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The sustained virologic response and elimination of HCV is widely viewed as a true cure of chronic hepatitis C as it associates with amelioration of histological liver damage and improved clinical outcomes. Therefore, the existence and clinical burden of occult HCV infection (OCI) has been a controversial issue for many years. In this review, we summarize recently published data that adds new information on the molecular and clinical background of OCI and its epidemiological significance. We also identify and discuss the most important methodological pitfalls, which can be a source of inconsistency between studies. Data that have accumulated so far, strongly support the existence of extrahepatic HCV replication in individuals negative for serum HCV-RNA by conventional clinical tests. OCI emerges as a condition where the immune system is unable to fully resolve infection but it is continuously stimulated by low levels of HCV antigens, leading to progression of liver pathology and extrahepatic HCV-related complications. Moreover, the development of monitoring strategies or management guidelines for OCI is still hampered by the lack of clear definition and the confusion regarding its clinical significance. Careful study design and the introduction of uniform protocols for the detection of low-level HCV-RNA are crucial for obtaining reliable data on OCI.

Chronic HBV infection affects more than 240 million people worldwide and is associated with a broad range of clinical manifestations including liver cirrhosis, liver failure and hepatocellular carcinoma. Because of the lack of an efficient cure for chronic hepatitis B, the main goal of antiviral therapy is the prevention of liver disease progression coupled with prolonged survival of patients. Because HBV viral load has been shown to be a crucial determinant of the progression of liver damage, these goals can be achieved as long as HBV replication can be suppressed. Unfortunately, long-term therapy with the low-to-moderate genetic barrier drugs, which are still recommended in a majority of developing countries, are strongly associated with HBV resistance development and treatment failure. In such cases, the precise and accurate determination of drug-resistant variants in an individual patient before treatment is important for a proper choice of first-line potent therapy. Nowadays, a number of techniques are available to study HBV quasispecies evolution. This review describes the advantages and limitations of various assays detecting drug-resistant HBV variants. Copyright © 2016 John WileySons, Ltd.

Hepatitis B virus (HBV) infection is one of the major human health problems worldwide. It is estimated that chronic HBV infection affects more than 350 million people globally. It is one of the leading causes of liver cirrhosis and hepatocellular carcinoma. High genetic variability is a characteristic feature of HBV as the viral polymerase lacks proofreading activity. The nucleotide substitution rate for HBV is 10-fold higher than for other DNA viruses. Genetic variations of HBV influence the clinical outcome of HBV infection. There are eight genotypes of hepatitis B virus (A-H) that have a distinct geographical distribution. There is clinical significance of HBV genotype in terms of disease activity, risk of progression to cirrhosis, the development of hepatocellular carcinoma and response to antiviral treatments. Moreover, polymorphism in HBV viral polymerase influences the development of HBV mutants resistant to nucleotide analogue treatment that is a consequence of treatment failure.

Liver is a key organ responsible for organism’s homeostasis. A proper function of this organ is crucial for detoxification of metabolic products and regulation of metabolic processes of macromolecules (proteins, lipids, carbohydrates). The most important infectious factors, leading to liver damage, are primary hepatotropic viruses, particularly those causing chronic inflammation of the organ (HBV, HCV, HDV), which may subsequently cause cirrhosis and/or primary hepatocellular carcinoma. There has been a growing interest in Helicobacter spp. liver infections as a potential factor promoting injury of the organ towards hepatocellular carcinoma. The association between hepatocellular carcinoma and the presence of Helicobacters in the liver has been well documented in animal models (Helicobacter hepaticus versus liver cancer in mice). Some reports also indicate similar association in humans, where the presence of Helicobacter antigens in patients with liver cancer is detected more often in comparison to healthy or chronically infected population. Although the molecular mechanisms underlying such a phenomenon are not well known, the knowledge on this subject has considerably increased during recent years. The review presents data on the association between the presence of Helicobacter spp. in the liver and injuries of the organ, as well as the role that is played by the bacteria in chronic liver diseases.

Iron overload observed in chronic hepatitis C (CHC) has been suggested to be one of the negative prognostic factors influencing liver disease progression and failure of treatment with recombinant interferon in monotherapy or in combination with ribavirin. The aim of this study was to assess occurrence of iron overload in relation to polymorphism of the HFE and the influence of both these factors on efficacy of antiviral treatment with pegylated interferon and ribavirin in patients with CHC.Liver function tests, serum indices of iron metabolism, and HFE mutations were assayed in 152 patients with CHC from Poland. Histopathological examination of the liver biopsy specimen was performed in 138 patients. Sixty-one patients were treated with pegylated interferon alfa-2 and ribavirin. The comparative analysis was performed in 2 groups of patients: those with and those without elevated serum indices of iron metabolism.Increased biochemical iron metabolism parameters correlated with older age, higher ALT activity, more advanced liver fibrosis and treatment failure. Iron deposits in liver specimens were not accompanied by exacerbation of necro-inflammatory activity and advanced fibrosis. Elevated biochemical values of iron metabolism parameters and presence of hepatic iron deposits correlated positively with C282Y mutations. The lack of sustained viral response after treatment with pegylated interferon and ribavirin was observed more frequently in carriers of HFE mutations.Iron overload was frequently detected in patients with CHC, and was associated only with C282Y alleles. Biochemical markers of iron overload and HFE gene mutations were negative prognostic factors of antiviral treatment.

The diagnosis of hereditary hemochromatosis (HH) is based on qualitative measurement of tissue iron concentration and genetic tests. The aim of this study was to evaluate the correlation between the presence of iron deposits in the liver and the HFE gene mutations in patients with chronic liver diseases (CLD).The 182 patients, age range 18-71 years, were hospitalized in Gdansk because of CLD. The C282Y, H63D and S65C HFE mutations were screened by PCR-RFLP analysis. Liver function tests, serological examinations for viral hepatitis, serum iron and ferritin concentration and semiquantitative assessment of liver iron were done in all subjects. Patients were divided into Group A without iron deposits in the liver, and Group B with deposits. The most frequent etiology of CLD was chronic hepatitis C.Biochemical parameters indicating iron storage and ALT activity were significantly higher in Group B. Either typical for diagnosis HH homozygotes C282Y/C282Y and combined heterozygotes C282Y/H63D or carriers of other HFE gene mutations were found significantly more frequently in Group B.The finding of iron deposits in routinely obtained liver specimen correlates with occurrence of the different HFE gene mutations.

The determination of gene expression levels in normal tissue is necessary for the analysis and interpretation of results of gene profiling studies in pathological samples. With the real-time reverse transcription-PCR technique, which enables one to detect the amplification rate during the process, assessment of the amount of gene transcript is fast and accurate. The most important problem in this type of analysis is the variability in the amount of genetic material between samples, caused mostly by changes in the efficiency of mRNA isolation and reverse transcription. Therefore, a reference gene to normalize sample variations is required. Quantification of the mRNA of the target and the reference gene in the sample ensures that the changes in transcript levels will influence both genes equally. To be used as a reference, a gene should show stable, unregulated expression in the analyzed sample type. Housekeeping genes (HKGs) fulfill this criterion and they are used for normalization purposes in most expression studies. However, transcript levels of HKGs can vary between different types of tissue (normal and pathological samples) and under different treatment conditions (drugs and chemicals). The aim of this study was to show the differences and the factors which can influence housekeeping gene expressions.

The frequent occurrence of metastases from the primary tumor present a major therapeutic problem in hepatocellular cancer because of the hematogenous spread of cancer cells. Standard imaging diagnostics methods do not allow for an early detection of relapse of the disease, as opposed to the analysis of molecular cell markers, especially mRNA-based methods, in peripheral blood samples by RT-PCR. Analysis of alphafetoprotein expression is the "gold standard" in the diagnostics of HCC at the protein and mRNA level because of its specificity for liver cancer. However, working out an analysis protocol is problematic and the utility of the marker in monitoring a patient's status in the perioperative period remains controversial. New HCC markers are being searched for among the highly liver-specific ones and those shared between various cancers types. Markers associated with freely circulating nucleic acids are also studied and quantitative assays are used. An assay for several markers simultaneously could give satisfactory results.

Hereditary hemochromatosis is now recognized as a very common inherited disease of the Caucasian population. It is defined as a disorder of unique clinicopathology caused by mutations of genes that control iron metabolism. Inappropriately increased intestinal iron absorption and accelerated recycling of iron by macrophages lead to progressive body iron accumulation and the generation of oxidative stress in tissues. This results in significant cellular damage, induction of inflammation, and fibrosis. Liver cirrhosis, hepatocellular carcinoma, diabetes mellitus, and cardiac insufficiency are diagnosed in the advanced phase of this disease. The natural course is modified by environmental factors and personal predisposition. Three forms of hemochromatosis with the pathophysiology of iron overload are described. Among them the classical form, juvenile hemochromatosis with severe course and circulatory insufficiency, and ferroportin disease are presented. Properly directed diagnostics makes early treatment protecting against disease progression and multiorgan insufficiency possible.

Hereditary hemochromatosis (HH) is a genetic metabolic disease characterized by increased intestinal iron absorption and progressive iron loading in the cells of various organs. Human body iron homeostasis involves a number of complicated processes, some of which are not identified yet. Genetic analysis of patients affected by HH recently led to the discovery of many novel proteins and mechanisms that can influence the uptake, transport, storage, and excretion of iron. It also showed that hemochromatosis is a very complex disease and that the type of mutation can influence its clinical manifestation. This review presents the current knowledge about the mechanisms of iron metabolism and describes the types of hereditary hemochromatosis and the mutations which induce the disease.

Hereditary hemochromatosis is one of the most frequent genetic disorders in Europeans, but its prevalence in Poland is still unknown. The aim of the study was an initial assessment of the prevalence of C282Y and H62D HFE gene mutations and their influence on the course of chronic hepatitis C. Forty-one patients were admitted to the Department of Infectious Diseases, Medical University of Gdansk in 2000-2004 because of chronic liver diseases with accompanying disturbances in iron metabolism. Genetic tests for the C282Y and H63D mutations were performed by PCR and restriction fragment length polymorphism (PCR-RFLP) analysis. The HFE gene mutations were confirmed in 24 of 41 (59%) cases with symptoms of chronic liver disease and iron overload, significantly more frequently in HCV-negative patients (12/14 vs. 12/27; chi2=8.28; p=0.05). The C282Y and H63D HFE gene mutations were detected in 16 of 41 (39%) and 9 of 41 (22%) cases, respectively. HCV-negative patients were C282Y carriers significantly more frequently than HCV-positive patients [9/14 vs. 2/27 C282Y homozygotes; 2/14 vs. 3/27 C282Y heterozygotes (p0.0001)]. The carrier state of the H63D HFE gene mutation was not significantly more frequent in HCV-positive than HCV-negative patients. HCV infection seems to be a negative predictive marker of HFE gene mutations in patients with iron overload. The relationship of H63D HFE gene mutations with chronic hepatitis C and the possible influence of HCV infection on iron metabolism needs further analysis.

Hepatitis B virus (HBV) infection is one of the major global epidemiological problems. The aim of our study was to determine the distribution of HBV genotypes in Poland since the data concerning the spread of HBV viruses in the central-eastern region of Europe is still very limited. HBV DNA was extracted from 58 serum samples. To quantify the level of HBV DNA the Roche Amplicor HBV Monitor Assay was used. To genotype and assign HBV subtypes DNA sequencing methods were performed. The HBV virus from 43 serum samples from hepatitis B infected patients was genotype A (74.1%), 12 cases had genotype D (20.7%), and 3 had the rare in Europe genotype F (5.2%). Prediction of HBV serological subtypes based on HBsAg sequencing showed almost 100% occurrence of subtype adw2 in the group of genotype A samples, three different subtypes in genotype D (ayw2, ayw3, and ayw4), and equal distribution of subtype adw4q- in all 3 cases of genotype F, also the most prevalent subtype in the Amerindians. Our results coincide with the general European HBV prevalence. However, HBV genotype F, which is not a common genotype in European countries, was detected and so was relatively high occurrence of genotype D, which may reflect historical and ethnical migration events in Poland in the past.

The proper application of quantitative real-time reverse transcription polymerase chain reaction (RT-PCR) for the relative quantification of a target gene in gene profiling studies requires reference genes to normalize sample variations. Stable housekeeping genes for this purpose have never been investigated in the liver tissue of patients with chronic hepatitis.Expression profiles of six functionally distinct housekeeping genes (ACTB, CYCC, GUS, HPRT1, PMM1, POLR2L) were examined by RT-PCR in liver specimens from 12 individuals with chronic hepatitis C or B. Two software programs, geNorm and NormFinder, were used to assess the expression stability of the studied genes.Crossing-point values of the candidate reference genes were recorded between 22 and 28. In three groups of patients (all patients, HCV patients, HBV patients) both programs identified GUS as the most stably expressed housekeeping gene (stability values: 0.275-0.360 and 0.095-0.107 determined by geNorm and NormFinder, respectively), followed by PMM1 (0.275-0.360 and 0.168-0.227), and POLR2L (0.347-0.397 and 0.319-0.388).The genes GUS and PMM1 are recommended for normalization purposes in gene expression studies of liver tissue from patients with chronic hepatitis C or B. Using these genes in combination will ensure very reliable results.

The polA gene of Escherichia coli coding for DNA polymerase I was cloned under the control of bacteriophage lambda promoter pL and gene N in a high copy number plasmid vector. The chromosomally located lambda cIts repressor gene kept the synthesis of the polA gene product at 28 degrees C at a low level. Raising the temperature to 43 degrees C resulted in inactivation of the repressor and overproduction of DNA polymerase I, which could easily be purified to homogeneity.