Genome-wide profiling of retroviral DNA integration and its effect on clinical pre-infusion CAR T-cell products

Shao, Lipei; Shi, Rongye; Zhao, Yingdong; Liu, Hui; Lu, Alexander; Ma, Jinxia; Cai, Yihua; Fuksenko, Tatyana; Pelayo, Alejandra; Shah, Nirali N.; Kochenderfer, James N.; Norberg, Scott M.; Hinrichs, Christian S.; Highfill, Steven L.; Somerville, Robert; Panch, Sandhya R.; Jin, Ping; Stroncek, David F.

doi:10.1186/s12967-022-03729-5

Cited by 20 publications

(13 citation statements)

References 50 publications

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“…We have previously described the bulk RNA sequencing procedures in detail [ 18 ]. In brief, total mRNA from CAR T-cell products was isolated using the miRNeasy Mini Kit.…”

Section: Methodsmentioning

confidence: 99%

Deciphering the importance of culture pH on CD22 CAR T-cells characteristics

Prochazkova,

Dreyzin,

Shao

et al. 2024

J Transl Med

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Background Chimeric antigen receptor (CAR) T-cells have demonstrated significant efficacy in targeting hematological malignancies, and their use continues to expand. Despite substantial efforts spent on the optimization of protocols for CAR T-cell manufacturing, critical parameters of cell culture such as pH or oxygenation are rarely actively monitored during cGMP CAR T-cell generation. A comprehensive understanding of the role that these factors play in manufacturing may help in optimizing patient-specific CAR T-cell therapy with maximum benefits and minimal toxicity. Methods This retrospective study examined cell culture supernatants from the manufacture of CAR T-cells for 20 patients with B-cell malignancies enrolled in a phase 1/2 clinical trial of anti-CD22 CAR T-cells. MetaFLEX was used to measure supernatant pH, oxygenation, and metabolites, and a Bio-Plex assay was used to assess protein levels. Correlations were assessed between the pH of cell culture media throughout manufacturing and cell proliferation as well as clinical outcomes. Next-generation sequencing was conducted to examine gene expression profiles of the final CAR T-cell products. Results A pH level at the lower range of normal at the beginning of the manufacturing process significantly correlated with measures of T-cell expansion and metabolism. Stable or rising pH during the manufacturing process was associated with clinical response, whereas a drop in pH was associated with non-response. Conclusions pH has potential to serve as an informative factor in predicting CAR T-cell quality and clinical outcomes. Thus, its active monitoring during manufacturing may ensure a more effective CAR T-cell product.

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“…We have previously described the bulk RNA sequencing procedures in detail [ 18 ]. In brief, total mRNA from CAR T-cell products was isolated using the miRNeasy Mini Kit.…”

Section: Methodsmentioning

confidence: 99%

Deciphering the importance of culture pH on CD22 CAR T-cells characteristics

Prochazkova,

Dreyzin,

Shao

et al. 2024

J Transl Med

Self Cite

View full text Add to dashboard Cite

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“…For instance, the integration site within the TET2 gene has been identified as a contributor to clonal expansion [164]. Therefore, the precise localization of the CAR vector in the genome of the T-cell is a crucial factor for successful CAR-T treatment [165,166]. Wang et al developed a method called EpiVIA for profiling chromatin accessibility and identifying lentiviral integration sites at both the cell population and single-cell levels [107].…”

Section: Integration Of Car-encoding Vectorsmentioning

confidence: 99%

Harnessing the Transcriptional Signatures of CAR-T-Cells and Leukemia/Lymphoma Using Single-Cell Sequencing Technologies

Liao,

Hsu,

Chiou

2024

IJMS

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Chimeric antigen receptor (CAR)-T-cell therapy has greatly improved outcomes for patients with relapsed or refractory hematological malignancies. However, challenges such as treatment resistance, relapse, and severe toxicity still hinder its widespread clinical application. Traditional transcriptome analysis has provided limited insights into the complex transcriptional landscape of both leukemia cells and engineered CAR-T-cells, as well as their interactions within the tumor microenvironment. However, with the advent of single-cell sequencing techniques, a paradigm shift has occurred, providing robust tools to unravel the complexities of these factors. These techniques enable an unbiased analysis of cellular heterogeneity and molecular patterns. These insights are invaluable for precise receptor design, guiding gene-based T-cell modification, and optimizing manufacturing conditions. Consequently, this review utilizes modern single-cell sequencing techniques to clarify the transcriptional intricacies of leukemia cells and CAR-Ts. The aim of this manuscript is to discuss the potential mechanisms that contribute to the clinical failures of CAR-T immunotherapy. We examine the biological characteristics of CAR-Ts, the mechanisms that govern clinical responses, and the intricacies of adverse events. By exploring these aspects, we hope to gain a deeper understanding of CAR-T therapy, which will ultimately lead to improved clinical outcomes and broader therapeutic applications.

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“…Moreover, if necessary, adding suicide elements to CAR could eliminate the potential transform risk caused by γ-retrovirus integration. Nevertheless, owing to the drawbacks of γ-retroviruses, such as their inability to infect non-dividing cells and the greater influence on the host transcriptome [ 427 ], lentivirus vectors have gradually replaced them in clinical trials [ 428 ].…”

Section: Gene Transduction Strategies In Actmentioning

confidence: 99%

Challenges and new technologies in adoptive cell therapy

Zhang,

Wan

2023

J Hematol Oncol

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Adoptive cell therapies (ACTs) have existed for decades. From the initial infusion of tumor-infiltrating lymphocytes to the subsequent specific enhanced T cell receptor (TCR)-T and chimeric antigen receptor (CAR)-T cell therapies, many novel strategies for cancer treatment have been developed. Owing to its promising outcomes, CAR-T cell therapy has revolutionized the field of ACTs, particularly for hematologic malignancies. Despite these advances, CAR-T cell therapy still has limitations in both autologous and allogeneic settings, including practicality and toxicity issues. To overcome these challenges, researchers have focused on the application of CAR engineering technology to other types of immune cell engineering. Consequently, several new cell therapies based on CAR technology have been developed, including CAR-NK, CAR-macrophage, CAR-γδT, and CAR-NKT. In this review, we describe the development, advantages, and possible challenges of the aforementioned ACTs and discuss current strategies aimed at maximizing the therapeutic potential of ACTs. We also provide an overview of the various gene transduction strategies employed in immunotherapy given their importance in immune cell engineering. Furthermore, we discuss the possibility that strategies capable of creating a positive feedback immune circuit, as healthy immune systems do, could address the flaw of a single type of ACT, and thus serve as key players in future cancer immunotherapy.

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Genome-wide profiling of retroviral DNA integration and its effect on clinical pre-infusion CAR T-cell products

Cited by 20 publications

References 50 publications

Deciphering the importance of culture pH on CD22 CAR T-cells characteristics

Deciphering the importance of culture pH on CD22 CAR T-cells characteristics

Harnessing the Transcriptional Signatures of CAR-T-Cells and Leukemia/Lymphoma Using Single-Cell Sequencing Technologies

Challenges and new technologies in adoptive cell therapy

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