Research Projects - 2010 - 2019

Approved projects

EpiRadBio

Molecular specificities of radiation-induced thyroid tumors

EpiRadBio - Validation of radiation-associated gain of chromosome band 7q11

A Sequence-based Approach to Identify Genetic Determinants of Tumorigenesis in Radiation-Induced Pediatric Papillary Thyroid Carcinomas

EpiRadBio - integrative analysis of molecular data

Validation of the gene signature differentiating exposed from non-exposed PTCs, obtained in the Genrisk-T project (no.: 036495) with an independent QPCR method

A detailed study of the somatic genomics of radiation induced thyroid cancer

Assessing the impact of radiation exposure on the development of medullary thyroid carcinoma

Anaplastic lymphoma kinase (ALK) – rearrangements in radiation-induced papillary thyroid carcinomas: a study on post Chernobyl tissue samples

Comprehensive Genomic Characterization of Radiation-Related Thyroid Cancer in Ukraine

Autoantibody biomarkers of malignancy in encapsulated follicular-patterned thyroid tumours

 

Project reference number: 001/2011

Principal Investigator: Dr K Unger, Helmholtz Centre, Munich, Germany

Email: unger@helmholtz-muenchen.de

EpiRadiBio

Summary of project:

The EU funded project EpiRadBio project seeks to model the cancer of the lung, breast and the thyroid after exposure to radiation in the low-dose range (cumulative dose < 100 mGy). The formalin-fixed paraffin-embedded (FFPE) papillary thyroid cancer tissue sections we apply for will be used in a work package of EpiRadBio that focuses on the cancer risk of papillary thyroid cancer. In another, recently finished EU funded project on young onset childhood thyroid carcinomas that also used CTB material we found that a gain of the chromosome band 7q11 was associated with exposure to low-dose ionising radiation (Heß et al., PNAS, in press). The FFPE tumour sections from patients, which are part of the UkrAm cohort and which come with estimates on radiation dose the patients have received will be used for validation and further characterisation of this marker. The FFPE sections will be used for in situ hybridisation (FISH) using 7q11 specific probes. DNA and total RNA will also be extracted from the FFPE sections. The DNA will be used for high-resolution array CGH and the total RNA for qRT-PCR mRNA expression analysis of candidate genes from the gained region. The copy number data and qRT-PCR data will be integrated with the dose estimates in order to identify a potential relationship between the radiation-associated biomarker and radiation dose. The resulting data will be provided to the modellers of the project who will use this information to build and refine their models on radiation risk of papillary thyroid cancer after exposure to low-dose ionising radiation.

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Project reference number: 002/2011
Principal Investigator: Dr C Ory, Commissariat à l’Energie Atomique, Département Sciences du vivant, Institut de radiobiologie cellulaire et moléculaire, Laboratoire de Cancérologie Expérimentale (CEA), France

Email: catherine.ory@cea.fr

Molecular specificities of radiation-induced thyroid tumors

Summary of project:

The constituted network to realise this program involved two teams well known in diagnosis and treatment of thyroid tumors and one team which were already implicated in the search of radiation-induced signatures in the thyroid and in the identification of the molecular mechanisms of radiation-induced tumorigenesis. To date, we focused our approach at the transcriptomic level. We wish now to analyse miRNA and mRNA deregulations in a series of post-Chernobyl thyroid tumors by microarray analysis: 1) to identify a radiation-induced miRNA and mRNA signatures. We will assess the robustness of these signatures for a potential use as a diagnostic tool alone or in combination. 2) to obtain an integrated miRNA/mRNA overview of radiation-induced tumorigenesis by taking advantage of the deregulated pathway identified by the transcriptomic approach. To date, no such integrated analysis has been performed as most of the studies focused on either transcriptome analysis or miRNA analysis separately. Ultimately, we will cross the obtained data with others results from analysis of post-radiotherapy tumors (Ory et al. 2011; Ugolin et al. PLosONE under revision).

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Project reference number: 003/2011
Principal Investigator: Dr K Unger, Helmholtz Centre, Munich, Germany

Email: unger@helmholtz-muenchen.de

EpiRadBio - Validation of radiation-associated gain of chromosome band 7q11

Summary of project:

The project using the applied biomaterial is an extension of the EU-funded GENRISK-T project and aims to validate a gain on chromosome band 7q11 that was found to be associated with papillary thyroid carcinomas from young patients (< 19 years) that were exposed to radiation from the Chernobyl fallout at very young age (median: 2 years). The validation set containing exposed and unexposed cases will be matched for age, morphology and residence - these criteria were already used for case selection of the GENRISK-T set. A high-definition array CGH platform will be used to validate the gain and to type for additional radiation-markers that are smaller in size and were therefore not detectable by 1Mb BAC array CGH that was used in GENRISK-T. Further, we will use RNA samples and paraffin sections for characterisation of expression candidate genes and proteins by qRT-PCR and immunohistochemistry. Fresh-frozen tissue from selected samples expressing the candidate gene CLIP2 from the gained region on 7q11 and those that do not express the gene will be analysed using a whole proteomics approach (liquid chromatography-tandem mass spectrometry, LC-MS/MS). The results will be used to identify the dysregulation networks in which CLIP2 is specifically involved. The projects aims to validate the radiation marker on chromosome band 7q11, to identify the networks that are dysregulated in tumours harbouring the marker and to find new markers that are associated with exposure to radiation.

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Project reference number: 004/2011
Principal Investigator: Dr L Hawthorn, Georgia Health Sciences University, USA

Email: lhawthorn@georgiahealth.edu

A Sequence-based Approach to Identify Genetic Determinants of Tumorigenesis in Radiation-Induced Pediatric Papillary Thyroid Carcinomas

Summary of project:

Cancer is a genetic disease, a concept which has been consistently observed for all tumors. Our approach is to survey the entire genome of these tumors to look for mutations and other perturbations that are involved in radiation-induced papillary thyroid carcinoma (RI-PTC) and create a genomic profile of this tumor. A new technology, termed Next-generation sequencing allows sequencing of the entire human genome in 8 days. We will begin by sequencing the DNA of 50 individual RI-PTC tumors from Chernobyl pediatric patients to look for mutations in genes. We will correlate this data with RNA sequencing from the same patient samples. This data will provide information about events that are taking place at the level of gene expression, providing information about over and under expressed genes and the expression of aberrant genes, and gene fusion products. This data will be compared to RIP-PTC in age matched patients who were not exposed to radiation to develop a radiation-specific profile. We have bioinformatic specialists in the group who will integrate these various kinds of data. This study will provide a comprehensive profile of RIP-PTC.

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Project reference number: 001/2012
Principal Investigator: Dr W van Wieringen, VU University Medical Centre, Amsterdam, The Netherlands

Email: w.vanwieringen@vumc.nl

EpiRadBio – integrative analysis of molecular data

Summary of project:

Within the scope of the EpiRadBio-project, Mark van de Wiel, Carel Peeters and Wessel van Wieringen from the department of Epidemiology & Biostatistics of the VU University Medical Center are responsible for integrative analysis of the molecular data from (radiation) exposed and non-exposed thyroid cancer samples.
Integrative analysis combines heterogeneous biological data, be it experimental (e.g., copy number, gene expression, microRNA expression) or from the biological literature (e.g., gene annotation, pathway information). Integration of data from multiple sources is imperative for a mechanistic understanding of cancer. By putting together partial views of a complex process like tumorgenesis, we may obtain a more accurate and complete picture of the molecular mechanisms underlying it. No off-the-shelf methodology for the statistical analysis of the data is available. We therefore aim to develop statistical models from the experimental data of these biological processes. Such models will enhance our ability to identify biomarkers and therapeutic targets more unambiguously and to interpret genotype information. This should enhance the understanding of what distinguishes the exposed from the non-exposed thyroid cancers. In addition, the biological insight these models provide is likely to result in more targeted follow-up experiments and efficient use of available resources.

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Project reference number: 002/2012
Principal Investigator: Professor B Jarzab, Maria Sklodowska-Curie Memorial Cancer Centre and Institute of Oncology, Gliwice, Poland

Email: bjarzab@io.gliwice.pl

Validation of the gene signature differentiating exposed from non-exposed PTCs, obtained in the Genrisk-T project (no.: 036495) with an independent QPCR method

Summary of project:

The aim of the study is to investigate transcriptomic profiles of papillary thyroid carcinomas that arose after expose to radioiodine fallout from Chernobyl power station and to low level radiocesium exposure present in the contaminated environment. This project is the continuation of a series of projects that are carry on to investigate the transcriptomic and genetic profile of radiation induced thyroid cancer.
As a first step of the study Affimetrix microarray technology was employed to define transcriptomic profiles in two cohorts of children matched on age, oblast and pathological type of tumour. At present we want to validate the results with qPCR.

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Project reference number 001/2013
Principal investigator: Professor GA Thomas, Imperial College, London

E-mail: geraldine.thomas@imperial.ac.uk

A detailed study of the somatic genomics of radiation induced thyroid cancer

Summary of project

It has long been accepted that cancers arise by the sequential accumulation of errors in the DNA of a clone of cells within a given tissue. This in part explains their long latency. However, recent studies using whole genome sequencing have suggested a different mechanism for some cancers, particularly those that arise in children. This mechanism is called chromothripsis and involves shattering of chromosomes and then restitching them together. This results in multiple small changes in the DNA that occur simultaneously rather than sequentially. The aim of this study is to use whole genome sequencing to identify novel mutations in radiation induced thyroid cancer, to identify changes in the mitochondrial genome and to investigate the frequency of chromothripsis in childhood thyroid cancer, especially with respect to radiation exposure.

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Project reference number: 001/2014
Principal investigator: Dr Elizabeth Grubbs, Department Surgical Oncology, MD Anderson Cancer Center, Houston, USA

E-mail: eggrubbs@mdanderson.org

Assessing the impact of radiation exposure on the development of medullary thyroid carcinoma

Summary of project

Convincing epidemiologic data has established a strong causative association between ionizing radiation and the development of papillary thyroid cancer (PTC). This finding was due, in large part, to studying those affected by the Chernobyl accident. More recently other solid tumors, such as lung and breast, have been associated with radiation. Medullary thyroid cancer (MTC), a rarer but more lethal thyroid cancer than PTC, has not been associated with radiation exposure to date. However, there appears to be a higher number of MTC cases than would be expected in the Chernobyl population. We would like to determine if there is a link between radiation and MTC by studying this population to look for mutations that are associated with radiation exposure. Additionally, because MTC is a hereditary condition in 25% of cases, we would also like to assess whether there could be a hereditary cause to MTC in this small geographic region. Such data will give us an insight into the mechanisms in which tumors are formed in MTC and potentially help us target ways to stop these tumors.

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Project reference number 002/2014
Principal Investigator: Mr S Eder, Bundeswehr Institute of Radiobiology, Munich Germany

E-mail: stefanfriedricheder@bundeswehr.org

Anaplastic lymphoma kinase (ALK) – rearrangements in radiation-induced papillary thyroid carcinomas: a study on post Chernobyl tissue samples

Summary of project

Previous analysis of data derived from the Chernobyl accident has shown strong correlation between absorbed doses of IR and the induction of papillary thyroid cancer (PTC). Specific genetic alterations, such as rearrangements of the RET oncogene, are linked to previous exposure to radioiodine. Recently, rearrangements of the anaplastic lymphoma kinase (ALK) gene have been found to be selectively expressed in papillary thyroid cancer (PTC) amongst atomic bomb survivors (ABS), but not in PTC patients lacking radiation exposure. In PTC, ALK rearrangements have been shown to be associated with tumour aggressiveness and, importantly, represent a possible pharmacologicaltarget for the compound Crizotinib. Interestingly, radiation-induced PTCs that show ALK rearrangements lack additional genetic alterations that are frequently found in sporadic thyroid cancer, such as RET, NTRK1, BRAF, or RAS; these findings underline the oncogenic potential of ALK rearrangements in radiation-induced PTC. We plan to investigate a possible correlation between radiation exposure and ALK rearrangements in PTC biospecimens from patients exposed to radioiodine in the context of the Chernobyl accident as well as in a control cohort of sporadic PTCs, performing fluorescence in situ hybridization (FISH) analyses. Furthermore, we intend to assess the mutation status of commonly altered oncogenes in PTC, such as BRAF or RAS, using pyrosequencing.

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Project reference number 003/2014
Principal Investigator: Dr S Channock, Division of Cancer Epidemiology and Genetics, National Cancer Institute, USA

E-mail: chanocks@mail.nih.gov

Comprehensive Genomic Characterization of Radiation-Related Thyroid Cancer in Ukraine

Summary of project

New advances in genomic characterization technologies afford new opportunities to comprehensively investigate the genetic basis of the established association between childhood exposure to iodine-131 (I-131) from the Chernobyl Nuclear Power Plant accident and risk of thyroid cancer. The opportunity to analyze a large set of thyroid cancers and normal tissue/blood from the Chernobyl Tissue Bank (CTB) could further our understanding of the molecular mechanisms of radiation carcinogenesis in humans based on careful evaluation of epidemiological risk factors and genomic alterations. Previously, we had reported a preliminary study of dose-related alterations in gene expression and chromosomal translocations in approximately 70 cases drawn from the Ukrainian-American (UkrAm) cohort component of the CTB biorepository. Recently, we have completed a pilot study in which we have conducted a comprehensive genomic characterization of 12 UkrAm cases, including paired fresh frozen and formalin-fixed paraffin-embedded tissue samples using the infrastructure and analytical pipeline of the Cancer Genome Atlas (TCGA) of the U.S.A. National Cancer Institute (NCI). This includes whole genome sequence analysis of RNA, DNA and micro-RNAs as well SNP and methylation microarrays of the tumor tissue. SNP microarray and DNA analysis was performed on peripheral blood for comparison of germline to somatic alterations. The success of the feasibility study establishes a strong scientific basis for extending this approach to a substantially larger study of thyroid cancer cases drawn from the CTB. Here, we propose conducting a comprehensive genomic characterization study of 500 papillary thyroid cancers (PTC) from the Ukraine using biological samples, information on radiation exposure, and demographic characteristics. The main objective of the study is to provide comprehensive, integrated characterization of the genomic, transcriptomic, and epigenomic landscapes of radiation-related PTC for comparison across a spectrum of I-131 exposure as well as a comparison with approximately 500 sporadic PTCs available from The Cancer Genome Atlas recently published in Cell. The proposed study has the potential to provide unique insights into the mechanisms of radiation carcinogenesis and to generate a rich data resource accessible to other investigators.

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Project reference number: 001/2015
Principal Investigator: Professor DV Kuprash, Engelhardt Institute of Molecular Biology, Moscow, Russia

Autoantibody biomarkers of malignancy in encapsulated follicular-patterned thyroid tumours

Summary of project

Circulating autoantibodies against tumor-associated antigens (TAA) represent a distinct class of cancer biomarkers, being extensively studied in many human neoplasms and recently entered a market (EarlyCDT®-Lung test for early diagnosis of lung cancer in high-risk group); however, TAA profiles of endocrine tumors and thyroid neoplasms in particular remain poorly explored. In our previous research, using immunoproteomic, selective screening and bioinformatic approaches and small serum sample set, we identified a number of candidate autoantibody biomarkers that may demonstrate discriminatory capacity with respect to benign and malignant encapsulated follicular-patterned thyroid tumors (EnFPT). In this project, we intend to perform a comprehensive analysis of serological reactivity of these autoantibodies across different groups of benign (follicular thyroid adenoma), malignant (follicular thyroid carcinoma, follicular variant of papillary thyroid carcinoma and encapsulated well-differentiated cancer not otherwise specified) and borderline (follicular and well-differentiated tumors of uncertain malignant potential) EnFPT. We also intend to study associations of autoantibody reactivity against these antigens with particular driver oncogenic events typical for EnFPT (RAS point mutations and PAX8-PPARg rearrangement), as well as to perform expression analysis of TAAs triggering autoantibody response in EnFPT compared to normal thyroid tissue. The ultimate goal of our research – to identify biologically relevant autoantibody signature that would be capable of pre-surgical discrimination of benign, malignant and probably borderline EnFPT.

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