Biology subjects

Ge, B.

Publications and source records attributed to Ge, B..

15 recordsLinked to original sources

bioRxiv2026

Maleic acid adjuvates BCG to induce CD4+CD8+ T cells and sterilize tuberculosis

Anti-tuberculosis (TB) immunity typically emphasizes CD4+ T and CD8+ T cells that only provide limited protection against Mycobacterium tuberculosis (Mtb) infection. The anti-TB function of CD4+CD8+ T cells remains unexplored, mostly due to the dogma that ThPOK and Runx3 antagonize each other to block their development and their scarcity. Here, we show that immunization of BCG (Bacillus Calmette-Gu&eacuterin) with Complete Freund's Adjuvant (CFA) markedly induced CD4+CD8+ T cells through the gut microbiota Clostridium butyricum or its metabolite maleic acid. Mtb-specific CD4+CD8+ T cells exhibited a broad T-cell receptor repertoire and sterilized Mtb infection by inducing SLAMF1 and neutrophil responses. Mechanistically, maleic acid interacted with PAK2 to promote STAT5 phosphorylation at Ser127, thus upregulating Ets1 expression. Direct binding of Ets1 to the Runx3 and ThPOK promoters orchestrated their expression to redirect the CD8+ T cell differentiation towards the CD4+CD8+ lineage. Moreover, immunization of BCG plus Clostridium butyricum or maleic acid sterilized Mtb infection in mouse models. These findings establish CD4+CD8+ T cells as superior immune effectors against Mtb, a concept that could fundamentally redirect the current paradigm for anti-TB vaccine development.

microbiology↗

bioRxiv2026

Caspase-14 recognizes and processes IL-1β in epithelial cells to drive anti-bacterial IgG production

Caspases-mediated processing of cytokines coordinates cell-autonomous defenses and induction of systemic inflammation 1. While caspase-1 processes IL-1{beta} and IL-18 2-5, human caspase-4 processes IL-18 mainly in monocytes 6. Caspase-14 is an exception, specializing in epidermal differentiation7,8, yet no cytokine target has been firmly established for caspase-14. Here, we report that recognition and IL-1{beta} maturation of IL-1{beta} by caspase-14 in epithelial cells determined anti-bacterial humoral immunity against Yersina pseudotuberculosis (Y. pseudotuberculosis) infection. Upon TAK1 inhibition by YopJ, activated caspase-8 cleaved caspase-14 at Asp 146, generating an active 16-kDa fragment, whose exposed pocket directly interacted with and cleaves pro-IL-1{beta} at Cys132. Moreover, conditional knock-out of caspase-14 in epithelial cells or knock-in of a caspase-inactive caspase-14C136A mutant impaired Y. pseudotuberculosis induced IL-1{beta} production and eliminated the total anti-Y. pseudotuberculosis IgG production, leading to uncontrolled Y. pseudotuberculosis infection. Thus, our findings establish caspase-14 as a processor of IL-1{beta} in epithelial cells to propel anti-bacterial humoral immunity, providing insights into the inflammation and vaccine development.

immunology↗

bioRxiv2025

A BCG toxic effector induces mitochondrial DNA compaction to refrain protective immunity

Innate immune memory typically emphasizes nuclear chromatin remodeling that determines transcriptional memory in monocytes and macrophages. Here, we show that compaction of mitochondrial DNA (mtDNA), governed by mitochondrial transcription factor A (TFAM) abundance and mtATP-dependent remodeling, defines the transcriptional and functional state of trained macrophages. While typical pathogen-associated molecular pattern (PAMPs) triggered mtDNA accessibility, Bacillus Calmette-Guerin (BCG) effector PE18 directly interacted with and activated SLC25A5 to reduce mtATP levels, thereby inhibiting TFAM degradation by AFG3L2. Accumulated TFAM restricts mtDNA accessibility, suppressing the transcription of the mtNd1 and thereby reducing mtNd1-mediated mtROS production, which diminishes the trained capacity of macrophages against secondary infections. Notably, BCG{Delta}pe18 maintains macrophages cytokine transcriptional capacity independent of classical nuclear histone modifications. Moreover, BCG{Delta}pe18 provides robust and lifelong protective immunity against Mycobacterium tuberculosis (Mtb) infection. These findings reveal mitochondrial genome as a regulatory entity in trained immunity, and suggest a potential strategy for improving vaccine performance.

immunology↗

bioRxiv2024

RING1 dictates GSDMD-mediated inflammatory response and host susceptibility to pathogen infection

RING1 is an E3 ligase component of the polycomb repressive complex 1 (PRC1) with known roles in chromatin regulation and cellular processes such as apoptosis and autophagy. However, its involvement in inflammation and pyroptosis needs to be better characterized. Here, we found that human RING1, but not RING2, promoted K48-linked ubiquitination of Gasdermin D (GSDMD) and acted as a negative regulator of pyroptosis and bacterial infection. Ring1 knockout mice increased the bacterial loads and mortality rate by treatment of S. typhimurium. Upon infection by M. tuberculosis (Mtb) H37Rv strain, RING1 deletion initially reduced bacterial loads but later increased lung inflammation and impaired immune defense responses in mice. Also, Ring1 knockout exacerbated acute sepsis induced by lipopolysaccharide (LPS). Mechanistically, RING1 directly interacts with GSDMD and ubiquitinates the K51 and K168 sites of GSDMD for K48-linked proteasomal degradation, thereby inhibiting pyroptosis. Inhibition of RING1 E3 ligase activity by mutation or small molecular compound increased GSDMD level and cell death during pyroptosis. Our findings reveal that RING1 dictates GSDMD-mediated inflammatory response and host susceptibility to pathogen infection, highlighting RING1 as a potential therapeutic target for combating infectious diseases. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/622030v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@e6d4a6org.highwire.dtl.DTLVardef@92f137org.highwire.dtl.DTLVardef@11a69c4org.highwire.dtl.DTLVardef@115dc0b_HPS_FORMAT_FIGEXP M_FIG Graphic Abstract C_FIG HighlightsO_LIE3 ubiquitin ligase RING1 targets GSDMD for proteasomal degradation. C_LIO_LIMice lacking RING1 are more vulnerable to S. typhimurium infection and LPS- induced sepsis. C_LIO_LIIn the early stages of M. tuberculosis (Mtb) infection, Ring1-/- mice exhibit efficient bacterial clearance. C_LIO_LIChronic inflammation in Ring1-/- mice impairs the ability to control Mtb in the late stages of infection. C_LI

cell biology↗

bioRxiv2024

Unveiling allopolyploidization-driven genome duplications through progressive analysis of deep genome skimming data

Whole-genome duplication (WGD) events are widespread across the Web of Life (WoL). Given the prevalence of WGDs in the polyploid Prunus (Rosaceae), this economically- and agriculturally-important angiosperm lineage provides an excellent model for exploring this mode of reticulation. We used the polyploid Prunus to demonstrate a progressive strategy for analyzing Deep Genome Skimming (DGS) data in the presence of WGDs. Phylogenomic discordance analyses indicated that allopolyploidization, rather than Incomplete Lineage Sorting (ILS), played a dominant role in the origin and dynamics of polyploid Prunus. This study underscores how a progressive strategy to identify WGD events at different depths in a phylogenetic tree reveals the nuances of evolutionary mechanisms driving allopolyploidization. We inferred that the continued uplift of the Himalayas from the Middle to Late Miocene drove the rapid diversification of the Eastern Asia endemic Maddenia clade, by facilitating frequent hybridization and allopolyploidization, specifically introgression between the Himalayas-Hengduan and the Central-Eastern China clades.

systems biology↗

bioRxiv2024

Expanded methylome and quantitative trait loci detection by long-read profiling of personal DNA

Structural variants (SVs) are omnipresent in human DNA, yet their genotype and methylation status is rarely characterized due to previous limitations in genome assembly and detection of modified nucleotides. Because of this, the extent to which these regions act as quantitative-trait loci is also largely unknown. Here, we generated a pangenome graph summarizing the SVs in 782 de novo assembled genomes obtained from the Genomic Answers for Kids rare disease cohort, that captures 14.6 million CpGs in DNA segments that are absent from the CHM13v2 assembly (SV-CpGs), expanding their number by 43.6%. Next, using 435 methylomes from the same samples, we genotyped a total of 7.99 million SV-CpGs, of which 5.18 million (64.8%) were found to be methylated (SV-5mCpGs) in at least one sample. To understand the provenance and impact of these novel SV-CpGs, we noted that non-repeat sequences were the leading contributor of SV-CpGs (3.3 x 106), followed by centromeric satellites (1.58 x 106), simple repeats (1.19 x 106), Alus (0.67 x 106), satellites (0.39 x 106), L1s (0.27 x 106), and SVAs (0.19 x 106). Meanwhile, the methylation rate of SV-CpGs was the highest in repeat sequences. Moreover, in contrast to Alus and L1s, centromeric satellites, simple repeats and SVA sequences were overrepresented in SV-5mCpGs compared to reference CpGs. Similarly, we established that non-reference CpGs were more than twice (37% vs. 15%) as likely to be variable, showing intermediate methylation levels in the population. Lastly, to explore if SVs detected in this pangenome are potentially causal for functional variation in population we measured methylation quantitative trait loci (SV-mQTLs) using CHM13v2 as a backbone. This revealed over 230,464 methylation bins within 100 kbp of a common SV (>5% MAF) showing significant association (at 5% FDR) with methylation variation. Finally, we assessed how many of these SVs-mQTLs were the leading QTL variant compared to SNVs and identified 65,659 methylation bins (28.5%) where the leading variant was an SV. In conclusion, our results demonstrate that graph genome references providing full SV structures in combination with the associated methylation variation reveal tens-of-thousands of QTLs that are more accurately mapped in personal genomes, underscoring the importance of assembly-based analyses of human traits.

bioinformatics↗

bioRxiv2023

Structural framework for the understanding spectroscopic and functional signatures of the cyanobacterial Orange Carotenoid Protein families

The Orange Carotenoid Protein (OCP) is a unique photoreceptor crucial for cyanobacterial photoprotection. Best studied Synechocystis sp. PCC 6803 OCP belongs to the large OCP1 family. Downregulated by the Fluorescence Recovery Protein (FRP) in low-light, high-light-activated OCP1 binds to the phycobilisomes and performs non-photochemical quenching. Recently discovered families OCP2 and OCP3 remain structurally and functionally underexplored, and no systematic comparative studies have ever been conducted. Here we present two first crystal structures of OCP2 from morphoecophysiologically different cyanobacteria and provide their comprehensive structural, spectroscopic and functional comparison with OCP1, the recently described OCP3 and all-OCP ancestor. Structures enable correlation of spectroscopic signatures with the effective number of hydrogen and discovered here chalcogen bonds anchoring the ketocarotenoid in OCP and rationalize the observed differences in OCP/FRP and OCP/phycobilisome functional interactions. These data are expected to foster OCP research and applications in optogenetics, targeted carotenoid delivery and cyanobacterial biomass engineering.

biochemistry↗

bioRxiv2023

Nightmare or delight: taxonomic circumscription meets reticulate evolution in the phylogenomic era

Phylogenetic studies in the phylogenomics era have demonstrated that reticulate evolution greatly impedes the accuracy of phylogenetic inference, and consequently can obscure taxonomic treatments. However, the systematics community lacks a broadly applicable strategy for taxonomic delimitation in groups identified to have pervasive reticulate evolution. The red-fruit genus, Stranvaesia, provides an ideal model for testing the effect of reticulation on generic circumscription when hybridization and allopolyploidy define a groups evolutionary history. Here, we conducted phylogenomic analyses integrating data from hundreds of single-copy nuclear (SCN) genes and plastomes, and interrogated nuclear paralogs to clarify the inter/intra-generic relationship of Stranvaesia and its allies in the framework of Maleae. Analyses of phylogenomic discord and phylogenetic networks showed that allopolyploidization and introgression promoted the origin and diversification of the Stranvaesia clade, a conclusion further bolstered by cytonuclear and gene tree discordance. The well-inferred phylogenetic backbone revealed an updated generic delimitation of Stranvaesia and a new genus, Weniomeles, characterized by purple-black fruits, trunk and/or branches with thorns, and fruit core with multilocular separated by a layer of sclereids and a cluster of sclereids at the top of the locules. Here, we highlight a broadly-applicable workflow for inferring how analyses of reticulate evolution in phylogenomic data can directly shape taxonomic revisions.

evolutionary biology↗

bioRxiv2021

Raman2RNA: Live-cell label-free prediction of single-cell RNA expression profiles by Raman microscopy

Single cell RNA-Seq (scRNA-seq) and other profiling assays have opened new windows into understanding the properties, regulation, dynamics, and function of cells at unprecedented resolution and scale. However, these assays are inherently destructive, precluding us from tracking the temporal dynamics of live cells, in cell culture or whole organisms. Raman microscopy offers a unique opportunity to comprehensively report on the vibrational energy levels of molecules in a label-free and non-destructive manner at a subcellular spatial resolution, but it lacks in genetic and molecular interpretability. Here, we developed Raman2RNA (R2R), an experimental and computational framework to infer single-cell expression profiles in live cells through label-free hyperspectral Raman microscopy images and multi-modal data integration and domain translation. We used spatially resolved single-molecule RNA-FISH (smFISH) data as anchors to link scRNA-seq profiles to the paired spatial hyperspectral Raman images, and trained machine learning models to infer expression profiles from Raman spectra at the single-cell level. In reprogramming of mouse fibroblasts into induced pluripotent stem cells (iPSCs), R2R accurately (r>0.96) inferred from Raman images the expression profiles of various cell states and fates, including iPSCs, mesenchymal-epithelial transition (MET) cells, stromal cells, epithelial cells, and fibroblasts. R2R outperformed inference from brightfield images, showing the importance of spectroscopic content afforded by Raman microscopy. Raman2RNA lays a foundation for future investigations into exploring single-cell genome-wide molecular dynamics through imaging data, in vitro and in vivo.

genomics↗

bioRxiv2021

Multi-omics analysis for potential inflammation-related genes involved in tumor immune evasion via extended application of epigenetic data

BackgroundAccumulating evidence suggests that inflammation-related genes may play key roles in tumor immune evasion. Programmed cell death ligand 1 (PD-L1) is an important immune checkpoint involved in mediating antitumor immunity. We performed multi-omics analysis to explore key inflammation-related genes affecting the transcriptional regulation of PD-L1 expression. MethodsThe open chromatin region of the PD-L1 promoter was mapped using the assay for transposase-accessible chromatin using sequencing (ATAC-seq) profiles. Correlation analysis of epigenetic data (ATAC-seq) and transcriptome data (RNA-seq) were performed to identify inflammation-related transcription factors whose expression levels were correlated with the chromatin accessibility of the PD-L1 promoter. Chromatin immunoprecipitation sequencing (ChIP-seq) profiles were used to confirm the physical binding of the TF STAT2 and the predicted binding regions. We also confirmed the results of the bioinformatics analysis with cell experiments. ResultsWe identified chr9:5449463-5449962 and chr9:5450250-5450749 as reproducible open chromatin regions in the PD-L1 promoter. Moreover, we observed a correlation between STAT2 expression and the accessibility of the aforementioned regions. Furthermore, we confirmed its physical binding through ChIP-seq profiles and demonstrated the regulation of PD-L1 by STAT2 overexpression in vitro. Multiple databases were also used for the validation of the results. ConclusionOur study identified STAT2 as a direct upstream TF regulating PD-L1 expression. The interaction of STAT2 and PD-L1 might be associated with tumor immune evasion in cancers, suggesting the potential value for tumor treatment.

immunology↗

bioRxiv2020

The genome analysis of Tripterygium wilfordii reveals TwCYP712K1 and TwCYP712K2 responsible for oxidation of friedelin in celastrol biosynthesis pathway

ABSTRACTTripterygium wilfordii is a Traditional Chinese Medicine (TCM) from family Celastraceae and celastrol is one of the strongest active ingredients belonging to friedelane-type pentacyclic triterpenoid, which has a large clinical application value of anti-tumor, immunosuppression, and obesity treatment. The first committed biosynthesis step of celastrol is the cyclization of 2, 3-oxidosqualene to friedelin, catalyzed by the oxidosqualene cyclase, while the rest of this pathway is still unclear. In this study, we reported a reference genome assembly of T. wilfordii with high-quality annotation by using a hybrid sequencing strategy (Nanopore, Bionano, Illumina HiSeq, and Pacbio), which obtained a 340.12 Mb total size and contig N50 reached 3.09 Mb. In addition, we successfully anchored 91.02% sequences into 23 pseudochromosomes using Hi-C technology and the super-scaffold N50 reached 13.03 Mb. Based on integration genome, transcriptom and metabolite analyses, as well as in vivo and in vitro enzyme assays, two CYP450 genes, TwCYP712K1 and TwCYP712K2 have been proven for C-29 position oxidation of friedelin to produce polpunonic acid, which clarifies the second biosynthesis step of celastrol. Syntenic analysis revealed that TwCYP712K1 and TwCYP712K2 derived from the common ancestor. These results have provided insight into illustrating pathways for both celastrol and other bioactive compounds found in this plant.Competing Interest StatementThe authors have declared no competing interest.View Full Text

plant biology↗

bioRxiv2019

Genome-wide Transcriptomic Analysis of the Response of Botrytis cinerea to Wuyiencin

Grey mould is caused by the ascomycetes Botrytis cinerea in a range of crop hosts. As a biological control agent, the nucleoside antibiotic wuyiencin has been industrially produced and widely used as an effective fungicide. To elucidate the effects of wuyiencin on the transcriptional regulation in B. cinerea, we, for the first time, report a genome-wide transcriptomic analysis of B. cinerea treated with wuyiencin. We could identify 2067 differentially expressed genes (DEGs); of them, 886 and 1181 genes were significantly upregulated and downregulated, respectively. Functional categorization indicated that genes involved in amino acid metabolism and those encoding putative secreted proteins were remarkably influenced in response to wuyiencin treatment. Moreover, the expression of genes involved in protein synthesis and energy metabolism (oxidative phosphorylation) and of those encoding ATP-binding cassette transporters was markedly upregulated, whereas that of genes participating in DNA replication, cell cycle, and stress response was downregulated. Furthermore, wuyiencin resulted in mycelial malformation and negatively influenced cell growth rate and conidial yield in B. cinerea. Our results suggest that this nucleoside antibiotic regulates all aspects of cell growth and differentiation in B. cinerea. To summarize, we identified candidate pathways and target genes that may offer insights into the protective and antagonistic mechanisms underlying the action of biological control agents.

microbiology↗

bioRxiv2019

LARP7 is a BRCA1 ubiquitinase substrate and regulates genome stability and tumorigenesis

Attenuated DNA repair leads to genomic instability and tumorigenesis. BRCA1/BARD1 are the best known tumor suppressors that promote homology recombination (HR) and arrest cell cycle at G2/M checkpoint. As E3 ubiquitin ligases, their ubiquitinase activity has been known to involve in the HR and tumor suppression, but the mechanism remains ambiguous. Here, we demonstrated upon genotoxic stress, BRCA1 together with BARD1 catalyzed the K48 ployubiquitination on LARP7, a 7SK RNA binding protein known to control RNAPII pausing, and thereby degraded it through 26S ubiquitin-proteasome pathway. Depleting LARP7 suppressed the expression of CDK1 complex, arrested cell at G2/M DNA damage checkpoint and reduced BRCA2 phosphorylation which thereby facilitated RAD51 recruitment to damaged DNA to enhance HR. Importantly, LARP7 depletion observed in breast patients lead to the chemoradiotherapy resistance both in vitro and in vivo. Together, this study unveils a mechanism by which BRCA1/BARD1 utilizes their E3 ligase activity to control HR and cell cycle, and highlights LARP7 as a potential target for cancer prevention and therapy.\n\nHighlightsO_LIDNA damage response downregulates LARP7 through BRCA1/BARD1\nC_LIO_LIBRCA1/BARD1 catalyzes the K48 polyubiquitination on LARP7\nC_LIO_LILARP7 promotes G2/M cell cycle transition and tumorigenesis via CDK1 complex\nC_LIO_LILARP7 disputes homology-directed repair that leads to tumor therapy resistance\nC_LI

molecular biology↗

bioRxiv2019

GSDMA drives the most replicated association with asthma in naïve CD4+ T cells

BackgroundThe 17q12-21 locus is the most replicated association with asthma. However, no study had described the genetic mechanisms underlying this association considering all genes of the locus in immune cell samples isolated from asthmatic and non-asthmatic individuals.\n\nObjectiveThis study takes benefit of samples from naive CD4+ T cells and eosinophils isolated from the same 200 individuals to describe specific interactions between genetic variants, gene expression and DNA methylation levels for the 17q12-21 asthma locus.\n\nMethods and ResultsAfter isolation of naive CD4+ T cells and eosinophils from blood samples, next generation sequencing was used to measure DNA methylation levels and gene expression counts. Genetic interactions were then evaluated considering genetic variants from imputed genotype data. In naive CD4+ T cells but not eosinophils, 20 SNPs in the fourth and fifth haplotype blocks modulated both GSDMA expression and methylation levels, showing an opposite pattern of allele frequencies and expression counts in asthmatics compared to controls. Moreover, negative correlations have been measured between methylation levels of CpG sites located within the 1.5 kb region from the transcription start site of GSDMA and its expression counts.\n\nConclusionAvailability of sequencing data from two key cell types isolated from asthmatic and non-asthmatic individuals allowed identifying a new gene in naive CD4+ T cells that drives the association with the 17q12-21 locus, leading to a better understanding of the genetic mechanisms taking place in it.

genetics↗

bioRxiv2018

Impact of using a personalized genome on histone ChIP-seq peak calls

BackgroundEpigenomic studies that use next generation sequencing experiments typically rely on the alignment of reads to a reference sequence. However, because of genetic diversity and the diploid nature of the human genome, we hypothesized that using a generic reference could lead to incorrectly mapped reads and bias downstream results.\n\nResultsWe show that accounting for genetic variation using a modified reference genome (MPG) or a denovo assembled genome (DPG) can alter histone H3K4me1 and H3K27ac ChIP-seq peak calls by either creating new personal peaks or by the loss of reference peaks. MPGs are found to alter approximately 1% of peak calls while DPGs alter up to 5% of peaks. We also show statistically significant differences in the amount of reads observed in regions associated with the new, altered and unchanged peaks. We report that short insertions and deletions (indels), followed by single nucleotide variants (SNVs), have the highest probability of modifying peak calls. A counter-balancing factor is peak width, with wider calls being less likely to be altered. Next, because high-quality DPGs remain hard to obtain, we show that using a graph personalized genome (GPG), represents a reasonable compromise between MPGs and DPGs and alters about 2.5% of peak calls. Finally, we demonstrate that altered peaks have a genomic distribution typical of other peaks. For instance, for H3K4me1, 518 personal-only peaks were replicated using at least two of three approaches, 394 of which were inside or within 10Kb of a gene.\n\nConclusionsAnalysing epigenomic datasets with personalized and graph genomes allows the recovery of new peaks enriched for indels and SNVs. These altered peaks are more likely to differ between individuals and, as such, could be relevant in the study of various human phenotypes.

bioinformatics↗