Emergence of a Stage-Dependent Human Liver Disease Signature with Directed Differentiation of Alpha-1 Antitrypsin-Deficient iPS Cells

Abstract

SummaryInduced pluripotent stem cells (iPSCs) provide an inexhaustible source of cells for modeling disease and testing drugs. Here we develop a bioinformatic approach to detect differences between the genomic programs of iPSCs derived from diseased versus normal human cohorts as they emerge during in vitro directed differentiation. Using iPSCs generated from a cohort carrying mutations (PiZZ) in the gene responsible for alpha-1 antitrypsin (AAT) deficiency, we find that the global transcriptomes of PiZZ iPSCs diverge from normal controls upon differentiation to hepatic cells. Expression of 135 genes distinguishes PiZZ iPSC-hepatic cells, providing potential clues to liver disease pathogenesis. The disease-specific cells display intracellular accumulation of mutant AAT protein, resulting in increased autophagic flux. Furthermore, we detect beneficial responses to the drug carbamazepine, which further augments autophagic flux, but adverse responses to known hepatotoxic drugs. Our findings support the utility of iPSCs as tools for drug development or prediction of toxicity.

Patient-specific hepatocyte-like cells derived from induced pluripotent stem cells model pazopanib-mediated hepatotoxicity

“…In a recent study, toxicity to valproic acid was modeled in iPSC-derived HLCs from two individuals with Alpers sydrome, characterized by mutations in POLG and increased sensitivity to valproic acid20. In another study, HLCs derived from alpha-1 antitrypsin (AAT)-deficient patient-specific iPSCs exhibited mutant AAT protein accumulation and autophagic flux reminiscent of the clinical disease21. These studies highlighted a known relationship between a specific rare genetic mutation and phenotype as reflected in patient-specific HLCs.…”

Prospective isolation of NKX2-1–expressing human lung progenitors derived from pluripotent stem cells

“…In contrast, GC3 was enriched in liver-lineage genes (APOA2 and FGB) as well as nonspecific mesenchymal genes (COL19A1 and S100A10). We have previously reported that in iPSC-derived hepatic cells, FGB represents the most upregulated transcript in the genome during hepaticdirected differentiation (45,46). Furthermore, in postnatal human tissues both APOA2 and FGB are transcripts specifically enriched in liver cells (gtexportal.org).…”

5-Hydroxymethylcytosine (5hmC), or How to Identify Your Favorite Cell

“…The adult liver is relatively rich in 5hmC content, and global redistributions of 5mC [67][68][69] and 5hmC [70] have been described during the fetal to adult liver transition. Specifically, liquid chromatography mass spectrometry (LC-MS) estimations indicate that 5hmC increases from 0.125% to 1% of the total cytosine content.…”