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Meng T, Liu J, Chang H, Qie R. Reverse predictive analysis of Rhizoma Pinelliae and Rhizoma Coptidis on differential miRNA target genes in lung adenocarcinoma. Medicine (Baltimore) 2023; 102:e32999. [PMID: 36800601 PMCID: PMC9936040 DOI: 10.1097/md.0000000000032999] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/19/2023] Open
Abstract
To use bioinformatics and network analysis to reveal the mechanism of "Rhizoma Pinelliae-Rhizoma Coptidis" herb pair in the treatment of lung adenocarcinoma. The target and pathway of "Rhizoma Pinelliae-Rhizoma Coptidis" herb pair in the treatment of lung adenocarcinoma were explored by online databases and network analysis tools, and the potential biomarkers of "Rhizoma Pinelliae-Rhizoma Coptidis" herb pair in the treatment of lung adenocarcinoma were predicted in reverse. A total of 59 traditional Chinese medicine compounds and 510 drug targets were screened in this study. A total of 25 micro-RNAs and 15,323 disease targets were obtained through GEO2R software analysis. In the end, 294 therapeutic targets and 47 core targets were obtained. A total of 186 gene ontology enrichment assays were obtained, and core therapeutic targets play multiple roles in biological processes, molecular functions, and cellular composition. Kyoto encyclopedia of genes and genomes pathway enrichment analysis showed that the core targets were mainly enriched in cancer-related pathways, immune-related pathways, endocrine-related pathways, etc, among which the non-small cell lung cancer pathway was the most significant core pathway. Molecular docking shows that the compound and the target have good binding ability. "Rhizoma Pinelliae-Rhizoma Coptidis" herb pair plays a mechanism of action in the treatment of lung adenocarcinoma through multiple targets and pathways. miR-5703, miR-3125, miR-652-5P, and miR-513c-5p may be new biomarkers for the treatment of lung adenocarcinoma.
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Affiliation(s)
- Tianwei Meng
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, China
| | - Jiawen Liu
- Graduate School, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, China
| | - Hong Chang
- Department of Pharmacy, Baotou Medical College, Baotou, Inner Mongolia, China
- * Correspondence: Hong Chang, Department of Pharmacy, Baotou Medical College, Baotou, Inner Mongolia, China (e-mail: )
| | - Rui Qie
- The First Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, China
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2
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Krishnan RH, Sadu L, Akshaya RL, Gomathi K, Saranya I, Das UR, Satishkumar S, Selvamurugan N. Circ_CUX1/miR-130b-5p/p300 axis for parathyroid hormone-stimulation of Runx2 activity in rat osteoblasts: A combined bioinformatic and experimental approach. Int J Biol Macromol 2023; 225:1152-1163. [PMID: 36427609 DOI: 10.1016/j.ijbiomac.2022.11.176] [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: 10/09/2022] [Revised: 10/31/2022] [Accepted: 11/17/2022] [Indexed: 11/23/2022]
Abstract
Parathyroid hormone (PTH) regulates the expression of bone remodeling genes by enhancing the activity of Runx2 in osteoblasts. p300, a histone acetyltransferase, acetylated Runx2 to activate the expression of its target genes. PTH stimulated the expression of p300 in rat osteoblastic cells. Increasing studies suggested the potential of non-coding RNAs (ncRNAs), such as microRNAs (miRNAs) and circular RNAs (circRNAs), in regulating gene expression under both physiological and pathological conditions. In this study, we hypothesized that PTH regulates Runx2 activity via ncRNAs-mediated p300 expression in rat osteoblastic cells. Bioinformatics and experimental approaches identified PTH-upregulation of miR-130b-5p and circ_CUX1 that putatively target p300 and miR-130b-5p, respectively. An antisense-mediated knockdown of circ_CUX1 was performed to determine the sponging activity of circ_CUX1. Knockdown of circ_CUX1 promoted miR-130b-5p activity and reduced p300 expression, resulting in decreased Runx2 acetylation in rat osteoblastic cells. Further, bioinformatics analysis identified the possible signaling pathways that regulate Runx2 activity and osteoblast differentiation via circ_CUX1/miR-130b-5p/p300 axis. The predicted circ_CUX1/miR-130b-5p/p300 axis might pave the way for better diagnostic and therapeutic approaches for bone-related diseases.
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Affiliation(s)
- R Hari Krishnan
- Department of Biotechnology, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - Lakshana Sadu
- Department of Biotechnology, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - R L Akshaya
- Department of Biotechnology, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - K Gomathi
- Department of Biotechnology, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - I Saranya
- Department of Biotechnology, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - Udipt Ranjan Das
- Department of Biotechnology, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - Sneha Satishkumar
- Department of Biotechnology, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - N Selvamurugan
- Department of Biotechnology, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India.
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Vijayalalitha R, Archita T, Juanitaa GR, Jayasuriya R, Amin KN, Ramkumar KM. Role of Long Non-Coding RNA in Regulating ER Stress Response to the Progression of Diabetic Complications. Curr Gene Ther 2023; 23:96-110. [PMID: 35927920 DOI: 10.2174/1566523222666220801141450] [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] [Received: 01/06/2022] [Revised: 04/08/2022] [Accepted: 04/22/2022] [Indexed: 11/22/2022]
Abstract
Chronic hyperglycemia damages the nerves and blood vessels, culminating in other vascular complications. Such complications enhance cytokine, oxidative and endoplasmic reticulum (ER) stress. ER is the primary organelle where proteins are synthesised and attains confirmatory changes before its site of destination. Perturbation of ER homeostasis activates signaling sensors within its lumen, the unfolded protein response (UPR) that orchestrates ER stress and is extensively studied. Increased ER stress markers are reported in diabetic complications in addition to lncRNA that acts as an upstream marker inducing ER stress response. This review focuses on the mechanisms of lncRNA that regulate ER stress markers, especially during the progression of diabetic complications. Through this systemic review, we showcase the dysfunctional lncRNAs that act as a leading cause of ER stress response to the progression of diabetic complications.
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Affiliation(s)
- Ramanarayanan Vijayalalitha
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - Tca Archita
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - George Raj Juanitaa
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - Ravichandran Jayasuriya
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - Karan Naresh Amin
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
| | - Kunka Mohanram Ramkumar
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur 603 203, Tamil Nadu, India
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4
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Zhang F, Cho WC. Therapeutic potential of RUNX1 and RUNX2 in bone metastasis of breast cancer. Expert Opin Ther Targets 2023; 27:413-417. [PMID: 37243490 DOI: 10.1080/14728222.2023.2219395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 05/15/2023] [Accepted: 05/25/2023] [Indexed: 05/28/2023]
Affiliation(s)
- Fei Zhang
- Department of Health Technology and Informatics, Hong Kong Polytechnic University, Hong Kong SAR, China
| | - William C Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong SAR, China
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Notch4 affects the proliferation and differentiation of deer antler chondrocytes through the Smad3/lncRNA27785.1 axis. Cell Signal 2022; 98:110429. [DOI: 10.1016/j.cellsig.2022.110429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 07/21/2022] [Accepted: 07/27/2022] [Indexed: 11/22/2022]
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Piperigkou Z, Tzaferi K, Makrokanis G, Cheli K, Karamanos NK. The microRNA-cell surface proteoglycan axis in cancer progression. Am J Physiol Cell Physiol 2022; 322:C825-C832. [PMID: 35294845 DOI: 10.1152/ajpcell.00041.2022] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Proteoglycans consist one of the major extracellular matrix class of biomolecules that demonstrate nodal roles in cancer progression. Μodern diagnostic and therapeutic approaches include proteoglycan detection and pharmacological targeting in various cancers. Proteoglycans orchestrate critical signaling pathways for cancer development and progression through dynamic interactions with matrix components. It is well established that the epigenetic signatures of cancer cells play critical role in guiding their functional properties and metastatic potential. Secreted microRNAs (miRNAs) reside in a complex network with matrix proteoglycans, thus affecting cell-cell and cell-matrix communication. This mini-review aims to highlight current knowledge on the proteoglycan-mediated signaling cascades that regulate miRNA biogenesis in cancer. Moreover, the miRNA-mediated proteoglycan regulation during cancer progression and mechanistic aspects on the way that proteoglycans affect miRNA expression are presented. Recent advances on the role of cell surface proteoglycans in exosome biogenesis and miRNA packaging and expression are also discussed.
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Affiliation(s)
- Zoi Piperigkou
- Biochemical Analysis and Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Patras, Greece.,Foundation for Research and Technology-Hellas (FORTH)/Institute of Chemical Engineering Sciences (ICE-HT), Patras, Greece
| | - Kyriaki Tzaferi
- Biochemical Analysis and Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Patras, Greece
| | - George Makrokanis
- Biochemical Analysis and Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Patras, Greece
| | - Konsatntina Cheli
- Biochemical Analysis and Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Patras, Greece
| | - Nikos K Karamanos
- Biochemical Analysis and Matrix Pathobiology Research Group, Laboratory of Biochemistry, Department of Chemistry, University of Patras, Patras, Greece.,Foundation for Research and Technology-Hellas (FORTH)/Institute of Chemical Engineering Sciences (ICE-HT), Patras, Greece
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7
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Bioinformatics Analysis Reveals the Related Role of miR-511-5p in the Progression of Breast Cancer. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:7146338. [PMID: 35186236 PMCID: PMC8853816 DOI: 10.1155/2022/7146338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 11/23/2022]
Abstract
Breast cancer remains a dangerous disease, and delving the molecular mechanism of breast cancer is still necessary. To illustrate the role of miR-511-5p, TCGA database was used to excavate the abundance of miR-511-5p, and the miR-511-5p level was measured in the pathological tissues and tumor cell lines. Moreover, the targets of miR-511-5p were identified with miRDIP and GEPIA and then were used for functional enrichment analysis. Besides, the targets of miR-511-5p were analyzed with the protein-protein interaction (PPI) network for the hub nodes, and then the expression levels of the hub nodes were visualized with the GEPIA database. The results showed that miR-511-5p was significantly downregulated in multiple types of tumor samples in the online database, and the downregulated miR-511-5p was also found in pathological tissues and tumor cell lines. Moreover, 48 genes were identified as the potential targets of miR-511-5p by miRDIP and GEPIA databases and enriched in cell cycle, PI3K/AKT, and P53 pathways. Besides, seven genes including BRCA1, FN1, CCNE1, CCND1, CHEK1, BUB3, and CDC25A were identified as the hub nodes by the PPI network, and CCNE1 and CHEK1 were confirmed to be related with the prognostic survival of the patients with breast cancer. In conclusion, the proofs in this study suggest that reduced miR-511-5p was a biomarker event for breast cancer, and CCNE1 and CHEK1 served as potential targets of miR-511-5p to involve the progression of breast cancer.
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Abedi M, Marateb HR, Mohebian MR, Aghaee-Bakhtiari SH, Nassiri SM, Gheisari Y. Systems biology and machine learning approaches identify drug targets in diabetic nephropathy. Sci Rep 2021; 11:23452. [PMID: 34873190 PMCID: PMC8648918 DOI: 10.1038/s41598-021-02282-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 11/12/2021] [Indexed: 11/15/2022] Open
Abstract
Diabetic nephropathy (DN), the leading cause of end-stage renal disease, has become a massive global health burden. Despite considerable efforts, the underlying mechanisms have not yet been comprehensively understood. In this study, a systematic approach was utilized to identify the microRNA signature in DN and to introduce novel drug targets (DTs) in DN. Using microarray profiling followed by qPCR confirmation, 13 and 6 differentially expressed (DE) microRNAs were identified in the kidney cortex and medulla, respectively. The microRNA-target interaction networks for each anatomical compartment were constructed and central nodes were identified. Moreover, enrichment analysis was performed to identify key signaling pathways. To develop a strategy for DT prediction, the human proteome was annotated with 65 biochemical characteristics and 23 network topology parameters. Furthermore, all proteins targeted by at least one FDA-approved drug were identified. Next, mGMDH-AFS, a high-performance machine learning algorithm capable of tolerating massive imbalanced size of the classes, was developed to classify DT and non-DT proteins. The sensitivity, specificity, accuracy, and precision of the proposed method were 90%, 86%, 88%, and 89%, respectively. Moreover, it significantly outperformed the state-of-the-art (P-value ≤ 0.05) and showed very good diagnostic accuracy and high agreement between predicted and observed class labels. The cortex and medulla networks were then analyzed with this validated machine to identify potential DTs. Among the high-rank DT candidates are Egfr, Prkce, clic5, Kit, and Agtr1a which is a current well-known target in DN. In conclusion, a combination of experimental and computational approaches was exploited to provide a holistic insight into the disorder for introducing novel therapeutic targets.
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Affiliation(s)
- Maryam Abedi
- grid.411036.10000 0001 1498 685XRegenerative Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hamid Reza Marateb
- grid.411750.60000 0001 0454 365XBiomedical Engineering Department, Engineering Faculty, University of Isfahan, Isfahan, Iran ,grid.6835.80000 0004 1937 028XDepartment of Automatic Control, Biomedical Engineering Research Center, Universitat Politècnica de Catalunya, BarcelonaTech (UPC), Barcelona, Spain
| | - Mohammad Reza Mohebian
- grid.25152.310000 0001 2154 235XDepartment of Electrical and Computer Engineering, University of Saskatchewan, Saskatoon, Canada
| | - Seyed Hamid Aghaee-Bakhtiari
- grid.411583.a0000 0001 2198 6209Bioinformatics Research Group, Mashhad University of Medical Sciences, Mashhad, Iran ,grid.411583.a0000 0001 2198 6209Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mahdi Nassiri
- grid.46072.370000 0004 0612 7950Department of Clinical Pathology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Yousof Gheisari
- Regenerative Medicine Research Center, Isfahan University of Medical Sciences, Isfahan, Iran. .,Department of Genetics and Molecular Biology, Isfahan University of Medical Sciences, Isfahan, Iran.
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