Here we describe a virus discovery protocol for a range of different virus genera, that can be applied to biopsy-sized tissue samples. Our viral enrichment procedure, validated using canine and human ...liver samples, significantly improves viral read copy number and increases the length of viral contigs that can be generated by de novo assembly. This in turn enables the Illumina next generation sequencing (NGS) platform to be used as an effective tool for viral discovery from tissue samples.
Non-alcoholic fatty liver disease (NAFLD) is an increasingly common condition, strongly associated with the metabolic syndrome, that can lead to progressive hepatic fibrosis, cirrhosis and hepatic ...failure. Subtle inter-patient genetic variation and environmental factors combine to determine variation in disease progression. A common non-synonymous polymorphism in TM6SF2 (rs58542926 c.449 C>T, p.Glu167Lys) was recently associated with increased hepatic triglyceride content, but whether this variant promotes clinically relevant hepatic fibrosis is unknown. Here we confirm that TM6SF2 minor allele carriage is associated with NAFLD and is causally related to a previously reported chromosome 19 GWAS signal that was ascribed to the gene NCAN. Furthermore, using two histologically characterized cohorts encompassing steatosis, steatohepatitis, fibrosis and cirrhosis (combined n=1,074), we demonstrate a new association, independent of potential confounding factors (age, BMI, type 2 diabetes mellitus and PNPLA3 rs738409 genotype), with advanced hepatic fibrosis/cirrhosis. These findings establish new and important clinical relevance to TM6SF2 in NAFLD.
Hepatocyte senescence is associated closely with fibrosis stage and an adverse outcome in chronic liver disease, but it is uncertain whether there is a causal relation with clinical manifestations of ...chronic liver disease, which was the subject of this study of the senescent hepatocyte gene signature. Senescence was induced in HepG2 cells using sub-lethal concentrations of H2O2. Gene expression of control and senescent HepG2 cells were studied. Comparison was made with patients with cirrhosis and three public microarray datasets. H2O2-treated HepG2 cells demonstrated characteristic cellular senescence. There was differential expression of 354 genes in senescence. Up-regulated genes in HepG2 senescence were also up regulated in patients with cirrhosis. The senescent hepatocyte gene signature distinguished liver disease from normal by unsupervised clustering in the public chronic liver disease microarray datasets, with enrichment of the senescence gene signature in all three datasets. The senescent hepatocyte gene signature included changes in cell cycle regulation, morphology, inflammation, signal transduction, metabolism and stellate cell activation, which alongside impaired synthetic function in senescence in vitro were consistent with manifestations of clinical liver disease, suggesting a close relation between hepatocyte senescence and manifestations of chronic liver disease including fibrosis and impaired synthetic function.
•HepG2 senescence model is highly relevant in human hepatocyte senescence studies.•Senescence signature differentiated disease from normal by unsupervised clustering.•Study suggests causal link between hepatocyte senescence and disease progression.
Hepatitis C virus (HCV) frequently causes chronic hepatitis, while spontaneous recovery from infection is infrequent. Persistence of HCV after self-limited (spontaneous) resolution of hepatitis C was ...rarely investigated. The current study aimed to assess incidence and robustness of HCV persistence after self-resolved hepatitis C in individuals with normal liver enzymes and undetectable virus by conventional tests. Applying high sensitivity HCV RNA detection approaches, we analyzed plasma and peripheral blood mononuclear cells (PBMC) from individuals with previous hepatitis C infection. Parallel plasma and PBMC from 24 such non-viraemic individuals followed for 0.3-14.4 (mean 6.4) years were examined. Additional samples from 9 of them were obtained 4.5-7.2 (mean 5.9) years later. RNA was extracted from 250 μl plasma and, if HCV negative, from ~5 ml after ultracentrifugation, and from ex vivo stimulated PBMC. PBMC with evidence of HCV replication from 4 individuals were treated with HCV protease inhibitor, telaprevir. HCV RNA was detected in 14/24 (58.3%) plasma and 11/23 (47.8%) PBMC obtained during the first collection. HCV RNA replicative strand was evident in 7/11 (63.6%) PBMC. Overall, 17/24 (70.8%) individuals carried HCV RNA at mean follow-up of 5.9 years. Samples collected 4.5-7.2 years later revealed HCV in 4/9 (44.4%) plasma and 5/9 (55.5%) PBMC, while 4 (80%) of these 5 PBMC demonstrated virus replicative strand. Overall, 6/9 (66.7%) individuals remained viraemic for up to 20.7 (mean 12.7) years. Telaprevir entirely eliminated HCV replication in the PBMC examined. In conclusion, our results indicate that HCV can persist long after spontaneous resolution of hepatitis C at levels undetectable by current testing. An apparently effective host immune response curtailing hepatitis appears insufficient to completely eliminate the virus. The long-term morbidity of asymptomatic HCV carriage should be examined even in individuals who achieve undetectable HCV by standard testing and their need for treatment should be assessed.
Natural killer (NK) cells provide a central defense against viral infection by using inhibitory and activation receptors for major histocompatibility complex class I molecules as a means of ...controlling their activity. We show that genes encoding the inhibitory NK cell receptor KIR2DL3 and its human leukocyte antigen C group 1 (HLA-C1) ligand directly influence resolution of hepatitis C virus (HCV) infection. This effect was observed in Caucasians and African Americans with expected low infectious doses of HCV but not in those with high-dose exposure, in whom the innate immune response is likely overwhelmed. The data strongly suggest that inhibitory NK cell interactions are important in determining antiviral immunity and that diminished inhibitory responses confer protection against HCV.
We genotyped 2,861 cases of primary biliary cirrhosis (PBC) from the UK PBC Consortium and 8,514 UK population controls across 196,524 variants within 186 known autoimmune risk loci. We identified 3 ...loci newly associated with PBC (at P<5×10(-8)), increasing the number of known susceptibility loci to 25. The most associated variant at 19p12 is a low-frequency nonsynonymous SNP in TYK2, further implicating JAK-STAT and cytokine signaling in disease pathogenesis. An additional five loci contained nonsynonymous variants in high linkage disequilibrium (LD; r2>0.8) with the most associated variant at the locus. We found multiple independent common, low-frequency and rare variant association signals at five loci. Of the 26 independent non-human leukocyte antigen (HLA) signals tagged on the Immunochip, 15 have SNPs in B-lymphoblastoid open chromatin regions in high LD (r2>0.8) with the most associated variant. This study shows how data from dense fine-mapping arrays coupled with functional genomic data can be used to identify candidate causal variants for functional follow-up.
In addition to the HLA locus, six genetic risk factors for primary biliary cirrhosis (PBC) have been identified in recent genome-wide association studies (GWAS). To identify additional loci, we ...carried out a GWAS using 1,840 cases from the UK PBC Consortium and 5,163 UK population controls as part of the Wellcome Trust Case Control Consortium 3 (WTCCC3). We followed up 28 loci in an additional UK cohort of 620 PBC cases and 2,514 population controls. We identified 12 new susceptibility loci (at a genome-wide significance level of P < 5 × 10⁻⁸) and replicated all previously associated loci. We identified three further new loci in a meta-analysis of data from our study and previously published GWAS results. New candidate genes include STAT4, DENND1B, CD80, IL7R, CXCR5, TNFRSF1A, CLEC16A and NFKB1. This study has considerably expanded our knowledge of the genetic architecture of PBC.
Hepatocellular carcinoma (HCC) has a poor prognosis with limited therapeutic options. We propose that local immune responses in patients with HCC are held in check by tumor-infiltrating CD4(+)CD25(+) ...T-regulatory lymphocytes (T(reg) cells), which suppress the activity and proliferation of effector CD4(+) and CD8(+) T cells. The phenotype and cell cycle status of tumor-infiltrating lymphocytes (TILs) in HCC were analyzed via immunohistochemistry of sections from patients undergoing surgery for HCC and via flow cytometry of peripheral blood mononuclear cells and TILs isolated from patients with HCC. Circulating and tumor-infiltrating T-cell function and activation status were assessed via proliferation and flow cytometry. More than 96% of TILs were quiescent as measured via Mcm-2 or Ki-67 expression, while less than 10% of CD8(+) T cells expressed perforin or granzyme B. CD4(+)CD25(+) T(reg) cells comprised 8.7% (1.4-13.8) of TILs and always exceeded the proportion in distant nontumor tissue (2.4% 1.5-5.6; P = .014). T(reg) cells isolated from HCC suppressed proliferation of autologous circulating CD4(+)CD25(-) cells and perforin expression and proliferation of autologous CD8(+) T cells. The proportion of circulating T(reg) cells in patients with HCC was similar in healthy controls (7.2% 1.2-23.3 and 9.2% 1.6-30.2, respectively), but the proportion of circulating T(reg) cells that were also transforming growth factor beta1(+) was elevated in HCC compared with controls (55.5% 8.2-73.9 and 2.0% 0-4.9, respectively; P = .003). In conclusion, TILs are compromised and contain a subpopulation of suppressive CD4(+)CD25(+)Foxp3(+) T(reg) cells. Functional deletion of tumor-infiltrating T(reg) cells could enhance tumor-specific immunotherapy.
Liver transplantation is an effective treatment for highly selected patients with hepatocellular carcinoma (HCC), but tumour recurrence remains an important cause of mortality. There are few data on ...the relation between the recurrence of HCC and lymphocytic infiltration following liver transplantation.
The tumour CD4
+
, CD8
+
, CD25
+
and Foxp3
+
lymphocyte infiltrate was assessed by immunohistochemistry in explant tissue of 69 patients who underwent liver transplantation for HCC between 1985 and 2001. The data were analysed according to HCC recurrence and factors known to be associated with outcome.
Tumour size (Hazard ratio (95% CI: 1.19 (1.02, 1.39),
P
=
0.03)), vascular invasion (
P
=
0.02), lymphocyte infiltration (
P
=
0.02) and CD4:CD8 ratio (
P
=
0.001) were identified as significant univariate predictors of tumour recurrence. On multivariate analysis CD4:8 ratio (
P
=
0.001), vascular invasion (
P
=
0.01), tumour size (
P
=
0.06) and reduced lymphocyte infiltration (
P
=
0.03) were significant independent predictors of recurrence. The presence of Foxp3
+
T-lymphocytes was not predictive of recurrence, but was associated with vascular invasion (FE
=
9.02,
P
=
0.04).
The data support the hypothesis that immune responses are important in HCC and that the phenotype of infiltrating lymphocytes is informative regarding prognosis.
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