In the classical form of ␣ 1 -antitrypsin deficiency, a mutant protein accumulates in a polymerized form in the endoplasmic reticulum (ER) of liver cells causing liver damage and carcinogenesis by a gain-of-toxic function mechanism. Recent studies have indicated that the accumulation of mutant ␣ 1 -antitrypsin Z in the ER specifically activates the autophagic response but not the unfolded protein response and that autophagy plays a critical role in disposal of insoluble ␣ 1 -antitrypsin Z. In this study, we used genomic analysis of the liver in a novel transgenic mouse model with inducible expression to screen for changes in gene expression that would potentially define how the liver responds to accumulation of this mutant protein. There was no unfolded protein response. Of several distinct gene expression profiles, marked up-regulation of regulator of G signaling (RGS16) was particularly notable. RGS16 did not increase when model systems were exposed to classical inducers of ER stress, including tunicamycin and calcium ionophore, or when a nonpolymerogenic ␣ 1 -antitrypsin mutant accumulated in the ER. RGS16 was up-regulated in livers from patients with ␣ 1 -antitrypsin deficiency, and the degree of up-regulation correlated with the hepatic levels of insoluble ␣ 1 -antitrypsin Z protein. Taken together, these results indicate that expression of RGS16 is an excellent marker for the distinct form of "ER stress" that occurs in ␣ 1 -antitrypsin deficiency, presumably determined by the aggregation-prone properties of the mutant protein that characterizes the deficiency.The histological hallmark of the classical form of ␣ 1 -antitrypsin (AT) 2 deficiency is liver cells containing periodic acidSchiffϩ/diastase-resistant globules. From many years of research on the disease, we now know that these globules represent rough endoplasmic reticulum (ER) distended by accumulation of the mutant ATZ molecule (where ATZ is the Z variant of ␣ 1 -antitrypsin). The wild type AT is a classical liverderived secretory glycoprotein that is delivered by the circulating blood to tissues to subserve its predominant function of inhibiting the neutrophil serine proteases neutrophil elastase, cathepsin G, and proteinase 3. The point mutation that characterizes the ATZ variant converts glutamate 342 to lysine and is sufficient to result in selective retention of the glycoprotein in the ER (reviewed in Refs. 1, 2). Thus, AT deficiency could be considered a prototype, naturally occurring "ER stress" state. Characterization of the structure of AT and its functional correlates led to the remarkable observation that the substitution of lysine for glutamate 342 conferred on the ATZ molecule a tendency to polymerize and aggregate (3, 4). Although it is still not clear whether the tendency to polymerize is the cause, or an effect, of ER retention, there is clear-cut evidence that polymers and aggregates of this molecule are formed in the ER, and there is growing evidence that these polymers and aggregates play a role in how liver cells respond and wh...