Scientists at the University of Birmingham and the Francis Crick Institute have discovered a new way in which cancer cells repair double-stranded breaks in DNA.

The findings were published in a paper titled,”H3K4 methylation by SETD1A/BOD1L facilitates RIF1-dependent NHEJ,” in the journal Molecular Cell on May 19, 2022. The work sheds light on how cancer cells respond to chemotherapy and radiotherapy, including how cancer cells may develop resistance to treatment. These insights could help develop precision medicine approaches for cancer patients.

The study results from a collaboration of the laboratories led by Martin Higgs, PhD, associate professor for genomics and rare disease and deputy director at the center for rare disease studies at the University of Birmingham, Grant Stewart, PhD, professor of cancer genetics at the institute of cancer and genomic sciences at the University of Birmingham, and Simon Boulton, PhD, senior group leader at the Francis Crick Institute and an honorary professor at University College London.

(From left to right) Martin Higgs, Grant Stewart and Simon Boulton and the senior authors of the study.

Double-strand breaks (DSBs) in DNA are a sign of trouble. They can crop up spontaneously upon exposure to excessive oxidation or ionizing radiation, or when an unwound region of DNA that’s undergoing active decoding (called a replication fork) collapses. They can also arise as part of a programmed system of cutting and joining sections of DNA during the development of the immune system (class switch recombination).

Repairing DSBs is vital for continued cellular health, and necessary in preventing cancer. Understanding how DSBs are repaired is pivotal in understanding cancer etiologies, predicting the efficacy of cancer treatments, and designing individualized treatments that exploit targeted DNA damage to eliminate cancer cells.

Cells have two established ways of repairing DSBs. The more slapdash and inherently error-prone way of repairing DSBs involves bringing the broken ends of DNA close to enable ligating enzymes to seal the break. This route, that does not require a template for repair and occurs throughout the cell cycle is called non-homologous end-joining (NHEJ).

The other way of repairing DSBs requires a template and therefore only occurs during the synthetic (S) or second growth (G2) phase of a cell cycle when a duplicated chromosome (sister chromatid) is available to serve as a template. This highly precise mode of repair called homologous recombination (HR) requires end-resection to generate a homologous template for repair.

Therefore, the first step in repairing DNA DSBs is deciding which of the two pathways are to be adopted. The 53BP1-RIF1-shieldin molecular pathway plays an important role in this decision. It prevents degradation at the broken ends of DNA DSBs, favoring NHEJ.  Earlier studies have shown that the repair protein called RIF1 interacts with damaged chromatin via phosphorylated 53BP1 to help bring the shield in complex to DSBs. But it has remained unclear whether other regulatory cues contribute to this mechanism.

Vital for DNA repair is the methylation of the histone protein, H3, at lysine-4 by SETD1A, a new study finds. This methylation promotes the accumulation of a protein called RIF1 at sites of DNA damage [Bayley et al, Molecular Cell, 2022].
The new study shows methylation of the DNA scaffolding protein histone H3, at its 4th residue (lysine) by the SETD1A-BOD1L protein duo recruits RIF1 to DSBs.

Higgs said, “Our three laboratories are interested in characterizing how DNA is repaired, and the genetic and epigenetic factors involved. A few years ago, we described a new DNA repair factor, BOD1L, and its role during DNA replication. During these initial studies on BOD1L, we also observed that it had a role in repairing DNA double-strand breaks, which led to this study. Since we also know from previous work that BOD1L interacts with the epigenetic modifier SETD1A, we combined work on both these genes.”

The current study pinpoints the roles of the proteins SETD1A and BOD1L in the DNA repair process. The team shows removing these proteins changes how DNA is repaired and alters the sensitivity of cancer cells to therapy. Specifically, the authors demonstrate blocking SETD1A or BOD1L expression or hindering H3K4 methylation allows unrestrained resection of DNA DSB ends and impairs NHEJ and class switch recombination.

In addition, the researchers found, when SETD1A is lost in patient cells, few RIF1 proteins made it to broken DSB ends. In cells lacking the breast cancer gene BRCA1, loss of SETD1A and subsequent loss of RIF1 recruitment to DSBs restored homologous recombination.  To clarify the mechanism, the authors demonstrated RIF1 binds directly to methylated H3K4. Furthermore, loss of SETD1A and BOD1L also made cancer cells resistant to a class of anti-cancer drugs called PARP inhibitors.

“There are three main findings from this paper. First, we have identified two new proteins (BOD1L and SETD1A) that are vital for repairing DNA double-strand breaks. Secondly, we have uncovered that epigenetic changes catalyzed by SETD1A regulate double-strand break repair at an entirely new level by controlling the repair protein RIF1. Lastly, loss of SETD1A confers resistance to targeted anti-cancer therapies in cells that are deficient for the tumor suppressor BRCA1,” said Higgs.

Higgs added, “This is the first time that these genes have been directly linked to DNA repair in cancer. This research has the potential to change how cancer patients are identified for treatment and how they become resistant to different drugs, which will improve treatment efficiency as well as patient outcomes.”

The team hopes the work will lead to the development of new inhibitors that re-sensitize treatment-resistant cancer cells. The team is currently pursuing experiments to understand how SETD1A and BOD1L regulate each other and control RIF1, and whether the findings of the current study have any clinical relevance in cancer patients.