977 research outputs found

    Molecular Genetics and Genomics of Hepatocellular Carcinoma

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    Small RNA transcriptomic analysis during chronic viral hepatitis and cancer

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    Hepatitis B virus (HBV) and hepatitis C virus (HCV) are unrelated non-cytopathic viruses that infect the liver. Hundreds of millions of people worldwide are chronic carriers of HBV or HCV, and together these viral infections are responsible for ~80% of hepatocellular carcinoma (HCC). Numerous reports suggest that certain microRNAs (miRNAs, small non-coding RNAs that regulate gene expression post-transcriptionally) are important in the pathogenesis of viral hepatitis, although very few studies have assessed them comprehensively. Furthermore, no study of viral hepatitis or HCC has analyzed other classes of small RNAs, such as tRNA-derived RNAs (tDRs). tDRs have recently been suggested to play a role in human health, although they have never been previously assessed in primary human tissue. Our goal was to characterize thoroughly the small RNA transcriptome in chronic viral hepatitis and HCC. We used high-throughput sequencing to conduct an unbiased profiling of small (14-40 nts) RNAs in liver from Japanese subjects with advanced hepatitis B or C and paired HCC. We also analyzed gene expression data (microarray) and determined that pathways controlling cholesterol homeostasis were among the most significantly altered in chronic viral hepatitis and especially in HCC. An integrative analysis of miRNA and gene expression data predicted several candidate master miRNA regulators of each disease state, including miR-21 and miR-27. We validated in cell culture the roles of miR-21 and miR-27 as regulators of cholesterol synthesis, suggesting that these two miRNAs may be responsible in part for cholesterol imbalance in chronic viral hepatitis and HCC. We next sought to assess tDRs in chronic viral hepatitis and liver cancer. From the small RNA-seq, we observed that tDRs were abundant and significantly increased in chronic viral hepatitis. Remarkably, tDR abundance exceeded that of miRNAs in most infected non-cancerous tissue. In cancer tissue, the total abundance of tDRs was reduced and the relative abundance of individual tDRs was altered. Despite the potential relevance of tDRs to human health and disease, there is no standardized nomenclature, and no method has yet been developed to quantify tDRs from small RNA-seq datasets. To ameliorate these limitations, I developed a publically available method called tDRmapper.Doctor of Philosoph

    Transcriptomic Analysis of Chronic Hepatitis B and C and Liver Cancer Reveals MicroRNA-Mediated Control of Cholesterol Synthesis Programs

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    ABSTRACT Chronic hepatitis B (CHB), chronic hepatitis C (CHC), and associated hepatocellular carcinoma (HCC) are characterized by cholesterol imbalance and dyslipidemia; however, the key regulatory drivers of these phenotypes are incompletely understood. Using gene expression microarrays and high-throughput sequencing of small RNAs, we performed integrative analysis of microRNA (miRNA) and gene expression in nonmalignant and matched cancer tissue samples from human subjects with CHB or CHC and HCC. We also carried out follow-up functional studies of specific miRNAs in a cell-based system. These studies led to four major findings. First, pathways affecting cholesterol homeostasis were among the most significantly overrepresented among genes dysregulated in chronic viral hepatitis and especially in tumor tissue. Second, for each disease state, specific miRNA signatures that included miRNAs not previously associated with chronic viral hepatitis, such as miR-1307 in CHC, were identified. Notably, a few miRNAs, including miR-27 and miR-224, were components of the miRNA signatures of all four disease states: CHB, CHC, CHB-associated HCC, and CHC-associated HCC. Third, using a statistical simulation method (miRHub) applied to the gene expression data, we identified candidate master miRNA regulators of pathways controlling cholesterol homeostasis in chronic viral hepatitis and HCC, including miR-21, miR-27, and miR-33. Last, we validated in human hepatoma cells that both miR-21 and miR-27 significantly repress cholesterol synthesis and that miR-27 does so in part through regulation of the gene that codes for the rate-limiting enzyme 3-hydroxy-3-methyl-glutaryl-coenzyme A (HMG-CoA) reductase ( HMGCR ). IMPORTANCE Hepatitis B virus (HBV) and hepatitis C virus (HCV) are phylogenetically unrelated hepatotropic viruses that persistently infect hundreds of millions of people world-wide, often leading to chronic liver disease and hepatocellular carcinoma (HCC). Chronic hepatitis B (CHB), chronic hepatitis C (CHC), and associated HCC often lead to cholesterol imbalance and dyslipidemia. However, the regulatory mechanisms underlying the dysregulation of lipid pathways in these disease states are incompletely understood. MicroRNAs (miRNAs) have emerged as critical modulators of lipid homeostasis. Here we use a blend of genomic, molecular, and biochemical strategies to identify key miRNAs that drive the lipid phenotypes of chronic viral hepatitis and HCC. These findings provide a panoramic view of the miRNA landscape in chronic viral hepatitis, which could contribute to the development of novel and more-effective miRNA-based therapeutic strategies

    Genetic and Epigenetic Regulation in Nonalcoholic Fatty Liver Disease (NAFLD)

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    Genetics and epigenetics play a key role in the development of several diseases, including nonalcoholic fatty liver disease (NAFLD). Family studies demonstrate that first degree relatives of patients with NAFLD are at a much higher risk of the disease than the general population. The development of the Genome Wide Association Study (GWAS) technology has allowed the identification of numerous genetic polymorphisms involved in the evolution of diseases (e.g., PNPLA3, MBOAT7). On the other hand, epigenetic changes interact with inherited risk factors to determine an individual’s susceptibility to NAFLD. Modifications of the histones amino-terminal ends are key factors in the maintenance of chromatin structure and gene expression (cAMP-responsive element binding protein H (CREBH) or SIRT1). Activation of SIRT1 showed potential against the physiological mechanisms related to NAFLD. Abnormal DNA methylation represents a starting point for cancer development in NAFLD patients. Besides, the evaluation of circulating miRNA profiles represents a promising approach to assess and non-invasively monitor liver disease severity. To date, there is no approved pharmacologic therapy for NAFLD and the current treatment remains weight loss with lifestyle modification and exercise. In this review, the status of research into relevant genetic and epigenetic modifiers of NAFLD progression will be discusse

    Biology and clinical application of regulatory RNAs in hepatocellular carcinoma

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    The majority of the human genome comprises of DNA genes that are translated into RNAs but not into proteins. These RNA molecules are named non‐coding RNAs (ncRNA). While in the past it was thought that ncRNAs would be redundant without relevant functions, it is now well established that ncRNAs identify a class of regulatory molecules that finely tune cell homeostasis and are deregulated in disease states, including Hepatocellular Carcinoma (HCC). Of note, the number of ncRNAs within a cell increases progressively with the complexity of the species indicating their essential role in the maintenance of regulatory networks that impact the intricacy of the organism. ncRNAs have been demonstrated to mediate HCC development and progression by affecting intrinsic cancer cell signaling and cross talk between malignant cells and the microenvironment. They hold promise as clinical biomarkers, but further evidence is warranted prior to translation and integration within clinical practice

    Cholangiocarcinoma 2020: the next horizon in mechanisms and management

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    [EN] Cholangiocarcinoma (CCA) includes a cluster of highly heterogeneous biliary malignant tumours that can arise at any point of the biliary tree. Their incidence is increasing globally, currently accounting for ~15% of all primary liver cancers and ~3% of gastrointestinal malignancies. The silent presentation of these tumours combined with their highly aggressive nature and refractoriness to chemotherapy contribute to their alarming mortality, representing ~2% of all cancer-related deaths worldwide yearly. The current diagnosis of CCA by non- invasive approaches is not accurate enough, and histological confirmation is necessary. Furthermore, the high heterogeneity of CCAs at the genomic, epigenetic and molecular levels severely compromises the efficacy of the available therapies. In the past decade, increasing efforts have been made to understand the complexity of these tumours and to develop new diagnostic tools and therapies that might help to improve patient outcomes. In this expert Consensus Statement, which is endorsed by the European Network for the Study of Cholangiocarcinoma, we aim to summarize and critically discuss the latest advances in CCA, mostly focusing on classification, cells of origin, genetic and epigenetic abnormalities, molecular alterations, biomarker discovery and treatments. Furthermore, the horizon of CCA for the next decade from 2020 onwards is highlightedJ.M.B. received EASL Registry Awards 2016 and 2019 (European CCA Registry, ENS-CCA). J.M.B. and M.J.P. were supported by: the Spanish Ministry of Economy and Competitiveness (J.M.B.: FIS PI12/00380, FIS PI15/01132, FIS PI18/01075 and Miguel Servet Programme CON14/00129; M.J.P.: FIS PI14/00399, FIS PI17/00022 and Ramon y Cajal Programme RYC-2015-17755, co-financed by “Fondo Europeo de Desarrollo Regional” (FEDER)); ISCIII CIBERehd; “Diputación Foral de Gipuzkoa” (J.M.B: DFG15/010, DFG16/004), and BIOEF (Basque Foundation for Innovation and Health Research: EiTB Maratoia BIO15/CA/016/BD); the Department of Health of the Basque Country (M.J.P.: 2015111100; J.M.B.: 2017111010), and “Fundación Científica de la Asociación Española Contra el Cancer” (AECC Scientific Foundation) (J.M.B.). J.M.B. and J.W.V. were supported by the European Commission Horizon 2020 programme (ESCALON project 825510). The laboratory of J.B.A. is supported by competitive grants from the Danish Medical Research Council, the Danish Cancer Society, and the Novo Nordisk and A.P. Møller Foundations. J.J.G.M. and R.I.R.M. were supported by the Carlos III Institute of Health, Spain (PI16/00598 and PI18/00428) and were co-financed by the European Regional Development Fund. J.M.B. and J.J.G.M. were supported by the Ministry of Science and Innovation, Spain (SAF2016-75197-R), and the “Asociación Española Contra el Cancer”, Spain (AECC-2017). R.I.R.M. was supported by the “Centro Internacional sobre el Envejecimiento”, Spain (OLD-HEPAMARKER, 0348-CIE-6-E). A.L. received funding from the Christie Charity. M.M. was supported by the Università Politecnica delle Marche, Ancona, Italy (040020_R.SCIENT.A_2018_MARZIONI_M_STRATEGICO_2017). M.S. was supported by the Yale Liver Center Clinical and Translational Core and the Cellular and Molecular Core (DK034989 Silvio O. Conte Digestive Diseases Research Center). C.C. is supported by grants from INSERM, Université de Rennes, INCa, and ITMO Cancer AVIESAN dans le cadre du Plan Cancer (Non-coding RNA in Cancerology: Fundamental to Translational), Ligue Contre le Cancer and Région Bretagne. J.Bruix was supported by grants from Instituto de Salud Carlos III (PI18/00763), AECC (PI044031) and WCR (AICR) 16-0026. A.F. was supported by grants from ISCIII (PI13/01229 and PI18/00542). CIBERehd is funded by the Instituto de Salud Carlos III. V.C., D.M., J. Bridgewater and P.I. are members of the European Reference Network - Hepatological Diseases (ERN RARE-LIVER). J.M.B. is a collaborator of the ERN RARE-LIVER

    Innovative Approaches To Identify Regulators Of Liver Regeneration

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    The mammalian liver possesses a remarkable ability to regenerate after injury to prevent immediate organ failure. However, amid a rising global burden of liver disease, the only curative treatment for patients with end-stage liver disease is transplantation. Elucidating the mechanisms underlying tissue repair and regrowth will enable identification of therapeutic targets to stimulate native liver regeneration, thereby circumventing the great paucity of available transplant organs. Here, utilizing the Fah-/- mouse model of liver repopulation, I applied transcriptomic and epigenomic techniques to investigate the changes occurring as hepatocytes restore organ mass following toxic injury. By labeling ribosomal or nuclear envelope proteins, I performed the first extensive characterization of gene expression and chromatin landscape changes specifically in repopulating hepatocytes in response to injury. Transcriptomic analysis showed that repopulating hepatocytes highly upregulate Slc7a11, a gene that encodes the cystine/glutamate antiporter. I demonstrated that ectopic Slc7a11 expression promotes liver regeneration and Slc7a11 mutation inhibits hepatocyte replication. Integrative bioinformatics analyses of chromatin accessibility revealed dynamic changes at promoters and liver-enriched enhancer regions that correlate with the activation of proliferation-associated genes and the repression of transcripts expressed in mature, quiescent hepatocytes. Furthermore, changes in chromatin accessibility and gene expression are associated with increased promoter binding of CCCTC-binding factor (CTCF) and decreased enhancer occupancy of hepatocyte nuclear factor 4α (HNF4α). In summary, my thesis work identifies Slc7a11 as a potential driver of liver regeneration, and provides insights into the complex crosstalk between chromatin accessibility and transcription factor occupancy to regulate gene expression in repopulating hepatocytes

    Computational Methods for the Analysis of Genomic Data and Biological Processes

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    In recent decades, new technologies have made remarkable progress in helping to understand biological systems. Rapid advances in genomic profiling techniques such as microarrays or high-performance sequencing have brought new opportunities and challenges in the fields of computational biology and bioinformatics. Such genetic sequencing techniques allow large amounts of data to be produced, whose analysis and cross-integration could provide a complete view of organisms. As a result, it is necessary to develop new techniques and algorithms that carry out an analysis of these data with reliability and efficiency. This Special Issue collected the latest advances in the field of computational methods for the analysis of gene expression data, and, in particular, the modeling of biological processes. Here we present eleven works selected to be published in this Special Issue due to their interest, quality, and originality

    Factors involved in the regulation of Long Interspersed-Nuclear-Elements (L1) retrotransposons in the context of Hepatocellular Carcinoma

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    PhD thesisHepatocellular carcinoma (HCC) generally develops on the background of a chronic liver disease following the accumulation of genetic damage and epigenetic alterations of growth regulatory genes, leading to activation of oncogenes and loss of function of tumour suppressor genes. Recent studies indicate that epigenetic aspects play an important role in the initiation of HCC. This includes dysregulation of repeat elements belonging to the Long Interspersed Nuclear Elements (LINE1 or L1) class. The L1 elements are autonomous mobile elements and upon activation contribute towards genomic instability via insertional mutagenesis. The thesis is aimed at understanding the factors leading to aberrant activation of retrotransposons and regulators of active retrotransposition in the context of HCC. All the liver cancer cell lines (Huh7, HepG2, Hep3B, PLC-PRF/5 and SK-Hep1) supported active retrotransposition in vitro irrespective of their basal L1 expression status or TP53 status. Since, active L1 retrotransposition through ‘Target Primed Reverse Transcription’ (TPRT) involves first DNA strand nicking by ORF2 endonuclease followed by second strand cleavage, we hypothesised that the DNA damage response pathways are involved in regulating the process. To decipher the influence of individual DNA repair pathway elements on the process of active retrotransposition, small molecule inhibitors towards ATM (KU-55933), DNA-PK (NU7441), ATR (VE-821), CHK1 (SRA737) and PARP (Rucaparib) were utilised. Overall, inhibition of ATR (Ataxia Telangiectasia And Rad3-Related Protein), a serine/threonine kinase involved in DNA replication stress and DNA damage signalling increased retrotransposition rate in all the cell lines. In addition, an increase in active retrotransposition was observed in Huh7 cell in presence of subgenomic copy of Hepatitis C Virus (HCV, a prevalent cause of HCC and contributes towards hepatocarcinogenesis by inducing oxidative stress, DNA damage and epigenetic changes in hepatocytes). Interestingly, the rate of retrotransposition remained higher in cells compared to control cell lines even when they were treated with PSI7977 (antiviral agent) successfully eliminating the viral genome from the cells. Hence, HCV upregulated active retrotransposition even beyond viral clearance and thus can contribute towards hepatocarcinogenesis by a ‘hit-and-run’ mechanism. Interrogating publicly available datasets - GSE84346 (RNAseq of Chronic HCV Hepatitis (CHC) patients and controls) and RNAseq data of non-tumour liver from the Cancer Genome Atlas HCC study - confirmed upregulation of L1 transcripts in chronic hepatitis patients liver. Hence, L1s can be activatedNewcastle University NUORS fellowship and JGW Patterson special gran

    The Contribution of Epigenetics to Cancer Immunotherapy

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    Altres ajuts: This work was supported by the the Cellex Foundation; and La Caixa Banking Foundation (LCF/PR/GN18/51140001).Effective anticancer immunotherapy treatments constitute a qualitative leap in cancer management. Nonetheless, not all patients benefit from such therapies because they fail to achieve complete responses, suffer frequent relapses, or develop potentially life-threatening toxicities. Epigenomic signatures in immune and cancer cells appear to be accurate and promising predictors of patient outcomes with immunotherapy. In addition, combined treatments with epigenetic drugs can exploit the dynamic nature of epigenetic changes to potentially modulate responses to immunotherapy. Candidate epigenetic biomarkers may provide a rationale for patient stratification and precision medicine, thus maximizing the chances of treatment success while minimizing unwanted effects. We present a comprehensive up-to-date view of potential epigenetic biomarkers in immunotherapy and discuss their advantages over other indicators
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