Krüppel-like zinc finger proteins in end-stage COPD lungs with and without severe alpha1-antitrypsin deficiency

Chronic obstructive pulmonary disease (COPD) includes a broad spectrum of respiratory symptoms and histopathological changes with varying degrees of severity, and it is typically diagnosed late in the course of disease when the patient presents with significant impairment [1, 2]. Different inflammatory cells (macrophages, neutrophils, CD8+ T lymphocytes) and several interrelated processes, such as chronic inflammation per se, proteinase/anti-proteinase imbalance, oxidative stress, apoptosis and replenishment of structural cells, are thought to contribute to the pathogenesis of COPD [3]. Given this complexity of COPD, the identification of biological markers of disease susceptibility and/or progression is of great importance [4]. DNA microarrays have been proven to be a powerful tool capable of biomarker discovery for various disease entities. Previous studies used this approach to characterize global gene expression patterns from lung tissue of patients with COPD, and to identify genes associated with disease severity. So far, these gene expression patterns have produced differing results likely due to differences in the types of patients enrolled and due to inherent heterogeneity of COPD.

An important fraction of COPD cases harbor a major genetic determinant, inherited ZZ (Glu342Lys) α1-antitrypsin deficiency (AATD). AAT is an acute phase protein, main inhibitor of neutrophil elastase and a modulator of host inflammatory responses [5]. It is well established that the Z variant of AAT forms polymers and is retained in the endoplasmic reticulum (ER) of the hepatocytes [6] which leads to markedly impede (up to 90%) levels of the circulating AAT protein. The lack of AAT predisposes a person to develop early onset, rapidly progressive COPD where emphysema is a major component [7] whereas the accumulation of abnormally folded AAT protein increases the risk to develop chronic liver disease. Cirrhosis in ZZ AATD individuals may become clinically apparent at any age, with the peak incidence typically occurring in elderly never-smokers who have survived without developing severe emphysema [8].

In an attempt to further improve our understanding of the complex molecular basis of AATD-related pathology, we aimed to investigate gene expression patterns in well matched end-stage COPD lungs from patients with and without inherited α1-antitrypsin deficiency (AATD). The identified genes differently expressed were then validated in separate groups of ZZ and MM end-stage COPD lung tissue and biopsies from liver cirrhosis patients using real time PCR. This strategy was used to confirm the reproducibility of our findings in different populations, which increases the probability of results being applicable to the wider population of COPD patients.

Tissues from explanted lungs of end-stage ZZ AATD-related COPD (n = 3) and non-AATD, MM COPD (n = 3) were used for gene expression analysis by Affymetrix. Detailed information about these patients can be found in Table 1 A. All patients had severe lung function impairment; however, none of the patients was a current smoker at the time of surgery and no one was treated with AAT augmentation therapy. Another cohort of lung specimens was used for laser-assisted microdissection, RNA extraction and RT-PCR analysis. Lung explants from MM COPD (n = 3) and ZZ COPD (n = 3) have been matched to the group of the cases used in Affymetrix analysis (Table 1 B). To avoid the regional variability of gene expression, we sampled lung tissue, several from central and peripheral regions. Liver biopsies were obtained from liver cirrhosis patients: 6 without [5 males and 1 female, mean age 56.8 ± 6.7 (SD)] and 4 with [males, mean age of 56.25 ± 6.9 (SD)] ZZ AATD. Additional RT-PCR analysis of selected genes was performed on surgical lung explants from end-stage ZZ emphysema cases with (n = 11, age 52.5 ± 2.1 (SD) years) and without AAT augmentation therapy (n = 6, age 44.7 ± 5.3 (SD) years).

To further explore lung tissue analysis using microarrays, we examined gene expression profiles in well matched end-stage (GOLD IV) COPD cases with ZZ AATD and without, “normal” MM COPD. Primarily, we wanted to find genes differentially expressed between MM and ZZ end-stage COPD and secondly, we sought for probable cluster(s) of genes which are able to stratify COPD cases by the genetic variant of AAT. It is important to point out that most patients with AATD-related emphysema are treated with AAT augmentation therapy. In order to make an appropriate match with “normal” MM COPD, we included non-augmented AATD cases which very much restricted the sample size of our cohort. We therefore deliberately used different cohorts of COPD and liver cirrhosis patients for the RT-PCR, because the replication of gene expression findings in a distinct cohort increases the likelihood of these results being applicable to wider populations of COPD patients.

Nevertheless, our results show that a relatively small number of genes is significantly differently expressed in end-stage ZZ lungs when compared to those from MM. Remarkably, out of 162 gene sets differently expressed between ZZ and MM-COPD lungs, 134 (82.7%) were up-regulated and only 28 (17.3%) were down-regulated in ZZ lungs. It is worth pointing out that among all up-regulated gene sets, the gene encoding α1-defensin (DEFA1) was one of the most highly (13-fold higher) expressed in ZZ compared to MM lung tissue. This finding was confirmed by RT-PCR analysis and is in line with previous studies showing that α-defensin concentrations are increased in individuals with AATD [23] and that patients with AATD have a milieu where high concentrations of α-defensins and low amounts of AAT potentiate the impact of α-defensins on lung injury [24, 25]. Remarkably, we could further verify in different cohorts that the expression of DEFA1 is higher in lungs from ZZ cases compared to MM COPD specimens. Based on this latter finding, we examined whether ZZ AAT deficiency-related emphysema patients treated with Prolastin® had lower DEFA1 expression in their lungs. Indeed, we found that augmentation therapy lowers DEFA1 expression when compared to untreated matched patients. Thus, our discovery that AAT influences DEFA1 gene expression opens new possibilities to further optimize augmentation therapies.

To our surprise, a set of genes including zinc finger protein 165, snail homolog 1 (Drosophila), and Krüppel-like transcription factors (KLFs) 4 (gut), 9 and 10, perfectly discriminated between patients with end-stage “normal” MM and ZZ AATD–related COPD (Figures 1 and 2). Further conformation in a different cohort of end-stage COPD lungs and in liver cirrhosis tissues showing that SNAI1, KLF9 and KLF10 are higher expressed in ZZ relative to MM AAT subjects, allows us to propose that the increased expression of zinc finger transcription factors is related to AATD. To our knowledge, so far only one study has shown an enhanced expression (2.1-fold) of Krüppel-related zinc finger protein (specifically undefined) in lung tissue from patients with AATD-associated emphysema when compared to normal lung tissue [26] and it has been shown that KLF4 mRNA is up-regulated more than 10-fold in mice lung tissue after endotoxin stimuli [27]. KLF10 was initially identified as a primary transforming growth factor beta (TGF-β)-inducible early gene in human osteoblasts [23]. KLF10 gene expression in the liver is shown to be regulated by glucose. This argues for a pleiotropic role of KLF10 in cellular biology by integrating antiproliferative, endocrine, metabolic, and circadian signals. As a matter of fact, genomic analysis of the liver in a transgenic mouse model with inducible expression of mutant Z and normal M variant of AAT protein unveiled a number of significantly more highly expressed genes in Z mice as an indicative of a TGF-β effect (among others KLF10) [28]. These data, together with our current findings suggest that induction of KLF10 gene expression might be specific for the ER stress state that is associated with the intracellular accumulation of aggregated Z AAT protein in the ER.

KLFs are critical regulators of many physiological processes and are involved in disorders such as cardiovascular disease, cancer, and inflammatory conditions. While numerous zinc finger proteins are expressed in the lung, only a few have been clearly implicated in lung homeostasis and disease. A recent study by Bhattacharya and co-workers [29] identified biomarker genes enriched in functions related to DNA binding and regulation of transcription which allow the prediction of disease in an unrelated data set, generated from patients with severe emphysema, with 97% accuracy. Although individual biomarkers in this study have not been identified, it is clearly shown that the selected genes include members of zinc finger–binding domain containing proteins. The patterns of KLF gene expression have not been considered in the pathobiology of AATD-associated COPD and warrants further investigation.

Lungs with end-stage emphysema display decreases in overall global gene expression, with pronounced increase in transcripts encoding pro-inflammatory mediators, immune-response proteins, and proteolytic enzymes. Some of these differentially-expressed genes are specifically linked to ZZ AATD-related emphysema. Results from the current study revealed a subgroup of genes from the zinc-finger family which perfectly segregated ZZ and MM COPD patients. This finding not only shows that these two types of emphysema can be distinguished from each other, but also provides a deeper insight into the pathophysiological mechanisms of lung emphysema with and without AATD.