Cerebrospinal fluid from Alzheimer’s patients has been analyzed to identify key proteins, genes, and cellular pathways responsible for the disease, uncovering potential therapeutic targets.
A wide range of genes have been associated with the onset of Alzheimer’s disease. However, the precise ways in which these genes contribute to the progression of neurodegeneration are still largely unknown, partly due to the difficulties in studying the brain of a living patient at a molecular level (1✔ ✔Trusted Source
Proteogenomic analysis of human cerebrospinal fluid identifies neurologically relevant regulation and implicates causal proteins for Alzheimer’s disease
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Using CSF to Identify Key Proteins and Genes in Alzheimer’s Disease
For the first time, researchers at Washington University School of Medicine in St. Louis have used cerebrospinal fluid (CSF) collected from living patients to investigate disease-related proteins and genes, identifying specific cellular pathways involved in the onset and progression of Alzheimer’s disease. Since these proteins are derived from CSF, they provide a reliable proxy for brain activity, with several potentially serving as targets for future therapies.
The findings are available in Nature Genetics.
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The Role of CSF Proteomics
The use of a patient’s CSF is a step forward for such studies and may be the best way to acquire relevant samples that help map out the constellation of protein activity, known as the proteome, said Carlos Cruchaga, Ph.D., the Barbara Burton and Reuben Morriss III professor of psychiatry and director of the NeuroGenomics and Informatics Center at WashU Medicine.
“Our goal is to identify risk-linked and protective genes, and also identify the causal role they play,” Cruchaga said. “To do that, we need to study human-derived data. That is why we decided to do a large proteomic study of cerebrospinal fluid, because we know that CSF is a good representation of the pathology of the disease.”
Cruchaga explained that similar investigations have relied on brain tissues collected postmortem, and therefore only provide information about the later stages of Alzheimer’s. Other studies have looked at blood plasma, which is not specific to the tissues affected by the disease.
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Genetic Markers in Alzheimer’s Research
In the past decade and a half of researching Alzheimer’s disease, scientists have increased the number of regions of our genome known to be associated with the condition from 10 to nearly 80. However, knowing the gene or region of DNA associated with the disease is only the first step. Linking an individual’s proteomic profile – that is, which proteins are active and to what degree – to their genetic code establishes a holistic view of the cellular activities in the brain. By comparing CSF samples from people with and without Alzheimer’s disease, the researchers could then identify which cellular pathways are dysfunctional.
“Sometimes within a region of DNA known to be associated with Alzheimer’s there are many genes, and we don’t know which of those genes are driving the medical condition,” Cruchaga said. “By adding the proteins to the analysis, we can determine the gene driving the association, determine the molecular pathway that they are part of, as well as to identify novel protein-to-protein interactions that otherwise will not be possible.”
Cruchaga and his collaborators had access to a rich database of information through the Knight-ADRC and the Dominantly Inherited Alzheimer Network (DIAN), which are based at WashU Medicine, as well as other studies through their collaborators. These studies were also able to provide the genetic information and CSF samples of 3,506 individuals, both healthy donors and those with Alzheimer’s disease.
Cross-referencing Genetic and Proteomic Data
The team cross-referenced proteomic data from the CSF samples with existing studies that had identified areas of the genome correlated with Alzheimer’s. From this process, they narrowed in on 1,883 proteins of the 6,361 in the CSF proteomic atlas. The investigators used three different established statistical analyses that can identify with high confidence genes and proteins that are part of the biological pathways leading to the disease. With this technique, they determined that 38 proteins are likely to have causal effects on Alzheimer’s progression; 15 of these can be targeted by medicines.
“The novelty and the strength of this analysis is that we have defined proteins that modify risk,” Cruchaga said. “So now that we have the causal steps, we can establish where the steps are leading to in the brain.”
CSF Proteomics as a Tool for Diverse Neurological Conditions
The immediate implications for understanding and developing treatments for Alzheimer’s from this study are significant, but Cruchaga said he believes that CSF proteomics may yield a treasure trove of information for many neurological conditions, ranging from Parkinson’s disease to schizophrenia.
“That’s the power of this approach – once you have an atlas of genetic variants, and that of the protein levels, you can apply this to any disease,” he said.
Metabolites as Biomarkers for Neurological Diseases
Proteins are not the only key to unlocking these conditions to be found in the CSF. Cruchaga is also investigating the potential of metabolites – substances released by cells when breaking down other compounds as part of their routine processes that are also found in CSF. In a separate paper, also published in Nature Genetics, he and his collaborators demonstrated the promise of this approach and reported associations between specific metabolites and conditions including Parkinson’s disease, diabetes, and dementia.
Reference:
- Proteogenomic analysis of human cerebrospinal fluid identifies neurologically relevant regulation and implicates causal proteins for Alzheimer’s disease – (https://www.nature.com/articles/s41588-024-01972-8)
Source-Eurekalert
