Biological Procedures Online最新文献

{"title":"Sheet Protector Strategy for Western Blot to Reduce Antibody Consumption and Incubation Time.","authors":"Sunmin Kwon, So Yeong Lee, Gun Kim","doi":"10.1186/s12575-025-00300-6","DOIUrl":"10.1186/s12575-025-00300-6","url":null,"abstract":"<p><strong>Background: </strong>Western blot is one of the most routinely conducted biochemical assays due to its technical ease and relatively low cost. The use of antibody is at the center of Western blot assay, providing great sensitivity and specificity. However, challenges can be posed when using a rare antibody stock. There have been efforts to improve the Western blot procedure to minimize the use of antibody, but these methods require specialized devices.</p><p><strong>Results: </strong>In this study, we hypothesized that the conventional large pool of antibody is not essential for detection and attempted applying only a small volume of antibody. We used sheet protector (SP), a common stationery material that protects office documents, to effectively distribute the antibody solution over the nitrocellulose (NC) membrane. This way, 20-150 µL antibody solution was sufficient for mini-sized membrane, which was adjustable depending on the size of the membrane. We confirmed that the sensitivity and specificity of this SP strategy was comparable to conventional (CV) method. The SP strategy brought a few additional advantages including: (1) antibody incubation without agitation (2), incubation at room temperature, and (3) faster detection on the order of minutes. Finally, we examined 15-min incubation SP protocol using time-series apoptosis samples.</p><p><strong>Conclusions: </strong>We propose that SP strategy is a universally accessible approach using a common consumable, greatly enhancing the efficiency of antibody consumption and incubation time in Western blot assays.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"27 1","pages":"37"},"PeriodicalIF":4.3,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12462392/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145136360","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":"SOCS3: An Immunological Biomarker Offering Potential Therapeutic Targets for Malignant Tumors.","authors":"Yan Zhang, Meiling Chu, Meina Ye, Yulian Yin, Hongfeng Chen","doi":"10.1186/s12575-025-00296-z","DOIUrl":"10.1186/s12575-025-00296-z","url":null,"abstract":"<p><p>Suppressor of Cytokine Signaling 3 (SOCS3) is a critical regulator of cytokine signaling, primarily acting through the Janus Kinase (JAK)/Signal Transducer and Activator of Transcription (STAT) pathway. It plays a significant role in the development and progression of various malignancies. Abnormal expression of SOCS3 in cancer cells is linked to dysregulated cell growth, migration, and apoptosis, driven by cytokines and hormones. This aberrant expression makes SOCS3 a potential biomarker for tumor diagnosis, prognosis, and gene therapy. Targeting SOCS3 may offer innovative strategies for cancer treatment. This review provides a comprehensive overview of SOCS3's molecular structure, its biological functions in tumors, underlying molecular mechanisms, and therapeutic strategies targeting SOCS3.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"27 1","pages":"36"},"PeriodicalIF":4.3,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12452022/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145124082","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":"Organotypic Culture of Adult Vascularized Porcine Retina Explants In Vitro on Nanotube Scaffolds.","authors":"Sabrina Friebe, Solveig Weigel, Mike Francke, Stefan G Mayr","doi":"10.1186/s12575-025-00301-5","DOIUrl":"10.1186/s12575-025-00301-5","url":null,"abstract":"<p><strong>Background: </strong>Organotypic long-term cultivation of vascularized retina explants is a major challenge for application in drug development, drug screening, diagnostics and future personalized medicine. With this background, an assay and protocol for organotypic culture of vascularized retina explants in vitro with optimum tissue integrity preservation is developed and demonstrated.</p><p><strong>Methods: </strong>Morphological, histologic and biochemical integrity as well as viability of vascularized retina explants are compared as function of cultivation time for differently structured nanotube scaffolds. In doing so, porcine retina explants obtained from a local slaughterhouse are employed as paradigm for vascularized retina.</p><p><strong>Conclusions: </strong>We demonstrate that titania nanotube arrays are highly promising as culturing scaffold of vascularized retina explants in vitro due to highly tunable surface properties regarding biomedical signaling. The unprecedented maintenance of tissue integrity allows for screening of pharmacological drugs and disease mechanisms in an ex-vivo test-based culture system with reduced need for animal experiments.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"27 1","pages":"35"},"PeriodicalIF":4.3,"publicationDate":"2025-09-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12418674/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145028865","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":"Evaluation of the HumanMethylationEPIC v2.0 Bead Chip Using Low Quality and Quantity DNA Samples.","authors":"Brando Poggiali, Mikkel Eriksen Dupont, Marie-Louise Kampmann, Athina Vidaki, Vania Pereira, Claus Børsting, Jacob Tfelt-Hansen, Jeppe Dyrberg Andersen","doi":"10.1186/s12575-025-00292-3","DOIUrl":"10.1186/s12575-025-00292-3","url":null,"abstract":"<p><strong>Background: </strong>The HumanMethylationEPIC v2.0 BeadChip (EPIC v2.0) microarray is a widely used tool for genome-wide DNA methylation (DNAm) analysis, designed for high-quality human DNA with a recommended input of 250 ng. However, in clinical and forensic settings, DNA samples may be of low quality and/or quantity (highly fragmented and/or available in low amounts). This study assessed the performance of the EPIC v2.0 on DNA samples with various combinations of average DNA fragment size (350, 230, 165, and 95 bp) and DNA input amount (100, 50, 20, and 10 ng), compared to a paired control sample analyzed under optimal conditions (high-quality DNA and 250 ng DNA input).</p><p><strong>Results: </strong>The best performance was obtained for samples with average DNA fragment size of 350 bp and 100 ng DNA input (~ 90% probe detection rate, r = 0.995, and median absolute beta value differences|Δβ| = 0.012 when compared with the control sample). Samples with lower average DNA fragment sizes and DNA input amount performed worse, with the lowest probe detection rate (~ 43%), r = 0.946, and the highest|Δβ| (0.038). Samples with average DNA fragment sizes of 95 bp and those with 165 bp at 10 ng DNA input failed to pass sample quality control (QC). CpG sites with intermediate DNAm values (β = 0.1-0.9) showed higher|Δβ| than the extreme DNAm values (β = 0-0.1, and β = 0.9-1). Finally, we assessed an application of DNAm by performing epigenetic age analysis, and observed mean absolute errors (MAEs) below 10 years for 350 bp samples across four epigenetic clocks.</p><p><strong>Conclusions: </strong>Both DNA fragment size and DNA input amounts affect DNAm analysis on the EPIC v2.0, with the investigated DNA fragment size having a greater impact than the investigated DNA input amount. DNAm measurements were achieved with the EPIC v2.0 microarray down to an average DNA fragment size of 165 bp and a 20 ng DNA input. Highly fragmented DNA (95 bp) did not result in usable DNAm analysis as all samples failed QC. Overall, our study demonstrates the potential and limitations of EPIC v2.0 microarray with low quality and quantity DNA samples.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"27 1","pages":"34"},"PeriodicalIF":4.3,"publicationDate":"2025-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12369268/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941447","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":"c-MET Inhibition Reverses the Osimertinib Resistance in Lung Circulating Tumor Cell Clusters and Suppresses Metastasis.","authors":"Zhipeng Zhang, Xinyi Lu, Jianhui Tian, Jiaxuan Li, Shihui Liu, Jiajun Liu, Bin Luo, Jialiang Yao, Yao Liu, Yanhong Wang, Wang Yao, Yun Yang, Wenji Shangguan, Zujun Que","doi":"10.1186/s12575-025-00295-0","DOIUrl":"10.1186/s12575-025-00295-0","url":null,"abstract":"<p><p>BACKGROUND: Circulating tumor cells (CTCs) serve as the “seeds” of tumor metastasis, and the clustering of CTCs is critically associated with tumor metastasis and the mortality of lung cancer patients. Inhibiting the survival of CTC clusters represents a pivotal strategy for anti-lung cancer metastasis therapy. This study is designed to explore the impact and underlying mechanism of lung cancer CTC clusters in mediating resistance to epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs), thereby offering novel insights into anti-lung cancer metastasis treatment. METHODS: Using the human lung adenocarcinoma CTC line CTC-TJH-01, we performed transcriptome analysis to identify differentially expressed genes. CCK-8, LDH, Calcein AM/EthD-1, and Annexin V-FITC/caspase-3 assays evaluated the effects of osimertinib, Tivantinib, or their combination on CTC-TJH-01 and A549 cell proliferation and apoptosis. RT-qPCR, western blot, and immunohistochemistry analyzed gene and protein expression. A lung metastasis mouse model was established by injecting CTC-TJH-01 clusters, with anatomical observation and H&E staining for evaluation. RESULTS: Our study demonstrated that CTC-TJH-01, A549, and H1975 cell clusters in suspension exhibited higher resistance to osimertinib compared to their adherent counterparts. Notably, the expression of the HGF gene was remarkably upregulated in CTC-TJH-01 cell clusters. Activation of the HGF/c-MET pathway was observed in CTC clusters, accompanied by a concurrent downregulation of EGFR protein expression. Significantly, the c-MET inhibitor Tivantinib, but not the HGF inhibitor SRI, effectively suppressed the survival of CTC-TJH-01 and A549 cell clusters. Moreover, Tivantinib, either as a single-agent or in combination with osimertinib, exerted a potent inhibitory effect on the in vivo metastasis of CTC-TJH-01 cell clusters. CONCLUSION: These findings indicate that CTC clusters contribute to resistance against EGFR-TKI treatment, and c-MET inhibitors hold promise as potential therapeutic agents for targeting CTC cluster survival to impede lung cancer metastasis. </p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"27 1","pages":"32"},"PeriodicalIF":4.9,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366314/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941460","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":"Refining Flow Cytometry-based Sorting of Plasma-derived Extracellular Vesicles.","authors":"Daniele Reverberi, Maria Chiara Ciferri, Nicole Rosenwasser, Alessandro Catino, Giuseppina Poppa, Ilaria Giusti, Vincenza Dolo, Rodolfo Quarto, Sara Santamaria, Monica Colombo, Simona Coco, Roberta Tasso","doi":"10.1186/s12575-025-00293-2","DOIUrl":"10.1186/s12575-025-00293-2","url":null,"abstract":"<p><p>BACKGROUND: Extracellular vesicles (EVs) are membrane-bound particles crucial for intercellular communication and serve as promising biomarkers for diseases, including cancer. Isolating and characterizing specific EV subpopulations, particularly those in plasma/serum, enhances biomarker precision and supports targeted therapies. Cancer-derived EVs often express unique surface markers, enabling distinction from other EVs. Accurate sorting of tumor-associated EVs provides insights into cancer progression, metastasis, and treatment response. RESULTS: This study presents a robust method for isolating and sorting CD9 + plasma EVs as a proof-of-concept for broader EV subpopulation analyses. Plasma EVs were isolated via sucrose cushion ultracentrifugation, optimizing purity and yield. Flow cytometry with fluorescence threshold triggering was fine-tuned to detect and sort CD9 + EVs, with instrument calibration and parameter adjustments mitigating swarming and improving sorting accuracy. Size exclusion chromatography further enhanced efficiency by reducing background noise. Sorted CD9 + EVs retained size and marker expression, including Syntenin, Alix, Flotillin-1, and CD9, which were enriched post-sorting. CONCLUSIONS: These advancements enable high-purity EV subpopulation isolation, facilitating applications such as identifying cancer biomarkers and developing EV-based targeted therapies. </p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"27 1","pages":"33"},"PeriodicalIF":4.9,"publicationDate":"2025-08-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12366389/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144941387","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 Role of the TIMP1/LINC01615 Axis as a Regulator of the EMT Pathway in Gastric Cancer.","authors":"Jiying Liu, Yeganeh Olyaee, Khatere Mokhtari, Chaoxiang Lv, Niloufar Salimian, Maliheh Entezari, Afshin Taheriazam, Mehrdad Hashemi, Mazaher Maghsoudloo, Ling Yuan","doi":"10.1186/s12575-025-00297-y","DOIUrl":"10.1186/s12575-025-00297-y","url":null,"abstract":"<p><strong>Objective: </strong>Gastric cancer (GCa) is a common malignancy where the epithelial-to-mesenchymal transition (EMT) pathway and lncRNAs are key to proliferation and metastasis. This study aimed to identify lncRNAs regulating the EMT pathway as therapeutic and diagnostic targets in GCa.</p><p><strong>Methods: </strong>We utilized the TCGA-STAD dataset and differential expression gene (DEG) analysis was performed to identify overlapping genes between DEGs and the EMT pathway. The LASSO feature reduction algorithm and ROC curve analysis were applied to prioritize candidate biomarkers. Additionally, immunological and immunotherapy analyses were conducted to evaluate the significance of TIMP1 in GCa. Pearson correlation analysis was performed between TIMP1 and all differentially expressed lncRNAs, and the most strongly correlated candidates were selected. Experimental validation of the results was carried out using RT-qPCR with 25 cancerous and 25 adjacent normal tissue samples in GCa.</p><p><strong>Results: </strong>DEG analysis identified 2,926 DEGs, among which 87 were associated with the EMT pathway. The LASSO algorithm reduced this list to 11 genes, and ROC curve analysis identified TIMP1 as a candidate biomarker in GCa. Higher TIMP1 expression was associated with improved response rates. Correlation analysis revealed that LINC01615 was most strongly co-regulated with TIMP1 in GCa. RT-qPCR confirmed that both TIMP1 and LINC01615 were significantly upregulated in tumor tissues compared to adjacent normal tissues, highlighting their potential as diagnostic biomarkers.</p><p><strong>Conclusion: </strong>A strong correlation between TIMP1 and LINC01615 suggests their role in promoting GCa proliferation, invasion, and metastasis. TIMP1/LINC01615 axis regulates the EMT pathway and is a potential biomarker and therapeutic target in GCa.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"27 1","pages":"31"},"PeriodicalIF":4.3,"publicationDate":"2025-08-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12363065/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144871268","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":"A Rare Case of Long-Term Survival in Stage IIIB Lung Adenocarcinoma: an 9-Year Follow-Up.","authors":"Jianing Chen, Li Liu, Qi Wang, Yan Wu, Jing Zhao, Li Wang, Lei Cheng, Huiming Zhu, Chunxia Su","doi":"10.1186/s12575-025-00291-4","DOIUrl":"10.1186/s12575-025-00291-4","url":null,"abstract":"<p><p>We report a rare case of long-term survival in a 59-year-old male patient diagnosed with stage IIIB lung adenocarcinoma. Despite disease progression following initial chemotherapy, the patient achieved prolonged survival through a combination of chemotherapy and radiotherapy. This case highlights the potential for extended survival in advanced lung cancer with multimodal treatment approaches.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"27 1","pages":"30"},"PeriodicalIF":4.3,"publicationDate":"2025-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12335796/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144811680","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":"Machine learning-driven multi-omics analysis identifies a prognostic gene signature associated with programmed cell death and metabolism in hepatocellular carcinoma.","authors":"Xiang Li, Donghao Yin, Jiahao Geng, Yanyu Xu, Zijing Xu, Xuemeng Yang, Quanwei Li, Zimeng Shang, Zhiyun Yang, Zhong Xu, Jiabo Wang, Enxiang Zhang, Xinhua Song","doi":"10.1186/s12575-025-00286-1","DOIUrl":"10.1186/s12575-025-00286-1","url":null,"abstract":"<p><p>BACKGROUND: Hepatocellular carcinoma (HCC) is the most prevalent primary liver malignancy, contributing significantly to global mortality due to limited therapeutic options. Programmed cell death (PCD) and metabolism are key cancer hallmarks, influencing tumor progression and treatment response. However, their association in HCC remains insufficiently characterized. METHODS: We utilized single-cell and bulk transcriptomic datasets to identify differentially expressed genes (DEGs) strongly associated with PCD and metabolism in HCC. Based on prognosis-related DEGs, patients and cells were stratified into high- and low-expression groups using corresponding computational algorithms. The intersecting DEGs from both datasets were analyzed using univariate Cox regression, and a prognostic risk score model was constructed through machine learning algorithms. The model was subsequently evaluated in the context of the immune microenvironment and its relevance to immunotherapeutic responses. Drug repurposing was pursued by integrating machine learning, deep learning, and molecular docking strategies to uncover potential therapeutic options. In parallel, consensus clustering analysis was performed to assess the grouping efficiency of the model-associated genes. Lastly, the expression of the model genes was evaluated in HCC mouse models and cell lines, and the biological function of a representative gene was further investigated through in vitro assays. RESULTS: We developed an 18-gene signature based on PCD and metabolism with strong predictive value for overall survival (OS) in HCC patients. Malignant cells with high PCD-Metabolism scores may promote HCC progression by influencing immune infiltration, fibroblast differentiation, and cancer-related pathways. The model also correlated with immunotherapy sensitivity. Leveraging a drug repurposing strategy guided by the PCD-Metabolism model, we identified triazolothiadiazine and fluvastatin as promising compounds targeting RCN2 and CDK4, respectively. Clustering analysis identified two HCC subtypes (C1 and C2), and the subtype enriched with high-risk patients was associated with inferior OS. Notably, CCT3, a key gene in the model, was enriched in tumor regions, and its silencing was found to inhibit the proliferation and migration of HCC cells while regulating ferroptosis- and autophagy-related markers. CONCLUSION: Our study established a PCD-Metabolism-based prognostic model for HCC, offering insights into disease biology and potential avenues for personalized therapy. </p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"27 1","pages":"29"},"PeriodicalIF":4.9,"publicationDate":"2025-08-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12335101/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144811681","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":"Comprehensive Insights into APOBEC Mutations in Thyroid Cancer: Prognostic and Therapeutic Discoveries.","authors":"Wei Luo, Feng Liu, Mengyu Li, Jialong Yu, Ziyun Liu, Xuan Cheng, Yue Huang, Yu Liu, Mei Tao, Yuqi Wang, Yiping Zou, Xiaobin Shang, Chao Yang, Xianhui Ruan, Yanchao Qin, Xiangqian Zheng","doi":"10.1186/s12575-025-00288-z","DOIUrl":"10.1186/s12575-025-00288-z","url":null,"abstract":"<p><strong>Background: </strong>The APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like) family plays a vital mutagenic role in diverse human malignancies. Nevertheless, the biological characteristics of APOBEC family members and their clinical significance in cancer have not been comprehensively explored. Our primary objective was to characterize the distribution and clinical relevance of APOBEC family members and their mutations across multiple cancer types, with a particular focus on thyroid carcinoma (THCA).</p><p><strong>Methods: </strong>In this study, we employed an integrated, multi-faceted approach combining diverse statistical and bioinformatics methods. Data sources included whole-exome sequencing (WES), targeted next-generation sequencing (NGS), bulk RNA sequencing (RNA-seq), single-cell RNA sequencing (scRNA-seq), Western blot assays, drug sensitivity analyses, and in vivo animal models.</p><p><strong>Results: </strong>APOBEC mutations occupy a significant position in the mutation landscape of THCA. High APOBEC mutation enrichment scores were strongly associated with poor prognosis, immune evasion, and increased risk of malignant progression in THCA patients. These mutations contribute to tumor advancement and influence cellular differentiation within the tumor microenvironment. Additionally, we developed a prognostic APOBEC mutagenesis model using machine learning, which was validated across multiple THCA cohorts. In vitro and in vivo experiments demonstrated that APOBEC2 inhibition effectively suppressed tumor proliferation, metastasis, and glycolytic activity, while simultaneously enhancing immune activation and boosting the efficacy of immune checkpoint inhibitors.</p><p><strong>Conclusion: </strong>Our study systematically characterizes APOBEC mutations across various cancer types and underscores their promise as biomarkers for aggressive tumor phenotypes, prognostic assessment, and immunotherapy response to THCA. These findings were accomplished through multi-omics sequencing and validated through comprehensive in vitro and in vivo experiments.</p>","PeriodicalId":8960,"journal":{"name":"Biological Procedures Online","volume":"27 1","pages":"28"},"PeriodicalIF":4.3,"publicationDate":"2025-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12297793/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144717380","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}