New gene linked to severe cases of Fanconi anemia microbiologystudy

Fanconi anemia is an aggressive, life-threatening disorder. Most individuals living with this rare genetic condition, characterized by bone marrow failure and cancer predisposition, survive into adulthood only with bone marrow transplantation and regular cancer screening.

But a new study demonstrates that mutations in one particular gene in the Fanconi anemia pathway result in an even more severe form of the disorder—and that many fetuses with this mutation do not survive to birth.

The sobering findings, published in the Journal of Clinical Investigation, identify this gene as FANCX and demonstrate just how essential it is to DNA repair.

“What’s so striking is the severity,” says Rockefeller’s Agata Smogorzewska, head of the Laboratory of Genome Maintenance. “We’re seeing a lot of miscarriages, or children not living very long, which illustrates the importance of this gene and the DNA repair pathway that it is associated with for many types of stem cells.”

From patient to pathway

Fanconi anemia is caused by mutations in genes that control a genomic repair process that removes covalent bonds between strands of DNA, called DNA interstrand crosslinks. But while the FANCX gene is clearly involved in that repair pathway, this particular gene never seemed to be mutated in Fanconi anemia patients.

“Cryo-EM structures showed that FANCX protein forms a tight complex with FANCB and FANCL, two other proteins whose deficiencies result in Fanconi anemia,” Smogorzewska says. “It was surprising that we didn’t know of any Fanconi anemia patients with FANCX mutations.”

Then one family in New York, who had multiple miscarriages and a newborn with developmental abnormalities incompatible with life, received care from a team at Icahn School of Medicine at Mount Sinai.

The physician–scientists ordered a blood test that diagnosed the fetuses and the newborn with Fanconi anemia, and New York University’s Undiagnosed Diseases Program used various sequencing techniques, including whole exome analysis, to demonstrate that changes in FANCX—then known as FAAP100—had occurred.

But the link between these genetic changes and the disease was only established through a collaboration between Smogorzewska’s lab—with experiments performed by Biomedical Fellow Benjamin Harrison—the NYU team led by Gilad Evrony, and the Mount Sinai team led by Bruce Gelb and Cassie Mintz. Together, the researchers confirmed the existence of a previously unknown, aggressive form of Fanconi anemia, driven by mutations in FANCX.

Testing demonstrated that the protein formed by FANCX was missing from the newborn, and that the newborn’s Fanconi anemia DNA repair pathway was unable to perform its duties without one normal copy of the gene.

It was then that FAAP100 officially gained the alias FANCX, signifying its status as one of the 23 genes now known to be mutated in patients with Fanconi anemia. The results established FANCX as a new Fanconi anemia gene causing an unusually aggressive disease.

“Sometimes you start with a pathway and find mutations in patients, but other times you start with the patients and define the pathway from there,” Smogorzewska says. “Fanconi anemia has often been the latter; most Fanconi anemia genes were identified after studying patients.”

Collaborating in rare disease research

Smogorzewska and colleagues began to suspect that Fanconi anemia patients hadn’t been presenting with FANCX mutations until now because these mutations are so severe. “Without this protein, it’s unlikely the fetus will survive,” Smogorzewska says. “If we begin to look for FANCX mutations in families with a lot of miscarriages, I suspect we’ll begin to discover many more parents who are carriers.”

Indeed, with the help of Kasturba Medical College in India, the team soon identified a second family with two miscarriages. Studies of the mutant protein from that family revealed a lack of normal function. Meanwhile, a group led by Detlev Schindler of the University of Würzburg in Germany had already presented a preliminary report on FAAP100 mutations in cell samples taken from a fetus four years earlier, also concluding that mutations in this gene caused Fanconi anemia.

That presentation at a symposium organized by the Fanconi Cancer Foundation led to coordination of publications, and Schindler’s paper was published in JCI at the same time as the paper by Smogorzewska and colleagues.

“The Foundation makes a lot of the important Fanconi anemia research possible,” Smogorzewska says. “Beyond the advocacy and grants, the symposium brings families, patients, clinicians, and researchers together and allows us to collaborate, compete and, in this case, co-publish.”

Beyond establishing FANCX as a Fanconi anemia gene and emphasizing the importance of this DNA repair pathway, the findings may help parents who are carriers start families. Smogorzewska envisions a future in which clinicians screen for FANCX mutations during IVF, selecting only healthy embryos for implantation. “We may soon be able to help families that carry these mutations prevent Fanconi anemia in future pregnancies,” Smogorzewska says. “We now know what we’re looking for.”