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Lack of significant ganglioside changes in Slc17a5 heterozygous mice: Relevance to FSASD and Parkinson's disease Slc17a5杂合小鼠缺乏显著神经节苷脂改变:与fssd和帕金森病相关
IF 2.3
Biochemistry and Biophysics Reports Pub Date : 2025-03-14 DOI: 10.1016/j.bbrep.2025.101979
Marya S. Sabir , Mahin S. Hossain , Laura Pollard , Marjan Huizing , William A. Gahl , Frances M. Platt , May Christine V. Malicdan
{"title":"Lack of significant ganglioside changes in Slc17a5 heterozygous mice: Relevance to FSASD and Parkinson's disease","authors":"Marya S. Sabir ,&nbsp;Mahin S. Hossain ,&nbsp;Laura Pollard ,&nbsp;Marjan Huizing ,&nbsp;William A. Gahl ,&nbsp;Frances M. Platt ,&nbsp;May Christine V. Malicdan","doi":"10.1016/j.bbrep.2025.101979","DOIUrl":"10.1016/j.bbrep.2025.101979","url":null,"abstract":"<div><div>Large population-based studies of Parkinson's disease (PD) have identified susceptibility genes, including <em>SLC17A5</em>. Biallelic mutations in <em>SLC17A5</em>, encoding the lysosomal sialic acid transporter sialin, cause the rare neurodegenerative disease, free sialic acid storage disorder (FSASD). To explore a potential biochemical link between FSASD and PD, we investigated ganglioside concentrations in a novel mouse model harboring the <em>Slc17a5</em> p.Arg39Cys (p.R39C) variant. Our analysis revealed no significant alterations in ganglioside concentrations in heterozygous p.R39C mice, warranting further studies into other potential links between PD and sialin defects.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 101979"},"PeriodicalIF":2.3,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143619880","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Eco-friendly synthesis of copper nanoparticles by using Ralstonia sp. and their antibacterial, anti-biofilm, and antivirulence activities 利用Ralstonia sp.环保合成铜纳米颗粒及其抗菌、抗生物膜和抗毒活性
IF 2.3
Biochemistry and Biophysics Reports Pub Date : 2025-03-13 DOI: 10.1016/j.bbrep.2025.101978
Narges Vakili , Morahem Ashengroph , Aram Sharifi , Musa Moetasam Zorab
{"title":"Eco-friendly synthesis of copper nanoparticles by using Ralstonia sp. and their antibacterial, anti-biofilm, and antivirulence activities","authors":"Narges Vakili ,&nbsp;Morahem Ashengroph ,&nbsp;Aram Sharifi ,&nbsp;Musa Moetasam Zorab","doi":"10.1016/j.bbrep.2025.101978","DOIUrl":"10.1016/j.bbrep.2025.101978","url":null,"abstract":"<div><div>Biosynthesized nanoparticles (NPs) created through environmentally friendly and low-toxicity methods show great potential for various nanotechnology applications. In particular, copper nanoparticles (Cu-NPs) are promising for medical uses. This study aims to explore the eco-friendly synthesis of Cu-NPs and their potential as a novel strategy to combat antimicrobial resistance. Cu-NPs were synthesized using <em>Ralstonia</em> sp. KF264453 and characterized with techniques including ultraviolet–visible (UV–Vis) spectroscopy, field emission scanning electron microscopy (FESEM), energy dispersive X-ray spectroscopy (EDX), dynamic light scattering (DLS), zeta potential analysis, X-ray diffraction (XRD), and Fourier transform infrared spectroscopy (FT-IR). The antibacterial properties of the NPs and their synergistic effects with common antibiotics were assessed. The study also investigated their impact on bacterial cell membrane disruption, biofilm formation, efflux pump activity, and motility. UV–Vis analysis indicated a significant absorption peak at 552 nm, confirming surface plasmon resonance (SPR) for Cu-NPs. FESEM images revealed predominantly spherical NPs with an average size of 69.7 nm. DLS measurements indicated a hydrodynamic diameter of 78.2 nm due to stabilizing biomolecules. A zeta potential of −5.1 mV suggested moderate colloidal stability, suitable for short-term biomedical applications. XRD analysis confirmed a face-centered cubic (FCC) crystalline structure with an average crystallite size of 45 nm. FT-IR spectra detected functional groups, indicating that proteins, carbohydrates, lipids, and amino acids may have contributed to the synthesis and stabilization of the NPs. Cu-NPs showed notable antibacterial efficacy, with minimum inhibitory concentrations (MIC) between 0.625 and 5 μg/mL and minimum bactericidal concentrations (MBC) ranging from 5 to 20 μg/mL. They improved the effectiveness of penicillin and cefixime, enhanced membrane permeability, inhibited biofilm formation, disrupted efflux pump activity in <em>Staphylococcus aureus</em> SA-1199B, and decreased swarming motility in <em>Pseudomonas aeruginosa</em>. Cu-NPs demonstrate strong antimicrobial activity, inhibit biofilm formation and efflux pump function, and enhance the effectiveness of conventional antibiotics. While they show promise in combating antimicrobial resistance, further research is needed to assess their clinical potential and safety for medical use.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 101978"},"PeriodicalIF":2.3,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143610945","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Hsa-miR-31-3p targets CLDN8 to compromise skin barrier integrity in psoriasis Hsa-miR-31-3p靶向CLDN8损害牛皮癣皮肤屏障完整性
IF 2.3
Biochemistry and Biophysics Reports Pub Date : 2025-03-13 DOI: 10.1016/j.bbrep.2025.101976
Yunhua Tu , Li Wang , Lijun An , Li He
{"title":"Hsa-miR-31-3p targets CLDN8 to compromise skin barrier integrity in psoriasis","authors":"Yunhua Tu ,&nbsp;Li Wang ,&nbsp;Lijun An ,&nbsp;Li He","doi":"10.1016/j.bbrep.2025.101976","DOIUrl":"10.1016/j.bbrep.2025.101976","url":null,"abstract":"<div><div>Skin barrier dysfunction in psoriasis has emerged as a significant concern, yet the underlying molecular mechanisms remain incompletely understood. This study investigates the role of hsa-miR-31-3p in regulating skin barrier function through its interaction with claudin-8 (CLDN8) in psoriasis. Through analysis of clinical samples and public datasets, we observed significantly impaired skin barrier function in psoriasis patients, characterized by increased transepidermal water loss and decreased stratum corneum hydration. Notably, CLDN8 expression was markedly downregulated in psoriatic lesions, while hsa-miR-31-3p levels were elevated. Bioinformatics analysis and molecular studies revealed that hsa-miR-31-3p directly targets the 3′UTR of CLDN8, leading to its downregulation. In vitro experiments demonstrated that both CLDN8 knockdown and hsa-miR-31-3p overexpression compromised the permeability barrier in keratinocytes. Furthermore, in an imiquimod-induced psoriasis mouse model, administration of mmu-miR-31-3p antagomir effectively ameliorated skin barrier damage, reduced inflammatory manifestations, and restored CLDN8 expression. These findings unveil a novel mechanism whereby hsa-miR-31-3p regulates skin barrier function through CLDN8 in psoriasis, suggesting potential therapeutic strategies targeting this pathway for psoriasis treatment.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 101976"},"PeriodicalIF":2.3,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143610944","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
In silico studies to understand the interactions of flavonoid inhibitor with nsp12-RNA dependent RNA polymerase of SARS-CoV-2 and its homologs 了解类黄酮抑制剂与SARS-CoV-2及其同源物的nsp12-RNA依赖性RNA聚合酶相互作用的计算机研究
IF 2.3
Biochemistry and Biophysics Reports Pub Date : 2025-03-13 DOI: 10.1016/j.bbrep.2025.101975
Shamiya Anwar Kizhakkiniyakath, Tejaswini Choudhury, Madhan Vishal Rajan, Sagar Rathee, Basant Meena , Gururao Hariprasad
{"title":"In silico studies to understand the interactions of flavonoid inhibitor with nsp12-RNA dependent RNA polymerase of SARS-CoV-2 and its homologs","authors":"Shamiya Anwar Kizhakkiniyakath,&nbsp;Tejaswini Choudhury,&nbsp;Madhan Vishal Rajan,&nbsp;Sagar Rathee,&nbsp;Basant Meena ,&nbsp;Gururao Hariprasad","doi":"10.1016/j.bbrep.2025.101975","DOIUrl":"10.1016/j.bbrep.2025.101975","url":null,"abstract":"<div><h3>Aim</h3><div>COVID 19 continues to be a major health concern. RNA dependent RNA polymerase of <em>SARS-CoV-2</em> which is crucial for replication is therefore a potential drug target.</div></div><div><h3>Methodology</h3><div>Based on experimental structures of RdRp from <em>SARS-CoV-2</em>, computational models were generated of its homologs from <em>SARS-C</em><em>o</em><em>V-1</em>, <em>MERS</em> and <em>Bat</em>. <em>SARS CoV-2</em> RdRp was used for virtual screening at nucleotide binding site with molecule from COCONUT Natural Products database using Glide. Complexes with the top inhibitor molecule were modelled using Discovery Studio and Desmond suite of programs.</div></div><div><h3>Results</h3><div><em>SARS-CoV-2</em> RdRp has a minimum of 80 % sequence similarity with its homologs, with the secondary structural elements, catalytic residues and metal binding residues being conserved. Certain residue variations in <em>SARS-CoV-2</em> RdRp seems to be responsible for the stability of the enzyme. Docking and simulation studies showed that a flavonoid molecule with Coconut ID: CNP0127177.0 (HHF318) has binding affinity in low nano-molar range against RdRp from <em>SARS-CoV-2</em> which was comparable or better than currently used inhibitors. This affinity stems from cationic-π with Arg555, and π-stacking interactions with a nucleobase of RNA. Molecule also engages with other residues that are crucial for its functions. This flavonoid molecule has similar physio-chemical properties like ATP towards <em>SARS-CoV-2</em> RdRp, and has low potency for human ATP binding proteins.</div></div><div><h3>Conclusion</h3><div>HHF318 is a potential inhibitor of <em>SARS-CoV-2</em> RdRp with good potency, specificity and pharmacokinetic properties for it to be developed as a drug candidate for COVID19.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 101975"},"PeriodicalIF":2.3,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143619887","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Epigenome editing-mediated restoration of FBN1 expression by demethylation of CpG island shore in porcine fibroblasts 表观基因组编辑介导的猪成纤维细胞CpG岛岸去甲基化恢复FBN1表达
IF 2.3
Biochemistry and Biophysics Reports Pub Date : 2025-03-11 DOI: 10.1016/j.bbrep.2025.101973
Rio Miyadai , Shiori Hinata , Yuya Amemiya , Satori Shigematsu , Kazuhiro Umeyama , Hiroshi Nagashima , Kenji Yamatoya , Jun Ohgane
{"title":"Epigenome editing-mediated restoration of FBN1 expression by demethylation of CpG island shore in porcine fibroblasts","authors":"Rio Miyadai ,&nbsp;Shiori Hinata ,&nbsp;Yuya Amemiya ,&nbsp;Satori Shigematsu ,&nbsp;Kazuhiro Umeyama ,&nbsp;Hiroshi Nagashima ,&nbsp;Kenji Yamatoya ,&nbsp;Jun Ohgane","doi":"10.1016/j.bbrep.2025.101973","DOIUrl":"10.1016/j.bbrep.2025.101973","url":null,"abstract":"<div><div>Fibrillin-1, an extracellular matrix protein encoded by the <em>FBN1</em> gene, is crucial for maintaining connective tissue integrity. Mutations in <em>FBN1</em> result in haploinsufficiency, leading to Marfan syndrome, in which the expression of functional <em>FBN1</em> is correlated with disease onset and severity. Recent studies suggest that <em>FBN1</em> expression is modulated by DNA methylation, particularly within the CpG island shores of its promoter region. In porcine models, <em>FBN1</em> mRNA levels have been found to correlate with the proportion of hypomethylated alleles in the CpG island shore region. In this study, we employed epigenome editing using the dCas9-TET1 system to induce targeted DNA demethylation within the <em>FBN1</em> CpG island shore, which became hypermethylated after a prolonged culture of porcine fetal fibroblast cells. This approach effectively reduced methylation in the targeted region, and cells expressing the dCas9-TET1 system maintained hypomethylation across multiple passages. Critically, DNA demethylation of the <em>FBN1</em> CpG island shore restored <em>FBN1</em> expression in heterozygous <em>FBN1</em> knockout fibroblasts, which developed stochastic hypermethylation after extended culture. These findings highlight the potential of DNA methylation manipulation to restore <em>FBN1</em> expression in cells with a haploinsufficient genetic background.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 101973"},"PeriodicalIF":2.3,"publicationDate":"2025-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143593789","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Characterization of lncRNA-protein interactions associated with Prostate cancer and Androgen receptors by molecular docking simulations 通过分子对接模拟表征lncrna与前列腺癌和雄激素受体相关的蛋白相互作用
IF 2.3
Biochemistry and Biophysics Reports Pub Date : 2025-03-09 DOI: 10.1016/j.bbrep.2025.101959
Barkha Khilwani , Bhumandeep Kour , Nidhi Shukla , Sugunakar Vuree , Abdul S. Ansari , Nirmal K. Lohiya , Prashanth Suravajhala , Renuka Suravajhala
{"title":"Characterization of lncRNA-protein interactions associated with Prostate cancer and Androgen receptors by molecular docking simulations","authors":"Barkha Khilwani ,&nbsp;Bhumandeep Kour ,&nbsp;Nidhi Shukla ,&nbsp;Sugunakar Vuree ,&nbsp;Abdul S. Ansari ,&nbsp;Nirmal K. Lohiya ,&nbsp;Prashanth Suravajhala ,&nbsp;Renuka Suravajhala","doi":"10.1016/j.bbrep.2025.101959","DOIUrl":"10.1016/j.bbrep.2025.101959","url":null,"abstract":"<div><div>Long non-coding RNA (lncRNAs) are known to be implicated in pathogenesis of a broad spectrum of malignancies. These are found to have a significant role as signal transduction mediators in cancer signaling pathways. Prostate Cancer (PCa) is emerging with increasing cases worldwide even as advanced approaches in clinical diagnosis and treatment of PCa are still challenging to address. To enhance patient stratification, there is an indefatigable need to understand risk that can allow new approaches of treatment based on prognosis. While PCa is known to have mediated androgen receptor (AR) stimulation, the latter plays a critical role in regulating transcription of genes via nuclear translocation which in turn leads to response to androgens. LncRNAs have been implicated in developing clinical diagnostic and prognostic biomarkers in a broad spectrum of cancers. In our present study, 12 lncRNAs identified from clinical samples from our erstwhile PCa patients were docked with PCa and AR targeted 36 proteins. We identified three lncRNAs, <em>viz.</em> SCARNA10, NPBWR1, ANKRD20A9P are common between the targeted proteins and discern that SCARNA10 lncRNA could serve as a prognostic signature for PCa and AR biogenesis. We also sought to check the coding potential of interfacial residues associated with lncRNA docking sites.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 101959"},"PeriodicalIF":2.3,"publicationDate":"2025-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143579909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Comprehensive in silico characterization of nonsynonymous SNPs in the human ezrin (EZR) gene and their role in disease pathogenesis 人ezrin (EZR)基因非同义snp的综合硅表征及其在疾病发病机制中的作用
IF 2.3
Biochemistry and Biophysics Reports Pub Date : 2025-03-08 DOI: 10.1016/j.bbrep.2025.101972
Sadia Akter , Mohtasim Fuad , Zimam Mahmud, Sonia Tamanna, Mohammad Sayem, Khalid Hasan Raj, Md. Zakir Hossain Howlader
{"title":"Comprehensive in silico characterization of nonsynonymous SNPs in the human ezrin (EZR) gene and their role in disease pathogenesis","authors":"Sadia Akter ,&nbsp;Mohtasim Fuad ,&nbsp;Zimam Mahmud,&nbsp;Sonia Tamanna,&nbsp;Mohammad Sayem,&nbsp;Khalid Hasan Raj,&nbsp;Md. Zakir Hossain Howlader","doi":"10.1016/j.bbrep.2025.101972","DOIUrl":"10.1016/j.bbrep.2025.101972","url":null,"abstract":"<div><div>Ezrin (EZR) is a crucial linker between the actin cytoskeleton and the plasma membrane. It interacts with proteins involved in cancer-related signaling pathways. To assess the impact of nonsynonymous single nucleotide polymorphisms (nsSNPs) on EZR structure and function, we employed bioinformatics tools (SIFT, PolyPhen-2, PROVEAN, PhD-SNP, SNPs&amp;GO, SuSPect, and FATHMM) and identified deleterious variants. Stability analyses using MUpro, mCSM, I-Mutant 2.0, and DynaMut2 revealed six destabilizing nsSNPs (F240S, H288D, I248T, L59Q, L125S, and L225P). Structural modeling using HOPE, MutPred2, AlphaFold, Swiss-Model, and protein-protein docking using HADDOCK 2.4 assessed the impact on the EZR-EBP50 complex. Binding free energy calculations, salt bridge analysis, and interface residue mapping further confirmed that the L225P, F240S, and I248T mutations significantly impaired EZR-EBP50 interaction, potentially disrupting key signaling pathways. Molecular dynamics simulations indicated that mutant EZR proteins exhibited reduced stability, flexibility, and hydrogen bonding. This first comprehensive in silico analysis of EZR highlights pathogenic nsSNPs that may contribute to disease progression. These findings provide a foundation for experimental validation and may inform targeted therapies for EZR-related pathologies.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 101972"},"PeriodicalIF":2.3,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143579908","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Three sample-sparing techniques to estimate the molar absorption coefficient of luminescent dyes 三种样品保留技术估算发光染料的摩尔吸收系数
IF 2.3
Biochemistry and Biophysics Reports Pub Date : 2025-03-08 DOI: 10.1016/j.bbrep.2025.101971
Jeffrey M. Schaub, Quinn A. Best, Cheng Zhao, Richard A. Haack, Qiaoqiao Ruan
{"title":"Three sample-sparing techniques to estimate the molar absorption coefficient of luminescent dyes","authors":"Jeffrey M. Schaub,&nbsp;Quinn A. Best,&nbsp;Cheng Zhao,&nbsp;Richard A. Haack,&nbsp;Qiaoqiao Ruan","doi":"10.1016/j.bbrep.2025.101971","DOIUrl":"10.1016/j.bbrep.2025.101971","url":null,"abstract":"<div><div>Luminescent dyes are commonly modified to improve their solubility, permeability, or spectral properties. However, changing the chemical structure influences the absorption of light and thus the compound-specific molar absorption coefficient (<em>ε</em>), which also confounds the compound's concentration in solution. The accurate determination of the molar absorption coefficient of new luminescent molecules is labor intensive and challenging when a limited amount of material is available for testing. To address this problem, we developed three techniques combined with UV–Vis spectrophotometry to closely approximate the molar absorption coefficient of various light-emitting dyes. The first technique uses Electrospray Mass Spectrometry to obtain a high-resolution incorporation ratio of a dye-labeled protein. The second approach utilizes covalent linking of the unknown dye to a dye with a known absorption coefficient. In the third method, we used fluorescence correlation spectroscopy to determine the fluorophore concentration in solution. We test each method with well-characterized fluorescent dyes and an uncharacterized chemilumiphore. Each technique produced calculated absorption coefficients comparable to the published reference values, although each presented unique limitations that reduced accuracy under certain conditions. Nevertheless, the techniques could be incorporated into current compound evaluation workflows and require only a small amount of sample, two significant advantages over traditional methods for characterizing new luminescent compounds.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 101971"},"PeriodicalIF":2.3,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143579902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Machine learning unravels the mysteries of glioma typing and treatment 机器学习揭开了神经胶质瘤分型和治疗的奥秘
IF 2.3
Biochemistry and Biophysics Reports Pub Date : 2025-03-07 DOI: 10.1016/j.bbrep.2025.101969
Ying Dang , Youhu Chen , Jie Chen , Guoqiang Yuan , Yawen Pan
{"title":"Machine learning unravels the mysteries of glioma typing and treatment","authors":"Ying Dang ,&nbsp;Youhu Chen ,&nbsp;Jie Chen ,&nbsp;Guoqiang Yuan ,&nbsp;Yawen Pan","doi":"10.1016/j.bbrep.2025.101969","DOIUrl":"10.1016/j.bbrep.2025.101969","url":null,"abstract":"<div><div>Gliomas, which are complex primary malignant brain tumors known for their heterogeneous and invasive nature, present substantial challenges for both treatment and prognosis. Recent advancements in whole-genome studies have opened new avenues for investigating glioma mechanisms and therapies. Through single-cell analysis, we identified a specific cluster of cancer cell-related genes within gliomas. By leveraging diverse datasets and employing non-negative matrix factorization (NMF), we developed a glioma subtyping method grounded in this identified gene set. Our exploration delved into the clinical implications and underlying regulatory frameworks of the newly defined subtype classification, revealing its intimate ties to glioma malignancy and prognostic outcomes. Comparative assessments between the identified subtypes revealed differences in clinical features, immune modulation, and the tumor microenvironment (TME). Using tools such as the <em>limma</em> R package, weighted gene co-expression network analysis (WGCNA), machine learning methodologies, survival analyses, and protein-protein interaction (PPI) networks, we identified key driver genes influencing subtype differentiation while quantifying associated outcomes. This study not only sheds light on the biological mechanisms within gliomas but also paves the way for precise molecular targeted therapies within this intricate disease landscape.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 101969"},"PeriodicalIF":2.3,"publicationDate":"2025-03-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143563669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Exploring the role of exosomal and non-exosomal non-coding RNAs in Kawasaki disease: Implications for diagnosis and therapeutic strategies against coronary artery aneurysms 探索外泌体和非外泌体非编码rna在川崎病中的作用:对冠状动脉瘤的诊断和治疗策略的意义
IF 2.3
Biochemistry and Biophysics Reports Pub Date : 2025-03-06 DOI: 10.1016/j.bbrep.2025.101970
Negar Jafari , Ali Zolfi Gol , Venus Shahabi Rabori , Mohammadreza Saberiyan
{"title":"Exploring the role of exosomal and non-exosomal non-coding RNAs in Kawasaki disease: Implications for diagnosis and therapeutic strategies against coronary artery aneurysms","authors":"Negar Jafari ,&nbsp;Ali Zolfi Gol ,&nbsp;Venus Shahabi Rabori ,&nbsp;Mohammadreza Saberiyan","doi":"10.1016/j.bbrep.2025.101970","DOIUrl":"10.1016/j.bbrep.2025.101970","url":null,"abstract":"<div><div>Kawasaki disease (KD) is an acute vasculitis primarily affecting children, with a potential risk of developing coronary artery aneurysms (CAAs) and cardiovascular complications. The emergence of non-coding RNAs (ncRNAs), including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), has provided insights into Kawasaki disease pathogenesis and opened new avenues for diagnosis and therapeutic intervention. Furthermore, polymorphism analysis of ncRNA genes offers significant insights into genetic predisposition to Kawasaki disease, facilitating tailored treatment approaches and risk assessment to improve patient outcomes. Exosomal ncRNAs, which are ncRNAs encapsulated within extracellular vesicles, have garnered significant attention as potential biomarkers for Kawasaki disease and CAA due to their stability and accessibility in biological fluids. This review comprehensively discusses the biogenesis, components, and potential of exosomal and non-exosomal ncRNAs in Kawasaki disease diagnosis and prognosis prediction. It also highlights the roles of non-exosomal ncRNAs, such as miRNAs, lncRNAs, and circRNAs, in Kawasaki disease pathogenesis and their implications as therapeutic targets. Additionally, the review explores the current diagnostic and therapeutic approaches for Kawasaki disease and emphasizes the need for further research to validate these ncRNA-based biomarkers in diverse populations and clinical settings.</div></div>","PeriodicalId":8771,"journal":{"name":"Biochemistry and Biophysics Reports","volume":"42 ","pages":"Article 101970"},"PeriodicalIF":2.3,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143549568","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","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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