Methods in cell biology最新文献_第7页

Epigenetic analysis in cancer research. 癌症研究中的表观遗传分析。

4区生物学

Methods in cell biology Pub Date : 2025-01-01 Epub Date: 2025-03-17 DOI: 10.1016/bs.mcb.2025.02.021

Lakshita Tyagi, Umesh Kumar, Shreeja Mishra, Simran, Garima Rathi, Deepak Parashar

{"title":"Epigenetic analysis in cancer research.","authors":"Lakshita Tyagi, Umesh Kumar, Shreeja Mishra, Simran, Garima Rathi, Deepak Parashar","doi":"10.1016/bs.mcb.2025.02.021","DOIUrl":"https://doi.org/10.1016/bs.mcb.2025.02.021","url":null,"abstract":"The understanding of cancer mechanisms has advanced, revealing the crucial roles of oncogenes, tumor suppressor genes, and epigenetics in cancer progression, making it the second deadliest disease. Genetic changes activating oncogenes and causing uncontrolled cell growth include the Philadelphia chromosome translocation and Ras mutations. Epigenetic alterations like histone modifications and DNA methylation can also disrupt gene regulation in cancer cells. The combination of genetic and epigenetic changes speeds up cancer spread and provides new targets for treatment. Abnormalities in chromatin structure affect gene activity, impacting cellular functions. DNA methylation patterns affect tumor suppressor genes and proto-oncogenes, closely linked to cancer development and spread. DNMT inhibitors, such as Decitabine and Azacytidine, target DNA methylation and show promise in treating certain blood disorders. Non-nucleoside inhibitors are being developed to reduce the toxicity of nucleoside analogs. Cancer treatments focus on histone modifications like acetylation and methylation, crucial for gene control. In has been demonstrated that inhibitors that targets the demethylases and histone methyltransferases stop the proliferation of cancer cells. The FDA has approved HDAC inhibitors such as Panobistat and Vorinostat to trat some types of blood cancer. Novel substances targeting HATs and HDACs, such as PU141 and C646, exhibit inhibitory effects on these enzymes, limiting cancer cell growth. Research is ongoing on natural substances with HDAC inhibitory action, such as apicidin and amamistatin. The effectiveness and safety of the epigenetic cancer treatment are being assessed in the clinical trials. Overall, the potential of epigenetic changes in cancer therapy offers hope for improved outcomes in challenging cancers.","PeriodicalId":18437,"journal":{"name":"Methods in cell biology","volume":"198 ","pages":"135-172"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145206771","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}

引用次数: 0

Matching model with mechanism: Appropriate rodent models for studying various aspects of diabetes pathophysiology. 与机制匹配的模型：适合研究糖尿病病理生理各方面的啮齿动物模型。

4区生物学

Methods in cell biology Pub Date : 2025-01-01 Epub Date: 2024-06-19 DOI: 10.1016/bs.mcb.2024.05.003

Lydia F Daniels Gatward, Aileen J F King

{"title":"Matching model with mechanism: Appropriate rodent models for studying various aspects of diabetes pathophysiology.","authors":"Lydia F Daniels Gatward, Aileen J F King","doi":"10.1016/bs.mcb.2024.05.003","DOIUrl":"10.1016/bs.mcb.2024.05.003","url":null,"abstract":"Many rodent models are available for preclinical diabetes research making it a challenge for researchers to choose the most appropriate one for their experimental question. To aid in this, models have classically been categorized according to which type of diabetes they represent, and further into whether the model is induced, spontaneous or the result of genetic manipulation. This fails to capture the complexity of pathogenesis seen in diabetes in humans. This includes pathogenesis specifically involving the beta cell, which is no longer considered to be innocuous in the development and progression of diabetes. In this chapter we explore rodent models that incorporate the initiating factors believed to be involved in type 1 diabetes (autoimmunity) and type 2 diabetes (insulin resistance), before further discussing rodents that can be used to model specific mechanisms involved in a failure of functional beta cell mass (impaired beta cell function and beta cell apoptosis). We segregate models of beta cell pathogenesis based on the beta cell stressor predominantly associated with phenotype, but it is important to consider that most rodent models will exhibit more than one beta cell stressor. Similarly, many models exhibit more than one pathogenic mechanism, for example the same model may show insulin resistance, impaired beta cell function as well as beta cell loss. This can complicate interpretation of results and should be considered, and the model thoroughly researched, during the experimental planning stage.","PeriodicalId":18437,"journal":{"name":"Methods in cell biology","volume":"192 ","pages":"39-68"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143039857","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}

引用次数: 0

Evaluating transcriptional tumour microenvironment response to immunotherapy using microarray analysis: From harvesting tumours to data analysis. 利用微阵列分析评估转录肿瘤微环境对免疫治疗的反应：从收集肿瘤到数据分析。

4区生物学

Methods in cell biology Pub Date : 2025-01-01 Epub Date: 2025-02-09 DOI: 10.1016/bs.mcb.2025.01.004

Olga Cormier, Maria Eugenia Davola, Susan Collins, Karen Mossman

{"title":"Evaluating transcriptional tumour microenvironment response to immunotherapy using microarray analysis: From harvesting tumours to data analysis.","authors":"Olga Cormier, Maria Eugenia Davola, Susan Collins, Karen Mossman","doi":"10.1016/bs.mcb.2025.01.004","DOIUrl":"https://doi.org/10.1016/bs.mcb.2025.01.004","url":null,"abstract":"In the recent years, a better understanding of the cellular and molecular processes that shape the dynamic balance of the immune system and the tumour has been gained. Accumulating evidence shows that cellular and acellular components in the tumour microenvironment (TME) can reprogram the response to immunotherapies. Transcriptome analyses of immunotherapy treatments have been invaluable for studying signalling pathways in cancer. Transcriptional characterization of tumours has allowed researchers to both predict the likely response to therapy as well as to evaluate the effect of therapy on tumours before any phenotypic changes are observed. Despite the rise of single-cell RNA sequencing (scRNAseq) it remains costly and technically challenging and, in many situations, unnecessarily detailed. Presented here is a protocol describing processing of tumours for microarray transcriptome analysis to evaluate the responses to therapy. This method has proven to be cost-effective in cases when broad transcriptional responses are being investigated.","PeriodicalId":18437,"journal":{"name":"Methods in cell biology","volume":"196 ","pages":"225-236"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144667967","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}

引用次数: 0

Next-generation deconvolution of the tumor microenvironment with omnideconv. 新一代肿瘤微环境反褶积技术的研究。

4区生物学

Methods in cell biology Pub Date : 2025-01-01 Epub Date: 2025-02-06 DOI: 10.1016/bs.mcb.2025.01.003

Lorenzo Merotto, Alexander Dietrich, Markus List, Francesca Finotello

{"title":"Next-generation deconvolution of the tumor microenvironment with omnideconv.","authors":"Lorenzo Merotto, Alexander Dietrich, Markus List, Francesca Finotello","doi":"10.1016/bs.mcb.2025.01.003","DOIUrl":"10.1016/bs.mcb.2025.01.003","url":null,"abstract":"The tumor microenvironment and, particularly, tumor-infiltrating immune cells can profoundly influence tumor progression and response to therapy. Deconvolution is a powerful computational technique to estimate cell-type fractions from bulk RNA sequencing (RNA-seq) data leveraging expression signatures specific to the cell types of interest. Recently, a new generation of deconvolution algorithms has emerged, making it possible to directly learn cell-type-specific signatures to be used for deconvolution from annotated single-cell RNA-seq (scRNA-seq) datasets. Thanks to their flexibility, these next-generation methods can extend deconvolution to any cell type, tissue, and organism for which a suitable single-cell reference is available. However, these methodologies are highly diverse in terms of programming languages, computational workflows, and input/output data, which complicate their usage and comparison. To overcome these challenges, we developed omnideconv, an R package that integrates several deconvolution methods, streamlining their usage and unifying their semantics. In this chapter, we demonstrate how omnideconv can be integrated with an annotated scRNA-seq dataset, comprising both malignant and normal cells from the breast cancer microenvironment, to quantify the cellular composition of bulk RNA-seq data from a cohort of breast cancer patients.","PeriodicalId":18437,"journal":{"name":"Methods in cell biology","volume":"196 ","pages":"87-112"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144667973","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}

引用次数: 0

Saphenous vein blood collection for different immune analyses of living mice. 活体小鼠不同免疫分析的隐静脉采血。

4区生物学

Methods in cell biology Pub Date : 2025-01-01 Epub Date: 2025-04-10 DOI: 10.1016/bs.mcb.2025.03.003

Kenny Misael Calvillo-Rodriguez, Kassandra Ofelia Rodriguez-Aguillon, Reyes Tamez-Guerra, Ana Carolina Martinez-Torres, Cristina Rodriguez-Padilla

引用次数: 0

Generation and functional evaluation of bispecific T cell engaging antibodies. 双特异性T细胞接合抗体的产生和功能评价。

4区生物学

Methods in cell biology Pub Date : 2025-01-01 Epub Date: 2025-03-13 DOI: 10.1016/bs.mcb.2025.02.012

Antonio Tapia-Galisteo, Rodrigo Lázaro-Gorines, Luis Álvarez-Vallina

{"title":"Generation and functional evaluation of bispecific T cell engaging antibodies.","authors":"Antonio Tapia-Galisteo, Rodrigo Lázaro-Gorines, Luis Álvarez-Vallina","doi":"10.1016/bs.mcb.2025.02.012","DOIUrl":"https://doi.org/10.1016/bs.mcb.2025.02.012","url":null,"abstract":"T cell engagers (TCE) are a class of bispecific antibodies that simultaneously target a tumor antigen and CD3, acting as a bridge between T cells and tumor cells. They promote the formation of T cell receptor (TCR)-independent canonical immune synapses and potent tumor-specific cytotoxic responses at extremely low concentrations. TCE-based immunotherapeutic have revolutionized the treatment landscape for hematological cancers. Structurally, TCE can be divided into non-IgG-like formats consisting of antibody fragments fused to an Fc-free polypeptide, and IgG-like formats containing an Fc region for construct dimerization. For the former, tandem single-chain variable fragment (scFv) are the most common design. They are potent and small molecules with high tissue penetration and improved tumor penetration, but also have a short serum half-life. To maintain effective serum antibody levels, they require continuous infusion or other strategies such as engineering T cells to secrete the TCE in situ. On the other hand, to enable monovalent CD3 interaction, the binding domains of IgG-like TCEs are usually heterodimerized by incorporating complementary docking mutations in the CH3 domains. In addition, most IgG-like TCEs contain engineered silent Fc to eliminate unwanted Fc interactions and mitigate potential toxicity, while retaining the potential for half-life extension. Here we present detailed protocols for the design, generation and validation of both non-IgG-like and IgG-like TCE, as well as their recombinant production and characterization. The methodology covers construct generation, antibody expression in mammalian systems and purification by chromatography. Finally, structural and functional characterization includes biophysical studies including in vitro and in vivo studies.","PeriodicalId":18437,"journal":{"name":"Methods in cell biology","volume":"199 ","pages":"167-186"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145313360","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}

引用次数: 0

Visualizing mitochondrial electron transport chain complexes and super-complexes during infection of human macrophages with Legionella pneumophila. 嗜肺军团菌感染人巨噬细胞时线粒体电子传递链复合物和超复合物的可视化。

4区生物学

Methods in cell biology Pub Date : 2025-01-01 Epub Date: 2024-03-07 DOI: 10.1016/bs.mcb.2024.01.003

Mariatou Dramé, Daniel Schator, Carmen Buchrieser, Pedro Escoll

{"title":"Visualizing mitochondrial electron transport chain complexes and super-complexes during infection of human macrophages with Legionella pneumophila.","authors":"Mariatou Dramé, Daniel Schator, Carmen Buchrieser, Pedro Escoll","doi":"10.1016/bs.mcb.2024.01.003","DOIUrl":"10.1016/bs.mcb.2024.01.003","url":null,"abstract":"The ultrastructure of mitochondria is pivotal for their respiratory activity. Thus, the regulation of the assembly of the super-complexes (SCs) of the mitochondrial electron transport chain (ETC) might be a core aspect of macrophage immunometabolism during bacterial infection. In order to study the impact of infection by Legionella pneumophila on the configuration of mitochondrial complexes and SCs in human macrophages, we have adapted and combined different methods such as cell sorting of infected cells, magnetic isolation of highly pure and functional mitochondria, quality control of mitochondrial purity by flow cytometry, and BN-PAGE (Blue-Native Polyacrylamide Gel Electrophoresis) coupled to Western Blot using near-infrared (NIR) fluorescence. The here presented protocol uses infected and non-infected human macrophage-like THP-1 cells and GFP-expressing L. pneumophila, but the method can be used to analyze the configuration of ETC complexes and SCs also in other mammalian cells and infected with different intracellular bacteria expressing a fluorescent protein.","PeriodicalId":18437,"journal":{"name":"Methods in cell biology","volume":"194 ","pages":"19-42"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586259","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}

引用次数: 0

Monitoring cellular dynamics upon infection using a holotomography-based approach. 使用基于全息成像的方法监测感染后的细胞动力学。

4区生物学

Methods in cell biology Pub Date : 2025-01-01 Epub Date: 2025-01-10 DOI: 10.1016/bs.mcb.2024.12.003

Ilaria Nunzi, Gloria D'Achille, Nada Dhaouadi, Fabio Marcheggiani, Caterina Licini, Mariangela Di Vincenzo, Monia Orciani, Gianluca Morroni, Saverio Marchi

引用次数: 0

A screening system to determine the effect of bacterial metabolites on MAdCAM-1 expression by transformed endothelial sinusoidal cells. 细菌代谢物对转化内皮窦细胞MAdCAM-1表达影响的筛选系统

4区生物学

Methods in cell biology Pub Date : 2025-01-01 Epub Date: 2024-02-26 DOI: 10.1016/bs.mcb.2024.01.007

Ai-Ling Tian, Marion Leduc, Marine Fidelle, Laurence Zitvogel, Guido Kroemer, Oliver Kepp

{"title":"A screening system to determine the effect of bacterial metabolites on MAdCAM-1 expression by transformed endothelial sinusoidal cells.","authors":"Ai-Ling Tian, Marion Leduc, Marine Fidelle, Laurence Zitvogel, Guido Kroemer, Oliver Kepp","doi":"10.1016/bs.mcb.2024.01.007","DOIUrl":"10.1016/bs.mcb.2024.01.007","url":null,"abstract":"Mucosal addressin cell adhesion molecule 1 (MAdCAM-1) expression in high endothelial venules is regulated by bacterial metabolites emanating from the gut and the interaction of MAdCAM-1 with α4β7 integrin mediates lymphocyte diapedesis into gut-associated secondary lymphoid tissues. MAdCAM-1 thus controls the abundance of circulating immunosuppressive T cells that can reach malignant tissue and compromise the therapeutic efficacy of anticancer immunotherapy. Here we describe a biosensor-based phenotypic assessment that facilitates the high throughput screening (HTS)-compatible assessment of MAdCAM-1 regulation in response to exposure to bacterial metabolites. This screening routine encompasses high endothelial venule cells expressing green fluorescent protein (GFP) under the control of the MAdCAM-1 promoter combined with robot-assisted bioimaging and a multistep image analysis pipeline. Altogether this system facilitates the discovery of bacterial composites that control anticancer immunity via the sequestration of Th17-specific regulatory T cells (Treg17) in the gut.","PeriodicalId":18437,"journal":{"name":"Methods in cell biology","volume":"194 ","pages":"119-133"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143586222","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}

引用次数: 0

Orthotopic model of tongue cancer for the study of head and neck squamous cell carcinoma in mice. 舌癌原位模型用于小鼠头颈部鳞状细胞癌的研究。

4区生物学

Methods in cell biology Pub Date : 2025-01-01 Epub Date: 2025-05-15 DOI: 10.1016/bs.mcb.2025.03.023

Sarah Adriana Scuderi, Fatima Domenica Elisa De Palma, Deborah Mannino, Maria Perez-Lanzon, Lionel Deroche, Marie Valet, Pierre Cordier, Jonathan G Pol, Guido Kroemer, Maria Chiara Maiuri

{"title":"Orthotopic model of tongue cancer for the study of head and neck squamous cell carcinoma in mice.","authors":"Sarah Adriana Scuderi, Fatima Domenica Elisa De Palma, Deborah Mannino, Maria Perez-Lanzon, Lionel Deroche, Marie Valet, Pierre Cordier, Jonathan G Pol, Guido Kroemer, Maria Chiara Maiuri","doi":"10.1016/bs.mcb.2025.03.023","DOIUrl":"https://doi.org/10.1016/bs.mcb.2025.03.023","url":null,"abstract":"Head and neck squamous cell carcinoma (HNSCC) is among the most prevalent human malignancies globally, with approximately 887,000 new cases diagnosed each year. Currently, the standard treatment for HNSCC involves surgery, followed by radiotherapy, chemotherapy and immunotherapy. However, despite these available treatments, the survival rate of patients with HNSCC remains low. A key factor in the development of HNSCC is genomic instability, which significantly influences several phases of the disease such as initiation and progression. Given the complexity of HNSCC, preclinical models are essential for exploring the mechanisms driving HNSCC progression, at the (epi)genetic (e.g., DNA mutations, histone modifications), cellular (e.g., resistance to cell death, autophagy) and histological (e.g., cancer-immunity cycle) levels. Moreover, such a model is precious for developing new therapies. In this context, we provide a comprehensive protocol outlining the steps required to establish a syngeneic orthotopic tongue mouse model, including cell preparation and injection steps. By implanting cells in their natural anatomical location within immunocompetent mice, this model allows to investigate interactions between the tumor and surrounding tissues, which can significantly influence tumor growth.","PeriodicalId":18437,"journal":{"name":"Methods in cell biology","volume":"197 ","pages":"179-192"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145033363","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}

引用次数: 0