Often mutated in cancer, the ATRX gene helps cells copy their DNA without damage. Crick scientists have uncovered new functions that leave ATRX-deficient cancer cells vulnerable.
Chromosomes with centromeres highlighted in green and telomeres highlighted in red at their ends. Credit: Tohru Takaki.
Every time a cell copies its DNA, parts of the genome are exposed and vulnerable to damage or errors. Molecular biologist Simon Boulton is interested in how cells spot and repair damage to their DNA, and what happens if this process fails if key genes are mutated.
“Lots of mutations in DNA repair genes are associated with cancers but we don’t often know how certain genetic changes alter DNA repair,” he says. “This is exactly the case with the ATRX gene– we know a bit about how it works but there are huge parts of the puzzle missing, affecting how we understand its role in cancer.”
ATRX mutations can arise in cancer but can also be inherited, causing ATRX syndrome, a developmental disorder linked to impaired DNA repair during critical periods of growth in childhood.
Keen to understand how ATRX mutations can stop a cell repairing DNA damage, and how this might lead to cancer or ATRX syndrome, Sandra Segura-Bayona, a postdoctoral research fellow in Simon’s team, used CRISPR gene editing to remove ATRX from cells and examine which other genes the cells needed to survive.
In a new research study, published in Nature Structural and Molecular Biology, Sandra discovered that cells deficient in ATRX become dependent on two other protein complexes, CST and 9-1-1. CST helps to replicate the protective telomere caps at the ends of DNA strands, and 9-1-1 supports the main site of DNA copying, called the replication fork.
“Both CST and 9-1-1 work by helping cells manage exposed single-stranded DNA, which are pieces of DNA that build up if replication is going awry,” says Sandra. “Clearing these single-stranded DNA stretches at the telomeres or the replication fork is critical for cells to maintain stable genomes.”
This finding led the team to consider whether removing ATRX and CST or 9-1-1 simultaneously might have a huge effect on the cell’s ability to repair DNA.
Sandra indeed confirmed that removing ATRX and either CST or 9-1-1 was lethal for the cell. “With ATRX and CST gone, single-stranded DNA built up at telomeres, causing them to break apart,” she says. “And with ATRX and 9-1-1 gone, single-stranded DNA built up at the replication fork and led to its collapse.” Surprisingly, both of these effects were independent of ARTX’s previously described roles, adding more to our understanding of its functions.
To further appreciate why loss of ATRX has such damaging effects, the team next looked at proteins at active replication forks, finding that an enzyme called FAM111A accumulates when ATRX is silenced. FAM111A promotes the formation of single stranded DNA, leading to an increased build-up of these damaging fragments.
Together these results suggest that different domains of ATRX act separately to manage distinct types of damage, one safeguarding replication, another protecting telomeres.
For Simon, the findings underline how critical losing ATRX is for a cell. “It’s clearly a linchpin for all these pathways that make sure DNA damage is repaired,” he says. “And now we’ve added two new separate roles for ATRX that haven’t been described before.”
Because the loss of both ATRX and CST or 9-1-1 are lethal for a cell, these dependencies could represent a new way to target ATRX-mutated cancers.
“Blocking CST or 9-1-1 in cancer cells with ATRX mutations could kill the cancer cells while sparing healthy cells,” says Simon. “We’d be removing the backup strategies the cancer has become dependent on.” His team is now researching how ATRX counteracts FAM111A’s activity to prevent DNA damage from being left unchecked, continuing the search for new ways to exploit vulnerabilities in cancers.
