Enhanced detection of early hepatocellular carcinoma by serum SELDI-TOF proteomic signature combined with alpha-fetoprotein marker.

BACKGROUND: Biomarkers for accurate diagnosis of early hepatocellular carcinoma (HCC) are limited in number and clinical validation. We applied SELDI-TOF-MS ProteinChip technology to identify serum profile for distinguishing HCC and liver cirrhosis (LC) and to compare the accuracy of SELDI-TOF-MS profile and alpha-fetoprotein (AFP) level in HCC diagnosis. PATIENTS AND METHODS: Serum samples were obtained from 120 HCC and 120 LC patients for biomarker discovery and validation studies. ProteinChip technology was employed for generating SELDI-TOF proteomic features and analyzing serum proteins/peptides. RESULTS: A diagnostic model was established by CART algorithm, which is based on 5 proteomic peaks with m/z values at 3324, 3994, 4665, 4795, and 5152. In the training set, the CART algorithm could differentiate HCC from LC subjects with a sensitivity and specificity of 98% and 95%, respectively. The results were assessed in blind validation using separate cohorts of 60 HCC and 60 LC patients, with an accuracy of 83% for HCC and 92% for LC patients. The diagnostic odd ratio (DOR) indicated that SELDI-TOF proteomic signature could achieve better diagnostic performance than serum AFP level at a cutoff of 20 ng/mL (AFP(20)) (92.72 vs 9.11), particularly superior for early-stage HCC (87% vs 54%). Importantly, a combined use of both tests could enhance the detection of HCC (sensitivity, 95%; specificity, 98%; DOR, 931). CONCLUSION: Serum SELDI-TOF proteomic signature, alone or in combination with AFP marker, promises to be a good tool for early diagnosis and/screening of HCC in at-risk population with liver cirrhosis

Falcon Optimization Algorithm for Bayesian Networks Structure Learning

In machine-learning, one of the useful scientific models for producing the structure of knowledge is Bayesian network, which can draw probabilistic dependency relationships between variables. The score and search is a method used for learning the structure of a Bayesian network. The authors apply the Falcon Optimization Algorithm (FOA) as a new approach to learning the structure of Bayesian networks. This paper uses the Reversing, Deleting, Moving and Inserting operations to adopt the FOA for approaching the optimal solution of Bayesian network structure. Essentially, the falcon prey search strategy is used in the FOA algorithm. The result of the proposed technique is compared with Pigeon Inspired optimization, Greedy Search, and Simulated Annealing using the BDeu score function. The authors have also examined the performances of the confusion matrix of these techniques utilizing several benchmark data sets. As shown by the evaluations, the proposed method has more reliable performance than the other algorithms including producing better scores and accuracy values

Primary liver cancer: Epidemiological and Biomarker Discovery Studies

With previous reports indicating changes in mortality, risk factors and management of primary liver cancer (PLC), evaluation of current trends in the incidence and mortality rates was indicated. Late diagnosis has been implicated to be a major contributor to the high fatality rates of PLC. This work aimed at: • studying trends of PLC by subcategories globally in general, and in England and Wales, in particular; • investigating liver-related morbidities of HIV infected patients in an African setting; and • discovering urinary biomarkers of hepatocellular carcinoma. The World Health Organisation (WHO) and Small Area Health Statistics Unit (SAHSU) databases were interrogated respectively, in order to achieve the first aim. The second aim was achieved through utilisation of databases of an African-based HIV treatment programme- AIDS Prevention Initiative in Nigeria (APIN), located in Jos, Nigeria. The European Union-funded Prevention of Liver Fibrosis and Cancer in Africa (PROLIFICA) case-control study in three West African countries was the platform through which urinary metabolic profiling was accomplished. Proton nuclear magnetic resonance spectroscopy (NMR) and parallel ultra-performance liquid chromatography mass spectrometry (UPLC-MS) were used for biomarker discovery studies. Mortality rates of intrahepatic bile duct carcinoma (IHBD) increased in all countries that were studied. Misclassification of hilar cholangiocarcinoma accounted for only a small increase in the rate of IHBD in England and Wales. With over 90% screening rate for viral hepatitides, the rates of hepatitis B (HBV), hepatitis C (HCV) and HBV/HCV in HIV-infected patients in the APIN programme were 17.8%, 11.3% and 2.5% respectively. There was attenuated immune response as well as significantly lower survival observed in HBV/HIV co-infection, relative to HIV mono-infected patients (p=0.0097). Whereas single urinary metabolites, including acetylcarnitine, N-acetylglutamate, betaine aldehyde, 3’-sialyllactose, methionine among others possessed high discriminatory power to diagnose HCC, a combination of three metabolites: 3’-sialyllactose, methionine and 9-decenoylcarnitine significantly outperformed serum alpha-fetoprotein (AFP) in the diagnosis of HCC in a cirrhosis population (area under the receiver operating characteristic curve; [urinary panel= 0.96] compared to [AFP = 0.64]). This work informs a critical assessment of current control strategies in the prevention of HCC, and potentially assists in the development of more affordable means of early detection of PLC for most affected regions of the world.Open Acces

Molecular pathogenesis of Helicobacter hepaticus induced liver disease

Thesis (Ph. D. in Molecular and Systems Bacterial Pathogenesis)--Massachusetts Institute of Technology, Biological Engineering Division, 2005.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Includes bibliographical references.Helicobacter hepaticus infection of A/JCr mice is a model of liver cancer resulting from chronic active inflammation. We monitored hepatic global gene expression profiles and correlated them to histological liver lesions in H. hepaticus infected and control male A/JCr mice at 3 months, 6 months, and 1 year of age. We used an Affymetrix-based oligonucleotide microarray platform on the premise that a specific genetic expression signature at isolated time points would be indicative of disease status. Model based expression index comparisons generated by dChip yielded consistent profiles of differential gene expression for H. hepaticus infected male mice with progressive liver disease versus uninfected control mice within each age group. Linear discriminant analysis and principal component analysis allowed segregation of mice based on combined age and lesion status, or age alone. Up-regulated genes present throughout the 12 month study involved inflammation, tissue repair, and host immune function. Upregulation of putative tumor and proliferation markers correlated with advancing hepatocellular dysplasia. Transcriptionally down-regulated genes in mice with liver lesions included those related to peroxisome proliferator, cholesterol, and steroid metabolism pathways. Transcriptional profiling of hepatic genes documented gene expression signatures in the livers of H. hepaticus infected male A/JCr mice with chronic progressive hepatitis and preneoplastic liver lesions, complemented the histopathological diagnosis, and suggested molecular targets for the monitoring and intervention of disease progression prior to the onset of hepatocellular neoplasia. Our laboratory, in collaboration with Professors Suerbaum and Schauer, recently identified a(cont.) 70kb genomic island in Helicobacter hepaticus strain ATCC 51488 as a putative pathogenicity island (HhPAI) (Suerbaum et al, PNAS, 2003). This region within H. hepaticus contains genes HH0233-HH0302, a differential GC content, several long tandem repeats but no flanking repeats, and three components of a type IV secretion system (T4SS). A/JCr mice were experimentally infected with three naturally occurring strains of H. hepaticus including the type strain H. hepaticus ATCC 51488 strain (Hh 3B1) isolated from A/JCr mice, MIT 96-1809 (Hh NET) isolated from mice shipped from the Netherlands, and MIT-96-284 (HhG) isolated from mice acquired from Germany.4 HhNET (missing most of the HhPAI) infected male A/JCR mice exhibited a significantly lower prevalence (p<.05) of hepatic lesions at 6 months post infection than Hh 3B1 with an intact HhPAI. Hh G also has a large segment of the genomic island deleted, but not as many genes are deleted as compared to Hh NET. Hh G also demonstrated a lower prevalence of hepatic lesions. This variable pathological effect was evident in male mice only. The severity of chronic active inflammation in the liver of the H. hepaticus infected A/JCr mice depended on H. hepaticus liver colonization levels. The in vivo results support the presence of the HhPAI as a legitimate virulence determinant and predictor of severity of liver lesions in H. hepaticus infected A/JCr male mice. To further determine the differences in virulence of the H. hepaticus strains Hh 3B1, Hh NET, Hh G and an isogenic mutant H. ...by Samuel R. Boutin.Ph.D.in Molecular and Systems Bacterial Pathogenesi

Dynamic Contrast Enhanced Computed Tomography Measurement of Perfusion in Hepatic Cancer

ABSTRACT In recent years, the incidence and mortality rate for hepatocellular carcinoma (HCC) have increased due to the emergence of hepatitis B, C and other diseases that cause cirrhosis. The progression from cirrhosis to HCC is characterized by abnormal vascularization and by a shift from a venous to an arterial blood supply. A knowledge of HCC vascularity which is manifested as alterations in liver blood flow may distinguish among different stages of liver disease and can be used to monitor response to treatment. Unfortunately, conventional diagnostic imaging techniques lack the ability to accurately quantify HCC vascularity. The purpose of this thesis was to validate and assess the diagnostic capabilities of dynamic contrast enhanced computed tomography (DCE-CT) and perfusion software designed to measure hepatic perfusion. Chapter 2 described a study designed to evaluate the accuracy and precision of hepatic perfusion measurement. The results showed a strong correlation between hepatic artery blood flow measurement with DCE-CT and radioactive microspheres under steady state in a rabbit model for HCC (VX2 carcinoma). Using repeated measurements and Monte Carlo simulations, DCE-CT perfusion measurements were found to be precise; with the highest precision in the tumor rim. In Chapter 3, we used fluorine-18 fluoro-2-deoxy-D-glucose (FDG) positron emission tomography and DCE-CT perfusion to determined an inverse correlation between glucose utilization and tumor blood flow; with an R of 0.727 (P \u3c 0.05). This suggests a limited supply of oxygen (possibly hypoxia) and that the tumor cells were surviving via anaerobic glycolysis. in In Chapter 4, hepatic perfusion data showed that thalidomide caused a reduction of tumor perfusion in the responder group during the first 8 days after therapy, P \u3c 0.05; while perfusion in the partial responder and control group remained unchanged, P \u3e 0.05. These changes were attributed to vascular remodeling and maturation resulting in a more functional network of endothelial tubes lined with pericytes. The results of this thesis demonstrate the accuracy and precision of DCE-CT hepatic perfusion measurements. It also showed that DCE-CT perfusion has the potential to enhance the functional imaging ability of hybrid PET/CT scanners and evaluate the efficacy of anti-angiogenesis therapy

The application of molecular profiling and proteomics in the study of liver cancers

MD ThesisBackground: Hepatocellular cancer [1] is increasing worldwide. The majority are detected too late for curative surgery as effective identification of the at risk population and their subsequent surveillance is inadequate. My specific aims were to study and characterise our own patients, evaluating the known and predicted biomarkers for HCC in patients with non-alcoholic fatty liver disease and exploring novel biomarker methodologies for the detection of either cirrhosis or HCC complicating it. Methods: Details of all HCC patients presenting to the Newcastle hepatopancreatobiliary (HPB) multidisciplinary team were recorded in an NHS intranet database, and a subset were consented for tissue collection. Established and candidate biomarkers were assessed in serum by western blotting and/or ELISA assay and the role of microarray analysis of HepG2 cells, and 2D-gel electrophoresis of immunodepleted serum in novel candidate biomarker identification were explored. Results: The number of HCC cases referred has increased dramatically over the last decade, as has the numbers arising in a background of non-alcoholic fatty liver disease (NAFLD). In our cohort, patients with earlier stage cancers detected by either - surveillance or incidentally had a better prognosis, but only 10% were eligible for definitive treatment. While HCC patients treated with liver transplant had an overall 5 year survival was 62.1%, the median survival of the transplant cohort was 137 months. Exploration of serum levels of Glypican 3, Squamous Cell Carcinoma Antigen-1 and follistatin were poor surveillance biomarkers, but the combination of Alpha-fetoprotein and Protrhombin induced by vitamin-K absence was encouraging. Serum proteomic analysis in a small subgroup identified four isoforms of apolipoproteins as well as CD5L as differentially expressed between patients with no cirrhosis, cirrhosis and HCC, although subsequent CD5L ELISA failed to confirm its ability to specifically detect HCC. Discussion: While the incidence of HCC is increasing, the prognosis for those affected remains poor. Biomarkers identifying both the at risk individuals and those with cancer are urgently required

Lung cancer risk test trial: study design, participant baseline characteristics, bronchoscopy safety, and establishment of a biospecimen repository

BACKGROUND: The Lung Cancer Risk Test (LCRT) trial is a prospective cohort study comparing lung cancer incidence among persons with a positive or negative value for the LCRT, a 15 gene test measured in normal bronchial epithelial cells (NBEC). The purpose of this article is to describe the study design, primary endpoint, and safety; baseline characteristics of enrolled individuals; and establishment of a bio-specimen repository. METHODS/DESIGN: Eligible participants were aged 50-90 years, current or former smokers with 20 pack-years or more cigarette smoking history, free of lung cancer, and willing to undergo bronchoscopic brush biopsy for NBEC sample collection. NBEC, peripheral blood samples, baseline CT, and medical and demographic data were collected from each subject. DISCUSSION: Over a two-year span (2010-2012), 403 subjects were enrolled at 12 sites. At baseline 384 subjects remained in study and mean age and smoking history were 62.9 years and 50.4 pack-years respectively, with 34% current smokers. Obstructive lung disease (FEV1/FVC \u3c0.7) was present in 157 (54%). No severe adverse events were associated with bronchoscopic brushing. An NBEC and matched peripheral blood bio-specimen repository was established. The demographic composition of the enrolled group is representative of the population for which the LCRT is intended. Specifically, based on baseline population characteristics we expect lung cancer incidence in this cohort to be representative of the population eligible for low-dose Computed Tomography (LDCT) lung cancer screening. Collection of NBEC by bronchial brush biopsy/bronchoscopy was safe and well-tolerated in this population. These findings support the feasibility of testing LCRT clinical utility in this prospective study. If validated, the LCRT has the potential to significantly narrow the population of individuals requiring annual low-dose helical CT screening for early detection of lung cancer and delay the onset of screening for individuals with results indicating low lung cancer risk. For these individuals, the small risk incurred by undergoing once in a lifetime bronchoscopic sample collection for LCRT may be offset by a reduction in their CT-related risks. The LCRT biospecimen repository will enable additional studies of genetic basis for COPD and/or lung cancer risk. TRIAL REGISTRATION: The LCRT Study, NCT 01130285, was registered with Clinicaltrials.gov on May 24, 2010

Synergisms of stem cell mobilisation and toll-like receptor 4 inhibition to treat the acute-on-chronic liver failure

Background: The acute-on-chronic liver failure (ACLF) is a complex disease with high mortality without effective therapeutic opportunities. A greater understanding of disease mechanisms is necessary to identify novel targets for disease modifying therapies. Systemic inflammation is central and toll-like receptor 4 (TLR4) may be an important pathway involved in activating immune cells. Granulocyte-colony stimulating factor (G-CSF) mobilises immunomodulatory stem- and immune cells and pivotal clinical studies provided promising results in liver disease. Aims: I aimed to understand the role of TLR4 in mediating inflammation and organ injury in ACLF. I also explored how G-CSF exerts its immunomodulatory capacities in ACLF and whether combing G-CSF with TLR4 signalling inhibition by TAK-242 might act synergistically. Methods: The first experimental part comprised human samples, and septic ACLF rodent models in which I evaluated the role of TLR4 in mediating inflammation and organ injury. The second clinical part was based on a multicentre interventional trial evaluating the impact of G-CSF on the outcome of humans with ACLF. In the third experimental part G-CSF and TAK-242 were used as therapy in a septic and in a sterile ACLF mouse model to evaluate synergisms of both therapies. Results: The first part showed that TLR4 signalling prompted cytokine release and organ injury causing deaths in ACLF. TLR4 signalling inhibition by TAK-242 prevented tissue injury and fatalities. The clinical trial revealed that G-CSF was ineffective in ACLF. In the septic mouse model of ACLF GCSF alone exaggerated the inflammatory response. The combinatory therapy G-CSF plus TAK-242 acted synergistically by reducing organ injury and promoting tissue repair. Conclusion: This study highlighted the complexity of ACLF and introduced TLR4 mediated inflammation as a central pathomechanistic element. It also emphasized that combinatory therapies may be necessary to address the whole spectrum of pathomechanisms involved in ACLF