Insertional transformation of hematopoietic cells by self-inactivating lentiviral and gammaretroviral vectors

Abstract

Gene transfer vectors may cause clonal imbalance and even malignant cell transformation by insertional upregulation of proto-oncogenes. Lentiviral vectors (LV) with their preferred integration in transcribed genes are considered less genotoxic than gammaretroviral vectors (GV) with their preference for integration next to transcriptional start sites and regulatory gene regions. Using a sensitive cell culture assay and a series of self-inactivating (SIN) vectors, we found that the lentiviral insertion pattern was approximately threefold less likely than the gammaretroviral to trigger transformation of primary hematopoietic cells. However, lentivirally induced mutants also showed robust replating, in line with the selection for common insertion sites (CIS) in the first intron of the Evi1 proto-oncogene. This potent proto-oncogene thus represents a CIS for both GV and LV, despite major differences in their integration mechanisms. Altering the vectors' enhancer-promoter elements had a greater effect on safety than the retroviral insertion pattern. Clinical grade LV expressing the Wiskott-Aldrich syndrome (WAS) protein under control of its own promoter had no transforming potential. Mechanistic studies support the conclusion that enhancer-mediated gene activation is the major cause for insertional transformation of hematopoietic cells, opening rational strategies for risk prevention.

Figures

Figure 1

Transforming activity of integrating vectors depends on vector background and content. (a) Vectors tested in the in vitro immortalization (IVIM) assay in the first set of experiments. We compared the IVIM frequency of three SIN-LV with different internal promoters (SFFV, PGK, and VAV) with an LTR-driven GV (SF91.eGFP.pre) and a SIN-GV (GV.SF.eGFP.pre). The latter represents the gammaretroviral equivalent of LV.SF.eGFP.pre. We also tested a SIN-LV that expresses WASP from the WAS promoter (LV.WASP.WAS). (b) Results of the IVIM assay: plotted are the replating frequencies corrected for the mean copy number as measured in the DNA of mass cultures taken 4 days after transduction. In none of the assays performed (n = 8), we obtained replating clones from untransduced cultures (mock), whereas SF91.eGFP.pre transduced cells always led to immortalized clones (n = 8). When transducing cells with the LV.SF.eGFP (n = 8) or LV.SF.eGFP.pre (n = 8), on average, every second assay developed replating clones (reduced incidence of immortalization, P = 0.0058 Fisher's exact test). In comparison, we have plotted results obtained with the GV.SF.eGFP.pre including previously published data indicated in gray,13 and the positive control, SF91.eGFP.pre. Horizontal bars indicate the median of all positive assays for a given vector. eGFP, enhanced green fluorescent protein; LTR, long terminal repeat; neg., negative; PGK, phosphoglycerate kinase; WAS, Wiskott–Aldrich syndrome.

Figure 2

Evi1 is a common insertion site for both gammaretroviral and lentiviral vectors. (a) Insertion sites identified in Evi1: in three of six independent lentiviral clones analyzed, we detected one insertion site in the first intron of Evi1 (long arrows with asterisks). The insertions were found within a region comprising about 11 kilobases in which most of the gammaretroviral vector (GV) insertions were detected so far. Previously reported insertion sites detected in in vitro immortalization clones are indicated as short hatched arrows (GV.SF.eGFP.pre) and short arrows (SF91.eGFP.pre).14 GV insertions recovered in leukemias and dominant clones in vivo in the mouse are indicated below the horizontal line.37 (b) Northern blot analysis showing strong upregulation of Evi1 transcript in all clones analyzed compared to the expression levels in mock-treated cells (left lane). (c) Evi1 expression levels in immortalized clones that were obtained and expanded in this study. All clones show strong upregulation of Evi1 mRNA when compared to the level in mock cells (grown for 2 weeks as mass culture).

Figure 3

Enhancer sequences are the driving force of replating activity. (a) LTR-driven GV were generated that carried deletions of the complete enhancer (NheI-AflII, 30–264), or promoter (AflII-AscI, 264–413), or the enhancer and promoter. The deletions were introduced in the vector SFβ91.eGFP.pre. After retroviral transduction, the deletions were present in both LTRs. Further vectors had specific mutations in transcription factor binding sites, either in the Ets binding site at position 139, or both Sp1 sites at positions 102 and 220. Those mutations were introduced in the SFα, an LTR with a deletion of the imperfect direct repeat of the enhancer array.23 (b) Vector constructs used in the IVIM assays in the second set of experiments. (c) Replating index derived in the IVIM assays performed with enhancer deletion and enhancer mutation vectors: the deletion of the SFFV enhancer (SFβ91.ΔE) from the viral LTR leaving the promoter intact abrogated the immortalization ability of the SFβ91.eGFP.pre as did the complete deletion of the viral enhancer–promoter (SFβ91.ΔE/P). The mutation of an Ets site reduced the replating frequency/copy number ~10 times (P = 0.03). The data points shown for the SFβ91.eGFP.pre contain those obtained in this experimental set (black) and data points that were obtained in the previous experiments as shown in Figure 1 (gray). eGFP, enhanced green fluorescent protein; LTR, long terminal repeat; neg, negative.