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Kaya M, Abuaisha A, Suer I, Emiroglu S, Abanoz F, Palanduz S, Cefle K, Ozturk S. Turmeric Inhibits MDA-MB-231 Cancer Cell Proliferation, Altering miR-638-5p and Its Potential Targets. Eur J Breast Health 2024; 20:102-109. [PMID: 38571691 PMCID: PMC10985573 DOI: 10.4274/ejbh.galenos.2024.2023-12-2] [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: 12/05/2023] [Accepted: 02/04/2024] [Indexed: 04/05/2024]
Abstract
Objective Recent research suggests curcumin extracted from the turmeric plant may inhibit the proliferation of cancer cells by controlling the expression of microRNAs (miRNAs). The effect of phenolic curcumin on miR-638-5p and potential target gene expressions in the triple negative breast cancer (TNBC) cell line MDA-MB-231 was investigated in this study. Materials and Methods GSE154255 and GSE40525 datasets were downloaded and analyzed using GEO2R to identify dysregulated miRNAs in TNBC. To find differently expressed genes in breast cancer (BRCA), The Cancer Genome Atlas Program data was examined. Utilizing in silico tools, KEGG, GO, and other enrichment analyses were performed. The databases miRNet, miRTarBase v8.0, and TarBase v.8 were used for miRNA and mRNA matching. Real-time quantitative reverse transcription polymerase chain reaction was used to examine the levels of miRNA and its targets in miRNA mimic transfected/curcumin-treated MDA-MB-231 cultures and controls. The cell viability detection kit-8 method was used to assess cell viability, and the scratch assay was used to conduct migration assessment. Results Bioinformatics analysis showed that miR-638-5p was significantly reduced in TNBC patients. Experimental results showed that miR-638-5p was upregulated in MDA-MB-231 treated with curcumin, while the potential target genes of miR-638-5p, CFL1, SIX4, MAZ, and CDH1 were downregulated. Mimic miR-638-5p transfection inhibited MDA-MB-231 cell proliferation and reduced migration and expression of CFL1, SIX4, and MAZ genes was decreased in mimic miR-638-5p transfected cells. Conclusion These findings suggest that curcumin exerts its anticancer effects on MDA-MB-231 cells by modulating the expression of miR-638-5p and its possible target genes.
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Affiliation(s)
- Murat Kaya
- Division of Medical Genetics, Department of Internal Medicine, Istanbul University-Istanbul Faculty of Medicine, Istanbul, Turkey
| | - Asmaa Abuaisha
- Department of Genetics, Institute of Graduate Studies in Health Sciences, Istanbul University, Istanbul, Turkey
| | - Ilknur Suer
- Department of Medical Genetics, Istanbul University-Istanbul Faculty of Medicine, Istanbul, Turkey
| | - Selman Emiroglu
- Division of Breast Surgery, Department of General Surgery, Istanbul University-Istanbul Faculty of Medicine, Istanbul, Turkey
- Department of Molecular and Medical Genetics, Biruni University Graduate School of Education, Istanbul, Turkey
| | - Fahrunnisa Abanoz
- Department of Genetics, Institute of Graduate Studies in Health Sciences, Istanbul University, Istanbul, Turkey
| | - Sukru Palanduz
- Division of Medical Genetics, Department of Internal Medicine, Istanbul University-Istanbul Faculty of Medicine, Istanbul, Turkey
| | - Kivanc Cefle
- Division of Medical Genetics, Department of Internal Medicine, Istanbul University-Istanbul Faculty of Medicine, Istanbul, Turkey
| | - Sukru Ozturk
- Division of Medical Genetics, Department of Internal Medicine, Istanbul University-Istanbul Faculty of Medicine, Istanbul, Turkey
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2
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Kariuki D, Asam K, Aouizerat BE, Lewis KA, Florez JC, Flowers E. Review of databases for experimentally validated human microRNA-mRNA interactions. Database (Oxford) 2023; 2023:7142843. [PMID: 37098414 PMCID: PMC10129384 DOI: 10.1093/database/baad014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 01/13/2023] [Accepted: 03/09/2023] [Indexed: 04/27/2023]
Abstract
MicroRNAs (miRs) may contribute to disease etiology by influencing gene expression. Numerous databases are available for miR target prediction and validation, but their functionality is varied, and outputs are not standardized. The purpose of this review is to identify and describe databases for cataloging validated miR targets. Using Tools4miRs and PubMed, we identified databases with experimentally validated targets, human data, and a focus on miR-messenger RNA (mRNA) interactions. Data were extracted about the number of times each database was cited, the number of miRs, the target genes, the interactions per database, experimental methodology and key features of each database. The search yielded 10 databases, which in order of most cited to least were: miRTarBase, starBase/The Encyclopedia of RNA Interactomes, DIANA-TarBase, miRWalk, miRecords, miRGator, miRSystem, miRGate, miRSel and targetHub. Findings from this review suggest that the information presented within miR target validation databases can be enhanced by adding features such as flexibility in performing queries in multiple ways, downloadable data, ongoing updates and integrating tools for further miR-mRNA target interaction analysis. This review is designed to aid researchers, especially those new to miR bioinformatics tools, in database selection and to offer considerations for future development and upkeep of validation tools. Database URL http://mirtarbase.cuhk.edu.cn/.
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Affiliation(s)
- Dorian Kariuki
- Department of Physiological Nursing, University of California, San Francisco, CA 94143, USA
| | - Kesava Asam
- Bluestone Center for Clinical Research, New York University, New York, CA 10010, USA
| | - Bradley E Aouizerat
- Bluestone Center for Clinical Research, New York University, New York, CA 10010, USA
- Department of Oral and Maxillofacial Surgery, New York University, New York, CA 10010, USA
| | - Kimberly A Lewis
- Department of Physiological Nursing, University of California, San Francisco, CA 94143, USA
| | - Jose C Florez
- Department of Medicine, Center for Genomic Medicine and Diabetes Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Programs in Metabolism and Medical & Population Genetics, Broad Institute, Cambridge, MA 02142, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Elena Flowers
- Department of Physiological Nursing, University of California, San Francisco, CA 94143, USA
- Institute for Human Genetics, University of California, San Francisco, CA 94143, USA
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3
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Bovari-Biri J, Garai K, Banfai K, Csongei V, Pongracz JE. miRNAs as Predictors of Barrier Integrity. BIOSENSORS 2023; 13:bios13040422. [PMID: 37185497 PMCID: PMC10136429 DOI: 10.3390/bios13040422] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 03/16/2023] [Accepted: 03/21/2023] [Indexed: 05/17/2023]
Abstract
The human body has several barriers that protect its integrity and shield it from mechanical, chemical, and microbial harm. The various barriers include the skin, intestinal and respiratory epithelia, blood-brain barrier (BBB), and immune system. In the present review, the focus is on the physical barriers that are formed by cell layers. The barrier function is influenced by the molecular microenvironment of the cells forming the barriers. The integrity of the barrier cell layers is maintained by the intricate balance of protein expression that is partly regulated by microRNAs (miRNAs) both in the intracellular space and the extracellular microenvironment. The detection of changes in miRNA patterns has become a major focus of diagnostic, prognostic, and disease progression, as well as therapy-response, markers using a great variety of detection systems in recent years. In the present review, we highlight the importance of liquid biopsies in assessing barrier integrity and challenges in differential miRNA detection.
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Affiliation(s)
- Judit Bovari-Biri
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, University of Pecs, 2 Rokus Str, H-7624 Pecs, Hungary
- Szentagothai Research Centre, University of Pecs, 20 Ifjusag Str, H-7624 Pecs, Hungary
| | - Kitti Garai
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, University of Pecs, 2 Rokus Str, H-7624 Pecs, Hungary
- Szentagothai Research Centre, University of Pecs, 20 Ifjusag Str, H-7624 Pecs, Hungary
| | - Krisztina Banfai
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, University of Pecs, 2 Rokus Str, H-7624 Pecs, Hungary
- Szentagothai Research Centre, University of Pecs, 20 Ifjusag Str, H-7624 Pecs, Hungary
| | - Veronika Csongei
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, University of Pecs, 2 Rokus Str, H-7624 Pecs, Hungary
- Szentagothai Research Centre, University of Pecs, 20 Ifjusag Str, H-7624 Pecs, Hungary
| | - Judit E Pongracz
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, University of Pecs, 2 Rokus Str, H-7624 Pecs, Hungary
- Szentagothai Research Centre, University of Pecs, 20 Ifjusag Str, H-7624 Pecs, Hungary
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4
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Macvanin MT, Gluvic Z, Radovanovic J, Essack M, Gao X, Isenovic ER. Diabetic cardiomyopathy: The role of microRNAs and long non-coding RNAs. Front Endocrinol (Lausanne) 2023; 14:1124613. [PMID: 36950696 PMCID: PMC10025540 DOI: 10.3389/fendo.2023.1124613] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/16/2023] [Indexed: 03/08/2023] Open
Abstract
Diabetes mellitus (DM) is on the rise, necessitating the development of novel therapeutic and preventive strategies to mitigate the disease's debilitating effects. Diabetic cardiomyopathy (DCMP) is among the leading causes of morbidity and mortality in diabetic patients globally. DCMP manifests as cardiomyocyte hypertrophy, apoptosis, and myocardial interstitial fibrosis before progressing to heart failure. Evidence suggests that non-coding RNAs, such as long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), regulate diabetic cardiomyopathy-related processes such as insulin resistance, cardiomyocyte apoptosis and inflammation, emphasizing their heart-protective effects. This paper reviewed the literature data from animal and human studies on the non-trivial roles of miRNAs and lncRNAs in the context of DCMP in diabetes and demonstrated their future potential in DCMP treatment in diabetic patients.
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Affiliation(s)
- Mirjana T. Macvanin
- Department of Radiobiology and Molecular Genetics, VINČA Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
- *Correspondence: Mirjana T. Macvanin,
| | - Zoran Gluvic
- University Clinical-Hospital Centre Zemun-Belgrade, Clinic of Internal Medicine, Department of Endocrinology and Diabetes, School of Medicine, University of Belgrade, Belgrade, Serbia
| | - Jelena Radovanovic
- Department of Radiobiology and Molecular Genetics, VINČA Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Magbubah Essack
- King Abdullah University of Science and Technology (KAUST), Computer, Electrical, and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST), Computer, Electrical, and Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
| | - Esma R. Isenovic
- Department of Radiobiology and Molecular Genetics, VINČA Institute of Nuclear Sciences - National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
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Shamloo-Dashtpagerdi R, Sisakht JN, Tahmasebi A. MicroRNA miR1118 contributes to wheat (Triticum aestivum L.) salinity tolerance by regulating the Plasma Membrane Intrinsic Proteins1;5 (PIP1;5) gene. JOURNAL OF PLANT PHYSIOLOGY 2022; 278:153827. [PMID: 36206620 DOI: 10.1016/j.jplph.2022.153827] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/05/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
microRNAs (miRNAs) are important regulators of various adaptive stress responses in crops; however, many details about associations among miRNAs, their target genes and physiochemical responses of crops under salinity stress remain poorly understood. We designed this study in a systems biology context and used a collection of computational, experimental and statistical procedures to uncover some regulatory functions of miRNAs in the response of the important crop, wheat, to salinity stress. Accordingly, under salinity conditions, wheat roots' Expressed Sequence Tag (EST) libraries were computationally mined to identify the most reliable differentially expressed miRNA and its related target gene(s). Then, molecular and physiochemical evaluations were carried out in a separate salinity experiment using two contrasting wheat genotypes. Finally, the association between changes in measured characteristics and wheat salinity tolerance was determined. From the results, miR1118 was assigned as a reliable salinity-responsive miRNA in wheat roots. The expression profiles of miR1118 and its predicted target gene, Plasma Membrane Intrinsic Proteins1,5 (PIP1;5), significantly differed between wheat genotypes. Moreover, results revealed that expression profiles of miR1118 and PIP1;5 significantly correlate to Relative Water Content (RWC), root hydraulic conductance (Lp), photosynthetic activities, plasma membrane damages, osmolyte accumulation and ion homeostasis of wheat. Our results suggest a plausible regulatory node through miR1118 adjusting the wheat water status, maintaining ion homeostasis and mitigating membrane damages, mainly through the PIP1;5 gene, under salinity conditions. To our knowledge, this is the first report on the role of miR1118 and PIP1;5 in wheat salinity response.
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Affiliation(s)
| | - Javad Nouripour Sisakht
- Department of Plant Production and Genetics, College of Agricultural Engineering, Isfahan University of Technology, Isfahan, Iran
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6
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Shamloo-Dashtpagerdi R, Lindlöf A, Tahmasebi S. Evidence that miR168a contributes to salinity tolerance of Brassica rapa L. via mediating melatonin biosynthesis. PHYSIOLOGIA PLANTARUM 2022; 174:e13790. [PMID: 36169653 DOI: 10.1111/ppl.13790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/20/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Melatonin is a master regulator of diverse biological processes, including plant's abiotic stress responses and tolerance. Despite the extensive information on the role of melatonin in response to abiotic stress, how plants regulate endogenous melatonin content under stressful conditions remains largely unknown. In this study, we computationally mined Expressed Sequence Tag (EST) libraries of salinity-exposed Chinese cabbage (Brassica rapa) to identify the most reliable differentially expressed miRNA and its target gene(s). In light of these analyses, we found that miR168a potentially targets a key melatonin biosynthesis gene, namely O-METHYLTRANSFERASE 1 (OMT1). Accordingly, molecular and physiochemical evaluations were performed in a separate salinity experiment using contrasting B. rapa genotypes. Then, the association between B. rapa salinity tolerance and changes in measured molecular and physiochemical characteristics was determined. Results indicated that the expression profiles of miR168a and OMT1 significantly differed between B. rapa genotypes. Moreover, the expression profiles of miR168a and OMT1 significantly correlated with more melatonin content, robust antioxidant activities, and better ion homeostasis during salinity stress. Our results suggest that miR168a plausibly mediates melatonin biosynthesis, mainly through the OMT1 gene, under salinity conditions and thereby contributes to the salinity tolerance of B. rapa. To our knowledge, this is the first report on the role of miR168a and OMT1 in B. rapa salinity response.
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Affiliation(s)
| | | | - Sirous Tahmasebi
- Seed and Plant Improvement Research Department, Fars Agricultural and Natural Resources Research and Education Center, AREEO, Shiraz, Iran
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7
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Jha N, Mangukia N, Gadhavi H, Patel M, Bhavsar M, Rawal R, Patel S. Small RNA sequencing and identification of papaya (Carica papaya L.) miRNAs with potential cross-kingdom human gene targets. Mol Genet Genomics 2022; 297:981-997. [PMID: 35570207 PMCID: PMC9107959 DOI: 10.1007/s00438-022-01904-3] [Citation(s) in RCA: 1] [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: 08/10/2021] [Accepted: 04/23/2022] [Indexed: 12/11/2022]
Abstract
Several studies have demonstrated potential role of plant-derived miRNAs in cross-kingdom species relationships by transferring into non-plant host cells to regulate certain host cellular functions. How nutrient-rich plants regulate host cellular functions, which in turn alleviate physiological and disease conditions in the host remains to be explored in detail. This computational study explores the potential targets, putative role, and functional implications of miRNAs derived from Carica papaya L., one of the most cultivated tropical crops in the world and a rich source of phytochemicals and enzymes, in human diet. Using the next-generation sequencing, -Illumina HiSeq2500, ~ 30 million small RNA sequence reads were generated from C. papaya young leaves, resulting in the identification of a total of 1798 known and 49 novel miRNAs. Selected novel C. papaya miRNAs were predicted to regulate certain human targets, and subsequent annotation of gene functions indicated a probable role in various biological processes and pathways, such as MAPK, WNT, and GPCR signaling pathways, and platelet activation. These presumptive target gene in humans were predominantly linked to various diseases, including cancer, diabetes, mental illness, and platelet disorder. The computational finding of this study provides insights into how C. papaya-derived miRNAs may regulate certain conditions of human disease and provide a new perspective on human health. However, the therapeutic potential of C. papaya miRNA can be further explored through experimental studies.
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Affiliation(s)
- Neha Jha
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Naman Mangukia
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
- BioInnovations, Bhayander (West), Mumbai, 401101, Maharashtra, India
| | - Harshida Gadhavi
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Maulik Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
- Advait Theragnostics Pvt. Ltd., Ahmedabad, Gujarat, India
| | - Mansi Bhavsar
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Rakesh Rawal
- Department of Biochemistry and Forensic Science, University School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India
| | - Saumya Patel
- Department of Botany, Bioinformatics and Climate Change Impacts Management, School of Sciences, Gujarat University, Ahmedabad, 380009, Gujarat, India.
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Gunel NS, Birden N, Kurt CC, Bagca BG, Shademan B, Sogutlu F, Ozates NP, Avci CB. Effect of valproic acid on miRNAs affecting histone deacetylase in a model of anaplastic thyroid cancer. Mol Biol Rep 2021; 48:6085-6091. [PMID: 34374891 DOI: 10.1007/s11033-021-06616-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/29/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND Thyroid cancer is the most common malignant tumor of the endocrine system seen in the thyroid gland. More than 90% of thyroid cancers comprise papillary thyroid cancer (PTC) and follicular thyroid cancer (FTC). Although anaplastic thyroid carcinoma (ATC) accounts for less than 2% of thyroid cancer. But patients' lifespan after diagnosis is about 6 months. Surgical interventions, radioactive iodine use, and chemotherapy are not sufficient in the treatment of ATC, so alternative therapies are needed. METHODS AND RESULTS The WST-1 assay test was performed to evaluate the anti-proliferative effects of Valproic acid (VPA). Also, the effect of VPA on miRNAs affecting histone deacetylase was determined by Quantitative RT-PCR. In the SW1736 cell line, IC50 dose for VPA was found 1.6 mg/ml. In our study, the level of oncogenic genes expression in cells treated with VPA, including miR-184, miR-222-5p, miR-124-3p, and miR-328-3p, decreased. Also, the expression of tumor inhibitory genes including miR-323-5p, miR-182-5p, miR-138-5p, miR-217, miR-15a-5p, miR-29b-3p, miR-324-5p and miR-101-5p increased significantly. CONCLUSIONS VPA can ad-just countless gene expression patterns, including microRNAs (miRNAs), by targeting histone deacetylase (HDAC). However, further studies are required for more accurate results.
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Affiliation(s)
- Nur Selvi Gunel
- Department of Medical Biology, Ege University Medical School, Izmir, Turkey
| | - Nihal Birden
- Department of Medical Biology, Ege University Medical School, Izmir, Turkey
| | | | - Bakiye Goker Bagca
- Department of Medical Biology, Ege University Medical School, Izmir, Turkey
| | - Behrouz Shademan
- Department of Medical Biology, Ege University Medical School, Izmir, Turkey
| | - Fatma Sogutlu
- Department of Medical Biology, Ege University Medical School, Izmir, Turkey
| | | | - Cigir Biray Avci
- Department of Medical Biology, Ege University Medical School, Izmir, Turkey.
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