Spatial CRISPR Unveils RNA Roles in Tumor Growth and Immunity
Publication Title: Large-scale, spatially resolved panoramic CRISPR screening in native tissue environments using Perturb-DBiT
Summary
- Question
- This study introduced Perturb-DBiT, a novel method for spatially resolved CRISPR screening in complex tissue environments. The researchers aimed to co-sequence single guide RNAs (sgRNAs) and total RNA transcriptomes within the same tissue section, enabling a detailed exploration of genetic perturbations and their effects on RNA regulation and tumor biology.
- Why it Matters
- Understanding how genetic modifications impact RNA biology and tumor behavior is critical for advancing cancer research and developing targeted therapies. Perturb-DBiT enables spatial mapping of genetic perturbations alongside RNA profiles, offering insights into tumor growth, migration, and immune interactions within their native tissue environment. This method provides a powerful tool for uncovering gene regulatory mechanisms that drive cancer progression and immune suppression, which could inform precision medicine and therapeutic strategies.
- Methods
- The researchers applied Perturb-DBiT in mouse and human tissue models, including immune-competent and metastatic cancer models. Using microfluidic devices, spatial barcodes were introduced to tissue sections, allowing the co-profiling of sgRNAs and RNA transcriptomes. This approach preserved tissue architecture while enabling unbiased sequencing of both coding and noncoding RNAs. The study utilized large-scale CRISPR libraries, including over 80,000 sgRNAs, to investigate gene perturbations in tumor and immune microenvironments.
- Key Findings
- Perturb-DBiT successfully linked genetic perturbations to changes in RNA regulation, including microRNAs, long noncoding RNAs, and transfer RNAs. It revealed how specific sgRNAs influence tumor growth, migration, and immune interactions. For example, sgRNAs targeting tumor suppressor genes like MT1E and S100A4 demonstrated distinct effects on tumor proliferation and immune suppression. Additionally, the method uncovered spatial patterns of RNA regulation, including miRNA-driven gene silencing and metabolic stress signatures tied to tRNA alterations.
- Implications
- This study highlights Perturb-DBiT's potential to transform cancer research by enabling spatial analysis of genetic and RNA interactions in complex tissues. The findings provide insights into tumor biology, immune evasion, and RNA regulatory networks, which are crucial for understanding cancer progression and developing targeted treatments. By preserving tissue architecture, Perturb-DBiT also offers a framework for studying other diseases where spatial context is critical.
- Next Steps
- The authors propose further validation of Perturb-DBiT across diverse tissue types and disease models. They also recommend integrating imaging-based spatial omics methods for higher resolution and expanding the approach to multimodal profiling, including protein analysis. Future research will focus on exploring the functional roles of noncoding RNAs and their interactions with genetic perturbations to uncover new therapeutic targets.
- Funding Information
- This research was supported by grants from the US National Institutes of Health (NIH), including U54CA274509, UH3CA257393, U54CA268083, RF1MH128876, U54AG079759, U54AG076043, U01CA294514, R01CA245313, and RM1MH132648 (all to R.F.), as well as R33CA281702 (to S.C.). Additional funding was provided by the Department of Defense (HT94252310472) and Foundation (CRI4964) grants to S.C. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Yale University also provided funding and support for this research.
Full Citation
Baysoy A, Tian X, Renauer P, Zhang F, Bai Z, Shi H, Yang M, Zhang D, Liu M, Li H, Tao B, Enninful A, Lu Y, Gao F, Wang G, Zhang W, Tran T, Patterson N, Sheng J, Bao S, Dong C, Xin S, Chen B, Zhong M, Rankin S, Guy C, Wang Y, Connelly J, Pruett-Miller S, Wang D, Xu M, Gerstein M, Chi H, Chen S, Fan R. Large-scale, spatially resolved panoramic CRISPR screening in native tissue environments using Perturb-DBiT. Nature Biotechnology 2026, 1-14. PMID: 42277225, DOI: 10.1038/s41587-026-03127-y.
This AI-assisted summary has been reviewed and approved by at least one of the study's authors to ensure it accurately reflects the research.
Authors
Alev Baysoy
First AuthorRong Fan
Last Author
Yale School of Medicine Authors
Other Authors
Research Themes
Concepts
- Protein-coding RNAs;
- MicroRNA-mRNA interactions;
- RNA regulation;
- CRISPR screens;
- Whole-transcriptome;
- RNA transcriptome;
- Native tissue environment;
- Pseudotime trajectories;
- Colonization model;
- RNA;
- Screened in vivo;
- Clonal dynamics;
- Complex tissues;
- Transcriptome;
- Impact of perturbations;
- SgRNA;
- Tumor migration;
- Sections in situ;
- Tissue sections in situ;
- Tissue environment;
- Mouse model;
- Tumor immune microenvironment;
- Syngeneic mouse model;
- Synergistic effect;
- Comprehensive view