Researchers at the Gaublomme lab have developed a novel optical pooled screening approach called CRISPRmap that enables the coupling of optical properties of single cells to targeted genetic perturbations. This groundbreaking technique allows for spatially resolved interrogation of gene function in tissues, unveiling both cell-intrinsic and cell-extrinsic effects that were previously inaccessible through in vitro studies. CRISPRmap opens new avenues for understanding genes involved in critical biological processes like immune cell recruitment, metastasis, angiogenesis, and more.
Unlocking Optical Phenotypes for Genetic Perturbation Studies
The traditional sequencing-based approaches for genetic studies often rely on cell lysis, which means they are unable to capture crucial information about cell morphology, protein subcellular localization, cell-cell interactions, extracellular matrix factors, and tissue organization. The Gaublomme lab’s CRISPRmap technology overcomes this limitation by enabling optical readout of genetic perturbations.
This approach allows researchers to map both the cell-intrinsic and cell-extrinsic effects of genetic modifications, which can provide invaluable insights into fundamental biological processes. For example, CRISPRmap can be used to study the recruitment of DNA damage repair proteins to DNA damage sites, as demonstrated in the study’s collaboration with the Ciccia lab at Columbia University Irving Medical Center.
Versatile Applications and Optimization for Broad Accessibility
The CRISPRmap technology is designed to be compatible with various CRISPR modalities and cell types, enabling a wide range of research applications in biology and medicine. The researchers have optimized the approach to be accessible to individual labs, as it does not rely on third-party sequencing reagents for barcode detection, and the readout dyes can be customized to match the microscopes available to researchers. Additionally, the CRISPRmap method is cost-effective, making it a viable option for many research groups.
The researchers envision CRISPRmap to be used for high-throughput genetic studies by measuring the responses of many cells to different genetic perturbations in parallel. This pooled analysis approach, where each cell expresses a barcode that identifies the CRISPR perturbation, allows for the simultaneous interrogation of a large number of genes and their effects.
Beyond studies of cancer cell lines, the researchers have also demonstrated the application of CRISPRmap in the tumor microenvironment, a key goal of the NIH Director’s New Innovator Award received by the Gaublomme lab. By combining the CRISPRmap barcode detection with multiplexed antibody staining, the researchers were able to visualize important features of the tumor, such as angiogenesis, extracellular matrix formation, and transcription factor nuclear translocation in the transplanted cells.
Exploring Gene Function in Complex Tissue Environments
The Gaublomme lab plans to further explore the impact of gene perturbations on tissue architecture and the interplay between cells in complex microenvironments. Future studies may focus on patient-derived organoids to study gene function in tissue-specific and disease-specific contexts.
The researchers envision CRISPRmap to be a powerful tool for elucidating optical phenotypes across a wide range of biological length scales, from molecular scales like DNA damage break foci in a single nucleus to cellular reorganization across whole organs. This versatility makes CRISPRmap applicable to a diverse range of research, from basic biology to the study of disease mechanisms and the optimization of therapeutic approaches in areas such as neurodegenerative diseases and cancer.
