Massively parallel assessment of human variants with base editor screens

Abstract

Base editor screens link sequence variation and gene function.

Predicting and interpreting large scale mutagenesis data using analyses of protein stability and conservation

“…Although it is possible to perform multiplexed assays on multiple genes in a single experiment ( Després et al, 2020; Jun et al, 2020; Hanna et al, 2021; Cuella-Martin et al, 2021 ), we are still far from able to probe all possible variants in all proteins by experiments. Thus, computational methods are important to predict and understand variant effects, and in some cases they may be even be more accurate than MAVEs for this purpose ( Jepsen et al, 2020; Frazer et al, 2020 ).…”

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.…”

“…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.…”