Abstract Non-alcoholic fatty liver disease (NAFLD) is a potentially progressive disorder, possibily leading to cirrhosis and hepatocellular carcinoma (HCC). Both acquired and genetic risk factors play an important role in disease progression. In this respect, the presence of metabolic comorbidities such as obesity and type two diabetes mellitus has been associated to a more severe phenotype, while genetic factors modulating hepatic lipid metabolism such as the variants in PNPLA3 (patatin-like phospholipase domain-containing protein 3), TM6SF2 (transmembrane 6 superfamily member 2), MBOAT7 (membrane bound O-acyltranferase domain containing 7), GCKR (glucokinase regulatory protein) and APOB (apolipoprotein B) have been demostrated to influence disease predisposition. Secondly, a consistent fraction of patients with liver disorders are diagnosed at advanced stage and in approximately one third of cases it is not possible to establish an etiological diagnosis (cryptogenic cirrhosis). By exploiting Whole Exome Sequencing (WES) technology, in this work we aimed to: 1) identify the prevalence of known pathogenic mutations in candidate genes mutated in genetic liver diseases and hereditary cancer syndromes in patients with HCC and cirrhosis due to NAFLD or cryptogenic disease, to compare it to that of healthy individuals and to evaluate in the aforementioned genes the burden of rare or novel mutations of unknown significance, that determine an alteration of protein sequence, and are therefore likely pathogenic; 2) test the functional and clinical significance of the mutations identified, by bioinformatics algorithms and in vitro assays; 3) identify novel genetic risk factors predisposing to progressive NAFLD; 4) implement a genetic risk score (GRS) aiming to improve the stratification of the risk of progressive NAFLD; 5) test the impact of WES on the clinical management of six patients with cryptogenic liver disease. Briefly, we detected an enrichment in pathogenic (p = 0.024), and likely pathogenic variants (p = 1.9*10−6), particularly in APOB (p = 0.047). APOB variants were associated with lower circulating triglycerides and higher HDL cholesterol (p < 0.01). A genetic risk score predicted NAFLD-HCC (OR 4.96, 3.29–7.55; p = 5.1*10−16), outperforming the diagnostic accuracy of common genetic risk variants, and of clinical risk factors (p < 0.05). Furthermore, in one third of the six patients with cryptogenic liver disease and aggressive phenotype it was possible to identify a probable genetic disorder expleining the phenotype. In conclusion, rare pathogenic variants in genes involved in liver disease and cancer predisposition are associated with NAFLD-HCC development. Genetic study by WES can represent a precious instrument for risk stratification and allow a Precision Medicine approach in the context of liver disease aimed at the targeted treatment of the underlying cause of the disease.

IMPACT OF WHOLE EXOME SEQUENCING (WES) ON THE CLINICAL MANAGEMENT OF PATIENTS WITH ADVANCED NONALCOHOLIC FATTY LIVER (NAFL) / S. Pelusi ; tutor: L. VALENTI. - : . Dipartimento di Fisiopatologia Medico-Chirurgica e dei Trapianti, 2021 Mar 26. ((33. ciclo, Anno Accademico 2020. [10.13130/pelusi-serena_phd2021-03-26].

IMPACT OF WHOLE EXOME SEQUENCING (WES) ON THE CLINICAL MANAGEMENT OF PATIENTS WITH ADVANCED NONALCOHOLIC FATTY LIVER (NAFL)

S. Pelusi
2021

Abstract

Abstract Non-alcoholic fatty liver disease (NAFLD) is a potentially progressive disorder, possibily leading to cirrhosis and hepatocellular carcinoma (HCC). Both acquired and genetic risk factors play an important role in disease progression. In this respect, the presence of metabolic comorbidities such as obesity and type two diabetes mellitus has been associated to a more severe phenotype, while genetic factors modulating hepatic lipid metabolism such as the variants in PNPLA3 (patatin-like phospholipase domain-containing protein 3), TM6SF2 (transmembrane 6 superfamily member 2), MBOAT7 (membrane bound O-acyltranferase domain containing 7), GCKR (glucokinase regulatory protein) and APOB (apolipoprotein B) have been demostrated to influence disease predisposition. Secondly, a consistent fraction of patients with liver disorders are diagnosed at advanced stage and in approximately one third of cases it is not possible to establish an etiological diagnosis (cryptogenic cirrhosis). By exploiting Whole Exome Sequencing (WES) technology, in this work we aimed to: 1) identify the prevalence of known pathogenic mutations in candidate genes mutated in genetic liver diseases and hereditary cancer syndromes in patients with HCC and cirrhosis due to NAFLD or cryptogenic disease, to compare it to that of healthy individuals and to evaluate in the aforementioned genes the burden of rare or novel mutations of unknown significance, that determine an alteration of protein sequence, and are therefore likely pathogenic; 2) test the functional and clinical significance of the mutations identified, by bioinformatics algorithms and in vitro assays; 3) identify novel genetic risk factors predisposing to progressive NAFLD; 4) implement a genetic risk score (GRS) aiming to improve the stratification of the risk of progressive NAFLD; 5) test the impact of WES on the clinical management of six patients with cryptogenic liver disease. Briefly, we detected an enrichment in pathogenic (p = 0.024), and likely pathogenic variants (p = 1.9*10−6), particularly in APOB (p = 0.047). APOB variants were associated with lower circulating triglycerides and higher HDL cholesterol (p < 0.01). A genetic risk score predicted NAFLD-HCC (OR 4.96, 3.29–7.55; p = 5.1*10−16), outperforming the diagnostic accuracy of common genetic risk variants, and of clinical risk factors (p < 0.05). Furthermore, in one third of the six patients with cryptogenic liver disease and aggressive phenotype it was possible to identify a probable genetic disorder expleining the phenotype. In conclusion, rare pathogenic variants in genes involved in liver disease and cancer predisposition are associated with NAFLD-HCC development. Genetic study by WES can represent a precious instrument for risk stratification and allow a Precision Medicine approach in the context of liver disease aimed at the targeted treatment of the underlying cause of the disease.
VALENTI, LUCA VITTORIO CARLO
Settore MED/03 - Genetica Medica
IMPACT OF WHOLE EXOME SEQUENCING (WES) ON THE CLINICAL MANAGEMENT OF PATIENTS WITH ADVANCED NONALCOHOLIC FATTY LIVER (NAFL) / S. Pelusi ; tutor: L. VALENTI. - : . Dipartimento di Fisiopatologia Medico-Chirurgica e dei Trapianti, 2021 Mar 26. ((33. ciclo, Anno Accademico 2020. [10.13130/pelusi-serena_phd2021-03-26].
Doctoral Thesis
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/2434/827810
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