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Rai V. Transcriptomics Revealed Differentially Expressed Transcription Factors and MicroRNAs in Human Diabetic Foot Ulcers. Proteomes 2024; 12:32. [PMID: 39585119 PMCID: PMC11587442 DOI: 10.3390/proteomes12040032] [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: 07/23/2024] [Revised: 09/19/2024] [Accepted: 10/31/2024] [Indexed: 11/26/2024] Open
Abstract
Non-healing diabetic foot ulcers (DFUs) not only significantly increase morbidity and mortality but also cost a lot and drain healthcare resources. Persistent inflammation, decreased angiogenesis, and altered extracellular matrix remodeling contribute to delayed healing or non-healing. Recent studies suggest an increasing trend of DFUs in diabetes patients, and non-healing DFYs increase the incidence of amputation. Despite the current treatment with offloading, dressing, antibiotics use, and oxygen therapy, the risk of amputation persists. Thus, there is a need to understand the molecular and cellular factors regulating healing in DFUs. The ongoing research based on proteomics and transcriptomics has predicted multiple potential targets, but there is no definitive therapy to enhance healing in chronic DFUs. Increased or decreased expression of various proteins encoded by genes, whose expression transcriptionally and post-transcriptionally is regulated by transcription factors (TFs) and microRNAs (miRs), regulates DFU healing. For this study, RNA sequencing was conducted on 20 DFU samples of ulcer tissue and non-ulcerated nearby healthy tissues. The IPA analysis revealed various activated and inhibited transcription factors and microRNAs. Further network analysis revealed interactions between the TFs and miRs and the molecular targets of these TFs and miRs. The analysis revealed 30 differentially expressed transcription factors (21 activated and 9 inhibited), two translational regulators (RPSA and EIF4G2), and seven miRs, including mir-486, mir-324, mir-23, mir-186, mir-210, mir-199, and mir-338 in upstream regulators (p < 0.05), while causal network analysis (p < 0.05) revealed 28 differentially expressed TFs (19 activated and 9 inhibited), two translational regulators (RPSA and EIF4G2), and five miRs including mir-155, mir-486, mir-324, mir-210, and mir-1225. The protein-protein interaction analysis revealed the interaction of various novel proteins with the proteins involved in regulating DFU pathogenesis and healing. The results of this study highlight many activated and inhibited novel TFs and miRs not reported in the literature so far, as well as the targeted molecules. Since proteins are the functional units during biological processes, alteration of gene expression may result in different proteoforms and protein species, making the wound microenvironment a complex protein interaction (proteome complexity). Thus, investigating the effects of these TFs and miRs on protein expression using proteomics and combining these results with transcriptomics will help advance research on DFU healing and delineate potential therapeutic strategies.
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Affiliation(s)
- Vikrant Rai
- Department of Translational Research, Western University of Health Sciences, 309 E. Second Street, Pomona, CA 91766-1854, USA
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He J, Wei C, Huang X, Zhang G, Mao J, Li X, Yang C, Zhang W, Tian K, Liu G. MiR-23b and miR-133 Cotarget TGFβ2/NOTCH1 in Sheep Dermal Fibroblasts, Affecting Hair Follicle Development. Cells 2024; 13:557. [PMID: 38534401 PMCID: PMC10969380 DOI: 10.3390/cells13060557] [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: 02/17/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 03/28/2024] Open
Abstract
Wool is produced and controlled by hair follicles (HFs). However, little is known about the mechanisms involved in HF development and regulation. Sheep dermal fibroblasts (SDFs) play a key role in the initial stage of HF development. Analyzing the molecular mechanism that regulates early HF development in superfine wool sheep is of great importance for better understanding the HF morphogenesis process and for the breeding of fine wool sheep. Here, we show that two microRNAs (miRNAs) affect the development of HFs by targeting two genes that are expressed by SDFs. Meanwhile, the overexpression and inhibition of oar-miR-23b and oar-miR-133 in SDFs cells and cell proliferation, apoptosis, and migration were further detected using a CCK-8 assay, an Annexin V-FITC assay, a Transwell assay, and flow cytometry. We found that oar-miR-23b, oar-miR-133, and their cotarget genes TGFβ2 and NOTCH1 were differentially expressed during the six stages of HF development in superfine wool sheep. Oar-miR-23b and oar-miR-133 inhibited the proliferation and migration of SDFs and promoted the apoptosis of SDFs through TGFβ2 and NOTCH1. oar-miR-23b and oar-miR-133 inhibited the proliferation and migration of SDFs by jointly targeting TGFβ2 and NOTCH1, thereby inhibiting the development of superfine wool HFs. Our research provides a molecular marker that can be used to guide the breeding of ultrafine wool sheep.
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Affiliation(s)
- Junmin He
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (C.W.); (G.Z.); (J.M.)
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Jinan 250100, China
| | - Chen Wei
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (C.W.); (G.Z.); (J.M.)
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Jinan 250100, China
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (X.H.); (X.L.); (C.Y.); (W.Z.)
| | - Guoping Zhang
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (C.W.); (G.Z.); (J.M.)
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Jinan 250100, China
| | - Jingyi Mao
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (C.W.); (G.Z.); (J.M.)
| | - Xue Li
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (X.H.); (X.L.); (C.Y.); (W.Z.)
| | - Cunming Yang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (X.H.); (X.L.); (C.Y.); (W.Z.)
| | - Wenjing Zhang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (X.H.); (X.L.); (C.Y.); (W.Z.)
| | - Kechuan Tian
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (C.W.); (G.Z.); (J.M.)
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Jinan 250100, China
| | - Guifen Liu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (J.H.); (C.W.); (G.Z.); (J.M.)
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Jinan 250100, China
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Yu H, Wang Y, Wang D, Yi Y, Liu Z, Wu M, Wu Y, Zhang Q. Landscape of the epigenetic regulation in wound healing. Front Physiol 2022; 13:949498. [PMID: 36035490 PMCID: PMC9403478 DOI: 10.3389/fphys.2022.949498] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 07/19/2022] [Indexed: 12/13/2022] Open
Abstract
Wound healing after skin injury is a dynamic and highly coordinated process involving a well-orchestrated series of phases, including hemostasis, inflammation, proliferation, and tissue remodeling. Epigenetic regulation refers to genome-wide molecular events, including DNA methylation, histone modification, and non-coding RNA regulation, represented by microRNA (miRNA), long noncoding RNA (lncRNA), and circular RNA (circRNA). Epigenetic regulation is pervasively occurred in the genome and emerges as a new role in gene expression at the post-transcriptional level. Currently, it is well-recognized that epigenetic factors are determinants in regulating gene expression patterns, and may provide evolutionary mechanisms that influence the wound microenvironments and the entire healing course. Therefore, this review aims to comprehensively summarize the emerging roles and mechanisms of epigenetic remodeling in wound healing. Moreover, we also pose the challenges and future perspectives related to epigenetic modifications in wound healing, which would bring novel insights to accelerated wound healing.
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Affiliation(s)
| | | | | | | | | | - Min Wu
- *Correspondence: Min Wu, ; Yiping Wu, ; Qi Zhang,
| | - Yiping Wu
- *Correspondence: Min Wu, ; Yiping Wu, ; Qi Zhang,
| | - Qi Zhang
- *Correspondence: Min Wu, ; Yiping Wu, ; Qi Zhang,
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Xie J, Wu W, Zheng L, Lin X, Tai Y, Wang Y, Wang L. Roles of MicroRNA-21 in Skin Wound Healing: A Comprehensive Review. Front Pharmacol 2022; 13:828627. [PMID: 35295323 PMCID: PMC8919367 DOI: 10.3389/fphar.2022.828627] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/10/2022] [Indexed: 12/12/2022] Open
Abstract
MicroRNA-21 (miR-21), one of the early mammalian miRNAs identified, has been detected to be upregulated in multiple biological processes. Increasing evidence has demonstrated the potential values of miR-21 in cutaneous damage and skin wound healing, but lack of a review article to summarize the current evidence on this issue. Based on this review, relevant studies demonstrated that miR-21 played an essential role in wound healing by constituting a complex network with its targeted genes (i.e., PTEN, RECK. SPRY1/2, NF-κB, and TIMP3) and the cascaded signaling pathways (i.e., MAPK/ERK, PI3K/Akt, Wnt/β-catenin/MMP-7, and TGF-β/Smad7-Smad2/3). The treatment effectiveness developed by miR-21 might be associated with the promotion of the fibroblast differentiation, the improvement of angiogenesis, anti-inflammatory, enhancement of the collagen synthesis, and the re-epithelialization of the wound. Currently, miRNA nanocarrier systems have been developed, supporting the feasibility clinical feasibility of such miR-21-based therapy. After further investigations, miR-21 may serve as a potential therapeutic target for wound healing.
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Affiliation(s)
- Jie Xie
- Department of Emergency Medicine, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China
| | - Weizhou Wu
- Department of Urology, Maoming People's Hospital, Guangdong, China
| | - Liying Zheng
- Postgraduate Pepartment, First Affiliated Hospital of Gannan Medical College, Ganzhou, China
| | - Xuesong Lin
- Department of Burn Surgery, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China
| | - Yuncheng Tai
- Department of Burn Surgery, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China
| | - Yajie Wang
- Department of Burn Surgery, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China
| | - Le Wang
- Department of Burn Surgery, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, China
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Cheng H, Zhang X, Li Y. Hydroxycamptothecin Impedes the Mesenchymal Stem Cells (MSCs)-Triggered Migrative Features of Breast Cancer Cells via Suppressing the Protein Kinase B/Mitogen-Activated Protein Kinase (AKT/MAPK) Activation in Bone Marrowmesenchymal Stem Cells. J BIOMATER TISS ENG 2022. [DOI: 10.1166/jbt.2022.2892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The current study aimed to dissect the impacts and mechanisms of hydroxycamptothecin on breast cancer. Collect conditioned medium from MSCs cells to apply it into the co-culture system of breast cancer cells, which were pre-treated with hydroxycamptothecin. The cell counting kit was
employed to measure the proliferation potential of cells, while the phosphorylation degrees of AKT/MAPKrelated proteins were examined via Western blotting. Then the cellular migration was test by transwell. Finally, the transcriptional and translational levels of IL-6 and RANTES in cells were
detected by real-time PCR and enzyme-linked immunosorbent assay. HC could remarkably influence the interplay between MSC and breast malignant cells, reduce the MSC-activated migrative behavior of breast malignant cells and impede the capability of MSC to maintain the migration of cancer cells.
RANTES and IL-6 exerted a synergistic induction in the migrative feature of breast cancer cells. HC could retard the migrating activities of breast cancer cells via diminishing the RANTES and IL-6 levels. Hydroxycamptothecin could impede the proliferative and migrative activities of MSC, of
which the impediment was accompanied by an inhibitory impact on the secretory production of two growth factors IL-6 and RANTES from MSC, thereby enhancing the migration of breast malignant cells.
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Affiliation(s)
- Hong Cheng
- Department of Breast Surgery, Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, 445000, China
| | - Xin Zhang
- Department of Oncology, Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, 445000, China
| | - Yinmou Li
- Department of Breast Surgery, Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, 445000, China
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Zhou K, Chang Y, Han B, Li R, Wei Y. MicroRNAs as crucial mediators in the pharmacological activities of triptolide (Review). Exp Ther Med 2021; 21:499. [PMID: 33791008 PMCID: PMC8005665 DOI: 10.3892/etm.2021.9930] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/18/2021] [Indexed: 12/19/2022] Open
Abstract
Triptolide is the main bioactive constituent isolated from the Chinese herb Tripterygium wilfordii Hook F., which possesses a variety of pharmacological properties. MicroRNAs (miRNAs/miRs) are short non-coding RNAs that regulate gene expression post-transcriptionally. miRNAs are implicated in several intracellular processes, whereby their dysregulation contributes to pathogenesis of various diseases. Thus, miRNAs have great potential as biomarkers and therapeutic targets for diseases, and are implicated in drug treatment. Previous studies have reported that specific miRNAs are targeted, and their expression levels can be altered following exposure to triptolide. Thus, miRNAs are emerging as crucial mediators in the pharmacological activities of triptolide. The present review summarizes current literature on miRNAs as target molecules in the pharmacological activities of triptolide, including antitumor, anti-inflammatory, immunosuppressive, renal protective, cardioprotective, antiangiogenesis activities and multiorgan toxicity effects. In addition, the diverse signaling pathways involved are discussed to provide a comprehensive understanding of the underlying molecular mechanisms of triptolide in the regulation of target miRNAs.
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Affiliation(s)
- Kun Zhou
- Shanxi Institute of Energy, Taiyuan, Shanxi 030600, P.R. China
| | - Yinxia Chang
- College of Chinese Medicine and Food Engineering, Shanxi University of Chinese Medicine, Jinzhong, Shanxi 030619, P.R. China
| | - Bo Han
- College of Basic Medicine, Shanxi University of Chinese Medicine, Jinzhong, Shanxi 030619, P.R. China
| | - Rui Li
- College of Chinese Medicine and Food Engineering, Shanxi University of Chinese Medicine, Jinzhong, Shanxi 030619, P.R. China
| | - Yanming Wei
- College of Chinese Medicine and Food Engineering, Shanxi University of Chinese Medicine, Jinzhong, Shanxi 030619, P.R. China
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