Fig 1.
A). Workflow summarizing the LCM islet proteome characterization. B). Tissue sections from nPOD human pancreas examined by microscopy under i) bright field; ii) autofluorescence; iii) stained with hematoxylin and eosin and iv) stained with insulin.
Fig 2.
Volcano plots and Venn diagrams showing protein expression in AAB+ and T1D cases versus non-diabetic cases.
A). Volcano plot of protein expression in islets from ND versus AAB+. B). Volcano plot of protein expression in islets from ND versus T1D. Volcano plots were constructed using fold-change and p values, enabling visualization of the relationship between fold change and statistical significance. The red boxes in volcano plots represent differentially proteins with statistical significance between ND vs AAB+ and T1D cases. C). Comparison of differentially expressed proteins between AAB+ and T1D versus controls. D) Significantly downregulated proteins between AAB+ and T1D versus controls. E). Significantly upregulated proteins between AAB+ and T1D versus controls.
Fig 3.
Gene ontology enrichment for differentially proteins between ND versus T1D cases.
The GO analysis was performed using Panther [15]. GO-CC denotes Cellular Component, GO-MF denotes Molecular Function and GO-BP, Biological Processes.
Fig 4.
STRING analysis (http://www.string-db.org) derived protein-protein interaction networks for 63 islet proteins that are differentially regulated in T1D compared to ND cases.
The network nodes represent proteins. Splice isoforms or post-translational modifications are collapsed, i.e., each node represents all proteins produced by a single, protein coding gene. Edges represent protein-protein associations. The associations are meant to be specific and meaningful with associated proteins jointly contributing to a shared function. This does not necessarily mean that the proteins are physically binding each other [18] (http://www.string-db.org).
Fig 5.
STRING analysis (http://www.string-db.org) derived protein-protein interaction networks for 39 islet proteins that are differentially regulated in AAB+ compared to ND cases.
The network nodes represent proteins. Splice isoforms or post-translational modifications are collapsed, i.e., each node represents all proteins produced by a single, protein coding gene. Edges represent protein-protein associations. The associations are meant to be specific and meaningful with associated proteins jointly contributing to a shared function. This does not necessarily mean that the proteins are physically binding each other [18] (http://www.string-db.org).
Table 1.
Summary of IPA Analysis AAB+ versus non-diabetic cases.
Table 2.
Summary of IPA analysis T1D versus non-diabetic cases.
Table 3.
Ten top differentially regulated molecules in IPA analysis T1D vs ND.
Table 4.
Ten top differentially regulated molecules in IPA analysis AAB+ vs ND.