Nature Communications: Zhejiang University Xie Anyong's team reveals the origin and mechanism of the characteristic mutation pattern of BRCA1-deficient tumors

Tumor genome sequencing revealed the complex mutational signatures of BRCA1-deficient tumors, including specific clustered point mutation enrichment, small fragment base additions and deletions (InDel), chromosomal translocation formation, and a large number of about 10 Kb tandem Tandem Duplication (TD); these mutational patterns document DNA damage events and aberrant repairs that cells encounter during tumorigenesi.

The Homologous Recombination Deficiency (HRD) prediction tool developed based on these characteristic mutational patterns has been used to predict the response to cancer drug PARP inhibitor therapy clinicall.

Endogenous DNA damage generated by normal cell metabolism under physiological conditions is the main culprit of genome instability, of which DNA single-strand break (SSB) is the most frequent DNA damage, and if it encounters a DNA replication fork, it will be converted into Single-ended DNA double-strand breaks (Double Strand Break, DSB.

Recently, the team of Pro.

The research team utilized the characteristics of CRISPR-Cas9 single-strand nickase (nCas9) target retention to efficiently induce single-end DSBs coupled with DNA replication derived from DNA single-strand nicks in cell.

The research team then analyzed the impact of BRCA1 deficiency on HR repair of single-terminal DSBs using an HR reporter system that can differentiate and quantify short-track gene conversion (STGC) and long-track gene conversion (LTGC.

In particular, the promotion of LTGC bias by BRCA1 deficiency has a pronounced DNA replication strand asymmetry, that is, BRCA1 deficiency is more likely to drive LTGC bias associated with lagging strand collapse, a result that correlates with strands of mutational patterns in BRCA1-deficient tumor.

Because replication-coupled single-end DSBs can also utilize a second single-end DSB generated by an inverted convergent replication fork for NHEJ, we analyzed such NHEJ efficiency and interface sequences using endogenous sites and found InDel frequencies in BRCA1-deficient cells The increase, especially the 11-80bp deletion product, was accompanied by an increase in the utilization of microhomology (Microhomology, MH) at the interface (Fi.

A TD of around 10 Kb is a characteristic mutational pattern of interest in BRCA1-deficient tumor.

FigureSchematic illustration of the mechanism by which aberrant replication-coupled single-terminal DSB repair induces characteristic mutational patterns in BRCA1-deficient tumors

This study not only helps to elucidate the functional differences of BRCA1 in the repair of paired-end DSBs and replication-coupled single-end DSBs, but more importantly, reveals that a major driver of the mutational pattern of BRCA1-deficient tumors is the production of replication-coupled single-end DSBs and the Repair anomalies rather than traditionally thought of as double-ended DSB.

The corresponding authors of the paper are Professor Xie Anyong and Feng Yili Distinguished Researcher from Run Run Shaw Hospital Affiliated to Zhejiang University School of Medicine and Zhejiang University Institute of Translational Medicin.

Original source:

Feng, Y.