Projects

Abstract

Thoracic aortic aneurysm (TAA) entails a high risk for aortic dissection and rupture, which is a prominent cause of death in Western countries. Prophylactic surgery significantly reduces the mortality risk, but complications are relatively common. Moreover, in severe TAA conditions aneurysms often develop at other locations afterwards, exposing patients to repeated surgeries and, thus, threats. Current drug options only modestly slow down dilatation, without preventing dissections or ruptures. Clearly, a game changer in TAA patient management would be the availability of medical therapies capable of stopping or reversing aneurysm formation. Functional characterization of the known TAA genes, especially those that are linked to syndromic TAA, in relevant cell and/or mouse models has already delivered valuable insights into the disease mechanisms, prompting pre-clinical drug testing in mice. The mechanistic picture is incomplete though, encumbering the development of additional, and especially more effective, therapies. Another prevailing issue is the inefficient and/or unsuccessful translation of pharmacological mouse results to the clinic. Few compounds make it to clinical trials due to the high costs, lengthy time frames and difficulties as to patient recruitment. Additionally, while TAA mouse models allow us to study and therapeutically target disease in an in vivo setting, efficiency of ensuing compounds might not be recapitulated in humans. Building on intriguing preliminary data and the unique availability of mutant/control Fbn1 and Ipo8 mice and human induced pluripotent stem cells, this project aims to contribute to the resolution of these issues by further unravelling and therapeutically targeting the mechanisms underlying syndromic TAA. Additionally, BREAK-OUT will provide proof-of-concept that patient-derived aorta-on-a-chip models can be used for pre-clinical TAA research.

Researcher(s)

• Promoter: Verstraeten Aline

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Impaired TGF-β signaling has been implied in thoracic aortic aneurysm and dissection (TAAD) related disorders such as Loeys-Dietz syndrome. Although pathogenic variants in genes coding for components of the TGF-β signaling pathway have been identified as causal for these diseases, the precise mechanisms by which these specific variants lead to pathology remain elusive. Since medial degeneration is the main pathological substrate for TAAD, vascular smooth muscle cell (VSMC) dysfunction is often considered as the main culprit, but the role of endothelial cells (ECs) is neglected. With this project, I will elucidate the TGF-β paradox by in vivo fluorescent light sheet imaging in zebrafish. I will use an innovative EC and VSMC specific fluorescent TGF-β reporter to study TGF-β signaling in real time in a zebrafish Tgfb2 knockout line. Elucidation of the true pathomechanisms will bring us closer to a curative therapy for life-threatening TAAD and pave the way for the identification of prognostic biomarkers of aortic disease severity.

Researcher(s)

• Promoter: Schepers Dorien

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Chondrodysplasias are skeletal disorders attributed to primary defects in hyaline cartilage. Disease severity differs considerably between subtypes, with some only inflicting joint abnormalities and others causing severe dwarfism or perinatal lethality. For many (severe) chondrodysplasias satisfactory therapies are lacking, prompting further research in the underlying disease mechanisms. Endoplasmatic reticulum (ER) stress, and the accompanying excess in chondrocyte apoptosis, have emerged as credible pathomechanisms in some chondrodysplasias, including COL2-pathies. In these conditions chaperone-oriented therapy represents an interesting pharmacological avenue. In this project, we will use iPSC-chondrocyte models to investigate whether ER stress and unfolded protein response (UPR) activation play a role in the etiology of BGN-related chondrodysplasia, which is a pathomechanistically unexplored form of serious dwarfism. IPSC-chondrocytes of patients suffering from severe but non-lethal COL2A1-related spondyloepiphyseal dysplasia congenita will be used as positive controls. Next, we will develop a novel iPSC-chondrocyte-based high-throughput microscopic high content assay, which will be used to pinpoint novel drug candidates (compound library screening) or existing drugs (repurposing) promoting protein folding in ER stress-related chondrodysplasias.

Researcher(s)

• Promoter: Verstraeten Aline
• Co-promoter: Peeters Silke

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Thoracic aortic aneurysms (TAAs) predispose to aortic dissection or rupture, a catastrophic event associated with an ultimate mortality rate of 80% and, hence, a prominent cause of morbidity and mortality in the Western population. If TAA is detected timely, prophylactic surgery can drastically reduce mortality rates but comes with a significant risk of complications. As there are currently no medical therapies capable of stopping or even reversing TAA formation, there is a high need for such medications. Although much progress has been made in our understanding of some mechanisms underlying TAA, we lack deep insight at the single cell resolution. The latter is essential if we want to develop more efficient drugs. Within this project we take advantage of the genetic knowledge of Marfan syndrome, a defined monogenic model for TAA development, and its related but opposing fibrillinopathies, stiff skin syndrome and acromelic dysplasia. These two conditions are also caused by pathogenic variants in FBN1 (gene coding for fibrillin-1) but do not present aortic aneurysm development. By studying the aorta in their respective mouse models at a single cell resolution, we aim to identify novel therapeutic targets which we will then test and validate in our already created iPSC derived cell models of these conditions. The anticipated findings will advance the pathomechanistic TAA knowledge beyond the current understanding and will pave the way for novel therapeutic strategies.

Researcher(s)

• Promoter: Loeys Bart
• Co-promoter: Peeters Silke

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Progressive dilatation of the thoracic aorta leads to the development of thoracic aortic aneurysms (TAAs), which are often asymptomatic but predispose to dissection and rupture. The latter are associated with high mortality rates. Even though over 40 TAA genes have been identified in the past, the cause remains elusive for the majority of patients (70% of familial and 85-90% of sporadic patients), despite exhaustive Mendelian whole exome sequencing efforts for both single nucleotide variants and copy number variant detection of the coding exons of these TAA genes. Moreover, all recently identified genes each only explain very small proportions (<1%) of previously genetically elusive TAA patients. Hence, there is a need to explore novel avenues that move beyond these traditional approaches. Various types of previously un(der)explored genetic variants may explain the missing TAA heritability. In this project, I will therefore determine (1) which proportion of sporadic TAA patients can genetically be explained by the presence of somatic mutation in affected aortic tissue using deep whole exome sequencing and (2) what is the role of (non-coding) structural variants in the development of TAA using short- and long-read whole genome sequencing.

Researcher(s)

• Promoter: Loeys Bart
• Fellow: Meester Josephina

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Pathogenic variants in biglycan cause two divergent phenotypes: Meester-Loeys syndrome (MRLS) and X-linked spondyloepimetaphyseal dysplasia (SEMDX). The latter is characterized by a disproportionate short stature and caused by missense variants. MRLS, on the other hand, is a syndromic form of thoracic aortic aneurysm that is caused by loss-of-function variants. Intriguingly, MRLS patients with partial biglycan deletions present with a more severe skeletal phenotype. To date, discriminative pathomechanisms explaining why certain biglycan mutations cause MRLS and others SEMDX remain elusive. This PhD project aims to answer this research question using induced pluripotent stem cells (iPSCs) of both patient groups and their respective (isogenic) controls. IPSC-based disease modeling provides a unique opportunity for pathomechanistic investigation in a patient-, variant- and cell type-specific manner. After the creation of disease-relevant patient-derived iPSC-vascular smooth muscle cells and -chondrocytes, I will identify cell type-specific differences between MRLS and SEMDX using (1) functional assays tailored to existing pathomechanistic insights, and (2) hypothesis-free transcriptomic and proteomic approaches. Finally, I will investigate the mutational effect of partial biglycan deletions to establish a specific MRLS genotype-phenotype association.

Researcher(s)

• Promoter: Loeys Bart
• Co-promoter: Meester Josephina
• Co-promoter: Verstraeten Aline
• Fellow: Hebert Anne

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Thoracic aortic aneurysm (TAA) denotes a progressive enlargement of the thoracic aorta, entailing a significant risk for life-threatening aortic dissection and/or rupture. At present, mouse models are often used to investigate and therapeutically target the molecular defects underlying TAA, as native aortic samples of patients and, especially, control individuals are hard to collect. Yet, murine in vivo studies are often lengthy and drug testing results did previously not always recapitulate in patients. With the advent of induced pluripotent stem cells (iPSCs), the field is closing in on apt solutions to faithfully model patient and control aortas in a dish. The currently available vascular smooth muscle cell (VSMC) or endothelial cell (EC) monocultures are still overly simplified, as they fail to adequately replicate the complex multilayered and multicellular structure of the aorta. Taking advantage of available iPSCs from syndromic TAA patients (FBN1 & IPO8), my project aims to 1) develop and consolidate the validity of the first iPSC-derived TAA aorta-on-a-chip models, comprising the two VSMC subtypes populating the native ascending aorta along with a layer of arterial ECs, and 2) use the established model to further investigate the disease mechanisms underlying the relatively unexplored IPO8 syndrome. The anticipated outcomes will contribute to the replacement of mouse models (3R principle) and expedite pathophysiological TAA research and drug discovery.

Researcher(s)

• Promoter: Verstraeten Aline
• Co-promoter: Loeys Bart
• Fellow: Fedoryshchenko Ivanna

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Thoracic aortic aneurysm (TAA) denotes a progressive enlargement of our body's largest artery, i.e. the aorta. It frequently remains unnoticed until aortic dissection and/or rupture occur, which are associated with high mortality rates. Although prophylactic aortic surgery can serve as a lifesaving event, it comes with important risks. Current drug therapies can only slow down TAA progression to some extent, but cannot fully prevent aortic dissections/ruptures. Better therapeutic options are clearly needed. TAA and the ensuing aortic complications are a hallmark of a rare connective tissue disorder, called Loeys-Dietz syndrome (LDS). While LDS-related TAA is relatively understudied as compared to other TAA conditions, it is an important study case considering its early onset and aggressive disease course. Taking advantage of the advent of the iPSC technology and our expertise in clinical and pathophysiological LDS research as well as iPSC-vascular smooth muscle cell and iPSC-endothelial cell disease modelling, we want to significantly expedite bench-to bedside translation of LDS research by developing and functionally validating iPSC-derived aorta-on-a-chip (AoC) models of TAA-presenting patients and isogenic controls. Upon demonstration of the known pathomechanisms and drug responses in SMAD3 mutant AoCs, we will investigate if our AoC models can also recapitulate between-patient variability in disease severity. In conclusion, we here take up the challenge to develop a novel pre-clinical tool allowing exploration and therapeutic targeting of LDS mechanisms in a human setting that more closely resembles the native aorta than ever before. The anticipated results will prove relevant for TAA in general, as the AoC expertise that will be acquired within the frame of this project can immediately be translated to other TAA conditions.

Researcher(s)

• Promoter: Verstraeten Aline
• Co-promoter: Loeys Bart
• Fellow: Bousbaa Amira

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Testing of repurposed drugs may lead to more effective treatment of core symptoms of Fragile X syndrome or in fact, of any neurological disorder. However, such an approach faces the challenge of having to test multiple drugs, likely in various concentrations each. This is a time-consuming and costly for current approaches, where preclinical testing is usually performed using large behavioral murine test batteries in combination with ex-vivo electrophysiological measurements. In this project, we propose to develop a highly versatile and innovative drug screening platform for Fragile X syndrome using a combination of live mouse tracker (LMT) and multi-electrode array (MEA). Standard behavioral test batteries will be replaced by a single LMT recording. This tracker is able to dissect up to 35 different behaviors of groups of up to four mice from a single 24-hour recording, providing a powerful first look at a drug's effectiveness. In addition, cultured primary neurons will be used for electrophysiological recordings of neuronal networks on the MEA. Drugs can be added on a daily basis, and the changes in the measures can assess the drugs. By combining LMT and MEA we aim to establish a ready-to-use, innovative and efficient drug screening platform for the preclinical validation of novel compounds and/or repurposed drugs for Fragile X syndrome, a prime example of a neurological disorder for translational medicine.

Researcher(s)

• Promoter: Kooy Frank

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

The attrition rate of novel drug candidates due to cardiotoxic adverse events remains a big challenge in the preclinical and clinical drug development. As such, it is pivotal for the pharmaceutical industry to identify these liabilities at early stages by applying sensitive and translatable assaysto predict potential harmful effects to the human cardiovascular system. The current project aims to develop and optimize an assay in human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CM) that combines impedance and multi-electrode array (MEA) measurements with cardiotoxicity biomarkers, in particular dysregulated microRNAs (miRNAs). To achieve this goal, commercially available hiPSC-CM were treated with a large set of drugs at clinically relevant concentrations, and drug responses were monitored for 72h on XCELLigence Real Time Cell Analysis (RTCA) Cardio ExtraCellular Recording (ECR) instrument measuring impedance and electrical changes. RT-qPCR on RNA extracted from the cell pellets was employed to study the upregulation of previously identified miRNAs candidates (Gryshkova et al. Arch of Toxicology, 2022). Several miRNAs were found to be upregulated in hiPSC-CM, especially in response to anthracycline drugs. hsa-miR-187-3p, hsa-miR-182-5p, hsa-miR-365a-5p, and hsa-miR-133b were upregulated with the highest fold changes in response to several treatments. In the past decade, several studies have confirmed the expression of dysregulated miRNAs in the blood/serum of patients with various diseases, spacing from oncological disorders to cardiovascular liabilities. Therefore, the investigation of miRNAs released in the supernatant of hiPSC-CM culture could confirm their utility as potential novel biomarkers of cardiotoxicity in the clinic. To assess the translatability of the already generated data and the effect of existing genetic cardiac liabilities on cardiotoxic drug exposure, the assays will be applied to in-house created hiPSC-CMs from patients carrying TTN and SCN5A mutations, causing cardiomyopathy and the cardiac arrhythmia Brugada syndrome respectively, and healthy control individuals (isogenic and unrelated controls). Impedance and electrophysiology will be measured on these cell lines by RTCA CardioECR and alteration in expression level of the selected miRNAs will be analyzed both in the cell pellet and the supernatant. In addition, expression level of the selected miRNAs will be analyzed in blood samples collected from the same individuals as well as a selection of cardio-oncology patients.

Researcher(s)

• Promoter: Alaerts Maaike
• Co-promoter: Guns Pieter-Jan

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Thoracic aortic aneurysm (TAA) stands for a pathological dilatation of the thoracic part of our body's largest artery, which entails a high risk for life-threatening aortic dissection and rupture. Prophylactic surgery significantly reduces the mortality risk, but complications are relatively common. Moreover, in severe TAA conditions aneurysms often develop at other locations afterwards, exposing patients to repeated surgeries and, thus, threats. Current drug options only modestly slow down dilatation, without preventing dissections or ruptures. Clearly, a game changer in TAA patient management would be the availability of medical therapies capable of stopping or reversing aneurysm formation. To develop such therapies, better pathomechanistic insights should be gained. To date, TAA insights have largely been acquired using single-gene functional genetic approaches. Disadvantages of such strategies include suboptimal exploration of less obvious disease culprits as well as the fact that the yet acquired insights may prove insufficient to develop a single efficient therapy for a genetically heterogeneous disease such as TAA. To find convergent TAA mechanisms, I used a hypothesis-free bulk transcriptomics approach on affected aortic root and ascending aorta samples from three distinct TAA mouse models and their respective wild-type littermates. A significant consistent dysregulation of several highly interesting candidate disease culprits (based on literature, other TAA transcriptomics datasets, phenotype of transgenic mice, etc.) was observed in all three models. Here, I aim to acquire preliminary evidence that neutralization of the top genes' expression levels in TAA-presenting Fbn1C1041G/+ mice can rescue the 3 TAA phenotype. To do so, crossbreeding of the TAA mouse with knockout or overexpression mice for the respective genes of interest will be done, after which the aorta of the different single- and double-transgenic offspring as well as their wildtype littermates will be phenotyped using echocardiography and histological stainings. Upon demonstration of phenotypic alleviation, additional offspring will be generated, whose aortic tissue samples will be subjected to standard molecular biology techniques to gain preliminary insights into the target genes' mode of action.

Researcher(s)

• Promoter: Verstraeten Aline

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Bicuspid aortic valve (BAV) is the most common congenital heart defect, affecting 1-2% of the general population. This aortic valve defect, which has a male predominance (3:1), is characterized by two semilunar leaflets instead of the normal three. BAV usually remains unnoticed, until patients develop clinical complications such as valvular dysfunction and/or thoracic aortic aneurysm (TAA, 20-30%). TAA is a pathological widening of the aorta in the thorax caused by vascular wall weakness, entailing a high risk for acute dissection and/or rupture (mortality rates ≥70%). Over the past decades, extensive gene discovery efforts have identified about 30 BAV/TAA-associated genes, explaining less than 6% of the BAV-related aortopathy patients. Their identification, and functional characterisation, have been key steps in acquiring our current molecular knowledge on this disease. Though, the still incomplete pathogenic picture hampers the identification of individuals at-risk for TAA, and the discovery of novel therapeutic targets to prevent and/or stop TAA formation. Our research group identified the SMAD6 gene as a novel cause for BAV/TAA disease, which accounts for 4.8% of the 6% genetically solved BAV-related aortopathy patients. More recently, I developed a Smad6 knockout mouse model mimicking human BAV-related aortopathy. In this project, I aim to identify disease-associated genes by using the transcriptomic profiling of Smad6-deficient mice with a highly penetrant outflow tract phenotype in order to prioritize, and strengthen the genetic link of novel and candidate genes with BAV-related aortopathy in humans. The project's anticipated outcomes will advance our current understanding on the molecular basis of the most important known genetic factor implicated in human BAV-related aortopathy.

Researcher(s)

• Promoter: Loeys Bart
• Co-promoter: Luyckx Ilse

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Cancer is a leading cause of death worldwide, accounting for nearly 10 million deaths in 2020. SOCan will contribute to the (early) diagnosis and follow up of cancer via a new disruptive detection platform, i.e. singlet oxygen-based photoelectrochemical detection of cancer biomarkers. Those biomarkers are increasingly discovered and validated, but the detection necessitates rapid, accurate and sensitive devices. To achieve this, the combined use of electrochemical detection with light-triggered sensor technology for the specific and sensitive detection of pre-selected DNA and RNA cancer biomarkers is proposed. The application of this technology on tissue and liquid biopsy samples will be a major contribution to the early detection of cancer. SOCan aligns with the EU Mission on Cancer and will lead to an affordable and sensitive diagnosis of cancer, reducing the time to result which allows faster and specific treatment, and thereby saving lives.

Researcher(s)

• Promoter: Van Camp Guy

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Over the last decade, four interfaculty research groups of the Center for Medical Genetics of the University of Antwerp have contributed significantly to the genetic underpinning of a wide range of heritable disorders. In the current project these groups will address two fundamental challenges: first, how can we better understand and predict the biological consequences of coding and non-coding variation in the human genome and second, how can we translate this understanding in new treatment strategies. In order to address these challenges we will apply state-of-the-art technology, including whole genome sequencing, long read sequencing (in collaboration with VIB), methylomics, single cell RNAseq and gene editing (CRISPR/Cas) into robust models systems such as advanced mouse and zebrafish models as well as induced pluripotent stem cells (iPSC) and Human Embryonic Stem Cells (hESCs). The four research groups have an established network with clinicians and industry to transfer genetic knowledge into biomarkers and to translate the new genetic insights into innovative therapies.

Researcher(s)

• Promoter: Loeys Bart

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Chondrodysplasias refer to a large and heterogeneous group of skeletal disorders caused by primary defects in hyaline cartilage. They have a combined prevalence of about 1/4000 births and differ considerably with respect to disease severity; with some only inflicting mild joint symptoms, and others coming with severe dwarfism or even perinatal lethality. Especially the complications that arise from major growth problems (e.g. respiratory difficulties, spinal cord compression, hydrocephaly) impact significantly on the patient's quality of life. For many chondrodysplasias no therapies are on the market yet. Over the past years, endoplasmatic reticulum (ER) stress and the resulting excess of apoptosis have emerged as convincing converging chondrodysplasia pathomechanisms. This project builds further on these findings and aims to significantly improve future chondrodysplasia patient management by 1) establishing the protocols to create and study iPSC-chondrocytes as well as to use them for high-throughput drug screening approaches, with a primary focus on COL2A1 and BGN-related dysplasias, 2) investigating whether ER stress and UPR activation play a role in the etiology of BGN-related chondrodysplasia (i.e. a pathomechanistically unexplored severe form of dwarfism), and 3) developing and applying a novel iPSC-chondrocyte-based high-throughput high content assay to discover putative drug candidates that promote protein folding in ER stress-related chondrodysplasias.

Researcher(s)

• Promoter: Verstraeten Aline
• Co-promoter: Meester Josephina
• Fellow: De Kinderen Pauline

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Thoracic aortic aneurysm (TAA) is an abnormal widening of the aorta in the chest, caused by the weakening of the aortic wall. TAAs can lead to rupture or dissection, a devastating complication with a mortality rate of 50%. Despite considerable efforts to gain insights on the molecular mechanisms underlying TAAs, there is currently no therapy that effectively stops or reverses TAA development. Single-cell RNA sequencing (scRNA-seq) is emerging as a ground-breaking technology to investigate gene expression at single-cell level and is opening new avenues to discover yet unexplored disease pathways. In my project, I will apply this technique to investigate a novel TAA disorder caused by bi-allelic pathogenic variants in the IPO8 gene, recently discovered in our Cardiogenomics research group. I will search for differentially expressed genes (DEGs) within the different aortic cell populations from an Ipo8-/- mouse model that recapitulates the human aortic aneurysmal phenotype. I will also investigate shared DEGs between Ipo8-/- mice and additional TAAs mouse models to find convergent disease pathways in clinically related TAA disorders. Subsequently, I will validate the role of the identified candidate culprits in mouse TAA development in a human setting, by using CRISPR-inhibition or -activation in iPSCs derived vascular smooth muscle cells or endothelial cells. The predicted outcomes will potentially pinpoint novel TAA drivers and hence, unveil potential new therapeutic targets.

Researcher(s)

• Promoter: Verstraeten Aline
• Co-promoter: Loeys Bart
• Co-promoter: Meester Josephina
• Fellow: Valdivia Callejon Irene

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Neuroendocrine neoplasms (NENs) exhibit clinical and biological heterogeneity, making diagnosis extremely challenging. Moreover, NENs tend to progress slowly necessitating long-term follow-up to monitor tumor growth and response to therapy. Current modalities for diagnosis and follow-up of NENs are primarily based on imaging and (repeated) tissue biopsies, but these suffer from several shortcomings which have a direct impact on patients' lives. Over the past few years, liquid biopsies have gained interest as a minimally-invasive way for rapid tumor detection and collection of molecular information of the tumor, with circulating tumor DNA (ctDNA) as one of the most promising new markers. This ctDNA is the fraction of cell-free DNA (cfDNA) released by the tumor, that reflects both the genetic and epigenetic alterations of the tumor. Consequently, this project aims to leverage liquid biopsies to improve diagnostic accuracy in NENs and enable real-time monitoring of NEN patients. For this purpose, NEN-specific molecular alterations namely copy number alterations and differentially methylated CpGs will be identified and selected to enable detection and quantification of ctDNA. Since the gold standard detection methods, shallow whole genome sequencing and methylation arrays, respectively, are unable to detect very low concentrations of ctDNA, two alternative and highly sensitive multiplex assays based on DNA sequencing and photoelectrochemistry, respectively, will be employed.

Researcher(s)

• Promoter: Van Camp Guy
• Co-promoter: De Wael Karolien
• Co-promoter: Op de Beeck Ken
• Co-promoter: Peeters Marc
• Fellow: Mariën Laura

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Thoracic aortic aneurysm (TAA) is an abnormal widening of the thoracic aorta caused by blood vessel wall weakness. TAAs entail a high risk for aortic rupture or dissection, commonly leading to sudden death. To date, genetic defects in >35 genes have been linked with TAA, providing a molecular cause for about 30% of patients. Their identification and functional characterization have been key in acquiring our current pathomechanistic aortopathy knowledge. Yet, the genetic and mechanistic picture for TAA is far from complete, hampering identification of predictive markers for aneurysm formation and development of therapies capable of stopping or reversing aneurysm formation. In search for novel TAA genes, our research group most recently identified recessive truncating IPO8 mutations as a novel cause of syndromic TAA. This project builds on this exciting finding, remarkable Ipo8-/- mouse background differences and the availability of IPO8 mutant iPSCs and isogenic controls. More specifically, we aim to significantly improve our current pathomechanistic insight in TAA caused by IPO8 deficiency based on 1) transcriptomics to unravel the involved biological pathways; and 2) identification of proteins and miRNAs with an abnormal cytosol/nucleus distribution upon IPO8 depletion. In the long term, this project's anticipated results will identify new targets for drug therapies, improving TAA patient management.

Researcher(s)

• Promoter: Loeys Bart
• Co-promoter: Meester Josephina
• Co-promoter: Verstraeten Aline
• Fellow: Buccioli Lucia

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Impaired TGF-ß signaling has been implied in thoracic aortic aneurysm and dissection (TAAD) related disorders such as Loeys-Dietz syndrome. Although pathogenic variants in genes coding for components of the TGF-ß signaling pathway have been identified as causal for these diseases, the precise mechanisms by which these specific variants lead to pathology remain elusive. Since medial degeneration is the main pathological substrate for TAAD, vascular smooth muscle cell (VSMC) dysfunction is often considered as the main culprit, but the role of endothelial cells (ECs) is neglected. Dysregulated endothelial nitric oxide (NO) signaling contributes to aneurysm development, but its link to TGF-ß signaling remains vague. With this project, I will elucidate the TGF-ß paradox and investigate the effect of impaired TGF-ß signaling on NO regulation by in vivo fluorescent light sheet imaging in zebrafish. I will use an innovative EC and VSMC specific fluorescent TGF-ß reporter to study TGF-ß signaling in real time in a zebrafish Tgfb2 knockout line. Next, by using a novel genetically encoded eNO probe (geNOps), I will investigate how impaired TGF-ß signaling affects NO regulation by in vivo imaging. Finally, I will identify therapeutic targets using an RNA sequencing approach on the novel zebrafish models I developed. This will bring us closer to a curative therapy for life-threatening TAAD and pave the way for the identification of prognostic biomarkers of aortic disease severity.

Researcher(s)

• Promoter: Loeys Bart
• Fellow: Schepers Dorien

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

The aorta is the body's main artery and supplies oxygenated blood to all parts of the body. Progressive dilatation of the aorta leads to the development of thoracic aortic aneurysms and dissections (TAADs), which are often asymptomatic but predispose to aortic dissection and rupture. The latter are associated with high mortality rates. In 2017, I identified mutations in BGN (Biglycan), an X-linked gene, as a novel cause of a severe syndromic form of TAAD, which shows clear clinical overlap with Marfan syndrome (MFS) and Loeys-Dietz syndrome (LDS), and is now designated as Meester-Loeys syndrome (MRLS). Based on the current knowledge, it remains unknown which molecular mechanisms explains how loss-of-function mutations in BGN lead to syndromic TAAD (MRLS). Within this project, I aim to further unravel the pathomechanism underlying MRLS using (single cell) transcriptomic approaches in an in vivo BALB/cA Bgn KO mouse model and validate these findings in an in vitro human iPSC-VSMC model. The expected results will be beneficial for genetic counselling and clinical follow-up of the families. Furthermore, they can lead to the development of more personalized preventive therapeutic strategies. In the long run, I anticipate that our research group will also use these mouse and cell models for drug compound screenings for syndromic TAAD.

Researcher(s)

• Promoter: Meester Josephina
• Co-promoter: Loeys Bart

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Fragile X syndrome (FXS) is the most common inherited cause of intellectual disability and autism. The mutational basis of FXS is the abnormal expansion and consequent hypermethylation of a CGG trinucleotide repeat in the promoter region of the fragile X mental retardation 1 (FMR1) gene, leading to transcriptional silencing and absence of fragile X mental retardation protein (FMRP). Current treatment is symptomatic and no specific drugs are available for the disorder yet. Several animal models have been developed to study FXS, of which the Fmr1 knockout (KO) mouse is the most studied. Over the past decades multiple studies have indicated an important role of FMRP in multiple cellular pathways, and several potential therapeutics showed efficacy in reversing symptoms in predominantly the Fmr1 KO mouse model. Unfortunately, the successes of the preclinical evaluations were rarely matched in clinical trials. However, essentially only therapies with drugs targeting individual pathways have been initiated. This oversimplification by targeting only one pathway at a time suggests that the use of a combination therapy, targeting multiple involved pathways simultaneously, is a promising new strategy in drug discovery for FXS. However, such an approach faces the challenge of having to test multiple compounds and a combination of a series of drugs, likely in various concentrations each. Most studies demonstrated rescue of symptoms based on a battery of behavioral tests and electrophysiological recordings that differ from laboratory to laboratory. This current approach is labor intensive, time consuming and costly, and therefore not fitted to screen for multiple drugs, nor combination therapies, where multiple drugs in multiple dosages need to be combined. Therefore, we have developed a standardized method to measure the effectiveness of different drugs in a uniform and versatile screening protocol. For electrophysiological measurements we have selected the multi electrode array (MEA) system, that can be used to determine the effects Fmr1 deletion on electrophysiology and neural network functioning. For the behavioral analysis, we use live mouse tracker (LMT) 24h recordings. This system is able to dissect up to 35 different (social) behaviors of up to four mice from a single 24 hours recording, and provides a first glance of the effectiveness of a drug. By combining the MEA and LMT we have developed a versatile, high throughput, innovative and efficient drug screening platform for fragile X syndrome. Additionally, this platform is the first universal system that has the potential to test multiple drugs under identical conditions in a single (same) laboratory.

Researcher(s)

• Promoter: Kooy Frank

Research team(s)

• Medical Genetics (MEDGEN)

Project website

Project type(s)

• Research Project

Abstract

Marfan syndrome (MFS) and acromelic dysplasias (AD) are caused by pathogenic variants in the fibrillin-1 (FBN1) gene. Remarkably, whereas MFS is characterized by aortic aneurysms and dissections, tall stature and arachnodactyly, AD patients present with short stature, brachydactyly, and no aortic involvement. To date, the divergent pathophysiological mechanisms explaining these contrasting phenotypes remain largely unknown. Loss of structural integrity of the microfibrils is proposed as the cause of MFS, while altered protein-protein interactions to the TB5 domain of FBN1 are thought to be at heart of the pathogenesis of AD. However, the alterations in protein interactions identified so far do not seem to fully explain the AD phenotype. Remarkably, increased transforming growth factor beta (TGF-β) signaling has been considered both in human and murine MFS aortic wall tissue and in fibroblasts of AD patients. As such, the exact functional consequences of the AD and MFS mutations on cell signaling pathways remain a matter of debate to date. The main questions remain: (1) why aortic disease is unique to MFS and (2) what is the exact role of the TB5 domain of FBN1? In this project, I want to decipher the pathomechanistic processes underlying these distinct aortic phenotypes by applying multi-omics approaches in murine and human (cellular) models of MFS and AD. The expected results may reveal novel (preventive) therapeutic targets, which is important to treat the life-threatening aortic aneurysms from which MFS patients are suffering.

Researcher(s)

• Promoter: Loeys Bart
• Co-promoter: Peeters Silke

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Resistance to stress and adversity is crucial because daily family life requires constant adaptation to changing challenging situations. This refers to resilience, which protects parents and children against the development of psychopathology. In light of this, there is an urge for research to underpin programs strengthening family resilience. We will study transmission of stress resilience between mother, father and child, to identify biobehavioral dynamics and factors contributing to resilience transmission in 500 families with children aged between 10 and 12 years. We start from the assumption that resilience transmission is a dynamic process whereby family members mutually affect each other's capacity to recover from stressful events. We predict that resilience transmission is related to biobehavioral family factors such as matching versus discordant family (epi-)genetic and endocrinological profiles, and family climate. We will also investigate whether transmission is linked to biobehavioral synchrony between family members. This latter refers to spontaneous synchronization between parent and child social behavior, their physiology, and between physiology of one and behavior of the other when confronted with stressors. Studying biobehavioral synchrony in the context of resilience transmission is highly innovative. It can lead to scientific breakthroughs, expanding our understanding of resilience and strategies to support families' resilience in the face of distress.

Researcher(s)

• Promoter: Kooy Frank

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Marfan syndrome (MFS) and acromelic dysplasias (AD) are caused by pathogenic variants in the fibrillin-1 (FBN1) gene. Remarkably, whereas MFS is characterized by thoracic aortic aneurysms (TAA), tall stature and arachnodactyly, AD patients present with short stature, brachydactyly, and no aortic involvement. Loss of structural integrity of the microfibrils is proposed as the cause of MFS, while altered protein interactions are thought to be at heart of the pathogenesis of AD. However, the alterations in protein interactions identified so far do not seem to fully explain the AD phenotype. Remarkably, increased transforming growth factor beta (TGF-?) signaling has been observed both in human and murine MFS aortic wall tissue and in fibroblasts of AD patients. As such, the exact functional consequences of AD and MFS mutations on cell signaling pathways remain a matter of debate. The main questions therefore remain: (1) which mechanisms explain why TAA is unique to MFS? And (2) why do heterozygous FBN1 mutations, both leading to increased TGF-? signaling, give rise to opposite skeletal phenotypes? In this project, I want to decipher the divergent pathomechanistic processes underlying these contrasting skeletal and aortic phenotypes by applying multi-omics approaches in murine and human (cellular) models of MFS and AD. The expected results may reveal novel therapeutic targets, which is especially important to treat the life-threatening TAA from which MFS patients are suffering.

Researcher(s)

• Promoter: Loeys Bart
• Co-promoter: Mortier Geert
• Fellow: Peeters Silke

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

COL4A1- and COL4A2-related disorders cause a broad spectrum of problems comprising abnormal brain development, brain hemorrhage at any age, aneurysms (local dilatations) of the brain arteries, but also eye or renal problems. In addition, COL4A1 was recently identified as a genetic modifier in Marfan syndrome. We studied the presence of COL4A1 and COL4A2 variants in two patient cohorts; a cerebral palsy (CP) and a TAA (thoracic aortic aneurysm) cohort. This led to a specific interest in the COL4A2 NC1 domain. A burden analysis demonstrated a statistically significant overrepresentation of COL4A2 NC1 variants in the CP cohort. Furthermore, we identified the NC1 variant p.Arg1662His in 3 TAA patients and 3 CP patients of Moroccan descent. In 5 cases in combination with the helical variant p.Met1355Thr. The latter is suggestive of a shared "risk haplotype". The p.Arg1662His variant was significantly overrepresented in Moroccan patients in our cohorts compared to a Moroccan control cohort. In addition, We will study the cellular effects of NC1 variants using patient fibroblasts in order to assess (1) the levels of endoplasmatic reticulum stress and activation of the unfolded protein response and (2) alterations in Akt-FAK-mTOR signaling and procaspase 8 and 9 expression. Fibroblasts were collected from patients harboring (1) the COL4A2 variant p.Arg1662His, (2) the COL4A2 variant p.Arg1662His in combination with the COL4A2 variant p.Met1355Thr and (3) the pathogenic COL4A2 p.Gly1353Ala as a positive control. Three wild-type fibroblasts are used as negative controls. Secondly, we will develop a zebrafish model to study the effect of COL4A2 NC1 variants. We will start with the introduction of the pathogenic COL4A2 p.Gly1353Ala variant and study the effect on zebrafish development using a fish that has fluorescent blood vessels in order to easily pick up abnormal vessels. We will study the occurrence of brain haemorrhage, changes in movement patterns and the basement membrane, a structure that stabilizes the wall of blood vessels and measure the aortic diameter. When a reliable read-out is identified, we will introduce NC1 variants in the zebrafish model to assess their effect. This project is the first study to investigate the contibution of specific COL4A2 NC1-domain variants in pathology. When our findings are corroborated by functional studies, it would also be the first identification of a population-specific COL4A2-related risk haplotype associated with cerebral and aortic vascular pathology, which is an important finding in the age of personalized medicine. Another novelty is the development and use of a zebrafish model to study functional effects of COL4A2 variants using (CRISPR)/Cas9 technology. The model would enable not only functional analysis of additional variants of unknown significance in cerebrovascular pathology and TAA, but additionally allows studies regarding the pathogenic mechanisms underlying different types of COL4A2-mutations. This will help in identifying potential therapeutic strategies. Eventually, the model is suited for testing of potential treatment strategies in vivo, enabling monitoring of the therapeutic effect, as well as unwanted side-effects.

Researcher(s)

• Promoter: Meuwissen Marije
• Co-promoter: Schepers Dorien
• Fellow: Nemegeer Merlijn

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Inherited Cardiac Arrhythmia (ICA) refers to a group of genetic disorders in which patients present with abnormal and potentially harmful heart rhythm. These episodes often go unnoticed, but can lead to sudden cardiac death. At present, over 60 ICA genes have been identified. Using novel next-generation sequencing technology it is possible to screen all ICA genes in a single molecular diagnostic test. This analysis allows the identification of clear disease-causing variants in patients, but also results in detection of a high number of genetic variants for which causality is unsure. These pose a major burden for the management of ICA patients. Therefore, the aim of this project is to develop a functional tool that allows to test the functional impact of these so-called 'variants of uncertain significance' (VUS). We will create an advanced model of 'human induced pluripotent stem cells (hiPSC)' with built-in special fluorescent proteins that report on calcium and voltage signals. Starting from these hiPSCs we will generate cardiomyocytes, cardiac fibroblasts and endothelial cells that we grow in a controlled mixture into cardiac microtissues (cMT). The electrical activity and calcium handling of these cMTs can then be monitored with a specialized confocal fluorescence microscope. To validate our tool, we will first introduce known disease-causing alterations into the genome of these transgenic hiPSCs and study the effect on the electrical activity of the derived cMTs. Next, we will apply this method to evaluate the functional effect of VUS identified in patients. This innovative approach will improve the molecular diagnostics of inherited cardiac arrhythmias and allow clinicians to deliver true personalized medicine.

Researcher(s)

• Promoter: Alaerts Maaike
• Fellow: Akdeniz Dogan

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Progressive dilatation of the aorta leads to the development of thoracic aortic aneurysms (TAAs), frequently resulting in aortic dissection or rupture. The latter events associate with an ultimate mortality rate of 50% and, hence, represent a prominent cause of morbidity and mortality in the Western population. Prophylactic surgery of TAA patients reduces the mortality rate down to about 5%, but comes with a relatively high risk of complications. Medical therapies capable of stopping or even reversing aneurysm formation are clearly highly needed, but are not available yet. Further deciphering of the mechanisms underlying TAA is essential to develop more efficient drugs. Owing to the advent of -omics technologies, it is now possible to dig into pan-TAA pathomechanisms in a hypothesis-free manner, opening new avenues to discover yet unexplored disease pathways and, hence, novel therapeutic targets. With this project, we want to be the first to take up the challenge of discovering convergent disease-linked pathways for TAA in a hypothesis-free manner using mouse and iPSC-derived cell models. The anticipated findings will advance the pathomechanistic TAA knowledge significantly beyond the current understanding and will greatly facilitate the development of novel therapeutic strategies.

Researcher(s)

• Promoter: Loeys Bart
• Co-promoter: Verstraeten Aline

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Malignant pleural mesothelioma (MPM) is mostly diagnosed in an advanced incurable stage and therefore, there is a need for new sensitive early detection biomarkers. DNA methylation is a promising field for biomarker detection and we are developing a novel technology that can detect tumour specific methylation signatures in a cost-effective manner. Exhaled breath condensates (EBCs) are an interesting novel source of liquid biopsies in MPM, next to classic blood plasma. We have exciting preliminary data showing that EBCs contain DNA fragments representing full genomes which may lead to a first truly non-invasive MPM detection test. We have preliminary data that an MPM specific methylation signature exists and that our new technology for detecting it works. We will further develop and optimise this new technology and validate it in tissue as well as in liquid biopsies such as blood and EBCs.

Researcher(s)

• Promoter: Van Camp Guy

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Thoracic aortic aneurysm (TAA) is an abnormal widening of the thoracic aorta caused by blood vessel wall weakness. TAAs entail a high risk for aortic rupture or dissection, commonly leading to sudden death. This dramatic event may leave family members of the deceased terrified and oblivious. To date, genetic defects in >30 genes have been linked with TAA, providing a molecular cause for about 30% of patients. Their identification and functional characterization have been key in acquiring our current pathomechanistic aortopathy knowledge. Yet, the genetic and mechanistic picture for TAA is far from complete, hampering identification of predictive markers for aneurysm formation and development of therapies capable of stopping or reversing aneurysm formation. In search for novel TAA genes, we most recently identified recessive truncating mutations in IPO8 as a novel cause of syndromic TAA. This project builds on this exciting finding. More specifically, we aim to significantly improve our current TAA pathomechanistic insight and future TAA patient management by (1) aortic phenotyping and functional characterization of an Ipo8 null mouse line, (2) validation of the mouse findings in the human context using patient- and control-derived iPSC-VSMCs, and (3) identifying putative drug compounds for IPO8-related aortopathy using a cell-based matrix metalloproteinase inhibition assay.

Researcher(s)

• Promoter: Verstraeten Aline
• Co-promoter: Luyckx Ilse

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Marfan syndrome (MFS) is an autosomal dominant connective tissue disorder with pleiotropic ocular, skeletal and cardiovascular manifestations. Morbidity and mortality are mostly determined by aortic root aneurysm, dissection and rupture. Although mutations in FBN1, coding for fibrillin-1, are the sole genetic MFS cause, there is a poor correlation between the MFS phenotype and the nature or location of the FBN1 variant. Wide intra- and interfamilial phenotypic variability, ranging from completely asymptomatic to sudden death at young age, is observed. The precise mechanisms underlying this variability remain elusive. In this project, we have selected an innovative strategy to fully understand the functional effects of the FBN1 mutation and discover genetic modifiers of MFS aortopathy with the following objectives: (1) CRISPR/Cas9 correction of the recurrent FBN1 p.Ile2585Thr in patient-derived iPSC-VSMCs and functional comparison to FBN1 mutant and control iPSC-VSMCs. (2) Whole genome and RNA-sequencing of patient iPSC-VSMCs at the extreme ends of the phenotypical spectrum for genetic modifier identification. (3) CRISPR-modification for validation of their modifying capacities. The understanding of the functional effects of the FBN1 mutation and the identification of genetic modifiers will advance the knowledge on aortopathy-mechanisms beyond current understanding, it will allow to individualize treatment protocols and will offer new leads to novel therapeutic targets.

Researcher(s)

• Promoter: Loeys Bart
• Co-promoter: Meester Josephina

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Dynamic mutations, stretches of repetitive DNA sequences that inherit unstably in pedigrees, are an important cause of intellectual disability and autism. In this project, we argue that the number of a specific class of dynamic mutations, the CGG-repeats is grossly underestimated. We focus in on CGG-repeats, as these have already been implicated in multiple disorders and moreover because these induce epigenetic silencing of associated repeats. Using the latest algorithms we will catalogue all repeats in the genome and annotate which ones are potentially prone to expansion. In a large patient cohort, we will search for expansions of any of those repeat. The repeat expansions will be experimentally validated. Up till now, the epigenetic changes accompanying dynamic mutations have been presented as an all or nothing effect. In this application, we will challenge this dogma and will more accurately define epigentic changes associated with the full range of CGG-repeats at several loci in the human genome. In addition, we will define one novel repeat expansion disorder by creating a cellular model and subject this to transcriptomic and neuronal network analysis. In summary, our project will increase our insights in the role CGG-repeats play in the human genome and in neurodevelopmental disease.

Researcher(s)

• Promoter: Kooy Frank
• Co-promoter: Vandeweyer Geert

Research team(s)

• Medical Genetics (MEDGEN)

Project website

Project type(s)

• Research Project

Abstract

Obesity is a complex disorder (with both lifestyle and genetic factors known to play a role in its development) affecting as much as 650 million people worldwide. Moreover, it induces excessive inflammation and oxidative stress and subsequently leads to the development of comorbidities such as non-alcoholic fatty liver disease (NAFLD). With a prevalance of 25% in general population and up to 90% in the obese population, NAFLD is currenty the most common chronic liver disease worldwide. On top of that, it can progress into life-threatening diseases such as liver cirrhosis. However, treatment options remain limited, especially for more advanced disease stages, indicating a need for better disease characterisation including elucidation of genetic risk factors that predispose to its development and early diagnosis. Consequently, in this project, we will investigate the role of the anti-inflammatory and anti-oxidative proteins paraoxonase (PON) 1 and 3, which are highly expressed in liver. To this end, our preliminary results showing a correlation between PON1 and NAFLD in an obesity cohort will be validated in a pon1 knockout model in zebrafish. PON3 will be examined in an in vitro HepG2 cell model and in a human obesity cohort. Ultimately, we will unravel the role of PON1 and PON3 in obesity and obesity-associated liver disease and elucidate the possible underlying mechanisms, being inflammation and oxidative stress.

Researcher(s)

• Promoter: Van Hul Wim
• Fellow: Van Dijck Evelien

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Colorectal cancer (CRC) and breast cancer are amongst the most common and deadliest cancers worldwide. Early detection through current screening programs for both cancers have reduced mortality, but important limitations of these methods, such as limited sensitivity, limited specificity and invasiveness, remain. There is a need for a new, minimally-invasive, cost-effective and very sensitive diagnostic test for screening and early cancer detection. Methylated circulating tumor DNA (metctDNA) biomarkers have shown great potential to discriminate between normal tissue and tumors. MetctDNA can be detected in a minimally-invasive manner using liquid biopsies, such as plasma. Currently, DNA methylation is studied using bisulfite conversion followed by next-generation sequencing or droplet digital PCR. However, disadvantages including DNA degradation, non-optimal sensitivity and specificity of subsequent techniques and limited multiplex capacities still need to be overcome. At this moment, there exists no efficient technique for the simultaneous analysis of several methylated regions in ctDNA in one assay. In our research group, we aim to develop a new, sensitive multi-region metctDNA based bisulfite-free detection technique. The technique will be used in this project to detect differential methylation signatures between normal tissue, pre-cancerous lesions and tumors. With this approach, we aim to develop a new and better assay for screening and detection of CRC and breast cancer.

Researcher(s)

• Promoter: Van Camp Guy
• Co-promoter: Op de Beeck Ken
• Co-promoter: Peeters Marc
• Co-promoter: Van Hal Guido
• Fellow: Neefs Isabelle

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Loeys-Dietz syndrome (LDS) is a genetic disorder presenting with thoracic aortic aneurysm (TAA), causing abnormal widening of the aorta, which leads to aortic rupture or dissection, a life-threatening complication that occurs unexpectedly. LDS is caused by genetic defects in six different genes of the TGF? pathway (TGFBR1/2, SMAD2/3, TGFB2/3), which is vital in the proper development of the body's connective tissue. Despite the progress in unraveling its genetic basis, there is a lack of understanding of the wide range of severity of cardiovascular involvement. In my project, I will focus on patients within families, carrying pathogenic SMAD3 variants, which show either no or early-onset aortic aneurysmal disease. I hypothesize that genetic modifiers of the primary SMAD3 mutation are the main contributors to the striking aortopathy variability in LDS-SMAD3 families. In this project, an innovative strategy will be used to identify genetic modifiers. I will perform genome-wide single nucleotide polymorphism-based linkage analysis on two large SMAD3 families and whole-genome sequencing on selected individuals, combined with SMAD3 iPSC-VSMC (induced pluripotent stem cell-derived vascular smooth muscle cells) model creation and characterization and subsequent CRISPR/Cas9-based validation of the identified modifier(s). The predicted outcomes will advance the LDS and TAA knowledge, contributing to the discovery and development of novel therapeutic targets and personalized medicine.

Researcher(s)

• Promoter: Loeys Bart
• Co-promoter: Alaerts Maaike
• Co-promoter: Verstraeten Aline
• Fellow: Velchev Joe Davis

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Brugada syndrome (BrS) is an inherited arrhythmic disorder and is estimated to account for up to 12% of all sudden cardiac death cases, especially in the young (< 40 years old). Only in circa 30% of BrS patients the underlying genetic cause can be identified with current diagnostic arrhythmia gene panels. Moreover, the use of these panels result in detection of numerous genetic "Variants of Uncertain Significance" (so called VUS), but currently functional models to prove their causality are lacking. Therefore, in my project I will create two proof-of-concept models for a known pathogenic CACNA1C mutation associated with BrS: a cardiomyocyte cell model, created from human stem cells, and a novel transgenic zebrafish model with built-in fluorescent calcium and voltage indicators. By functionally characterising these models with innovative imaging and electrophysiological techniques, I will assess the mutation's effect on a cellular level and in the whole heart, proving its contribution to disease causation. After validating these models, I will apply this strategy to functionally assess the pathogenicity of two VUS identified in two BrS patients. Ultimately, by establishing the use of these state-of-the-art study models to predict the pathogenicity of BrS-related VUS, a more accurate risk stratification and proficient use of specialized prevention strategies can be implemented in the future, potentially also for other electrical disorders of the heart.

Researcher(s)

• Promoter: Loeys Bart
• Co-promoter: Alaerts Maaike
• Co-promoter: Knapen Dries
• Co-promoter: Labro Alain
• Co-promoter: Schepers Dorien
• Co-promoter: Snyders Dirk
• Fellow: Vandendriessche Bert

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

My mission is to consolidate and expand my cardiogenetics research group of the University of Antwerp as a center of excellence that aims to identify the genetic causes and underlying pathogenetic mechanisms of both common and rare genetic disorders affecting the cardiovascular system, in particular aortic aneurysmal disorders and primary inheritable arrhythmias. It will be the ultimate goal to translate our genetic and pathomechanistic discoveries into an improvement of the quality of life of patients.

Researcher(s)

• Promoter: Loeys Bart
• Fellow: Loeys Bart

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

This project aims to upgrade the current electrophysiology technologies at UAntwerpen by acquiring a state-of-the-art MicroElectrode Array platform (MEA). To study the electrophysiological properties of excitable cells, currently patch-clamping is the gold standard. However, this is an extremely labour-intensive and invasive technique, limited to short-term measurements of individual cells at single time points. On the other hand, MEAs enable high-throughput non-invasive longitudinal real‐time measurements of functional cellular networks, without disrupting important cell-cell contacts, and thus provide a more physiologically relevant model. The multi-well format allows repeated recordings from cell cultures grown under various experimental conditions, including the opportunity to rapidly screen large drug libraries. Based on these advantages, multi-well MEAs are the most suitable instrument for functionally elucidating the pathomechanisms of neurological/cardiac disorders by performing (1) cardiac activity assays: measurement of field and action potentials from (iPSC-)cardiomyocytes to investigate wave-form, propagation and irregular beating; (2) neural activity assay based on three key measures: frequency of action potential firing, synchrony as measure for synaptic strength and oscillation as hallmark for neuronal organization in time; (3) (iPSC-)vascular smooth muscle contractility assay based on impedance alterations.

Researcher(s)

• Promoter: Loeys Bart
• Co-promoter: Kooy Frank
• Co-promoter: Labro Alain
• Co-promoter: Ponsaerts Peter
• Co-promoter: Rademakers Rosa
• Co-promoter: Snyders Dirk
• Co-promoter: Timmerman Vincent
• Co-promoter: Weckhuysen Sarah

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Cardiovascular diseases are worldwide the leading cause of mortality (31% of all deaths, WHO) and disability. These diseases include heart failure, coronary artery disease, hypertension, cerebrovascular and peripheral vascular diseases. Dysfunction of endothelial cells (ECs) lining the inner wall of the vasculature is a major initiator that fuels the progression of cardiovascular disease. Mutations in genes encoding different components of the bone morphogenetic protein (BMP) pathway cause various severe vascular diseases such as hereditary hemorrhagic telangiectasia (HHT), bicuspid aortic valve with thoracic aortic aneurysms (BAV/TAA) and pulmonary arterial hypertension (PAH) (Goumans et al., Cold Spring Harbor Persp. Biol. 2018). BMPs are secreted factors that belong to the larger transforming growth factor (TGF)β family. Signaling by BMPs contributes to the morphological, functional and molecular differences ('heterogeneity') among ECs in different vessel types like arteries, veins, lymphatic vessels and in different organs. Understanding how BMP signaling co-regulates EC heterogeneity in homeostasis and how its deregulation can contribute to disease is key to obtain insights in the genesis of vessel-type restricted disorders and design improved disease-tailored therapies with reduced side effects. The BMP pathway is an important therapeutic target in vascular disease, with several BMP modulators being used already in clinic. The BMP signaling output critically depends on the cellular context in the vessel wall which includes flow hemodynamics, inflammation, interplay with other "vascular" signaling cascades and the interaction of ECs with peri-endothelial cells and surrounding matrix. The BMP community – which has long remained bone-centered – is joining forces relatively recently in vascular biology within Europe. We feel momentum to team-up with the present multidisciplinary network consortium consisting of 8 'Flemish' teams from 3 Universities (A. Zwijsen (KUL1), E.A. Jones (KUL2), B. Loeys/A. Verstraeten (UA), A. Luttun (KUL3), R. Quarck/M. Delcroix (KUL4), P. Segers (UGent) and H. Van Oosterwyck (KUL5),) and 6 external teams (M.J. Goumans (NL1), F. Itoh (JP), P. Knaus (DE), F. Lebrin (NL2/FR2), G. Valdimarsdottir (IS) and M. Vikkula (BE)) to jointly address how i) dysfunctional BMP pathways contribute to vessel (instability) diseases, ii) how impaired BMP signaling affects mechanobiology (interpretation of flow, cellular tractions, matrix stiffness) in the vessel wall and iii) validate promising BMP-based vessel repair strategies across our different models. The various partners of this WOG network study different aspects of BMP/TGFβ signaling and/or vascular (mechano)biology and disease (see further). Within this multidisciplinary consortium, we aim to accelerate the unraveling of BMP-mediated mechanisms of EC heterogeneity and mechanotransduction to refine and improve etiology-based vascular repair strategies, a major challenge in curing vessel-related diseases. Our objectives are to: i) increase critical mass in Flanders on BMP signaling and its interplay with mechanotransduction in vascular diseases and boost trans- and interdisciplinary collaborations within this consortium, to underscore faster commonalities and specificities of (impaired) BMP functions in different vascular beds and vessel (instability) diseases; ii) model and validate vessel normalization strategies in our various physiopathological systems and translate results to a clinical setting; iii) create an "incubator" environment and solid basis for future successful funding applications (leverage); iv) expose and challenge each other's work at an early stage to strengthen and increase research output and competitiveness; v) increase visibility of all the teams in Flanders and internationally, propel the junior talents in the teams and deliver high-quality trained PhDs/masters/bachelors.

Researcher(s)

• Promoter: Loeys Bart

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Cardiovascular diseases are worldwide the leading cause of mortality (31% of all deaths, WHO) and disability. These diseases include heart failure, coronary artery disease, heart disease, hypertension, cerebrovascular and peripheral vascular diseases. Dysfunction of endothelial cells (ECs) lining the inner wall of the vasculature is a major initiator that fuels the progression of cardiovascular disease. Mutations in genes encoding different components of the bone morphogenetic protein (BMP) pathway cause various severe vascular diseases such as hereditary hemorrhagic telangiectasia, bicuspid aortic valve with thoracic aortic aneurysms and pulmonary arterial hypertension. BMPs are secreted factors that belong to the larger transforming growth factor (TGF)β family. Signaling by BMPs contributes to the morphological, functional and molecular differences ('heterogeneity') among ECs in different vessel types like arteries, veins, lymphatic vessels and in different organs. Understanding how BMP signaling co-regulates EC heterogeneity in homeostasis and how its deregulation can contribute to disease is key to obtain insights in the genesis of vessel-type restricted disorders and design improved disease-tailored therapies with reduced side effects.

Researcher(s)

• Promoter: Verstraeten Aline

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Neurodevelopmental disorders (NDD) are disorders which affect learning ability. Since genetic defects in many genes are linked to NDD's, diagnosis and treatment are difficult. Moreover, for the majority of NDD patients, the genetic cause remains unknown. However, there is growing evidence that for different NDDs a common molecular pathway is affected. For example, there is an enrichment of genes involved in chromatin remodelling. Disorders caused by mutations in genes regulating chromatin remodelling are called chromatinopathies. In this project, we want to study five distinct chromatinopathies: Kabuki, Kleefstra, Gabriele-de Vries, Helsmoortel-Van der Aa and a syndromic type of autism caused by mutations in KMT2D, EHMT1, YY1, ADNP and CHD8 respectively. The rationale for studying these five disorders is that the corresponding genes are involved in shared biological processes and that they have overlapping clinical features. We thus hypothesize that mutations in these five genes give rise to unique as well as common downstream effects in gene transcription and translation.

Researcher(s)

• Promoter: Kooy Frank
• Co-promoter: Vandeweyer Geert
• Fellow: Van Rossem Kirsten

Research team(s)

• Medical Genetics (MEDGEN)

Project website

Project type(s)

• Research Project

Abstract

Marfan syndrome (MFS) is an autosomal dominant connective tissue disorder with pleiotropic ocular, skeletal and cardiovascular manifestations. Morbidity and mortality are mostly determined by aortic root aneurysm, dissection and rupture. Although mutations in FBN1, coding for fibrillin-1, are the sole genetic MFS cause, there is a poor correlation between the MFS phenotype and the nature or location of the FBN1 variant. Wide intra- and interfamilial phenotypic variability, ranging from completely asymptomatic to sudden death at young age, is observed. The precise mechanisms underlying this variability remain elusive. In this project, I have selected an innovative strategy to fully understand the functional effects of the FBN1 mutation and discover genetic modifiers of MFS aortopathy with the following objectives: (1) CRISPR/Cas9 correction of the recurrent FBN1 p.Ile2585Thr in patient-derived iPSC-VSMCs and functional comparison to FBN1 mutation and control iPSC-VSMCs. (2) Whole genome sequencing, and RNA-seq of patient iPSCVSMCs at the extreme ends of the phenotypical spectrum for genetic modifier identification. (3) CRISPR-modification for validation of their modifying capacities. The understanding of the functional effects of the FBN1 mutation and the identification of genetic modifiers will advance the knowledge on aortopathy-mechanisms beyond current understanding, it will allow to individualize treatment protocols and will offer new leads to novel therapeutic targets.

Researcher(s)

• Promoter: Loeys Bart
• Co-promoter: Verstraeten Aline
• Fellow: Van Den Heuvel Lotte

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Connective tissue disease (CTD) refers to a large and diverse group of disorders affecting the protein-rich tissues that support our body's organ systems. Patients most typically present with skin, spinal cord, eye, heart, blood vessel and/or skeletal manifestations. CTDs can either be inherited or provoked by environmental factors. With respect to hereditary CTD, an increasing number of genetic causes has been discovered over the past ten years owing to the advent of high-throughput DNA sequencing technologies. In-depth investigation of these defects' molecular mode of action at the cellular and tissue level is now increasingly needed in order to complete the mechanistic CTD puzzles and to facilitate the development of novel drug therapies. I will establish a research group that aims to address these CTD needs, with a primary focus on thoracic aortic aneurysm and dissection (TAAD) and skeletal dysplasia. TAAD denotes an abnormal widening and/or rupture of the largest human artery, i.e. the aorta, and entails a high risk for sudden death due to severe internal bleeding. It is estimated to account for 1-2% of all deaths in the Western population. Skeletal dysplasias are a group of more than 200 disorders that affect bone and cartilage growth, resulting in abnormal skeleton shape and size. At first glance, these two conditions might seem oddly dissimilar. From a molecular point of view they have quite a lot in common though. Different defects in a set of genes have been shown to cause both TAAD and skeletal dysplasia. Moreover, significant overlap exists with regard to the yet described dysregulated subcellular processes. By comprehensively studying the entire disease continuum, I will contribute synergistically to a better understanding of the disease mechanisms and, hence, the treatment of both separate clinical entities. Three major strategic research pillars have been defined on which I desire to concentrate: (1) identification of the DNA variants that explain why some subjects carrying a certain disease-causing genetic defect are more severely affected than others with that identical defect (i.e. modifier variants); (2) elucidation of the molecular mode of action of disease-causing and disease-modifying genetic variants; and (3) discovery of novel disease-remedying drug compounds as well as the genetic determinants that explain variation in drug response between patients. The experimental set-up will be determined in a project-by-project manner, but will typically involve high-throughput DNA, RNA and/or protein analyses (-omics) as well as classical molecular biology strategies in relevant mouse and induced pluripotent stem cell (iPSC)-derived models. IPSCs are somatic cells (e.g. from skin or blood) that have been reprogrammed to pluripotent cells, and can be differentiated into virtually any cell type of interest. Patient- and control-derived iPSC-vascular smooth muscle cells and iPSC-chondrocytes will be used (i.e. relevant TAAD and skeletal dysplasia cell types, respectively) because of limited access to their native counterparts.

Researcher(s)

• Promoter: Verstraeten Aline
• Fellow: Verstraeten Aline

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

GENOMED is an interfaculty consortium of four research groups and Center of Excellence at the University of Antwerp. The general aim of GENOMED is to enhance genetic research in biomedical sciences by application of state-of-the-art technologies such as next generation sequencing (NGS), induced pluripotent stem cells (iPSC) and gene editing (CRISPR/Cas). In the past few years, GENOMED has focused on exome sequencing which has led to new gene discoveries but now anticipates that whole genome sequencing (WGS) will become the next standard genetic analysis and an essential step towards personalized medicine. The future research within GENOMED will focus on two major challenges: first, the development of technologies that allow better understanding of the biological meaning of both coding and noncoding genetic variants in the human genome, and second, the translation of these new genetic findings into better diagnostics and treatment. At present, the major bottleneck with NGS is the ability to distinguish causal mutations from benign variants. The study of the functional effect of these variants will be key in the understanding of the disease biology but also necessary for the translation into personalized medicine. It will require robust and efficient systems to explore the functional consequences of these variants by using in vitro cell cultures (especially iPSC) and/or animal models (mouse, zebrafish) that are representative for the human disorder. To address the second challenge, the consortium will establish collaborations with clinicians and industry to transfer genetic knowledge into biomarkers and to translate the new genetic insights into innovative therapies.

Researcher(s)

• Promoter: Loeys Bart
• Promoter: Mortier Geert
• Co-promoter: Kooy Frank
• Co-promoter: Loeys Bart
• Co-promoter: Van Camp Guy
• Co-promoter: Van Hul Wim

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

The maintenance contracts for our NGS devices (MiSeq and HiSeq1500) are partly covered by BOF funding. These devices were gained by Hercules funding. They make next generation sequencing for research purposes possible.

Researcher(s)

• Promoter: Loeys Bart
• Promoter: Mortier Geert

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

We apply for BOF support for involvement of Catalyze for an application in Call topic: Horizon Europe - EIC pathfinder Challenge: Cardiogenomics (HORIZON-EIC-2022-PATHFINDERCHALLENGES-01-03) Deadline October 19, 2022 Anticipated evaluation outcome: March 2023 Start project: July 2023

Researcher(s)

• Promoter: Loeys Bart

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

A progressive widening of the aorta (called aortic aneurysm) affecting our body's main blood vessel in the chest (thorax) can lead to a catastrophic event with a tear or rupture of the aortic wall (dissection or rupture). Unfortunately, a thoracic aortic aneurysm most often remains asymptomatic until catastrophic dissections or ruptures happen. These latter complications are a major cause of sudden cardiac death in the western world. Currently, aortic aneurysms are mostly detected incidentally upon imaging studies for other medical indications. Although not perfect, follow-up of the diameter of the aorta by imaging studies is considered the best predictor of the aortic dissection risk. At present, there are no markers in the blood (called biomarkers) that can predict the presence of a thoracic aortic aneurysm or the occurrence of a thoracic aortic dissection. Identification of such a biomarker would be of great help in the faster and easier diagnosis and follow-up of thoracic aortic aneurysm and dissection. Upon investigation of aneurysmal aortic gene expression profiles of three different symptomatic mouse models of Marfan and Loeys-Dietz syndrome, we observed high expression of a novel gene in all three models. This gene encodes for a growth factor that has not previously been associated with the pathogenesis of thoracic aortic aneurysm. Although the molecule has been linked to metabolism and cancer, its highest expression is in the aortic wall. In this study we would like to investigate if serum levels of this growth factor in Marfan and Loeys-Dietz syndrome mice correspond to their thoracic aortic aneurysm severity and progression. We will validate the findings in serum samples of patients with thoracic aortic aneurysm and dissection. If successful, the latter model can be used in future projects to test therapeutic compounds with the "simple" measurement of the levels of this growth factor as the outcome parameter. In summary, if successful our project will provide the strong foundations of future research that will further explore whether serum levels of this growth factor can detect asymptomatic thoracic aortic aneurysm, monitor disease progression and predict aortic dissection.

Researcher(s)

• Promoter: Loeys Bart
• Co-promoter: Verstraeten Aline

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Marfan syndrome (MFS) and acromelic dysplasias (AD) are caused by pathogenic variants in the fibrillin-1 (FBN1) gene. Remarkably, whereas MFS is characterized by aortic aneurysms and dissections, tall stature and arachnodactyly, AD patients present with short stature, brachydactyly, and no aortic involvement. To date, the divergent pathophysiological mechanisms explaining these contrasting phenotypes remain largely unknown. Loss of structural integrity of the microfibrils is proposed as the cause of MFS, while altered protein-protein interactions to the TB5 domain of FBN1 are thought to be at heart of the pathogenesis of AD. However, the alterations in protein interactions identified so far do not seem to fully explain the AD phenotype. Remarkably, increased transforming growth factor beta (TGF-β) signaling has been considered both in human and murine MFS aortic wall tissue and in fibroblasts of AD patients. As such, the exact functional consequences of the AD and MFS mutations on cell signaling pathways remain a matter of debate to date. The main questions remain: (1) why aortic disease is unique to MFS and (2) what is the exact role of the TB5 domain of FBN1? In this project, I want to decipher the pathomechanistic processes underlying these distinct aortic phenotypes by applying multi-omics approaches in murine and human (cellular) models of MFS and AD. The expected results may reveal novel (preventive) therapeutic targets, which is important to treat the life-threatening aortic aneurysms from which MFS patients are suffering.

Researcher(s)

• Promoter: Peeters Silke

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Progressive dilatation of the aorta leads to the development of thoracic aortic aneurysms, which are often asymptomatic but predispose to aortic dissection and rupture. The latter are associated with high mortality rates. In 2017, I identified loss-of-function (LOF) mutations in BGN, an X-linked gene, as a novel cause of a severe syndromic form of thoracic aortic aneurysms and dissections (TAAD) and is now designated as Meester-Loeys syndrome (MRLS). The general aim of this proposal is to identify which cell type is the main driver of the development of syndromic TAAD in patients with a BGN mutation. This key question will be addressed by taking advantage of the innovative single cell RNA-sequencing approach in a BGN knock-out mouse model.

Researcher(s)

• Promoter: Meester Josephina

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

This is a gift that was awarded to expand our work on the Helsmoortel Van der Aa syndrome. It has been used, among other things, to facilitate the Neurodevelopmental disorders conference of September 2022.

Researcher(s)

• Promoter: Kooy Frank

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Cerebral palsy (CP) is a clinical descriptive term that defines a heterogeneous group of non- progressive, neurodevelopmental disorders of motor impairment, which co-occur with a wide range of medical conditions, such as intellectual disability (ID), speech and language deficits, autism, epilepsy and visual and/or hearing impairment. It is the most frequent cause of motor impairment in children, with an important impact on quality of life and a prevalence ranging from 1.5 to 2.5 in 1000 live births. The causes of CP are quite variable. Recent studies demonstrate an important contribution of genetic causes. However, a common mechanism of action of the genes associated with CP is largely unknown. This prompted us to perform genetic analysis in our CP-patient cohort using Single Nucleotide Polymorphism (SNP) array and Whole Exome Sequencing (WES). In this project, we investigate the hypothesis that a subset of genetic causes of CP affect ATG9A transport and subsequently lead to a dysregulation of autophagy. Autophagy is a self-degradative cellular process that removes redundant/dysfunctional proteins, organelles or pathogens. Autophagy was already demonstrated to be an important neuroprotective mechanism against hypoxia-ischemia and glutamate excitotoxicity in animal models. This hypothesis is based on: 1. The important contribution of pathogenic de novo missense variants in KIF1A in our CP cohort (identified in 7/ 141 CP cases). KIF1A is a member of the kinesin motor protein family and is responsible for cargo transport along microtubular tracts. A major cargo of KIF1A is ATG9A, a key regulator of autophagy induction at the presynaptic synapses. 2. In the AP-4 deficiency syndrome, the first known genetic cause of CP, mislocalisation of ATG9A was already demonstrated to be the causal mechanism for the CP phenotype. 3. The identification of likely pathogenic variants in known CP genes (KIF5C) and interesting novel CP candidate genes (KLC3, KLC4, MAP7D2, MAP7D3) that may affect ATG9A transport. In the project, we will study the effect of 1) KIF1A variants and of 2) variants in other CP (candidate) genes on ATG9A and the autophagy process in patients' and controls' fibroblasts. Furthermore, we perform RNA-sequencing in blood and fibroblasts to determine a common expression profile leading to an "autophagy dysregulation" signature. This signature could have important future clinical relevance in screening for potential autophagy dysregulation and monitoring future treatment strategies targeting autophagy.

Researcher(s)

• Promoter: Meuwissen Marije
• Fellow: Thys Liene

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Many advances in systemic therapies have significantly improved the survival of patients with metastatic colorectal cancer (mCRC). However, there is a high variability of therapeutic responses among patients and determining the optimal personalized treatment plan is challenging. Conventional monitoring of the therapy response is based on imaging as suggested in RECIST 1.1 and measurements of tumormarkers (e.g. CEA) derived from plasma. However, radiological assessments are usually limited in frequency (radiation exposure, costs, logistics,…), have a detection limit, are not suited for small metastases and cannot describe intrinsic characteristics of each tumor. Therefore, other predictive biomarkers of treatment outcomes and disease progression are of great value to enable early therapy response evaluation and early change of therapy avoiding unnecessary side effects, enhancing efficacy and minimizing costs. Quantification of ctDNA in real-time renders information on tumor characteristics and has been shown to be associated with treatment responses in mCRC. Recently, our research group has shown that quantifying ctDNA through the methylation analysis of NPY in circulating DNA is a good marker for total tumor burden and can therefore be used for the follow-up of mCRC patients. It could be demonstrated that the amount of circulating tumor DNA (ctDNA) in plasma, measured using NPY ddPCR methylation assays, decreased immediately (14 days) after treatment start. The amount of ctDNA remained low or undetectable in patients undergoing curative metastasectomy, while the amount of ctDNA increased in patients showing progressive disease. As progressive disease might be detected earlier using liquid biopsies as compared to observations by radiographic evaluation, the use of liquid biopsies might be a promising tool to guide treatment options. The aim of this study is to determine the optimal cutoff value of the liquid biopsy test (using a ROC curve based on the data of this study). This cutoff value will be used in a follow-up study to detect progressive disease in patients with metastatic colorectal cancer treated with first-line FOLFOX/FOLFIRI and panitumumab. Additionally, the follow-up trial will determine if ctDNA detects progression earlier than conventional used imaging techniques and will estimate the effect on progression-free survival in case therapy is guided by NPY methylation levels in liquid biopsy. Furthermore, in the LEAD-IN FOLICOLOR Trial we will exploratively compare liquid biopsies to tumor markers (CEA and/or CA19.9) in their ability to predict progressive disease. This innovative study will add evidence to the clinical relevance of ctDNA during treatment.

Researcher(s)

• Promoter: Van Camp Guy

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Each year, an estimated 8.2 million people die of cancer. With appropriate detection methods and treatment, many of these deaths would be avoidable. Due to the high incidence and mortality rates, early and accurate diagnosis is paramount for a quick and adequate treatment of patients. Until recently, no truly non-invasive diagnostic methods for the detection of cancer existed. An attractive novel method is the detection of abnormally expressed biological markers manifested during carcinogenesis in so called "liquid biopsies". Liquid biopsy is a technique in which non-solid biological tissues such as urine, stool or peripheral blood, are sampled and analysed for disease diagnosis. The analysis of Circulating tumor DNA (CtDNA) in cancer patients is not new and has been performed in the past. However, until now, a strong focus existed on the detection of tumor specific mutations, which has several limitations. The use of methylation markers instead of mutation markers has many advantages and is understudied. We have recently published GSDME as a highly sensitive and specific methylation biomarker for both breast and colorectal cancer. We wish to build upon these data and extend our search for suitable cancer detection biomarkers genome wide. One of the problems with liquid biopsy nucleic acid biomarkers is the limited sensitivity for early detection. Indeed, in early stages of carcinogenesis, many tumor types have low concentrations of CtDNA. Sensitivity can be increased by measuring a multitude of markers simultaneously. However, to date, no efficient techniques exist that allow multi-region methylation analysis in plasma. Therefore, in this project, we will design a novel technique, next generation high resolution methylation detection in plasma of cancer patients and develop a novel multi-region pan-cancer detection assay, based on genome wide methylation tumor data. We believe that this novel technology is able to increase sensitivity 100 - 1000 fold while reducing the cost more than a 100 fold compared to the standard technologies that are used nowadays. Finally, we will validate our novel technique and assay in clinical samples.

Researcher(s)

• Promoter: Van Camp Guy
• Co-promoter: Fransen Erik
• Co-promoter: Peeters Marc

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

The aorta is the body's main artery and supplies oxygenated blood to all parts of the body. A dilatation of the thoracic aorta leads to the development of thoracic aortic aneurysms (TAA). These weakened regions are vulnerable to tearing and this often results in sudden death. In 2016, we identified BGN (Biglycan) as a novel cause of a severe form of TAA, which is now called Meester-Loeys syndrome (MLS). In parallel with our observations, different mutations in BGN were described as the cause of X-linked spondylo-epi-metaphyseal dysplasia (X-SEMD), which is characterized by short stature. Based on the current knowledge, it remains unknown which mechanisms explain why some mutations in BGN lead to X-SEMD and others lead to MLS and why only MLS patients with BGN deletions also develop skeletal symptoms. This project aims to answer these questions by addressing the following objectives: (1) characterization of the disease phenotypes and pathomechanisms in dedicated mouse models of TAA and X-SEMD, (2) the verification of the functional differences between BGN mutations causing MLS versus X-SEMD in a human cell model and (3) the identification of the role of an alternative splice form of the biglycan protein in the development of skeletal features in MLS.

Researcher(s)

• Promoter: Loeys Bart
• Co-promoter: Meester Josephina
• Co-promoter: Mortier Geert

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Each year, an estimated 8.2 million people die of cancer. With appropriate detection methods and treatment, many of these deaths would be avoidable. However, current methods for detection and analysis of treatment response still suffer from major disadvantages. An attractive novel method is the detection of abnormally expressed biological markers manifested during carcinogenesis in so called "liquid biopsies". Liquid biopsy is a technique in which non-solid biological tissues such as urine, stool or peripheral blood, are sampled and analysed for disease diagnosis. The analysis of CtDNA (DNA originating from the tumor and present in the blood) in cancer patients is not new and has been performed in the past. However, until now, a strong focus existed on the detection of tumor specific mutations, which has several limitations, such as limited sensitivity. The use of methylation markers instead of mutation markers has many advantages, such as a potentially much higher sensitivity, and is understudied. We have recently published GSDME as a highly sensitive and specific methylation biomarker for both breast and colorectal cancer. In addition, we have analyzed 12 additional frequent cancer types, and we have strong preliminary data that GSDME is about equally sensitive in each of these 14 tumor types analyzed. These data show that GSDME has strong potential as the first true pan-cancer biomarker. In part A of the project, we will focus on GSDME, and test it as a true biomarker in a clinical setting. Next to detection markers, there is also a need for better follow-up markers. Follow-up of cancer patients is currently performed based on clinical, radiologic and tumor marker evaluation, which has limitations. Better follow-up markers have the potential to detect resistance or disease progression earlier. We aim to expand further on these concepts and conduct a clinical trial where we will evaluate the use of GSDME methylation analysis in liquid biopsies as a tool to guide treatment in metastatic colorectal patients and to explore whether GSDME has potential as a follow up biomarker (WP2). Moreover, GSDME has an interesting physiological function. Recent papers have identified Gasdermins, including GSDME, as a completely new type of regulated cell death executioners (RCD). Recently, it was proven that the N-terminal part of GSDME induces RCD through pore-formation and this is a key antitumor mechanism that is inactivated in several tumor types. In a third work package of part A, we will further investigate these fundamental aspects of the GSDME gene and study its involvement in carcinogenesis. One of the problems with liquid biopsy nucleic acid biomarkers is the limited sensitivity for early detection. Indeed, in early stages of carcinogenesis, many tumor types have low concentrations of CtDNA. Sensitivity can be increased by measuring a multitude of markers simultaneously. However, to date, no efficient techniques exist that allow multi-region methylation analysis in plasma. Therefore, in part B of this project, we will design a novel technique that is able to do this. In a previous unpublished analysis, we have shown that the cancer methylome contains a multitude of differentially methylated makers, that hold the potential to be used as pan-cancer biomarkers, and we have developed a bioinformatics analysis pipeline to detect and rank these according to their discriminating power. Using these data, we will develop a novel multi-region pan-cancer detection assay using our novel technique. We believe that our technology is able to increase sensitivity 100 - 1000 fold while reducing the cost more than a 100 fold compared to the standard technologies that are currently used for CtDNA biomarkers. Finally, we will validate our novel pan-cancer detection assay in the clinical samples that were collected in part A.

Researcher(s)

• Promoter: Van Camp Guy
• Co-promoter: Fransen Erik
• Co-promoter: Peeters Marc

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Sudden death in the young is primarily caused by inherited diseases of the heart. These conditions are frequently caused by mutations in genes responsible for maintaining a regular heartbeat. Many genes that can cause sudden death have already been identified. However, for an important portion of patients, the genetic test reveals a genetic variant with unknown significance. With this project, we intend to create a new model to study the effects of these mutations on the heart in vivo. We will generate a new zebrafish line, in which cardiac electrical and chemical calcium signals will be converted into fluorescent light signals. As zebrafish are translucent during the first days of development, this animal model lends itself perfectly to visualize these signals in vivo. We will use the new zebrafish line to improve our understanding of one specific cardiac disorder, catecholaminergic polymo hic ventricular tachycardia (CPVT). This condition is characterized by abnormal calcium signaling in the heart, and as such our method will be highly suitable to study CPVT. Both in the literature and in our own cardiogenetics clinic, several CPVT families with an uncertain inheritance pattern have been discovered. With my assay we intend to expose the mechanisms of CPVT in these families and hereby clarify the results of the genetic tests and contribute to future diagnostic testing in CPVT.

Researcher(s)

• Promoter: Schepers Dorien

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

With an estimated 8.8 million deaths yearly, the cancer burden weighs heavily on populations globally. Early detection of cancer is one of the key aspects that results in improved patient prognosis. In this respect, the analysis of circulating tumor DNA in plasma is potentially a major enhancement over currently used imaging, immunochemincal or histopathological methods. Highly sensitive and specific biomarkers for the most common types of cancer are currently still lacking however. In light of recent publications, DNA methylation holds great promise as a tumour marker, but it is yet to be fully explored in the context of liquid biopsies. Our preliminary data shows that CpG methylation can be used to effectively detect cancer and determine different tumors. Our research group is developing a new, robust, and cost-effective diagnostic assay using methylation markers, termed MeD-smMIPs-seq. This assay will combine methylated DNA sequencing with single molecule molecular inversion probes to target highly informative CpGs and achieve high diagnostic sensitivity while reducing assay costs. The aim of this project is first to identify the most informative differentially methylated regions genome-wide, that can be used as cancer biomarkers in this assay. Secondly, we aim to develop the bioinformatics framework required for new experimental design and downstream data analysis. Finally, we will validate the assay and the computational pipeline in the context of liquid biopsies.

Researcher(s)

• Promoter: Van Camp Guy
• Co-promoter: Peeters Marc
• Fellow: Ibrahim Joe

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Despite the unprecedented number of recent novel disease gene identifications in neurodevelopmental disorders such as intellectual disability, autism, or schizophrenia, our understanding of the pathogenicity mechanisms and associated clinical spectra are limited. We are an existing, established and productive ERA-NET neuron consortium. In our ongoing network, we studied mutations in ADNP, originally identified as a gene involved in syndromic autism, using a suite of cellular and animal models and tools developed. Since our results obtained in the ongoing project indicated a much broader clinical phenotype than anticipated and linking ADNP to multiple dimensions of epigenetic regulation, we now propose to apply our resources to investigate the involvement of the epigenome in the phenotypical presentation of mental disorders, using ADNP as a model. Our work will be based on the materials we generated in the ongoing application, including unique cellular and specifically for this project created animal models of the disorder. The work plan consists of six work packages, including disease characterization in patients and animal models, transcriptomics and epigenomics, functional analysis, mosaicism analysis, data integration and preclinical drug testing. These results will enable a full characterization of the consequences of the ADNP mutation that can be linked to the specific aspects of the diseases caused by ADNP mutations.

Researcher(s)

• Promoter: Kooy Frank

Research team(s)

• Medical Genetics (MEDGEN)

Project website

Project type(s)

• Research Project

Abstract

Heterozygous missense mutations in the collagen type II-encoding gene COL2A1 explain about 95% and 70% of the hypochondrogenesis and spondyloepiphyseal dysplasia congenita patients, respectively, as well as a smaller fraction of patients with closely related phenotypes. Prior functional characterization of iPSC-derived and transdifferentiated chondrocytes of carriers of COL2A1 missense mutations revealed increased expression of endoplasmatic reticulum (ER) stress and apoptosis markers in addition to reduced levels of cartilage matrix proteins. Abnormal procollagen folding is considered a key pathogenic skeletal dysplasia mechanism, rendering chaperone-oriented therapy an interesting pharmacological avenue. Subjecting iPSC-chondrocytes of a COL2A1 glycine substitution carrier to a drug library comprising roughly 2,400 chaperone agonists and antagonists, we aim to identify a highly potent novel drug for skeletal dysplasias attributed to COL2A1 missense mutations. To evaluate the compounds' efficiency in restoring the cellular phenotype, integrated high content quantification of collagen type II as well as apoptosis and ER stress markers will be done. The most interesting compounds will be tested in knock-in COL2A1 mice to establish in vivo performance.

Researcher(s)

• Promoter: Verstraeten Aline
• Fellow: De Kinderen Pauline

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Thoracic aortic aneurysm and dissection (TAAD) is an important cause of morbidity and mortality in the western world. As 20% of all affected individuals have a positive family history, the genetic contribution to the development of TAAD is significant. Over the last decade dozens of genes were identified underlying syndromic and non-syndromic forms of TAAD. Although mutations in these disease culprits do not yet explain all cases, their identification and functional characterization were essential in deciphering three key aortic aneurysm/dissection patho-mechanisms: disturbed extracellular matrix homeostasis, dysregulated TGFbeta signaling and altered aortic smooth muscle cell contractility. Owing to the recent advent of next-generation sequencing technologies, I anticipate that the identification of additional genetic TAAD causes will remain quite straightforward in the coming years. Importantly, in many syndromic and non-syndromic families, significant non-penetrance and both inter- and intra-familial clinical variation are observed. So, although the primary genetic underlying mutation is identical in all these family members, the clinical spectrum varies widely from completely asymptomatic to sudden death due to aortic dissection at young age. The precise mechanisms underlying this variability remain largely elusive. Consequently, a better understanding of the functional effects of the primary mutation is highly needed and the identification of genetic variation that modifies these effects is becoming increasingly important. In this project, I carefully selected four different innovative strategies to discover mother nature's own modifying capabilities in human and mouse aortopathy. The identification of these genetic modifiers will advance the knowledge significantly beyond the current understanding, individualize current treatment protocols to deliver true precision medicine and offer promising new leads to novel therapeutic strategies.

Researcher(s)

• Promoter: Loeys Bart

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Obesity constitutes a major health problem, partly due to the increasing prevalence and secondly because of its associated morbidity. It is associated with increased amounts of adipose tissue as well as fat accumulation in non-adipose tissue such as liver and skeletal muscle. Accumulation of ectopic fat in the liver (non-alcoholic fatty liver disease, NAFLD) is a strong independent marker of dyslipidaemia and insulin resistance predisposing to the development of type 2 diabetes. Besides high caloric diet and lack of physical activity, pesticide exposure and endocrine disruptor pollutants are now also increasingly recognized as an "obesogenic" risk factor. Remarkably, recent genome- and epigenome wide associations studies highlight crosstalk of many obesity-associated genetic variants and environmental factors (diet, pesticides, exercise, alcohol consumption, smoking, drugs, medication) with DNA methylation changes at proximal promoters and enhancers. For example, we recently found a strong association between the paraoxonase 1 (PON1) p.Q192R genotype with pesticide exposure and adverse epigenetic (re)programming of endocrine pathways in obesity and high body fat content. PON members hydrolyze several pesticides, a number of exogenous and endogenous lactones and metabolizes toxic oxidized lipids of low density lipoproteins (LDL) and HDL. A decrease in PON1 expression promotes adverse lipid metabolism and is an important risk factor for cardiometabolic disease and has recently been found to be associated with childhood and adult obesity, liver steatosis and its more severe subtype of steatohepatitis. Differences in PON2 have been associated with obesity susceptibility in brown/white adipose tissue. Given the crucial role of PON members in protecting from adverse environmental exposure and from obesity, there is an urgent need for further molecular and clinical research on (epi)genetic PON(1-3) regulation mechanisms in this area. In this GOA, we want to further investigate associations of clinical characterized obesity phenotypes with PON(1-3) genetic variants/polymorphisms, associated epigenetic DNA methylation variation and PON(1-3) expression in samples (i.e. blood, serum, adipose or liver) of clinical patient cohorts diagnosed with obesity, NAFLD/NASH, in relation to adverse pesticide exposure or following therapeutic medical intervention (liraglutide or bariatric surgery). Functional investigation of genetic-epigenetic regulatory crosstalk of PON(1-3) expression in response to pollutant exposure or following medical interventions will be further investigated in relation to biochemical parameters of obesity/liver steatosis/adipocyte differentiation in cell models in vitro as well as in zebrafish in vivo. As such, a better understanding of variable PON(1-3) regulation of obesity-associated traits by adverse obesogenic pollutants or healthy intervention strategies may offer new perspectives to prevent obesity and/or promote cardiometabolic health.

Researcher(s)

• Promoter: Van Hul Wim
• Co-promoter: Francque Sven
• Co-promoter: Knapen Dries
• Co-promoter: Vanden Berghe Wim

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Thoracic aortic aneurysm (TAA) is an abnormal widening of the thoracic aorta caused by blood vessel wall weakness. TAAs entail a high risk for aortic rupture or dissection, commonly leading to sudden death. This dramatic event may leave family members of the deceased terrified and oblivious. To date, genetic defects in >30 genes have been linked with TAA, providing a molecular cause for about 30% of patients. Their identification and functional characterization have been key in acquiring our current aortopathy knowledge. Yet, the genetic and mechanistic picture for TAA is far from complete, hampering identification of predictive markers for aneurysm formation and development of therapies capable of stopping or reversing aneurysm formation. In search for novel TAA genes, the Antwerp Cardiogenetics research group most recently identified recessive truncating mutations in IPO8 as a novel cause of syndromic TAA. My PhD project builds on this exciting finding. More specifically, I aim to significantly improve our current TAA pathomechanistic insight and future TAA patient management by (1) investigating IPO8 as a novel syndromic TAA gene through characterization of an Ipo8 null mouse line, (2) elucidating the IPO8-related pathomechanisms using patient- and control-derived cell lines, and (3) identifying putative drug compounds for IPO8-related aortopathy using a cell-based matrix metalloproteinase inhibition assay.

Researcher(s)

• Promoter: Loeys Bart
• Co-promoter: Verstraeten Aline
• Fellow: Van Gucht Ilse

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project

Abstract

Researcher(s)

• Promoter: Van Hul Wim
• Co-promoter: Van Camp Guy

Research team(s)

• Medical Genetics (MEDGEN)

Project type(s)

• Research Project