The field of rheumatoid arthritis (RA) is moving into identification of patients as early as possible and the ultimate aim is to prevent RA becoming a chronic disease. To this end, we studied the... Show moreThe field of rheumatoid arthritis (RA) is moving into identification of patients as early as possible and the ultimate aim is to prevent RA becoming a chronic disease. To this end, we studied the phase of Clinically Suspect Arthralgia (CSA). Patients with arthralgia that were considered by the rheumatologist to have an increased risk to progress to RA (CSA) had indeed an increased risk of RA. In addition, subclinical MRI-inflammation preceded clinical arthritis with a few months. Future research will shed more light on processes underlying progression from CSA to RA and effectiveness of treatment initiation in the CSA phase. The severity of the course of RA is variable between patients and this cannot be yet accurately predicted. In this thesis, we performed studies that contributed to the understanding of these differences in severity. Three genetic risk factors for more severe joint damage progression (two non-HLA and one HLA variation) and one for arthritis persistence were identified. Further research on functional implications of the identified variants and whether they might be useful as biomarkers to guide treatment decisions is needed. Show less
Deelen, J.; Akker, E.B. van den; Trompet, S.; Heemst, D. van; Mooijaart, S.P.; Slagboom, P.E.; Beekman, M. 2016
A large part of the human genome consists of repetitive DNA. In this thesis two human diseases have been studied in which deregulation of repetitive DNA is a central feature: facioscapulohumeral... Show moreA large part of the human genome consists of repetitive DNA. In this thesis two human diseases have been studied in which deregulation of repetitive DNA is a central feature: facioscapulohumeral muscular dystrophy (FSHD) and immunodeficiency, centromere instability and facial anomalies (ICF) syndrome. FSHD is caused by the misexression of the transcription factor DUX4 in skeletal muscle. DUX4 is encoded in the D4Z4 repeat array and is silenced in healthy somatic tissues. In this thesis, several aspects of the epigenetic deregulation of DUX4 in FSHD are described. We have analysed possible correlations between disease severity and epigenetic organization of the D4Z4 repeat. Next we showed that cellular ageing results in deregulation of genomic regions like D4Z4. Moreover, we show that SMCHD1 is the main epigenetic repressor of DUX4 in somatic cells. We next showed that DUX4 misexpression results in the activation of an FSHD candidate gene, FRG2. Finally, we report the generation of a transgenic mouse model for FSHD. The disease mechanism of ICF syndrome remains to be elucidated. However, in this thesis we identify two new ICF disease genes. We highlight a role for all four known ICF genes in repressing repetitive DNA, suggesting functional convergence of these genes. Show less
Paneque, M.; Turchetti, D.; Jackson, L.; Lunt, P.; Houwink, E.; Skirton, H. 2016
Jasmonates (JAs) are crucial plant signaling molecules that regulate defense responses against wounding, insects and necrotrophic pathogens. The biosynthesis of JAs is regulated by a positive... Show moreJasmonates (JAs) are crucial plant signaling molecules that regulate defense responses against wounding, insects and necrotrophic pathogens. The biosynthesis of JAs is regulated by a positive feedback loop. This thesis reveals the transcriptional regulatory mechanism behind this positive feedback loop in Arabidopsis. The studies show that the bHLH-domain transcription factors MYC2, MYC3 and MYC4 positively regulate most JAs biosynthesis genes directly and by controlling the expression of ORA47 gene, encoding a regulator of JAs biosynthesis. Show less
Advances in technology have turned modern biology into a data-intensive enterprise. The advent of high-output technologies like Microarrays and Next-generation sequencing technologies has resulted... Show moreAdvances in technology have turned modern biology into a data-intensive enterprise. The advent of high-output technologies like Microarrays and Next-generation sequencing technologies has resulted in researchers grappling not just with huge volumes but also multiple types of data. While generation and storage of high-quality data are an important research focus, it is increasingly recognized that translating data into actionable information and insight is a critical research challenge. To infer reliable conclusions from the data, it is often necessary to integrate large amounts of heterogeneous data with different formats and semantics. Given the breadth and volume of data involved, this goal is best achieved through automated methods and tools for data integration and workflow management. This thesis presents automated strategies that combine bioinformatics and statistical methods to identify novel biomarkers in high-throughput OMICs datasets pertaining to the metabolic syndrome and to gain mechanistic insight into the underlying biological processes. An underlying theme in this thesis is data-driven approaches that generate plausible hypothesis which is followed by experimental verification. Show less
Messemaker, T.C.; Huizinga, T.W.; Kurreeman, F. 2015
The ultimate goal of translational colon and rectal cancer research is to turn these types of cancer into curable or manageable chronic diseases. The approach to achieve this is to enable... Show moreThe ultimate goal of translational colon and rectal cancer research is to turn these types of cancer into curable or manageable chronic diseases. The approach to achieve this is to enable clinicians to make (adjuvant) treatment decisions, based on the individual patient characteristics and individual characteristics of a patient__s tumor. Identification of new prognostic and predictive biomarkers, based on the biology of individual tumor characteristics, is therefore warranted to further refine the current TNM classification. This thesis describes the use of molecular techniques for the identification of prognostic biomarkers for clinical outcome in (sporadic) colon and rectal cancer. We here present compelling candidate biomarker combinations for validation in further studies. Retrospective and prospective validation of these prognostic biomarker combinations in international and independent patient series is therefore the crucial next step. Additionally, the presented studies stress the importance of -1- combining biomarkers based on tumor biology, -2- integrative analysis of cancer hallmark related processes at all different cellular regulatory levels (genetics, epigenetics and protein level), -3- assessment of tissue specificity between colon and rectal tumors, and -4- studying age-related effects in future colorectal cancer research. Show less
Rheumatoid arthritis is a chronic auto-immune disorder, of which persistent synovitis, bone erosions and auto-antibody formation are characteristic features. Although the etiology of the disease... Show moreRheumatoid arthritis is a chronic auto-immune disorder, of which persistent synovitis, bone erosions and auto-antibody formation are characteristic features. Although the etiology of the disease remains largely unknown, it is established that genetic risk factors play a pivotal role in disease pathology. Both family and twin studies have shown that the genetic contribution to the disease can be estimated around 50%. In the current thesis the genetic contribution of non-HLA genes to RA susceptibility was further investigated and the functional relevance of these loci was explored. The studies described were able to establish several previously identified risk factors in a statistical robust manner. Also novel genetic risk factors that are associated with RA susceptibility could be identified, as well as risk factors that are conferred to specific subgroups of the disease. Show less
Juvenile idiopathic arthritis (JIA) is a non-common disease in children that can persist into adulthood. JIA is considered to be an auto-immune disease. Genetic factors play a role in the... Show moreJuvenile idiopathic arthritis (JIA) is a non-common disease in children that can persist into adulthood. JIA is considered to be an auto-immune disease. Genetic factors play a role in the pathogenesis. In a new cohort of JIA patients from North-West European descent genetic candidate gene association studies have been performed. In this cohort we have discovered new associations with the susceptibility of JIA and the genes/loci TRAF1/C5, 4q27, CD226 and CD28. These genes have already been associated with other auto-immune diseases and might be part of a shared common auto-immune susceptibility. Also genetic association with the course of disease has been studied, revealing an association of VTCN1 and the severity of JIA defined by the percentage of active disease in the first two years. VTCN1 encodes B7-H4 that is involved in the co-stimulation of T-cells and inhibits the immune-response. Until the precise role of VTCN1 will be clarified, the genetic association might be of use in predicting the course of disease and might be a lead point for new treatment. Show less
Primary vascular tumors of bone are a heterogeneous group. Numerous terms have been introduced as well as different classification systems. However, so far none of them have been generally accepted... Show morePrimary vascular tumors of bone are a heterogeneous group. Numerous terms have been introduced as well as different classification systems. However, so far none of them have been generally accepted.Therefor, there is a need for more specific morphological, immunohistochemical and molecular tools to support the classification of different vascular tumors of bone. In this thesis, we attempt to delineate the high-grade malignant vascular tumors of bone based on histomorphological criteria, protein expression profile based on a large panel of oncogenes, tumor-suppressor genes and signaling molecules, and molecular data. Moreover, we compared our dataset with a small groups of angiosarcoma of soft tissue in order to see whether these are truly different tumors or whether they should be regarded as one entity with a different localization. Finally, we question whether the rare vascular tumor previously designated as "haemangiopericytoma of bone" is a true entity or should rather be regarded as a growth pattern. Show less
Although much research effort has been put into the development of new antidepressant drugs, the process of developing a drug often fails at the stage of large randomized controlled trials (RCTs)... Show moreAlthough much research effort has been put into the development of new antidepressant drugs, the process of developing a drug often fails at the stage of large randomized controlled trials (RCTs) in which an initially promising compound appears to lack efficacy after all. Several experimental medicine models have been proposed as preclinical tools in order to predict drug efficacy before the stage large RCTs. Among the various experimental medicine models, the cognitive neuropsychological model has been proposed as a tool to predict the efficacy of antidepressant drug even before the stage of large scale and expensive RCTs. We applied the cognitive neuropsychological model of drug action to test antidepressant effects of a novel compound (ARA290) and a well-known compound (L-tryptophan). We further investigated the model by tapping into HPA-axis reactivity and social decision making as additional outcomes, and investigated their interaction with a genetic marker. Show less