The principal end-stage lung diseases of this group include cystic fibrosis, bronchiectasis, and emphysema.

Cystic fibrosis: Life expectancy in cystic fibrosis (CF) has improved substantially over the last 75 years, with a median predicted survival now approaching 40 years; however CF and non-CF bronchiectasis are the most important chronic suppurative diseases requiring lung transplantation, usually bilateral lung transplantation. The availability of stored explanted CF lungs has significantly supported research into pathogenesis, providing also detailed histopathological reports. CF is caused by mutations in the gene encoding the CF transmembrane conductance regulator (CFTR) protein [5]; however, the pathophysiology of CF lung disease remains incompletely understood. In particular the contribution of inflammation, airway remodeling, and other factors remain undefined. A better knowledge of the disease in particular the true onset (usually it begins before symptoms) is extremely important for suggesting new preventions and treatments. The lack of an animal model that mirrors CF in humans has delayed progress in discovering the origins of the lung disease [6]. Lung disease such as that in humans does not develop in mice with cftr mutations, even if new animal models have recently been successfully generated [7]. Interesting findings coming from the study of explanted lungs are now changing the pathogenetic view. Fibro-obliterative processes either isolated to the airways, i.e., obliterative bronchiolitis, or as a part of organizing pneumonia of a bronchiolitis obliterans-organizing pneumonia pattern are frequently detected. This has renewed the pathogenesis of the disease with more interest in the small airways instead of large airways, which has been the main area of clinical and pathologic interest. Other important data frequently detected from careful morphological studies is the presence of emphysema, until recently considered minimal [8, 9]. Mets et al. assessing by morphometry explanted lungs of 20 CF patients and found that emphysema is common and age related [10]. Emphysema might become an increasingly important disease component in the aging CF population. This finding appears of particular importance due to the fact that life expectancy of CF patients has dramatically increased in the last decades.

Other associated pathologic lesions that can be detected in end-stage CF and non-CF bronchiectasis lungs are Aspergillus or mycobacterial infections and neuroendocrine lesions (i.e., carcinoids and tumorlet); both lesions are important and should be described in the diagnostic report for more careful monitoring of recipients.

Among restrictive forms idiopathic pulmonary fibrosis (IPF) represents the most frequent referral end-stage lung disease. IPF, the most common form of idiopathic interstitial pneumonias, is a chronic, progressive, irreversible, and usually lethal lung disease often occurring in middle-aged and elderly adults (median age at diagnosis 66 years, range 55–75 years) [16]. The annual incidence of IPF is rising and is estimated to be between 4 · 6 and 16 · 3 per 100,000 people, and the prevalence is 13–20 cases per 100,000 [17–19]. The main histopathological features of IPF, named usual interstitial pneumonia, is characterized by a heterogeneous appearance with areas of subpleural/paraseptal fibrosis and honeycombing alternating with areas of less affected or normal parenchyma (spatial heterogeneity). Small areas of active fibrosis called fibroblast foci are present in the background of collagen deposition, and they reflect the temporal heterogeneity of the process. Inflammation is usually mild and consists of a patchy lymphoplasmacytic interstitial infiltrate. All these pathologic changes can be also detected in end-stage disease of explant lungs. More inflammation and moreover a temporally uniform distribution of the lesions are present in other interstitial lung diseases (desquamative interstitial pneumonia, nonspecific interstitial pneumonia, acute interstitial pneumonia, hypersensitivity pneumonia, collagen vascular diseases) which should be distinguished from UIP/IPF due to a better responsiveness to steroid treatment, better prognosis, and rarely indication for lung transplantation [19]. Multidisciplinary teams with high expertise and experience have been recommended by several authors to obtain a more correct final diagnosis [5, 18]. In our internal audit, both minor and major discrepancies were found in explanted lungs with a clinical diagnosis of IPF [3]. One of the most important lesions detected in our IPF explanted lungs was the presence of lung cancer; all our recipients with unsuspected neoplasia had a poor posttransplant follow-up (death or disease recurrence).

Today the increased diagnostic sensitivity of noninvasive techniques (such as high-resolution computed tomography scan) particularly if performed in referral centers have significantly reduced the use of lung biopsy [19]. Thus explanted lungs now represent an important tissue source available for any type of research. Many recent views about the IPF/UIP pathogenesis have just come from the study of native lungs. The recent hypothesis of IPF pathogenesis indicates that injured and hyperplastic alveolar epithelial cells are able to release cytokines causing proliferation of fibroblasts/myofibroblasts and deposition of extracellular matrix. Among profibrogenetic cytokines, transforming growth factor β (TGF β) represents the key growth factor which leads to mesenchymal differentiation, myofibroblast infiltration, and proliferation. Interestingly, the molecular pathways aberrantly activated in IPF seem to be the same involved in epithelial-mesenchymal communications occurring in lung development and differentiation [20].

Our experience, studying a large number of IPF native lungs, demonstrated that there is an abnormal epithelial renewal with diffuse signs of morphological changes through variegated cellular alterations, such as hyperplasia, atypia, squamous metaplasia, and various degrees of dysplasia [21, 22]. In particular, hyperplasic lesions and epithelial atypia have often been detected in highly remodeled lung areas as honeycomb.

This area represents a site of high instability at risk of neoplastic transformation, which are more frequently of squamous type [23–30]. Serpin B3/B4, a clade B serpin involved in several pathways including apoptosis/proliferation imbalance, has been found overexpressed in patients with squamous cell carcinoma type of different organs [31–38] and in metaplastic/dysplastic area of IPF lungs. Different works, in vitro and in vivo (both human and animal), have demonstrated a strict influence between serpin B3 and TGF-ß [39, 40]. Apoptosis/proliferation imbalance with a significant gain of epithelial proliferation has recently been demonstrated in bleomycin-induced lung damage using serpin B3 transgenic mice [40]. The overexpression of serpin B3/B4, particularly the isoform B4, in IPF patients may be an important factor in the resistance of injured epithelial cells to apoptosis, thus leading to progressive lesions at high risk of malignant transformation. Interestingly our group found a direct relationship between serpin B3/B4 and TGF-β expression [22, 39]. The ov-serpins have been shown to render cells more resistant to apoptotic cell death, and proapoptotic effect of TGF-β might represent a counterbalancing mechanism leading to accumulation of fibrosis as a secondary effect. Epithelial mesenchymal transition, typically ascribed to TGF-ß [41], has also been related to serpin B3 [42]. The study has provided evidence that the antiprotease activity of serpin could be implicated in the TGF-ß induction.

Another important aspect extensively explored in lung tissue sampled from IPF native lungs concerns the investigation of viral infection as a contributing etiological factor [43]. Several studies have implicated viral infection as a cause of epithelial injury and therefore an important factor in its pathogenesis [44–61]. Among viral agents herpes viruses, in particular Epstein-Barr virus (EBV), have been suggested as principal cofactors (as initiating or exacerbating agents) of fibrotic lung disease, and treatment with ganciclovir has been shown to attenuate disease progression in a subgroup of patients [62]. Our experience demonstrated a different phenotype of virus-positive IPF patients. In particular virus-positive IPF cases showed more pronounced vessel remodeling and a higher mean pulmonary arterial pressure (mPAP) and significantly higher primary graft dysfunction after transplantation. While there is large mechanistic evidence of epithelial herpesvirus-associated alveolar injury, the effect of these viruses on the pulmonary vasculature in IPF merits investigation. A deeper knowledge of viral-induced pathways in endothelial cells could give new insights for a targeted therapeutic approach to pulmonary hypertension, one of the most important IPF complications.

Pulmonary hypertension, either primary or secondary origin, is considered an important indication for lung transplantation (with and without the heart). Patients with pulmonary hypertension secondary congenital heart disease and patients with end-stage thromboembolic pulmonary hypertension are usually diagnosed on native lungs at transplantation. However chronic thromboembolic pulmonary hypertension is now rarely considered an indication for transplantation being treated surgically by pulmonary thrombectomy. There is an increasing focus on the cellular and molecular pathogenesis of idiopathic pulmonary hypertension. Animal models do not reproduce the morphological features of human pulmonary hypertension, thus it is mandatory that the human tissue available through transplantation is adequately studied. Many studies have given significant improvement in the understanding of pathogenesis and evolution of plexiform lesions leading to better clinical staging and more effective treatment strategies [63]. Explanted lungs were also successfully used for several studies focusing on key biomarkers such as the expression of genes for bone morphogenetic protein receptor type II (BMPR2) and TGF-β type I and II receptors [64]. The group of Papworth studying explanted lungs with primary pulmonary hypertension demonstrated that TGF-β R1 and RII co-localized to vascular endothelium in the normal pulmonary circulation, with reduced expression of TGF-β RII subtype in plexiform and intimal lesions of primary pulmonary hypertension [64]. Evidence is emerging that germline and/or somatic mutations in key cell growth regulatory genes play a role in the development of idiopathic sporadic and familial pulmonary hypertension [65]. Our group studied lungs with pulmonary hypertension (primary and secondary forms) and demonstrated increased intrapulmonary endothelial progenitor cells (EPC), suggesting that these cells may contribute to vascular remodeling [66]. The localization of specific cell markers and the identification of EPC are very likely to have an impact on therapy for both pre- and posttransplant conditions.

Hyperacute rejection is an early complication of transplantation, caused by the presence in the recipient of preformed donor-directed antibodies. It occurs within 24–48 h of graft implantation and should be suspected when the lungs become markedly congested and edematous with the production of copious frothy bloodstained sputum from the bronchial orifice of the graft. The histologic features of hyperacute rejection include diffuse alveolar damage, alveolar hemorrhage, interstitial pneumonia, and vasculitis. As only a few well-documented cases of hyperacute rejection of the lung have recently been reported in the literature [69, 70], it was not included in the working formulation. Ancillary techniques are useful for the final diagnosis: immunofluorescence may show IgG and complement (C3d and C4d) deposition in the alveolar septa. Immunohistochemistry for C4d should be interpreted as positive only when strongly stained deposition are detected.

The diagnosis is based on the presence of perivascular or airway inflammatory infiltrates that are composed mainly of activated lymphocytes, few eosinophils, neutrophils, and plasma cells (grade A). Lymphocytic bronchiolitis can also be observed and is characterized by bronchiolar inflammatory cell infiltrates with epithelial cell ulceration in severe forms (grade B). The histologic grade is based on the intensity and distribution of the infiltrate (Table 16.1; Fig. 16.1a–d).

Chronic rejection is primarily manifested as bronchiolitis obliterans (grade C). It is the most significant complication limiting long-term survival, affecting up to 50 % of patients 3 years after transplantation. Previous episodes of acute rejections are the most well-recognized risk factor. Since bronchiolitis obliterans (BO) is a patchy process and diagnostic yield of transbronchial biopsy is low, pulmonary functional tests are considered as more sensitive tools: when the decline is greater than 10 % of baseline, a clinical diagnosis of BO syndrome is made (without pathologic confirmation) and graded from 1 to 3 based on the degree of loss of lung function [71] (Table 16.1; Fig. 16.2a).

Chronic vascular rejection (grade D) is characterized by fibrointimal thickening of arteries and veins, with or without inflammatory infiltrates (Table 16.1; Fig. 16.2b).

Cytomegalovirus (CMV) infection is the most important cause of pneumonia. Primary infection, through blood transfusion or transmitted in the graft, may cause very severe disease in the allograft with systemic spread. Reactivation in a seropositive recipient may cause clinical disease that is less severe than in seronegative recipients. A prophylactic regimen has significantly reduced the severity and the frequency of CMV pneumonia [79–81]. CMV pneumonia is diagnosed in transbronchial biopsies by finding the classical single intranuclear and multiple small cytoplasmic inclusions in an enlarged cell. Treated patients may show more frequently smudged eosinophilic inclusions which may be difficult to identify as CMV. In these cases the use of in situ hybridization or immunohistochemistry against immediate-early antigen could be extremely useful [82, 83]. Routine histology with immunohistochemistry and/or in situ hybridization shows however low sensitivity in CMV detection often leading to underdiagnosis and/or delayed diagnosis of CMV pneumonitis. Increasing interest has focused on more sensitive molecular detection techniques both applied to transbronchial biopsy and overall to bronchoalveolar lavage. Although the critical threshold of viral load (4.6 × 10⁴ and 5.0 × 10⁵) is not yet completely validated, several works have proposed CMV quantification in bronchoalveolar lavage to have a higher sensitivity in the differentiation of patients with active CMV disease from latently infected patients, and they suggested that molecular quantitative assay on bronchoalveolar lavage should replace traditional culture and also CMV DNA assay in the blood [84–86]. The use of these ancillary techniques is overall useful to differentiate histological changes from acute rejection particularly when both diseases coexist and inclusions are sparse. Indeed CMV is known to be associated with an increased incidence of allograft dysfunction, possibly through upregulation of MHC class I and class II antigens in alveolar cells [87, 88]. In severe infection, diffuse alveolar damage is the prevalent histological finding. Adenovirus infection is more common in children, and scattered adults and pediatric patients develop serious pneumonias due to other respiratory viruses (e.g., respiratory syncytial virus, rhinovirus, parainfluenza, influenza).