Yingwu Chen, Kai Chen, Xinqiang Zhu, Xiaoli Wang, Feifan Leng, Yonggang Wang
{"title":"Effect of Different Diet Formulas on Production Performance and Rumen Bacterial Diversity of Fattening Beef Cattle.","authors":"Yingwu Chen, Kai Chen, Xinqiang Zhu, Xiaoli Wang, Feifan Leng, Yonggang Wang","doi":"10.1007/s12033-025-01402-y","DOIUrl":"https://doi.org/10.1007/s12033-025-01402-y","url":null,"abstract":"<p><p>The effect of beef cattle (Angus vs. Simmental) feeds with various diet formulas on the production performance, blood biochemical indexes, beef quality, and rumen bacterial diversity were investigated. Corn silage, sorghum silage, and the mixture of corn silage and sorghum silage were used as experimental materials to compare the feeding effect of different proportions of feed. The results showed that fattening cattle fed diets containing 75% or 100% sweet sorghum (DMD and DME) had a daily gain of 0.85-0.92 kg. The fattening rate of cattle fed with 50% sweet sorghum (DMC) was 54.78%. There were no adverse effects on beef quality and blood physiological and biochemical indexes in each group. In terms of rumen bacterial diversity, the flora of rumen fluid mainly contains Firmicutes and Bacteroidetes. Prevotella and Succinic acid were the dominant groups in the known genera of rumen fluid bacteria. Compared with the cattle fed with corn silage alone, the growth performance, slaughter performance, blood physicochemical indexes, and rumen diversity of cattle fed with mixed silage of sweet sorghum and corn showed similar or excellent traits.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586306","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Evolving Landscape of Emerging Virus Diagnosis: Challenges and Innovations.","authors":"Anoop Kumar, Supriya Saini, Anupkumar Anvikar, Neelima Mishra, Gauri Misra","doi":"10.1007/s12033-025-01385-w","DOIUrl":"https://doi.org/10.1007/s12033-025-01385-w","url":null,"abstract":"<p><p>Emerging and re-emerging viruses (like Spanish flu, SARS-CoV-2, etc.) have substantially impacted global public health since the early twentieth century. These outbreaks are unpredictable and novel viruses are difficult to understand due to emerging variations. Advanced virology and diagnostic technologies have revolutionized viral diagnostics, enabling accurate early identification and successful treatment and containment. Next-generation sequencing (NGS) technologies, such as metagenomics and whole-genome sequencing, have played a crucial role in the detection and monitoring of emerging viruses, such as SARS-CoV-2 and its variants. Advanced diagnostic methods, such as digital PCR, CRISPR-based tools, and serological techniques like ELISA, enhance viral detection's sensitivity, specificity, and speed. Research has shown that innovations such as lateral flow immunoassays, biosensors, and aptamers have the potential to significantly enhance diagnostic accuracy in various fields. The integration of AI in diagnostics aids researchers in understanding viral evolution and outbreak management, offering new avenues for rapid response. This review aims to examine the latest advancements in virus diagnosis technologies, identify unresolved accuracy and detection issues, and discuss emerging ideas that are transforming the future of viral diagnostics. It is important to improve early identification, rendering the system more cost-effective and adaptable to new viral threats.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143557343","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Biogenic Nickel Oxide Nanoparticles: Synthesis, Characterization and Biomedical Potential.","authors":"Akankshya Dash, Chinnasamy Ragavendran, Ranjith Rajendran","doi":"10.1007/s12033-025-01413-9","DOIUrl":"https://doi.org/10.1007/s12033-025-01413-9","url":null,"abstract":"<p><p>Green-synthesized nanoparticles provide an eco-friendly approach to nanotechnology, reducing harmful chemical use and environmental impact. This study focuses on the green synthesis of nickel oxide nanoparticles (FV-NiO NPs) using Fioria vitifolia. Synthesized NPs were characterization by UV, XRD, FTIR, SEM, and TEM revealed spherical, well-dispersed particles (17-168 nm) with a UV-Visible absorption peak at 247 nm. EDAX analysis confirmed their composition: 55.02% Ni, 22.77% O, 18.49% C, and 3.71% Na. FV-NiO NPs exhibited potent antibacterial activity at 100 µg/mL against Escherichia coli (21.1 ± 0.2 mm inhibition) and Enterococcus faecalis (24.6 ± 0.5 mm inhibition). Furthermore, anti-inflammatory activity showed 68.3% inhibition at 200 µg/mL, while antioxidant assays demonstrated 78.64% DPPH and 68.21% ABTS inhibition at 100 µg/mL. Antitumour assays revealed an IC<sub>50</sub> of 28.15 µg/mL against A549 lung cancer cells. Photocatalytic studies indicated 88.9% degradation efficiency of Reactive Black 5 dye under visible light. Zebrafish embryo assays demonstrated dose-dependent toxicity, influencing body length, heart rate, hatchability, and survival rates, confirming the nanoparticles' biosafety. These results highlight FV-NiO NPs as promising candidates for biomedical and environmental applications.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143557342","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Expression of Serum Inflammatory Factors in Patients with Acute Ischemic Stroke Complicated with Type 2 Diabetes Mellitus and Its Relationship with the Formation and Stability of Carotid Atherosclerotic Plaque.","authors":"Xia Chen, Juan Li, Fang Zhang, Ruixia Wang","doi":"10.1007/s12033-025-01405-9","DOIUrl":"https://doi.org/10.1007/s12033-025-01405-9","url":null,"abstract":"<p><p>To explore the stability of carotid plaques and their relationship with biomarkers in patients with acute ischemic stroke (AIS) complicated with type 2 diabetes mellitus (T2DM). A retrospective analysis was conducted on 160 cases of AIS patients with T2DM. They were divided into plaque group, intima thickening group (CG), and normal intima group (DG). 95 plaque patients were grouped: stable plaque group (AG) and unstable plaque group (BG). Serum indicators and carotid intima-media thickness (IMT) were collated, and Pearson correlation analysis (PCA) and multiple logistic regression analysis (MLRA) were performed. As against CG, AG and BG had higher levels of high-sensitivity C-reactive protein (hs-CRP), homocysteine (HCY), and IMT (P < 0.05). The carotid IMT in patients suggested an obvious positive correlation with hs-CRP and HCY (P < 0.001). Hs-CRP and HCY had an obvious positive impact on the formation of carotid plaques; as against AG, BG had higher levels of hs-CRP, HCY, total cholesterol (TC), and IMT (P < 0.05). The stability of patients' carotid arteries suggested an obvious positive correlation with hs-CRP and TC (P < 0.05), and HCY (P < 0.001). The levels of hs-CRP, TC, and HCY had an obvious positive impact on the IMT of patients (P < 0.05). High levels of hs-CRP, TC, and HCY have a positive impact on the stability of carotid plaques and are independent risk factors for plaque instability.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":""},"PeriodicalIF":2.4,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143542731","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Molecular BiotechnologyPub Date : 2025-03-01Epub Date: 2024-03-06DOI: 10.1007/s12033-024-01107-8
Fanhao Kong, Siwen Yang, Ruimeng Shi, Yanyu Peng
{"title":"The Up-Regulated Expression of Mitochondrial Membrane Molecule RHOT1 in Gastric Cancer Predicts the Prognosis of Patients and Promotes the Malignant Biological Behavior of Cells.","authors":"Fanhao Kong, Siwen Yang, Ruimeng Shi, Yanyu Peng","doi":"10.1007/s12033-024-01107-8","DOIUrl":"10.1007/s12033-024-01107-8","url":null,"abstract":"<p><p>Gastric cancer (GC) remains a major disease of high morbidity and mortality worldwide despite advances in diagnosis and treatment. Ras homolog family member T1 (RHOT1) plays an important role in several cancers. Our study aimed to analyze RHOT1 expression, to assess the relationship between its expression and the prognosis of patients, and know the impact of RHOT1 on GC cells. The Cancer Genome Atlas (TCGA) RNA-seq data was used for gene expression analysis, survival and prognostic analysis. Nomograms were created to analyze the pathological factors of GC patients. RHOT1 expression was up-regulated by analyzed TCGA-Stomach adenocarcinoma (STAD) data and verified by Polymerase Chain Reaction (PCR) assay in GC tissues and cell lines. Furthermore, RHOT1 up-regulation was significantly associated with shorter survival of GC patients. At last, after silencing the expression of RHOT1 in AGS cell lines, we found that the proliferative ability of the cells was significantly reduced, the cell invasion ability was significantly inhibited, the cell migration ability was also significantly weakened, the cell cycle was arrested in the G0/G1 phase, and apoptosis was significantly increased. So RHOT1 could impact the apoptosis, proliferation, invasion, and migration behavior of GC cells. We trust RHOT1 has the potential to become a new oncogene biomarker for diagnosis and prognosis as well as a new therapeutic target in GC.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"1095-1108"},"PeriodicalIF":2.4,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140049931","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"The Interplay Between Epilepsy and Parkinson's Disease: Gene Expression Profiling and Functional Analysis.","authors":"Xiaolong Wu, Kailiang Wang, Jingjing Wang, Penghu Wei, Huaqiang Zhang, Yanfeng Yang, Yinchun Huang, Yihe Wang, Wenli Shi, Yongzhi Shan, Guoguang Zhao","doi":"10.1007/s12033-024-01103-y","DOIUrl":"10.1007/s12033-024-01103-y","url":null,"abstract":"<p><p>The results of many epidemiological studies suggest a bidirectional causality may exist between epilepsy and Parkinson's disease (PD). However, the underlying molecular landscape linking these two diseases remains largely unknown. This study aimed to explore this possible bidirectional causality by identifying differentially expressed genes (DEGs) in each disease as well as their intersection based on two respective disease-related datasets. We performed enrichment analyses and explored immune cell infiltration based on an intersection of the DEGs. Identifying a protein-protein interaction (PPI) network between epilepsy and PD, and this network was visualised using Cytoscape software to screen key modules and hub genes. Finally, exploring the diagnostic values of the identified hub genes. NetworkAnalyst 3.0 and Cytoscape software were also used to construct and visualise the transcription factor-micro-RNA regulatory and co-regulatory networks, the gene-microRNA interaction network, as well as gene-disease association. Based on the enrichment results, the intersection of the DEGs mainly revealed enrichment in immunity-, phosphorylation-, metabolism-, and inflammation-related pathways. The boxplots revealed similar trends in infiltration of many immune cells in epilepsy and Parkinson's disease, with greater infiltration in patients than in controls. A complex PPI network comprising 186 nodes and 512 edges were constructed. According to node connection degree, top 15 hub genes were considered the kernel targets of epilepsy and PD. The area under curve values of hub gene expression profiles confirmed their excellent diagnostic values. This study is the first to analyse the molecular landscape underlying the epidemiological link between epilepsy and Parkinson's disease. The two diseases are closely linked through immunity-, inflammation-, and metabolism-related pathways. This information was of great help in understanding the pathogenesis, diagnosis, and treatment of the diseases. The present results may provide guidance for further in-depth analysis about molecular mechanisms of epilepsy and PD and novel potential targets.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"1035-1053"},"PeriodicalIF":2.4,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140059953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Molecular BiotechnologyPub Date : 2025-03-01Epub Date: 2024-03-15DOI: 10.1007/s12033-024-01120-x
Nagesh Kishan Panchal, Poorva Samdani, Tiasa Sengupta, Sabina Evan Prince
{"title":"Computational Analysis of Non-synonymous SNPs in ATM Kinase: Structural Insights, Functional Implications, and Inhibitor Discovery.","authors":"Nagesh Kishan Panchal, Poorva Samdani, Tiasa Sengupta, Sabina Evan Prince","doi":"10.1007/s12033-024-01120-x","DOIUrl":"10.1007/s12033-024-01120-x","url":null,"abstract":"<p><p>Ataxia telangiectasia-mutated (ATM) protein kinase, a key player in cellular integrity regulation, is known for its role in DNA damage response. This study investigates the broader impact of ATM on cellular processes and potential clinical manifestations arising from mutations, aiming to expand our understanding of ATM's diverse functions beyond conventional roles. The research employs a comprehensive set of computational techniques for a thorough analysis of ATM mutations. The mutation data are curated from dbSNP and HuVarBase databases. A meticulous assessment is conducted, considering factors such as deleterious effects, protein stability, oncogenic potential, and biophysical characteristics of the identified mutations. Conservation analysis, utilizing diverse computational tools, provides insights into the evolutionary significance of these mutations. Molecular docking and dynamic simulation analyses are carried out for selected mutations, investigating their interactions with Y2080D, AZD0156, and quercetin inhibitors to gauge potential therapeutic implications. Among the 419 mutations scrutinized, five (V1913C, Y2080D, L2656P, C2770G, and C2930G) are identified as both disease causing and protein destabilizing. The study reveals the oncogenic potential of these mutations, supported by findings from the COSMIC database. Notably, Y2080D is associated with haematopoietic and lymphoid cancers, while C2770G shows a correlation with squamous cell carcinomas. Molecular docking and dynamic simulation analyses highlight strong binding affinities of quercetin for Y2080D and AZD0156 for C2770G, suggesting potential therapeutic options. In summary, this computational analysis provides a comprehensive understanding of ATM mutations, revealing their potential implications in cellular integrity and cancer development. The study underscores the significance of Y2080D and C2770G mutations, offering valuable insights for future precision medicine targeting-specific ATM. Despite informative computational analyses, a significant research gap exists, necessitating essential in vitro and in vivo studies to validate the predicted effects of ATM mutations on protein structure and function.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"1201-1221"},"PeriodicalIF":2.4,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140137036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Molecular BiotechnologyPub Date : 2025-03-01Epub Date: 2024-03-09DOI: 10.1007/s12033-024-01112-x
Dongjuan Chen, Jun Yang, Ting Zhang, Xuemei Li, Qiliang Xiong, Shaofeng Jiang, Chen Yi
{"title":"Mechanistic Investigation of Calcium Channel Regulation-Associated Genes in Pulmonary Arterial Hypertension and Signatures for Diagnosis.","authors":"Dongjuan Chen, Jun Yang, Ting Zhang, Xuemei Li, Qiliang Xiong, Shaofeng Jiang, Chen Yi","doi":"10.1007/s12033-024-01112-x","DOIUrl":"10.1007/s12033-024-01112-x","url":null,"abstract":"<p><p>Pulmonary arterial hypertension (PAH) is a severe cardiopulmonary disorder with complex causes. Calcium channel blockers have long been used in its treatment. Our study aimed to validate experimental results showing increased calcium ion concentration in PAH patients. We investigated the impact of genes related to calcium channel regulation on PAH development and developed an accurate diagnostic model. Clinical trial data from serum of 18 healthy individuals and 18 patients with PAH were retrospectively analyzed. Concentrations of calcium and potassium ions were determined and compared. Datasets were retrieved, selecting genes associated with calcium ion release. R packages processed the datasets, filtering 174 common genes, and conducting Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses. Six hub genes were identified, and nomogram and logistic regression prediction models were constructed. Random forest filtered cross genes, and a diagnostic model was developed and validated using an artificial neural network. The 174 intersection genes related to calcium ions showed significant correlations with biological processes, cellular components, and molecular functions. Six key genes were obtained by constructing a protein-protein interaction network. A diagnostic model with high accuracy (> 90%) and diagnostic capability (AUC = 0.98) was established using a neural network algorithm. This study validated the experimental results, identified key genes associated with calcium ions, and developed a highly accurate diagnostic model using a neural network algorithm. These findings provide insights into the role of calcium release genes in PAH and demonstrate the potential of the diagnostic model for clinical application. However, due to limitations in sample size and a lack of prognosis data, the regulatory mechanisms of calcium ions in PAH patients and their impact on the clinical prognosis of PAH patients still need further exploration in the future.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"1122-1136"},"PeriodicalIF":2.4,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140068524","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Molecular BiotechnologyPub Date : 2025-03-01Epub Date: 2024-03-15DOI: 10.1007/s12033-024-01110-z
Taewon Yang, Hyunjoo Hwang, Kibum Kim, Yerin Kim, Richard D Cummings, Yong Kyoo Shin, Taejin Lee, Kisung Ko
{"title":"Plant-Produced Therapeutic Crizanlizumab Monoclonal Antibody Binds P-Selectin to Alleviate Vaso-occlusive Pain Crises in Sickle Cell Disease.","authors":"Taewon Yang, Hyunjoo Hwang, Kibum Kim, Yerin Kim, Richard D Cummings, Yong Kyoo Shin, Taejin Lee, Kisung Ko","doi":"10.1007/s12033-024-01110-z","DOIUrl":"10.1007/s12033-024-01110-z","url":null,"abstract":"<p><p>Sickle Cell Disease (SCD) is a severe genetic disorder causing vascular occlusion and pain by upregulating the adhesion molecule P-selectin on endothelial cells and platelets. It primarily affects infants and children, causing chronic pain, circulatory problems, organ damage, and complications. Thus, effective treatment and management are crucial to reduce SCD-related risks. Anti-P-selectin antibody Crizanlizumab (Crimab) has been used to treat SCD. In this study, the heavy and light chain (HC and LC) genes of anti-P-Selectin antibody Crimab were cloned into a plant expression binary vector. The HC gene was under control of the duplicated 35S promoter and nopaline synthase (NOS) terminator, whereas the LC gene was under control of the potato proteinase inhibitor II (PIN2) promoter and PIN2 terminator. Agrobacterium tumefaciens LBA4404 was used to transfer the genes into the tobacco (Nicotiana tabacum cv. Xanthi) plant. In plants the genomic PCR and western blot confirmed gene presence and expression of HC and LC Crimab proteins in the plant, respectively. Crimab was successfully purified from transgenic plant leaf using protein A affinity chromatography. In ELISA, plant-derived Crimab (Crimab<sup>P</sup>) had similar binding activity to P-selectin compared to mammalian-derived Crimab (Crimab<sup>M</sup>). In surface plasmon resonance, the K<sub>D</sub> (dissociation binding constant) and response unit values were lower and higher than Crimab<sup>P</sup>, respectively. Taken together, these results demonstrate that the transgenic plant can be applied to produce biofunctional therapeutic monoclonal antibody.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"834-844"},"PeriodicalIF":2.4,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140140479","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Molecular BiotechnologyPub Date : 2025-03-01Epub Date: 2024-03-21DOI: 10.1007/s12033-024-01114-9
Tingting Liu, Wen Ji, Xue Cheng, Lin Lv, Xiaohui Yu, Na Wang, Mengcong Li, Tinghua Hu, Zhihong Shi
{"title":"Revealing a Novel Methylated Integrin Alpha-8 Related to Extracellular Matrix and Anoikis Resistance Using Proteomic Analysis in the Immune Microenvironment of Lung Adenocarcinoma.","authors":"Tingting Liu, Wen Ji, Xue Cheng, Lin Lv, Xiaohui Yu, Na Wang, Mengcong Li, Tinghua Hu, Zhihong Shi","doi":"10.1007/s12033-024-01114-9","DOIUrl":"10.1007/s12033-024-01114-9","url":null,"abstract":"<p><p>Genomic epigenetics of extracellular matrix (ECM) play an important role in lung adenocarcinoma (LUAD). Our study identified a signature of potential prognostic genes associated with ECM and constructed immune risk-related prognosis model in LUAD. We downloaded mRNAs transcriptome data, miRNAs expression data, and clinical patient information for LUAD based on The Cancer Genome Atlas. \"Limma, clusterProfiler, ggplot2\" R packages and GSEA were used to analyze meaningful genes and explore potential biological function. A competing endogenous RNA network was constructed to reveal the mechanism of ECM-related genes. Combined with clinical LUAD patients' characteristics, univariate and multivariate Cox regression analyses were used to build prognostic immune risk model. Next, we calculated AUC value of ROC curve, and explored survival probability of different risk groups. A total of 2966 mRNAs were differently expressed in LUAD samples and normal samples. Function enrichment analyses proved mRNAs were associated with many tumor pathways, such as cell adhesion, vascular smooth muscle contraction, and cell cycle. There were 18 mRNAs related to ECM receptor signaling pathway, and 7 mRNAs expressions were correlated with EGFR expression, but only 5mRNAs were associated with the long-term prognosis. Based on Integrin alpha-8 (ITGA8) molecule, we identified potential 3 miRNAs from several databases. The promoter of ITGA8 was higher-methylated and lower-expressed in LUAD. And lower-expressed group has poor prognosis for patients. 66 immunomodulators related to ITGA8 were performed to construct immune correlation prediction model (p < 0.05). Comprehensive analyses of ITGA8 revealed it combined focal adhesion kinase to activate PI3K/AKT signaling pathway to influence the occurrence and development of LUAD. A novel immune prognostic model about ITGA8 was constructed and verified in LUAD patients. Combined with non-coding genes and genomic epigenetics, identification of potential biomarkers provided new light on therapeutic strategy for clinical patients.</p>","PeriodicalId":18865,"journal":{"name":"Molecular Biotechnology","volume":" ","pages":"1137-1155"},"PeriodicalIF":2.4,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140184879","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}