NUS Cancer Science Institute's Spatial Perturb-Seq: Revolutionizing Single-Cell Genomics in Nature Communications

Singapore's research landscape has just witnessed a groundbreaking advancement from the Cancer Science Institute of Singapore (CSI) at the National University of Singapore (NUS), in collaboration with the Genome Institute of Singapore (GIS) under A*STAR. Researchers have unveiled Spatial Perturb-Seq, a pioneering method that revolutionizes single-cell functional genomics by enabling the study of gene functions within the intact architecture of living tissues. Published yesterday in the prestigious Nature Communications, this innovation addresses longstanding limitations in traditional single-cell analysis, promising transformative insights into complex diseases like cancer and neurodegeneration.

Spatial Perturb-Seq combines in vivo CRISPR gene editing with high-resolution spatial transcriptomics, allowing scientists to perturb multiple genes simultaneously in their native tissue context. Unlike conventional approaches that dissociate cells, disrupting spatial relationships and biasing cell type representation, this technique preserves tissue structure while capturing single-cell resolution data. Led by first author Dr. Kimberle Shen from GIS and senior authors Dr. Wei Leong Chew and Dr. Shyam Prabhakar—who holds joint appointments at GIS, NTU's Lee Kong Chian School of Medicine, and NUS CSI—the method was demonstrated in mouse brain tissues targeting neurodegenerative disease risk genes.

The Challenge of Single-Cell Genomics in Tissue Context

Single-cell RNA sequencing (scRNA-seq), or single-cell genomics, has transformed biology by revealing cellular heterogeneity at unprecedented detail. It profiles thousands of genes per cell, identifying rare populations and states missed by bulk methods. However, dissociating tissues for scRNA-seq introduces artifacts: fragile cells die, tough ones dominate, and spatial information—crucial for understanding cell-cell interactions—is lost. In cancer, tumor microenvironments (TME) rely on precise spatial organization; disrupting it obscures how genes influence neighbors.

Spatial transcriptomics technologies like Stereo-seq and Xenium map gene expression in tissue sections, but they lack functional perturbation. CRISPR screens (pooled perturbations) reveal gene functions, and Perturb-seq merges them with scRNA-seq for single-cell readout. Yet, spatial integration was missing—until Spatial Perturb-Seq.

How Spatial Perturb-Seq Works: A Step-by-Step Breakdown

The method starts with designing a library of single-guide RNAs (sgRNAs) targeting genes of interest, packaged into adeno-associated virus (AAV) vectors for in vivo delivery. Stereotaxic injection into mouse brain targets specific regions, where CRISPR-Cas9 knocks out genes in individual cells.

1. Perturbation Delivery: AAV-sgRNA library infects cells randomly, perturbing one or few genes per cell.
2. Tissue Harvest: After weeks, brains are harvested intact.
3. Spatial Profiling: Sections undergo Stereo-seq (MGI Tech) or Xenium (10x Genomics) for spatial transcriptomics, capturing sgRNA barcodes and gene expression.
4. Single-Cell Validation: Dissociated cells for scRNA-seq confirm perturbations.
5. Analysis: Tools like Seurat, BANKSY integrate data, mapping perturbations to spatial positions and effects.

This pipeline bypasses dissociation biases, enabling true in situ functional screens.

Key Findings from Mouse Brain Applications

Applied to 12 neurodegenerative risk genes (e.g., APOE, TREM2), Spatial Perturb-Seq revealed:

• Cell-autonomous effects: e.g., APOE knockout altered lipid metabolism in neurons.
• Non-cell-autonomous effects: Perturbations in microglia influenced distant neurons via dysregulated signaling pathways like synaptic transmission.
• Spatial patterns: Knockouts clustered in specific brain layers, highlighting microenvironmental dependencies.
• Pathway insights: Identified neuronal communication disruptions, linking genetics to spatial dysfunction.

Data deposited in GEO (GSE274447, GSE274058), enabling global reuse.

Development at NUS CSI and Singapore's Synergy

Dr. Shyam Prabhakar's expertise in single-cell analytics bridged GIS's wet-lab innovation with NUS CSI's cancer focus. GIS's Spatial and Single Cell Genomics Platform provided MERFISH and analytics infrastructure. Funded by Singapore's National Medical Research Council and A*STAR, this exemplifies Singapore's biotech ecosystem, where NUS, NTU, and A*STAR collaborate seamlessly.

NUS CSI, established to accelerate cancer translation, leverages this for TME studies—critical as tumors evolve spatially.

Implications for Cancer Research

Though demonstrated in brain, Spatial Perturb-Seq's power shines for cancer. Tumor heterogeneity and TME drive resistance; spatial perturbations can map drivers like immune evasion or metastasis in situ. CSI's mandate positions it to adapt for patient-derived organoids or xenografts, accelerating precision oncology. References prior works like Perturb-map in lung cancer highlight synergies.

In Singapore, with rising cancer incidence, this bolsters national efforts like the Cancer Research Masterplan.

Singapore's Rising Star in Genomics Innovation

Singapore invests heavily in biotech: S$25B RIE2025, GIS's platforms, NUS's Yong Loo Lin School. Spatial Perturb-Seq joins milestones like long-read RNA atlases. For aspiring researchers, opportunities abound at higher-ed jobs in genomics.

Future Outlook: Broader Applications and Challenges

Next: Human tissues via organoids, multiplexing more genes, integration with multi-omics. Challenges: AAV tropism optimization, computational scaling. Globally, it could redefine functional screens for TME regulators, drug discovery.

In Singapore, expect pilots in cancer models, aligning with Precision Health Strategy.

Careers in Single-Cell Genomics at NUS and Beyond

This breakthrough opens doors. NUS CSI seeks postdocs, bioinformaticians; GIS offers computational roles. Skills: CRISPR design, spatial omics, R/Python. Check research jobs, academic CV tips. Rate profs at Rate My Professor.

Photo by Robert Zunikoff on Unsplash

Spatial Perturb-Seq cements NUS CSI's leadership, propelling Singapore in global genomics. Explore higher ed jobs, university jobs, career advice.