In research, genetic screens are powerful tools to reveal genes responsible for specific biological functions. The choice of the best method among existing technologies for screens is not easy and the experimental set-up can be a challenge. A recently published review authored by Dr Anne Schuster and colleagues from LIH serves as a comprehensive overview on RNAi and CRISPR screening technology, including a critical assessment of different approaches and advice on how to get robust and reproducible results and how to analyse data.
In the recent years the NorLux Neuro-Oncology Laboratory in LIH’s Department of Oncology has gained extensive experience with high-throughput screening to identify gene functions and novel treatment targets in the context of brain cancer. Generated as a real team effort within the research unit, with Prof Simone Niclou and Dr Anna Golebiewska as senior authors, the review presents the current state-of-the-art in high-throughput genetic screening. It was published end of August 2018 in the prestigious Cell Press journal Trends in Biotechnology (impact factor: 13.578).
The article serves as a valuable guide on gene perturbation technologies based on RNA interference (RNAi) or the CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeat)/CRISPR-associated protein 9) system. It focusses in particular on the so-called “pooled” genetic screens that simultaneously target a large number of genes or regulatory elements in a single batch and require the introduction of a library of perturbations into a population of cells. Such screens are more cost-effective and less labour-intensive than single-well screens.
The review presents the advantages and pitfalls of the technologies at hand to manipulate the genome by knock-down, overexpression or editing. ‘Designing and performing a pooled genetic screen requires detailed knowledge in molecular biology, sequencing technology as well as biostatistics and high-throughput data analysis’, states Dr Golebiewska. ‘This can be very demanding for researchers with limited experience. Therefore we highlight crucial aspects of study design and protocol steps, and provide an overview of the main algorithms available to analyse data and select hits.’ Following the fast development of genome editing and manipulation techniques in the recent years, the screening technologies are constantly evolving and the authors envisage exciting opportunities in the near future, particularly for challenging biological systems such as brain cancer.
The research of the authors is supported by LIH, the Luxembourg Cancer Foundation “Fondation Cancer”, FNRS-Télévie and the Luxembourg National Research Fund (FNR).
Link to publication: https://doi.org/10.1016/j.tibtech.2018.08.002