Using next-generation CRISPR tool, scientists create unprecedented molecular map of human immune response

In a landmark-scale study, scientists at the Gladstone Institutes have created a complex map of how the immune system works, examining the detailed molecular structures governing human T cells using the next-generation CRISPR tool known as the base edition name.

Their paper, “Base editing mutagenesis maps functional alleles to regulate human T cell activity,” published in Naturereveals detailed insights that could help overcome the limitations of current immunotherapies and identify new drug targets for a wide range of diseases, including autoimmune diseases and cancer.

Led by Gladstone principal investigator Alex Marson, MD, Ph.D., the team dove deep into T cell DNA, identifying specific nucleotides (the basic units of genetic information in DNA ) that influence how immune cells respond to stimuli. In total, they examined more than 100,000 sites on nearly 400 genes present in functional human T cells.

Nucleotides serve as the basic code for building proteins in cells. So, by identifying these specific units of DNA, scientists now clearly know the exact locations within the proteins that regulate immune responses essential to health. The results serve as a target, marking sites that can be targeted by future immunomodulatory drugs.

“We have created incredibly precise and informative maps of DNA sequences and protein sites that fine-tune real human immune responses,” says Marson, also director of the Gladstone-UCSF Institute for Genomic Immunology and the Parker Institute for cancer immunotherapy at the Gladstone Institutes. .

“Our mapped sites provide insight into mutations found in patients with immune disorders. The enormous genetic dataset also functions as a sort of cheat sheet, explaining the biochemical code that will help us program future immunotherapies against cancer, autoimmunity, infections and beyond.”

T cells play a central role in immune response and regulation, making them of particular interest to scientists seeking to solve complex diseases such as cancer or immune disorders. Over the past decade, the Marson lab and others have developed CRISPR gene-editing technology to study how primary immune cells function.

For this study, the team went further, leveraging a new CRISPR-based technology known as base editing to make more targeted changes to hundreds or even thousands of DNA sites on individual genes, thus giving a much more nuanced picture at high resolution.

Because the study was conducted using primary T cells from human blood donors, the results are of high clinical relevance, noted Ralf Schmidt, MD, co-first author of the paper. Schmidt, a medical researcher at the Medical University of Vienna, is a former postdoctoral researcher at the Gladstone Institutes.

“This study focuses on the genetic basis of immune cell functions,” explains Schmidt. “We can now interrogate T cells with nucleotide resolution, generating blueprints for drug development, diagnostics and other scientific endeavors.”

With immense stores of data generated from more than 100,000 sites on T cells, computational genomics has become an essential part of the study. Carl Ward, Ph.D., a postdoctoral researcher at Gladstone and co-first author, led the team’s efforts in this area, relying on important measurements of cellular function to create what he hopes serve as an indispensable resource for immunologists and drug developers. look alike.

“We can now assign functions to specific mutations that have remained a mystery,” says Ward. “Our detailed functional maps can also be combined with existing datasets and AI tools to amplify our findings and predict new avenues of investigation.”

Ward notes that the new Nature This study is just the beginning of a new chapter of discoveries about immune cells: “Our tools to solve diseases are going to get better and better,” he says. “We are approaching the point where we can use these maps to design therapies that can adjust T cell function for cancer treatments or reduce it to treat autoimmune diseases.”