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Asberger J, Berner K, Bicker A, Metz M, Jäger M, Weiß D, Kreutz C, Juhasz-Böss I, Mayer S, Ge I, Erbes T. In Vitro microRNA Expression Profile Alterations under CDK4/6 Therapy in Breast Cancer. Biomedicines 2023; 11:2705. [PMID: 37893081 PMCID: PMC10604872 DOI: 10.3390/biomedicines11102705] [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: 07/25/2023] [Revised: 09/16/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Breast cancer is the most common type of cancer worldwide. Cyclin-dependent kinase inhibition is one of the backbones of metastatic breast cancer therapy. However, there are a significant number of therapy failures. This study evaluates the biomarker potential of microRNAs for the prediction of a therapy response under cyclin-dependent kinase inhibition. METHODS This study comprises the analysis of intracellular and extracellular microRNA-expression-level alterations of 56 microRNAs under palbociclib mono as well as combination therapy with letrozole. Breast cancer cell lines BT-474, MCF-7 and HS-578T were analyzed using qPCR. RESULTS A palbociclib-induced microRNA signature could be detected intracellularly as well as extracellularly. Intracellular miR-10a, miR-15b, miR-21, miR-23a and miR-23c were constantly regulated in all three cell lines, whereas let-7b, let-7d, miR-15a, miR-17, miR-18a, miR-20a, miR-191 and miR301a_3p were regulated only in hormone-receptor-positive cells. Extracellular miR-100, miR-10b and miR-182 were constantly regulated across all cell lines, whereas miR-17 was regulated only in hormone-receptor-positive cells. CONCLUSIONS Because they are secreted and significantly upregulated in the microenvironment of tumor cells, miRs-100, -10b and -182 are promising circulating biomarkers that can be used to predict or detect therapy responses under CDK inhibition. MiR-10a, miR-15b, miR-21, miR-23a and miR-23c are potential tissue-based biomarkers.
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Affiliation(s)
- Jasmin Asberger
- Department of Obstetrics and Gynecology, Medical Center—University Hospital Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Kai Berner
- Department of Obstetrics and Gynecology, Medical Center—University Hospital Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Anna Bicker
- Department of Obstetrics and Gynecology, Medical Center—University Hospital Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Department of Obstetrics and Gynecology, St. Josefs-Hospital Wiesbaden, 65189 Wiesbaden, Germany
| | - Marius Metz
- Department of Obstetrics and Gynecology, Medical Center—University Hospital Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Markus Jäger
- Department of Obstetrics and Gynecology, Medical Center—University Hospital Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Daniela Weiß
- Department of Obstetrics and Gynecology, Medical Center—University Hospital Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Clemens Kreutz
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Institute of Medical Biometry and Statistics, Medical Center – University of Freiburg, 79104 Freiburg, Germany
| | - Ingolf Juhasz-Böss
- Department of Obstetrics and Gynecology, Medical Center—University Hospital Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
| | - Sebastian Mayer
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Department of Gynaecology and Obstetrics, Hospital Krumbach, 86381 Krumbach, Germany
| | - Isabell Ge
- Department of Obstetrics and Gynecology, Medical Center—University Hospital Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Department of Obstetrics and Gynaecology, University Hospital of Basel, 4056 Basel, Switzerland
| | - Thalia Erbes
- Department of Obstetrics and Gynecology, Medical Center—University Hospital Freiburg, 79106 Freiburg, Germany
- Faculty of Medicine, University of Freiburg, 79106 Freiburg, Germany
- Department of Gynaecology and Obstetrics, Diako Mannheim, 68135 Mannheim, Germany
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2
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El-Husseiny AA, Abdelmaksoud NM, Mageed SSA, Salman A, Zaki MB, El-Mahdy HA, Ismail A, Abd-Elmawla MA, El-Husseiny HM, Abulsoud AI, Elshaer SS, Elsakka EGE, Fathi D, El-Dakroury WA, Doghish AS. miRNAs orchestration of salivary gland cancer- Particular emphasis on diagnosis, progression, and drug resistance. Pathol Res Pract 2023; 248:154590. [PMID: 37295259 DOI: 10.1016/j.prp.2023.154590] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 05/31/2023] [Accepted: 06/03/2023] [Indexed: 06/12/2023]
Abstract
Cancer of the salivary glands is one of the five major types of head and neck cancer. Due to radioresistance and a strong propensity for metastasis, the survival rate for nonresectable malignant tumors is dismal. Hence, more research is needed on salivary cancer's pathophysiology, particularly at the molecular level. The microRNAs (miRNAs) are a type of noncoding RNA that controls as many as 30% of all genes that code for proteins at the posttranscriptional level. Signature miRNA expression profiles have been established in several cancer types, suggesting a role for miRNAs in the incidence and progression of human malignancies. Salivary cancer tissues were shown to have significantly aberrant levels of miRNAs compared to normal salivary gland tissues, supporting the hypothesis that miRNAs play a crucial role in the carcinogenesis of salivary gland cancer (SGC). Besides, several SGC research articles reported potential biomarkers and therapeutic targets for the miRNA-based treatment of this malignancy. In this review, we will explore the regulatory impact of miRNAs on the processes underlying the molecular pathology of SGC and provide an up-to-date summary of the literature on miRNAs that impacted this malignancy. We will eventually share information about their possible use as diagnostic, prognostic, and therapeutic biomarkers in SGC.
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Affiliation(s)
- Ahmed A El-Husseiny
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt; Department of Biochemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City 11829, Cairo, Egypt
| | - Nourhan M Abdelmaksoud
- Department of Biochemistry, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Sherif S Abdel Mageed
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Aya Salman
- Department of Biochemistry, Faculty of Pharmacy, Egyptian Russian University, Badr City 11829, Cairo, Egypt
| | - Mohamed Bakr Zaki
- Department of Biochemistry, Faculty of Pharmacy, University of Sadat City, Menoufia 32897, Egypt
| | - Hesham A El-Mahdy
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Ahmed Ismail
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Mai A Abd-Elmawla
- Department of Biochemistry, Faculty of Pharmacy, Cairo University, Cairo, Egypt
| | - Hussein M El-Husseiny
- Department of Surgery, Anesthesiology, and Radiology, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh, Elqaliobiya, 13736, Egypt; Cooperative Department of Veterinary Medicine, Faculty of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai Cho, Fuchu-shi, Tokyo 183-8509, Japan
| | - Ahmed I Abulsoud
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt; Department of Biochemistry, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt.
| | - Shereen Saeid Elshaer
- Department of Biochemistry, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt; Department of Biochemistry and Molecular Biology, Faculty of Pharmacy (Girls), Al-Azhar University, Nasr city, Cairo 11823, Egypt
| | - Elsayed G E Elsakka
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt
| | - Doaa Fathi
- Department of Biochemistry, Faculty of Pharmacy, Heliopolis University, Cairo 11785, Egypt
| | - Walaa A El-Dakroury
- Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt
| | - Ahmed S Doghish
- Department of Biochemistry, Faculty of Pharmacy, Badr University in Cairo (BUC), Badr City, Cairo 11829, Egypt; Faculty of Pharmacy (Boys), Al-Azhar University, Nasr City 11231, Cairo, Egypt.
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3
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Fariha A, Hami I, Tonmoy MIQ, Akter S, Al Reza H, Bahadur NM, Rahaman MM, Hossain MS. Cell cycle associated miRNAs as target and therapeutics in lung cancer treatment. Heliyon 2022; 8:e11081. [PMID: 36303933 PMCID: PMC9593298 DOI: 10.1016/j.heliyon.2022.e11081] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 08/17/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022] Open
Abstract
Lung cancer is the primary cause of cancer related deaths worldwide. Limited therapeutic options and resistance to existing drugs are the major hindrances to the clinical success of this cancer. In the past decade, several studies showed the role of microRNA (miRNA) driven cell cycle regulation in lung cancer progression. Therefore, these small nucleotide molecules could be utilized as promising tools in lung cancer therapy. In this review, we highlighted the recent advancements in lung cancer therapy using cell cycle linked miRNAs. By highlighting the roles of the specific cell cycle core regulators affiliated miRNAs in lung cancer, we further outlined how these miRNAs can be explored in early diagnosis and treatment strategies to prevent lung cancer. With the provided information from our review, more medical efforts can ensure a potential breakthrough in miRNA-based lung cancer therapy.
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Affiliation(s)
- Atqiya Fariha
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Ithmam Hami
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | | | - Shahana Akter
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Hasan Al Reza
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | - Newaz Mohammed Bahadur
- Department of Applied Chemistry and Chemical Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md. Mizanur Rahaman
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh,Corresponding author.
| | - Md Shahadat Hossain
- Department of Biotechnology & Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh,Corresponding author.
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4
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De Santis C, Götte M. The Role of microRNA Let-7d in Female Malignancies and Diseases of the Female Reproductive Tract. Int J Mol Sci 2021; 22:ijms22147359. [PMID: 34298978 PMCID: PMC8305730 DOI: 10.3390/ijms22147359] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 02/06/2023] Open
Abstract
microRNAs are small noncoding RNAs that regulate gene expression at the posttranscriptional level. Let-7d is a microRNA of the conserved let-7 family that is dysregulated in female malignancies including breast cancer, ovarian cancer, endometrial cancer, and cervical cancer. Moreover, a dysregulation is observed in endometriosis and pregnancy-associated diseases such as preeclampsia and fetal growth restriction. Let-7d expression is regulated by cytokines and steroids, involving transcriptional regulation by OCT4, MYC and p53, as well as posttranscriptional regulation via LIN28 and ADAR. By downregulating a wide range of relevant mRNA targets, let-7d affects cellular processes that drive disease progression such as cell proliferation, apoptosis (resistance), angiogenesis and immune cell function. In an oncological context, let-7d has a tumor-suppressive function, although some of its functions are context-dependent. Notably, its expression is associated with improved therapeutic responses to chemotherapy in breast and ovarian cancer. Studies in mouse models have furthermore revealed important roles in uterine development and function, with implications for obstetric diseases. Apart from a possible utility as a diagnostic blood-based biomarker, pharmacological modulation of let-7d emerges as a promising therapeutic concept in a variety of female disease conditions.
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MESH Headings
- Aging
- Animals
- Biomarkers
- Biomarkers, Tumor
- Breast Neoplasms/drug therapy
- Breast Neoplasms/genetics
- Cell Line, Tumor
- Female
- Fertility/genetics
- Gene Expression Regulation
- Gene Expression Regulation, Neoplastic
- Genes, Tumor Suppressor
- Genital Diseases, Female/drug therapy
- Genital Diseases, Female/genetics
- Genital Neoplasms, Female/drug therapy
- Genital Neoplasms, Female/genetics
- Humans
- Mice
- MicroRNAs/genetics
- MicroRNAs/physiology
- Molecular Targeted Therapy
- Pregnancy
- Pregnancy Complications/genetics
- RNA, Neoplasm/antagonists & inhibitors
- RNA, Neoplasm/genetics
- RNA, Neoplasm/physiology
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5
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Ghafouri-Fard S, Shoorei H, Anamag FT, Taheri M. The Role of Non-Coding RNAs in Controlling Cell Cycle Related Proteins in Cancer Cells. Front Oncol 2020; 10:608975. [PMID: 33330110 PMCID: PMC7734207 DOI: 10.3389/fonc.2020.608975] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 10/27/2020] [Indexed: 12/12/2022] Open
Abstract
Cell cycle is regulated by a number of proteins namely cyclin-dependent kinases (CDKs) and their associated cyclins which bind with and activate CDKs in a phase specific manner. Additionally, several transcription factors (TFs) such as E2F and p53 and numerous signaling pathways regulate cell cycle progression. Recent studies have accentuated the role of long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) in the regulation of cell cycle. Both lncRNAs and miRNAs interact with TFs participating in the regulation of cell cycle transition. Dysregulation of cell cycle regulatory miRNAs and lncRNAs results in human disorders particularly cancers. Understanding the role of lncRNAs, miRNAs, and TFs in the regulation of cell cycle would pave the way for design of anticancer therapies which intervene with the cell cycle progression. In the current review, we describe the role of lncRNAs and miRNAs in the regulation of cell cycle and their association with human malignancies.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamed Shoorei
- Department of Anatomical Sciences, Faculty of Medicine, Birjand University of Medical Sciences, Birjand, Iran
| | | | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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6
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Ren M, Yang L, Li D, Yang L, Su Y, Su X. Cell Cycle Regulation by Berberine in Human Melanoma A375 Cells. Bull Exp Biol Med 2020; 169:491-496. [PMID: 32915362 DOI: 10.1007/s10517-020-04916-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Indexed: 01/24/2023]
Abstract
We studied the effects of berberine on the proliferation, apoptosis, and migration of skin melanoma A375 cells, as well as cell cycle-related miRNAs and their target genes, CDK1, CDK2, and cyclins D1 and A. The inhibitory effect of berberine on the growth of A375 cells was evaluated by MTT assay. Cell apoptosis was detected by trypan blue staining. Cell migration was assessed by the scratch test. Cell cycle phases were determined by flow cytometry. The levels of miRNA-582-5p and miRNA-188-5, and mRNA of their target genes encoding CDK1, CDK2, and cyclins D1 and A were measured by qRT-PCR. The expression of cell cycle-related proteins (CDK1, CDK2, and cyclins D1 and A) was determined by Western blotting. Berberine inhibited the proliferation of A375 cells in a time- and dose-dependent manner and significantly and dose-dependently enhanced cell apoptosis. Scratch assay showed an inhibitory effect of berberine on migration of A375 cells. Berberine in low concentrations (20 and 40 μM) caused cell cycle arrest in the S and G2/M phases, while treatment with high concentrations of berberine (60 and 80 μM) arrested cell-cycle in the G2/M phase. The increase in berberine concentration led to an increase in miRNA-582-5p and miRNA-188-5p expression and a decrease in the expression of mRNA for the corresponding target genes encoding CDK1, CDK2, and cyclins D1 and A. Western blotting also revealed reduced expression of CDK1, CDK2, and cyclins D1 and A. Thus, berberine suppressed the growth and migration of human melanoma cells and promoted their apoptosis. Berberine can increase the expression of cell cycle-related miRNAs and cause degradation of the corresponding target genes, thereby blocking the cell cycle progression and inhibiting the melanoma A375 cells.
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Affiliation(s)
- Min Ren
- Department of Dermatology, Affiliated Hospital of Inner Mongolia Medical University, Huhhot, Inner Mongolia, P.R. China
| | - Lihui Yang
- Department of Dermatology, Affiliated Hospital of Inner Mongolia Medical University, Huhhot, Inner Mongolia, P.R. China
| | - Dongxia Li
- Department of Dermatology, Affiliated Hospital of Inner Mongolia Medical University, Huhhot, Inner Mongolia, P.R. China.
| | - Ling Yang
- Clinical Medical Research Center, Inner Mongolia Medical University, Huhhot, Inner Mongolia, P.R. China
| | - Yila Su
- Clinical Medical Research Center, Inner Mongolia Medical University, Huhhot, Inner Mongolia, P.R. China
| | - Xiulan Su
- Clinical Medical Research Center, Inner Mongolia Medical University, Huhhot, Inner Mongolia, P.R. China
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7
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Modulatory Effect of Indoles on the Expression of miRNAs Regulating G1/S Cell Cycle Phase in Breast Cancer Cells. Appl Biochem Biotechnol 2020; 192:1208-1223. [PMID: 32710170 DOI: 10.1007/s12010-020-03378-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/23/2020] [Indexed: 12/13/2022]
Abstract
Indole-3-carbinol (I3C) is a naturally occurring glucosinolate found in Brassica vegetables that is usually converted in gastric acidic environment to the efficient metabolite 3,3'-diindolylmethane (DIM). Both indoles (I3C and DIM) are known chemopreventive agents for various cancers including breast cancer. This study aimed to investigate the influence of both indoles on the tumor suppressor miRNAs (let-7a-e, miR-15a, miR-16, miR-17-5p, miR-19a, and miR-20a) and oncomiRs (miR-181a, miR-181b, miR-210, miR-221, and miR-106a), which are controlling the cell cycle key regulators: cyclin-dependent kinases (CDKs), CDK inhibitor p27Kip1, and cyclin D1. Our results indicated that both indoles generally elevated the expression of the tumor suppressor miRNAs let-7a-e, miR-19a, miR-17-5p, and miR-20a and decreased the expression of the oncomiR list. Both indoles were able to significantly suppress the expression of CDK4 and CDK6 as well as the apoptotic markers Bcl-2 and survivin. Both indoles decreased cyclin-D1 protein, where I3C decreased cytoplasmic and nuclear cyclin-D1 significantly. Cytoplasmic and nuclear P27Kip1 showed overexpression following treatment with I3C higher than that detected following DIM treatment. This study provides a mechanistic elucidation of the previously reported cell cycle arrest by I3C and DIM in breast cancer cells suggesting that this effect could be through modulation of miRNAs expression that, in turn, regulates the genetic network controlling the G1/S phase in cell cycle progression.
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8
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Behl T, Kumar C, Makkar R, Gupta A, Sachdeva M. Intercalating the Role of MicroRNAs in Cancer: As Enemy or Protector. Asian Pac J Cancer Prev 2020; 21:593-598. [PMID: 32212783 PMCID: PMC7437313 DOI: 10.31557/apjcp.2020.21.3.593] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Indexed: 12/18/2022] Open
Abstract
Objective: The transformation in cells at genetic levels stimulatesthe proliferation of cancer. The current review highlights the role of miRNA in management of cancer by altering processes of body at cellular levels. Methods: A deep research on the literature available till date for miRNA in cancer was conducted using various medical sites like PubMed, MEDLINE from internet and data was collected. The articles were majorly preferred in English language. Results: The development of normal cells into cancerous cells is a multivalent procedure highlighting numerous responsible factors. During the progression of cancer, the role of oncogene and tumor suppressor genes outshines at different levels of tumorogenesis. Metastasis poses highest threat in cancer progression and fabricates obstacles to clinicians and researchers in preventing formation of tumor on secondary sites. The mesenchymal-epithelial transition (MET) and epithelial mesenchymal transition (EMT) induce dissemination and ultimately progression of cancer. Conclusion: A comprehensive knowledge of the altered genes and the mechanism by which they induce formation of tumor is essential as they contribute in proliferating cancer at various stages, aggravating clinical symptoms. Hence miRNAs can be efficiently employed as an emerging treatment therapy for cancer.
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Affiliation(s)
- Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Chanchal Kumar
- Vallabhbhai Patel Chest Institute, University of Delhi, Delhi, India
| | - Rashita Makkar
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Amit Gupta
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
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9
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Guo ZH, You ZH, Yi HC. Integrative Construction and Analysis of Molecular Association Network in Human Cells by Fusing Node Attribute and Behavior Information. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 19:498-506. [PMID: 31923739 PMCID: PMC6951835 DOI: 10.1016/j.omtn.2019.10.046] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/07/2019] [Accepted: 10/21/2019] [Indexed: 11/27/2022]
Abstract
Detecting whether a pair of biomolecules associate is of great significance in the study of molecular biology. Hence, computational methods are urgently needed as guidance for practice. However, most of the previous prediction models influenced by reductionism focused on isolated research objects, which have their own inherent defects. Inspired by holism, a machine-learning-based framework called MAN-node2vec is proposed to predict multi-type relationships in the molecular associations network (MAN). Specifically, we constructed a large-scale MAN composed of 1,023 miRNAs, 1,649 proteins, 769 long non-coding RNAs (lncRNAs), 1,025 drugs, and 2,062 diseases. Then, each biomolecule in MAN can be represented as a vector by its attribute learned by k-mer, etc. and its behavior learned by node2vec. Finally, the random forest classifier is applied to carry out the relationship prediction task. The proposed model achieved a reliable performance with 0.9677 areas under the curve (AUCs) and 0.9562 areas under the precision curve (AUPRs) under 5-fold cross-validation. Also, additional experiments proved that the proposed global model shows more competitive performance than the traditional local method. All of these provided a systematic insight for understanding the synergistic interactions between various molecules and diseases. It is anticipated that this work can bring beneficial inspiration and advance to related systems biology and biomedical research.
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Affiliation(s)
- Zhen-Hao Guo
- Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhu-Hong You
- Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Hai-Cheng Yi
- Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi 830011, China; University of Chinese Academy of Sciences, Beijing 100049, China
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10
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Wu L, Yang K, Gui Y, Wang X. Nicotine-upregulated miR-30a arrests cell cycle in G1 phase by directly targeting CCNE2 in human periodontal ligament cells. Biochem Cell Biol 2019; 98:354-361. [PMID: 31689122 DOI: 10.1139/bcb-2019-0156] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The consumption of nicotine via smoking tobacco has been reported to stimulate the occurrence and progression of periodontitis. Many studies have demonstrated that nicotine prevents the regeneration of periodontal tissues primarily by inhibiting the proliferation of human periodontal ligament (PDL) cells. However, the mechanisms underlying this process are still unclear. Therefore, we investigated whether nicotine-upregulated miR-30a inhibited the proliferation of human PDL cells by downregulating cyclin E2 (CCNE2), in vitro. Quantitative real-time PCR analysis revealed that nicotine upregulated the expression of miR-30a in human PDL cells. In addition, nicotine inhibited the proliferation of human PDL cells by inducing cell cycle arrest. To support this hypothesis, we showed that nicotine downregulated the expression of CCNE2 in human PDL cells, whereas inhibition of miR-30a restored CCNE2 expression that had been downregulated by nicotine. Furthermore, using luciferase reporter assays, we found that miR-30a directly interacts with the CCNE2 3'UTR. In conclusion, these findings indicate that nicotine-upregulated miR-30a inhibits the proliferation of human PDL cells by downregulating the expression of CCNE2.
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Affiliation(s)
- Lizheng Wu
- Department of Stomatology, Characteristic Medical Center of the Chinese people's Armed Police Force, Tianjin, China.,State Key Laboratory of Military Stomatology, Department of Pediatric Dentistry, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Kuan Yang
- Department of Orthodontics, College of Stomatology, Xi'an Jiaotong University
| | - Yajie Gui
- Department of Stomatology, Characteristic Medical Center of the Chinese people's Armed Police Force, Tianjin, China
| | - Xiaojing Wang
- State Key Laboratory of Military Stomatology, Department of Pediatric Dentistry, School of Stomatology, The Fourth Military Medical University, Xi'an, Shaanxi, China
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11
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Chou CH, Shrestha S, Yang CD, Chang NW, Lin YL, Liao KW, Huang WC, Sun TH, Tu SJ, Lee WH, Chiew MY, Tai CS, Wei TY, Tsai TR, Huang HT, Wang CY, Wu HY, Ho SY, Chen PR, Chuang CH, Hsieh PJ, Wu YS, Chen WL, Li MJ, Wu YC, Huang XY, Ng FL, Buddhakosai W, Huang PC, Lan KC, Huang CY, Weng SL, Cheng YN, Liang C, Hsu WL, Huang HD. miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions. Nucleic Acids Res 2019; 46:D296-D302. [PMID: 29126174 PMCID: PMC5753222 DOI: 10.1093/nar/gkx1067] [Citation(s) in RCA: 1256] [Impact Index Per Article: 251.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 10/25/2017] [Indexed: 01/16/2023] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs of ∼ 22 nucleotides that are involved in negative regulation of mRNA at the post-transcriptional level. Previously, we developed miRTarBase which provides information about experimentally validated miRNA-target interactions (MTIs). Here, we describe an updated database containing 422 517 curated MTIs from 4076 miRNAs and 23 054 target genes collected from over 8500 articles. The number of MTIs curated by strong evidence has increased ∼1.4-fold since the last update in 2016. In this updated version, target sites validated by reporter assay that are available in the literature can be downloaded. The target site sequence can extract new features for analysis via a machine learning approach which can help to evaluate the performance of miRNA-target prediction tools. Furthermore, different ways of browsing enhance user browsing specific MTIs. With these improvements, miRTarBase serves as more comprehensively annotated, experimentally validated miRNA-target interactions databases in the field of miRNA related research. miRTarBase is available at http://miRTarBase.mbc.nctu.edu.tw/.
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Affiliation(s)
- Chih-Hung Chou
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Sirjana Shrestha
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Chi-Dung Yang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Institute of Population Health Sciences, National Health Research Institutes, Miaoli, 350, Taiwan
| | - Nai-Wen Chang
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 106, Taiwan
| | - Yu-Ling Lin
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Center for Bioinformatics Research, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Kuang-Wen Liao
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Wei-Chi Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Ting-Hsuan Sun
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Siang-Jyun Tu
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Wei-Hsiang Lee
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Clinical Research Center, Chung Shan Medical University Hospital, Taichung, 402, Taiwan
| | - Men-Yee Chiew
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Chun-San Tai
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Ting-Yen Wei
- Interdisciplinary Program of Life Science, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Tzi-Ren Tsai
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Hsin-Tzu Huang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Chung-Yu Wang
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Hsin-Yi Wu
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Shu-Yi Ho
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Pin-Rong Chen
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Cheng-Hsun Chuang
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Pei-Jung Hsieh
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Yi-Shin Wu
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Wen-Liang Chen
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Meng-Ju Li
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Department of Pediatrics, National Taiwan University Hospital Hsinchu Branch, Hsinchu, 300, Taiwan
| | - Yu-Chun Wu
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Xin-Yi Huang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Fung Ling Ng
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Waradee Buddhakosai
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Pei-Chun Huang
- Delivery Room, Department of Nursing, National Taiwan University Hospital Hsinchu Branch, Hsinchu, 300, Taiwan
| | - Kuan-Chun Lan
- Institute of Molecular Medicine and Bioengineering, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Chia-Yen Huang
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Gynecologic Cancer Center, Department of Obstetrics and Gynecology, Cathay General Hospital, Taipei, 106, Taiwan
| | - Shun-Long Weng
- Department of Obstetrics and Gynecology, Hsinchu Mackay Memorial Hospital, Hsinchu, 300, Taiwan.,Mackay Medicine, Nursing and Management College, Taipei, 112, Taiwan.,Department of Medicine, Mackay Medical College, New Taipei City, 252, Taiwan
| | - Yeong-Nan Cheng
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Chao Liang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan
| | - Wen-Lian Hsu
- Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan
| | - Hsien-Da Huang
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Department of Biological Science and Technology, National Chiao Tung University, Hsinchu, 300, Taiwan.,Warshel Institute for Computational Biology, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong Province, 518172, China.,School of Science and Engineering, The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong Province, 518172, China
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12
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Cui X, Guo Y, Wang Q, Li X. MiR‐199‐3p–Dnmt3a–STAT3 signalling pathway in ovalbumin‐induced allergic rhinitis. Exp Physiol 2019; 104:1286-1295. [PMID: 31124216 DOI: 10.1113/ep087751] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 05/23/2019] [Indexed: 12/12/2022]
Affiliation(s)
- Xinhua Cui
- Department of Otolaryngology–Head and Neck SurgeryQianfoshan Hospital Affiliated to Shandong University 16766 Jingshi Road Jinan 250014 Shandong China
- Department of Otolaryngology–Head and Neck SurgeryQilu Hospital of Shandong University, NHC key laboratory of Otolaryngology 107 West Wenhua Road Jinan 250012 Shandong China
| | - Ying Guo
- Department of Otolaryngology–Head and Neck SurgeryQianfoshan Hospital Affiliated to Shandong University 16766 Jingshi Road Jinan 250014 Shandong China
| | - Qirong Wang
- Department of Otolaryngology–Head and Neck SurgeryQianfoshan Hospital Affiliated to Shandong University 16766 Jingshi Road Jinan 250014 Shandong China
| | - Xuezhong Li
- Department of Otolaryngology–Head and Neck SurgeryQilu Hospital of Shandong University, NHC key laboratory of Otolaryngology 107 West Wenhua Road Jinan 250012 Shandong China
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13
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Chen S, Chen Y, Gao Y, Zuo Y, Zhou X. Effect of single-nucleotide polymorphism in pri-microRNA-124 on poststroke motor function recovery. J Cell Biochem 2019; 120:7125-7132. [PMID: 30548296 DOI: 10.1002/jcb.27986] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 10/08/2018] [Indexed: 01/24/2023]
Abstract
BACKGROUND Stroke is a leading cause of long-term disability and further one of the main causes of motor impairment. The current study aimed to investigate whether miR-124 polymorphism (rs531564) influences the motor function of patients after stroke. METHODS In total, 56 patients with stroke-induced motor dysfunction were enrolled. Box and block test (BBT) and Fugl-Meyer assessment (FMA) were performed to evaluate the motor functions in all participants. Computation analysis, luciferase activity, PCR assays, and Western blot analysis were performed to reveal the molecular mechanism underlying the effect of miR-124 polymorphism on motor functions. RESULTS The 56 participants were genotyped as CC, CG, and GG, respectively. The serum miR-124 was significantly upregulated in the CC group than that in the GC and GG groups. According to the result of FMA or BBT, there was no obvious difference in upper and lower limb motor functions between CC and CG/GG groups 1 week after the treatment. In addition, scores of BBT and FMA exhibited apparent improvement in both groups at 1 month and 3 months after the treatment. Furthermore, improvements in the CG/GG groups were more significant as compared with those in the CC group. CDK4 was a target of miR-124, and the effect of miR-124 on the motor function recovery might be mediated by CDK4. CONCLUSION The presence of a minor allele, G, of miR-124 polymorphism (rs531564) reduced the expression of miRNA and upregulated the expression of CDK4, which may contribute to the effect of rs531564 on the motor function recovery in poststroke patients.
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Affiliation(s)
- Shangjun Chen
- Neurosurgery Department, No. 215 Hospital of Shaanxi Nuclear Industry, Xianyang, Shaanxi, China
| | - Yuhong Chen
- Neurosurgery Department, People's Hospital of Tongchuan, Tongchuan, Shaanxi, China
| | - Yadong Gao
- Neurosurgery Department, People's Hospital of Tongchuan, Tongchuan, Shaanxi, China
| | - Yi Zuo
- Neurosurgery Department, No. 215 Hospital of Shaanxi Nuclear Industry, Xianyang, Shaanxi, China
| | - Xiaowei Zhou
- Neurosurgery Department, No. 215 Hospital of Shaanxi Nuclear Industry, Xianyang, Shaanxi, China
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14
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Tetik Vardarlı A, Düzgün Z, Erdem C, Kaymaz BT, Eroglu Z, Çetintas VB. Matrine induced G0/G1 arrest and apoptosis in human acute T-cell lymphoblastic leukemia (T-ALL) cells. Bosn J Basic Med Sci 2018; 18:141-149. [PMID: 29045804 DOI: 10.17305/bjbms.2017.2457] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/08/2017] [Accepted: 10/09/2017] [Indexed: 12/13/2022] Open
Abstract
Matrine, a natural product extracted from the root of Sophora flavescens, is a promising alternative drug in different types of cancer. Here, we aimed to investigate the therapeutic effects and underlying molecular mechanisms of matrine on human acute lymphoblastic leukemia (ALL) cell line, CCRF-CEM. Cell viability and IC50 values were determined by WST-1 cell cytotoxicity assay. Cell cycle distribution and apoptosis rates were analyzed by flow cytometry. Expression patterns of 44 selected miRNAs and 44 RNAs were analyzed by quantitative reverse transcription polymerase chain reaction (qRT-PCR) using the Applied Biosystems 7500 Fast Real-Time PCR System. Matrine inhibited cell viability and induced apoptosis of CCRF-CEM cells in a dose-dependent manner. Cell cycle analysis demonstrated that matrine-treated CCRF-CEM cells significantly accumulated in the G0/G1 phase compared with the untreated control cells. hsa-miR-376b-3p (-37.09 fold, p = 0.008) and hsa-miR-106b-3p (-16.67 fold, p = 0.028) expressions were decreased, whereas IL6 (95.47 fold, p = 0.000011) and CDKN1A (140.03 fold, p = 0.000159) expressions were increased after matrine treatment. Our results suggest that the downregulation of hsa-miR-106b-3p leads to the upregulation of target p21 gene, CDKN1A, and plays a critical role in the cell cycle progression by arresting matrine-treated cells in the G0/G1 phase.
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15
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Mullany LE, Herrick JS, Sakoda LC, Samowitz W, Stevens JR, Wolff RK, Slattery ML. miRNA involvement in cell cycle regulation in colorectal cancer cases. Genes Cancer 2018; 9:53-65. [PMID: 29725503 PMCID: PMC5931252 DOI: 10.18632/genesandcancer.167] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Uncontrolled cell replication is a key component of carcinogenesis. MicroRNAs (miRNAs) regulate genes involved in checkpoints, DNA repair, and genes encoding for key proteins regulating the cell cycle. We investigated how miRNAs and mRNAs in colorectal cancer subjects interact to regulate the cell cycle. Using RNA-Seq data from 217 individuals, we analyzed differential expression (carcinoma minus normal mucosa) of 123 genes within the cell cycle pathway with differential miRNA expression, adjusting for age and sex. Multiple comparison adjustments for gene/miRNA associations were made at the gene level using an FDR <0.05. Differentially expressed miRNAs and mRNAs were tested for associations with colorectal cancer survival. MRNA and miRNA sequences were compared to identify seed region matches to support biological interpretation of the observed associations. Sixty-seven mRNAs were dysregulated with a fold change (FC) <0.67 or >1.50. Thirty-two mRNAs were associated with 48 miRNAs; 102 of 290 total associations had identified seed matches; of these, ten had negative beta coefficients. Hsa-miR-15a-5p and hsa-miR-20b-5p were associated with colorectal cancer survival with an FDR <0.05 (HR 0.86 95% CI 0.79, 0.94; HR 0.83 95% CI 0.75, 0.91 respectively). Our findings suggest that miRNAs impact mRNA translation at multiple levels within the cell cycle.
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Affiliation(s)
- Lila E Mullany
- Division of Epidemiology, University of Utah, Salt Lake City, Ut, USA
| | | | - Lori C Sakoda
- Division of Research, Kaiser Permanente Northern California, CA, USA
| | - Wade Samowitz
- Department of Pathology, University of Utah, Salt Lake City, Ut, USA
| | - John R Stevens
- Department of Mathematics and Statistics, Utah State University, Logan, Ut, USA
| | - Roger K Wolff
- Division of Epidemiology, University of Utah, Salt Lake City, Ut, USA
| | - Martha L Slattery
- Division of Epidemiology, University of Utah, Salt Lake City, Ut, USA
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16
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Different levels of let-7d expression modulate response of FaDu cells to irradiation and chemotherapeutics. PLoS One 2017; 12:e0180265. [PMID: 28665983 PMCID: PMC5493379 DOI: 10.1371/journal.pone.0180265] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 06/13/2017] [Indexed: 12/19/2022] Open
Abstract
The implication of the let-7 family in cancer development is multifaceted. The family acts as tumor suppressor miRNA although overexpression of let-7 has also been described in many types of cancer, including head and neck squamous cell carcinoma (HNSCC). The aim of this study includes whether different expression levels of let-7d has an influence on chemo- and radiosensitivity. FaDu cell line models with a gradually increased level of let-7d (models from A to E) were generated with the lentiviral system. Expression levels of pluripotency, chemo-radioresistance/apoptosis, and targets of mRNAs were analyzed by real-time reverse transcription-PCR (qRT-PCR). Radiosensitivity was analyzed using a clonogenic assay after irradiation. Response to cisplatin, 5-FU, doxorubicin, and paclitaxel was done with MTT assay. Statistically significant decrease of K-RAS (p = 0.0369) and CASPASE3 (p = 0.0342) were observed with the growing expression level of let-7d. Cisplatin, 5-FU and doxorubicin caused similar decreased of cell survival with the increase of let-7d level (p = 0.004, post-trend p = 0.046; p = 0.004, post trend p = 0.0005 and p<0.0001, post trend p = 0.0001, respectively). All models were resistant to paclitaxel, irrespective of let-7d expression levels. Only two of the generated models (A and C) were radiosensitive (p = 0.0002). Conclusion: the above results indicated that the level of let-7d expression is an important factor for cell response to irradiation and chemotherapeutics.
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17
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Pujol-López M, Ortega-Paz L, Garabito M, Brugaletta S, Sabaté M, Paula Dantas A. miRNA Update: A Review Focus on Clinical Implications of miRNA in Vascular Remodeling. AIMS MEDICAL SCIENCE 2017. [DOI: 10.3934/medsci.2017.1.99] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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18
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Gao Y, Peng J, Ren Z, He NY, Li Q, Zhao XS, Wang MM, Wen HY, Tang ZH, Jiang ZS, Wang GX, Liu LS. Functional regulatory roles of microRNAs in atherosclerosis. Clin Chim Acta 2016; 460:164-71. [DOI: 10.1016/j.cca.2016.06.044] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 06/29/2016] [Accepted: 06/30/2016] [Indexed: 01/24/2023]
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19
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Frixa T, Donzelli S, Blandino G. Oncogenic MicroRNAs: Key Players in Malignant Transformation. Cancers (Basel) 2015; 7:2466-85. [PMID: 26694467 PMCID: PMC4695904 DOI: 10.3390/cancers7040904] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 12/02/2015] [Accepted: 12/11/2015] [Indexed: 01/17/2023] Open
Abstract
MicroRNAs (miRNAs) represent a class of non-coding RNAs that exert pivotal roles in the regulation of gene expression at the post-transcriptional level. MiRNAs are involved in many biological processes and slight modulations in their expression have been correlated with the occurrence of different diseases. In particular, alterations in the expression of miRNAs with oncogenic or tumor suppressor functions have been associated with carcinogenesis, malignant transformation, metastasis and response to anticancer treatments. This review will mainly focus on oncogenic miRNAs whose aberrant expression leads to malignancy.
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Affiliation(s)
- Tania Frixa
- Translational Oncogenomics Laboratory, Regina Elena National Cancer Institute, 00144 Rome, Italy.
| | - Sara Donzelli
- Translational Oncogenomics Laboratory, Regina Elena National Cancer Institute, 00144 Rome, Italy.
| | - Giovanni Blandino
- Translational Oncogenomics Laboratory, Regina Elena National Cancer Institute, 00144 Rome, Italy.
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20
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Sun L, Shen YL, Liu HJ, Hu YJ, Kang YL, Huang WY. The expression of response gene to complement 32 on renal ischemia reperfusion injury in rat. Ren Fail 2015; 38:276-81. [PMID: 26652201 DOI: 10.3109/0886022x.2015.1120118] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
To investigate the expression of response gene to complement 32 (RGC32) in rat with acute kidney injury (AKI) and to explore the role of RGC32 in renal injury and repair induced by ischemia reperfusion. Rats were randomly divided into two groups, including sham operation group (n = 48) and acute ischemia reperfusion injury (IRI) group (n = 48). Rats were sacrificed following reperfusion 2 h, 6 h, 24 h, 48 h, 72 h, 1 week (w), 2 w, and 4 w. The distribution and expression of RGC32 in renal tissue were observed by means of immunohistochemistry. The mean density of the images detected by Image-Pro Plus 6 was designated as the representative RGC32 expression levels. Meanwhile, RGC32 mRNA expression was measured by qPCR. RGC32 mainly expressed in cytoplasm of proximal tubular epithelial cells. However, RGC32 did not express in renal interstitium and vessels. The expression levels of RGC32 measured by immunohistochemistry at different reperfusion time were 0.0168 ± 0.0029, 0.0156 ± 0.0021, 0.0065 ± 0.0013, 0.0075 ± 0.0013, 0.0096 ± 0.0014, 0.0132 ± 0.0016, 0.0169 ± 0.0014, 0.0179 ± 0.0022, respectively. Compared with the sham group, the level of RGC32 expression in IRI group was significant lower at 24 h, 48 h, 72 h after IRI (p < 0.05). The expression levels of RGC32 mRNA at different reperfusion time measured by qPCR were corroborated the immunohistochemistry finding. The in vitro experiments show the expression of α-SMA and extracellular matrix expression increased signification when the RGC32 was silenced. Our data showed that the RGC32 expression in AKI rat decreased significantly reduces with different reperfusion time and performs a time-dependent manner. RGC32 may play an important role in the pathogenesis of AKI following IRI and repair in rat.
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Affiliation(s)
- Lei Sun
- a Department of Nephrology and Rheumatology , Shanghai Children's Hospital, Children's Hospital of Shanghai Jiaotong University , Shanghai , P.R. China
| | - Yun-Lin Shen
- a Department of Nephrology and Rheumatology , Shanghai Children's Hospital, Children's Hospital of Shanghai Jiaotong University , Shanghai , P.R. China
| | - Hua-Jie Liu
- a Department of Nephrology and Rheumatology , Shanghai Children's Hospital, Children's Hospital of Shanghai Jiaotong University , Shanghai , P.R. China
| | - Yu-Jie Hu
- a Department of Nephrology and Rheumatology , Shanghai Children's Hospital, Children's Hospital of Shanghai Jiaotong University , Shanghai , P.R. China
| | - Yu-Lin Kang
- a Department of Nephrology and Rheumatology , Shanghai Children's Hospital, Children's Hospital of Shanghai Jiaotong University , Shanghai , P.R. China
| | - Wen-Yan Huang
- a Department of Nephrology and Rheumatology , Shanghai Children's Hospital, Children's Hospital of Shanghai Jiaotong University , Shanghai , P.R. China
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21
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Li J, Bei Y, Liu Q, Lv D, Xu T, He Y, Chen P, Xiao J. MicroRNA-221 is required for proliferation of mouse embryonic stem cells via P57 targeting. Stem Cell Rev Rep 2015; 11:39-49. [PMID: 25086570 DOI: 10.1007/s12015-014-9543-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Factors responsible for the rapid proliferative properties of embryonic stem (ES) cells are largely unknown. MicroRNA-221/222 (miR-221/222) regulate proliferation in many somatic cells, however, their roles in proliferation of ES cells are unclear. In this study, E14 mouse ES cells proliferation was determined by total cell counting, Cell Counting Kit (CCK-8), size of colonies and cell cycle analysis, while apoptosis and necrosis using Annexin V and propidium iodide staining. miR-221 inhibitor decreased proliferation of ES cells without inducing apoptosis and necrosis. miR-221 mimic, miR-222 mimic and miR-222 inhibitor did not affect ES cells proliferation. The expression level of miR-221 remained unchanged upon embryoid body (EB) formation. ES cells with miR-221 inhibition maintained an undifferentiated state, as indicated by unchanged alkaline phosphatase enzyme activity and Sox2, Nanong, and Oct4 expressions. P57 was post-transcriptionally regulated by miR-221 in ES cells. P57 knockdown completely abolished the inhibition effects of ES cells proliferation observed in miR-221 reduction, further indicating that miR-221 inhibition is likely to mediate its antiproliferative effects via P57 expression. To exclude that the function of miR-221 in ES cells is E14 specific, the effects of miR-221 mimic and inhibitor in size of colonies and cell cycle of R1 mouse ES cells were also determined and similar effects in inhibiting proliferation were achieved with miR-221 inhibition. Therefore, miR-221 is required for mouse ES cells proliferation via P57 targeting. This study indicates that miR-221 is among the regulators that control ES cells proliferation and might be used to influence the fate of ES cells.
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Affiliation(s)
- Jin Li
- Regeneration Lab and Experimental Center of Life Sciences, School of Life Science, Shanghai University, 333 Nan Chen Road, Shanghai, 200444, China
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Van Roey K, Davey NE. Motif co-regulation and co-operativity are common mechanisms in transcriptional, post-transcriptional and post-translational regulation. Cell Commun Signal 2015; 13:45. [PMID: 26626130 PMCID: PMC4666095 DOI: 10.1186/s12964-015-0123-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 11/24/2015] [Indexed: 01/01/2023] Open
Abstract
A substantial portion of the regulatory interactions in the higher eukaryotic cell are mediated by simple sequence motifs in the regulatory segments of genes and (pre-)mRNAs, and in the intrinsically disordered regions of proteins. Although these regulatory modules are physicochemically distinct, they share an evolutionary plasticity that has facilitated a rapid growth of their use and resulted in their ubiquity in complex organisms. The ease of motif acquisition simplifies access to basal housekeeping functions, facilitates the co-regulation of multiple biomolecules allowing them to respond in a coordinated manner to changes in the cell state, and supports the integration of multiple signals for combinatorial decision-making. Consequently, motifs are indispensable for temporal, spatial, conditional and basal regulation at the transcriptional, post-transcriptional and post-translational level. In this review, we highlight that many of the key regulatory pathways of the cell are recruited by motifs and that the ease of motif acquisition has resulted in large networks of co-regulated biomolecules. We discuss how co-operativity allows simple static motifs to perform the conditional regulation that underlies decision-making in higher eukaryotic biological systems. We observe that each gene and its products have a unique set of DNA, RNA or protein motifs that encode a regulatory program to define the logical circuitry that guides the life cycle of these biomolecules, from transcription to degradation. Finally, we contrast the regulatory properties of protein motifs and the regulatory elements of DNA and (pre-)mRNAs, advocating that co-regulation, co-operativity, and motif-driven regulatory programs are common mechanisms that emerge from the use of simple, evolutionarily plastic regulatory modules.
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Affiliation(s)
- Kim Van Roey
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), 69117, Heidelberg, Germany.
- Health Services Research Unit, Operational Direction Public Health and Surveillance, Scientific Institute of Public Health (WIV-ISP), 1050, Brussels, Belgium.
| | - Norman E Davey
- Conway Institute of Biomolecular and Biomedical Sciences, University College Dublin, Dublin 4, Ireland.
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23
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The mystery of let-7d - a small RNA with great power. Contemp Oncol (Pozn) 2014; 18:293-301. [PMID: 25477749 PMCID: PMC4248056 DOI: 10.5114/wo.2014.44467] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 05/16/2014] [Accepted: 06/18/2014] [Indexed: 12/21/2022] Open
Abstract
miRNAs belong to a class of small non-coding RNAs which can modulate gene expression. Disturbances in their expression and function may cause cancer formation, progression and cell response to various types of stress. The let-7 family is one of the most studied groups of miRNAs. The family contains 13 members with similar sequences and a wide spectrum of target genes. In this paper, we mostly focus on one member of the family – let-7d. This miRNA is dysregulated in many types of cancers. It can be over- or down-expressed, and it acts as a tumor suppressor or oncogene. It regulates various genes such as LIN28, C-MYC, K-RAS, HMGA2 and IMP-1. Moreover, let-7d has a significant impact on epithelial-to-mesenchymal transition (EMT) and formation of cancer initiating cells which are resistant to irradiation and chemical exposure and responsible for cancer metastasis. Let-7d can serve as a prognostic and predictive marker for personalization of the treatment. Let-7d is a small RNA with great power, but in different cell genetic backgrounds it acts in different ways, which makes this molecule still mysterious.
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Leotta M, Biamonte L, Raimondi L, Ronchetti D, Di Martino MT, Botta C, Leone E, Pitari MR, Neri A, Giordano A, Tagliaferri P, Tassone P, Amodio N. A p53-dependent tumor suppressor network is induced by selective miR-125a-5p inhibition in multiple myeloma cells. J Cell Physiol 2014; 229:2106-16. [PMID: 24819167 DOI: 10.1002/jcp.24669] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Revised: 03/31/2014] [Accepted: 05/09/2014] [Indexed: 02/06/2023]
Abstract
The analysis of deregulated microRNAs (miRNAs) is emerging as a novel approach to disclose the regulation of tumor suppressor or tumor promoting pathways in tumor cells. Targeting aberrantly expressed miRNAs is therefore a promising strategy for cancer treatment. By miRNA profiling of primary plasma cells from multiple myeloma (MM) patients, we previously reported increased miR-125a-5p levels associated to specific molecular subgroups. On these premises, we aimed at investigating the biological effects triggered by miR-125a-5p modulation in MM cells. Expression of p53 pathway-related genes was down-regulated in MM cells transfected with miR-125a-5p mimics. Luciferase reporter assays confirmed specific p53 targeting at 3'UTR level by miR-125a-5p mimics. Interestingly, bone marrow stromal cells (BMSCs) affected the miR-125a-5p/p53 axis, since adhesion of MM cells to BMSCs strongly up-regulated miR-125a-5p levels, while reduced p53 expression. Moreover, ectopic miR-125a-5p reduced, while miR-125-5p inhibitors promoted, the expression of tumor suppressor miR-192 and miR-194, transcriptionally regulated by p53. Lentiviral-mediated stable inhibition of miR-125a-5p expression in wild-type p53 MM cells dampened cell growth, increased apoptosis and reduced cell migration. Importantly, inhibition of in vitro MM cell proliferation and migration was also achieved by synthetic miR-125a-5p inhibitors and was potentiated by the co-expression of miR-192 or miR-194. Taken together, our data indicate that miR-125a-5p antagonism results in the activation of p53 pathway in MM cells, underlying the crucial role of this miRNA in the biopathology of MM and providing the molecular rationale for the combinatory use of miR-125a inhibitors and miR-192 or miR-194 mimics for MM treatment.
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Affiliation(s)
- Marzia Leotta
- Department of Experimental and Clinical Medicine, Magna Graecia University, Medical Oncology Unit, T. Campanella Cancer Center, Salvatore Venuta University Campus, Catanzaro, Italy
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Wu J, Lv Q, He J, Zhang H, Mei X, Cui K, Huang N, Xie W, Xu N, Zhang Y. MicroRNA-188 suppresses G1/S transition by targeting multiple cyclin/CDK complexes. Cell Commun Signal 2014; 12:66. [PMID: 25304455 PMCID: PMC4200121 DOI: 10.1186/s12964-014-0066-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 09/30/2014] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Accelerated cell cycle progression is the common feature of most cancers. MiRNAs can act as oncogenes or tumor suppressors by directly modulating cell cycle machinery. It has been shown that miR-188 is upregulated in UVB-irradiated mouse skin and human nasopharyngeal carcinoma CNE cells under hypoxic stress. However, little is known about the function of miR-188 in cell proliferation and growth control. RESULTS Overexpression of miR-188 inhibits cell proliferation, tumor colony formation and G1/S cell cycle transition in human nasopharyngeal carcinoma CNE cells. Using bioinformatics approach, we identify a series of genes regulating G1/S transition as putative miR-188 targets. MiR-188 inhibits both mRNA and protein expression of CCND1, CCND3, CCNE1, CCNA2, CDK4 and CDK2, suppresses Rb phosphorylation and downregulates E2F transcriptional activity. The expression level of miR-188 also inversely correlates with the expression of miR-188 targets in human nasopharyngeal carcinoma (NPC) tissues. Moreover, studies in xenograft mouse model reveal that miR-188 is capable of inhibiting tumor initiation and progression by suppressing target genes expression and Rb phosphorylation. CONCLUSIONS This study demonstrates that miR-188 exerts anticancer effects, via downregulation of multiple G1/S related cyclin/CDKs and Rb/E2F signaling pathway.
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Affiliation(s)
- Jiangbin Wu
- School of Life Sciences, Tsinghua University, Beijing, 100084, PR China. .,Division of Life Science, Key Lab in Healthy Science and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, PR China.
| | - Qing Lv
- School of Life Sciences, Tsinghua University, Beijing, 100084, PR China. .,Division of Life Science, Key Lab in Healthy Science and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, PR China.
| | - Jie He
- Division of Life Science, Key Lab in Healthy Science and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, PR China.
| | - Haoxiang Zhang
- School of Life Sciences, Tsinghua University, Beijing, 100084, PR China. .,Division of Life Science, Key Lab in Healthy Science and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, PR China.
| | - Xueshuang Mei
- ENT Department, Peking University Shenzhen Hospital, Shenzhen, 518055, PR China.
| | - Kai Cui
- School of Life Sciences, Tsinghua University, Beijing, 100084, PR China. .,Division of Life Science, Key Lab in Healthy Science and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, PR China.
| | - Nunu Huang
- School of Life Sciences, Tsinghua University, Beijing, 100084, PR China. .,Division of Life Science, Key Lab in Healthy Science and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, PR China.
| | - Weidong Xie
- Division of Life Science, Key Lab in Healthy Science and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, PR China.
| | - Naihan Xu
- Division of Life Science, Key Lab in Healthy Science and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, PR China.
| | - Yaou Zhang
- Division of Life Science, Key Lab in Healthy Science and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, PR China.
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Jamshidi-Adegani F, Langroudi L, Shafiee A, Mohammadi-Sangcheshmeh A, Ardeshirylajimi A, Barzegar M, Azadmanesh K, Naderi M, Arefian E, Soleimani M. Mir-302 cluster exhibits tumor suppressor properties on human unrestricted somatic stem cells. Tumour Biol 2014; 35:6657-64. [PMID: 24705778 DOI: 10.1007/s13277-014-1844-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 03/12/2014] [Indexed: 02/03/2023] Open
Abstract
Many studies have reported that miR-302-367 cluster acts in different ways in various cell types. For instance, this cluster is shown to have a potential role in stemness regulation in embryonic stem cells (ESCs). On the other hand, this cluster inhibits the tumorigenicity of human pluripotent stem cells by coordinated suppression of CDK2 and CDK4/6 cell cycle pathways. Indeed, this cluster has a significant posttranscriptional impact on cell cycle progression. Previous reports have shown the participation of miR-302-367 cluster in cell cycle regulation of hESCs, MCF7, HepG2, and Teta-2 embryonal teratocarcinoma cells, but its effect on unrestricted somatic stem cells (USSCs) as a new source of human somatic stem cells from the umbilical cord blood remains to be elucidated. Therefore, in this study, we aimed to investigate the effect of miR-302-367 cluster on cell proliferation by MTT assay, cell cycle analysis, and colony formation assay. In addition, the expression of candidate cell cycle regulatory performance and tumor suppressor genes was determined. In this study, for the first time, we found that miR-302-367 cluster not only did not reprogram human USSCs into a pluripotent ESC-like state, but also inhibited the proliferation of human USSCs. Moreover, analyzing the cell cycle curve revealed a significant apoptotic phase upon viral introduction of miR-302-367. Our gene expression study revealed the overexpression of candidate genes after transduction of USSCs with miR-302-367 cluster. In conclusion, the controversial role of miR-302-367 in different cell types may provide better understanding for its role in stemness level and its antitumorigenicity potential in different contexts.
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Cheng C, Ung M, Grant GD, Whitfield ML. Transcription factor binding profiles reveal cyclic expression of human protein-coding genes and non-coding RNAs. PLoS Comput Biol 2013; 9:e1003132. [PMID: 23874175 PMCID: PMC3708869 DOI: 10.1371/journal.pcbi.1003132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 05/24/2013] [Indexed: 12/02/2022] Open
Abstract
Cell cycle is a complex and highly supervised process that must proceed with regulatory precision to achieve successful cellular division. Despite the wide application, microarray time course experiments have several limitations in identifying cell cycle genes. We thus propose a computational model to predict human cell cycle genes based on transcription factor (TF) binding and regulatory motif information in their promoters. We utilize ENCODE ChIP-seq data and motif information as predictors to discriminate cell cycle against non-cell cycle genes. Our results show that both the trans- TF features and the cis- motif features are predictive of cell cycle genes, and a combination of the two types of features can further improve prediction accuracy. We apply our model to a complete list of GENCODE promoters to predict novel cell cycle driving promoters for both protein-coding genes and non-coding RNAs such as lincRNAs. We find that a similar percentage of lincRNAs are cell cycle regulated as protein-coding genes, suggesting the importance of non-coding RNAs in cell cycle division. The model we propose here provides not only a practical tool for identifying novel cell cycle genes with high accuracy, but also new insights on cell cycle regulation by TFs and cis-regulatory elements. Cell cycle is a complex and highly supervised process that must proceed with regulatory precision to achieve successful cellular division. Microarray time course experiments have been successfully used to identify cell cycle regulated genes but with several limitations, e.g. less effective in identifying genes with low expression. We propose a computational approach to predict cell cycle genes based on TF binding data and motif information in their promoters. Specifically, we take advantage of ChIP-seq TF binding data generated by the ENCODE project and the TF binding motif information available from public databases. These data were processed and utilized as predictor for predicting cell cycle genes using the Random Forest method. Our results show that both the trans- TF features and the cis- motif features are predictive to cell cycle genes, and a combination of the two types features can further improve prediction accuracy. We apply our model to a complete list of GENCODE promoters to predict novel cell cycle driving promoters for both protein-coding genes and non-coding RNAs such as lincRNAs. We find that a similar percentage of lincRNAs are cell cycle regulated as protein-coding genes, suggesting the importance of non-coding RNAs in cell cycle division.
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Affiliation(s)
- Chao Cheng
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA.
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28
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Chen KC, Juo SHH. MicroRNAs in atherosclerosis. Kaohsiung J Med Sci 2012; 28:631-40. [DOI: 10.1016/j.kjms.2012.04.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 02/20/2012] [Indexed: 02/04/2023] Open
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29
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Wang F, Zhao XQ, Liu JN, Wang ZH, Wang XL, Hou XY, Liu R, Gao F, Zhang MX, Zhang Y, Bu PL. Antagonist of microRNA-21 improves balloon injury-induced rat iliac artery remodeling by regulating proliferation and apoptosis of adventitial fibroblasts and myofibroblasts. J Cell Biochem 2012; 113:2989-3001. [PMID: 22565856 DOI: 10.1002/jcb.24176] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Molecular pathways involved in adventitial fibroblasts (AFs) and myofibroblasts (MFs) proliferation and apoptosis contribute to vascular remodeling. MicroRNA-21 (miR-21) plays an important role in regulating cellular proliferation and apoptosis of many cell types; however, the effect of miR-21 on AFs and MFs is still unknown. In this study, we found that miR-21 was expressed in AFs and overexpressed in MFs. Inhibition of miR-21 decreased proliferation and increased apoptosis of AFs and MFs, and overexpression of miR-21 with pre-miR-21 had the reverse effect. Programmed cell death 4 (PDCD4), related to cell proliferation and apoptosis, was validated as a direct target of miR-21 by dual-luciferase reporter assay and gain and loss of function of miR-21 in AFs and MFs. PDCD4 knockdown with siRNA partly rescued the reduced proliferation with miR-21 inhibition and alleviated the increased apoptosis induced by miR-21 inhibition in AFs and MFs. Moreover, increasing PDCD4 expression by miR-21 inhibition significantly decreased JNK/c-Jun activity. In contrast, decreasing PDCD4 expression by pre-miR-21 treatment increased JNK/c-Jun activity, while the effect of miR-21 inhibition on JNK/c-Jun activity could be rescued by PDCD4 siRNA. Moreover, miR-21 inhibition could regulate proliferation and apoptosis of vascular AFs and MFs in vivo. Furthermore, miR-21 inhibition reversed vascular remodeling induced by balloon injury. In summary, our findings demonstrate that miR-21 may have a critical role in regulating proliferation and apoptosis of AFs and MFs, and PDCD4 is a functional target gene involved in the miR-21-mediated cellular effects in vascular remodeling by a miR-21/PDCD4/JNK/c-Jun pathway.
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Affiliation(s)
- Fei Wang
- The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education and Chinese Ministry of Public Health, Department of Cardiology, Shandong University Qilu Hospital, Jinan, Shandong Province, China
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miRT: a database of validated transcription start sites of human microRNAs. GENOMICS PROTEOMICS & BIOINFORMATICS 2012. [PMID: 23200141 PMCID: PMC5054196 DOI: 10.1016/j.gpb.2012.08.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
MicroRNAs (miRNAs) are small endogenous non-coding RNAs of about 22 nt in length that take crucial roles in many biological processes. These short RNAs regulate the expression of mRNAs by binding to their 3′-UTRs or by translational repression. Many of the current studies focus on how mature miRNAs regulate mRNAs, however, very limited knowledge is available regarding their transcriptional loci. It is known that primary miRNAs (pri-miRs) are first transcribed from the DNA, followed by the formation of precursor miRNAs (pre-miRs) by endonuclease activity, which finally produces the mature miRNAs. Till date, many of the pre-miRs and mature miRNAs have been experimentally verified. But unfortunately, identification of the loci of pri-miRs, promoters and associated transcription start sites (TSSs) are still in progress. TSSs of only about 40% of the known mature miRNAs in human have been reported. This information, albeit limited, may be useful for further study of the regulation of miRNAs. In this paper, we provide a novel database of validated miRNA TSSs, miRT, by collecting data from several experimental studies that validate miRNA TSSs and are available for full download. We present miRT as a web server and it is also possible to convert the TSS loci between different genome built. miRT might be a valuable resource for advanced research on miRNA regulation, which is freely accessible at: http://www.isical.ac.in/~bioinfo_miu/miRT/miRT.php.
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31
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MicroRNA turnover: when, how, and why. Trends Biochem Sci 2012; 37:436-46. [PMID: 22921610 DOI: 10.1016/j.tibs.2012.07.002] [Citation(s) in RCA: 207] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 07/16/2012] [Accepted: 07/16/2012] [Indexed: 12/18/2022]
Abstract
MicroRNAs (miRNAs) are short (∼22 nucleotide) RNAs that are important for the regulation of numerous biological processes. Accordingly, the expression of miRNAs is itself tightly controlled by mechanisms acting at the level of transcription as well as processing of miRNA precursors. Recently, active degradation of mature miRNAs has been identified as another mechanism that is important for miRNA homeostasis. Here we review the molecular factors and cellular conditions that promote miRNA turnover. We also discuss what is known about the physiological relevance of miRNA decay.
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Lichner Z, Mejia-Guerrero S, Ignacak M, Krizova A, Bao TT, Girgis AHF, Youssef YM, Yousef GM. Pleiotropic action of renal cell carcinoma-dysregulated miRNAs on hypoxia-related signaling pathways. THE AMERICAN JOURNAL OF PATHOLOGY 2012; 180:1675-87. [PMID: 22326755 DOI: 10.1016/j.ajpath.2011.12.030] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 12/19/2011] [Accepted: 12/27/2011] [Indexed: 01/05/2023]
Abstract
The von Hippel-Lindau (VHL) gene is lost in ≈ 70% of all renal cell carcinomas (RCCs); however, increasing evidence supports the involvement of alternative mechanisms in the regulation of VHL expression, including suppression by microRNAs (miRNAs). miRNAs are small, noncoding RNA molecules that regulate gene expression through binding to target mRNAs. In this study, we found that miRNAs, which are dysregulated in cases of RCC, can target multiple members of RCC-related signaling pathways. Importantly, both VHL and the hypoxia-inducible factor 1-α gene are experimentally validated and are likely direct targets of miR-17-5p and miR-224, as shown by both luciferase assay and Western blot analysis. We found a negative correlation between miR-17-5p and its two predicted targets, VEGF-A and EGLN3, and between miR-224 and its targets SMAD4 and SMAD5 in RCC specimens, suggesting that downstream signaling pathways are also modulated by clear cell RCC-dysregulated miRs. Results from our bioinformatics analysis show that a single miRNA molecule can target multiple components of the same pathway and that multiple miRNAs can target the same molecule. Our results also indicate that miRNAs represent a mechanism for the inactivation of VHL in cases of RCC and can elucidate a new dimension in cancer pathogenesis. As such, miRNAs exemplify new potential therapeutic targets with a significant effect on both tumor growth and metastatic potential.
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Affiliation(s)
- Zsuzsanna Lichner
- Department of Laboratory Medicine, Keenan Research Centre in the Li Ka Shing Knowledge Institute St. Michael's Hospital, Toronto, Ontario, Canada
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Castañeda CA, Agullo-Ortuño MT, Fresno Vara JA, Cortes-Funes H, Gomez HL, Ciruelos E. Implication of miRNA in the diagnosis and treatment of breast cancer. Expert Rev Anticancer Ther 2012; 11:1265-75. [PMID: 21916580 DOI: 10.1586/era.11.40] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Breast cancer (BC) comprises a group of different diseases characterized by changes in tissue structure and gene expression. Recent advances in molecular biology have shed new light on the participation of genes and their products in the biology of BC. MicroRNAs (miRNAs) are small noncoding endogenous RNA molecules that appear to modulate the expression of more than a third of human genes, and their implications in cancer have grasped the attention of the scientific community. Recently, several studies have described the association between miRNA expression profiles and pathological and clinical BC features. Moreover, these molecules represent a new type of molecular marker that can identify prognosis and guide the management of BC patients. With the increasing understanding of miRNA networks and their impact in the biology of BC, as well as the development of viable strategies to modulate specific miRNAs, we could improve the treatment of this disease.
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Izumiya M, Tsuchiya N, Okamoto K, Nakagama H. Systematic exploration of cancer-associated microRNA through functional screening assays. Cancer Sci 2011; 102:1615-21. [PMID: 21668585 DOI: 10.1111/j.1349-7006.2011.02007.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
MicroRNA (miRNA), non-coding RNA of approximately 22 nucleotides, post-transcriptionally represses expression of its target genes. miRNA regulates a variety of biological processes such as cell proliferation, cell death, development, stemness and genomic stability, not only in physiological conditions but also in various pathological conditions such as cancers. More than 1000 mature miRNA have been experimentally identified in humans and mice, yet the functions of a vast majority of miRNA remain to be elucidated. Identification of novel cancer-associated miRNA seems promising considering their possible application in the development of novel cancer therapies and biomarkers. Currently, there are two major approaches to identify miRNA that are associated with cancer: expression profiling study and functional screening assay. The former approach is widely used, and a large number of studies have shown aberrant miRNA expression profiles in cancer tissues compared with their non-cancer counterparts. Although aberrantly expressed miRNA are potentially good biomarkers, in most cases a majority of them do not play causal roles in cancers when functional assays are performed. In contrast, the latter approach allows screening of 'driver' miRNA with cancer-associated phenotypes, such as cell proliferation and cell invasion. Thus, this approach might be suitable in finding crucial targets of novel cancer therapy. The combination of both types of approaches will contribute to further elucidation of the cancer pathophysiology and to the development of a novel class of cancer therapies and biomarkers.
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Affiliation(s)
- Masashi Izumiya
- Division of Cancer Development System, National Cancer Center Research Institute, Tokyo, Japan
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35
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Oliveira KC, Carvalho MLP, Maracaja-Coutinho V, Kitajima JP, Verjovski-Almeida S. Non-coding RNAs in schistosomes: an unexplored world. AN ACAD BRAS CIENC 2011; 83:673-94. [DOI: 10.1590/s0001-37652011000200026] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2011] [Accepted: 04/28/2011] [Indexed: 11/21/2022] Open
Abstract
Non-coding RNAs (ncRNAs) were recently given much higher attention due to technical advances in sequencing which expanded the characterization of transcriptomes in different organisms. ncRNAs have different lengths (22 nt to >1, 000 nt) and mechanisms of action that essentially comprise a sophisticated gene expression regulation network. Recent publication of schistosome genomes and transcriptomes has increased the description and characterization of a large number of parasite genes. Here we review the number of predicted genes and the coverage of genomic bases in face of the public ESTs dataset available, including a critical appraisal of the evidence and characterization of ncRNAs in schistosomes. We show expression data for ncRNAs in Schistosoma mansoni. We analyze three different microarray experiment datasets: (1) adult worms' large-scale expression measurements; (2) differentially expressed S. mansoni genes regulated by a human cytokine (TNF-α) in a parasite culture; and (3) a stage-specific expression of ncRNAs. All these data point to ncRNAs involved in different biological processes and physiological responses that suggest functionality of these new players in the parasite's biology. Exploring this world is a challenge for the scientists under a new molecular perspective of host-parasite interactions and parasite development.
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Trompeter HI, Abbad H, Iwaniuk KM, Hafner M, Renwick N, Tuschl T, Schira J, Müller HW, Wernet P. MicroRNAs MiR-17, MiR-20a, and MiR-106b act in concert to modulate E2F activity on cell cycle arrest during neuronal lineage differentiation of USSC. PLoS One 2011; 6:e16138. [PMID: 21283765 PMCID: PMC3024412 DOI: 10.1371/journal.pone.0016138] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Accepted: 12/14/2010] [Indexed: 12/19/2022] Open
Abstract
Background MicroRNAs are short (∼22 nt) non-coding regulatory RNAs that control gene expression at the post-transcriptional level. Here the functional impact of microRNAs on cell cycle arrest during neuronal lineage differentiation of unrestricted somatic stem cells from human cord blood (USSC) was analyzed. Methodology/Principal Findings Expression profiling revealed downregulation of microRNAs miR-17, -20a, and -106b in USSC differentiated into neuronal lineage but not in USSC differentiated into osteogenic lineage. Transfection experiments followed by Ki67 immunostainings demonstrated that each of these microRNAs was able to promote proliferation of native USSC and to prevent in part cell cycle arrest during neuronal lineage differentiation of USSC. Bioinformatic target gene predictions followed by experimental target gene validations revealed that miR-17, -20a, and -106b act in a common manner by downregulating an overlapping set of target genes mostly involved in regulation and execution of G1/S transition. Pro-proliferative target genes cyclinD1 (CCND1) and E2F1 as well as anti-proliferative targets CDKN1A (p21), PTEN, RB1, RBL1 (p107), RBL2 (p130) were shown as common targets for miR-17, -20a, and -106b. Furthermore, these microRNAs also downregulate WEE1 which is involved in G2/M transition. Most strikingly, miR-17, -20a, and -106b were found to promote cell proliferation by increasing the intracellular activity of E2F transcription factors, despite the fact that miR-17, -20a, and -106b directly target the transcripts that encode for this protein family. Conclusions/Significance Mir-17, -20a, and -106b downregulate a common set of pro- and anti-proliferative target genes to impact cell cycle progression of USSC and increase intracellular activity of E2F transcription factors to govern G1/S transition.
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Affiliation(s)
- Hans-Ingo Trompeter
- University Düsseldorf, Medical Faculty, Institute for Transplantation Diagnostics and Cell Therapeutics, Düsseldorf, Germany
| | - Hassane Abbad
- University Düsseldorf, Medical Faculty, Institute for Transplantation Diagnostics and Cell Therapeutics, Düsseldorf, Germany
| | - Katharina M. Iwaniuk
- University Düsseldorf, Medical Faculty, Institute for Transplantation Diagnostics and Cell Therapeutics, Düsseldorf, Germany
| | - Markus Hafner
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Rockefeller University, New York, New York, United States of America
| | - Neil Renwick
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Rockefeller University, New York, New York, United States of America
| | - Thomas Tuschl
- Howard Hughes Medical Institute, Laboratory of RNA Molecular Biology, Rockefeller University, New York, New York, United States of America
| | - Jessica Schira
- Molecular Neurobiology Laboratory, Medical Faculty, Department of Neurology, University Düsseldorf, Düsseldorf, Germany
| | - Hans Werner Müller
- Molecular Neurobiology Laboratory, Medical Faculty, Department of Neurology, University Düsseldorf, Düsseldorf, Germany
| | - Peter Wernet
- University Düsseldorf, Medical Faculty, Institute for Transplantation Diagnostics and Cell Therapeutics, Düsseldorf, Germany
- * E-mail:
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37
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Chegini N. Uterine microRNA signature and consequence of their dysregulation in uterine disorders. Anim Reprod 2010; 7:117-128. [PMID: 22328907 PMCID: PMC3275910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023] Open
Abstract
MicroRNA (miRNA) has emerged as key post-transcriptional regulator and through this mechanism control many normal developmental and physiological processes. Conversely, aberrant expression of some miRNAs has been correlated with various disorders, more specifically, development and progression of malignancy. Endometrium is a dynamic tissue which undergoes extensive cyclic changes in preparation for embryo implantation during reproductive years, as well as changes that occur following menopause, and establishment of benign and malignant uterine disorders. These processes are highly regulated by ovarian steroids and locally expressed genes in response to steroid hormone receptor-mediated signaling and include genes related to inflammatory reaction, apoptosis, cell-cycle progression, angiogenesis and tissue remodeling. Here we present an overview of our current understanding of uterine miRNA biogenesis and highlights their potential regulatory functions in cellular processes relevant to normal uterine physiological and pathological disorders such as endometriosis, dysfunctional uterine bleeding and endometrial cancer. Understanding the expression, regulation and functional aspects of miRNAs in uterine environment under normal and various disorders may lead to their potential utilization as diagnostic as well as therapeutic tool.
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Affiliation(s)
- Nasser Chegini
- Corresponding author: , Phone: (352) 273-7566; Fax: (352) 392-6994
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38
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Hulsmans M, Holvoet P. The vicious circle between oxidative stress and inflammation in atherosclerosis. FASEB J 2009; 25:2515-27. [PMID: 19968738 DOI: 10.1096/fj.11-181149] [Citation(s) in RCA: 171] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The initial event in atherogenesis is the increased transcytosis of low density lipoprotein, and its subsequent deposition, retention and modification in the subendothelium. It is followed by the infiltration of activated inflammatory cells from the coronary circulation into the arterial wall. There they secrete reactive oxygen species (ROS) and produce oxidized lipoproteins capable of inducing endothelial cell apoptosis, and thereby plaque erosion. Activated T lymphocytes, macrophages and mast cells, accumulate in the eroded plaque where they secrete a variety of proteases capable of inducing degradation of extracellular proteins, thereby rendering the plaques more prone to rupture. This review summarizes the recent advancements in the understanding of the roles of ROS and oxidized lipoproteins in the activation of inflammatory cells and inducing signalling pathways related to cell death and apoptosis. In addition, it presents evidence that this vicious circle between oxidative stress and inflammation does not only occur in the diseased arterial wall, but also in adipose tissues. There, oxidative stress and inflammation impair adipocyte maturation resulting in defective insulin action and adipocytokine signalling. The latter is associated with increased infiltration of inflammatory cells, loss of anti-oxidant protection and cell death in the arterial wall.
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Affiliation(s)
- Maarten Hulsmans
- Atherosclerosis and Metabolism Unit, Department of Cardiovascular Diseases, Katholieke Universiteit Leuven, Belgium
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