STEP-UP - Single cell transcriptome and epigenome profiling to better understand organ development failure in MRKH patients

• Applicants: André Koch, Ph.D.; Professorin Dr. K. Katharina Rall; Professorin Julia M. Schulze-Hentrich, Ph.D.
• Subject Area: Gynaecology and Obstetrics
• Term: since 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 514121636

Mayer-Rokitansky-Küster-Hauser is a rare syndrome manifesting with aplasia or severe hypoplasia of uterine structures. Even though extensive studies have been performed, for the majority of cases the etiology remains unclear. In the first funding period, we sought to identify genetic causes in discordant twins as well as sporadic cases of MRKH using genome sequencing. However, no clear pathogenic differences were detected suggesting a minor role of genetics in MRKH etiology. In addition, we profiled endometrial tissue of uterus rudiments in a large cohort of MRKH patients using RNA sequencing and revealed widespread perturbations of gene activity that point at epigenetic regulation to play a role in MRKH which we now aim to better understand in this follow-up project. Similarly, transcriptome analyses of long-term expandable organoid cultures from the endometrium of MRKH patients, identified an array of dysregulated genes that are implicated in the interaction of epithelial cells with the extracellular matrix and/or the stromal compartment of endometrium in the uterine rudiments. Therefore, we hypothesize that in MRKH crucial interactions between epithelial and stromal cells might be impaired and need to be further investigated in this follow-up project. In four work packages, we propose to (i) characterize MRKH patient organoids using single-cell RNA- and ATAC-sequencing and DNA methylome analysis, (ii) investigate stromal cells derived from MRKH patients using single-cell RNA- and ATAC-sequencing and DNA methylome analysis, (iii) transcriptionally and epigenetically profile co-cultures of endometrial organoid models and stromal cells, and (iv) computationally analyze, integrate, and validate these data. The expected results will not only help to better understand the pathogenic origins of MRKH syndrome but also enable possible treatment opportunities to improve patients quality of life. While uterus transplantation has emerged as a highly promising approach for woman suffering from MRKH syndrome, it remains ethically and technically challenging. Using patient-specific cells for uterus reconstruction could overcome these limitations, but requires an in-depth understanding of their functionality and their interactions. Here, we aim to achieve this goal by combining our versatile endometrial organoid and co-culturing techniques with state-of-the art profiling approaches and computational analysis pipelines.

• DFG Programme: Research Grants
• Co-Investigator: Professorin Dr. Sara Brucker