Microbiota regulates the TET1-mediated DNA hydroxymethylation program in innate lymphoid cell differentiation.

Innate lymphoid cell precursors (ILCPs) develop into distinct subsets of innate lymphoid cells (ILCs) with specific functions. The epigenetic program underlying the differentiation of ILCPs into ILC subsets remains poorly understood. Here, we reveal the genome-wide distribution and dynamics of the DNA methylation and hydroxymethylation in ILC subsets and their respective precursors. Additionally, we find that the DNA hydroxymethyltransferase TET1 suppresses ILC1 but not ILC2 or ILC3 differentiation. TET1 deficiency promotes ILC1 differentiation by inhibiting TGF-ß signaling. Throughout ILCP differentiation at postnatal stage, gut microbiota contributes to the downregulation of TET1 level. Microbiota decreases the level of cholic acid in the gut, impairs TET1 expression and suppresses DNA hydroxymethylation, ultimately resulting in an expansion of ILC1s. In adult mice, TET1 suppresses the hyperactivation of ILC1s to maintain intestinal homeostasis. Our findings provide insights into the microbiota-mediated epigenetic programming of ILCs, which links microbiota-DNA methylation crosstalk to ILC differentiation.

Exploring the immunological landscape of osteomyelitis through mendelian randomization analysis.

Background: Osteomyelitis is a severe bone marrow infection, whose pathogenesis is not yet fully understood. This study aims to explore the causal relationship between immune cell characteristics and osteomyelitis, hoping to provide new insights for the prevention and treatment of osteomyelitis. Methods: Based on two independent samples, this study employed a two-sample Mendelian randomization (MR) analysis to assess the causal relationship between 731 immune cell characteristics (divided into seven groups) and osteomyelitis. Genetic variants were used as proxies for risk factors to ensure that the selected instrumental variables meet the three key assumptions of MR analysis. Genome-Wide Association Studies (GWAS) data for immune characteristics were obtained from the public GWAS catalog, while data for osteomyelitis was sourced from the FinnGen. Results: At a significance level of 0.05, 21 immune phenotypes were identified as having a causal relationship with osteomyelitis development. In the B cell group, phenotypes such as Memory B cell % B cell (percentage of memory B cells within the total B cell population, % finger cell ratio), CD20- %B cell (percentage of B cells that do not express the CD20 marker on their surface), and Memory B cell % lymphocyte showed a positive causal relationship with osteomyelitis, while Naive-mature B cell %B cell and IgD-CD38-absolute cell counts (AC) phenotypes showed a negative causal relationship. In addition, specific immune phenotypes in the conventional dendritic cells (cDCs) group, Myeloid cell group, TBNK (T cells, B cells, natural killer cells) cell group, T cell maturation stage, and Treg cell group also showed significant associations with osteomyelitis. Through reverse MR analysis, it was found that osteomyelitis had no significant causal impact on these immune phenotypes, suggesting that the occurrence of osteomyelitis may not affect these immune cell phenotypes. Conclusion: To our knowledge, this is the first study to shed light on the causal relationship between specific immune cell characteristics and the development of osteomyelitis, thereby providing a new perspective to understand the immune mechanism of osteomyelitis. These findings are significant for formulating targeted prevention and treatment strategies, and hold promise to improve the treatment outcomes for patients with osteomyelitis.

Endogenous chemicals guard health through inhibiting ferroptotic cell death.

Ferroptosis is a new form of regulated cell death caused by iron-dependent accumulation of lethal polyunsaturated phospholipids peroxidation. It has received considerable attention owing to its putative involvement in a wide range of pathophysiological processes such as organ injury, cardiac ischemia/reperfusion, degenerative disease and its prevalence in plants, invertebrates, yeasts, bacteria, and archaea. To counter ferroptosis, living organisms have evolved a myriad of intrinsic efficient defense systems, such as cyst(e)ine-glutathione-glutathione peroxidase 4 system (cyst(e)ine-GPX4 system), guanosine triphosphate cyclohydrolase 1/tetrahydrobiopterin (BH4) system (GCH1/BH4 system), ferroptosis suppressor protein 1/coenzyme Q10 system (FSP1/CoQ10 system), and so forth. Among these, GPX4 serves as the only enzymatic protection system through the reduction of lipid hydroperoxides, while other defense systems ultimately rely on small compounds to scavenge lipid radicals and prevent ferroptotic cell death. In this article, we systematically summarize the chemical biology of lipid radical trapping process by endogenous chemicals, such as coenzyme Q10 (CoQ10), BH4, hydropersulfides, vitamin K, vitamin E, 7-dehydrocholesterol, with the aim of guiding the discovery of novel ferroptosis inhibitors.

T12-L3 Nerve Transfer-Induced Locomotor Recovery in Rats with Thoracolumbar Contusion: Essential Roles of Sensory Input Rerouting and Central Neuroplasticity.

Locomotor recovery after spinal cord injury (SCI) remains an unmet challenge. Nerve transfer (NT), the connection of a functional/expendable peripheral nerve to a paralyzed nerve root, has long been clinically applied, aiming to restore motor control. However, outcomes have been inconsistent, suggesting that NT-induced neurological reinstatement may require activation of mechanisms beyond motor axon reinnervation (our hypothesis). We previously reported that to enhance rat locomotion following T13-L1 hemisection, T12-L3 NT must be performed within timeframes optimal for sensory nerve regrowth. Here, T12-L3 NT was performed for adult female rats with subacute (7-9 days) or chronic (8 weeks) mild (SCImi: 10 g × 12.5 mm) or moderate (SCImo: 10 g × 25 mm) T13-L1 thoracolumbar contusion. For chronic injuries, T11-12 implantation of adult hMSCs (1-week before NT), post-NT intramuscular delivery of FGF2, and environmentally enriched/enlarged (EEE) housing were provided. NT, not control procedures, qualitatively improved locomotion in both SCImi groups and animals with subacute SCImo. However, delayed NT did not produce neurological scale upgrading conversion for SCImo rats. Ablation of the T12 ventral/motor or dorsal/sensory root determined that the T12-L3 sensory input played a key role in hindlimb reanimation. Pharmacological, electrophysiological, and trans-synaptic tracing assays revealed that NT strengthened integrity of the propriospinal network, serotonergic neuromodulation, and the neuromuscular junction. Besides key outcomes of thoracolumbar contusion modeling, the data provides the first evidence that mixed NT-induced locomotor efficacy may rely pivotally on sensory rerouting and pro-repair neuroplasticity to reactivate neurocircuits/central pattern generators. The finding describes a novel neurobiology mechanism underlying NT, which can be targeted for development of innovative neurotization therapies.

Microsphere-Enabled Modular Formation of Miniaturized In Vitro Breast Cancer Models.

In search of effective therapeutics for breast cancers, establishing physiologically relevant in vitro models is of great benefit to facilitate the clinical translation. Despite extensive progresses, it remains to develop the tumor models maximally recapturing the key pathophysiological attributes of their native counterparts. Therefore, the current study aimed to develop a microsphere-enabled modular approach toward the formation of in vitro breast tumor models with the capability of incorporating various selected cells while retaining spatial organization. Poly (lactic-co-glycolic acid) microspheres (150-200 mm) with tailorable pore size and surface topography are fabricated and used as carriers to respectively lade with breast tumor-associated cells. Culture of cell-laden microspheres assembled within a customized microfluidic chamber allowed to form 3D tumor models with spatially controlled cell distribution. The introduction of endothelial cell-laden microspheres into cancer-cell laden microspheres at different ratios would induce angiogenesis within the culture to yield vascularized tumor. Evaluation of anticancer drugs such as doxorubicin and Cediranib on the tumor models do demonstrate corresponding physiological responses. Clearly, with the ability to modulate microsphere morphology, cell composition and spatial distribution, microsphere-enabled 3D tumor tissue formation offers a high flexibility to satisfy the needs for pathophysiological study, anticancer drug screening or design of personalized treatment.

FOXO1 orchestrates the intestinal homeostasis via neuronal signaling in group 3 innate lymphoid cells.

The neuro-immune regulation is associated with homeostasis of the intestine. Intestinal group 3 innate lymphoid cells (ILC3s) are tissue-resident lymphocytes whose functions are affected by the intestine niche. However, how a gut neuronal signal coordinates the immune response of ILC3s is largely unknown. Here, we found that cyclic adenosine monophosphate (cAMP) signaling exacerbated the inflammatory response and attenuated the expression level of the transcription factor forkhead box O1 (FOXO1) in ILC3s. Deficiency of FOXO1 drove the hyperactivation of ILC3s and resulted in gut inflammation independently of T cells. Mechanistically, FOXO1 promoted the transcription of neuropeptide receptor VIPR2 and inhibited the transcription of adrenoceptor ADRA2A in ILC3s. FOXO1-related regulation of VIPR2 and ADRA2A signaling balanced the activation of ILC3s under steady condition or during colitis. Moreover, chronic stress elevated cAMP level and downregulated FOXO1 level, exacerbating intestinal inflammation. Our findings reveal that FOXO1 balances the activation of ILC3s via VIP and adrenergic signaling and regulates intestinal homeostasis.

Tissue-resident Lachnospiraceae family bacteria protect against colorectal carcinogenesis by promoting tumor immune surveillance.

The intestinal microbiota plays an important role in colorectal cancer (CRC) progression. However, the effect of tissue-resident commensal bacteria on CRC immune surveillance remains poorly understood. Here, we analyzed the intratissue bacteria from CRC patient colon tissues. We found that the commensal bacteria belonging to the Lachnospiraceae family, including Ruminococcus gnavus (Rg), Blautia producta (Bp), and Dorea formicigenerans (Df), were enriched in normal tissues, while Fusobacterium nucleatum (Fn) and Peptostreptococcus anaerobius (Pa) were abundant in tumor tissues. Tissue-resident Rg and Bp reduced colon tumor growth and promoted the activation of CD8+ T cells in immunocompetent mice. Mechanistically, intratissue Rg and Bp degraded lyso-glycerophospholipids that inhibited CD8+ T cell activity and maintained the immune surveillance function of CD8+ T cells. Lyso-glycerophospholipids alone promoted tumor growth that was abrogated with Rg and Bp injection. Collectively, intratissue Lachnospiraceae family bacteria facilitate the immune surveillance function of CD8+ T cells and control colorectal cancer progression.

The neuropeptide CGRP enters the macrophage cytosol to suppress the NLRP3 inflammasome during pulmonary infection.

The NLRP3 inflammasome plays an essential role in resistance to bacterial infection. The nervous system secretes multiple neuropeptides affecting the nervous system as well as immune cells. The precise impact of the neuropeptide CGRP on NLRP3 inflammasome activation is still unclear. Here, we show that CGRP negatively regulates the antibacterial process of host cells. CGRP prevents NLRP3 inflammasome activation and reduces mature IL-1ß secretion. Following NLRP3 inflammasome stimulation that triggers endosome leakage, CGRP internalized to endosomal compartments is released into the cell cytosol. Cytosolic CGRP binds directly to NLRP3 and dismantles the NLRP3-NEK7 complex, which is crucial for NLRP3 inflammasome activation. CGRP administration exacerbates bacterial infection, while the treatment with a CGRP antagonist has the opposite effect. Our study uncovers a unique role of CGRP in inhibiting inflammasome activation during infections, which might shed new light on antibacterial therapies in the future.

Maturation and specialization of group 2 innate lymphoid cells through the lung-gut axis.

Innate lymphoid cells (ILC) are abundant in mucosal tissues. They serve critical functions in anti-pathogen response and tissue homeostasis. However, the heterogenous composition of ILCs in mucosal sites and their various maturation trajectories are less well known. In this study, we characterize ILC types and functions from both the lung and the small intestine, and identify their tissue-specific markers. We find that ILC2s residing in the lung express CCR2, whereas intestinal ILC2s express CCR4. Through the use of CCR2 and CCR4 reporter mice, we show that ILC2s undergo translocation via the lung-gut axis upon IL-33 treatment. This trajectory of ILC2s is also observed at the postnatal stage. Allergen-induced activation of lung ILC2s affects the homeostasis of gut ILC2s. Together, our findings implicate that ILCs display tissue-specific features in both the lung and gut, and ILC2s mature along the lung-gut axis in particular homeostatic and inflammatory conditions.

Trained immunity in the mucosal diseases.

Immune memory is well known as a signature of the adaptive immune system. Recently, enhanced responses to subsequent triggers are also observed in innate immune system, termed trained immunity (TI). Awakening of innate immune memory is required for host defense, such as anti-pathogen and anti-tumor responses. However, hyper-reactivation of trained innate immune cells also gives rise to undesirable inflammation. Mucosa immune system serves as the first defense line against pathogens. Trained immunity of mucosal immune system is tightly associated with the outcomes of mucosal diseases. In this review, we discuss the role of trained immunity in mucosal-associated diseases and the underlying mechanisms. We summarize the metabolic and epigenetic changes of trained immune cells and highlight their potential in clinical treatment. This article is categorized under: Infectious Diseases > Molecular and Cellular Physiology.

Combined addition of biochar and garbage enzyme improving the humification and succession of fungal community during sewage sludge composting.

The influences of combination of garbage enzyme and biochar on total organic carbon (TOC) degradation, humification and the fungal succession during sewage sludge (SS) composting were established. Results showed that the GE and BC + GE treatments significantly increased the enzyme activity of fluorescein diacetate hydrolase (FDA) and increased the TOC degradation rate by 9.8% and 21.9% relative to control. The excitation-emission matrix (EEM) combined with the percentage fluorescence response (Pi, n) also proved that the combination of BC and GE promoted fulvic acid-like and humic-like substances production, and thus increased humification. Furthermore, the combination of BC and GE effectively decreased the relative abundance of Unclassified_k_Fugni, while increased the abundance of Ascomycota and Basidiomycota compared with control. The four genera, Pseudeurotium, Talaromyces, Trichoderma, and Penicillium, were the main fungi for the humification. Comparatively, the combined of BC and GE showed the optimal performance for TOC degradation and humification during SS composting.

SARS-CoV-2 nucleocapsid suppresses host pyroptosis by blocking Gasdermin D cleavage.

SARS-CoV-2 is an emerging coronavirus that causes dysfunctions in multiple human cells and tissues. Studies have looked at the entry of SARS-CoV-2 into host cells mediated by the viral spike protein and human receptor ACE2. However, less is known about the cellular immune responses triggered by SARS-CoV-2 viral proteins. Here, we show that the nucleocapsid of SARS-CoV-2 inhibits host pyroptosis by blocking Gasdermin D (GSDMD) cleavage. SARS-CoV-2-infected monocytes show enhanced cellular interleukin-1ß (IL-1ß) expression, but reduced IL-1ß secretion. While SARS-CoV-2 infection promotes activation of the NLRP3 inflammasome and caspase-1, GSDMD cleavage and pyroptosis are inhibited in infected human monocytes. SARS-CoV-2 nucleocapsid protein associates with GSDMD in cells and inhibits GSDMD cleavage in vitro and in vivo. The nucleocapsid binds the GSDMD linker region and hinders GSDMD processing by caspase-1. These insights into how SARS-CoV-2 antagonizes cellular inflammatory responses may open new avenues for treating COVID-19 in the future.

Dynamic regulation of innate lymphoid cells in the mucosal immune system.

The mucosal immune system is considered a local immune system, a term that implies regional restriction. Mucosal tissues are continually exposed to a wide range of antigens. The regulation of mucosal immune cells is tightly associated with the progression of mucosal diseases. Innate lymphoid cells (ILCs) are abundant in mucosal barriers and serve as first-line defenses against pathogens. The subtype changes and translocation of ILCs are accompanied by the pathologic processes of mucosal diseases. Here, we review the plasticity and circulation of ILCs in the mucosal immune system under physiological and pathological conditions. We also discuss the signaling pathways involved in dynamic ILC changes and the related targets in mucosal diseases.

Comparative evaluation of biochar, pelelith, and garbage enzyme on nitrogenase and nitrogen-fixing bacteria during the composting of sewage sludge.

This study investigated the effects of garbage enzyme (GE), pelelith (PL), and biochar (BC) on nitrogen (N) conservation, nitrogenase (Nase) and N-fixing bacteria during the composting of sewage sludge. Results showed that the addition of GE, PL, and BC reduced NH3 emissions by 40.9%, 29.3%, and 67.4%, and increased the NO3-N contents of the end compost by 161.4, 88.2, and 105.8% relative to control, respectively, thus increasing the TN content. Three additives improved Nase, cellulase, and fluorescein diacetate hydrolase (FDA) activities and the abundances of nifH gene, and the largest increase was BC, followed by PL and GE. In addition, the additives also markedly influenced the succession of N-fixing bacteria, and significantly increased the abundance of Proteobacteria during the whole process. The BC and PL additions strengthened the sensitivity of N-fixing bacteria to environmental variables, and FDA, TN, moisture content, and NO3-N significantly affected the N-fixing bacteria at genus level.

Garbage enzymes effectively regulated the succession of enzymatic activities and the bacterial community during sewage sludge composting.

This study evaluated nitrogen transformation, enzymatic activities and bacterial succession during sewage sludge composting with and without garbage enzymes (GE and CK, respectively). The results showed that GE addition significantly increased fluorescein diacetate hydrolase (FDA), cellulase, and nitrogenase activities during the composting process. GE addition reduced the cumulative NH3 emissions by 66.5%, increased the peak NH4-N content by 26.3% and increased the total nitrogen (TN) content of the end compost by 39.2% compared to CK. Microbiological analysis revealed that GE addition significantly increased the relative abundance of Firmicutes during the thermophilic and cooling phases relative to CK. The selected factors affected the bacterial community composition in the following order: NH4-N > TOC > FDA > TN > C/N. Network analysis also showed that the enzymes were secreted mainly by Bacillus and norank_f_Caldilineaceae in GE, while they were secreted primarily by norank_f_Methylococcaceae in CK during the composting process.

Effects of urease inhibitors on enzymatic activities and fungal communities during the biosolids composting.

This study evaluated the influences of urease inhibitors (UIs) on nitrogen conversion, enzyme activities, and fungal communities during aerobic composting. Results showed that UI addition reduced NH3 emissions by 22.2% and 21.5% and increased the total nitrogen (TN) content by 9.7% and 14.3% for the U1 (0.5% UI of the dry weight of the mixture) and U2 (1% UI of the dry weight of the mixture) treatments, respectively. The addition of UI inhibited the enzyme activity during thermophilic stage while increased enzyme activity during the cool and maturity stages. Ascomycota, Basidiomycota and unclassified fungi were the main phyla, and Ascomycota increased significantly during the maturity period. Network analysis showed that Aspergillus, Penicillium, Trichoderma, Talaromyces, Peseudeurotium, and Exophiala were the main "connecting" genera. The redundancy analysis (RDA) showed that the fungal community was mainly influenced by temperature, DOC, pH, and urease. The results suggested that UI was an effective additive for nitrogen conservation and the increase of enzyme activity reduce nitrogen loss and promote enzyme activity during biosolids composting.

Use of additives in composting informed by experience from agriculture: Effects of nitrogen fertilizer synergists on gaseous nitrogen emissions and corresponding genes (amoA and nirS).

The effects of two nitrogen fertilizer synergists (urease inhibitor, UI; nitrification inhibitor, NI) on NH3 and N2O emissions and the successions of the amoA and nirS genes during composting were assessed. Results showed that the UI and UI + NI treatments reduced NH3 emissions by 26.3% and 24.3%, respectively, and N2O emissions were reduced by 63.9% for UI + NI treatment but were not reduced by UI. The addition of UI and NI significantly reduced the abundance of the nirS gene during thermophilic stage, while significantly increased that of the amoA gene during maturation stage. Crenarchaeota was the principal nitrifying archaeal phylum and was significantly affected by pH. Proteobacteria was the main denitrifying bacterial phylum, whose relative abundance was higher for UI + NI treatment than the other treatments. PICRUSt analysis showed that the addition of UI and NI inhibited enzymatic activity related to N transformation during thermophilic stage while enriching enzymatic activity during maturation phase.

Ribosomal protein S11 influences glioma response to TOP2 poisons.

Topoisomerase II poisons are one of the most common class of chemotherapeutics used in cancer. We and others had shown that a subset of glioblastomas, the most malignant of all primary brain tumors in adults, is responsive to TOP2 poisons. To identify genes that confer susceptibility to this drug in gliomas, we performed a genome-scale CRISPR knockout screen with etoposide. Genes involved in protein synthesis and DNA damage were implicated in etoposide susceptibility. To define potential biomarkers for TOP2 poisons, CRISPR hits were overlapped with genes whose expression correlates with susceptibility to this drug across glioma cell lines, revealing ribosomal protein subunit RPS11, 16, and 18 as putative biomarkers for response to TOP2 poisons. Loss of RPS11 led to resistance to etoposide and doxorubicin and impaired the induction of proapoptotic gene APAF1 following treatment. The expression of these ribosomal subunits was also associated with susceptibility to TOP2 poisons across cell lines from gliomas and multiple other cancers.

High-level expression of highly active and thermostable trehalase from Myceliophthora thermophila in Aspergillus niger by using the CRISPR/Cas9 tool and its application in ethanol fermentation.

Trehalase catalyzes the hydrolysis of the non-reducing disaccharide trehalose. The highly active trehalase MthT from Myceliophthora thermophila was screened from the trehalase genes of six species of filamentous fungi. An ingenious multi-copy knock-in expression strategy mediated by the CRISPR/Cas9 tool and medium optimization were used to improve MthT production in Aspergillus niger, up to 1698.83 U/mL. The protein background was dramatically abated due to insertion. The recombinant MthT showed optimal activity at pH 5.5 and 60 °C, and exhibited prominent thermal stability between 50 and 60 °C under acid conditions (pH 4.5-6.5). The ethanol conversion rate (ethanol yield/total glucose) was significantly improved by addition of MthT (51.88%) compared with MthT absence (34.38%), using 30% starch saccharification liquid. The results of this study provided an effective strategy, established a convenient platform for heterologous expression in A. niger and showed a potential strategy to decrease production costs in industrial ethanol production.