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Morrison HA, Hoyt KJ, Mounzer C, Ivester HM, Barnes BH, Sauer B, McGowan EC, Allen IC. Expression profiling identifies key genes and biological functions associated with eosinophilic esophagitis in human patients. FRONTIERS IN ALLERGY 2023; 4:1239273. [PMID: 37692891 PMCID: PMC10484407 DOI: 10.3389/falgy.2023.1239273] [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: 06/16/2023] [Accepted: 08/10/2023] [Indexed: 09/12/2023] Open
Abstract
Introduction Eosinophilic Esophagitis (EoE) is a chronic allergic disease characterized by progressive inflammation of the esophageal mucosa. This chronic inflammatory disorder affects up to 50 per 100,000 individuals in the United States and Europe yet is limited in treatment options. While the transcriptome of EoE has been reported, few studies have examined the genetics among a cohort including both adult and pediatric EoE populations. To identify potentially overlooked biomarkers in EoE esophageal biopsies that may be promising targets for diagnostic and therapeutic development. Methods We used microarray analysis to interrogate gene expression using esophageal biopsies from EoE and Control subjects with a wide age distribution. Analysis of differential gene expression (DEGs) and prediction of impaired pathways was compared using conventional transcriptome analysis (TAC) and artificial intelligence-based (ADVAITA) programs. Principal Components Analysis revealed samples cluster by disease status (EoE and Control) irrespective of clinical features like sex, age, and disease severity. Results Global transcriptomic analysis revealed differential expression of several genes previously reported in EoE (CCL26, CPA3, POSTN, CTSC, ANO1, CRISP3, SPINK7). In addition, we identified differential expression of several genes from the MUC and SPRR families, which have been limited in previous reports. Discussion Our findings suggest that there is epithelial dysregulation demonstrated by DEGs that may contribute to impaired barrier integrity and loss of epidermal cell differentiation in EoE patients. These findings present two new gene families, SPRR and MUC, that are differentially expressed in both adult and pediatric EoE patients, which presents an opportunity for a future therapeutic target that would be useful in a large demographic of patients.
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Affiliation(s)
- Holly A. Morrison
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States
| | - Kacie J. Hoyt
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States
| | - Christina Mounzer
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States
| | - Hannah M. Ivester
- Graduate Program in Translational Biology, Medicine, and Health, Virginia Polytechnic Institute and State University, Roanoke, VA, United States
| | - Barrett H. Barnes
- Division of Pediatric Gastroenterology/Nutrition, Department of Pediatrics, University of Virginia School of Medicine, Charlottesville, VA, United States
| | - Bryan Sauer
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA, United States
| | - Emily C. McGowan
- Division of Allergy and Clinical Immunology, Department of Medicine, University of Virginia School of Medicine, Charlottesville, VA, United States
- Division of Allergy and Clinical Immunology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Irving C. Allen
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States
- Graduate Program in Translational Biology, Medicine, and Health, Virginia Polytechnic Institute and State University, Roanoke, VA, United States
- Department of Basic Science Education, Virginia Tech Carilion School of Medicine, Roanoke, VA, United States
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Jeong Y, Song J, Lee Y, Choi E, Won Y, Kim B, Jang W. A Transcriptome-Wide Analysis of Psoriasis: Identifying the Potential Causal Genes and Drug Candidates. Int J Mol Sci 2023; 24:11717. [PMID: 37511476 PMCID: PMC10380797 DOI: 10.3390/ijms241411717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
Psoriasis is a chronic inflammatory skin disease characterized by cutaneous eruptions and pruritus. Because the genetic backgrounds of psoriasis are only partially revealed, an integrative and rigorous study is necessary. We conducted a transcriptome-wide association study (TWAS) with the new Genotype-Tissue Expression version 8 reference panels, including some tissue and multi-tissue panels that were not used previously. We performed tissue-specific heritability analyses on genome-wide association study data to prioritize the tissue panels for TWAS analysis. TWAS and colocalization (COLOC) analyses were performed with eight tissues from the single-tissue panels and the multi-tissue panels of context-specific genetics (CONTENT) to increase tissue specificity and statistical power. From TWAS, we identified the significant associations of 101 genes in the single-tissue panels and 64 genes in the multi-tissue panels, of which 26 genes were replicated in the COLOC. Functional annotation and network analyses identified that the genes were associated with psoriasis and/or immune responses. We also suggested drug candidates that interact with jointly significant genes through a conditional and joint analysis. Together, our findings may contribute to revealing the underlying genetic mechanisms and provide new insights into treatments for psoriasis.
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Affiliation(s)
- Yeonbin Jeong
- Department of Life Sciences, Dongguk University, Seoul 04620, Republic of Korea
| | - Jaeseung Song
- Department of Life Sciences, Dongguk University, Seoul 04620, Republic of Korea
| | - Yubin Lee
- Department of Life Sciences, Dongguk University, Seoul 04620, Republic of Korea
| | - Eunyoung Choi
- Department of Life Sciences, Dongguk University, Seoul 04620, Republic of Korea
| | - Youngtae Won
- Department of Life Sciences, Dongguk University, Seoul 04620, Republic of Korea
| | - Byunghyuk Kim
- Department of Life Sciences, Dongguk University-Seoul, Goyang 10326, Republic of Korea
| | - Wonhee Jang
- Department of Life Sciences, Dongguk University, Seoul 04620, Republic of Korea
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Roy T, Banang-Mbeumi S, Boateng ST, Ruiz EM, Chamcheu RCN, Kang L, King JA, Walker AL, Nagalo BM, Kousoulas KG, Esnault S, Huang S, Chamcheu JC. Dual targeting of mTOR/IL-17A and autophagy by fisetin alleviates psoriasis-like skin inflammation. Front Immunol 2023; 13:1075804. [PMID: 36741386 PMCID: PMC9889994 DOI: 10.3389/fimmu.2022.1075804] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/28/2022] [Indexed: 01/19/2023] Open
Abstract
Psoriasis is a chronic autoimmune inflammatory skin disorder characterized by epidermal hyperplasia and aberrant immune response. In addition to aberrant cytokine production, psoriasis is associated with activation of the Akt/mTOR pathway. mTOR/S6K1 regulates T-lymphocyte activation and migration, keratinocytes proliferation and is upregulated in psoriatic lesions. Several drugs that target Th1/Th17 cytokines or their receptors have been approved for treating psoriasis in humans with variable results necessitating improved therapies. Fisetin, a natural dietary polyphenol with anti-oxidant and anti-proliferative properties, covalently binds mTOR/S6K1. The effects of fisetin on psoriasis and its underlying mechanisms have not been clearly defined. Here, we evaluated the immunomodulatory effects of fisetin on Th1/Th17-cytokine-activated adult human epidermal keratinocytes (HEKa) and anti-CD3/CD28-stimulated inflammatory CD4+ T cells and compared these activities with those of rapamycin (an mTOR inhibitor). Transcriptomic analysis of HEKa revealed 12,713 differentially expressed genes (DEGs) in the fisetin-treated group compared to 7,374 DEGs in the rapamycin-treated group, both individually compared to a cytokine treated group. Gene ontology analysis revealed enriched functional groups related to PI3K/Akt/mTOR signaling pathways, psoriasis, and epidermal development. Using in silico molecular modeling, we observed a high binding affinity of fisetin to IL-17A. In vitro, fisetin significantly inhibited mTOR activity, increased the expression of autophagy markers LC3A/B and Atg5 in HEKa cells and suppressed the secretion of IL-17A by activated CD4+ T lymphocytes or T lymphocytes co-cultured with HEKa. Topical administration of fisetin in an imiquimod (IMQ)-induced mouse psoriasis model exhibited a better effect than rapamycin in reducing psoriasis-like inflammation and Akt/mTOR phosphorylation and promoting keratinocyte differentiation and autophagy in mice skin lesions. Fisetin also significantly inhibited T-lymphocytes and F4/80+ macrophage infiltration into skin. We conclude that fisetin potently inhibits IL-17A and the Akt/mTOR pathway and promotes keratinocyte differentiation and autophagy to alleviate IMQ-induced psoriasis-like disease in mice. Altogether, our findings suggest fisetin as a potential treatment for psoriasis and possibly other inflammatory skin diseases.
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Affiliation(s)
- Tithi Roy
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe, LA, United States
| | - Sergette Banang-Mbeumi
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe, LA, United States
- School of Nursing and Allied Health Sciences, Louisiana Delta Community College, Monroe, LA, United States
| | - Samuel T. Boateng
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe, LA, United States
| | - Emmanuelle M. Ruiz
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
| | - Roxane-Cherille N. Chamcheu
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe, LA, United States
| | - Lin Kang
- Biomedical Research, Edward Via College of Osteopathic Medicine, Monroe, LA, United States
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Tech, Blacksburg, VA, United States
| | - Judy A. King
- Department of Pathology and Translational Pathobiology, Louisiana State University Health Sciences Center, Shreveport, LA, United States
| | - Anthony L. Walker
- School of Clinical Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe, LA, United States
| | - Bolni Marius Nagalo
- Department of Pathology, University of Arkansas for Medical Sciences (UAMS), Little Rock, AR, United States
- The Winthrop P. Rockefeller Cancer Institute, UAMS, Little Rock, AR, United States
| | - Konstantin G. Kousoulas
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, United States
| | - Stephane Esnault
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine, School of Medicine and Public Health, Madison, WI, United States
| | - Shile Huang
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA, United States
- Department of Hematology and Oncology, Louisiana State University Health Sciences Center, Shreveport, LA, United States
- Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA, United States
| | - Jean Christopher Chamcheu
- School of Basic Pharmaceutical and Toxicological Sciences, College of Pharmacy, University of Louisiana at Monroe, Monroe, LA, United States
- Department of Pathology and Translational Pathobiology, Louisiana State University Health Sciences Center, Shreveport, LA, United States
- Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA, United States
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Transcriptomic Analysis Reveals Genetic Cross-Talk between Periodontitis and Hypothyroidism. DISEASE MARKERS 2022; 2022:5736394. [PMID: 35450027 PMCID: PMC9017577 DOI: 10.1155/2022/5736394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/14/2022] [Indexed: 01/01/2023]
Abstract
Background. Aim of this bioinformatics study based on transcriptomic analysis was to reveal the cross-talk between periodontitis (PD) and hypothyroidism (HT). Methods. The gene expression datasets GSE18152 and GSE176153 of HT and GSE10334, GSE16134, and GSE173078 of PD were downloaded through the Gene Expression Omnibus (GEO) database. Differential Expression Genes (DEG) between cases and controls in each microarray were assessed by using the “limma” (linear models for microarray data) R package (|log2 fold change (FC)| >0 and
-value <0.05). To analyze the cross-talk effect between HT and PD, the intersection of DEG of HT and PD was selected. To investigate the biological function of cross-talk genes, the gene ontology (GO) functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were applied. Protein-Protein Interaction (PPI) network was constructed using Cytoscape software. Top 10 cross-talk genes were screened, and the expression values of these 10 genes were extracted. ROC analysis was performed by using the pROC package and GGplot2 package of R language to predict the classification accuracy. Results. The overlapping DEG between HT and PD were 107 cross-talk genes. The results revealed that developmental process (
-value =1.06E-21) was the most significantly enriched biological process, followed by cell differentiation (
-value =8.49E-18) and immune system process (
-value =6.78E-11). KEGG analysis showed that Complement and coagulation cascades (
-value =2.29E-05), Hematopoietic cell lineage (
-value =2.66E-05), Phospholipase D signaling pathway (
-value =0.034367878) and Chemokine signaling pathway (
-value =0.04946333) were significantly enriched. The top 10 genes with most connections were LCE1B, LCE2B, LCE2A, LCE2C, LCE1C, LCE1F, ITGAM, C1QB, TREM2, and CD19. The AUC values of the two datasets of HT were both greater than 65% (GSE18152 = 81.42%, GSE176153 = 68.75%). AUC values of three datasets of PD were all greater than 60% (GSE10334 = 69.23%, GSE16134 = 73.72%, GSE173078 = 81.6%). Conclusions. A genetic cross-talk between HT and PD was detected, whereby LCE family genes appeared to play the most important role.
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Alam J, Yazdanpanah G, Ratnapriya R, Borcherding N, de Paiva CS, Li D, Guimaraes de Souza R, Yu Z, Pflugfelder SC. IL-17 Producing Lymphocytes Cause Dry Eye and Corneal Disease With Aging in RXRα Mutant Mouse. Front Med (Lausanne) 2022; 9:849990. [PMID: 35402439 PMCID: PMC8983848 DOI: 10.3389/fmed.2022.849990] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/24/2022] [Indexed: 11/22/2022] Open
Abstract
Purpose To investigate IL-17 related mechanisms for developing dry eye disease in the Pinkie mouse strain with a loss of function RXRα mutation. Methods Measures of dry eye disease were assessed in the cornea and conjunctiva. Expression profiling was performed by single-cell RNA sequencing (scRNA-seq) to compare gene expression in conjunctival immune cells. Conjunctival immune cells were immunophenotyped by flow cytometry and confocal microscopy. The activity of RXRα ligand 9-cis retinoic acid (RA) was evaluated in cultured monocytes and γδ T cells. Results Compared to wild type (WT) C57BL/6, Pinkie has increased signs of dry eye disease, including decreased tear volume, corneal barrier disruption, corneal/conjunctival cornification and goblet cell loss, and corneal vascularization, opacification, and ulceration with aging. ScRNA-seq of conjunctival immune cells identified γδ T cells as the predominant IL-17 expressing population in both strains and there is a 4-fold increased percentage of γδ T cells in Pinkie. Compared to WT, IL-17a, and IL-17f significantly increased in Pinkie with conventional T cells and γδ T cells as the major producers. Flow cytometry revealed an increased number of IL-17+ γδ T cells in Pinkie. Tear concentration of the IL-17 inducer IL-23 is significantly higher in Pinkie. 9-cis RA treatment suppresses stimulated IL-17 production by γδ T and stimulatory activity of monocyte supernatant on γδ T cell IL-17 production. Compared to WT bone marrow chimeras, Pinkie chimeras have increased IL-17+ γδ T cells in the conjunctiva after desiccating stress and anti-IL-17 treatment suppresses dry eye induced corneal MMP-9 production/activity and conjunctival goblet cell loss. Conclusion These findings indicate that RXRα suppresses generation of dry eye disease-inducing IL-17 producing lymphocytes s in the conjunctiva and identifies RXRα as a potential therapeutic target in dry eye.
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Affiliation(s)
- Jehan Alam
- Department of Ophthalmology, Ocular Surface Center, Baylor College of Medicine, Houston, TX, United States
| | - Ghasem Yazdanpanah
- Department of Ophthalmology, Ocular Surface Center, Baylor College of Medicine, Houston, TX, United States
| | - Rinki Ratnapriya
- Department of Ophthalmology, Baylor College of Medicine, Houston, TX, United States
| | - Nicholas Borcherding
- Department of Pathology, Washington University School of Medicine, St. Louis, MO, United States
| | - Cintia S. de Paiva
- Department of Ophthalmology, Ocular Surface Center, Baylor College of Medicine, Houston, TX, United States
| | - DeQuan Li
- Department of Ophthalmology, Ocular Surface Center, Baylor College of Medicine, Houston, TX, United States
| | - Rodrigo Guimaraes de Souza
- Department of Ophthalmology, Ocular Surface Center, Baylor College of Medicine, Houston, TX, United States
- Department of Ophthalmology, University of São Paulo, São Paulo, Brazil
| | - Zhiyuan Yu
- Department of Ophthalmology, Ocular Surface Center, Baylor College of Medicine, Houston, TX, United States
| | - Stephen C. Pflugfelder
- Department of Ophthalmology, Ocular Surface Center, Baylor College of Medicine, Houston, TX, United States
- *Correspondence: Stephen C. Pflugfelder
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