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Lin Q, Cai B, Ke R, Chen L, Ni X, Liu H, Lin X, Wang B, Shan X. Integrative bioinformatics and experimental validation of hub genetic markers in acne vulgaris: Toward personalized diagnostic and therapeutic strategies. J Cosmet Dermatol 2024; 23:1777-1799. [PMID: 38268224 DOI: 10.1111/jocd.16152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/10/2023] [Indexed: 01/26/2024]
Abstract
BACKGROUND Acne vulgaris is a widespread chronic inflammatory dermatological condition. The precise molecular and genetic mechanisms of its pathogenesis remain incompletely understood. This research synthesizes existing databases, targeting a comprehensive exploration of core genetic markers. METHODS Gene expression datasets (GSE6475, GSE108110, and GSE53795) were retrieved from the GEO. Differentially expressed genes (DEGs) were identified using the limma package. Enrichment analyses were conducted using GSVA for pathway assessment and clusterProfiler for GO and KEGG analyses. PPI networks and immune cell infiltration were analyzed using the STRING database and ssGSEA, respectively. We investigated the correlation between hub gene biomarkers and immune cell infiltration using Spearman's rank analysis. ROC curve analysis validated the hub genes' diagnostic accuracy. miRNet, TarBase v8.0, and ChEA3 identified miRNA/transcription factor-gene interactions, while DrugBank delineated drug-gene interactions. Experiments utilized HaCaT cells stimulated with Propionibacterium acnes, treated with retinoic acid and methotrexate, and evaluated using RT-qPCR, ELISA, western blot, lentiviral transduction, CCK-8, wound-healing, and transwell assays. RESULTS There were 104 genes with consistent differences across the three datasets of paired acne and normal skin. Functional analyses emphasized the significant enrichment of these DEGs in immune-related pathways. PPI network analysis pinpointed hub genes PTPRC, CXCL8, ITGB2, and MMP9 as central players in acne pathogenesis. Elevated levels of specific immune cell infiltration in acne lesions corroborated the inflammatory nature of the disease. ROC curve analysis identified the acne diagnostic potential of four hub genes. Key miRNAs, particularly hsa-mir-124-3p, and central transcription factors like TFEC were noted as significant regulators. In vitro validation using HaCaT cells confirmed the upregulation of hub genes following Propionibacterium acnes exposure, while CXCL8 knockdown reduced pro-inflammatory cytokines, cell proliferation, and migration. DrugBank insights led to the exploration of retinoic acid and methotrexate, both of which mitigated gene expression upsurge and inflammatory mediator secretion. CONCLUSION This comprehensive study elucidated pivotal genes associated with acne pathogenesis, notably PTPRC, CXCL8, ITGB2, and MMP9. The findings underscore potential biomarkers, therapeutic targets, and the therapeutic potential of agents like retinoic acid and methotrexate. The congruence between bioinformatics and experimental validations suggests promising avenues for personalized acne treatments.
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Affiliation(s)
- Qian Lin
- Department of Plastic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Plastic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China
| | - Beichen Cai
- Department of Plastic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Plastic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China
| | - Ruonan Ke
- Department of Plastic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Plastic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, Fujian, China
| | - Lu Chen
- Department of Plastic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Plastic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Xuejun Ni
- Department of Plastic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Plastic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
| | - Hekun Liu
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China
| | - Xinjian Lin
- Department of Plastic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Plastic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Key Laboratory of Gastrointestinal Cancer (Fujian Medical University), Ministry of Education, Fuzhou, Fujian, China
| | - Biao Wang
- Department of Plastic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Plastic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
- Fujian Key Laboratory of Translational Research in Cancer and Neurodegenerative Diseases, Institute for Translational Medicine, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, Fujian, China
| | - Xiuying Shan
- Department of Plastic Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, China
- Department of Plastic Surgery, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, China
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Bahmyari S, Khatami SH, Taghvimi S, Rezaei Arablouydareh S, Taheri-Anganeh M, Ghasemnejad-Berenji H, Farazmand T, Soltani Fard E, Solati A, Movahedpour A, Ghasemi H. MicroRNAs in Male Fertility. DNA Cell Biol 2024; 43:108-124. [PMID: 38394131 DOI: 10.1089/dna.2023.0314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024] Open
Abstract
Around 50% of all occurrences of infertility are attributable to the male factor, which is a significant global public health concern. There are numerous circumstances that might interfere with spermatogenesis and cause the body to produce abnormal sperm. While evaluating sperm, the count, the speed at which they migrate, and their appearance are the three primary characteristics that are analyzed. MicroRNAs, also known as miRNAs, are present in all physiological fluids and tissues. They participate in both physiological and pathological processes. Researches have demonstrated that the expression of microRNA genes differs in infertile men. These genes regulate spermatogenesis at various stages and in several male reproductive cells. Hence, microRNAs have the potential to act as useful indicators in the diagnosis and treatment of male infertility and other diseases affecting male reproduction. Despite this, additional research is necessary to determine the precise miRNA regulation mechanisms.
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Affiliation(s)
- Sedigheh Bahmyari
- Department of Reproductive Biology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyyed Hossein Khatami
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sina Taghvimi
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Sahar Rezaei Arablouydareh
- Reproductive Health Research Center, Clinical Research Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Mortaza Taheri-Anganeh
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Research Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Hojat Ghasemnejad-Berenji
- Reproductive Health Research Center, Clinical Research Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Tooba Farazmand
- Departmant of Gynecology, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran
| | - Elahe Soltani Fard
- Department of Molecular Medicine, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Arezoo Solati
- Department of Reproductive Biology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
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Mohamed HA, Abdelkafy AE, Khairy RMM, Abdelraheim SR, Kamel BA, Marey H. MicroRNAs and cytokines as potential predictive biomarkers for COVID-19 disease progression. Sci Rep 2023; 13:3531. [PMID: 36864077 PMCID: PMC9979137 DOI: 10.1038/s41598-023-30474-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 02/23/2023] [Indexed: 03/04/2023] Open
Abstract
Host microRNAs can influence the cytokine storm associated SARS-CoV-2 infection and proposed as biomarkers for COVID-19 disease. In the present study, serum MiRNA-106a and miRNA-20a were quantified by real time-PCR in 50 COVID-19 patients hospitalized at Minia university hospital and 30 healthy volunteers. Profiles of serum inflammatory cytokines (TNF-α, IFN-γ, and IL-10) and TLR4 were analyzed by Eliza in patients and controls. A highly significant decrease (P value = 0.0001) in the expressions of miRNA-106a and miRNA-20a was reported in COVID-19 patients compared to controls. A significant decrease in the levels of miRNA-20a was also reported in patients with lymphopenia, patients having chest CT severity score (CSS) > 19 and in patients having O2 saturation less than 90%. Significantly higher levels of TNF-α, IFN-γ, IL-10 and TLR4 were reported in patients compared to controls. IL-10 and TLR4 levels were significantly higher in patients having lymphopenia. TLR-4 level was higher in patients with CSS > 19 and in patients with hypoxia. Using univariate logistic regression analysis, miRNA-106a, miRNA-20a, TNF-α, IFN-γ, IL-10 and TLR4 were identified as good predictors of disease. Receiver operating curve showed that the downregulation of miRNA-20a in patients having lymphopenia, patients with CSS > 19 and patients with hypoxia could be a potential biomarker with AUC = 0.68 ± 0.08, AUC = 0.73 ± 0.07 and AUC = 0.68 ± 0.07 respectively. Also, ROC curve showed accurate association between the increase of serum IL-10 and TLR-4 and lymphopenia among COVID-19 patients with AUC = 0.66 ± 0.08 and AUC = 0.73 ± 0.07 respectively. ROC curve showed also that serum TLR-4 could be a potential marker for high CSS with AUC = 0.78 ± 0.06. A negative correlation was detected between miRNA-20a with TLR-4 (r = - 0.30, P value = 0.03). We concluded that, miR-20a, is a potential biomarker of COVID-19 severity and blockade of IL-10 and TLR4 may constitute a novel therapy for COVID-19 patients.
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Affiliation(s)
- Hatem A. Mohamed
- grid.411806.a0000 0000 8999 4945Department of Biochemistry, Faculty of Medicine, Minia University, Minia, Egypt
| | - Aya Eid Abdelkafy
- grid.411806.a0000 0000 8999 4945Department of Biochemistry, Faculty of Medicine, Minia University, Minia, Egypt
| | - Rasha M. M. Khairy
- grid.411806.a0000 0000 8999 4945Department of Microbiology and Immunology, Faculty of Medicine, Minia University, Minia, 61511 Egypt
| | - Salama R. Abdelraheim
- grid.411806.a0000 0000 8999 4945Department of Biochemistry, Faculty of Medicine, Minia University, Minia, Egypt
| | - Bothina Ahmed Kamel
- grid.411806.a0000 0000 8999 4945Department of Biochemistry, Faculty of Medicine, Minia University, Minia, Egypt
| | - Heba Marey
- grid.411806.a0000 0000 8999 4945Department of Biochemistry, Faculty of Medicine, Minia University, Minia, Egypt
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Ying H, Ebrahimi M, Keivan M, Khoshnam SE, Salahi S, Farzaneh M. miRNAs; a novel strategy for the treatment of COVID-19. Cell Biol Int 2021; 45:2045-2053. [PMID: 34180562 PMCID: PMC8426984 DOI: 10.1002/cbin.11653] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/08/2021] [Accepted: 06/17/2021] [Indexed: 11/09/2022]
Abstract
Coronavirus disease 2019 (COVID‐19) is the seventh member of the bat severe acute respiratory syndrome family. COVID‐19 can fuse their envelopes with the host cell membranes and deliver their genetic material. COVID‐19 attacks the respiratory system and stimulates the host inflammatory responses, enhances the recruitment of immune cells, and promotes angiotensin‐converting enzyme 2 activities. Patients with confirmed COVID‐19 may have experienced fever, dry cough, headache, dyspnea, acute kidney injury, acute respiratory distress syndrome, and acute heart injury. Several strategies such as oxygen therapy, ventilation, antibiotic or antiviral therapy, and renal replacement therapy are commonly used to decrease COVID‐19‐associated mortality. However, these approaches may not be good treatment options. Therefore, the search for an alternative‐novel therapy is urgently important to prevent the disease progression. Recently, microRNAs (miRNAs) have emerged as a promising strategy for COVID‐19. The design of oligonucleotide against the genetic material of COVID‐19 might suppress virus RNA translation. Several previous studies have shown that host miRNAs play an antiviral role and improve the treatment of patients with COVID‐19. miRNAs by binding to the 3′‐untranslated region (UTR) or 5′‐UTR of viral RNA play an important role in COVID‐19‐host interplay and viral replication. miRNAs interact with multiple pathways and reduce inflammatory biomarkers, thrombi formation, and tissue damage to accelerate the patient outcome. The information in this review provides a summary of the current clinical application of miRNAs for the treatments of patients with COVID‐19.
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Affiliation(s)
- Hao Ying
- Zhuji People's Hospital of Zhejiang Province, Zhuji Affiliated Hospital of Shaoxing University, Zhuji, China
| | - Mohsen Ebrahimi
- Neonatal and Children's Health Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mona Keivan
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Seyed Esmaeil Khoshnam
- Persian Gulf Physiology Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Sarvenaz Salahi
- Minimally Invasive Surgery Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Maryam Farzaneh
- Fertility, Infertility and Perinatology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Candidate reference genes for quantitative gene expression analysis in Lagerstroemia indica. Mol Biol Rep 2021; 48:1677-1685. [PMID: 33575959 DOI: 10.1007/s11033-021-06209-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/29/2021] [Indexed: 10/22/2022]
Abstract
Quantitative gene expression analysis by qPCR requires reference genes for normalization. Lagerstroemia indica (crape myrtle) is a popular ornamental plant in the world, but suitable endogenous reference genes are lacking. To find suitable reference genes, we evaluated the stabilities of nine candidate genes in six experimental data sets: six different tissues, three leaf colors, nine flower colors, and under three abiotic stresses (salt, drought, cold) using four statistical algorithms. A target gene LiMYB56 (homolog of Arabidopsis MYB56) was used to verify the authenticity and accuracy of the candidate reference genes. The results showed that the combination of two stably expressed reference genes, rather than a single reference gene, improved the accuracy of the qPCR. LiEF1α-2 + LiEF1α-3 was best for the tissue, salt treatment, and drought treatment sets; LiEF1α-2 + LiEF1α-1 was optimal for leaf color; LiEF1α-2 + LiACT7 was optimal for cold treatment; and LiUBC + LiEF1α-1 was best for the flower color set. Notably, LiEF1α-2 had high expression stability in all six experimental sets, implying it may be a good reference gene for expression studies in L. indica. Our results will facilitate future gene expression studies in L. indica.
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