Acta biochimica et biophysica Sinica最新文献

The intestinal microbiota plays critical roles in regulating immunity and inflammation through intricate interactions between microbial metabolites and diverse immune cells. Dendritic cells (DCs), the most potent professional antigen-presenting cells, are essential for sensing the complicated microbiota environment and subsequently initiating and regulating adaptive immune responses. While the commensal microbiota typically mediates DC-triggered immune tolerance and thus the maintenance of intestinal homeostasis, epithelial injury or pathogenic infection generally drives the proinflammatory function of DCs, contributing to harmful inflammation and intestinal disorders. Various microbiota metabolites (such as short-chain fatty acids, bile acids, and tryptophan derivatives) play critical roles in modulating the developmental and functional diversity of DCs through metabolic, epigenetic, or signaling reprogramming. In this review, we discuss the metabolic crosstalk between the intestinal microbiota and DCs and its pivotal function in orchestrating the balance between intestinal homeostasis and pathogenic inflammation. We also discuss future directions to better elucidate the microbiota-DC dialog in intestinal immunity and develop therapeutic approaches for manipulating the microbiota-DC axis against inflammatory disorders.

Acrolein, a highly reactive α,β-unsaturated aldehyde found in cigarette smoke, automobile exhaust, industrial emissions, combustion byproducts, cooking and cyclophosphamide chemotherapy, has raised serious health concerns, although the precise mechanism remains unclear. This study is designed to examine the impact of this pervasive environmental pollutant on myocardial geometry and function alongside the underlying cellular mechanisms. Adult C57BL/6 mice are challenged with acrolein (2.5 mg/kg/day, i.p., for 20 days) prior to the evaluation of myocardial geometry and function. Acrolein exposure evokes evident cardiac remodeling (interstitial fibrosis), compromised echocardiographic (enlarged LVESD, compromised ejection fraction and fractional shortening), cardiomyocyte contractile and intracellular Ca ²⁺ capacities [decreased peak shortening, maximal velocity of shortening and relengthening (±dL/dt), and electrically stimulated rise in Fura-2 fluorescence intensity (ΔFFI), prolonged time-to-90% relengthening (TR ₉₀) and intracellular Ca ²⁺ decay], accompanied by overt mitochondrial damage (ultrastructure, aconitase and mitochondrial protein contents), free radical buildup, apoptosis (Bax, Caspase-3, and Bcl2) and cuproptosis (upregulated SLC31A1, DLAT and FDX1), downregulated the Fe-S cluster proteins ACO2 and NDUFS8 alongside unchanged ATP7A and the ferroptosis markers GPX4 and SLC7A11. The levels of copper-sensing protein metal response element binding transcription factor 2 (MTF2), but not MTF1, are increased by acrolein insult. CB-DOCK2 analysis predicts an interaction between acrolein and the MTF2 dimer within its DNA-binding regions. In vivo administration of the cuproptosis inhibitor tetrathiomolybdate (TTM), the mitochondrial antioxidant mitoTEMPO or the nonselective MTF2 inhibitor actinomycin D alleviates acrolein-evoked cardiomyocyte dysfunction (decreased PS, ±dL/dt, and prolonged TR ₉₀). These findings indicate that acrolein evoked cardiac functional anomalies possibly through MTF2-related control of cuproptosis.

Nuclear factor I (NFI) transcription factors play essential roles in multiple aspects of nervous system development, including radial glia maturation, neurogenesis, gliogenesis, and brain morphogenesis. Numerous NFI variants have been identified in individuals with neurodevelopmental disorders, yet the molecular basis of their pathogenicity remains unclear. The absence of resolved NFI-DNA complex structures continues to impede mechanistic insights and therapeutic exploration. Here, we define the oligomeric states of NFIA and NFIC, and determine the crystal structures of the NFIC homodimer, as well as the NFIA and NFIC monomers lacking their dimerization region, in complexes with double-stranded DNAs. Structural analysis reveals the molecular mechanism underlying NFI dimerization and recognition of a dyad-symmetric TGGCA(N3)TGCCA sequence motif, and demonstrates that dimerization enhances both DNA-binding affinity and specificity of NFI proteins. The functional importance of key NFI residues and DNA bases involved in the protein-DNA interaction is further validated by mutagenesis and binding assays. Additionally, we systematically evaluate the effects of the neurodevelopmental disorders-associated NFI mutations on DNA binding of NFIA, providing insights into their potential pathogenic mechanisms. Together, our findings elucidate the structural basis of NFI dimerization and dyad-symmetric DNA recognition and highlight pathogenic variants for further mechanistic studies in neurodevelopmental disorders.

The molecular mechanisms underlying Klebsiella pneumoniae (KP) resistance to phages have not been fully elucidated, especially those involving the quorum-sensing (QS) system and the global regulator H-NS. In this work, we investigate the relationship between H-NS and QS in phage resistance by detecting transcriptional variation under phage pressure with RT-qPCR. LuxS and lsr operon knockout strains are generated via CRISPR editing, and H-NS-overexpressing mutants are constructed using plasmid-based overexpression. We also determine phage susceptibility by measuring the efficiency of plating (EOP). The capsular uronic acid content and phage adsorption efficiency are evaluated. The results show that phage pressure strongly downregulates luxS and lsr operon gene expressions but upregulates the transcription of H-NS. Knockout of either luxS/ lsr operon genes or overexpression of H-NS results in diminished phage sensitivity and the downregulation of CPS synthase genes. However, these changes do not reduce the capsular uronic acid content or affect phage adsorption rates, suggesting that H-NS-mediated resistance is independent of capsular modulation. In addition, this H-NS-QS regulatory link is conserved between HvKP and CRKP. H-NS enhances phage resistance by suppressing QS through a mechanism independent of capsular polysaccharide modulation, as evidenced by unaltered phage adsorption and statistically insignificant changes in capsular uronic acid. This provides a novel explanation for a resistance mechanism involving intracellular defenses ( e. g., abortive infection) and provides possible avenues for improving phage therapy targeting multidrug-resistant K. pneumoniae.

Brown adipose tissue (BAT) is a heat-generating organ burning significant amounts of calories from fatty acids and glucose. The importance of glucose metabolism in the context of thermogenic function has been underlined by several studies. However, fructose metabolism and consequences of fructose overfeeding are poorly studied in BAT. Here we provide evidence that brown adipocytes use fructose as a substrate, however to a lesser extent than glucose. Furthermore, our data suggest that carbohydrate response element binding protein (ChREBP) and its target glucose transporter 5 (GLUT5) are not essential for fructose uptake and metabolism in BAT. Notably, we report that high fructose feeding has no effect on ChREBP activity and thus de novo fatty acid synthesis in BAT as opposed to liver and intestine. Instead, excessive carbohydrate loading of brown adipocytes induced by both, high-fructose feeding and impairment of ChREBP-dependent glucose metabolism, causes a massive accumulation of hexosylceramide species, as revealed by mass spectrometry-based lipidomics. Based on our data we hypothesize a reprogramming of fructose utilization upon impaired carbohydrate metabolism from canonical glycolysis and pentose phosphate pathway towards glycosphingolipid synthesis.

Given the critical role of the cGAS-STING pathway in antitumor immunity, this study investigates the functional role of STING in head and neck squamous cell carcinoma (HNSCC) to evaluate the therapeutic potential of STING agonists. Analysis of the TCGA-HNSC dataset reveals that elevated expression of the STING-encoding gene TMEM173 is significantly correlated with increased M1 macrophage infiltration and enrichment of macrophage polarization-related signaling pathways. In vitro experiments in which RAW 264.7 cells are co-cultured with tumor cell-conditioned medium demonstrate that the STING agonist MSA-2 effectively reprograms tumor-induced M2-polarized macrophages toward the M1 phenotype. This MSA-2-induced M1 polarization is accompanied by increased expressions of IFN-α, IFN-β, IFN-γ, TNF-α, and IL-6, while the STING inhibitor H-151 reverses these effects. Flow cytometry further reveals that MSA-2 treatment reduces PD-1 and increases MHC II expression on macrophages. Immunohistochemical analysis of clinical samples confirms that high STING expression is correlated with increased numbers of CD68⁺ and CD80⁺ (M1-like) macrophages. In support of translational relevance, analysis of single-cell RNA-seq data from HNSCC patients receiving neoadjuvant immunotherapy indicates that TMEM173 is expressed primarily in T cells and macrophages and that the cGAS-STING pathway score is significantly higher in patients who respond to treatment. Collectively, these findings provide systematic clinical and experimental evidence supporting the potential of STING agonists, such as MSA-2, to enhance antitumor immunity in HNSCC, particularly when combined with immunotherapy.

Long noncoding RNAs (lncRNAs) are essential in regulating the development and progression of different types of cancer. However, our insights into their impact and mechanisms in papillary thyroid carcinoma (PTC) are still insufficient. In this study, we investigate the effects of the ferroptosis-associated long noncoding RNA LINC02432 on PTC, which recognizes ferroptosis as a critical mechanism in cancer biology and lncRNAs as significant factors in various malignancies. To identify lncRNAs associated with ferroptosis in PTC, we conduct bioinformatics analyses and perform functional assays to evaluate the biological impact of LINC02432 on PTC cells, as well as its relationship with ferroptosis. Mechanistic studies employ methods such as western blot analysis, flow cytometry, and real-time PCR. Our analysis of transcriptome data from TCGA reveals that LINC02432 is the only lncRNA consistently identified by all 10 machine learning methods used, and its expression is significantly downregulated in PTC. Overexpression of LINC02432 in PTC cells inhibits cell proliferation and migration while promoting ferroptosis through inactivation of the NRF2 pathway. LINC02432 knockdown in PTC cells yields the opposite result. These findings highlight the potential of LINC02432 as a tumor suppressor in PTC progression, offering new insights into the mechanisms underlying the development and progression of this malignancy.

The diverse antibodies of adaptive immunity comprise an antibody repertoire that combats various pathogens. This repertoire is shaped by both intrinsic antibody gene diversification and extrinsic cellular selection. Conversely, an antibody repertoire contains multiple layers of immunological information, including the history of pathogen exposure. High-throughput sequencing-based antibody repertoire cloning approaches have revealed unexpected features of adaptive immunity. However, our understanding of antibody repertoire data is still in its infancy. In this review, we introduce the emerging concepts and discuss the application of deep learning approaches to understanding antibody repertoires. First, we introduce the definition and functional features of antibody clonotype. Next, we review the evolution of antibody clonotypes and discuss potential antibody repertoire-directed vaccination approaches. Lastly, we summarize the application of deep learning in predicting antibody binding, generating specific antibodies, and making immunologic diagnoses. Recently, artificial intelligence (AI) has made revolutionary progress in biology. Leveraging high-dimensional antibody repertoire information, deep learning models have the potential to transform our understanding of antibody repertoire.

Cryptococcus gattii causes cryptococcosis and life-threatening cryptococcal meningitis. Currently, the pathogenic virulence mechanisms of C. gattii remain a significant area of ongoing research with considerable unexplored aspects. On the basis of our established research, a sub-cluster of strains with independent evolutionary relationships from WM276 in the phylogenetic analysis of VGI-type strains is identified. In vivo infection experiments on this sub-branch of strains reveal that there are hypervirulent strains and hypovirulent strains among these strains, and the virulence differences are significant ( P  < 0.001). Bioinformatic interrogation of differentially expressed genes reveals that the catalase-encoding gene CGB_J0620W, CAT2, is a pivotal virulence-associated gene. The hypervirulent clinical isolate G4 (G4-WT) is selected as the parental strain, from which an isogenic CAT2-knockout mutant ( cat2Δ) is constructed via homologous recombination, which shows increased sensitivity to oxidative stress, as well as growth defects in response to hyperosmosis, 5-fluorocytosine, fluconazole and amphotericin B. The cat2Δ::CAT2 strain exhibits phenotypic restoration to wild type (WT). In the mouse experiments, significant differences in survival ( P  < 0.001), pulmonary fungal burden ( P  < 0.01), and alveolar structural damage are observed between the WT and cat2Δ strains, which are completely different from C. neoformans. Moreover, comparative transcriptome analysis is performed on the WT and cat2Δ strains, which reveals that enzymes encoded by CAT2 may be involved in oxidative stress, metabolism and sugar transport. In conclusion, this study may explain the differences in virulence among different genetic evolutionary processes of a sub-cluster of the VGI geneotype of C. gattii and provide a theoretical basis for targeted therapy in a specific genotype population in the future.

The evolutionarily conserved nucleosome assembly protein 1 (NAP1) functions as a histone chaperone for H2A-H2B, regulating nucleosome assembly and maintaining chromatin integrity. However, the dynamic and variable nature of the interactions between acidic NAP1 and basic H2A-H2B has obscured the molecular basis of its chaperoning activity. Here, we report the crystal structures of Caenorhabditis elegans NAP1 (CeNAP1) in complex with Xenopus laevis H2A-H2B (XlH2A-H2B) and with C. elegans H2A.Z-H2B (CeH2A.Z-H2B) at 3.35 Å and 2.8 Å, respectively. In our structures, H2A/H2A.Z-H2B binds to the acidic concave surface of CeNAP1 in three distinct poses, with two in the CeNAP1-XlH2A-H2B complex and one in the CeNAP1-CeH2A.Z-H2B complex. These poses are different from the two poses observed in the previously reported CeNAP1-CeH2A/H2A.Z-H2B structures. The predominant interaction involves engagement of the acidic CeNAP1 α6-carboxy-terminal (C-terminal) tail by the basic H2A/H2A.Z αN-α1 region, stabilized by salt bridges and electrostatic interactions. A comparative analysis of all five known poses reveals that H2A/H2A.Z-H2B can shift approximately 20.7 Å along the α6-C-terminal tail-C'-terminal tail-α6' axis. These findings demonstrate a sliding binding mode of H2A/H2A.Z-H2B on NAP1, providing new mechanistic insights into nucleosome assembly activity of histone chaperones.