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Singh P, Solanki R, Tasneem A, Suri S, Kaur H, Shah SR, Dohare R. Screening of miRNAs as prognostic biomarkers and their associated hub targets across Hepatocellular carcinoma using survival-based bioinformatics approach. J Genet Eng Biotechnol 2024; 22:100337. [PMID: 38494261 DOI: 10.1016/j.jgeb.2023.100337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
BACKGROUND The hepatocellular carcinoma (HCC) incident rate is gradually increasing yearly despite all the research and efforts taken by scientific communities and governing bodies. Approximately 90% of all liver cancer cases belong to HCC. Usually, HCC patients approach the treatment in the late stages of this malignancy which becomes the primary cause of high mortality rate. The knowledge about molecular pathogenesis of HCC is limited and needs more attention from researchers to identify the driver genes and miRNAs, which causes to translate this information into clinical practice. Therefore, the key regulators identification of miRNA-mRNA regulatory network is essential to identify HCC-associated genes. METHODOLOGY We extracted microRNA (miRNA) and messenger RNA (mRNA) expression datasets of normal and tumor HCC patient samples from UCSC Xena followed by identifying differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs). Univariate and multivariate cox-proportional hazard models were utilized to identify DEMs having significant association with overall survival (OS). Kaplan-Meier (KM) plotter was used to validate the presence of prognostic DEMs. A risk-score model was used to evaluate the effectiveness of KM-plotter validated DEMs combination on risk of samples. Target DEGs of prognostic miRNAs were identified via sources such as miRTargetLink and miRWalk followed by their validation in an external microarray cohort and enrichment analysis. RESULTS 562 DEGs and 388 DEMs were identified followed by seven prognostic miRNAs (i.e., miR-19a, miR-19b, miR-30d-5p, miR-424-5p, miR-3677-5p, miR-3913-5p, miR-7705) post univariate, multivariate, risk-score model evaluation and KM-plotter analyses. ANLN, MRO, CPEB3 were their targets and were also validated in GSE84005 dataset. CONCLUSIONS The findings of this study decipher that most significant miRNAs and their identified target genes have association with apoptosis, inflammation, cell cycle regulation and cancer-related pathways, which appear to contribute to HCC pathogenesis and therefore, the discovery of new targets.
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Affiliation(s)
- Prithvi Singh
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Rubi Solanki
- School of Interdisciplinary Sciences and Technology, Jamia Hamdard, New Delhi 110062, India
| | - Alvea Tasneem
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Simran Suri
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Harleen Kaur
- Department of Computer Science and Engineering, School of Engineering Sciences and Technology, Jamia Hamdard, New Delhi 110062, India
| | - Sapna Ratan Shah
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Ravins Dohare
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi 110025, India.
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2
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Han W, Wang W, Wang Q, Maduray K, Hao L, Zhong J. A review on regulation of DNA methylation during post-myocardial infarction. Front Pharmacol 2024; 15:1267585. [PMID: 38414735 PMCID: PMC10896928 DOI: 10.3389/fphar.2024.1267585] [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: 07/26/2023] [Accepted: 01/25/2024] [Indexed: 02/29/2024] Open
Abstract
Myocardial infarction (MI) imposes a huge medical and economic burden on society, and cardiac repair after MI involves a complex series of processes. Understanding the key mechanisms (such as apoptosis, autophagy, inflammation, and fibrosis) will facilitate further drug development and patient treatment. Presently, a substantial body of evidence suggests that the regulation of epigenetic processes contributes to cardiac repair following MI, with DNA methylation being among the notable epigenetic factors involved. This article will review the research on the mechanism of DNA methylation regulation after MI to provide some insights for future research and development of related drugs.
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Affiliation(s)
- Wenqiang Han
- National Key Laboratory for Innovation and Transformation of Luobing Theory, The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Wenxin Wang
- National Key Laboratory for Innovation and Transformation of Luobing Theory, The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Qinhong Wang
- National Key Laboratory for Innovation and Transformation of Luobing Theory, The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Kellina Maduray
- National Key Laboratory for Innovation and Transformation of Luobing Theory, The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Li Hao
- Department of Gerontology, The First Affiliated Hospital of Shandong First Medical University and Shandong Provincial Qianfoshan Hospital, Jinan, China
| | - Jingquan Zhong
- National Key Laboratory for Innovation and Transformation of Luobing Theory, The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
- Department of Cardiology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao, China
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Mohammed A, Shaker OG, Khalil MAF, Abu-El-Azayem AK, Samy A, Fathy SA, AbdElguaad MMK, Mahmoud FAM, Erfan R. Circulating miR-206, miR-181b, and miR-21 as promising biomarkers in hypothyroidism and their relationship to related hyperlipidemia and hepatic steatosis. Front Mol Biosci 2024; 11:1307512. [PMID: 38370005 PMCID: PMC10869530 DOI: 10.3389/fmolb.2024.1307512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/08/2024] [Indexed: 02/20/2024] Open
Abstract
Background: Thyroid hormones (THs) signaling has profound effects on many physiological processes. The regulation of THs signaling in various tissues involves the action of microRNAs (miRNAs) on thyroid deiodinases and receptors. THs regulate the expression of certain miRNAs and their target messenger RNAs (mRNAs) in various tissues and cells. The modulation of miRNA levels by THs affects their functions in processes such as liver lipid metabolism, skin physiology, and muscle and heart performance. Aim: This research aimed to investigate miR-181b, miR-206, and miR-21 in the serum of patients with subclinical and overt hypothyroidism to determine their possible role in the diagnosis of the disease and their relationship to clinical disorders related to hypothyroidism. Methods: This study included ninety participants, divided evenly into three groups as follows: patients with overt hypothyroidism diagnosed clinically, radiologically, and by investigation, subclinical hypothyroid patients, and healthy volunteers. The patients had a thorough medical history and underwent a clinical examination. Laboratory tests included plasma cholesterol, LDL, HDL, TGs, liver and renal function tests, CBC, fasting insulin, HOMA-IR, HbA1c, TSH, and free T4. The serum levels of miR-21, miR-206, and miR-181b were measured using qRT-PCR. Results: miR-206 and miR-181b levels were higher in the subclinical group, followed by the hypothyroid and control groups. For miR-21, there was a significantly lower mean value in both the hypothyroid and subclinical groups than in the control group, with no difference between the two groups. Both miR-206 and miR-181b showed a significant negative association with albumin and free T4 levels and a significant direct association with GGT, ALT, AST, creatinine, uric acid, TGs, TC, LDL, TSH, thyroid volume, and CAP score. The same correlation pattern was observed for miR-181b, except that it was not significantly correlated with the TGs. For miR-21 levels, there was a significant positive correlation with albumin, free T4 level, and kPa score and a negative correlation with GGT, ALT, AST, creatinine, uric acid, HOMA-IR, HbA1c, TC, LDL, TSH, and CAP score. Cases with F1 kPa score and S2 CAP scores had significantly higher averages for miR-206 and miR-181b, with a p-value of 0.05. Moreover, miR-21 levels were significantly lower in the S2 CAP score group. Conclusion: These miRNAs (miR-206, miR-181b, and miR-21) may be used as diagnostic biomarkers for hypothyroidism. They may be used as therapeutic targets to control dyslipidemia and hepatic steatosis during hypothyroid disease.
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Affiliation(s)
- Asmaa Mohammed
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Olfat G. Shaker
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Mahmoud A. F. Khalil
- Department of Microbiology and Immunology, Faculty of Pharmacy, Fayoum University, Fayoum, Egypt
| | - Abeer K. Abu-El-Azayem
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Amira Samy
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | - Shaimaa A. Fathy
- Department of Internal Medicine, Diabetes and Endocrinology, Faculty of Medicine, Cairo University, Cairo, Egypt
| | | | - Fatma A. M. Mahmoud
- Department of Tropical Medicine, Faculty of Medicine, Fayoum University, Fayoum, Egypt
| | - Randa Erfan
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Cairo University, Cairo, Egypt
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4
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Bertol BC, Massaro JD, Debortoli G, Santos ALP, de Araújo JNG, Giorgenon TMV, Costa e Silva M, de Figueiredo-Feitosa NL, Collares CVA, de Freitas LCC, Soares EG, Neder L, Silbiger VN, Calado RT, Maciel LMZ, Donadi EA. BRAF, TERT and HLA-G Status in the Papillary Thyroid Carcinoma: A Clinicopathological Association Study. Int J Mol Sci 2023; 24:12459. [PMID: 37569841 PMCID: PMC10419559 DOI: 10.3390/ijms241512459] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
As BRAF, TERT, HLA-G, and microRNAs have been individually associated with papillary thyroid carcinoma (PTC), we aimed to evaluate the individual and collaborative role of these markers in PTC in the same patient cohort. HLA-G and BRAF tumor expression was evaluated by immunohistochemistry. Using molecular methods, BRAFV600E and TERT promoter mutations were evaluated in thyroid fine needle aspirates. MicroRNA tumor profiling was investigated using massively parallel sequencing. We observed strong HLA-G (67.96%) while BRAF (62.43%) staining was observed in PTC specimens. BRAF overexpression was associated with poor response to therapy. The BRAFV600E (52.9%) and TERTC228T (13%) mutations were associated with extrathyroidal extension, advanced-age, and advanced-stage cancer. The TERT rs2853669 CC+TC genotypes (38%) were overrepresented in metastatic tumors. Nine modulated microRNAs targeting the BRAF, TERT, and/or HLA-G genes were observed in PTC and involved with cancer-related signaling pathways. The markers were individually associated with PTC features, emphasizing the synergistic effect of BRAFV600E and TERTC228T; however, their collaborative role on PTC outcome was not fully demonstrated. The differentially expressed miRNAs targeting the BRAF and/or HLA-G genes may explain their increased expression in the tumor milieu.
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Affiliation(s)
- Bruna C. Bertol
- Postgraduate Program of Basic and Applied Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Juliana D. Massaro
- Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (J.D.M.); (M.C.e.S.); (C.V.A.C.)
| | - Guilherme Debortoli
- Department of Anthropology, University of Toronto, Mississauga, ON L5L 1C6, Canada;
| | - André L. P. Santos
- Department of Medical Imaging, Hematology, and Clinical Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (A.L.P.S.); (R.T.C.)
| | - Jéssica N. G. de Araújo
- Department of Clinical Analysis and Toxicology, Federal University of Rio Grande do Norte, Natal 59012-570, Brazil; (J.N.G.d.A.); (V.N.S.)
| | - Tatiana M. V. Giorgenon
- Division of Endocrinology and Metabolism, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (T.M.V.G.); (N.L.d.F.-F.); (L.M.Z.M.)
| | - Matheus Costa e Silva
- Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (J.D.M.); (M.C.e.S.); (C.V.A.C.)
| | - Nathalie L. de Figueiredo-Feitosa
- Division of Endocrinology and Metabolism, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (T.M.V.G.); (N.L.d.F.-F.); (L.M.Z.M.)
| | - Cristhianna V. A. Collares
- Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (J.D.M.); (M.C.e.S.); (C.V.A.C.)
| | - Luiz Carlos C. de Freitas
- Department of Ophthalmology, Otorhinolaryngology and Head and Neck Surgery, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil;
| | - Edson G. Soares
- Department of Pathology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (E.G.S.); (L.N.)
| | - Luciano Neder
- Department of Pathology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (E.G.S.); (L.N.)
| | - Vivian N. Silbiger
- Department of Clinical Analysis and Toxicology, Federal University of Rio Grande do Norte, Natal 59012-570, Brazil; (J.N.G.d.A.); (V.N.S.)
| | - Rodrigo T. Calado
- Department of Medical Imaging, Hematology, and Clinical Oncology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (A.L.P.S.); (R.T.C.)
| | - Léa M. Z. Maciel
- Division of Endocrinology and Metabolism, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (T.M.V.G.); (N.L.d.F.-F.); (L.M.Z.M.)
| | - Eduardo A. Donadi
- Postgraduate Program of Basic and Applied Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil
- Division of Clinical Immunology, Department of Medicine, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (J.D.M.); (M.C.e.S.); (C.V.A.C.)
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Shih ML, Lawal B, Cheng SY, Olugbodi JO, Babalghith AO, Ho CL, Cavalu S, Batiha GES, Albogami S, Alotaibi SS, Lee JC, Wu ATH. Large-scale transcriptomic analysis of coding and non-coding pathological biomarkers, associated with the tumor immune microenvironment of thyroid cancer and potential target therapy exploration. Front Cell Dev Biol 2022; 10:923503. [PMID: 35990603 PMCID: PMC9384576 DOI: 10.3389/fcell.2022.923503] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 06/30/2022] [Indexed: 12/11/2022] Open
Abstract
Papillary thyroid carcinoma (PTC) is the most prevalent endocrine malignancy with a steadily increasing global incidence in recent decades. The pathogenesis of PTC is poorly understood, and the present diagnostic protocols are deficient. Thus, identifying novel prognostic biomarkers to improve our understanding of the mechanisms of pathogenesis, diagnosis, and designing therapeutic strategies for PTC is crucial. In this study, we integrated 27 PTC transcriptomic datasets and identified overlapping differentially expressed genes (DEGs) and differentially expressed microRNAs, collectively known as thyroid tumor-enriched proteins (TTEPs), and TTEmiRs, respectively. Our integrated bioinformatics analysis revealed that TTEPs were associated with tumor stages, poor surgical outcomes, distant metastasis, and worse prognoses in PTC cohorts. In addition, TTEPs were found to be associated with tumor immune infiltrating cells and immunosuppressive phenotypes of PTC. Enrichment analysis suggested the association of TTEPs with epithelial-to-mesenchymal transition (EMT), cell-matrix remodeling, and transcriptional dysregulation, while the TTEmiRs (miR-146b-5p and miR-21-5p) were associated with the modulation of the immune response, EMT, migration, cellular proliferation, and stemness. Molecular docking simulations were performed to evaluate binding affinities between TTEPs and antrocinnamomin, antcin, and antrocin, the bioactive compounds from one of the most reputable Taiwan indigenous medicinal plants (Antrodia camphorata). Our results revealed that antcin exhibited higher binding efficacies toward FN1, ETV5, and NRCAM, whereas antrocin demonstrated the least. Among the targets, fibronectin (FN1) demonstrated high ligandability potential for the compounds whereas NRCAM demonstrated the least. Collectively, our results hinted at the potential of antcin for targeting TTEPs. In conclusion, this comprehensive bioinformatics analysis strongly suggested that TTEPs and TTEmiRs could be used as potential diagnostic biomarker signatures and be exploited as potential targets for therapeutics development.
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Affiliation(s)
- Ming-Lang Shih
- Division of General Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Bashir Lawal
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei, Taiwan
- Graduate Institute for Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Sheng-Yao Cheng
- Department of Otolaryngology-Head and Neck Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | | | - Ahmad O Babalghith
- Medical Genetics Department, Faculty of Medicine, Umm al-Qura Univeristy, Mecca, Saudi Arabia
| | - Ching-Liang Ho
- Division of Hematology and Oncology Medicine, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Simona Cavalu
- Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
| | - Sarah Albogami
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Saqer S. Alotaibi
- Department of Biotechnology, College of Science, Taif University, Taif, Saudi Arabia
| | - Jih-Chin Lee
- Department of Otolaryngology-Head and Neck Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
- *Correspondence: Jih-Chin Lee, ; Alexander T. H. Wu,
| | - Alexander T. H. Wu
- The PhD Program of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Clinical Research Center, Taipei Medical University Hospital, Taipei Medical University, Taipei, Taiwan
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, Taiwan
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan
- *Correspondence: Jih-Chin Lee, ; Alexander T. H. Wu,
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Ma X, Wang Z, Zhang C, Bian Y, Zhang X, Liu X, Cao Y, Zhao Y. Association of SNPs in the FK-506 binding protein (FKBP5) gene among Han Chinese women with polycystic ovary syndrome. BMC Med Genomics 2022; 15:149. [PMID: 35787810 PMCID: PMC9254403 DOI: 10.1186/s12920-022-01301-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 06/30/2022] [Indexed: 11/10/2022] Open
Abstract
Background Polycystic ovary syndrome (PCOS) is a common endocrine disorder in premenopausal women, whose etiology remains uncertain, although it is known to be highly heterogeneous and genetically complex. PCOS often presents with hyperandrogenism symptoms. The present study aimed to determine whether polymorphisms in the FK-506 binding protein 5 (FKBP5) gene (androgen target gene) are associated with an association for PCOS and hyperandrogenism. Methods This is a case–control study, and association analyses were conducted. A total of 13 single-nucleotide polymorphisms (SNPs) in the FKBP5 gene were evaluated in 775 PCOS patients who were diagnosed based on the Rotterdam Standard and 783 healthy Chinese Han women. Associations between FKBP5 SNPs and hormone levels were investigated. These 13 SNPs were genotyped using the Sequenom MassARRAY system, and an association analysis between the phenotype and alleles and genotypes were conducted. Results The genotype frequencies for the rs1360780 and rs3800373 SNPs differed significantly between the PCOS cases and healthy controls (p = 0.025, OR is 1.63 (1.05–2.53) and p = 0.029, OR is 1.59 (1.03–2.45) respectively under co-dominant model). Moreover, the genotype frequencies and genetic model analysis for the SNPs rs1360780, rs9470080, rs9296158, rs1043805 and rs7757037 differed significantly between the hyperandrogenism and non-hyperandrogenism groups of PCOS patients. The TT genotype of rs1360780, the TT genotype of rs9470080, the TT genotype of rs1043805 or the GG genotype of rs7705037 (ORs are 2.13 (1.03–4.39), 1.81 (1.03–3.17), 2.94 (1.32–6.53) and 1.72 (1.04–2.84) respectively) were correlated with androgen level of PCOS patients. Conclusion Our study showed that FKBP5 gene polymorphisms are associated with PCOS generally (rs1360780 and rs3800373) and with the hyperandrogenism subtype specifically (rs1360780, rs9470080, rs9296158, rs1043805 and rs7757037).
Supplementary Information The online version contains supplementary material available at 10.1186/s12920-022-01301-0.
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Affiliation(s)
- Xinyue Ma
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, 250012, Shandong, China
| | - Zhao Wang
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, 250012, Shandong, China
| | - Changming Zhang
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, 250012, Shandong, China
| | - Yuehong Bian
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, 250012, Shandong, China
| | - Xin Zhang
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, 250012, Shandong, China
| | - Xin Liu
- Central Laboratory, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, China
| | - Yongzhi Cao
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China. .,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China. .,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China. .,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, 250012, Shandong, China.
| | - Yueran Zhao
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, China. .,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China. .,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China. .,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, 250012, Shandong, China. .,Central Laboratory, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250021, Shandong, China.
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Asare A, Yao H, Lara OD, Wang Y, Zhang L, Sood AK. Race-associated molecular changes in gynecologic malignancies. CANCER RESEARCH COMMUNICATIONS 2022; 2:99-109. [PMID: 35992327 PMCID: PMC9390975 DOI: 10.1158/2767-9764.crc-21-0018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The difference in cancer morbidity and mortality between individuals of different racial groups is complex. Health disparities provide a framework to explore potential connections between poor outcomes and individuals of different racial backgrounds. This study identifies genomic changes in African-American patients with gynecologic malignancies, a population with well-established disparities in outcomes. Our data explore whether social health disparities might mediate interactions between the environment and tumor epigenomes and genomes that can be identified. Using The Cancer Genetic Ancestry Atlas, which encodes data from The Cancer Genome Atlas by ancestry and allows for systematic analyses of sequencing data by racial group, we performed large-scale, comparative analyses to identify novel targets with alterations in methylation, transcript, and microRNA expression between tumors from women of European American or African American racial groups across all gynecologic malignancies. We identify novel discrete genomic changes in these complex malignancies and suggest a framework for identifying novel therapeutic targets for future investigation.
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Affiliation(s)
- Amma Asare
- Department of Obstetrics and Gynecology, Baylor College of Medicine, Houston, Texas
| | - Hui Yao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Olivia D. Lara
- Department of Obstetrics and Gynecology, NYU Langone Health, New York
| | - Ying Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lin Zhang
- Department of Obstetrics and Gynecology, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Anil K. Sood
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Corresponding Author: Anil K. Sood, Department of Gynecologic Oncology and Reproductive Medicine, Unit 1362, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030. Phone: 713-745-5266; E-mail:
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8
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Papaioannou M, Chorti AG, Chatzikyriakidou A, Giannoulis K, Bakkar S, Papavramidis TS. MicroRNAs in Papillary Thyroid Cancer: What Is New in Diagnosis and Treatment. Front Oncol 2022; 11:755097. [PMID: 35186709 PMCID: PMC8851242 DOI: 10.3389/fonc.2021.755097] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Accepted: 12/08/2021] [Indexed: 12/12/2022] Open
Abstract
Introduction Papillary thyroid cancer (PTC) accounts for up to 80% of thyroid malignancies. New diagnostic and therapeutic options are suggested including innovative molecular methods. MicroRNAs (miRNAs) are nonprotein coding single-stranded RNAs that regulate many cell processes. The aim of the present study is to review the deregulated miRNAs associated with PTCs. Methods A bibliographic research was conducted, resulting in 272 articles referred to miRNAs and PTC. Regarding our exclusion criteria, 183 articles were finally included in our review. Results A remarkably large number of miRNAs have been found to be deregulated during PTC manifestation in the literature. The deregulated miRNAs are detected in tissue samples, serum/plasma, and FNA samples of patients with PTC. These miRNAs are related to several molecular pathways, involving genes and proteins responsible for important biological processes. MiRNA deregulation is associated with tumor aggressiveness, including larger tumor size, multifocality, extrathyroidal extension, lymphovascular invasion, lymph node and distant metastasis, and advanced tumor node metastasis stage. Conclusion MiRNAs are proposed as new diagnostic and therapeutic tools regarding PTC. They could be essential biomarkers for PTC diagnosis applied in serum and FNA samples, while their contribution to prognosis is of great importance.
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Affiliation(s)
- Maria Papaioannou
- Laboratory of Biological Chemistry, School of Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Angeliki G. Chorti
- 1st Propedeutic Department of Surgery, American Hellenic Educational Progressive Association (AHEPA) University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anthoula Chatzikyriakidou
- Laboratory of Medical Biology, School of Medicine, Faculty of Health Science, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Kleanthis Giannoulis
- 1st Propedeutic Department of Surgery, American Hellenic Educational Progressive Association (AHEPA) University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sohail Bakkar
- Department of Surgery, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - Theodosios S. Papavramidis
- 1st Propedeutic Department of Surgery, American Hellenic Educational Progressive Association (AHEPA) University Hospital, Aristotle University of Thessaloniki, Thessaloniki, Greece
- *Correspondence: Theodosios S. Papavramidis,
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9
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Rogucki M, Buczyńska A, Krętowski AJ, Popławska-Kita A. The Importance of miRNA in the Diagnosis and Prognosis of Papillary Thyroid Cancer. J Clin Med 2021; 10:4738. [PMID: 34682861 PMCID: PMC8537372 DOI: 10.3390/jcm10204738] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 12/14/2022] Open
Abstract
In recent years, the global incidence of thyroid cancer has been increasing. Despite the significant progress in the diagnostic tools applied for papillary thyroid cancer (PTC) diagnosis, commonly used methods require undergoing invasive diagnostic procedures, such as liquid biopsy, which still, in some cases, remains imprecise. In this case, novel screening and diagnostic biomarkers are still being evaluated using highly specialized techniques, which could increase PTC detection. Currently, a number of genes and proteins associated with PTC development are currently under investigation to assess their clinical utility. Accordingly, a literature search was undertaken to collect novel information about the diagnosis of and prognosis for PTC with a particular emphasis on the role of microRNA (miRNA) evaluation. The early identification of novel biomarkers is essential for facilitating appropriate therapeutic decisions. Moreover, the evaluation of plasma- and serum-derived miRNA measurements could be considered as equivalent thyroid cancer screening tools in the future. On the other hand, the PTC pathogenesis could be evaluated further with the use of miRNA evaluation, which may bring novel insights for potential medical target determination.
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Affiliation(s)
- Mariusz Rogucki
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15-276 Bialystok, Poland; (A.J.K.); (A.P.-K.)
| | - Angelika Buczyńska
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland;
| | - Adam Jacek Krętowski
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15-276 Bialystok, Poland; (A.J.K.); (A.P.-K.)
- Clinical Research Centre, Medical University of Bialystok, 15-276 Bialystok, Poland;
| | - Anna Popławska-Kita
- Department of Endocrinology, Diabetology and Internal Medicine, Medical University of Bialystok, 15-276 Bialystok, Poland; (A.J.K.); (A.P.-K.)
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10
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Sun CX, Liu BJ, Su Y, Shi GW, Wang Y, Chi JF. MiR-181a promotes cell proliferation and migration through targeting KLF15 in papillary thyroid cancer. Clin Transl Oncol 2021; 24:66-75. [PMID: 34312797 DOI: 10.1007/s12094-021-02670-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/10/2021] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Papillary thyroid cancer (PTC) is the predominant histological type of thyroid cancer, accounting for 80% of thyroid cancers. MiR-181a is a novel microRNA that is usually upregulated in multiple cancers. This study aims to explore the role and underlying mechanism of miR-181a in PTC. METHODS CCK8 and Transwell assays were performed to evaluate cell viability and migration. The mRNA level of miR-181a and KLF15 was calculated by qRT-PCR. The protein level of E-Cadherin, N-Cadherin and GAPDH was evaluated by western blot. Dual luciferase assay was conducted to validate that miR-181a directly targeting the 3'-UTR of KLF15 mRNA in TPC-1 cells. RESULTS We observed that miR-181a was overexpressed and KLF15 was low expressed in PTC tissues and cell lines. Upregulation of miR-181a or downregulation of KLF15 predicted poor outcomes in PTC patients. MiR-181a improved cell growth of PTC, migration and epithelial-mesenchymal transition (EMT) in TPC-1 cells. KLF15 was a target gene of miR-181a and its expression was mediated by miR-181a. KLF15 partially reversed the facilitating effect of miR-181a on cell proliferation and migration in TPC-1 cells. CONCLUSION We discovered that miR-181a served as an oncogene downregulating KLF15, thereby inhibiting cell proliferation, migration and the EMT. These findings demonstrate that miR-181a plays a significant role in PTC progression and could be a therapeutic target for PTC.
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Affiliation(s)
- C X Sun
- Department of Endocrinology, Yantaishan Hospital, Yantai, 264000, Shandong, China
| | - B J Liu
- Operation Room, Rizhao Hospital of TCM, Rizhao, 276800, Shandong, China
| | - Y Su
- Operation Room, Qingdao Hospital of Traditional Chinese Medicine, Qingdao Hiser Hospital, Qingdao, 266033, Shandong, China
| | - G W Shi
- Health Management Center, Zhangqiu District People's Hospital, Jinan, 250200, Shandong, China
| | - Y Wang
- Health Management Center, Zhangqiu District People's Hospital, Jinan, 250200, Shandong, China
| | - J F Chi
- Department of Endocrinology, Jinan Central Hospital, 105 Jiefang Road, Lixia District, Jinan, 250013, Shandong, China.
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11
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Park JL, Kim SK, Jeon S, Jung CK, Kim YS. MicroRNA Profile for Diagnostic and Prognostic Biomarkers in Thyroid Cancer. Cancers (Basel) 2021; 13:632. [PMID: 33562573 PMCID: PMC7916038 DOI: 10.3390/cancers13040632] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 02/02/2021] [Accepted: 02/02/2021] [Indexed: 02/07/2023] Open
Abstract
The challenge in managing thyroid nodules is to accurately diagnose the minority of those with malignancy. We aimed to identify diagnostic and prognostic miRNA markers for thyroid nodules. In a discovery cohort, we identified 20 candidate miRNAs to differentiate between noninvasive follicular thyroid neoplasms with papillary-like nuclear features (NIFTP) and papillary thyroid carcinomas (PTC) by using the high-throughput small RNA sequencing method. We then selected three miRNAs (miR-136, miR-21, and miR-127) that were differentially expressed between the PTC follicular variant and other variants in The Cancer Genome Atlas data. High expression of three miRNAs differentiated thyroid cancer from nonmalignant tumors, with an area under curve (AUC) of 0.76-0.81 in an independent cohort. In patients with differentiated thyroid cancer, the high-level expression of the three miRNAs was an independent indicator for both distant metastases and recurrent or persistent disease. In patients with PTC, a high expression of miRNAs was associated with an aggressive histologic variant, extrathyroidal extension, distant metastasis, or recurrent or persistent disease. Three miRNAs may be used as diagnostic markers for differentiating thyroid cancers from benign tumors and tumors with extremely low malignant potential (NIFTP), as well as prognostic markers for predicting the risk of recurrent/persistent disease for differentiated thyroid cancer.
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Affiliation(s)
- Jong-Lyul Park
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea;
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea;
| | - Seon-Kyu Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea;
- Department of Bioinformatics, University of Science and Technology, Daejeon 34141, Korea
| | - Sora Jeon
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea;
| | - Chan-Kwon Jung
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea;
- Department of Hospital Pathology, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
| | - Yong-Sung Kim
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea;
- Department of Functional Genomics, University of Science and Technology, Daejeon 34141, Korea
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12
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Hou S, Xie X, Zhao J, Wu C, Li N, Meng Z, Cai C, Tan J. Downregulation of miR-146b-3p Inhibits Proliferation and Migration and Modulates the Expression and Location of Sodium/Iodide Symporter in Dedifferentiated Thyroid Cancer by Potentially Targeting MUC20. Front Oncol 2021; 10:566365. [PMID: 33489878 PMCID: PMC7821393 DOI: 10.3389/fonc.2020.566365] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 11/17/2020] [Indexed: 11/13/2022] Open
Abstract
The dedifferentiation of differentiated thyroid cancer (DTC) is a challenging problem for radioactive iodine (131I) treatment, also known as radioiodine refractory differentiated thyroid cancer (RAIR-DTC). The purpose of this study was to further explore the mechanism of the redifferentiation of dedifferentiated thyroid cancer. Ineffective and effective groups of 131I therapy were analyzed and compared in both our clinical and TCGA samples. Whole-exome sequencing, mutation analysis, transcriptome analysis, and in vitro functional experiments were conducted. FLG, FRG1, MUC6, MUC20, and PRUNE2 were overlapping mutation genes between our clinical cases, and the TCGA cases only appeared in the ineffective group. The expression of miR-146b-3p target MUC20 was explored. The expression levels of miR-146b-3p and MUC20 were significantly increased, and the inhibition of miR-146b-3p expression significantly inhibited proliferation and migration, promoted apoptosis, regulated the expression and location of thyroid differentiation-related genes, and sodium/iodide symporter (NIS) in dedifferentiated thyroid cancer cells (WRO). Thus, miR-146b-3p potentially targets MUC20 participation in the formation of DTC dedifferentiation, resulting in resistance to 131I and the loss of the iodine uptake ability of DTC cancer foci, promoting refractory differentiated thyroid cancer. miR-146b-3p may be a potentially therapeutic target for the reapplication of 131I therapy in dedifferentiated thyroid cancer patients.
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Affiliation(s)
- Shasha Hou
- Department of Nuclear Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Xiaorui Xie
- Department of Pediatrics, Tianjin Medical University General Hospital, Tianjin, China
| | - Jing Zhao
- Department of Ultrasound, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Cailan Wu
- Department of Nuclear Medicine, Tianjin Fourth Central Hospital, Tianjin, China
| | - Ning Li
- Department of Nuclear Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Zhaowei Meng
- Department of Nuclear Medicine, Tianjin Medical University General Hospital, Tianjin, China
| | - Chunquan Cai
- Department of Pediatrics, Tianjin Children's Hospital, Tianjin, China
| | - Jian Tan
- Department of Nuclear Medicine, Tianjin Medical University General Hospital, Tianjin, China
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13
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Cui Y, Hunt A, Li Z, Birkin E, Lane J, Ruge F, Jiang WG. Lead DEAD/H box helicase biomarkers with the therapeutic potential identified by integrated bioinformatic approaches in lung cancer. Comput Struct Biotechnol J 2020; 19:261-278. [PMID: 33425256 PMCID: PMC7779375 DOI: 10.1016/j.csbj.2020.12.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/02/2020] [Accepted: 12/08/2020] [Indexed: 02/07/2023] Open
Abstract
DEAD/H box helicases are implicated in lung cancer but have not been systematically investigated for their clinical significance and function. In this study, we aimed to evaluate the potential of DEAD/H box helicases as prognostic biomarkers and therapeutic targets in lung cancer by integrated bioinformatic analysis of multivariate large-scale databases. Survival and differential expression analysis of these helicases enabled us to identify four biomarkers with the most significant alterations. These were found to be the negative prognostic factors DDX11, DDX55 and DDX56, and positive prognostic factor DDX5. Pathway enrichment analysis indicates that MYC signalling is negatively associated with expression levels of the DDX5 gene while positively associated with that of DDX11, DDX55 and DDX56. High expression levels of the DDX5 gene is associated with low mutation levels of TP53 and MUC16, the two most frequently mutated genes in lung cancer. In contrast, high expression levels of DDX11, DDX55 and DDX56 genes are associated with high levels of TP53 and MUC16 mutation. The tumour-infiltrated CD8 + T and B cells positively correlate with levels of DDX5 gene expression, while negatively correlate with that of the other three DEAD box helicases, respectively. Moreover, the DDX5-associated miRNA profile is distinguished from the miRNA profiles of DDX11, DDX55 and DDX56, although each DDX has a different miRNA signature. The identification of these four DDX helicases as biomarkers will be valuable for prognostic prediction and targeted therapeutic development in lung cancer.
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Affiliation(s)
- Yuxin Cui
- Cardiff China Research Collaborative, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Adam Hunt
- Cardiff China Research Collaborative, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Zhilei Li
- Department of Pharmacy, Zhujiang Hospital of Southern Medical University, Guangzhou 510282, PR China
| | - Emily Birkin
- Cardiff & Vale University Health Board, University Hospital of Wales, Heath Park, Cardiff CF14 4XW, UK
| | - Jane Lane
- Cardiff China Research Collaborative, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Fiona Ruge
- Cardiff China Research Collaborative, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Wen G Jiang
- Cardiff China Research Collaborative, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
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14
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Kumar S, Gonzalez EA, Rameshwar P, Etchegaray JP. Non-Coding RNAs as Mediators of Epigenetic Changes in Malignancies. Cancers (Basel) 2020; 12:E3657. [PMID: 33291485 PMCID: PMC7762117 DOI: 10.3390/cancers12123657] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 12/12/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are untranslated RNA molecules that regulate gene expressions. NcRNAs include small nuclear RNAs (snRNAs), small nucleolar RNAs (snoRNAs), ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), circular RNAs (cRNAs) and piwi-interacting RNAs (piRNAs). This review focuses on two types of ncRNAs: microRNAs (miRNAs) or short interfering RNAs (siRNAs) and long non-coding RNAs (lncRNAs). We highlight the mechanisms by which miRNAs and lncRNAs impact the epigenome in the context of cancer. Both miRNAs and lncRNAs have the ability to interact with numerous epigenetic modifiers and transcription factors to influence gene expression. The aberrant expression of these ncRNAs is associated with the development and progression of tumors. The primary reason for their deregulated expression can be attributed to epigenetic alterations. Epigenetic alterations can cause the misregulation of ncRNAs. The experimental evidence indicated that most abnormally expressed ncRNAs impact cellular proliferation and apoptotic pathways, and such changes are cancer-dependent. In vitro and in vivo experiments show that, depending on the cancer type, either the upregulation or downregulation of ncRNAs can prevent the proliferation and progression of cancer. Therefore, a better understanding on how ncRNAs impact tumorigenesis could serve to develop new therapeutic treatments. Here, we review the involvement of ncRNAs in cancer epigenetics and highlight their use in clinical therapy.
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Affiliation(s)
- Subhasree Kumar
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA; (S.K.); (E.A.G.)
| | - Edward A. Gonzalez
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA; (S.K.); (E.A.G.)
| | - Pranela Rameshwar
- Department of Medicine, Hematology/Oncology, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, NJ 07103, USA
| | - Jean-Pierre Etchegaray
- Department of Biological Sciences, Rutgers University, Newark, NJ 07102, USA; (S.K.); (E.A.G.)
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15
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Peñaloza E, Soto-Carrasco G, Krause BJ. MiR-21-5p directly contributes to regulating eNOS expression in human artery endothelial cells under normoxia and hypoxia. Biochem Pharmacol 2020; 182:114288. [PMID: 33075314 DOI: 10.1016/j.bcp.2020.114288] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/14/2020] [Accepted: 10/14/2020] [Indexed: 12/22/2022]
Abstract
Clinical conditions associated with hypoxia and oxidative stress, such as fetal growth restriction (FGR), results in endothelial dysfunction. Previous reports show that changes in eNOS expression under these conditions are tightly controlled by DNA methylation and histone posttranslational modifications. However, the contribution of an orchestrating epigenetic mechanism, such as miRNAs, on the NO-related genes expression has not been addressed. We aimed to determine the levels of miRNAs highly expressed in normal endothelial cells (EC), miR-21 and miR-126, in FGR human umbilical artery EC (HUAEC), and their effects on hypoxia-dependent regulation of both, NO-related and oxidative stress-related genes. Results were validated by transcriptome analysis of HUAEC cultured under chronic low oxygen conditions. Cultured FGR-HUAEC showed decreased hsa-miR-21, DDAH1, SOD1, and NRF2, but increased miR-126, NOX4, and eNOS levels, compared with controls. MiR-21-5p levels in FGR were associated with increased hg-miR-21 gene promoter methylation, with no changes in hg-miR-126 gene promoter methylation. HUAEC exposed to hypoxia showed a transient increase in eNOS and DDAH11, paralleled by decrease miR-21-5p levels, but no changes in miR-126-3p and the other genes under study. Transcriptome profiling showed an inverse relationship among miR-21 and several transcripts targeted by miR-21 in HUAEC exposed to hypoxia, meanwhile miR-21-5p-mimic decreased eNOS and DDAH1 transcripts stability, blocking their induction by hypoxia. Consequently, FGR programs a hypoxia-related miRNA that contributes to the regulation of the NO pathway, involving a direct effect of miR-21-5p on eNOS transcript stability, not previously reported. Moreover, hypoxia downregulates miR-21-5p, contributing to increasing the expression of NO-related genes in arterial endothelial cells.
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Affiliation(s)
- Estefania Peñaloza
- Instituto de Ciencias de la Salud, Universidad de O'Higgins, Rancagua, Chile
| | | | - Bernardo J Krause
- Instituto de Ciencias de la Salud, Universidad de O'Higgins, Rancagua, Chile.
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16
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Chen Y, Wang K, Shang M, Zhao S, Zhang Z, Yang H, Chen Z, Du R, Wang Q, Chen B. Exploration of DNA Methylation-Driven Genes in Papillary Thyroid Carcinoma Based on the Cancer Genome Atlas. J Comput Biol 2020; 28:99-114. [PMID: 32790501 DOI: 10.1089/cmb.2019.0471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Although the incidence of thyroid carcinoma is reported to be the highest among malignancies of endocrine system, its diagnosis is still unsatisfactory. This study sought to explore the key DNA methylation-driven genes in the development of papillary thyroid carcinoma (PTC) via a bioinformatic analysis based on the Cancer Genome Atlas (TCGA) database and was validated using the Gene Expression Omnibus (GEO) database. The level 3 DNA methylation, mRNA expression, and clinical data of 499 patients with PTC were obtained from the TCGA database. The R package LIMMA, edgeR, and MethylMix were applied to explore the DNA methylation-driven genes in PTC. The ConsensusPathDB software, DAVID, and STRING databases were used for Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes pathway analyses, as well as protein/protein interaction network construction individually. To verify the result, the explored genes were validated using GSE97466 data set retrieved from the GEO database. Fifty-seven (57) methylation-driven genes were detected via MethylMix based on a beta mixture model that compared the DNA methylation state of tumor tissues with that of the normal tissues. Eventually, three genes (TNFRSF1A, CLDN1, and CASP1) were identified to be the most potential biomarkers for the diagnosis or treatment of PTC. These results suggest the crucial roles of TNFRSF1A, CLDN1, and CASP1 in the tumorigenesis of PTC and provide a vital bioinformatic basis for further experimental validations and clinical applications.
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Affiliation(s)
- Yanwei Chen
- Department of Medical Ultrasound, Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China
| | - Keke Wang
- Department of Medical Ultrasound, Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China
| | - Mengyuan Shang
- Department of Medical Ultrasound, Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China
| | - Shuangshuang Zhao
- Department of Medical Ultrasound, Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China
| | - Zheng Zhang
- Department of Medical Ultrasound, Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China
| | - Haizhen Yang
- Department of Medical Ultrasound, Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China
| | - Zheming Chen
- Department of Medical Ultrasound, Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China
| | - Rui Du
- Department of Medical Ultrasound, Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China
| | - Qilong Wang
- Department of Pharmaceutics, School of Pharmacy and Center for Drug/Gene Delivery and Tissue Engineering, Jiangsu University, Zhenjiang, People's Republic of China
| | - Baoding Chen
- Department of Medical Ultrasound, Affiliated Hospital of Jiangsu University, Zhenjiang, People's Republic of China
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17
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Karimzadeh MR, Pourdavoud P, Ehtesham N, Qadbeigi M, Asl MM, Alani B, Mosallaei M, Pakzad B. Regulation of DNA methylation machinery by epi-miRNAs in human cancer: emerging new targets in cancer therapy. Cancer Gene Ther 2020; 28:157-174. [PMID: 32773776 DOI: 10.1038/s41417-020-00210-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 07/24/2020] [Accepted: 07/29/2020] [Indexed: 12/13/2022]
Abstract
Disruption in DNA methylation processes can lead to alteration in gene expression and function that would ultimately result in malignant transformation. In this way, studies have shown that, in cancers, methylation-associated silencing inactivates tumor suppressor genes, as effectively as mutations. DNA methylation machinery is composed of several genes, including those with DNA methyltransferases activity, proteins that bind to methylated cytosine in the promoter region, and enzymes with demethylase activity. Based on a prominent body of evidence, DNA methylation machinery could be regulated by microRNAs (miRNAs) called epi-miRNAs. Numerous studies demonstrated that dysregulation in DNA methylation regulators like upstream epi-miRNAs is indispensable for carcinogenesis; consequently, the malignant capacity of these cells could be reversed by restoring of this regulatory system in cancer. Conceivably, recognition of these epi-miRNAs in cancer cells could not only reveal novel molecular entities in carcinogenesis, but also render promising targets for cancer therapy. In this review, at first, we have an overview of the methylation alteration in cancers, and the effect of this phenomenon in miRNAs expression and after that, we conduct an in-depth discussion about the regulation of DNA methylation regulators by epi-miRNAs in cancer cells.
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Affiliation(s)
- Mohammad Reza Karimzadeh
- Department of medical Genetics, School of Medicine, Bam University of Medical Sciences, Bam, Iran
| | | | - Naeim Ehtesham
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Masood Movahedi Asl
- Non-Communicable Diseases Research Center, Endocrinology and Metabolism Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Behrang Alani
- Department of Applied Cell Sciences, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Meysam Mosallaei
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Bahram Pakzad
- Department of Internal Medicine, School of Medicine, Isfahan University of Medical Science, Isfahan, Iran.
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Kenney MC, Nashine S. Further understanding of epigenetic dysfunction of the retinal pigment epithelium in AMD. EXPERT REVIEW OF OPHTHALMOLOGY 2020; 15:221-231. [PMID: 33732291 DOI: 10.1080/17469899.2020.1767597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Introduction Modulation of epigenetic mechanisms that contribute to retinal development may render the eye susceptible to age-related macular degeneration (AMD). Progression of AMD involves alterations of epigenome such as CpG methylation and histone modifications, and study of the epigenetic regulation of molecular/ cellular pathways associated with AMD might identify target epigenetic markers for treatment of AMD. Areas covered In this review, we provide an overview of the influence of epigenetic factors on signaling pathways/ related genes associated with AMD, mainly hypoxia, angiogenesis, inflammation, complement, and oxidative stress; and discuss the critical role of microRNAs in AMD. Expert Opinion Better understanding of epigenetic-mediated and microRNA-mediated regulation of the AMD disease-related pathways would help to assess the risk of developing AMD besides providing valuable insight on potential target candidates for AMD therapy.
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Affiliation(s)
- Maria Cristina Kenney
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA, USA.,Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, CA, USA
| | - Sonali Nashine
- Department of Ophthalmology, Gavin Herbert Eye Institute, University of California Irvine, Irvine, CA, USA
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Lu J, Tan T, Zhu L, Dong H, Xian R. Hypomethylation Causes MIR21 Overexpression in Tumors. MOLECULAR THERAPY-ONCOLYTICS 2020; 18:47-57. [PMID: 32637580 PMCID: PMC7321816 DOI: 10.1016/j.omto.2020.05.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 05/22/2020] [Indexed: 12/13/2022]
Abstract
miR-21 is an oncogenic microRNA (miRNA) that is upregulated in many solid tumors. However, the effect of MIR21 hypomethylation on miR-21 expression in tumors and the mechanism of miR-21 DNA demethylation remain unclear. In this study, we confirmed that the expression of miR-21 was significantly increased in multiple tumors. We analyzed eight types of cancer, including breast cancer (BRCA), lung adenocarcinoma (LUAD), renal and renal clear cell carcinoma (KIRC), bladder urothelial carcinoma (BLCA), hepatocellular carcinoma (LIHC), lung squamous cell cancer (LUSC), renal papillary cell carcinoma (KIRP), and pancreatic adenocarcinoma (PAAD). MIR21 DNA methylation levels were elevated in these cancers. CpG loci located approximately 200 bp upstream of the transcription initiation site strongly affect MIR21 expression. We also confirmed MIR21 hypomethylation by pyrosequencing of fresh clear cell renal cell carcinoma (ccRCC) samples. Demethylating agent was proved to increase hsa-miR-21-5p level in HEK293T cells, while knockdown of DNA demethylases TET3 and TDG decreased MIR21 expression. In addition, we showed that the cg02515217 CpG locus in MIR21 promoter was a conserved binding site of transcription factors CEBPB, MEIS3, and TEAD4, which were co-expressed with miR-21 in tumors. These observations identified that gene hypomethylation regulated the expression of MIR21 in tumors.
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Affiliation(s)
- Jun Lu
- Fuzhou General Clinical College, Fujian Medical University, Fuzhou, China.,900 Hospital of the Joint Logistics Team, Fuzhou, China.,Fujian Provincial Key Laboratory of Transplant Biology, Dongfang Hospital (900 Hospital of the Joint Logistics Team), Xiamen University, Fuzhou, China
| | - Ting Tan
- Fuzhou General Clinical College, Fujian Medical University, Fuzhou, China.,900 Hospital of the Joint Logistics Team, Fuzhou, China
| | - Ling Zhu
- Fuzhou General Clinical College, Fujian Medical University, Fuzhou, China.,900 Hospital of the Joint Logistics Team, Fuzhou, China.,Fujian Provincial Key Laboratory of Transplant Biology, Dongfang Hospital (900 Hospital of the Joint Logistics Team), Xiamen University, Fuzhou, China
| | - Huiyue Dong
- Fuzhou General Clinical College, Fujian Medical University, Fuzhou, China.,900 Hospital of the Joint Logistics Team, Fuzhou, China.,Fujian Provincial Key Laboratory of Transplant Biology, Dongfang Hospital (900 Hospital of the Joint Logistics Team), Xiamen University, Fuzhou, China
| | - Ronghua Xian
- Fuzhou General Clinical College, Fujian Medical University, Fuzhou, China.,900 Hospital of the Joint Logistics Team, Fuzhou, China
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20
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Boresowicz J, Kober P, Rusetska N, Maksymowicz M, Paziewska A, Dąbrowska M, Zeber-Lubecka N, Kunicki J, Bonicki W, Ostrowski J, Siedlecki JA, Bujko M. DNA Methylation Influences miRNA Expression in Gonadotroph Pituitary Tumors. Life (Basel) 2020; 10:E59. [PMID: 32413978 PMCID: PMC7281098 DOI: 10.3390/life10050059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 12/30/2022] Open
Abstract
microRNAs are involved in pathogenesis of cancer. DNA methylation plays a role in transcription of miRNA-encoding genes and may contribute to changed miRNA expression in tumors. This issue was not investigated in pituitary neuroendocrine tumors (PitNETs) previously. DNA methylation patterns, assessed with HumanMethylation450K arrays in 34 PitNETs and five normal pituitaries, were used to determine differentially methylated CpGs located at miRNA genes. It showed aberrant methylation in regions encoding for 131 miRNAs. DNA methylation data and matched miRNA expression profiles, determined with next-generation sequencing (NGS) of small RNAs, were correlated in 15 PitNETs. This showed relationship between methylation and expression levels for 12 miRNAs. DNA methylation and expression levels of three of them (MIR145, MIR21, and MIR184) were determined in the independent group of 80 tumors with pyrosequencing and qRT-PCR and results confirmed both aberrant methylation in PitNETs and correlation between methylation and expression. Additionally, in silico target prediction was combined with analysis of established miRNA profiles and matched mRNA expression pattern, assessed with amplicon-based NGS to indicate putative target genes of epigenetically deregulated miRNAs. This study reveals aberrant DNA methylation in miRNA-encoding genes in gonadotroph PitNETs. Methylation changes affect expression level of miRNAs that regulate putative target genes with tumorigenesis-relevant functions.
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Affiliation(s)
- Joanna Boresowicz
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (J.B.); (P.K.); (N.R.); (J.A.S.)
| | - Paulina Kober
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (J.B.); (P.K.); (N.R.); (J.A.S.)
| | - Natalia Rusetska
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (J.B.); (P.K.); (N.R.); (J.A.S.)
| | - Maria Maksymowicz
- Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland;
| | - Agnieszka Paziewska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.P.); (M.D.); (J.O.)
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, 01-813 Warsaw, Poland;
| | - Michalina Dąbrowska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.P.); (M.D.); (J.O.)
| | - Natalia Zeber-Lubecka
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, 01-813 Warsaw, Poland;
| | - Jacek Kunicki
- Department of Neurosurgery, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (J.K.); (W.B.)
| | - Wiesław Bonicki
- Department of Neurosurgery, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (J.K.); (W.B.)
| | - Jerzy Ostrowski
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (A.P.); (M.D.); (J.O.)
- Department of Gastroenterology, Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, 01-813 Warsaw, Poland;
| | - Janusz A. Siedlecki
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (J.B.); (P.K.); (N.R.); (J.A.S.)
| | - Mateusz Bujko
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland; (J.B.); (P.K.); (N.R.); (J.A.S.)
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21
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Li J, Zhang S, Zou Y, Wu L, Pei M, Jiang Y. miR-145 promotes miR-133b expression through c-myc and DNMT3A-mediated methylation in ovarian cancer cells. J Cell Physiol 2020; 235:4291-4301. [PMID: 31612498 DOI: 10.1002/jcp.29306] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 09/30/2019] [Indexed: 12/11/2022]
Abstract
Ovarian cancer presents as malignant tumors in the female reproductive system with high mortality. MicroRNAs are involved in the progression of ovarian cancer; however, the regulatory relationship among miRs remains unclear. In our study, we verified that both miR-145 and miR-133b messenger RNA (mRNA) levels in ovarian cancer tissues were lower than in normal ovarian tissues, and their mRNA level in serum of patients with ovarian cancer was reduced. We demonstrated miR-145 targeted c-myc, and c-myc interacted physically with DNMT3A in ovarian cancer cells. We confirmed that c-myc recruited DNMT3A to the miR-133b promoter. miR-133b overexpression also inhibited target gene PKM2 expression along with the Warburg effect. Our results indicate that miR-145 inhibited the Warburg effect through miR-133b/PKM2 pathways, which may improve approaches to ovarian cancer diagnosis and treatment.
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Affiliation(s)
- Jie Li
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Songlin Zhang
- Department of Structural Heart Disease, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yuliang Zou
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Lei Wu
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Meili Pei
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yu Jiang
- Department of Gynecology and Obstetrics, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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22
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Doukas SG, Vageli DP, Lazopoulos G, Spandidos DA, Sasaki CT, Tsatsakis A. The Effect of NNK, A Tobacco Smoke Carcinogen, on the miRNA and Mismatch DNA Repair Expression Profiles in Lung and Head and Neck Squamous Cancer Cells. Cells 2020; 9:E1031. [PMID: 32326378 PMCID: PMC7226174 DOI: 10.3390/cells9041031] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 04/04/2020] [Accepted: 04/19/2020] [Indexed: 02/07/2023] Open
Abstract
Tobacco smoking is a common risk factor for lung cancer and head and neck cancer. Molecular changes such as deregulation of miRNA expression have been linked to tobacco smoking in both types of cancer. Dysfunction of the Mismatch DNA repair (MMR) mechanism has also been associated with a poor prognosis of these cancers, while a cross-talk between specific miRNAs and MMR genes has been previously proposed. We hypothesized that exposure of lung and head and neck squamous cancer cells (NCI and FaDu, respectively) to tobacco-specific nitrosamine 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) is capable of altering the expression of MSH2 and MLH1, key MMR components, by promoting specific miRNA deregulation. We found that either a low (1 μM) or high (2 μM) dose of NNK induced significant upregulation of "oncomirs" miR-21 and miR-155 and downregulation of "tumor suppressor" miR-422a, as well as the reduction of MMR protein and mRNA expression, in NCI and FaDu, compared to controls. Inhibition of miR-21 restored the NNK-induced reduced MSH2 phenotype in both NCI and FaDu, indicating that miR-21 might contribute to MSH2 regulation. Finally, NNK exposure increased NCI and FaDu survival, promoting cancer cell progression. We provide novel findings that deregulated miR-21, miR-155, and miR-422a and MMR gene expression patterns may be valuable biomarkers for lung and head and neck squamous cell cancer progression in smokers.
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Affiliation(s)
- Sotirios G. Doukas
- Department of Forensic Sciences and Laboratory of Toxicology, Medical School, University of Crete, 71003 Heraklion, Greece; (S.G.D.); (A.T.)
- Department of Surgery, The Yale Larynx Laboratory, New Haven, CT 06510, USA;
| | - Dimitra P. Vageli
- Department of Surgery, The Yale Larynx Laboratory, New Haven, CT 06510, USA;
| | - George Lazopoulos
- Department of Cardiothoracic Surgery, Medical School, University of Crete, 71110 Heraklion, Greece;
| | - Demetrios A. Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, 71110 Heraklion, Greece;
| | - Clarence T. Sasaki
- Department of Surgery, The Yale Larynx Laboratory, New Haven, CT 06510, USA;
| | - Aristidis Tsatsakis
- Department of Forensic Sciences and Laboratory of Toxicology, Medical School, University of Crete, 71003 Heraklion, Greece; (S.G.D.); (A.T.)
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23
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Wang Y, Hao Y, Zhang H, Xu L, Ding N, Wang R, Zhu G, Ma S, Yang A, Yang Y, Wu K, Jiang Y, Zhang H, Jiang Y. DNA Hypomethylation of miR-30a Mediated the Protection of Hypoxia Postconditioning Against Aged Cardiomyocytes Hypoxia/Reoxygenation Injury Through Inhibiting Autophagy. Circ J 2020; 84:616-625. [PMID: 32115441 DOI: 10.1253/circj.cj-19-0915] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Ischemic postconditioning (IPostC) is an endogenous protective mechanism to reduce ischemia-reperfusion (I/R) injury. However, whether IPostC protects aged cardiomyocytes against I/R injury is not fully understood. Considering the protective function of microRNA 30a (miR-30a) against ischemia-induced injury in H9C2 cells, its role in the protective effects of IPostC on I/R injury of aged cardiomyocytes was investigated further.Methods and Results:To mimic I/R and IPostC in vitro, the aged cardiomyocyte model for hypoxia postconditioning (HPostC) treatment was established by 9 days of incubation with 8 mg/mL D-galactose and then followed by exposure to hypoxic environment. HPostC significantly alleviated hypoxia/reoxygenation (H/R) injury and reduced autophagy of aged cardiomyocytes, as evidenced by decreased LC3B-II expression and increased p62 by Western blot. Quantified by quantitative real-time polymerase chain reaction (qRT-PCR), miR-30a was increased in aged cardiomyocytes treated with HPostC compared with I/R injury group. Overexpression of miR-30a by LV3-rno-miR-30a mimic promoted cardioprotective effect of HPostC in aged cardiomyocytes by suppressing BECN1-mediated autophagy, all of which was abrogated by knockdown of miR-30a expression. Epigenetic analyses demonstrated that HPostC reduced DNA methyltransferase 3b-mediated DNA hypomethylation levels at miR-30a promoter, leading to upregulation of miR-30a. CONCLUSIONS HPostC protected aged cardiomyocytes survival against H/R injury via DNMT3b-dependent activation of miR-30a. miR-30a could be a potential therapeutic target for ischemic myocardial infarction.
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Affiliation(s)
- YanHua Wang
- Department of Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University
- NHC Key Laboratory of Metabolic Cardiovascular Diseases Research, Ningxia Medical University
- Ningxia Key Laboratory of Vascular Injury and Repair Research
| | - YinJu Hao
- NHC Key Laboratory of Metabolic Cardiovascular Diseases Research, Ningxia Medical University
- Department of Pharmacology, Ningxia Medical University
- Ningxia Key Laboratory of Vascular Injury and Repair Research
| | - Hui Zhang
- Department of Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University
- NHC Key Laboratory of Metabolic Cardiovascular Diseases Research, Ningxia Medical University
- Ningxia Key Laboratory of Vascular Injury and Repair Research
| | - LingBo Xu
- Department of Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University
- NHC Key Laboratory of Metabolic Cardiovascular Diseases Research, Ningxia Medical University
- Ningxia Key Laboratory of Vascular Injury and Repair Research
| | - Ning Ding
- Department of Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University
- NHC Key Laboratory of Metabolic Cardiovascular Diseases Research, Ningxia Medical University
- Ningxia Key Laboratory of Vascular Injury and Repair Research
| | - Rui Wang
- Department of Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University
- NHC Key Laboratory of Metabolic Cardiovascular Diseases Research, Ningxia Medical University
- Ningxia Key Laboratory of Vascular Injury and Repair Research
| | - GuangRong Zhu
- Department of Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University
- NHC Key Laboratory of Metabolic Cardiovascular Diseases Research, Ningxia Medical University
- Ningxia Key Laboratory of Vascular Injury and Repair Research
| | - ShengChao Ma
- Department of Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University
- NHC Key Laboratory of Metabolic Cardiovascular Diseases Research, Ningxia Medical University
- Ningxia Key Laboratory of Vascular Injury and Repair Research
| | - AnNing Yang
- Department of Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University
- NHC Key Laboratory of Metabolic Cardiovascular Diseases Research, Ningxia Medical University
- Ningxia Key Laboratory of Vascular Injury and Repair Research
| | - Yong Yang
- People's Hospital in Ningxia Hui Autonomous Region
| | - Kai Wu
- NHC Key Laboratory of Metabolic Cardiovascular Diseases Research, Ningxia Medical University
- Ningxia Key Laboratory of Vascular Injury and Repair Research
| | - YuanXu Jiang
- Department of Pharmacology, Ningxia Medical University
| | - HuiPing Zhang
- NHC Key Laboratory of Metabolic Cardiovascular Diseases Research, Ningxia Medical University
- Ningxia Key Laboratory of Vascular Injury and Repair Research
- Department of Prenatal Diagnosis Center, General Hospital of Ningxia Medical University
| | - YiDeng Jiang
- Department of Pathophysiology, School of Basic Medical Sciences, Ningxia Medical University
- NHC Key Laboratory of Metabolic Cardiovascular Diseases Research, Ningxia Medical University
- Ningxia Key Laboratory of Vascular Injury and Repair Research
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24
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Hu Y, Wu F, Liu Y, Zhao Q, Tang H. DNMT1 recruited by EZH2-mediated silencing of miR-484 contributes to the malignancy of cervical cancer cells through MMP14 and HNF1A. Clin Epigenetics 2019; 11:186. [PMID: 31810492 PMCID: PMC6898970 DOI: 10.1186/s13148-019-0786-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 11/24/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Emerging evidence indicates that dysregulation of microRNAs (miRNAs) contributes to cervical cancer (CC) tumorigenesis and development. Previous work showed that miR-484 which regulated the EMT process was obviously downregulated in CC. However, little is known about the precise mechanism. RESULTS We found that the deficiency of EZH2-recruited DNA methyltransferases DNMT1 reduced the CpG methylation of miR-484 promoter and then increased the miR-484 expression. Furthermore, the cell membrane-bound matrix metalloproteinase (MMP14) and the hepatocyte nuclear factor 1A (HNF1A) were found to be downregulated by miR-484. miR-484 repressed the expression of MMP14 and HNF1A inhibiting CC growth and metastasis in vitro and in vivo. Upregulation of MMP14 and HNF1A promotes the CC cell adhesion and EMT, all of which contribute to cell motility and metastasis. Moreover, miR-484 negatively regulates the WNT/MAPK and TNF signaling pathway by downregulating HNF1A and MMP14 respectively. Thus, miR-484, who is downregulated by DNMT1-mediated hypermethylation in its promoter, functions as a tumor suppressor by inhibiting MMP14 and HNF1A expression in CC. CONCLUSION Our finding characterizes miR-484 as a key suppressive regulator in CC metastasis and reveals a DNMT1-mediated epigenetic mechanism for miR-484 silencing, expanding our understanding of the molecular mechanism underlying CC progression and metastasis.
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Affiliation(s)
- Yang Hu
- Tianjin Life Science Research Center, Tianjin Laboratory of Inflammation Biology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Department of Pathogen Biology, Basic Medical School, Tianjin Medical University, 22 Qi-Xiang-Tai Road, Tianjin, 300070, China
| | - Fuxia Wu
- Tianjin Life Science Research Center, Tianjin Laboratory of Inflammation Biology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Department of Pathogen Biology, Basic Medical School, Tianjin Medical University, 22 Qi-Xiang-Tai Road, Tianjin, 300070, China
| | - Yankun Liu
- The Cancer Institute, Tangshan People's Hospital, Tangshan, 063001, China
| | - Qian Zhao
- Department of Cell Biology, Tianjin Medical University, Tianjin, 300070, China
| | - Hua Tang
- Tianjin Life Science Research Center, Tianjin Laboratory of Inflammation Biology, Collaborative Innovation Center of Tianjin for Medical Epigenetics, Department of Pathogen Biology, Basic Medical School, Tianjin Medical University, 22 Qi-Xiang-Tai Road, Tianjin, 300070, China.
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25
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Tavakolian S, Goudarzi H, Torfi F, Faghihloo E. Evaluation of microRNA-9 and -192 expression levels as biomarkers in patients suffering from breast cancer. Biomed Rep 2019; 12:30-34. [PMID: 31839947 DOI: 10.3892/br.2019.1257] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 10/02/2019] [Indexed: 12/18/2022] Open
Abstract
Given the global outbreak of breast cancer and its debilitating effect on women's health, it is not surprising that tremendous efforts have been made with an aim of shedding more light on the mechanisms involved in the pathogenesis of this type of cancer. Among the long list of risk factors associated with this malignancy, recently, the role of microRNAs (miRNAs or miRs) has turned into a hotspot for breast cancer investigations. miRNAs approximately 20 nucleotides in length and are located in either an exon or an intron, playing a role in the regulation of gene expression. In the present study, we extracted RNA from both the serum and cancerous tissue of breast cancer patients and after synthesizing the cDNA, we performed quantitative PCR to determine the expression levels of miR-9 and miR-192. The resulting data revealed that while the mRNA expression level of miR-9 was significantly decreased in the breast cancer tissues, there was no noticeable change in the expression level of this miRNA in the serum samples. Likewise, we found that the marked downregulation of miR-192 was only restricted to the cancerous tissues, but was not found in the serum of patients. Based on the meaningful downregulation of the expression of miR-9 and miR-192, this study provides a plausible framework for these miRNAs as effective biomarkers for breast cancer patients.
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Affiliation(s)
- Shaian Tavakolian
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran
| | - Hossein Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran
| | - Farhad Torfi
- Surgical Ward, Taleghani Hospital, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran
| | - Ebrahim Faghihloo
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran
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26
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Li Y, Chen F, Chu J, Wu C, Li Y, Li H, Ma H. miR-148-3p Inhibits Growth of Glioblastoma Targeting DNA Methyltransferase-1 (DNMT1). Oncol Res 2019; 27:911-921. [PMID: 30982493 PMCID: PMC7848282 DOI: 10.3727/096504019x15516966905337] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
To date, miR-148-3p and DNMT1–recombinant human runt-related transcription factor 3 (RUNX3) axis have been linked to cell proliferation, migration, and invasion; however, their roles and relationships in human glioblastoma multiforme (GBM) are still not clear. Here we found that the expression of miR-148-3p in glioma tissues was decreased compared with adjacent nontumor tissues and correlated with WHO grade, tumor size, and prognosis as well as DNMT1 and RUNX3 expressions. Compared with NHA cells, the expression of miR-148-3p in U87 and U251 cells was also downregulated and accompanied with upregulation of DNMT1 and hypermethylation level of RUNX3 promoter region. miR-148-3p overexpression induced apoptosis and cell cycle arrest of U87 and U251 cells, and affected cell migration and invasion. miR-148-3p mimics effectively suppressed the expression of DNMT1 and methylation of RUNX3 promoter, finally upregulating RUNX3 expression. Mechanistically, the 3′-untranslated region (3′-UTR) of DNMT1 was a direct target of miR-148-3p. Overexpression of miR-148-3p or inhibition of DNMT1 induced the expression of E-cadherin and reduced the expressions of N-cadherin, vimentin, MMP-2, and MMP-9. In conclusion, miR-148-3p directly repressed the expression of DNMT1 and inhibited proliferation, migration, and invasion by regulating DNMT1–RUNX3 axis and the epithelial–mesenchymal transition in GBM. Our findings provide a new foundation for treatment of patients with GBM.
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Affiliation(s)
- Yongtao Li
- Department of Neurosurgery, Tengzhou Central People's Hospital, Tengzhou, Shandong, P.R. China
| | - Fanyu Chen
- Department of Neurosurgery, Tengzhou Central People's Hospital, Tengzhou, Shandong, P.R. China
| | - Jiancheng Chu
- Department of Neurosurgery, Tengzhou Central People's Hospital, Tengzhou, Shandong, P.R. China
| | - Chao Wu
- Department of Neurosurgery, Tengzhou Central People's Hospital, Tengzhou, Shandong, P.R. China
| | - Yuan Li
- School of Medicine, Shandong University, Jinan, Shandong, P.R. China
| | - Heng Li
- School of Medicine, Shandong University, Jinan, Shandong, P.R. China
| | - Hongxin Ma
- Department of Neurosurgery, Tengzhou Central People's Hospital, Tengzhou, Shandong, P.R. China
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27
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Barros-Filho MC, Pewarchuk M, Minatel BDC, Sage AP, Marshall EA, Martinez VD, Rock LD, MacAulay G, Kowalski LP, Rogatto SR, Garnis C, Lam WL. Previously undescribed thyroid-specific miRNA sequences in papillary thyroid carcinoma. J Hum Genet 2019; 64:505-508. [DOI: 10.1038/s10038-019-0583-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 02/04/2019] [Accepted: 02/11/2019] [Indexed: 12/12/2022]
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