{"title":"Computational screening of filamin mechanical binding proteins using AlphaFold2.","authors":"Jennifer Johnson, Nicanor González-Morales","doi":"10.1139/bcb-2025-0194","DOIUrl":"10.1139/bcb-2025-0194","url":null,"abstract":"<p><p>Filamins are dimeric actin-binding protein that play a critical role in mechanical signaling. They contain a mechanosensory region (MSR) that naturally folds into a globular closed conformation. Under mechanical stress, the MSR unfolds into an open conformation, exposing binding sites for numerous proteins. Filamins are involved in diverse cellular functions, and their mechanical binding targets are highly context-dependent. In this study, we employed AlphaFold2 modelling for screening proteins that specifically recognize the open conformation of filamins. We focused on the <i>Drosophila melanogaster</i> filamin, Cheerio, and conducted a biased screen to identify mechanical binding proteins. We selected the top 132 hits from the initial screening for further characterization. All identified binding proteins specifically recognize the open conformation of the MSR and not the closed conformation. Interestingly, the binding regions of these proteins lack obvious sequence similarity. While some false positives were identified, they could be effectively filtered out based on the secondary structure formed at the binding interface. This study provides a framework for identifying specifically filamin interactions in mechanosignaling.</p>","PeriodicalId":8775,"journal":{"name":"Biochemistry and Cell Biology","volume":" ","pages":"1-11"},"PeriodicalIF":2.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144798053","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}
{"title":"Antibiofilm activities of lactoferricin-related Trp- and Arg-rich antimicrobial hexapeptides against pathogenic <i>Staphylococcus aureus</i> and <i>Pseudomonas aeruginosa</i> strains.","authors":"Gopal Ramamourthy, Hans J Vogel","doi":"10.1139/bcb-2024-0183","DOIUrl":"10.1139/bcb-2024-0183","url":null,"abstract":"<p><p>Recently, several antimicrobial peptides (AMPs), varying in length from 12 to 37 residues, have been shown to act as antibiofilm agents. Here, we report a study of 23 hexapeptides modeled after four different Trp- and Arg-rich AMPs, including the RRWQWR-NH<sub>2</sub> peptide, derived from bovine lactoferrin. They were tested against the pathogenic Gram-negative <i>Pseudomonas aeruginosa</i> PAO1 strain and a Gram-positive <i>Staphylococcus aureus</i> MRSA strain. Both strains were engineered to express the green fluorescent protein (GFP) protein, and fluorescence detection was used to measure the ability of the peptides to prevent biofilm formation (minimum biofilm inhibitory concentration (MBIC)) or to cause the breakdown of established biofilms (minimum biofilm eradication concentration (MBEC)). Similar antibiofilm activities were obtained with the standard crystal violet dye assay. Most Trp- and Arg-rich hexapeptides displayed a potent antibiofilm activity against the Gram-positive <i>S. aureus</i> MRSA strain. In particular, hexapeptides with 3 Arg and 3 Trp were very effective, especially when they contained the three Trp in sequence. Somewhat unexpectedly, the antimicrobial (MIC) values correlated with the MBIC and MBEC values, which has not been seen for several other AMP/antibiofilm peptides. Our results demonstrate that short Trp- and Arg-rich peptides merit further studies as antibiofilm agents that could be deployed to address part of the antimicrobial resistance problem.</p>","PeriodicalId":8775,"journal":{"name":"Biochemistry and Cell Biology","volume":" ","pages":"1-18"},"PeriodicalIF":2.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142456994","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}
Valerie S Mayorga, Rafaella Navarro, Victor D Torres Roldan, Meritxell Urtecho, Silvia Tipe, Bea Calvert, Laura A Wright, Theresa J Ochoa
{"title":"Efficacy of lactoferrin supplementation in pediatric infections: a systematic review and meta-analysis.","authors":"Valerie S Mayorga, Rafaella Navarro, Victor D Torres Roldan, Meritxell Urtecho, Silvia Tipe, Bea Calvert, Laura A Wright, Theresa J Ochoa","doi":"10.1139/bcb-2024-0181","DOIUrl":"10.1139/bcb-2024-0181","url":null,"abstract":"<p><p>Pediatric infections account for approximately one-third of all deaths in children under 5 years globally. Lactoferrin (LF) supplementation has the potential to reduce infection-related morbidity due to its antimicrobial, anti-inflammatory, and immunoregulatory properties. We conducted a systematic review and meta-analysis of oral LF supplementation randomized controlled trials in population under 18 years old. The primary outcomes were infection-associated outcomes: late onset sepsis (LOS), diarrhea, and upper respiratory infections (URIs). We also analyzed mortality among LOS studies. Of 1594 citations identified, 25 studies met eligibility criteria, including 10 studies of LOS, 14 of diarrhea, and 8 of URI. LF supplementation was associated with fewer patients with culture-proven or probable neonatal LOS compared to placebo (odds ratio (OR): 0.60; 95% confidence interval (CI): 0.42-0.86), with fewer patients with diarrhea compared to placebo in children (OR: 0.56; 95% CI: 0.41-0.75), and no significant fewer patients with URI (OR: 0.61; 95% CI: 0.27-1.40). Before LF can be used as a public health intervention, it is necessary to refine some aspects of the design of future trials. Ideally these trials should be conducted in countries with the highest burden of infections, where the potential benefit is expected to have the largest impact.</p>","PeriodicalId":8775,"journal":{"name":"Biochemistry and Cell Biology","volume":" ","pages":"1-23"},"PeriodicalIF":2.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143021954","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}
{"title":"E2F8 facilitates malignant phenotypes of muscle-invasive bladder cancer via increasing MCM7 expression.","authors":"Li-Yun Liu, Liang Tian, Ling-Huan Gao, Hai-Jun Cui, Xue-Mei Li, Yue-Hong Li","doi":"10.1139/bcb-2024-0083","DOIUrl":"10.1139/bcb-2024-0083","url":null,"abstract":"<p><p>E2F transcription factor 8 (E2F8) is an important regulator of the cell cycle. In this study, we first assessed the expression of E2F8 in bladder cancer and examined its effects in the malignant phenotypes of bladder cancer cell lines. We found that E2F8 was upregulated in bladder cancer tissues, and the increased expression was positively associated with higher clinical stage. E2F8 knockdown suppressed bladder cancer cell proliferation, accompanied by the performance of G1 phase arrest and the upregulated Cyclin D1 protein expression. The migrative and invasive capability was reduced in E2F8-depleted bladder cancer cells. Cisplatin resistance is an important cause of bladder cancer relapse. E2F8 downregulation facilitated cisplatin-induced apoptosis of bladder cancer cells. MCM7 is regulated by E2F and has been shown to participate in bladder cancer. There was a positive correlation between E2F8 and MCM7 expression in bladder cancer. We confirmed that E2F8 bound to the promoter region of MCM7 and activated MCM7 transcription. MCM7 overexpression abrogated the suppressive effects of E2F8 knockdown on malignant phenotypes of bladder cancer cells. We also demonstrated that E2F8 knockdown suppressed bladder cancer progression in vivo. In conclusion, we verify that E2F8 functioned in bladder cancer, and might exert its function via MCM7.</p>","PeriodicalId":8775,"journal":{"name":"Biochemistry and Cell Biology","volume":" ","pages":"1-14"},"PeriodicalIF":2.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142725360","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}
Samaneh Matoo, Prashun Acharya, Sadika T J Tonu, Jasvinder Bharaj, Ashwini Mudaliyar, Katherine Holmes, Nicole Roeser, Natalie Hill, Basmala Touny, Regan VanderPol, Scott W Crawley
{"title":"CDHR5 splice isoform cooperation promotes apical targeting of the brush border cadherin.","authors":"Samaneh Matoo, Prashun Acharya, Sadika T J Tonu, Jasvinder Bharaj, Ashwini Mudaliyar, Katherine Holmes, Nicole Roeser, Natalie Hill, Basmala Touny, Regan VanderPol, Scott W Crawley","doi":"10.1139/bcb-2025-0044","DOIUrl":"10.1139/bcb-2025-0044","url":null,"abstract":"<p><p>Cadherin-related family member 5 (CDHR5) is an adhesion molecule that is highly enriched in the microvilli found on the surface of transporting epithelial cells of the gut and kidney. CDHR5 localizes to the distal tips of these microvilli as part of an adhesion complex that drives assembly of microvilli into a cohesive apical brush border, a hallmark feature of polarized transporting epithelial cells. Loss of CDHR5 correlates with poor prognosis of colon cancer patients, while forced over-expression of CDHR5 in colorectal cancer cell lines blocks their ability to form tumors in mice. Despite acting as an apparent tumor suppressor, how CDHR5 targets to the apical domain of transporting epithelial cells to exert its tumor suppressor effects is poorly understood. Here, we show that CDHR5 is expressed as three dominant splice isoforms in intestinal epithelial cells that differ only in the presence and composition of a membrane-proximal extracellular mucin-like domain. When present in the CDHR5 ectodomain, this mucin-like domain restricted targeting of the cadherin to apical microvilli. Importantly, we show that this restriction could be bypassed through apparent hetero-oligomer formation between the splice isoforms that have the mucin-like domain and the isoform that does not.</p>","PeriodicalId":8775,"journal":{"name":"Biochemistry and Cell Biology","volume":" ","pages":"1-11"},"PeriodicalIF":2.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144741058","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}
Xia Jiang, Liming Wu, Rong Zhou, Miaohua Quan, Xiaoliang Xiang
{"title":"Galanthamine promotes neuronal differentiation and neurite outgrowth of neural progenitor/stem cells by up-regulating IGF-2.","authors":"Xia Jiang, Liming Wu, Rong Zhou, Miaohua Quan, Xiaoliang Xiang","doi":"10.1139/bcb-2025-0058","DOIUrl":"10.1139/bcb-2025-0058","url":null,"abstract":"<p><p>Galanthamine, an alkaloid derived from the Amaryllidaceae family, serves as an acetylcholinesterase inhibitor. Due to its central cholinergic properties, this compound is being actively studied as a potential treatment for Alzheimer's disease. However, the broader scope of its biological effects remains poorly understood. In this study, we explored the therapeutic potential of galanthamine in promoting neuronal differentiation and enhancing neurite outgrowth in neural stem and progenitor cells (NSPCs). Our detailed analysis demonstrated notable changes in neuronal morphology and complexity during maturation following galanthamine exposure. Notably, the compound significantly increased the proportion of neurons with multiple neurites, indicating its ability to stimulate neurite formation and foster the development of complex neuronal networks. Furthermore, galanthamine treatment led to a marked rise in the number of mature-appearing neurons, distinguished by elongated and intricate dendrites, highlighting its potential to enhance neural plasticity and repair mechanisms. Importantly, we also identified that galanthamine facilitates neuronal differentiation in NSPCs by up-regulating the insulin-like growth factor 2 signaling pathway. Collectively, these findings provide valuable insights into galanthamine's role in Alzheimer's disease and emphasize its promise as a therapeutic agent for this neurodegenerative disorder.</p>","PeriodicalId":8775,"journal":{"name":"Biochemistry and Cell Biology","volume":" ","pages":"1-9"},"PeriodicalIF":2.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144940709","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}
{"title":"Bovine lactoferrin suppresses the proliferation of endometriotic stromal cells via the PI3K/Akt/mTOR pathway.","authors":"Akiko Nakamura, Yuji Tanaka, Shunichiro Tsuji, Tsukuru Amano, Akie Takebayashi, Akimasa Takahashi, Ayako Inatomi, Tetsuro Hanada, Takashi Murakami","doi":"10.1139/bcb-2025-0014","DOIUrl":"10.1139/bcb-2025-0014","url":null,"abstract":"<p><p>The most common medical therapy for endometriosis suppresses ovulation, which is a barrier for patients planning pregnancy. To address this issue, we focused on the cell proliferation-suppressing effects of lactoferrin, which reportedly in various malignant tumours. Despite being a benign disease, endometriotic cells have similar characteristics to malignant tumours, which may be involved in its onset and progression. Endometriotic and endometrial stromal cells were obtained from patients with endometriosis. After culture with 1 mg/mL of bovine lactoferrin, cell proliferation was significantly suppressed in endometriotic stromal cells compared to controls, but this remained unchanged in endometrial stromal cells. Bovine lactoferrin also significantly increased the number of endometriotic stromal cells in the G0/G1 phase and significantly decreased those in the S phase, and suppressed the protein expression of phosphorylated-AKT, phosphorylated-mTOR, phosphorylated-S6K, and cyclin D1. Bovine lactoferrin inhibits the transition from the G1 to the S phase by suppressing the PI3K/Akt/mTOR pathway and reducing the synthesis of cyclin D1, thereby arresting the cell cycle at the G1 phase. Bovine lactoferrin suppressed the proliferation of endometriotic stromal cells without suppressing the proliferation of endometrial stromal cells. Lactoferrin, which allows for pregnancy and lactation during administration, has potential as a novel therapeutic candidate for endometriosis.</p>","PeriodicalId":8775,"journal":{"name":"Biochemistry and Cell Biology","volume":" ","pages":"1-8"},"PeriodicalIF":2.1,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144257224","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}
Karanveer S Johal, Sandra A Youssef, Samira M Ibrahim, Lina A Dizon-Mapula, Isabella R Galluzzo, Gilda Stefanelli
{"title":"Srcap loss alters H2A.Z-dependent and neuronal differentiation-related gene expression in N2A cells.","authors":"Karanveer S Johal, Sandra A Youssef, Samira M Ibrahim, Lina A Dizon-Mapula, Isabella R Galluzzo, Gilda Stefanelli","doi":"10.1139/bcb-2024-0294","DOIUrl":"10.1139/bcb-2024-0294","url":null,"abstract":"<p><p>The chromatin remodeler SRCAP plays a critical role in depositing the histone variant H2A.Z, which is essential for transcriptional regulation, chromatin accessibility, and neurodevelopmental processes. Despite its known importance, the mechanisms by which SRCAP regulates H2A.Z dynamics during neuronal differentiation remain poorly understood. Here, we investigated the impact of Srcap knockdown on H2A.Z incorporation and transcriptional regulation in N2A cells. Chromatin immunoprecipitation revealed reduced H2A.Z occupancy at activity-dependent and neurodevelopmental genes upon Srcap knockdown, confirming Srcap's role in H2A.Z deposition. Interestingly, CBP recruitment and global histone H3 acetylation were unaffected by Srcap knockdown at steady-state conditions, suggesting an H2A.Z-specific function of Srcap. We also observed that retinoic acid-induced neuronal differentiation leads to dynamic changes in H2A.Z levels at developmental loci, which are disrupted in Srcap-deficient cells. Gene expression analysis revealed altered expression of neurodevelopmental genes in the absence of Srcap, correlating with reduced H2A.Z occupancy. Together, these findings demonstrate that Srcap is essential for regulating H2A.Z dynamics and gene expression during neuronal differentiation, offering new insights into its role in chromatin remodelling and its potential involvement in neurodevelopmental disorders.</p>","PeriodicalId":8775,"journal":{"name":"Biochemistry and Cell Biology","volume":" ","pages":"1-12"},"PeriodicalIF":2.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143603877","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}
{"title":"Retraction: Active vitamin D activates chondrocyte autophagy to reduce osteoarthritis via mediating the AMPK-mTOR signaling pathway.","authors":"","doi":"10.1139/bcb-2025-0020","DOIUrl":"10.1139/bcb-2025-0020","url":null,"abstract":"","PeriodicalId":8775,"journal":{"name":"Biochemistry and Cell Biology","volume":"103 ","pages":"1"},"PeriodicalIF":2.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143497611","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}
{"title":"Lysosomal enzyme processing and trafficking in the social amoeba <i>Dictyostelium discoideum</i>.","authors":"Sean V Condie, William D Kim, Robert J Huber","doi":"10.1139/bcb-2025-0062","DOIUrl":"10.1139/bcb-2025-0062","url":null,"abstract":"<p><p><i>Dictyostelium discoideum</i> is a single-celled protist that undergoes multicellular development in response to nutrient deprivation. For close to a century, <i>D. discoideum</i> has been used as a model system for studying conserved cellular and developmental processes such as chemotaxis, cell adhesion, and cell differentiation. In the later decades of the 20th century, intensive research efforts examined the synthesis, trafficking, and activity of lysosomal enzymes in <i>D. discoideum</i>. Subsequent work revealed that lysosomes are essential for all stages of the <i>D. discoideum</i> life cycle and the genome encodes dozens of homologs of human lysosomal enzymes, including those associated with lysosomal storage diseases. Additionally, protocols for examining the trafficking and activity of lysosomal enzymes in <i>D. discoideum</i> are well-established. Here, we provide a comprehensive up-to-date review that summarizes our current knowledge of lysosomal enzyme processing and trafficking in <i>D. discoideum</i>, with an eye towards re-establishing <i>D. discoideum</i> as a model eukaryote for studying the functions of conserved lysosomal enzymes and the pathways that regulate their trafficking.</p>","PeriodicalId":8775,"journal":{"name":"Biochemistry and Cell Biology","volume":" ","pages":"1-11"},"PeriodicalIF":2.4,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143762980","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}