Biology subjects

Ziebell, F.

Publications and source records attributed to Ziebell, F..

5 recordsLinked to original sources

bioRxiv2026

High-throughput platforms for genetic perturbation screening using CRISPR/Cas9 in human iPSC-derived macrophages for drug discovery

Human induced Pluripotent Stem Cell (hiPSC) models have revolutionised drug discovery, offering high translational relevance for recapitulating disease biology and thereby the potential to help reduce drug attrition. Macrophages are pivotal for maintaining tissue homeostasis and orchestrating immune responses; their dysregulation underpins several diseases, including autoinflammatory disorders, neurodegeneration, and cancer. Therapeutically targeting this cell type presents an attractive strategy to simultaneously influence multiple cellular mediators and functions. We have established a scalable, semi-automated, and physiologically relevant hiPSC-derived macrophage model, rigorously characterised through deep comparative multi-omics. We have also integrated our hiPSC-derived macrophage platform with large-scale CRISPR screening workflows designed for parallel genetic interrogation of thousands of gene targets, in both arrayed and pooled formats. In this manuscript, we apply those genetic screening methods to hiPSC-derived macrophages and showcase how genetic perturbations alter pro- and anti-inflammatory transcriptional signatures and significantly impact functional phenotypes in this cell model. This integrated approach allows for the exploration of novel genetic insights linked to causal disease biology, advancing myeloid cell-associated target discovery across a broad spectrum of therapeutic areas.

immunology↗

bioRxiv2025

A quantitative approach to discover nonlinear signaling linking combinatorial environments with cellular responses

Cells constantly integrate diverse inputs from the extracellular environment, yet our understanding of how cells effectively process information from multiple cues at the same time remains limited. We utilized an integrated imaging platform and RNAseq analysis to investigate the combined effects of growth factors on cellular signaling and gene expression. Paired stimuli by receptor ligands revealed diverse signaling signatures-- ranging from antagonism to synergy--driving global signaling programs and gene expression. Notably, correlation networks based on signaling signatures identified vulnerabilities in cancer cells when compared to synergistic drug combinations. Profiling kinase and phosphatase activities uncovered a crucial interplay, where cellular sensitivity and phospho-turnover dynamics are modulated by input history through coordinated basal kinase and phosphatase activities. Our novel methodology sheds light on cellular processing of multiple cues, elucidating intricate mechanisms underlying cellular adaptation to extracellular environmental variations. Based on previous preprint: doi: https://doi.org/10.1101/346957

cell biology↗

bioRxiv2019

Biological Plasticity Rescues Target Activity in CRISPR Knockouts

Gene knockouts (KOs) are efficiently engineered through CRISPR-Cas9-induced frameshift mutations. While DNA editing efficiency is readily verified by DNA sequencing, a systematic understanding of the efficiency of protein elimination has been lacking. Here, we devised an experimental strategy combining RNA-seq and triple-stage mass spectrometry (SPS-MS3) to characterize 193 genetically verified deletions targeting 136 distinct genes generated by CRISPR-induced frameshifts in HAP1 cells. We observed residual protein expression for about one third of the quantified targets, at variable levels from low to original, and identified two causal mechanisms, translation reinitiation leading to N-terminally truncated target proteins, or skipping of the edited exon leading to protein isoforms with internal sequence deletions. Detailed analysis of three truncated targets, BRD4, DNMT1 and NGLY1, revealed partial preservation of protein function. Our results imply that systematic characterization of residual protein expression or function in CRISPR-Cas9 generated KO lines is necessary for phenotype interpretation.

bioengineering↗

bioRxiv2018

A combinatorial extracellular code tunes the intracellular signaling network activity to distinct cellular responses

Cells constantly survey a complex set of inputs that is processed by the intracellular signaling network, but little is known of how cells integrate input information from more than one cue. We employed a FRET biosensor-based imaging platform to study the effect of combinatorial growth factor levels on the signaling network in human cells. We found that pairwise stimuli caused distinct concentration- and ratio-dependent signaling states through signaling signatures such as antagonism, additivity and synergy. The unique signaling states correlated with differential gene expression and non-additive transcription patterns. We further elucidated how a signal-rich environment can fine-tune the signaling network and adjust physiological outcomes, by kinase and phosphatase activity profiling. We describe how complex extracellular conditions affect phospho-turnover and the basal phosphorylation status. Thus, we provide mechanistic insights into cellular processing of multiple cues and explain part of the complexity of cellular adaptation to changes in the extracellular environment.

cell biology↗

bioRxiv2017

Revealing Age-Related Changes of Adult Hippocampal Neurogenesis

In the adult hippocampus, neural stem cells (NSCs) continuously produce new neurons that integrate into the neuronal network to modulate learning and memory. The amount and quality of newly generated neurons decline with age, which can be counteracted by increasing intrinsic Wnt activity in NSCs. However, the precise cellular changes underlying this age-related decline or its rescue through Wnt remain unclear. The present study combines development of a mathematical model and experimental data to address features controlling stem cell dynamics. We show that available experimental data fit a model in which quiescent NSCs can either become activated to divide or undergo depletion events, consisting of astrocytic transformation and apoptosis. Additionally, we demonstrate that aged NSCs remain longer in quiescence and have a higher probability to become re-activated versus being depleted. Finally, our model explains that high NSC-Wnt activity leads to longer time in quiescence while augmenting the probability of activation.

systems biology↗