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Liver Diseases, Genetics and Epigenetics
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Liver Diseases, Genetics and Epigenetics

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (20 June 2023) | Viewed by 15954

Special Issue Editors

Dr. Stefania Grimaudo

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Guest Editor
Section of Gastroenterology and Hepatology, Dipartimento di Promozione della Salute, University of Palermo, Palermo, Italy
Interests: liver disease; NAFLD; NASH; chronic hepatitis C; chronic hepatitis B; hepatocellular carcinoma; liver fibrosis; gene profiling; SNPs; transcriptomic analysis; GWAS
Special Issues, Collections and Topics in MDPI journals
Dr. Rosaria Maria Pipitone

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Guest Editor
Section of Gastroenterology and Hepatology, Dipartimento Di Promozione Della Salute, University of Palermo, Palermo, Italy
Interests: study of molecular mechanisms involved in MAFLD development and progression in terms of MASH and HCC; evaluation of the effects of compounds and phytonutrient administration, potentially capable of improving the lipid and glucose metabolic profiles, as well as steatosis and hepatic fibrosis, on in vitro models of continuous human hepatoma cell lines (HepG2) and hepatic stellate cells (LX2)
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Liver diseases are characterized by a wide variability in terms of development and progression not only due to different aetiologies, but also to acquired and inherited individual factors. Numerous genome-wide association studies showed that genetic background can condition hepatic inflammation, fibrosis progression and hepatocellular carcinoma (HCC) development both in viral and metabolic liver diseases. Among single-nucleotide polymorphisms (SNPs), the common variants in the patatin‐like phospholipase domain–containing protein 3 (PNPLA3)/ADIPONUTRIN (rs738409 C/T) are identified as major genetic risk factors for nonalcoholic fatty liver disease (NAFLD) development, while the transmembrane 6 superfamily member 2 E167K variant is strongly associated with the histological progression of liver damage in NAFLD patients. On the other hand, the rs12979860 C>T polymorphism in the interferon (IFN) lambda 4 locus was identified as a major predictor of spontaneous and alpha–IFN-induced viral eradication during hepatitis C infection. Together with genetic backgrounds, emerging studies suggest the involvement of epigenetic mechanisms in the occurrence and progression of liver disease. Epigenetic modifications, including DNA methylation, histone modifications, chromatin remodelling and noncoding-RNA-mediated mechanisms, play a key role in the complex niche of liver physiopathology. The Special Issue, entitled “Liver Diseases, Genetics and Epigenetics”, in International Journal of Molecular Science, will include a selection of original papers and reviews. The knowledge in these fields could be strategically vital for understanding variations in disease phenotypes, providing better risk stratification for disease progression. Moreover, identifying keys genes and pathways could be useful for the development of new diagnostic/prognostic biomarkers with clinical and translational implications.

Dr. Stefania Grimaudo
Dr. Rosaria Maria Pipitone
Guest Editors

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Keywords

  • liver disease
  • NAFLD (nonalcoholic fatty liver disease)
  • NASH (nonalcoholic steatohepatitis)
  • transcriptomic analysis
  • HCC (hepatocellular carcinoma)
  • genetic background
  • epigenetics
  • chronic hepatitis B
  • chronic hepatitis C
  • GWAS

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Published Papers (5 papers)

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Research

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14 pages, 1725 KiB  
Article
A Single Nucleotide Polymorphism rs1010816 Predicts Sorafenib Therapeutic Outcomes in Advanced Hepatocellular Carcinoma
by Chih-Lang Lin, Kung-Hao Liang, Ching-Chih Hu, Cheng-Hung Chien, Li-Wei Chen, Rong-Nan Chien, Yang-Hsiang Lin and Chau-Ting Yeh
Int. J. Mol. Sci. 2023, 24(2), 1681; https://doi.org/10.3390/ijms24021681 - 14 Jan 2023
Cited by 1 | Viewed by 2233
Abstract
Sorafenib is currently a targeted agent widely used in the treatment of advanced hepatocellular carcinoma (aHCC). However, to date there is still a lack of a reliable marker capable of predicting sorafenib therapeutic responses. Here, we conducted a genome-wide association study (GWAS) to [...] Read more.
Sorafenib is currently a targeted agent widely used in the treatment of advanced hepatocellular carcinoma (aHCC). However, to date there is still a lack of a reliable marker capable of predicting sorafenib therapeutic responses. Here, we conducted a genome-wide association study (GWAS) to identify candidate single-nucleotide polymorphism outcome predictors in aHCC patients. A total of 74 real-world sorafenib-treated aHCC patients were enrolled for GWAS and outcome analysis. GWAS showed that rs1010816 (p = 2.2 × 10−7) was associated with sorafenib therapeutic response in aHCC patients. Kaplan–Meier analysis indicated that the “TT” genotype was significantly associated with a favorable therapeutic response but not significantly associated with overall survival (OS). Univariate followed by multivariate Cox proportional hazard analysis showed that ascites, main portal vein thrombosis, lower platelet count, lower total sorafenib doses, higher PALBI score in model A and higher ALBI grade in model B were significantly associated with a shorter OS. Subgroup analysis showed that only in alcoholic aHCC patients treated by sorafenib, rs1010816 “TT” genotype was significantly associated with longer OS (p = 0.021). Sorafenib had a favorable therapeutic outcome in alcoholic aHCC patients carrying rs1010816 “TT” genotype. Full article
(This article belongs to the Special Issue Liver Diseases, Genetics and Epigenetics)
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20 pages, 3213 KiB  
Article
A Mitophagy-Related Gene Signature for Subtype Identification and Prognosis Prediction of Hepatocellular Carcinoma
by Chang Liu, Zhen Wu, Liping Wang, Qian Yang, Ji Huang and Jichang Huang
Int. J. Mol. Sci. 2022, 23(20), 12123; https://doi.org/10.3390/ijms232012123 - 12 Oct 2022
Cited by 17 | Viewed by 4618
Abstract
Globally, hepatocellular carcinoma (HCC) is the sixth most common cancer. In this study, the correlation between mitophagy and HCC prognosis was evaluated using data from The Cancer Genome Atlas (TCGA). Clinical and transcriptomic data of HCC patients were downloaded from TCGA dataset, and [...] Read more.
Globally, hepatocellular carcinoma (HCC) is the sixth most common cancer. In this study, the correlation between mitophagy and HCC prognosis was evaluated using data from The Cancer Genome Atlas (TCGA). Clinical and transcriptomic data of HCC patients were downloaded from TCGA dataset, and mitophagy-related gene (MRG) datasets were obtained from the Molecular Signature Database. Then, a consensus clustering analysis was performed to classify the patients into two clusters. Furthermore, tumor prognosis, clinicopathological features, functional analysis, immune infiltration, immune checkpoint (IC)-related gene expression level, tumor stem cells, ferroptosis status, and N6-methyladenosine analysis were compared between the two clusters. Finally, a mitophagy-related signature was developed. Two clusters (C1 and C2) were identified using the consensus clustering analysis based on the MRG signature. Patients with the C1 subtype exhibited upregulated pathways with better liver function, downregulated cancer-related pathways, lower cancer stem cell scores, lower Tumor Immune Dysfunction and Exclusion scores (TIDE), different ferroptosis status, and better prognosis compared with the patients with the C2 subtype. The C2 subtype was characterized by the increased grade of HCC, as well as the increased number of immune-related pathways and m6A-related genes. Higher immune scores were also observed for the C2 subtype. A signature containing four MRGs (PGAM5, SQSTM1, ATG9A, and GABARAPL1) which can accurately predict the prognosis of HCC patients was then identified. This four-gene signature exhibited a predictive effect in five other cancer types, namely glioma, uveal melanoma, acute myeloid leukemia, adrenocortical carcinoma, and mesothelioma. The mitophagy-associated subtypes of HCC were closely related to the immune microenvironment, immune checkpoint-related gene expression, cancer stem cells, ferroptosis status, m6A, prognosis, and HCC progression. The established MRG signature could predict prognosis in patients with HCC. Full article
(This article belongs to the Special Issue Liver Diseases, Genetics and Epigenetics)
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11 pages, 1269 KiB  
Article
Impact of a Loss-of-Function Variant in HSD17B13 on Hepatic Decompensation and Mortality in Cirrhotic Patients
by Antonio Gil-Gómez, Ángela Rojas, María R. García-Lozano, Rocío Muñoz-Hernández, Rocío Gallego-Durán, Douglas Maya-Miles, Rocío Montero-Vallejo, Sheila Gato, Javier Gallego, Rubén Francés, Germán Soriano, Javier Ampuero and Manuel Romero-Gómez
Int. J. Mol. Sci. 2022, 23(19), 11840; https://doi.org/10.3390/ijms231911840 - 6 Oct 2022
Cited by 7 | Viewed by 2471
Abstract
A common splice variant in HSD17B13 (rs72613567:TA) was recently found to be associated with a reduced risk of developing chronic liver disease in NAFLD patients and a reduced risk of progression to advanced fibrosis and cirrhosis. In this study, we aimed to evaluate [...] Read more.
A common splice variant in HSD17B13 (rs72613567:TA) was recently found to be associated with a reduced risk of developing chronic liver disease in NAFLD patients and a reduced risk of progression to advanced fibrosis and cirrhosis. In this study, we aimed to evaluate the prognosis of cirrhotic patients harboring this variant. We performed a retrospective analysis on 483 prospectively recruited patients from four different hospitals in Spain, followed-up for at least 5 years. We collected clinical, demographic, and biochemical data, and we performed a genotyping analysis for common variants previously associated with liver disease risk (HSD17B13 rs72613567:TA and PNPLA3 rs738409). Patients homozygous for the TA allele showed a higher MELD score (p = 0.047), Child–Turcotte–Pugh score (p = 0.014), and INR levels (p = 0.046), as well as decreased albumin (p = 0.004) at baseline. After multivariate analysis, patients with the “protective” variant indeed had an increased risk of hepatic decompensation [aHR 2.37 (1.09–5.06); p = 0.029] and liver-related mortality [aHR 2.32 (1.20–4.46); p = 0.012]. Specifically, these patients had an increased risk of developing ascites (Log-R 11.6; p < 0.001), hepatic encephalopathy (Log-R 10.2; p < 0.01), and higher mortality (Log-R 14.1; p < 0.001) at 5 years of follow-up. Interactions with the etiology of the cirrhosis and with the variant rs738409 in PNPLA3 are also described. These findings suggest that the variant rs72613567:TA in HSD17B13 has no protective effect, but indeed increases the risk of decompensation and death in patients with advanced chronic liver disease. Full article
(This article belongs to the Special Issue Liver Diseases, Genetics and Epigenetics)
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12 pages, 913 KiB  
Article
Single Nucleotide Polymorphisms of Toll-like Receptor 4 in Hepatocellular Carcinoma—A Single-Center Study
by Theodoros Androutsakos, Athanasios-Dimitrios Bakasis, Abraham Pouliakis, Maria Gazouli, Christos Vallilas and Gregorios Hatzis
Int. J. Mol. Sci. 2022, 23(16), 9430; https://doi.org/10.3390/ijms23169430 - 21 Aug 2022
Cited by 10 | Viewed by 2194
Abstract
Hepatocellular carcinoma (HCC) is the most common primary liver tumor leading to significant morbidity and mortality; its exact genetic background is largely unrecognized. Toll-like receptor-4 (TLR4) reacts with lipopolysaccharides, molecules found in the outer membrane of Gram-negative bacteria. In damaged liver, TLR4 expression [...] Read more.
Hepatocellular carcinoma (HCC) is the most common primary liver tumor leading to significant morbidity and mortality; its exact genetic background is largely unrecognized. Toll-like receptor-4 (TLR4) reacts with lipopolysaccharides, molecules found in the outer membrane of Gram-negative bacteria. In damaged liver, TLR4 expression is upregulated, leading to hepatic inflammation and injury. We tried to investigate the role of the two most common single-nucleotide polymorphisms (SNPs) of TLR4 in HCC-genesis. Aged > 18 years old, cirrhotic patients were included in this study. Exclusion criteria were non-HCC tumors and HIV co-infection. TLR4 SNPs association with HCC occurrence was the primary endpoint, and associations with all-cause and liver-related mortality, as well as time durations between diagnosis of cirrhosis and HCC development or death and diagnosis of HCC and death were secondary endpoints. A total of 52 out of 260 included patients had or developed HCC. TLR4 SNPs showed no correlation with primary or secondary endpoints, except for the shorter duration between HCC development and death in patients with TLR4 mutations. Overall, TLR4 SNPs showed no correlation with carcinogenesis or deaths in patients with liver cirrhosis; patients with TLR4 SNPs that developed HCC had lower survival rates, a finding that should be further evaluated. Full article
(This article belongs to the Special Issue Liver Diseases, Genetics and Epigenetics)
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Review

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12 pages, 774 KiB  
Review
Role of B Lymphocytes in the Pathogenesis of NAFLD: A 2022 Update
by Chu-Jun Deng, Tak-Ho Lo, Ka-Ying Chan, Xiang Li, Meng-Yao Wu, Zou Xiang and Chi-Ming Wong
Int. J. Mol. Sci. 2022, 23(20), 12376; https://doi.org/10.3390/ijms232012376 - 16 Oct 2022
Cited by 17 | Viewed by 3398
Abstract
Non-alcoholic fatty liver disease and its related complications are becoming one of the most important health problems globally. The liver functions as both a metabolic and an immune organ. The crosstalk between hepatocytes and intrahepatic immune cells plays a key role in coordinating [...] Read more.
Non-alcoholic fatty liver disease and its related complications are becoming one of the most important health problems globally. The liver functions as both a metabolic and an immune organ. The crosstalk between hepatocytes and intrahepatic immune cells plays a key role in coordinating a dual function of the liver in terms of the protection of the host from antigenic overload as a result of receiving nutrients and gut microbiota antigenic stimulation via facilitating immunologic tolerance. B cells are the most abundant lymphocytes in the liver. The crucial role of intrahepatic B cells in energy metabolism under different immune conditions is now emerging in the literature. The accumulating evidence has demonstrated that the antibodies and cytokines produced by B cells in the microenvironment play key and distinct roles in the pathogenesis of non-alcoholic fatty liver disease (NAFLD). Herein, we have aimed to consolidate and update the current knowledge about the pathophysiological roles of B cells as well as the underlying mechanisms in energy metabolism. Understanding how B cells can exacerbate and suppress liver damage by exploiting the antibodies and cytokines they produce will be of great importance for designing B-cell targeting therapies to treat various liver diseases. Full article
(This article belongs to the Special Issue Liver Diseases, Genetics and Epigenetics)
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