ISCOMS Research Fellowships projects 2017

Project A: Chromosomal instability in cancer and ageing

Supervisor: Floris Foijer PhD

Department: European Research Institute for the Biology of Ageing (ERIBA), UMCG

Capacity: 1 student

Project introduction:

Each cell division, our complete genome is replicated and segregated equally over the two emerging daughter cells. Cancer cells have an intrinsic tendency to missegregate chromosomes occasionally, a process known as chromosomal instability or CIN. CIN results in cells with an abnormal chromosomal content, a state defined as aneuploid. Indeed, more than two out of three cancers are aneuploid, suggesting that CIN somehow contributes to the transition of normal cells into cancer cells.

Paradoxically, CIN and the resulting aneuploidy pose a growth disadvantage to non-cancer cells, suggesting that cancer cells have found ways to cope with the detrimental consequences of aneuploidy. In our lab, we try to map and understand how aneuploid cells transform into aneuploid cancer cells. We developed state of the art mouse models, in which we can provoke CIN in tissues of choice at time points of choice. Using these models, we have shown that whereas CIN is indeed detrimental for some stem cells, it is remarkably well tolerated by epidermal cells, although aneuploid mouse epidermis appears prematurely aged (Foijer et al, PNAS 2013). Furthermore, we found that CIN alone is not sufficient for cancer, but that predisposing mutations (such as p53 inactivation) are required for aneuploidy to contribute to malignancy (Foijer et al, PNAS 2014). The main aim of the lab is to develop new intervention strategies that can selectively kill aneuploid cells. For this, we need to better understand the biology of aneuploid cells and which (epi)genetic alterations are required to transform aneuploid cells into their malignant counterpart.

In this IRF project, you will be exposed to the exiting field of chromosome biology, which includes time lapse microscopy, cytogenetics, mouse models, pre-clinical intervention and state of the art technology such as single cell sequencing (also see Bakker et al, Genome Biology 2016), RNA sequencing. While two weeks won’t be sufficient to finish a full project, your IRF stay will reveal how we try to fulfil our mission to identify aneuploidy-killing compound. More importantly, you will also learn whether the field of chromosomal instability is a field for you to pursue in your future research avenues.

Project B: Ageing Biology and Stem Cells

Supervisor: Prof. Gerald de Haan PhD

Field: Hematopoietic stem cells, ageing, leukemia, genetics, epigenetics

Group:  Aeging Biology and stem cells

Capacity: 1 student

Project introduction:

The aim of studies our lab is to understand the mechanisms that specify normal hematopoietic stem cell functioning from birth to death. Blood cells have a limited lifespan, and are replenished constantly by bone marrow stem cells. Although this process is highly efficient, with age hematopoietic stem cells (HSC) function worse, and this coincides with the incidence of various hematological diseases, including leukemia. In our lab we try to find the cell-intrinsic mechanisms that contribute to loss of hematopoietic stem cell activity.

We have a particular interest in the role of epigenetic modifications in stem cell ageing. Polycomb Repressive Complexes (PRC) modify and read epigenetic marks on chromatin, and cause chromatin compaction or relaxation. A decade ago we discovered that overexpression of the PRC2 protein Ezh2 can prevent exhaustion of HSCs. More recently, we showed that the presence of PRC1 Cbx proteins dictate whether HSCs selfrenew or rather differentiate, and thus serve as a toggle between these two fate choices.

HSCs from distinct inbred strains of mice display widely varying ageing characteristics. In an effort to determine the cause for these genetic differences, we have performed extensive genome-wide mRNA and mciroRNA expression analyses. In these screens we identified the microRNA125 family as a candidate of selfrenewing genes. Strikingly, miR-125 is able to induce transplantable stem cell activity in hematopoietic committed cells. This suggests that it is possible to re-introduce cellular potential cells that have lost this potential.

We have developed tools that allows us to label individual HSCs with a DNA barcode and follow the clonal progeny of labelled cells. This method has allowed us to determine clonal contributions of aged vs. young HSCs, but also the distributions of HSCs throughout the skeleton after transplantation. We showed at the clonal level that old stem cells produce fewer mature cells than their young counterparts.

ISCOMS students will be taking part in one of the above projects.

Project C: Gene regulation in ageing and age-related diseases

Supervisor: Cornelis F. Calkhoven PhD

Department: European Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen (UMCG)

Capacity: 1 student

Project description:

Ageing, metabolic disorders and cancer share common biological mechanisms. Cellular factors that are involved in sensing nutrient (food) and energy availability are decisively involved in ageing and lifespan determination as well as in the development of age-related diseases like cancer or metabolic diseases. The primary research focus of the Calkhoven lab is determining how metabolic and other growth signals control the expression of specific sets of genes that can alter the organism’s normal function or contribute to disease.

Currently, the Calkhoven lab studies a specific pathway (mTORC1-pathway) that senses if enough nutrients and energy are available to regulate cell growth through the control of protein synthesis and/or other metabolic processes. The Calkhoven lab is particularly interested in the function of mRNA control elements, protein factors and microRNAs that are involved in mTORC1-controlled processes. Using mouse models they examine the function of these elements, and other factors, on organismal health and life span determination. In addition, they study the modification of gene regulatory proteins by cellular metabolites and how this regulates cell function under different nutritional conditions. With the aim of ‘translating’ the fundamental research into clinical-pharmacological applications, the lab is also involved in developing reporter systems for potential compound screening strategies.

Project D: Molecular eating: feed your microbes to support immunity

Supervisor: Prof. Paul de Vos PhD

Department: Pathology and Medical Biology

Capacity: 2 students

Project introduction:

The human gut harbours trillions of microbes. Current estimates are that the human gut harbours a tenfold more microbes than human cells and contains 150 times more genes than the human genome. The recent change of the traditional view that gut microbiota effects are not only limited to fermentation of food components but also influence immune status has led to the realisation that these microbes can impact health on different levels and are instrumental for maintaining health. During recent years, it has been demonstrated that microbes in the intestine can easily be influenced by external factors such as diet and antibiotics which may disturb the microbiota-host interactions in an undesirable way and can ultimately lead to disease. An imbalance in microbiota communities in the intestine is implicated in a large number of Western diseases. This correlates with lowering of dietary fibers in Western diets. We found evidence that beneficial effects of dietary fibers are highly dependent on its chemical structure. Some structures serve as food for the microbiota and support production of degradation products with beneficial effects on the immune system. Other chemical structures however, bind directly to sensors on immune cells and support or regulate immune processes directly. Unravelling the mechanisms on how molecular components in our food stimulate immune regulation can lead to prevention and treatment of disease.

Project E: Nephrology

Coordinators:

Department: Research Department Nephrology, University Medical Center Groningen

Department of Internal Medicine, Division of Nephrology.

Graduate School of Medical Sciences;

Groningen Research Institute for Drug Exploration (GUIDE)

Capacity: 1 student

Project introduction:

In the Research Department of Nephrology, various projects are running using diverse methodologies (see 1-6). Please motivate your interest for the specific topic (being either clinical, epidemiological, human- or animal in vivo- or in vitro experiments) to indicate what sub-project interests you most.

  1. Patients with renal disease and progressive renal function loss are being studied with respect to the mechanisms via which the urinary protein leakage results in renal function loss. Both non-diabetic and diabetic renal disease are studied. Most of these patients are included in clinical trials to study the efficacy of regimens to lower proteinuria and to prevent progressive renal function loss.
  1. Our centre also has a large population of renal transplant recipients. These patients are monitored very closely, and currently regimens aimed at increasing the duration of graft function as well as patient survival are being studied. A major focus point is on the involvement of viral infections in chronic renal transplant dysfunction.
  1. General population cohorts PREVEND and LifeLines are studied to detect which parameters lead to initiation of progressive renal function loss and its complications. The natural progression is followed to study possible causes of morbidity and mortality in relation to renal parameters.
  1. Lifestyle and the kidney. Many lifestyle factors are involved in the risk of long-term renal function loss. These include nutritional habits, such as excess caloric intake leading to obesity and diabetes, excess sodium intake and sedentary lifestyle and smoking. The mechanisms of renal damage induced by these lifestyle factors are being studied in patients as well as in laboratory animals. Furthermore, the effect of lifestyle intervention measures on the course of renal disease is being studied. Nutritional monitoring is part of this project.
  1. Various animal (rat) models of proteinuria and progressive renal disease are being studied, in order to unravel the mechanisms of renal damage and to optimise antiproteinuric and renoprotective treatments. Focus points are the RAAS – Vitamin D – FGF23 axis; progression of structural tubulo-interstitial changes; and the interplay of proteinuria and dyslipidemia.
  1. Innate immunity and the kidney. Within this research line, we try to unravel the role of the innate immune system (complement system, leukocytes, chemokines) in chronic renal damage in proteinuria and transplanted kidneys. By intervention of novel heparin (or such)-related drugs we aim to reduce the contribution of inflammation in chronic renal tissue remodeling. Research is largely done in experimental models of renal disease.

Project F: Stem cell therapy to treat radiation-induced side effects

Supervisor: Prof. Rob P. Coppes PhD

Department: Departments of Cell Biology and Radiation Oncology, University Medical Center Groningen (UMCG)

Capacity: 1 student

Xerostomia (dry mouth syndrome) can be caused by dysfunctional salivary glands (SG) due to ageing, radiotherapy for head and neck tumours and autoimmune diseases such as Sjögren’s syndrome. About 25% of the elderly and 40% of the patients treated for head and neck cancer suffer from oral dryness leading to impaired speech, chewing, taste and swallowing, higher susceptibility for infections, and caries. These sequelae severely affect the patient’s wellbeing and quality of life.

A lack of viable stem cells able to maintain glandular homeostasis underlies age and radiotherapy induced SG dysfunction. Therefore, stem cell therapy could ameliorate xerostomia. Indeed, recently we showed that transplantation of mouse or human SG stem cells can rescue murine SG from radiation damage. For patients receiving radiotherapy, collection of stem cells before cancer treatment seems feasible. However, the definitive salivary gland stem cell has not been characterised yet. This project will attempt to understand the mechanisms behind stem cell maintenance and differentiation, to allow stem cell therapy in the future.

Project set-up

The student will participate in the culturing and testing of salivary gland or other tissues stem cells in vitro. Primary cells are obtained from mouse or human tissues and cultured as organoids.  Dispersed single cells selected with FACS for the expression of stem cell markers are passaged to Matrigel to form secondary spheres and organoids. The expression of genes and stem cell markers involved in the stemness of these cells are investigated. Involved signalling pathways will be manipulated to assess their role in stem cell maintenance, expansion and differentiation.

Project G: Nuclear Medicine

Supervisor: Walter Noordzij MD

Department: Department of Nuclear Medicine

Capacity: 1 student

Project introduction:
Nuclear medicine is a field that uses radioactivity for imaging and therapy. The radioactive molecules are attached to substances that are used in all kinds of bodily processes. For example, a glucose analogue is used to visualise high metabolic processes, such as primary tumours and their metastases. The effective radioactive dose to the patient is very low, due to the low amount of radioactivity and short half-life of the isotopes.

Project set-up:
In this research programme you will investigate the role of this glucose analogue (fluorine-18 labelled fluorodesoxyglucose, or FDG) in staging patients with melanoma. Up to now, all patients undergo total body scanning, i.e. from the top of the skull until the toes. However, in patients with a primary tumour located above the groin, scanning from top of the skull to mid-thigh may be sufficient. The consequent reduction in scanning time is potentially of benefit for both the patient and the departments’ logistics.

You will analyse scans of melanoma patients regarding the site of the primary tumour and the location of the metastases. You should be able to answer the question to what amount a reduction in scanning time would have consequences in staging the patients. So, will we under stage some patients? Will that have consequences for therapeutic options?

Project H: Immunogenetics of Autoimmune Diseases

Supervisor: Prof. Cisca N. Wijmenga PhD

coordinator: Dr. Sebo Withoff

Department: Department of Genetics

Capacity: 1 student

Project introduction:

The Immunogenetics group of professor Cisca Wijmenga (chair of the Department of Genetics of the UMCG) investigates the role of genetic variation in the aetiology of autoimmune diseases (e.g. celiac disease, inflammatory bowel disease and multiple sclerosis) and on the role of the gut microbiome in health and disease.

The data used for these studies are mostly generated by next generation sequencing. The generation of the data and the analyses requires a broad range of scientific expertise. In her group, a dynamic and highly interactive environment is created in which bioinformaticians, geneticists, statisticians, molecular biologists and immunologists work together closely.

Important findings published by prof. Wijmenga are (a) the shared genetics of autoimmune diseases, (b) 95% of the autoimmune disease associated single nucleotide polymorphisms (SNPs) affect gene expression rather than gene function, (c) eQTL effects of GWAS SNPs on long non-coding RNAs (lncRNAs), (d) the enrichment of ‘lymphocyte specific’ long intergenic non-coding RNAs (lincRNAs) in celiac disease associated loci, and a range of environmental factors affecting the human microbiome.

The currently ongoing research is for a large part focused on the prioritisation of SNPs, genes, pathways and cell types affected in autoimmune diseases, on in vitro experiments to validate the function of the prioritised candidates (with currently a strong interest in the mechanisms of lncRNAs) and on determining how host genetics affects microbiome composition.

Depending on the interest of the student, we will try to design a working plan for the two-week internship.

Project I: Positive Airway pressure and cardiovascular outcomes in coronary artery disease patients with nonsleepy sleep apnea – a multistate analysis

Supervisor: C.H. zu Eulenburg PhD

Department: Departments of Epidemiology, Unit for Medical Statistics and Decision Making

Capacity: 1 student

Project introduction:

In patients with coronary artery disease (CAD), obstructive sleep apnea (OSA) is a common problem. Continuous positive airway pressure (CPAP) is the standard treatment for these patients, when they report daytime sleepiness. In patients who do not report sleepiness at daytime, CPAP is not prescribed so far.

The effect of CPAP in CAD patients with OSA without daytime sleepiness was recently investigated in a randomized controlled trial, The RICCADSA trial by Y Peker et al. (2016). The researchers investigated the effect of CPAP on the time to first event of repeat revascularisation, myocardial infarction, stroke, or cardiovascular mortality. The primary result of the study was insignificant, indicating that the CPAP device did not reduce these events.

Multistate models are a flexible statistical toolbox to analyse different event types or components of a composite endpoint separately. With this technique, it is possible to test treatment effects on different event types, and also to set those different event types into perspective. Performing a multistate analysis on the RICCADSA data could lead to new insights into effect associations.

Every multistate analysis starts with a model specification. In this step, the potential courses on how the patients go through their disease are modelled. In this interesting project, you will be included in this model building process. After having defined the structure of the disease states, you will perform first analyses of the events observed.

Project J: Cardiothoracic surgery

Department: Cardiothoracic Surgery University Medical Center Groningen (UMCG).
Supervisor: Prof. M. Mariani MD PhD
Capacity: 2 students

Project introduction:
The Cardiothoracic Surgery is part of the Thoracic Center of the University Medical Center Groningen, which consist of a Cardiology department and department of Cardiothoracic Surgery. The Cardiothoracic department has a total of 94 beds, and  four surgical operating rooms. On an annual basis the department performs ca. 1.700 surgical interventions. The department participates in several clinical and research projects among other in Transplantation/Organ preservation (Heart, Lung and Heart-Lung transplantations), Aortic Surgery,  Aortic and Mitral valve sparing surgery, Atrial Fibrillation, Minimal Invasive Surgery and off-pump coronary surgery.

The department participates in several  multi-disciplinary programmes.

For the ISCOMS Research Fellowships we require an open minded student, with basic statistics skills. The student must be able to speak English fluently and write correctly.

Project K: Imaging Atherosclerosis: Which way to choose?

Supervisors: Hendrikus H. Boersma PhD, Prof. Clark J. Zeebregts PhD, Prof. Riemer H. Slart PhD

Department: Nuclear Medicine/ Clinical Pharmacy and Pharmacology/ Vascular Surgery

Capacity: 1 student

Project introduction:
Cardiovascular events associated with progressive atherosclerosis constitute the number one cause of death in Western societies today. Atherosclerosis originates from chronic inflammation of the arteries characterised by enhanced infiltration of leukocytes, uptake of lipoprotein particles, proliferation of smooth muscle and endothelial cells, and apoptosis of foam cells. Myocardial infarction and stroke, the most serious of the atherosclerotic sequelae, can result from expansion and destabilisation of atherosclerotic lesions, leading to plaque rupture and subsequent thrombotic events. Prevention of serious cardiovascular events has, not surprisingly, been linked to early diagnosis and detection of vulnerable atherosclerotic lesions.

Vascular properties that are thought to differ between vulnerable and quiescent atherosclerotic lesions generally include the inflammatory status, morphology, degree of stenosis, cap thickness and stability, and proteinase activity of the atherosclerotic plaque. Attempts to quantitate these differences as a means of assessing cardiovascular risk have focused on the design of non-invasive imaging agents that detect the accumulation of immune cells, expression of metalloproteinase activity, heightened consumption of glucose, and cell death of cells within the vascular bed. Although such strategies show considerable promise for identification of vulnerable plaque, they also suffer from some degree of non-specificity, because each strategy also images healthy cells involved in other processes.

In an effort to add another tool to the arsenal of methods for the detection of vulnerable plaque, our lab has undertaken the imaging of sites of accumulation of activated macrophages within the vasculature. Our 2-week plan with the IRF student would be to let him/her make a tour through our research and labs to discover which targets are really suitable to image the vulnerable plaque and its relation to other diseases. We will undertake literature research, visits to other related research groups as well as some lab experiments.

Project L: Epigenetic programming of adult disease

Supervisor: Torsten Plösch PhD

Department: Obstetrics and Gynaecology

Capacity: 2 students

Project introduction

Our research is focused on the influence of the early foetal and neonatal environment on the health of the offspring at adult age. Specifically, we study how disturbances in maternal-foetal nutrient supply during pregnancy and how early postnatal nutrition influence later metabolic regulation. The key idea is that nutrients or other biologically active molecules induce epigenetic changes in the placenta, embryo, foetus or newborn that persist into adulthood and hence change the susceptibility to develop chronic disease (metabolic programming, epigenetic programming).

Our projects therefore focuses on several aspects of early development: in material from early human pregnancy we aim to identify epigenetic changes preceding developmental complications. On the other hand, we study how maternal diabetes, maternal lifestyle or pregnancy complications such as preeclampsia can lead to epigenetic modifications in the placenta or the offspring.

Our work forms a bridge from foetal physiology via epigenetics to long-term health outcome. The students will get the opportunity to work on epigenetic mechanisms in cell systems or samples obtained from animal or human studies.

Project M: Diamond magnetometry for biomedical applications

Department: biomedical engineering

Supervisor: dr. R. Schirhagl

Capacity: 3 students

Project introduction:
Diamond magnetometry is a new method, which allows magnetic resonance measurements in the nanoscale. It is based on fluorescent defects in diamond, which changes its optical properties in a changing magnetic surrounding. This has the striking advantage that optical transitions are easier to measure then magnetic transitions themselves. As a result this method currently holds the world record sensitivity for magnetic resonance measurements. In addition, one can do magnetic resonance measurements without the need of a magnetic resonance machine.
The goal of my group is to apply this method, which emerged from the quantum information field, to biological applications. More concrete we are interested in monitoring free radicals that are generated when cells are under stress. This stress can be due to the impact of a pathogen, a drug or simply the ageing process. We hope to learn from this experiments where exactly the radicals are generated within the cell, which ones play a role and under which conditions they appear. To achieve this goal we introduce diamond nanoparticle sensors into cells while monitoring their optical signal.
We are pioneering this field with a young (founded in 2013), interdisciplinary and international team consisting of physicists, biologists, chemists and engineers from all over the world.
We are particularly interested in hosting people from these backgrounds for our IRF. We especially appreciate it if people are potentially interested in pursuing a longer project (internship, bachelor, master or PhD) later with the group. Useful skills are: cell culturing, imaging, optics, toxicity tests, oxidative stress, surface chemistry, drug delivery. For more information please contact me at romana.schirhagl@gmail.com.

Project N: Culturomics; a means to isolate and identify putative next generation probiotics.

Supervisor: Eleni Sibbald-Tsompanidou PhD

Department: Molecular Bacteriology, Medical Microbiology

Capacity: 2 students

Project introduction:

The human body carries about 100-trilion microorganisms in its intestines. Interestingly, the metabolic activities performed by the gut microbiota resemble those of an organ, which lead to the term ‘forgotten’ organ. The gut microbiota benefit the host mostly by fermenting undigested carbohydrates to short-chain fatty acids, such as butyrate, propionate, acetate and lactate. Aberrant compositions of the gut microbiota have been linked to several diseases. Our aim is to identify beneficial gut microbiota that could restore microbial imbalances relevant for prevention or treatment of disease. Unfortunately, culturing and identifying beneficial anaerobic bacteria can be troublesome and elaborate.

Therefore, we established a broad-range culturing method using a variety of carbohydrate substrates, which allowed us to culture isolates that belong to the most abundant bacterial species in the human gut. We used Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI TOF MS) to identify the bacteria to genus and/or species level. Since MALDI TOF MS can only identify species of which there is a reference spectrum present in the database, we used 16S rRNA sequencing to identify isolates that could not be identified by MALDI TOF MS.

In this project, you will use fecal samples to isolate beneficial anaerobic bacteria and you will use MALDI TOF MS in order to identify the bacteria species present in the fecal samples. Furthermore, you will perform 16 rRNA gene sequencing in order to identify bacteria that are non-identified by MALDI TOF MS.

Setup of the experiments:

  • Isolations of anaerobic bacteria from fecal samples.
  • Identification of the fecal bacteria using MALDI TOF MS.
  • PCR of the 16 rRNA gene of non-identified bacteria.
  • Sequencing of the 16 rRNA gene.
  • Analyses of the 16 rRNA gene sequencing results.

Project O: Understanding the pathophysiology of Shock-mediated organ failure in order to improve the clinical care of critically-ill patients

Supervisor: Dr. J. Moser

Department: Critical Care

Capacity: 2 students

Project introduction:

Every day, critically ill patients in ICUs worldwide develop failure of vital organs. This happens usually as a result of infection (sepsis) or injury (trauma or surgery). This so called multiple organ dysfunction syndrome (MODS) leads to increased mortality among ICU patients. If patients survive MODS, their increased morbidity and mortality persists long after their ICU stay. Worldwide the incidence of sepsis is increasing mainly due to the ageing population, as well as the growing problem of antibiotic resistance. Currently, there is no effective treatment beyond supportive care, emphasizing the urgent need for a better understanding of the pathophysiological and molecular mechanisms in order to identify new therapeutic approaches.

One of the failing organs in septic patients is the kidney. If patients survive, they have an increased risk of developing chronic kidney disease (CKD) and/or end stage renal disease (ESRD), which can result in dialysis dependency. The underlying mechanisms of sepsis-induced kidney failure are still unknown. However, one of the major pathophysiological consequences is loss of microvascular integrity and exaggerated microvascular inflammation. Current research projects focus on understanding aberrant microvascular integrity and inflammation. In these studies a variety of experimental techniques including immunostaining, western blotting, qRT-PCR and ELISA are used to analyze in vitro cell studies, using kidney tissue from in vivo sepsis models and patient material.

Project P: Novel regulators of the kinase mammalian target of rapamycin (mTOR)

 Researchers: Prof. Dr. K. Thedieck, Lab for Metabolic Signaling

Department: Pediatrics

Capacity: 2 students

 Nature of the research

This is a fundamental research project using biochemical, cell and molecular biology techniques to analyze the mTOR signaling network. Depending on the interests of the applicant proteomic and metabolomics approaches and/or computational modeling may be part of the project.

Fields of Study: metabolic signaling

Background / introduction

mTOR, the mammalian target of the anti-cancer drug rapamycin, is a central controller of metabolism and ageing. mTOR is dysregulated in most cancers as well as in metabolic and neurodegenerative diseases, and is therefore of major biomedical interest as a drug target and biomarker. The kinase mTOR is at the center of a large signaling network and exists in two structurally and functionally distinct multiprotein complexes, named mTOR complex 1 (mTORC1) and mTORC2. mTORC1, in response to growth factors (insulin), nutrients (amino acids), energy (ATP), and stress (reactive oxygen species) controls growth related processes such as translation, ribosome biogenesis, and autophagy. mTORC2 is also a central metabolic regulator which is involved in lipid and glucose homeostasis.

Research question / problem definition

mTOR, via a complex kinase network, regulates virtually all anabolic processes at the cellular and organismal level. But how are specific metabolic responses to specific metabolic inputs achieved? We hypothesize that different molecular networks transduce specific metabolic stimuli and mTOR-dependent metabolic responses. Hence, we aim to identify novel mTOR network components and their interconnection in relation to specific metabolic inputs. To this end, our lab analyses the mTOR interactome and phosphotargets with proteomic and biochemical methods1. To deal with mTOR network complexity, systems biology approaches are adopted to unravel novel regulatory connections governing mTOR’s activity and outputs2-4. We functionally investigate novel mTOR regulators by cell biological approaches. For example, we investigate regulators which control mTOR activity and cellular survival under stress5,6, and we unravel mTOR crosstalk with other signaling networks such as TGFbeta7. For further information see http://www.rug.nl/staff/k.thedieck/research .

Workplan

The aim of this project is to elucidate novel links between mTOR and its metabolic inputs. Metabolic, pharmacological, and stress interventions will be utilized to delineate the molecular mechanisms of mTOR regulation and their relevance for the cellular stress response, growth and survival. Techniques/approaches that will be used include cell culture, imaging, biochemistry, molecular biology, RNAi, proteomics, computational modeling.

Project Q: Effects of age on brain control of standing balance

Department: Kinesiology (Human Movement Science)

Coordinators:  Prof. Hortobágyi PhD, Tulika Nandi (PhD candidate)

Type of research: Basic Sciences, laboratory
Field: Kinesiology

Capacity: 2 students

Project introduction:
Standing balance becomes less stable when the base of support becomes narrow. How and if at all the brain and the primary motor cortex is involved in this control is unclear. The purpose of this study is to examine the responses to magnetic brain stimulation during standing with a normal stand, wide stand, and a tandem stand. The project will primarily examine circuits in the primary motor cortex involved in inhibition. This project is part of a PhD thesis.

 Goals:
– To become familiar with magnetic brain stimulation methods used in movement neuroscience;
– To determine the motor control mechanisms of standing balance;
– To determine the effects of old age on the motor cortical control of standing balance.

Approach:
Students participate in laboratory sessions where they will watch and then execute data collection using magnetic brain stimulation. We also use peripheral nerves stimulation under certain conditions. Data analyses are done using Matlab scripts. A PhD and / or a masters student will supervise the project.

Project R: Genomics for Infection Prevention

Supervisor: Dr. John W.A. Rossen

Department: Medical Microbiology

Capacity: 2 students

Project introduction

Dr. John W. A. Rossen has a 25-year history in molecular microbiology and more than 100 peer reviewed publications (> 55 in the last five years; H-index 26). He is Assistant Professor at the University of Groningen, PI in the research group “Genomics for Infection Prevention” and head of the molecular unit which has implemented the use of next generation sequencing for routine clinical microbiology and infection prevention.

This next generation sequencing is used to determine the genetic relationship between pathogens (used to guide infection prevention measures) and for the molecular detection and further characterization of (emerging) pathogens. To be able to determine this relationship, analysis   for revealing (new) antibiotic resistance mechanisms and for determining the virulence of pathogens resulting in improved risk assessment and infection prevention are required. In addition, based on comparing whole genomes of bacteria, tailor-made diagnostic tests are developed used for specific detection of outbreak and or virulent bacterial strains.

Recently, the research group started to implement deep (DNA and RNA) sequencing as a tool for diagnosing severely ill patients suspected to suffer from an infection. Moreover, sequencing an analysis are used to get more insight into the pathogenesis of the pathogen. Several PhD students, Post-Docs and technicians work together to investigate not only patient samples, but also samples taken from animals, food, and water – thereby achieving the one health principle in microbiology.

e-mail: j.w.a.rossen@rug.nl

Project S: Pathophysiology of cholestatic liver diseases: mechanisms and targets for therapy

Coordinators: Prof. Han J. Moshage PhD, Prof. Klaas Niko Faber PhD

Department: Hepatology

Capacity: 2 students

Background:

Chronic liver diseases are characterized by the progressive loss of hepatocytes, the functional liver cells, as a result of cell death. Several toxic factors presenting in the chronically injured liver contribute to cell death, e.g. reactive oxygen species, pro-apoptotic cytokines like TNF and bile acids. Cell death is the consequence of either necrosis (or passive cell death) or apoptosis (programmed cell destruction). In contrast to necrosis, apoptosis is an active and strongly regulated process and therefore amenable to intervention. At the same time, during chronic liver diseases, there is proliferation of connective tissue cells in the liver, the so-called stellate cells and activation of liver-specific macrophages: the Kupffer cells. The proliferation and activation of stellate cells and Kupffer cells leads to liver inflammation and fibrosis.

To treat the detrimental effects of chronic liver diseases, i.e. death of hepatocytes, activation of Kupffer cells and proliferation of stellate cells, we need to know the exact actions of toxic factors, present during liver diseases, on hepatocytes, Kupffer cells and stellate cells.

A major cause of chronic liver diseases is chronic cholestasis, the accumulation of bile in the liver, due to disturbances in the enterohepatic circulation of bile. Therefore, it is very important to elucidate the mechanisms of bile homeostasis and to be able to correct any disturbances in bile homeostasis. Recently, an important role of vitamin A has been discovered in maintaining bile homeostasis.

Goals of our studies are:
1) to elucidate the effects of relevant toxic factors present in the chronically injured liver;
2) to prevent cell death induced by these factors by manipulating signal transduction pathways;

3) to elucidate the mechanisms of regulation of bile flow and, in particular, the role of vitamin A in this regulation.

Approach

The research of the department is very much focused on laboratory work. It involves both in vivo and in vitro (cultured hepatocytes, Kupffer cells and stellate cells). The IRF-student participates actively in the research of the department and will be supervised by PhD students/technicians and Master’s students of the department. Techniques used will include: hepatocyte/stellate cell isolation and culture, assays for apoptosis (caspase activity, nuclear condensation), intervention in intracellular apoptosis and signal-transduction pathways, assays for cell proliferation, mRNA isolation and real time PCR, Western blotting and immunofluorescence microscopy.

Project T: Extrafine particle treatment in smokers with asthma

Department: Pulmonary Diseases
Coordinators: M. van den Berge PhD
Type of research: Bio-informatics
Field: Pulmonology
Capacity: 2 students

Project introduction

For many years inhaled corticosteroids (ICS) constitute the corner stone of asthma treatment. This generally results in less symptoms, improves lung function, and reduces airway hyperresponsiveness (AHR). Asthma patients who smoke, however, benefit less from ICS treatment, experience worse symptoms and have more severe airflow obstruction, compared to non-smoking asthmatics. Nevertheless, asthmatics smoke as often as the general population.

Smoking is, even in non-asthmatics, one of the strongest inducers of small airways disease (SAD). Cigarette smoke consists of particles with a diameter of 0.1-1 µm, which can affect even the smallest airways. It has been shown that smoking leads to inhomogeneous ventilation of the small airways in healthy subjects, as measured with single and multiple breath nitrogen washout tests. This may explain the observations of earlier studies that treatment with non-extrafine particle ICS, which mainly deposit in the larger airways, is less effective in smokers with asthma, with respect to symptoms and pulmonary function improvement.

Since it may be particularly important to treat the small airways in smokers and ex-smokers with asthma, we have recently compared the effects of treatment with extrafine particle ICS to a clinically equivalent dose of non-extrafine particle treatment. Extrafine particle ICS treatment improved small airway function to the same extent as non-extrafine particle ICS treatment in current and ex-smokers with asthma. In ex-smokers, we observed greater corticosteroid treatment responsiveness than in current smokers. We speculate that this difference in effect may be greater for extrafine particle compared to non-extrafine ICS, but this remains to be confirmed in future studies.

Goals of our studies are:

  • to find clinical predictors for a favourable corticosteroid responsiveness in smokers and ex-smokers with asthma.
  • to identify those asthma patients who benefit more from extrafine particle treatment

Approach

The student analyses extensive clinical and genomics data from a clinical study under close supervision of PhD students of the department.

Project U: Personalised medicine and targeted pharmacological therapy for diabetes mellitus type 2

Supervisors: dr. J.F.M. (Job) van Boven

Department: Clinical Pharmacy & Pharmacology

Capacity: 1 student

The department of Clinical Pharmacy & Pharmacology of the University Medical Center Groningen (UMCG) performs preclinical, translational and clinical research. Research is focusing on personalised medicine and targeted pharmacological therapy, mostly applied to diabetes mellitus type 2 (and its cardiovascular and nephropathic complications) and infectious diseases. Topics within personalised medicine include optimisation of pharmacotherapy (individual response variability, therapeutic drug monitoring, pharmacogenetics, biomarkers, molecular imaging), conducting large clinical trials with investigational medicinal products, drug utilisation research (real-world outcomes such as medication adherence, safety and cost-effectiveness) and development and regulatory assessment of new drugs and dosage forms.

We offer a 2-week IRF project that will focus on medication adherence in patients with diabetes mellitus type 2. How common is non-adherence to glucose regulating medication in The Netherlands? Which patient, clinical and product factors influence the extent of non-adherence? What can we do to optimise adherence? To assess these issues, you can make use of our in-house database (GIANTT, www.giantt.nl) with anonymised patient records of over 20,000 patients with diabetes type 2 and learn from our experienced multidisciplinary team of physicians, pharmacists and clinical researchers.

For questions regarding this project, please contact: dr. J.F.M. van Boven, assistant professor of Drug Utilization Research (j.f.m.van.boven@umcg.nl)

Project V: Medical Immunology: at the crossroad between research and diagnostic testing

Supervisor: Dr. B.J. Kroesen

Department: Rheumatology

Capacity: 1 student

Our laboratory:

The Medical Immunology laboratory is part of the larger UMCG-department Laboratory Medicine which facilitates diagnostic tests and procedures, research and education in relation to the daily practice of patient care. The Medical Immunology laboratory is dedicated mainly to performing and development of diagnostic tests in relation to autoimmune diseases and allergy.

Our daily practice:

The diagnosis of an allergic disease or an autoimmune disease requires a multidisciplinary approach in which the laboratory specialist and the clinician interact to perform the right test and come to the right interpretation of the test results. This requires in-depth knowledge of the added value and limitations of laboratory tests in relation to the typical signs and symptoms by which the patients present themselves in the clinic. In this respect, our laboratory strives to offer tests that allow a diagnosis in an efficient, unequivocal and cost-effective way.

The IRF-project:

The project aims to help with the introduction and validation of a fixation method that is classically used to help in defining the true specificity of anti-neutrophil cytoplasmic antibodies (ANCA). Using this fixation, one may better distinguish a true peri-nulear ANCA (pANCA) from a false-positive pANCA due to the presence of anti-nuclear antibodies (ANA).

Project W: Microglia in multiple sclerosis (MS) and aging

Department: Neuroscience, section Medical Physiology
Coordinators:  Prof. Jon D. Laman PhD and Bart Eggen PhD
Type of research: Basic Sciences, laboratory
Field: Molecular Biology, Immunology, Neuroscience
Capacity: 1 student

Project introduction:

Microglia are routinely considered to be the prime immune cell type of the brain, involved both in protection against infection and injury, and in detrimental inflammation. Although this is true, microglia functions are much broader and include interactions with astrocytes, synaptic pruning, and likely also cognition and behaviour. Very recent studies have established that microglia develop independent from blood monocytes, and they are replaced regularly over lifetime of rodents and humans. Several groups including our own identified microglia transcriptome profiles, mostly in mice, but also in humans (paper resubmitted February 2017). Contributions of microglia to MS lesion activity and ageing are under intense study, but yet poorly known.

Goals of our studies

  • To elucidate microglia functions in MS lesion stages and during the ageing process
  • To identify microglia transcriptome profiles under different conditions
  • To develop and apply single cell approaches
  • To identify potential drugable pathways and functionalities

Approach

The research of the department is very much focused on laboratory work, both in vivo using mice and non-human primates, and in vitro (cultured microglia, organotypic slice cultures). The student participates actively in the research of the department and will be supervised by PhD students/technicians and Master students of the department. Techniques used will include: isolation of microglia from mouse and human samples, culture systems, assays for microglia function, mRNA isolation and real time PCR, Western blotting and immunofluorescence microscopy.

Project X: G-quadruplex DNA structures, a novel tool influencing genome stability

European Research Institute for the Biology of Ageing (ERIBA)

Coordinators: Katrin Paeschke PhD

Type of research: Basic Sciences, laboratory

Field: Molecular biology, Genetics

Capacity: 2 students

Project introduction:

Cancer is still one of the most common causes of death. During ageing the risk of cancer development increases dramatically and although our knowledge about its causes has improved, an attempt at finding a cure is still pertinent. Identification of molecular processes at protein level that are associated with cancer development will bring us one step closer to find it.

During cancer, multiple processes are misregulated such as DNA replication and DNA repair. Many different factors regulate replication and repair. Interestingly, it was shown that DNA structures themself can directly regulate those processes. An interesting example of a DNA structure is the G-quadruplex (G4). Scientist revealed that G4s have the potential to regulate replication and repair. However, misregulation of these structures results in genome instability (mutations, deletions) observed during cancer development. In the past, we and others showed that G4 formation and unfolding requires specific proteins. Mutations or loss of these proteins results in misregulation of G4s and consequently misregulation of biological processes G4s participate in.

Goals of our studies are:

– to identify and characterise proteins that regulate G4s;

– to elucidate the function of G4 during DNA repair;

– to understand the causes and consequences of G4 formation/ and unformation for genome stability.

Approach

To address these research questions, we focus on in vivo and in vitro experiments in the laboratory. We are using human tissue culture cells as well as the eukaryote S. cerevisiae. The students will participate actively in our research.

Project Y: Targeting Parkinson’s disease: From biochemistry to pharmacology with AKAP, PKA and LRRK2

Department: Molecular Pharmacology (Pharmacy) and Biochemistry (GBB)
Coordinators: Prof. Martina SchmidtArjan Kortholt PhD
Type of research: Basic Sciences, translational pharmacology, laboratory
Field: Pharmacology, Biochemistry, Drug Screening
Capacity: 2 students

Project introduction:
Parkinson’s disease (PD) is the second most common neurodegenerative disease world-wide and affects an estimated 1 in 1000 people in Europe. Mutations in Leucine-rich repeat kinase 2 (LRRK2) have been found in five to six per cent of patients with familial PD, and also have been associated with sporadic PD. LRRK2 belongs to the Roco family of complex proteins, which are characterized by the presence of Leucine-rich-repeats (LRR), a Ras-like guanine nucleotide binding domain called Roc, a dimerization domain called COR and often also a kinase domain.

Despite a vast amount of research on LRRK2 was conducted in the past years, the cellular and pathological functions are still not completely understood. However, Steger et al. recently identified a subgroup of Rab proteins as the first bona fide kinase substrate and it is now generally believed that this LRRK2/Rab pathway functions at the interface of vesicular trafficking, mitochondrial functioning and autophagy. The pathways regulating and linking LRRK2 PD-mediated mitochondrial dysregulation and abnormal autophagy are only partly identified. Interestingly, accumulating evidence links protein kinase A and LRRK2 signaling in neuron and microglia functions, a process involving AKAP1 as member of the A-kinase anchoring family. Like AKAP1 and PKA, LRRK2 shows an enhanced localization to the outer mitochondrial membrane, however the mechanism is not well understood.

Goals of our studies are:

  • To link the function of LRRK2 with mitochondrial dysfunction;
  • To screen for potential mitochondrial preserving drugs allowing neuronal longevity;
  • To characterise multi-protein complexes in their complex 3D organisation.

Approach

The Kortholt lab (LRRK2 biochemistry and structure) and the Schmidt lab (AKAPs and translational pharmacology) combine all the expertise essential to gain further insight into the next step of novel PD therapeutics. We expect to gain insights into the molecular mode of action of a distinct subset of LRRK2 inhibitors, which have been shown to be brain permeable but to cause severe kidney and lung abnormalities. The combined expertise in both laboratories make it feasible to unravel the cause of unwanted side effects of available LRRK2 inhibitors. We have access to neuronal cell lines, but also to primary (immortalized) structural lung cells, animal models and patient cohorts. The students will be supervised by PhD students, master students and technicians.