CRISPR screening provides map of immune system regulators

Scientists have created the first retroviral CRISPR-Cas9 gene editing library to explore the regulation of mouse T cells, which are key cells in the immune system. They have mapped the most important genes for controlling T helper cells, and identified several new regulatory genes. These could help scientists looking to develop new treatments to activate the immune system against infection or to attack tumour cells.

Published in Cell, the study deciphers the complex control mechanism, with many different genes involved in both activation and development of T helper cells. Understanding what regulates T cell development could also help find new drugs against auto-immune diseases such as allergies or rheumatoid arthritis, caused by an over-active immune system.

The immune system protects the body against infection and tumours, and T helper type 2 cells (Th2) are a key component of this, releasing specific chemicals to tell the body to kill invaders. T helper cells are switched on when an invader is detected. They then need to develop down exactly the right pathway to best help remove that specific infection, a process known as differentiation. However, it is unclear exactly what signals activate these cells or tell them how to develop and which chemical signals to release.

To investigate this, the researchers created a new genome-wide CRISPR library of 88,000 guides that enabled them to switch off each of the 20,000 genes from mouse Th2 cells. After mimicking an infection in cultured Th2 cells, they studied how switching off each single gene in the genome affected the activation or differentiation. They found many different genes involved in regulating Th2 development, and defined the gene regulatory network.

The two processes are tightly coupled and are jointly controlled by many transcription factors, metabolic genes, and cytokine/receptor pairs. There are only a small number of genes regulating differentiation without any role in activation. By combining biochemical and genetic data, the authors provide an atlas for Th2 differentiation, validating known regulators and identifying factors, such as Pparg and Bhlhe40, as part of the core regulatory network governing Th2 helper cell fates.

Joint first author said: "This is the first ever unbiased genome-wide analysis of the activation and differentiation of T helper cells, helping us understand which signals are involved in immune system regulation. Our study shows that many different types of genes impact both activation and differentiation of these immune cells, indicating how closely linked those two processes are."

It is vital that the activation and differentiation of the Th2 cells is well controlled. Ineffective Th2 cells leave an infection unchecked, whereas if they are too active the body can attack itself in autoimmunity. The study identified several new regulatory genes, and discovered that the transcription factor PPARG is particularly important for regulating Th2 cells.

https://www.sanger.ac.uk/news/view/crispr-study-reveals-new-immune-system-regulators