Research team
Expertise
Dr. Bart Cuypers (Msc. 2013, PhD 2018) is FWO post-doc and a bioinformatics scientist who uses multi 'omic and machine learning methods to unravel the molecular biology and drug-resistance mechanisms of pathogens, as well as their host responses. Currently, his post-doctoral at the interface the Adrem Data Lab (University of Antwerp, Antwerp, Belgium). Bart Cuypers has a background in biology (BSc) and cell- and systems biology (MSc). During his PhD, he studied the functional impact and adaptive role of aneuploidy and gene copy number variation in the protozoan parasite Leishmania, a pathogen of which the molecular biology is still elusive. As such, he worked on the collection, analysis, integration and interpretation of (epi-) genomics, transcriptomics, proteomics and metabolomics data over a wide array of genetic backgrounds, life stages and resistance profiles. As such, he has both wet-lab and computational experience. His post-doc focussed on unravelling the (poorly characterised) post-transcriptional regulatory chain of Leishmania by integration of third generation sequencing data (PacBio) with ribosome profiling and proteomics. Bart Cuypers has obtained several competitive grants and fellowships. Firstly, he has started his career with an FWO Aspirant fellowship (2013) and later continued with and FWO post-doc fellowship (2018). To strengthen his post-doc project, he has obtained additional BOF funding (BOF KP, 2019) as well as an FWO credit for post-docs (2020) and a credit for a long research stay abroad at the Notredame Lab (7 months, 2019-2020). He is co-promotor the SB fellowship of Katlijn de Meulenaere (2019) that investigates Plasmodium vivax reticulocyte invasion pathways and ligand candidates using a multi-omic approach. Finally, he obtained an award from the UA research council for promising young researchers (2015). In total this accounts to more than 660 000 euro in acquired funding. As a bioinformatics enthusiast and strong supporter of interdisciplinary research Bart Cuypers has a leading role in the International Society for Computational Biology Student Council (Executive team, treasurer) a global network of more than 2000 master students, PhD students and young post-docs that are passionate about computational biology. He is one of the main organisers of the International Society for Computational Biology Student Council webinar programme (ISCB Academy). Further, Bart is involved in several research consortia, such as BIOMINA (Biomedical Informatics Research Network, Antwerp, steering committee member) and the Tuberculosis ‘Omics Research Consortium (TORCH). He also represents the Institute of Tropical Medicine (ITM) in the CalcUA Supercomputer User Board, is member of the academic council at ITM and Faculty of Science Faculty Board at UA. Keywords: Systems Biology, Multi 'omics, Data Mining, Molecular Biology, Molecular Parasitology.
A framework to deduce the convoluted repertoire and epitope hierarchy of human T cell responses in visceral leishmaniasis: patient meets in silico.
Abstract
Visceral leishmaniasis (VL) is one of the most severe parasitic infectious diseases with 0.4 million cases annually. There are currently no vaccines for VL, although there is evidence of acquired T cell-mediated immunity and resistance to reinfection. Indeed, VL vaccine development is severely hampered by the absence of a good animal model and the multitude of possible Leishmania antigens that remain uncharacterized because of the low-throughput screening methodologies currently applied. As such, there is a complete lack of insight in epitope reactivity, epitope dominance hierarchy and antigenic variation. In this project, we aim to unlock this status quo by implementing a patient-centered framework integrated with in silico epitope prediction tools and in vitro immunopeptidomics that can comprehensively deduce and confirm the Leishmania epitope hierarchy in patients. Additionally, we will phenotype and monitor the human Leishmania-specific T-cell response and repertoire during the complete course of infection using single-cell RNAseq, single-cell TCRseq and CITE-seq. These recent, state-of-the art tools allow unprecedented resolution by providing an exhaustive, timely and high-throughput immune profiling. We believe that this framework can be directly wheeled for diagnostic tools and to expedite vaccine development against Leishmania and serve as a proof of concept for similar complex eukaryotic pathogens.Researcher(s)
- Promoter: Laukens Kris
- Co-promoter: Cuypers Bart
- Fellow: de Vrij Nicky
Research team(s)
Project type(s)
- Research Project
Elucidating the link between HLA-presentome and different clinical presentations of cutaneous leishmaniasis with Nanopore HLA genotyping.
Abstract
Infection with Leishmania parasites can lead to a wide spectrum of clinical manifestations. These range from diverse cutaneous presentations to a deadly systemic visceral disease, each being associated with infection by a specific set of Leishmania species. As of yet, knowledge on the host-pathogen interactions underpinning this diverse clinical spectrum is scarce. In our recent work, we have demonstrated a link between HLA genotype and susceptibility to the development of leishmaniasis, leading us to hypothesize that differential T cell antigen presentation shaped by HLA diversity may be a key driver of the development of different clinical presentations of leishmaniasis. In this project, we aim to uncover whether and how differential antigen presentation and HLA diversity is associated with the different cutaneous presentations. We will do so by combining Oxford Nanopore sequencing for HLA genotyping with state-of-the-art in silico antigen presentation predictions. Samples will be derived from Ethiopian patients infected with L. aethiopica, as this species can cause all different forms of cutaneous leishmaniasis.Researcher(s)
- Promoter: Cuypers Bart
Research team(s)
Project type(s)
- Research Project
Uncover and compare the human immunopeptidome of Leishmania across the clinical spectrum.
Abstract
Infection with the Leishmania parasite can lead to a wide spectrum of clinical presentations, ranging from diverse cutaneous presentations (localized, mucocutaneous, disseminated) to a deadly systemic disease (visceral leishmaniasis). Yet, the underlying factors driving this disease spectrum remain mostly unknown. Although Leishmania is an obligatory intracellular parasite surviving in the phagolysosome of key antigen presenting cells, it remains mostly unexplored whether the complex host-parasite interplay translates in an altered net effect on the MHC-presented peptidome to T cells (giving rise to a differential antigen-specific T cell repertoire), and whether and how this is associated with certain disease presentations that have distinct immunopathology patterns. Although attempts were made in murine models, discordant data has often been found between experimental in vivo models, in vitro settings and patients regarding the host immune response after Leishmania infection. By applying a new high-throughput MS-based method on an unique set of patient tissue samples, we aim to perform the first comprehensive screening of the antigenic repertoire and study whether and how this differs between in vitro and in vivo conditions, blood and tissue compartments, and across the clinical presentations.Researcher(s)
- Promoter: Baggerman Geert
- Co-promoter: Cuypers Bart
- Co-promoter: Meysman Pieter
- Co-promoter: Pepermans Elise
Research team(s)
Project type(s)
- Research Project
Unraveling the post-transcriptional regulatory chain in Leishmania by multi'omic integration.
Abstract
Trypanosomatids are protozoan parasites which have evolved a gene expression system that is remarkably different from other Eukaryotes. Instead of being individually controlled by transcription factors, Trypanosomatid genes are transcribed constitutively in long arrays of tens to hundreds of functionally unrelated genes. In this study, we aim to understand how Trypanosomatids, despite this constitutive transcription system, can generate and regulate the major diversity in transcript and protein levels that is typically observed during their life cycle. Using Leishmania donovani as a model system, we will carry out the first deep characterization of transcript isoforms (using long-read PacBio sequencing) and their degree of translation ('translatome'), during the parasite's life cycle. Using state-of-the art pattern mining and machine learning approaches we will then identify mRNA sequence and structural patterns that play a role in modulating transcript stability and/or their translation efficiency. Finally, we will generate an integrated, systems biology model of protein production and its post-transcriptional regulation in Leishmania, validated by previously collected multi-?omic data. The study will lead to novel insights in the post-transcriptional regulatory chain of Trypansomatids, which remains poorly understood to this date.Researcher(s)
- Promoter: Cuypers Bart
Research team(s)
Project type(s)
- Research Project
Elucidating the role of alternative trans-splicing in the mRNA abundance regulation of Leishmania.
Abstract
Leishmania is a genus of protozoan parasites that cause the disease leishmaniasis in humans and a wide array of vertebrate animals. The parasite exhibits a remarkable gene expression system where genes lack individual RNA polymerase II promoters and are therefore not individually controllable by transcription factors. Instead, genes are transcribed constitutively in long polycistronic units of functionally unrelated genes and co-transcriptionally processed to individual mRNAs per gene during a process called 'trans-splicing'. During trans-splicing, mRNAs receive a fixed 39 nucleotide sequence at their 5' end called 'spliced-leader'. The location where this spliced-leader is added is variable, resulting in different possible transcript lengths for a single gene (alternative trans-splicing). The abundance of mRNA per gene appears to be regulated entirely post-transcriptionally, however, it is currently unclear how this occurs. This project aims to determine the role of alternative trans-splicing in the mRNA abundance regulation of Leishmania. As this process determines the length of the transcript, we hypothesise that it affect the abundance of a transcript by altering its stability and/or included regulatory motifs. For the first time, we will make use of long read mRNA sequencing (PacBio) to study the changes in transcript repertoires during different life stages of Leishmania donovani. Additionally, we aim to identify the motifs and/or RNA structural patterns which regulate the location and usage frequency of alternative trans-splicing and polyadenylation sites. This will be investigated making use of state-of-the art pattern finding and classification approaches.Researcher(s)
- Promoter: Cuypers Bart
Research team(s)
Project type(s)
- Research Project
A study of the plasmodium vivax reticulocyte invasion pathways and ligan candidates, with special attention to the promising PvTRAg and PvRBP multigenic families.
Abstract
Plasmodium vivax is one of the 5 species causing malaria in humans, and the leading cause of malaria outside Africa. A key step in P. vivax infection is the invasion of reticulocytes (young red blood cells) by the parasite. This invasion is made possible through several interactions between host receptors (reticulocyte membrane) and parasite ligands. While these interactions are well studied for P. falciparum, they remain elusive (and are not comparable) in P. vivax, due to the inability of long-term cultures. However, identifying parasite ligands and characterising the pathways used by the parasite to enter reticulocytes is essential for drug and vaccine development, and is the question that lies at the core of this project. In order to achieve P. vivax elimination, a better understanding of the ligands involved in invasion is necessary. We hypothesize that alternate pathways are used by P. vivax to invade reticulocytes, and that the PvTRAg and PvRBP multigenic families contain important invasion ligands. Therefore, we will carry out the first study integrating newly characterized P. vivax invasion phenotypes with transcriptomic and (epi-)genomic data in field isolates. As such, we expect to advance the knowledge on the role and regulation of PvTrag and PvRBP families in invasion and to discover new potential ligands. Candidate target ligands will be validated by ex vivo invasion assays, and will finally help us to identify the most suited drug and vaccine candidates.Researcher(s)
- Promoter: Laukens Kris
- Co-promoter: Cuypers Bart
- Fellow: De Meulenaere Katlijn
Research team(s)
Project type(s)
- Research Project
A multi-omic approach to characterize gene dosage compensation in Leishmania.
Abstract
Leishmania is a protozoan parasite with a remarkable tolerance for aneuploidy, while this phenomenon is often deleterious in other organisms. The result of aneuploidy is that all genes of an affected chromosome have an altered gene dosage (i.e. more or less copies) compared to the euploid situation. In Leishmania, we have previously shown that the majority of transcripts and proteins follow dosage changes in a same in vitro condition, while for the remaining products dosage compensation occurs by an unknown mechanism. This project investigates whether (i) dosage compensation occurs by alterations of transcript stability, translation efficiency and/or protein stability, driven by specific transcript and protein biomolecular features and (ii) whether dosage compensation regulation is modulated during the life cycle. As such, we will determine the relative contribution of each regulation layer to the overall compensation and establish a conceptual model of dosage compensation in Trypanosomatids. This is the first integrated multi-omic of dosage compensation in Leishmania, but also in Trypanosomatids in general. The study will lead to novel insights in how this compensation is regulated in aneuploid cells, and investigate if this has a life-stage specific component to it. These fundamental mechanisms are still incompletely understood in all eukaryotes and trough this study, we believe it is possible to gain insights in potentially hitherto unrevealed regulatory mechanisms in eukaryotes.Researcher(s)
- Promoter: Laukens Kris
- Co-promoter: Dujardin Jean-Claude
- Fellow: Cuypers Bart
Research team(s)
Project type(s)
- Research Project
Finding the cause of leishmaniasis relapse after treatment with miltefosine using untargeted proteomics.
Abstract
The protozoan parasite Leishmania donovani is responsible for the disease visceral leishmaniasis (VL) in the Indian Subcontinent. Each year, an estimated 200 000-400 000 people contract VL, which is almost always fatal if left untreated. Sodium stibogluconate (SSG) has been used for decades for the treatment of leishmaniasis, but is now being replaced by miltefosine (MIL) and amphotericin B due to toxicity and widespread drug resistance. However, recent reports indicate a significant decrease in the efficacy of MIL with 20% of the patients relapsing within 12 months after treatment. Remarkably, and in contrast with SSG resistance, this relapse could not be related to reinfection, drug quality, drug exposure, or drug-resistant parasites which poses major questions about the cause of this treatment relapse. In a previous study we showed that parasites isolated from MIL relapse patients did have a different phenotype compared to the MIL cure Leishmania donovanii. However, it is not clear what the molecular basis of this difference is, if it is causal or not, and if other mechanisms could be involved. Therefore, the goal of this study is to find which molecular features are causing the observed leishmaniasis relapse after MIL treatment and the related increase in infectivity. Untargeted 'omics studies are particularly suited for this task, since in this case, there is no prior knowledge of which mechanisms could be involved. Out of all functional levels (genome, transcriptome, proteome and metabolome) the proteome is the level that translates genomic variety into metabolic and functional changes. Therefore, this study will characterize the proteomic differences between MIL cure and MIL relapse Leishmania isolates in order to find out what is causing this relapse.Researcher(s)
- Promoter: Cuypers Bart
Research team(s)
Project type(s)
- Research Project
A systems biology approach for a comprehensive understanding of development and adaptation in Leishmania donovani.
Abstract
This PhD project will undertake a systems biology approach to improve the understanding of Leishmania development and adaptation using a holistic view of cellular processes. As such, our goal is to stepwise unravel the complexity of the interactions between the different 'omic levels.Researcher(s)
- Promoter: Dujardin Jean-Claude
- Co-promoter: Laukens Kris
- Fellow: Cuypers Bart
Research team(s)
Project type(s)
- Research Project
A systems biology approach for a comprehensive understanding of development and adaptation in Leishmania donovani.
Abstract
This PhD project will undertake a systems biology approach to improve the understanding of Leishmania development and adaptation using a holistic view of cellular processes. As such, our goal is to stepwise unravel the complexity of the interactions between the different 'omic levels.Researcher(s)
- Promoter: Dujardin Jean-Claude
- Co-promoter: Laukens Kris
- Fellow: Cuypers Bart
Research team(s)
Project type(s)
- Research Project