Multi-faceted approach to screening genes and proteins improves accuracy

12 May 2016

Ilaria Gori in the High Throughput Screening Laboratory where the genomic screening for this work was carried out. (Ilaria is now in Caroline Hill’s research group).

Image: Ilaria Gori in the High Throughput Screening Laboratory where the genomic screening for this work was carried out. (Ilaria is now in Caroline Hill’s research group).

Researchers at the Francis Crick Institute have developed a new way to screen genes or proteins when looking for factors that play a role in biological pathways. The approach reduces the usual problems of false positives and false negatives.

Using this new approach they discovered a role in the cellular response to UV-induced DNA damage for a protein called Serine-Threonine Kinase 19 (STK19), which is frequently mutated in patients with melanoma but has otherwise been poorly understood.

Dr Jesper Svejstrup of the Crick explained: "Almost any modern genetic or proteomic screen results in hundreds, often thousands of interesting candidates, but it is frequently impossible to determine which ones are worth pursuing. This is because any screening approach gives rise to a very high percentage of false positives and false negatives."

Q-Exactive Orbitrap mass spectrometer at the Proteomics Science and Technology Platform at Clare Hall. This technology was used to identify and quantify all peptides used in this study.

Q-Exactive Orbitrap mass spectrometer at the Proteomics Science and Technology Platform at Clare Hall. This technology was used to identify and quantify all peptides used in this study. (Click to view larger image)

 

 

 

 

 

 

 

 

 

  

 

To try and overcome this problem, the scientists used a 'multi-omic' approach, in which the same process is attacked from several distinct angles. They used a mixture of proteomic approaches - screening based on protein interactions, modifications to proteins before and after DNA damage - and genomic screening for genes related to DNA damage.

Only proteins that scored highly in two or more screens were considered interesting, which Dr Svejstrup said dramatically increased the trust in such candidates.

He added: "We uncovered a large number of proteins/genes with poorly understood molecular function, many of them disease genes, using this new approach. We suggest that the approach can be used for uncovering new factors in any cellular pathway or process."

This unique approach was made possible due to the wide-ranging expertise at the Crick, where proteomic analysis is facilitated by the expertise in the Protein Analysis and Proteomics laboratory led by Bram Snijders, and genomic screening is made possible by the High Throughput Screening Laboratory led by Mike Howell. Bioinformatic support was provided by the Bioinformatics and Biostatistics Laboratory led by Aengus Stewart.

The paper, Multiomic Analysis of the UV-Induced DNA Damage Response, is published in Cell Reports.

  • By combining multiple methods for screening genes and proteins, scientists have cut down on false positives and negatives and improved accuracy of results.
  • While our genome is all our DNA and genes, our proteome is the entire set of proteins needed in our body to carry out all its functions. Screening many of these genes (genomics) or proteins (proteomics) at once can help scientists find specific ones that play a role in whatever process they're studying.
  • The Francis Crick Institute teams worked with colleagues from the Stowers Institute for Medical Research in Kansas City, Missouri, USA. The work was supported by the Francis Crick Institute, the European Research Council, and Worldwide Cancer Research (formerly known as the Association for International Cancer Research).