Extended Data Fig. 10: Annotation and benchmark of trophoblast in vitro models.

a: Dot plots showing normalised, log-transformed and variance-scaled expression of genes (Y-axis) characteristic of trophoblast cell states (X-axis) in primary trophoblast organoids (PTO, left) and trophoblast stem cell (TSC, right) models. Marked in red are genes that differ from the in vivo observed expression pattern. b: Dot plot showing normalised, log-transformed and variance-scaled expression of genes (X-axis) of signalling molecules known to be upregulated in in vivo trophoblast invasion plotted in trophoblast organoids (Y-axis). c: UMAP (uniform manifold approximation and projection) scatterplot of PTO single-cell RNA sequencing (scRNA-seq data, n = 26,853 cells) coloured by predicted cell state (top left) and probability (top center) according to our logistic regression model. Only in vivo data from donor P13 (snRNA-seq) was considered for the training. Confusion matrix with predictions on test set based on common features with PTO (Top right). UMAP scatterplot of TSC scRNA-seq data (n = 9957 cells) coloured by predicted cell state (bottom left) and probability (bottom center) according to our logistic regression model. Only in vivo data from donor P13 (snRNA-seq) was considered for the training. Confusion matrix with predictions on test set based on common features with TSC (Bottom right). d: UMAP scatterplot of scRNA-seq data (n = 23,519 cells) from¹³ re-annotated using markers from Fig. 1e. e: (Left and center) Integrated manifold (in vivo and in vitro) using scVI and coloured by cell state and specific conditions. Integration is performed with scVI. (Top right) Table displaying organoid-independent annotation for each scVI-integrated cluster. Organoid annotation matching in vivo labels displayed in green, discordant annotation in red. f: Violin plot showing normalised and log-transformed expression of differentially expressed genes (DEGs, limma, FDR < 0.05, with Bonferroni correction for multiple hypotheses testing) when comparing early EVT-2 in PTO vs in vivo EVT-2. (Right) Violin plot showing normalised and log-transformed expression of DEG when comparing iEVT in TSC vs in vivo iEVT. Primary trophoblast organoids (PTO), trophoblast stem cells (TSC), trophoblast organoid media (TOM), syncytiotrophoblast (SCT), villous cytotrophoblast (VCT), cytotrophoblast cell column (CCC), proliferative (p), extravillous trophoblast (EVT), interstitial EVT (iEVT), giant cells (GC), endovascular EVT (eEVT).