Single-Cell Transcriptomics in Computational Biology and Toxicology
Our single-cell transcriptomics projects aim to harness this advanced method to reveal cell-type specific molecular responses to chemical perturbations. Building on our extensive expertise in this field, which began with the Helmholtz Incubator project Sparse2Big, we continue to innovate and lead in the analysis of single-cell transcriptomics data.
The primary goal of our single-cell transcriptomics research is to understand how different cell types within an organism respond at a molecular level to various chemical exposures. By identifying these specific responses, we can gain valuable insights into the mechanisms of toxicity and the potential risks posed by different chemicals.
Our team has a long-standing history of excellence in single-cell transcriptomics, particularly in data analysis. Starting from the Sparse2Big project, we have analyzed different imputation methods to facilitate the data analysis of large but sparse data sets and participated in various single-cell projects with clinical and toxicological background that allow us to handle and interpret the complex data generated by single-cell transcriptomics.
Our research is not just about advancing scientific knowledge; it also
has practical implications for regulatory purposes. By shaping
single-cell transcriptomic data analysis, we aim to provide robust,
reproducible, and detailed insights that can inform regulatory decisions
and ensure safer chemical use.
Model Systems
To achieve our objectives, we utilize a variety of advanced model systems, each offering unique insights into cellular responses:
Human Retina Organoids: These organoids provide a relevant model for studying the effects of chemicals on human retinal cells, helping us to understand potential impacts on vision and ocular health.
Human Placenta Organoids: By studying placenta organoids, we can investigate how chemicals might affect fetal development and maternal health, offering critical insights into reproductive toxicology.
Zebrafish Larvae: Zebrafish (Danio rerio) are a versatile model organism that allows for the observation of chemical effects on a whole organism level, providing comprehensive data on developmental and systemic responses.
Related own publications:
Reliability of human retina organoid generation from hiPSC-derived neuroepithelial cysts (2023).
Front Cell Neurosci 2023 Oct 6:17:1166641
https://doi.org/10.3389/fncel.2023.1166641
HBEGF-TNF induce a complex outer retinal pathology with photoreceptor cell extrusion in human organoids (2022).
Nat Commun 13, 6183
https://doi.org/10.1038/s41467-022-33848-y
Benchmarking scRNA-seq imputation tools with respect to network
inference highlights deficits in performance at high levels of sparsity
(2021).
https://doi.org/10.1101/2021.04.02.438193
Related own data sets:
Reliability of human retinal organoid generation from hiPSC-derived neuroepithelial cysts (2023).
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE237007
Single-cell RNASeq analysis of human retinal organoids generated from hiPSC derived of a healthy donor patient (2022).
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE174215
HBEGF-TNF induces a complex retinal pathology with macular degeneration hallmarks in human organoids (2022).
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE146641