Epigenetic Suppression of Transgenic T-cell Receptor Expression via Gamma-Retroviral Vector Methylation in Adoptive Cell Transfer Therapy

Abstract

Transgenic T-cell receptor (TCR) adoptive cell therapies recognizing tumor antigens are associated with robust initial response rates, but frequent disease relapse. This usually occurs in the setting of poor long-term persistence of cells expressing the transgenic TCR, generated using murine stem cell virus (MSCV) γ -retroviral vectors. Analysis of clinical transgenic adoptive cell therapy products in vivo revealed that despite strong persistence of the transgenic TCR DNA sequence over time, its expression was profoundly decreased over time at the RNA and protein levels. Patients with the greatest degrees of expression suppression displayed signifi cant increases in DNA methylation over time within the MSCV promoter region, as well as progressive increases in DNA methylation within the entire MSCV vector over time. These increases in vector methylation occurred independently of its integration site within the host genomes. These results have signifi cant implications for the design of future viral vector gene-engineered adoptive cell transfer therapies. SIGNIFICANCE:Cellular immunotherapies' reliance on retroviral vectors encoding foreign genetic material can be vulnerable to progressive acquisition of DNA methylation and subsequent epigenetic suppression of the transgenic product in TCR adoptive cell therapy. This must be considered in the design of future generations of cellular immunotherapies for cancer. intRoDuctionGenetically engineered adoptive cell therapy (ACT) is revolutionizing cancer treatment, with sustained clinical responses seen in a variety of malignancies. Current approaches utilize retroviral or lentiviral vectors for ex vivo transduction of a patient's T cells to express either a cancer antigen-specifi c T-cell receptor (TCR) or a chimeric antigen receptor (CAR). These reinfused cells then create a focused antitumor response in a variety of cancer subtypes ( 1, 2 ). However, although these Cancer Research.

BET bromodomain protein inhibition reverses chimeric antigen receptor extinction and reinvigorates exhausted T cells in chronic lymphocytic leukemia

“…However, loss of vector-driven transcriptional activity in cells containing proviral DNA has been observed early after transduction (52), which drastically limits the efficacy of vector-based gene delivery platforms. Although attempts to optimize vector design, particularly with γ-retroviruses, have augmented transgene expression, these systems remain susceptible to promoter shutdown (16,53).…”

“…The level and duration of cell-surface CAR expression may also be an important T cell-intrinsic factor influencing clinical efficacy, and receptor extinction as a potential mechanism of resistance has not been widely explored in the context of CAR T cell therapy. The half-life of transgenic antigen receptor expression has been previously implicated as a major determinant of clinical responses to TCR-engineered T cells (15,16). Transgene shutdown, as defined by an immediate silencing or a gradual decrease in gene expression after differentiation or proliferation of cells transduced with integrating viruses, can occur through multiple epigenetic processes, potentially leading to poor clinical responses to adoptive cell therapies (17).…”

Epigenetic Profiling and Response to CD19 Chimeric Antigen Receptor T-Cell Therapy in B-Cell Malignancies

“…Our results strengthen the notion that the molecular profiles of the cells used in adoptive cell therapy is of great value for determining treatment success. This approach has also been proposed for immune checkpoint inhibitors ( 13 , 14 ). Thus, biomarkers of the efficacy of adoptive cell therapy, similar to those cited here ( 5–9 , 37 ), and the DNA methylation markers discovered in our study almost certainly await discovery.…”

“…DNA methylation is altered in cancer ( 10 , 11 ), affecting the immune system and immunotherapy efficacy ( 12 ). In this regard, DNA methylation signatures are associated with clinical response to programmed cell death protein 1 checkpoint blockade ( 13 ) and the DNA methylation status of the vector for transgenic T-cell receptor adoptive cell therapy relates to changes in tumor burden ( 14 ). For these reasons, we decided to assess the effects of the DNA methylation landscape of preinfused CART19 cells on the clinical outcome of patients with B-cell malignancies.…”

Recent progress in targeted delivery vectors based on biomimetic nanoparticles

“…Similarly, in a child with junctional epidermolysis bullosa, the human epidermis can be regenerated entirely by autologous transgenic keratinocyte cultures via retroviral vectors 297 . Another clinical study indicated that γ retroviral vector showed epigenetic suppression of transgenic T-cell receptor expression through the vector methylation in adoptive cell transfer therapy 298 . Moreover, the anticancer vaccine based on an alphaviral vector enhanced HER2-specific memory CD8 + T cells and exhibited obvious inhibition of breast cancer in clinical testing 299 .…”