Combined Use of Laser Capture Microdissection and cDNA Microarray Analysis Identifies Locally Expressed Disease-Related Genes in Focal Regions of Psoriasis.

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Combined Use of Laser Capture Microdissection and cDNA Microarray Analysis Identifies Locally Expressed Disease-Related Genes in Focal Regions of Psoriasis Vulgaris Skin Lesions Hiroshi Mitsui, Mayte Suárez-Fariñas, Daniel A. Belkin, Natasha Levenkova, Judilyn Fuentes-Duculan, Israel Coats, Hideki Fujita, James G. Krueger Journal of Investigative Dermatology Volume 132, Issue 6, Pages 1615-1626 (June 2012) DOI: 10.1038/jid.2012.33 Copyright © 2012 The Society for Investigative Dermatology, Inc Terms and Conditions

Figure 1 Immunohistochemical staining patterns were correlated with complementary DNA (cDNA) microarray data. (a) CCL27 was expressed in the basal layer of non-lesional epidermis. (b) CRIP1 was expressed in the granular layer of non-lesional epidermis. (c) STAT-1 stained in the cytosol of cells in non-lesional epidermis, whereas it stained in the nuclei of cells in lesional epidermis and dermis. (d–f) CCR7 and CCL19 were positive in dermal aggregates in lesional skin, whereas CCL21 was detected neither in non-lesional nor lesional skin. (g, h) CXCL13 (three out of five samples) and CXCR5 (six out of eight samples) were detected in lesional dermis. (i) CD20+ cells (three out of five samples) were also found in lesional dermis. Arrows indicate the positive layers and cells. Bar=100μm. Journal of Investigative Dermatology 2012 132, 1615-1626DOI: (10.1038/jid.2012.33) Copyright © 2012 The Society for Investigative Dermatology, Inc Terms and Conditions

Figure 2 Characterization of lymphoid tissue–like structures in lesional skin. (a) Both CCR7 and CCL19 were localized in dermal aggregates of the lesional skin. (b) LAMP3/DC-LAMP was co-expressed with CCR7. (c) CD3 was also co-expressed with CCR7. (d) CCL19 expression was detected on CD11c+ and (e) LAMP3/DC-LAMP+ dendritic cells, (f) as well as on CD3+ T cells. We also stained CXCR5 in combination with CXCL13 and CD20. (g) Both CXCL13 and CXCR5 stained in dermal aggregates of lesional skin and (h) CXCR5 co-stained with CD20. White arrows indicate the double-positive cells. White lines represent epidermal–dermal junctions. Bar=100μm. Journal of Investigative Dermatology 2012 132, 1615-1626DOI: (10.1038/jid.2012.33) Copyright © 2012 The Society for Investigative Dermatology, Inc Terms and Conditions

Figure 3 Unique detection of differentially expressed genes (DEGs) by laser capture microdissection (LCM) samples compared with bulk skin sample. (a, b) Scatter plots of log2FCH (fold change) of bulk versus epidermis (EPI) and reticular dermis (RD). Black lines: identity lines; gray lines: ±2 FCH; red lines: robust linear regression estimates. (c) Percentage of probe sets with larger absolute FCH in LCM samples than in bulk. Pink bars: all probe sets; red bars: probe sets considering ∣FCH∣>2.0. (d, e) Venn diagrams of bulk, EPI, and RD psoriasis transcriptome. (f, g) Proportion of unique EPI-, RD-, and bulk-related probe sets that appear in 1, 2, or 3 of the published Affymetrix studies (considering HU133A2.0 probe sets), or in the next-generation sequencing (NGS) transcriptome. The width of each bar depicts the number in each category. (h) Reverse-transcribe PCR (RT-PCR) fold changes of the top eight unconfirmed downregulated genes using bulk tissue samples (n=9). FDR, false discovery rate; psDEGs, psoriatic transcriptome. Journal of Investigative Dermatology 2012 132, 1615-1626DOI: (10.1038/jid.2012.33) Copyright © 2012 The Society for Investigative Dermatology, Inc Terms and Conditions