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Proteome-wide characterization of signalling interactions in the hippocampal CA4/DG subfield of patients with Alzheimer's disease.

Ho Kim J, Franck J, Kang T, Heinsen H, Ravid R, Ferrer I, Hee Cheon M, Lee JY, Shin Yoo J, Steinbusch HW, Salzet M, Fournier I, Mok Park Y - Sci Rep (2015)

Bottom Line: We also used a bioinformatics approach to examine upstream signalling interactions of the 113 regulated proteins.Five upstream signalling (IGF1, BDNF, ZAP70, MYC, and cyclosporin A) factors showed novel interactions in AD hippocampi.Taken together, these results demonstrate a novel platform that may provide new strategies for the early detection of AD and thus its diagnosis.

View Article: PubMed Central - PubMed

Affiliation: 1] Center for Cognition and Sociality, Institute for Basic Science, Daejeon 305-811, Republic of Korea [2] Mass Spectrometry Research Center, Korea Basic Science Institute, 804-1 Yangcheong-ri, Ochang-eup, Cheongwon-gun, Chungbuk 363-883, Republic of Korea.

ABSTRACT
Alzheimer's disease (AD) is the most common form of dementia; however, mechanisms and biomarkers remain unclear. Here, we examined hippocampal CA4 and dentate gyrus subfields, which are less studied in the context of AD pathology, in post-mortem AD and control tissue to identify possible biomarkers. We performed mass spectrometry-based proteomic analysis combined with label-free quantification for identification of differentially expressed proteins. We identified 4,328 proteins, of which 113 showed more than 2-fold higher or lower expression in AD hippocampi than in control tissues. Five proteins were identified as putative AD biomarkers (MDH2, PCLO, TRRAP, YWHAZ, and MUC19 isoform 5) and were cross-validated by immunoblotting, selected reaction monitoring, and MALDI imaging. We also used a bioinformatics approach to examine upstream signalling interactions of the 113 regulated proteins. Five upstream signalling (IGF1, BDNF, ZAP70, MYC, and cyclosporin A) factors showed novel interactions in AD hippocampi. Taken together, these results demonstrate a novel platform that may provide new strategies for the early detection of AD and thus its diagnosis.

No MeSH data available.


Related in: MedlinePlus

Strategy for identifying putative biomarkers of AD.(A) Experimental scheme for analysis of regulated proteins from post-mortem AD tissues using mass spectrometry-based proteomic analysis with label-free quantification. (B) Protein prioritization scheme for the selection of candidate proteins for verification.
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f1: Strategy for identifying putative biomarkers of AD.(A) Experimental scheme for analysis of regulated proteins from post-mortem AD tissues using mass spectrometry-based proteomic analysis with label-free quantification. (B) Protein prioritization scheme for the selection of candidate proteins for verification.

Mentions: To select meaningful proteins from total identified proteins in AD and control hippocampi, we performed a systematic data-mining strategy using an in-house protocol that involved four stages (Fig. 1). A total of 5,784 proteins from AD and control hippocampal tissues were extensively profiled by high-resolution nanoLC/MS throughout stage 1 (Fig. 1B). We identified 4,328 unique proteins from five AD hippocampus samples (2,085) and five control samples (2,243) (Fig. 2A,B) using a minimum of one unique peptide and a protein FDR of ≤1%. Thereafter, we adopted a ratio cut-off of ≥1.8 and ≤0.56 and obtained 113 proteins (52 upregulated proteins and 61 downregulated proteins; stage 3) (Table 1) for the refinedverification set; stage 4 (Fig. 1B). Recently, our institution14 identified 5,971 proteins in AD hippocampal tissues by off-gel fractionation, and profiled these proteins by using a high-resolution mass spectrometer with collision-induced dissociation and electron transfer dissociation. Fig. 2C shows the number of identified proteins in the CA4 and DG subfields and the entire hippocampus.


Proteome-wide characterization of signalling interactions in the hippocampal CA4/DG subfield of patients with Alzheimer's disease.

Ho Kim J, Franck J, Kang T, Heinsen H, Ravid R, Ferrer I, Hee Cheon M, Lee JY, Shin Yoo J, Steinbusch HW, Salzet M, Fournier I, Mok Park Y - Sci Rep (2015)

Strategy for identifying putative biomarkers of AD.(A) Experimental scheme for analysis of regulated proteins from post-mortem AD tissues using mass spectrometry-based proteomic analysis with label-free quantification. (B) Protein prioritization scheme for the selection of candidate proteins for verification.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4462342&req=5

f1: Strategy for identifying putative biomarkers of AD.(A) Experimental scheme for analysis of regulated proteins from post-mortem AD tissues using mass spectrometry-based proteomic analysis with label-free quantification. (B) Protein prioritization scheme for the selection of candidate proteins for verification.
Mentions: To select meaningful proteins from total identified proteins in AD and control hippocampi, we performed a systematic data-mining strategy using an in-house protocol that involved four stages (Fig. 1). A total of 5,784 proteins from AD and control hippocampal tissues were extensively profiled by high-resolution nanoLC/MS throughout stage 1 (Fig. 1B). We identified 4,328 unique proteins from five AD hippocampus samples (2,085) and five control samples (2,243) (Fig. 2A,B) using a minimum of one unique peptide and a protein FDR of ≤1%. Thereafter, we adopted a ratio cut-off of ≥1.8 and ≤0.56 and obtained 113 proteins (52 upregulated proteins and 61 downregulated proteins; stage 3) (Table 1) for the refinedverification set; stage 4 (Fig. 1B). Recently, our institution14 identified 5,971 proteins in AD hippocampal tissues by off-gel fractionation, and profiled these proteins by using a high-resolution mass spectrometer with collision-induced dissociation and electron transfer dissociation. Fig. 2C shows the number of identified proteins in the CA4 and DG subfields and the entire hippocampus.

Bottom Line: We also used a bioinformatics approach to examine upstream signalling interactions of the 113 regulated proteins.Five upstream signalling (IGF1, BDNF, ZAP70, MYC, and cyclosporin A) factors showed novel interactions in AD hippocampi.Taken together, these results demonstrate a novel platform that may provide new strategies for the early detection of AD and thus its diagnosis.

View Article: PubMed Central - PubMed

Affiliation: 1] Center for Cognition and Sociality, Institute for Basic Science, Daejeon 305-811, Republic of Korea [2] Mass Spectrometry Research Center, Korea Basic Science Institute, 804-1 Yangcheong-ri, Ochang-eup, Cheongwon-gun, Chungbuk 363-883, Republic of Korea.

ABSTRACT
Alzheimer's disease (AD) is the most common form of dementia; however, mechanisms and biomarkers remain unclear. Here, we examined hippocampal CA4 and dentate gyrus subfields, which are less studied in the context of AD pathology, in post-mortem AD and control tissue to identify possible biomarkers. We performed mass spectrometry-based proteomic analysis combined with label-free quantification for identification of differentially expressed proteins. We identified 4,328 proteins, of which 113 showed more than 2-fold higher or lower expression in AD hippocampi than in control tissues. Five proteins were identified as putative AD biomarkers (MDH2, PCLO, TRRAP, YWHAZ, and MUC19 isoform 5) and were cross-validated by immunoblotting, selected reaction monitoring, and MALDI imaging. We also used a bioinformatics approach to examine upstream signalling interactions of the 113 regulated proteins. Five upstream signalling (IGF1, BDNF, ZAP70, MYC, and cyclosporin A) factors showed novel interactions in AD hippocampi. Taken together, these results demonstrate a novel platform that may provide new strategies for the early detection of AD and thus its diagnosis.

No MeSH data available.


Related in: MedlinePlus