Biology subjects

Yildiz, D.

Publications and source records attributed to Yildiz, D..

3 recordsLinked to original sources

bioRxiv2026

Physiological re-replication during human stem cell differentiation

During defined developmental windows in Drosophila, controlled re-replication generates physiological gene amplification. Although gene amplification has also been observed during human stem cell differentiation, re-replication in human cells has largely been linked to tumor-associated genome instability. Here, we demonstrate that re-replication likewise operates as a physiological mechanism in human stem cells. Using Rerep-Seq and DNA fiber-combing, we identify distinct phases of re-replication during the differentiation of human myoblasts into myotubes and during the lineage commitment of mesenchymal stem cells toward adipogenic, osteogenic, chondrogenic, and neuronal fates. In all differentiation systems examined, re-replication occurred within defined temporal windows. FACS-isolated re-replicating cells exhibited elevated gene expression using RNA-Seq specifically within re-replicated genomic regions. Moreover, re-replicated DNA was detected as extranuclear DNA. These findings support a model in which cells that do not undergo re-replication, and thus avoid increased chromosomal instability, may nonetheless boost the expression of differentiation-relevant genes by acquiring re-replicated DNA released from neighboring re-replicating cells. We propose that human stem cells exploit an evolutionarily conserved re-replication mechanism to transiently increase gene copy number and thereby meet the heightened protein demands associated with differentiation.

genomics↗

bioRxiv2023

Extracellular release of a disintegrin and metalloproteinases orchestrates periodontal disease severity

Periodontal diseases are amongst the most common pathologies worldwide with a high risk for the development of systemic complications. Periodontal disease is driven by oral pathogens such as Porphyromonas gingivalis and the release of inflammatory cytokines. These cytokines (e.g. TNF) or their receptors (IL-1R) are substrates of a disintegrin and metalloproteinases (ADAMs). In a comparative approach, we observed an increase of ADAM8 protein expression and activity in the sulcus fluid of periodontal disease patients correlating with the disease stage. In contrast, the induced ADAM10 expression was decreased. In vitro mechanistic studies revealed that both Porphyromonas gingivalis infection and the resulting cytokine release orchestrated the release of soluble ADAM8 by keratinocytes and neutrophils as soluble ectodomain and on exosomes, respectively. Furthermore, ADAM8 regulated the release of ADAM10 and MMP9, thereby potentially influencing wound healing and tissue destruction. Thus, the dysregulation of the cell-associated and extracellular ADAM proteolytic activity mainly driven by ADAM8 may be an essential regulatory element in periodontal disease onset and progression. This potential as novel local treatment option should be addressed in future translational studies.

immunology↗

bioRxiv2023

Modeling of lung-liver interaction during infection in a human microfluidic organ-on-a-chip

BackgroundInfections of the respiratory tract such as pneumonia or COVID-19 cause high mortality and morbidity worldwide. Organ-on-a-chip (OC) technologies have been developed in the last years to establish human-based disease models, to study basic disease mechanisms and to provide a tool to speed up drug development. The aim of this study was to establish a lung-liver microfluidic system to study the interaction of both organ modules during infection. MethodsA two organ (lung / liver) microfluidic system was established using primary human bronchial (HBECs) or alveolar type epithelial cells (ATC) for the lung module and Huh-7 cells for the liver module. Inactivated non typeable Haemophilus influenzae (NTHi) and Pseudomonas aeruginosa PAO1 (PAO1) were applied to the lung module. Secreted mediators were screened by dot-blot analysis and quantified. The effect of lung epithelial bacterial stimulation on the liver cell transcriptome was analyzed by mRNA sequencing. ResultsLung and liver cells established stable cultures in a circulatory microfluidic system. Activation of HBECs or ATCs with NTHi or PAO1 resulted in the secretion of multiple inflammatory mediators into the microfluidic medium including TNF-, monocyte chemotactic protein-1 (MCP-1) and macrophage inflammatory protein-3 (MIP-3). Addition of lung cells and application of bacterial onto the HBECs module resulted in the gross change of the transcriptome of the liver cell module. Gene ontology enrichment analysis showed the induction of various pathways involved in host defense, metabolisms, repair, and acute phase response. InterpretationIn conclusion, a two-organ lung/liver microfluidic system was established to study the interaction of the organ modules during infection. Mediators released from epithelial culture modules into the microfluidic circulation after exposure to bacterial pathogens significantly modify the gene expression patterns of liver cells. FundingThis research was funded by the German Federal Ministry of Education and Research (BMBF), 031L0153 VISION "Alternativmethoden zum Tierversuch" and the Dr. Rolf M. Schwiete Stiftung.

cell biology↗