Biology subjects

De Ridder, K.

Publications and source records attributed to De Ridder, K..

3 recordsLinked to original sources

bioRxiv2026

Lung cancer-fueled emergency myelopoiesis is characterized by an increase of S100A9+ and LCN2+ hematopoietic stem and progenitor cells

The pivotal role of tumor infiltrating myeloid cells in lung cancer composition and response to therapy is universally recognized. Nevertheless, their main cradle being the bone marrow (BM), remains vastly understudied owing to the spatiotemporal complexity of hematopoiesis and its hard to access anatomical location. Therefore, the BM niche of lung cancer subjects remains understudied which is why we integrated transcriptional and translational single-cell profiling, ELISA and two-photon microscopy to characterize the medullary hematopoietic compartment in orthotopic lung cancer-bearing mice with validation in human non-small cell lung cancer (NSCLC) samples. In brief we found that lung cancer remotely alters the entire hematopoietic process resulting in higher levels of hematopoietic stem cells (HSCs), myeloid and lymphoid multipotent progenitors (MPPs) and downstream predominance of Granulocyte Monocyte Progenitors (GMP), early Granulocyte Progenitors (GP) and Common Monocyte Progenitors (cMoP) at the expense of mature neutrophils and B cells. Furthermore, a significant increase in the expression and secretion of S100A9 and Lipocalin-2 (LCN2), was characteristic across the entire hematopoietic trajectory in lung cancer-bearing mice and patients. In vivo inhibition of S100A9 with Tasquinimod reduced tumor growth, irrespective of its combination with immunotherapy. In addition, it altered the secretion profile of S100A9 but also LCN2 in the BM, suggesting that S100A9 serves as an upstream regulator of LCN2 and holds therapeutic premise to treat immunotherapy refractory lung cancer.

immunology↗

bioRxiv2025

Longitudinal cell-free DNA methylome and fragmentome profiles in health uncover signatures of cell type and demographic origin

Cell-free DNA (cfDNA) is a powerful analyte for liquid biopsy applications. However, the composition and fragmentation of cfDNA in health remains incompletely characterized. Here, we profiled 432 plasma cfDNA samples from healthy individuals using targeted enzymatic methyl-sequencing, allowing cell-type of origin inference and assessment of fragmentation features. Both in a diurnal and a cross-sectional cohort, we observed that cfDNA levels and cellular contributions show lower variability within than between individuals. Hematopoietic lineages are the dominant cfDNA sources, with interindividual variability particularly evident in granulocyte contributions. Demographic factors such as sex, age and body mass index (BMI) contribute to changes in the contribution of various blood cell types, and cfDNA concentrations are 1.6-fold higher in early morning collections (P = 1.8 x 10-5). By integrating cell-type-specific cfDNA methylation, fragment size and dinucleotide end motif information, we demonstrate distinct associations of these characteristics with specific cell types. Granulocyte-derived fragments showed a consistent enrichment in mononucleosomal sizes (P = 3.5 x 10-54) and CC end motifs, while also cfDNA from non-hematopoietic cells exhibited distinct size and end-motif profiles. In addition, we observed hypomethylated DNA to be associated with shorter fragment sizes and altered end-motif frequencies, emphasizing interactions between DNA methylation, nuclease activity and chromatin context in shaping cfDNA features. Together, our results provide a view on processes and cell types involved in cfDNA biogenesis in healthy individuals. They underscore that demographic variables and sampling time should be considered for cfDNA-based assay design, but also highlight novel opportunities to improve the representation of specific cell types in cfDNA, thus providing a foundation for optimizing cfDNA diagnostics by leveraging multiple axes of information.

genomics↗

bioRxiv2025

Maternal Vitamin C Deficiency and Genetic Risk Factors Contribute to Congenital Defects through Dysregulation of DNA Methylation.

AbstractMaternal dietary insufficiencies can reshape the fetal epigenome during gestation, contributing to birth defects and developmental disorders. Vitamin C (VitC) is a critical co-factor for Ten-Eleven- Translocation (TET) DNA demethylases, but the impact of its deficiency on embryonic development has gone largely unappreciated. Here, we show that maternal VitC deficiency in L-gulonolactone oxidase (Gulo)-deficient mice, which like humans are unable to synthesize VitC, can cause highly penetrant developmental delays and malformations in non-inbred embryos during the vulnerable period of gastrulation. DNA hypermethylation in Gulo-/- embryonic neural tissues of susceptible strains increases with VitC dose reduction and with the severity of embryonic pathologies, coinciding with hallmarks of TET1 dysfunction. A moderate reduction in VitC status is sufficient to induce DNA hypermethylation and cause neural tube defects. Our results suggest that promoting timely VitC supplementation by at-risk pregnant mothers may prevent a range of birth defects and enhance health outcomes of future generations.

developmental biology↗