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Simultaneous skin biome and keratinocyte genomic capture reveals microbiome differences by depth of sampling

Published:April 19, 2020DOI:https://doi.org/10.1016/j.jaci.2020.04.004
      Atopic dermatitis (AD) is a multifactorial, inflammatory skin condition affecting up to 20% of children, with approximately 60% of patients experiencing disease onset within the first year of life.
      • Weidinger S.
      • Novak N.
      Atopic dermatitis.
      AD varies in clinical presentation and phenotypes are difficult to define. Noninvasive methods to sample the skin are necessary to enable investigations of AD and improve disease phenotyping. Skin tape stripping is a common dermatologic procedure used to collect keratinocytes and other resident skin cells.
      • Zeeuwen P.L.
      • Boekhorst J.
      • van den Bogaard E.H.
      • de Koning H.D.
      • van de Kerkhof P.M.
      • Saulnier D.M.
      • et al.
      Microbiome dynamics of human epidermis following skin barrier disruption.
      Current noninvasive methods result in poor keratinocyte nucleic acid yields, requiring pooling of multiple tapes for downstream assays, such as proteomics
      • Clausen M.L.
      • Slotved H.C.
      • Krogfelt K.A.
      • Agner T.
      Tape stripping technique for stratum corneum protein analysis.
      • Reisdorph N.
      • Armstrong M.
      • Powell R.
      • Quinn K.
      • Legg K.
      • Leung D.
      • et al.
      Quantitation of peptides from non-invasive skin tapings using isotope dilution and tandem mass spectrometry.
      • Leung D.Y.M.
      • Calatroni A.
      • Zaramela L.S.
      • LeBeau P.K.
      • Dyjack N.
      • Brar K.
      • et al.
      The nonlesional skin surface distinguishes atopic dermatitis with food allergy as a unique endotype.
      and transcriptomics.
      • Dyjack N.
      • Goleva E.
      • Rios C.
      • Kim B.E.
      • Bin L.
      • Taylor P.
      • et al.
      Minimally invasive skin tape strip RNA sequencing identifies novel characteristics of the type 2-high atopic dermatitis disease endotype.
      Pooling of tapes helps to increase the yield of material necessary for downstream assays, but it masks key differences that may be present as a function of the depth of sampling. The current study uniquely uses dissolvable tape strips, originally designed for hydrographic applications, for simultaneous collection of the skin microbiome, keratinocyte epigenetics, and keratinocyte gene expression to characterize the surface biome and the ensuing underlying host skin innate response. Our data demonstrate differences in gene expression and microbial ecology with each individual tape, an observation that would have been masked by tape pooling. Furthermore, our findings highlight that the local environment is dependent on the depth of sampling. These attributes make this methodology a powerful clinical and research tool to enhance our understanding of normal skin and skin diseases.
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