br Author Contributions br Acknowledgments br Introduction A

Author Contributions
Acknowledgments
Introduction Alpha-1 antitrypsin deficiency (AATD) is a common genetic cause of both liver and lung disease affecting an estimated 3.4 million patients worldwide (de Serres, 2002). The most common disease variant is caused by an inherited single death associated protein kinase pair mutation of the SERPINA1 gene that results in a glutamate to lysine substitution (Glu342Lys) and production of a mutant version of the protease inhibitor AAT, known as Z AAT (Brantly et al., 1988). Z AAT protein is prone to misfolding and polymerization and has reduced capacity to inactivate neutrophil elastase, its primary substrate, resulting in both toxic gain-of-function and loss-of-function phenotypes (Brantly et al., 1988; Crystal, 1990; Lomas et al., 1992; Perlmutter and Pierce, 1989). AATD has proven difficult to model experimentally in mice and in human primary or immortalized cells, a factor that has limited the progress of research aimed either at elucidating mechanisms of disease or developing new treatment approaches. Studies based on transgenic PiZ mice or immortalized cell lines engineered to express the human mutant Z AAT allele or on primary human hepatocytes have provided significant insights into the pathogenesis of AATD-associated liver disease. These studies have demonstrated that polymerization of Z AAT protein in the ER results in activation of an ER overload response (Hidvegi et al., 2005; Lawless et al., 2004), characterized by chronic activation of the proinflammatory transcription factor NF-κB (Pahl and Baeuerle, 1995), together with activation of ER stress-specific caspases (Hidvegi et al., 2005). Each of these models, however, has shortcomings that potentially limit its ability to delineate the mechanisms of a disease that develops over time in human liver tissue. Recently, the discovery of induced pluripotent stem cells (iPSCs) (Takahashi and Yamanaka, 2006) has made it possible to model a variety of genetic diseases in vitro using patient-derived stem cells (Ebert et al., 2009; Park et al., 2008; Rashid et al., 2010). The differentiated progeny of patient-derived iPSCs provide disease-relevant cells in an individual patient’s genetic background, potentially allowing personalized, in vitro assessments of disease pathogenesis and treatment responsiveness. As with human clinical trials, however, studies utilizing multiple patient-derived iPSC lines introduce the complexity of genetic variability. This experimental approach increases the likelihood that findings will be generalizable to a population rather than specific to an individual, but also potentially decreases the signal-to-noise ratio. Here we sought to apply an iPSC-based approach to study generalizable effects of the Z mutation, rather than the effects of any single individual’s genetic background. To do so, we incorporated iPSC lines derived from multiple individuals homozygous for the Z allele (termed PiZZ), ensuring the inclusion of genetic heterogeneity. We found that the transcriptional profile of iPSCs derived from individuals homozygous for the Z allele diverges from normal controls only upon differentiation to the hepatic stage, when the AAT gene is expressed. Expression of 135 genes distinguishes PiZZ iPSC-hepatic cells from controls at this stage, providing potential clues to liver disease pathogenesis. PiZZ iPSC-hepatic cells model key features of AATD-associated liver disease, including intracellular accumulation and reduced secretion of AAT protein as well as increased autophagic flux. Augmented autophagic flux can be further enhanced in iPSC-hepatic cells upon treatment with the drug carbamazepine (CBZ), an observation first made in transgenic PiZ mice (Hidvegi et al., 2010) that has important implications for treating patients with AATD-related liver disease. Finally PiZZ iPSC-hepatic cells exhibit increased sensitivity to a panel of hepatotoxic drugs, including the common analgesic acetaminophen, confirming their potential application as tools for drug discovery or prediction of toxicity.