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Multiomics analysis reveals dermokine as a regulator of keratinocyte differentiation and adhesion
Vahap Canbay, Till Wüstemann, Weihua Tian, Tobias A. Beyer, Camilla Reiter Elbæk, Michael Stumpe, Gaetana Restivo, Chatpakorn Christiansen, Anabel Migenda Herranz, Susanne Mailand, Jürg Hafner, Rune Busk Damgaard, Steffen Goletz, Jörn Dengjel, Ulrich auf dem Keller, Chiara Francavilla
Vahap Canbay, Till Wüstemann, Weihua Tian, Tobias A. Beyer, Camilla Reiter Elbæk, Michael Stumpe, Gaetana Restivo, Chatpakorn Christiansen, Anabel Migenda Herranz, Susanne Mailand, Jürg Hafner, Rune Busk Damgaard, Steffen Goletz, Jörn Dengjel, Ulrich auf dem Keller, Chiara Francavilla
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Research Article Cell biology Dermatology

Multiomics analysis reveals dermokine as a regulator of keratinocyte differentiation and adhesion

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Abstract

Impaired adhesion and differentiation of keratinocytes is a hallmark of several skin diseases, but only some of the factors that regulate these processes have been identified. Here, we studied the role of isoform-rich dermokine — a wound- and tumor-regulated protein — in keratinocytes using a combination of multiomics and functional approaches. CRISPR/Cas9-induced knockout of dermokine isoforms in human keratinocytes inhibited differentiation of these cells in 3-dimensional organotypic skin cultures, which was confirmed by quantitative proteomics. In 2-dimensional monocultures, dermokine deficiency affected the proteome and phosphoproteome as revealed by mass spectrometry. We found reduced abundance of differentiation-specific proteins and increased phosphorylation of the cell adhesion protein p120 (catenin δ-1). The adhesive strength of dermokine-knockout keratinocytes was impaired, which was rescued by p120 knockdown or ROCK inhibition. Finally, we verified the correlation between decreased dermokine expression and increased p120 phosphorylation in human non-healing wounds. These results identify dermokine as a regulator of keratinocyte adhesion and differentiation, involving at least in part its effect on p120 phosphorylation and ROCK. Our data point to a function of dermokine in the pathogenesis of chronic wounds.

Authors

Vahap Canbay, Till Wüstemann, Weihua Tian, Tobias A. Beyer, Camilla Reiter Elbæk, Michael Stumpe, Gaetana Restivo, Chatpakorn Christiansen, Anabel Migenda Herranz, Susanne Mailand, Jürg Hafner, Rune Busk Damgaard, Steffen Goletz, Jörn Dengjel, Ulrich auf dem Keller, Chiara Francavilla

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Figure 1

Targeted proteomics validates the knockout of dermokine in human keratinocytes.

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Targeted proteomics validates the knockout of dermokine in human keratin...
(A) Schematic of the genetic loci encoding the different dermokine isoforms and locations of guide RNAs (gRNA 1 and gRNA 2) targeting isoform-specific exons. (B and C) Methodologies used to delete dermokine in keratinocytes through either chemical transfection (B) or the FluidFM CRISPR approach (C). After transfection and clonal expansion, WT, DMKN αβ–/–, or DMKN βγ–/– keratinocytes were used for the generation of 3D organotypic skin cultures. (D) Schematic of the protein domains of the dermokine isoforms and of the 5 isoform-specific and proteotypic peptides used for targeted proteomics analysis. (E and F) Proteotypic dermokine peptide abundances are log2-transformed fold changes of summed transition areas from DMKN βγ–/– (E) or DMKN αβ–/– (F) relative to WT keratinocytes analyzed by targeted proteomics. N = 3 different 3D organotypic skin cultures. Statistical significance was calculated using 2-sided Student’s t tests on log2-transformed intensities, with multiple-testing correction performed using the Benjamini-Hochberg false discovery rate.

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