CRISPR screens guide the way for PARP and ATR inhibitor biomarker discovery

Abstract

DNA repair pathways are heavily studied for their role in cancer initiation and progression. Due to the large amount of inherent DNA damage in cancer cells, tumor cells profoundly rely on proper DNA repair for efficient cell cycle progression. Several current chemotherapeutics promote excessive DNA damage in cancer cells, thus leading to cell death during cell cycle progression. However, if the tumor has efficient DNA repair mechanisms, DNA‐damaging therapeutics may not be as effective. Therefore, directly inhibiting DNA repair pathways alone and in combination with chemotherapeutics that cause DNA damage may result in improved clinical outcomes. Nevertheless, tumors can acquire resistance to DNA repair inhibitors. It is essential to understand the genetic mechanisms underlying this resistance. Genome‐wide CRISPR screening has emerged as a powerful tool to identify biomarkers of resistance or sensitivity to DNA repair inhibitors. CRISPR knockout and CRISPR activation screens can be designed to investigate how the loss or overexpression of any human gene impacts resistance or sensitivity to specific inhibitors. This review will address the role of CRISPR screening in identifying biomarkers of resistance and sensitivity to DNA repair pathway inhibitors. We will focus on inhibitors targeting the PARP1 and ATR enzymes, and how the biomarkers identified from CRISPR screens can help inform the treatment plan for cancer patients.

Optimized minimal genome-wide human sgRNA library

“…2; Supplementary Table 2). We chose the Brunello library as a benchmark as it has been widely used in many CRISPR-based knockout screening experiments 11,27,[34][35][36][37][38] since it was designed. And when comparing the prediction scores of on-target efficiencies, the Rule2 score of the Brunello library showed the second-best performance besides H-mLib (Supplementary Fig.…”

Complementary CRISPR genome-wide genetic screens in PARP10-knockout and overexpressing cells identify synthetic interactions for PARP10-mediated cellular survival

“…Genome-wide CRISPR genetic screening has emerged as a powerful tool for revealing novel functions of genes, as well as for identifying clinically-relevant genetic interactions such as the discovery of genetic markers of sensitivity or resistance to novel therapeutic drugs [22,23]. In this work, we employed complementary CRISPR genome-wide genetic loss-of-function screening to identify genes required for proliferation of PARP10overexpressing and PARP10-knockout cells.…”

“…In recent years, genome-wide CRISPR genetic screens have emerged as powerful tools for identifying clinically-relevant genetic interactions, such as synthetic lethality interactions, as well as genetic biomarkers of drug response [22,23]. Here, we employed complementary CRISPR loss-of-function genome-wide screening to identify genes required for proliferation of PARP10overexpressing and PARP10-knockout cells.…”

BRCAness, DNA gaps, and gain and loss of PARP inhibitor–induced synthetic lethality

“…It is worth noting that recent CRISPR/Cas9 loss-of-function screens have served as a powerful and unbiased tool to explore synthetic lethal interactions with PARPis in BRCA-proficient and -deficient cells ( 118 ). In addition to ALC1 ( 115 ), RNase H2 was identified as a strong synthetic lethal screen hit with olaparib ( 119 ).…”