Project 1 : An integrative network-based approach to unravel dysregulations in PD in vitro models

Supervisor: Prof. Dr. Antonio del Sol, Computational Biology Group and Prof. Dr. Jens Schwamborn at the Luxembourg Centre for Systems Biomedicine (LCSB) 

PhD Student: Céline Barlier

Project descriptionThe Computational Biology Group works on an exciting project that aims to integrate different layers of cellular regulation to better understand cellular disease-related dysregulations in the context of the neurodegeneration. In particular, we develop a computational integrative model of gene regulatory and signaling networks to identify disease-related genes, biomarkers and signaling pathways. In this highly collaborative project we will develop mathematical and computational models for delineating the dysregulations that arise under neurodegenerative disease conditions. Specific focus will be made on gene regulatory network reconstruction both using and improving existing approaches in the lab and by developing novel approaches without relying on prior knowledge data based on application of new mathematical formalisms. Integration of different layers of regulatory information in a core component of the project and we will develop computational methods to integrate diverse experimental data to build predictive computational models that could be tested experimentally. 

Project 2 : The contribution of the mitochondrial DNA and neuromelanin to inflammasome activation in idiopathic PD

Supervisor: Prof. Dr. Anne Grünewald and Prof. Dr. Jens Schwamborn, Luxembourg Centre for Systems Biomedicine (LCSB) 

PhD Student: Semra Smajic

Project description: The PhD project will focus on the role of neuromelanin in the pathogenesis of Parkinson’s disease (PD) and explore potential links between neuromelanin and mitochondrial genome integrity. Neuromelanin is a product of dopamine oxidation and binds metals, aggregated proteins and environmental toxins, thereby reducing the noxious effects of these compounds. Neuromelanin-positive nigral neurons show higher levels of deleted mtDNA molecules. To study the relationship between neuromelanin formation, oxidative stress, and mtDNA integrity in vivo, we will generate midbrain-specific organoids from PD patients. Organoids are the sole cell culture system in which neuromelanin formation has been reported to date. The project is embedded in the interdisciplinary scientific environment at the LCSB.

Project 3: Morphological and functional heterogeneity of hippocampal microglia in late-onset Alzheimer’s Disease post-mortem samples

Supervisor: Prof. Dr. Michel Mittelbronn (Luxembourg Centre for Neuropathology), Dr. Alexander Skupin (Integrative Cell Signalling Group) at the Luxembourg Centre for Systems Biomedicine (LCSB), Dr. David S. Bouvier (Integrative Cell Signalling Group) at the Luxembourg Centre for Systems Biomedicine (LCSB).

PhD Student: Sonja Fixemer

Project description: The phenotypic heterogeneity of microglia complexifies our understanding of their role in Alzheimer’s Disease (AD). The hippocampus is one of the most vulnerable brain regions in AD with an atrophy particularly severe in the Cornu Ammonis (CA) 1 subregion. Indeed, it remains controversial whether microglia have protective effects or exacerbate neurodegeneration. This appeals for a precise characterization of microglia signatures in AD patients’ brains. The aim of this project is to characterize and classify microglia responses in the AD hippocampus and to evaluate the contribution of microglia in its deterioration. Various hippocampal subregions (CA1, CA3 and Dentate Gyrus) from human post-mortem brain samples from AD patients and age-matched controls are analyzed by immunohistofluorescence, high- and super-resolution 3D microscopy, semi-automated computational pipeline MICMAC (Microglia and Immune Cell Morphological Analysis and Classification) and single-nuclei RNA sequencing. Preliminary results suggest that some subgroups of microglia might be directly involved in disease progression and could contribute to CA1 vulnerability.

Project 4: Role of metabolite repair, a new type of molecular quality control, in the protection against neurodegeneration

Supervisor: Dr. Carole Linster, Enzymology & Metabolism Group at the Luxembourg Centre for Systems Biomedicine (LCSB) 

PhD Student: Myrto Patraskaki

Project description: In 2011, we discovered two enzymes (NAXD and NAXE) that repair damaged and inactive forms of NADH and NADPH, two central cofactors of cellular metabolism. Based on the conservation of NAXD and NAXE across virtually all known living species and the essential role of the cofactors that those enzymes contribute to preserve, we predicted a fundamental role for NAXD and NAXE in maintaining a normal cellular function. Observations from the clinical world recently provided support for this hypothesis, given that mutations in the repair genes have been found in young children suffering from an eventually fatal disease characterized by severe, febrile-induced neurodegeneration.

Important questions that need to be addressed now concern the mechanism through which those mutations cause severe neurological impairments and which therapeutic interventions could slow down or even prevent the unfavorable course of the disease. We will address those questions by establishing and analyzing cellular or whole organism models of the disease, applying Crispr/Cas9 technology and metabolomics as well as imaging-based phenotypic approaches, respectively. These models and defined phenotypic readouts will then be used to test small molecule therapeutic treatments.

Project 5: Identification of the earliest PD pathogenic mechanisms using humanized mouse models

Supervisors: Dr. Pierre Garcia and Dr. Manuel Buttini, Prof. Dr. Michel Mittelbronn, Luxembourg Centre for Systems Biomedicine (LCSB), the University of Luxembourg, and Luxembourg Center for Neuropathology (LCNP).

PhD Student: Alessia Sciortino

Project description: The Neuropathology/Neurodegeneration group, which is part of the recently formed trans-institutional Luxembourg Centre for Neuropathology, is carrying out an interdisciplinary project that uses mouse as a model organism to identify early molecular events associated with Parkinson’s disease initiation. The project will cover integration of phenotypic mouse model analyses with transcriptomic profiling and functional activity measurements of susceptible neuron populations in an effort to identify Parkinson’s-linked pathological events that occur before neuron dysfunction and loss. We may also perform functional validation of identified molecular entities in select in vitro or in vivo models, and test their potential as early Parkinson’s disease biomarkers.

This is a project embedded in large multi-disciplinary effort, and will combine experimental lab work, behavioral and pathological mouse model phenotyping, and bioinformatical analysis of gene expression profiling data. The Neuropathology/Neurodegeneration group uses genetic and induced mouse models of Parkinson’s disease to understand disease initiation and progression at the whole organism level and translate the findings into identification of meaningful new therapeutic targets and biomarkers. The applied combination of the various mouse models, their phenotypic and functional analyses, and expression profiling will pave way for the identification of the early molecular events and biomarkers of Parkinson’s disease. 

Project 6: Nanoparticle-based and Quantitative Susceptibility weighted imaging based MRI in the diagnosis of neurodegenerative diseases

Supervisor: Prof. Dr. Frank Hertel, Interventional Neuroscience Group at the Luxembourg Centre for Systems Biomedicine (LCSB) 

PhD Student: Beatriz Garcia

Project description: The Interventional Neuroscience – Next Generation Neurosurgery Group is an interdisciplinary research team developing innovative technologies for Neurosurgery / Neuroscience.
This project is part of a doctoral training unit at the LCSB focusing on biological and computational analysis and modelling of neurodegenerative disorders, especially Parkinson’s disease (PD).
Within the project, special Magnetic resonance imaging (MRI) technologies should be developed and applied. A focus will be on quantitative, as well as on nanoparticle-based MRI. These technologies will be analyzed in small animal models, postmortem and patient MRI datasets.
The project is embedded in an interdisciplinary working group consisting of medical doctors, computer scientists and biologists. The work will also include a narrow international collaboration with 2 groups, well established for nanoparticle design and quantitative MR-imaging, respectively.

Project 7: Knowledge platform for the storage and analysis of heterogeneous biomedical data in a Parkinson’s disease (PD) context and with a focus on reproducible science 

Supervisors: Prof. Dr. Reinhard Schneider, Bioinformatics Core Facility, LCSB

PhD Student: Nikola de Lange

Project description: The project focuses on developing and implementing informatics tools to facilitate the next generation of experimental biomedical research, covering the complete data integration, design and implementation for the various "-omics" data originating from the other DTU projects. Basically, the project will be in the middle of all the other projects, making the connection between them by designing a database platform to collect and process all the different types of data generated, in order to facilitate further consult and analysis using statistical and machine learning methods. The goals will be the identification and integration of molecular mechanisms into networks applying state-of-the-art visualization and computational modelling technologies

Project 8: Integration of genomic, transcriptomic and epigenomic data for the functional identification of age of onset modifiers in a LRRK2 G2019S PD background

Supervisors: Dr. Lasse Sinkkonen, Life Sciences Research Unit (LSRU), and Prof. Dr. Rejko Krüger Luxembourg Centre for Systems Biomedicine (LCSB) 

PhD Student: Borja Gomes

Project description: The Epigenetics Team (LSRU) and the Clinical & Experimental Neuroscience group (LCSB) are jointly carrying out an interdisciplinary project that aims to generate and integrate genome-wide epigenomic data from patient-specific iPSC-derived dopaminergic neurons with existing whole-genome sequencing analysis to identify age-of-onset modifiers in Parkinson’s disease. Moreover, we will perform functional validation of the identified modifiers in the relevant cell lines through genome-editing and analysis of neuronal phenotypes.

This is a collaborative project combining experimental lab work and bioinformatic analysis of next generation sequencing. The Epigenetics Team integrates computational approaches and experimental biology to understand cellular function and gene regulation in development and disease at the genome-wide level. The Clinical & Experimental Neuroscience group focuses on the elucidation of cellular mechanisms leading to neurodegeneration in Parkinson’s disease. Harvesting on the unique interdisciplinary setting this project will combine expertise from cellular reprogramming, in vitro disease-modeling, functional genomics, human genetics, and genome engineering to uncover the genetic modifiers of age of onset in Parkinson’s disease. 

Project 9: Elucidating the role of epigenetic histone modifications in the modulation of PD pathogenesis

Supervisors: Dr. Manuel Buttini and Prof. Dr. Michel Mittelbronn, Luxembourg Centre for Systems Biomedicine (LCSB), and Dr. Lasse Sinkkonen, Life Sciences Research Unit (LSRU) 

PhD Student: Sergio Helgueta Romero

Project description: The Epigenetics Team (LSRU) and the Neuropathology group (LCSB) carrying out an interdisciplinary project that uses mouse as a model organism to characterize the hierarchy of molecular events of Parkinson’s disease progression by integration of phenotypic mouse model analyses with transcriptomic and epigenomic profiling. Moreover, we will perform functional validation of the identified modifiers in the relevant mouse PD models and test the translatability of the identified molecular changes into early biomarkers in human.

This is a collaborative project combining experimental lab work, behavioral and pathological mouse model phenotyping, and bioinformatics analysis of next generation sequencing data. The Epigenetics Team integrates computational approaches and experimental biology to understand cellular function and gene regulation in development and disease at the genome-wide level. The Neuropathology group uses genetic and induced murine models of Parkinson’s disease to understand disease initiation and progression at the whole organism level and translate the findings into identification of meaningful new therapeutic targets and biomarkers. The applied combination of the various mouse models, phenotypic analysis, and functional genomics will pave way for the identification of the early molecular events and biomarkers of Parkinson’s disease.

Project 10: Search for novel PD biomarkers originating from increased molecular damage and/or deficient molecular quality control systems

Supervisors: Dr. Carole Linster, Enzymology & Metabolism Group, LCSB, and Dr. Fay Betsou, Chief Scientific Officer, IBBL.

PhD Student: position open

Project description: The Parkinson associated protein DJ-1 has recently been shown to have a robust deglycase activity towards nucleotides and amino acids modified by the reactive dicarbonyl metabolites, glyoxal and methylglyoxal. Protein and DNA glycation adducts produced by exposure to glyoxal and methylglyoxal were also shown to be repaired in vitroby DJ-1. Glyoxal and methylglyoxal can be formed physiologically by lipid peroxidation and as by-product of glycolysis, respectively. Glycation adducts of deoxyguanosine (dG) have previously been shown to reach similar cellular levels than 8-oxodG, a commonly used marker of DNA oxidation. Both glycated and oxidized dG derivatives can be measured in biological samples, including plasma and urine. Stable isotope dilution LC-MS/MS is the analytical method of choice, but immunoassays also exist to measure both types of DNA damage markers (8-oxodG CEdG ELISA kits). Given the recent findings concerning DJ-1 function, we propose here to evaluate glycated dG derivatives as biomarkers for PD. This is further motivated by the observation that diabetes mellitus is a risk factor for PD and other previous findings indicating a link between protein glycation and PD. A second avenue that can be explored depending on time and project progress, is the evaluation of glucosylceramide and derivatives as potential biomarkers for PD. Glucosylceramide is the substrate of glucocerebrosidase (GBA1), mutations in which lead to increased risk of developing PD. In this project, analyses will be performed both on DJ-1 (and GBA1) mutant cell and/or whole organism models as well as PD patient derived material. In collaboration with IBBL, different types of biospecimens (plasma, urine, CSF, fibroblast extracts) as well as pre-analytical sample processing procedures will be optimized for detection of the markers of interest. Cell culture experiments and LC-MS method development and analyses will be performed at LCSB. Ideally, the project will conclude with a biomarker validation phase at IBBL.

Project 11: The pathogenic role of novel PD-associated Miro1 and mitochondrial chaperone TRAP1 variants in mitochondrial dysfunction and impaired dynamics leading to neurodegeneration 

Supervisor: Prof. Dr. Rejko Krüger, Clinical and Experimental Neuroscience Group at the Luxembourg Centre for Systems Biomedicine (LCSB) 

PhD Student: Axel Chemla

Project description: The Clinical and Experimental Neuroscience Group intends to work on an exciting project on pathogenic pathways leading to neurodegeneration in Parkinson’s disease. We will generate iPSC-based neuronal cell models and corresponding isogenic control lines in order to analyze midbrain-specific phenotypes caused by mutations in the TRAP1and RHOT1gene. 

The project will focus on functional characterization of iPSC-derived neurons, including the analysis of e.g. mitochondrial respiration, ATP synthesis rate, respiratory chain complex activities, calcium signaling, mitochondrial transport, electrophysiology and mitochondrial quality control. Moreover, all cellular phenotypes established will undergo a comprehensive compound screening campaign on a newly established automated stem cell culturing and screening platform (Beckman automation) in our laboratory.

Project 12: Lysosomal and mitochondria dysfunction in human disease specific, iPSC derived, microglia contributes to dopaminergic neuron degeneration

Supervisor: Prof. Dr. Jens Schwamborn, Luxembourg Centre for Systems Biomedicine (LCSB) 

PhD Student: Ugnė Dubonytė

Project descriptionIn this project we will derive human microglia from induced pluripotent stem cells (iPSCs). This will be done from healthy controls as well as from Parkinson’s disease (PD) specific lines with defined mutations (e.g. in SNCA and LRRK2), matching isogenic controls where the mutation is corrected and PD specific lines from idiopathic patients. In these microglia the activity of mitochondria and lysosomes will be determined via imaging approaches, metabolomics measurements, seahorse measurements etc. In a next step patient specific microglia will be integrated into human brain organoids. These organoids are generated from the same iPSCs following our published protocol (Monzel et al., 2017, Stem Cell Reports). After integration the effect of microglia on dopaminergic neuron degeneration and disease associated protein aggregation shall be investigated. Eventually, we will attempt to rescue disease specific effects by small molecule drug treatment. 

Project 13: Experimentally induced aging in human midbrain organoids intensifies decline in organellar quality and exacerbates cellular phenotypes

Supervisor: Prof. Dr. Jens Schwamborn, Prof. Dr. Antonio del Sol and Dr. Alexander Skupin, Luxembourg Centre for Systems Biomedicine (LCSB

PhD Student: Nathasia Mudiwa Muwanigwa

Project description: This is a joint project between the Schwamborn, del Sol and Skupin labs. Here, it will be investigated how aging affects cellular- and organellar quality in Parkinson’s disease (PD) relevant models. The main model that will be used here are patient specific midbrain organoids (described in Monzel et al., 2017, Stem Cell Reports) that are derived from induced pluripotent stem cells (iPSCs). In order to induce aging the iPSCs for organoid generation will be engineered in a way that they inducible express Progerin, which has been shown to induce aging in dopaminergic neurons (Milleret al., 2013). In aged organoids, disease associated phenotypes will be analyzed at various levels. Besides imaging approaches also single cell sequencing shall be used intensively. Mapping the single cell sequencing data to available transcriptomics data from embryonic development and adult human (La Manno et al., 2016) will allow us to assess how much aging can be induced and what the cellular consequences are. In a final series of experiments it shall be investigated whether small molecule treatment can inhibit aging or age associated phenotypes.

Project 14: Effects of α-synuclein on astrocytic metabolism: mechanisms underlying PD

Supervisor: Prof. Dr. Anne Grünewald and Prof. Dr. Rejko Krüger, Luxembourg Centre for Systems Biomedicine (LCSB) 

PhD Student: Patrycja Mulica

The Molecular and Functional Neurobiology and the Clinical and Experimental Neuroscience teams will focus on the study of alpha-synuclein, a protein that is etiologically linked to Parkinson’s disease (PD) and characteristically aggregates and forms deposits at the level of neurons and glial cells of diseased patients. Much effort has recently been put into the elucidation of both alpha-synuclein physiological and pathological roles in neurons, in the context of PD. However, our innovative project challenges the neurocentric view of PD and will focus on the study of alpha-synuclein effects in the astrocytic lineage. Particularly, the project will address the possible metabolic alterations elicited by alpha-synuclein in iPSC-derived astrocytes, affecting their neuronal supportive roles. 

Project 15: Deciphering the genetic architecture of Parkinson’s disease in the Luxembourgish population

Supervisor: Prof. Dr. Rejko Krüger, Luxembourg Centre for Systems Biomedicine (LCSB)

PhD Student: Sinthuja Pachchek

Parkinson disease (PD) is one of the most common neurodegenerative diseases, which is characterized by motor features such as bradykinesia, rigidity and tremor. In addition, it also causes several non-motor symptoms including depression, cognitive decline, sleep abnormalities, reduced olfaction and autonomic dysfunction.

Hence, the research topic of the thesis focuses on the Luxembourgish population, the deeply phenotyped and genotyped LuxPARK dataset, the first Luxembourg PD cohort, will be used. The LuxPARK PD cohort will is planned to have 1600 clinical samples obtained from 800 patients and 800 controls until the end of the NCER project. The dataset provides three types of data set. The first one is Neurochip genotyping data. All samples are genotyped on the Illumina NeuroChip, which was specifically designed to integrate rare and common variants related to neurodegenerative diseases. To improve the call rates the LuxPARK NeuroChip genotypes were called together with additional 11,000 PD and 10000 control samples from the JPND COURAGE-PD project that are also available for further analysis. The second data type is whole genome sequencing (WGS) data from LuxPARK Familial PD cases with unknown genetic cause. The third type is clinical data obtained for all participants over time. The results from the Luxembourg cohort will be combined with available data sets like the PPMI cohort, Oxford cohort and the data from the JPND COURAGE-PD consortium.

The main goal of the proposed project is the clinico-genetic stratification of PD within the Luxembourgish population. Various clinico-genetic analysis will be performed including the identification of patients with GBA mutations, the analysis of polygenic risk, the integrate Quantitative Trait Locus (QTL) analysis using available omics data like microbiome and expression data, in-depth WGS analysis to identify potential new PD-causing genes or variants, copy number analysis and analysis of the genetic contribution of mitochondrial genes for sporadic cases PD.

Project 16: Identification and characterization of novel, aging related disease mechanisms in iPSC-based midbrain dopaminergic neurons derived from Parkinson’s disease patients

Supervisor: Dr. Ulf Nehrbass, Luxembourg Institute of Health

PhD Student: Jennifer Phan

The number of people diagnosed with Parkinson’s disease (PD) continues to increase, making it one of the most common age-related neurodegenerative diseases. On average, patients diagnosed with PD are in their 60s, but cases with early onset at younger age have been reported. To understand whether similar pathways are involved or whether the disease etiology in early and late onset PD are independent, we intend to subject cells from patients with early onset (EOPD), late onset (LOPD) Parkinson’s disease and healthy controls to a deep comparative analysis. Midbrain dopaminergic neurons will be derived from patients using the induced pluripotent stem cells technology.

To start the project, we will use patients carrying SNCA mutation as EOPD references, whereas LOPD will be started from a LRRK2 G2019S background. Differentiated midbrain dopaminergic neurons from LOPD and EOPD patients will be compared to each other and with their isogenic wildtype controls. Genetic and targeted proteomic analyses, in conjunction with imaging based morphometric profiling, will be performed on both 2D cell cultures as well as 3D ‘mini-brain’ organoids. Differential pathways between LOPD and EOPD patient-derived disease models could be causative mechanisms of action, leading to disease. Ideally, this would allow to us investigate whether these mechanisms are present in idiopathic LOPD and EOPD patients. It would also allow analysis in a more systematic way, in which genes other than the isogenic controls might rescue disease phenotypes. This approach could contribute to the understanding of Parkinson’s disease and provide a potential diagnostic tool.

Project 17: Mathematical modeling of critical transitions in epithelial and mesenchymal cell population                                                                                    

Supervisor: Dr. Alexander Skupin, Luxembourg Centre for Systems Biomedicine (LCSB)

PhD Student: Françoise Kemp

Cell fate is characterized by incremental changes of the internal gene regulatory network. Perturbations of this program can lead disease development such as in cancer or neurodegeneration. Our mechanistic understanding of the underlying mechanisms is still incomplete but recent experimental and theoretical developments indicate critical transitions as a generic dynamical feature of differentiation.

We are therefore developing a dynamic systems approach for such tipping points. Here, we apply such an approach to breast cancer which is a heterogeneous disease portrayed by the ability of stem cells to change their identity. During the epithelial-mesenchymal transition (EMT), a polarized, immotile epithelial cell goes through multiple biochemical changes and acquire mesenchymal, migrational and invasive properties. The shift towards a mesenchymal phenotype promotes metastasis and tumour recurrence. After the intra-vasation and extra-vasation, cells must retransform to epithelial phenotype referred as mesenchymal-epithelial transition (MET) in order to grow in the distant tissue. However, the mechanisms involved in trans-differentiation by EMT and MET are not well-understood.

The project will show how mathematical modelling can be used to understand the cell population dynamics of EMT and MET in the framework of tipping points. Understanding these critical transitions may pave the way for the development of novel therapeutics in breast cancer but the methodology will also support new insights into neurodegeneration.

Project 18: Striatal neurodevelopment at single cell resolution in rats during the asusceptibility period of schizophrenia

Supervisor: Prof. Dr. Jens Schwamborn and Dr. Alexander Skupin, Luxembourg Centre for Systems Biomedicine (LCSB) of the University of Luxembourg.

PhD Student: Dimitrios Kyriakis

The striatum is a critical component of the motor and reward systems. It receives glutaminergic and dopaminergic inputs from various sources and is the primary input layer of the basal ganglia. For this purpose, the striatum translates cortical activity from dorsal striatum into adaptive motor actions and the activity from ventral striatum to mediate reward, cognition, and reinforcement.

Dysfunctions of the striatum are associated with motor dysfunctions and neuropsychiatric disorders. An important neurodevelopmental process occurs during the second postnatal week in rats, which is analogous to the second trimester of limbic development in humans. Disruption of this process is thought to impact the formation of important network connections both within the striatum and within target brain areas. Stress, nutritional deficiencies or infection experienced by the mother during this time increase the likelihood of the offspring for developing neuropsychiatric disease and in particular schizophrenia.

By performing Drop-Seq, a single-cell RNA sequencing (scRNA-seq) technique, we comprehensively characterized the transcriptome of the cells present in the striatum during this developmental step at 4 time-points. Applying our computational analysis pipeline for single-cell data allowed us to analyze the cellular heterogeneity and identify distinct subpopulations of cells involved in the striatal neurodevelopment and its potential impact on schizophrenia and neurodegenerative disease.