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Machine learning applied to atopic dermatitis transcriptome reveals distinct therapy‐dependent modification of the keratinocyte immunophenotype

Machine learning applied to atopic dermatitis transcriptome reveals distinct therapy‐dependent modification of the keratinocyte immunophenotype
Machine learning applied to atopic dermatitis transcriptome reveals distinct therapy‐dependent modification of the keratinocyte immunophenotype

Background: Atopic dermatitis (AD) arises from a complex interaction between an impaired epidermal barrier, environmental exposures, and the infiltration of T helper (Th)1/Th2/Th17/Th22 T cells. Transcriptomic analysis has advanced our understanding of gene expression in cells and tissues. However, molecular quantitation of cytokine transcripts does not predict the importance of a specific pathway in AD or cellular responses to different inflammatory stimuli. Objectives: To understand changes in keratinocyte transcriptomic programmes in human cutaneous disease during development of inflammation and in response to treatment. Methods: We performed in silico deconvolution of the whole-skin transcriptome. Using co-expression clustering and machine-learning tools, we resolved the gene expression of bulk skin (seven datasets, n = 406 samples), firstly, into keratinocyte phenotypes identified by unsupervised clustering and, secondly, into 19 cutaneous cell signatures of purified populations from publicly available datasets. Results: We identify three unique transcriptomic programmes in keratinocytes – KC1, KC2 and KC17 – characteristic of immune signalling from disease-associated Th cells. We cross-validate those signatures across different skin inflammatory conditions and disease stages and demonstrate that the keratinocyte response during treatment is therapy dependent. Broad-spectrum treatment with ciclosporin ameliorated the KC17 response in AD lesions to a nonlesional immunophenotype, without altering KC2. Conversely, the specific anti-Th2 therapy, dupilumab, reversed the KC2 immunophenotype. Conclusions: Our analysis of transcriptomic signatures in cutaneous disease biopsies reveals the effect of keratinocyte programming in skin inflammation and suggests that the perturbation of a single axis of immune signal alone may be insufficient to resolve keratinocyte immunophenotype abnormalities.

0007-0963
1-10
Clayton, Kalum
499fec32-9297-45bd-9207-5ba699734844
Vallejo Pulido, Andres
27bc0b94-0c40-4fd1-9533-7e267d588c0a
Sirvent Bernal, Sofia
c8c68bc8-a5a7-456d-899d-6e48ccfac02f
Davies, James David
a93b4fc9-80a2-4620-ada6-c12f05c5ee38
Porter, Gemma
5f0c0ee9-ed05-41de-8552-8ad7390fc7a8
Reading, Isabel
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Lim, Fei Ling
5d565505-ce8e-40e3-8418-3e9875255629
Ardern-Jones, Michael
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Polak, Marta
e0ac5e1a-7074-4776-ba23-490bd4da612d
Clayton, Kalum
499fec32-9297-45bd-9207-5ba699734844
Vallejo Pulido, Andres
27bc0b94-0c40-4fd1-9533-7e267d588c0a
Sirvent Bernal, Sofia
c8c68bc8-a5a7-456d-899d-6e48ccfac02f
Davies, James David
a93b4fc9-80a2-4620-ada6-c12f05c5ee38
Porter, Gemma
5f0c0ee9-ed05-41de-8552-8ad7390fc7a8
Reading, Isabel
6f832276-87b7-4a76-a9ed-b4b3df0a3f66
Lim, Fei Ling
5d565505-ce8e-40e3-8418-3e9875255629
Ardern-Jones, Michael
7ac43c24-94ab-4d19-ba69-afaa546bec90
Polak, Marta
e0ac5e1a-7074-4776-ba23-490bd4da612d

Clayton, Kalum, Vallejo Pulido, Andres, Sirvent Bernal, Sofia, Davies, James David, Porter, Gemma, Reading, Isabel, Lim, Fei Ling, Ardern-Jones, Michael and Polak, Marta (2020) Machine learning applied to atopic dermatitis transcriptome reveals distinct therapy‐dependent modification of the keratinocyte immunophenotype. British Journal of Dermatology, 0, 1-10. (doi:10.1111/bjd.19431).

Record type: Article

Abstract

Background: Atopic dermatitis (AD) arises from a complex interaction between an impaired epidermal barrier, environmental exposures, and the infiltration of T helper (Th)1/Th2/Th17/Th22 T cells. Transcriptomic analysis has advanced our understanding of gene expression in cells and tissues. However, molecular quantitation of cytokine transcripts does not predict the importance of a specific pathway in AD or cellular responses to different inflammatory stimuli. Objectives: To understand changes in keratinocyte transcriptomic programmes in human cutaneous disease during development of inflammation and in response to treatment. Methods: We performed in silico deconvolution of the whole-skin transcriptome. Using co-expression clustering and machine-learning tools, we resolved the gene expression of bulk skin (seven datasets, n = 406 samples), firstly, into keratinocyte phenotypes identified by unsupervised clustering and, secondly, into 19 cutaneous cell signatures of purified populations from publicly available datasets. Results: We identify three unique transcriptomic programmes in keratinocytes – KC1, KC2 and KC17 – characteristic of immune signalling from disease-associated Th cells. We cross-validate those signatures across different skin inflammatory conditions and disease stages and demonstrate that the keratinocyte response during treatment is therapy dependent. Broad-spectrum treatment with ciclosporin ameliorated the KC17 response in AD lesions to a nonlesional immunophenotype, without altering KC2. Conversely, the specific anti-Th2 therapy, dupilumab, reversed the KC2 immunophenotype. Conclusions: Our analysis of transcriptomic signatures in cutaneous disease biopsies reveals the effect of keratinocyte programming in skin inflammation and suggests that the perturbation of a single axis of immune signal alone may be insufficient to resolve keratinocyte immunophenotype abnormalities.

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bjd.19431 - Accepted Manuscript
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Accepted/In Press date: 30 July 2020
e-pub ahead of print date: 30 July 2020

Identifiers

Local EPrints ID: 443532
URI: http://eprints.soton.ac.uk/id/eprint/443532
ISSN: 0007-0963
PURE UUID: e93c6abb-be6e-4bd4-8091-d2dffa6ca688
ORCID for Kalum Clayton: ORCID iD orcid.org/0000-0002-1143-3931
ORCID for Andres Vallejo Pulido: ORCID iD orcid.org/0000-0002-4688-0598
ORCID for Sofia Sirvent Bernal: ORCID iD orcid.org/0000-0003-0050-8579
ORCID for Isabel Reading: ORCID iD orcid.org/0000-0002-1457-6532

Catalogue record

Date deposited: 28 Aug 2020 16:31
Last modified: 30 Jul 2021 04:01

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Contributors

Author: Kalum Clayton ORCID iD
Author: Andres Vallejo Pulido ORCID iD
Author: Sofia Sirvent Bernal ORCID iD
Author: James David Davies
Author: Gemma Porter
Author: Isabel Reading ORCID iD
Author: Fei Ling Lim
Author: Marta Polak

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