Additional file 2 of Neutrophil and mononuclear leukocyte pathways and upstream regulators revealed by serum proteomics of adult and juvenile dermatomyositis
Creators: name: Sparling, A. Clare
name: Ward, James M.
name: Sarkar, Kakali
name: Schiffenbauer, Adam
name: Farhadi, Payam Noroozi
name: Smith, Michael A.
name: Rahman, Saifur
name: Zerrouki, Kamelia
name: Miller, Frederick W.
name: Li, Jian-Liang
name: Casey, Kerry A.
name: Rider, Lisa G.
Publisher: name: figshare
Year: 2024
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Physiology
subject: Pharmacology
subject: Chemical Sciences not elsewhere classified
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer

description: Supplementary Material 2: Additional File 2: Supplementary Figure 1. Differentially regulated proteins shared in both adult and juvenile dermatomyositis (DM, JDM). The Venn diagram depicts the overlap between the differentially regulated proteins in the DM (n = 48) and JDM (n = 32) analyses. Adult controls were used in the DM analysis and pediatric controls were used in the JDM analysis. Twelve additional proteins (not shown) were identified in the combined DM and JDM analysis, which included: ADAMTS8, APOC1, ANGPT1, B2M, CHI3L1, IGFBP7, IL1RL1, IL1R2, IL6R, PPY, RETN, and SERPINA7. Abbreviations: DM, adult dermatomyositis; JDM, juvenile dermatomyositis. Additional File 2: Supplementary Figure 2. Protein-protein correlations in juvenile dermatomyositis (JDM) patients associated with neutrophil, monocyte, and dendritic cell expression. (A) JDM protein clustering of the 78 differentially expressed proteins. Correlations that met the thresholds of p &lt;0.05 and |Spearman’s rank correlation coefficient| &gt; 0.4 were clustered. (B) The largest protein cluster, boxed in panel A, was further examined. (C) Relative expression levels of the clustered proteins in immune cells. Abbreviations: JDM, juvenile dermatomyositis; NA, not applicable. Additional File 2: Supplementary Figure 3. Protein-protein correlations in adult dermatomyositis (DM) and juvenile dermatomyositis (JDM) patients associated with interferons. (A) DM protein clustering of the 78 differentially expressed proteins. Correlations that met the thresholds of p &lt;0.05 and |Spearman’s rank correlation coefficient| &gt; 0.4 were clustered. (B) The second largest DM protein cluster, boxed in panel A, was further examined. (C) JDM protein clustering of the 78 differentially expressed proteins. Correlations that met the thresholds were clustered. (D) The second largest JDM protein cluster, boxed in panel C, was further examined. Abbreviations: DM, adult dermatomyositis; JDM, juvenile dermatomyositis; NA, not applicable. Additional File 2: Supplementary Figure 4. Significant correlations between serum muscle enzyme levels and proteins from the Rules-based Medicine platform in patients with adult dermatomyositis (DM) and juvenile dermatomyositis (JDM). Serum levels of lactate dehydrogenase (LDH), aldolase, and creatine kinase were correlated with proteins from the Rules-Based Medicine (RBM) proteomics platform. Correlations that met the thresholds of p &lt;0.05 and |Spearman’s rank correlation coefficient| &gt; 0.5 are displayed. Red indicates a positive correlation; blue indicates a negative correlation. (A) The left heatmap depicts correlations in patients with DM. (B) The right heatmap depicts correlations in patients with JDM. Proteins that were part of the 78 differentially expressed proteins are starred. RBM protein names are used in the heatmaps. Abbreviations: RBM, Rules-Based Medicine; DM, adult dermatomyositis; JDM, juvenile dermatomyositis; LDH, lactate dehydrogenase. Additional File 2: Supplementary Table 2. Top five canonical pathways associated with differentially expressed proteins in adult dermatomyositis (DM) and juvenile dermatomyositis (JDM). Pathways shared between DM and JDM are bolded. Shared proteins between DM and JDM in the same pathways are indicated in bold. Abbreviations: DM, adult dermatomyositis; JDM, juvenile dermatomyositis. Additional File 2: Supplementary Table 3. Top five molecular and cellular functions associated with differentially expressed proteins in adult dermatomyositis (DM) and juvenile dermatomyositis (JDM). Molecular and cellular functions shared between DM and JDM are bolded. Shared proteins between DM and JDM in the same molecular and cellular functions are indicated in bold. Abbreviations: DM, adult dermatomyositis; JDM, juvenile dermatomyositis. Additional File 2: Supplementary Table 4. Predicted upstream regulators of differentially expressed proteins in adult dermatomyositis (DM) and juvenile dermatomyositis (JDM). Upstream regulators shared between DM and JDM are bolded. Shared proteins between DM and JDM under the same upstream regulators are indicated in bold. Abbreviations: DM, adult dermatomyositis; JDM, juvenile dermatomyositis.