Biology subjects

Dong, T.

Publications and source records attributed to Dong, T..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Regulatory genome annotation of 33 insect species

Annotation of newly-sequenced genomes frequently includes genes, but rarely covers important non-coding genomic features such as the cis-regulatory modules--e.g., enhancers and silencers--that regulate gene expression. Here, we begin to remedy this situation by developing a workflow for rapid initial annotation of insect regulatory sequences, and provide a searchable database resource with enhancer predictions for 33 genomes. Using our previously-developed SCRMshaw computational enhancer prediction method, we predict over 2.8 million regulatory sequences along with the tissues where they are expected to be active, in a set of insect species ranging over 360 million years of evolution. Extensive analysis and validation of the data provides several lines of evidence suggesting that we achieve a high true-positive rate for enhancer prediction. One, we show that our predictions target specific loci, rather than random genomic locations. Two, we predict enhancers in orthologous loci across a diverged set of species to a significantly higher degree than random expectation would allow. Three, we demonstrate that our predictions are highly enriched for regions of accessible chromatin. Four, we achieve a validation rate in excess of 70% using in vivo reporter gene assays. As we continue to annotate both new tissues and new species, our regulatory annotation resource will provide a rich source of data for the research community and will have utility for both small-scale (single gene, single species) and large-scale (many genes, many species) studies of gene regulation. In particular, the ability to search for functionally-related regulatory elements in orthologous loci should greatly facilitate studies of enhancer evolution even among distantly related species.

genomics↗

bioRxiv2023

LLPS condensates of Fha initiate the inside-out assembly of the type VI secretion system

The type VI secretion system (T6SS) is one of the most powerful nanomachines employed by Gram-negative pathogens for penetrating diverse cell envelopes, including bacteria and fungi, to deliver potent effectors into target cells. While the membrane-anchored contractile tubular structure of the T6SS is well characterized, the assembly process remains poorly understood. The prevailing model suggests that the assembly of T6SS initiates from its outer-membrane component. Here, we report a distinct model that the cytoplasmic protein Fha initiates T6SS assembly in Acidovorax citrulli, an important plant pathogen. Fha dictates the formation of the inner-membrane complex and the baseplate, and directly interacts with these key components. Importantly, imaging and biochemical assays reveal that Fha undergoes liquid-liquid phase separation (LLPS), forming condensates that selectively recruit essential T6SS proteins, which are otherwise dispersed in cells. Fha also exhibited conserved functions in human pathogens Vibrio cholerae and Pseudomonas aeruginosa. These findings unveil an inside-first LLPS-driven model for T6SS assembly and suggest LLPS might be broadly involved in mediating the assembly of bacterial macromolecular complexes and facilitating interspecies interactions and pathogenesis. Significance statementThe T6SS plays a pivotal role in interspecies competition and host-microbe interactions by delivering toxins to various prokaryotes and eukaryotes. Its crucial function relies on a membrane-anchored macromolecular structure comprising at least 13 conserved components. However, the mechanisms governing the efficient assembly of its diverse cytosolic and membrane-bound components remain elusive. Here, we identify Fha, a conserved cytosolic protein, as a key initiator of T6SS assembly. Fha recruits multiple structural and effector components, forming LLPS condensates. Fha homologs of plant and human pathogens exhibit conserved functions. Our findings not only unveil an inside-first assembly model for the T6SS, initiating from inner-membrane and baseplate components, but also suggest LLPS may have a broader impact on bacterial physiology beyond intracellular activities.

microbiology↗

bioRxiv2023

Evolution-guided large language model is a predictor of virus mutation trends

The increasing frequency of emerging viral infections necessitates a rapid human response, highlighting the cost-effectiveness of computational methods. However, existing computational approaches are limited by their input forms or incomplete functionalities, preventing a unified prediction of diverse viral variation drivers and hindering in-depth applications. To address this issue, we propose a unified evolution-driven framework for predicting virus variation drivers, named E2VD, which is guided by virus evolutionary traits priors. With evolution-inspired design, E2VD comprehensively and significantly outperforms state-of-the-art methods across various virus variation drivers prediction tasks. Moreover, E2VD effectively captures the fundamental patterns of virus evolution. It not only distinguishes different types of mutations but also accurately identifies rare beneficial mutations that are critical for virus to survival, while maintains generalization capabilities on different viral lineages. Importantly, with predicted biological drivers, E2VD perceives virus evolutionary trends, in which potential high-risk mutation sites are accurately recommended. Overall, E2VD represents a unified, structure-free, and interpretable approach for analyzing and predicting viral evolutionary fitness, providing an ideal alternative to costly wet-lab measurements to accelerate responses to emerging viral infections.

bioinformatics↗

bioRxiv2023

Presence of NCOR1+/CD4+ T cells in tertiary lymphoid organ predicts favorable prognosis in pancreatic ductal adenocarcinoma

CD4+ T cells have critical roles in anti-tumour immunity and its differentiation is known to be regulated by the nuclear receptor co-repressor 1 (NCOR1). Previous studies suggested that high CD4+ T cells are associated with a favourable prognosis in patients with pancreatic ductal adenocarcinoma (PDAC). However, the prognostic significance of NCOR1 in PDAC is still missing. In this study, the pathological impact of NCOR1 and CD4 has been analysed by multiplex immunohistochemistry in 100 PADC patients. NCOR1 expression in tertiary lymphoid organs is positively associated with the good prognosis of PDAC patients, while its expression in tumour tissue is not. Furthermore, the presence of NCOR1+/CD4+ T cells in tertiary lymphoid organs predicts a favourable prognosis in PDAC. Mechanistically, upregulation of NCOR1 expression in CD4+ T cells increases the release of TNF-, which induces the apoptosis of the tumor cells in vitro. Together, our data highlighted the tumour suppressive role of NCOR1+/CD4+ T cells in PDAC.

cancer biology↗

bioRxiv2023

Proximity proteomics reveals UCH-L1 as an essential regulator of NLRP3 mediated IL-1β production in human macrophages and microglia

Activation of the NACHT, LRR family pyrin domain containing 3 (NLRP3) inflammasome complex is an essential innate immune signalling mechanism. To reveal how human NLRP3 inflammasome assembly and activation are controlled, in particular by components of the ubiquitin system, proximity labelling, affinity purification and RNAi screening approaches were performed. Our study provides an intricate time-resolved molecular map of different phases of NLRP3 inflammasome activation. Also, we show that ubiquitin C-terminal hydrolase 1 (UCH-L1) interacts with the NACHT domain of NLRP3. Downregulation of UCH-L1 decreases pro-IL-1{beta} levels. UCH-L1 chemical inhibition with small molecules interfered with NLRP3 puncta formation and ASC oligomerization, leading to altered IL-1{beta} cleavage and secretion, particularly in microglia cells, which exhibited elevated UCH-L1 expression as compared to monocytes/macrophages. Altogether, we profiled NLRP3 inflammasome activation dynamics and highlight UCH-L1 as an important modulator of NLRP3-mediated IL-1{beta} production, suggesting that a pharmacological inhibitor of UCH-L1 may decrease inflammation-associated pathologies.

biochemistry↗

bioRxiv2023

Discovery of peptides for targeted delivery of mRNA lipid nanoparticles to cystic fibrosis lung epithelia

For cystic fibrosis (CF) patients, a lung targeted gene therapy would significantly alleviate pulmonary complications associated with morbidity and mortality. However, mucus in the airways and cell entry pose huge delivery barriers for local gene therapy. Here, we used phage display technology to select for and identify mucus- and cell-penetrating peptides against primary human bronchial epithelial cells (pHBECs) from CF patients cultured at air-liquid interface (ALI). At ALI, pHBECs produce mucus and reflect CF disease pathology, making it a clinically relevant model. Using this model, we discovered a lead candidate peptide, and incorporated it into lipid nanoparticles (LNPs) to deliver mRNA to pHBECs and mouse lungs in vivo. Compared to LNPs without our peptide, peptide-LNPs demonstrated 7.8-fold and 4.8-fold higher mRNA expression in vitro and in vivo, respectively. Since gene delivery to pHBECs is a significant challenge, we are encouraged by these results and anticipate that our peptide could be used to successfully deliver CF gene therapies in future work.

bioengineering↗

bioRxiv2023

Deep spatial proteomic exploration of severe COVID-19-related pulmonary injury in post-mortem specimens

The lung, as a primary target of SARS-CoV-2, exhibits heterogeneous microenvironment accompanied by various histopathological changes following virus infection. However, comprehensive insight into the protein basis of COVID-19-related pulmonary injury with spatial resolution is currently deficient. Here, we generated a region-resolved quantitative proteomic atlas of seven major pathological structures within the lungs of COVID-19 victims by integrating histological examination, laser microdissection, and ultrasensitive proteomic technologies. Over 10,000 proteins were quantified across 71 dissected FFPE post-mortem specimens. By comparison with control samples, we identified a spectrum of COVID-19-induced protein and pathway dysregulations in alveolar epithelium, bronchial epithelium, and pulmonary blood vessels, providing evidence for the proliferation of transitional-state pneumocytes. Additionally, we profiled the region-specific proteomes of hallmark COVID-19 pulmonary injuries, including bronchiole mucus plug, pulmonary fibrosis, airspace inflammation, and hyperplastic alveolar type 2 cells. Bioinformatic analysis revealed the enrichment of cell-type and functional markers in these regions (e.g. enriched TGFBI in fibrotic region). Furthermore, we identified the up-regulation of proteins associated with viral entry, host restriction, and inflammatory response in COVID-19 lungs, such as FURIN and HGF. Collectively, this study provides spatial proteomic insights for understanding COVID-19-caused pulmonary injury, and may serve as a valuable reference for improving therapeutic intervention for severe pneumonia.

systems biology↗

bioRxiv2023

A Highly Efficient Aorta-Gonad-Mesonephros-Like Definitive Hemogenic Endothelium From Human Pluripotent Stem Cells

Summary/AbstractHuman pluripotent stem cells are a tremendous tool to model early human development and disease including their use in the in vitro generation of blood cell fates. Hematopoietic progenitors and stem cells are the primary source of blood and the immune system from early development to adulthood and arise through successive waves of hemogenic mesoderm either in the yolk sac or embryo proper. Researchers have long sought a tractable human model for observing and distinguishing these waves of hematopoiesis in the dish for human developmental and disease modeling. Here we report a high-efficiency method for differentiating human pluripotent stem cells into an aorta-gonad-mesonephros-like definitive hemogenic mesoderm capable of giving rise to definitive hematopoietic progenitor and stem cells. The hematopoietic progenitor and stem cells exhibit robust multilineage in vitro colony forming potential. Gene expression analysis and single cell sequencing strongly support the developmental timing and notion that the pluripotent stem cell derived hematopoietic stem and progenitors are strikingly like bone fide hematopoietic stem cells. The hematopoietic progenitors can be subsequently differentiated into polarized macrophage and T-cells in vitro. Minimal silencing was observed upon differentiation of the pluripotent stem cells to hematopoietic lineages when conducting gene editing. Finally, upon engraftment into immunodeficient animals the hematopoietic progenitors and stem cells differentiate into multiple lineages including B-cells, T-cells, NK-cells, and monocytes.

developmental biology↗

bioRxiv2023

Early-life obesogenic environment integrates immunometabolic and epigenetic signatures governing neuroinflammation

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/537874v1_ufig1.gif" ALT="Figure 1"> View larger version (34K): org.highwire.dtl.DTLVardef@1bb1277org.highwire.dtl.DTLVardef@b978dborg.highwire.dtl.DTLVardef@adafc8org.highwire.dtl.DTLVardef@efa0f3_HPS_FORMAT_FIGEXP M_FIG Early life trauma and obesogenic diet effects of feeding control.Consumption of a Western-like high-saturated fat diet (WD, 42% kcal from fat) during adolescence in combination with (2) Exposure to early-life psychosocial stress leads to (3) changes in brain neurocircuitry and metabolic dysregulation. These alterations lead to (4) stress susceptibility, (5) emotional and feeding dysregulation, and (6) obesity. Dysregulation of feeding control and obesity leads to increased hedonic feeding and engages individuals in a cycle of aberrant feeding behaviors. C_FIG BackgroundChildhood overweight/obesity is associated with the development of stress-related psychopathology. However, the pathways connecting childhood obesity to stress susceptibility remain poorly understood. Here, we used a systems biology approach to determine linkages underlying obesity-induced stress susceptibility. MethodsSixty-two (62) adolescent Lewis rats (PND21) were fed for four weeks with a Western-like high-saturated fat diet (WD, 41% kcal from fat) or a matched control diet (CD, 13% kcal from fat). Subsequently, a group of rats (n = 32) was exposed to a well-established 31-day model of predator exposures and social instability (PSS). The effects of the WD and PSS were assessed with a comprehensive battery of behavioral tests, DTI (diffusion tensor imaging), NODDI (neurite orientation dispersion and density imaging), high throughput 16S ribosomal RNA gene sequencing for gut microbiome profiling, hippocampal microglia morphological and gene analysis, and gene methylation status of the stress marker, FKBP5. Parallel experiments were performed on human microglial cells (HMC3) to examine molecular mechanisms by which palmitic acid primes these cells to aberrant responses to cortisol. ResultsRats exposed to the WD and PSS exhibited deficits in sociability indices and increased fear and anxiety-like behaviors, food consumption, and body weight. WD and PSS interacted to alter indices of microstructural integrity within the hippocampal formation (subiculum) and subfields (CA1). Microbiome diversity and taxa distribution revealed that WD/PSS exposure caused significant shifts in the diversity of gut dominant bacteria and decreased the abundance of various members of the Firmicutes phylum, including Lachnospiracae NK4A136. Interestingly, the WD and PSS synergized to promote hippocampal microglia morphological and gene signatures implicated in neuroinflammation. These alterations were associated with changes in the microbiome, and in the expression and methylation status of the corticosterone receptor chaperone rat gene Fkbp5. HMC3 responses to cortisol were markedly disrupted after incubating cells in palmitate, shown by morphological changes and pro-inflammatory cytokine expression and release. Notably, these effects were partly mediated by the human FKBP5 gene. ConclusionsThe combination of psychosocial stress and poor diet during adolescence has a deleterious synergistic impact on brain health. This study enhances our understanding of mechanisms and adaptations by which obesogenic environments shape the maturational trajectories of common neurobiological correlates of resilience. HighlightsO_LIObesogenic diet consumption during adolescence leads to stress-induced anxiety-like behaviors in rats. C_LIO_LIExposure to an obesogenic environment during adolescence alters indices of hippocampal microstructural integrity. C_LIO_LIObesogenic diet and chronic stress promote selective gut microbiota dysbiosis. C_LIO_LIObesogenic diet and chronic stress synergize to expand putative pro-inflammatory microglia populations in the CA1 subfield of the hippocampus. C_LIO_LIObesogenic diet and chronic stress influence hippocampal Fkbp5 gene methylation status at specific sites. C_LIO_LIFKBP5 integrates microglial pro-inflammatory signals under obesogenic conditions. C_LI

neuroscience↗

bioRxiv2023

Activation of peroxisome proliferator-activated receptor-gamma prevents monocrotaline-induced pulmonary arterial hypertension by suppressing of nuclear factor-kappa B mediated autophagy

To investigate the molecular mechanisms underlying autophagy inducing pulmonary vascular remodeling and rosiglitazone inhibiting pulmonary arterial hypertension (PAH). Monocrotaline (MCT) was intraperitoneally injection to induce the rat PAH model. The right ventricular hypertrophy index (RVHI), right ventricle systolic pressure (RVSP), percentage of medial wall thickness (%MT) and histomorphologic analyses were performed to evaluate the development of PAH. The translocation of nuclear factor-kappa B (NF-{kappa}B) p65 subunit from cytosol to nucleus, the protein expression levels of LC3B, Beclin 1 and RND3 were determined by western blot. Furthermore, NF-{kappa}B inhibitor, pyrrolidine dithiocarbamate (PDTC) and peroxisome proliferator-activated receptor-{gamma} (PPAR{gamma}) activator, rosiglitazone, were used to inhibit the activation of NF-{kappa}B and activate PPAR{gamma} signaling, respectively. MCT injection dramatically induced PAH models in rats as manifested by the increased RVSP, RVHI, and %MT. In addition, the activation of NF-{kappa}B and autophagy were significantly enhanced and the RND3 were markedly decreased in MCT-induced PAH in rat. However, these effects could be significantly suppressed either by the supplementation of PDTC or rosiglitazone. NF-{kappa}B promotes the development of PAH by activation of autophagy and consequent down-regulation of RND3 expression. Activation of PPAR{gamma} suppresses autophagy by inhibiting NF-{kappa}B in MCT-induced PAH. Our results not only uncovered the mechanisms of PPAR{gamma} activator in the protection of PAH but also provided potential therapeutic target for PAH treatment.

biochemistry↗

bioRxiv2023

Computational design of N-linked glycans for high throughput epitope profiling

Efficient identification of epitopes is crucial for drug discovery and design as it enables the selection of optimal epitopes, expansion of lead antibody diversity, and verification of binding interface. Although high resolution low throughput methods like X-ray crystallography can determine epitopes or protein-protein interactions accurately, they are time-consuming and can only be applied to a limited number of complexes. To overcome these limitations, we have developed a rapid computational method that incorporates N-linked glycans to mask epitopes or protein interaction surfaces, thereby providing an atomistic mapping of these regions. Using human coagulation factor IXa (fIXa) as a model system, we could rapidly and reliably delineate epitopes through the insertion of N-linked glycans that efficiently disrupt binding in a site-selective manner. To validate the efficacy of our method, we conducted ELISA experiments and high-throughput yeast surface display assays. Furthermore, X-ray crystallography was employed to verify the results, thereby recapitulating through the method of N-linked glycans an atomistic resolution mapping of the epitope.

bioengineering↗

bioRxiv2023

Two haplotype-resolved genomes of highly heterozygous AAB allotriploid bananas provide insights into subgenome asymmetric evolution and banana wilt control

Bananas (Musa spp.) are one of the most important tropical fruits and staple food, which are of great significance to human societies. Plantain and Silk are two important banana subgroups, which are both triploid hybrids (AAB) between the wild diploid Musa acuminata and M. balbisiana. In this study, we reported the first haplotype-resolved genome assembly of Plantain and Silk bananas with genome size of approximately 1.4 Gb. We discovered widespread asymmetric evolution in the subgenomes of Plantain and Silk, which could be linked to frequent homologous exchanges (HEs) events. This is the first study to uncover the genetic makeup of triploid banana and verify that subgenome B harbors a rich source of resistance genes. Of the 88,078 and 94,988 annotated genes in Plantain and Silk, only 58.5% and 59.4% were present in all three subgenomes, with >50% genes containing differently expressed alleles in different haplotypes. We also found that Plantain is more resistant to banana Fusarium wilt, exhibiting a much faster defense response after pathogenic fungi infection. Many differentially expressed genes in abscisic acid, ethylene, jasmonic acid and salicylic acid pathways were identified in Plantain. Our analysis revealed that MpMYB36 promotes the biosynthesis of secondary cell wall and deposition of lignin by directly binding to the promoter of MpPAL and MpHCT, which allows Plantain to inhibit the penetration of early infection. Moreover, the insertion of the key carotenoid synthesis gene (CRTISO) may be the potential genetic basis for the richness of carotenoids in Plantain. Our study provides an unprecedented genomic basis for basic research and the development of elite germplasm in cultivated bananas.

plant biology↗

bioRxiv2022

Large clones of pre-existing T cells drive early immunity against SARS-COV-2 and LCMV infection.

We analyzed the dynamics of the earliest T cell response to SARS-COV-2. A wave of TCRs strongly but transiently expand during infection, frequently peaking the same week as the first positive PCR test. These expanding TCR CDR3s were enriched for sequences functionally annotated as SARS-COV-2 specific. Most epitopes recognized by the expanding TCRs were highly conserved between SARS-COV-2 strains, but not with circulating human coronaviruses. Many expanding CDR3s were also present at high precursor frequency in pre-pandemic TCR repertoires. A similar set of early response TCRs specific for lymphocytic choriomeningitis virus epitopes were also found at high frequency in the pre-infection naive repertoire. High frequency naive precursors may allow the T cell response to respond rapidly during the crucial early phases of acute viral infection. One-Sentence SummaryHigh frequency naive precursors underly the rapid T cell response during the crucial early phases of acute viral infection.

immunology↗

bioRxiv2022

Systematic mutagenesis reveals critical effector functions in the assembly and dueling of the H1-T6SS in Pseudomonas aeruginosa

Pseudomonas aeruginosa is an important human pathogen that can cause severe wound and lung infections. It employs the type VI secretion system (H1-T6SS) as a molecular weapon to carry out a unique dueling response to deliver toxic effectors to neighboring sister cells or other microbes after sensing an external attack. However, the underlying mechanism for such dueling is not fully understood. Here, we examined the role of all H1-T6SS effectors and VgrG proteins in assembly and signal sensing by ectopic expression, combinatorial deletion and point mutations, and imaging analyses. Expression of effectors targeting the cell wall and membrane resulted in increased H1-T6SS assembly. Deletion of individual effector and vgrG genes had minor- to-moderate effects on H1-T6SS assembly and dueling activities. The dueling response was detectable in the P. aeruginosa mutant lacking all H1-T6SS effector activities. In addition, double deletions of vgrG1a with either vgrG1b or vgrG1c and double deletions of effector genes tse5 and tse6 severely reduced T6SS assembly and dueling activities, suggesting their critical role in T6SS assembly. Collectively, these data highlight the diverse roles of effectors in not only dictating antibacterial functions but also their differential contributions to the assembly of the complex H1-T6SS apparatus.

microbiology↗

bioRxiv2022

A dueling-competent signal-sensing module guides precise delivery of cargo proteins into target cells by engineered Pseudomonas aeruginosa

To recognize and manipulate a specific microbe of a crowded community is a highly challenging task in synthetic biology. Here, we introduce a highly-selective protein delivery platform, termed DUEC, which responds to direct contact of attacking cells by engineering the tit-for-tat/dueling response of H1-T6SS (type VI secretion system) in Pseudomonas aeruginosa. Using a Cre-recombinase-dependent reporter, we screened H1-T6SS secreted substrates and developed Tse6N as the most effective secretion tag for Cre delivery. DUEC cells can discriminately deliver the Tse6N-Cre cargo into the cytosol of T6SS+ but not T6SS- Vibrio cholerae cells in a mixed population. These data demonstrate that the DUEC cell is not only a prototypical physical-contact sensor and delivery platform but also may be coupled with recombination-based circuits with the potential for complex tasks in mixed microbial communities.

microbiology↗

bioRxiv2022

Automated assembly of high-density carbon fiber electrode arrays for single unit electrophysiological recordings

ObjectiveCarbon fiber (CF) is good for chronic neural recording due to the small diameter (7 {micro}m), high Youngs modulus, and low electrical resistance, but most high-density carbon fiber (HDCF) arrays are manually assembled with labor-intensive procedures and limited by the accuracy and repeatability of the operator handling. A machine to automate the assembly is desired. ApproachThe HDCF array assembly machine contains: 1) a roller-based CF extruder, 2) a motion system with three linear and one rotary stages, 3) an imaging system with two digital microscope cameras, and 4) a laser cutter. The roller-based extruder automatically feeds single CF as raw material. The motion system aligns the CF with the array backend then places it. The imaging system observes the relative position between the CF and the backend. The laser cutter cuts off the CF. Two image processing algorithms are implemented to align the CF with the support shanks and circuit connection pads. Main resultsThe machine was capable of precisely handling 6.8 m carbon fiber electrodes. Each electrode was placed into a 12 m wide trenches in a silicon support shank. Two HDCF arrays with 16 CF electrodes populated on 3 mm shanks (with 80 m pitch) were fully assembled. Impedance measurements were found to be in good agreement with manual assembled arrays. One HDCF array was implanted in the motor cortex in an anesthetized rat and was able to detect single unit activity. SignificanceThis machine can eliminate the manual labor-intensive handling, alignment and placement of single carbon fiber during assembly, providing a proof-of-concepts towards fully automated HDCF array assembly and batch production.

bioengineering↗

bioRxiv2022

SARS-CoV-2 mutations affect proteasome processing to alter CD8+ T cell responses

Viral CD8+ epitopes are generated by the cellular turnover of viral proteins, predominantly by the proteasome. Mutations located within viral epitopes can result in escape from memory T cells but the contribution of mutations in flanking regions of epitopes in SARS-CoV-2 has not been investigated. Focusing on two of the most dominant SARS-CoV-2 nucleoprotein CD8+ epitopes, we identified mutations in epitope flanking regions and investigated the contribution of these mutations to antigen processing and T cell activation using SARS-CoV-2 nucleoprotein transduced B cell lines and in vitro proteasomal processing of peptides. We found that decreased NP9-17-B*27:05 CD8+ T cell responses to the NP-Q7K mutation correlated with lower epitope surface expression, likely due to a lack of efficient epitope production by the proteasome, suggesting immune escape caused by this mutation. In contrast, NP-P6L and NP-D103N/Y mutations flanking the NP9-17-B*27:05 and NP105-113-B*07:02 epitopes, respectively, increased CD8+ T cell responses associated with enhanced epitope production by the proteasome. Our results provide evidence that SARS-CoV-2 mutations outside the epitope could have a significant impact on antigen processing and presentation, thereby contributing to escape from immunodominant T cell responses. Alternatively, mutations could enhance antigen processing and efficacy of T cell recognition, opening new avenues for improving future vaccine designs. One Sentence SummaryNatural mutations in the flanking regions of known immunodominant SARS-CoV-2 nucleoprotein epitopes can decrease CD8+ T cell responses leading to partial escape.

immunology↗

bioRxiv2021

DETIRE: A Hybrid Deep Learning Model for identifying Viral Sequences from Metagenomes

A metagenome contains all DNA sequences from an environmental sample, including viruses, bacteria, fungi, actinomycetes and so on. Since viruses are of huge abundance and have caused vast mortality and morbidity to human society in history as a kind of major pathogens, detecting viruses from metagenomes plays a crucial role in analysing the viral component of samples and is the very first step for clinical diagnosis. However, detecting viral fragments directly from the metagenomes is still a tough issue because of the existence of huge number of short sequences. In this paper, a hybrid Deep lEarning model for idenTifying vIral sequences fRom mEtagenomes (DETIRE), is proposed to solve the problem. Firstly, the graph-based nucleotide sequence embedding strategy is utilized to enrich the expression of DNA sequences by training an embedding matrix. Then the spatial and sequential features are extracted by trained CNN and BiLSTM networks respectively to improve the feature expression of short sequences. Finally, the two set of features are weighted combined for the final decision. Trained by 220,000 sequences of 500bp subsampled from the Virus and Host RefSeq genomes, DETIRE identifies more short viral sequences (<1,000bp) than three latest methods, DeepVirFinder, PPR-Meta and CHEER. DETIRE is freely available at https://github.com/crazyinter/DETIRE.

bioinformatics↗