Acta Biochimica et Biophysica Sinica•2025•DOI: 10.3724/abbs.2024235
Activated astrocytes and their associated inflammatory responses play critical roles in the pathogenesis of hypoxic-ischemic brain damage (HIBD). Gastrodin (GAS), an anti-inflammatory herbal agent, is known to suppress microglial activation. Here, we investigate whether it exerts a similar effect on activated astrocytes and whether it acts through S100B/RAGE-Smad3 signaling. The expression changes of S100B/RAGE-Smad3 signaling pathway-related proteins, inflammatory factors and A1/A2 astrocyte markers were detected by ELISA, western blot analysis, immunofluorescence and immunohistochemistry. The results show that GAS decreases the expression of sRAGE in the brain tissue and S100B in the serum and brain tissue of HIBD mice. However, it promotes the expression of sRAGE in the serum of HIBD mice. Moreover, GAS inhibits the expressions of RAGE, p-Smad3, TNF-α, and C3 (A1 astrocyte marker), and promotes the expressions of S100A10 (A2 astrocyte marker) and BDNF in HIBD model mice, as well as in oxygen glucose deprivation (OGD)-treated TNC-1 astrocytes. The immunofluorescence and immunohistochemical results of RAGE and p-Smad3, as well as the immunofluorescence results of C3 and S100A10, reveal the same trend. Interestingly, FPS-ZM1 (a specific inhibitor of RAGE) inhibits the expressions of p-Smad3, TNF-α, C3, and S100A10, but promotes that of BDNF compared with those in the OGD group. The combination of GAS and FPS-ZM1 further decreases the expression of C3. These results indicate that GAS can inhibit the activation of Smad3 through S100B/RAGE signaling and regulate the expression of A1/A2-type astrocytes.
Acta Biochimica et Biophysica Sinica•2025•DOI: 10.3724/abbs.2025040
Iron, an ancient and essential transition metal, is involved in various biological functions, including oxygen transport, DNA synthesis, heme production, and iron-sulfur clusters, which participate in electron transport, DNA repair, and other cellular processes. However, excessive iron can lead to oxidative stress, lipid peroxidation, and cell damage. Thus, maintaining the iron content within an appropriate safe range and maintaining the balance of iron metabolism play crucial roles in both cellular function and human health [1]. An important aspect of maintaining the balance of iron homeostasis is the regulation of the iron uptake system. In Saccharomyces cerevisiae, cells can either obtain iron from the external environment via the non-reducing siderophore transport system or transport iron from the extracellular space to the intracellular space via the reducing iron transport system [2]. Iron uptake system-related genes are regulated mainly by the transcription factor Aft1p. During iron deficiency, Aft1p translocates into the nucleus, binds to genes involved in iron metabolism, and regulates the expressions of genes involved in iron uptake systems [3]. In addition, when there is a problem in the synthesis of iron-sulfur clusters in the mitochondria, such as the lack of the iron chaperone Yfh1p, which promotes the synthesis of iron-sulfur clusters, the transcription and nuclear entry of the transcription factor Aft1p are also activated, thereby regulating the expressions of iron metabolism-related genes [4]. In addition to transcription factors, gene expression is also regulated by histones and their modifications at the epigenetic level. For example, histone H3K4 methylation is related to gene activation, H3K36 methylation plays an important role in the elongation of transcription, and histone acetylation results in the loss of nucleosome structure and facilitates gene expression [5]. Therefore, histone modifications should also play important roles in the regulation of iron homeostasis. The relationship between histone modifications and iron homeostasis has been reported in the literature. For example, the DNA methylation-binding protein MBD5 can change histone acetylation in the promoter region of the ferritin gene by recruiting the histone acetylase KAT2A protein [6]. Histone acetylation has also been reported to be reduced in iron-deficient environments [7,8], and direct effects of histone acetylation on iron homeostasis gene loci have also been reported both in C. albicans [9] and mammals [10]. More recently, the histone H3-H4 tetramer was found to be a copper reductase enzyme, and H3-mediated Cu+ toxicity is a major determinant of the cellular functional pool of iron-sulfur (Fe-S) clusters [11,12]. However, information on the role of histone modifications in the regulation of iron homeostasis is limited. The mechanism by which and how histone modifications are involved in the transcriptional regulation of iron uptake-related genes or the iron deficiency response require further investigation. To determine whether histone acetylation and methylation are involved in the iron deficiency response, we first deleted the histone acetylase genes, including GCN5 (histones H2B and H3 N-terminal lysine acetylase, partial deletion of the ADA2 interaction sequence [13]), RTT109 (H3 lysine 9 and 56 acetylase), SAS2 (H4 lysine 16 acetylase), and YNG2 (subunit of the histone acetyltransferase complex NuA4 for acetylation of histone H4 or histone H2A) in the wild-type (WT) strain, as well as the histone methyltransferases SET1 (H3 lysine 4 methyltransferase), SET2 (H3 lysine 36 methyltransferase) and DOT1 (H3 lysine 79 methyltransferase). The genomic deletions were confirmed by colony PCR and genomic coverage analysis, as depicted in Supplementary Figures S1 and S2. The sensitivity of single histone modification enzyme mutants to iron deficiency induced by the iron chelator bathophenanthroline disulfonate (BPS) was tested. As shown in Supplementary Figure S3, the histone acetylation-related mutants gcn51–316, rtt109Δ, sas2Δ, and yng2Δ did not exhibit significant growth defects compared with the WT on the YPD + BPS plate. None of the histone methyltransferase knockout strains presented significant growth defects. As a positive control, the iron-responsive transcription factor gene AFT1 knockout strain grew slowly on YPD + BPS plates. It is possible that histone modifications do not have a strong effect on the equilibrium status of iron deficiency but still regulate transcription induction during the iron deficiency response. To investigate the role of histone modifications during the induction of the iron deficiency response, the expressions of iron response genes in the wild-type and mutant strains before and 4 h after BPS treatment were examined.
Acta Biochimica et Biophysica Sinica•2025•DOI: 10.3724/abbs.2024142
Fluorogenic RNA aptamers are in vitro-selected RNA molecules capable of binding to specific fluorophores, significantly increasing their intrinsic fluorescence. Over the past decade, the color palette of fluorescent RNA aptamers has greatly expanded. The emergence and development of these fluorogenic RNA aptamers has introduced a powerful approach for visualizing RNA localization and transport with high spatiotemporal resolution in live cells. To date, a variety of tertiary structures of fluorogenic RNA aptamers have been determined using X-ray crystallography or NMR spectroscopy. Many of these fluorogenic RNA aptamers feature base quadruples or base triples in their fluorophore-binding sites. This review summarizes the structure-based investigations of fluorogenic RNA aptamers, with a focus on their overall folds, ligand-binding pockets and fluorescence activation mechanisms. Additionally, the exploration of how structures guide rational optimization to enhance RNA visualization techniques is discussed.
Acta Biochimica et Biophysica Sinica•2024•DOI: 10.3724/abbs.2024062
Ubiquitin-conjugation enzyme E2C (UBE2C) is a crucial component of the ubiquitin-proteasome system that is involved in numerous cancers. In this study, we find that UBE2C expression is significantly increased in mouse embryos, a critical stage during skeletal muscle development. We further investigate the function of UBE2C in myogenesis. Knockdown of UBE2C inhibits C2C12 cell differentiation and decreases the expressions of MyoG and MyHC, while overexpression of UBE2C promotes C2C12 cell differentiation. Additionally, knockdown of UBE2C, specifically in the tibialis anterior muscle (TA), severely impedes muscle regeneration in vivo. Mechanistically, we show that UBE2C knockdown reduces the level of phosphorylated protein kinase B (p-Akt) and promotes the degradation of Akt. These findings suggest that UBE2C plays a critical role in myoblast differentiation and muscle regeneration and that UBE2C regulates myogenesis through the Akt signaling pathway.
Chinese Traditional and Herbal Drugs•2026•DOI: 10.7501/j.issn.0253-2670.2026.16.20261605
Property prediction of traditional Chinese medicine (TCM) molecules remains constrained by their complex ring systems and conformational flexibility. Conventional graph neural networks (GNNs) treat molecules as topological graphs, discarding bond length and angle strain information critical for accurate property estimation. This study introduces the flexibility-ring enhanced graph neural network (FRGNN), which augments the graph isomorphism network (GIN) with edge descriptors encoding bond length strain and angle strain, and incorporates multiple favorable conformations to construct multi-graph data. The model was evaluated on two TCM databases comprising 37,822 molecules across seven key molecular properties, benchmarked against three state-of-the-art (SOTA) GNN models and two basic GNN models. FRGNN achieved an average root mean square error (RMSE) reduction of 8.63% relative to the second-best model across all seven tasks. For molecules containing polycyclic and macrocyclic structures, the RMSE reduction reached 10.04%. These results demonstrate that FRGNN outperforms existing SOTA small-molecule property prediction models on TCM compounds, offering a robust computational approach for complex natural product characterization. The incorporation of flexibility and ring-specific descriptors addresses a critical gap in molecular representation learning, enabling more accurate predictions for structurally diverse TCM constituents.
Chinese Journal of Tissue Engineering Research•2026•DOI: 10.12307/2026.21299
BACKGROUND: Neurogenic heterotopic ossification frequently occurs within 1 to 3 months following spinal cord injury or traumatic brain injury, characterized by abnormal bone formation in periarticular soft tissues. The precise pathogenesis remains unclear, underscoring the urgent need for systematic research to inform clinical management. OBJECTIVE: To summarize recent advances in animal models of neurogenic heterotopic ossification and elucidate its underlying mechanisms, with a particular focus on the pathological differentiation of osteogenic precursor cells, remodeling of the local tissue microenvironment, and the interplay between neural regulation and neurogenic heterotopic ossification formation. METHODS: PubMed, CNKI, and SinoMed were searched from inception to January 2025. Chinese search terms included 'neurogenic heterotopic ossification, spinal cord injury, traumatic brain injury, heterotopic ossification'; English search terms included 'Neurogenic Heterotopic Ossification, spinal cord injury, Traumatic brain injury, ossification, heterotopic, Central nervous system'. Literature related to animal models and mechanisms of neurogenic heterotopic ossification was included to summarize key pathogenic processes. RESULTS AND CONCLUSION: The recruitment and aberrant osteogenic differentiation of osteogenic precursor cells (mainly fibro-adipogenic progenitors) are regulated by local microenvironmental factors such as hypoxia, inflammation, and angiogenesis. Neurotrophic factors, calcitonin gene-related peptide, and substance P promote aberrant ossification through neuro-immune interactions. Future research should construct a systematic molecular map, explore core signaling pathways, and develop novel targeted interventions to achieve early identification and individualized treatment of neurogenic heterotopic ossification, thereby improving patient outcomes.