Biology subjects

Melsen, J. E.

Publications and source records attributed to Melsen, J. E..

4 recordsLinked to original sources

bioRxiv2026

Multi-omic profiling of human thymic B cells reveals intrathymic Ig-class switching and differentiation into multiple memory B cell subsets

Primarily recognized as the site for T cell development, the thymus supports a complex interplay between thymic stromal cells and developing thymocytes, which is essential for T cell maturation and the establishment of central tolerance. Emerging evidence indicates that thymic B cells contribute to tolerance induction by functioning as antigen-presenting cells. However, their developmental pathways and functional roles remain poorly understood. Using tissue mass cytometry, we localized B cells in the thymus and their orientation towards other cells in the medulla. We characterized the heterogeneity of thymic B cells using single-cell RNA sequencing of cells isolated from human thymi, identifying naive, germinal center-like, plasma cell, and multiple memory B cell populations. We identified a distinct pre-B cell subset with local thymic B cell development potential, that can develop due to the inhibition of Notch signaling by Deltex1, a Notch antagonist. Using BCR repertoire analysis, we explored clonal diversity, somatic hypermutation patterns and class switch recombination of thymic B cells. Spectral flow cytometry further validated the surface phenotype of thymic B cell populations and confirmed the presence of distinct CD21-CD27- memory compartments with heterogeneous surface immunoglobulin isotype usage. In doing so we provide novel insights into the unique biology of human thymic B cells, their development, and their differentiation in the human thymus. We conclude that the human thymus supports local B cell development and differentiation into medullary memory-like populations that undergo class switching with limited somatic hypermutation, suggesting secondary lymphoid-like B cell programs adapted to central tolerance induction. One Sentence SummaryThe human thymus is not only a primary lymphoid organ for T cell development, but also a secondary site for the development and maturation of unique populations of B cells.

immunology↗

bioRxiv2026

Mapping human natural killer cell development in tonsil

Secondary lymphoid tissue, including tonsil, supports human NK cell development, but the spatial organization and tissue niches that drive this differentiation remain undefined. Here, we used single cell analysis of cyclic immunofluorescence to generate a comprehensive atlas of human NK cell development in tonsil. By integrating regional localization, chemokine signaling, cytokine availability, and cell phenotype, we show that NK cell differentiation follows a reproducible spatial trajectory defined by stage-specific cell-cell interactions. CD34+ NK cell progenitors are found in the interfollicular domain in proximity to high endothelial venules, consistent with this route of progenitor entry into tissue. Mature NK cells are primarily found in the T cell-rich parafollicular domain, where they interact with other NK cells and T cell subsets. Local inflammation increases NK cell frequency in tissue through both proliferation of NK progenitors and increased frequency of mature NK cells. Finally, we identify a subset of tonsil stromal cells that support differentiation of NK cells in vitro and proliferation of NK precursors in situ. Together, these findings demonstrate that spatial localization defines human NK cell development and provide an in situ definition of niches that support human NK cell differentiation in tonsil.

immunology↗

bioRxiv2024

Immunophenotyping of T cells combined with Vβ antibodies identifies long lasting CMV related T cell expansions with a consistent TIGIT and PD-1 phenotype

Simultaneous analysis of T cell receptor repertoire and T cell phenotype is of high relevance to gain a deeper understanding on the T cell response in terms of differentiation, kinetics and persistence. Also it is currently unknown how the repertoire of immune checkpoints on T cells evolves over time. To fully capture the heterogenous response, TCR repertoire and T cell phenotype analysis is preferably performed at the single-cell level, but this is costly and analytically challenging. Therefore, we developed a flow cytometry based method that allows for simultaneous characterization of the T cell TCR V{beta} and the phenotype. We generated a 9-tube 24-color panel with antibodies against maturation and activation markers, and 24 TCR V{beta} chains. Peripheral blood mononuclear cells from 5 healthy controls were analyzed, revealing the presence of oligoclonal expansions. Within the CD27+CD28+ memory T cell population, oligoclonal expansions were characterized by a T regulatory, or KLRG1+CCR7-CD27low phenotype. Within the late CD27- and/or CD28-memory T cells, the populations with the lowest TCR V{beta} diversity expressed CX3CR1. As a proof of principle, we demonstrate the dynamics of circulating oligoclonal T cell expansions that emerged following hematopoietic stem cell transplantation in the presence of CMV in 2 patients. We provide evidence that oligoclonal T cells transferred from donor to recipient can be traced up to at least 2.5 years while maintaining its phenotype. Mostly TIGIT and PD-1 were critical in defining T cell expansions, while CD45RA, CD57, CD56 and NKG2A were variably expressed. Overall, we developed a phenotype based method to trace T cell populations, that is widely applicable to different settings in which the T cell response needs to be monitored.

immunology↗

bioRxiv2023

Mapping human natural killer cell development in pediatric tonsil by imaging mass cytometry & high-resolution microscopy

Natural killer (NK) cells develop from CD34+ progenitors in a stage-specific manner defined by changes in cell surface receptor expression and function. Secondary lymphoid tissues, including tonsil, are sites of human NK cell development. Here we present new insights into human NK cell development in pediatric tonsil using cyclic immunofluorescence and imaging mass cytometry. We show that NK cell subset localization and interactions are dependent on NK cell developmental stage and tissue residency. NK cell progenitors are found in the interfollicular domain in proximity to cytokine-expressing stromal cells that promote proliferation and maturation. Mature NK cells are primarily found in the T-cell rich parafollicular domain engaging in cell-cell interactions that differ depending on their stage and tissue residency. The presence of local inflammation results in changes in NK cell interactions, abundance, and localization. This study provides the first comprehensive atlas of human NK cell development in secondary lymphoid tissue.

immunology↗