β-Tricalcium phosphate (β-TCP), frequently employed for bone tissue regeneration, can induce inflammation during the initial phases of implantation within the organism. However, mechanisms by which β-TCP nanoparticles (NPs) cause this inflammatory response is rarely reported. This project aims to investigate the causes of the macrophage inflammatory response induced by β-TCP NPs. Here, macrophage-like RAW264.7 cells were co-cultured with conditioned medium containing β-TCP NPs to identify the pathways through which β-TCP NPs influence inflammation and polarization of macrophages. This effect is achieved by modulating mitochondrial oxidative stress in the immune microenvironment. The results demonstrated that β-TCP NPs caused mitochondrial swelling, increased intracellular calcium ions, reduced mitochondrial membrane potential, as well as decreased the level of adenosine triphosphate (ATP) and translocase of outer mitochondrial membrane 20 (TOMM20). These NPs further lead to mitochondrial oxidative damage. These alterations promoted the polarization of macrophage to M1-type. Exogenous mitochondrial-targeted antioxidants could block this M1-type macrophage polarization. The findings of this work suggest that β-TCP NPs induce macrophage inflammation and contribute to M1 macrophage polarization, primarily through the activation of mitochondrial oxidative stress. These insights could guide the development of improved β-TCP formulations to mitigate inflammatory responses in bone regeneration applications.
{"title":"β-Tricalcium phosphate nanoparticles induce macrophage polarization to M1-type through mitochondrial oxidative stress activation","authors":"Yunbing Chen , Xinping Li , Hongyi Yang, Gaoying Ran, Lifang Zhang, Shuguang Zeng","doi":"10.1016/j.biocel.2025.106868","DOIUrl":"10.1016/j.biocel.2025.106868","url":null,"abstract":"<div><div>β-Tricalcium phosphate (β-TCP), frequently employed for bone tissue regeneration, can induce inflammation during the initial phases of implantation within the organism. However, mechanisms by which β-TCP nanoparticles (NPs) cause this inflammatory response is rarely reported. This project aims to investigate the causes of the macrophage inflammatory response induced by β-TCP NPs. Here, macrophage-like RAW264.7 cells were co-cultured with conditioned medium containing β-TCP NPs to identify the pathways through which β-TCP NPs influence inflammation and polarization of macrophages. This effect is achieved by modulating mitochondrial oxidative stress in the immune microenvironment. The results demonstrated that β-TCP NPs caused mitochondrial swelling, increased intracellular calcium ions, reduced mitochondrial membrane potential, as well as decreased the level of adenosine triphosphate (ATP) and translocase of outer mitochondrial membrane 20 (TOMM20). These NPs further lead to mitochondrial oxidative damage. These alterations promoted the polarization of macrophage to M1-type. Exogenous mitochondrial-targeted antioxidants could block this M1-type macrophage polarization. The findings of this work suggest that β-TCP NPs induce macrophage inflammation and contribute to M1 macrophage polarization, primarily through the activation of mitochondrial oxidative stress. These insights could guide the development of improved β-TCP formulations to mitigate inflammatory responses in bone regeneration applications.</div></div>","PeriodicalId":50335,"journal":{"name":"International Journal of Biochemistry & Cell Biology","volume":"189 ","pages":"Article 106868"},"PeriodicalIF":2.8,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145158799","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-23DOI: 10.1016/j.biocel.2025.106867
Linshan Xie , Rong Xu , Huining Liu , Man Na , Qikai Qin , Fei Xu , Raymond C. Stevens , Yan Liu
The biased agonism of glucagon-like peptide-1 receptor (GLP-1R) plays a key role in the efficacy and side effects of drugs used to treat type II diabetes mellitus and obesity. Despite its therapeutic potential, the mechanisms underlying GLP-1R biased agonism remain poorly understood. In this study, we investigate the role of the extracellular domain (ECD) in GLP-1R signaling bias through saturation mutagenesis at seven key sites. We examined 126 mutations and identified several that selectively abolished β-arrestin recruitment while retaining cAMP production. Additionally, we employed a large language model (LLM) to interpret the functional impacts of these mutations, uncovering correlations between sequence features and signaling outcome. These findings provide new insight into the "two-domain" model of class B1 G protein-coupled receptors (GPCRs), highlighting the ECD's role in biased agonism and offering novel information for designing more effective and selective GLP-1R agonists.
{"title":"Characterizing the role of extracellular domain in GLP-1R biased agonism","authors":"Linshan Xie , Rong Xu , Huining Liu , Man Na , Qikai Qin , Fei Xu , Raymond C. Stevens , Yan Liu","doi":"10.1016/j.biocel.2025.106867","DOIUrl":"10.1016/j.biocel.2025.106867","url":null,"abstract":"<div><div>The biased agonism of glucagon-like peptide-1 receptor (GLP-1R) plays a key role in the efficacy and side effects of drugs used to treat type II diabetes mellitus and obesity. Despite its therapeutic potential, the mechanisms underlying GLP-1R biased agonism remain poorly understood. In this study, we investigate the role of the extracellular domain (ECD) in GLP-1R signaling bias through saturation mutagenesis at seven key sites. We examined 126 mutations and identified several that selectively abolished β-arrestin recruitment while retaining cAMP production. Additionally, we employed a large language model (LLM) to interpret the functional impacts of these mutations, uncovering correlations between sequence features and signaling outcome. These findings provide new insight into the \"two-domain\" model of class B1 G protein-coupled receptors (GPCRs), highlighting the ECD's role in biased agonism and offering novel information for designing more effective and selective GLP-1R agonists.</div></div>","PeriodicalId":50335,"journal":{"name":"International Journal of Biochemistry & Cell Biology","volume":"189 ","pages":"Article 106867"},"PeriodicalIF":2.8,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145151893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-23DOI: 10.1016/j.biocel.2025.106866
Yongwei Du , Fangtian Xu , Shengwang Miao , Bo Zhou , Jianwen Mo , Zhen Liu
<div><h3>Background</h3><div>Ferroptosis occurs in osteoblasts in a diabetic environment, which impairs osteoblast number and function, promotes osteoblast death, destroys bone homeostasis, and eventually contributes to type 2 diabetic osteoporosis (T2DOP). Chromobox protein homolog 7 (CBX7) deficiency plays a positive role in bone formation and skeletal development. Besides, CBX7 interference has been reported to protect against disease development by inhibiting ferroptosis. This study focuses on determining whether CBX7 is involved in the progression of T2DOP by regulating osteoblast ferroptosis and explore the underlying mechanism.</div></div><div><h3>Methods</h3><div>The bone tissues of 28 patients with T2DOP (the research group) and severe bone trauma (the control group) were collected, and CBX7 expression in bone tissues was detected through RT-qPCR and western blotting. Mouse pre-osteoblast MC3T3-E1 cells were treated with high glucose (HG; 25 mM) for 72 h to establish an <em>in vitro</em> model of T2DOP. The effects of CBX7 knockdown or overexpression on ferroptosis in HG-treated MC3T3-E1 cells were assessed by examining the levels of intracellular Fe<sup>2 +</sup> , lipid peroxidation, ROS, MDA, 4‑HNE, GSH, and ferroptosis regulatory proteins SLC7A11 and GPX4. The osteogenic differentiation of HG-treated MC3T3-E1 cells after knocking down or overexpressing CBX7 was assessed by performing ALP and ARS staining and measuring the levels of osteogenesis markers (ALP, RUNX2, and OCN). Whether CBX7 knockdown affects osteoblast differentiation and ferroptosis by regulating the Nrf2 pathway was validated by using the Nrf2 inhibitor ML385. Furthermore, Sprague Dawley (SD) rats were fed a high-fat diet and injected with streptozotocin to induce type 2 diabetes (T2DM), followed by the induction of T2DOP for 2 months and subsequently the determination of the anti-osteoporotic, anti-ferroptotic, and pro-osteogenic effects of CBX7 deficiency <em>in vivo</em>.</div></div><div><h3>Results</h3><div>CBX7 expression was markedly increased in the bone tissues of T2DOP patients compared to control patients. HG stimulation enhanced CBX7 expression, intracellular Fe<sup>2+</sup>, lipid peroxidation, ROS, MDA, and 4‑HNE levels but attenuated GSH, SLC7A11, and GPX4 levels in MC3T3-E1 cells. These effects of HG were reversed by CBX7 knockdown but were intensified by CBX7 overexpression. CBX7 silencing antagonized while CBX7 overexpression enhanced the inhibitory effects of HG treatment on the osteogenic differentiation of MC3T3-E1 cells. CBX7 knockdown promoted Nrf2 expression and nuclear translocation in HG-treated MC3T3-E1 cells and CBX7 showed potential protein interaction with Nrf2. The inhibition of CBX7 depletion on HG-induced ferroptosis in MC3T3-E1 cells and its promotion on the osteogenic differentiation of MC3T3-E1 cells were abrogated by ML385. Additionally, CBX7 silencing ameliorated bone mass loss and bone microstructure destruction, reduced MDA and i
{"title":"Chromobox protein homolog 7 (CBX7) deficiency inhibits osteoblast ferroptosis by activating the Nrf2 function in type 2 diabetic osteoporosis","authors":"Yongwei Du , Fangtian Xu , Shengwang Miao , Bo Zhou , Jianwen Mo , Zhen Liu","doi":"10.1016/j.biocel.2025.106866","DOIUrl":"10.1016/j.biocel.2025.106866","url":null,"abstract":"<div><h3>Background</h3><div>Ferroptosis occurs in osteoblasts in a diabetic environment, which impairs osteoblast number and function, promotes osteoblast death, destroys bone homeostasis, and eventually contributes to type 2 diabetic osteoporosis (T2DOP). Chromobox protein homolog 7 (CBX7) deficiency plays a positive role in bone formation and skeletal development. Besides, CBX7 interference has been reported to protect against disease development by inhibiting ferroptosis. This study focuses on determining whether CBX7 is involved in the progression of T2DOP by regulating osteoblast ferroptosis and explore the underlying mechanism.</div></div><div><h3>Methods</h3><div>The bone tissues of 28 patients with T2DOP (the research group) and severe bone trauma (the control group) were collected, and CBX7 expression in bone tissues was detected through RT-qPCR and western blotting. Mouse pre-osteoblast MC3T3-E1 cells were treated with high glucose (HG; 25 mM) for 72 h to establish an <em>in vitro</em> model of T2DOP. The effects of CBX7 knockdown or overexpression on ferroptosis in HG-treated MC3T3-E1 cells were assessed by examining the levels of intracellular Fe<sup>2 +</sup> , lipid peroxidation, ROS, MDA, 4‑HNE, GSH, and ferroptosis regulatory proteins SLC7A11 and GPX4. The osteogenic differentiation of HG-treated MC3T3-E1 cells after knocking down or overexpressing CBX7 was assessed by performing ALP and ARS staining and measuring the levels of osteogenesis markers (ALP, RUNX2, and OCN). Whether CBX7 knockdown affects osteoblast differentiation and ferroptosis by regulating the Nrf2 pathway was validated by using the Nrf2 inhibitor ML385. Furthermore, Sprague Dawley (SD) rats were fed a high-fat diet and injected with streptozotocin to induce type 2 diabetes (T2DM), followed by the induction of T2DOP for 2 months and subsequently the determination of the anti-osteoporotic, anti-ferroptotic, and pro-osteogenic effects of CBX7 deficiency <em>in vivo</em>.</div></div><div><h3>Results</h3><div>CBX7 expression was markedly increased in the bone tissues of T2DOP patients compared to control patients. HG stimulation enhanced CBX7 expression, intracellular Fe<sup>2+</sup>, lipid peroxidation, ROS, MDA, and 4‑HNE levels but attenuated GSH, SLC7A11, and GPX4 levels in MC3T3-E1 cells. These effects of HG were reversed by CBX7 knockdown but were intensified by CBX7 overexpression. CBX7 silencing antagonized while CBX7 overexpression enhanced the inhibitory effects of HG treatment on the osteogenic differentiation of MC3T3-E1 cells. CBX7 knockdown promoted Nrf2 expression and nuclear translocation in HG-treated MC3T3-E1 cells and CBX7 showed potential protein interaction with Nrf2. The inhibition of CBX7 depletion on HG-induced ferroptosis in MC3T3-E1 cells and its promotion on the osteogenic differentiation of MC3T3-E1 cells were abrogated by ML385. Additionally, CBX7 silencing ameliorated bone mass loss and bone microstructure destruction, reduced MDA and i","PeriodicalId":50335,"journal":{"name":"International Journal of Biochemistry & Cell Biology","volume":"189 ","pages":"Article 106866"},"PeriodicalIF":2.8,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145151910","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-22DOI: 10.1016/j.biocel.2025.106865
Zhenxing Liu , Jingye Zhao , Lei Zhang , Xiaoting Wu , Jiamiao Liu , Yuanrui Mei , Shuyan Liu , Jieru Lin , Hongyan Li , Xiaoye Qi , Fuping Lu , Huabing Zhao , Aipo Diao
Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by impaired skin barrier function and immune dysregulation. Autophagy, a lysosome-dependent degradation pathway essential for removing unnecessary components, plays a crucial role in maintaining cellular homeostasis. Defective autophagy has been implicated in AD pathogenesis, and enhancing autophagic activity represents a viable therapeutic strategy. This study investigated the potential of the natural saponin escin to ameliorate AD through autophagy activation. We demonstrated that escin induced autophagy in HaCaT keratinocytes and mitigated tight junction (TJ) barrier disruption in an AD-like cell model stimulated with IL-4 and IL-13. Notably, silencing ATG7, an essential autophagy-related protein, abrogated the barrier-restorative effects of escin. Furthermore, in a 2,4-dinitrochlorobenzene (DNCB)-induced murine model of AD, escin treatment ameliorated AD-like skin lesions, reduced mast cell infiltration, and decreased cutaneous levels of the pro-inflammatory cytokines IL-4, IL-13, and IFN-γ. Escin administration also restored the epidermal expression of key TJ proteins, Claudin-1 and ZO-1. Mechanistically, escin promoted the nuclear translocation of transcription factor EB (TFEB) and upregulated the expression of genes involved in autophagy and lysosome biogenesis. These protective effects were associated with the activation of the AMPK-mTORC1-TFEB signaling pathway. Collectively, our findings indicate that escin enhances autophagy and restores skin barrier function, highlighting its potential as a novel therapeutic agent for AD treatment.
{"title":"Escin alleviates DNCB-induced atopic dermatitis-like symptoms by promoting autophagy activation and tight junction barrier restoration","authors":"Zhenxing Liu , Jingye Zhao , Lei Zhang , Xiaoting Wu , Jiamiao Liu , Yuanrui Mei , Shuyan Liu , Jieru Lin , Hongyan Li , Xiaoye Qi , Fuping Lu , Huabing Zhao , Aipo Diao","doi":"10.1016/j.biocel.2025.106865","DOIUrl":"10.1016/j.biocel.2025.106865","url":null,"abstract":"<div><div>Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by impaired skin barrier function and immune dysregulation. Autophagy, a lysosome-dependent degradation pathway essential for removing unnecessary components, plays a crucial role in maintaining cellular homeostasis. Defective autophagy has been implicated in AD pathogenesis, and enhancing autophagic activity represents a viable therapeutic strategy. This study investigated the potential of the natural saponin escin to ameliorate AD through autophagy activation. We demonstrated that escin induced autophagy in HaCaT keratinocytes and mitigated tight junction (TJ) barrier disruption in an AD-like cell model stimulated with IL-4 and IL-13. Notably, silencing ATG7, an essential autophagy-related protein, abrogated the barrier-restorative effects of escin. Furthermore, in a 2,4-dinitrochlorobenzene (DNCB)-induced murine model of AD, escin treatment ameliorated AD-like skin lesions, reduced mast cell infiltration, and decreased cutaneous levels of the pro-inflammatory cytokines IL-4, IL-13, and IFN-γ. Escin administration also restored the epidermal expression of key TJ proteins, Claudin-1 and ZO-1. Mechanistically, escin promoted the nuclear translocation of transcription factor EB (TFEB) and upregulated the expression of genes involved in autophagy and lysosome biogenesis. These protective effects were associated with the activation of the AMPK-mTORC1-TFEB signaling pathway. Collectively, our findings indicate that escin enhances autophagy and restores skin barrier function, highlighting its potential as a novel therapeutic agent for AD treatment.</div></div>","PeriodicalId":50335,"journal":{"name":"International Journal of Biochemistry & Cell Biology","volume":"189 ","pages":"Article 106865"},"PeriodicalIF":2.8,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145139104","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-19DOI: 10.1016/j.biocel.2025.106864
Chloé Richard , Charlène Pourpe , Guillaume Fourneaux , Gwendal Cueff , Laurent Parry , Cécile Coudy-Gandilhon , Jonas Kindberg , Alina L. Evans , Andrea Miller , Guillemette Gauquelin-Koch , Christophe Tatout , Cécile Polge , Daniel Taillandier , Fabrice Bertile , Etienne Lefai , Lydie Combaret
Muscle atrophy is observed in several pathophysiological situations, including physical inactivity, leading to negative health consequences, without any effective treatment currently available. Conversely, brown bears resist muscle atrophy during hibernation, despite prolonged physical inactivity and fasting. We previously reported that hibernating brown bear serum increases protein content in human myotubes and inhibits proteolysis. To go further, we deciphered here the transcriptional effects of brown bear serum in human myotubes using large-scale transcriptomics. After 48 h, the winter-hibernating bear serum (WBS) induced a specific transcriptomic program, affecting mostly biological pathways related to muscle growth and BMP signalling, compared to the summer-active bear (SBS) serum. WBS predominantly reduced, at mRNA and protein levels, activators and inhibitors of BMP signalling, which is associated with muscle mass maintenance. Moreover, BMP activity was more responsive to a stimulation by BMP7 at supra-physiological concentrations in human myotubes cultured in WBS versus SBS conditions. Meanwhile, WBS also up-regulated expression of genes encoding repressors of the pro-atrophic TGF-β pathway, decreased phosphorylated SMAD3 nuclear protein levels, and down-regulated TGF-β target genes. Furthermore, WBS treatment resulted in reduced TGF-β signalling responsiveness in human myotubes stimulated with TGF-β3 at physiological concentrations. Overall, even though WBS induced larger transcriptomic changes in the BMP compared to TGF-β pathway, the functional consequences were more pronounced for the TGF-β pathway with a marked inhibition. This study suggests that bioactive compounds in WBS may protect human muscle cells during catabolic situations, by regulating the TGF-β/BMP balance. These findings open new perspectives for therapies targeting muscle atrophy.
{"title":"Hibernating brown bear serum modulates the balance of TGF-β and BMP pathways in human muscle cells","authors":"Chloé Richard , Charlène Pourpe , Guillaume Fourneaux , Gwendal Cueff , Laurent Parry , Cécile Coudy-Gandilhon , Jonas Kindberg , Alina L. Evans , Andrea Miller , Guillemette Gauquelin-Koch , Christophe Tatout , Cécile Polge , Daniel Taillandier , Fabrice Bertile , Etienne Lefai , Lydie Combaret","doi":"10.1016/j.biocel.2025.106864","DOIUrl":"10.1016/j.biocel.2025.106864","url":null,"abstract":"<div><div>Muscle atrophy is observed in several pathophysiological situations, including physical inactivity, leading to negative health consequences, without any effective treatment currently available. Conversely, brown bears resist muscle atrophy during hibernation, despite prolonged physical inactivity and fasting. We previously reported that hibernating brown bear serum increases protein content in human myotubes and inhibits proteolysis. To go further, we deciphered here the transcriptional effects of brown bear serum in human myotubes using large-scale transcriptomics. After 48 h, the winter-hibernating bear serum (WBS) induced a specific transcriptomic program, affecting mostly biological pathways related to muscle growth and BMP signalling, compared to the summer-active bear (SBS) serum. WBS predominantly reduced, at mRNA and protein levels, activators and inhibitors of BMP signalling, which is associated with muscle mass maintenance. Moreover, BMP activity was more responsive to a stimulation by BMP7 at supra-physiological concentrations in human myotubes cultured in WBS versus SBS conditions. Meanwhile, WBS also up-regulated expression of genes encoding repressors of the pro-atrophic TGF-β pathway, decreased phosphorylated SMAD3 nuclear protein levels, and down-regulated TGF-β target genes. Furthermore, WBS treatment resulted in reduced TGF-β signalling responsiveness in human myotubes stimulated with TGF-β3 at physiological concentrations. Overall, even though WBS induced larger transcriptomic changes in the BMP compared to TGF-β pathway, the functional consequences were more pronounced for the TGF-β pathway with a marked inhibition. This study suggests that bioactive compounds in WBS may protect human muscle cells during catabolic situations, by regulating the TGF-β/BMP balance. These findings open new perspectives for therapies targeting muscle atrophy.</div></div>","PeriodicalId":50335,"journal":{"name":"International Journal of Biochemistry & Cell Biology","volume":"189 ","pages":"Article 106864"},"PeriodicalIF":2.8,"publicationDate":"2025-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145096627","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-16DOI: 10.1016/j.biocel.2025.106863
Wei Huang , Guanhua Deng , Qinghua Zhang, Fengquan Lv, Dehuan Xie, Chen Ren, Shasha Du, Peixin Tan
<div><h3>Background</h3><div>Radiation induced lung injury (RILI) is a common complication in patients undergoing thoracic radiotherapy. At present, there are no effective early diagnostic biomarkers, and clinical treatment methods are very limited, which poses a huge challenge to the management of cancer patients. Oxidative stress has been recognized as a key mediator of aging and disease. Therefore, this study integrated multiple omics data in mice and advanced bioinformatics and machine learning methods to systematically analyze the molecular features associated with oxidative stress, and screened for clinically relevant biomarkers and molecular mechanisms of RILI. This study aims to provide a timely and practical theoretical basis for the early diagnosis and targeted intervention of RILI.</div></div><div><h3>Method</h3><div>We implemented a comprehensive approach that integrated both bulk RNA and single-cell RNA sequencing analyses, utilizing advanced bioinformatics methodologies. These encompassed techniques aimed at eliminating batch effects to facilitate smooth data integration, executing differential expression analyses, and applying weighted gene co-expression network analysis (WGCNA). Furthermore, we developed a diagnostic model for RILI utilizing random forest and support vector machine (SVM) algorithms. We also conducted Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA). To evaluate immune cell infiltration, we employed Single-Sample Gene-Set Enrichment Analysis (ssGSEA) alongside the CIBERSORT algorithm. We then investigated the expression and interactions of module genes across various cell populations utilizing data derived from single-cell RNA sequencing. Ultimately, the expression of module genes in irradiated lung tissues were validate by reverse transcription–polymerase chain reaction (RT-PCR) and immunohistochemistry (IHC).</div></div><div><h3>Results</h3><div>Our study identified a total of 286 differentially expressed genes (DEGs). Among these, we confirmed 61 genes related to oxidative stress (OSRDEGs). We constructed nine co-expression modules, four of which showed a significant association with RILI, encompassing 53 genes from these modules. A diagnostic model with AUC over 0.9 was constructed and further refined to include five key genes: Stk4, Aaas, Ets1, Sesn2, and Kit, which were validated for accuracy through LASSO regression. The model genes were found to be enriched in crucial pathways, particularly the MAPK signaling pathway. A direct relationship between Ets1 and Kit was found, which extended to 20 functionally similar proteins identified through GeneMANIA. Additionally, we noted significant changes in the infiltration patterns of 13 immune cell types, including Activated B cells and Activated CD4 T cells. Sens2 and Kit were found highly expressed in granulocytes and endothelial cells, respectively. In mouse models of RILI, Sesn2 and Aaas were significantl
{"title":"Integrated bulk and single-cell RNA sequencing identifies oxidative stress signatures of radiation-induced lung injury in mice through machine learning","authors":"Wei Huang , Guanhua Deng , Qinghua Zhang, Fengquan Lv, Dehuan Xie, Chen Ren, Shasha Du, Peixin Tan","doi":"10.1016/j.biocel.2025.106863","DOIUrl":"10.1016/j.biocel.2025.106863","url":null,"abstract":"<div><h3>Background</h3><div>Radiation induced lung injury (RILI) is a common complication in patients undergoing thoracic radiotherapy. At present, there are no effective early diagnostic biomarkers, and clinical treatment methods are very limited, which poses a huge challenge to the management of cancer patients. Oxidative stress has been recognized as a key mediator of aging and disease. Therefore, this study integrated multiple omics data in mice and advanced bioinformatics and machine learning methods to systematically analyze the molecular features associated with oxidative stress, and screened for clinically relevant biomarkers and molecular mechanisms of RILI. This study aims to provide a timely and practical theoretical basis for the early diagnosis and targeted intervention of RILI.</div></div><div><h3>Method</h3><div>We implemented a comprehensive approach that integrated both bulk RNA and single-cell RNA sequencing analyses, utilizing advanced bioinformatics methodologies. These encompassed techniques aimed at eliminating batch effects to facilitate smooth data integration, executing differential expression analyses, and applying weighted gene co-expression network analysis (WGCNA). Furthermore, we developed a diagnostic model for RILI utilizing random forest and support vector machine (SVM) algorithms. We also conducted Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA). To evaluate immune cell infiltration, we employed Single-Sample Gene-Set Enrichment Analysis (ssGSEA) alongside the CIBERSORT algorithm. We then investigated the expression and interactions of module genes across various cell populations utilizing data derived from single-cell RNA sequencing. Ultimately, the expression of module genes in irradiated lung tissues were validate by reverse transcription–polymerase chain reaction (RT-PCR) and immunohistochemistry (IHC).</div></div><div><h3>Results</h3><div>Our study identified a total of 286 differentially expressed genes (DEGs). Among these, we confirmed 61 genes related to oxidative stress (OSRDEGs). We constructed nine co-expression modules, four of which showed a significant association with RILI, encompassing 53 genes from these modules. A diagnostic model with AUC over 0.9 was constructed and further refined to include five key genes: Stk4, Aaas, Ets1, Sesn2, and Kit, which were validated for accuracy through LASSO regression. The model genes were found to be enriched in crucial pathways, particularly the MAPK signaling pathway. A direct relationship between Ets1 and Kit was found, which extended to 20 functionally similar proteins identified through GeneMANIA. Additionally, we noted significant changes in the infiltration patterns of 13 immune cell types, including Activated B cells and Activated CD4 T cells. Sens2 and Kit were found highly expressed in granulocytes and endothelial cells, respectively. In mouse models of RILI, Sesn2 and Aaas were significantl","PeriodicalId":50335,"journal":{"name":"International Journal of Biochemistry & Cell Biology","volume":"189 ","pages":"Article 106863"},"PeriodicalIF":2.8,"publicationDate":"2025-09-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145087980","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-09-04DOI: 10.1016/j.biocel.2025.106861
Meiqi Sun , Hua Fang , Jiashu Zhang , Mengyao Wang , Peng Jiang , LiLi Ma , Huanyu Jin , Wei Zhang
Silicosis is a fatal occupational lung disease characterized by persistent inflammation and irreversible fibrosis. However, the pathogenesis of silicosis is currently unclear. In this study, a mouse model of silicosis was established by intranasal instillation of silica, and transcriptomic alterations in lung tissues were assessed by mRNA-sequencing. Cholesterol 25-hydroxylase (Ch25h) was upregulated in silicotic lung tissues and alveolar macrophages. Lentivirus-mediated Ch25h knockdown was then employed to assess its functional role in vivo. It was found that Ch25h knockdown alleviated associated pathological changes, including pulmonary injury and fibrosis. Additionally, Ch25h significantly modulated NLRP3 inflammasome activity in vivo and in vitro. Knockdown of Ch25h inhibited the secretion of inflammatory factor (IL-1α, IL-1β, and IL-18), decreased the protein level of cleaved caspase-1 and GSDMD-N in macrophages, and reduced potassium ion efflux and lactate dehydrogenase (LDH) release. Notably, ASC (apoptosis-related spotted protein) oligomerization was suppressed by Ch25h downregulation, suggesting that Ch25h was required for the inflammasome assembly. Our findings suggest that Ch25h may contribute to silicosis development by regulating NLRP3 inflammasome activation and pyroptosis, warranting further investigation as a possible therapeutic target.
{"title":"Resistance to silicosis progression in mice with Ch25h downregulation: The involvement of NLRP3 inflammasome","authors":"Meiqi Sun , Hua Fang , Jiashu Zhang , Mengyao Wang , Peng Jiang , LiLi Ma , Huanyu Jin , Wei Zhang","doi":"10.1016/j.biocel.2025.106861","DOIUrl":"10.1016/j.biocel.2025.106861","url":null,"abstract":"<div><div>Silicosis is a fatal occupational lung disease characterized by persistent inflammation and irreversible fibrosis. However, the pathogenesis of silicosis is currently unclear. In this study, a mouse model of silicosis was established by intranasal instillation of silica, and transcriptomic alterations in lung tissues were assessed by mRNA-sequencing. Cholesterol 25-hydroxylase (Ch25h) was upregulated in silicotic lung tissues and alveolar macrophages. Lentivirus-mediated Ch25h knockdown was then employed to assess its functional role in vivo. It was found that Ch25h knockdown alleviated associated pathological changes, including pulmonary injury and fibrosis. Additionally, Ch25h significantly modulated NLRP3 inflammasome activity in vivo and in vitro. Knockdown of Ch25h inhibited the secretion of inflammatory factor (IL-1α, IL-1β, and IL-18), decreased the protein level of cleaved caspase-1 and GSDMD-N in macrophages, and reduced potassium ion efflux and lactate dehydrogenase (LDH) release. Notably, ASC (apoptosis-related spotted protein) oligomerization was suppressed by Ch25h downregulation, suggesting that Ch25h was required for the inflammasome assembly. Our findings suggest that Ch25h may contribute to silicosis development by regulating NLRP3 inflammasome activation and pyroptosis, warranting further investigation as a possible therapeutic target.</div></div>","PeriodicalId":50335,"journal":{"name":"International Journal of Biochemistry & Cell Biology","volume":"189 ","pages":"Article 106861"},"PeriodicalIF":2.8,"publicationDate":"2025-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145005125","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-25DOI: 10.1016/j.biocel.2025.106853
Leyli Naraghi , Alexey Koval , Vladimir L. Katanaev , S.Mahmoud A Najafi
Syndecans are a family of four-member transmembrane heparan sulfate proteoglycans that bind to various extracellular biomolecules, such as Wnt ligands, via their heparan sulfate chains, thereby controlling a variety of cellular processes. When dysregulated, syndecans can affect tumorigenesis and cancer progression by modulating key signaling pathways involved in the regulation of biological functions. Aberrant activation of Wnt/β-catenin signaling is a hallmark of many human tumors, including breast cancer. Studying the interplay between syndecans and Wnt signaling in human cancers is beneficial for identifying new therapeutic strategies, understanding tumor behavior and improving patient outcomes. Syndecan-2 is predominantly expressed by mesenchymal cells, and its overexpression in tumors of epithelial origin appears to induce aggressive behavior. Here, by measuring β-catenin cytoplasmic stabilization and transcriptional activity, we show that syndecan-2 expression significantly enhances the sensitivity of HEK293T cells and BT-20 triple-negative breast cancer cells to Wnt3a-induced activation of Wnt/β-catenin signaling. In addition, CRISPR/Cas9-mediated deletion of SDC2, the gene encoding syndecan-2, reduced β-catenin transcriptional activity in BT-20 cells in response to Wnt3a stimulation. This reduction was rescued by the re-expression of SDC2. Collectively, our results demonstrate that syndecan-2 is a positive regulator of canonical Wnt signaling. These results also suggest that syndecan-2 is a potential clinical target for inhibiting the progression of some human cancers.
{"title":"Syndecan-2 positively regulates Wnt/β-catenin signaling in breast cancer cells","authors":"Leyli Naraghi , Alexey Koval , Vladimir L. Katanaev , S.Mahmoud A Najafi","doi":"10.1016/j.biocel.2025.106853","DOIUrl":"10.1016/j.biocel.2025.106853","url":null,"abstract":"<div><div>Syndecans are a family of four-member transmembrane heparan sulfate proteoglycans that bind to various extracellular biomolecules, such as Wnt ligands, via their heparan sulfate chains, thereby controlling a variety of cellular processes. When dysregulated, syndecans can affect tumorigenesis and cancer progression by modulating key signaling pathways involved in the regulation of biological functions. Aberrant activation of Wnt/β-catenin signaling is a hallmark of many human tumors, including breast cancer. Studying the interplay between syndecans and Wnt signaling in human cancers is beneficial for identifying new therapeutic strategies, understanding tumor behavior and improving patient outcomes. Syndecan-2 is predominantly expressed by mesenchymal cells, and its overexpression in tumors of epithelial origin appears to induce aggressive behavior. Here, by measuring β-catenin cytoplasmic stabilization and transcriptional activity, we show that syndecan-2 expression significantly enhances the sensitivity of HEK293T cells and BT-20 triple-negative breast cancer cells to Wnt3a-induced activation of Wnt/β-catenin signaling. In addition, CRISPR/Cas9-mediated deletion of <em>SDC2</em>, the gene encoding syndecan-2, reduced β-catenin transcriptional activity in BT-20 cells in response to Wnt3a stimulation. This reduction was rescued by the re-expression of <em>SDC2</em>. Collectively, our results demonstrate that syndecan-2 is a positive regulator of canonical Wnt signaling. These results also suggest that syndecan-2 is a potential clinical target for inhibiting the progression of some human cancers.</div></div>","PeriodicalId":50335,"journal":{"name":"International Journal of Biochemistry & Cell Biology","volume":"188 ","pages":"Article 106853"},"PeriodicalIF":2.8,"publicationDate":"2025-08-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144916779","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-23DOI: 10.1016/j.biocel.2025.106852
Azubuike P. Ebokaiwe , Lingyu Li , Ting Peng , Emmanuel M. Njoya , Zongyuan Zhou , Euslar Nnenna Onu , Guolin Zhang , Wang Fei
New therapeutic approaches are essential in the fight against breast cancer, which remains one of the top causes of mortality globally. Innovative and efficient methods of treating and preventing cancer has become expedient since its incidence rates are rising globally. Combining herbal extracts and chemotherapy have drawn a lot of attention in recent times as a cutting-edge cancer prevention approach. The wild parasitic plant Loranthus micranthus is extensively distributed throughout the world and is well-known for its therapeutic uses. Previous preclinical investigations indicated that the leaves and stem extracts of L. micranthus had the potential to suppress breast cancer. Investigating the anticancer effects of L. micranthus extracts through network pharmacology analysis, in vitro and in vivo experiments is the goal of the current study. Network pharmacology analysis revealed 207 targets and 30 bioactive phytoconstituents of L. micranthus associated with the metabolism of breast cancer. L. micranthus controlled the metabolism of tryptophan and nitrogen in breast cancer, according to KEGG analysis and in silico models. The results of the experiment showed that L. micranthus significantly reduced the synthesis of kynurenine in interferon-γ (IFN-γ)-stimulated breast cancer cells, downregulated important proteins involved in tryptophan catabolism, and produced no cytotoxic effects in human breast cancer cells (MCF 7 and MDA-MB 231) at the administered doses. The viability of T cells co-cultured with IFN-γ-treated breast cancer cells was also markedly enhanced by L. micranthus pre-treatment. The in vivo investigation showed a similar outcome, with L. micranthus treatment suppressing the inflammatory response, IDO activity/expression, lowering kynurenine levels, blocking CTLA-4 immune checkpoint and finally increasing the CD4+ T cell population in rats with DMBA-induced breast cancer.
{"title":"Anti-cancer effect of Loranthus micranthus via downregulation of inflammation, tryptophan catabolism and kynurenine synthesis","authors":"Azubuike P. Ebokaiwe , Lingyu Li , Ting Peng , Emmanuel M. Njoya , Zongyuan Zhou , Euslar Nnenna Onu , Guolin Zhang , Wang Fei","doi":"10.1016/j.biocel.2025.106852","DOIUrl":"10.1016/j.biocel.2025.106852","url":null,"abstract":"<div><div>New therapeutic approaches are essential in the fight against breast cancer, which remains one of the top causes of mortality globally. Innovative and efficient methods of treating and preventing cancer has become expedient since its incidence rates are rising globally. Combining herbal extracts and chemotherapy have drawn a lot of attention in recent times as a cutting-edge cancer prevention approach. The wild parasitic plant <em>Loranthus micranthus</em> is extensively distributed throughout the world and is well-known for its therapeutic uses. Previous preclinical investigations indicated that the leaves and stem extracts of <em>L. micranthus</em> had the potential to suppress breast cancer. Investigating the anticancer effects of <em>L. micranthus</em> extracts through network pharmacology analysis, in vitro and in vivo experiments is the goal of the current study. Network pharmacology analysis revealed 207 targets and 30 bioactive phytoconstituents of <em>L. micranthus</em> associated with the metabolism of breast cancer. <em>L. micranthus</em> controlled the metabolism of tryptophan and nitrogen in breast cancer, according to KEGG analysis and in silico models. The results of the experiment showed that <em>L. micranthus</em> significantly reduced the synthesis of kynurenine in interferon-γ (IFN-γ)-stimulated breast cancer cells, downregulated important proteins involved in tryptophan catabolism, and produced no cytotoxic effects in human breast cancer cells (MCF 7 and MDA-MB 231) at the administered doses. The viability of T cells co-cultured with IFN-γ-treated breast cancer cells was also markedly enhanced by <em>L. micranthus</em> pre-treatment. The in vivo investigation showed a similar outcome, with <em>L. micranthus</em> treatment suppressing the inflammatory response, IDO activity/expression, lowering kynurenine levels, blocking CTLA-4 immune checkpoint and finally increasing the CD4<sup>+</sup> T cell population in rats with DMBA-induced breast cancer.</div></div>","PeriodicalId":50335,"journal":{"name":"International Journal of Biochemistry & Cell Biology","volume":"188 ","pages":"Article 106852"},"PeriodicalIF":2.8,"publicationDate":"2025-08-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144894777","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2025-08-20DOI: 10.1016/j.biocel.2025.106851
Qiao Ling , Manqi Cao , Hua-an Zhang , Xinjie Li , Wenhao Wang , Zhuohua Wang , Qingrong Sun , Zhijuan Liang , Weiyi Huang , Mengxuan Wang , Xin Li , Chuwen Lin , Xuan Jiang , Ji-An Pan , Xiaoxue Peng
The KCTD gene family is conserved across species, yet the knowledge of its function is limited. Recently, increasing studies focused on KCTD5 emerged. The functions of KCTD5 and its associations with various diseases were revealed. However, the function of KCTD5 in vivo has remained elusive. We generated Kctd5+/- mice with the Kctd5 gene’s exon 2 deleted using CRISPR/Cas9 technology. Breeding experiments on Kctd5+/- mice showed that only Kctd5+/- and Kctd5+/+ mice could be born normally, while Kctd5-/- embryos died in early embryonic development. Compared to Kctd5+/+ mice, Kctd5+/- mice have a shorter lifespan and exhibit spleen enlargement, abnormal blood cell counts, and metabolic disorders, including elevated cholesterol and triglyceride levels. Genome-wide gene expression analysis revealed that KCTD5 may affect the PPAR signaling pathway and subsequent the expression of Apo family genes, thereby regulating lipid metabolism. In summary, our study identified a previously unrecognized role of KCTD5 in regulating lipid metabolism and KCTD5 deficiency-induced animal phenotype, and revealed multiple correlations between KCTD5 and various molecules in mice.
{"title":"Heterozygous Kctd5 knockout mice exhibit abnormal lipid metabolism","authors":"Qiao Ling , Manqi Cao , Hua-an Zhang , Xinjie Li , Wenhao Wang , Zhuohua Wang , Qingrong Sun , Zhijuan Liang , Weiyi Huang , Mengxuan Wang , Xin Li , Chuwen Lin , Xuan Jiang , Ji-An Pan , Xiaoxue Peng","doi":"10.1016/j.biocel.2025.106851","DOIUrl":"10.1016/j.biocel.2025.106851","url":null,"abstract":"<div><div>The KCTD gene family is conserved across species, yet the knowledge of its function is limited. Recently, increasing studies focused on KCTD5 emerged. The functions of KCTD5 and its associations with various diseases were revealed. However, the function of KCTD5 <em>in vivo</em> has remained elusive. We generated <em>Kctd5</em><sup>+/-</sup> mice with the <em>Kctd5</em> gene’s exon 2 deleted using CRISPR/Cas9 technology. Breeding experiments on <em>Kctd5</em><sup>+/-</sup> mice showed that only <em>Kctd5</em><sup>+/-</sup> and <em>Kctd5</em><sup>+/+</sup> mice could be born normally, while <em>Kctd5</em><sup>-/-</sup> embryos died in early embryonic development. Compared to <em>Kctd5</em><sup>+/+</sup> mice, <em>Kctd5</em><sup>+/-</sup> mice have a shorter lifespan and exhibit spleen enlargement, abnormal blood cell counts, and metabolic disorders, including elevated cholesterol and triglyceride levels. Genome-wide gene expression analysis revealed that KCTD5 may affect the PPAR signaling pathway and subsequent the expression of Apo family genes, thereby regulating lipid metabolism. In summary, our study identified a previously unrecognized role of KCTD5 in regulating lipid metabolism and KCTD5 deficiency-induced animal phenotype, and revealed multiple correlations between KCTD5 and various molecules in mice.</div></div>","PeriodicalId":50335,"journal":{"name":"International Journal of Biochemistry & Cell Biology","volume":"188 ","pages":"Article 106851"},"PeriodicalIF":2.8,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144892029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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