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Biology subjects

Zhu, G.

Publications and source records attributed to Zhu, G..

At least 37 records · Page 2Linked to original sources

HPV16 E6 oncoprotein promotes microhomology-mediated viral integration by upregulating POLQ expression

Integration of the high-risk Human Papillomavirus 16 (HPV16) genome into the host chromosome, frequently driven by microhomology-mediated end joining (MMEJ), is a critical step in the carcinogenesis of HPV-associated tumors. However, the mechanisms by which viral oncoproteins manipulate the error-prone MMEJ pathway remain poorly defined. Here, we demonstrate that the HPV16 E6 oncoprotein upregulates MMEJ to facilitate viral genome integration. This heightened MMEJ activity is driven by a marked increase in the protein levels of DNA Polymerase Theta (POLQ), a central enzyme of the MMEJ pathway. Mechanistically, we show that the elevation of POLQ levels in response to HPV16 E6 expression is dependent on the host E3 ubiquitin ligase UBE3A/E6AP but is independent of p53 degradation. E6 activates UBE3A to promote the ubiquitination and degradation of RAD23A, a shuttle protein required for delivering polyubiquitinated POLQ to the proteasome. Consequently, the loss of functional RAD23A phenocopies the effect of HPV16 E6, leading to POLQ stabilization and increased MMEJ activity. By elucidating the E6-UBE3A-RAD23A-POLQ axis, our findings reveal a novel mechanism through which HPV manipulates the host DNA repair machinery to promote its integration and oncogenic potential.

molecular biology↗

Elevated Temperatures Representing Heatwave Conditions Shift Active Nitrifying Communities and Their Viruses in Tidal Flats and Agricultural Soils

Global heatwave intensification associated with climate change will impact the nitrogen cycle, yet its effect on specific nitrifier groups or their interactions with viruses remains unclear. Using 13CO2-DNA-based stable isotope probing (SIP) coupled with metagenomics, we show that elevated temperatures associated with heatwave conditions restructure active nitrifying communities and their viruses in Yangtze River estuary tidal flats and adjacent agricultural soils. In tidal flats, high temperatures shifted active ammonia-oxidizing archaea and bacteria (AOA and AOB), and nitrite-oxidizing bacteria (NOB) from marine to terrestrial ecotypes. In contrast, heatwave conditions stimulated terrestrial ecotypes of AOA but suppressed AOB in agricultural soils. 13C-labeled nitrifier-infecting viruses also showed temperature-driven shifts in activity, lifestyle, and auxiliary metabolic genes in concert with hosts. Notably, AOA viruses carried the plastocyanin gene, potentially augmenting host metabolism. These findings demonstrate heatwaves drive complex shifts in nitrifier communities and their interactions with viruses, impacting global nutrient cycling under climate extremes.

microbiology↗

Widespread genomic heterogeneity at the type II NAD(P)H dehydrogenase locus predisposes Cryptosporidium to clofazimine resistance

The parasite Cryptosporidium is a leading cause of life-threatening diarrheal disease, and effective treatment is not available. The discovery of potent anti-Cryptosporidium activity of clofazimine, offered the opportunity to repurpose a drug already used to treat leprosy and tuberculosis. However, clofazimine failed in a human trial, which was attributed to poor bioavailability. Here, we observed differential susceptibility among parasite isolates which we exploit to map the mode of action to type II NADH dehydrogenase (NDH2) in an unbiased genetic cross. Targeted genetic ablation of NDH2 resulted in profound clofazimine resistance, and biochemical studies demonstrated NDH2 mediated electron transfer to clofazimine. Through genomic analyses we uncovered heterogeneity at the NDH2 locus for C. parvum and C. hominis and widespread carriage of a conserved attenuated allele across multiple continents. This heterogeneity allows parasites genomically linked through frequent sexual recombination to adjust to changing NDH2 requirements and predisposes Cryptosporidium to evade clofazimine treatment.

microbiology↗

Engineering circular guide RNA and CRISPR-Cas13d-encoding mRNA for the RNA editing of Adar1 in triple-negative breast cancer immunotherapy

Clustered regularly interspaced short palindromic repeat Cas endonuclease (CRISPR-Cas) systems, such as RNA-editing CRISPR-Cas13d, are poised to advance the gene therapy of various diseases. However, their clinical development has been challenged by 1) the limited biostability of linear guide RNAs (lgRNAs) susceptible to degradation, 2) the immunogenicity of prokaryotic microorganism-derived Cas proteins in human that restrains their long-term therapeutic efficacy, and 3) off-targeting gene editing caused by the prolonged Cas expression from DNA vectors. Here, we report the development of highly stable circular gRNAs (cgRNAs) and transiently-expressing Cas13d-encoding mRNA for efficient CRISPR-Cas13d editing of target mRNA. We first optimized cgRNA for CRISPR-Cas13d editing of adenosine deaminase acting on RNA type I (Adar1) transcript for the combination immunotherapy of triple negative breast cancer (TNBC). cgRNAs were synthesized by enzymatic ligation of lgRNA precursors. cgRNAs enhanced biostability with comparable Cas13d-binding affinity relative to lgRNA. Next, using ionizable lipid nanoparticles (LNPs), we co-delivered the resulting Adar1-targeting cgRNA with an mRNA encoding RfxCas13d (mRNA-RfxCas13d), a widely used Cas13d variant, to TNBC cells. As a result, relative to lgRNA, cgRNA significantly enhanced the efficiency of Adar1 knockdown with minimal collateral activity, which sensitized the cancer cells for cytokine-mediated cell apoptosis. In a 4T1 murine TNBC tumor model in syngeneic mice, Adar1-targeting cgRNA outperformed lgRNA for tumor immunotherapy in combination with immune checkpoint blockade (ICB). Collectively, these results demonstrate the great potential of cgRNA and mRNA-RfxCas13d for RNA-targeted gene editing.

bioengineering↗

Decoding functional genes across species with annotation-independent machine learning

Dissecting the genetic basis of complex traits across species is a challenge for traditional low-throughput, species-specific methods. To overcome these limitations, we introduce a computational framework that integrates cross-species comparative genomics and machine learning to identify functional genes for shared phenotypes, independent of prior annotation. Our method links orthologous gene group (OG) profiles to specific traits, enabling the powerful discovery of functional genes across diverse evolutionary clades. For plant-arbuscular mycorrhizal symbiosis, a notoriously difficult system, our model pinpointed a regulatory network by identifying 27 core plant-AM symbiosis genes among its top 50 candidate OGs, including the critical receptor SYMRK. The approach also proved highly effective for identifying functional genes related to the tested vertebrate skeletal development and multiple bacterial traits. Most notably, for bacterial motility, our model not only identified 63 known motility genes from the top 100 candidate OGs (of which 78 are present in Escherichia coli) but also guided the experimental validation of three novel essential genes. This annotation-independent strategy represents a paradigm shift in functional genomics, offering a scalable and universal engine to decode the genetic architecture of complex traits and illuminate the vast functional dark matter across the tree of life.

genomics↗

Disruption of Microhomology-mediated End-joining in Ewing Sarcoma

Ewing sarcoma (EwS) is a group of bone and soft tissue cancers in children and young adults. Since EwS cells have pronounced sensitivity to radiation and chemotherapy-induced DNA damage, the role of the oncoprotein, EWS-FLI1, in DNA repair is likely. Here, we demonstrate that EWS-FLI1 causes a defect in microhomology-mediated end-joining (MMEJ) repair. EWSR1 is a splicing factor that promotes the faithful splicing of the POLQ pre-mRNA, required for the expression of POL{Theta}, a critical protein in the MMEJ pathway. Expression of EWS-FLI1, or loss of EWSR1, causes exon 25 skipping of the POLQ transcript, decreased POL{Theta} expression, impaired MMEJ, and cellular sensitivity to inhibitors of the Fanconi Anemia (FA), NHEJ, or HR pathways, through the mechanism of synthetic lethality. Knockdown of EWS-FLI1 expression restores POL0 mitotic foci and increases MMEJ activity. Inhibitors of the FA, NHEJ, or HR therefore may provide a targeted therapy for patients with EwS. Highlights- Ewing sarcoma tumors have a deficiency in POL{theta} expression and a corresponding loss of MMEJ activity - EWSR1 is a splicing factor that interacts with other splicing factors such as FUBP1 and KHSRP/FUBP2 to accurately splice the POLQ mRNA. - The EWS-FLI1 fusion oncoprotein, or loss of EWSR1, causes a splicing defect, leading to exon25 skipping of the POLQ pre-mRNA and loss of POL{theta} expression - The MMEJ deficiency of EwS cells results in cellular sensitivity to inhibitors of Fanconi Anemia, Homologous Recombination or Non-Homologous End-Joining - Exon 25 skipping of POLQ mRNA is a predictive biomarker for HR inhibitors in human cancers

cancer biology↗

A Computational Framework for Analysis of cfDNA Fragmentation Profiles

Circulating cell-free DNA (cfDNA) has emerged as a promising non-invasive medium for studying tumor molecular profiles. Non-random fragmentation patterns in plasma cfDNA, particularly around nucleosome-depleted regions (NDRs) near transcription start sites (TSS), have been shown to reflect epigenetic regulation and gene expression. In this study, coverage profiles of the NDR were utilized to derive an NDR score, which was subsequently used as a proxy for inferring gene expression. To reduce transcript-to-transcript variability and enhance the clarity of these expression-associated signals, we implement a method for GC-bias correction of cfDNA samples. A computational framework (NDRDiff) was then developed to enable comparative analyses of NDR score profiles across different sample groups. The GC-bias correction preserved the overall trend of the NDR signal while improving the separation of gene expression levels, as demonstrated by comparisons of healthy donor cfDNA samples with matched blood RNA-seq data. Validation on a simulated dataset showed that NDRDiff achieved an area under the precision-recall curve (AUPRC) of 0.916, outperforming a standard t-test (AUPRC of 0.777). When applied to a comparison of healthy donor cfDNA and metastatic colorectal cancer (mCRC) cfDNA, NDRDiff identified 531 differential NDR score (DNS) genes that facilitated clear separation between the two groups. These DNS genes were found to correlate with tumor fraction estimates (down-regulated DNS genes: Pearson R = 0.89, p < 0.05; up-regulated DNS genes: Pearson R = -0.88, p < 0.05) and included CLDN4, BIN2, and IRAG2, which exhibit strong associations with colorectal cancer or blood cell expression signatures. Gene set enrichment analysis further revealed enrichment of colon and other gastrointestinal tissue signatures. Collectively, these findings underscore the potential of NDR-based cfDNA analysis as a minimally invasive tool for monitoring tumor-related molecular features in cancer.

cancer biology↗

Next-Generation saRNA Platforms: Systematic Screening and Engineering Enhances Superior Protein Expression and Organ-Specific Targeting for RNA Therapeutics

Self-amplifying RNA (saRNA), derived from alphaviruses, encodes nonstructural proteins (NSP1-4) that form a replicase complex, enabling prolonged and amplified protein expression at lower doses than conventional mRNA. However, its high immunogenicity and limited replication efficiency require optimization for improved protein expression. Here, we systematically optimized a widely used Venezuelan Equine Encephalitis Virus (VEEV)-based saRNA by refining its capping structure, nucleotide modifications, polyA tail length, and regulatory elements, achieving over 10-fold enhancement in protein expression compared to the wild-type. Additionally, we screened 28 alphavirus-derived saRNA constructs in vitro, selecting the top 3 candidates Everglades virus (EVEV), Mosso das Pedras virus (MDPV), and Rio Negro virus (RNV) for in vivo evaluation using SM102 lipid nanoparticle (LNP) formulations and luciferase reporters. These optimized saRNAs demonstrated sustained expression and distinct extrahepatic tissue-specific biodistribution, notably high spleen targeting compared to conventional mRNA. Such organ-specific expression profiles present novel strategies for targeted RNA therapeutics, and further integration with advanced delivery technologies could enhance the precision, efficacy, and therapeutic potential of mRNA-based treatments. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/644708v1_ufig1.gif" ALT="Figure 1"> View larger version (56K): org.highwire.dtl.DTLVardef@1eed9bdorg.highwire.dtl.DTLVardef@192815org.highwire.dtl.DTLVardef@196a8e9org.highwire.dtl.DTLVardef@2b6e53_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOTOC figureC_FLOATNO C_FIG

molecular biology↗

CD45-mediated apoptosis and IL2R downregulation by serine proteases from diarrheagenic bacteria

Most enteropathogens secrete one or more members of the serine protease autotransporters of Enterobacteriaceae (SPATE). We previously demonstrated that SPATE cleaves various O-linked glycoproteins on leukocytes, including the tyrosine phosphatase CD45RO. SPATE impairs leukocyte functions and triggers apoptosis in activated T cells in vitro. Here, we show that SPATE produced by pathogenic E. coli, Shigella, and the mouse pathogen Citrobacter rodentium cleaves not only CD45RO but also CD45 isoforms containing exons A and B. We found that the cleavage of CD45 in primary T cells from both human and murine sources correlated with decreased IL2RA (CD25) surface expression in a concentration-dependent manner. SPATE did not cleave CD25 or affect T cell activation. However, SPATE requires CD45 expression for the depletion of CD25 in activated T cells, as SPATE did not significantly impact CD25 in the Jurkat J45.01 cell line, which lacks CD45. More importantly, we discovered that J45.01 cells resisted SPATE-mediated apoptosis, whereas apoptotic wild-type Jurkat cells exhibited decreased surface expression of CD25. Furthermore, we observed that mice infected with C. rodentium lacking SPATE displayed lower mortality, delayed intestinal colonization, reduced inflammatory cytokines, and decreased leukocyte infiltration in the lamina propria while having a higher number of CD25+ T cells compared to mice infected with wild-type CR or the CR SPATE mutant expressing Crc2 in trans. Our data suggest that SPATE-producing pathogens trigger T-cell apoptosis through CD45 via a mechanism akin to IL2 deprivation, demonstrating that SPATE can act as immunomodulators at various levels of the immune system. SIGNIFICANCEWe have demonstrated for the first time that serine proteases (C2S) from clinically relevant pathogens, such as E. coli pathotypes and Shigella, can cleave leukocyte glycoproteins, including the tyrosine phosphatase CD45, which play crucial roles in cellular and immune functions. In this study, we discovered that C2S induces apoptosis in activated T cells through a previously unknown mechanism resembling IL-2 deprivation, mediated by CD45. Furthermore, we found that C2S is essential for bacterial virulence in vivo. This suggests that pathogens producing C2S may possess previously undescribed immunoregulatory functions that enhance their survival in the host and contribute to the disease process by eliminating T cells through the targeting of CD45 and the IL-2 receptor.

microbiology↗

Benchmarking AlphaFold3-like Methods for Protein-Peptide Complex Prediction

Protein-short peptide interactions are central mechanisms regulating signal transduction, chaperone functions, and drug targeting design. However, the precise prediction of their complex structures has long been constrained by the limited accuracy of traditional methods. The breakthrough of AlphaFold2 resolved the challenge of predicting protein monomer structures. Its derivative method, AlphaFold2-multimer, surpassed traditional docking approaches in predicting protein complexes, yet its accuracy remains suboptimal. AlphaFold3 and its replication models, such as Protenix, Chai-1, and Boltz-1, have further improved prediction accuracy for protein-protein interactions. To evaluate the performance of these methods in protein-short peptide structure prediction, this study conducted predictions and comprehensive comparisons on two benchmark datasets of protein-short peptide complexes. One dataset did not intentionally exclude structures from the training set of these methods, while the other did. For the former, the results demonstrate that the new-generation structural method significantly increased the success rate under stringent criteria (Fnat[&ge;] 0.8) to 70-80%, compared to AlphaFold2-multimer (53%), with Protenix achieving the highest accuracy at 80.8%. For the second dataset, AlphaFold2-multimer showed consistent performance, but the success rates of the new-generation methods all dropped significantly (to 40-56%). Our analysis suggests that the main challenge for the performance decline comes from the accurate prediction of binding sites. For all datasets, A multi-method combination strategy enabled a higher-quality prediction success rate compared to the individual models, highlighting synergistic advantages among methods. Notably, inter-model consistency analysis provided an efficient metric for selecting optimal predictions.

bioinformatics↗

The response of ETV6-NTRK3 condensates to TRK inhibitors elucidates their precise phase separationmechanism

NTRK fusion oncoproteins are considered to mediate oncogenesis in multiple rare cancers. These fusion oncoproteins form cytoplasmic kinase condensates to hyper-activate downstream signaling pathways. However, their responses to TRK inhibitors have not been investigated. Here we show that TRK inhibitors induce a quantity increasement and liquid-to-solid transition of ETV6-NTRK3 condensates. During this process, the ETV6-NTRK3 condensates undergo rapid dissolution and subsequent reemergence, with entirely altered components. We proposed a novel phase separation model for ETV6-NTRK3 that both ETV6 and NTRK3 fragments contribute to the condensates formation. These findings refresh the understanding of the phase separation mechanism of NTRK fusion proteins and provide basis for phenotype-based TRK inhibitor screening strategy.

cell biology↗

The protein translation initiation machinery is targetable for developing fast-killing therapeutics against the zoonotic Cryptosporidium parvum

Cryptosporidium parvum is a zoonotic apicomplexan parasite that causes moderate to severe watery diarrhea in humans and animals. It is one of the two major cryptosporidial species that infect humans, particularly those with weak or compromised immunity (e.g., children and AIDS patients). C. parvum is also one of the major pathogens causing diarrhea in neonatal farm ruminants (e.g., calves). However, fully effective drugs are still unavailable for medical or veterinary use to treat cryptosporidiosis. In the past decade or two, a number of key enzymes in the core metabolic pathways of Cryptosporidium have been explored as drug targets (e.g., energy metabolism, fatty acid synthesis, nucleotide synthesis, protein synthesis and modification), while the protein translation initiation machinery has been unexplored. Here, we report that C. parvum eukaryotic initiation factor 4A (CpeIF4A), a DEAD-box RNA helicase and part of the eIF4F complex (composed of eIF4A, eIF4E, and eIF4G), can be targeted for developing anti-cryptosporidial therapeutics. CpeIF4A can be inhibited by the selective inhibitor rocaglamide-A (Roc-A; a natural product from Aglaia plants). The inhibition of CpeIF4A activity by Roc-A impedes protein synthesis in the sporozoites of C. parvum (IC50 = 3.65-3.80 M) via tight binding to the CpeIF4A-RNA complex (Kd = 33.7 nM). This efficaciously lowers parasite growth in vitro (EC50 = 1.77 nM; selectivity index >1000) and oocyst production in vivo in IFN-{gamma} knockout mice (with a rapid drop on the second day post-administration at 0.5 mg/kg/day). These findings indicate that CpeIF4A can serve as a novel drug target, and that Roc-A is a promising anti-cryptosporidial lead compound for therapeutic development and structural optimization. Author summaryCryptosporidium parvum is a globally distributed protozoan parasite that infect both humans and animals. Cryptosporidial infection in hosts with weak or compromised immunity (e.g., AIDS patients, children or calves) can be severe or deadly, but fully effective treatments are yet unavailable. In the past decade or two, a number of potential drug targets in the core metabolic pathways in Cryptosporidium have been explored, but the protein translation machinery has been unexplored. Here, we report that the C. parvum eukaryotic initiation factor 4A (CpeIF4A), one of the key components in the protein translational machinery, can be targeted for developing fast-killing anti-cryptosporidial therapeutics. We show that CpeIF4A can be inhibited by the selective inhibitor rocaglamide-A (Roc-A), consequently suppressing the protein synthesis in the parasite via tight binding to the CpeIF4A-RNA complex. This efficaciously inhibits the parasite growth both in vitro and in vivo. The killing of C. parvum by Roc-A is fast and irreversible (parasiticidal). Our data indicate that the protein translational machinery is a novel drug target for developing fast-killing anti-cryptosporidial therapeutics, and that Roc-A is a promising lead compound for therapeutic development and structural optimization.

microbiology↗

Evolution of Salmonella Chromosomes and Its Influence on Gene Expression and Chromosomal Conformation

Salmonella is one of the most important bacterial pathogens in the world, causing an estimated 120 million infections each year. There is considerable diversity, with [~]2,600 serovars, but it remains unclear how the genomes have evolved as the species and subspecies of Salmonella differentiate. Here, we have reconstructed the ancient orthologous chromosomes of each major Salmonella lineage and traced their evolutionary process. In total, 911 rearrangement events were identified, with 64% of events occurring in a locus-specific way. Using RNA sequencing and multi-strain association analysis, we demonstrate that genetic rearrangements have a significant effect on gene expression across Salmonella lineages. Moreover, we perform chromosome conformation capture (3C) sequencing analysis, which demonstrates large variations for the organization of ter chromosomal interaction domains among Salmonella lineages. In conclusion, our work delineates the evolutionary trajectory of Salmonella chromosomes, and demonstrates the influence of rearrangements on gene expression profiles and chromosomal conformation. ImportanceThis study reconstructed the ancient orthologous chromosomes of the Salmonella genus, species and well-recognized subspecies, by which the trajectory of gene flow caused by genetic rearrangements was delineated chronologically. The rearrangements show apparent hotspot distribution property and are enriched with genes important for bacterial fitness. Correlation analysis further disclosed the general influence of the rearrangements on gene expression and the organization and conformation of chromosome interaction domains. The results provide new insights on the evolution of Salmonella chromosomes, especially the genetic rearrangements and their epigenetic consequences.

microbiology↗

Genome-wide investigation of outer membrane protein families under mosaic evolution in Escherichia coli

Several genes in Gram-negative bacteria encoding outer membrane proteins (OMPs) have been reported to show patterns of mosaic evolution featured by mixture of negative selection and local recombination. Here, we proposed a strategy, and applied it to screen OMPs under mosaic evolution in Escherichia coli in the genome level. In total, 21 OMP families, including 16 new ones, were detected with the typical patterns of mosaic evolution. An abosolute majority of the protein families are conserved in E. coli for the composition, genomic loci and the overall structures. Highly Variable Regions (HVRs) can be recognized, which are frequently located extracellularly within the protruding loops. There are only limited number of major HVR sequence types, within which positively selected sites can be detected ocassionally. Based on the simulated results of multiple models, the OMPs under mosaic evolution are often with good antigenicity, with HVRs of various sequence types coinciding with the B-cell epitopes of the strongest immunogenicity. The study futher broadened our understanding of the characteristics of mosaic evolution and the functions of OMPs in Gram-negative bacteria, laying an important foundation for their potential translational applications. ImportanceIt is important to understand the evolutionary mechanisms of bacterial OMP-encoding genes, which would facilitate the development of anti-bacterial reagents. This study made the first genome-wide screening of bacterial OMPs under mosaic evolution, and increased the list of candidate OMP families by 3 folds in E. coli, far more than we expected. The study further confirmed the hypothesis about the evolutionary, micro-evolutionary and structural features of these OMPs, and facilitated the functional theory of mosaic evolution. Moreover, the findings of limited HVR sequence types and strong immunogenicity of HVRs paved important foundation for application of these OMPs and their HVRs in development of antibodies or other anti-bacterial treatment.

microbiology↗

Multi-modal profiling identifies CD4+CXCR5+PD-1- Tfh cells as prognostic and predictive biomarkers for response to R-CHOP therapy in human DLBCL

Despite the improvements in clinical outcomes for patients with Diffuse Large B-Cell Lymphoma (DLBCL), a significant proportion of those patients still face challenges with refractory/relapsed (R/R) disease after receiving first-line R-CHOP treatment. Characterizing the heterogeneity of the tumor microenvironment (TME) in diffuse large B cell lymphoma (DLBCL) is crucial for understanding relapsed/refractory disease. However, the complex and diverse nature of the TME has impeded progress. Here, using single-cell RNA sequencing(scRNA-seq), we explored the DLBCL landscape at single-cell resolution, profiling 77,344 cells from both primary and relapsed DLBCL patients. We further investigated the shared and distinct molecular and cellular features of tumor microenvironment in both primary and relapsed DLBCL tumors by integrating next-generation DNA sequencing data and multiple scRNA-seq datasets from total 72,351 cells. Our results demonstrated that there was a significant decrease of CD4+CXCR5+PD-1- Tfh cells, along with excessive activation of the TNF-NF{kappa}B signaling pathways in malignant B cells in R/R disease. Furthermore, by using multiplex IHC, we confirmed that CD4+CXCR5+PD-1- Tfh cells are prognostic and predictive biomarkers for response to R-CHOP treatment. As a proof of concept, we successfully generated mutilplexed images of CD4+CXCR5+PD-1- Tfh cells from a single DAPI staining in human DLBCL tissues through using generative artificial intelligence. Our study offers critical insights into the heterogeneity and molecular features of DLBCL, shedding light on the crucial role of CD4+CXCR5+PD-1- Tfh cells in the recurrent process. HighlightsO_LIShared and distinct molecular and cellular features of tumor microenvironment in both primary and relapsed DLBCL tumors; C_LIO_LIThe characteristic of relapsed DLBCL TME is a dysfunctional immune microenvironment with a significant decrease of CD4+CXCR5+PD-1- Tfh cells. C_LIO_LICD4+CXCR5+PD-1- Tfh cells are prognostic and predictive biomarkers for response to R-CHOP treatment C_LIO_LIDetermination of CD4+CXCR5+PD-1- Tfh cells in human DLBCL tissues through using generative artificial intelligence. C_LI

immunology↗

Proteolysis-targeting vaccines (PROTAVs) for robust tumor combination immunotherapy

Protein/peptide subunit vaccines are promising to promote the tumor therapeutic efficacy of immune checkpoint blockade (ICB). However, current protein/peptide vaccines elicit limited antitumor T cell responses, leading to suboptimal therapeutic efficacy. Here, we present proteolysis-targeting vaccines (PROTAVs) that facilitate antigen proteolytic processing and cross-presentation to potentiate T cell responses for robust ICB combination immunotherapy of melanoma. PROTAVs are modular conjugates of protein/peptide antigens, E3 ligase-binding ligands, and linkers. In antigen-presenting cells (APCs), PROTAVs bind to E3 ligases to rapidly ubiquitinate PROTAV antigens, facilitating antigen proteolytic processing by proteasome, and thereby promoting antigen cross-presentation to T cells and potentiating CD8+ T cell responses. We developed a melanoma PROTAV using a tandem peptide of trivalent melanoma-associated antigens. Co-delivered by lipid nanoparticles (LNPs) with bivalent immunostimulant adjuvants, this PROTAV promotes the quantity and quality of melanoma-specific CD8+ T cells in mice. Further, combining PROTAV and ICB ameliorates the immunosuppressive melanoma microenvironment. As a result, PROTAV and ICB combination enhances melanoma complete regression rates and eradicated 100% large BrafV600E melanoma without recurrence in syngeneic mice. PROTAVs hold the potential for robust tumor combination immunotherapy.

bioengineering↗

Integrated single-cell RNA-seq analysis revealed PTN secreted by fibroblasts acting on itself and macrophages via SDC4 ligand in myocardial hypertrophy

BackgroundHypertrophic cardiomyopathy (HCM) is characterized by massive myocardial hypertrophy, which is the most frequent cause of sudden death and can lead to heart failure (HF) or stroke. The objective of this study was to explore the communication network among various cells in the heart of pathological HCM derived from transverse aortic constriction (TAC) mouse model, and investigate the potential mechanism through data mining, biological informatics analysis, and experimental validation. Methods and ResultsThe integrated analyses including CellChat, Seurat, gene ontology (GO), pseudo-time trajectory analysis, and weighted gene co-expression network analysis (WGCNA) were performed based on the single-cell RNA-seq data (scRNA-seq). In vitro tests were conducted to verify bioinformatic analysis findings through enzyme-linked immunosorbent assay (ELISA), real-time quantitative PCR (RT-qPCR), Edu staining, and transwell assay. In vivo tests were also performed to further verify bioinformatic analysis findings by western blot and immunofluorescence assays based on our established TAC mouse model with myocardial hypertrophy. Our results showed that in the heart of TAC mouse, the interaction between cardiac fibroblasts and macrophages was most common, and the increasing pleiotrophin (PTN) secreted by cardiac fibroblasts could promote themselves proliferation or invasion as well as stimulate macrophage activation to release inflammatory cytokines, such as TNF-, IL-6, Cox-2, Cd83, Egr2, and IL-10 through acting on its ligand recombinant Syndecan 4 (SDC4), which may affect cardiomyocyte normal function and eventually cause HCM. This study first demonstrated that PTN derived from cardiac fibroblasts may act on SDC4 to play crucial role in myocardial hypertrophy, which may be a potential therapeutic targets for patients with pathological HCM. ConclusionsIn this study, the complex interaction network between cardiac fibroblasts and macrophages of TAC mice based on the scRNA-seq data was investigated, and we found that the increasing PTN secreted by cardiac fibroblasts under cardiac pressure overload could promote themselves proliferation or invasion as well as stimulate macrophage activation to release inflammatory cytokines through acting on SDC4 ligand, which may affect cardiomyocyte normal function and eventually cause HCM. In addition, our study suggested that PTN derived from cardiac fibroblasts may act on SDC4 ligand to play crucial role in myocardial hypertrophy, which may be a potential therapeutic targets for patients with pathological HCM.

cell biology↗

Human birth tissue products as a regenerative medicine to inhibit post-surgical pain through multi-modal action

Pain after surgery causes significant suffering. Opioid analgesics cause severe side effects and accidental death. Therefore, there is an urgent need to develop non-opioid therapies for managing post-surgical pain. Local application of Clarix Flo (FLO), a human amniotic membrane (AM) product, attenuated established post-surgical pain hypersensitivity without exhibiting known side effects of opioid use in mice. This effect was achieved through direct inhibition of nociceptive dorsal root ganglion (DRG) neurons via CD44-dependent pathways. We further purified the major matrix component, the heavy chain-hyaluronic acid/pentraxin 3 (HC-HA/PTX3) from human AM that has greater purity and water solubility than FLO. HC-HA/PTX3 replicated FLO-induced neuronal and pain inhibition. Mechanistically, HC-HA/PTX3 induced cytoskeleton rearrangements to inhibit sodium current and high-voltage activated calcium current on nociceptive neurons, suggesting it is a key bioactive component mediating pain relief. Collectively, our findings highlight the potential of naturally derived biologics from human birth tissues as an effective non-opioid treatment for post-surgical pain. Moreover, we unravel the underlying mechanisms of pain inhibition induced by FLO and HC-HA/PTX3.

neuroscience↗