Chromatin Opening Elements Mitigate Silencing of Transgenes During iPS Cell to Macrophage or Lymphocyte Differentiation

Claire Aibel1, Abigail Blatchford1, Christopher B. Rohde1, Matthew Angel1
1Factor Bioscience Inc., Cambridge, MA

Mol Ther, Vol 32, No 4S1, 2024


Induced pluripotent stem cell (iPSC)-derived therapies hold potential for increased scalability, broader accessibility, and superior production of genetically identical cells compared to traditional allogeneic approaches. Clonal populations of immune cells expressing therapeutic transgenes can be generated from gene-edited iPSCs. Synthetic promoters are often paired with such transgenes, as they can drive high levels of protein expression and avoid genomic disruption associated with the use of endogenous promoters. However, synthetic promoters can become silenced during differentiation or, conversely, induce expression above a therapeutic range. Therefore, there is a need to engineer regulatory elements that can withstand differentiation and drive clinically relevant levels of a desired protein in multiple therapeutic cell types. We designed novel sequences consisting of a synthetic promoter, EF1α or SFC, and an upstream ubiquitous chromatin opening element (UCOE). We generated iPSC lines containing a GFP reporter under EF1α alone, EF1α with a UCOE (uEF1α), or SFC with a UCOE (uSFC) inserted into the AAVS1 safe harbor locus. The iPSCs were differentiated via static culture into lymphocytes (CD7+) or macrophages (CD14+, CD33+), which displayed expected surface marker expression. We found that uEF1α, compared to EF1α alone, promoted not only higher baseline GFP expression levels in both iPSCs and differentiated cells, but also less differentiation-induced silencing. In iPSCs, the percentages of GFP+ cells were similar (EF1α = 97.9%, uEF1α = 98.1%), but median fluorescence intensity (MFI) among the GFP+ cells was 1.6-fold higher under uEF1αthan under EF1α. In the iPSC-derived lymphocytes, the percentage of GFP+ cells was 36.5-fold higher under uEF1α (73%) than under EF1α (2%). Comparison of GFP expression before and after differentiation to lymphocytes indicated that 96% of EF1α cells, but only 25% of uEF1α cells, underwent silencing. Of the GFP+ lymphocytes, the MFI was 7.5-fold higher under uEF1α than under EF1α. In the iPSC-derived macrophages, the percentage of GFP+ cells was 13-fold higher under uEF1α (78%) than under EF1α (6%). These data indicate that, during differentiation to macrophages, 92% of EF1α cells, but only 20% of uEF1α cells, underwent silencing. Of the GFP+ macrophages, the MFI was 2.1-fold higher under uEF1α than under EF1α. Furthermore, we found that the addition of a UCOE did not confer constitutively high gene expression but rather could be modulated through promoter selection to achieve clinically relevant expression levels. uSFC iPSCs were differentiated in parallel with the uEF1α iPSCs into macrophages. The percentage of GFP+ macrophages under uSFC was 17% (compared to 78% under uEF1α), and among the GFP+ population, the MFI was 4-fold higher under uEF1α than under uSFC. These results suggest that pairing a UCOE with a weaker promoter, such as SFC, could be beneficial when lower transgene expression is desired. In summary, we demonstrate novel UCOE-containing regulatory sequences that mitigate silencing during differentiation of iPSCs into lymphocytes or macrophages. These sequence elements may prove useful in engineering cells with functional transgenes encoding therapeutic proteins, and could contribute to the development of effective engineered iPSC-based therapies.