BMC Molecular and Cell Biology最新文献

{"title":"Targeting METTL16 attenuates mesangial cell viability and fibrosis in a high-glucose state by suppressing m6A modification and the expression of RAP1B.","authors":"Weixu Wang, Yanhong Luo","doi":"10.1186/s12860-025-00559-3","DOIUrl":"10.1186/s12860-025-00559-3","url":null,"abstract":"<p><strong>Background: </strong>Methyltransferase-like 16 (METTL16) is involved in regulating kidney disease progression. This study aimed to investigate the effect of METTL16 on the progression of diabetic kidney disease (DKD) and its potential mechanism.</p><p><strong>Methods: </strong>SV40-MES13 cells were transfected with METTL16 siRNA (siMETTL16), scramble control (siNC), or RAP1B siRNA (siRAP1B) under low glucose (LG) or high glucose (HG) conditions. Subsequently, RNA immunoprecipitation (RIP) assays, cell viability assays, EdU staining, TUNEL staining, ROS staining, and MDA detection were carried out.</p><p><strong>Results: </strong>In SV40-MES13 cells, cell viability, the number of EdU-positive cells, the MDA level, METTL16 mRNA, and protein levels were greater in the HG groups than in the control group. Moreover, cell viability, the number of EdU-positive cells, and VIMENTIN protein levels were lower, whereas the apoptosis rate and ROS and MDA levels were greater in the HG + siMETTL16 group than in the HG + siNC group. RAP1B mRNA and protein levels and N⁶-methyladenosine modification levels were greater in the HG group than in the control group but lower in the HG + siMETTL16 group than in the HG + siNC group. Furthermore, the METTL16 protein bound to the RAP1B mRNA. Compared with those in the HG + siNC group, cell viability, the number of EdU-positive cells, and VIMENTIN protein levels were decreased, whereas the ROS and MDA levels were increased in the HG + siRAP1B group.</p><p><strong>Conclusion: </strong>METTL16 knockdown attenuates cell viability and fibrosis by reducing m6A modification and the expression of RAP1B in high glucose-treated mesangial cells, suggesting the potential of METTL16 as a treatment target for DKD.</p>","PeriodicalId":9099,"journal":{"name":"BMC Molecular and Cell Biology","volume":"26 1","pages":"32"},"PeriodicalIF":2.7,"publicationDate":"2025-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12570422/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145386910","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impact of mouse tracheal basal cell expansion medium on formation and metabolic characteristics of tracheospheres.","authors":"Joseph E Druso, Reem Aboushousha, Maximillian MacPherson, Cuixia Erickson, Vitor Mori, Elise Hickman, Alexander R D'Amico, David Seward, Julie A Reisz, Julia E Rager, Yvonne Janssen-Heininger, Elizabeth Corteselli","doi":"10.1186/s12860-025-00554-8","DOIUrl":"10.1186/s12860-025-00554-8","url":null,"abstract":"<p><p>BACKGROUND: Airway basal cells have been shown to play important roles in lung disease, prompting their use in research involving 3-dimensional (3D) organoid culture. Mouse tracheal basal cells (MTBC) represent a key model in understanding the differentiation of airway basal cells in normal development and diseased states. The isolation, expansion, and culture media of basal cells can affect their capacity to maintain stemness and properly differentiate, thereby introducing unknown experimental variables. As MTBC use in 3D organoid culture proceeds, there is an increasing need for comparative studies to identify unknown experimental variables. In this study, we examined the effects of MTBC expansion media on the differentiation and tracheosphere-forming ability in 3D culture. METHODS: MTBC were isolated from mouse tracheas, and three commonly used airway basal cell media were compared during MTBC expansion in cell culture (hereafter referred to as Media 1, 2, and 3). Following expansion, MTBC were cultured identically in 3D conditions to analyze tracheosphere-forming capability. Image analyses were performed to characterize tracheosphere count, size, and morphology, while metabolic and transcriptomic signatures were analyzed to assess MTBC differentiation in 3D culture. RESULTS: Expansion of MTBC in the three distinct media resulted in subsequent 3D tracheospheres that displayed unique metabolite and gene expression profiles, accompanied by overall changes in tracheosphere count and size. MTBC expanded in Medium 1 displayed lower levels of TCA cycle intermediates, along with lowered expression of differentiation markers Foxj1 and Scgb1a1, compared to MTBC expanded in Media 2 or 3. Pathway analysis showed an upregulation of idiopathic pulmonary fibrosis signaling pathways in tracheospheres cultured from MTBC expanded in Media 2 or 3. CONCLUSION: This study identified several key differences in tracheosphere-forming ability of MTBC resulting from MTBC expansion media and highlights the importance of transparency in cell culture protocols, particularly those involving stem cells or 3D culture. </p>","PeriodicalId":9099,"journal":{"name":"BMC Molecular and Cell Biology","volume":"26 1","pages":"31"},"PeriodicalIF":3.0,"publicationDate":"2025-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12536532/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145336232","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Subtype-specific divergent roles of calpain-1 and calpain-2 in basal A triple-negative breast cancer.","authors":"Göklem Üner, Erdal Bedir, Petek Ballar Kirmizibayrak","doi":"10.1186/s12860-025-00556-6","DOIUrl":"10.1186/s12860-025-00556-6","url":null,"abstract":"<p><strong>Background: </strong>CAPN-1 and CAPN-2, two ubiquitously expressed calpains, have been implicated in cancer progression, but their distinct roles in breast cancer remain poorly defined. This study aims to define the opposing roles of CAPN-1 and CAPN-2 in breast cancer progression, with a focus on their regulatory impact on cell proliferation. Since these calpains may have different functions in the mammary gland, we aimed to investigate the possible antagonistic roles of CAPN-1 and CAPN-2 in breast cancer progression, focusing on their expression patterns and functional impact on cell proliferation.</p><p><strong>Methods and results: </strong>We analyzed breast cancer cell lines using immunoblotting and real-time cellular assays, showing that HCC1937 cells exhibit an opposite expression pattern of CAPN-1 and CAPN-2 compared to non-cancerous breast cells. CAPN-1 promoted cancer cell survival and negatively regulated CAPN-2 at both the protein and mRNA levels, whereas CAPN-2 suppressed proliferation. Additionally, the calpain activator AG-08 triggered cell death through CAPN-2 but not CAPN-1. In silico analysis confirmed higher CAPN-1 and lower CAPN-2 expression levels in breast cancer samples compared to normal tissue.</p><p><strong>Conclusions: </strong>These findings indicate that CAPN-1 and CAPN-2 may exert antagonistic roles in breast cancer, but importantly, this effect was restricted to HCC1937 cells, representing a basal A TNBC subtype. Validation in additional basal A models and patient-derived samples will be essential to confirm these results. Our study, therefore, provides preliminary, model-specific insights into calpain regulation in TNBC and suggests that future therapeutic strategies should carefully account for subtype heterogeneity.</p>","PeriodicalId":9099,"journal":{"name":"BMC Molecular and Cell Biology","volume":"26 1","pages":"29"},"PeriodicalIF":2.7,"publicationDate":"2025-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12532864/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145306667","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In situ proximity ligation assay for analysing spatial interactions between ciliary proteins.","authors":"Thorsten Pfirrmann, Ulrich Rüther, Christoph Gerhardt","doi":"10.1186/s12860-025-00555-7","DOIUrl":"10.1186/s12860-025-00555-7","url":null,"abstract":"<p><strong>Background: </strong>Cilia are small, hair-like structures on the surface of most eukaryotic cells. They are composed of distinct substructures: the basal body, the transition zone, and the axoneme. Proper ciliary function is crucial for human health, and defects can result in a group of disorders known as ciliopathies. Many ciliopathy-associated mutations affect genes encoding proteins of the ciliary transition zone, a key structural and regulatory region at the base of the cilium. Understanding the molecular composition and interactions within subciliary compartments, such as the transition zone, is essential to elucidate their role in ciliary function and disease.</p><p><strong>Results: </strong>Protein interaction studies have played a central role in uncovering the functional landscape of subciliary compartments. In this context, the in situ proximity ligation assay (in situ PLA) has emerged as a valuable tool to investigate whether two proteins are located in close proximity (less than 40 nm) within the cellular environment, implying potential interaction. In situ PLA uses primary antibodies to recognise target proteins, followed by secondary antibodies conjugated with oligonucleotides (PLA probes). When two probes are sufficiently close, added circle-forming oligonucleotides can hybridise and ligate to form a circular DNA strand. This DNA circle serves as a template for rolling circle amplification, which is then detected through hybridisation with fluorescently labelled oligonucleotides. The resulting signals can be visualised using fluorescence microscopy, enabling precise spatial mapping of protein proximities in cells.</p><p><strong>Conclusions: </strong>The in situ PLA technique offers a powerful means of detecting protein proximities in subciliary compartments with high spatial resolution. This method supports the identification of novel protein interactions and contributes to a deeper understanding of subciliary architecture and its disruption in ciliopathies.</p>","PeriodicalId":9099,"journal":{"name":"BMC Molecular and Cell Biology","volume":"26 1","pages":"30"},"PeriodicalIF":2.7,"publicationDate":"2025-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12532946/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145306676","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Immune gene expression in salmon keratocytes upon bacterial exposure.","authors":"Marie Kristin Mikkelborg, Antonette Skram Helgestad, Roy Ambli Dalmo, Dhivya Borra Thiyagarajan","doi":"10.1186/s12860-025-00553-9","DOIUrl":"10.1186/s12860-025-00553-9","url":null,"abstract":"<p><p>BACKGROUND: Pathogens pose a significant threat to farmed salmon, adversely affecting their health and welfare, which results in substantial economic losses. The outermost skin epithelial cells, including skin keratocytes, serve as a critical defense barrier against environmental stressors, such as bacterial infections. Understanding the features and properties of these cells, particularly skin keratocytes, is essential as they play a crucial role in wound healing and tissue regeneration. Additionally, we were curious whether corneal epithelial cells (corneal keratocytes), which protect the fish eye, exhibit similar features and immune functions. RESULTS: To investigate the properties of skin keratocytes, we utilized flow cytometry to analyze scale-derived cells. The analysis revealed that more than 85% of the cells were skin keratocytes, although the remaining cells could not be characterized using this method. Microscopic analysis confirmed that the majority of these cells exhibited the typical morphology of keratocytes and were positive for a pan-keratin antibody. To assess the immune function of skin keratocytes, we exposed scale-derived keratocytes to various fish pathogenic bacteria and evaluated their ability to ingest bacteria and examined the regulation of innate immune genes. Additionally, we analyzed the expression of immune-related markers, including mhcii, in both skin and corneal cells. CONCLUSION: Our findings demonstrated that scale-derived skin keratocytes internalized bacteria within 3–6 hours of exposure. This bacterial interaction led to the significant upregulation of several key immune-related genes. Interestingly, both skin and corneal cells expressed mhcii, suggesting a potential role in adaptive immunity in addition to their participation in innate immune responses. These results highlight the vital role of skin and corneal cells in the innate immune response against bacterial infections and their possible contribution to adaptive immunity. </p>","PeriodicalId":9099,"journal":{"name":"BMC Molecular and Cell Biology","volume":"26 1","pages":"28"},"PeriodicalIF":3.0,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12462119/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145136425","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rescue of ciliogenesis and hyperglutamylation mutant phenotype in AGBL5^-/- cell model of retinitis pigmentosa.","authors":"Suly S Villa-Vasquez, Liliya Nazlamova, Reuben J Pengelly, David I Wilson, Diana Baralle, Gabrielle Wheway","doi":"10.1186/s12860-025-00551-x","DOIUrl":"10.1186/s12860-025-00551-x","url":null,"abstract":"<p><p>Retinitis pigmentosa (RP) affects around 1 in 4000 individuals and represents approximately 25% of cases of vision loss in adults, through death of retinal rod and cone photoreceptor cells. It remains a largely untreatable disease, and research is needed to identify potential targets for therapy. Mutations in 94 different genes have been identified as causing RP, including AGBL5 which encodes the main deglutamylase that regulates and maintains functional levels of cilia tubulin glutamylation, which is essential to initiate ciliogenesis, maintain cilia stability and motility. In this study we use CRISPR-mutated AGBL5 clonal retinal pigmented epithelial cell lines to characterise the cilia defects and hyperglutamylation in these cells and identify potential targets for treatment. We demonstrate rescue of glutamylation to wild-type levels and restoration of ciliogenesis in AGBL5 mutant cells through exogenous expression of AGBL5, and independently through both stable genomic mutation and transient siRNA knockdown of TTLL5, which encodes a tubulin glutamylase. This identifies two potential routes to treatment for patients with RP associated with mutations in AGBL5 which will need to be explored further in retinal organoid models of this disease.</p>","PeriodicalId":9099,"journal":{"name":"BMC Molecular and Cell Biology","volume":"26 1","pages":"27"},"PeriodicalIF":2.7,"publicationDate":"2025-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12418683/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145028907","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolutionary and structural insights into DNMTs and TETs: decoding their functional heterogeneity and oncogenic roles in methylation regulation.","authors":"Siqi Yang, Xinyi Li, Lingling Bao, Jiafu Cui, Jing Liu, Shan Cong, Yongchun Zuo","doi":"10.1186/s12860-025-00552-w","DOIUrl":"https://doi.org/10.1186/s12860-025-00552-w","url":null,"abstract":"<p><p>DNA methylation in mammals is dynamically regulated by DNMTs and TETs. Despite their critical roles, comparative structural analyses of these protein families have been relatively scarce. To address the above problems, this study first constructed a phylogenetic tree of DNMT and TET proteins to investigate their evolutionary relationships. Furthermore, the structural exploration revealed that both protein families possess conserved β-sheet structures and exhibit the characteristics of alternating β-sheets in their catalytic domains. Interestingly, DNMTs contain more α helices and fewer loops compared to TETs. Several notable structural changes were discovered, including unique flexibility of the CXXC domain and divergences in DNA binding mechanisms among DNMT1, TET1, and TET3. Additionally, the results showed that a distinctive loop present in DNMT2 may indicate its specialized functional role. This research provides fundamental evolutionary and structural insights into DNMT and TET proteins, emphasizing their significance in tissue-specific distribution and cancer signaling, thereby establishing a foundation for future investigations in the field of epigenetics.</p>","PeriodicalId":9099,"journal":{"name":"BMC Molecular and Cell Biology","volume":"26 1","pages":"26"},"PeriodicalIF":2.7,"publicationDate":"2025-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12392533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144942601","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cell biology of Dictyostelium.","authors":"Robert J Huber, Paul A Steimle, Cynthia K Damer","doi":"10.1186/s12860-025-00550-y","DOIUrl":"10.1186/s12860-025-00550-y","url":null,"abstract":"<p><p>The Cell Biology of Dictyostelium article collection highlights the benefits of using Dictyostelium as a model system for studying fundamental cellular processes. The studies compiled in this collection showcase the many ways Dictyostelium is used to enhance our understanding of the eukaryotic cell.</p>","PeriodicalId":9099,"journal":{"name":"BMC Molecular and Cell Biology","volume":"26 1","pages":"25"},"PeriodicalIF":2.7,"publicationDate":"2025-08-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12362907/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144882103","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Indian medicinal phytocompounds for targeting apoptosis and high-penetrance genes in triple-negative breast cancer: an in-silico exploration.","authors":"Reshmi Kumari, Satarupa Banerjee","doi":"10.1186/s12860-025-00548-6","DOIUrl":"10.1186/s12860-025-00548-6","url":null,"abstract":"<p><p>Triple-negative breast cancer (TNBC) presents a significant therapeutic challenge due to its aggressive nature, lack of hormone receptors, and limited targeted treatment options. The complexity of the disease is further compounded by mutations in high-penetrance genes such as BRCA1, BRCA2, and BAX, along with other apoptotic genes involved in tumorigenesis, apoptosis, and drug resistance. Targeting these genes through innovative therapeutic approaches is crucial for improving treatment outcomes. This in-silico study explores the potential of phytochemicals as natural, multi-targeted therapeutic agents against high-penetrance and apoptotic genes implicated in TNBC. Using the IMPPAT 2.0 database, 300 phytochemicals were systematically screened based on their pharmacokinetic properties and toxicity profiles to identify promising candidates. Among them, Bayogenin exhibited strong binding to BRCA2 (-9.3 kcal/mol) and PALB2 (-8.7 kcal/mol), surpassing the FDA-approved drug Olaparib in molecular docking studies. Molecular dynamics simulations over 200 ns further confirmed the stability of these phytochemical-protein complexes, showing consistent root mean square deviation, hydrogen bonding, and free energy profiles. These findings highlight the therapeutic potential of phytochemicals and their possible advantages over existing TNBC treatments. By targeting key molecular pathways, this study provides insights into the development of natural, multi-targeted therapeutic strategies, emphasizing their translational relevance for TNBC therapy.</p>","PeriodicalId":9099,"journal":{"name":"BMC Molecular and Cell Biology","volume":"26 1","pages":"24"},"PeriodicalIF":2.7,"publicationDate":"2025-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12312594/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144752258","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In vivo genetic labeling of primary cilia in developing astrocytes.","authors":"Rachel Bear, Claire Wei, Tamara Caspary","doi":"10.1186/s12860-025-00547-7","DOIUrl":"10.1186/s12860-025-00547-7","url":null,"abstract":"<p><strong>Background: </strong>Astrocyte cilia are largely understudied due to the lack of available tools. Astrocyte research advanced with the establishment of Aldh1l1-Cre^ERT2, an inducible Cre line that specifically targets the astrocyte lineage. Here, we develop and compare genetic models that label astrocyte cilia in the developing prefrontal cortex (PFC) using Aldh1l1-Cre^ERT2 and Cre-dependent cilia reporters. We evaluate these models by testing different tamoxifen-induction protocols and quantifying the percentage of astrocytes labeled with the cilia reporters.</p><p><strong>Results: </strong>We show that tamoxifen dosage impacts the expression of cilia reporters in astrocytes. We uncover the maximum cilia-labeling efficiency using recombined, constitutively-expressed cilia reporters.</p><p><strong>Conclusion: </strong>The data reveal that only a subset of SOX9- positive astrocytes in the PFC possess cilia throughout development. Our work highlights the utility of Cre-Lox systems to target specific cell types and the importance of carefully validating genetic models.</p>","PeriodicalId":9099,"journal":{"name":"BMC Molecular and Cell Biology","volume":"26 1","pages":"23"},"PeriodicalIF":3.0,"publicationDate":"2025-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12288362/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144706239","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}