Disrupting DNA Loops Could Be Potential Strategy to Reduce Tumor Proliferation

Baylor College of Medicine researchers report that they discover the mechanism by which normal brain cells regulate the expression of the NFIA, or nuclear factor IA, gene, which is important for both normal brain development and brain tumor growth. The team, which believes its discovery will eventually help improve treatments for brain tumors, published its study (“Glia-Specific Enhancers and Chromatin Structure Regulate NFIA Expression and Glioma Tumorigenesis”) in Nature Neuroscience.

“By examining the regulation of the transcription factor NFIA in the developing spinal cord, we identified long-range enhancers that recapitulate NFIA expression across glial and neuronal lineages in vivo. Complementary genetic studies found that Sox9–Brn2 and Isl1–Lhx3 regulate enhancer activity and NFIA expression in glial and neuronal populations,” write the investigators. “Chromatin conformation analysis revealed that these enhancers and transcription factors form distinct architectures within these lineages in the spinal cord. In glioma models, the glia-specific architecture is present in tumors, and these enhancers are required for NFIA expression and contribute to glioma formation.”

“By delineating three-dimensional mechanisms of gene expression regulation, our studies identify lineage-specific chromatin architectures and associated enhancers that regulate cell fate and tumorigenesis in the CNS.”

“We began this project by studying how three components that regulate the expression of the NFIA gene interact with each other in the developing spinal cord in animal models,” explains corresponding author Benjamin Deneen, Ph.D., associate professor of neuroscience at the Center for Stem Cell and Regenerative Medicine and member of the Dan L Duncan Comprehensive Cancer Center at Baylor College of Medicine.

The scientists focused on glial cells, which represent 70% of the cells in the CNS and support the functions of the neurons.

Dr. Deneen and his colleagues looked at how three levels of gene regulation coordinated their activities to regulate NFIA gene expression. They studied enhancers, transcription factors, and the three-dimensional architecture of the associated DNA.

The team identified enhancers involved in the regulation of NFIA gene expression using a nontraditional approach. They did not rely on bioinformatics to infer which sections of DNA probably have enhancer activity. Instead, they used living chick embryos to identify enhancer elements in the spinal cord associated with the NFIA gene expression.

“Our chick spinal cord system is a powerful model for screening and proving enhancer function,” said Dr. Deneen, who also is a member of Jan and Dan Duncan Neurological Research Institute at Texas Children’s Hospital. “The system allowed us to identify multiple enhancers that operate in specific locations in the DNA and at different times, enabling us to pinpoint the transcription factors that regulate them. We also were able to determine how the DNA strands formed distinct 3D architectures (DNA loops) that brought enhancers and transcription factor together closer to the NFIA gene, which led to the production of the NFIA protein.”

According to Dr. Deneen, the researchers then studied glioma, a deadly form of brain cancer, with a 5-year progression-free survival rate of less than 5%.

“We had previously shown that NFIA is important for glioma formation,” said first author Stacey Glasgow, Ph.D., a postdoctoral fellow in the Deneen lab. “In this study we wanted to know whether the 3D DNA loops we saw in normal glial cells also formed in glioma and what would happen if we disrupted them.”

The team found that the DNA loops they had observed in normal glial cells also were present in glioma cells. When they disrupted the DNA loops in normal glial cells, the cells did not express the NFIA gene and did not go on to show their expected development. When the researchers disrupted the DNA loops in glioma cells, the cells decreased the expression of NFIA and reduced proliferation.

“Altogether, our results open the possibility for a new approach to treat glioma in the future,” notes Dr. Deneen. “Disrupting the DNA loops required for NFIA expression could be a potential strategy to indirectly reduce NFIA expression and, as a result, reduce tumor proliferation.”