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Makrodimitris, S. (author), Pronk, I.B. (author), Abdelaal, T.R.M. (author), Reinders, M.J.T. (author)Multi-omic analyses are necessary to understand the complex biological processes taking place at the tissue and cell level, but also to make reliable predictions about, for example, disease outcome. Several linear methods exist that create a joint embedding using paired information per sample, but recently there has been a rise in the...review 2024
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Singh, A. (author), Biharie, K. (author), Reinders, M.J.T. (author), Mahfouz, A.M.E.T.A. (author), Abdelaal, T.R.M. (author)Motivation: Single-cell technologies allow deep characterization of different molecular aspects of cells. Integrating these modalities provides a comprehensive view of cellular identity. Current integration methods rely on overlapping features or cells to link datasets measuring different modalities, limiting their application to experiments...journal article 2023
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van der Sluis, Tetje C. (author), Beyrend, Guillaume (author), van der Gracht, Esmé T.I. (author), Abdelaal, T.R.M. (author), Jochems, Simon P. (author), Belderbos, Robert A. (author), Wesselink, Thomas H. (author), van Duikeren, Suzanne (author), Arens, Ramon (author)Immune checkpoint therapy (ICT) has the power to eradicate cancer, but the mechanisms that determine effective therapy-induced immune responses are not fully understood. Here, using high-dimensional single-cell profiling, we interrogate whether the landscape of T cell states in the peripheral blood predict responses to combinatorial targeting...journal article 2023
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Zhang, Yun (author), Miller, Jeremy A. (author), Park, Jeongbin (author), Lelieveldt, B.P.F. (author), Abdelaal, T.R.M. (author), Dzyubachyk, O. (author), Lein, Ed S. (author), Scheuermann, Richard H. (author)With the advent of multiplex fluorescence in situ hybridization (FISH) and in situ RNA sequencing technologies, spatial transcriptomics analysis is advancing rapidly, providing spatial location and gene expression information about cells in tissue sections at single cell resolution. Cell type classification of these spatially-resolved cells...journal article 2023
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Koppejan, Hester (author), Beyrend, Guillaume (author), Hameetman, Marjolijn (author), Abdelaal, T.R.M. (author), Toes, René E.M. (author), van Gaalen, Floris A. (author)Objective: Mass cytometry (MC) immunoprofiling allows high-parameter phenotyping of immune cells. We set to investigate the potential of MC immuno-monitoring of axial spondyloarthritis (axSpA) patients enrolled in the Tight Control SpondyloArthritis (TiCoSpA) trial. Methods: Fresh, longitudinal PBMCs samples (baseline, 24, and 48 weeks) from...journal article 2023
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Heezen, L. G.M. (author), Abdelaal, T.R.M. (author), van Putten, M. (author), Aartsma-Rus, A. (author), Mahfouz, A.M.E.T.A. (author), Spitali, P. (author)Duchenne muscular dystrophy is caused by mutations in the DMD gene, leading to lack of dystrophin. Chronic muscle damage eventually leads to histological alterations in skeletal muscles. The identification of genes and cell types driving tissue remodeling is a key step to developing effective therapies. Here we use spatial transcriptomics in...journal article 2023
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Li, Na (author), Zhu, Junhui (author), Chen, Peiru (author), Bao, Chuntong (author), Wang, Jun (author), Abdelaal, T.R.M. (author), Chen, Dexi (author), Zhu, Sibo (author), Wang, Wenjing (author)Due to the increase in bacterial resistance, improving the anti-infectious immunity of the host is rapidly becoming a new strategy for the prevention and treatment of bacterial pneumonia. However, the specific lung immune responses and key immune cell subsets involved in bacterial infection are obscure. Actinobacillus pleuropneumoniae (APP)...journal article 2023
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Eltager, M.A.M.E. (author), Abdelaal, T.R.M. (author), Charrout, M. (author), Mahfouz, A.M.E.T.A. (author), Reinders, M.J.T. (author), Makrodimitris, S. (author)Deep generative models, such as variational autoencoders (VAE), have gained increasing attention in computational biology due to their ability to capture complex data manifolds which subsequently can be used to achieve better performance in downstream tasks, such as cancer type prediction or subtyping of cancer. However, these models are...journal article 2023
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Thomsen, L.C.V. (author), Kleinmanns, Katrin (author), Anandan, Shamundeeswari (author), Gullaksen, Stein Erik (author), Abdelaal, T.R.M. (author), Iversen, Grete Alrek (author), Akslen, Lars Andreas (author), McCormack, Emmet (author), Bjørge, Line (author)The prognosis of high-grade serous ovarian carcinoma (HGSOC) is poor, and treatment selection is challenging. A heterogeneous tumor microenvironment (TME) characterizes HGSOC and influences tumor growth, progression, and therapy response. Better characterization with multidimensional approaches for simultaneous identification and...journal article 2023
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Li, Chang (author), Thijssen, Julian (author), Kroes, Thomas (author), de Boer, Mitchell (author), Abdelaal, T.R.M. (author), Höllt, T. (author), Lelieveldt, B.P.F. (author)In spatial transcriptomics (ST) data, biologically relevant features such as tissue compartments or cell-state transitions are reflected by gene expression gradients. Here, we present SpaceWalker, a visual analytics tool for exploring the local gradient structure of 2D and 3D ST data. The user can be guided by the local intrinsic...journal article 2023
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van Unen, Vincent (author), Ouboter, Laura F. (author), Li, Na (author), Schreurs, Mette (author), Abdelaal, T.R.M. (author), Kooy-Winkelaar, Yvonne (author), Beyrend, Guillaume (author), Höllt, T. (author), Maljaars, P. W.Jeroen (author), Mearin, M. Luisa (author), Mahfouz, A.M.E.T.A. (author), Witte, Anne M.C. (author), Clemens, Cornelis H.M. (author), Abraham, Sunje (author), Escher, Johanna C. (author), Lelieveldt, B.P.F. (author), Pascutti, M. Fernanda (author), van der Meulen – de Jong, Andrea E. (author), Koning, Frits (author)Chronic intestinal inflammation underlies inflammatory bowel disease (IBD). Previous studies indicated alterations in the cellular immune system; however, it has been challenging to interrogate the role of all immune cell subsets simultaneously. Therefore, we aimed to identify immune cell types associated with inflammation in IBD using high...journal article 2022
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Eltager, M.A.M.E. (author), Abdelaal, T.R.M. (author), Mahfouz, A.M.E.T.A. (author), Reinders, M.J.T. (author)Motivation: Single-cell multi-omics assays simultaneously measure different molecular features from the same cell. A key question is how to benefit from the complementary data available and perform cross-modal clustering of cells. Results: We propose Single-Cell Multi-omics Clustering (scMoC), an approach to identify cell clusters from data...journal article 2022
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Pardieck, Iris N. (author), van der Sluis, Tetje C. (author), van der Gracht, Esmé T.I. (author), Veerkamp, Dominique M.B. (author), Behr, Felix M. (author), van Duikeren, Suzanne (author), Beyrend, Guillaume (author), Rip, Jasper (author), Abdelaal, T.R.M. (author)Understanding the mechanisms and impact of booster vaccinations are essential in the design and delivery of vaccination programs. Here we show that a three dose regimen of a synthetic peptide vaccine elicits an accruing CD8<sup>+</sup> T cell response against one SARS-CoV-2 Spike epitope. We see protection against lethal SARS-CoV-2 infection...journal article 2022
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Brouwer, Thomas P. (author), de Vries, Natasja L. (author), Abdelaal, T.R.M. (author), Li, Zheng (author), Ruano, Dina (author), Fariña, Arantza (author), Lelieveldt, B.P.F. (author), Morreau, Hans (author), Vahrmeijer, Alexander L. (author)BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy in need of effective (immuno)therapeutic treatment strategies. For the optimal application and development of cancer immunotherapies, a comprehensive understanding of local and systemic immune profiles in patients with PDAC is required. Here, our goal was to...journal article 2022
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Abdelaal, T.R.M. (author)Single-cell technologies have emerged as powerful tools to analyze complex tissues at the single-cell resolution, resolving the cellular heterogeneity within a tissue through the discovery of different cell populations. Over the past decade, single-cell technologies have greatly developed allowing the profiling of various molecular features...doctoral thesis 2021
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van der Gracht, Esmé T.I. (author), Beyrend, Guillaume (author), Abdelaal, T.R.M. (author), Pardieck, Iris N. (author), Wesselink, Thomas H. (author), van Haften, Floortje J. (author), van Duikeren, Suzanne (author), Koning, Frits (author), Arens, Ramon (author)SummaryFactors that govern the complex formation of memory T cells are not completelyunderstood. A better understanding of thedevelopment of memory Tcell hetero-geneity is however required to enhance vaccination and immunotherapy ap-proaches. Here we examined the impact of pathogen- and tissue-specific cueson memory CD8+T cell heterogeneity...journal article 2021
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Anandan, Shamundeeswari (author), Thomsen, Liv Cecilie V. (author), Gullaksen, Stein Erik (author), Abdelaal, T.R.M. (author), Kleinmanns, Katrin (author), Skavland, Jørn (author), Bredholt, Geir (author), Gjertsen, Bjørn Tore (author), McCormack, Emmet (author), Bjørge, Line (author)Improved molecular dissection of the tumor microenvironment (TME) holds promise for treating high-grade serous ovarian cancer (HGSOC), a gynecological malignancy with high mortality. Reliable disease-related biomarkers are scarce, but single-cell mapping of the TME could identify patient-specific prognostic differences. To avoid technical...journal article 2021
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Abdelaal, T.R.M. (author), Mourragui, S.M.C. (author), Mahfouz, A.M.E.T.A. (author), Reinders, M.J.T. (author)Single-cell technologies are emerging fast due to their ability to unravel the heterogeneity of biological systems. While scRNA-seq is a powerful tool that measures whole-transcriptome expression of single cells, it lacks their spatial localization. Novel spatial transcriptomics methods do retain cells spatial information but some methods can...journal article 2020
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Abdelaal, T.R.M. (author), van Unen, Vincent (author), Höllt, T. (author), Koning, Frits (author), Reinders, M.J.T. (author), Mahfouz, A.M.E.T.A. (author)Mass cytometry by time-of-flight (CyTOF) is a valuable technology for high-dimensional analysis at the single cell level. Identification of different cell populations is an important task during the data analysis. Many clustering tools can perform this task, which is essential to identify “new” cell populations in explorative experiments....journal article 2019
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Abdelaal, T.R.M. (author), Michielsen, L.C.M. (author), Cats, Davy (author), Hoogduin, Dylan (author), Mei, Hailiang (author), Reinders, M.J.T. (author), Mahfouz, A.M.E.T.A. (author)Background: Single-cell transcriptomics is rapidly advancing our understanding of the cellular composition of complex tissues and organisms. A major limitation in most analysis pipelines is the reliance on manual annotations to determine cell identities, which are time-consuming and irreproducible. The exponential growth in the number of...journal article 2019
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