Single-nuclei RNA-sequencing fails to detect molecular dysregulation in the preeclamptic placenta
Background: Single-cell RNA-sequencing has revolutionized our understanding of tissue complexity in health and disease. In the pregnancy-specific hypertensive disorder preeclampsia we previously applied the method toreveal massive transcriptional dysregulation across all placental cell classes in early-onset, but not late-onset preeclampsia, compared to gestation-matched controls. However, the placenta’s maternal-fetal interface, the syncytium, is multinucleated and largely inaccessible to cell dissociation. Nuclei isolation and single-nuclei RNA-seq may therefore be preferable in this and other inaccessible clinical tissues; not least due to ease of handling and compatibility with long-term tissue freezing and storage. Yet, nuclei contain a subsample of the cells’ full transcriptional profile, and mature transcripts critical to cellular function and disease processes may be missed.Here, we compare single-cell (sc) and single-nuclei (sn) RNA-seq on placentae from pregnancies with early-onset preeclampsia and controls.
Results: Mature syncytium was sampled substantially more efficiently by nuclei extraction. However, scRNA-seq was more sensitive, alleviating fine-level cell type assignment. In snRNA-seq, nuclei across placental cell classes further suffered ambient contamination of trophoblast transcripts. In preeclamptic samples, disease-related transcriptional dysregulation, including stress in stromal cells and vasculature, and massive inflammatory signature of myeloid immune cells were undetected from nuclei.
Conclusions: Our study reveals important advantages of cell dissociation over nuclei extraction for comprehensive single-cell transcriptomics studies of the placenta, especially to understand cell-type resolved dysregulation in pathologies. Yet, to address the dilemma of underrepresentation of the placenta’s multinucleated syncytium, studies will benefit from complementary nuclei sampling.
