Neurodegenerative diseases like Alzheimer’s (AD), Parkinson’s (PD), and dementia with Lewy bodies (DLB) affect millions worldwide, yet effective treatments remain elusive. Researchers at Sanford Burnham Prebys are using advanced sequencing techniques to explore how these diseases alter brain cell RNA, opening new avenues for understanding their biological foundations.
A team led by Jerold Chun, Professor in the Degenerative Diseases Program, recently published findings in eNeuro highlighting the use of single-nucleus RNA sequencing (snRNAseq) to examine messenger RNA (mRNA) changes in diseased brain cells. This study builds on Chun’s earlier work, which established snRNAseq as a critical tool for studying human brain transcriptomes.
Mapping Brain RNA with Precision
Unlike traditional methods, snRNAseq isolates the nuclei of cells, bypassing contamination from the surrounding material. “Because of the brain’s complex intermixture of cells that can have thousands of connections, other single-cell technologies are more apt to be contaminated by the stuff around the cell that you don’t want,” Chun explained. This precision allows scientists to analyze RNA molecules, which carry the instructions for building proteins, within each cell.
The team combined short-read and long-read sequencing to capture a comprehensive view of RNA sequences. Short-read sequencing, which examines 100 to 150 base pairs at a time, relies on mapping these snippets to a reference genome. While effective for many applications, this method struggles with complex variants.
“Short-read sequencing struggles with certain kinds of sequence variants, so to better capture these, we also used long-read sequencing,” said Chun. Long-read sequencing analyzes RNA sequences of up to 30,000 base pairs without needing a reference genome, providing a clearer view of RNA diversity.
New Discoveries in Brain Transcriptomes
The researchers analyzed over 165,000 cells from post-mortem brain tissue samples from 25 donors, including individuals with AD, DLB, and PD, as well as controls without neurodegenerative diseases. They focused on 50 genes previously associated with these conditions, applying targeted long-read sequencing to uncover mRNA variations.
The results were striking. The team identified novel mRNA sequences for all 50 target genes, many of which had gone undetected in earlier studies. “By combining short- and long-read sequencing, we found vast mRNA isoform diversity in these genes, even those that were not differentially expressed in the short-read data,” said Christine Liu, the study’s first author.
Chun added that these findings align with prior research showing that three-quarters of the mRNAs in the brain transcriptome remain unknown. “We still have a lot left to learn about these new mRNAs and how they change with disease,” he said.
Implications for Neurodegenerative Disease
One key question emerging from this study is whether the newly identified mRNA isoforms produce novel proteins within diseased brain cells. “New mRNA isoforms mean new potential proteins within diseased brains and cells,” Chun emphasized. These proteins could represent untapped opportunities for therapeutic intervention. While the study’s immediate focus is on understanding the RNA landscape in neurodegeneration, the findings may eventually contribute to the development of targeted treatments for these debilitating diseases.
Publication Details
Liu, C. S., Park, C., Ngo, T., Saikumar, J., Palmer, C. R., Shahnaee, A., ... & Chun, J. (2024). RNA isoform diversity in human neurodegenerative diseases. eneuro, 11(12).
A team led by Jerold Chun, Professor in the Degenerative Diseases Program, recently published findings in eNeuro highlighting the use of single-nucleus RNA sequencing (snRNAseq) to examine messenger RNA (mRNA) changes in diseased brain cells. This study builds on Chun’s earlier work, which established snRNAseq as a critical tool for studying human brain transcriptomes.
Mapping Brain RNA with Precision
Unlike traditional methods, snRNAseq isolates the nuclei of cells, bypassing contamination from the surrounding material. “Because of the brain’s complex intermixture of cells that can have thousands of connections, other single-cell technologies are more apt to be contaminated by the stuff around the cell that you don’t want,” Chun explained. This precision allows scientists to analyze RNA molecules, which carry the instructions for building proteins, within each cell.
The team combined short-read and long-read sequencing to capture a comprehensive view of RNA sequences. Short-read sequencing, which examines 100 to 150 base pairs at a time, relies on mapping these snippets to a reference genome. While effective for many applications, this method struggles with complex variants.
“Short-read sequencing struggles with certain kinds of sequence variants, so to better capture these, we also used long-read sequencing,” said Chun. Long-read sequencing analyzes RNA sequences of up to 30,000 base pairs without needing a reference genome, providing a clearer view of RNA diversity.
New Discoveries in Brain Transcriptomes
The researchers analyzed over 165,000 cells from post-mortem brain tissue samples from 25 donors, including individuals with AD, DLB, and PD, as well as controls without neurodegenerative diseases. They focused on 50 genes previously associated with these conditions, applying targeted long-read sequencing to uncover mRNA variations.
The results were striking. The team identified novel mRNA sequences for all 50 target genes, many of which had gone undetected in earlier studies. “By combining short- and long-read sequencing, we found vast mRNA isoform diversity in these genes, even those that were not differentially expressed in the short-read data,” said Christine Liu, the study’s first author.
Chun added that these findings align with prior research showing that three-quarters of the mRNAs in the brain transcriptome remain unknown. “We still have a lot left to learn about these new mRNAs and how they change with disease,” he said.
Implications for Neurodegenerative Disease
One key question emerging from this study is whether the newly identified mRNA isoforms produce novel proteins within diseased brain cells. “New mRNA isoforms mean new potential proteins within diseased brains and cells,” Chun emphasized. These proteins could represent untapped opportunities for therapeutic intervention. While the study’s immediate focus is on understanding the RNA landscape in neurodegeneration, the findings may eventually contribute to the development of targeted treatments for these debilitating diseases.
Publication Details
Liu, C. S., Park, C., Ngo, T., Saikumar, J., Palmer, C. R., Shahnaee, A., ... & Chun, J. (2024). RNA isoform diversity in human neurodegenerative diseases. eneuro, 11(12).