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A Highly Sensitive Tissue-specific qRT-PCR-based Assay for Detection of Melanoma Cells in Tumor-Draining Lymph Nodes 一种高度敏感的组织特异性qrt - pcr检测肿瘤引流淋巴结黑色素瘤细胞的方法
Current protocols Pub Date : 2025-04-26 DOI: 10.1002/cpz1.70139
Kristian M. Hargadon, Travis B. Goodloe III
{"title":"A Highly Sensitive Tissue-specific qRT-PCR-based Assay for Detection of Melanoma Cells in Tumor-Draining Lymph Nodes","authors":"Kristian M. Hargadon,&nbsp;Travis B. Goodloe III","doi":"10.1002/cpz1.70139","DOIUrl":"https://doi.org/10.1002/cpz1.70139","url":null,"abstract":"<p>Melanoma invasion of regional lymph nodes, a critical event in the progression of this disease, is well documented as a poor prognostic factor for patients with melanoma. Assessing lymph node involvement is therefore a routine part of the diagnostic workup for patients presenting with melanoma at a T stage of ≥T2a. In clinical settings, the status and degree of melanoma lymph node involvement is traditionally characterized by histopathological analysis of tissue obtained during a sentinel lymph node biopsy, a labor-intensive and costly approach that requires technically challenging sample preparation and interpretation by a trained pathologist. Alternative approaches that might reduce the financial burden and turnaround time of a sentinel lymph node biopsy workup are therefore desirable. Likewise, the ability to accurately assess lymph node invasion by melanoma in experimental settings is necessary to gain new insights into mechanisms of distant metastasis and tumor-associated immune suppression. With these applications in mind, we recently developed, and describe herein, a tissue-specific qRT-PCR-based protocol for detecting melanoma cells within tumor-draining lymph nodes. Using murine models of lymph-node-invasive and lymph-node-noninvasive melanoma cell lines and a melanin-biosynthesis-pathway-specific <i>Trp2</i> gene expression assay, we validated this method as a highly sensitive strategy for assessing lymph node involvement by melanoma. © 2025 Wiley Periodicals LLC.</p><p><b>Basic Protocol 1</b>: Growth and maintenance of murine melanoma cell cultures</p><p><b>Basic Protocol 2</b>: Extraction and quantification of RNA from murine melanoma cultures</p><p><b>Basic Protocol 3</b>: cDNA synthesis via reverse transcription</p><p><b>Basic Protocol 4</b>: Probe and primer design for TaqMan-based qPCR</p><p><b>Basic Protocol 5</b>: qPCR analysis of tissue-specific <i>Trp2</i> gene expression</p><p><b>Basic Protocol 6</b>: <i>In vitro</i> validation of qRT-PCR <i>Trp2</i> gene expression assay for detection of melanoma cells in murine whole lymph node preparations</p><p><b>Basic Protocol 7</b>: <i>In vivo</i> validation of qRT-PCR <i>Trp2</i> gene expression assay for detection of melanoma cells in murine tumor-draining lymph nodes</p>","PeriodicalId":93970,"journal":{"name":"Current protocols","volume":"5 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143877827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Cryptococcus neoformans Biofilm Formation and Quantification 新型隐球菌生物膜的形成与定量
Current protocols Pub Date : 2025-04-25 DOI: 10.1002/cpz1.70133
Oscar Romero, Davier Gutierrez-Gongora, Jennifer Geddes-McAlister
{"title":"Cryptococcus neoformans Biofilm Formation and Quantification","authors":"Oscar Romero,&nbsp;Davier Gutierrez-Gongora,&nbsp;Jennifer Geddes-McAlister","doi":"10.1002/cpz1.70133","DOIUrl":"https://doi.org/10.1002/cpz1.70133","url":null,"abstract":"<p><i>Cryptococcus neoformans</i> is an opportunistic fungal pathogen that heads the Fungal Priority Pathogen List published by the World Health Organization (WHO) in 2022. This pathogen is a primary cause of death for immunocompromised individuals (e.g., those with HIV/AIDS, the elderly, immunotherapy recipients), causing approximately 118,000 deaths yearly worldwide. <i>C. neoformans</i> relies on virulence factors that include a polysaccharide capsule, melanin, extracellular enzymes, and thermotolerance to initiate and sustain host infection. Additionally, similar to other fungal pathogens (e.g., <i>Candida albicans</i>), <i>C. neoformans</i> may develop a biofilm organization linked to more persistent cryptococcal infections. Cryptococcal biofilms are highlighted in cases of cryptococcal meningitis, in which biofilm-like structures form that are highly resistant to host immune response and to antifungal therapies. In this regard, fungal biofilm formation has become an important area of study as a means to improve our understanding of the mechanisms regulating biofilm formation and infection and to advance the discovery of antibiofilm therapeutics. To assess biofilm properties and compare across treatments, quantification and evaluation of cell viability are important. Herein, we describe a standardized method to establish a cryptococcal biofilm and quantify total biomass and cell viability. © 2025 The Author(s). <i>Current Protocols</i> published by Wiley Periodicals LLC.</p><p><b>Basic Protocol 1</b>: Culturing and biofilm formation</p><p><b>Basic Protocol 2</b>: Biofilm quantification</p><p><b>Alternate Protocol</b>: Biofilm viability assay</p>","PeriodicalId":93970,"journal":{"name":"Current protocols","volume":"5 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cpz1.70133","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143875570","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
Enhancing Visual Discrimination Task: Optimized Mouse Motivation in the Touchscreen Paradigm 增强视觉辨别任务:在触屏范式下优化鼠标动机
Current protocols Pub Date : 2025-04-25 DOI: 10.1002/cpz1.70126
Jeremy Jehl, Fabrice Riet, Aline Simonet, Yann Herault
{"title":"Enhancing Visual Discrimination Task: Optimized Mouse Motivation in the Touchscreen Paradigm","authors":"Jeremy Jehl,&nbsp;Fabrice Riet,&nbsp;Aline Simonet,&nbsp;Yann Herault","doi":"10.1002/cpz1.70126","DOIUrl":"https://doi.org/10.1002/cpz1.70126","url":null,"abstract":"<p>Mouse models are essential for understanding gene function, environmental interaction, and brain structure and function. This is reinforced by the ability of mice to perform complex behavioral tasks. Still, their cognitive assessments often rely on aversive paradigms, such as fear conditioning and the Morris water maze. A promising alternative is the automated touchscreen platform, which enables cognitive tests comparable to those used in humans, such as the Cambridge Neuropsychological Test Automated Battery (CANTAB). This approach enhances standardization and reduces stress by employing appetitive reinforcement. Although widely used in non-human primates, touchscreen testing remains underutilized in rodents despite its potential for cross-species cognitive research. Motivation is key to successful touchscreen tasks, often achieved through water restriction, which mice tolerate well. However, water restriction is a stressful condition, combining negative and positive reinforcement. Here, we propose an alternative that uses citric acid (CA) water to avoid classical food privation in the touchscreen paradigm to mitigate mice's stress. By creating a strong contrast with the reward, we increase the reward's positive valence. We used the touchscreen visual discrimination task to assess the effectiveness of CA water in enhancing motivation. Our results show that administering CA water on training days while allowing access to plain water on weekends reduces the learning phase duration without causing significant weight loss in wild-type C57BL/6J mice. In addition, we observed a strong commitment to performing the pattern dissociation task. This approach offers a welfare-friendly alternative for maintaining motivation in touchscreen-based cognitive tasks while minimizing stress. © 2025 Wiley Periodicals LLC.</p><p><b>Basic Protocol</b>: Pattern dissociation paradigm using sour water</p>","PeriodicalId":93970,"journal":{"name":"Current protocols","volume":"5 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143875571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Leveraging the MethMotif Toolkit to Characterize Context-Specific Features and Roles of Methylation Sensitive Transcription Factors 利用MethMotif工具包表征甲基化敏感转录因子的环境特异性特征和作用
Current protocols Pub Date : 2025-04-25 DOI: 10.1002/cpz1.70129
Matthew Dyer, Gastongay Siu, Denis Thieffry, Touati Benoukraf
{"title":"Leveraging the MethMotif Toolkit to Characterize Context-Specific Features and Roles of Methylation Sensitive Transcription Factors","authors":"Matthew Dyer,&nbsp;Gastongay Siu,&nbsp;Denis Thieffry,&nbsp;Touati Benoukraf","doi":"10.1002/cpz1.70129","DOIUrl":"https://doi.org/10.1002/cpz1.70129","url":null,"abstract":"<p>This article presents a comprehensive guide for using the MethMotif platform, which includes the MethMotif database, the TFregulomeR R package, and a new R library, Forked-TF, designed specifically for analyzing leucine-zipper transcription factors (TFs) that bind DNA as dimers. The MethMotif platform integrates transcription factor binding site (TFBS) motifs with DNA methylation profiles, providing an in-depth analysis of how methylation modulates TF binding across different cell types and conditions. The protocols are organized into three main workflows: (1) Exploration of transcription factor dimerization partners, (2) visualization of methylation-specific TF motifs using TFregulomeR, and (3) characterization of leucine-zipper TF binding patterns with a focus on dimerization. Using the platform's MethMotif database, users can retrieve ChIP-seq and DNA methylation data, intersect TFBS peak regions, and generate TFBS-methylation-informed motif logos. A case study of CEBPB in K562 cells is included to demonstrate the use of the platform, showing how to identify TF dimers, analyze their co-binding behavior, and visualize the impact of DNA methylation on binding specificity. The protocols also provide step-by-step instructions for software installation, data input formats, and interpretation of results, making it accessible to researchers with varying levels of computational expertise. Through these protocols, users can uncover how DNA methylation and TF dimerization influence gene regulatory networks, with a focus on leucine-zipper TFs in a cell-type-specific context. © 2025 The Author(s). Current Protocols published by Wiley Periodicals LLC.</p><p><b>Basic Protocol 1</b>: Exploration of transcription factor dimerization partners</p><p><b>Support Protocol 1</b>: Software installation</p><p><b>Support Protocol 2</b>: Docker installation</p><p><b>Support Protocol 3</b>: Verifying installation</p><p><b>Basic Protocol 2</b>: Visualization of alternative cofactors</p><p><b>Basic Protocol 3</b>: Characterization of bZIP partners/cofactors</p><p><b>Basic Protocol 4</b>: Context-independent and context-dependent analysis</p>","PeriodicalId":93970,"journal":{"name":"Current protocols","volume":"5 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cpz1.70129","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143875573","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
Label-Free Quantification of Protein Density in Living Cells 活细胞中蛋白密度的无标记定量
Current protocols Pub Date : 2025-04-24 DOI: 10.1002/cpz1.70130
Robert J. Clements, Ruixin Guo, Jonathan C. Petruccelli, Michael A. Model
{"title":"Label-Free Quantification of Protein Density in Living Cells","authors":"Robert J. Clements,&nbsp;Ruixin Guo,&nbsp;Jonathan C. Petruccelli,&nbsp;Michael A. Model","doi":"10.1002/cpz1.70130","DOIUrl":"https://doi.org/10.1002/cpz1.70130","url":null,"abstract":"<p>Intracellular water content, W, and protein concentration, P, are essential characteristics of living cells. Healthy cells maintain them within a narrow range, but often become dehydrated under severe stress; moreover, persistent loss of water (an increase in P) can lead to apoptotic death. It is very likely that protein concentration affects cellular metabolism and signaling through macromolecular crowding (MC) effects, to which P is directly related, but much remains unknown in this area. Obviously, in order to study the biological roles and regulation of MC in living cells, one needs a method to measure it. Simple and accurate measurements of P in adherent cells can be based on its relationship to refractive index. The latter can be derived from two or more (depending on the algorithm) mutually defocused brightfield images processed by the transport-of-intensity equation (TIE) that must be complemented by a determination of volume. Here, we describe the experimental considerations for both TIE imaging and for a particular method of cell volume measurement, transmission-through-dye (TTD). We also introduce an ImageJ plugin for solving TIE. TIE and TTD are fully compatible with each other as well as with fluorescence. A similar approach can be applied to subcellular organelles; however, in this case, the volume must be determined differently.© 2025 The Author(s). <i>Current Protocols</i> published by Wiley Periodicals LLC.</p><p><b>Basic Protocol 1</b>: Sample preparation for TIE with or without TTD</p><p><b>Basic Protocol 2</b>: Acquisition of TIE and TTD images</p><p><b>Basic Protocol 3</b>: Calibration of TIE</p><p><b>Basic Protocol 4</b>: Measurement of the absorption coefficient of the medium used for TTD</p><p><b>Basic Protocol 5</b>: Image processing using Fiji</p><p><b>Support Protocol 1</b>: Installation and use of TIE plugin</p><p><b>Support Protocol 2</b>: Automation of the double TTD/TIE processing using a Fiji macro</p>","PeriodicalId":93970,"journal":{"name":"Current protocols","volume":"5 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/cpz1.70130","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143871532","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
Getting Started with Machine Learning for Experimental Biochemists and Other Molecular Scientists 实验生物化学家和其他分子科学家的机器学习入门
Current protocols Pub Date : 2025-04-21 DOI: 10.1002/cpz1.70085
Matthew J. K. Vince, Kristin A. Hughes, Anastasiya Buzuk, Deborah L. Perlstein, Lauren A. Viarengo-Baker, Adrian Whitty
{"title":"Getting Started with Machine Learning for Experimental Biochemists and Other Molecular Scientists","authors":"Matthew J. K. Vince,&nbsp;Kristin A. Hughes,&nbsp;Anastasiya Buzuk,&nbsp;Deborah L. Perlstein,&nbsp;Lauren A. Viarengo-Baker,&nbsp;Adrian Whitty","doi":"10.1002/cpz1.70085","DOIUrl":"https://doi.org/10.1002/cpz1.70085","url":null,"abstract":"<p>Machine learning (ML) is rapidly gaining traction in many areas of experimental molecular science for elucidating relationships and patterns in large or complex data sets. Historically, ML was largely the preserve of those with specialized training in fields such as statistics or cheminformatics. Increasingly, however, ML methodologies are becoming part of the standard toolkit for experimental scientists across a range of disciplines. For scientists without a significant background in computer science or statistics, lowering the barrier of entry to these ML techniques is important to broadening access to these powerful methods. Here we provide detailed, step-by-step protocols for performing four ML methods that are particularly useful for applications in biochemistry, cell biology, and drug discovery: hierarchical clustering, principal component analysis (PCA), partial least squares discriminant analysis (PLSDA), and partial least squares regression (PLSR). The protocols are written for the widely used software MATLAB, but no prior experience with MATLAB is required to use them. We include an explanation of each step, pitched at a level to be understood by investigators without any prior experience with ML, MATLAB, or any kind of coding. We also highlight the scientific issues pertaining to selecting and scaling the data to be analyzed. Throughout, we emphasize the relationship between the scientific question and how to choose data and methods that will allow it to be addressed in a meaningful way. Our aim is to provide a basic introduction that will equip experimental chemical biologists, chemists, and other biomedical scientists with the knowledge required to use ML to aid in the design of experiments, the formulation and data-driven testing of hypotheses, and the analysis of experimental data. © 2025 Wiley Periodicals LLC.</p><p><b>Basic Protocol 1</b>: Clustering</p><p><b>Basic Protocol 2</b>: Principal component analysis</p><p><b>Basic Protocol 3</b>: Partial least squares-discriminant analysis</p><p><b>Basic Protocol 4</b>: Partial least squares regression</p>","PeriodicalId":93970,"journal":{"name":"Current protocols","volume":"5 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143852716","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Reverse-Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) for Viral Detection — A Case Study 用于病毒检测的反转录酶环路介导等温扩增(RT-LAMP)--案例研究
Current protocols Pub Date : 2025-04-21 DOI: 10.1002/cpz1.70127
Ashley Hassman, Renée Richie Casey, Colby Rouchka, Diego Sunino, Felix Veloz Espinal, Mona Youssef
{"title":"Reverse-Transcriptase Loop-Mediated Isothermal Amplification (RT-LAMP) for Viral Detection — A Case Study","authors":"Ashley Hassman,&nbsp;Renée Richie Casey,&nbsp;Colby Rouchka,&nbsp;Diego Sunino,&nbsp;Felix Veloz Espinal,&nbsp;Mona Youssef","doi":"10.1002/cpz1.70127","DOIUrl":"https://doi.org/10.1002/cpz1.70127","url":null,"abstract":"<p>An assay and protocol framework are provided for utilizing reverse-transcriptase loop-mediated isothermal amplification (RT-LAMP) at the point-of-care for diagnosing and monitoring a hypothetical zoonotic viral outbreak in a resource-limited area. This manuscript utilizes a previously published decision tree algorithm to determine an appropriate molecular diagnostic point-of-care test that can effectively address the outbreak presented in the hypothetical case study. © 2025 Wiley Periodicals LLC.</p>","PeriodicalId":93970,"journal":{"name":"Current protocols","volume":"5 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143852717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Flow Cytometric Bone Marrow Evaluation in Suspected Myelodysplastic Neoplasms 疑似骨髓增生异常肿瘤的流式细胞术骨髓评估
Current protocols Pub Date : 2025-04-21 DOI: 10.1002/cpz1.70137
Veronika Ecker, Martha-Lena Müller, Wolfgang Kern
{"title":"Flow Cytometric Bone Marrow Evaluation in Suspected Myelodysplastic Neoplasms","authors":"Veronika Ecker,&nbsp;Martha-Lena Müller,&nbsp;Wolfgang Kern","doi":"10.1002/cpz1.70137","DOIUrl":"https://doi.org/10.1002/cpz1.70137","url":null,"abstract":"<p>Myelodysplastic neoplasms (MDS) are acquired heterogeneous clonal hematopoietic stem cell neoplasms, clinically characterized by progressively ineffective hematopoiesis and an increased risk of acute myeloid leukemia. MDS are accompanied by an inflammatory microenvironment and genome instability. Signs of dysplasia can occur in the erythroid, myeloid, monocytic, and megakaryocytic cell lineages and result in anemia, neutropenia, and thrombocytopenia. Multi-parameter flow cytometry can be used to detect aberrant antigen expression patterns typical of MDS, which correlate with cytomorphologically identified dysplasias and provide important information for diagnosis and prognosis. Characteristic findings include an increase in myeloid progenitor cells; aberrant myeloid and erythroid maturation; aberrant marker expression on progenitor cells, granulocytes, and monocytes, which corresponds to lineage infidelity, under-/overexpression, or asynchronous expression; and an increase in monocytes and progenitor cells in chronic myelomonocytic leukemia. The latter represents an independent disease entity with a similar phenotype. In addition, flow cytometry can rule out other causes of cytopenia, such as lymphoma, acute leukemias, paroxysmal nocturnal hemoglobinuria, or systemic mastocytosis with associated hematologic neoplasm. To analyze those features, the European LeukemiaNet recommends a set of markers together with important technical aspects. At least three distinct aberrations in at least two lineages are associated with a high likelihood of MDS. © 2025 Wiley Periodicals LLC.</p><p><b>Basic Protocol</b>: Flow cytometric bone marrow evaluation in suspected myelodysplastic neoplasms</p>","PeriodicalId":93970,"journal":{"name":"Current protocols","volume":"5 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143852718","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Isolation and Characterization of Extracellular Vesicles from Natural Killer Cells 天然杀伤细胞胞外囊泡的分离与表征
Current protocols Pub Date : 2025-04-12 DOI: 10.1002/cpz1.70125
Sara G. Dosil, Francisco Sánchez-Madrid, Lola Fernández-Messina
{"title":"Isolation and Characterization of Extracellular Vesicles from Natural Killer Cells","authors":"Sara G. Dosil,&nbsp;Francisco Sánchez-Madrid,&nbsp;Lola Fernández-Messina","doi":"10.1002/cpz1.70125","DOIUrl":"https://doi.org/10.1002/cpz1.70125","url":null,"abstract":"<p>Natural killer (NK) cells are critical components of the immune system, recognized for their ability to identify and eliminate target cells undergoing various forms of stress. Beyond their direct cytotoxic activity, NK cells secrete extracellular vesicles (EVs), which serve as mediators of intercellular communication. These vesicles play an essential role in modulating immune responses and influencing tumoral and post-infection microenvironments. In this study, we present a detailed methodology for the isolation and expansion of human primary NK cells, the accumulation of their EVs, and the subsequent procedures for their isolation and characterization. © 2025 Wiley Periodicals LLC.</p><p><b>Basic Protocol 1</b>: NK cell isolation and expansion</p><p><b>Basic Protocol 2</b>: NK-EV purification using ultracentrifugation</p><p><b>Alternate Protocol</b>: NK-EV isolation using size exclusion chromatography</p><p><b>Basic Protocol 3</b>: Characterization of NK-EVs</p>","PeriodicalId":93970,"journal":{"name":"Current protocols","volume":"5 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143822270","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Synthesis of Prodrug-Type Oligonucleotides Modified With a Galactosylated Self-Immolative Linker Cleavable by β-Galactosidase 半乳糖基化自牺牲连接体修饰前药型寡核苷酸的合成,可被β-半乳糖苷酶切割
Current protocols Pub Date : 2025-04-07 DOI: 10.1002/cpz1.70128
Kento Miyaji, Yoshiaki Masaki, Kohji Seio
{"title":"Synthesis of Prodrug-Type Oligonucleotides Modified With a Galactosylated Self-Immolative Linker Cleavable by β-Galactosidase","authors":"Kento Miyaji,&nbsp;Yoshiaki Masaki,&nbsp;Kohji Seio","doi":"10.1002/cpz1.70128","DOIUrl":"https://doi.org/10.1002/cpz1.70128","url":null,"abstract":"<p>This protocol describes procedures for the preparation of a modified thymidine conjugated with galactose via a self-immolative linker at the <i>O</i>4-position, and the synthesis of β-galactosidase-responsive prodrug-type oligodeoxynucleotides (ONs) containing these modified thymidines. These prodrug-ONs are designed to be activated in response to β-galactosidase, enabling targeted activation in specific cells or tissues and potentially contributing to the reduction of adverse effects. © 2025 Wiley Periodicals LLC.</p><p><b>Basic Protocol 1</b>: Preparation of <i>O</i>4-modified thymidine phosphoramidite <b>7</b></p><p><b>Basic Protocol 2</b>: Preparation of <i>O</i>4-modified thymidine phosphoramidite <b>15</b></p><p><b>Support Protocol 1</b>: Preparation of triazolyl thymidine derivative <b>1</b></p><p><b>Support Protocol 2</b>: Preparation of benzyl alcohol derivative <b>2</b></p><p><b>Basic Protocol 3</b>: Preparation of β-galactosidase-responsive <b>ODNs 1</b> to <b>5</b></p>","PeriodicalId":93970,"journal":{"name":"Current protocols","volume":"5 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143786886","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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