Role of functional genomics in identifying cancer drug resistance and overcoming cancer relapse

Abstract

Functional genomics is an emerging field focused on elucidating the functions of genes or proteins, which can help solve challenges related to reliable cancer therapy. One of the main challenges currently faced by cancer therapy is the variations in the number of mutations in patients, leading to drug resistance and cancer relapses. Drug intrinsic or acquired resistance, is generally associated with most cancer relapses. There are advanced tools that can help identify the mutant genes in cancer tissues causing cancer drug resistance (CDR). Such tools include but are not limited to DNA and RNA sequencing as well assynthetic lethality gene screen (CRISPR)-based diagnosis. This review discusses the role of functional genomics in understanding CDR and finding tools for discovering drug target genes for cancer therapy.

Fig. 1

Mechanisms of therapeutic resistance in cancer. Therapeutic resistance in cancer cells typically has two types: (a) intrinsic resistance, pre-existed sub-clones shown in cancer colonies, and cancer relapse early in cancer cell treatment. (b)The acquired resistance is a new mutation shown by the drug-induced mutation forming a clonal mutation or stem cancer mutation shown in the blood-stream as soluble molecules.

Fig. 2

Single-cell isolation and sequencing. Drop-Seq protocol is an advanced technology that produces a gene expression map made of an individual cell. Then, the mRNA Seq is performed from a large number of cells. That started sample collection using liquid or tissue biopsy. This method relies on droplet microfluidics and library preparation for NGS: droplets allow for swift and effective separation of the cells in one tissue using low reagent volumes. NGS allows for a fast and massive number of cell analyses in single-cell gene expression. The resulting study showed the cell clustering and function maps, as well as the single-cell expression profile.

Fig. 3

Cell-based screening to identify resistance genes in solid tumor cells using pooled CRISPR/Cas9 libraries. CRISPR/Cas-based genetic screening strategy to swiftly identify drug resistance mutations in targeted genes. The screening discovers the local genetic changes shaped by CRISPR-Cas-induced non-homologous end-joining (NHEJ) repair to induce several functional in-frame mutations. The screening was validated using large sgRNA building libraries fused with pairs of drug targets that are already known to be recognized.

Fig. 4

The principle of CRISPR/Cas9-mediated genome editing is to treat solid tumors and overcome drug resistance in cancer. These small-molecule inhibitors can be used later as new targeted therapy.