Clinical utility of genomic analysis in adults with idiopathic liver disease

Abstract

Background & aims: Adult patients suffering from liver disease of unknown cause represent an understudied and underserved population. The use of whole-exome sequencing (WES) for the assessment of a broader spectrum of non-oncological diseases, among adults, remains poorly studied. We assessed the utility of WES in the diagnosis and management of adults with unexplained liver disease despite comprehensive evaluation by a hepatologist and with no history of alcohol overuse.

Methods: We performed WES and deep phenotyping of 19 unrelated adult patients with idiopathic liver disease recruited at a tertiary academic health care center in the US.

Results: Analysis of the exome in 19 cases identified 4 monogenic disorders in 5 unrelated adults. Patient 1 suffered for 18 years from devastating complications of undiagnosed type 3 familial partial lipodystrophy due to a deleterious heterozygous variant in PPARG. Molecular diagnosis enabled initiation of leptin replacement therapy with subsequent normalization of liver aminotransferases, amelioration of dyslipidemia, and decreases in daily insulin requirements. Patients 2 and 3 were diagnosed with MDR3 deficiency due to recessive mutations in ABCB4. Patient 4 with a prior diagnosis of non-alcoholic steatohepatitis was found to harbor a mitochondrial disorder due to a homozygous pathogenic variant in NDUFB3; this finding enabled initiation of disease preventive measures including supplementation with antioxidants. Patient 5 is a lean patient with hepatic steatosis of unknown etiology who was found to have a damaging heterozygous variant in APOB.

Conclusions: Genomic analysis yielded an actionable diagnosis in a substantial number (∼25%) of selected adult patients with chronic liver disease of unknown etiology. This study supports the use of WES in the evaluation and management of adults with idiopathic liver disease in clinical practice.

Lay summary: We performed whole-exome sequencing in 19 adult patients with unexplained liver disease after an unrevealing conventional work-up performed by a hepatologist. In 5 cases, genomic analysis led to a diagnosis and informed treatment and management of the disease. Therefore, we suggest using whole-exome sequencing in the evaluation and management of adults with unexplained liver disease.

Keywords: Genetic diagnosis; Germline mutations; Precision medicine; Undiagnosed liver disease; Whole-exome sequencing.

Figure 1.

Liver histology, genetic and laboratory findings in patient 1. (A) Liver parenchyma shows marked steatosis with moderate steatohepatitis (H&E stain, 40x). (B) Trichrome stain of liver biopsy tissue shows portal, periportal and perisnusoidal fibrosis consistent with stage 2 fibrosis (Brunt grading and staging system) (20x). (C) Pedigree depicts proband and unaffected subjects in black and white symbols, respectively, with Sanger sequencing chromatograms of the proband and her unaffected parents. PPARG alleles are denoted WT (wild-type) or Mut (p.Gly161Val). The PPARG p.Gly161Val variant is heterozygous in the proband and absent in both parents. (D) Location of Gly-161 in PPARG and its conservation across species. The patient’s variant is in a highly conserved DNA-binding domain (DBD) of the PPARG protein. Amino acid positions identical to the human reference are highlighted in yellow. N-terminal transactivation domain (AF1), highly conserved DNA-binding domain (DBD), C-terminal ligand-binding domain (LBD). (E) Triglycerides and leptin levels before (no shadow) and after (depicted by a gray shadow) initiation of leptin replacement therapy. (F) ALT/AST levels before (no shadow) and after (depicted by a gray shadow) initiation of leptin replacement therapy. LLN, lower limit of normal; ULN, upper limit of normal.

Figure 2.

Liver histology and genetic findings in patients 2 and 3. (A) Trichrome stain for patient 2 reveals fibrous septa with nodule formation consistent with cirrhosis (10x). (B) Cytokeratin 7 immunohistochemical staining (depicted in brown) for patient 2 shows ductular proliferation (10x). (C) Pedigree depicts patient 2 and unaffected subjects shown in black and white symbols, respectively. (D) Sanger sequencing chromatograms of the proband (patient 2) and her unaffected mother and son. The patient harbors two variants in ABCB4, p.Arg549Cys and p.Ala934Thr, whereas her mother and her son solely carry one of these variants each, p.Arg549Cys and p.Ala934Thr, respectively. (E, F) Conservation of Arg-549 and Ala-934 across species, respectively. Amino acid positions identical to the human reference are highlighted in yellow. (G) Liver parenchyma (H&E stain) from patient 3 showing cirrhosis (4x). (H, I) Liver parenchyma (H&E stain) from patient 3 at lower and higher magnification, respectively, revealing portal/septal chronic inflammation, ductular proliferation, and marked cholestasis (10x and 20x). (J) Copper stain of liver parenchyma for patient 3 supporting marked cholestasis (40x).

Figure 3.

Liver biopsies of patients 4 and 5. (A, B) Patient 4 liver parenchyma shows near normal histology with minimal macrovesicular steatosis (small and large droplet fat) (H&E stain) at lower (20x) and higher magnification (40x), respectively. (C) Electron microscopic findings for patient 4 is suggestive of a mitochondrial abnormality, with hepatocytes showing different sized lipid droplets (scale bar, 2 microns). (D) Hepatic parenchyma (H&E stain) from patient 5 shows predominantly macrovesicular steatosis with minimal steatohepatitis (10x).

Figure 4.

Schematic representation of multidisciplinary Genome Rounds in Adult Hepatology. It merges genotype-phenotype information with the goal of recognizing unappreciated phenotypic features by standard clinical examination, providing a diagnosis and new therapeutic options, and establishing adequate family counseling in adults. gDNA, genomic DNA.