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Blood transcriptomics of drug-naïve sporadic Parkinson's disease patients.

Calligaris R, Banica M, Roncaglia P, Robotti E, Finaurini S, Vlachouli C, Antonutti L, Iorio F, Carissimo A, Cattaruzza T, Ceiner A, Lazarevic D, Cucca A, Pangher N, Marengo E, di Bernardo D, Pizzolato G, Gustincich S - BMC Genomics (2015)

Bottom Line: Functional annotations were assigned using GO, DAVID, GSEA to unveil significant enriched biological processes in the differentially expressed genes.Together with neuronal apoptosis, lymphocyte activation and mitochondrial dysfunction, already found in previous analysis of PD blood and post-mortem brains, we unveiled transcriptome changes enriched in biological terms related to epigenetic modifications including chromatin remodeling and methylation.It identifies changes in crucial components of chromatin remodeling and methylation machineries as early events in sporadic PD suggesting epigenetics as target for therapeutic intervention.

View Article: PubMed Central - PubMed

Affiliation: Area of Neuroscience, International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy. calliga@sissa.it.

ABSTRACT

Background: Parkinson's disease (PD) is a chronic progressive neurodegenerative disorder that is clinically defined in terms of motor symptoms. These are preceded by prodromal non-motor manifestations that prove the systemic nature of the disease. Identifying genes and pathways altered in living patients provide new information on the diagnosis and pathogenesis of sporadic PD.

Methods: Changes in gene expression in the blood of 40 sporadic PD patients and 20 healthy controls ("Discovery set") were analyzed by taking advantage of the Affymetrix platform. Patients were at the onset of motor symptoms and before initiating any pharmacological treatment. Data analysis was performed by applying Ranking-Principal Component Analysis, PUMA and Significance Analysis of Microarrays. Functional annotations were assigned using GO, DAVID, GSEA to unveil significant enriched biological processes in the differentially expressed genes. The expressions of selected genes were validated using RT-qPCR and samples from an independent cohort of 12 patients and controls ("Validation set").

Results: Gene expression profiling of blood samples discriminates PD patients from healthy controls and identifies differentially expressed genes in blood. The majority of these are also present in dopaminergic neurons of the Substantia Nigra, the key site of neurodegeneration. Together with neuronal apoptosis, lymphocyte activation and mitochondrial dysfunction, already found in previous analysis of PD blood and post-mortem brains, we unveiled transcriptome changes enriched in biological terms related to epigenetic modifications including chromatin remodeling and methylation. Candidate transcripts as CBX5, TCF3, MAN1C1 and DOCK10 were validated by RT-qPCR.

Conclusions: Our data support the use of blood transcriptomics to study neurodegenerative diseases. It identifies changes in crucial components of chromatin remodeling and methylation machineries as early events in sporadic PD suggesting epigenetics as target for therapeutic intervention.

No MeSH data available.


Related in: MedlinePlus

RT-qPCR validation experiments of selected transcripts. The box plots show the natural logarithms of the relative gene expression levels (calculated by dividing the RT-qPCR values by the geometric mean of the HKs PGK1 and UBC raw quantities) for the individual genes (a and b) in blood samples of 12 de novo PD patients and 12 age- and sex-matched HCs. The statistical significance was calculated by t-test (*p < 0.05, **p < 0.01, ***p < 0.001)
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Fig2: RT-qPCR validation experiments of selected transcripts. The box plots show the natural logarithms of the relative gene expression levels (calculated by dividing the RT-qPCR values by the geometric mean of the HKs PGK1 and UBC raw quantities) for the individual genes (a and b) in blood samples of 12 de novo PD patients and 12 age- and sex-matched HCs. The statistical significance was calculated by t-test (*p < 0.05, **p < 0.01, ***p < 0.001)

Mentions: Genes for validation were selected from the candidates list of biomarkers commonly obtained with R-PCA, PUMA and SAM analysis (Additional file 9). Four transcripts were chosen among the ones with the most significant P-values (p < 0.0003) and tested with RT-qPCR. Data were normalized to the geometric mean of PGK and UBC, the most reliable reference genes. These were identified using TaqMan® array human endogenous control cards (Applied Biosystems, Foster City, CA, USA) as reported in Materials and methods section and in Additional file 13. As shown in Fig. 2a, statistically significant results from RT-qPCR analysis were achieved for Chromobox homolog 5 (CBX5) (P = 2.88E-02), Transcription factor 3 (TCF3) (P = 5.12E-04), Dedicator of cytokinesis 10 (DOCK10) (P = 1.52E-02) and Mannosidase, alpha class 1C (MAN1C1) (P = 1.15E-03). Overall, these RT-qPCR data validate expression changes identified through array analysis with a different technology and on an independent set of samples.Fig. 2


Blood transcriptomics of drug-naïve sporadic Parkinson's disease patients.

Calligaris R, Banica M, Roncaglia P, Robotti E, Finaurini S, Vlachouli C, Antonutti L, Iorio F, Carissimo A, Cattaruzza T, Ceiner A, Lazarevic D, Cucca A, Pangher N, Marengo E, di Bernardo D, Pizzolato G, Gustincich S - BMC Genomics (2015)

RT-qPCR validation experiments of selected transcripts. The box plots show the natural logarithms of the relative gene expression levels (calculated by dividing the RT-qPCR values by the geometric mean of the HKs PGK1 and UBC raw quantities) for the individual genes (a and b) in blood samples of 12 de novo PD patients and 12 age- and sex-matched HCs. The statistical significance was calculated by t-test (*p < 0.05, **p < 0.01, ***p < 0.001)
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4625854&req=5

Fig2: RT-qPCR validation experiments of selected transcripts. The box plots show the natural logarithms of the relative gene expression levels (calculated by dividing the RT-qPCR values by the geometric mean of the HKs PGK1 and UBC raw quantities) for the individual genes (a and b) in blood samples of 12 de novo PD patients and 12 age- and sex-matched HCs. The statistical significance was calculated by t-test (*p < 0.05, **p < 0.01, ***p < 0.001)
Mentions: Genes for validation were selected from the candidates list of biomarkers commonly obtained with R-PCA, PUMA and SAM analysis (Additional file 9). Four transcripts were chosen among the ones with the most significant P-values (p < 0.0003) and tested with RT-qPCR. Data were normalized to the geometric mean of PGK and UBC, the most reliable reference genes. These were identified using TaqMan® array human endogenous control cards (Applied Biosystems, Foster City, CA, USA) as reported in Materials and methods section and in Additional file 13. As shown in Fig. 2a, statistically significant results from RT-qPCR analysis were achieved for Chromobox homolog 5 (CBX5) (P = 2.88E-02), Transcription factor 3 (TCF3) (P = 5.12E-04), Dedicator of cytokinesis 10 (DOCK10) (P = 1.52E-02) and Mannosidase, alpha class 1C (MAN1C1) (P = 1.15E-03). Overall, these RT-qPCR data validate expression changes identified through array analysis with a different technology and on an independent set of samples.Fig. 2

Bottom Line: Functional annotations were assigned using GO, DAVID, GSEA to unveil significant enriched biological processes in the differentially expressed genes.Together with neuronal apoptosis, lymphocyte activation and mitochondrial dysfunction, already found in previous analysis of PD blood and post-mortem brains, we unveiled transcriptome changes enriched in biological terms related to epigenetic modifications including chromatin remodeling and methylation.It identifies changes in crucial components of chromatin remodeling and methylation machineries as early events in sporadic PD suggesting epigenetics as target for therapeutic intervention.

View Article: PubMed Central - PubMed

Affiliation: Area of Neuroscience, International School for Advanced Studies (SISSA), via Bonomea 265, 34136, Trieste, Italy. calliga@sissa.it.

ABSTRACT

Background: Parkinson's disease (PD) is a chronic progressive neurodegenerative disorder that is clinically defined in terms of motor symptoms. These are preceded by prodromal non-motor manifestations that prove the systemic nature of the disease. Identifying genes and pathways altered in living patients provide new information on the diagnosis and pathogenesis of sporadic PD.

Methods: Changes in gene expression in the blood of 40 sporadic PD patients and 20 healthy controls ("Discovery set") were analyzed by taking advantage of the Affymetrix platform. Patients were at the onset of motor symptoms and before initiating any pharmacological treatment. Data analysis was performed by applying Ranking-Principal Component Analysis, PUMA and Significance Analysis of Microarrays. Functional annotations were assigned using GO, DAVID, GSEA to unveil significant enriched biological processes in the differentially expressed genes. The expressions of selected genes were validated using RT-qPCR and samples from an independent cohort of 12 patients and controls ("Validation set").

Results: Gene expression profiling of blood samples discriminates PD patients from healthy controls and identifies differentially expressed genes in blood. The majority of these are also present in dopaminergic neurons of the Substantia Nigra, the key site of neurodegeneration. Together with neuronal apoptosis, lymphocyte activation and mitochondrial dysfunction, already found in previous analysis of PD blood and post-mortem brains, we unveiled transcriptome changes enriched in biological terms related to epigenetic modifications including chromatin remodeling and methylation. Candidate transcripts as CBX5, TCF3, MAN1C1 and DOCK10 were validated by RT-qPCR.

Conclusions: Our data support the use of blood transcriptomics to study neurodegenerative diseases. It identifies changes in crucial components of chromatin remodeling and methylation machineries as early events in sporadic PD suggesting epigenetics as target for therapeutic intervention.

No MeSH data available.


Related in: MedlinePlus