A New Chapter in the Molecular Understanding of the Human Placenta: Breakthroughs in Spatial Multiomics

Background and Research Questions

The placenta is the first fetal organ to develop during human pregnancy and plays a critical role in ensuring successful gestation and healthy fetal development. Despite its importance, our understanding of the molecular mechanisms and developmental processes underlying placental function is limited. The placenta serves as the key interface for maternal-fetal physical and nutritional exchange, while also ensuring fetal growth and well-being through immune regulation and metabolic adaptation.

In recent years, single-cell technologies such as single-cell RNA sequencing (scRNA-seq) and spatial omics analysis have been applied to investigate placental heterogeneity and cell-cell interactions. However, several major challenges remain: insufficient molecular resolution, studies limited to single data dimensions (e.g., transcriptomics or epigenomics alone), and a lack of systematic spatial characterization of the maternal-fetal interface (MFI). Addressing these challenges is crucial for understanding placental development, pregnancy-related disorders (e.g., preeclampsia and gestational diabetes), and tumor-like behaviors of the placenta.

Motivated by these gaps, the research team conducted an original investigation into the molecular architecture of the placenta. By integrating multimodal spatial single-cell omics techniques, they aimed to create a comprehensive molecular atlas of the early human placenta and uncover its developmental regulatory mechanisms.

Publication and Research Team

This study was published in the leading medical journal Nature Medicine (Volume 30, December 2024), titled “Spatial Multiomic Landscape of the Human Placenta at Molecular Resolution”. The research was a collaborative effort by scientists from top institutions such as Massachusetts General Hospital (MGH), Harvard Medical School, the Broad Institute, and the Medical University of Vienna. The corresponding authors are Dr. Fei Chen, Dr. Sandra Haider, and Dr. Jian Shu.

Research Workflow and Experimental Strategy

The study was conducted in multiple stages to provide an in-depth spatial multiomics analysis, integrating single-nucleus transcriptomics and epigenomics with spatial mapping to systematically characterize the molecular structure of the human placenta in early pregnancy (6–11 weeks). The research workflow and innovative methodologies include the following key steps:

1. Sample Collection and Preparation

The team obtained early first-trimester placental samples (eight donors at gestational weeks 6–11) from legal pregnancy terminations. The placental tissues were dissected into segments, cryopreserved immediately, and used for subsequent single-nucleus isolation, single-cell sequencing, and spatial tissue sectioning.

2. Single-Cell Multiomics Sequencing

Through single-nucleus RNA sequencing (snRNA-seq) and single-nucleus Assay for Transposase-Accessible Chromatin Sequencing (snATAC-seq), the study analyzed 36,456 nuclei that passed stringent quality control measures. These nuclei were predominantly fetal (98.6%) with a small maternal component (1.4%). By integrating gene expression and chromatin accessibility data, the team resolved 17 major cell subtypes, including villous cytotrophoblasts (vCTBs), extravillous trophoblasts (EVTs), syncytiotrophoblasts (STBs), endothelial cells, fibroblasts, and Hofbauer cells (fetal macrophages).

3. Spatial Multiomics Technology

To spatially resolve gene expression and chromatin accessibility within the tissue, the researchers employed three complementary spatial techniques: - Slide-tags: A barcoding-based spatial multiomics approach combining transcriptomics and epigenomics for single nuclei in tissue sections.
- Starmap In Situ Sequencing (Starmap-ISS): RNA-based spatial in situ sequencing to profile 1,001 highly variable genes across the placenta.
- Starmap In Situ Hybridization (Starmap-ISH): Targeted spatial expression mapping of 48 carefully selected marker genes in distinct tissue regions.

By integrating these methods, the team constructed a detailed single-cell, high-dimensional spatial map of the placenta.

4. Data Analysis and Computational Predictions

Using diverse analytical techniques, including unsupervised clustering, ChromVAR motif enrichment analysis, differential accessibility calculations, and transcription factor binding prediction, the researchers identified domains of regulatory chromatin (DORCs) and deciphered regulatory networks linked to trophoblast differentiation. They also used the CellRank algorithm to predict trophoblast differentiation trajectories based on chromatin accessibility dynamics.

Key Findings and Results

1. Cellular Diversity and Differentiation Trajectories

The study successfully reconstructed trophoblast differentiation trajectories, tracing the transition from progenitor villous cytotrophoblasts (vCTB progenitors) to invasive EVTs and functional STBs. Key transcription factors (e.g., FoxP1, TP63) were identified, unveiling complex regulatory networks underlying trophoblast differentiation.

2. Chromatin Regulation and Gene Networks

The researchers identified 43,622 chromatin accessibility peaks significantly linked to gene expression, revealing more than 1,000 DORCs. These DORCs highlighted trophoblast-specific genes (e.g., MYCN, FOXF1) that are finely regulated to maintain functionality and differentiation potential.

3. Discovery of Novel Genes and Functional Elements

The team uncovered numerous novel genes implicated in invasion and immune modulation, such as ERVH48-1 and ANXA1. ERVH48-1, for instance, may regulate early trophoblast function by preventing premature fusion.

4. Spatially Specific Signaling Pathways

Spatial analysis revealed signaling pathways between maternal tissues (e.g., fibroblasts) and placental trophoblasts, such as the PTN-SDC4 pathway, which may adapt the pregnancy immune microenvironment.

Conclusions and Implications

This study represents a groundbreaking achievement in spatial multiomics, creating the first comprehensive molecular atlas of the early human placenta. These findings shed light on the molecular mechanisms underlying early placental function and open new possibilities for diagnosing and intervening in pregnancy-related disorders, such as preeclampsia and gestational complications.

The research also provides novel insights into tumor-like behaviors of the placenta, such as invasion and immune evasion, offering a theoretical framework for further exploration of connections between placental biology and cancer.

Research Highlights and Future Directions

• Technological Innovation: Integration of three complementary spatial techniques significantly enhanced resolution and data coverage.
  
• Discovery of Novel Genes: Functional insights into ERVH48-1 and FOXP1 highlight the unparalleled complexity of the placenta.
  
• Multilayered Analysis: Comprehensive characterization of the placenta was achieved by integrating chromatin, gene expression, and spatial data.
  

Future work will focus on functional validation of these key genes and regulatory networks, as well as spatial analysis of the placenta in other species or disease models. Such efforts will drive interdisciplinary advances in maternal-fetal medicine and oncology research.