International Journal of Molecular Sciences

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28 pages, 5814 KiB

Open AccessArticle

Systems Biology Methods via Genome-Wide RNA Sequences to Investigate Pathogenic Mechanisms for Identifying Biomarkers and Constructing a DNN-Based Drug–Target Interaction Model to Predict Potential Molecular Drugs for Treating Atopic Dermatitis

by Sheng-Ping Chou, Yung-Jen Chuang and Bor-Sen Chen

Int. J. Mol. Sci. 2024, 25(19), 10691; https://doi.org/10.3390/ijms251910691 - 4 Oct 2024

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Abstract

This study aimed to construct genome-wide genetic and epigenetic networks (GWGENs) of atopic dermatitis (AD) and healthy controls through systems biology methods based on genome-wide microarray data. Subsequently, the core GWGENs of AD and healthy controls were extracted from their real GWGENs by [...] Read more.

This study aimed to construct genome-wide genetic and epigenetic networks (GWGENs) of atopic dermatitis (AD) and healthy controls through systems biology methods based on genome-wide microarray data. Subsequently, the core GWGENs of AD and healthy controls were extracted from their real GWGENs by the principal network projection (PNP) method for Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation. Then, we identified the abnormal signaling pathways by comparing the core signaling pathways of AD and healthy controls to investigate the pathogenesis of AD. Then, IL-1β, GATA3, Akt, and NF-κB were selected as biomarkers for their important roles in the abnormal regulation of downstream genes, leading to cellular dysfunctions in AD patients. Next, a deep neural network (DNN)-based drug–target interaction (DTI) model was pre-trained on DTI databases to predict molecular drugs that interact with these biomarkers. Finally, we screened the candidate molecular drugs based on drug toxicity, sensitivity, and regulatory ability as drug design specifications to select potential molecular drugs for these biomarkers to treat AD, including metformin, allantoin, and U-0126, which have shown potential for therapeutic treatment by regulating abnormal immune responses and restoring the pathogenic signaling pathways of AD. Full article

(This article belongs to the Special Issue Molecular Research on Skin Disease: From Pathology to Therapy)

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21 pages, 5607 KiB

Open AccessArticle

Comparative Analysis of the Cutaneous Microbiome in Psoriasis Patients and Healthy Individuals—Insights into Microbial Dysbiosis: Final Results

by Diana Sabina Radaschin, Alina Viorica Iancu, Alexandra Mariana Ionescu, Gabriela Gurau, Elena Niculet, Florin Ciprian Bujoreanu, Cristina Beiu, Alin Laurentiu Tatu and Liliana Gabriela Popa

Int. J. Mol. Sci. 2024, 25(19), 10583; https://doi.org/10.3390/ijms251910583 - 1 Oct 2024

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Abstract

Psoriasis is one of the most frequent chronic inflammatory skin diseases and exerts a significant psychological impact, causing stigmatization, low self-esteem and depression. The pathogenesis of psoriasis is remarkably complex, involving genetic, immune and environmental factors, some of which are still incompletely explored. [...] Read more.

Psoriasis is one of the most frequent chronic inflammatory skin diseases and exerts a significant psychological impact, causing stigmatization, low self-esteem and depression. The pathogenesis of psoriasis is remarkably complex, involving genetic, immune and environmental factors, some of which are still incompletely explored. The cutaneous microbiome has become more and more important in the pathogenesis of inflammatory skin diseases such as acne, rosacea, atopic dermatitis and psoriasis. Dysbiosis of the skin microbiome could be linked to acute flare ups in psoriatic disease, as recent studies suggest. Given this hypothesis, we conducted a study in which we evaluated the cutaneous microbiome of psoriasis patients and healthy individuals. In our study, we collected multiple samples using swab sampling, adhesive tape and punch biopsies. Our results are similar to other studies in which the qualitative and quantitative changes found in the cutaneous microbiome of psoriasis patients are different than healthy individuals. Larger, standardized studies are needed in order to elucidate the microbiome changes in psoriasis patients, clarify their role in the pathogenesis of psoriasis, decipher the interactions between the commensal microorganisms of the same and different niches and between microbiomes and the host and identify new therapeutic strategies. Full article

(This article belongs to the Special Issue Molecular Research on Skin Disease: From Pathology to Therapy)

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10 pages, 1643 KiB

Open AccessCommunication

Missing Heritability in Albinism: Deep Characterization of a Hungarian Albinism Cohort Raises the Possibility of the Digenic Genetic Background of the Disease

by Nikoletta Nagy, Margit Pal, Jozsef Kun, Bence Galik, Peter Urban, Marta Medvecz, Beata Fabos, Alexandra Neller, Aliasgari Abdolreza, Judit Danis, Viktoria Szabo, Zhuo Yang, Stefanie Fenske, Martin Biel, Attila Gyenesei, Eva Adam and Marta Szell

Int. J. Mol. Sci. 2024, 25(2), 1271; https://doi.org/10.3390/ijms25021271 - 20 Jan 2024

Cited by 1 | Viewed by 1582

Abstract

Albinism is characterized by a variable degree of hypopigmentation affecting the skin and the hair, and causing ophthalmologic abnormalities. Its oculocutaneous, ocular and syndromic forms follow an autosomal or X-linked recessive mode of inheritance, and 22 disease-causing genes are implicated in their development. [...] Read more.

Albinism is characterized by a variable degree of hypopigmentation affecting the skin and the hair, and causing ophthalmologic abnormalities. Its oculocutaneous, ocular and syndromic forms follow an autosomal or X-linked recessive mode of inheritance, and 22 disease-causing genes are implicated in their development. Our aim was to clarify the genetic background of a Hungarian albinism cohort. Using a 22-gene albinism panel, the genetic background of 11 of the 17 Hungarian patients was elucidated. In patients with unidentified genetic backgrounds (n = 6), whole exome sequencing was performed. Our investigations revealed a novel, previously unreported rare variant (N687S) of the two-pore channel two gene (TPCN2). The N687S variant of the encoded TPC2 protein is carried by a 15-year-old Hungarian male albinism patient and his clinically unaffected mother. Our segregational analysis and in vitro functional experiments suggest that the detected novel rare TPCN2 variant alone is not a disease-causing variant in albinism. Deep genetic analyses of the family revealed that the patient also carries a phenotype-modifying R305W variant of the OCA2 protein, and he is the only family member harboring this genotype. Our results raise the possibility that this digenic combination might contribute to the observed differences between the patient and the mother, and found the genetic background of the disease in his case. Full article

(This article belongs to the Special Issue Molecular Research on Skin Disease: From Pathology to Therapy)

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16 pages, 3231 KiB

Open AccessArticle

Diagnostic Algorithm to Subclassify Atypical Spitzoid Tumors in Low and High Risk According to Their Methylation Status

by Jose Francisco González-Muñoz, Beatriz Sánchez-Sendra and Carlos Monteagudo

Int. J. Mol. Sci. 2024, 25(1), 318; https://doi.org/10.3390/ijms25010318 - 25 Dec 2023

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Abstract

Current diagnostic algorithms are insufficient for the optimal clinical and therapeutic management of cutaneous spitzoid tumors, particularly atypical spitzoid tumors (AST). Therefore, it is crucial to identify new markers that allow for reliable and reproducible diagnostic assessment and can also be used as [...] Read more.

Current diagnostic algorithms are insufficient for the optimal clinical and therapeutic management of cutaneous spitzoid tumors, particularly atypical spitzoid tumors (AST). Therefore, it is crucial to identify new markers that allow for reliable and reproducible diagnostic assessment and can also be used as a predictive tool to anticipate the individual malignant potential of each patient, leading to tailored individual therapy. Using Reduced Representation Bisulfite Sequencing (RRBS), we studied genome–wide methylation profiles of a series of Spitz nevi (SN), spitzoid melanoma (SM), and AST. We established a diagnostic algorithm based on the methylation status of seven cg sites located in TETK4P2 (Tektin 4 Pseudogene 2), MYO1D (Myosin ID), and PMF1-BGLAP (PMF1-BGLAP Readthrough), which allows the distinction between SN and SM but is also capable of subclassifying AST according to their similarity to the methylation levels of Spitz nevi or spitzoid melanoma. Thus, our epigenetic algorithm can predict the risk level of AST and predict its potential clinical outcomes. Full article

(This article belongs to the Special Issue Molecular Research on Skin Disease: From Pathology to Therapy)

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28 pages, 3972 KiB

Open AccessArticle

Mass Spectrometry Analysis of Shark Skin Proteins

by Etty Bachar-Wikstrom, Braham Dhillon, Navi Gill Dhillon, Lisa Abbo, Sara K. Lindén and Jakob D. Wikstrom

Int. J. Mol. Sci. 2023, 24(23), 16954; https://doi.org/10.3390/ijms242316954 - 29 Nov 2023

Cited by 1 | Viewed by 1783

Abstract

The mucus layer covering the skin of fish has several roles, including protection against pathogens and mechanical damage in which proteins play a key role. While proteins in the skin mucus layer of various common bony fish species have been explored, the proteins [...] Read more.

The mucus layer covering the skin of fish has several roles, including protection against pathogens and mechanical damage in which proteins play a key role. While proteins in the skin mucus layer of various common bony fish species have been explored, the proteins of shark skin mucus remain unexplored. In this pilot study, we examine the protein composition of the skin mucus in spiny dogfish sharks and chain catsharks through mass spectrometry (NanoLC-MS/MS). Overall, we identified 206 and 72 proteins in spiny dogfish (Squalus acanthias) and chain catsharks (Scyliorhinus retifer), respectively. Categorization showed that the proteins belonged to diverse biological processes and that most proteins were cellular albeit a significant minority were secreted, indicative of mucosal immune roles. The secreted proteins are reviewed in detail with emphasis on their immune potentials. Moreover, STRING protein–protein association network analysis showed that proteins of closely related shark species were more similar as compared to a more distantly related shark and a bony fish, although there were also significant overlaps. This study contributes to the growing field of molecular shark studies and provides a foundation for further research into the functional roles and potential human biomedical implications of shark skin mucus proteins. Full article

(This article belongs to the Special Issue Molecular Research on Skin Disease: From Pathology to Therapy)

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24 pages, 5027 KiB

Open AccessArticle

Antitumor Effect of Poplar Propolis on Human Cutaneous Squamous Cell Carcinoma A431 Cells

by Chuang Zhang, Yuanyuan Tian, Ao Yang, Weihua Tan, Xiaoqing Liu and Wenchao Yang

Int. J. Mol. Sci. 2023, 24(23), 16753; https://doi.org/10.3390/ijms242316753 - 25 Nov 2023

Cited by 1 | Viewed by 1550

Abstract

Propolis is a gelatinous substance processed by western worker bees from the resin of plant buds and mixed with the secretions of the maxillary glands and beeswax. Propolis has extensive biological activities and antitumor effects. There have been few reports about the antitumor [...] Read more.

Propolis is a gelatinous substance processed by western worker bees from the resin of plant buds and mixed with the secretions of the maxillary glands and beeswax. Propolis has extensive biological activities and antitumor effects. There have been few reports about the antitumor effect of propolis against human cutaneous squamous cell carcinoma (CSCC) A431 cells and its potential mechanism. CCK-8 assays, label-free proteomics, RT–PCR, and a xenograft tumor model were employed to explore this possibility. The results showed that the inhibition rate of A431 cell proliferation by the ethanol extract of propolis (EEP) was dose-dependent, with an IC₅₀ of 39.17 μg/mL. There were 193 differentially expressed proteins in the EEP group compared with the control group (p < 0.05), of which 103 proteins (53.37%) were upregulated, and 90 proteins (46.63%) were downregulated. The main three activated and suppressed Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were extracellular matrix (ECM)-receptor interaction, amoebiasis, cell adhesion molecules (CAMs), nonalcoholic fatty liver disease (NAFLD), retrograde endocannabinoid signaling, and Alzheimer’s disease. The tumor volume of the 100 mg/kg EEP group was significantly different from that of the control group (p < 0.05). These results provide a theoretical basis for the potential treatment of human CSCC A431 cell tumors using propolis. Full article

(This article belongs to the Special Issue Molecular Research on Skin Disease: From Pathology to Therapy)

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Review

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27 pages, 2546 KiB

Open AccessReview

Pathophysiological Roles of Ion Channels in Epidermal Cells, Immune Cells, and Sensory Neurons in Psoriasis

by Hyungsup Kim, Mi Ran Choi, Seong Ho Jeon, Yongwoo Jang and Young Duk Yang

Int. J. Mol. Sci. 2024, 25(5), 2756; https://doi.org/10.3390/ijms25052756 - 27 Feb 2024

Viewed by 2309

Abstract

Psoriasis is a chronic inflammatory skin disease characterized by the rapid abnormal growth of skin cells in the epidermis, driven by an overactive immune system. Consequently, a complex interplay among epidermal cells, immune cells, and sensory neurons contributes to the development and progression [...] Read more.

Psoriasis is a chronic inflammatory skin disease characterized by the rapid abnormal growth of skin cells in the epidermis, driven by an overactive immune system. Consequently, a complex interplay among epidermal cells, immune cells, and sensory neurons contributes to the development and progression of psoriasis. In these cellular contexts, various ion channels, such as acetylcholine receptors, TRP channels, Ca²⁺ release-activated channels, chloride channels, and potassium channels, each serve specific functions to maintain the homeostasis of the skin. The dysregulation of ion channels plays a major role in the pathophysiology of psoriasis, affecting various aspects of epidermal cells, immune responses, and sensory neuron signaling. Impaired function of ion channels can lead to altered calcium signaling, inflammation, proliferation, and sensory signaling, all of which are central features of psoriasis. This overview summarizes the pathophysiological roles of ion channels in epidermal cells, immune cells, and sensory neurons during early and late psoriatic processes, thereby contributing to a deeper understanding of ion channel involvement in the interplay of psoriasis and making a crucial advance toward more precise and personalized approaches for psoriasis treatment. Full article

(This article belongs to the Special Issue Molecular Research on Skin Disease: From Pathology to Therapy)

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17 pages, 2388 KiB

Open AccessReview

Cannabinoids and Their Receptors in Skin Diseases

by Eun Hee Yoo and Ji Hyun Lee

Int. J. Mol. Sci. 2023, 24(22), 16523; https://doi.org/10.3390/ijms242216523 - 20 Nov 2023

Cited by 9 | Viewed by 6579

Abstract

The therapeutic application of cannabinoids has gained traction in recent years. Cannabinoids interact with the human endocannabinoid system in the skin. A large body of research indicates that cannabinoids could hold promise for the treatment of eczema, psoriasis, acne, pruritus, hair disorders, and [...] Read more.

The therapeutic application of cannabinoids has gained traction in recent years. Cannabinoids interact with the human endocannabinoid system in the skin. A large body of research indicates that cannabinoids could hold promise for the treatment of eczema, psoriasis, acne, pruritus, hair disorders, and skin cancer. However, most of the available data are at the preclinical stage. Comprehensive, large-scale, randomized, controlled clinical trials have not yet been fully conducted. In this article, we describe new findings in cannabinoid research and point out promising future research areas. Full article

(This article belongs to the Special Issue Molecular Research on Skin Disease: From Pathology to Therapy)

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