In biliary atresia diagnostic biopsy is no longer the norm [14]. Jaundiced neonates with acholic stool and atretic gallbladder on ultrasound proceed to operative cholangiogram. If atresia is confirmed, which can affect varying portions of the extrahepatic biliary tree, Kasai portoenterostomy is performed. The removed hilar plate shows fibro-inflammatory obliteration of the ducts, and multiple small duct profiles are often seen. Biopsy is only carried out in atypical cases, and the peripheral liver shows the manifestations of large bile duct obstruction often with prominent ductular bile plugging (Fig. 3.2). In early biopsies appropriately sized bile ducts are usually identifiable, whereas children who come to transplantation often have a paucity of intrahepatic bile ducts, a presumed manifestation of ongoing large duct obstruction despite Kasai procedure. It should be noted that one of the manifestations of alpha-1 antitrypsin deficiency (A1ATd) in a neonatal biopsy is a biliary picture mimicking large duct obstruction. Other biopsy manifestations in A1ATd include either bile duct paucity or a neonatal hepatitis-like pattern and/or periportal steatosis.

It is occasionally observed that babies with suspected biliary atresia (clinically and histologically) have an operative cholangiogram showing patent but thin and tortuous large bile ducts. This has been termed “neonatal sclerosing cholangitis”. This condition is believed to be rare and is poorly defined, with no specific histological clues in a peripheral liver biopsy. Familial occurrence has suggested an autosomal recessive inheritance. There can be extrahepatic manifestations, notably in the skin in “neonatal ichthyosis sclerosing cholangitis syndrome” related to mutations in the claudin 1 gene [15]. The long-term course is likely to be a progression to biliary cirrhosis.

In these conditions the portal tracts lack an appropriately sized bile duct, i.e. a duct of similar calibre to, and in close proximity to, the hepatic artery branch. It is always important to distinguish the bile duct proper from marginal ductules (Fig. 3.2). In normal subjects the ratio of the bile ducts to portal tracts is 0.9–1.8. Paucity is said to be present if the ratio is less than 0.4 [16].

Ductal plate malformation is a generic term encompassing a group of phenotypically and genetically heterogeneous conditions under the umbrella term of fibropolycystic syndromes. Cysts are variably present in the liver and kidneys. Congenital hepatic fibrosis (CHF) is the classical example in the liver. The ductal plate malformation (DPM) arises when the hepatoblasts, which condense around the primitive portal tract to form the embryonic ductal plate, subsequently fail to undergo the normal sequence of events involved in remodelling leading to the formation of a single duct. The persisting ductal plate structures have a distinctive appearance in a liver biopsy. They are typically located at the periphery of portal tracts and have complex profiles with an incomplete circular arrangement. They may also be dilated and plugged with bile. The ductular reaction, which occurs in many chronic biliary diseases, has a similar anatomical location to DPM, and distinction between these two processes may sometimes be difficult. Ductular reaction is characterised by smaller biliary structures, which are more tightly aggregated and have a narrow or inconspicuous lumen. CHF is often also associated with loss of portal veins – affected portal tracts consequently have a sclerotic appearance due to the absence of portal vein branches, which are normally larger than the bile ducts and hepatic arteries. The parenchyma, in uncomplicated cases, is strikingly normal.

In cystic fibrosis, as management of the respiratory manifestations improves, liver disease is emerging as an important cause of morbidity. The effects on the liver are very patchy and referred to as “focal biliary fibrosis”. Biopsies are unlikely to be representative of the liver as a whole but may show portal biliary features, and the ductules classically contain inspissated eosinophilic secretions associated with an infiltrate of neutrophil polymorphs. Cystic fibrosis (CF) is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Mutations causing CF do not seem to be a cause of PSC, but polymorphisms in the CFTR gene have been investigated, and those associated with reduction or non-function of the CFTR protein product confer protection against PSC when compared with non-diseased controls [21].

PFIC is a term describing a group of conditions, usually diagnosed in infancy, which, as the name implies, can be progressive and can be considered in the differential diagnosis of chronic biliary tract disease in childhood. Underlying genetic defects are known and should ideally be used for the nomenclature of these conditions [17, 22]. Types “1” and “2” present in infancy, and, importantly, affected babies have a low gamma glutamyl transferase (GGT) despite severe cholestasis. Type 1 (ATP8B1/ATP8B1FIC1) can have extrahepatic manifestations, whilst type 2 (ABCB11/ABCB11 bile salt export pump, BSEP) is confined to the liver. Histologically, type 1 shows a bland canalicular cholestasis and type 2 the non-specific pattern of “neonatal hepatitis” where cholestasis is accompanied by giant cell change of hepatocytes and extramedullary haemopoiesis. The bile in type 1 has a characteristic ultrastructural appearance, but the diagnosis is best established by genetic testing. Type 3 (ABCB4/ABCB4 MDR3 – functional interaction with ATP8B1) is more likely to have a post-infantile presentation, and GGT is raised here. Histologically there is a progressive biliary fibrosis without distinguishing features. Duct paucity and sclerosing bile duct lesions are not typically seen in PFIC but have been recognised as an occasional finding in adults with MDR-3 deficiency [23]. Less pathogenic mutations in the genes mentioned here can cause intermittent cholestatic episodes (benign recurrent intrahepatic cholestasis, BRIC). Cholestasis might also be precipitated by drug exposure – oral contraceptives in teenage girls, for example. Biopsies in this setting typically show a bland bilirubinostasis.

PBC is a disease characterised by inflammatory damage to small (interlobular) bile ducts. The classical florid duct lesion involves lymphocytic or granulomatous destruction of the bile ducts resulting in bile duct loss. The presence of florid destructive cholangitis has a high diagnostic specificity for PBC – however, these lesions are patchy in distribution and are only seen in approximately 30–50% of liver biopsies [24, 25]. More frequently, as discussed earlier, liver biopsies show features compatible with a diagnosis of chronic biliary disease, and the final diagnosis of PBC thus requires correlation with other relevant findings.

It is now increasingly accepted that PBC can be diagnosed on the basis of the clinical, biochemical and immunological findings, and liver biopsy is thus no longer required for the routine diagnosis of PBC [26, 27]. Liver biopsy continues to play an important diagnostic role in atypical cases (e.g. AMA-negative PBC) and in cases where there may be a dual pathology (e.g. PBC and fatty liver disease). Liver biopsy is also recommended in the assessment of patients suspected to have an “overlap syndrome” with autoimmune hepatitis. In addition to showing histological features compatible with PBC, the diagnosis of PBC-AIH “overlap syndrome” requires the presence of at least moderate interface hepatitis [26, 28]. A recent study suggested that classical histological features of AIH such as hepatocyte rosettes, emperipolesis and lobular hepatitis are less frequent and/or severe in PBC patients with interface hepatitis than in people with “pure” AIH [29]. The severity of inflammatory activity has been shown to predict subsequent progression to cirrhosis and liver failure, and there is some evidence to suggest that PBC patients with unusually prominent “hepatic features” may consequently benefit from treatment with immunosuppressive therapy [30, 31].

PSC is a disease that affects bile ducts of all sizes (intrahepatic and extrahepatic). There is emerging evidence to suggest that PSC may have a number of different subtypes, which differentially involve ducts of different sizes – amongst adults with PSC, approximately 5–15% appear to have disease confined to small ducts, whilst 10% have disease only or predominantly involving large ducts.

The classical fibrosing duct lesions seen in PSC mainly involve medium-sized (septal) bile ducts and are thus seen infrequently (<20% of cases) in liver biopsies, which mainly sample smaller ducts [24]. The early stages are characterised by foci of loose concentric periductal fibrosis (“onion skin”-like) often accompanied by varying numbers of periductal inflammatory cells. As the disease progresses, there is formation of more dense acellular fibrosis associated with progressive obliteration of the bile duct lumen, eventually resulting in complete replacement of the original duct by a nodule of fibrous tissue (nodular scar). Features of fibrosing cholangiopathy can also be seen in a number of diseases where sclerosing cholangitis occurs as a secondary phenomenon. Some examples of diseases associated with secondary sclerosing cholangitis are included in Table 3.2. Small (interlobular) ducts may occasionally show periductal fibrosis, but more typically disappear without trace (“vanishing bile duct syndrome”). A recent study has suggested that basement membrane thickening in interlobular ducts (demonstrated by PAS-diastase staining) may be a useful diagnostic feature of PSC [32]. Large bile ducts are typically dilated, ulcerated and inflamed – resulting in the characteristic beading appearance seen radiologically. Biopsies are rarely obtained from large bile ducts, except in the investigation of cases suspected to have developed hilar cholangiocarcinoma. A detailed discussion of the approaches used to establish a tissue diagnosis of cholangiocarcinoma is beyond the scope of this article. A recent study of PSC hepatectomy specimens obtained at liver transplantation has suggested that hyperplasia of peribiliary glands may be important in the pathogenesis, both of periductal fibrosis and of neoplastic transformation in large bile ducts [33]. Two other studies have identified arterial abnormalities in PSC, including enlargement, mural thickening and fibrointimal hyperplasia, although the functional significance of these findings is uncertain [34, 35].