T-lymphocyte senescence and hepatitis C virus infection

Hepatitis C virus (HCV) infection is a leading cause of cirrhosis and hepatocellular carcinoma. The degree of fibrosis progression and treatment-related outcomes are critically dependent on the age of the infected individual. Progressive ageing is associated with a decline in the efficacy of adaptive immune system function. T-lymphocytes from aged subjects demonstrate multiple phenotypic and functional changes, including telomere shortening. Short telomeres are associated with poor proliferative capacity, pro-inflammatory responses and increased mortality in clinical studies. This research aimed to study telomere length changes in T-lymphocytes in chronic HCV infection and its relationship to clinical endpoints. Further, the intracellular signalling changes in T-lymphocytes with short telomeres were studied in subjects with chronic HCV. Short CD4+ T-lymphocyte telomeres were associated with the presence of severe hepatic fibrosis independent of other known factors. Telomere length was associated with blood markers of hepatic damage and dysfunction as well as histological markers of inflammation and fibrosis. Further, on prospective follow-up, short CD4+ telomere length at enrolment predicted progression to clinical endpoints of hepatic decompensation, development of hepatocellular carcinoma and death. Short CD4+ telomere length predicted a failure to respond to anti-viral treatment for HCV infection. Unexpectedly, subjects with non-viraemic HCV had short CD8+ telomere length. Liver biopsy tissue from a cohort of subjects with non-viraemic HCV was studied and demonstrated significant inflammation or fibrosis in most. To study the IFN-α signalling pathway in cells with short telomeres, I utilised the phospho-histone γ-H2AX, a downstream signal from short telomeres. CD8+ T-lymphocytes expressing γ-H2AX had the form and function of cells with end-stage differentiation. γ-H2AX+ cells had a pro-inflammatory cytokine secretion profile with high expression of IFN-γ and low IL-2. Further γ-H2AX+ cells were unable to respond to exogenous IFN-α by phosphorylating Stat1. This failure was attributable to a post-receptor defect. T-lymphocyte telomere length changes in HCV may underpin the effect of age on clinical and treatment-related outcome. Short telomeres are associated with intracellular signalling defects which may explain the failure to respond to anti-viral therapy.My salary costs for the duration of this project were supported by a Clinical Research Training Fellowship from the Wellcome Trust and a scholarship from the Raymond and Beverley Sackler Foundation. Consumable expenses were supported by the Wellcome Trust, the Cambridge Hepatology endowment fund, the Frank Litchfield charitable trust and an unrestricted consumables grant from Roche (UK) pharmaceuticals

Children’s experience and attitudes towards the police, personal safety and public spaces: findings from the 2009/10 British Crime Survey interviews with children aged 10 to 15, supplementary volume 3 to Crime in England and Wales 2009/10

The British Crime Survey (BCS) is a face-to-face victimisation survey of around 46,000 adults resident in households in England and Wales. The survey has been carried out since 19821, asking adults aged 16 or over about their experiences of crime in the 12 months prior to interview as well as their attitudes towards different crime-related issues such as the police, criminal justice system, and perceptions of crime and anti-social behaviour. One of the key recommendations of crime statistics reviews carried out in 2006 was that the BCS should be extended to include populations currently not covered by the survey, for example, people aged under 16 (Smith, 2006; Statistics Commission, 2006). An announcement was made in May 2008 that the BCS would be extended to include children aged 10 to 15 following independent expert advice (Pickering et al., 2008). After a period of testing, development and consultation, data collection began in January 2009. A methodological report detailing all aspects of this process was published on 21 October 2010 (see Fitzpatrick et al., 2010)

Ageing, telomeres, senescence, and liver injury

Populations in developed countries continue to grow older and an understanding of the ageing process to allow healthy ageing carries important medical implications. Older individuals are more susceptible to most acquired liver disorders and more vulnerable to the consequences of liver disease. Accordingly, age is a critical determinant of outcome for hepatitis C virus infection and liver transplantation. In this review we describe changes in the ageing liver and discuss mechanisms of senescence at the cellular level. In particular, we focus on mechanisms by which inflammation, oxidative stress, and oncogenic stress accelerate cellular senescence. In the setting of chronic hepatic injury and inflammation, cellular senescence functions as an essential stress-response mechanism to limit the proliferation of damaged cells and reduce the risk of malignancy, but this benefit is achieved at the expense of senescence-related organ dysfunction. The dual role of cell senescence in chronic liver disease will make this an intriguing but challenging area for future clinical interventions

γ-H2AX+CD8+ T lymphocytes cannot respond to IFN-α, IL-2 or IL-6 in chronic hepatitis C virus infection

Background & AimsAge is the dominant prognostic factor influencing the natural history of hepatitis C virus (HCV) infection and treatment response. Accelerated lymphocyte telomere shortening in HCV infection correlates with adverse clinical outcomes. Critical telomere shortening generates double-stranded DNA breaks (DSB) inducing the DNA damage response, leading to replicative senescence. The phenotype and function of CD8+ T lymphocytes and the in vitro response to IFN-α in relation to the DNA damage response were investigated in patients with chronic HCV infection.MethodsCD8+ T lymphocytes with DSB were identified by expression of γ-H2AX (Ser-139) in 134 HCV-exposed subjects and 27 controls. Telomere length was determined by flow-FISH; cytokine expression by intracellular cytokine staining; in vitro responses to IFN-α, IL-2 or IL-6 by phospho-STAT1 (Y701) or phospho-STAT5 (Y694) expression.ResultsThe proportion of circulating CD8+γ-H2AX+ T lymphocytes rose with increasing fibrosis stage (p=0.0023). CD8+γ-H2AX+ T lymphocytes were enriched in liver compared to blood (p=0.03). CD8+γ-H2AX+ T lymphocytes demonstrated increased IFN-γ (p=0.02) and reduced IL-2 expression (p=0.02). CD8+γ-H2AX+ T lymphocytes failed to phosphorylate STAT1 in response to IFN-α compared to unfractionated CD8+ T lymphocytes (p <0.0001). More widespread failure of Jak/Stat signalling in CD8+γ-H2AX+ T lymphocytes was suggested by impaired phosphorylation of STAT1 with IL-6 (p=0.002) and STAT5 with IL-2 (p=0.0039) compared to unfractionated CD8+ T-lymphocytes.ConclusionsIn chronic HCV infection, CD8+γ-H2AX+ T lymphocytes are highly differentiated with shortened telomeres, are more frequent within the liver, are associated with severe fibrosis and fail to activate Jak/Stat pathways in response to IFN-α, IL-2 or IL-6, perhaps explaining treatment failure in those with severe fibrosis

Machine learning for the life-time risk prediction of Alzheimer’s disease: a systematic review

Alzheimer’s disease is a neurodegenerative disorder and the most common form of dementia. Early diagnosis may assist interventions to delay onset and reduce the progression rate of the disease. We systematically reviewed the use of machine learning algorithms for predicting Alzheimer’s disease using single nucleotide polymorphisms and instances where these were combined with other types of data. We evaluated the ability of machine learning models to distinguish between controls and cases, while also assessing their implementation and potential biases. Articles published between December 2009 and June 2020 were collected using Scopus, PubMed and Google Scholar. These were systematically screened for inclusion leading to a final set of 12 publications. Eighty-five per cent of the included studies used the Alzheimer's Disease Neuroimaging Initiative dataset. In studies which reported area under the curve, discrimination varied (0.49–0.97). However, more than half of the included manuscripts used other forms of measurement, such as accuracy, sensitivity and specificity. Model calibration statistics were also found to be reported inconsistently across all studies. The most frequent limitation in the assessed studies was sample size, with the total number of participants often numbering less than a thousand, whilst the number of predictors usually ran into the many thousands. In addition, key steps in model implementation and validation were often not performed or unreported, making it difficult to assess the capability of machine learning models

Robustness of radiomic features in CT images with different slice thickness, comparing liver tumour and muscle

Abstract: Radiomic image features are becoming a promising non-invasive method to obtain quantitative measurements for tumour classification and therapy response assessment in oncological research. However, despite its increasingly established application, there is a need for standardisation criteria and further validation of feature robustness with respect to imaging acquisition parameters. In this paper, the robustness of radiomic features extracted from computed tomography (CT) images is evaluated for liver tumour and muscle, comparing the values of the features in images reconstructed with two different slice thicknesses of 2.0 mm and 5.0 mm. Novel approaches are presented to address the intrinsic dependencies of texture radiomic features, choosing the optimal number of grey levels and correcting for the dependency on volume. With the optimal values and corrections, feature values are compared across thicknesses to identify reproducible features. Normalisation using muscle regions is also described as an alternative approach. With either method, a large fraction of features (75–90%) was found to be highly robust (< 25% difference). The analyses were performed on a homogeneous CT dataset of 43 patients with hepatocellular carcinoma, and consistent results were obtained for both tumour and muscle tissue. Finally, recommended guidelines are included for radiomic studies using variable slice thickness

Functional skewing of the global CD8 T cell population in chronic hepatitis B virus infection

The inflamed liver in chronic hepatitis B virus (HBV) infection (CHB) is characterized by a large influx of non–virus-specific CD8 T cells. Little is known about the functional capacity of these lymphocytes, which could provide insights into mechanisms of failure of viral control and liver damage in this setting. We compared the effector function of total circulating and intrahepatic CD8 T cells in CHB patients and healthy donors. We demonstrated that CD8 T cells from CHB patients, regardless of their antigen specificity, were impaired in their ability to produce interleukin-2 and proliferate upon TCR-dependent stimulation. In contrast, these CD8 T cells had preserved production of the proinflammatory cytokines interferon-γ and tumor necrosis factor-α. This aberrant functional profile was partially attributable to down-regulation of the proximal T cell receptor signaling molecule CD3ζ, and could be corrected in vitro by transfection of CD3ζ or replenishment of the amino acid arginine required for its expression. We provide evidence for depletion of arginine in the inflamed hepatic microenvironment as a potential mechanism for these defects in global CD8 T cell signaling and function. These data imply that polarized CD8 T cells within the HBV-infected liver may impede proliferative antiviral effector function, while contributing to the proinflammatory cytokine environment

CD94-NKG2A recognition of human leukocyte antigen (HLA)-E bound to an HLA class I leader sequence

The recognition of human leukocyte antigen (HLA)-E by the heterodimeric CD94-NKG2 natural killer (NK) receptor family is a central innate mechanism by which NK cells monitor the expression of other HLA molecules, yet the structural basis of this highly specific interaction is unclear. Here, we describe the crystal structure of CD94-NKG2A in complex with HLA-E bound to a peptide derived from the leader sequence of HLA-G. The CD94 subunit dominated the interaction with HLA-E, whereas the NKG2A subunit was more peripheral to the interface. Moreover, the invariant CD94 subunit dominated the peptide-mediated contacts, albeit with poor surface and chemical complementarity. This unusual binding mode was consistent with mutagenesis data at the CD94-NKG2A–HLA-E interface. There were few conformational changes in either CD94-NKG2A or HLA-E upon ligation, and such a “lock and key” interaction is typical of innate receptor–ligand interactions. Nevertheless, the structure also provided insight into how this interaction can be modulated by subtle changes in the peptide ligand or by the pairing of CD94 with other members of the NKG2 family. Differences in the docking strategies used by the NKG2D and CD94-NKG2A receptors provided a basis for understanding the promiscuous nature of ligand recognition by NKG2D compared with the fidelity of the CD94-NKG2 receptors

Lipid Remodeling in Hepatocyte Proliferation and Hepatocellular Carcinoma.

BACKGROUND AND AIMS: Hepatocytes undergo profound metabolic rewiring when primed to proliferate during compensatory regeneration and in hepatocellular carcinoma (HCC). However, the metabolic control of these processes is not fully understood. In order to capture the metabolic signature of proliferating hepatocytes, we applied state-of-the-art systems biology approaches to models of liver regeneration, pharmacologically and genetically activated cell proliferation, and HCC. APPROACH AND RESULTS: Integrating metabolomics, lipidomics, and transcriptomics, we link changes in the lipidome of proliferating hepatocytes to altered metabolic pathways including lipogenesis, fatty acid desaturation, and generation of phosphatidylcholine (PC). We confirm this altered lipid signature in human HCC and show a positive correlation of monounsaturated PC with hallmarks of cell proliferation and hepatic carcinogenesis. CONCLUSIONS: Overall, we demonstrate that specific lipid metabolic pathways are coherently altered when hepatocytes switch to proliferation. These represent a source of targets for the development of therapeutic strategies and prognostic biomarkers of HCC.J.L.G., Z.H. and M.V. are funded by the Medical Research Council (MRC grant MC UP A90 1006 & MC PC 13030). J.L.G. and Z.H. are supported by the Imperial Biomedical Research Centre, NIHR. M.A., A.V-P., F.O., Q.M.A. and M.V. are members of the EPoS consortium, which is funded by the Horizon 2020 Framework Program of the European Union under Grant Agreement 634413. F.O. is supported by MRC program grants (MR/K0019494/1 and MR/R023026/1). J.L is supported by MRC PhD studentship and a CRUK program grant (C18342/A23390). M.V. and A.V-P. are supported by MRC MDU and MRC DMC (MC UU 12012/2). Q.M.A. received additional research support from The Liver Research Trust and is a Newcastle NIHR Biomedical Research Centre investigator. M.A., M.V., A.V-P. and J.L.G. received research support from the Evelyn Trust and the NIHR Cambridge Biomedical Research Centre (Gastroenterology Theme)