Researchers in Brazil have identified a group of co-expressed genes that are dysregulated in induced pluripotent stem cell (iPSC)-derived neuronal cells from patients with autism spectrum disorder (ASD), and which could potentially be used as a biomarker or even therapeutic target for the neurodevelopmental disorder. The study results, reported by scientists at the University of São Paulo’s Institute of Biosciences (IB-USP), indicate that a common gene expression profile my underpin ASD, regardless of the DNA mutations in any autistic individual.
“We found a group of genes that’s dysregulated in neural progenitor cells, which give rise to neurons, and in neurons themselves,” said Maria Rita dos Santos e Passos-Bueno, PhD, a professor at IB-USP. “The study bore out the hypothesis that, while the origin of autism is multifactorial and different in each person, these different alterations can lead to the same problems in the functioning of their neurons,” added first author Karina Griesi Oliveira, PhD, a researcher in the Albert Einstein Israeli Education and Research Institute (IIEP).
The results indicate that while the DNA of individuals with autism may harbor different alterations, the activity of these genes is similar in people with the disorder, and differs from that of the same genes in the brains of people without autism. The investigators reported on their study in Molecular Psychiatry, in a paper titled, “Transcriptome of iPSC-derived neuronal cells reveals a module of co-expressed genes consistently associated with autism spectrum disorder.”
ASD is a neurodevelopmental disorder that affects at least 1% of the population, and is characterized by impaired social-communicative skills and by repetitive behaviors, the authors wrote. Diagnosis of suspected cases generally can’t be made through imaging or blood tests, and while it has long been recognized that genetic factors play an important role in ASD, considerable variability in genetic background makes diagnosis and treatment of the disorder on a genomic basis difficult. About 100 genes have already been linked with the disorder, and another thousand are being studied, the investigators noted. “A major genetic error causes autism in some 30% of patients, but the origin of the disorder is multifactorial in 70%, with several alterations to DNA causing clinical symptoms, so that interpretation of the genetic data is still complex,” Passos-Bueno explained.
Despite the large number of candidate ASD-associated genes, there does seem to be some convergence on a few final common effectors or molecular pathways, however, “… suggesting that the different genetic variants associated with the disease may lead to similar functional consequences which might be reflected in the transcriptional level, protein level or, lately, in the regulation of specific cellular mechanisms,” the team commented.
Whole transcriptome studies carried out to investigate differentially expressed gene profiles associated with ASD have mainly used post-mortem brain tissue from ASD individuals, but this doesn’t capture ASD-related dysregulated gene expression that may occur only transiently during prenatal development. More recent developments in cellular reprogramming mean that it is now possible to generate neural progenitor cells (NPCs) and neurons from ASD patients, as in vitro models that might better recapitulate the features of the developing brain.
For their study, the team generated iPSC lineages from stem cells derived from teeth. “We took dental pulp cells from people with and without autism, and from these, we created pluripotent stem cells, which can be transformed into any type of cell,” said Oliveira. “In this way, we were able to create in the laboratory neural cells with the same genomes as those of the patients.”
Five individuals with high-functioning autism and one with low-functioning autism were enrolled in the study. The six individuals had heterogeneous genetic profiles. A control group comprised of six healthy subjects. The iPSCs derived from the tooth stem cells were reprogrammed into cell types that would simulate two stages in the development of the human brain, i.e., neural progenitor cells, which give rise to neurons, and neurons at a stage equivalent to those of a fetus between the 16th and 20th weeks of gestation.
The researchers then analyzed the transcriptomes of the neural progenitor cells and neurons. “By counting the RNA molecules, we were able to determine gene expression with a considerable degree of precision,” Oliveira said. Using mathematical models to determine which genes were differentially expressed between the groups with and without autism, the researchers highlighted genes involved in synaptic function and neurotransmitter release, essentially, a group of genes that modulates communication among neurons, which influences brain function. “Taken together, these exploratory analyses point to some putative proteins that may act as molecular links between NPC and neuron transcriptome dysregulation seen in ASD patients,” the investigators commented.
The set of genes identified, some of which have been linked with autism in previous research, displayed increased activity in neurons. “Some of them were dysregulated in iPSC-derived neural cells from autists studied in other research, and in neurons from postmortem brain tissue belonging to individuals with autism, validating the method,” Passos-Bueno said. “Although these results should be interpreted with caution due to the limited number of samples included in this analysis, these possible molecular regulatory links between modules in NPC and in neurons deserve further investigation,” the authors stated.
Interestingly, a second analysis using postmortem tissue data showed decreased gene expression at the time of death. “We don’t know the reason for the difference, but it’s consistent evidence that expression of this group of genes is involved in autism spectrum disorder,” Oliveira commented. “Comparison of our results with previous transcriptome studies using both iPSC-derived neuronal cells and postmortem brain tissue revealed the consistent dysregulation of a module of synaptic molecules, which may represent a subset of genes exhibiting a pattern of expression that could be used as a biomarker for ASD,” the team concluded.
The dysregulation appeared to affect communication among neurons in the subjects of the study, which was conducted in Brazil. The discovery could improve diagnosis, which is currently based on the clinical analysis of symptoms. [RIDC HUG-CELL]
The results provided additional evidence to suggest that autism begins to develop during gestation. “The study points to a disturbance in fetal neurodevelopment that alters neuronal functioning, so that the child is born with altered gene expression,” suggested Passos-Bueno, who is affiliated with the Human Genome and Stem Cell Research Center (HUG-CELL), a Research, Innovation and Dissemination Center (RIDC) supported by São Paulo Research Foundation – FAPESP and hosted by the University of São Paulo (USP).
The team said identification of the dysregulated module of co-expressed synaptic genes could be considered one of the most consistent findings for ASD to date, pointing to a central role in disease pathology. “Therefore, this module should be carefully considered when exploring genetic variants in ASD individuals, its expression pattern might be used as a biomarker for the disease and, especially, it should be explored as a potential target for disease treatment.”