Novel Regulatory Sequences Drive Persistent Transgene Expression During Directed Differentiation of iPSCs to Lymphocytes and Macrophages

Claire Aibel1, Abigail Blatchford1, Taeyun Kim1, Christopher B. Rohde1, Matthew Angel1

1Factor Bioscience Inc., Cambridge, MA

 

2024 ISSCR Annual Meeting

Cell therapies derived from knock-in human induced pluripotent stem cells (iPSCs) hold potential for increased scalability, broader accessibility, and superior production of genetically identical immune cells that express therapeutic transgenes. Such transgenes are often paired with synthetic promoters, which can drive high levels of protein expression but are often silenced during differentiation. To address this issue, we designed novel sequences comprising a synthetic promoter (EF1α or SFC), an upstream ubiquitous chromatin opening element (UCOE), and a GFP reporter. These sequences (GFP under EF1α alone, EF1α with a UCOE (uEF1α), SFC alone, or SFC with a UCOE (uSFC)) were inserted into the AAVS1 safe harbor locus of mRNA-reprogrammed iPSCs, which were then differentiated via static culture into lymphocytes and macrophages. The gene-edited iPSCs expressed the pluripotency markers TRA-1-60 (wild type = 96.9%, SFC = 99.9%, uSFC = 99.9%, EF1α = 95.2%, uEF1α = 99.9%) and TRA-1-81 (wild type = 97.0%, SFC = 99.8%, uSFC = 99.9%, EF1α = 99.9%, uEF1α = 99.9%) and yielded comparable numbers of CD34+ hematopoietic progenitor cells upon differentiation (CD34+ cells as a percentage of iPSCs initially seeded: wild type = 4.4%, SFC = 5.0%, uSFC = 2.3%, EF1α = 3.8%, uEF1α = 4.1%). EF1α and uEF1α iPSC-derived lymphocytes were positive for CD7, and EF1α, uEF1α, and uSFC iPSC-derived macrophages were positive for CD13, CD14, CD33, and CD45. Furthermore, we found that uEF1α exhibited less differentiation-induced gene silencing than did EF1α. GFP expression in EF1α and uEF1α iPSCs was uniformly high (98.4% and 99.9%, respectively); however, in the iPSC-derived lymphocytes, the percentage of GFP+ cells was 36.5-fold higher under uEF1α (73%) than under EF1α (2%), and in the iPSC-derived macrophages, the percentage of GFP+ cells was 13-fold higher under uEF1α (78%) than under EF1α (6%). In summary, we present novel synthetic regulatory sequences that mitigate silencing during differentiation of iPSCs into lymphocytes or macrophages without interfering with differentiation or introducing unintended phenotypic changes. 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.