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Transcriptomic analysis of healthy and PE patients
For gene expression differences between the normal (Normal) group and PE patients, the differential expression by the R package limma in the merged datasets was analyzed. A total of 89 DEGs were identified (p < 0.05 and |log2FC| > 0.5), 69 upregulated genes and 20 downregulated genes for GSE75010 (Figure 1A). There are 2,097 differentially expressed genes, and 1,121 are upregulated, and 976 are downregulated (Figure 1B). There are 7,633 DEGs for the GSE60438 dataset with 3,371 upregulated genes and 4,262 downregulated genes (Figure 1C). The substantial differences in DEG numbers across the three datasets likely reflect differences in sample size, tissue origin (placental villi vs. decidua basalis), and PE severity classification, which further underscores the value of taking the intersection across datasets to identify robust common DEGs.
Functional enrichment analysis of DEGs
For the systematic identification of key DEGs associated with PE, Venn analysis was done on the DEGs from the GSE75010, GSE10588, and GSE60438 PE datasets, and ultimately identified 56 common DEGs (Figure 2A). A PPI network was constructed for these 56 common DEGs using the online platform STRING (interaction score ≥0.15), and the top 20 hub genes were further identified based on their degree of connectivity within the network, ranked using Cytoscape software (Figure 2B). Based on such genes, GO enrichment was also performed to explore potential functionalities in BP, CC, and MF (Figure 2C). The DEGs were most likely enriched in hormone secretion and regulation of transmembrane receptor serine/threonine kinase signaling. In terms of cells, the genes were mainly localized to focal adhesions, cell–substrate junctions, and a variety of vesicle- and lysosome-related genes. In molecular functions, the enriched terms were prolyl hydroxylase activity, hormone activity, and transmembrane transport of lipid-related molecules. These results suggest that the DEGs may play important roles in placental cell signaling, cell-matrix interaction, and endocrine-related function maintenance. At the same time, it was found that KEGG pathway enrichment yielded the DEG most likely to be enriched in cytokine–cytokine receptor interaction, cell adhesion molecule interaction, and the TGF-β and HIF-1 signaling pathways (Figure 2D). Enrichment of certain virus-related terms (e.g., Hepatitis viruses, Ebolavirus) likely reflects non-specific overlap with shared immune-regulatory genes rather than a direct biological association with PE; the interpretive focus therefore remains on inflammation-, adhesion-, and hypoxia-related pathways. These pathways are related to inflammatory response, cell adhesive-mediated, and hypoxia-related signaling and may have an influence on PE progression by varying the immune-inflammatory status and cell-cell communication in the placental microenvironment.
Machine learning identifies SASH1 as a key gene in PE
To identify key prognostic genes, four machine learning methods were applied for feature selection. LASSO regression with cross-validation showed that the model achieved the minimum cross-validation error when log(λ.min) = -3.8075. Genes with non-zero coefficients at this λ value were selected as key features identified by LASSO (Figure 3A–B). The Boruta algorithm evaluates feature importance by comparison with shadow features. Genes with importance values higher than shadowMax were labeled as Confirmed and considered key candidate genes, whereas those with importance values lower than shadowMin were labeled as Rejected and regarded as having no significant contribution. Genes between these two thresholds were labeled as Tentative, indicating potential but uncertain importance (Figure 3C). SVM-RFE analysis demonstrated that when 40–50 features were retained, the cross-validation accuracy reached the highest or near-highest level, suggesting optimal predictive performance at this feature scale (Figure 3D). The moderate cross-validation accuracy (~0.6) indicates that no single algorithm performed optimally for this dataset; a multi-algorithm intersection strategy was therefore adopted to enhance the robustness of feature selection. XGBoost quantified the relative importance of genes using Gain values, thereby identifying features with higher contributions to model prediction (Figure 3E). Venn intersection analysis of the results from the four methods identified SASH1 as the only overlapping gene. Although SASH1 was classified as Tentative by the Boruta algorithm, its consistent selection across all three other algorithms supports its de Susignation as a consensus candidate gene (Figure 3F).
Single-cell analysis
The cellular heterogeneity and molecular processes in PE placental tissues were investigated. Cells were quality-filtered based on the number of detected genes, number of RNA counts, and percentage of mitochondrial gene expression. Low-quality cells (less than 200 detected genes or with more than 20% mitochondrial gene content) were removed to obtain a high-quality single-cell sample for downstream analysis. The quality control metrics and identification of highly variable genes are shown in Supplementary Figure 1A–B. After normalizing and identifying highly variable genes, principal component analysis (PCA) was performed using the top 2,000 highly variable genes and significant principal components using JackStraw analysis and ElbowPlot analysis (Supplementary Figure 2A–B).
Based on the principal components, uniform manifold approximation and projection (UMAP) was used to reduce dimensionality and perform unsupervised clustering, where all cells were classified into 22 clusters, highlighting the high cellular heterogeneity in placental tissue (Figure 4A). By studying cluster-specific marker gene expression and visualizing DEGs in a heatmap (Figure 4B), each cluster was annotated based on a canonical marker and projected back onto the UMAP embedding (Figure 4C). Based on this major placental cell populations, including B cells/plasma cells, endothelial cells, fibroblasts/stromal cells, macrophages/dendritic cells, natural killer cells, T cells, and trophoblast cells were identified. Comparisons between control and PE groups reveal that several types of cells present a substantial relative distribution in PE placentas, suggesting remodeling of the placental microenvironment (Figure 4D).
Tissue origin and disease status were used to track cells in the same UMAP embedding based on tissue source (decidua vs. villi) and disease grouping (control vs. PE) (Figure 4E). Cell number distribution was partially separated by tissue origin, while cells from different disease groups were highly interconnected. This suggests that PE does not substantially rearrange the entire transcriptomic structure, but may have effects on individual cell populations or on particular molecular features. SASH1 expression was mapped onto the UMAP to explore its distribution among placental cell populations (Figure 4F–G). SASH1 shows strong cell type-specific expression, with notable differences between decidual and villous cell populations. Statistical comparison of SASH1 expression between PE and control groups across cell types (Wilcoxon rank-sum test) revealed significant differences in multiple placental cell populations, with the most pronounced elevation observed in trophoblast cells from PE samples (Figure 4H). This finding provides single-cell-level evidence that SASH1 dysregulation is particularly pronounced in the trophoblast compartment, supporting the use of the HTR-8/SVneo trophoblast cell line for subsequent functional experiments.
SASH1 knockdown inhibits hypoxia-induced trophoblast apoptosis and inflammatory responses
To validate the bioinformatic predictions, a PE-related trophoblast cell model was established under hypoxic conditions (1% O2). qPCR and Western blot analyses were performed to assess SASH1 expression (Figure 5A–B). Compared with normoxic HTR-8/SVneo cells, hypoxia-treated cells showed significantly increased SASH1 mRNA and protein expression levels, providing preliminary experimental validation of the bioinformatic results. To evaluate the effect of SASH1 knockdown on PE-related pathological processes, SASH1 was silenced in hypoxia-treated HTR-8/SVneo cells. Quantitative PCR and Western blot analyses (Figure 5C–D) showed that SASH1 expression was significantly reduced in all sh-SASH1 groups compared with the sh-NC group. Among them, sh-SASH1#3 exhibited the highest knockdown efficiency and was therefore selected for subsequent experiments. TUNEL staining and ELISA were performed under three conditions: normoxic control (Normal), hypoxia with negative control shRNA (Hypoxia + sh-NC), and hypoxia with SASH1 knockdown (Hypoxia + sh-SASH1). Compared with the Normal group, the Hypoxia + sh-NC group exhibited significantly increased apoptosis and elevated secretion of pro-inflammatory cytokines IL-1β, IL-6, and TNF-α, confirming hypoxia-induced trophoblast injury. SASH1 knockdown markedly attenuated these effects, reducing apoptosis (Figure 5E) and cytokine levels (Figure 5F) to levels approaching those of the Normal group, suggesting that SASH1 knockdown can largely rescue hypoxia-induced trophoblast apoptosis and inflammatory responses. To further establish the causal role of SASH1, gain-of-function experiments were performed. qPCR and Western blot confirmed successful SASH1 overexpression in HTR-8/SVneo cells (Figure 5G–H). Under normoxic conditions, SASH1 overexpression (OE-SASH1) significantly increased trophoblast apoptosis and pro-inflammatory cytokine secretion compared with the OE-NC group, recapitulating the hypoxia-induced phenotype (Figure 5I–J). Taken together, the loss- and gain-of-function data establish that SASH1 is both necessary and sufficient to drive trophoblast apoptosis and inflammatory responses, confirming its causal role in PE-related pathology.
P-EXOS suppresses hypoxia-induced trophoblast apoptosis and inflammatory responses by modulating SASH1
P-EXOS is considered to have potential therapeutic value in PE. In this study, bioinformatics analysis suggested that SASH1 is associated with exosome-related signaling pathways (as indicated by GO and KEGG enrichment, Figure 2C–D), leading us to hypothesize that P-EXOS may exert a protective effect in PE by regulating SASH1. Prior to functional studies, isolated P-EXOS were first characterized. Western blot analysis confirmed the presence of exosome marker proteins PLAP, CD63, and TSG101, with no detectable expression of the Golgi marker GM130, indicating high purity of the isolated vesicles. Transmission electron microscopy further revealed typical cup-shaped vesicular structures (Figure 6A–B). To verify whether P-EXOS could be efficiently internalized by target cells, immunofluorescence staining was performed to assess the cellular uptake of P-EXOS. Compared with the control group, HTR-8/SVneo cells treated with P-EXOS exhibited prominent co-localization signals in the merged images, indicating that P-EXOS were effectively internalized by HTR-8/SVneo cells (Figure 6C).
Subsequently, HTR-8/SVneo cells were co-cultured with P-EXOS under hypoxic conditions. Both quantitative PCR and Western blot assays showed a pronounced reduction in SASH1 mRNA and protein levels in the P-EXOS-treated group compared with controls (Figure 6D–E), providing initial evidence for a regulatory interaction between P-EXOS and SASH1. Consistent with these molecular changes, TUNEL staining revealed a substantial attenuation of hypoxia-induced apoptosis in HTR-8/SVneo cells following P-EXOS treatment (Figure 6F). At the same time, ELISA assays demonstrated markedly decreased secretion of pro-inflammatory cytokines, including IL-6, IL-1β, and TNF-α (Figure 6G).
To determine whether the protective effects of P-EXOS are mechanistically dependent on SASH1 suppression, a rescue experiment was performed under hypoxic conditions. Cells overexpressing SASH1 (OE-SASH1 + P-EXOS) were compared with negative control cells (OE-NC + P-EXOS). SASH1 overexpression significantly abolished the protective effects of P-EXOS, as evidenced by increased apoptosis (Figure 6H) and elevated pro-inflammatory cytokine secretion (Figure 6I) compared with the OE-NC + P-EXOS group. These results demonstrate that the protective effect of P-EXOS is mediated specifically through the suppression of SASH1, rather than through parallel pathways, underscoring the therapeutic potential of P-EXOS in PE.
DATA AVAILABILITY:
The datasets supporting the findings of this study are publicly available and were obtained from the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/), with accession numbers GSE75010, GSE10588, GSE60438, and GSE183338. Cell type annotation was performed with reference to the Cell Classification Database (https://ngdc.cncb.ac.cn/celltaxonomy/). Uncropped Western blot images and all other raw experimental data supporting the findings of this study are provided in the Supplementary Raw Data folder.

Figure 1: Identification of DEGs in PE placental and decidual tissues across three independent datasets. (A) Volcano plot of DEGs between 157 PE placental samples and 173 non-PE placental samples from the combined GSE75010 dataset. (B) Volcano plot of DEGs between severe PE placental samples (n = 17) and normal placental samples (n = 26) from the GSE10588 dataset. (C) Volcano plot of DEGs between PE decidual samples and normotensive control decidual samples from the GSE60438 dataset. DEGs were identified using p < 0.05 and |log2FC| > 0.5. Please click here to view a larger version of this figure.

Figure 2: Functional enrichment and PPI analysis of common DEGs associated with pre-eclampsia. (A) Venn diagram of DEGs identified from PE-related datasets GSE75010, GSE10588, and GSE60438. (B) PPI network of the top 20 hub genes selected from the 56 common DEGs based on degree of connectivity, ranked using Cytoscape software (STRING interaction score ≥0.15). (C) GO and KEGG enrichment analyses of the common DEGs are presented as bar plots. (D) GO and KEGG enrichment analyses of the common DEGs, presented as chord diagrams. Please click here to view a larger version of this figure.

Figure 3: Machine learning-based screening of candidate hub genes associated with pre-eclampsia. (A) LASSO regression analysis showing coefficient profiles of candidate genes. (B) Selection of the optimal regularization parameter (λ) by LASSO regression using cross-validation. (C) Boruta algorithm. (D) SVM-RFE analysis. (E) XGBoost algorithm. (F) Venn diagram showing the intersection of candidate genes identified by LASSO, Boruta, SVM-RFE, and XGBoost algorithms. Abbreviations: LASSO = least absolute shrinkage and selection operator; SVM-RFE = support vector machine recursive feature elimination. Please click here to view a larger version of this figure.

Figure 4: Single-cell transcriptomic analysis reveals cell type-specific SASH1 expression patterns in pre-eclampsia. (A) UMAP clustering of the single-cell dataset. (B) Top five marker annotation analysis of the PE single-cell transcriptome dataset GSE183338. (C) Annotation of cell subpopulations. (D) Bar plot showing the distribution of cell proportions in control and PE samples. (E) UMAP plot colored by tissue origin (decidua and villi) and disease status (control and PE). (F) UMAP plot showing SASH1 expression in placental cell populations grouped by tissue origin (decidua and villi). (G) UMAP plot showing SASH1 expression in placental cell populations grouped by disease status (control and PE). (H) Violin plot showing the expression distribution of SASH1 across different placental cell types. ns p > 0.05; *p < 0.05; **p < 0.01; ***p < 0.001. Abbreviations: UMAP = uniform manifold approximation and projection; ns = not significant. Please click here to view a larger version of this figure.

Figure 5: SASH1 regulates hypoxia-induced trophoblast apoptosis and inflammation. (A) qPCR analysis of SASH1 mRNA expression and densitometric quantification of SASH1 protein levels in HTR-8/SVneo cells under normal and hypoxic conditions. (B) Representative Western blot images corresponding to the densitometric data shown in (A). (C) qPCR analysis of SASH1 mRNA expression and densitometric quantification of SASH1 protein levels in hypoxia-treated HTR-8/SVneo cells transfected with sh-NC or sh-SASH1 constructs (sh-SASH1#1, sh-SASH1#2, and sh-SASH1#3). (D) Representative Western blot images corresponding to the densitometric data shown in (C). (E) TUNEL staining of HTR-8/SVneo cells in the Normal, Hypoxia + sh-NC, and Hypoxia + sh-SASH1(#3) groups. Scale bar = 20 µm. (F) ELISA analysis of inflammatory cytokines (IL-1β, IL-6, and TNF-α) in the Normal, Hypoxia + sh-NC, and Hypoxia + sh-SASH1(#3) groups. (G) qPCR analysis of SASH1 mRNA expression and densitometric quantification of SASH1 protein levels in HTR-8/SVneo cells transfected with OE-NC or OE-SASH1 constructs. (H) Representative Western blot images corresponding to the densitometric data shown in (G). (I) TUNEL staining of HTR-8/SVneo cells in the Normal + OE-NC and Normal + OE-SASH1 groups. Scale bar = 20 µm. (J) ELISA analysis of inflammatory cytokines (IL-1β, IL-6, and TNF-α) in the Normal + OE-NC and Normal + OE-SASH1 groups. *p < 0.05; **p < 0.01; ***p < 0.001. Data are represented as mean ± SD from three independent biological replicates (n = 3). Please click here to view a larger version of this figure.

Figure 6: P-EXOS alleviates hypoxia-induced trophoblast injury via suppression of SASH1. (A) Western blot analysis of P-EXOS marker proteins PLAP, CD63, and TSG101, with GM130 serving as a negative control. (B) Transmission electron microscopy (TEM) analysis of P-EXOS morphology. Scale bar = 1.0 µm. (C) Confocal laser scanning microscopy images showing uptake of PKH67-labeled P-EXOS (green) in HTR-8/SVneo cells (red). Nuclei were counterstained with DAPI (blue). Scale bar = 20 µm. (D) qPCR analysis of SASH1 mRNA expression and densitometric quantification of SASH1 protein levels in HTR-8/SVneo cells in the Control and P-EXOS groups. (E) Representative Western blot images corresponding to the densitometric data shown in (D). (F) TUNEL staining of HTR-8/SVneo cells in the Control and P-EXOS groups. Scale bar = 20 µm. (G) ELISA analysis of inflammatory cytokines (IL-1β, IL-6, and TNF-α) in hypoxia-treated HTR-8/SVneo cells in the Control and P-EXOS groups. (H) TUNEL staining of HTR-8/SVneo cells in the OE-NC + P-EXOS and OE-SASH1 + P-EXOS groups. Scale bar = 20 µm. (I) ELISA analysis of inflammatory cytokines (IL-1β, IL-6, and TNF-α) in hypoxia-treated HTR-8/SVneo cells in the OE-NC + P-EXOS and OE-SASH1 + P-EXOS groups. Abbreviations: P-EXOS = placenta-derived exosomes; TEM = transmission electron microscopy; PLAP = placental alkaline phosphatase; TSG101 = tumor susceptibility gene 101. *p < 0.05; **p < 0.01. Data are represented as mean ±SD from three independent biological replicates (n = 3). Please click here to view a larger version of this figure.
Supplementary Figure 1: Quality control of single-cell RNA-seq data. (A) Violin plot of gene expression levels after quality control. (B) Variable feature plot showing highly variable genes identified after quality control.Please click here to download this file.
Supplementary Figure 2: Determination of statistically significant principal components for single-cell clustering. (A) JackStraw dot plot used to identify statistically significant principal components. (B) Elbow dot plot showing the variance explained by principal components.Please click here to download this file.
Supplementary Table 1: shRNA target sequences used for SASH1 knockdown. shRNA target sequences (5′–3′) for the negative control (sh-NC) and three SASH1-targeting constructs (sh-SASH1#1, sh-SASH1#2, and sh-SASH1#3) used for gene silencing.Please click here to download this file.
Supplementary Table 2: Primer sequences used for quantitative PCR. Forward and reverse primer sequences (5′–3′) for SASH1 and β-actin (internal reference control) used in qPCR analysis.Please click here to download this file.