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Ismail NH, Mussa A, Al-Khreisat MJ, Mohamed Yusoff S, Husin A, Al-Jamal HAN, Johan MF, Islam MA. Dysregulation of Non-Coding RNAs: Roles of miRNAs and lncRNAs in the Pathogenesis of Multiple Myeloma. Noncoding RNA 2023; 9:68. [PMID: 37987364 PMCID: PMC10660696 DOI: 10.3390/ncrna9060068] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
The dysregulation of non-coding RNAs (ncRNAs), specifically microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), leads to the development and advancement of multiple myeloma (MM). miRNAs, in particular, are paramount in post-transcriptional gene regulation, promoting mRNA degradation and translational inhibition. As a result, miRNAs can serve as oncogenes or tumor suppressors depending on the target genes. In MM, miRNA disruption could result in abnormal gene expression responsible for cell growth, apoptosis, and other biological processes pertinent to cancer development. The dysregulated miRNAs inhibit the activity of tumor suppressor genes, contributing to disease progression. Nonetheless, several miRNAs are downregulated in MM and have been identified as gene regulators implicated in extracellular matrix remodeling and cell adhesion. miRNA depletion potentially facilitates the tumor advancement and resistance of therapeutic drugs. Additionally, lncRNAs are key regulators of numerous cellular processes, such as gene expression, chromatin remodeling, protein trafficking, and recently linked MM development. The lncRNAs are uniquely expressed and influence gene expression that supports MM growth, in addition to facilitating cellular proliferation and viability via multiple molecular pathways. miRNA and lncRNA alterations potentially result in anomalous gene expression and interfere with the regular functioning of MM. Thus, this review aims to highlight the dysregulation of these ncRNAs, which engender novel therapeutic modalities for the treatment of MM.
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Affiliation(s)
- Nor Hayati Ismail
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Ali Mussa
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Department of Biology, Faculty of Education, Omdurman Islamic University, Omdurman 11111, Sudan
- Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, Tamil Nadu, India
| | - Mutaz Jamal Al-Khreisat
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Shafini Mohamed Yusoff
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Azlan Husin
- Department of Internal Medicine, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Hamid Ali Nagi Al-Jamal
- School of Biomedicine, Faculty of Health Sciences, Universiti Sultan Zainal Abidin (UniSZA), Kuala Nerus 21300, Terengganu, Malaysia
| | - Muhammad Farid Johan
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Md Asiful Islam
- WHO Collaborating Centre for Global Women’s Health, Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
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Liu T, Jiang C. Effects of heat-sensitive moxibustion plus Chinese medication on the expression of serum inflammatory indicators and microRNAs in patients with multiple myeloma after chemotherapy. JOURNAL OF ACUPUNCTURE AND TUINA SCIENCE 2023. [DOI: 10.1007/s11726-023-1358-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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Taheri F, Ebrahimi SO, Heidari R, Pour SN, Reiisi S. Mechanism and function of miR-140 in human cancers: A review and in silico study. Pathol Res Pract 2023; 241:154265. [PMID: 36509008 DOI: 10.1016/j.prp.2022.154265] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/27/2022] [Accepted: 12/03/2022] [Indexed: 12/12/2022]
Abstract
MicroRNA-140 (miR-140) acts as a tumor suppressor and plays a vital role in cell biological functions such as cell proliferation, apoptosis, and DNA repair. The expression of this miRNA has been shown to be considerably decreased in cancer tissues and cell lines compared with normal adjacent tissues. Consequently, aberrant expression of some miR-140 target genes can lead to the initiation and progression of various human cancers, such as breast cancer, gastrointestinal cancers, lung cancer, and prostate cancer. The dysregulation of the miR-140 network also affects cell proliferation, invasion, metastasis, and apoptosis of cancer cells by affecting various signaling pathways. Besides, up-regulation of miR-140 could enhance the efficacy of chemotherapeutic agents in different cancer. We aimed to cover most aspects of miR-140 function in cancer development and address its importance in different stages of cancer progression.
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Affiliation(s)
- Forough Taheri
- Department of Genetics, Sharekord Branch, Islamic Azad University, Sharekord, Iran
| | - Seyed Omar Ebrahimi
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran
| | - Razieh Heidari
- Department of Medical Biotechnology, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Somaye Nezamabadi Pour
- Department of Obstetrics and Gynecology, School of Medicine, Bam University of Medical Sciences, Bam, Iran
| | - Somayeh Reiisi
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran.
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Qi D, Li H, Wang S, Wang S, Zheng R, Liu N, Han B, Liu L. Construction of ceRNA network and key gene screening in cervical squamous intraepithelial lesions. Medicine (Baltimore) 2022; 101:e31928. [PMID: 36482542 PMCID: PMC9726336 DOI: 10.1097/md.0000000000031928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND This study aimed to construct an endogenous competition network for cervical squamous intraepithelial lesions using differential gene screening. METHODS GSE149763 was used to screen differentially expressed long non-coding RNAs (lncRNAs) and mRNAs to predict correlated microRNAs (miRNAs). The correlated miRNAs and GSE105409 were used to screen differentially expressed miRNAs for differential co-expression analysis, and the co-expressed differentially expressed miRNAs were used to predict correlated mRNAs. Differentially expressed mRNAs, miRNAs, and lncRNAs were visualized, and differential gene screening, enrichment, and pathway analysis were performed. RESULTS The ceRNA network of cervical squamous intraepithelial was successfully established and a potential differentially expressed network was identified. The key genes were VEGFA and FOS, and the key pathway was the MAPK signaling pathway. CONCLUSIONS The differential expression and potential effects of the lncRNA BACH1-IT1/miR-140-5p/VEGFA axis, key genes, VEGFA and FOS, and MAPK signaling in CIN were clarified, and the occurrence and potential effects of CIN were further clarified. The underlying molecular mechanism provides a certain degree of reference for subsequent treatments and experimental research.
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Affiliation(s)
- Ding Qi
- Heilongjiang University of Traditional Chinese Medicine, Heilongjiang, China
| | - Hongmei Li
- The 2nd Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Heilongjiang, China
| | - Shuoqi Wang
- Heilongjiang University of Traditional Chinese Medicine, Heilongjiang, China
| | - Shimeng Wang
- Heilongjiang University of Traditional Chinese Medicine, Heilongjiang, China
| | - Rui Zheng
- Heilongjiang University of Traditional Chinese Medicine, Heilongjiang, China
| | - Ning Liu
- Heilongjiang University of Traditional Chinese Medicine, Heilongjiang, China
| | - Buwei Han
- Heilongjiang University of Traditional Chinese Medicine, Heilongjiang, China
| | - Li Liu
- The 1st Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Heilongjiang, China
- * Correspondence: Li Liu, Department of Gynecology, The 1st Affiliated Hospital of Heilongjiang University of Traditional Chinese Medicine, Harbin, Heilongjiang 150036, China (e-mail: )
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Souza OF, Popi AF. Role of microRNAs in B-Cell Compartment: Development, Proliferation and Hematological Diseases. Biomedicines 2022; 10:biomedicines10082004. [PMID: 36009551 PMCID: PMC9405569 DOI: 10.3390/biomedicines10082004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/29/2022] [Accepted: 08/14/2022] [Indexed: 11/24/2022] Open
Abstract
B-cell development is a very orchestrated pathway that involves several molecules, such as transcription factors, cytokines, microRNAs, and also different cells. All these components maintain the ideal microenvironment and control B-cell differentiation. MicroRNAs are small non-coding RNAs that bind to target mRNA to control gene expression. These molecules could circulate in the body in a free form, protein-bounded, or encapsulated into extracellular vesicles, such as exosomes. The comprehension of the role of microRNAs in the B-cell development was possible based on microRNA profile of each B-cell stage and functional studies. Herein, we report the knowledge about microRNAs in the B-cell the differentiation, proliferation, and also in hematological malignancies.
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Network pharmacology approach and molecular docking to explore the potential mechanism of Wu-Wei-Wen-Tong Chubi capsules in rheumatoid arthritis. Naunyn Schmiedebergs Arch Pharmacol 2022; 395:1061-1073. [PMID: 35670824 DOI: 10.1007/s00210-022-02260-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Accepted: 05/24/2022] [Indexed: 10/18/2022]
Abstract
Network pharmacology, a holistic approach based on the theory of biological network technology, integrates information from biological systems, drugs, and diseases. Here, this theory was used to predict the targets of Wu-Wei-Wen-Tong Chubi capsule (WWWT) to explore the mechanism in the treatment of rheumatoid arthritis (RA). The ingredients of each herbal medicine in WWWT were collected from the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP), and the active ingredients were screened through bioavailability (OB) ≥30% and drug-likeness (DL) ≥ 0.18. SwissTargetPrection and TCMSP were utilized to calculate and predict the targets of active ingredients. RA-related targets were obtained by searching the Genecards and OMIM databases. The common targets of RA and WWWT were used for gene ontology (GO), KEGG pathway enrichment, protein-protein interaction (PPI) analysis, and molecular docking. And then, four key genes were screened for subsequent verification experiments. In total, 90 active compounds and 330 potential targets of WWWT, 1310 targets of RA, and 135 intersection targets were found. Additionally, GO and pathway analysis identified 4610 significant GO terms and 147 significant KEGG pathways. Based on the PPI network, 11 key genes including IL-6, MMP-9, and TNF-α were screened out for molecular docking. Molecular docking showed that these key genes have good binding activities to active compounds of WWWT such as oroxylin a, kaempferol, and luteolin. Simultaneously, Western blot experimental validation demonstrated that the protein expressions of IL-6, MMP-9, TNF-α, and VEGFA significantly decreased after WWWT treatment. The mechanism of WWWT in treating RA involves multiple active compounds acting on multiple targets, and multiple pathways, which provides an important reference for further elucidation the mechanism and clinical applications of WWWT in the treatment of RA.
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Fan YX, Wu JH, Yin SJ, Zhou T, Huang YH, Meng R, Wang P, He GH. Associations of FOXP3 gene polymorphisms with susceptibility and severity of preeclampsia: A meta-analysis. Am J Reprod Immunol 2022; 88:e13554. [PMID: 35441756 DOI: 10.1111/aji.13554] [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: 01/05/2022] [Revised: 03/10/2022] [Accepted: 04/12/2022] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVE FOXP3 single nucleotide polymorphisms (SNPs) were recently elucidated to influence the development of preeclampsia (PE), but the results on this issue still remained controversial. Thus, a meta-analysis was implemented to systematically investigate the roles of FOXP3 SNPs in PE. METHODS Eligible publications were identified by retrieving relevant electronic databases. Meanwhile, the association intensity was estimated by calculating odds ratios (ORs) and 95% confidence intervals (CIs) in various genetic models. RESULTS Totally eight investigations involving 3446 subjects were enrolled in the final meta-analysis. The AC and AC + CC genotypes of FOXP3 rs3761548 were related to the susceptibility of PE in over-dominant (OR = 1.19, 95%CI = 1.02-1.38, P = 0.03) and recessive (OR = 0.59, 95% CI: 0.36-0.97, P = 0.04) models. Furthermore, correlation between rs2232365 and PE was observed in recessive model (GG vs. GA + AA) (OR = 0.79, 95%CI: 0.65-0.97, P = 0.03). Moreover, rs2232365 GA and GG + GA genotypes were associated with the severity of PE. However, rs4824747, rs3761547 and rs2280883 polymorphisms had no significant impact on PE susceptibility. CONCLUSIONS FOXP3 rs3761548 and rs2232365 SNPs influenced the PE susceptibility and therefore may be potential biomarkers for prediction of PE risk.
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Affiliation(s)
- Yu-Xin Fan
- Department of Clinical Pharmacy, The 920th Hospital of Joint Logistics Support Force, Kunming, China.,College of Pharmacy, Dali University, Dali, China
| | - Jiang-Hai Wu
- Department of Clinical Pharmacy, The 920th Hospital of Joint Logistics Support Force, Kunming, China.,Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Sun-Jun Yin
- Department of Clinical Pharmacy, The 920th Hospital of Joint Logistics Support Force, Kunming, China
| | - Tao Zhou
- Department of Clinical Pharmacy, The 920th Hospital of Joint Logistics Support Force, Kunming, China
| | - Yan-Hua Huang
- Department of Clinical Pharmacy, The 920th Hospital of Joint Logistics Support Force, Kunming, China
| | - Rui Meng
- Department of Clinical Pharmacy, The 920th Hospital of Joint Logistics Support Force, Kunming, China
| | - Ping Wang
- Department of Clinical Pharmacy, The 920th Hospital of Joint Logistics Support Force, Kunming, China
| | - Gong-Hao He
- Department of Clinical Pharmacy, The 920th Hospital of Joint Logistics Support Force, Kunming, China
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Zhang T, Wang LL, Guan J, Zhou Y, Cheng P, Zou L. MicroRNA-125a/b-5p promotes malignant behavior in multiple myeloma cells and xenograft tumor growth by targeting DIS3. Kaohsiung J Med Sci 2022; 38:574-584. [PMID: 35394705 DOI: 10.1002/kjm2.12534] [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: 09/26/2021] [Revised: 12/17/2021] [Accepted: 01/26/2022] [Indexed: 11/11/2022] Open
Abstract
Multiple myeloma (MM) is a hematological malignancy with a high prevalence and is characterized by the clonal expansion of malignant plasma cells. As a new tumor suppressor, defective in sister chromatid joining (DIS3) was reported to be a gene closely related to MM. This study elucidated the biological functions and underlying mechanisms of DIS3 in MM. DIS3 mRNA and protein levels were detected using RT-qPCR and western blotting, respectively. Methyl thiazolyl tetrazolium assays, flow cytometry analyses, Transwell assays, and wound healing assays were performed to detect the proliferation, apoptosis, invasion, and migration of MM cells. The binding relationship between miR-125a/b-5p and DIS3 was verified using luciferase reporter assays and RNA pulldown assays. Xenograft tumor models were established in nude mice to investigate the effects of miR-125a/b-5p and DIS3 on tumor growth in vivo. DIS3 levels were downregulated in MM cells, and DIS3 upregulation inhibited the malignant behaviors of MM cells. Mechanistically, miR-125a/b-5p directly targeted the 3' untranslated region of DIS3. The expression of miR-125a/b-5p was upregulated in MM cells, miR-125a/b-5p knockdown inhibited the malignant behaviors of MM cells, and the inhibitory effect was reversed by DIS3 downregulation. The results of in vivo experiments indicated that miR-125a/b-5p promoted tumor growth by downregulating DIS3. Overall, miR-125a/b-5p promotes MM cellular processes and xenograft tumor growth by targeting DIS3.
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Affiliation(s)
- Ting Zhang
- Department of Hematology, Wuhan No.1 Hospital, Wuhan, China
| | - Lan-Lan Wang
- Department of Hematology, Wuhan No.1 Hospital, Wuhan, China
| | - Jun Guan
- Department of Hematology, Wuhan No.1 Hospital, Wuhan, China
| | - Ying Zhou
- Department of Hematology, Wuhan No.1 Hospital, Wuhan, China
| | - Ping Cheng
- Department of Hematology, Wuhan No.1 Hospital, Wuhan, China
| | - Liang Zou
- Department of Hematology, Wuhan No.1 Hospital, Wuhan, China
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Mahajan M, Sitasawad S. miR-140-5p Attenuates Hypoxia-Induced Breast Cancer Progression by Targeting Nrf2/HO-1 Axis in a Keap1-Independent Mechanism. Cells 2021; 11:12. [PMID: 35011574 PMCID: PMC8750786 DOI: 10.3390/cells11010012] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 11/03/2021] [Accepted: 11/04/2021] [Indexed: 01/02/2023] Open
Abstract
Hypoxia and oxidative stress significantly contribute to breast cancer (BC) progression. Although hypoxia-inducible factor 1α (Hif-1α) is considered a key effector of the cellular response to hypoxia, nuclear factor erythroid 2-related factor 2 (Nrf2), a master antioxidant transcription factor, is a crucial factor essential for Hif-1α-mediated hypoxic responses. Hence, targeting Nrf2 could provide new treatment strategies for cancer therapy. miRNAs are potential regulators of hypoxia-responsive genes. In a quest to identify novel hypoxia-regulated miRNAs involved in the regulation of Nrf2, we found that miR-140-5p significantly affects the expression of Nrf2 under hypoxia. In our study, miR-140-5p expression is downregulated in BC cells under hypoxic conditions. We have identified Nrf2 as a direct target of miR-140-5p, as confirmed by the luciferase assay. Knockdown of miR-140-5p under normoxic conditions significantly enhanced Nrf2/HO-1 signaling and tumor growth, angiogenesis, migration, and invasion in BC. In contrast, overexpression of miR-140-5p under hypoxic conditions revealed opposite results. Further silencing Nrf2 expression mimicked the miR-140-5p-induced anti-tumor effects. Consistent with the knockdown of miR-140-5p in vitro, mice injected with miR-140-5p-KD cells exhibited dramatically reduced miR-140-5p levels, increased Nrf2 levels, and increased tumor growth. In contrast, tumor growth is potently suppressed in mice injected with miR-140-5p-OE cells. Collectively, the above results demonstrate the importance of the Nrf2/HO-1 axis in cancer progression and, thus, targeting Nrf2 by miR-140-5p could be a better strategy for the treatment of Nrf2-driven breast cancer progression.
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Affiliation(s)
| | - Sandhya Sitasawad
- Redox Biology Laboratory, National Centre for Cell Science (NCCS), Pune 411007, India; or
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Norouzian M, Rahimzadeh M, Rajaee M, Arabpour F, Naderi N. FoxP3 gene promoter polymorphism affects susceptibility to preeclampsia. Hum Immunol 2016; 77:1232-1238. [PMID: 27614018 DOI: 10.1016/j.humimm.2016.09.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Revised: 07/17/2016] [Accepted: 09/06/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND Preeclampsia (PE) is a multifactorial pregnancy disorder and is a major cause of maternal morbidity and mortality. Despite intense study, the pathophysiology of preeclampsia remains enigmatic. Recent studies have reported that regulatory T cells (Tregs) is linked with PE. It is well identified that FoxP3/Scurfin is involved in development and function of Tregs. However, the association between PE and the FoxP3 gene polymorphism has not been sufficiently investigated. In this study, we hypothesized that polymorphisms of the FoxP3 may be related to PE. METHODS We assessed the relationship between four single-nucleotide polymorphisms (SNPs) in the FoxP3 genes with sequence-specific primers (PCR-SSP) in 81 PE patients and 90 age-matched controls. RESULT We identified significant difference of rs4824747 GG genotype frequency between the PE and control groups. Women with GG genotypes exhibited higher (OR=6.25, 95% CI=2.63-14.85; P<0.0001) risk of developing PE. None of the other investigated SNPs (rs2232365, rs3761547 and rs3761548) showed significant association with PE. CONCLUSION We suggest that FoxP3 polymorphisms (rs4824747) could be a potential contributor for the development of PE in Iranian women.
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Affiliation(s)
- Marzieh Norouzian
- Molecular Medicine Research Center, Department of Immunology, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mahsa Rahimzadeh
- Molecular Medicine Research Center, Department of Biochemistry, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Minoo Rajaee
- Department of Midwifery, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Fahimeh Arabpour
- Molecular Medicine Research Center, Department of Immunology, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Nadereh Naderi
- Molecular Medicine Research Center, Department of Immunology, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran.
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Guo L, Tsai SQ, Hardison NE, James AH, Motsinger-Reif AA, Thames B, Stone EA, Deng C, Piedrahita JA. Differentially expressed microRNAs and affected biological pathways revealed by modulated modularity clustering (MMC) analysis of human preeclamptic and IUGR placentas. Placenta 2013; 34:599-605. [PMID: 23639576 DOI: 10.1016/j.placenta.2013.04.007] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 03/25/2013] [Accepted: 04/05/2013] [Indexed: 01/12/2023]
Abstract
INTRODUCTION This study focuses on the implementation of modulated modularity clustering (MMC) a new cluster algorithm for the identification of molecular signatures of preeclampsia and intrauterine growth restriction (IUGR), and the identification of affected microRNAs METHODS Eighty-six human placentas from normal (40), growth-restricted (27), and preeclamptic (19) term pregnancies were profiled using Illumina Human-6 Beadarrays. MMC was utilized to generate modules based on similarities in placental transcriptome. Gene Set Enrichment Analysis (GSEA) was used to predict affected microRNAs. Expression levels of these candidate microRNAs were investigated in seventy-one human term placentas as follows: control (29); IUGR (26); and preeclampsia (16). RESULTS MMC identified two modules, one representing IUGR placentas and one representing preeclamptic placentas. 326 differentially expressed genes in the module representing IUGR and 889 differentially expressed genes in a module representing preeclampsia were identified. Functional analysis of molecular signatures associated with IUGR identified P13K/AKT, mTOR, p70S6K, apoptosis and IGF-1 signaling as being affected. Analysis of variance of GSEA-predicted microRNAs indicated that miR-194 was significantly down-regulated both in preeclampsia (p = 0.0001) and IUGR (p = 0.0304), and miR-149 was significantly down-regulated in preeclampsia (p = 0.0168). DISCUSSION Implementation of MMC, allowed identification of genes disregulated in IUGR and preeclampsia. The reliability of MMC was validated by comparing to previous linear modeling analysis of preeclamptic placentas. CONCLUSION MMC allowed the elucidation of a molecular signature associated with preeclampsia and a subset of IUGR samples. This allowed the identification of genes, pathways, and microRNAs affected in these diseases.
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Affiliation(s)
- L Guo
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, USA
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