Overlap between Central and Peripheral Transcriptomes in Parkinson’s Disease but Not Alzheimer’s Disease
Abstract
:1. Introduction
2. Results
2.1. Non-Overlapping Sample Subset Selection Using Differentially Expressed Genes
2.2. ML-Based Ranking of Genes in BA9 (or DLPFC) from AD and PD
2.3. Diagnosis of AD and PD by Profiling Peripheral Blood Biomarkers Using ML
2.4. Correspondence between Peripheral Blood and Brain in NDs
3. Discussion
4. Materials and Methods
4.1. Data Collection
4.2. Workflow Implementation and Data Processing
4.3. Transcriptomic Data Normalisation and Expression Analysis
4.4. Analysis of Genes Associated with NDs by Machine Learning (ML)
4.5. Gene Ontology and Pathway Enrichment Analysis
4.6. Gene–Gene Interaction and Gene Co-Expression Network Analysis
5. Conclusions
6. Potential Limitations and Future Prospective
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Condition | PBMC | WB | DLPFC/BA9 | PBMC | WB | DLPFC/BA9 |
---|---|---|---|---|---|---|
Total Number of Samples | Final Number of Samples | |||||
Parkinson’s Disease | 47 | 38 | 172 | 6 | 20 | 126 |
Alzheimer’s Disease | 33 | 54 | 155 | 22 | 48 | 101 |
Cognitively-Healthy Controls | 78 | 74 | 184 | 25 | 42 | 162 |
Tissue | Contrast | Number of DEGs | Top GO-BPs | Genes |
---|---|---|---|---|
DLPFC/BA9 | AD-vs.-ctrl | 8948 | 1-Intracellular transport 2-Cellular component organisation 3-Cellular protein localisation 4-Organelle organisation 5-Protein localisation 6-mRNA metabolic process 7-Peptide transport 8-Nitrogen compound transport | hondroitin sulfate proteoglycan 5 (CSPG5), DAAM1, SEPTIN9, kinesin family member 5C (KIF5C), Unc-51 like autophagy activating kinase 1 (ULK1), Ubiquitin-specific protease 9, X-LINKED (Usp9X), RAP2A, Transforming growth factor beta regulator 4 (TBRG4), TAP binding protein (TAPBP), Solute aarrier family 6 member 8 (SLC6A8) |
DLPFC/BA9 | PD-vs.-ctrl | 12,043 | 1-Intracellular transport 2-Cellular protein localization 3-Cellular component organisation 4-Protein localisation 5-Intracellular protein transport 6-Cellular protein metabolic process 7-Catabolic process 8-mRNA metabolic process | RANBP1, Spire type actin nucleation factor 1 (SPIRE1), Solute carrier family 9 member A3 (SLC9A3), SEPTIN9, Peroxisomal biogenesis factor 10 (PEX10), VTI1B, Transmembrane protein 132A (TMEM132A), Trans-golgi network protein 2 (TGOLN2), Phosphotriesterase-related protein (PTER), Poly(RC) binding protein 2 (PCBP2) |
DLPFC/BA9 | AD-vs.-PD | 8554 | 1-Intracellular transport 2-Cellular protein localisation 3-Protein localisation 4-Cellular component organisation 5-Intracellular protein transport 6-Organelle organisation 7-Peptide transport 8-Nitrogen compound transport | VPS41, SEPTIN9, ULK1, dishevelled associated activator of morphogenesis 1 (DAAM1), Dishevelled associated activator of morphogenesis 2 (DAAM2), Transmembrane P24 Trafficking Protein 7 (TME D7), Golgi reassembly-stacking protein 2 (GORASP2), TAPBP, SLC6A8 |
WB | AD-vs.-ctrl | 740 | 1-SRP-dependent co-translational protein targeting to membrane 2-Nuclear-transcribed mRNA catabolic process, nonsense-mediated decay 3-Viral process 4-Viral transcription 5-Nuclear-transcribed mRNA catabolic process 6-Protein localisation to membrane | Ribosomal protein L31 (RPL31), Ribosomal protein L32 (RPL32), SMG5, H2AX, LSM4, Adaptor related protein complex 3 subunit delta 1 (AP3D1) |
WB | PD-vs.-ctrl | 5641 | 1-Granulocyte activation 2-Neutrophil degranulation 3-Neutrophil activation involved in immune response 4-Leukocyte degranulation 5-Neutrophil activation 6-Neutrophil mediated immunity 7-Myeloid leukocyte activation 8-Leukocyte activation involved in immune response | Vesicle associated membrane protein 8 (VAMP8), Myeloid differentiation primary response 88 (MYD88), Spleen associated tyrosine kinase (SYK), HCK, C-X-C Motif chemokine receptor 2 (CXCR2), WD repeat domain 1 (WDR1), Fc alpha receptor (FCAR), TYROBP, SYK |
WB | AD-vs.-PD | 3143 | 1-Neutrophil activation 2-Neutrophil activation involved in immune response 3-Neutrophil degranulation 4-Neutrophil mediated immunity 5-Myeloid leukocyte activation 6-Leukocyte activation 7-Regulated exocytosis 8-Vesicle-mediated transport | CXCR2, C-C motif chemokine ligand 5 (CCL5), Fc epsilon receptor Ig (FCER1G), TYRO protein tyrosine kinase binding protein (TYROBP), Stimulator of interferon response CGAMP interactor 1 (STING1), Major histocompatibility complex, class I, B (HLA-B), Major histocompatibility complex, class I, C (HLA-C), WDR-1, Peroxiredoxin 1 (PRDX1), PRDX2, Synaptogyrin 2 (SYNGR2), Myosin heavy chain 9 (MYH9), Reticulon 3 (RTN3), COPI coat complex subunit gamma 1 (COPG1), Perilipin 3 (PLIN3), ERGIC and Golgi 3 (ERGIC3) |
PBMC | AD-vs.-ctrl | 3921 | 1-mRNA metabolic process 2-Intracellular transport 3-Cellular protein localisation 4-Translational initiation 5-Cellular metabolic processes 6-Cotranslational protein targeting to membrane 7-Protein targeting to ER 8-SRP-dependent cotranslational protein targeting to membrane | Poly(RC) binding protein 2 (PCBP2), RNA binding protein 1 (RNABP1), SEPTIN9, ATP binding cassette subfamily E member 1 (ABCE1), Exosome component 10 (EXOSC10), SEC61 translocon subunit alpha 1 (SEC61A1), Translocation associated membrane protein 1 (TRAM1), Signal recognition particle 14 (SRP14), SRP receptor subunit alpha (SRPRA), Ribosomal protein L31 (RPL31), Ubiquitin A-52 residue ribosomal protein fusion product 1 (UBA52) |
PBMC | PD-vs.-ctrl | 8202 | 1-Immune system process 2-Viral process 3-Cellular metabolic process 4-cell activation 5-Immune response 6-Cell activation involved in immune response 7-Myeloid leukocyte activation 8-Leukocyte activation involved in immune response | Major histocompatibility complex, class II, DQ alpha 1 (HLA-DQA1), Major histocompatibility complex, class II, DR beta 1 (HLA-DRB1), Major histocompatibility complex, class I, F (HLA-F), HLA-C, Major histocompatibility complex, class I, E (HLA-E), Exosome component 1 (EXOSC1), TIMP metallopeptidase inhibitor 1 (TIMP-1), Golgi brefeldin a resistant Guanine nucleotide exchange factor 1 (GBF1), TYROBP, SYK |
PBMC | AD-vs.-PD | 6599 | 1-Viral process 2-Cellular metabolic process 3-Cellular component organisation 4-Intracellular transport 5-Cellular protein localisation 6-mRNA metabolic process 7-Nitrogen compound metabolic process 8-Immune system process | SPEN, Voltage dependent anion channel 1 (VDAC1), C-X-C motif chemokine receptor 4 (CXCR4), Exosome component 10 (EXOSC10), Formin Like 2 (FMNL2), RAB14, SEPTIN9, Poly(RC) binding protein 2 (PCBP2), Nitrilase 1 (NIT1), AT-Rich interaction domain 5B (ARID5B), DPA1, Leucine rich repeat containing G protein-coupled receptor 4 (LGR4), Ficolin 1 (FCN1), ETS proto-oncogene 1, transcription factor (ETS1), Macrophage expressed 1 (MPEG1) |
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Hooshmand, K.; Halliday, G.M.; Pineda, S.S.; Sutherland, G.T.; Guennewig, B. Overlap between Central and Peripheral Transcriptomes in Parkinson’s Disease but Not Alzheimer’s Disease. Int. J. Mol. Sci. 2022, 23, 5200. https://doi.org/10.3390/ijms23095200
Hooshmand K, Halliday GM, Pineda SS, Sutherland GT, Guennewig B. Overlap between Central and Peripheral Transcriptomes in Parkinson’s Disease but Not Alzheimer’s Disease. International Journal of Molecular Sciences. 2022; 23(9):5200. https://doi.org/10.3390/ijms23095200
Chicago/Turabian StyleHooshmand, Kosar, Glenda M. Halliday, Sandy S. Pineda, Greg T. Sutherland, and Boris Guennewig. 2022. "Overlap between Central and Peripheral Transcriptomes in Parkinson’s Disease but Not Alzheimer’s Disease" International Journal of Molecular Sciences 23, no. 9: 5200. https://doi.org/10.3390/ijms23095200