Brazilian researchers create cell atlas for brain malformation associated with severe epilepsy

Using a single-cell sequencing technique, it was possible to characterize the different cell types present in the brain lesion. The result paves the way for specific treatments against focal cortical dysplasia.

By Luciana Constantino  |  Agência FAPESP – Using a single-cell sequencing technique, Brazilian researchers have created the first cell atlas of focal cortical dysplasia (FCD), a malformation of the cerebral cortex that leads to drug-resistant epilepsy. These cases are most common in children and adolescents, accounting for up to 50% of epilepsy surgeries in this age group.

With the atlas, it was possible to characterize the different cell types present in the brain lesion and determine which ones are involved in the disease. The result opens the way for the development of new specific treatments for this type of dysplasia.

The molecular mechanisms responsible for epileptic seizures in patients with FCD are poorly understood. People with severe cases can have between 40 and 50 seizures a day, with loss of consciousness and falls. When medications fail to control the seizures, surgery is an option, but it carries risks, such as vision, hearing and speech problems.

In a study published in the journal iScience, the researchers were able to map at cellular resolution both transcriptional changes – involved in the process of converting DNA into messenger RNA (the “recipe” for making proteins) – and epigenetic changes (modifying gene expression through biochemical processes without changing the DNA sequence). These mechanisms regulate how genes are activated or deactivated to produce proteins and other functional molecules, known as gene expression.

The study also identified subpopulations of neurons, microglia and astrocytes involved in the disease. This group of cells forms the cerebral cortex and ensures the functioning, protection and adaptation of the nervous system.

The research identified a specific neuronal population in FCD patients characterized by the expression of NEFM+ neurofilament (a neuronal protein), which includes the so-called dysmorphic neurons. These are abnormal cells found in the cortex of these patients that are responsible for the altered synapses that cause epileptic seizures.

As for microglia (immune system cells located in the brain), two subpopulations were discovered, called CD74+ and CD83+. These may be associated with immune activation and neuroinflammation.

“Using an advanced genomic technique, we obtained a cellular and therefore extremely detailed view of this brain malformation. We identified profound cellular changes in the cortex of these patients, including the loss of neurons in the upper layers, as well as immature astrocytes and populations of microglia expanded in the lesions and associated with inflammation. This cell atlas is of great importance for understanding the mechanisms and seeking specific therapies that can target the identified cells,” explains computational biologist Diogo Veiga, corresponding author of the article, to Agência FAPESP.

A researcher at the School of Medical Sciences of the State University of Campinas (FCM-UNICAMP), Veiga is part of the team at the Brazilian Institute of Neuroscience and Neurotechnology (BRAINN), a Research, Innovation and Dissemination Center (RIDC) funded by FAPESP.

In the work that began in 2021, the group generated a dataset of 61,525 single cells from 11 clinical samples of focal cortical dysplasia lesions obtained from patients undergoing surgery and from controls. Single-cell sequencing is an advanced molecular biology technique that allows genetic material (DNA or RNA) to be analyzed individually, providing a detailed view of cellular heterogeneity and revealing much more specific characteristics of the lesions studied.

One of the challenges was analyzing the amount of data. “We spent a long time developing the computational workflow and testing different approaches to be able to identify these subpopulations associated with the disease,” says Veiga, who highlights the contribution of his PhD thesis student Isabella Cotta Galvão, first author of the article.

The work has been presented at national and international events, including the Human Cell Atlas Latin America Symposium in July 2024, which brought together researchers in the field of single-cell genomics.

In order to increase knowledge on the topic in Brazil, researchers Iscia Lopes-Cendes and Jaqueline Geraldis, both from FCM-UNICAMP and authors of the article, organized the event “Single-Cell Omic Fusion: Navigating Spatial Omics in Biomedical Research” last November. The workshop marked the launch of Single-Cell and Spatial Omics Brazil, a scientific community dedicated to fostering collaboration and advancing this field in the country.

Epilepsy, a neurological disease with no cure, affects approximately 50 million people worldwide, according to the World Health Organization (WHO). In Brazil, there are an estimated 2 million cases. Last year, the largest study ever published on the subject in the world revealed a kind of “genetic architecture” of the disease, identifying 26 areas of the genome associated with the disorder. Brazil was the only Latin American country represented through BRAINN (read more at: agencia.fapesp.br/51140).

Next steps

The results of the study have been incorporated into the CellxGene cell database, which is part of the Human Cell Atlas Consortium. Founded in 2016, the consortium has more than 3 thousand members in 99 countries, bringing together biologists, clinicians, technologists, physicists, computer scientists, software engineers and mathematicians.

As a result, other groups can use this data in their research and try to find more targeted treatments for focal cortical dysplasia. “This type of data sharing is essential today to accelerate progress in medical research. We’re making available data generated with public money, returning society’s investment for the benefit of all,” says Lopes-Cendes.

Veiga says his group is now using the same single-cell technique to study infant brain development and another type of dysplasia to see if there are any similarities.

The research was also supported by FAPESP through four other projects (19/07382-2; 22/01530-2; 20/06168-4; 19/08259-0).

The article “Multimodal single-cell profiling reveals neuronal vulnerability and pathological cell states in focal cortical dysplasia” can be read at www.cell.com/iscience/fulltext/S2589-0042%2824%2902562-8.