Functional interrogation of DNA damage response variants with base editing screens

High-throughput base editing: a promising technology for precision medicine and drug discovery

“…Recently, two resource papers (Hanna et al 1 and Cuella-Martin et al 2 ) were published describing high-throughput large-scale functional assessment of tens of thousands of human single-nucleotide variants (SNVs) across multiple cell lines by base editing in single pooled screens.…”

“…At least three different cell lines were co-transduced with lentiviral BEs and sgRNA libraries targeting every NGG/PAM sequence (N: unknown base) within the coding regions of the 47 genes 1 and 86 DNA damage response genes 2 , with a total library size of 12,141 1 and ~37,000 2 sgRNAs, respectively. The multiplicity of infection was around 0.4 so that 20–40% of the cells were transduced, resulting in a heterogeneous population of transduced (mostly one sgRNA/cell) and non-transduced cells.…”

“…Application of the BEs and pooled screening approach in the induced pluripotent stem cells (iPSCs) disease modelling by generating isogenic iPSC lines offers an unprecedented opportunity in high-throughput drug discovery, safety pharmacology and elucidation of the pathological mechanisms underlying polygenic complex diseases involving the association of more than one genetic variants (schizophrenia and autism spectrum disorders), sporadic diseases for which the genetic causes were not known from the family history (Alzheimer’s disease), diseases with late-onset of phenotypic changes (Brugada syndrome and early repolarization syndrome) and diseases that involve the interaction of a multitude of phenotypic cells (amyotrophic lateral sclerosis). High-throughput screening with BEs 1 , 2 combined with the human iPSC (hiPSC)-based disease modelling will revolutionize the personalized medicine by filling several gaps hindering the exploitation potential of the hiPSCs as a powerful therapeutic tool 4 . However, the low editing efficiency in iPSC should be improved.…”

“…The pooled screen with BEs will greatly benefit from the optimization of editing window, phenotypic resolution and editing specificity for every assay 2 . Also, the novel dual-function BEs that can simultaneously induce both A → G and C → T in the same target site could be a powerful approach for many therapeutic applications.…”

“…Also, the novel dual-function BEs that can simultaneously induce both A → G and C → T in the same target site could be a powerful approach for many therapeutic applications. Although both studies 1 , 2 made significant progress in the CBE-based identification and correction of genes with pathological SNVs, the consequences of such corrections for the stability of the rest of the genome, which stands under ‘evolutionary pressure’ are unknown. Indeed, evolutionary perspective on human diseases should be taken into consideration when it comes to personalized medicine.…”