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• Publications

  Cutting edge: characterization of human tissue-resident memory T Cells at different infection sites in patients with tuberculosis

  CD4+ regulatory T cells (Tregs) are acutely activated by traumatic injury, which suggests that they may react to injury with similar kinetics as memory T cells. …

• Publications

  Cutting edge: characterization of human tissue-resident memory T Cells at different infection sites in patients with tuberculosis

  Tissue-resident memory T cells (TRMs) have a key role in mediating the host defense against tuberculosis (TB) in mice, but their human counterparts have not been well characterized. …

• Publications

  Immunophenotyping and intracellular staining of fixed whole blood for mass cytometry (CyTOF)

  Non-invasive methods to obtain biological samples and single cell technologies are much sought after, as they provide an opportunity to comprehensively study human diseases …

• Publications

  Monogenic inflammatory bowel disease: It's never too late to make a diagnosis

  More than 50 different monogenic disorders have been identified as directly causing inflammatory bowel diseases, typically manifesting in the first years of life. We present the clinical course and immunological work-up of an adult patient who presented in adolescent years with an atypical gastrointestinal phenotype and was diagnosed more than two decades later with a monogenic disorder with important therapeutic implications. …

• Publications

  High-dimensional analysis of circulating and tissue-derived myeloid-derived suppressor cells from patients with glioblastoma

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• Publications

  Progress and applications of mass cytometry in sketching immune landscapes

  The immune plasticity is expressed in the remarkably heterogeneous milieus, including circulation and different tissues, during the homeostasis or during the various disease states.1 An array of adaptive responses, including training, priming, exhaustion, and tolerance, has been distinguished in adaptive and innate immunocytes. Precise classification of cell subpopulations with overlapping phenotypes and simultaneous interrogation of the phenotypic and functional properties of single cells in basal state and after their exposure to exogenous stimuli are of great significance. …

• From Bivariate to Multivariate Analysis of Cytometric Data: Overview of Computational Methods and Their Application in Vaccination Studies

  Flow and mass cytometry are used to quantify the expression of multiple extracellular or intracellular molecules on single cells, allowing the phenotypic and functional characterization of complex cell populations. Multiparametric flow cytometry is particularly suitable for deep analysis of immune responses after vaccination, as it allows to measure the frequency, the phenotype, and the functional features of antigen-specific cells. …

• Recent Advances in Computer-Assisted Algorithms for Cell Subtype Identification of Cytometry Data

  The progress in the field of high-dimensional cytometry has greatly increased the number of markers that can be simultaneously analyzed producing datasets with large numbers of parameters. Traditional biaxial manual gating might not be optimal for such datasets. To overcome this, a large number of automated tools have been developed to aid with cellular clustering of multi-dimensional datasets. Here were review two large categories of such tools; unsupervised and supervised clustering tools. After a thorough review of the popularity and use of each of the available unsupervised clustering tools, we focus on the top six tools to discuss their advantages and limitations. Furthermore, we employ a publicly available dataset to directly compare the usability, speed, and relative effectiveness of the available unsupervised and supervised tools. Finally, we discuss the current challenges for existing methods and future direction for the new generation of cell type identification approaches. …

• Publications

  Mass cytometry provides unprecedented insight into the role of B cells during the pathogenesis of multiple sclerosis

  In recent years, it has become clear that B cells play a prominent role in the pathogenesis of multiple sclerosis (MS). This is most evident when considering the effectiveness of anti-CD20 monoclonal therapeutics including rituximab and ocrelizumab. In fact many successful therapeutics alter the level of switched memory B cells. …

• The role of single-cell technology in the study and control of infectious diseases

  The advent of single-cell research in the recent decade has allowed biological studies at an unprecedented resolution and scale. In particular, single-cell analysis techniques such as Next-Generation Sequencing (NGS) and Fluorescence-Activated Cell Sorting (FACS) have helped show substantial links between cellular heterogeneity and infectious disease progression. …

• A cancer biologist’s primer on machine learning applications in high-dimensional cytometry”

  The application of machine learning and artificial intelligence to high-dimensional cytometry data sets has increasingly become a staple of bioinformatic data analysis over the past decade. This is especially true in the field of cancer biology, where protocols for collecting multiparameter single-cell data in a high-throughput fashion are rapidly developed. …

• Publications

  Mass cytometry—A tool for the curious Networking in Berlin

  In the past decade, mass cytometry has been revolutionizing cytomics due to its ability for high‐dimensional characterization of single cells using isotopetagged antibodies enabling the simultaneous interrogation of 40+ protein targets. It thereby captures the complexity of cellular systems at unprecedented depth and has been key to advances in human systems biology, in particular in the field of immunology and cancer biology. Cytomics by mass cytometry has also become an integral part of multi‐OMICS studies …

• Publications

  IgG3+ B cells are associated with the development of multiple sclerosis

  Disease‐modifying therapies (DMTs) targeting B cells are amongst the most effective for preventing multiple sclerosis (MS) progression. …

• Publications

  A network of immune and microbial modifications underlies viral persistence in the gastrointestinal tract

  Many pathogens subvert intestinal immunity to persist within the gastrointestinal tract (GIT); yet, the underlying mechanisms that enable sanctuary specifically in this reservoir are unclear. …

• Publications

  HIV efficiently infects T cells from the endometrium and remodels them to promote systemic viral spread

  The female reproductive tract (FRT) is the most common site of infection during HIV transmission to women, but viral remodeling complicates characterization of cells targeted for infection. …

• Publications

  Stimulation of strength controls the rate of initiation but not the molecular organization of TCR-induced signalling

  Millions of naïve T cells with different TCRs may interact with a peptide-MHC ligand, but very few will activate. Remarkably, this fine control is orchestrated using a limited set of intracellular machinery. …

• Publications

  Integrated RNA Sequencing and Single-Cell Mass Cytometry Reveal a Novel Role of LncRNA HOXA-AS2 in Tumorigenesis and Stemness of Hepatocellular Carcinoma

  Accumulating evidence indicates that long non-coding RNAs (lncRNAs) play critical roles in the development of many cancer types. …

• Publications

  PAI-1-dependent inactivation of SMAD4-modulated junction and adhesion complex in obese endometrial cancer

  ASC infiltration in endometrial tumor microenvironments positively correlates with BMI …

• Publications

  The identification and functional analysis of CD8+PD-1+CD161+ T cells in hepatocellular carcinoma

  Hepatocellular carcinoma (HCC) is one of the most common primary liver cancers, ranking the fourth leading cause of cancer-related death worldwide …

• Technologies for assessing vaccine responses in the very young

  Many vaccines are administered to young children in order to prevent infectious diseases early in life. At the same time, most of these vaccines are not developed specifically with the immune system of young children in mind and our understanding of how newborn immune systems differ from adult counterparts is incomplete. …