Patterns of chromosomal copy-number alterations in intrahepatic cholangiocarcinoma

International audienceBackground: Intrahepatic cholangiocarcinomas (ICC) are relatively rare malignant tumors associated with a poor prognosis. Recent studies using genome-wide sequencing technologies have mainly focused on identifying new driver mutations. There is nevertheless a need to investigate the spectrum of copy number aberrations in order to identify potential target genes in the altered chromosomal regions. The aim of this study was to characterize the patterns of chromosomal copy-number alterations (CNAs) in ICC. Methods: 53 patients having ICC with frozen material were selected. In 47 cases, DNA hybridization has been performed on a genomewide SNP array. A procedure with a segmentation step and a calling step classified genomic regions into copy-number aberration states. We identified the exclusively amplified and deleted recurrent genomic areas. These areas are those showing the highest estimated propensity level for copy loss (resp. copy gain) together with the lowest level for copy gain (resp. copy loss). We investigated ICC clustering. We analyzed the relationships between CNAs and clinico-pathological characteristics. Results: The overall genomic profile of ICC showed many alterations with higher rates for the deletions. Exclusively deleted genomic areas were 1p, 3p and 14q. The main exclusively amplified genomic areas were 1q, 7p, 7q and 8q. Based on the exclusively deleted/amplified genomic areas, a clustering analysis identified three tumors groups: the first group characterized by copy loss of 1p and copy gain of 7p, the second group characterized by 1p and 3p copy losses without 7p copy gain, the last group characterized mainly by very few CNAs. From univariate analyses, the number of tumors, the size of the largest tumor and the stage were significantly associated with shorter time recurrence. We found no relationship between the number of altered cytobands or tumor groups and time to recurrence. Conclusion: This study describes the spectrum of chromosomal aberrations across the whole genome. Some of the recurrent exclusive CNAs harbor candidate target genes. Despite the absence of correlation between CNAs and clinico-pathological characteristics, the co-occurence of 7p gain and 1p loss in a subgroup of patients may suggest a differential activation of EGFR and its downstream pathways, which may have a potential effect on targeted therapies

Features Ranking Techniques for Single Nucleotide Polymorphism Data

Identifying biomarkers like single nucleotide polymorphisms (SNPs) is an important topic in biomedical applications. Such SNPs can be associated with an individual’s metabolism of drugs, which make these SNPs targets for drug therapy, and useful in personalized medicine applications. Yet another important application is that SNPs can be associated with an individual’s genetic predisposition to develop a disease. Identifying these associations allow proactive steps to be taken to hinder, delay or eliminate the disease. However, the problem is challenging; data are high dimensional and incomplete, and features (SNPs) are correlated. The goal of this thesis is to propose features ranking methods to reduce the number of selected features and the computational cost required to select these features in a binary classification task. The main idea of the hypothesis is that specific values within a feature might be useful in predicting specific classes, while other values are not. In this context, three heuristic methods are applied to select the best features. The methods are applied to the Wellcome Trust Case Control Consortium (WTCCC1) dataset, and evaluated on Texas A&M University Qatar’s High Performance Computing platform. The results show that the classification accuracy achieved by the proposed methods is comparable to the baseline. However, one of the proposed methods reduced the execution time of the feature selection and the number of features required to achieve similar accuracy in the baseline by 40% and 47% respectively

Patterns of chromosomal copy-number alterations in intrahepatic cholangiocarcinoma

BACKGROUND: Intrahepatic cholangiocarcinomas (ICC) are relatively rare malignant tumors associated with a poor prognosis. Recent studies using genome-wide sequencing technologies have mainly focused on identifying new driver mutations. There is nevertheless a need to investigate the spectrum of copy number aberrations in order to identify potential target genes in the altered chromosomal regions. The aim of this study was to characterize the patterns of chromosomal copy-number alterations (CNAs) in ICC. METHODS: 53 patients having ICC with frozen material were selected. In 47 cases, DNA hybridization has been performed on a genomewide SNP array. A procedure with a segmentation step and a calling step classified genomic regions into copy-number aberration states. We identified the exclusively amplified and deleted recurrent genomic areas. These areas are those showing the highest estimated propensity level for copy loss (resp. copy gain) together with the lowest level for copy gain (resp. copy loss). We investigated ICC clustering. We analyzed the relationships between CNAs and clinico-pathological characteristics. RESULTS: The overall genomic profile of ICC showed many alterations with higher rates for the deletions. Exclusively deleted genomic areas were 1p, 3p and 14q. The main exclusively amplified genomic areas were 1q, 7p, 7q and 8q. Based on the exclusively deleted/amplified genomic areas, a clustering analysis identified three tumors groups: the first group characterized by copy loss of 1p and copy gain of 7p, the second group characterized by 1p and 3p copy losses without 7p copy gain, the last group characterized mainly by very few CNAs. From univariate analyses, the number of tumors, the size of the largest tumor and the stage were significantly associated with shorter time recurrence. We found no relationship between the number of altered cytobands or tumor groups and time to recurrence. CONCLUSION: This study describes the spectrum of chromosomal aberrations across the whole genome. Some of the recurrent exclusive CNAs harbor candidate target genes. Despite the absence of correlation between CNAs and clinico-pathological characteristics, the co-occurence of 7p gain and 1p loss in a subgroup of patients may suggest a differential activation of EGFR and its downstream pathways, which may have a potential effect on targeted therapies

Desarrollo y validación de un índice pronóstico de la respuesta del virus de la hepatitis C al tratamiento con interferón pegilado y ribavirina en pacientes coinfectados por el virus de la inmudeficiencia humana

Tesis doctoral inédita realizada en la Universidad Autónoma de Madrid, Facultad de Medicina, Facultad de Medicina, Departamento de Medicina. Fecha de lectura: 16 Julio de 2010

A PROBABILISTIC APPROACH TO DATA INTEGRATION IN BIOMEDICAL RESEARCH: THE IsBIG EXPERIMENTS

Indiana University-Purdue University Indianapolis (IUPUI)Biomedical research has produced vast amounts of new information in the last decade but has been slow to find its use in clinical applications. Data from disparate sources such as genetic studies and summary data from published literature have been amassed, but there is a significant gap, primarily due to a lack of normative methods, in combining such information for inference and knowledge discovery. In this research using Bayesian Networks (BN), a probabilistic framework is built to address this gap. BN are a relatively new method of representing uncertain relationships among variables using probabilities and graph theory. Despite their computational complexity of inference, BN represent domain knowledge concisely. In this work, strategies using BN have been developed to incorporate a range of available information from both raw data sources and statistical and summary measures in a coherent framework. As an example of this framework, a prototype model (In-silico Bayesian Integration of GWAS or IsBIG) has been developed. IsBIG integrates summary and statistical measures from the NIH catalog of genome wide association studies (GWAS) and the database of human genome variations from the international HapMap project. IsBIG produces a map of disease to disease associations as inferred by genetic linkages in the population. Quantitative evaluation of the IsBIG model shows correlation with empiric results from our Electronic Medical Record (EMR) – The Regenstrief Medical Record System (RMRS). Only a small fraction of disease to disease associations in the population can be explained by the linking of a genetic variation to a disease association as studied in the GWAS. None the less, the model appears to have found novel associations among some diseases that are not described in the literature but are confirmed in our EMR. Thus, in conclusion, our results demonstrate the potential use of a probabilistic modeling approach for combining data from disparate sources for inference and knowledge discovery purposes in biomedical research

Study of the Phenotypic Characteristics and Genetic Risk Factors of Primary Sclerosing Cholangitis

Primary sclerosing cholangitis (PSC) is a progressive chronic cholestatic liver disease, affecting young males predominantly. It causes stricturing of the intrahepatic and extrahepatic bile ducts, often leading to biliary cirrhosis, with an increased risk of colorectal and hepato-biliary malignancy. It is commonly associated with inflammatory bowel disease (IBD). Specific medical therapy is ineffective and for patients who develop end-stage liver disease, liver transplantation remains the only definitive treatment option. The UK PSC study was set up in 2008 to recruit patients with PSC, to collect clinical data and DNA samples, to study phenotypic characteristics and the role of genetic risk factors in PSC. To date, more than 2,000 patients have been recruited from UK hospitals, making it the largest independent PSC cohort worldwide. I studied the phenotypic characteristics of the cohort and identified an increased risk of requiring liver transplantation in patients with both intrahepatic and extrahepatic bile duct disease, in comparison to those with disease limited to intrahepatic ducts. Further study of the clinical and laboratory parameters, helped develop a UK PSC risk score, which allowed risk stratification of patients with PSC at the time of diagnosis. I performed a replication/candidate gene study followed by a genome wide association study in a cohort of 1,030 and 1,020 patients respectively with 5,162 controls. Genome-wide signficant association was identified at two novel loci: 10p15 and 12q24, containing candidate genes Il2RA and SH2B3/ATXN2 respectively. These genes have important roles in adaptive immune pathways, implicating an immue mediated disease process in the pathogenesis of PSC. As part of UK PSC, I also contributed to two large scale genome wide association studies in an international collaboration, which identified 13 novel loci associated with PSC. The UK PSC cohort is a unique national resource of patients with PSC and further deep phenotyping and quality of life studies are planned, in addition to undertaking clinical trials for novel therapeutic agents. The study of phenotypic characteristics and genetic association, undertaken in patients with PSC are described in this thesis.UK PSC support group Norwegian PSC charit

A multi-modality approach for enhancing the diagnosis of cholangiocarcinoma

Background: Cholangiocarcinoma (CC) is a malignancy of the bile ducts and mortality is high as patients present too late for curative surgery. In most cases of CC the aetiology is unknown, whilst diagnosis and staging are challenging. The hepatobiliary system excretes carcinogenic toxins and genetic mutations in biliary transporters lead to dysfunction and cholestasis, potentially contributing to cholangiocarcinogenesis. Polymorphisms in the NKG2D receptor have previously been associated with CC in primary sclerosing cholangitis (PSC). Such a role has not been investigated in sporadic CC. CC is difficult to diagnose, particularly in those with PSC. The transition from benign to malignant biliary disease is likely to be reflected in changes to the plasma proteome. However, current plasma biomarkers do not reliably distinguish benign from malignant biliary strictures. Elevation of neutrophil gelatinase-associated lipocalin (NGAL) has been demonstrated in the bile of patients with CC but has not been investigated as a plasma protein biomarker. Staging of CC is inaccurate, with only a minority of operated patients cured. Higher resolution MRI would improve diagnosis and staging. The work presented in this thesis represents a multimodality approach to enhance the diagnosis of CC: Genetic studies: Genetic variation in major biliary transporter proteins, and the NKG2D receptor, were investigated. Single nucleotide polymorphisms (SNPs) in candidate genes were selected using HapMap. DNA from 173 CC patients and 265 healthy controls was genotyped. SNPs in ABCB11, MDR3 and ATP8B1 were nominally associated with altered susceptibility to CC, suggesting a potential role in cholangiocarcinogenesis. The previous association of NKG2D variation with CC in PSC was not replicated in sporadic CC, suggesting a possible difference in pathogenesis. Protein studies: Plasma from subjects with CC, benign disease, and from healthy controls was studied. Two proteomic techniques, liquid chromatography-tandem mass spectrometry (LCMS/ MS) and surfaced enhanced laser desorption ionization time-of-flight MS (SELDITOF MS), were utilised. Differentially expressed proteins were identified where possible. LC-MS/MS fully identified six proteins that were differentially expressed in CC compared to gall stone disease patients. SELDI-TOF MS identified seven m/z peaks that showed significant utility in discriminating CC from PSC controls. An ELISA approach was used to study plasma NGAL levels in CC. Although differentially expressed between CC and healthy control groups, the utility of NGAL in discriminating CC from PSC was limited. Imaging studies: An endoscope-mounted MR coil and intraductal MR detector coil were developed. Quantitative resolution and signal-to-noise-ratio (SNR) testing, and qualitative tissue discrimination appraisal, were undertaken. Sub-0.7mm resolution and excellent SNRs have been demonstrated. High-resolution has been demonstrated in imaged tissue. Imaging with the new devices compares favourably with endoscopic ultrasound imaging

In vivo Partial Reprogramming by Bacteria Promotes Adult Liver Organ Growth without Fibrosis and Tumorigenesis

Ideal therapies for regenerative medicine or healthy aging require healthy organ growth and rejuvenation, but no organ-level approach is currently available. Using Mycobacterium leprae (ML) with natural partial cellular reprogramming capacity and its animal host nine-banded armadillos, we present an evolutionarily refined model of adult liver growth and regeneration. In infected armadillos, ML reprogram the entire liver and significantly increase total liver/body weight ratio by increasing healthy liver lobules, including hepatocyte proliferation and proportionate expansion of vasculature, and biliary systems. ML-infected livers are microarchitecturally and functionally normal without damage, fibrosis, or tumorigenesis. Bacteria-induced reprogramming reactivates liver progenitor/developmental/fetal genes and upregulates growth-, metabolism-, and anti-aging-associated markers with minimal change in senescence and tumorigenic genes, suggesting bacterial hijacking of homeostatic, regeneration pathways to promote de novo organogenesis. This may facilitate the unraveling of endogenous pathways that effectively and safely re-engage liver organ growth, with broad therapeutic implications including organ regeneration and rejuvenation