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A prognostic gene signature and subtype-specific drug sensitivity in TNBC revealed by single-cell and bulk RNA sequencing: Insights into stemness and tumor heterogeneity 单细胞和大量RNA测序揭示了TNBC的预后基因特征和亚型特异性药物敏感性:对干细胞和肿瘤异质性的见解
IF 4.2 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-10-01 Epub Date: 2025-06-18 DOI: 10.1016/j.ymeth.2025.06.007
Do Thi Minh Xuan , Doan Phuong Quy Nguyen , Van Thi Ngoc Tram , Hoang Dang Khoa Ta
Triple-negative breast cancer (TNBC) remains one of the most aggressive Triple-negative breast cancer (TNBC) remains one of the most aggressive and therapeutically challenging breast cancer subtypes, largely due to its lack of targetable receptors and its intrinsic chemoresistance. In this study, we applied an integrative multi-omics approach − combining single-cell RNA sequencing (scRNA-seq) with bulk transcriptomic, epigenomic, and mutational analyses, to investigate the cellular heterogeneity and underlying mechanisms of drug resistance in TNBC. Analysis of the scRNA-seq dataset (GSE176078) revealed a complex tumor microenvironment with a highly plastic cancer epithelial subpopulation (Cluster C4) exhibiting elevated multipotency and distinct intercellular communication patterns. Concurrently, unsupervised clustering of TCGA-BRCA data delineated three molecular subtypes (CS1, CS2, and CS3) with unique biological and metabolic profiles, where CS3 notably exhibited unique molecular features associated with chromatin remodeling and high proliferative activity, suggesting distinct therapeutic vulnerabilities. An overlap analysis between scRNA-seq and bulk RNA-seq data identified 220 common differentially expressed genes (DEGs), from which a four-gene prognostic signature (CTSF, GBP1, BCL2A1, and EMP1) was derived. This signature robustly stratified patients by overall survival across both internal and external cohorts. Overall, our findings provide critical insights into the molecular drivers of chemoresistance in TNBC and offer a foundation for personalized therapeutic strategies.
三阴性乳腺癌(TNBC)仍然是最具侵袭性和治疗挑战性的乳腺癌亚型之一,主要是由于其缺乏靶向受体和内在的化疗耐药。在这项研究中,我们采用了综合多组学方法-将单细胞RNA测序(scRNA-seq)与大量转录组学、表观基因组学和突变分析相结合,研究TNBC的细胞异质性和潜在的耐药机制。对scRNA-seq数据集(GSE176078)的分析揭示了一个复杂的肿瘤微环境,具有高度可塑性的癌症上皮亚群(C4簇),表现出更高的多能性和不同的细胞间通讯模式。同时,TCGA-BRCA数据的无监督聚类描绘了具有独特生物学和代谢谱的三种分子亚型(CS1、CS2和CS3),其中CS3明显表现出与染色质重塑和高增殖活性相关的独特分子特征,表明不同的治疗脆弱性。scRNA-seq和大量RNA-seq数据之间的重叠分析确定了220个常见差异表达基因(deg),从中衍生出四基因预后特征(CTSF, GBP1, BCL2A1和EMP1)。这一特征通过内部和外部队列的总生存率对患者进行了有力的分层。总的来说,我们的研究结果为TNBC化疗耐药的分子驱动因素提供了重要的见解,并为个性化治疗策略提供了基础。
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引用次数: 0
Immunoinformatics-based multi-epitope vaccine design using transforming growth factor beta-2 proprotein (TGFB2) for glioblastoma multiforme (GBM): GVac 基于免疫信息学的多形性胶质母细胞瘤(GBM)转化生长因子-2蛋白(TGFB2)多表位疫苗设计
IF 4.2 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-10-01 Epub Date: 2025-07-06 DOI: 10.1016/j.ymeth.2025.07.001
Deniz Tülümen , Esra Aydemir , Furkan Ayaz
Glioblastoma multiforme (GBM), a malignant glioma, is a central nervous system tumor with a high mortality rate in the world. Despite its high mortality rate, there is no effective treatment yet. Classical treatment methods are usually applied to patients, but patients lose their lives in a short time. A strong vaccine or drug that will extend the life of patients has not yet emerged. In this study, various bioinformatic analyses were performed on the Transforming growth factor beta-2 proprotein (TGFB2) belonging to GBM, and a multi-epitope vaccine design was made. These analyses include allergenicity, antigenicity and toxicity tests, various epitope selections, molecular docking, molecular dynamics simulation and immune simulation analyses. As a result of all analyses, a vaccine candidate called GVac was revealed. Gvac is enhanced with an adjuvant called batroxicidin (BatxC), an antimicrobial peptide. While analyses of Gvac generally yield strong results, it offers the potential to be used in various clinical studies if carried forward. With developing technologies, it is now necessary to move away from classical treatment methods and apply to treatment methods that can provide faster and more effective results. This is also the aim of this study. Gvac may offer hope to GBM patients awaiting treatment around the world and the studies need to be carried forward.
多形性胶质母细胞瘤(GBM)是一种恶性胶质瘤,是世界上死亡率较高的中枢神经系统肿瘤。尽管死亡率很高,但目前还没有有效的治疗方法。经典的治疗方法通常适用于患者,但患者会在短时间内失去生命。一种能够延长患者生命的强效疫苗或药物尚未出现。本研究对GBM的转化生长因子β -2蛋白(TGFB2)进行了多种生物信息学分析,并进行了多表位疫苗设计。这些分析包括致敏性、抗原性和毒性测试、各种表位选择、分子对接、分子动力学模拟和免疫模拟分析。作为所有分析的结果,一种名为GVac的候选疫苗被发现。Gvac用一种叫做抗细菌毒素(BatxC)的佐剂增强,BatxC是一种抗菌肽。虽然对Gvac的分析通常会产生强有力的结果,但如果继续进行下去,它将提供用于各种临床研究的潜力。随着技术的发展,现在有必要摆脱传统的治疗方法,采用能够提供更快、更有效结果的治疗方法。这也是本研究的目的。Gvac可能为世界各地等待治疗的GBM患者带来希望,这些研究需要继续进行。
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引用次数: 0
A simple, accurate method for the measurement of lysosomal activity 测定溶酶体活性的一种简单、准确的方法。
IF 4.3 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-10-01 Epub Date: 2025-07-24 DOI: 10.1016/j.ymeth.2025.07.008
Yoshito Iwai , Yuriko Furuya , Yuji Oguro , Keiji Yamamoto
Lysosomes are responsible for the degradation of intra- and extracellular components and are thus essential for the quality control of proteins and organelles. Lysosomal dysfunction leads to lysosomal storage diseases, and it is therefore important to identify which types of stress cause functional abnormalities. Lysosomal function is generally evaluated by measuring the enzyme activity of lysosomes with fluorescent dyes. However, fluorescence microscopy can lead to different outcomes due to variations in the field of view, the analysis software used, and the parameter settings. We therefore developed a method that uses only a microplate reader and DQ Green BSA, a dye that emits fluorescence upon lysosomal degradation, to ascertain lysosomal activity. HEK293 cells were treated with DQ Green BSA with or without bafilomycin A1 and lysates extracted using cell lysis buffer. Fluorescence intensities and protein concentrations in the cell lysates were then measured using a microplate reader and the bicinchoninic acid method, respectively, and the fluorescence intensity divided by the protein concentration. Results indicated a significant lysosome inhibitor-induced dose-dependent decrease in the lysosomal activity. The Z’-factor of 0.77 obtained using the proposed method is a significant improvement over the − 0.06 obtained using the conventional method. The versatility of the method was evaluated with different cell types, cell lysis buffers, inhibitors, and protease substrates. These results suggest that the method works regardless of the cells or reagents used, and indicates the relative simplicity and accuracy of the proposed method compared to the currently utilized method.
溶酶体负责细胞内和细胞外成分的降解,因此对蛋白质和细胞器的质量控制至关重要。溶酶体功能障碍导致溶酶体贮积病,因此确定哪些类型的应激导致功能异常是很重要的。溶酶体的功能一般是通过荧光染料测定溶酶体的酶活性来评价的。然而,由于视野、使用的分析软件和参数设置的变化,荧光显微镜可以导致不同的结果。因此,我们开发了一种方法,仅使用微孔板读取器和DQ Green BSA(一种在溶酶体降解时发出荧光的染料)来确定溶酶体的活性。用含或不含巴菲霉素A1的DQ Green BSA和放射免疫沉淀缓冲液提取的裂解物处理HEK293细胞。然后分别使用微孔板读取器和比辛醌酸法测量细胞裂解液中的荧光强度和蛋白质浓度,并将荧光强度除以蛋白质浓度。结果显示溶酶体抑制剂诱导溶酶体活性呈剂量依赖性降低。该方法得到的Z′因子为0.77,比传统方法得到的 - 0.06有显著提高。用不同的细胞类型、细胞裂解缓冲液、抑制剂和蛋白酶底物对该方法的通用性进行了评估,结果表明,无论使用何种细胞或试剂,该方法都有效,表明与目前使用的方法相比,所提出的方法相对简单和准确。
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引用次数: 0
Development of capillary electrophoresis method to measure albumin thiol oxidation in dystrophic humans and animal models of Duchenne muscular dystrophy. 毛细管电泳法测定营养不良人和杜氏肌营养不良动物模型白蛋白硫醇氧化的建立。
IF 4.3 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-10-01 Epub Date: 2025-07-31 DOI: 10.1016/j.ymeth.2025.07.010
Angelo Patrick R Bautista, Jessica R Terrill, Marisa N Duong, Gabriella Angelica, Irene Tsioutsias, Christopher P James, Aude Lafoux, Corinne Huchet, Peter G Arthur

Inflammatory responses evident in many diseases involve the generation of oxidants which can cause oxidant-induced post-translational modifications to proteins. Albumin, the most abundant plasma protein, contains a free thiol group which is susceptible to oxidative modification. We propose that albumin thiol oxidation (AlbOx) could be a useful biomarker to monitor changes in inflammatory activity and oxidative stress. To measure AlbOx in humans and animal models, we developed a fast, sensitive, simple, and reproducible capillary electrophoresis method (CE-AlbOx). This method can analyse total, reversible, and irreversible oxidation of albumin. The method only requires a small volume of sample (<10 μL blood), has an intra/interday variation of <2 %, and has a total run time of 17 min. We validated the usefulness of AlbOx as a biomarker of chronic inflammation by analysing samples from patients with, and animal models of, Duchenne muscular dystrophy (DMD), a disease associated with chronic inflammation. The main findings in this study are (1) dystrophic humans and animals have higher oxidised albumin compared to healthy controls, (2) mouse albumin has two reactive cysteine groups, and (3) our method is the first to quantify the different oxidation states of mouse albumin. In conclusion, we have developed a new method to measure albumin oxidation in humans and animals using capillary electrophoresis. The simple methodology of the CE-AlbOx method makes it advantageous to current methods and can be readily used as a biomarker of inflammation and oxidative stress in both humans and animal models.

在许多疾病中明显的炎症反应涉及氧化剂的产生,氧化剂可引起氧化诱导的蛋白质翻译后修饰。白蛋白是最丰富的血浆蛋白,它含有一个易受氧化修饰的游离巯基。我们提出白蛋白硫醇氧化(AlbOx)可能是监测炎症活性和氧化应激变化的有用生物标志物。为了测定人类和动物模型中的AlbOx,我们开发了一种快速、灵敏、简单、可重复的毛细管电泳方法(CE-AlbOx)。该方法可分析白蛋白的完全氧化、可逆氧化和不可逆氧化。这种方法只需要少量的样品(
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引用次数: 0
3DCellComposer − A versatile pipeline utilizing 2D cell segmentation methods for 3D cell segmentation 3DCellComposer -利用2D细胞分割方法进行3D细胞分割的多功能管道。
IF 4.3 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-10-01 Epub Date: 2025-07-28 DOI: 10.1016/j.ymeth.2025.07.007
Haoran Chen , Ted Zhang, Matthew Ruffalo, Robert F. Murphy
Cell segmentation is crucial in bioimage informatics, as its accuracy directly impacts conclusions drawn from cellular analyses. While many approaches to 2D cell segmentation have been described, 3D cell segmentation has received much less attention. 3D segmentation faces significant challenges, including limited training data availability due to the difficulty of the task for human annotators, and inherent three-dimensional complexity. As a result, existing 3D cell segmentation methods often lack broad applicability across different imaging modalities. To address this, we developed a generalizable approach for using 2D cell segmentation methods to produce accurate 3D cell segmentations. We implemented this approach in 3DCellComposer, a versatile, open-source package that allows users to choose any existing 2D segmentation model appropriate for their tissue or cell type(s) without requiring any additional training. Importantly, we have enhanced our open source CellSegmentationEvaluator quality evaluation tool to support 3D images. It provides metrics that allow selection of the best approach for a given imaging source and modality, without the need for human annotations to assess performance. Using these metrics, we demonstrated that our approach produced high-quality 3D segmentations of multichannel tissue images. 3DCellComposer, when paired with well-trained 2D segmentation models, provides an important alternative to acquiring human-annotated 3D images for new sample types or imaging modalities and then training 3D segmentation models using them. It is expected to be of significant value for large scale projects such as the Human BioMolecular Atlas Program.
细胞分割在生物图像信息学中是至关重要的,因为它的准确性直接影响细胞分析得出的结论。虽然许多二维细胞分割的方法已经被描述,但三维细胞分割却很少受到关注。3D分割面临着巨大的挑战,包括由于人类注释者的任务困难而导致的训练数据可用性有限,以及固有的三维复杂性。因此,现有的三维细胞分割方法往往缺乏对不同成像模式的广泛适用性。为了解决这个问题,我们开发了一种可推广的方法,用于使用2D细胞分割方法来产生准确的3D细胞分割。我们在3DCellComposer中实现了这种方法,这是一个通用的开源软件包,允许用户选择适合其组织或细胞类型的任何现有2D分割模型,而无需任何额外的培训。重要的是,我们已经增强了我们的开源CellSegmentationEvaluator质量评估工具,以支持3D图像。它提供的指标允许为给定的成像源和模式选择最佳方法,而不需要人工注释来评估性能。使用这些指标,我们证明了我们的方法产生了高质量的多通道组织图像的3D分割。3DCellComposer与训练有素的2D分割模型配对时,为获取新的样本类型或成像模式的人工注释3D图像提供了重要的替代方案,然后使用它们训练3D分割模型。预计对人类生物分子图谱计划等大型项目具有重要价值。
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引用次数: 0
Interpretable multimodal learning for tumor protein-metal binding: Progress, challenges, and perspectives 肿瘤蛋白-金属结合的可解释多模式学习:进展、挑战和前景。
IF 4.3 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-10-01 Epub Date: 2025-07-21 DOI: 10.1016/j.ymeth.2025.07.004
Xiaokun Liu , Sayedmohammadreza Rastegari , Yijun Huang , Sxe Chang Cheong , Weikang Liu , Wenjie Zhao , Qihao Tian , Hongming Wang , Yingjie Guo , Shuo Zhou , Sina Tabakhi , Xianyuan Liu , Zheqing Zhu , Wei Sang , Haiping Lu
In cancer therapeutics, protein-metal binding mechanisms critically govern the pharmacokinetics and targeting efficacy of drugs, thereby fundamentally shaping the rational design of anticancer metallodrugs. While conventional laboratory methods used to study such mechanisms are often costly, low throughput, and limited in capturing dynamic biological processes, machine learning (ML) has emerged as a promising alternative. Despite increasing efforts to develop protein-metal binding datasets and ML algorithms, the application of ML in tumor protein-metal binding remains limited. Key challenges include a shortage of high-quality, tumor-specific datasets, insufficient consideration of multiple data modalities, and the complexity of interpreting results due to the “black box” nature of complex ML models. This paper summarizes recent progress and ongoing challenges in using ML to predict tumor protein-metal binding, focusing on data, modeling, and interpretability. We present multimodal protein-metal binding datasets and outline strategies for acquiring, curating, and preprocessing them for training ML models. Moreover, we explore the complementary value provided by different data modalities and examine methods for their integration. We also review approaches for improving model interpretability to support more trustworthy decisions in cancer research. Finally, we offer our perspective on research opportunities and propose strategies to address the scarcity of tumor protein data and the limited number of predictive models for tumor protein-metal binding. We also highlight two promising directions for effective metal-based drug design: integrating protein-protein interaction data to provide structural insights into metal-binding events and predicting structural changes in tumor proteins after metal binding.
在癌症治疗中,蛋白质-金属结合机制对药物的药代动力学和靶向疗效起着至关重要的作用,从而从根本上决定了抗癌金属药物的合理设计。虽然用于研究此类机制的传统实验室方法通常成本高,吞吐量低,并且在捕获动态生物过程方面受到限制,但机器学习(ML)已成为一种有前途的替代方法。尽管越来越多的人致力于开发蛋白质-金属结合数据集和ML算法,但ML在肿瘤蛋白质-金属结合中的应用仍然有限。主要挑战包括缺乏高质量的肿瘤特异性数据集,对多种数据模式的考虑不足,以及由于复杂ML模型的“黑箱”性质而导致解释结果的复杂性。本文总结了利用机器学习预测肿瘤蛋白-金属结合的最新进展和面临的挑战,重点是数据、建模和可解释性。我们提出了多模态蛋白质-金属结合数据集,并概述了获取、管理和预处理这些数据集用于训练ML模型的策略。此外,我们还探讨了不同数据模式提供的互补价值,并研究了它们整合的方法。我们还回顾了提高模型可解释性的方法,以支持癌症研究中更可靠的决策。最后,我们提出了我们对研究机会的看法,并提出了解决肿瘤蛋白质数据稀缺和肿瘤蛋白质-金属结合预测模型数量有限的策略。我们还强调了有效的基于金属的药物设计的两个有希望的方向:整合蛋白质-蛋白质相互作用数据以提供金属结合事件的结构见解和预测金属结合后肿瘤蛋白的结构变化。
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引用次数: 0
DEF-DSVM: A deep ensemble feature learning and deepSVM approach for multifaceted analysis and diagnosis of Alzheimer's disease from EEG signals. DEF-DSVM:一种深度集成特征学习和深度支持向量机方法,用于脑电信号中阿尔茨海默病的多方面分析和诊断。
IF 4.3 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-10-01 Epub Date: 2025-08-06 DOI: 10.1016/j.ymeth.2025.08.003
Shabnam Hesari, Hamidreza Ghaffari, Khosro Rezaee

Early detection of Alzheimer's disease (AD) and its precursor, mild cognitive impairment (MCI), is paramount for timely intervention and effective disease management. This study introduces a novel computer-aided diagnostic model that leverages electroencephalogram (EEG) data to precisely identify and classify AD and MCI. A comprehensive preprocessing pipeline is employed, incorporating discrete wavelet transform (DWT) for EEG signal decomposition into relevant subbands and subsequent signal windowing to address non-stationarity. Spectrograms derived from these preprocessed signals serve as input for a deep ensemble feature learning and deep support vector machine (DEF-DSVM) architecture. The DEF-DSVM model significantly enhances the accuracy of diagnosing both MCI and AD, achieving an impressive 98.17% accuracy rate that surpasses contemporary state-of-the-art methods. Beyond diagnostic precision, the model effectively identifies specific EEG subbands-namely alpha, theta, and delta-instrumental in elucidating the pathophysiology of AD and MCI. The structure's generalizability and robustness are validated using the Figshare dataset, encompassing, AD, MCI, and control classes. To ensure a rigorous assessment of the model's performance, the Leave-One-Subject-Out (LOSO) cross-validation procedure is employed in lieu of the traditional K-fold approach, mitigating the risk of overoptimistic performance estimates and providing a more accurate reflection of the model's ability to generalize to novel, unseen subjects. Further evaluation of the method's generalizability through its application to an EEG dataset related to attention deficit hyperactivity disorder (ADHD) highlights its broader clinical utility across various neurodegenerative disorders. These findings establish the DEF-DSVM model as a reliable and potent tool for the early diagnosis and monitoring of AD and MCI, offering substantial accuracy gains and demonstrating its potential for widespread application across different neurological conditions.

早期发现阿尔茨海默病(AD)及其前兆轻度认知障碍(MCI)对于及时干预和有效的疾病管理至关重要。本研究介绍了一种新的计算机辅助诊断模型,该模型利用脑电图(EEG)数据来精确识别和分类AD和MCI。采用了一套综合的预处理流程,将离散小波变换(DWT)用于脑电信号的相关子带分解和后续的信号窗口处理,以解决非平稳性问题。从这些预处理信号中得到的频谱图作为深度集成特征学习和深度支持向量机(DEF-DSVM)架构的输入。DEF-DSVM模型显著提高了MCI和AD的诊断准确率,达到了令人印象深刻的98.17%,超过了当代最先进的方法。除了诊断精度,该模型有效地识别特定的脑电图亚带-即α, θ和δ -有助于阐明AD和MCI的病理生理。使用Figshare数据集(包括AD、MCI和控制类)验证了该结构的通用性和鲁棒性。为了确保对模型的性能进行严格的评估,我们采用了留一个主体(LOSO)交叉验证程序来代替传统的K-fold方法,从而降低了过于乐观的性能估计的风险,并提供了更准确的反映模型推广到新的、看不见的主体的能力。通过将该方法应用于与注意缺陷多动障碍(ADHD)相关的脑电图数据集,进一步评估了该方法的泛化性,突出了其在各种神经退行性疾病中的广泛临床应用。这些发现建立了DEF-DSVM模型作为早期诊断和监测AD和MCI的可靠和有效的工具,提供了大量的准确性提高,并展示了其在不同神经系统疾病中的广泛应用潜力。
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引用次数: 0
Multi-filter based signed heterogeneous graph convolutional networks for predicting activating/inhibiting drug-target interactions 基于多滤波器的预测药物-靶标相互作用激活/抑制的签名异构图卷积网络。
IF 4.2 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-09-01 Epub Date: 2025-05-15 DOI: 10.1016/j.ymeth.2025.05.005
Ming Chen , Haike Li , Yunhan Pan , Yinglong Dai , Xiujuan Lei , Yi Pan
The prediction of mechanisms within drug-target interactions (DTIs) can boost the drug discovery process, which has traditionally relied on time-consuming and expensive laboratory experiments. Despite much more attention has been paid to predicting DTIs, but few studies focused on their activating/inhibiting mechanisms. In this work, we model DTIs on signed heterogeneous networks, through categorizing activating/inhibiting DTIs into signed links, and accordingly introducing the coherence/incoherence between drugs on a common target to construct signed drug-drug links. We propose a multi-filter based signed heterogeneous graph convolutional network (MFSHGCN) for drugs and targets embedding, via employing dual filters on both the signed drug-drug sub-graph and the signed DTI sub-graph to converge the spectral information from positive and negative edges. We further put forward an end-to-end framework to predict activation and inhibition within DTIs. The comparison results demonstrate the introduction of coherence/incoherence of drug pairs and the design of our multi-filter system can effectively improve the prediction metrics, even without relying on rich node information and interactions from drug pairs or target pairs. Case studies on breast cancer and lung cancer confirm the model's feasibility.
药物-靶标相互作用(DTIs)机制的预测可以促进药物发现过程,这一过程传统上依赖于耗时且昂贵的实验室实验。尽管对dti的预测已经引起了广泛的关注,但对其激活/抑制机制的研究却很少。在这项工作中,我们在签名异构网络上建模dti,通过将激活/抑制dti分类为签名链接,并相应地引入共同靶标上药物之间的一致性/不一致性来构建签名药物-药物链接。本文提出了一种基于多滤波器的药物和目标嵌入的有签名异构图卷积网络(MFSHGCN),通过对有签名药物-药物子图和有签名DTI子图使用双重滤波器来收敛正负边的谱信息。我们进一步提出了一个端到端的框架来预测dti内的激活和抑制。对比结果表明,即使不依赖于丰富的节点信息和药物对或目标对的相互作用,引入药物对的相干性/非相干性以及我们设计的多滤波器系统也可以有效地提高预测指标。乳腺癌和肺癌的案例研究证实了该模型的可行性。
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引用次数: 0
Quorum sensing: An essential factor in culturing the human promyelocytic leukemia cell line HL-60 and its neutrophil-related functions 群体感应:人早幼粒细胞白血病HL-60细胞培养及其中性粒细胞相关功能的重要因素。
IF 4.2 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-09-01 Epub Date: 2025-05-20 DOI: 10.1016/j.ymeth.2025.05.008
Danfeng Li , Tian Yang , Siyuan Ma , Xinwei Lyu , Cheng Hu , Jiayin Yan , Lihong Guo , Jiali Tan
HL-60 cells are frequently employed as a standard in vitro model for neutrophil research and extensively utilized. However, the cultivation of HL-60 cells presents a recurring challenge. Historically, cell culture density has been ignored in the consistency of culture conditions. Here, we optimized the culture protocol and explored the impact of culture density on HL-60 cells. Additionally, we investigated the differentiated rate and antibacterial potential of differentiated HL-60 (dHL-60) neutrophils across varying cell density cultures. The findings revealed a positive correlation between cell proliferation activity and cell density, suggesting that increased density facilitates enhanced cell proliferation. Furthermore, as the density of the cell culture increased, there was a concomitant rise in the differentiation rate of HL-60 cells into neutrophils upon stimulation. Importantly, this elevated density also led to significantly higher levels of mitochondrial reactive oxygen species (ROS) production and bacterial phagocytosis. Further investigation revealed that small extracellular vesicles (sEVs) are crucial communicator in quorum sensing within HL-60 cells. Supplementation of HL60-derived sEVs (hEVs) in low-density cell populations resulted in a restoration of cell proliferation, in dose-dependent tendency. Conversely, the inhibition of EV-secretion in HL-60 cells restrains cell growth and proliferation. Overall, our study not only optimized the HL-60 cell culture protocol but also elucidated the critical role of culture density in enhancing HL-60 cell proliferation and antibacterial activity. This finding offers a noteworthy consideration for in vitro experiments of HL-60 cells and suggests the involvement of a quorum sensing mechanism within the neutrophil microenvironment.
HL-60细胞经常被用作中性粒细胞研究的标准体外模型,并被广泛应用。然而,HL-60细胞的培养提出了一个反复出现的挑战。从历史上看,细胞培养密度在培养条件的一致性中被忽略了。本实验优化培养方案,探讨培养密度对HL-60细胞的影响。此外,我们研究了HL-60 (dHL-60)中性粒细胞在不同细胞密度培养中的分化率和抗菌潜力。研究结果显示细胞增殖活性与细胞密度呈正相关,表明细胞密度增加有利于细胞增殖。此外,随着细胞培养密度的增加,HL-60细胞在刺激下向中性粒细胞的分化率也随之上升。重要的是,这种升高的密度也导致线粒体活性氧(ROS)产生和细菌吞噬水平显著提高。进一步的研究表明,小的细胞外囊泡(sev)是HL-60细胞群体感应的重要通讯载体。在低密度细胞群中补充hl60衍生的sEVs (hEVs)导致细胞增殖恢复,并呈剂量依赖趋势。相反,抑制HL-60细胞中ev的分泌会抑制细胞的生长和增殖。总的来说,我们的研究不仅优化了HL-60细胞培养方案,而且阐明了培养密度在促进HL-60细胞增殖和抗菌活性方面的关键作用。这一发现为HL-60细胞的体外实验提供了值得注意的考虑,并表明中性粒细胞微环境中参与了群体感应机制。
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引用次数: 0
Enhancing biliary tract cancer diagnosis using AI-driven 3D optical diffraction tomography 人工智能驱动的三维光学衍射断层扫描增强胆道癌诊断。
IF 4.2 3区 生物学 Q1 BIOCHEMICAL RESEARCH METHODS Pub Date : 2025-09-01 Epub Date: 2025-06-06 DOI: 10.1016/j.ymeth.2025.06.003
Se Woo Park , Hee Chan Moon , Seok Jin Hong , Anna Choi , Seung-Lee Lee , Da Hae Park , Eun Shin , Jung Hyun Jo , Dong Hee Koh , Jin Lee , Jong-Uk Hou , Kyong Joo Lee
Biliary tract cancer is associated with distinct metabolic alterations, particularly in lipid metabolism. This study aimed to classify biliary tract cancer cells automatically based on lipid droplet (LD) characteristics using three-dimensional (3D) optical diffraction tomography (ODT) combined with convolutional neural networks (CNNs). Human biliary tract cancer cell lines (SNU1196, SNU308, and SNU478) and a normal cholangiocyte cell line (H69) were cultured to evaluate the LD volume, mass, and count. We generated 3D refractive index tomograms and developed a CNN-based diagnostic system for automated classification. The biliary tract cancer cells exhibited significantly increased LD volume, mass, and count compared with those of normal cholangiocytes, reflecting distinct metabolic profiles. The EfficientNet-b3 model achieved an area under the curve (AUC) of 0.982 and an accuracy of 93.79%. Incorporating LD metadata, such as volume and dry mass, improved performance, yielding an AUC of 0.997 and an accuracy of 97.94%. Combining LD metadata with multi-view score fusion enhanced diagnostic performance (AUC: 0.999, accuracy: 98.61%). Further, LayerCAM analysis revealed that the model focused on LD-rich cytoplasmic regions, thereby aligning with known metabolic phenotypes. Overall, our findings demonstrate the diagnostic potential of LD characteristics and support the clinical utility of 3D ODT combined with deep learning for early detection of biliary tract cancer and future multimodal applications.
胆道癌与明显的代谢改变有关,尤其是脂质代谢。本研究旨在利用三维光学衍射断层扫描(ODT)结合卷积神经网络(cnn),基于脂滴(LD)特征对胆道癌细胞进行自动分类。培养人胆道癌细胞系(SNU1196、SNU308和SNU478)和正常胆管细胞系(H69),评估LD的体积、质量和计数。我们生成了3D折射率断层图,并开发了一个基于cnn的自动分类诊断系统。与正常胆管细胞相比,胆道癌细胞的LD体积、质量和计数明显增加,反映了不同的代谢特征。effentnet -b3模型的曲线下面积(AUC)为0.982,准确度为93.79%。结合LD元数据,如体积和干质量,提高了性能,AUC为0.997,准确率为97.94%。结合LD元数据和多视图评分融合提高了诊断性能(AUC: 0.999,准确率:98.61%)。此外,LayerCAM分析显示,该模型专注于富含ld的细胞质区域,从而与已知的代谢表型一致。总的来说,我们的研究结果证明了LD特征的诊断潜力,并支持3D ODT结合深度学习在胆道癌早期检测中的临床应用,以及未来的多模式应用。
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