Applying Lipid Nanoparticles to Gene Therapy JCRnEDITORS HokkaidoUni CRISPR Cas9 genetics nanomedicine
Gene therapy—and the whole of biology—has been transformed with the advent of the genetic modification technique known as CRISPR-Cas9 in 2012. It has only started being used in clinical studies to treat some human diseases.
Yusuke Sato, Study Corresponding Author and Assistant Professor, Faculty of Pharmaceutical Sciences, Hokkaido University Hideyoshi Harashima, Study Corresponding Author and Professor, Faculty of Pharmaceutical Sciences, Hokkaido University
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ShrinkCRISPR: a flexible method for differential fitness analysis of CRISPR-Cas9 screen data - BMC BioinformaticsBackground CRISPR screens provide large-scale assessment of cellular gene functions. Pooled libraries typically consist of several single guide RNAs (sgRNAs) per gene, for a large number of genes, which are transduced in such a way that every cell receives at most one sgRNA, resulting in the disruption of a single gene in that cell. This approach is often used to investigate effects on cellular fitness, by measuring sgRNA abundance at different time points. Comparing gene knockout effects between different cell populations is challenging due to variable cell-type specific parameters and between replicates variation. Failure to take those into account can lead to inflated or false discoveries. Results We propose a new, flexible approach called ShrinkCRISPR that can take into account multiple sources of variation. Impact on cellular fitness between conditions is inferred by using a mixed-effects model, which allows to test for gene-knockout effects while taking into account sgRNA-specific variation. Estimates are obtained using an empirical Bayesian approach. ShrinkCRISPR can be applied to a variety of experimental designs, including multiple factors. In simulation studies, we compared ShrinkCRISPR results with those of drugZ and MAGeCK, common methods used to detect differential effect on cell fitness. ShrinkCRISPR yielded as many true discoveries as drugZ using a paired screen design, and outperformed both drugZ and MAGeCK for an independent screen design. Although conservative, ShrinkCRISPR was the only approach that kept false discoveries under control at the desired level, for both designs. Using data from several publicly available screens, we showed that ShrinkCRISPR can take data for several time points into account simultaneously, helping to detect early and late differential effects. Conclusions ShrinkCRISPR is a robust and flexible approach, able to incorporate different sources of variations and to test for differential effect on cell fitness at the gene l
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From anti-antibiotics to extinction therapy: How evolutionary thinking can transform medicineThe word 'evolution' may bring to mind dusty dinosaur bones, but it impacts our health every day. For example, even though antibiotics were invented only a century ago, the evolution of antibiotic resistance is already a major concern. The rise in modern health problems such as obesity can also be traced back to evolutionary principles.
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