{"id":3175,"date":"2024-05-17T22:43:35","date_gmt":"2024-05-17T13:43:35","guid":{"rendered":"https:\/\/misterx95.myds.me\/wordpress\/?p=3175"},"modified":"2024-05-17T22:48:29","modified_gmt":"2024-05-17T13:48:29","slug":"journal-club-2024-05-10","status":"publish","type":"post","link":"https:\/\/misterx95.myds.me\/wordpress\/?p=3175","title":{"rendered":"Journal Club: 2024.05.10"},"content":{"rendered":"\n<p>Allergy.&nbsp;2024 Mar 13.&nbsp;doi: 10.1111\/all.16086.&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38477552\/#\"><\/a><\/p>\n\n\n\n<p style=\"font-size:30px\">RNA-sequencing of paired tape-strips and skin biopsies in atopic dermatitis reveals key differences<\/p>\n\n\n\n<p><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/?term=Fritz+B&amp;cauthor_id=38477552\">Blaine Fritz<\/a><sup>&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38477552\/#full-view-affiliation-1\">1<\/a><\/sup>,&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/?term=Halling+AS&amp;cauthor_id=38477552\">Anne-Sofie Halling<\/a><sup>&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38477552\/#full-view-affiliation-2\">2<\/a><\/sup>,&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/?term=Cort+ID&amp;cauthor_id=38477552\">Isabel D\u00edaz-Pin\u00e9s Cort<\/a><sup>&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38477552\/#full-view-affiliation-1\">1<\/a><\/sup>,&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/?term=Christensen+MO&amp;cauthor_id=38477552\">Maria Oberl\u00e4nder Christensen<\/a><sup>&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38477552\/#full-view-affiliation-2\">2<\/a><\/sup>,&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/?term=R%C3%B8nnstad+ATM&amp;cauthor_id=38477552\">Amalie Thorsti M\u00f8ller R\u00f8nnstad<\/a><sup>&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38477552\/#full-view-affiliation-2\">2<\/a><\/sup>,&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/?term=Olesen+CM&amp;cauthor_id=38477552\">Caroline Meyer Olesen<\/a><sup>&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38477552\/#full-view-affiliation-2\">2<\/a><\/sup>,&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/?term=Knudgaard+MH&amp;cauthor_id=38477552\">Mette Hjorslev Knudgaard<\/a><sup>&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38477552\/#full-view-affiliation-3\">3<\/a><\/sup>,&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/?term=Zachariae+C&amp;cauthor_id=38477552\">Claus Zachariae<\/a><sup>&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38477552\/#full-view-affiliation-3\">3<\/a>&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38477552\/#full-view-affiliation-4\">4<\/a><\/sup>,&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/?term=Heegaard+S&amp;cauthor_id=38477552\">Steffen Heegaard<\/a><sup>&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38477552\/#full-view-affiliation-4\">4<\/a><\/sup>,&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/?term=Thyssen+JP&amp;cauthor_id=38477552\">Jacob P Thyssen<\/a><sup>&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38477552\/#full-view-affiliation-2\">2<\/a>&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38477552\/#full-view-affiliation-4\">4<\/a><\/sup>,&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/?term=Bjarnsholt+T&amp;cauthor_id=38477552\">Thomas Bjarnsholt<\/a><sup>&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38477552\/#full-view-affiliation-1\">1<\/a>&nbsp;<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38477552\/#full-view-affiliation-5\">5<\/a><\/sup><\/p>\n\n\n\n<ul id=\"full-view-identifiers\">\n<li>PMID:&nbsp;<strong>38477552<\/strong><\/li>\n\n\n\n<li>DOI:&nbsp;<a target=\"_blank\" rel=\"noreferrer noopener\" href=\"https:\/\/doi.org\/10.1111\/all.16086\">10.1111\/all.16086<\/a><\/li>\n<\/ul>\n\n\n\n<h2>Abstract<\/h2>\n\n\n\n<p><strong>Background:&nbsp;<\/strong>Skin tape-strips and biopsies are widely used methods for investigating the skin in atopic dermatitis (AD). Biopsies are more commonly used but can cause scarring and pain, whereas tape-strips are noninvasive but sample less tissue. The study evaluated the performance of skin tape-strips and biopsies for studying AD.<\/p>\n\n\n\n<p><strong>Methods:&nbsp;<\/strong>Whole-transcriptome RNA-sequencing was performed on paired tape-strips and biopsies collected from lesional and non-lesional skin from AD patients (n = 7) and non-AD controls (n = 5). RNA yield, mapping efficiency, and differentially expressed genes (DEGs) for the two methods (tape-strip\/biopsy) and presence of AD (AD\/non-AD) were compared.<\/p>\n\n\n\n<p><strong>Results:&nbsp;<\/strong>Tape-strips demonstrated a lower RNA yield (22 vs. 4596 ng) and mapping efficiency to known genes (28% vs. 93%) than biopsies. Gene-expression profiles of paired tape-strips and biopsies demonstrated a medium correlation (R<sup>2<\/sup>&nbsp;= 0.431). Tape-strips and biopsies demonstrated systematic differences in measured expression levels of 6483 genes across both AD and non-AD samples. Tape-strips preferentially detected many itch (CCL3\/CCL4\/OSM) and immune-response (CXCL8\/IL4\/IL5\/IL22) genes as well as markers of epidermal dendritic cells (CD1a\/CD207), while certain cytokines (IL18\/IL37), skin-barrier genes (KRT2\/FLG2), and dermal fibroblasts markers (COL1A\/COL3A) were preferentially detected by biopsies. Tape-strips identified more DEGs between AD and non-AD (3157 DEGs) then biopsies (44 DEGs). Tape-strips also detected higher levels of bacterial mRNA than biopsies.<\/p>\n\n\n\n<p><strong>Conclusions:&nbsp;<\/strong>This study concludes that tape-strips and biopsies each demonstrate respective advantages for measuring gene-expression changes in AD. Thus, the specific skin layers and genes of interest should be considered before selecting either method.<\/p>\n\n\n\n<p><strong>Keywords:&nbsp;<\/strong>RNA sequencing; atopic dermatitis; biopsies; inflammation; tape-strips.<\/p>\n\n\n\n<p id=\"copyright\">\u00a9 2024 The Authors. Allergy published by European Academy of Allergy and Clinical Immunology and John Wiley &amp; Sons Ltd.<\/p>\n\n\n\n<div class=\"wp-block-file\"><object class=\"wp-block-file__embed\" data=\"https:\/\/misterx95.myds.me\/wordpress\/wp-content\/uploads\/2024\/05\/RNA-sequencing-of-paired-tape-strips-and-skin-biopsies-in-atopic-dermatitis-reveals-key-differences.pdf\" type=\"application\/pdf\" style=\"width:100%;height:600px\" aria-label=\"Embed of RNA-sequencing-of-paired-tape-strips-and-skin-biopsies-in-atopic-dermatitis-reveals-key-differences.\"><\/object><a id=\"wp-block-file--media-1e66b1a8-b953-45e4-8b4c-1915a0557312\" href=\"https:\/\/misterx95.myds.me\/wordpress\/wp-content\/uploads\/2024\/05\/RNA-sequencing-of-paired-tape-strips-and-skin-biopsies-in-atopic-dermatitis-reveals-key-differences.pdf\">RNA-sequencing-of-paired-tape-strips-and-skin-biopsies-in-atopic-dermatitis-reveals-key-differences<\/a><a href=\"https:\/\/misterx95.myds.me\/wordpress\/wp-content\/uploads\/2024\/05\/RNA-sequencing-of-paired-tape-strips-and-skin-biopsies-in-atopic-dermatitis-reveals-key-differences.pdf\" class=\"wp-block-file__button wp-element-button\" download aria-describedby=\"wp-block-file--media-1e66b1a8-b953-45e4-8b4c-1915a0557312\">Download<\/a><\/div>\n","protected":false},"excerpt":{"rendered":"<p>Allergy.&nbsp;2024 Mar 13.&nbsp;doi: 10.1111\/all.16086.&nbsp; RNA-sequencing of paired tape-strips and skin biopsies in atopic dermatitis reveals key differences Blaine Fritz&nbsp;1,&nbsp;Anne-Sofie Halling&nbsp;2,&nbsp;Isabel D\u00edaz-Pin\u00e9s Cort&nbsp;1,&nbsp;Maria Oberl\u00e4nder Christensen&nbsp;2,&nbsp;Amalie Thorsti M\u00f8ller R\u00f8nnstad&nbsp;2,&nbsp;Caroline Meyer Olesen&nbsp;2,&nbsp;Mette Hjorslev Knudgaard&nbsp;3,&nbsp;Claus Zachariae&nbsp;3&nbsp;4,&nbsp;Steffen Heegaard&nbsp;4,&nbsp;Jacob P Thyssen&nbsp;2&nbsp;4,&nbsp;Thomas Bjarnsholt&nbsp;1&nbsp;5 Abstract Background:&nbsp;Skin tape-strips and biopsies are widely used methods for investigating the skin in atopic dermatitis (AD). Biopsies are [&hellip;]<\/p>\n","protected":false},"author":15,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"site-sidebar-layout":"default","site-content-layout":"","ast-site-content-layout":"","site-content-style":"default","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"","ast-breadcrumbs-content":"","ast-featured-img":"","footer-sml-layout":"","theme-transparent-header-meta":"","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"default","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"ast-content-background-meta":{"desktop":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}}},"categories":[1],"tags":[],"_links":{"self":[{"href":"https:\/\/misterx95.myds.me\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/3175"}],"collection":[{"href":"https:\/\/misterx95.myds.me\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/misterx95.myds.me\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/misterx95.myds.me\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/15"}],"replies":[{"embeddable":true,"href":"https:\/\/misterx95.myds.me\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=3175"}],"version-history":[{"count":5,"href":"https:\/\/misterx95.myds.me\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/3175\/revisions"}],"predecessor-version":[{"id":3185,"href":"https:\/\/misterx95.myds.me\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/3175\/revisions\/3185"}],"wp:attachment":[{"href":"https:\/\/misterx95.myds.me\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=3175"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/misterx95.myds.me\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=3175"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/misterx95.myds.me\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=3175"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}