When analyzing transcriptome sequences in childhood brain cancer samples, Jessica Tsai, a pediatric oncologist at the Dana-Farber Cancer Institute, was surprised to find that many of the samples expressed Forkhead Box R2 (FOXR2), a gene located on the X chromosome and normally expressed only in the testis. 

FOXR2 is part of a large family of highly conserved transcription factors that play a role in homeostasis and cellular stability. Scientists identified FOXR2 as an oncogene in many cancers. However, the mechanisms by which FOXR2 induces tumor formation are not well understood.

Along with her team led by pediatric neurologist Pratiti Bandopadhayay of the Broad Institute of MIT and Harvard and the Dana-Farber Cancer Institute, Tsai searched cancer databases, analyzed cultures of human cells, and sequenced tumor genes in animal models to investigate why FOXR2 expression increases in so many cancers. 

After screening 10,000 adult and pediatric cancers samples, the team found that FOXR2 was abnormally expressed in more than 70 percent of all cancer types, including adult melanomas, non-small cell lung cancers, and pediatric neuroblastoma and brain tumors (1,2). 

The researchers also discovered that almost 80 percent of the tumors expressing FOXR2 initiated transcription at a new region of the DNA, FOXR2 Exon-3. They found that the FOXR2 Exon-3 promoter is required for FOXR2 expression in cancer cells, and that hypomethylation of the region on the X chromosome around the FOXR2 gene activates this promoter.

“The idea of FOXR2 being uniquely epigenetically regulated to induce oncogenesis agnostic of tumor type is really exciting because it highlights the importance of having a common permissive cell state for cancer initiation,” said Eric Rahrmann, a cancer researcher at the Cancer Research UK Cambridge Institute who was not involved in the study. 

The team next investigated which genes the FOXR2 transcription factors targeted in cancer samples, and they found that FOXR2 bound to the DNA sequences that normally associate with E26 transformation-specific (ETS) transcription factors (ETS TFs), which control the expression of genes with a variety of cellular functions. 

“FOXR2 and ETS TFs can interact on DNA and actually turn genes on and off, which can cause cancer,” said Timothy Phoenix, coauthor of the study and a pharmaceutical researcher at the University of Cincinnati. 

Developing cancer therapies that inhibit FOXR2 expression is of interest to cancer researchers because it is not usually expressed in healthy cells. While healthy testis cells do express FOXR2, there is a unique barrier system called the blood-testis-barrier that could exclude a potential FOXR2-targeted treatment.

Finding a way to disrupt the interaction of FOXR2 with partner proteins to render it nonfunctional is one potential therapeutic strategy, said Rahrmann. “If we could prevent the formation of the FOXR2 protein complex that binds to the DNA or specifically prevent the binding to the DNA, it is possible it may stop cancer from progressing.” 

“The fact that FOXR2 is only expressed after development in the testis means that you might be able to provoke an immune response against it,” said David Largaespada, a geneticist at the University of Minnesota Medical School, who provided feedback about the study data to the authors.

Even though researchers have a better understanding about what FOXR2 is doing in cancer, they still don’t understand exactly how it functions. Phoenix and his team hope to identify the specific proteins with which FOXR2 interacts, which will allow them to identify potential therapeutic targets.

References

1. Tsai, J.W. et al. FOXR2 is an epigenetically regulated pan-cancer oncogene that activates ETS transcriptional circuits. Cancer Res  82, 2980–3001 (2022).
2. Liu, A.P.Y. and Northcott, P.A. Pursuing FOXR2-driven oncogenesis. Cancer Res  82, 2977–2979 (2022).