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DeepOmicsAE: Representing Signaling Modules in Alzheimer's Disease with Deep Learning Analysis of Proteomics, Metabolomics, and Clinical Data
Published on: December 15, 2023
Discovering Biomarkers and Pathways Shared by Alzheimer's Disease and Ischemic Stroke to Identify Novel Therapeutic
Md Rezanur Rahman1, Tania Islam2, Md Shahjaman3
1Department of Biochemistry and Biotechnology, School of Biomedical Science, Khwaja Yunus Ali University, Sirajgonj 6751, Bangladesh. rezanur12@yahoo.com.
Insights
Researchers identified common molecular links between Alzheimer's disease (AD) and ischemic strokes (IS). This study reveals shared gene expression patterns and pathways, offering new insights into disease progression and potential therapeutic targets for both conditions.
Area of Science:
- Neuroscience
- Genomics
- Biochemistry
Background:
- Alzheimer's disease (AD) is a progressive neurodegenerative disorder causing severe dementia.
- Ischemic strokes (IS) are recognized risk factors for AD, yet underlying molecular mechanisms remain unclear.
- Understanding shared molecular pathways is crucial for predicting disease progression and identifying therapeutic targets.
Purpose of the Study:
- To identify common molecular biomarkers and pathways in both ischemic strokes (IS) and Alzheimer's disease (AD).
- To elucidate potential mechanistic and gene expression links between IS and AD.
- To discover novel therapeutic strategies by analyzing protein-drug interactions.
Main Methods:
- Analysis of microarray gene expression datasets for IS and AD.
- Application of combinatorial statistical methods to identify commonly dysregulated transcripts.
- Utilized Gene Ontology (GO), KEGG pathway, and protein-protein interaction (PPI) analyses.
Main Results:
- Identified 26 common dysregulated transcripts (22 unique genes) in IS and AD.
- Revealed altered molecular pathways including MAPK signaling, alcoholism, and amino acid metabolism.
- Identified key pathway hub proteins (e.g., PDE9A, GNAO1) and transcription factors (e.g., SPIB, SMAD3).
Conclusions:
- Established novel putative links between IS and AD at the transcript level.
- Highlighted PDE9A as a potential therapeutic target with interactions to caffeine and other compounds.
- Provided foundational insights into the shared molecular pathology of IS and AD.
Abstract:
Background and objectives: Alzheimer's disease (AD) is a progressive neurodegenerative disease that results in severe dementia. Having ischemic strokes (IS) is one of the risk factors of the AD, but the molecular mechanisms that underlie IS and AD are not well understood. We thus aimed to identify common molecular biomarkers and pathways in IS and AD that can help predict the progression of these diseases and provide clues to important pathological mechanisms. Materials and Methods: We have analyzed the microarray gene expression datasets of IS and AD. To obtain robust results, combinatorial statistical methods were used to analyze the datasets and 26 transcripts (22 unique genes) were identified that were abnormally expressed in both IS and AD. Results: Gene Ontology (GO) and KEGG pathway analyses indicated that these 26 common dysregulated genes identified several altered molecular pathways: Alcoholism, MAPK signaling, glycine metabolism, serine metabolism, and threonine metabolism. Further protein-protein interactions (PPI) analysis revealed pathway hub proteins PDE9A, GNAO1, DUSP16, NTRK2, PGAM2, MAG, and TXLNA. Transcriptional and post-transcriptional components were then identified, and significant transcription factors (SPIB, SMAD3, and SOX2) found. Conclusions: Protein-drug interaction analysis revealed PDE9A has interaction with drugs caffeine, γ-glutamyl glycine, and 3-isobutyl-1-methyl-7H-xanthine. Thus, we identified novel putative links between pathological processes in IS and AD at transcripts levels, and identified possible mechanistic and gene expression links between IS and AD.
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