Calcium signaling instructs NIPBL recruitment at active enhancers and promoters via distinct mechanisms to reconstruct genome compartmentalization.

During developmental progression the genomes of immune cells undergo large-scale changes in chromatin folding. However, insights into signaling pathways and epigenetic control of nuclear architecture remain rudimentary. Here, we found that in activated neutrophils calcium influx rapidly recruited the cohesin-loading factor NIPBL to thousands of active enhancers and promoters to dictate widespread changes in compartment segregation. NIPBL recruitment to enhancers and promoters occurred with distinct kinetics. The induction of NIPBL-binding was coordinate with increased P300, BRG1 and RNA polymerase II occupancy. NIPBL-bound enhancers were associated with NFAT, PU.1, and CEBP cis elements, whereas NIPBL-bound promoters were enriched for GC-rich DNA sequences. Using an acute degradation system, we found that the histone acetyltransferases P300 and CBP maintained H3K27ac abundance and facilitated NIPBL occupancy at enhancers and that active transcriptional elongation is essential to maintain H3K27ac abundance. Chromatin remodelers, containing either of the mutually exclusive BRG1 and BRM ATPases, promoted NIPBL recruitment at active enhancers. Conversely, at active promoters, depletion of BRG1 and BRM showed minimal effect on NIPBL occupancy. Finally, we found that calcium signaling in both primary innate and adaptive immune cells swiftly induced NIPBL occupancy. Collectively, these data reveal how transcriptional regulators, histone acetyltransferases, chromatin remodelers, and transcription elongation promote NIPBL occupancy at active enhancers while the induction of NIPLB occupancy at promoters is primarily associated with GC-rich DNA sequences.

Upon microbial challenge, human neutrophils undergo rapid changes in nuclear architecture and chromatin folding to orchestrate an immediate inflammatory gene program.

Differentiating neutrophils undergo large-scale changes in nuclear morphology. How such alterations in structure are established and modulated upon exposure to microbial agents is largely unknown. Here, we found that prior to encounter with bacteria, an armamentarium of inflammatory genes was positioned in a transcriptionally passive environment suppressing premature transcriptional activation. Upon microbial exposure, however, human neutrophils rapidly (<3 h) repositioned the ensemble of proinflammatory genes toward the transcriptionally permissive compartment. We show that the repositioning of genes was closely associated with the swift recruitment of cohesin across the inflammatory enhancer landscape, permitting an immediate transcriptional response upon bacterial exposure. We found that activated enhancers, marked by increased deposition of H3K27Ac, were highly enriched for cistromic elements associated with PU.1, CEBPB, TFE3, JUN, and FOSL2 occupancy. These data reveal how upon microbial challenge the cohesin machinery is recruited to an activated enhancer repertoire to instruct changes in chromatin folding, nuclear architecture, and to activate an inflammatory gene program.

Comprehensive characterization of neutrophil genome topology.

Neutrophils are responsible for the first line of defense against invading pathogens. Their nuclei are uniquely structured as multiple lobes that establish a highly constrained nuclear environment. Here we found that neutrophil differentiation was not associated with large-scale changes in the number and sizes of topologically associating domains (TADs). However, neutrophil genomes were enriched for long-range genomic interactions that spanned multiple TADs. Population-based simulation of spherical and toroid genomes revealed declining radii of gyration for neutrophil chromosomes. We found that neutrophil genomes were highly enriched for heterochromatic genomic interactions across vast genomic distances, a process named supercontraction. Supercontraction involved genomic regions located in the heterochromatic compartment in both progenitors and neutrophils or genomic regions that switched from the euchromatic to the heterochromatic compartment during neutrophil differentiation. Supercontraction was accompanied by the repositioning of centromeres, pericentromeres, and long interspersed nuclear elements (LINEs) to the neutrophil nuclear lamina. We found that Lamin B receptor expression was required to attach centromeric and pericentromeric repeats but not LINE-1 elements to the lamina. Differentiating neutrophils also repositioned ribosomal DNA and mininucleoli to the lamina-a process that was closely associated with sharply reduced ribosomal RNA expression. We propose that large-scale chromatin reorganization involving supercontraction and recruitment of heterochromatin and nucleoli to the nuclear lamina facilitates the folding of the neutrophil genome into a confined geometry imposed by a multilobed nuclear architecture.

Fibrocyte: A missing piece in the pathogenesis of fibrous epulis.

OBJECTIVES: To explore the role of fibrocytes in the recurrence and calcification of fibrous epulides. METHODS: Different subtypes of fibrous epulides and normal gingival tissue specimens were first collected for histological and immunofluorescence analyses to see if fibrocytes were present and whether they differentiated into myofibroblasts and osteoblasts upon stimulated by transforming growth factor-ß1 (TGF-ß1). Electron microscopy and elemental analysis were used to characterize the extracellular microenvironment in different subtypes of fibrous epulides. Human peripheral blood mononuclear cells (PBMCs) were subsequently isolated from in vitro models to mimic the microenvironment in fibrous epulides to identify whether TGF-ß1 as well as the calcium and phosphorus ion concentration in the extracellular matrix (ECM) of a fibrous epulis trigger fibrocyte differentiation. RESULTS: Fibrous epulides contain fibrocytes that accumulate in the local inflammatory environment and have the ability to differentiate into myofibroblasts or osteoblasts. TGF-ß1 promotes fibrocytes differentiation into myofibroblasts in a concentration-dependent manner, while TGF-ß1 stimulates the fibrocytes to differentiate into osteoblasts when combined with a high calcium and phosphorus environment. CONCLUSIONS: Our study revealed fibrocytes play an important role in the fibrogenesis and osteogenesis in fibrous epulis, and might serve as a therapeutic target for the inhibition of recurrence of fibrous epulides.

A combined protein toxin screening based on the transcriptome and proteome of Solenopsis invicta.

BACKGROUND: Multi-omics technology provides a good tool to analyze the protein toxin composition and search for the potential pathogenic factors of Solenopsis invicta, under the great harm of the accelerated invasion in southern China. METHODS: Species collection, functional annotation, toxin screening, and 3D modeling construction of three interested toxins were performed based on the successfully constructed transcriptome and proteome of S. invicta. RESULTS: A total of 33,231 unigenes and 721 proteins were obtained from the constructed transcriptome and proteome, of which 9,842 (29.62%) and 4,844 (14.58%) unigenes, as well as 469 (65.05%) and 71 (99.45%) proteins were annotated against the databases of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes, respectively. After comparing with the uniprot toxin database, a total of 316 unigenes and 47 proteins (calglandulin, venom allergen 3, and venom prothrombin activator hopsarin-D, etc.) were successfully screened. CONCLUSIONS: The update of annotations at the transcriptome and proteome levels presents a progression in the comprehension of S. invicta in China. We also provide a protein toxin list that could be used for further exploration of toxicity as well as its antagonistic strategy by S. invicta.

Synthesis of harmine-nitric oxide donor derivatives as potential antitumor agents.

To further improve the anti-tumor activity of Harmine (HM), we took the hybridization approach and synthesized harmine derivatives-furoxan hybrids containing nitric oxide (NO) releasing parts by connecting NO donors with anti-tumor active fragments to harmine. Then, the synthesized compounds were evaluated for their in vitro cytotoxicity against five human cancer cell lines. Among them, compound 10 was found to have the strongest antiproliferative activity against HepG2 (IC50 = 1.79 µM). In addition, compound 10 produced high levels of NO in vitro, verifying that the release of NO was closely correlated to the antiproliferative activity. In addition, Compound 10 also showed good plasma stability. Finally, we also preliminarily investigated the acute toxicity of compound 10 in mice and assessed the absorption of compound 10 by Caco-2 cell permeability assay. In brief, the remarkable biological characteristics of the new harmine derivatives-furoxan hybrids may make them promising candidates for human cancer intervention.

Toxicity evaluation, toxin screening and its intervention of the jellyfish Phacellophora camtschatica based on a combined transcriptome-proteome analysis.

BACKGROUND: The application of multi-omics technologies provides a new perspective to solve three main problems including species identification, toxin screening and effective antagonist conformation in the studies of marine toxic jellyfish. METHODS: A series of transcriptome-proteome based analysis accompanied with toxicity evaluations were performed for the ornamental jellyfish Phacellophora camtschatica. RESULTS: Through combined morphological observation and Cytochrome c oxidase subunit Ⅰ (CO1) molecular alignment, the sample jellyfish was identified as P. camtschatica. A total of 25,747 unigenes and 3058 proteins were obtained from the successfully constructed transcriptome and proteome, in which 6869 (26.68%) and 6618 (25.70%) unigenes, as well as 2536 (82.93%) and 2844 (93.00%) proteins were annotated against the databases of Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), respectively. The jellyfish displayed obvious in vivo lethal effects with significant increases of multi-organ functional indexes as well as in vitro activities. Total of 62 toxins from 120 toxin-related unigenes were screened including 16 metalloproteases, 11 phospholipases and others. Moreover, 11 toxins were further screened by using the erythrocyte model, where the zinc metalloproteinase nas-15-like (1) was the most abundant. Finally, Diltiazem greatly improved the survival rate while EDTA slightly prolonged the survival time in ICR mice. CONCLUSION: P. camtschatica is a poisonous jellyfish with diversified toxic components, in which metalloproteinase probably plays an important role in toxicities, and excessive Ca2+ entry may be the main mechanism of systemic lethal toxicity.

The role of mitophagy in the mechanism of genioglossal dysfunction caused by chronic intermittent hypoxia and the protective effect of adiponectin.

PURPOSE: Dysfunction of the genioglossus muscle is important in the pathogenesis of obstructive sleep apnea due to chronic intermittent hypoxia (CIH). Mitochondrial impairment resulting from hypoxia is mitigated by mitophagy to avoid cell apoptosis in cardiomyocytes. This project was designed to explore the effects of CIH on mitophagy in the genioglossus muscle and the impact of adiponectin (Ad). METHODS: One hundred eighty male SD rats were randomly divided into 3 groups (normal control [NC], CIH, and CIH + Ad groups), with 60 rats in each group observed for 5 weeks. Comparisons of serum Ad levels, mitochondrial structure and function, mitophagy, and cell apoptosis in the genioglossus were made at different time points. RESULTS: (1) The CIH group was significantly different from the NC group as follows: During the first 3 weeks, serum Ad levels, the reactive oxygen species (ROS), relative proteins and mRNA of mitophagy, autophagy biomarker LC3-II, and autophagosomes increased, while during the last 2 weeks, most parameters decreased. (2) There was no difference among the 3 groups in mitochondrial structure and function-associated mRNA during the first 3 weeks, while damaged mitochondrial structures were growing during the last 2 weeks. Exacerbation of apoptosis was also detected in the last 2 weeks. (3) All of the damage was partially alleviated in the CIH + Ad group in contrast to CIH group at the end of this study. CONCLUSION: Disturbances of genioglossal mitophagy could be related to damaged mitochondrial structure and function induced by CIH, which could be alleviated by supplementation of exogenous Ad via increasing mitophagy.

The distinct microbial community in Aurelia coerulea polyps versus medusae and its dynamics after exposure to 60Co-γ radiation.

Radiation (e.g., nuclear leakage) is a common harmful factor in the ocean that potentially affects the microbial community in nearby benthic hosts such as jellyfish polyps, which is essential for the maintenance of jellyfish populations and high-quality medusae. After comparison with the microbial community of medusae, the effect of 60Co-γ on the microbial community in Aurelia coerulea polyps was dynamically tested using 16S rRNA gene sequencing. Our results suggested that Proteobacteria (76.19 ± 3.24%), Tenericutes (12.93 ± 3.20%) and Firmicutes (8.33 ± 1.06%) are most abundant in medusae, while Proteobacteria (29.49 ± 2.29%), Firmicutes (46.25 ± 5.59%), and Bacteroidetes (20.16 ± 2.65%) are the top three phyla in polyps. After 60Co-γ radiation, the proportion of Proteobacteria increased from 29.49 ± 2.29% to 59.40 ± 3.09% over 5 days, while that of Firmicutes decreased from 46.25 ± 5.59% to 13.58 ± 3.74%. At the class level, Gammaproteobacteria continually increased during the 5 days after radiation exposure, whereas Bacilli declined, followed by partial recovery, and Alphaproteobacteria and Flavobacteriia remained almost unchanged. Intriguingly, Staphylococcus from Firmicutes and three other genera, Rhodobacter, Vibrio, and Methylophaga, from Proteobacteria greatly overlapped according to their KEGG functions. It is concluded that the microbial community in A. coerulea polyps is distinct from that in the medusae and is greatly affected by 60Co-γ exposure, with a growth (0-3 d) period and a redistribution (3-5 d) period. The dynamic change in the microbial community is probably an important self-defense process in response to external interference that is regulated by the host's physiological characteristics and the intense interspecific competition among symbiotic microbes with similar functions and functional redundancies.

Cell-type-specific control of enhancer activity by H3K9 trimethylation.

Cell-type-specific control of gene expression is critical for the development of multicellular organisms. To investigate the mechanisms which underlie this, we have studied the regulation of the model genes Mdc and Il12b, whose stimulus-induced expression is tightly restricted to specific cells of the immune system. Surprisingly, we find that neither the promoter nor the enhancer sequences of these genes are sufficient to direct this cell-type specificity. Instead, the activities of upstream enhancers are repressed in nonexpressing cells by high levels of trimethylated H3K9 in their flanking regions. Genome-wide analysis indicates that this manner of regulation is shared by numerous enhancers of cell-type-specific genes. In dendritic cells and macrophages, the stimulus-induced demethylase Jmjd2d controls H3K9me3 levels at these regions, and is thereby required for Mdc and Il12b transcription. By experimentally assaying multiple enhancers in a variety of cell types, we show that regulation by H3K9me3 is a widely used mechanism which imparts specificity to the activities of otherwise broadly functional enhancers.

First report of sparganosis manifested by pleuritis and decreased peripheral blood eosinophils in Jiangsu province, China.

Sparganosis is a parasitic infection caused by the metacestode stage of Spirometra mansoni and some other related diphyllobothriidean cestodes. Although various internal organs were involved in sparganum infection, pulmonary and pleural involvement is rarely reported. We herein report an uncommon form of sparganosis manifested by pleuritis and decreased peripheral blood eosinophils. Sparganum worms were found in the pleural effusion accidentally and confirmed by pathological diagnosis. After being treated with praziquantel for 10 days, the patient's symptoms, laboratory examinations, and imaging findings were improved gradually.

A feed-forward circuit controlling inducible NF-κB target gene activation by promoter histone demethylation.

Activation of transcription from a silenced state is crucial to achieve specific gene expression in many biological contexts. Methylation of lysine 9 on histone H3 (H3K9) is widely associated with transcriptional silencing, and its disappearance is linked to the activation of several inflammatory genes by NF-κB. Here we describe that this event is controlled by a feed-forward circuit catalyzed by the activity of the histone demethylase Aof1 (also known as Lsd2/Kdm1b). We find that Aof1 is required for removal of dimethyl H3K9 at specific promoters, and thereby it controls stimulus-induced recruitment of NF-κB and gene expression. However, Aof1 is itself recruited by interaction with the c-Rel subunit of NF-κB, which is found at low levels associated with promoters in unstimulated cells. Thus, at these tightly regulated genes, NF-κB functions both as a transcriptional activator and as an upstream targeting signal that marks promoters to be derepressed by histone demethylation.

A hierarchical Bilayered scaffold for periodontal complex structure regeneration.

The periodontal tissue comprises alveolar bone, cementum, and periodontal ligament (PDL), forming a highly hierarchical architecture. Although current therapies could regenerate the hard tissue well, the simultaneous reconstruction of hard and soft tissue remains a great clinical challenge with the major difficulty in highly orientated PDL regeneration. Using the unidirectional freeze-casting method and biomimetic mineralization technique, we construct a hierarchical bilayer scaffold with the aligned chitosan scaffold with ZIF-8 resembling PDL, and intrafibrillarly mineralized collagen resembling alveolar bone. The hierarchical bilayer scaffold exhibits different geomorphic clues and chemical microenvironments to realize a perfect simulation of the natural periodontal hierarchical architecture. The aligned scaffold with ZIF-8 could induce the fibrogenic differentiation of bone mesenchymal stromal cells (BMSCs), and the mineralized scaffold could induce osteogenic differentiation of BMSCs. The hierarchical bilayer scaffold could simulate periodontal complex tissue, exhibiting great promise for synchronized multi-tissue regeneration of periodontal tissue.

Joint GWAS and WGCNA Identify Genes Regulating the Isoflavone Content in Soybean Seeds.

Isoflavone is a secondary metabolite of the soybean phenylpropyl biosynthesis pathway with physiological activity and is beneficial to human health. In this study, the isoflavone content of 205 soybean germplasm resources from 3 locations in 2020 showed wide phenotypic variation. A joint genome-wide association study (GWAS) and weighted gene coexpression network analysis (WGCNA) identified 33 single-nucleotide polymorphisms and 11 key genes associated with soybean isoflavone content. Gene ontology enrichment analysis, gene coexpression, and haplotype analysis revealed natural variations in the Glyma.12G109800 (GmOMT7) gene and promoter region, with Hap1 being the elite haplotype. Transient overexpression and knockout of GmOMT7 increased and decreased the isoflavone content, respectively, in hairy roots. The combination of GWAS and WGCNA effectively revealed the genetic basis of soybean isoflavone and identified potential genes affecting isoflavone synthesis and accumulation in soybean, providing a valuable basis for the functional study of soybean isoflavone.

Microbial Diversity and Screening for Potential Pathogens and Beneficial Bacteria of Five Jellyfish Species-Associated Microorganisms Based on 16S rRNA Sequencing.

Jellyfish, microorganisms, and the marine environment collectively shape a complex ecosystem. This study aimed to analyze the microbial communities associated with five jellyfish species, exploring their composition, diversity, and relationships. Microbial diversity among the species was assessed using 16S rRNA gene sequencing and QIIME analysis. Significant differences in bacterial composition were found, with distinct dominant taxa in each species: Mycoplasmataceae (99.21%) in Aurelia coerulea, Sphingomonadaceae (22.81%) in Cassiopea andromeda, Alphaproteobacteria_unclassified (family level) (64.09%) in Chrysaora quinquecirrha, Parcubacteria_unclassified (family level) (93.11%) in Phacellophora camtschatica, and Chlamydiaceae (35.05%) and Alphaproteobacteria_unclassified (family level) (38.73%) in Rhopilema esculentum. C. andromeda showed the highest diversity, while A. coerulea exhibited the lowest. Correlations among dominant genera varied, including a positive correlation between Parcubacteria_unclassified (genus level) and Chlamydiaceae_unclassified (genus level). Genes were enriched in metabolic pathways and ABC transporters. The most abundant potential pathogens at the phylum level were Proteobacteria, Tenericutes, Chlamydiae, and Epsilonbacteraeota. The differing microbial compositions are likely influenced by species and their habitats. Interactions between jellyfish and microorganisms, as well as among microorganisms, showed interdependency or antagonism. Most microbial gene functions focused on metabolic pathways, warranting further study on the relationship between pathogenic bacteria and these pathways.

Exploring the Link Between Autophagy-Lysosomal Dysfunction and Early Heterotopic Ossification in Tendons.

Heterotopic ossification (HO), the pathological formation of bone within soft tissues such as tendon and muscle, is a notable complication resulting from severe injury. While soft tissue injury is necessary for HO development, the specific molecular pathology responsible for trauma-induced HO remains a mystery. The previous study detected abnormal autophagy function in the early stages of tendon HO. Nevertheless, it remains to be determined whether autophagy governs the process of HO generation. Here, trauma-induced tendon HO model is used to investigate the relationship between autophagy and tendon calcification. In the early stages of tenotomy, it is observed that autophagic flux is significantly impaired and that blocking autophagic flux promoted the development of more rampant calcification. Moreover, Gt(ROSA)26sor transgenic mouse model experiments disclosed lysosomal acid dysfunction as chief reason behind impaired autophagic flux. Stimulating V-ATPase activity reinstated both lysosomal acid functioning and autophagic flux, thereby reversing tendon HO. This present study demonstrates that autophagy-lysosomal dysfunction triggers HO in the stages of tendon injury, with potential therapeutic targeting implications for HO.

Biomimetic Self-Maturation Mineralization System for Enamel Repair.

Enamel repair is crucial for restoring tooth function and halting dental caries. However, contemporary research often overlooks the retention of organic residues within the repair layer, which hinders the growth of dense crystals and compromises the properties of the repaired enamel. During the maturation of natural enamel, the organic matrix undergoes enzymatic processing to facilitate further crystal growth, resulting in a highly mineralized tissue. Inspired by this process, a biomimetic self-maturation mineralization system is developed, comprising ribonucleic acid-stabilized amorphous calcium phosphate (RNA-ACP) and ribonuclease (RNase). The RNA-ACP induces initial mineralization in the form of epitaxial crystal growth, while the RNase present in saliva automatically triggers a biomimetic self-maturation process. The mechanistic study further indicates that RNA degradation prompts conformational rearrangement of the RNA-ACP, effectively excluding the organic matter introduced earlier. This exclusion process promotes lateral crystal growth, resulting in the generation of denser enamel-like apatite crystals that are devoid of organic residues. This strategy of eliminating organic residues from enamel crystals enhances the mechanical and physiochemical properties of the repaired enamel. The present study introduces a conceptual biomimetic mineralization strategy for effective enamel repair in clinical practice and offers potential insights into the mechanisms of biomineral formation.

Bacteria-mediated resistance of neutrophil extracellular traps to enzymatic degradation drives the formation of dental calculi.

Dental calculi can cause gingival bleeding and periodontitis, yet the mechanism underlying the formation of such mineral build-ups, and in particular the role of the local microenvironment, are unclear. Here we show that the formation of dental calculi involves bacteria in local mature biofilms converting the DNA in neutrophil extracellular traps (NETs) from being degradable by the enzyme DNase I to being degradation resistant, promoting the nucleation and growth of apatite. DNase I inhibited NET-induced mineralization in vitro and ex vivo, yet plasma DNases were ineffective at inhibiting ectopic mineralization in the oral cavity in rodents. The topical application of the DNA-intercalating agent chloroquine in rodents fed with a dental calculogenic diet reverted NET DNA to its degradable form, inhibiting the formation of calculi. Our findings may motivate therapeutic strategies for the reduction of the prevalence of the deposition of bacteria-driven calculi in the oral cavity.

Advances in materials-based therapeutic strategies against osteoporosis.

Osteoporosis is caused by the disruption in homeostasis between bone formation and bone resorption. Conventional management of osteoporosis involves systematic drug administration and hormonal therapy. These treatment strategies have limited curative efficacy and multiple adverse effects. Biomaterials-based therapeutic strategies have recently emerged as promising alternatives for the treatment of osteoporosis. The present review summarizes the current status of biomaterials designed for managing osteoporosis. The advantages of biomaterials-based strategies over conventional systematic drug treatment are presented. Different anti-osteoporotic delivery systems are concisely addressed. These materials include injectable hydrogels and nanoparticles, as well as anti-osteoporotic bone tissue engineering materials. Fabrication techniques such as 3D printing, electrostatic spinning and artificial intelligence are appraised in the context of how the use of these adjunctive techniques may improve treatment efficacy. The limitations of existing biomaterials are critically analyzed, together with deliberation of the future directions in biomaterials-based therapies. The latter include discussion on the use of combination strategies to enhance therapeutic efficacy in the osteoporosis niche.

Optimization of Lactoferrin-Derived Amyloid Coating for Enhancing Soft Tissue Seal and Antibacterial Activity of Titanium Implants.

A poor seal of the titanium implant-soft tissue interface provokes bacterial invasion, aggravates inflammation, and ultimately results in implant failure. To ensure the long-term success of titanium implants, lactoferrin-derived amyloid is coated on the titanium surface to increase the expression of cell integrins and hemidesmosomes, with the goal of promoting soft tissue seal and imparting antibacterial activity to the implants. The lactoferrin-derived amyloid coated titanium structures contain a large number of amino and carboxyl groups on their surfaces, and promote proliferation and adhesion of epithelial cells and fibroblasts via the PI3K/AKT pathway. The amyloid coating also has a strong positive charge and possesses potent antibacterial activities against Staphylococcus aureus and Porphyromonas gingivalis. In a rat immediate implantation model, the amyloid-coated titanium implants form gingival junctional epithelium at the transmucosal region that resembles the junctional epithelium in natural teeth. This provides a strong soft tissue seal to wall off infection. Taken together, lactoferrin-derived amyloid is a dual-function transparent coating that promotes soft tissue seal and possesses antibacterial activity. These unique properties enable the synthesized amyloid to be used as potential biological implant coatings.