Polina Shcherbakova, PhD

Research Topics

DNA polymerase defects in human cancers 

Genetic instability has long been known as a hallmark of human cancers. Tumor cells can contain up to several thousands of genetic alterations. Mutations in oncogenes and tumor suppressor genes play a key role in the initiation and progression of cancer. In addition, tumors contain numerous random mutations, most of which are present in only a small proportion of the cells in a tumor. This genetic heterogeneity provides endless opportunities for tumor evolution and rapid emergence of resistance to therapy. The mechanisms underlying the high genome instability in most cancers are unknown. Recent sequencing of cancer genomes revealed that tumors with the highest number of mutations and families with some of the most severe hereditary cancer predisposition syndromes carry defects in the replicative DNA polymerase genes. The prevailing but not extensively tested theory is that these defects reduce the fidelity of the replicative enzymes and, thus, result in multiple errors when the genomic DNA is duplicated and a copy is passed on to the daughter cell. Our laboratory investigates the mechanisms through which DNA polymerase defects cause hypermutated cancers, with the long-term goal of learning to control the genome instability to reduce cancer incidence, delay progression and improve therapy outcome.

Mechanisms of DNA damage-induced mutagenesis

Replicative polymerases have evolved to copy DNA with high fidelity only when presented with undamaged DNA templates. However, cellular DNA is continuously attacked by endogenous and exogenous genotoxicants. Although cells possess DNA repair pathways that remove various types of damage, DNA damage occurs throughout the cell cycle, including during the S-phase. The replication machinery, therefore, often encounters lesions that create obstacles for the replicative DNA polymerases. At the turn of the century, specialized polymerases that have the ability to bypass lesions in template DNA were discovered. The translesion synthesis helps the cells to overcome the replication block, but the specialized enzymes are inaccurate and generate mutations during copying of the damaged region. We study the mechanisms that lead to the recruitment of error-prone polymerases to sites of DNA lesions and, thus, promote DNA damage-induced mutagenesis. We also study the mechanisms that restrict access of the error-prone enzymes to the rest of the genome (to undamaged DNA), where their participation in DNA synthesis would be more harmful than helpful.

The role of non-canonical DNA structures in mutagenesis

While the majority of cellular DNA exists in the classical double helical “B-form”, certain sequences adopt unusual secondary structures, such as hairpins, cruciforms, slipped structures, G-quadruplex, triplex and Z-DNA. These non-canonical structures inhibit the progression of replication. Using the yeast model, our laboratory discovered that error-prone DNA polymerases are recruited not only to the sites of DNA damage, but also to templates with small hairpins formed by very short (4-6 bases) inverted repeat sequences that are widespread in all genomes. The bypass of hairpins by the error-prone enzymes results in mutations, including complex DNA changes where several nucleotides in a row are replaced by a completely different sequence taken from an alternative hairpin-free template. While short inverted repeats present a relatively minor challenge to normal cells, they become a major source of replication stalling and mutation when the activity of replicative polymerases is reduced due to genetic defects or treatment with therapeutic replication inhibitors. Accordingly, we call this phenomenon Defective-Replisome-Induced Mutagenesis (DRIM). Guided by the knowledge we have gained from the yeast system, we are now developing approaches to study the DRIM pathway in human cells.