Gene Regulatory Network Analysis and Engineering Directs Development and Vascularization of Multilineage Human Liver Organoids

Jeremy J. Velazquez, Ryan LeGraw, Farzaneh Moghadam, Yuqi Tan, Jacquelyn Kilbourne, Joseph C. Maggiore, Joshua Hislop, Silvia Liu, Davy Cats, Susana M. Chuva de Sousa Lopes, Christopher Plaisier, Patrick Cahan, Samira Kiani, Mo R. Ebrahimkhani

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


Pluripotent stem cell (PSC)-derived organoids have emerged as novel multicellular models of human tissue development but display immature phenotypes, aberrant tissue fates, and a limited subset of cells. Here, we demonstrate that integrated analysis and engineering of gene regulatory networks (GRNs) in PSC-derived multilineage human liver organoids direct maturation and vascular morphogenesis in vitro. Overexpression of PROX1 and ATF5, combined with targeted CRISPR-based transcriptional activation of endogenous CYP3A4, reprograms tissue GRNs and improves native liver functions, such as FXR signaling, CYP3A4 enzymatic activity, and stromal cell reactivity. The engineered tissues possess superior liver identity when compared with other PSC-derived liver organoids and show the presence of hepatocyte, biliary, endothelial, and stellate-like cell populations in single-cell RNA-seq analysis. Finally, they show hepatic functions when studied in vivo. Collectively, our approach provides an experimental framework to direct organogenesis in vitro by systematically probing molecular pathways and transcriptional networks that promote tissue development. Informed by computational analyses, Velazquez et al, exercised overexpression of ATF5, PROX1 transcription factors, and CRISPR-mediated activation of CYP3A4 to advance the maturity and vascularity of human iPSC-derived fetal liver organoids in vitro. The findings highlight the importance of integrative systems and synthetic biology to engineer multicellular systems.

Original languageEnglish (US)
Pages (from-to)41-55.e11
JournalCell Systems
Issue number1
StatePublished - Jan 20 2021


  • Cas9
  • gene circuit
  • gene regulatory network
  • genetic engineering
  • induced pluripotent stem cells
  • liver
  • maturation
  • organoids
  • synthetic biology

ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Histology
  • Cell Biology


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