations of Chinese Soybean Gene Bank (CNSGB) germplasm

In Chinese National Soybean GeneBank (CNSGB), we have collected more than 30,000 soybean accessions. However, data sharing for soybean remains an especially sensitive question, and how to share the genome variations within rule frame has been bothering the soybean germplasm workers for a long time. Here we release a big data source named Soybean Functional Genomics & Breeding database (SoyFGB v2.0) (https://sfgb.rmbreeding.cn/), which embed a core collection of 2,214 soybean resequencing genome (2K-SG) from the CNSGB germplasm. This source presents a unique example which may help elucidating the following three major functions for multiple genome data mining with general interests for plant researchers. 1) On-line analysis tools are provided by the Analysis module for haplotype mining in high-throughput genotyped germplasms with different methods. 2) Variations for 2K-SG are provided in SoyFGB v2.0 by Browse module which contains two functions of SNP and InDel. Together with the Gene (SNP & InDel) function embedded in Search module, the genotypic information of 2K-SG for targeting gene / region is accessible. 3) Scaled phenotype data of 42 traits, including 9 quality and 33 quantitative traits are provided by SoyFGB v2.0. With the scaled-phenotype data search and seed request tools under a control list, the germplasm information could be shared without direct downloading the unpublished phenotypic data or information of sensitive germplasms. In a word, the mode of data mining and sharing underlies SoyFGB v2.0 may inspire more ideas for works on genome resources of not only soybean but also the other plants.

genomics↗

bioRxiv2021

Broad neutralization of SARS-CoV-2 variants by an inhalable bispecific single-domain antibody

The effectiveness of SARS-CoV-2 vaccines and therapeutic antibodies has been limited by the continuous emergence of viral variants, and by the restricted diffusion of antibodies from circulation into the sites of respiratory virus infection. Here, we report the identification of two highly conserved regions on Omicron variant RBD recognized by broadly neutralizing antibodies. Based on this finding, we generated a bispecific single-domain antibody that was able to simultaneously and synergistically bind these two regions on a single Omicron variant RBD as revealed by Cryo-EM structures. This inhalable antibody exhibited exquisite neutralization breadth and therapeutic efficacy in mouse models of SARS-CoV-2 infections. The structures also deciphered an uncommon cryptic epitope within the spike trimeric interface that may have implications for the design of broadly protective SARS-CoV-2 vaccines and therapeutics.

immunology↗

bioRxiv2021

OptDesign: Identifying Optimum Design Strategies in Strain Engineering for Biochemical Production

Computational tools have been widely adopted for strain optimisation in metabolic engineering, contributing to numerous success stories of producing industrially relevant biochemicals. However, most of these tools focus on single metabolic intervention strategies (either gene/reaction knockout or amplification alone) and rely on hypothetical optimality principles (e.g., maximisation of growth) and precise gene expression (e.g., fold changes) for phenotype prediction. This paper introduces OptDesign, a new two-step strain design strategy. In the first step, OptDesign selects regulation candidates that have a noticeable flux difference between the wild type and production strains. In the second step, it computes optimal design strategies with limited manipulations (combining regulation and knockout) leading to high biochemical production. The usefulness and capabilities of OptDesign are demonstrated for the production of three biochemicals in E. coli using the latest genome-scale metabolic model iML1515, showing highly consistent results with previous studies while suggesting new manipulations to boost strain performance. Source code is available at https://github.com/chang88ye/OptDesign.

bioinformatics↗

bioRxiv2021

Robust Single-cell Matching and Multi-modalAnalysis Using Shared and Distinct FeaturesReveals Orchestrated Immune Responses

The ability to align individual cellular information from multiple experimental sources, techniques and systems is fundamental for a true systems-level understanding of biological processes. While single-cell transcriptomic studies have transformed our appreciation for the complexities and contributions of diverse cell types to disease, they can be limited in their ability to assess protein-level phenotypic information and beyond. Therefore, matching and integrating single-cell datasets which utilize robust protein measurements across multiple modalities is critical for a deeper understanding of cell states, and signaling pathways particularly within their native tissue context. Current available tools are mainly designed for single-cell transcriptomics matching and integration, and generally rely upon a large number of shared features across datasets for mutual Nearest Neighbor (mNN) matching. This approach is unsuitable when applied to single-cell proteomic datasets, due to the limited number of parameters simultaneously accessed, and lack of shared markers across these experiments. Here, we introduce a novel cell matching algorithm, Matching with pARtIal Overlap (MARIO), that takes into account both shared and distinct features, while consisting of vital filtering steps to avoid sub-optimal matching. MARIO accurately matches and integrates data from different single-cell proteomic and multi-modal methods, including spatial techniques, and has cross-species capabilities. MARIO robustly matched tissue macrophages identified from COVID-19 lung autopsies via CODEX imaging to macrophages recovered from COVID-19 bronchoalveolar lavage fluid via CITE-seq. This cross-platform integrative analysis enabled the identification of unique orchestrated immune responses within the lung of complement-expressing macrophages and their impact on the local tissue microenvironment. MARIO thus provides an analytical framework for unified analysis of single-cell data for a comprehensive understanding of the underlying biological system.

bioinformatics↗

bioRxiv2021

Identification of a promiscuous conserved CTL epitope within the SARS-CoV-2 spike protein

The COVID-19 disease caused by infection with SARS-CoV-2 and its variants is devastating to the global public health and economy. To date, over a hundred COVID-19 vaccines are known to be under development and the few that have been approved to fight the disease are using the spike protein as the primary target antigen. Although virus neutralizing epitopes are mainly located within the RBD of the spike protein, the presence of T cell epitopes, particularly the CTL epitopes that are likely to be needed for killing infected cells, has received comparatively little attention. In this study, we predicted several potential T cell epitopes with web-based analytic tools, and narrowed them down from several potential MHC-I and MHC-II epitopes by ELIspot and cytolytic assays to a conserved MHC-I epitope. The epitope is highly conserved in current viral variants including the most recent Omicron and compatible with presentation by most HLA alleles worldwide. In conclusion, we identified a CTL epitope suitable for evaluating the CD8+ T cell-mediated cellular response and potentially for addition into future COVID-19 vaccine candidates to maximize CTL responses against SARS-CoV-2.

immunology↗