Pub Date : 2026-01-03DOI: 10.1016/j.bbrc.2025.153224
Akanksha Kulshreshtha, Sonika Bhatnagar
Integrative Biology research has deepened our understanding of various diseases particularly by elucidating the impact of nonsynonymous single nucleotide polymorphisms (nsSNPs) on disease and diagnosis. PCSK9 is an important cholesterol regulator, and genetic variations in this protein can influence cardiovascular risk. Loss-of-function (LOF) mutations in PCSK9 gene are linked to reduced plasma LDL cholesterol levels and prevent hypercholesterolemia. This study investigated the influence of nsSNPs of PCSK9 found in the Indian population to assess their impact on protein stability, dynamics and interaction with the LDL receptor (LDLR). Molecular dynamics Simulation were carried out on wild type PCSK9-LDLR and LOF PCSK9-LDLR complexes and revealed that R93C, N298D, and A511V mutations destabilize the PCSK9–LDLR complex, with A511V, a variant unique to the Indian population showing complete loss of all contacts with LDLR. Further analysis confirmed the structural instability of these LOF variants, suggesting their potential role in altered lipid regulation. The structure and dynamics of LDLR complex formation in wild type versus three LOF variants provides a basis for prediction of LOF of PCSK9 and may facilitate drug design and personalized low risk assessment for hypercholesterolemia leading to heart disease.
{"title":"Impact of loss-of-function variations of PCSK9 on LDLR interaction and dynamics: Implications for heart function","authors":"Akanksha Kulshreshtha, Sonika Bhatnagar","doi":"10.1016/j.bbrc.2025.153224","DOIUrl":"10.1016/j.bbrc.2025.153224","url":null,"abstract":"<div><div>Integrative Biology research has deepened our understanding of various diseases particularly by elucidating the impact of nonsynonymous single nucleotide polymorphisms (nsSNPs) on disease and diagnosis. PCSK9 is an important cholesterol regulator, and genetic variations in this protein can influence cardiovascular risk. Loss-of-function (LOF) mutations in PCSK9 gene are linked to reduced plasma LDL cholesterol levels and prevent hypercholesterolemia. This study investigated the influence of nsSNPs of PCSK9 found in the Indian population to assess their impact on protein stability, dynamics and interaction with the LDL receptor (LDLR). Molecular dynamics Simulation were carried out on wild type PCSK9-LDLR and LOF PCSK9-LDLR complexes and revealed that R93C, N298D, and A511V mutations destabilize the PCSK9–LDLR complex, with A511V, a variant unique to the Indian population showing complete loss of all contacts with LDLR. Further analysis confirmed the structural instability of these LOF variants, suggesting their potential role in altered lipid regulation. The structure and dynamics of LDLR complex formation in wild type versus three LOF variants provides a basis for prediction of LOF of PCSK9 and may facilitate drug design and personalized low risk assessment for hypercholesterolemia leading to heart disease.</div></div>","PeriodicalId":8779,"journal":{"name":"Biochemical and biophysical research communications","volume":"799 ","pages":"Article 153224"},"PeriodicalIF":2.2,"publicationDate":"2026-01-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145897947","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 : 2026-01-02DOI: 10.1016/j.bbrc.2026.153238
Ailing Huang , Cheng Li , Hui Wu , Wenli Sun , Shanshan Huo , Juan Wang , Yanling Wu , Tianlei Ying , Fei Yu
The neuraminidase (NA) of influenza A virus (IAV) is an important antiviral target. However, antibodies require precise recognition of the catalytic pocket to exert antiviral effects, making them difficult to obtain through conventional screening. Traditional IgG antibodies also suffer from poor aerosolization efficiency, limiting their effectiveness for respiratory delivery. Human single-domain antibodies (sdAbs) with only the variable domain of the heavy chain (VH) show great potential in combating respiratory viral infections because of their small molecular weight and superior inhalable properties; however, sdAbs often lose stability or binding activity when isolated directly from parental IgG antibodies. To overcome these barriers and accelerate the acquisition of fully human sdAbs targeting the NA active pocket, we extracted the VH domain from broadly neutralizing anti-NA IgG and applied scaffold grafting followed by affinity recovery. Ultimately, we obtained two fully human sdAbs with favorable physicochemical properties that inhibited H5N8 NA enzymatic activity, with IC50 values of 0.82 and 0.59 μg mL−1. This work enabled the originally insoluble VH fragment of IgG to be expressed in a stable and soluble form and restored its NA-binding activity from undetectable levels to the nanomolar range, providing insights into engineering fully human sdAbs capable of targeting structurally constrained viral enzymes and suitable for inhalable influenza therapeutics.
{"title":"Development of human single-domain antibodies against influenza based on NA-targeting IgG","authors":"Ailing Huang , Cheng Li , Hui Wu , Wenli Sun , Shanshan Huo , Juan Wang , Yanling Wu , Tianlei Ying , Fei Yu","doi":"10.1016/j.bbrc.2026.153238","DOIUrl":"10.1016/j.bbrc.2026.153238","url":null,"abstract":"<div><div>The neuraminidase (NA) of influenza A virus (IAV) is an important antiviral target. However, antibodies require precise recognition of the catalytic pocket to exert antiviral effects, making them difficult to obtain through conventional screening. Traditional IgG antibodies also suffer from poor aerosolization efficiency, limiting their effectiveness for respiratory delivery. Human single-domain antibodies (sdAbs) with only the variable domain of the heavy chain (VH) show great potential in combating respiratory viral infections because of their small molecular weight and superior inhalable properties; however, sdAbs often lose stability or binding activity when isolated directly from parental IgG antibodies. To overcome these barriers and accelerate the acquisition of fully human sdAbs targeting the NA active pocket, we extracted the VH domain from broadly neutralizing anti-NA IgG and applied scaffold grafting followed by affinity recovery. Ultimately, we obtained two fully human sdAbs with favorable physicochemical properties that inhibited H5N8 NA enzymatic activity, with IC<sub>50</sub> values of 0.82 and 0.59 μg mL<sup>−1</sup>. This work enabled the originally insoluble VH fragment of IgG to be expressed in a stable and soluble form and restored its NA-binding activity from undetectable levels to the nanomolar range, providing insights into engineering fully human sdAbs capable of targeting structurally constrained viral enzymes and suitable for inhalable influenza therapeutics.</div></div>","PeriodicalId":8779,"journal":{"name":"Biochemical and biophysical research communications","volume":"798 ","pages":"Article 153238"},"PeriodicalIF":2.2,"publicationDate":"2026-01-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145910004","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 : 2025-12-31DOI: 10.1016/j.bbrc.2025.153173
Yang Xu , Bin Yuan , Mingjun Zhang
Objective
Airborne environmental contaminants are established carcinogens. This investigation elucidates the mechanistic contributions to pulmonary adenocarcinoma (LUAD) pathogenesis.
Methods
Transcriptomic profiling through differential expression analysis and weighted gene co-expression network analysis (WGCNA) identified malignancy-associated molecular targets. Computational screening of environmental toxicology databases yielded airborne contaminant-responsive genes that were subsequently cross-referenced with LUAD-associated targets. An integrative analytical framework incorporating artificial intelligence-driven pattern recognition, systems toxicology, and computational structural biology characterizes contaminant-macromolecule interactions. Expression-based patient stratification enabled pathway enrichment investigation of CA4-related oncogenic processes.
Results
Systematic evaluation of eight atmospheric pollutants (benzene, sulfur dioxide, nitric oxide, carbon monoxide, nitrogen dioxide, toluene, ozone, and benzo[a]pyrene) identified 265 molecular interactors, including 58 putative LUAD mediators. Predictive modeling established five central regulators exhibiting significant alterations in expression (CA4 and CAT suppression; SPP1, CDH1, and TIMP1 elevation; all P < 0.05). In silico structural analysis demonstrated high-affinity binding between the prototypical polycyclic aromatic hydrocarbon benzo[a]pyrene (BaP) and carbonic anhydrase IV protein.
Conclusions
Air pollution may promote LUAD via specific gene regulation. The identified hub genes and validated CA4-Benzo[a]pyrene interactions provided mechanistic insights for further research.
{"title":"Unraveling the molecular mechanisms of air pollution-induced lung adenocarcinoma through machine learning, network toxicology, and molecular docking","authors":"Yang Xu , Bin Yuan , Mingjun Zhang","doi":"10.1016/j.bbrc.2025.153173","DOIUrl":"10.1016/j.bbrc.2025.153173","url":null,"abstract":"<div><h3>Objective</h3><div>Airborne environmental contaminants are established carcinogens. This investigation elucidates the mechanistic contributions to pulmonary adenocarcinoma (LUAD) pathogenesis.</div></div><div><h3>Methods</h3><div>Transcriptomic profiling through differential expression analysis and weighted gene co-expression network analysis (WGCNA) identified malignancy-associated molecular targets. Computational screening of environmental toxicology databases yielded airborne contaminant-responsive genes that were subsequently cross-referenced with LUAD-associated targets. An integrative analytical framework incorporating artificial intelligence-driven pattern recognition, systems toxicology, and computational structural biology characterizes contaminant-macromolecule interactions. Expression-based patient stratification enabled pathway enrichment investigation of CA4-related oncogenic processes.</div></div><div><h3>Results</h3><div>Systematic evaluation of eight atmospheric pollutants (benzene, sulfur dioxide, nitric oxide, carbon monoxide, nitrogen dioxide, toluene, ozone, and benzo[a]pyrene) identified 265 molecular interactors, including 58 putative LUAD mediators. Predictive modeling established five central regulators exhibiting significant alterations in expression (CA4 and CAT suppression; SPP1, CDH1, and TIMP1 elevation; all P < 0.05). In silico structural analysis demonstrated high-affinity binding between the prototypical polycyclic aromatic hydrocarbon benzo[a]pyrene (BaP) and carbonic anhydrase IV protein.</div></div><div><h3>Conclusions</h3><div>Air pollution may promote LUAD via specific gene regulation. The identified hub genes and validated CA4-Benzo[a]pyrene interactions provided mechanistic insights for further research.</div></div>","PeriodicalId":8779,"journal":{"name":"Biochemical and biophysical research communications","volume":"797 ","pages":"Article 153173"},"PeriodicalIF":2.2,"publicationDate":"2025-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145882130","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 : 2025-12-31DOI: 10.1016/j.bbrc.2025.153222
Gelin Jin , Chenxuan Yang , Qinqin Deng , Longjiang Wu , Wang Chen , Zhuoying Chen
The CRISPR/Cas9 system revolutionizes genome engineering, yet optimizing the stability and expression levels of single-guide RNA (sgRNA) is crucial for achieving more effective gene regulation. Transfer RNAs (tRNA), known for their inherent stability, present a valuable solution. In this study, we developed a chimeric tRNA-sgRNA (tgRNA) by integrating sgRNA into the anticodon stem of a Sephadex aptamer-human HBV ε tRNA (SeptRNA) scaffold, resulting in the formation of SeptgRNA. When applied to target the E. coli ampC and ompA genes, SeptgRNA exhibited significantly increased accumulation compared to conventional sgRNAs. To overcome potential steric hindrance from the tRNA scaffold, we utilized CRISPR interference (CRISPRi) by co-expressing SeptgRNA with deactivated Cas9 (dCas9), which effectively suppressed DNA transcription. This approach demonstrated superior gene expression suppression compared to traditional sgRNA-based CRISPRi. Molecular docking and molecular dynamics simulations revealed that the SeptRNA scaffold stabilizes the sgRNA stem-loop architecture and enhances the stability of the dCas9-tgRNA-DNA ternary complex. Our findings provide proof-of-concept for the use of chimeric tgRNAs in gene knockdown, highlighting their potential for increased expression levels and improved stability. This study advances the CRISPR/Cas9 toolkit and underscores the versatility of tRNA scaffolds in genetic engineering applications.
{"title":"Establishing a chimeric tRNA-sgRNA scaffold and computational basis for enhanced CRISPR interference","authors":"Gelin Jin , Chenxuan Yang , Qinqin Deng , Longjiang Wu , Wang Chen , Zhuoying Chen","doi":"10.1016/j.bbrc.2025.153222","DOIUrl":"10.1016/j.bbrc.2025.153222","url":null,"abstract":"<div><div>The CRISPR/Cas9 system revolutionizes genome engineering, yet optimizing the stability and expression levels of single-guide RNA (sgRNA) is crucial for achieving more effective gene regulation. Transfer RNAs (tRNA), known for their inherent stability, present a valuable solution. In this study, we developed a chimeric tRNA-sgRNA (tgRNA) by integrating sgRNA into the anticodon stem of a Sephadex aptamer-human HBV ε tRNA (SeptRNA) scaffold, resulting in the formation of SeptgRNA. When applied to target the <em>E. coli ampC</em> and <em>ompA</em> genes, SeptgRNA exhibited significantly increased accumulation compared to conventional sgRNAs. To overcome potential steric hindrance from the tRNA scaffold, we utilized CRISPR interference (CRISPRi) by co-expressing SeptgRNA with deactivated Cas9 (dCas9), which effectively suppressed DNA transcription. This approach demonstrated superior gene expression suppression compared to traditional sgRNA-based CRISPRi. Molecular docking and molecular dynamics simulations revealed that the SeptRNA scaffold stabilizes the sgRNA stem-loop architecture and enhances the stability of the dCas9-tgRNA-DNA ternary complex. Our findings provide proof-of-concept for the use of chimeric tgRNAs in gene knockdown, highlighting their potential for increased expression levels and improved stability. This study advances the CRISPR/Cas9 toolkit and underscores the versatility of tRNA scaffolds in genetic engineering applications.</div></div>","PeriodicalId":8779,"journal":{"name":"Biochemical and biophysical research communications","volume":"798 ","pages":"Article 153222"},"PeriodicalIF":2.2,"publicationDate":"2025-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145882971","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 : 2025-12-31DOI: 10.1016/j.bbrc.2025.153198
Yan-Xia Ma , Shan-Wen Wei , Hao-Nan Zhang , Ming-Ming Zou , Saijilafu
The regenerative capacity of the adult mammalian central nervous system is severely limited, posing a significant challenge for functional recovery after injury. To explore novel approaches to support neuronal regeneration, this study examined the role of Caspr1 as an inhibitor of axonal regeneration. Caspr1 expression was downregulated in dorsal root ganglion neurons in a rodent model of nerve injury and absent from regenerating axons, but localized to the neuronal soma membrane. Functional assays revealed that knocking down Caspr1 in cultured central and peripheral neurons using targeted siRNA significantly enhanced axon growth. Silencing Caspr1 in sensory neurons and retinal ganglion cells promoted the regeneration of sensory axons and the optic nerve, respectively. We further identified Nfasc as a key downstream mediator, and that Nfasc expression was negatively regulated by Caspr1. Taken together, these findings identify Caspr1 as a potent negative regulator of axonal regeneration and the novel Caspr1-Nfasc pathway as a promising therapeutic target for the axonal regeneration of mature neurons following injury.
{"title":"Caspr1 silencing promotes axon regeneration in both peripheral and central nervous systems via negative regulation of neurofascin","authors":"Yan-Xia Ma , Shan-Wen Wei , Hao-Nan Zhang , Ming-Ming Zou , Saijilafu","doi":"10.1016/j.bbrc.2025.153198","DOIUrl":"10.1016/j.bbrc.2025.153198","url":null,"abstract":"<div><div>The regenerative capacity of the adult mammalian central nervous system is severely limited, posing a significant challenge for functional recovery after injury. To explore novel approaches to support neuronal regeneration, this study examined the role of Caspr1 as an inhibitor of axonal regeneration. Caspr1 expression was downregulated in dorsal root ganglion neurons in a rodent model of nerve injury and absent from regenerating axons, but localized to the neuronal soma membrane. Functional assays revealed that knocking down Caspr1 in cultured central and peripheral neurons using targeted siRNA significantly enhanced axon growth. Silencing Caspr1 in sensory neurons and retinal ganglion cells promoted the regeneration of sensory axons and the optic nerve, respectively. We further identified Nfasc as a key downstream mediator, and that Nfasc expression was negatively regulated by Caspr1. Taken together, these findings identify Caspr1 as a potent negative regulator of axonal regeneration and the novel Caspr1-Nfasc pathway as a promising therapeutic target for the axonal regeneration of mature neurons following injury.</div></div>","PeriodicalId":8779,"journal":{"name":"Biochemical and biophysical research communications","volume":"799 ","pages":"Article 153198"},"PeriodicalIF":2.2,"publicationDate":"2025-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145923563","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 : 2025-12-31DOI: 10.1016/j.bbrc.2025.153236
Jay Bhushan Jawale , Monal Yuwanati , Sambath Baskaran , M. Senthil Murugan , Parthiban Anaikutti
Oral squamous cell carcinoma (OSCC) continues to pose a considerable health challenge worldwide, often exhibiting poor response to conventional therapies and high recurrence rates. In search of novel chemotherapeutic agents, fused heterocycles such as naphthyridine and isoindoline-1,3-dione derivatives have shown considerable promise due to their biological activity. This study aimed to synthesize, characterize, and evaluate the anticancer potential of a novel compound, 2-(7-hydroxy-1,8-naphthyridin-2-yl)isoindoline-1,3-dione (3), against human oral carcinoma (KB) cells. The structure of the molecule was characterized through FT-IR, 1H NMR, and 13C NMR spectroscopy. The anti-cancer activities of synthesized compound (3) was evaluated and exhibited a significant anticancer effect with an IC50 of 23.60 ± 5.54 μM against human oral carcinoma KB cells. Mechanistic studies performed on the compound (3) and treated cells showed increased intracellular, decreased mitochondrial membrane potential, and evident nuclear condensation. DFT studies indicate that isoindoline-naphthyridine (3) exhibits significant binding affinity and molecular stability. Furthermore, the molecular docking results demonstrate that isoindoline-naphthyridine binds effectively within the ATP-binding clefts of both EGFR and HER2.
{"title":"Biological assessment of a novel isoindoline-naphthyridine derivative with anticancer potential in oral squmaous cell carcinoma: In vitro and In silico approach","authors":"Jay Bhushan Jawale , Monal Yuwanati , Sambath Baskaran , M. Senthil Murugan , Parthiban Anaikutti","doi":"10.1016/j.bbrc.2025.153236","DOIUrl":"10.1016/j.bbrc.2025.153236","url":null,"abstract":"<div><div>Oral squamous cell carcinoma (OSCC) continues to pose a considerable health challenge worldwide, often exhibiting poor response to conventional therapies and high recurrence rates. In search of novel chemotherapeutic agents, fused heterocycles such as naphthyridine and isoindoline-1,3-dione derivatives have shown considerable promise due to their biological activity. This study aimed to synthesize, characterize, and evaluate the anticancer potential of a novel compound, 2-(7-hydroxy-1,8-naphthyridin-2-yl)isoindoline-1,3-dione (<strong>3)</strong>, against human oral carcinoma (KB) cells. The structure of the molecule was characterized through FT-IR, <sup>1</sup>H NMR, and <sup>13</sup>C NMR spectroscopy. The anti-cancer activities of synthesized compound (<strong>3)</strong> was evaluated and exhibited a significant anticancer effect with an IC<sub>50</sub> of 23.60 ± 5.54 μM against human oral carcinoma KB cells. Mechanistic studies performed on the compound (<strong>3</strong>) and treated cells showed increased intracellular, decreased mitochondrial membrane potential, and evident nuclear condensation. DFT studies indicate that isoindoline-naphthyridine (<strong>3</strong>) exhibits significant binding affinity and molecular stability. Furthermore, the molecular docking results demonstrate that isoindoline-naphthyridine binds effectively within the ATP-binding clefts of both EGFR and HER2.</div></div>","PeriodicalId":8779,"journal":{"name":"Biochemical and biophysical research communications","volume":"798 ","pages":"Article 153236"},"PeriodicalIF":2.2,"publicationDate":"2025-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145876738","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 : 2025-12-31DOI: 10.1016/j.bbrc.2025.153177
Jun Jiang , Fangzhou Ye , Jiayi Wang , Huanqing Li , Songhua Bei , Xiaohong Zhang , Li Feng
Background
A recently identified type of copper-induced cell death that may contribute to tumor development is cuprotosis. However, uncertainty surrounds its molecular regulation mechanism in colorectal cancer (CRC). Clarifying the regulation mechanism of SLC7A11 in CRC cell cuproptosis was the goal of this investigation.
Methods
To identify the genes associated with cuproptosis, we combined transcriptome data from TCGA-COAD and GSE83889. Functional experiments including cell viability assays, colony formation, Western blotting, glutathione metabolism analysis, lipid peroxidation staining, and ROS measurements, were performed in CRC cells following SLC7A11 knockdown and treatment with the copper ionophore elesclomol–Cu. Rescue experiments were conducted using exogenous glutathione (GSH) and SLC7A11 inhibitors (erastin, SASP) to validate the mechanisms.
Results
Bioinformatics analysis identified SLC7A11 as a cuproptosis-related gene markedly elevated in CRC and linked with a poor prognosis. Knockdown or pharmacological inhibition of SLC7A11 enhanced elesclomol-Cu-induced cell death, increased intracellular Cu2+ accumulation, and aggravated oxidative stress. Mechanistically, SLC7A11 silencing disrupted glutathione and cystine metabolism, suppressed GPX4 activity, and altered the expression of key cuproptosis regulators. Exogenous glutathione partially reversed these effects. Furthermore, inhibition of SLC7A11 using erastin or SASP drugs enhanced goblet apoptosis and further reduced CRC cell viability.
Conclusion
SLC7A11 knockdown regulates intracellular redox balance through the GSH-GPX4 axis, thereby promoting cellular cuproptosis. Targeting SLC7A11 can enhance the sensitivity of CRC cells to copper ionophores and may represent a novel therapeutic strategy to enhance cuproptosis of CRC cells.
{"title":"Targeting SLC7A11 sensitizes colorectal cancer cells to elesclomol–Cu–induced cuproptosis via the GSH-GPX4 axis","authors":"Jun Jiang , Fangzhou Ye , Jiayi Wang , Huanqing Li , Songhua Bei , Xiaohong Zhang , Li Feng","doi":"10.1016/j.bbrc.2025.153177","DOIUrl":"10.1016/j.bbrc.2025.153177","url":null,"abstract":"<div><h3>Background</h3><div>A recently identified type of copper-induced cell death that may contribute to tumor development is cuprotosis. However, uncertainty surrounds its molecular regulation mechanism in colorectal cancer (CRC). Clarifying the regulation mechanism of <em>SLC7A11</em> in CRC cell cuproptosis was the goal of this investigation.</div></div><div><h3>Methods</h3><div>To identify the genes associated with cuproptosis, we combined transcriptome data from TCGA-COAD and GSE83889. Functional experiments including cell viability assays, colony formation, Western blotting, glutathione metabolism analysis, lipid peroxidation staining, and ROS measurements, were performed in CRC cells following <em>SLC7A11</em> knockdown and treatment with the copper ionophore elesclomol–Cu. Rescue experiments were conducted using exogenous glutathione (GSH) and <em>SLC7A11</em> inhibitors (erastin, SASP) to validate the mechanisms.</div></div><div><h3>Results</h3><div>Bioinformatics analysis identified <em>SLC7A11</em> as a cuproptosis-related gene markedly elevated in CRC and linked with a poor prognosis. Knockdown or pharmacological inhibition of <em>SLC7A11</em> enhanced elesclomol-Cu-induced cell death, increased intracellular Cu<sup>2+</sup> accumulation, and aggravated oxidative stress. Mechanistically, <em>SLC7A11</em> silencing disrupted glutathione and cystine metabolism, suppressed GPX4 activity, and altered the expression of key cuproptosis regulators. Exogenous glutathione partially reversed these effects. Furthermore, inhibition of <em>SLC7A11</em> using erastin or SASP drugs enhanced goblet apoptosis and further reduced CRC cell viability.</div></div><div><h3>Conclusion</h3><div><em>SLC7A11</em> knockdown regulates intracellular redox balance through the GSH-GPX4 axis, thereby promoting cellular cuproptosis. Targeting <em>SLC7A11</em> can enhance the sensitivity of CRC cells to copper ionophores and may represent a novel therapeutic strategy to enhance cuproptosis of CRC cells.</div></div>","PeriodicalId":8779,"journal":{"name":"Biochemical and biophysical research communications","volume":"799 ","pages":"Article 153177"},"PeriodicalIF":2.2,"publicationDate":"2025-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145923561","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 : 2025-12-30DOI: 10.1016/j.bbrc.2025.153225
Yu Xie, Yue Shi, Yinan Hong, Xiaojun Wang, Hong Pan, Yiwen Wang, Yuzhi Xing, Hongbo Li
Ginsenoside F2 has multiple biological effects, such as cardiovascular protection, antioxidant. However, ginsenoside F2 is extremely low in natural ginseng plants; it can be obtained by deglycosylation of ginsenoside Rb1. In this paper, high-performance liquid chromatography, fourier transform infrared spectroscopy, ultraviolet spectroscopy, and fluorescence spectroscopy were used to study the molecular mechanism of β-glucanase in the conversion of rare ginsenoside F2. The ability of β-glucanase to convert ginsenoside Rb1 into ginsenoside F2 was examined. Molecular dynamics simulation and molecular docking were used to identify the putative binding site of β-glucanase and ginsenoside Rb1 as well as the optimal binding conformation. The results showed that β-glucanase and ginsenosides Rb1 and Rd can spontaneously interact with each other. the dynamic binding process of the active site during the conversion of ginsenoside Rb1 to F2 by β-glucanase was verified by spectroscopic experiments, and the molecular basis of the conformational relationship was elucidated and validated by molecular simulations. This study established a multi-scale research approach by integrating spectroscopic analysis with molecular simulation. This methodology not only optimized the process for converting Rb1 to F2 by β-glucanase but also elucidated the structural basis of its regioselectivity at the molecular level. This work not only provides a paradigm for elucidating the transformation mechanism of glycosidases but also establishes an efficient route for producing precious rare ginsenosides.
{"title":"Optimization of the process and kinetic mechanism of ginsenoside Rb1 conversion by β-glucanase","authors":"Yu Xie, Yue Shi, Yinan Hong, Xiaojun Wang, Hong Pan, Yiwen Wang, Yuzhi Xing, Hongbo Li","doi":"10.1016/j.bbrc.2025.153225","DOIUrl":"10.1016/j.bbrc.2025.153225","url":null,"abstract":"<div><div>Ginsenoside F2 has multiple biological effects, such as cardiovascular protection, antioxidant. However, ginsenoside F2 is extremely low in natural ginseng plants; it can be obtained by deglycosylation of ginsenoside Rb1. In this paper, high-performance liquid chromatography, fourier transform infrared spectroscopy, ultraviolet spectroscopy, and fluorescence spectroscopy were used to study the molecular mechanism of β-glucanase in the conversion of rare ginsenoside F2. The ability of β-glucanase to convert ginsenoside Rb1 into ginsenoside F2 was examined. Molecular dynamics simulation and molecular docking were used to identify the putative binding site of β-glucanase and ginsenoside Rb1 as well as the optimal binding conformation. The results showed that β-glucanase and ginsenosides Rb1 and Rd can spontaneously interact with each other. the dynamic binding process of the active site during the conversion of ginsenoside Rb1 to F2 by β-glucanase was verified by spectroscopic experiments, and the molecular basis of the conformational relationship was elucidated and validated by molecular simulations. This study established a multi-scale research approach by integrating spectroscopic analysis with molecular simulation. This methodology not only optimized the process for converting Rb1 to F2 by β-glucanase but also elucidated the structural basis of its regioselectivity at the molecular level. This work not only provides a paradigm for elucidating the transformation mechanism of glycosidases but also establishes an efficient route for producing precious rare ginsenosides.</div></div>","PeriodicalId":8779,"journal":{"name":"Biochemical and biophysical research communications","volume":"797 ","pages":"Article 153225"},"PeriodicalIF":2.2,"publicationDate":"2025-12-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145877622","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 : 2025-12-30DOI: 10.1016/j.bbrc.2025.153223
Jiang Wu , Yuying Yang , Shan yuan , Guangze Hu , Rui Gao , Shangquan Gan
Ischemic stroke is a complex polygenic disorder, in which microRNAs (miRNAs) have been implicated in various physiological and pathological processes. However, the specific regulatory networks and mechanisms involving brain miRNAs in the development of stroke remain inadequately elucidated. In this study, a middle cerebral artery occlusion (MCAO) model was established in Sprague-Dawley rats to simulate cerebral ischemia. Deep sequencing was performed to profile miRNA expression in the cerebral cortex after stroke, with an emphasis on identifying pivotal miRNAs. Key differentially expressed miRNAs (DEMis) and their potential target mRNAs were validated by quantitative reverse-transcription PCR (qRT-PCR), showing strong concordance with sequencing results. Cluster analysis revealed distinct miRNA expression patterns between MCAO and control cortical tissues. Gene Ontology (GO) enrichment analysis indicated that target genes of DEMis were significantly associated with stroke-relevant pathways, including calcium transmembrane transport, axon guidance, and MAPK and PI3K signaling pathways. Additionally, by combining DEMis target genes with differentially expressed genes (DEGs) obtained from high-throughput sequencing, we identified 376 disease-related target genes and constructed a miRNA-mRNA regulatory network of key DEGs. Through this analysis, we discovered three novel miRNAs (novel-miR-398, novel-miR-544, and novel-miR-1808) and ten miRNAs previously reported in stroke or other diseases. The target genes of these miRNAs are involved in post-stroke processes such as oxidative stress, apoptosis, inflammatory response, and nerve regeneration through endogenous competition mechanisms. Our findings suggested that miRNAs significantly contributed to the regulation of post-stroke pathophysiological processes, offering potential new targets for therapeutic intervention and advancing our understanding of the molecular mechanisms underlying stroke.
缺血性脑卒中是一种复杂的多基因疾病，其中microRNAs （miRNAs）参与了多种生理和病理过程。然而，涉及脑mirna在卒中发展中的具体调控网络和机制仍未充分阐明。本研究建立了Sprague-Dawley大鼠大脑中动脉闭塞（MCAO）模型，模拟脑缺血。研究人员对脑卒中后大脑皮层的miRNA表达进行了深度测序，重点是鉴定关键miRNA。通过定量反转录PCR （qRT-PCR）对关键差异表达miRNAs （DEMis）及其潜在靶mrna进行验证，结果与测序结果具有较强的一致性。聚类分析显示MCAO和对照皮质组织之间存在不同的miRNA表达模式。基因本体（Gene Ontology， GO）富集分析表明，DEMis靶基因与脑卒中相关通路显著相关，包括钙跨膜转运、轴突引导、MAPK和PI3K信号通路。此外，通过将DEMis靶基因与高通量测序获得的差异表达基因（differential expression genes, DEGs）结合，我们鉴定出376个疾病相关靶基因，并构建了关键DEGs的miRNA-mRNA调控网络。通过这项分析，我们发现了三个新的mirna （novel- mir -398， novel- mir -544和novel- mir -1808）和十个先前报道的与中风或其他疾病相关的mirna。这些mirna的靶基因通过内源性竞争机制参与脑卒中后的过程，如氧化应激、细胞凋亡、炎症反应和神经再生。我们的研究结果表明，mirna对脑卒中后病理生理过程的调节有重要作用，为治疗干预提供了潜在的新靶点，并促进了我们对脑卒中分子机制的理解。
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Pub Date : 2025-12-29DOI: 10.1016/j.bbrc.2025.153218
Qingcheng Guo , Yunfei Fu , Xiaoqi Ma , Jihao Xing , Yudai Kawamoto , Atomu Yamaguchi , Chengzhou Xiong , Mikiko Uemura , Hidemi Fujino , Noriaki Maeshige
Background
Skeletal muscle–derived extracellular vesicles (SkM-EVs) are promising mediators of intercellular communication, yet practical strategies to safely and efficiently enhance their release remain limited. Vibration is a non-invasive, parameter-controlled mechanical stimulus that is already widely used in musculoskeletal rehabilitation, making it an attractive candidate for enhancing SkM-EV release. However, it remains unclear whether vibration increases EV release and which vibration parameter (amplitude, frequency, or acceleration) regulates this effect. Accordingly, we investigated the parameter dependence of this process and the corresponding effective intensity.
Methods
Differentiated C2C12 myotubes were exposed to sinusoidal vibration using a custom-built device. Two parameter-decoupled series were designed: an acceleration-variation series and an amplitude-variation series. EVs were isolated by ultracentrifugation and analyzed by western blotting and tunable resistive pulse sensing (TRPS). RNA sequencing with gene set enrichment analysis (GSEA) was used to identify pathways associated with vibration-induced EV secretion.
Results
Vibration did not reduce cell viability. SkM-EV concentration remained unchanged across acceleration conditions but significantly increased under medium-amplitude (MAm) stimulation. Transcriptomic analysis showed that MAm downregulated Wnt signaling and upregulated the NOD-like receptor pathway, with specific upregulation of Rab27a and Nlrp4e.
Conclusion
Vibration promotes SkM-EV secretion in an amplitude-dependent manner, with the medium-amplitude (MAm) condition being the most effective. This effect appears to be mediated by modulation of the Wnt–Rab27a axis and NLR–Nlrp4e signaling.
骨骼肌来源的细胞外囊泡（skm - ev）是一种很有前途的细胞间通讯介质，但安全有效地促进其释放的实用策略仍然有限。振动是一种非侵入性、参数控制的机械刺激，已广泛应用于肌肉骨骼康复，使其成为增强SkM-EV释放的有吸引力的候选者。然而，目前尚不清楚振动是否会增加EV释放，以及哪种振动参数（振幅、频率或加速度）调节这种影响。因此，我们研究了该过程的参数依赖性和相应的有效强度。方法采用特制装置对分化后的C2C12肌管进行正弦振动。设计了两个参数解耦序列：加速度变化序列和幅值变化序列。采用超离心分离ev， western blotting和可调电阻脉冲传感（TRPS）对其进行分析。RNA测序和基因集富集分析（GSEA）被用于鉴定振动诱导EV分泌的相关途径。结果振动不影响细胞活力。SkM-EV浓度在加速条件下保持不变，但在中振幅（MAm）刺激下显著增加。转录组学分析显示，MAm下调Wnt信号通路，上调nod样受体通路，并特异性上调Rab27a和Nlrp4e。结论振动促进SkM-EV分泌具有幅值依赖性，其中中幅值（MAm）条件下效果最好。这种效应似乎是通过调节Wnt-Rab27a轴和NLR-Nlrp4e信号通路介导的。
{"title":"Amplitude dependence in extracellular vesicle release from cultured myotubes under vibration stimulation","authors":"Qingcheng Guo , Yunfei Fu , Xiaoqi Ma , Jihao Xing , Yudai Kawamoto , Atomu Yamaguchi , Chengzhou Xiong , Mikiko Uemura , Hidemi Fujino , Noriaki Maeshige","doi":"10.1016/j.bbrc.2025.153218","DOIUrl":"10.1016/j.bbrc.2025.153218","url":null,"abstract":"<div><h3>Background</h3><div>Skeletal muscle–derived extracellular vesicles (SkM-EVs) are promising mediators of intercellular communication, yet practical strategies to safely and efficiently enhance their release remain limited. Vibration is a non-invasive, parameter-controlled mechanical stimulus that is already widely used in musculoskeletal rehabilitation, making it an attractive candidate for enhancing SkM-EV release. However, it remains unclear whether vibration increases EV release and which vibration parameter (amplitude, frequency, or acceleration) regulates this effect. Accordingly, we investigated the parameter dependence of this process and the corresponding effective intensity.</div></div><div><h3>Methods</h3><div>Differentiated C2C12 myotubes were exposed to sinusoidal vibration using a custom-built device. Two parameter-decoupled series were designed: an acceleration-variation series and an amplitude-variation series. EVs were isolated by ultracentrifugation and analyzed by western blotting and tunable resistive pulse sensing (TRPS). RNA sequencing with gene set enrichment analysis (GSEA) was used to identify pathways associated with vibration-induced EV secretion.</div></div><div><h3>Results</h3><div>Vibration did not reduce cell viability. SkM-EV concentration remained unchanged across acceleration conditions but significantly increased under medium-amplitude (MAm) stimulation. Transcriptomic analysis showed that MAm downregulated Wnt signaling and upregulated the NOD-like receptor pathway, with specific upregulation of Rab27a and Nlrp4e.</div></div><div><h3>Conclusion</h3><div>Vibration promotes SkM-EV secretion in an amplitude-dependent manner, with the medium-amplitude (MAm) condition being the most effective. This effect appears to be mediated by modulation of the Wnt–Rab27a axis and NLR–Nlrp4e signaling.</div></div>","PeriodicalId":8779,"journal":{"name":"Biochemical and biophysical research communications","volume":"797 ","pages":"Article 153218"},"PeriodicalIF":2.2,"publicationDate":"2025-12-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145882135","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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