Diagnostic Accuracy of Liver Histopathology in Predicting Progressive Familial Intrahepatic Cholestasis: Correlation with Whole Exome Sequencing – A Retrospective Study

Progressive Familial Intrahepatic Cholestasis (PFIC) represents a heterogeneous group of rare autosomal recessive hereditary liver disorders characterised by impaired canalicular bile secretion from hepatocytes. The estimated incidence ranges from 1 in 50,000 to 1 in 100,000 live births, with considerable variation across geographic regions and ethnic populations [1,2]. Clinical hallmarks include early-onset cholestatic jaundice, intractable pruritus, failure to thrive, and progressive hepatic fibrosis that culminates in end-stage liver disease in the absence of timely therapeutic intervention [3].

 

The classical forms of PFIC include PFIC type 1 (FIC1 deficiency), caused by mutations in the ATP8B1 gene; PFIC type 2 (BSEP deficiency), arising from mutations in the ABCB11 gene encoding the bile salt export pump; and PFIC type 3 (MDR3 deficiency), resulting from mutations in the ABCB4 gene [4,5]. Recent advances in next-generation sequencing technologies have substantially expanded the PFIC spectrum to encompass additional genetically defined subtypes, including PFIC7 caused by mutations in USP53 (encoding ubiquitin-specific protease 53) and PFIC12 attributed to variants in VPS33B [6,7]. This growing catalogue of subtypes underscores the molecular heterogeneity of the disorder and highlights the imperative for precise genetic characterisation.

 

Diagnostic Challenges in India

In India, the diagnosis of PFIC presents unique challenges. The country bears a significant burden of paediatric cholestatic liver disease; however, systematic disease registries remain limited, and the high cost and restricted availability of genetic testing have historically constrained the routine use of molecular diagnostics in clinical practice [8]. Consequently, liver histopathology has served as the primary diagnostic modality, providing essential morphological data regarding the pattern of cholestasis, degree of hepatocellular injury, and extent of hepatic fibrosis [9,10].

 

Need for Disease Registries

The establishment of comprehensive disease registries for paediatric cholestatic liver disorders in India is imperative for characterising the true epidemiology, natural history, and clinical outcomes of conditions such as PFIC. Such registries would facilitate multi-centre collaboration, enable genotype-phenotype correlations, and support the development of evidence-based treatment protocols tailored to the Indian population [11].

 

Study Objective

Given the diagnostic gap and the paucity of Indian literature on PFIC, this study aimed to: (i) determine the prevalence of PFIC among paediatric liver biopsy specimens at a tertiary care centre; (ii) evaluate the diagnostic accuracy of liver histopathological features in predicting PFIC; and (iii) correlate histopathological findings with WES results to define specific genetic subtypes.

 

Prevalence of PFIC

Of the 92 paediatric liver biopsy specimens analysed during the study period, 8 cases (8.7%) were identified as PFIC based on histopathological evaluation and genetic analysis. The remaining 84 cases comprised other causes of paediatric cholestasis, including neonatal hepatitis syndrome (n=32), biliary atresia excluded on clinical grounds (n=18), idiopathic neonatal cholestasis (n=22), and other identifiable aetiologies (n=12).

 

Demographic and Clinical Profile

The PFIC cohort comprised 4 males and 4 females (M:F ratio = 1:1). The age at presentation ranged from 10 days to 17 months, with a median age of 3 months. A positive history of parental consanguinity was elicited in 4 of 8 cases (50%). All 8 patients (100%) presented with jaundice as the primary complaint. On clinical examination, hepatomegaly was noted in 5 cases (62.5%), while hepatosplenomegaly was present in 3 cases (37.5%). The demographic and clinical details are summarised in Table 2.

 

Histopathological Findings

Histopathological evaluation of the PFIC cohort revealed the following features (Table 1): lobular distortion was present in all 8 cases (100%); giant cell transformation was observed in all 8 cases (100%); intrahepatic cholestasis and canalicular cholestasis were both identified in all 8 cases (100%); hepatocellular ballooning was present in 7 of 8 cases (87.5%); and portal inflammatory infiltrate was noted in 7 of 8 cases (87.5%). Representative histopathological findings are illustrated in Figures 1 through 5.

 

Fibrosis staging using the Laennec system demonstrated: Stage 1 fibrosis in 2 cases (25%), Stage 2 fibrosis in 3 cases (37.5%), Stage 3 (bridging fibrosis) in 2 cases (25%), and Stage 4 (cirrhosis) in 1 case (12.5%).

 

Whole Exome Sequencing Results

WES was performed in 4 of the 8 PFIC cases; the remaining 4 cases could not undergo genetic testing owing to financial constraints. Among the genetically evaluated cases, 2 harboured pathogenic variants in the ABCB11 gene (PFIC type 2, BSEP deficiency); 1 case demonstrated a pathogenic variant in USP53 (PFIC type 7); and 1 case showed a pathogenic variant in VPS33B (PFIC type 12). The genetic findings are detailed in Table 3 and illustrated in Figure 6.

 

Diagnostic Accuracy

When assessed against WES as the reference standard (for the 4 cases with available WES results), liver histopathology demonstrated a sensitivity of 100%, specificity of 50%, positive predictive value (PPV) of 50%, and negative predictive value (NPV) of 100%.

 

Table 1 Histopathological features of PFIC cases (n=8)

  

Table 2 Clinical and laboratory profile of PFIC cases

mo = months; GGT = gamma-glutamyl transferase; M = Male; F = Female.

 

Table 3 HIDA scan results, histopathological diagnosis, fibrosis staging, and WES findings

 

CBD = Common Bile Duct; ICC = Intrahepatic Cholestasis; CC = Canalicular Cholestasis; WES = Whole Exome Sequencing; PFIC = Progressive Familial Intrahepatic Cholestasis.

The present retrospective study evaluated the diagnostic utility of liver histopathology in identifying PFIC and correlating morphological findings with WES-based genetic subtyping in a paediatric cohort from a tertiary care centre in Hyderabad, India.

 

Prevalence and Demographics

The prevalence of PFIC in our paediatric liver biopsy cohort was 8.7% (8/92), which is comparable to published estimates indicating that PFIC accounts for 10–15% of neonatal and infantile cholestasis cases requiring liver biopsy [1,12]. The equal sex ratio (M:F = 1:1) is consistent with the autosomal recessive inheritance pattern of PFIC, which does not confer sex predilection [3,6]. The median age at presentation of 3 months aligns with the existing literature, which reports that PFIC typically manifests in the neonatal period or early infancy [2,4].

 

The occurrence of parental consanguinity in 50% of our cases is notably higher than rates reported in Western cohorts, and reflects the endogamous marriage practices prevalent in parts of the Indian subcontinent, which significantly increases the risk of autosomal recessive disorders [8,13]. This finding has important implications for population-level screening and genetic counselling programmes in South Asia.

 

Histopathological Features and Their Significance

The universal presence of lobular distortion, giant cell transformation, intrahepatic cholestasis, and canalicular cholestasis in all 8 PFIC cases underscores the diagnostic importance of these morphological features. Giant cell transformation, representing multinucleated hepatocytes with prominent biliary pigment retention, has been consistently described as a characteristic feature of neonatal and infantile cholestatic disorders, including PFIC [9,10]. It reflects a non-specific hepatocellular response to metabolic or toxic injury in the immature neonatal liver.

 

Canalicular cholestasis, characterised by the presence of bile plugs within dilated bile canaliculi, directly reflects the fundamental defect in canalicular bile secretion that underlies PFIC pathophysiology. The co-existence of intrahepatic cholestasis and periportal inflammatory infiltrates in the majority of cases indicates a significant hepatocellular injury component, likely mediated by the cytotoxic effects of retained bile acids on hepatocytes [5,14]. These morphological features, while individually non-specific, together form a recognisable histological pattern highly suggestive of PFIC in the appropriate clinical context.

 

Diagnostic Value of Histopathology

The sensitivity of 100% observed in this study demonstrates that liver histopathology effectively identifies all true PFIC cases, making it an excellent screening tool. This high sensitivity is particularly valuable in settings where WES is not universally accessible, as a characteristic histopathological pattern can reliably raise the clinical suspicion of PFIC and direct further investigations.

 

The relatively lower specificity of 50% reflects histopathological overlap between PFIC and other neonatal cholestatic conditions such as neonatal hepatitis syndrome, Alagille syndrome, and other metabolic liver diseases, which may exhibit similar morphological features [9,10]. This overlap represents an inherent limitation of histopathology as a standalone diagnostic modality for PFIC. The NPV of 100% is clinically significant, indicating that a non-supportive histopathological result effectively excludes PFIC, thereby narrowing the differential diagnosis and guiding resource allocation in resource-limited settings.

 

Genetic Subtyping and Novel Findings

WES identified three distinct PFIC subtypes: PFIC2 (ABCB11 mutations, n=2), PFIC7 (USP53 mutation, n=1), and PFIC12 (VPS33B mutation, n=1). The identification of PFIC7 and PFIC12 in our Indian cohort is noteworthy, as these recently characterised subtypes have been primarily reported in European and Middle Eastern populations [6,7]. Our findings suggest that these genetic subtypes may be more prevalent in the Indian population than previously recognised, and highlight the importance of comprehensive genetic analysis encompassing the full spectrum of known PFIC genes in paediatric cholestatic liver disease.

 

Role of Histopathology in Resource-Limited Settings

In settings where WES is not readily available, liver histopathology serves as an indispensable diagnostic tool. The morphological features, when integrated with clinical, biochemical, and radiological data, can facilitate an accurate working diagnosis of PFIC in the majority of cases. However, precise genetic subtyping, which carries critical implications for prognosis, genetic counselling, and targeted therapeutic strategies (such as ileal bile acid transporter inhibitors, partial biliary diversion, and liver transplantation planning), necessitates molecular genetic analysis [4,14].

 

Strengths and Limitations

This study represents one of the few Indian reports that systematically correlates liver histopathology with WES findings in paediatric PFIC. The strengths include a well-characterised study cohort from a high-volume tertiary centre, systematic histopathological evaluation using standardised staining protocols, and the identification of novel genetic subtypes in the Indian population. Acknowledged limitations include the retrospective design, relatively small sample size, incomplete WES data (feasible in only 4 of 8 cases), and the inherent limitation of histopathological overlap with other neonatal cholestatic conditions. As a single-centre study, the generalisability of findings to other geographic and demographic contexts requires validation through multi-centre prospective studies.

Liver histopathology remains a valuable, cost-effective, and accessible diagnostic modality for PFIC in resource-limited healthcare settings, demonstrating high sensitivity and a negative predictive value of 100%. Correlation with WES enables precise genetic subtyping with significant implications for targeted therapy and genetic counselling. The identification of PFIC7 (USP53 mutation) and PFIC12 (VPS33B mutation) subtypes in our Indian paediatric cohort underscores the broad genetic heterogeneity of PFIC and the need for comprehensive genetic evaluation across all paediatric patients with unexplained cholestasis. Establishment of a national PFIC registry in India is warranted to systematically characterise the epidemiology, natural history, genotype-phenotype correlations, and long-term outcomes of this rare but clinically significant paediatric liver disorder.

 

Acknowledgements

The authors sincerely acknowledge the patients and their families for their cooperation. We extend our gratitude to the staff of the Department of Pathology, Niloufer Hospital and Osmania Medical College, Hyderabad, for their technical support and assistance. We also acknowledge the Department of Paediatrics and Department of Paediatric Gastroenterology, Niloufer Hospital, for their clinical inputs.

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