Programmable apoptosis circuits enable subtractive engineering of stem cell-derived organoids and embryoids.

Pluripotent stem cell-derived multicellular systems provide a promising platform for studying development and disease. However, they do not faithfully mirror their in vivo counterparts due to the presence of aberrant cells. Similarly, aberrant cell types emerge during tissue development in multicellular organisms but are effectively removed via proofreading mechanisms that often exploit apoptosis. Yet, the design and engineering of such processes are notably absent from current approaches for building stem cell-derived multicellular systems. We address this gap by introducing a "subtractive multicellular engineering" approach, using genetic circuits that integrate logic-gated computing and synthetic apoptosis. Through this approach, we enhance tissue maturity in human pluripotent stem cell-derived liver organoids. Additionally, we demonstrate the versatility of this approach in a human post-implantation embryo model, where it improves pro-amniotic cavity development, a key morphogenetic feature. Our results establish a framework for building tissues in vitro via controlled elimination of aberrant cells during morphogenesis.