Methods in cell biologyPub Date : 2025-01-01Epub Date: 2025-03-18DOI: 10.1016/bs.mcb.2025.02.023
Preeti Jain, Nitika Joshi, Sadhna Aggarwal
{"title":"Cell culture techniques for cancer research.","authors":"Preeti Jain, Nitika Joshi, Sadhna Aggarwal","doi":"10.1016/bs.mcb.2025.02.023","DOIUrl":"https://doi.org/10.1016/bs.mcb.2025.02.023","url":null,"abstract":"<p><p>Cancer is perceived as difficult to treat due to its capacity to manifest in different forms and lack of knowledge of mechanical details. Advances in the analytical techniques relevant to boosting cancer research require an hour. With the help of cell culture techniques, several significant advances in cancer research have been made in the recent past. The main difficulty associated with cell culture techniques of cancer research is to create an in vivo tumor microenvironment cost-effectively. Here, in this chapter, we have discussed the different protocols for utilizing cell culture techniques in cancer research. The 2D, 3D, scaffold and organoid based cell culture techniques have been covered in detail. In addition, we have presented a comparative analysis, including advantages and disadvantages of each type of cell culture technique. Moreover, the assays, which can be used for assessing the quality of cancer cell lines, have been listed in detail.</p>","PeriodicalId":18437,"journal":{"name":"Methods in cell biology","volume":"198 ","pages":"27-71"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145206803","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}
Methods in cell biologyPub Date : 2025-01-01Epub Date: 2025-03-11DOI: 10.1016/bs.mcb.2025.02.019
Wasiur Rahman Choudhury, Rama Rao Damerla, K Devaraja
{"title":"Liquid biopsy and circulating tumor cell analysis.","authors":"Wasiur Rahman Choudhury, Rama Rao Damerla, K Devaraja","doi":"10.1016/bs.mcb.2025.02.019","DOIUrl":"https://doi.org/10.1016/bs.mcb.2025.02.019","url":null,"abstract":"<p><p>This chapter introduces to the indications, biofluids used and laboratory methods of liquid biopsy. A detailed description of preanalytical factors, extraction methods, enrichment methods, quality control, storage and analysis of various targets of liquid biopsy such as Circulating Tumor Nucleic Acids, Circulating Tumor Cells, Extracellular Vesicles, and Tumor-educated platelets has been included.</p>","PeriodicalId":18437,"journal":{"name":"Methods in cell biology","volume":"198 ","pages":"313-357"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145206854","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}
Methods in cell biologyPub Date : 2025-01-01Epub Date: 2024-11-19DOI: 10.1016/bs.mcb.2024.10.008
Noor A M Bakker, Claudia Burrello, Karin E de Visser
{"title":"Ex vivo assessment of human neutrophil motility and migration.","authors":"Noor A M Bakker, Claudia Burrello, Karin E de Visser","doi":"10.1016/bs.mcb.2024.10.008","DOIUrl":"10.1016/bs.mcb.2024.10.008","url":null,"abstract":"<p><p>Neutrophils are pivotal in orchestrating tumor-induced systemic inflammation and are increasingly recognized for their critical involvement in both the initiation and progression of cancer. A fundamental facet of neutrophil biology is their migratory capacity, which enables them to extravasate and infiltrate tumors in other tissues, where they carry out essential effector functions. Unraveling the intricate mechanisms of neutrophil motility and migration is crucial for comprehending immune responses and inflammatory processes, shedding light on their substantial contribution to cancer progression. Here, we provide a comprehensive protocol to assess direct ex vivo motility and migration of freshly isolated human neutrophils, offering valuable insights into their behavior.</p>","PeriodicalId":18437,"journal":{"name":"Methods in cell biology","volume":"191 ","pages":"115-133"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008115","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}
Methods in cell biologyPub Date : 2025-01-01Epub Date: 2024-11-19DOI: 10.1016/bs.mcb.2024.10.004
Silvia Santopolo, Cecilia Ciancaglini, Francesca Romana Mariotti, Lorenzo Moretta, Linda Quatrini
{"title":"In vitro ILC differentiation from human HSCs.","authors":"Silvia Santopolo, Cecilia Ciancaglini, Francesca Romana Mariotti, Lorenzo Moretta, Linda Quatrini","doi":"10.1016/bs.mcb.2024.10.004","DOIUrl":"10.1016/bs.mcb.2024.10.004","url":null,"abstract":"<p><p>The Innate Lymphoid Cells (ILCs) are a family of innate immune cells composed by the Natural Killer (NK) cells and the helper ILCs (hILCs) (ILC1, ILC2, ILC3), both developing from a common ILC precursor (ILCP) derived from hematopoietic stem cells (HSCs). A correct ILC reconstitution is crucial, particularly in patients receiving HSC transplantation (HSCT), the only therapeutic option for many adult and pediatric high-risk hematological malignancies. Indeed, mainly thanks to their cytotoxic activity, NK cells have a strong Graft-versus-Leukemia (GvL) effect. On the other hand, hILCs, that are mainly tissue resident, are involved in tissue repair and homeostasis, Graft-versus-Host Disease (GvHD) prevention and immune response to infections. Unlike NK cell development, hILC-poiesis is still poorly characterized in humans. Here, we provide a protocol for the in vitro ILC differentiation from healthy donor peripheral blood-derived CD34<sup>+</sup> HSCs. This could represent a useful model to dissect the molecular mechanisms by which the distinct ILC subsets are generated from ILCP leading to the development of novel strategies to improve the HSCT clinical outcome.</p>","PeriodicalId":18437,"journal":{"name":"Methods in cell biology","volume":"191 ","pages":"41-57"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008130","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}
Methods in cell biologyPub Date : 2025-01-01Epub Date: 2024-11-19DOI: 10.1016/bs.mcb.2024.10.017
Sophia Stock, Luisa Fertig, Vivien Doreen Menkhoff, Thaddäus Strzalkowski, Manuel Caruso, Sebastian Kobold
{"title":"Retrovirus-based manufacturing of chimeric antigen receptor-modified T cells for cancer therapy research.","authors":"Sophia Stock, Luisa Fertig, Vivien Doreen Menkhoff, Thaddäus Strzalkowski, Manuel Caruso, Sebastian Kobold","doi":"10.1016/bs.mcb.2024.10.017","DOIUrl":"10.1016/bs.mcb.2024.10.017","url":null,"abstract":"<p><p>Treatment with autologous chimeric antigen receptor (CAR)-modified T cells can achieve outstanding clinical response rates in heavily pretreated patients with B and plasma cell malignancies. However, relapses occur, and they limit the efficacy of this promising treatment approach. The complex GMP-compliant production and high treatment costs cause that CAR T cells cannot yet be used in a broad population. Among others, CAR T cell therapy has evolved regarding vector design and manufacturing process. Optimal production of CAR T cells is not yet defined, far from being standardized. Quality, cellular composition and immunophenotype of the administered CAR T cells are influenced by the manufacturing protocol and therefore play a crucial role for therapeutic success. For the gene transfer, viral and non-viral strategies are available. Retrovirus-based protocols for CAR T cell production offer advantages in terms of stable gene integration, sufficient transduction efficiency, proven clinical success, and scalability. Here, we detail a retrovirus-based generation protocol of human CAR-modified T cells for experimental immunotherapeutic treatment of cancer cells. For the CAR generation, HEK-293-based packaging cell lines, CD3<sup>+</sup> selection, CD3/CD28-coated bead-based activation and IL-2/IL-15-mediated expansion were used. This protocol can be applied for every possible CAR construct after being successfully transfected in HEK-293-based packaging cell lines.</p>","PeriodicalId":18437,"journal":{"name":"Methods in cell biology","volume":"191 ","pages":"329-352"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008161","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}
Methods in cell biologyPub Date : 2025-01-01Epub Date: 2024-11-14DOI: 10.1016/bs.mcb.2024.10.015
Mireia Cruz De Los Santos, Andreas Lundqvist
{"title":"Evaluation of lymphocyte infiltration into cancer spheroids by immunofluorescent staining and 3D imaging.","authors":"Mireia Cruz De Los Santos, Andreas Lundqvist","doi":"10.1016/bs.mcb.2024.10.015","DOIUrl":"10.1016/bs.mcb.2024.10.015","url":null,"abstract":"<p><p>In recent years, three-dimensional (3D) cultures of tumor cells has emerged as an important tool in cancer research. The significance of 3D cultures, such as tumor spheroids, lies in their ability to mimic the in vivo tumor microenvironment more precisely, offering a nuanced understanding of immune responses within the context of tumor progression. In fact, the infiltration of cytotoxic lymphocytes is key to determining patients' prognosis in several types of cancer and response to immunotherapy. Therefore, harnessing the cytotoxic and infiltration potential of immune cells is a promising avenue for developing effective therapies. This protocol offers a straightforward approach for analyzing infiltrating lymphocytes in tumor spheroids by confocal microscopy imaging. Although it specifically involves utilizing tumor spheroids and culture with autologous tumor-infiltrating T lymphocytes (TILs), the protocol can be adapted for other immune cell types, such as NK cells.</p>","PeriodicalId":18437,"journal":{"name":"Methods in cell biology","volume":"191 ","pages":"269-287"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143008111","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}
Methods in cell biologyPub Date : 2025-01-01Epub Date: 2024-08-12DOI: 10.1016/bs.mcb.2024.07.005
Camille Daviaud, María Cecilia Lira, Claire Vanpouille-Box, Mara De Martino
{"title":"Stereotactic injection of murine brain tumor cells for neuro-oncology studies.","authors":"Camille Daviaud, María Cecilia Lira, Claire Vanpouille-Box, Mara De Martino","doi":"10.1016/bs.mcb.2024.07.005","DOIUrl":"10.1016/bs.mcb.2024.07.005","url":null,"abstract":"<p><p>Glioblastomas (GBMs) are the most common and aggressive brain tumors, with a poor prognosis. Effective preclinical models are crucial to investigate GBM biology and develop novel treatments. Syngeneic models, which consist in injecting murine GBM cells into mice with a similar genetic background, offer reproducibility, cost-effectiveness, and an intact immune system, making them ideal for immunotherapy research. This chapter presents a comprehensive protocol for stereotactic injection of murine GBM cells into immunocompetent mice to induce intracranial GBM. The protocol covers cell culture, anesthesia, surgical procedures, and post-operative care, allowing the reliable induction of orthotopic brain tumors. This method can be used to study anti-GBM therapies, including immunotherapies, and has the potential to accelerate the development of effective treatments.</p>","PeriodicalId":18437,"journal":{"name":"Methods in cell biology","volume":"192 ","pages":"181-188"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143039911","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}
Methods in cell biologyPub Date : 2025-01-01Epub Date: 2024-11-08DOI: 10.1016/bs.mcb.2024.09.001
Sophie Goyard, Amandine Schneider, Jerko Ljubetic, Nicolas Inacio, Marie Juzans, Céline Cuche, Pascal Bochet, Vincenzo Di Bartolo, Andrés Alcover, Thierry Rose
{"title":"Measuring interaction force between T lymphocytes and their target cells using live microscopy and laminar shear flow chambers.","authors":"Sophie Goyard, Amandine Schneider, Jerko Ljubetic, Nicolas Inacio, Marie Juzans, Céline Cuche, Pascal Bochet, Vincenzo Di Bartolo, Andrés Alcover, Thierry Rose","doi":"10.1016/bs.mcb.2024.09.001","DOIUrl":"10.1016/bs.mcb.2024.09.001","url":null,"abstract":"<p><p>Understanding the immunological synapse formation and dynamics can be enriched by measuring cell-cell interaction forces and their kinetics. Microscopy imaging reveals structural organization of the synapse, while physical methods detail its mechanical construction. Various techniques have been reported for measuring forces needed to rupture the interface between a T lymphocyte and its target cell but most of them measure one pair at a time. We describe here a laminar shear flow-based method that exerts dragging forces on T cell-target cells pairs immobilized on the surface of a flow chamber. Increasing flow rate allows us to observe the detachment of hundreds of cell conjugates on the wide field of a light transmission microscope. Monitoring precisely the flow rate gradient exerted on T cells readily yields synapse rupture measurements. Dragging forces are measured at the point of rupture as a linear function of the flow speed in minutes from 10pN to 20nN for each cell pair among a statistically representative cell population in the whole field of view of a single experiment. The output cells can be collected in multi-well plate sorted in the increasing order of rupture forces. We used this approach to unveil the involvement of the cytoskeleton regulator adenomatous polyposis coli (APC) in the stability of immunological synapses formed between human cytotoxic T cell and tumor target cells. APC is a polarity regulator and tumor suppressor associated with familial adenomatous polyposis and colorectal cancer. Reduced APC expression impairs T cell adhesion with tumor target cells suggesting an impact of APC mutation in anti-tumor immune defense.</p>","PeriodicalId":18437,"journal":{"name":"Methods in cell biology","volume":"193 ","pages":"175-200"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143370861","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}
Methods in cell biologyPub Date : 2025-01-01Epub Date: 2025-03-04DOI: 10.1016/bs.mcb.2025.02.003
Cecilia Pesini, Pilar M Lanuza, Julián Pardo, Diego Sánchez-Martínez, Ariel Ramírez-Labrada
{"title":"Expansion and activation of NK cells supported by accessory cells. Phenotypic and functional characterization.","authors":"Cecilia Pesini, Pilar M Lanuza, Julián Pardo, Diego Sánchez-Martínez, Ariel Ramírez-Labrada","doi":"10.1016/bs.mcb.2025.02.003","DOIUrl":"https://doi.org/10.1016/bs.mcb.2025.02.003","url":null,"abstract":"<p><p>Natural Killer cells (NK) are cytotoxic lymphocytes from the innate immune system that recognize and eliminate virally infected and tumor cells. Accordingly, manipulation of NK cells has been the focus of several immunotherapy protocols aimed at eradicating cancer cells. Allogeneic NK cell therapy was initially described over two decades ago, emphasizing KIR-mismatch's importance in preventing NK cell inhibition and promoting cytotoxicity and tumor elimination without inducing graft-versus-host disease (GvHD). While unstimulated NK cells have shown limited antitumoral activity in adoptive cell therapy, various activation and expansion protocols have been proposed to enhance their cytotoxic potential. Activated and expanded allogeneic NK cells, especially with the rise of chimeric antigen receptor (CAR) therapies, have attracted significant attention from academic and commercial sectors. Protocols typically involve using cytokines and stimulatory cells, such as Epstein-Barr virus (EBV)-transformed lymphoblastoid B cell lines (LCLs) or K562 leukemic cells, before or after NK cell enrichment. Here we present two different standardized protocols for NK cell activation and expansion, offering insights into NK cell-based immunotherapies for cancer treatment. We also present a comprehensive methodology for assessing NK cell-mediated cytotoxicity against Neuroblastoma cell lines in both 2D and 3D cultures. The comprehensive methodology presented here lays the foundation for further research in the field, driving advancements in NK cell-based therapies against malignancies.</p>","PeriodicalId":18437,"journal":{"name":"Methods in cell biology","volume":"196 ","pages":"237-250"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144667968","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}
Methods in cell biologyPub Date : 2025-01-01Epub Date: 2025-03-17DOI: 10.1016/bs.mcb.2025.02.001
Kathryn A Jacobs, Gabriele Bergers
{"title":"Guidelines for the assessment of high endothelial venule functionality and health.","authors":"Kathryn A Jacobs, Gabriele Bergers","doi":"10.1016/bs.mcb.2025.02.001","DOIUrl":"https://doi.org/10.1016/bs.mcb.2025.02.001","url":null,"abstract":"<p><p>High endothelial venules (HEVs) are specialized blood vessels that act as the entry point for lymphocytes into the lymph node. These vessels have a unique cuboidal morphology and modified sugar coating, which favors the entry process. A major challenge in studying these vessels is that isolating and culturing them leads to the loss of their phenotype, making in vivo assessment the only reliable method for their examination. Moreover, there is a current need for consensus guidelines to assess alterations in HEVs. Therefore, we have developed a manual for the assessment of HEV alterations under stress, such as during inflammation or lymph node metastasis, at the protein level via immunofluorescence staining and at the RNA level via single-cell RNA sequencing.</p>","PeriodicalId":18437,"journal":{"name":"Methods in cell biology","volume":"196 ","pages":"1-15"},"PeriodicalIF":0.0,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144667969","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}