New Screening Tool Unveils Impact of Disease-Causing Mutations

Scientists have developed a new screening tool to uncover how genetic changes affect gene activity and can lead to diseases such as cancer, autoimmunity, neurodegeneration, and cardiovascular disease. This new tool enables the investigation of thousands of DNA mutations identified by genetic studies in one experiment, guiding the development of advanced diagnostics and treatments.

The technique, called scSNV-seq, enables researchers to rapidly assess the impact of thousands of genetic changes in cells that have never been screened before, directly connecting these changes to how those cells operate. This provides a comprehensive view for researchers to pinpoint the disease-causing mutations, offering crucial insights for developing targeted therapies.

In the new study, published in Genome Biology, researchers from the Wellcome Sanger Institute and their collaborators at Open Targets and EMBL’s European Bioinformatics Institute (EMBL-EBI) applied scSNV-seq to the blood cancer gene, JAK1. The technique accurately assessed the impact of JAK1 mutations, revealing for the first time that certain mutations caused a "halfway house" phenotype cycling between different states. It wasn’t possible to make such observations with previous approaches.

The technique is designed to demonstrate versatility across cell types, including hard-to-culture primary cells, like T cells and stem cell-derived neurons, as well as various editing methods, such as base editing and prime editing. Applied on a large scale, scSNV-seq could transform understanding of the genetic changes driving cancer and decoding genetic risk for Alzheimer’s, arthritis, diabetes, and other autoimmune diseases.

Advances in human genetics combined with the increasing affordability of DNA sequencing technologies have unveiled hundreds of thousands of disease-related genetic variants that are increasing at a staggering rate. Yet, tools to interpret them lag, sometimes relying on tedious manual processes.

Impact of gene editing on cellular activity and phenotypes

When using advanced gene-editing tools to introduce defined genetic mutations, using current screening methods, it is difficult to distinguish between cells where the editing did not work and those where it successfully introduced a harmless change without affecting the cell's behavior.

Researchers from the Wellcome Sanger Institute and their collaborators set out to address this with a new screening technique, scSNV-seq, which directly couples the specific genetic information in the genotype of a cell to its gene activity. The team tested the effectiveness of scSNV-seq by altering specific DNA bases within the JAK1 gene, which is linked to inflammation and cancer, to study their effects on cell behavior.

They demonstrated that scSNV-seq could accurately categorize different types of genetic changes into three categories: benign, causing loss of function, and altering function. They showed certain mutations caused an intermediate phenotype cycling between different states—an observation not possible under existing approaches.

Dr Sarah Cooper, a senior staff scientist at the Wellcome Sanger Institute and first author of the study, said, “In an era where the rate of genetic variant discovery outpaces our ability to interpret their effects, scSNV-seq fills a major gap for studying challenging cells like T cells and neurons. We are already using it to shed light on the impact of Alzheimer's and Parkinson's risk variants on brain cells.”

Andrew Bassett, PhD, head of Cellular and Gene Editing Research at the Wellcome Sanger Institute and senior author of the study, said, “Our technique is able to directly connect effects of mutations to how a cell behaves, revealing downstream impacts that previous technologies alone cannot deliver. The technique speeds up the identification of causal genetic mutations, which will allow better diagnosis and deepens our molecular understanding of diseases, paving the way for more targeted and effective treatments.”

- This press release was originally published on the Wellcome Sanger Institute website