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Proteomic changes during experimental de- and remyelination in the corpus callosum

Szilagyi, Gabor T., Nawrocki, Arkadiusz M., Eros, Krisztian, Schmidt, Janos, Fekete, Katalin, Elkjaer, Maria L., Hyrlov, Kirsten H., Larsen, Martin R., Illes, Zsolt, Gallyas, Ferenc·2020·PLOS ONE
DOI 10.1371/journal.pone.0230249PMC PMC7145428
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Fig 1 Cluster analysis. Mice were treated or not (C) with 0.2% cuprizone in their food for 4 weeks then were sacrificed after termination of the treatment (4wD), and 2 (2dR) or 14 (2wR) days later. Cluster analysis of 3183 unmodified (A and C) and 1703 single- or multi phosphorylated and/or gycosylated proteins (B and D) identified in corpus callosum homogenate of the mice were performed by using the Perseus software platform (http://www.perseus-framework.org). Heat maps (A and B) and pattern of protein concentration changes in the treatment groups (C and D) are presented. The concentrations were normalised to those of C group and were expressed in log2(fold change) values. Heat map scales are z score based, number of the proteins in a given cluster (A and B) as well as cluster ID next to a given cluster pattern (C and D) are indicated.
Fig 1 Cluster analysis. Mice were treated or not (C) with 0.2% cuprizone in their food for 4 weeks then were sacrificed after termination of the treatment (4wD), and 2 (2dR) or 14 (2wR) days later. Cluster analysis of 3183 unmodified (A and C) and 1703 single- or multi phosphorylated and/or gycosylated proteins (B and D) identified in corpus callosum homogenate of the mice were performed by using the Perseus software platform (http://www.perseus-framework.org). Heat maps (A and B) and pattern of protein concentration changes in the treatment groups (C and D) are presented. The concentrations were normalised to those of C group and were expressed in log2(fold change) values. Heat map scales are z score based, number of the proteins in a given cluster (A and B) as well as cluster ID next to a given cluster pattern (C and D) are indicated.CC BY · PubMed Central
Fig 2 Venn diagrams for the proteins significantly altered in the experimental groups. Distribution of unmodified (A) and single- or multi phosphorylated and/or gycosylated proteins (B) among the different experimental groups are presented. Numbers indicate the number of the proteins in Tables 1 and 2.
Fig 2 Venn diagrams for the proteins significantly altered in the experimental groups. Distribution of unmodified (A) and single- or multi phosphorylated and/or gycosylated proteins (B) among the different experimental groups are presented. Numbers indicate the number of the proteins in Tables 1 and 2.CC BY · PubMed Central
Fig 3 Immunohistochemical analysis of phosphorylation during de- and remyelination. We performed immunohistochemistry utilising phospho (p)-Ser, p-Thr and p-Tyr specific primary antibodies on brain sections of the animals (n = 3) from all four treatment groups. Representative sections are presented (A). For quantitative assessment of phosphorylation during de- and remyelination (B), all nuclei and staining artefacts were eliminated from the sections, and staining intensities of corpus callosum were normalised by an expert blind to the experiment to background i.e. left and right retrosplenial area, ventral part, layer 1 (lightly stained area containing few nuclei left and right to the arrow in A) by using Molecular Devices’ MetaXpress® image analyser software. Data are presented mean ± standard deviation % of the background (n = 3). Filled, dark grey, open and light grey bars denote control, 4-week demyelination, 2-day and 2-week remyelination groups, respectively. * significantly different from C; # significantly different from 4W.
Fig 3 Immunohistochemical analysis of phosphorylation during de- and remyelination. We performed immunohistochemistry utilising phospho (p)-Ser, p-Thr and p-Tyr specific primary antibodies on brain sections of the animals (n = 3) from all four treatment groups. Representative sections are presented (A). For quantitative assessment of phosphorylation during de- and remyelination (B), all nuclei and staining artefacts were eliminated from the sections, and staining intensities of corpus callosum were normalised by an expert blind to the experiment to background i.e. left and right retrosplenial area, ventral part, layer 1 (lightly stained area containing few nuclei left and right to the arrow in A) by using Molecular Devices’ MetaXpress® image analyser software. Data are presented mean ± standard deviation % of the background (n = 3). Filled, dark grey, open and light grey bars denote control, 4-week demyelination, 2-day and 2-week remyelination groups, respectively. * significantly different from C; # significantly different from 4W.CC BY · PubMed Central
Fig 4 Venn diagrams for the shortlisted proteins. Those proteins of Tables 1 and 2 that were PANTHER unclassified or belonged to a biological process of smaller than 50% over- or under-representation were deleted from the list. Distribution of the 157 remaining unmodified and single- or multi phosphorylated and/or gycosylated proteins among the different experimental groups (see Fig 1) are presented. Remyelination only proteins are shaded.
Fig 4 Venn diagrams for the shortlisted proteins. Those proteins of Tables 1 and 2 that were PANTHER unclassified or belonged to a biological process of smaller than 50% over- or under-representation were deleted from the list. Distribution of the 157 remaining unmodified and single- or multi phosphorylated and/or gycosylated proteins among the different experimental groups (see Fig 1) are presented. Remyelination only proteins are shaded.CC BY · PubMed Central
Fig 5 IPA regulator network analysis of RO proteins. IPA regulator network analysis was performed on the 2dR and 2wR groups of RO proteins. The resulting network is presented (A). Occurrence of the network orthologues among genes expressed differentially between human multiple sclerosis lesion types vs. NAWM [20] was studied by using the edgeR package (3.8) software [19]. The results are presented as a heat map. Key for molecule shapes and colors as well as relationship labels is published on http://qiagen.force.com/KnowledgeBase/articles/Basic_Technical_Q_A/Legend. Significant changes represented by node coloring based on the fold changes in protein levels.
Fig 5 IPA regulator network analysis of RO proteins. IPA regulator network analysis was performed on the 2dR and 2wR groups of RO proteins. The resulting network is presented (A). Occurrence of the network orthologues among genes expressed differentially between human multiple sclerosis lesion types vs. NAWM [20] was studied by using the edgeR package (3.8) software [19]. The results are presented as a heat map. Key for molecule shapes and colors as well as relationship labels is published on http://qiagen.force.com/KnowledgeBase/articles/Basic_Technical_Q_A/Legend. Significant changes represented by node coloring based on the fold changes in protein levels.CC BY · PubMed Central

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Metadata

Authors
Szilagyi, G. T., Nawrocki, A. M., Eros, K., Schmidt, J., Fekete, K., Elkjaer, M. L., Hyrlov, K. H., Larsen, M. R., Illes, Z., & Gallyas, F.
ORCID
Gallyas, Ferenc
Venue
PLOS ONE
Publisher
Public Library of Science (PLoS)
Published
2020-04-09
Volume
15
Issue
4
Pages
e0230249
ISSN
1932-6203
DOI
10.1371/journal.pone.0230249
PMC
PMC7145428
Cited by
8
References
3
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (vor)

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Szilagyi, G. T., Nawrocki, A. M., Eros, K., Schmidt, J., Fekete, K., Elkjaer, M. L., Hyrlov, K. H., Larsen, M. R., Illes, Z., & Gallyas, F. (2020). Proteomic changes during experimental de- and remyelination in the corpus callosum. PLOS ONE. https://doi.org/10.1371/journal.pone.0230249