A 3'-untranslated region variant (rs2289046) of insulin receptor substrate 2 gene is associated with susceptibility to nonalcoholic fatty liver disease.

PURPOSE: Nonalcoholic fatty liver disease (NAFLD) is an increasing global health concern defined by excessive hepatic fat content in the absence of excessive alcohol consumption. Regarding the key role of insulin and insulin resistance in NAFLD, we investigated whether insulin receptor substrate 1 (IRS1) and insulin receptor substrate 2 (IRS2) gene variants were associated with NAFLD risk. METHODS: In this case-control study, 305 subjects including 151 cases with biopsy-proven NAFLD and 154 controls were enrolled. All the subjects were genotyped for IRS1 (rs1801278) and IRS2 (rs2289046) gene variants using PCR-RFLP method. RESULTS: Our findings showed that the IRS2 rs2289046 "GG+AG" genotype compared with "AA" genotype to be a marker of decreased NAFLD susceptibility and the difference remained significant even after adjustment for confounding factors including age, BMI, sex, smoking status, systolic blood pressure, and diastolic blood pressure (P=0.014; OR=0.50, 95%CI= 0.29-0.87). Furthermore, the IRS2 "G" allele was significantly underrepresented in the cases with NAFLD than controls (P=0.026 ; OR=0.62, 95%CI=0.41-0.94). However, no significant difference was found for IRS1 rs1801278 gene variant. CONCLUSIONS: This study suggests, for the first time, that the IRS2 gene rs2289046 variant may play a role in NAFLD susceptibility. Nevertheless, this observation warrants further investigations in other populations.

HCC complicated by PVT: Outcome and the role of anticoagulation therapy.

Background: This retrospective study investigated the clinical impact of PVT on the course of patients with HCC who were and were not treated with anticoagulation (AC). Methods: We retrospectively evaluated a cohort of 60 patients diagnosed with HCC and PVT. Nine patients were excluded for lack of follow-up. HCC, PVT diagnosis, and imaging follow-up were performed using contrast-enhanced computed tomography or MRI. Of the 51 patients evaluated, 12 received AC and 39 did not. Results: Forty-two patients were male; mean age was 60.3 years. Mean survival after HCC diagnosis was 32.9 months; after PVT diagnosis, it was 18.4 months. No symptoms directly related to PVT development were reported. AC therapy was initiated for 12 patients and had to be discontinued for 3 patients because of complications. AC was not associated with a difference in PVT progression (49% in non-AC group vs. 50% in AC group). After adjusting for age, HCC type (single vs. multifocal), and Child-Pugh score, AC was associated with an improved survival after HCC diagnosis (adjusted hazard ratio [HR] = 0.37; 95% confidence interval [CI] 0.14 to 0.99) and after PVT diagnosis (HR = 0.34; 95% CI 0.13 to 0.88). Conclusion: Patients with HCC complicated by PVT in both AC and non-AC groups had a similar rate of progression. Neither group had symptoms attributable to PVT. Possible AC-related complications need to be considered before proceeding with therapy in patients with HCC and PVT. AC may be associated with a survival advantage in patients with HCC and PVT.

The Multifaceted Contributions of Chromatin to HIV-1 Integration, Transcription, and Latency.

The capacity of the human immunodeficiency virus (HIV-1) to establish latent infections constitutes a major barrier to the development of a cure for HIV-1. In latent infection, replication competent HIV-1 provirus is integrated within the host genome but remains silent, masking the infected cells from the activity of the host immune response. Despite the progress in elucidating the molecular players that regulate HIV-1 gene expression, the mechanisms driving the establishment and maintenance of latency are still not fully understood. Transcription from the HIV-1 genome occurs in the context of chromatin and is subjected to the same regulatory mechanisms that drive cellular gene expression. Much like in eukaryotic genes, the nucleosomal landscape of the HIV-1 promoter and its position within genomic chromatin are determinants of its transcriptional activity. Understanding the multilayered chromatin-mediated mechanisms that underpin HIV-1 integration and expression is of utmost importance for the development of therapeutic strategies aimed at reducing the pool of latently infected cells. In this review, we discuss the impact of chromatin structure on viral integration, transcriptional regulation and latency, and the host factors that influence HIV-1 replication by regulating chromatin organization. Finally, we describe therapeutic strategies under development to target the chromatin-HIV-1 interplay.

Liver transplant for viral hepatitis and fulminant hepatic failure.

Since the introduction of hepatitis B immunoglobulin and nucleoside/nucleotide antivirals in the 1990's, outcomes of LT for hepatitis B virus (HBV)-related liver disease, regardless of whether for decompensated cirrhosis, hepatocellular carcinoma satisfying Milan criteria or fulminant hepatic failure (FHF), have been favorable with results comparable if not better to other liver transplant recipients. Unfortunately the same optimism does not hold true for hepatitis C which differs from post- transplant hepatitis B in many ways, most striking of which are the limited options for treatment of recurrent hepatitis C (HCV). As time has passed, the initial enthusiasm for liver transplantation for HCV has waned as the original excellent five year survival rates have now translated into disappointing medium- and long-term survival data. Cirrhosis can also develop in between 10-25% of patients by five years post-transplant which in turn has led to recurrent HCV-related cirrhosis emerging as an important yet controversial indication for retransplantation. A variety of diseases can cause FHF with drug-related hepatotoxicity, particularly from acetaminophen accounting for 50-60% of cases in United Kingdom and the United States while viral hepatitis appears to be declining as a cause. Although FHF is a relatively rare disease affecting approximately 2000 patients per year in the United States, it is associated with high morbidity and mortality without transplantation yet only 25% of patients in the United States undergo liver transplantation. This review article will discuss liver transplantation for HBV and HCV and will conclude with reviewing the etiology, epidemiology and management of FHF.

Identification of a new human mtDNA polymorphism (A14290G) in the NADH dehydrogenase subunit 6 gene.

Leber's hereditary optic neuropathy (LHON) is a maternally inherited form of retinal ganglion cell degeneration leading to optic atrophy in young adults. Several mutations in different genes can cause LHON (heterogeneity). The ND6 gene is one of the mitochondrial genes that encodes subunit 6 of complex I of the respiratory chain. This gene is a hot spot gene. Fourteen Persian LHON patients were analyzed with single-strand conformational polymorphism and DNA sequencing techniques. None of these patients had four primary mutations, G3460A, G11788A, T14484C, and G14459A, related to this disease. We identified twelve nucleotide substitutions, G13702C, T13879C, T14110C, C14167T, G14199T, A14233G, G14272C, A14290G, G14365C, G14368C, T14766C, and T14798C. Eleven of twelve nucleotide substitutions had already been reported as polymorphism. One of the nucleotide substitutions (A14290G) has not been reported. The A14290G nucleotide substitution does not change its amino acid (glutamic acid). We looked for base conservation using DNA star software (MEGALIGN program) as a criterion for pathogenic or nonpathogenic nucleotide substitution in A14290G. The results of ND6 gene alignment in humans and in other species (mouse, cow, elegans worm, and Neurospora crassa mold) revealed that the 14290th base was not conserved. Fifty normal controls were also investigated for this polymorphism in the Iranian population and two had A14290G polymorphism (4%). This study provides evidence that the mtDNA A14290G allele is a new nonpathogenic polymorphism. We suggest follow-up studies regarding this polymorphism in different populations.

Identification of a new human mtDNA polymorphism (A14290G) in the NADH dehydrogenase subunit 6 gene

Leber's hereditary optic neuropathy (LHON) is a maternally inherited form of retinal ganglion cell degeneration leading to optic atrophy in young adults. Several mutations in different genes can cause LHON (heterogeneity). The ND6 gene is one of the mitochondrial genes that encodes subunit 6 of complex I of the respiratory chain. This gene is a hot spot gene. Fourteen Persian LHON patients were analyzed with single-strand conformational polymorphism and DNA sequencing techniques. None of these patients had four primary mutations, G3460A, G11788A, T14484C, and G14459A, related to this disease. We identified twelve nucleotide substitutions, G13702C, T13879C, T14110C, C14167T, G14199T, A14233G, G14272C, A14290G, G14365C, G14368C, T14766C, and T14798C. Eleven of twelve nucleotide substitutions had already been reported as polymorphism. One of the nucleotide substitutions (A14290G) has not been reported. The A14290G nucleotide substitution does not change its amino acid (glutamic acid). We looked for base conservation using DNA star software (MEGALIGN program) as a criterion for pathogenic or nonpathogenic nucleotide substitution in A14290G. The results of ND6 gene alignment in humans and in other species (mouse, cow, elegans worm, and Neurospora crassa mold) revealed that the 14290th base was not conserved. Fifty normal controls were also investigated for this polymorphism in the Iranian population and two had A14290G polymorphism (4 percent). This study provides evidence that the mtDNA A14290G allele is a new nonpathogenic polymorphism. We suggest follow-up studies regarding this polymorphism in different populations.

Selective gene regulation by SWI/SNF-related chromatin remodeling factors.

Chromatin is a highly dynamic structure that plays a key role in the orchestration of gene expression patterns during cellular differentiation and development. The packaging of DNA into chromatin generates a barrier to the transcription machinery. The two main strategies by which cells alleviate chromatin-mediated repression are through the action of ATP-dependent chromatin remodeling complexes and enzymes that covalently modify the histones. Various signaling pathways impinge upon the targeting and activity of these enzymes, thereby controlling gene expression in response to physiological and developmental cues. Chromatin structure also underlies many so-called epigenetic phenomena, leading to the mitotically stable propagation of differential expression of genetic information. Here, we will focus on the role of SWI/SNF-related ATP-dependent chromatin remodeling complexes in developmental gene regulation. First, we compare different models for how remodelers can act in a gene-selective manner, and either cooperate or antagonize other chromatin-modulating systems in the cell. Next, we discuss their functioning during the control of developmental gene expression programs.

Chromatin silencing and activation by Polycomb and trithorax group proteins.

The Polycomb group (PcG) of repressors and the trithorax group (trxG) of activators maintain the correct expression of several key developmental regulators, including the homeotic genes. PcG and trxG proteins function in distinct multiprotein complexes that are believed to control transcription by changing the structure of chromatin, organizing it into either a 'closed' or an 'open' conformation. The hallmark of gene regulation by PcG/trxG proteins is that it can lead to a mitotically stable pattern of gene expression, often referred to as epigenetic regulation. Although much remains to be learned, recent studies have provided insights into how this epigenetic switch is set, how PcG/trxG proteins might be linked to cis-acting DNA elements and what potential mechanisms underlie stable inheritance of gene expression status over multiple cell divisions. Finally, the study of the evolutionarily conserved PcG/trxG factors has recently gained additional urgency with the realization that they play a pertinent role in certain human cancers.

The Drosophila brahma complex is an essential coactivator for the trithorax group protein zeste.

The trithorax group (trxG) of activators and Polycomb group (PcG) of repressors are believed to control the expression of several key developmental regulators by changing the structure of chromatin. Here, we have sought to dissect the requirements for transcriptional activation by the Drosophila trxG protein Zeste, a DNA-binding activator of homeotic genes. Reconstituted transcription reactions established that the Brahma (BRM) chromatin-remodeling complex is essential for Zeste-directed activation on nucleosomal templates. Because it is not required for Zeste to bind to chromatin, the BRM complex appears to act after promoter binding by the activator. Purification of the Drosophila BRM complex revealed a number of novel subunits. We found that Zeste tethers the BRM complex via direct binding to specific subunits, including trxG proteins Moira (MOR) and OSA. The leucine zipper of Zeste mediates binding to MOR. Interestingly, although the Imitation Switch (ISWI) remodelers are potent nucleosome spacing factors, they are dispensable for transcriptional activation by Zeste. Thus, there is a distinction between general chromatin restructuring and transcriptional coactivation by remodelers. These results establish that different chromatin remodeling factors display distinct functional properties and provide novel insights into the mechanism of their targeting.

Addition of positively charged tripeptide to N-terminus of the Fos basic region leucine zipper domain: implications on DNA bending, affinity, and specificity.

GKH-Fos(139-211)/Jun(248-334) (GKH: glycine-lysine-histidine) is a modified Fos/Jun heterodimer designed to contain a metal binding motif in the form of a GKH tripeptide at the amino terminus of Fos bZIP domain dimerized with the Jun basic region leucine zipper (bZIP) domain. We examined the effect of the addition of positively charged GKH motif to the N-terminus of Fos(139-211) on the DNA binding characteristics of the Fos(139-211)/Jun(248-334) heterodimer. Binding studies indicate that while the nonspecific DNA binding affinity of the GKH modified heterodimer increases 4-fold, it specifically binds the activating protein-1 (AP-1) site 6-fold less tightly than the control unmodified counterpart. Furthermore, helical phasing analysis indicates that GKH-Fos(139-211)/Jun(248-334) and control Fos(139-211)/Jun(248-334) both bend the DNA at the AP-1 site toward the minor groove. However, due to the presence of the positively charged GKH motif on Fos, the degree of the induced bend by GKH- Fos(139-211)/Jun(248-334) is greater than that induced by the unmodified Fos/Jun heterodimer. Our results suggest that the unfavorable energetic cost of the increased DNA bending by GKH-Fos(139-211)/Jun(248-334) results in a decrease in both specificity and affinity of binding of the heterodimer to the AP-1 site. These findings may have important implications in protein design as well in our understanding of DNA bending and factors responsible for the functional specificity of different members of the bZIP family of transcription factors.