Researchers at The Translational Genomics Research Institute (TGen) and Barrow Neurological Institute say they have detected repetitive expansions (cryptic exons) in the C9ORF72 gene in the brain cells from patients with Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The team noted that it is the first time that disease-linked cryptic exons have been identified in single cells.
The findings, reported in the journal Acta Neuropathologica, could help researchers understand how cryptic exons affect cell function and which cells are most vulnerable to the dysfunction of the TDP-43 protein which drives the erroneous gene splicing.
“By examining single cells from individuals diagnosed with ALS, FTD or both, we are able to investigate which cells are most vulnerable to the genetic changes that cause disease, and which cells are more protected. This can help us understand the underlying cell processes involved in these diseases more clearly” said Kendall Van Keuren-Jensen, PhD, professor in the neurogenomics division and deputy director of scientific resources at TGen.
While previous researchers have described the presence of these cryptic exons in the spinal cord and brain tissues from people with ALS and FTD, there have been no findings about which specific cells contained them.
To discover cellular identity, the investigators examined post-mortem tissues of ALS and FTD patients with the C9ORF72 repetitive expansions. The researchers used single-nuclei RNA on the samples to look for cryptic exons in specific cells. The TGen team employed deeper sequencing than most studies, which in the search for the cryptic Exons, according to study co-author Eric Alsop, PhD, a computational scientist at TGen.
The search uncovered cryptic exons in the STMN2 and KALRN genes in the frontal cortext of the brains of patients with both diseases, but the highest frequency of crypton exons were found in FTD patients. So of the cells types found had already been linked to FTD, so the different approach taken to uncover them in this study “may further confirm them as a vulnerable cell type in the disease,” said study co-author Rita Sattler, PhD, a Barrow professor in the department of translational neuroscience.
In addition, the researchers uncovered some interesting differences of how likely brain cells were to containing cryptic exons—differences that could. be related to the different trajectories of disease development of either ALS or FTD.
There was also some evidence of gene dysregulation in some of the exon-bearing cells. However Sattler noted that this study only had post-mortem tissue to use in the study, which represented the end-stage of the disease for the patients. “We see these changes, but are they related to dying cells, or real transcriptional changes that are associated with those cells with TDP-43 pathology?” he asked.
Finding an answer to this question is the next phase of the TGen study of cryptic exons. Lauren M. Gittings, PhD, a postdoctoral fellow in the Sattler Lab, will undertake this work in the near future, this time with patient derived cells that will be used to create cortical neurons.
“She’s going to dive deeper into that biology by looking at the presence of these cryptic exons in the [KALRN] gene, and whether it plays a role in the degeneration that occurs in ALS and FTD,” Gittings said. “We’re going to look for the presence of the cryptic exons in these cells over time, to complement the post-mortem studies.”