BMC Molecular and Cell Biology最新文献

{"title":"Conserved structural topologies in RNase A-like and trypsin-like serine proteases: a sequence-based folding analysis.","authors":"K M Ahsanul Kabir, Takuya Takahashi, Takeshi Kikuchi","doi":"10.1186/s12860-025-00542-y","DOIUrl":"https://doi.org/10.1186/s12860-025-00542-y","url":null,"abstract":"<p><strong>Background: </strong>Protein folding is a complex process in which amino acid sequences encode the information required for a polypeptide chain to fold into its functional three-dimensional (3D) structure. Many proteins share common substructures and recurring secondary structure elements that contribute to similar 3D folding patterns, even across different protein families. This study examines two distinct groups of proteins, the RNase A-like fold and the trypsin-like serine protease fold, classified by SCOPe. These proteins share only some substructures that contribute to their folding cores. Despite minimal sequence identity, they exhibit partial structural similarities in their 3D topologies. We used a sequence-based approach, including inter-residue average distance statistics and contact frequency prediction, to explore these folding characteristics. Structural observations guided further analyses of conserved hydrophobic residue packing, highlighting key folding units within each fold.</p><p><strong>Results: </strong>Our analysis predicted two compact regions within each protein group. Interactions between these regions form a partially shared topology. We identified conserved hydrophobic residues critical to these interactions, suggesting a common mechanism for establishing these structural features. Despite overall structural differences between the RNase A-like and trypsin-like folds, our findings emphasize the presence of a shared partial folding core.</p><p><strong>Conclusions: </strong>The partially shared structural features in the RNase A-like and trypsin-like serine protease folds reflect a convergent folding mechanism. This mechanism underscores the evolutionary adaptation of protein folding, where distinct folds can still retain critical, conserved structural motifs. These findings highlight how proteins with overall different topologies can evolve to share key folding features, demonstrating the elegance and efficiency of protein evolution.</p>","PeriodicalId":9099,"journal":{"name":"BMC Molecular and Cell Biology","volume":"26 1","pages":"16"},"PeriodicalIF":2.4,"publicationDate":"2025-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144172259","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":"Optimizing mesenchymal stem cell therapy: from isolation to GMP-compliant expansion for clinical application.","authors":"Michael E Williams, Federica Banche Niclot, Sara Rota, Jaesang Lim, Janaina Machado, Ricardo de Azevedo, Katia Castillo, Samuel Adebiyi, Ranga Sreenivasan, Daniel Kota, Patrick C Mcculloch, Francesca Taraballi","doi":"10.1186/s12860-025-00539-7","DOIUrl":"https://doi.org/10.1186/s12860-025-00539-7","url":null,"abstract":"<p><strong>Background: </strong>Mesenchymal stem cells (MSCs) are promising for cell-based therapies targeting a wide range of diseases. However, challenges in translating MSC-based therapies to clinical applications necessitate standardized protocols following Good Manufacturing Practices (GMP) guidelines. This study aimed at developing GMP-complained protocols for FPMSCs isolation and manipulation, necessary for translational research, by (1) optimize culture of MSCs derived from an infrapatellar fat pad (FPMSC) condition through animal-free media comparison and (2) establish feasibility of MSC isolation, manufacturing and storage under GMP-compliance (GMP-FPMSC).</p><p><strong>Methods: </strong>FPMSCs from three different patients were isolated following established protocols and the efficacy of two animal component-free media formulations in the culturing media were evaluated. The impact of different media formulations on cell proliferation, purity, and potency of MSCs was evaluated through doubling time, colony forming unit assay, and percentage of MSCs, respectively. Furthermore, the isolation and expansion of GMP-FPMSCs from four additional donors were optimized and characterized at each stage according to GMP requirements. Viability and sterility were checked using Trypan Blue and Bact/Alert, respectively, while purity and identity were confirmed using Endotoxin, Mycoplasma assays, and Flow Cytometry. The study also included stability assessments post-thaw and viability assessment to determine the shelf-life of the final GMP-FPMSC product. Statistical analyses were conducted using one-way ANOVA with Tukey's Multiple Comparisons.</p><p><strong>Results: </strong>The study demonstrated that FPMSCs exhibited enhanced proliferation rates when cultured in MSC-Brew GMP Medium compared to standard MSC media. Cells cultured in this media showed lower doubling times across passages, indicating increased proliferation. Additionally, higher colony formation in FPMSCs cultured in MSC-Brew GMP Medium were observed, supporting enhanced potency. Data from our GMP validation, including cells from 4 different donors, showed post-thaw GMP-FPMSC maintained stem cell marker expression and all the specifications required for product release, including > 95% viability (> 70% is required) and sterility, even after extended storage (up to 180 days), demonstrating the reproducibility and potential of GMP-FPMSCs for clinical use as well as the robustness of the isolation and storage protocols.</p><p><strong>Conclusions: </strong>The study underscores the feasibility of FPMSCs for clinical uses under GMP conditions and emphasizes the importance of optimized culture protocols to improve cell proliferation and potency in MSC-based therapies.</p>","PeriodicalId":9099,"journal":{"name":"BMC Molecular and Cell Biology","volume":"26 1","pages":"15"},"PeriodicalIF":2.4,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12054297/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143968592","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":"PYGO2 regulates IL10 and plays immunosuppressive role through ESCC progression.","authors":"Fereshteh Ahmadian Shalchi, Nayyerehalsadat Hosseini, Fatemeh Nourmohammadi, Mohammad Arian Ahmadian Shalchi, Mohammad Mahdi Forghanifard","doi":"10.1186/s12860-025-00540-0","DOIUrl":"https://doi.org/10.1186/s12860-025-00540-0","url":null,"abstract":"<p><strong>Background: </strong>Esophageal squamous cell carcinoma (ESCC), one of the most aggressive carcinomas of the gastrointestinal tract, is the sixth most common cause of cancer-related death. Wnt pathway plays a pivotal role in cell proliferation and differentiation. PYGO2 and IL10 are involved in this pathway. Our aim in this study was to examine the correlation between PYGO2 and IL10 expression in ESCC patients and cell lines.</p><p><strong>Methods: </strong>Relative-comparative real time-PCR (RT-qPCR) was used to evaluate the PYGO2 and IL10 mRNA expression profile in 58 non-treated ESCC compared to their margin normal tissues. Expression of PYGO2 was induced in KYSE-30 and YM1 ESCC lines and IL10 expression was analyzed.</p><p><strong>Results: </strong>The results revealed the significant overexpression of PYGO2 and IL10 mRNA in 31.0% and 51.7% of ESCCs, respectively. The PYGO2 and IL10 overexpression was significantly correlated to each other (p = 0.007). Concomitant overexpression of the genes was significantly associated to grade of tumor differentiation (p < 0.01), and tumor depth of invasion (p < 0.05). Induced expression of PYGO2 caused a meaningful change in IL10 expression in ESCC cells.</p><p><strong>Conclusion: </strong>PYGO2 may regulate IL10 through Wnt/β-catenin signaling pathway, suggesting a possible oncogenic role for PYGO2/IL10 axis in ESCC tumorigenesis. Considering the involvement of IL10 as an anti-inflammatory cytokine and PYGO2 role in elevated tumor invasion and metastasis, possible functional interaction between these factors may promote a process which induces invasion and malignant phenotype in ESCC.</p>","PeriodicalId":9099,"journal":{"name":"BMC Molecular and Cell Biology","volume":"26 1","pages":"14"},"PeriodicalIF":2.4,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12038969/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143969447","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":"The formin FMNL2 plays a role in the response of melanoma cells to substrate stiffness.","authors":"Joshua D Clugston, Sarah Fox, James L Harden, John W Copeland","doi":"10.1186/s12860-025-00538-8","DOIUrl":"https://doi.org/10.1186/s12860-025-00538-8","url":null,"abstract":"<p><strong>Background: </strong>Cells constantly sense and respond to changes in their local environment to adapt their behaviour and morphology. These external stimuli include chemical and mechanical signals, and much recent work has revealed the complexity of the cellular response to changes in substrate stiffness. We investigated the effects of substrate stiffness on the morphology and motility of A2058 human melanoma cells. FMNL2, a formin protein associated with actin cytoskeleton dynamics, regulates melanoma cell morphology and motility, but its role in stiffness sensing remains unclear. This study examines how A2058 cells respond to substrates of varying stiffness and evaluates the impact of FMNL2 depletion on these responses.</p><p><strong>Results: </strong>We found that with increasing substrate stiffness the cells transitioned from a rounded cell morphology to progressively more elongated morphologies with a concomitant increase in actin stress fiber alignment. Depletion of FMNL2 expression amplified these morphological changes, with knockdown cells showing consistently greater elongation and more pronounced stress fiber alignment compared to controls. Notably, the orientational order parameter (S) revealed higher alignment of actin filaments along the cell's long axis in knockdown cells. Substrate stiffness also affected cell motility, indicated by an apparent optimal stiffness that maximized motility followed by a notable decrease in distance travelled during migration on progressively stiffer substrates. This decrease was largely attributable to a decrease in the time the cells spent in motion as the substrate stiffness increased. FMNL2 depletion significantly exacerbated this effect, with knockdown cells traveling shorter net distances and spending less time moving across all substrates.</p><p><strong>Conclusions: </strong>This study demonstrates that substrate stiffness profoundly influences A2058 melanoma cell morphology and motility, with FMNL2 playing a pivotal regulatory role. Our observations suggest that FMNL2 is critical for maintaining motility and morphological adaptability under increased stiffness. Loss of FMNL2 enhanced stress fiber alignment and cell elongation while impairing motility, particularly on stiff substrates, revealing FMNL2 as a mechanosensitive effector. This work highlights the need to study metastatic cell behaviour on substrates with biologically relevant properties and provides the foundation for future effort to determine the mechanism by which FMNL2 participates in the melanoma cell response to substrate stiffness.</p>","PeriodicalId":9099,"journal":{"name":"BMC Molecular and Cell Biology","volume":"26 1","pages":"13"},"PeriodicalIF":2.4,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12039054/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143966292","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":"N-actylcysteine inhibits diethyl phthalate-induced inflammation via JNK and STAT pathway in RAW264.7 macrophages.","authors":"Jin Hee Kim, Jae Hoon Lee, Yoon Jung Koo, Jong Wook Song","doi":"10.1186/s12860-025-00537-9","DOIUrl":"https://doi.org/10.1186/s12860-025-00537-9","url":null,"abstract":"<p><strong>Background: </strong>Phthalates are plasticizers that cause inflammation in several cell types and adversely affect the health of humans and animals. Nacetylcysteine (NAC) has been shown to exert antioxidant effects in various diseases. However, the effect of NAC on diethyl phthalate (DEP)-induced toxicity in macrophages has not yet been elucidated. In this study, we investigated the effect and underlying mechanisms of NAC on DEP-induced inflammation in RAW264.7 macrophages. RAW264.7 macrophages were pretreated with NAC for 2 h followed by exposure to DEP. We investigated the effect of NAC on NO, reactive oxygen species (ROS), prostaglandin E2 (PGE2), and glutathione (GSH) levels following DEP exposure. In addition, pathway-related genes including cyclooxygenase-2 (COX-2), inducible nitric oxide synthase (iNOS), mitogen-activated protein kinase (MAPK), and signal transducer and activator of transcription (STAT) were evaluated using western blot.</p><p><strong>Results: </strong>Treatment with 100 and 300 µM DEHP, DBP, and DEP significantly increased the protein levels of cyclooxygenase-2 (COX-2) and inducible nitric oxide synthase (iNOS) compared with those in the control group. However, NAC pretreatment downregulated the levels of NO, PGE2, and ROS, elevated GSH levels, and suppressed the mRNA levels of inflammatory cytokines such as interleukin (IL)-1β, IL-6, COX-2, and iNOS compared with those in the DEP-treated group. In addition, NAC significantly reduced the levels of p-JNK and p-STAT1/3 in RAW264.7 macrophages treated with DEP.</p><p><strong>Conclusions: </strong>NAC pretreatment inhibits DEP-induced inflammation via the MAPK/JNK and STAT1/3 pathways in macrophages.</p>","PeriodicalId":9099,"journal":{"name":"BMC Molecular and Cell Biology","volume":"26 1","pages":"12"},"PeriodicalIF":2.4,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12001441/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143969321","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":"Canine intestinal organoids as a platform for studying MHC class II expression in epithelial cells.","authors":"Meg Nakazawa, Itsuma Nagao, Yoko M Ambrosini","doi":"10.1186/s12860-025-00536-w","DOIUrl":"10.1186/s12860-025-00536-w","url":null,"abstract":"<p><strong>Backgrounds: </strong>The interplay between intestinal epithelial cells (IECs), the immune system, and the gut microbiome is pivotal for maintaining gastrointestinal homeostasis and mediating responses to ingested antigens. IECs, capable of expressing Major Histocompatibility Complex (MHC) class II molecules, are essential in modulating immune responses, especially CD4 + T cells, in both physiological and pathological contexts. The expression of MHC class II on IECs, regulated by the class II transactivator (CIITA) and inducible by cytokine IFN-γ, has been traditionally associated with professional antigen-presenting cells but is now recognized in the context of inflammatory conditions such as inflammatory bowel disease (IBD). In veterinary medicine, particularly among canine populations, MHC (or Dog Leukocyte Antigen, DLA) expression on IECs underlines its significance in intestinal immune pathologies, yet remains underexplored. This study aims to leverage canine intestinal organoids as a novel in vitro model to elucidate MHC class II expression dynamics and their implications in immune-mediated gastrointestinal diseases, bridging the gap between basic research and clinical application in canine health.</p><p><strong>Results: </strong>Canine colonoids derived from healthy dogs showed significant expression of MHC class II and its promoter gene, CIITA, after IFN-γ treatment. This MHC class II induction was even more pronounced in differentiated colonoids cultured in Wnt-3a-depleted medium.</p><p><strong>Conclusions: </strong>This study provides insights into the role of IECs as antigen-presenting cells and demonstrates the use of intestinal organoids for investigating epithelial immune responses in inflammatory conditions.</p>","PeriodicalId":9099,"journal":{"name":"BMC Molecular and Cell Biology","volume":"26 1","pages":"11"},"PeriodicalIF":2.4,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11980282/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143810455","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":"Quantitative phosphoproteomics reveals that nestin is a downstream target of dual leucine zipper kinase during retinoic acid-induced neuronal differentiation of Neuro-2a cells.","authors":"Guillaume St-Cyr, Daniel Garneau, Nicolas Gévry, Richard Blouin","doi":"10.1186/s12860-025-00535-x","DOIUrl":"10.1186/s12860-025-00535-x","url":null,"abstract":"<p><strong>Background: </strong>Dual leucine zipper kinase (DLK) is critical for neurite outgrowth in the developing nervous system and during nerve regeneration, but the underlying mechanisms remain largely unknown. To address this issue, we generated stable shRNA-mediated DLK-depleted Neuro-2a cell lines and analyzed their phosphoproteome after induction of neuronal differentiation by retinoic acid (RA).</p><p><strong>Results: </strong>Here, we report the identification of 32 phosphopeptides that exhibited significant differences in relative abundance between control and DLK-depleted cells. Two of the most downregulated phosphopeptides identified after DLK depletion were derived from nestin, a type VI intermediate filament (IF) protein typically expressed in neural progenitor cells. The reduced abundance of these phosphopeptides in response to DLK knockdown was validated using parallel reaction monitoring (PRM)-based quantitative proteomics and paired with a concomitant reduction in nestin mRNA and protein expression, indicating that the decrease in nestin phosphorylation was due to a decrease in total nestin in DLK-depleted cells compared to control cells. This DLK-mediated regulation of nestin expression had no apparent effect on neurite formation because nestin knockdown alone was not sufficient to impair RA-induced neurite extension in parental Neuro-2a cells, and nestin overexpression failed to rescue the neurite outgrowth defect observed in DLK-depleted Neuro-2a cells.</p><p><strong>Conclusions: </strong>Together, these results demonstrate that nestin is a novel downstream target of DLK signaling but not a mediator of its ability to promote neurite outgrowth during neuronal differentiation.</p>","PeriodicalId":9099,"journal":{"name":"BMC Molecular and Cell Biology","volume":"26 1","pages":"10"},"PeriodicalIF":2.4,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11938613/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143717941","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":"Differentiation of Wharton's jelly-derived mesenchymal stromal cells into hepatocyte-like cells using a refined method.","authors":"Afsoon Afshari, Negar Azarpira, Sara Pakbaz","doi":"10.1186/s12860-025-00534-y","DOIUrl":"10.1186/s12860-025-00534-y","url":null,"abstract":"<p><strong>Background: </strong>The production of functional hepatocyte cells in enough quantities is of paramount importance for the replacement of lost hepatocytes. In this investigation, a series of 7-mimic microRNAs was harnessed to induce the differentiation of Wharton's jelly-derived mesenchymal stromal cells (WJ-MSCs) into hepatocyte-like cells (HLC) through the application of two distinct techniques: transfection agents and electroporation. The results were then compared with those of HLCs differentiated through the consumption of chemical compounds.</p><p><strong>Results: </strong>Different time points (48 h, 72 h, and 96 h), unlike concentrations of mimic miRNAs (100 pM, and 200 pM), and dissimilar combinations of mimic-miRNAs (4-mimic and 7-mimic miRNAs) were selected to assess the stage of differentiated cells through electroporation and lipofection methods. For chemical differentiation, a two-step chemical hepatic differentiation protocol was used (for 21 days). The expression level of eleven key genes that were selected to estimate the stage of produced HLCs by each method were tested at different time points, concentrations and combination of mimic-miRNA. Results demonstrated that the 7-miR-mimics/72 h culture method by electroporation, then the 7-miR-mimics/72 h culture method by lipofection, and finally the chemical differentiation (72 h culture) showed the best result for differentiation. Furthermore, the period in which HLCs are maintained under culture conditions is important, as prolonged culture (more than 72 h) leads to cell loss.</p><p><strong>Conclusion: </strong>In conclusion, the results demonstrated that the 7-miR cocktail delivered by electroporation after 72 h effectively promoted the acquisition of hepatocyte-like characteristics which was evidenced by a significant decrease in the Oct4 stemness factor and an increase in the expression of ALB, TAT, AAT, CYP, G6P and HNF4A.</p>","PeriodicalId":9099,"journal":{"name":"BMC Molecular and Cell Biology","volume":"26 1","pages":"9"},"PeriodicalIF":2.4,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11874389/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143540121","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":"Assessment of XCI skewing and demonstration of XCI escape region based on single-cell RNA sequencing: comparison between female Grave's disease and control.","authors":"In-Cheol Baek, Soo Yeun Sim, Byung-Kyu Suh, Tai-Gyu Kim, Won Kyoung Cho","doi":"10.1186/s12860-025-00533-z","DOIUrl":"10.1186/s12860-025-00533-z","url":null,"abstract":"<p><strong>Background: </strong>The reactivation and loss of mosaicism hypothesis due to X chromosome inactivation (XCI) skewing and escape could influence gender differences in autoimmune diseases. XCI selectively inactivates one of the two X chromosomes in females.</p><p><strong>Methods: </strong>To estimate XCI skewing and the occurrence of XCI escape, we conducted a normal female (NF) without a history of autoimmune thyroid disease (AITD) and a patient with Grave's disease (GD) based on a thyroid diagnosis. After single-cell RNA sequencing, heterozygous variants were converted and transformed. XCI skewing was calculated using the formula and the skewing degree was defined. NF/GD genes were compared using correction methods. Positions are heterozygous within a single cell as indicated by a unique barcode.</p><p><strong>Results: </strong>XCI skewing showed 45.8%/48.9% relatively random, 29.4%/27.0% skewing, 24.6%/23.7% severe skewing, and 0.2%/0.4% extreme severe skewing. 24.8%/24.1% in NF/GD exhibited severe skewing or higher. A total of 13 genes were significantly associated with XCI skewing ratios in NF/GD cells. In total, 371/250 nucleotide positions with only one barcode (representing a unique cell) were identified for XCI escape. A total of 143/52 nucleotide positions spanned 20/6 genes, and 12/1 genes were identified as XCI escapes.</p><p><strong>Conclusions: </strong>These results could aid in understanding the immunogenetics of gender differences in various autoimmune disease pathophysiologies.</p>","PeriodicalId":9099,"journal":{"name":"BMC Molecular and Cell Biology","volume":"26 1","pages":"8"},"PeriodicalIF":2.4,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11786500/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143073833","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":"Method for determining of cytotoxicity based on the release of fluorescent proteins.","authors":"Dmitry Lifanov, Dulamsuren Zorigt, Evgenya Shabalina, Abdullah Khalil, Konstantin Gorbunov, Elena Petersen","doi":"10.1186/s12860-025-00532-0","DOIUrl":"10.1186/s12860-025-00532-0","url":null,"abstract":"<p><p>This paper describes a method for determining the cytotoxicity of chemical compounds based on the detection of fluorescent proteins-in this case, green fluorescent protein (GFP) and red fluorescent protein (RFP), which are released into the medium from dead cells. This method is similar in principle to the lactate dehydrogenase test (LDH test), but it does not require a reaction with a chromogenic substrate. This method also makes it possible to independently determine the viability of different lines when used in cocultures. Experiments were performed on a classical monolayer, spheroids and 3D cultures in alginate hydrogel. Capecitabine was used as a model cytotoxic agent. We included liver cells (Huh7) in a coculture model and determined changes in the cytotoxicity levels of capecitabine against NCI-H1299 cells. The experimental part also found that there were differences in sensitivity to capecitabine depending on the type of 3D cultures used.</p>","PeriodicalId":9099,"journal":{"name":"BMC Molecular and Cell Biology","volume":"26 1","pages":"7"},"PeriodicalIF":2.4,"publicationDate":"2025-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11776130/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143057914","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}