Project Details
Projekt
Deciphering Immune Cell Function in the Testis and Epididymis by Single-Cell Transcriptomics, Spatial Proteomics and Integrative Bioinformatics (Central Project Z1 of the FOR 5644 ‘INFINITE’)
Subject Area
Reproductive Medicine, Urology
Term
since 2024
Project identifier
Deutsche Forschungsgemeinschaft (DFG) - Project number 515636567
Advancing research of immune cell function in testis and epididymis as proposed in the FOR ‘INFINITE’ heavily depends on modern high-throughput methodologies. Understanding cell-specific gene-regulatory events and their impact on cellular networks in diseased and normal tissues requires central access to transcriptomic approaches like RNA-seq and related techniques. These methods allow the efficient detection and quantification of all expressed transcripts in a given population of cells by Next Generation Sequencing (NGS) and enable identification of gene regulatory networks and inference of upstream signaling pathways. A major challenge in the study area is to understand the heterogeneity, development, differentiation and especially the microenvironment of different leukocyte cell types in the spatial context of the testis and epididymis under normal and diseased conditions. NGS applications have advanced dramatically since the advent of droplet-based single-cell RNA-sequencing (scRNA-seq) approaches. In contrast to classical approaches like microscopy or cytometry, scRNA-seq allows classification of individual single cells based on their transcriptome rather than surface markers. Using this approach has revealed an extreme heterogeneity of immune cells in general and helped to unveil a high number of leukocyte subpopulation in the testis and epididymis in preparatory work, which helped to shape the aims of INFINITE projects. Although scRNA-seq has transformed our understanding by providing unprecedented resolution of transcriptomics differences between cell types, spatial information of individual cells is lost during tissue dissociation. This in turn is provided on the protein level by co-detection by indexing (CODEX). This method allows multiplexed tissue imaging and relies on DNA-conjugated antibodies and the cyclic addition and removal of complementary fluorescently labelled DNA probes. Thereby, CODEX reveals insight into the tissue architecture and cellular organization in a high-throughput manner. The central project Z will provide an integrative platform delivering NGS-based and CODEX technologies to the projects of the FOR. We will provide established experimental procedures and the necessary equipment to process biological samples in addition to the bioinformatics and systems biology methods needed for their interpretation. This ensures the standardized and reproducible analysis for a state-of-the-art interpretation of the highly complex data to put them in an organ context. Furthermore, this central project will develop specific software solutions tailored for the projects to address their specific questions of study. Moreover, this central project will provide training opportunities for PhD students and postdocs in order to familiarise them with up to date bioinformatics analysis strategies, especially for the analysis of transcriptomic and CODEX data.
DFG Programme
Research Units
