Frontiers in Molecular Biosciences最新文献

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Dynamic contrast-enhanced MRI-based radiomics model of intra-tumoral kinetic heterogeneity for predicting breast cancer molecular subtypes. 基于动态增强mri的肿瘤内动力学异质性放射组学模型用于预测乳腺癌分子亚型。
IF 3.9 3区 生物学
Frontiers in Molecular Biosciences Pub Date : 2025-07-18 eCollection Date: 2025-01-01 DOI: 10.3389/fmolb.2025.1635296
Yue Cheng, Ran Ren, Yu Xu, Shaofeng Duan, Jilei Zhang, Zhongyuan Bao
{"title":"Dynamic contrast-enhanced MRI-based radiomics model of intra-tumoral kinetic heterogeneity for predicting breast cancer molecular subtypes.","authors":"Yue Cheng, Ran Ren, Yu Xu, Shaofeng Duan, Jilei Zhang, Zhongyuan Bao","doi":"10.3389/fmolb.2025.1635296","DOIUrl":"https://doi.org/10.3389/fmolb.2025.1635296","url":null,"abstract":"<p><strong>Objectives: </strong>This study aims to segment intra-tumoral subregions of breast cancer based on kinetic heterogeneity using dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI). It also aims to construct a radiomics model of the whole tumor and washout region to predict molecular subtypes and human epidermal growth factor receptor 2 (HER2) status.</p><p><strong>Methods: </strong>A total of 124 patients with biopsy-confirmed breast cancer were randomly divided into training and test sets in a 7:3 ratio. Quantitative analysis of breast cancer kinetic heterogeneity parameters based on DCE-MRI data was performed, dividing tumors into three subregions (Persistent, Washout, and Plateau) according to the type of voxel-level contrast enhancement. Radiomics features of the washout region and the whole tumor were extracted from the first phase of DCE-MRI enhancement. The area under the receiver operating characteristic curve (AUC) and decision curve analysis (DCA) were used to evaluate the performance of the model.</p><p><strong>Results: </strong>The radiomics model using tumor subregion (washout region) features related to kinetic heterogeneity showed the best performance for differentiating between patients with Luminal, HER2, and HER2 status, with AUC values in the train set of 0.924, 0.876, and 0.816, respectively. Exhibiting an AUC value higher than that obtained with the whole tumor and the kinetic heterogeneity parameters. DCA curves showed that the washout region model was more effective in predicting Luminal and HER2-status subtypes, compared to the whole tumor region model.</p><p><strong>Conclusion: </strong>Radiomics analysis of washout areas from high-resolution DCE-MRI breast scans has the potential to better identify molecular subtypes of breast cancer non-invasively.</p>","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"12 ","pages":"1635296"},"PeriodicalIF":3.9,"publicationDate":"2025-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12313481/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144775074","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}
引用次数: 0
Proteomic and structural comparison between cilia from primary ciliary dyskinesia patients with a DNAH5 defect. DNAH5缺陷原发性纤毛运动障碍患者纤毛的蛋白质组学和结构比较。
IF 3.9 3区 生物学
Frontiers in Molecular Biosciences Pub Date : 2025-07-17 eCollection Date: 2025-01-01 DOI: 10.3389/fmolb.2025.1593810
Charlotte de Ceuninck van Capelle, Leo Luo, Alexander Leitner, Stefan A Tschanz, Philipp Latzin, Sebastian Ott, Tobias Herren, Loretta Müller, Takashi Ishikawa
{"title":"Proteomic and structural comparison between cilia from primary ciliary dyskinesia patients with a DNAH5 defect.","authors":"Charlotte de Ceuninck van Capelle, Leo Luo, Alexander Leitner, Stefan A Tschanz, Philipp Latzin, Sebastian Ott, Tobias Herren, Loretta Müller, Takashi Ishikawa","doi":"10.3389/fmolb.2025.1593810","DOIUrl":"10.3389/fmolb.2025.1593810","url":null,"abstract":"<p><strong>Introduction: </strong>Primary ciliary dyskinesia (PCD) is a genetic disorder affecting motile cilia across various organs, leading to recurrent respiratory infections, subfertility, and laterality defects. While several diagnostic tools exist-such as high-speed video microscopy, immunofluorescence staining, electron microscopy, and genetic screening-the relationship between different pathogenic variants within a single PCD gene and their effects on ciliary composition, structure, and clinical phenotype remains poorly understood.</p><p><strong>Methods: </strong>To investigate this, we analyzed cilia from PCD patients with different mutations in axonemal dynein heavy chain <i>dnah5</i> using mass spectrometry and cryo-electron tomography. These methods allowed us to examine both the protein composition and ultrastructural organization of motile cilia in affected individuals.</p><p><strong>Results: </strong>Though all analyzed patients present similarly in traditional diagnostic methods, we observed differences in axonemal composition among patients carrying different <i>dnah5</i> mutations. Specific reductions in ciliary components varied between individuals, indicating a mutation-specific impact. Notably, proteins such as VWA3B, KIAA1430/CFAP97, and DTHD1-not previously identified as components of human respiratory motile cilia-were detected in wild type cilia, but not in patient cilia. Lastly, we confirmed some changes in protein abundance in the 96-nm repeated unit of the axoneme between wild-type and PCD samples.</p><p><strong>Discussion: </strong>These findings suggest that mutations in <i>dnah5</i> result in varied and specific alterations in axonemal composition, reflecting the heterogeneity of the disease at the molecular level. The discovery of novel ciliary proteins and mutation-specific differences enhances our understanding of the complexity of PCD pathogenesis and may inform future diagnostic and therapeutic strategies.</p>","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"12 ","pages":"1593810"},"PeriodicalIF":3.9,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12310455/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144759633","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}
引用次数: 0
Development of a human colorectal carcinoma cell-based platform for studying inducible nitric oxide synthase expression and nitric oxide signaling dynamics. 人类结直肠癌细胞诱导型一氧化氮合酶表达和一氧化氮信号动力学研究平台的建立。
IF 3.9 3区 生物学
Frontiers in Molecular Biosciences Pub Date : 2025-07-17 eCollection Date: 2025-01-01 DOI: 10.3389/fmolb.2025.1637230
Xi Chen, Elizabeth A Grimm, Yong Qin
{"title":"Development of a human colorectal carcinoma cell-based platform for studying inducible nitric oxide synthase expression and nitric oxide signaling dynamics.","authors":"Xi Chen, Elizabeth A Grimm, Yong Qin","doi":"10.3389/fmolb.2025.1637230","DOIUrl":"10.3389/fmolb.2025.1637230","url":null,"abstract":"<p><strong>Introduction: </strong>Inducible nitric oxide synthase (iNOS) plays a critical role in inflammatory signaling and tumor immunology, contributing to both pro- and anti-tumor effects depending on the cellular context. While iNOS induction has been linked to immune activation and tumor progression, its expression in cancer cells is highly variable and often inconsistently reported across different tumor models. To address this gap, we developed a well-defined <i>in vitro</i> platform using the human colorectal adenocarcinoma cell line DLD-1 to model stimulus-dependent iNOS expression and nitric oxide (NO) signaling.</p><p><strong>Methods: </strong>DLD-1 cells were stimulated with a pro-inflammatory cytokine cocktail (lipopolysaccharide [LPS], interleukin-1β [IL-1β], and interferon-γ [IFN-γ]), resulting in marked upregulation of iNOS at both the mRNA and protein levels. iNOS specificity was confirmed using targeted siRNA knockdown. Functional assessment of NO production was performed using the Nitrate/Nitrite Colorimetric Assay Kit and the ENO-30 NOx Analyzer. Induction of iNOS was further associated with elevated levels of reactive nitrogen species (RNS), reactive oxygen species (ROS), and protein nitration, including 3-nitrotyrosine, detected by immunohistochemistry and Western blot.</p><p><strong>Results: </strong>Upon stimulation, DLD-1 cells consistently expressed enzymatically active, full-length human iNOS and produced biologically relevant levels of NO and downstream nitrosative stress markers. Treatment with selective iNOS inhibitors significantly reduced nitrite accumulation, confirming the functional activity of iNOS and the model's applicability for pharmacologic evaluation of NO-modulatory compounds.</p><p><strong>Discussion: </strong>Our findings establish the DLD-1 cell line as a reproducible and well-controlled in vitro system for studying inducible iNOS expression and downstream NO/RNS signaling in human epithelial cancer cells. This platform provides a valuable tool for mechanistic studies, screening of iNOS-targeted agents, and resolving discrepancies in iNOS detection across experimental models in cancer biology.</p>","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"12 ","pages":"1637230"},"PeriodicalIF":3.9,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12310501/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144759632","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}
引用次数: 0
The role of epigenetics in pulmonary fibrosis: recent advances in mechanistic insights and therapeutic implications. 表观遗传学在肺纤维化中的作用:机制见解和治疗意义的最新进展。
IF 3.9 3区 生物学
Frontiers in Molecular Biosciences Pub Date : 2025-07-17 eCollection Date: 2025-01-01 DOI: 10.3389/fmolb.2025.1647300
Jingru Huang, Jianfeng Qin, Yuguang Zhu, Ao Shen
{"title":"The role of epigenetics in pulmonary fibrosis: recent advances in mechanistic insights and therapeutic implications.","authors":"Jingru Huang, Jianfeng Qin, Yuguang Zhu, Ao Shen","doi":"10.3389/fmolb.2025.1647300","DOIUrl":"10.3389/fmolb.2025.1647300","url":null,"abstract":"<p><p>Pulmonary fibrosis (PF) is a fatal disease characterized by progressive fibrosis of lung tissue, with a key pathological feature of excessive accumulation of extracellular matrix. PF occurs from complicated origins, while emerging findings have suggested the involvement of the environmental factors in the risk of PF through epigenetic regulation. This article will discuss how recent advances in epigenetic alterations of DNA methylation, RNA methylation, histone modifications, and non-coding RNAs contribute to PF development through molecular mechanisms and cellular processes, including fibroblast-to-myofibroblast transition (FMT), epithelial-to-mesenchymal transition (EMT), alveolar epithelial cell injury and immune cell interactions in the past 5 years.</p>","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"12 ","pages":"1647300"},"PeriodicalIF":3.9,"publicationDate":"2025-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12310491/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144759634","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}
引用次数: 0
An overview of current research on the modulation of NLRP3 inflammasome by traditional Chinese medicine to combat acute pancreatitis. 中药调节NLRP3炎性体抗急性胰腺炎的研究现状综述。
IF 3.9 3区 生物学
Frontiers in Molecular Biosciences Pub Date : 2025-07-16 eCollection Date: 2025-01-01 DOI: 10.3389/fmolb.2025.1634132
Xiongjie He, Jia Xia, Qi Chen, Zhaozhao Huang, Juanjuan Lu, Yisong Ren
{"title":"An overview of current research on the modulation of NLRP3 inflammasome by traditional Chinese medicine to combat acute pancreatitis.","authors":"Xiongjie He, Jia Xia, Qi Chen, Zhaozhao Huang, Juanjuan Lu, Yisong Ren","doi":"10.3389/fmolb.2025.1634132","DOIUrl":"10.3389/fmolb.2025.1634132","url":null,"abstract":"<p><p>Acute pancreatitis (AP), a life-threatening gastrointestinal emergency, is characterized by acute onset, rapid clinical deterioration, and high mortality rates, imposing profound long-term health burdens and socioeconomic costs on patients and healthcare systems. Current therapeutic strategies focus on supportive care, as no curative therapies exist to halt AP progression. Traditional Chinese medicine (TCM), with its multi-target, multi-component, and multi-pathway pharmacological properties, has emerged as a promising therapeutic drug against inflammation-driven pathologies, including AP. This review systematically discussed the assembly, activation, and pathogenic contributions of the NOD-like receptor family pyrin domain-containing 3 (NLRP3) inflammasome in AP pathogenesis. Mechanistically, NLRP3 activation exacerbated pancreatic injury through caspase-1-dependent maturation of interleukin-1β (IL-1β) and gasdermin D (GSDMD)-mediated pyroptosis, perpetuating systemic inflammation. We systematically summarized the research progress of TCM in the treatment of AP by reducing pancreatic necrosis, neutrophil infiltration, and intestinal barrier dysfunction through targeting NLRP3 inflammasome, as well as its clinical evidence. Collectively, this review highlights the translational potential of TCM as an adjunctive therapy for AP through NLRP3 inflammasome inhibition, offering mechanistic insights and evidence-based support for its integration into integrative medicine strategies.</p>","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"12 ","pages":"1634132"},"PeriodicalIF":3.9,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12307185/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144752883","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}
引用次数: 0
Identification and validation of integrated stress-response-related genes as biomarkers for age-related macular degeneration. 作为年龄相关性黄斑变性生物标志物的综合应激反应相关基因的鉴定和验证。
IF 3.9 3区 生物学
Frontiers in Molecular Biosciences Pub Date : 2025-07-16 eCollection Date: 2025-01-01 DOI: 10.3389/fmolb.2025.1583237
Jingyi Niu, Ling Jin, Yijun Hu, Yiting Wang, Xiaoning Hao, Wenwen Geng, Ruirui Ma
{"title":"Identification and validation of integrated stress-response-related genes as biomarkers for age-related macular degeneration.","authors":"Jingyi Niu, Ling Jin, Yijun Hu, Yiting Wang, Xiaoning Hao, Wenwen Geng, Ruirui Ma","doi":"10.3389/fmolb.2025.1583237","DOIUrl":"10.3389/fmolb.2025.1583237","url":null,"abstract":"<p><strong>Background: </strong>Age-related macular degeneration (AMD) is a prevalent ocular condition associated with aging, serving as a significant contributor to vision loss among middle-aged and older individuals. Studies have shown that AMD and integrated stress response (ISR) are associated with oxidative stress, but no specific molecular mechanisms have been identified. Therefore, this study aimed to identify potential biomarkers for AMD through bioinformatics analysis based on the transcriptome database and integrated stress response related genes (ISR-RGs).</p><p><strong>Methods: </strong>Transcriptomic data GSE76237, GSE247168, and ISR-RGs were sourced from public databases and related literature. The biomarkers associated with AMD were identified by differentially expressed gene (DEG) analysis, intersection of common DEGs, and ISR-RGs machine algorithm. After that, nomograms, GSEA, and immune infiltration analysis were performed for the biomarkers. The effects of transcription factors (TFs) and miRNAs on biomarkers were then explored by constructing a TF-biomarker-miRNA regulatory network. In addition, potential effective drugs of the biomarkers were explored by constructing a biomarker-effective drug interaction network. Finally, we verified the gene expression of the biomarkers by RT-qPCR.</p><p><strong>Results: </strong>We obtained 2,567 and 1,454 DEGs in GSE76237 and GSE247168, respectively. The up- and downregulated genes shared in both datasets were intersected with ISR-RGs taken to obtain eight candidate genes. SLFN11 and GRIN1 were identified as common biomarkers for AMD. An analysis of the nomogram model of biomarkers revealed good diagnostic predictive abilities (AUC > 0.7). SLFN11 and GRIN1 were mainly enriched in pathways such as proteasome, lysosome, and neuroactive ligand receptor interaction. In addition, the disease group's monocyte expression was significantly higher than that of the control group in GSE76237 (p < 0.01). We obtained thirteen relevant miRNAs and 27 TFs by prediction, with three shared TFs, and seventeen potentially effective drugs were predicted. RT-qPCR validation showed in AMD patients, and SLFN11 and GRIN1 expression was significantly higher than controls (p < 0.05). Only SLFN11 expression was consistent with the bioinformatics analysis.</p><p><strong>Conclusion: </strong>SLFN11 and GRIN1 were identified as AMD biomarkers, exhibiting robust diagnostic performance and providing new insights into the condition.</p>","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"12 ","pages":"1583237"},"PeriodicalIF":3.9,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12307159/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144752884","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}
引用次数: 0
Expression and clinical significance of S100A8/9 in adults with secondary phagocytic lymphohistiocytosis. S100A8/9在成人继发性吞噬性淋巴组织细胞增多症中的表达及临床意义
IF 3.9 3区 生物学
Frontiers in Molecular Biosciences Pub Date : 2025-07-15 eCollection Date: 2025-01-01 DOI: 10.3389/fmolb.2025.1607352
Ziwei Fang, Xin Gao, Limin Duan, Jujuan Wang, Tian Tian, Ji Xu, Yongqian Shu, Guangli Yin, Hongxia Qiu
{"title":"Expression and clinical significance of S100A8/9 in adults with secondary phagocytic lymphohistiocytosis.","authors":"Ziwei Fang, Xin Gao, Limin Duan, Jujuan Wang, Tian Tian, Ji Xu, Yongqian Shu, Guangli Yin, Hongxia Qiu","doi":"10.3389/fmolb.2025.1607352","DOIUrl":"10.3389/fmolb.2025.1607352","url":null,"abstract":"<p><strong>Introduction: </strong>The study aimed to investigate the diagnostic and prognostic value of serum S100A8/9 levels with sHLHa, a high-mortality multiorgan inflammatory syndrome with no reliable clinical biomarkers, where calreticulin's role is unclear.</p><p><strong>Methods: </strong>This was a study of 67 newly diagnosed sHLHa patients. 48 patients met criteria and were analyzed. ELISA detected S100A8/9 levels in patients and controls. The optimal classification threshold for S100A8/9 was determined to be 2.44 µg/mL by restricted cubic spline (RCS) curve analysis. Patients were categorized. Correlations, diagnostic efficacy, survival differences, and prognosis impacts were analyzed.</p><p><strong>Results: </strong>Serum S100A8/9 levels in sHLHa patients were greater than in healthy controls. Various analyses showed its diagnostic and prognostic value. ANC<1.0 × 10<sup>9</sup>/L and high S100A8/9 expression group were independent risk factors for poor prognosis in patients with sHLHa. It's correlated with liver function indicators and HScore.</p><p><strong>Discussion: </strong>This study evaluates S100A8/9 in sHLHa diagnosis and prognosis. S100A8/9 levels are useful for differentiating patients, providing etiologic and survival info. They show a nonlinear positive correlation with survival and a threshold effect. Serum S100A8/9 levels offer potential biomarkers, and further studies are needed.</p>","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"12 ","pages":"1607352"},"PeriodicalIF":3.9,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12304547/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144741789","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}
引用次数: 0
An integrated approach for analyzing spatially resolved multi-omics datasets from the same tissue section. 用于分析来自同一组织切片的空间分辨多组学数据集的集成方法。
IF 3.9 3区 生物学
Frontiers in Molecular Biosciences Pub Date : 2025-07-15 eCollection Date: 2025-01-01 DOI: 10.3389/fmolb.2025.1614288
Thao Tran, Felicia Wee, Craig Ryan Joseph, Wanqiu Zhang, Jeffrey Chun Tatt Lim, Zhen Wei Neo, Li Yen Chong, Francis Hong Xin Yap, Nathan Heath Patterson, Marc Claesen, Alice Ly, Joe Yeong
{"title":"An integrated approach for analyzing spatially resolved multi-omics datasets from the same tissue section.","authors":"Thao Tran, Felicia Wee, Craig Ryan Joseph, Wanqiu Zhang, Jeffrey Chun Tatt Lim, Zhen Wei Neo, Li Yen Chong, Francis Hong Xin Yap, Nathan Heath Patterson, Marc Claesen, Alice Ly, Joe Yeong","doi":"10.3389/fmolb.2025.1614288","DOIUrl":"10.3389/fmolb.2025.1614288","url":null,"abstract":"<p><p>Recent advances in spatial transcriptomics (ST) and spatial proteomics (SP) technologies have enabled high-dimensional molecular profiling at single-cell resolution, providing deeper insights into the tumour-immune microenvironment. However, these modalities are typically applied to separate tissue sections, limiting direct comparisons across molecular layers. We developed a wet-lab and computational framework to perform and integrate ST and SP from the same tissue section, as demonstrated on human lung cancer samples. Applying ST, SP, and hematoxylin and eosin (H&E) staining from the same section ensured consistency in tissue morphology and spatial context. Computational registration using Weave software allowed accurate alignment and annotation transfer across modalities. This co-registered dataset enabled single-cell level comparisons of RNA and protein expression, revealed segmentation accuracy and transcript-protein correlation analyses within individual cells. Notably, we observed systematic low correlations between transcript and protein levels-consistent with prior findings-now resolved at cellular resolution. Our approach highlights the feasibility and utility of performing spatially-resolved multi-omics analysis on the same section without compromising data quality, facilitating concordance studies and region-specific analysis of immune and tumour markers, and ultimately advancing our understanding of disease heterogeneity at the molecular level.</p>","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"12 ","pages":"1614288"},"PeriodicalIF":3.9,"publicationDate":"2025-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12304548/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144741788","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}
引用次数: 0
Editorial: Ironome: a still untapped frontier. 社论:电子商务:一个尚未开发的领域。
IF 3.9 3区 生物学
Frontiers in Molecular Biosciences Pub Date : 2025-07-14 eCollection Date: 2025-01-01 DOI: 10.3389/fmolb.2025.1651154
Gloria C Ferreira, Vladimir N Uversky, Zoubida Karim
{"title":"Editorial: Ironome: a still untapped frontier.","authors":"Gloria C Ferreira, Vladimir N Uversky, Zoubida Karim","doi":"10.3389/fmolb.2025.1651154","DOIUrl":"10.3389/fmolb.2025.1651154","url":null,"abstract":"","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"12 ","pages":"1651154"},"PeriodicalIF":3.9,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12301187/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144729352","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}
引用次数: 0
Untargeted plasma metabolite detection in sudden sensorineural hearing loss: identifying key metabolic signatures. 突发性感音神经性听力损失的非靶向血浆代谢物检测:识别关键代谢特征。
IF 3.9 3区 生物学
Frontiers in Molecular Biosciences Pub Date : 2025-07-14 eCollection Date: 2025-01-01 DOI: 10.3389/fmolb.2025.1567064
Rongyue Ma, Huangruici Zhang, Weijie Wang, Changping Yu, Guohang Xiong, Qing Li, Yan Wang, Li Zhou, Yu Zhang, Min Li, Min Guo
{"title":"Untargeted plasma metabolite detection in sudden sensorineural hearing loss: identifying key metabolic signatures.","authors":"Rongyue Ma, Huangruici Zhang, Weijie Wang, Changping Yu, Guohang Xiong, Qing Li, Yan Wang, Li Zhou, Yu Zhang, Min Li, Min Guo","doi":"10.3389/fmolb.2025.1567064","DOIUrl":"10.3389/fmolb.2025.1567064","url":null,"abstract":"<p><strong>Background: </strong>Sudden sensorineural hearing loss (SSNHL) is a common otological disorder with complex etiologies and unclear pathophysiology. This study aimed to detect and analyze plasma metabolites in SSNHL, identify potential biomarkers, and uncover underlying metabolic mechanisms.</p><p><strong>Methods: </strong>A cohort of 64 SSNHL, classified into four subtypes (low-frequency, high-frequency, flat and total deafness type), and 53 normal controls (NC) were recruited. Plasma samples were collected and analyzed by high-performance liquid chromatography-mass spectrometry (LC-MS). Metabolite profiling was performed, followed by multivariate statistical analyses, including orthogonal projections to latent structures-discriminant analysis (OPLS-DA) and partial least-squares discriminant analysis (PLS-DA) to find differentially expressed metabolites between the groups.</p><p><strong>Results: </strong>The results showed significant differences in the plasma metabolome when comparing each of the four SSNHL types with NC. A total of 130 differentially expressed metabolites were identified, with sphingosine, anthranilic acid, and 6-hydroxyflavanone (6-HF) being prominent examples. Were prominent. Pathway enrichment analysis indicated that these metabolites were mainly involved in central carbon metabolism, protein digestion and absorption, aminoacyl-tRNA biosynthesis, mineral absorption, etc.</p><p><strong>Conclusion: </strong>These findings imply that plasma metabolite profiling holds promise as a non-invasive approach for screening biomarkers in SSNHL. The identified differential metabolites and associated metabolic pathways may offer novel perspectives on the pathophysiology of SSNHL, presenting potential targets for future therapeutic interventions.</p>","PeriodicalId":12465,"journal":{"name":"Frontiers in Molecular Biosciences","volume":"12 ","pages":"1567064"},"PeriodicalIF":3.9,"publicationDate":"2025-07-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12301207/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144729343","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}
引用次数: 0
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