Current Methodology Advances in Cell Therapy Applications

A special issue of Methods and Protocols (ISSN 2409-9279).

Deadline for manuscript submissions: 25 September 2025 | Viewed by 2973

Special Issue Editors

Department of Microbiology, Immunology and Genetics, Health Science Center, University of North Texas, Fort Worth, TX 76107, USA
Interests: cellular reprogramming; induced pluripotent stem cells; iPSCs; bromodomain extra terminal (BET) protein; epigenetics; molecular biology; cell biology
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Guest Editor
Department of Physiology and Pharmacology, Sapienza University, 00185 Rome, Italy
Interests: cell biology; molecular biology; transcriptional regulation; cardiac and skeletal muscle physiology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Cell Therapy per definition uses cellular material that is injected or transplanted into a patient with the aim of treating a disease. Cell Therapy approaches are naturally diverse. Approaches can use autologous (i.e., patient self-derived) material or allogeneic cells (derived from either genetically matched donors or from engineered stem cells). One prominent and well-studied example of Cell Therapy applications are autologous CAR T therapies, where patient T cells are genetically engineered to express specific tumor-targeting chimeric antigen receptors. CAR T therapies have proven to be an efficient treatment for a variety of hematologic cancers. Alternatively, stem cell-derived allogeneic therapies use genetically engineered human stem cells or human-induced pluripotent stem cells that will later be differentiated into the desired effector cells, ensuring a much wider target range. Such allogeneic therapy will provide almost unlimited material and can be applied to a larger number of patients. Cell-based therapies are a rapidly developing field with high medical interest. Cell Therapy development uses cutting-edge techniques that are constantly optimized in several fields: generation of appropriate cell sources, genetic engineering of donor cells, differentiation protocols for stem cell-based products and aspects of safety studies, and rigorous quality assurance procedures for Cell Therapy products.

This Special Issue of Methods and Protocols wants to bridge all these efforts and to collect recent advances in methods, procedures, and protocols for all areas of Cell Therapy applications. We are very much looking forward to receiving your invaluable contributions.

Dr. Kejin Hu
Dr. Lucia Monaco
Dr. Philip Hublitz
Guest Editors

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Keywords

  • cell therapy
  • autologous
  • allogeneic
  • stem cell-based therapies
  • T cell engineering
  • immuno-oncology
  • tissue repair

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Published Papers (2 papers)

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14 pages, 1963 KiB  
Article
K562 Chronic Myeloid Leukemia Cells as a Dual β3-Expressing Functional Cell Line Model to Investigate the Effects of Combined αIIbβ3 and αvβ3 Antagonism
by Amal A. Elsharif, Laurence H. Patterson, Steven D. Shnyder and Helen M. Sheldrake
Methods Protoc. 2025, 8(4), 73; https://doi.org/10.3390/mps8040073 - 5 Jul 2025
Viewed by 618
Abstract
Several of the integrin family of cell adhesion receptors have been popular targets for the development of anticancer agents, but with little clinical success to date. Cancer cells usually express multiple redundant integrins; one hypothesis for the lack of efficacy of current antagonists [...] Read more.
Several of the integrin family of cell adhesion receptors have been popular targets for the development of anticancer agents, but with little clinical success to date. Cancer cells usually express multiple redundant integrins; one hypothesis for the lack of efficacy of current antagonists is their high selectivity for a single integrin. To address this, we developed a functional dual-β3-expressing cell model to investigate the effects of combined αIIbβ3/αvβ3 antagonism. We established that treating K562 chronic myeloid leukemia cells with 0.04 μM phorbol 12-myristate 13-acetate (PMA) for 40 h significantly upregulates functional αIIbβ3 and αvβ3 integrins. This optimized method provides a reliable platform for adhesion and detachment assays, enabling the characterization of dual integrin targeting strategies. Using this model, we demonstrate that combining αIIbβ3 and αvβ3 antagonists (GR144053 and cRGDfV) synergistically enhances inhibition of cell adhesion and promotes cell detachment compared to single-agent treatments. Our findings establish a reproducible approach for studying dual β3 integrin targeting, which can be used to investigate potential strategies for overcoming integrin redundancy in cancer therapeutics. Full article
(This article belongs to the Special Issue Current Methodology Advances in Cell Therapy Applications)
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19 pages, 4506 KiB  
Protocol
Analysis of Processing, Post-Maturation, and By-Products of shRNA in Gene and Cell Therapy Applications
by Zhenyi Hong, Nikola Tesic and Xavier Bofill-De Ros
Methods Protoc. 2025, 8(2), 38; https://doi.org/10.3390/mps8020038 - 7 Apr 2025
Viewed by 1278
Abstract
Short hairpin RNAs (shRNAs) are potent tools for gene silencing, offering therapeutic potential for gene and cell therapy applications. However, their efficacy and safety depend on precise processing by the RNA interference machinery and the generation of minimal by-products. In this protocol, we [...] Read more.
Short hairpin RNAs (shRNAs) are potent tools for gene silencing, offering therapeutic potential for gene and cell therapy applications. However, their efficacy and safety depend on precise processing by the RNA interference machinery and the generation of minimal by-products. In this protocol, we describe how to systematically analyze the processing of therapeutic small RNAs by DROSHA and DICER1 and their incorporation into functional AGO complexes. Using standard small RNA sequencing and tailored bioinformatic analysis (QuagmiR), we evaluate the different steps of shRNA maturation that influence processing efficiency and specificity. We provide guidelines for troubleshooting common design pitfalls and off-target effects in transcriptome-wide profiling to identify unintended mRNA targeting via the miRNA-like effect. We provide examples of the bioinformatic analysis that can be performed to characterize therapeutic shRNA. Finally, we provide guidelines for troubleshooting shRNA designs that result in suboptimal processing or undesired off-target effects. This protocol underscores the importance of rational shRNA design to enhance specificity and reduce biogenesis by-products that can lead to off-target effects, providing a framework for optimizing the use of small RNAs in gene and cell therapies. Full article
(This article belongs to the Special Issue Current Methodology Advances in Cell Therapy Applications)
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