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Pažur K, Francuzik W, El-Mahmoud H, Kraft M, Worm M. Proteomic, miRNA and bacterial biomarker patterns in atopic dermatitis patients and their course upon anti-IL-4Rα therapy. J Eur Acad Dermatol Venereol 2024; 38:1749-1759. [PMID: 38379385 DOI: 10.1111/jdv.19911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 01/23/2024] [Indexed: 02/22/2024]
Abstract
BACKGROUND Identification of biomarkers is required for a systems medicine approach and personalized treatment in atopic dermatitis (AD). These biomarkers may not only aid in diagnosing but also might be suitable to predict the effectiveness of targeted treatment. OBJECTIVE We aimed to identify proteomic, microbial and miRNA biomarkers in AD patients and investigated their course in relation to the clinical response upon anti-IL-4Rα therapy. METHODS Proteomic and miRNA screening was performed in AD patients in comparison to healthy controls. Differentially regulated serum proteins, miRNA and selected skin microbiota were measured consecutively in 50 AD patients before and upon systemic dupilumab treatment. A random forest classifier was used to predict the outcome of dupilumab therapy based on the initial biomarker patterns. RESULTS We identified 27 proteomic candidates, miRNA and three microbial strains to be dysregulated in AD. CCL17, CCL13, CCL22, E-selectin and BDNF were differently regulated and significantly associated with treatment response. In contrast, neither the microbial composition nor the miRNA pattern was associated with treatment response upon dupilumab treatment. CONCLUSION AD patients display defined dysregulations regarding their systemic proteomic serum profile, miRNA patterns and their skin microbiome. The proteomic profile and selected skin bacteria changed profoundly upon anti-IL-4Rα therapy which was associated with an overall clinical response. This was not seen in miRNA-related biomarkers. Our findings support the hypothesis that biomarker profiles reflect treatment responses and may in the future be used to develop a personalized medicine approach for the treatment of AD patients.
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Affiliation(s)
- K Pažur
- Department of Dermatology, Venereology and Allergology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - W Francuzik
- Department of Dermatology, Venereology and Allergology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - H El-Mahmoud
- Department of Dermatology, Venereology and Allergology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
| | - M Kraft
- Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - M Worm
- Department of Dermatology, Venereology and Allergology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
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2
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Grafanaki K, Antonatos C, Maniatis A, Petropoulou A, Vryzaki E, Vasilopoulos Y, Georgiou S, Gregoriou S. Intrinsic Effects of Exposome in Atopic Dermatitis: Genomics, Epigenomics and Regulatory Layers. J Clin Med 2023; 12:4000. [PMID: 37373692 DOI: 10.3390/jcm12124000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/03/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Atopic dermatitis (AD) or atopic eczema is an increasingly manifested inflammatory skin disorder of complex etiology which is modulated by both extrinsic and intrinsic factors. The exposome includes a person's lifetime exposures and their effects. We recently reviewed the extrinsic exposome's environmental risk factors that contribute to AD. The periods of pregnancy, infancy, and teenage years are recognized as crucial stages in the formation of AD, where the exposome leads to enduring impacts on the immune system. However, research is now focusing on the interactions between intrinsic pathways that are modulated by the extrinsic exposome, including genetic variation, epigenetic modifications, and signals, such as diet, stress, and microbiome interactions. As a result, immune dysregulation, barrier dysfunction, hormonal fluctuations, and skin microbiome dysbiosis are important factors contributing to AD development, and their in-depth understanding is crucial not only for AD treatment but also for similar inflammatory disorders.
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Affiliation(s)
- Katerina Grafanaki
- Department of Dermatology-Venereology, School of Medicine, University of Patras, 26504 Patras, Greece
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Charalabos Antonatos
- Laboratory of Genetics, Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
| | - Alexandros Maniatis
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Antonia Petropoulou
- Department of Biochemistry, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Eleftheria Vryzaki
- Department of Dermatology-Venereology, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Yiannis Vasilopoulos
- Laboratory of Genetics, Section of Genetics, Cell Biology and Development, Department of Biology, University of Patras, 26504 Patras, Greece
| | - Sophia Georgiou
- Department of Dermatology-Venereology, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Stamatis Gregoriou
- Department of Dermatology-Venereology, Faculty of Medicine, Andreas Sygros Hospital, National and Kapodistrian University of Athens, 16121 Athens, Greece
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3
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Dopytalska K, Czaplicka A, Szymańska E, Walecka I. The Essential Role of microRNAs in Inflammatory and Autoimmune Skin Diseases-A Review. Int J Mol Sci 2023; 24:ijms24119130. [PMID: 37298095 DOI: 10.3390/ijms24119130] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/17/2023] [Accepted: 05/19/2023] [Indexed: 06/12/2023] Open
Abstract
The etiopathogenesis of autoimmune skin diseases is complex and still not fully understood. The role of epigenetic factors is emphasized in the development of such diseases. MicroRNAs (miRNAs), a group of non-coding RNAs (ncRNAs-non-coding RNAs), are one of the important post-transcriptional epigenetic factors. miRNAs have a significant role in the regulation of the immune response by participating in the process of the differentiation and activation of B and T lymphocytes, macrophages, and dendritic cells. Recent advances in research on epigenetic factors have provided new insights into the pathogenesis and potential diagnostic and therapeutic targets of many pathologies. Numerous studies revealed a change in the expression of some microRNAs in inflammatory skin disorders, and the regulation of miRNA expression is a promising therapeutic goal. This review presents the state of the art regarding changes in the expression and role of miRNAs in inflammatory and autoimmune skin diseases, including psoriasis, atopic dermatitis, vitiligo, lichen planus, hidradenitis suppurativa, and autoimmune blistering diseases.
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Affiliation(s)
- Klaudia Dopytalska
- Department of Dermatology, Centre of Postgraduate Medical Education, 02-507 Warsaw, Poland
- Department of Dermatology, The National Institute of Medicine of the Ministry of the Interior and Administration, 02-507 Warsaw, Poland
| | - Anna Czaplicka
- Department of Dermatology, Centre of Postgraduate Medical Education, 02-507 Warsaw, Poland
- Department of Dermatology, The National Institute of Medicine of the Ministry of the Interior and Administration, 02-507 Warsaw, Poland
| | - Elżbieta Szymańska
- Department of Dermatology, Centre of Postgraduate Medical Education, 02-507 Warsaw, Poland
- Department of Dermatology, The National Institute of Medicine of the Ministry of the Interior and Administration, 02-507 Warsaw, Poland
| | - Irena Walecka
- Department of Dermatology, Centre of Postgraduate Medical Education, 02-507 Warsaw, Poland
- Department of Dermatology, The National Institute of Medicine of the Ministry of the Interior and Administration, 02-507 Warsaw, Poland
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Nousbeck J, McAleer MA, Irvine AD. Peripheral Blood Gene Expression Profile of Infants with Atopic Dermatitis. JID INNOVATIONS 2023; 3:100165. [PMID: 36699197 PMCID: PMC9868882 DOI: 10.1016/j.xjidi.2022.100165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 11/06/2022] Open
Abstract
To enhance the understanding of molecular mechanisms and mine previously unidentified biomarkers of pediatric atopic dermatitis, PBMC gene expression profiles were generated by RNA sequencing in infants with atopic dermatitis and age-matched controls. A total of 178 significantly differentially expressed genes (DEGs) (115 upregulations and 63 downregulations) were seen, compared with those in healthy controls. The DEGs identified included IL1β, TNF, TREM1, IL18R1, and IL18RAP. DEGs were validated by real-time RT- qPCR in a larger number of samples from PBMCs of infants with atopic dermatitis aged <12 months. Using the DAVID (Database for Annotation, Visualization and Integrated Discovery) database, functional and pathway enrichment analyses of DEGs were performed. Gene ontology enrichment analysis showed that DEGs were associated with immune responses, inflammatory responses, regulation of immune responses, and platelet activation. Pathway analysis indicated that DEGs were enriched in cytokine‒cytokine receptor interaction, immunoregulatory interactions between lymphoid and nonlymphoid cells, hematopoietic cell lineage, phosphoinositide 3-kinase‒protein kinase B signaling pathway, NK cell‒mediated cytotoxicity, and platelet activation. Furthermore, the protein‒protein interaction network was predicted using the STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) database and visualized with Cytoscape software. Finally, on the basis of the protein‒protein interaction network, 18 hub genes were selected, and two significant modules were obtained. In conclusion, this study sheds light on the molecular mechanisms of pediatric atopic dermatitis and may provide diagnostic biomarkers and therapeutic targets.
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Affiliation(s)
- Janna Nousbeck
- National Children's Research Centre, Dublin, Ireland.,Clinical Medicine, School of Medicine, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | - Maeve A McAleer
- National Children's Research Centre, Dublin, Ireland.,Department of Paediatric Dermatology, Children's Health Ireland at Crumlin, Dublin, Ireland
| | - Alan D Irvine
- National Children's Research Centre, Dublin, Ireland.,Clinical Medicine, School of Medicine, Trinity College Dublin, The University of Dublin, Dublin, Ireland.,Department of Paediatric Dermatology, Children's Health Ireland at Crumlin, Dublin, Ireland
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Identification of novel candidate genes and predicted miRNAs in atopic dermatitis patients by bioinformatic methods. Sci Rep 2022; 12:22067. [PMID: 36543921 PMCID: PMC9772328 DOI: 10.1038/s41598-022-26689-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Atopic dermatitis (AD) is a common, chronic inflammatory dermatosis with relapsing eruptions. Our study used bioinformatics to find novel candidate differentially expressed genes (DEGs) and predicted miRNAs between AD patients and healthy controls. The Mesh term "atopic dermatitis" was retrieved to obtain DEGs in GEO datasets. DEGs between AD patients and healthy controls were analyzed using GEO2R. Overlapping DEGs between different datasets were obtained with use of Draw Venn software. GO and KEGG enrichment analyses were conducted by the use of DAVID. STRING and miRWalk were used to individually analyze PPI networks, interactions of candidate genes and predicted miRNAs. A total of 571 skin samples, as retrieved from 9 databases were assessed. There were 225 overlapping DEGs between lesioned skin samples of AD patients and that of healthy controls. Nineteen nodes and 160 edges were found in the largest PPI cluster, consisting of 17 up-regulated and 2 down-regulated nodes. Two KEGG pathways were identified, including the cell cycle (CCNB1, CHEK1, BUB1B, MCM5) and p53 (CCNB1, CHEK1, GTSE1) pathways. There were 56 nodes and 100 edges obtained in the miRNA-target gene network, with has-miR-17-5p targeted to 4 genes and has-miR-106b-5p targeted to 3 genes. While these findings will require further verification as achieved with experiments involving in vivo and in vitro modles, these results provided some initial insights into dysfunctional inflammatory and immune responses associated with AD. Such information offers the potential to develop novel therapeutic targets for use in preventing and treating AD.
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Anti-Inflammatory microRNAs for Treating Inflammatory Skin Diseases. Biomolecules 2022; 12:biom12081072. [PMID: 36008966 PMCID: PMC9405611 DOI: 10.3390/biom12081072] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 02/07/2023] Open
Abstract
Skin inflammation occurs due to immune dysregulation because of internal disorders, infections, and allergic reactions. The inflammation of the skin is a major sign of chronic autoimmune inflammatory diseases, such as psoriasis, atopic dermatitis (AD), and lupus erythematosus. Although there are many therapies for treating these cutaneous inflammation diseases, their recurrence rates are high due to incomplete resolution. MicroRNA (miRNA) plays a critical role in skin inflammation by regulating the expression of protein-coding genes at the posttranscriptional level during pathogenesis and homeostasis maintenance. Some miRNAs possess anti-inflammatory features, which are beneficial for mitigating the inflammatory response. miRNAs that are reduced in inflammatory skin diseases can be supplied transiently using miRNA mimics and agomir. miRNA-based therapies that can target multiple genes in a given pathway are potential candidates for the treatment of skin inflammation. This review article offers an overview of the function of miRNA in skin inflammation regulation, with a focus on psoriasis, AD, and cutaneous wounds. Some bioactive molecules can target and modulate miRNAs to achieve the objective of inflammation suppression. This review also reports the anti-inflammatory efficacy of these molecules through modulating miRNA expression. The main limitations of miRNA-based therapies are rapid biodegradation and poor skin and cell penetration. Consideration was given to improving these drawbacks using the approaches of cell-penetrating peptides (CPPs), nanocarriers, exosomes, and low-frequency ultrasound. A formulation design for successful miRNA delivery into skin and target cells is also described in this review. The possible use of miRNAs as biomarkers and therapeutic modalities could open a novel opportunity for the diagnosis and treatment of inflammation-associated skin diseases.
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Bosma AL, Ascott A, Iskandar R, Farquhar K, Matthewman J, Langendam MW, Mulick A, Abuabara K, Williams HC, Spuls PI, Langan SM, Middelkamp-Hup MA. Classifying atopic dermatitis: a systematic review of phenotypes and associated characteristics. J Eur Acad Dermatol Venereol 2022; 36:807-819. [PMID: 35170821 PMCID: PMC9307020 DOI: 10.1111/jdv.18008] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 12/10/2021] [Accepted: 01/18/2022] [Indexed: 11/28/2022]
Abstract
Atopic dermatitis is a heterogeneous disease, accompanied by a wide variation in disease presentation and the potential to identify many phenotypes that may be relevant for prognosis and treatment. We aimed to systematically review previously reported phenotypes of atopic dermatitis and any characteristics associated with them. Ovid EMBASE, Ovid MEDLINE and Web of Science were searched from inception till the 12th of February 2021 for studies attempting to classify atopic dermatitis. Primary outcomes are atopic dermatitis phenotypes and characteristics associated with them in subsequent analyses. A secondary outcome is the methodological approach used to derive them. In total, 8,511 records were found. By focusing only on certain clinical phenotypes, 186 studies were eligible for inclusion. The majority of studies were hospital-based (59%, 109/186) and cross-sectional (76%, 141/186). The number of included patients ranged from seven to 526,808. Data-driven approaches to identify phenotypes were only used in a minority of studies (7%, 13/186). Ninety-one studies (49%) investigated a phenotype based on disease severity. A phenotype based on disease trajectory, morphology and eczema herpeticum was investigated in 56 (30%), 22 (12%) and 11 (6%) studies, respectively. Thirty-six studies (19%) investigated morphological characteristics in other phenotypes. Investigated associated characteristics differed between studies. In conclusion, we present an overview of phenotype definitions used in literature for severity, trajectory, morphology and eczema herpeticum, including associated characteristics. There is a lack of uniform and consistent use of atopic dermatitis phenotypes across studies.
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Affiliation(s)
- A L Bosma
- Department of Dermatology, UMC, location Academic Medical Center, University of Amsterdam, Amsterdam Public Health, Infection and Immunity, Amsterdam, The Netherlands
| | - A Ascott
- Department of Dermatology, University Hospitals Sussex NHS Foundation Trust, Worthing, United Kingdom
| | - R Iskandar
- Faculty of Epidemiology and Population Health, School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - J Matthewman
- Department of Non-communicable disease epidemiology, School of Hygiene and Tropical Medicine, London, United Kingdom
| | - M W Langendam
- Department of Epidemiology and Data Science, UMC, location Amsterdam Medical Center, University of Amsterdam, Amsterdam Public Health research institute, Amsterdam, The Netherlands
| | - A Mulick
- Faculty of Epidemiology and Population Health, School of Hygiene and Tropical Medicine, London, United Kingdom
| | - K Abuabara
- Department of Dermatology, University of California San Francisco, United States
| | - H C Williams
- Centre of Evidence-Based Dermatology, University of Nottingham, United Kingdom
| | - P I Spuls
- Department of Dermatology, UMC, location Academic Medical Center, University of Amsterdam, Amsterdam Public Health, Infection and Immunity, Amsterdam, The Netherlands
| | - S M Langan
- Department of Dermatology, UMC, location Academic Medical Center, University of Amsterdam, Amsterdam Public Health, Infection and Immunity, Amsterdam, The Netherlands.,Faculty of Epidemiology and Population Health, School of Hygiene and Tropical Medicine, London, United Kingdom
| | - M A Middelkamp-Hup
- Department of Dermatology, UMC, location Academic Medical Center, University of Amsterdam, Amsterdam Public Health, Infection and Immunity, Amsterdam, The Netherlands
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Ghumra W, Lee N, Whitehouse H, Bhutani R, Lagos D, Layton AM. MicroRNAs as biomarkers of atrophic scarring in acne: a cross-sectional analysis of 41 patients. Clin Exp Dermatol 2021; 46:1495-1503. [PMID: 34101224 DOI: 10.1111/ced.14792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/07/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Acne is the commonest inflammatory dermatosis seen worldwide. Atrophic acne scarring is a frequent complication, which can arise from acne of any severity. Micro (mi)RNAs are noncoding RNA molecules of 19-25 nucleotides that function as post-transcriptomic mediators of gene expression. They have demonstrated differential expression in various pathologies, such as eczema and psoriasis, allowing for a unique miRNA 'signature' profile to be established for different disease states. AIM To establish a miRNA signature for acne, and acne-associated atrophic scarring and to identify if a pattern of circulating miRNA is evident in patients who are prone to scarring. METHODS In total, 41 participants were consecutively recruited to this study. Circulating miRNA was quantified from plasma samples in all 41 patients, while in 8 patients, and in a further validation cohort of 9 patients, whole miRNAome was undertaken from tissue specimens, which included lesional, normal and where present, scarred skin. RESULTS Three miRNAs, miR-223, miR-21 and miR-150, were statistically significantly overexpressed in acne lesions, and notably, in clinically uninvolved skin in participants prone to scarring. In this subgroup, we also found statistically significantly elevated levels of circulating miRNA-21 and miRNA-150. CONCLUSION The presence of elevated levels of these specific miRNAs in the serum of patients with acne raises the potential of a blood test to identify those at risk of scarring, allowing for earlier intervention with effective therapy.
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Affiliation(s)
- W Ghumra
- Department of Dermatology, Harrogate District Hospital, Harrogate District and NHS Foundation Trust, Harrogate, Yorkshire, UK
| | - N Lee
- Department of Dermatology, Harrogate District Hospital, Harrogate District and NHS Foundation Trust, Harrogate, Yorkshire, UK
| | - H Whitehouse
- Department of Dermatology, Harrogate District Hospital, Harrogate District and NHS Foundation Trust, Harrogate, Yorkshire, UK
| | - R Bhutani
- Department of Dermatology, Harrogate District Hospital, Harrogate District and NHS Foundation Trust, Harrogate, Yorkshire, UK
| | - D Lagos
- Hull York Medical School and York Biomedical Research Institute, University of York, York, UK
| | - A M Layton
- Department of Dermatology, Harrogate District Hospital, Harrogate District and NHS Foundation Trust, Harrogate, Yorkshire, UK
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Polak ME. Early life regulation of inflammation in atopic dermatitis by microRNA. Br J Dermatol 2020; 184:391-392. [PMID: 32951210 DOI: 10.1111/bjd.19475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 07/26/2020] [Indexed: 01/15/2023]
Affiliation(s)
- M E Polak
- Clinical and Experimental Sciences, Sir Henry Wellcome Laboratories, Faculty of Medicine, University of Southampton, Southampton, UK
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