Progress in the study of AATD from 1990 to 2010 proceeded in different directions. The AATD disease mechanism underwent progressive clarification. The most frequent AAT variant associated with severe deficiency, Glu
342Lys, also referred to as PI*Z, was shown to form polymers and accumulate within hepatocytes [
30], causing the deficiency in the bloodstream. This led to the hypothesis of a divergent mechanism for lung and liver disease in AATD: a deficiency mechanism (“loss-of-function”) in lung disease, and an add-on, related to the misfolding of the protein (“gain-of-function”), a conformational mechanism in liver disease [
31,
32]. This Manichean view was however complicated by evidence that PI*Z polymers may also be detected and likely produced within the lung [
33], thus suggesting that the add-on mechanism could also contribute to lung disease. A large series of AATD patients were studied in the United States and United Kingdom during this period, and greatly contributed to our knowledge on the clinical presentation and natural history of lung disease associated with AATD, in terms of mortality, FEV
1 decline, and exacerbations [
34‐
36], as well as the associated liver disease [
37]. The epidemiology of AATD received great attention after the publication of the worldwide analysis by Fredrick de Serres: in his estimation, albeit in part refined in numerous subsequent publications, ca. 30,000,000 individuals are at risk for adverse health effects due to different AATD genotypes [
38]. Replacement therapy with
i.v. infusion of purified human plasma protein was licensed in the last decade of the Twentieth Century, and progressively became available. As a result, thousands of patients with lung disease associated with AATD have been safely treated [
39,
40]: a meta-analysis of observational studies confirmed efficacy with the decreasing decline of lung function in treated patients with an initial FEV
1 between 30 and 65% predicted [
41]. A number of alternative treatments for AATD have been proposed, ranging from inhalation therapy to recombinant and transgenic AAT, from gene therapy to regenerative medicine [
42‐
45]: none of these options has so far gone beyond the experimental stage. AATD played a critical role in the last two decades in building one of the most long-lived and respected hypotheses for the development of common pulmonary emphysema: the theory of an imbalance between proteinases and proteinase inhibitors, took shape, which evolved over the years, with the biochemical evidence of emphysema in subjects lacking AAT [
46].
At the beginning of the last 1990’s, compared with AATD, PAP lagged behind in terms of knowledge on pathogenesis. But it quickly made up for lost time: in 1994 two papers demonstrated simultaneously and serendipitously that mice lacking GM-CSF (granulocyte-macrophage colony-stimulating factor) developed a lung disease similar to human PAP [
47,
48]. These data showed that GM-CSF is critical for surfactant homeostasis in the lung, leading to subsequent studies and evidence that PAP was related to impaired surfactant catabolism by alveolar macrophages [
49]. However the etiology of surfactant impairment in PAP remained unexplained until 1999, when Koh Nakata and coworkers demonstrated the presence of polyclonal, neutralizing anti-GM-CSF autoantibodies (GMAbs) in patients with “idiopathic” PAP [
50]. Shortly thereafter, the pathogenesis of PAP in GM-CSF-deficient mice was elucidated in a study demonstrating that pulmonary GM-CSF is required for the terminal differentiation of alveolar macrophages [
51]. Subsequently, passive transfer studies in non-human primates injected with purified human PAP patient-derived GMAbs provided proof of their role in pathogenesis of PAP in humans (and of the critical role of GM-CSF in terminal differentiation of alveolar macrophages in primates) [
52]. These and other studies helped to define the previously designated “idiopathic” PAP as an autoimmune disorder and led to a new classification of surfactant disorders, including secondary PAP and rare forms of hereditary PAP [
53]. The progressive evolution and improvements in the WLL technique over the years dramatically changed the natural course of the disease, which was originally charged with a mortality of approximately 30%, it progressively became a disease with a substantially favorable prognosis [
21]. In the 70% of PAP patients a single WLL is enough to provide a prolonged period free of disease and/or symptoms [
54]. Although WLL is a relatively safe procedure in experienced hands, it is however an invasive procedure, not exempt from severe complications. Therefore based on novel pathogenesis insights, novel therapeutic options have sprung [
55]. To restore appropriate GM-CSF signaling, impaired by the presence of GMAbs, supplementation with exogenous recombinant GM-CSF has been proposed, first by subcutaneous injection, and then by inhalation [
56,
57]; results were substantially better with the latter delivery method. Considering the mechanisms underlying the autoimmune form of PAP, a biological approach seemed reasonable. An open-label trial investigating Rituximab treatment which depletes the CD20 B-cell population provided intriguing, preliminary results [
58].