NOD-like receptor signaling and inflammasome-related pathways are highlighted in psoriatic epidermis
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1 Supplementary Information NOD-like receptor signaling and inflammasome-related pathways are highlighted in psoriatic epidermis Mari H. Tervaniemi, Shintaro Katayama, Tiina Skoog, H. Annika Siitonen, Jyrki Vuola, Kristo Nuutila, Raija Sormunen, Anna Johnsson, Sten Linnarsson, Sari Suomela, Esko Kankuri, Juha Kere, and Outi Elomaa
2 a b c PL.09 PN.09 C.05 d Figure S1. Split-thickness skin grafts (SG). The SGs consist mainly of the epidermis, as seen from the figures (a), (b), and (c). The samples were harvested using a dermatome (Zimmer ) with fixed setting for thickness (d). a b
3 c Figure S2. Gene expression profiles of up- and downregulated pathways in psoriatic lesions. Heat maps of genes involved in the NLR signaling (Run2; Run1 shown in Figure 1) (a), lysosome (Run2; Run1 shown in Figure 1) (b), and pathways in cancer (c). Lysosome includes several V-ATPase and cathepsin genes that are upregulated in PL samples. Pathways in cancer is identifiable among both the upregulated and downregulated DEGs of PL. The heat map (c) shows only the downregulated genes. Color key: red represents upregulation and blue downregulation, according to the intensity of the color (row Z-score).
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8 Figure S3. Expression of the NLR-pathway key component transcripts shown in box plots. Plots are based on the spike-in normalized gene expression data of RNAseq. a qpcr primers: Forward Reverse CARD6 AGGCGACCTGTCAGCATTTT TTAAAACTTCATGCCTTAAGCCGC IFI16 AACCACGTTGAAACCAAGACT TGCGTTCAGCACCATCACTT PYCARD GTTCAAGCTGAAGCTGCTGTCG GTGAGGTCCAAGGCGTCCAT IL8 TCTGTGTGAAGGTGCAGTTTTG TGGGGTGGAAAGGTTTGGAGT RPLP13 CTCAAGGTCGTGCGTCTGAA TGGCTGTCACTGCCTGGTACT GAPDH GAGTCAACGGATTTGGTCGT CATGGGTGGAATCATATTGG
9 Normal rabbit IgG NOD2 PYCARD b PL.02 PL.08 c d NLRP10 CARD6 e PL PN C f Figure S4. Expression of the NLR-signaling related genes in psoriatic and control epidermis. (a) Confirmation of changes in the expression of CARD6, IFI16, PYCARD, and IL8, with qpcr. Two control genes were used for normalization: RPLP13 and GAPHD. The samples were compared to the sample C.04, which therefore has the value 1. (b) NOD2 has induced expression in PL epidermis, which varies between individuals: staining in PL.02 sample is moderate whereas in PL.08 it is highly upregulated when compared with corresponding PN samples. (c) IEM of PL skin shows PYCARD clusters in connection with membrane structures that resemble desmosomes. (d) In the higher magnification of immunostaining in PL skin CARD6 is observable as cytoplasmic granules. The IEM reveals abundant CARD6 in keratinocyte contacts as well. (e) Immunohistochemistry (IH) with antibody against NLRP10 reveals strong expression in control as well as in psoriatic skin (PL and PN). (f) Control stainings with normal rabbit IgG are negative. IH scale bars: 50μm. IEM scale bars: 500nm.
10 Figure S5. Expression of the fibroblast marker genes shown in box plots. Plots are based on the spike-in normalized gene expression data of RNAseq. The Run1 contains samples: 02C, 04C, 05C, 07C, 10C, 11C, 12C, 02PN, 03PN, 06PN, 02PL, 03PL, 06PL, and 08PL. The Run2 contains samples: 02C, 04C, 05C, 07C, 09C, 10C, 11C, 12C, 14C, 05PN, 09PN, 05PL, and 09PL. All the triplicates of each sample are shown as pink spots. We selected the fibroblast markers COL3A1 and COL1A2 and examined their expression. We could see a slight decrease in the expression of these markers in some of the samples, which might be due to the thickened architecture of the epidermis.
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12 c chrm:1673 GCTAAACCTAGCCCCAAACCCACTCCACCTTACTACCAG (~ 95% of total alignments at this site) d
13 Fold change e qpcr primers: Forward Reverse MTRNR2 (FE404545) CACTCCACCTTACTACCAGACAAC GGTACTATATCTATTGCGCCAGGT MTRNR2L1 (FE163258) AGGACATCCCAATGGTGCAG ACCTGGATTACTCCGGTCTGA RNA18S5 GTGAAACTGCGAATGGCTC CGTCGGCATGTATTAGCTC Mottaghi-Dastjerdi et al. 2014: MTRNR2L1 (FE163258) CGCAGGCCCTAAACTACCAG TGCTACTGTCGATGTGGACC 2,5 2 1,5 1 MTRNR2 Mottaghi-MTRNR2L1 MTRNR2L1 0,5 0 C.05 C.07 PN.02 PN.05 PL.02 PL.05 Figure S6: Differentially expressed genes in non-lesional psoriatic skin. (a) Heat map of DEGs from the PNvsC comparison; gene expressions in samples (PL, PN, and C) of the Run2. Color key: red represents upregulated and blue downregulated expression levels according to the intensity of the color (row Z-score). The gene name includes transcript first exon (TFE) code. The most highly upregulated transcript in PN samples, ChrM_FE404545, represents MTRNR2 and shows no induction in PL. Heat map of the Run1 is shown in Figure 5. (b) Box plots of ChrM_FE404545_o and MTRNR2L1_FE163258_c. Plots are based on the spike-in normalized gene expression data of RNAseq. (c) Chromosomal localization of C.02 reads shown in UCSC genome browser: ChrM_FE404545_o reads map at the start site of the MTRNR2 gene and (d) MTRNR2L1 reads align with the 3 -end region of the gene. (e) MTRNR2 and MTRNR2L1 expressions were studied in SG samples (PL, PN, and C) by qpcr. Here presented data from a representative experiment where RNA18S5 was used as a reference and the data compared here to C.05 (PCR target regions shown in c and d). We were unable to detect significant difference between the sample groups with qpcr.
NOD-like receptor signaling and inflammasome-related pathways are highlighted in psoriatic epidermis. Tervaniemi, Mari H.
https://helda.helsinki.fi NOD-like receptor signaling and inflammasome-related pathways are highlighted in psoriatic epidermis Tervaniemi, Mari H. 2016-03-15 Tervaniemi, M H, Katayama, S, Skoog, T, Siitonen,
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DOI:.38/ncb3399 a b c d FSP DAPI 5mm mm 5mm 5mm e Correspond to melanoma in-situ Figure a DCT FSP- f MITF mm mm MlanaA melanoma in-situ DCT 5mm FSP- mm mm mm mm mm g melanoma in-situ MITF MlanaA mm mm
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Supplementary Figure 1
Supplementary Figure 1 Constitutive EGFR signaling does not activate canonical EGFR signals (a) U251EGFRInd cells with or without tetracycline exposure (24h, 1µg/ml) were treated with EGF for 15 minutes
Nature Medicine: doi: /nm.4322
1 2 3 4 5 6 7 8 9 10 11 Supplementary Figure 1. Predicted RNA structure of 3 UTR and sequence alignment of deleted nucleotides. (a) Predicted RNA secondary structure of ZIKV 3 UTR. The stem-loop structure
Fig. S1. Upregulation of K18 and K14 mrna levels during ectoderm specification of hescs. Quantitative real-time PCR analysis of mrna levels of OCT4
Fig. S1. Upregulation of K18 and K14 mrna levels during ectoderm specification of hescs. Quantitative real-time PCR analysis of mrna levels of OCT4 (n=3 independent differentiation experiments for each
Supplementary Figures
Supplementary Figures Supplementary Figure 1. Heatmap of GO terms for differentially expressed genes. The terms were hierarchically clustered using the GO term enrichment beta. Darker red, higher positive
Supplementary Figures and Tables
Supplementary Figures and Tables Supplementary Figure 1. Study design and sample collection. S.japonicum were harvested from C57 mice at 8 time points after infection. Total number of samples for RNA-Seq:
SUPPLEMENTARY FIGURES
SUPPLEMENTARY FIGURES Figure S1. Clinical significance of ZNF322A overexpression in Caucasian lung cancer patients. (A) Representative immunohistochemistry images of ZNF322A protein expression in tissue
(a) Significant biological processes (upper panel) and disease biomarkers (lower panel)
Supplementary Figure 1. Functional enrichment analyses of secretomic proteins. (a) Significant biological processes (upper panel) and disease biomarkers (lower panel) 2 involved by hrab37-mediated secretory
Title: Epigenetic mechanisms underlying maternal diabetes-associated risk of congenital heart disease
1 Supplemental Materials 2 3 Title: Epigenetic mechanisms underlying maternal diabetes-associated risk of congenital heart disease 4 5 6 Authors: Madhumita Basu, 1 Jun-Yi Zhu, 2 Stephanie LaHaye 1,3, Uddalak
sequences of a styx mutant reveals a T to A transversion in the donor splice site of intron 5
sfigure 1 Styx mutant mice recapitulate the phenotype of SHIP -/- mice. (A) Analysis of the genomic sequences of a styx mutant reveals a T to A transversion in the donor splice site of intron 5 (GTAAC
Supplementary Figure 1. Metabolic landscape of cancer discovery pipeline. RNAseq raw counts data of cancer and healthy tissue samples were downloaded
Supplementary Figure 1. Metabolic landscape of cancer discovery pipeline. RNAseq raw counts data of cancer and healthy tissue samples were downloaded from TCGA and differentially expressed metabolic genes
Lung Met 1 Lung Met 2 Lung Met Lung Met H3K4me1. Lung Met H3K27ac Primary H3K4me1
a Gained Met-VELs 1.5 1.5 -.5 Lung Met 1 Lung Met Lung Met 3 1. Lung Met H3K4me1 Lung Met H3K4me1 1 Lung Met H3K4me1 Lung Met H3K7ac 1.5 Lung Met H3K7ac Lung Met H3K7ac.8 Primary H3K4me1 Primary H3K7ac
SUPPLEMENTARY INFORMATION
SUPPLEMENTARY INFORMATION Supplementary Figure 1. Generation of a conditional allele of the Kindlin-2 gene. (A) A restriction map of the relevant genomic region of Kindlin-2 (top), the targeting construct
SUPPLEMENTARY INFORMATION
DOI: 10.1038/ncb2607 Figure S1 Elf5 loss promotes EMT in mammary epithelium while Elf5 overexpression inhibits TGFβ induced EMT. (a, c) Different confocal slices through the Z stack image. (b, d) 3D rendering
Supplementary Figure 1. AdipoR1 silencing and overexpression controls. (a) Representative blots (upper and lower panels) showing the AdipoR1 protein
Supplementary Figure 1. AdipoR1 silencing and overexpression controls. (a) Representative blots (upper and lower panels) showing the AdipoR1 protein content relative to GAPDH in two independent experiments.