CNPEM study in Science Signaling advances understanding of neurodevelopmental disorders

Researchers have identified a previously unknown role for chloride in regulating a protein essential for brain function

A study led by scientists from the CNPEM (Brazilian Center for Research in Energy and Materials), located in Campinas (SP), has identified a previously unknown mechanism in the functioning of an important human protein: the chloride ion is capable of directly interfering with the activity of a substance essential for proper neurological development. The study was published this week in Science Signaling, an international scientific journal specializing in research on cell signaling.

Although still in the realm of basic research, the study represents a significant advance in understanding the molecular mechanisms behind DDX3X syndrome, a rare genetic condition that affects brain development. “Before considering a treatment, it is essential to understand what happens at the molecular level in these disorders. This work helps to build that fundamental scientific foundation”, says CNPEM researcher Juliana Oliveira.

This discovery opens up new possibilities for future research and may, in the long term, contribute to the development of therapeutic strategies aimed at improving the quality of life of patients with these neurodevelopmental disorders.

The work was conducted by researchers from CNPEM, with the participation of other Brazilian institutions, and investigated the DDX3X protein, which is fundamental for RNA processing and has already been associated with intellectual disabilities and alterations in brain development.

Previously known primarily for its role in the chemical balance of cells, chloride has revealed a much more active role. The scientists have demonstrated that this ion binds  itself directly to the DDX3X protein, interfering with its enzymatic activity and cellular function. In practice, this interaction reduces the protein’s ability to perform an essential function: separating RNA strands, like a zipper, a crucial step for genetic information to be correctly used by cells.

“We have identified a new type of molecular regulation, connecting the balance of ions within the cell to the functioning of a key brain protein,” highlights Ivan Rosa e Silva, CNPEM researcher and one of those responsible for the study.

Furthermore, the study showed that chloride also influences the formation of so-called “stress granules,” cellular structures that help protect genetic material in adverse situations, a process that is especially important during the development of the nervous system. By separating proteins and RNAs like water and oil, the cell forms condensates that control vital processes. Biomolecular condensates have been cited by scientists as one of the most transformative discoveries in modern biology.

Among the authors of the study are CNPEM researchers Ivan Rosa e Silva, Juliana Oliveira, Paula Prado, Felipe Benevenutti, and a multidisciplinary team of more than 20 Brazilian scientists in areas such as structural biology, biochemistry, and neuroscience.

In addition to ongoing CNPEM’s funding from the Ministry of Science, Technology and Innovation (MCTI), the research was supported by the National Council for Scientific and Technological Development (CNPq) and by the São Paulo Research Foundation (FAPESP).

Neurological diseases and DDX3X

DDX3X is a protein found in human cells that plays an essential role in the functioning of genetic material. It acts in the processing of RNA, the molecule responsible for transforming the information from DNA into proteins, helping to “open” these structures so that they can be used correctly.

When mutations occur in the DDX3X gene, this process can be impaired. These changes are associated with a neurodevelopmental disorder characterized primarily by intellectual disability, as well as, in some cases, alterations in brain formation.

Because it is located on the X chromosome, the condition is more common in women and manifests itself during pregnancy, during the period of nervous system formation.

One of the main highlights of the research was the analysis of a specific mutation in the DDX3X protein, identified in patients with more severe clinical presentations of the neurodevelopmental disorder.

The researchers observed that this alteration compromises the protein’s interaction with chloride, impairing its regulation and function. This imbalance can affect fundamental processes in brain development.

According to the study, mutations in DDX3X alter the formation of cellular structures known as condensates, small “droplets” that organize molecules within the cell. Under normal conditions, these structures are dynamic and functional, but with mutation, they become more rigid and dysfunctional, which can compromise cellular function.

State-of-the-art technology

To reach these results, the scientists used an integrative approach, combining different experimental techniques and advanced computational methods. The approach included nuclear magnetic resonance, fluorescence microscopy, synchrotron light techniques, and experiments on living cells.

Part of the experiments were carried out at Sirius, the Brazilian synchrotron light source that has one of the most advanced particle accelerators in the world. This allowed the protein structure to be analyzed at the atomic level using X-ray crystallography and to investigate the dynamics of condensates over time using the modern X-ray Photon Correlation Spectroscopy (XPCS) technique, in the Manacá and Cateretê beamlines.

The work also continues a previous study by the group published in 2021, when a previously unknown mutation identified in a Brazilian patient was characterized. In this new phase, the researchers deepened the analysis by investigating a more severe mutation, broadening the understanding of the disease’s mechanisms.