Additional file 2: of Looking beyond the brain to improve the pathogenic understanding of Parkinson’s disease: implications of whole transcriptome profiling of Patients’ skin

The comparative gene expression list from RNA-sequencing analysis of skin samples from Parkinson’s Disease patients and controls. An excel file of all regulated genes between Parkinson’s Disease patients and control skin samples from RNA-sequencing analysis, which includes a column form of data including the geneID, log2FC, logCPM, p-value, FDR, the HGNC identifier and the name of the gene. (XLSX 1752 kb

Additional file 1: Table S1. of Looking beyond the brain to improve the pathogenic understanding of Parkinson’s disease: implications of whole transcriptome profiling of Patients’ skin

Demographic and clinical characteristic of patients with Parkinson’s Disease. * MMSE was not obtained from patient nr.5; PIGD, postural instability gait disorder; MDS-UPDRS, Movement Disorders Society Unified Parkinson’s Disease Rating Scale, scores range from 0 to 260 (higher scores indicating more severe disability; [18, 19]). Hoehn and Yahr stages from 1 to 5 (higher scores indicating more severe disability, [20]). Schwab and England scores range from 0 to 100 (lower scores indicating more severe disability; [21]). MMSE, mini mental state examination, scores range from 0 to 30 (scores under 24 indicating dementia; [22]). Table S2. The cellular and mitochondrial metabolism pathways affected in Parkinson’s disease versus normal skin. Table S3. The protein metabolism pathways affected in Parkinson’s disease versus normal skin. Table S4. The skin homeostasis pathways affected in Parkinson’s disease versus normal skin. Table S5. The nuclear pathways affected in Parkinson’s disease versus normal skin. Table S6. The signalling/tumorigenicity pathways affected in Parkinson’s disease versus normal skin. Table S7. The immune pathways affected in Parkinson’s disease versus normal skin. Table S8. Differentially expressed genes in Parkinson’s disease versus normal skin validated by qRT-PCR. Gene names: serum amyloid A-1 and A-2 (SAA-1,-2), haemoglobin α-2 (HBA-2), calmodulin-like 6 (CALML-6), DiGeorge syndrome critical region gene 6-like (DGCR-6 L), cystatin E/M (CST E/M), olfactory receptor family 2 subfamily H member 2 (OR2HR), reactive oxygen species modulator 1 (ROMO-1), ADAM-like decysin 1 (ADAMDEC), hypocretin (orexin) neuropeptide precursor (HCRT), killer cell lectin-like receptor subfamily C member 3 (KLRC-3), apolipoprotein C-1 (APOC-1).). Table S9. Demographic and clinical characteristic of patients with Parkinson’s Disease used in the qRT-PCR analysis. (DOCX 97 kb

Blood serum metabolome of atopic dermatitis: Altered energy cycle and the markers of systemic inflammation - Fig 4

<p><b>PCA plots based only on metabolites that were found to be significant in untargeted analysis for positive (A) and combined (B) datasets.</b> Red circles—cases; blue squares—controls. Points on both plots are visually separable and form very clear clusters that correlate with phenotypes.</p

Targeted analysis results from non-paired t-test where atopic dermatitis patients’ serum metabolites were compared to controls.

<p>Targeted analysis results from non-paired t-test where atopic dermatitis patients’ serum metabolites were compared to controls.</p

Melanocytes in the Skin – Comparative Whole Transcriptome Analysis of Main Skin Cell Types

<div><p>Melanocytes possess several functions besides a role in pigment synthesis, but detailed characteristics of the cells are still unclear. We used whole transcriptome sequencing (RNA-Seq) to assess differential gene expression of cultivated normal human melanocytes with respect to keratinocytes, fibroblasts and whole skin. The present results reveal cultivated melanocytes as highly proliferative cells with possible stem cell-like properties. The enhanced readiness to regenerate makes melanocytes the most vulnerable cells in the skin and explains their high risk of developing into malignant melanoma.</p></div

Untargeted analysis results from Mann-Whitney Wilcox test where atopic dermatitis patients’ serum metabolites were compared to controls.

<p>Untargeted analysis results from Mann-Whitney Wilcox test where atopic dermatitis patients’ serum metabolites were compared to controls.</p

PCA plot for targeted analysis based on the significantly different metabolites.

<p>Red circles—cases; blue squares—controls. The groups are visually separable, although there is still a significant overlap between samples. It is important to note that PCs explain much more variance than in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0188580#pone.0188580.g001" target="_blank">Fig 1</a>.</p

PCA plot for targeted analysis based on the whole data.

<p>Red circles—cases; blue squares—controls. Initially, both groups largely overlap, also PCs explain a modest amount of variance.</p

The number of differentially expressed genes in each study group - melanocyte (MC), keratinocyte (KC), fibroblast (FB) and whole skin (Skin).

<p>Red triangles – upregulated genes, blue triangles – downregulated genes.</p

Comparative pathway analysis of MC and KC, FB and whole skin.

<p>Red plots indicate pathways, which were prominently expressed in MC. Blue plots mark pathways, which were downregulated in MC (A, B, C) and concomitantly upregulated in the whole skin (A), KC (B) and FB (C), respectively. The word sizes in wordclouds are defined by the p-values.</p