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Zeng Q, Zou D, Liu N, Wei Y, Yang J, Wu W, Han F, He R, Guo R. Association of miR-196a2 and miR-27a polymorphisms with gestational diabetes mellitus susceptibility in a Chinese population. Front Endocrinol (Lausanne) 2023; 14:1127336. [PMID: 37113490 PMCID: PMC10127250 DOI: 10.3389/fendo.2023.1127336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/20/2023] [Indexed: 04/08/2023] Open
Abstract
IntroductionMiR-196a2 and miR-27a play a key role in the regulation of the insulin signaling pathway. Previous studies have indicated that miR-27a rs895819 and miR-196a2 rs11614913 have a strong association with type 2 diabetes (T2DM), but very few studies have investigated their role in gestational diabetes mellitus (GDM).MethodsA total of 500 GDM patients and 502 control subjects were enrolled in this study. Using the SNPscan™ genotyping assay, rs11614913 and rs895819 were genotyped. In the data treatment process, the independent sample t test, logistic regression and chi-square test were used to evaluate the differences in genotype, allele, and haplotype distributions and their associations with GDM risk. One-way ANOVA was conducted to determine the differences in genotype and blood glucose level.ResultsThere were obvious differences in prepregnancy body mass index (pre-BMI), age, systolic blood pressure (SBP), diastolic blood pressure (DBP) and parity between GDM and healthy subjects (P < 0.05). After adjusting for the above factors, the miR-27a rs895819 C allele was still associated with an increased risk of GDM (C vs. T: OR=1.245; 95% CI: 1.011-1.533; P = 0.039) and the TT-CC genotype of rs11614913-rs895819 was related to an increased GDM risk (OR=3.989; 95% CI: 1.309-12.16; P = 0.015). In addition, the haplotype T-C had a positive interaction with GDM (OR=1.376; 95% CI: 1.075-1.790; P=0.018), especially in the 18.5 ≤ pre-BMI < 24 group (OR=1.403; 95% CI: 1.026-1.921; P=0.034). Moreover, the blood glucose level of the rs895819 CC genotype was significantly higher than that of the TT and TC genotypes (P < 0.05). The TT-CC genotype of rs11614913-rs895819 showed that the blood glucose level was significantly higher than that of the other genotypes.DiscussionOur findings suggest that miR-27a rs895819 is associated with increased GDM susceptibility and higher blood glucose levels.
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Affiliation(s)
- Qiaoli Zeng
- Department of Internal Medicine, Shunde Women and Children’s Hospital (Maternity and Child Healthcare Hospital of Shunde Foshan), Guangdong Medical University, Foshan, Guangdong, China
- State Key Laboratory of Quality Research in Chinese Medicine, School of Pharmacy, Macau University of Science and Technology, Taipa, Macau, China
- Guangdong Engineering Research Center of Chinese Medicine & Disease Susceptibility, Jinan University, Guangzhou, Guangdong, China
- Key Laboratory of Research in Maternal and Child Medicine and Birth Defects, Guangdong Medical University, Foshan, Guangdong, China
- Matenal and Child Research Institute, Shunde Women and Children’s Hospital (Maternity and Child Healthcare Hospital of Shunde Foshan), Guangdong Medical University, Foshan, Guangdong, China
| | - Dehua Zou
- State Key Laboratory of Quality Research in Chinese Medicine, School of Pharmacy, Macau University of Science and Technology, Taipa, Macau, China
- Guangdong Engineering Research Center of Chinese Medicine & Disease Susceptibility, Jinan University, Guangzhou, Guangdong, China
| | - Na Liu
- Department of Pediatrics, Shunde Women and Children’s Hospital (Maternity and Child Healthcare Hospital of Shunde Foshan), Guangdong Medical University, Foshan, Guangdong, China
| | - Yue Wei
- Department of Ultrasound, Shunde Women and Children’s Hospital (Maternity and Child Healthcare Hospital of Shunde Foshan), Guangdong Medical University, Foshan, Guangdong, China
- Department of Ultrasound, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Jing Yang
- Department of Obstetric, Shunde Women and Children’s Hospital (Maternity and Child Healthcare Hospital of Shunde Foshan), Guangdong Medical University, Foshan, Guangdong, China
| | - Weibiao Wu
- Medical Genetics Laboratory, Shunde Women and Children’s Hospital (Maternity and Child Healthcare Hospital of Shunde Foshan), Guangdong Medical University, Foshan, Guangdong, China
| | - Fengqiong Han
- Department of Obstetric, Shunde Women and Children’s Hospital (Maternity and Child Healthcare Hospital of Shunde Foshan), Guangdong Medical University, Foshan, Guangdong, China
- *Correspondence: Fengqiong Han, ; Rongrong He, ; Runmin Guo,
| | - Rongrong He
- State Key Laboratory of Quality Research in Chinese Medicine, School of Pharmacy, Macau University of Science and Technology, Taipa, Macau, China
- Guangdong Engineering Research Center of Chinese Medicine & Disease Susceptibility, Jinan University, Guangzhou, Guangdong, China
- *Correspondence: Fengqiong Han, ; Rongrong He, ; Runmin Guo,
| | - Runmin Guo
- Department of Internal Medicine, Shunde Women and Children’s Hospital (Maternity and Child Healthcare Hospital of Shunde Foshan), Guangdong Medical University, Foshan, Guangdong, China
- Key Laboratory of Research in Maternal and Child Medicine and Birth Defects, Guangdong Medical University, Foshan, Guangdong, China
- Matenal and Child Research Institute, Shunde Women and Children’s Hospital (Maternity and Child Healthcare Hospital of Shunde Foshan), Guangdong Medical University, Foshan, Guangdong, China
- Department of endocrinology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
- *Correspondence: Fengqiong Han, ; Rongrong He, ; Runmin Guo,
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Bozgeyik E, Bozgeyik İ. Non-coding RNA variations in oral cancers: a comprehensive review. Gene 2022; 851:147012. [DOI: 10.1016/j.gene.2022.147012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 10/11/2022] [Accepted: 10/24/2022] [Indexed: 11/04/2022]
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Khan MS, Rahman B, Haq TU, Jalil F, Khan BM, Maodaa SN, Al-Farraj SA, El-Serehy HA, Shah AA. Deciphering the Variants Located in the MIR196A2, MIR146A, and MIR423 with Type-2 Diabetes Mellitus in Pakistani Population. Genes (Basel) 2021; 12:genes12050664. [PMID: 33925232 PMCID: PMC8146332 DOI: 10.3390/genes12050664] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/07/2021] [Accepted: 04/09/2021] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs) are small non-coding RNA molecules that control the post-transcriptional gene expression. They play a pivotal role in the regulation of important physiological processes. Variations in miRNA genes coding for mature miRNA sequences have been implicated in several diseases. However, the association of variants in miRNAs genes with Type 2 Diabetes Mellitus (T2DM) in the Pakistani population is rarely reported. Therefore, the current study was designed to investigate the association of rs11614913 T/C (MIR196A2), rs2910164 G/C (MIR146A), and rs6505162 C/A (MIR423) in clinicopathological proven T2DM patients and gender-matched healthy controls. The tetra-primer amplification refractory mutation system-polymerase chain (ARMS-PCR) reaction method was used to determine the genotypes and to establish the association of each variant with T2DM through inherited models. In conclusion, the present study showed that variants rs11614913 T/C and rs2910164 G/C were linked with the risk of T2DM. The data suggested that rs11614913 T/C and rs2910164 G/C could be considered as novel risk factors in the pathogenesis of T2DM in the Pakistani population.
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Affiliation(s)
- Muhammad Sohail Khan
- Department of Biotechnology, University of Malakand, Chakdara 18800, Pakistan; (M.S.K.); (B.R.); (T.U.H.)
| | - Bashir Rahman
- Department of Biotechnology, University of Malakand, Chakdara 18800, Pakistan; (M.S.K.); (B.R.); (T.U.H.)
| | - Taqweem Ul Haq
- Department of Biotechnology, University of Malakand, Chakdara 18800, Pakistan; (M.S.K.); (B.R.); (T.U.H.)
| | - Fazal Jalil
- Department of Biotechnology, Abdul Wali Khan University Mardan (AWKUM), Mardan 23200, Pakistan;
| | - Bilal Muhammad Khan
- University Institute of Biochemistry and Biotechnology, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi 46300, Pakistan;
- National Center of Industrial Biotechnology, Pir Mehr Ali Shah Arid Agriculture University, Rawalpindi 46300, Pakistan
| | - Saleh N. Maodaa
- Department of Zoology, College of Science, King Saud University, Riyadh l1451, Saudi Arabia; (S.N.M.); (S.A.A.-F.); (H.A.E.-S.)
| | - Saleh A. Al-Farraj
- Department of Zoology, College of Science, King Saud University, Riyadh l1451, Saudi Arabia; (S.N.M.); (S.A.A.-F.); (H.A.E.-S.)
| | - Hamed A. El-Serehy
- Department of Zoology, College of Science, King Saud University, Riyadh l1451, Saudi Arabia; (S.N.M.); (S.A.A.-F.); (H.A.E.-S.)
| | - Aftab Ali Shah
- Department of Biotechnology, University of Malakand, Chakdara 18800, Pakistan; (M.S.K.); (B.R.); (T.U.H.)
- Correspondence:
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Analysis of microRNA-34a expression profile and rs2666433 variant in colorectal cancer: a pilot study. Sci Rep 2020; 10:16940. [PMID: 33037254 PMCID: PMC7547073 DOI: 10.1038/s41598-020-73951-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 09/23/2020] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs (miRNAs) are implicated in every stage of carcinogenesis and play an essential role as genetic biomarkers of cancer. We aimed to evaluate microRNA-34a gene (MIR34A) expression in colorectal cancer (CRC) tissues compared with non-cancer one and to preliminarily explore the association of one related variant to CRC risk. A total of 116 paraffin-embedded colon specimens were enrolled. MiR-34a was quantified by qPCR, and rs2666433 (A/G) genotyping was performed by TaqMan Real-Time PCR. Also, the somatic mutation burden was assessed. MIR34A expression in the CRC specimens was significantly upregulated (median = 21.50, IQR: 7.0–209.2; P = 0.001) relative to the non-cancer tissues. Allele (A) was highly prevalent in CRC tissues represented 0.56 (P < 0.001). AA/AG genotype carriers were 5.7 and 2.8 more likely to develop cancer than GG carriers. Tumor-normal tissue paired analysis revealed genotype concordance in 33 out of 58 tissue samples. Approximately 43% of the specimens showed a tendency for G to A shift. Additionally, a higher frequency of somatic mutation (92%) was observed in adenocarcinoma (P = 0.006). MIR34A expression and gene variant did not show associations with the clinicopathological data. However, G > A somatic mutation carriers had more prolonged DFS and OS. Bioinformatics analysis revealed miR-34a could target 30 genes that are implied in all steps of CRC tumorigenesis. In conclusion, this study confirms MIR34A upregulation in CRC tissues, and its rs2666433 (A/G) variant showed association with CRC and a high somatic mutation rate in cancer tissues. MiR-34a could provide a novel targeted therapy after validation in large-scale studies.
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miR-3188 (rs7247237-C>T) Single-Nucleotide Polymorphism Is Associated With the Incidence of Vascular Complications in Chinese Patients With Type 2 Diabetes. J Cardiovasc Pharmacol 2020; 74:62-70. [PMID: 31274844 DOI: 10.1097/fjc.0000000000000681] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
miR-3188, one of the earliest discovered microRNAs, is involved in regulating the mTOR-p-PI3K/AKT pathway, thus affecting the progression of diabetic complications. In this study, we observed that the miR-3188 (rs7247237-C>T) polymorphism not only affected the production of nitric oxide (NO) production in endothelial cells, but also significantly associated with the incidence of vascular complications in Chinese patients with type 2 diabetes. Mechanistic analyses indicate that miR-3188 (rs7247237-T) polymorphism inhibited its own expression and upregulated the expression of gstm1 and trib3, which impairs NO production in human endothelial cells through inactivating AKT/eNOS signal transduction pathway. In addition, our clinical retrospective study indicated that, compared with patients with the CC genotype (n = 351), patients with rs7247237 TT + CT genotypes (n = 580) exhibited an increased risk of major vascular events during intensive glucose control treatment (hazard ratio = 1.560; 95% CI: 1.055-2.307, P = 0.025). Simultaneously, the risk of major vascular events was marginally decreased in patients with the CC genotype during intensive glucose control treatment compared with standard treatment (hazard ratio = 0.666; 95% CI: 0.433-1.016, P = 0.053). Our findings indicate that the miR-3188 (rs7247237-C>T) polymorphism is associated with the incidence of vascular complications in Chinese patients with type 2 diabetes, likely due to its remarkable effect on miR-3188 expression.
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SiamiGorji S, Jorjani I, Tahamtan A, Moradi A. Effects of microRNAs polymorphism in cancer progression. Med J Islam Repub Iran 2020; 34:3. [PMID: 32284927 PMCID: PMC7139258 DOI: 10.34171/mjiri.34.3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Indexed: 02/06/2023] Open
Abstract
MicroRNAs (miRNAs) are known as a new class of small RNAs (18-25 nucleotides) that regulate gene expression at multiple levels from transcription to translation. Considering the important role of miRNAs in cell proliferation, differentiation, and apoptosis, any variations in their expression can contribute to various anomalies, such as tumorigenesis. Single-nucleotide polymorphisms (SNPs) have received much attention as potential genetic markers for diseases due to their advantage of being present at a high frequency in the human genome. SNPs can occur in different parts of the miRNA genes (primary, precursor, and mature) which result in pathological conditions. In this study, recent findings related to the effects of SNPs in miRNAs on their biogenesis and functions and their role in cancer development and progression are discussed. This review was performed using PubMed to search for related reports. The identified effects may be useful for clinical decision-making and providing important new information about the pathophysiology of miRNAs.
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Affiliation(s)
- Simin SiamiGorji
- Department of Biology, Faculty of Basic Science, Gonbad Kavous University, Gonbad kavous, Golestan, Iran
| | - Isa Jorjani
- Department of Biology, Faculty of Basic Science, Gonbad Kavous University, Gonbad kavous, Golestan, Iran
| | - Alireza Tahamtan
- Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Abdolvahab Moradi
- Department of Microbiology, School of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
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Viera GM, Salomao KB, de Sousa GR, Baroni M, Delsin LEA, Pezuk JA, Brassesco MS. miRNA signatures in childhood sarcomas and their clinical implications. Clin Transl Oncol 2019; 21:1583-1623. [PMID: 30949930 DOI: 10.1007/s12094-019-02104-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 03/27/2019] [Indexed: 02/06/2023]
Abstract
Progresses in multimodal treatments have significantly improved the outcomes for childhood cancer. Nonetheless, for about one-third of patients with Ewing sarcoma, rhabdomyosarcoma, or osteosarcoma steady remission has remained intangible. Thus, new biomarkers to improve early diagnosis and the development of precision-targeted medicine remain imperative. Over the last decade, remarkable progress has been made in the basic understanding of miRNAs function and in interpreting the contribution of their dysregulation to cancer development and progression. On this basis, this review focuses on what has been learned about the pivotal roles of miRNAs in the regulation of key genes implicated in childhood sarcomas.
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Affiliation(s)
- G M Viera
- Ribeirao Preto School of Medicine, University of Sao Paulo, Ribeirao Preto, Brasil
| | - K B Salomao
- Ribeirao Preto School of Medicine, University of Sao Paulo, Ribeirao Preto, Brasil
| | - G R de Sousa
- Ribeirao Preto School of Medicine, University of Sao Paulo, Ribeirao Preto, Brasil
| | - M Baroni
- Ribeirao Preto School of Medicine, University of Sao Paulo, Ribeirao Preto, Brasil
| | - L E A Delsin
- Ribeirao Preto School of Medicine, University of Sao Paulo, Ribeirao Preto, Brasil
| | - J A Pezuk
- Anhanguera University of Sao Paulo, UNIAN/SP, Sao Paulo, Brasil
| | - M S Brassesco
- Faculty of Philosophy, Sciences and Letters at Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, Brasil.
- Departamento de Biologia, FFCLRP-USP, Av. Bandeirantes, 3900, Bairro Monte Alegre, Ribeirao Preto, SP, CEP 14040-901, Brazil.
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Kim EG, Kim JO, Park HS, Ryu CS, Oh J, Jun HH, Kim JW, Kim NK. Genetic associations between the miRNA polymorphisms miR-130b (rs373001), miR-200b (rs7549819), and miR-495 (rs2281611) and colorectal cancer susceptibility. BMC Cancer 2019; 19:480. [PMID: 31117970 PMCID: PMC6532172 DOI: 10.1186/s12885-019-5641-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 04/26/2019] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Recent studies have extensively investigated the role of miRNAs in colorectal cancer (CRC), and several associations have been reported. In addition, single nucleotide polymorphisms (SNPs) in promoter regions of miRNAs have been shown to affect miRNA expression. Therefore, we aimed to analyze the effect of miRNA polymorphisms on CRC susceptibility. METHODS We conducted association studies on the relationships between the miRNA polymorphisms miR-130bT > C rs373001, miR-200bT > C rs7549819, and miR-495A > C rs2281611 and CRC with 472 CRC patients and 399 control subjects in Korea. RESULTS Multivariate logistic regressions of the CRC subgroups showed that the miR-495CC genotype associated with rectal cancer (AA+AC vs. CC; adjusted odds ratio (AOR) for CC, 1.592; 95% confidence interval (CI), 1.071-2.368; P = 0.022). The gene-environment combinatorial analysis showed that the combination of miR-495A > C and low plasma folate contributed to an increased risk of rectal cancer (AA+AC vs. CC; AOR for CC, 3.829; 95% CI, 1.577-9.300; P = 0.003). In the survival analysis, miR-200bT > C associated with CRC patient mortality (TT vs TC + CC; adjusted hazard ratio for TC + CC, 0.592; 95% CI, 0.373-0.940; P = 0.026). CONCLUSION In this study, we found that miR-200b and miR-495 polymorphisms are involved in CRC susceptibility and prognosis.
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Affiliation(s)
- Eun-Gyo Kim
- Department of Biomedical Science, College of Life Science, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam, 13488 South Korea
| | - Jung Oh Kim
- Department of Biomedical Science, College of Life Science, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam, 13488 South Korea
| | - Han Sung Park
- Department of Biomedical Science, College of Life Science, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam, 13488 South Korea
| | - Chang Soo Ryu
- Department of Biomedical Science, College of Life Science, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam, 13488 South Korea
| | - Jisu Oh
- Department of Internal Medicine, CHA Bundang Medical Center, CHA University, 59 Yatap-ro, Bundang-gu, Seongnam, 13496 South Korea
| | - Hak Hoon Jun
- Department of Surgery, CHA Bundang Medical Center, CHA University, 59 Yatap-ro, Bundang-gu, Seongnam, 13496 South Korea
| | - Jong Woo Kim
- Department of Surgery, CHA Bundang Medical Center, CHA University, 59 Yatap-ro, Bundang-gu, Seongnam, 13496 South Korea
| | - Nam Keun Kim
- Department of Biomedical Science, College of Life Science, CHA University, 335 Pangyo-ro, Bundang-gu, Seongnam, 13488 South Korea
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Wei GJ, Yuan MQ, Jiang LH, Lu YL, Liu CH, Luo HC, Huang HT, Qi ZQ, Wei YS. A Genetic Variant of miR-34a Contributes to Susceptibility of Ischemic Stroke Among Chinese Population. Front Physiol 2019; 10:432. [PMID: 31068831 PMCID: PMC6491571 DOI: 10.3389/fphys.2019.00432] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 03/28/2019] [Indexed: 12/22/2022] Open
Abstract
miRNAs are small non-coding RNAs modulating gene expression, and variants in miRNA genes are involved in the pathogenesis of ischemic stroke (IS). However, the effect of miR-34a polymorphisms on IS susceptibility has rarely been reported. In the present study, we investigated the association between rs12128240, rs2666433, and rs6577555 of the miR-34a gene and IS susceptibility. Snapshot assay was used to detect miR-34a polymorphisms in 548 IS patients and 560 controls. Relative expression of miR-34a was measured by quantitative real-time PCR. We found that rs2666433 was associated with a significantly increased risk of IS (AA vs. GG: OR = 1.61, 95% CI = 1.05-2.52, P = 0.031; AA vs. GG+GA: OR = 1.58, 95% CI = 1.05-2.45, P = 0.026). For the IS subtypes, rs2666433 was associated with large artery atherosclerosis (AA vs. GG: OR = 2.09, 95% CI = 1.16-3.51, P = 0.007; AA vs. GG+GA: OR = 2.02, 95% CI = 1.15-3.33, P = 0.007; A vs. G: OR = 1.36, 95% CI = 1.07-1.81, P = 0.021). Additionally, the level of miR-34a was significantly up-regulated in IS patients compared to the controls (P < 0.001), and patients with rs2666433 AA genotype had a higher level of miR-34a than those with GG+GA genotypes (P < 0.001). Furthermore, increased level of homocysteine was observed in IS patients compared to the controls (P < 0.001), especially in patients carrying the rs2666433AA genotype compared to those carrying the rs2666433 GG+GA genotypes (P < 0.001). However, no significant association between rs12128240 or rs6577555 and IS was found. Collectively, our study found the association between miR-34a polymorphisms and the risk of IS among the Chinese population. The results may provide an explanation for etiology of IS and a potential biomarker or therapeutic target for IS. HIGHLIGHTS-MiR-34a rs2666433 polymorphism was associated with an increased risk of ischemic stroke.-The level of miR-34a was significantly up-regulated in ischemic stroke patients compared with controls, and patients with rs2666433 AA genotype had a higher level miR-34a than those with GG+GA genotypes.-Furthermore, increased level of homocysteine was showed in IS patients compared to controls, and in patients carrying the rs2666433AA compared to those carrying the rs2666433 GG+GA.
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Affiliation(s)
- Gui-Jiang Wei
- Department of Cell Biology, Medical College of Guangxi University, Nanning, China
- Department of Medical Laboratory, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Ming-Qing Yuan
- Department of Cell Biology, Medical College of Guangxi University, Nanning, China
| | - Li-He Jiang
- Department of Cell Biology, Medical College of Guangxi University, Nanning, China
| | - Yu-Lan Lu
- Department of Medical Laboratory, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Chun-Hong Liu
- Department of Medical Laboratory, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Hong-Cheng Luo
- Department of Medical Laboratory, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Hua-Tuo Huang
- Department of Medical Laboratory, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, China
| | - Zong-Quan Qi
- Department of Cell Biology, Medical College of Guangxi University, Nanning, China
| | - Ye-Sheng Wei
- Department of Cell Biology, Medical College of Guangxi University, Nanning, China
- Department of Medical Laboratory, Affiliated Hospital of Guilin Medical University, Guilin, China
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Kalapanida D, Zagouri F, Gazouli M, Zografos E, Dimitrakakis C, Marinopoulos S, Giannos A, Sergentanis TN, Kastritis E, Terpos E, Dimopoulos MA. Evaluation of pre-mir-34a rs72631823 single nucleotide polymorphism in triple negative breast cancer: A case-control study. Oncotarget 2018; 9:36906-36913. [PMID: 30651924 PMCID: PMC6319339 DOI: 10.18632/oncotarget.26385] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 11/03/2018] [Indexed: 12/19/2022] Open
Abstract
Aim The purpose of this study is to evaluate the role of pre-miR34a rs72631823 as potential risk factor and/or prognostic marker in patients with triple negative breast cancer. Methods 114 samples of DNA from paraffin embedded breast normal tissues of patients with triple negative breast cancer and 124 samples of healthy controls were collected and analyzed for pre-miR34a rs72631823 polymorphism. Results Pre-miR34a rs72631823 A allele was associated with increased TNBC risk both in univariate and multivariate analysis. The number of pre-miR34a rs72631823 AA subjects was very small and the association did not reach significance (p = 0.176, Fisher’s exact test). The examined polymorphism was not associated with overall survival at the univariate or multivariate Cox regression analysis (adjusted HR = 1.60, 95%CI: 0.64–3.96 for miR34 rs72631823 GA/AA vs. GG). Conclusion Our case-control study suggests that pre-miR34a rs72631823 A allele is associated with increased triple negative breast cancer risk.
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Affiliation(s)
- Despoina Kalapanida
- Department of Clinical Therapeutics, Alexandra Hospital, Medical School, University of Athens, Athens, Greece
| | - Flora Zagouri
- Department of Clinical Therapeutics, Alexandra Hospital, Medical School, University of Athens, Athens, Greece
| | - Maria Gazouli
- Department of Basic Medical Sciences, Laboratory of Biology, University of Athens School of Medicine, Athens, Greece.,Laboratory of Cell and Gene Therapy, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Eleni Zografos
- Department of Basic Medical Sciences, Laboratory of Biology, University of Athens School of Medicine, Athens, Greece.,Laboratory of Cell and Gene Therapy, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Constantine Dimitrakakis
- Department of Obstetrics and Gynaecology, Alexandra Hospital, Medical school, University of Athens, Athens, Greece
| | - Spyridon Marinopoulos
- Department of Obstetrics and Gynaecology, Alexandra Hospital, Medical school, University of Athens, Athens, Greece
| | - Aris Giannos
- Department of Obstetrics and Gynaecology, Alexandra Hospital, Medical school, University of Athens, Athens, Greece
| | - Theodoros N Sergentanis
- Department of Clinical Therapeutics, Alexandra Hospital, Medical School, University of Athens, Athens, Greece
| | - Efstathios Kastritis
- Department of Clinical Therapeutics, Alexandra Hospital, Medical School, University of Athens, Athens, Greece
| | - Evangelos Terpos
- Department of Clinical Therapeutics, Alexandra Hospital, Medical School, University of Athens, Athens, Greece
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Martin-Guerrero I, Bilbao-Aldaiturriaga N, Gutierrez-Camino A, Santos-Zorrozua B, Dolžan V, Patiño-Garcia A, Garcia-Orad A. Variants in the 14q32 miRNA cluster are associated with osteosarcoma risk in the Spanish population. Sci Rep 2018; 8:15414. [PMID: 30337581 PMCID: PMC6194014 DOI: 10.1038/s41598-018-33712-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 09/26/2018] [Indexed: 12/11/2022] Open
Abstract
Association studies in osteosarcoma risk found significant results in intergenic regions, suggesting that regions which do not codify for proteins could play an important role. The deregulation of microRNAs (miRNAs) has been already associated with osteosarcoma. Consequently, genetic variants affecting miRNA function could be associated with risk. This study aimed to evaluate the involvement of all genetic variants in pre-miRNAs described so far in relationship to the risk of osteosarcoma. We analyzed a total of 213 genetic variants in 206 pre-miRNAs in two cohorts of osteosarcoma patients (n = 100) and their corresponding controls (n = 256) from Spanish and Slovenian populations, using Goldengate Veracode technology (Illumina). Four polymorphisms in pre-miRNAs at 14q32 miRNA cluster were associated with osteosarcoma risk in the Spanish population (rs12894467, rs61992671, rs58834075 and rs12879262). Pathway enrichment analysis including target genes of these miRNAs pointed out the WNT signaling pathways overrepresented. Moreover, different single nucleotide polymorphism (SNP) effects between the two populations included were observed, suggesting the existence of population differences. In conclusion, 14q32 miRNA cluster seems to be a hotspot for osteosarcoma susceptibility in the Spanish population, but not in the Slovenian, which supports the idea of the existence of population differences in developing this disease.
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Affiliation(s)
- Idoia Martin-Guerrero
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country, UPV/EHU, Leioa, Spain
| | - Nerea Bilbao-Aldaiturriaga
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursery, UPV/EHU, Leioa, Spain
| | - Angela Gutierrez-Camino
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursery, UPV/EHU, Leioa, Spain
| | - Borja Santos-Zorrozua
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursery, UPV/EHU, Leioa, Spain
| | - Vita Dolžan
- Institute of Biochemistry, Faculty of Medicine, Ljubljana, Slovenia
| | - Ana Patiño-Garcia
- Laboratory of Pediatrics, University Clinic of Navarra, Pamplona, Spain
| | - Africa Garcia-Orad
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursery, UPV/EHU, Leioa, Spain. .,BioCruces Health Research Institute, Barakaldo, Spain.
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Chen Y, Tang W, Liu C, Lin J, Wang Y, Zhang S, Chen G, Zheng X. miRNA-146a rs2910164 C>G polymorphism increased the risk of esophagogastric junction adenocarcinoma: a case-control study involving 2,740 participants. Cancer Manag Res 2018; 10:1657-1664. [PMID: 29983589 PMCID: PMC6025765 DOI: 10.2147/cmar.s165921] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Purpose The miRNA-146a rs2910164 C>G polymorphism may contribute to the development of cancer. However, the association between this polymorphism and the risk of esophagogastric junction adenocarcinoma (EGJA) remains unclear. In the present study, we carried out a case–control study to explore the potential relationship between miRNA-146a rs2910164 C>G polymorphism and EGJA risk. Patients and methods In total, 1,063 EGJA patients and 1,677 cancer-free controls were enrolled. The SNPscan™ genotyping assay, a patented technology, was used to test the genotyping of miRNA-146a rs2910164 C>G polymorphism. Results We found that miRNA-146a rs2910164 C>G polymorphism was associated with a risk of developing EGJA (additive model: adjusted odds ratio (OR), 1.27; 95% CI, 1.07–1.51; P=0.006; homozygote model: adjusted OR, 1.31; 95% CI, 1.03–1.65; P=0.027 and dominant model: adjusted OR, 1.36; 95% CI, 1.15–1.60; P<0.001). After adjustment for the Bonferroni correction, these associations were also found in additive and dominant genetic models. In the subgroup analyses, after adjustment by sex, age, alcohol consumption, and smoking status, results of multiple logistic regression analysis indicated that miRNA-146a rs2910164 C>G polymorphism increased the risk of EGJA in males, females, <64 years old, ≥64 years old, never smoking, and never drinking subgroups. Conclusion The current study highlights that the miRNA-146a rs2910164 C>G polymorphism increased the risk of EGJA in eastern Chinese Han population.
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Affiliation(s)
- Yu Chen
- Department of Medical Oncology, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, Fujian Province, China.,Cancer Bio-Immunotherapy Center, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, Fujian Province, China.,Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian Province, China,
| | - Weifeng Tang
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Chao Liu
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu Province, China
| | - Jing Lin
- Department of Medical Oncology, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, Fujian Province, China.,Cancer Bio-Immunotherapy Center, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, Fujian Province, China
| | - Yafeng Wang
- Department of Cardiology, The People's Hospital of Xishuangbanna Dai Autonomous Prefecture, Jinghong, Yunnan Province, China
| | - Sheng Zhang
- Department of General Surgery, Changzhou No. 3 People's Hospital, Changzhou, Jiangsu Province, China
| | - Gang Chen
- Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian Province, China, .,Department of Pathology, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, Fujian Province, China,
| | - Xiongwei Zheng
- Fujian Provincial Key Laboratory of Translational Cancer Medicine, Fuzhou, Fujian Province, China, .,Department of Pathology, Fujian Cancer Hospital and Fujian Medical University Cancer Hospital, Fuzhou, Fujian Province, China,
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13
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Genetic susceptibility to bone and soft tissue sarcomas: a field synopsis and meta-analysis. Oncotarget 2018; 9:18607-18626. [PMID: 29719630 PMCID: PMC5915097 DOI: 10.18632/oncotarget.24719] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 03/07/2018] [Indexed: 12/18/2022] Open
Abstract
Background The genetic architecture of bone and soft tissue sarcomas susceptibility is yet to be elucidated. We aimed to comprehensively collect and meta-analyze the current knowledge on genetic susceptibility in these rare tumors. Methods We conducted a systematic review and meta-analysis of the evidence on the association between DNA variation and risk of developing sarcomas through searching PubMed, The Cochrane Library, Scopus and Web of Science databases. To evaluate result credibility, summary evidence was graded according to the Venice criteria and false positive report probability (FPRP) was calculated to further validate result noteworthiness. Integrative analysis of genetic and eQTL (expression quantitative trait locus) data was coupled with network and pathway analysis to explore the hypothesis that specific cell functions are involved in sarcoma predisposition. Results We retrieved 90 eligible studies comprising 47,796 subjects (cases: 14,358, 30%) and investigating 1,126 polymorphisms involving 320 distinct genes. Meta-analysis identified 55 single nucleotide polymorphisms (SNPs) significantly associated with disease risk with a high (N=9), moderate (N=38) and low (N=8) level of evidence, findings being classified as noteworthy basically only when the level of evidence was high. The estimated joint population attributable risk for three independent SNPs (rs11599754 of ZNF365/EGR2, rs231775 of CTLA4, and rs454006 of PRKCG) was 37.2%. We also identified 53 SNPs significantly associated with sarcoma risk based on single studies.Pathway analysis enabled us to propose that sarcoma predisposition might be linked especially to germline variation of genes whose products are involved in the function of the DNA repair machinery. Conclusions We built the first knowledgebase on the evidence linking DNA variation to sarcomas susceptibility, which can be used to generate mechanistic hypotheses and inform future studies in this field of oncology.
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Bhaumik P, Ghosh P, Biswas A, Ghosh S, Pal S, Sarkar B, Kumar Dey S. Rare Intronic Variations inTP73Gene Found in Patients with Alzheimer’sDisease. INT J HUM GENET 2018. [DOI: 10.1080/09723757.2017.1421438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Pranami Bhaumik
- Department of Biotechnology, School of Biotechnology and Biological Sciences, Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly known as West Bengal University of Technology) BF – 142, Salt Lake City, Sector I. Kolkata 700 064, West Bengal, India
| | - Priyanka Ghosh
- Department of Biotechnology, School of Biotechnology and Biological Sciences, Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly known as West Bengal University of Technology) BF – 142, Salt Lake City, Sector I. Kolkata 700 064, West Bengal, India
| | - Atanu Biswas
- Department of Neurology, Bangur Institute of Neurosciences, 52/1A, S.N. Pandit Street, Kolkata 700 025, West Bengal, India
| | - Sujay Ghosh
- Department of Zoology, University of Calcutta, (Ballygunge Science College Campus), 35 Ballygunge Circular Road., Kolkata 700 019, West Bengal, India
| | - Sandip Pal
- Department of Neurology, Burdwan Medical College, Burdwan 713 104, West Bengal, India
| | - Biswanath Sarkar
- DNA Laboratory, Anthropological Survey of India, 27 Jawaharlal Nehru Road Kolkata 700 016, West Bengal, India
| | - Subrata Kumar Dey
- Department of Biotechnology, School of Biotechnology and Biological Sciences, Maulana Abul Kalam Azad University of Technology, West Bengal (Formerly known as West Bengal University of Technology) BF – 142, Salt Lake City, Sector I. Kolkata 700 064, West Bengal, India
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Kushlinskii NE, Fridman MV, Braga EA. Molecular mechanisms and microRNAs in osteosarcoma pathogenesis. BIOCHEMISTRY (MOSCOW) 2016; 81:315-28. [DOI: 10.1134/s0006297916040027] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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16
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Abstract
MicroRNA molecules have a variety of roles in cellular development and proliferation processes, including normal osteogenesis. These effects are exerted through post-translational inhibition of target genes. Altered miRNA expression has been demonstrated in several cancers, both in the tumor tissue and in the peripheral circulation. This may influence carcinogenesis if the specific miRNA targets are encoded by tumor suppressor genes or oncogenes. To date, most research investigating the role of microRNAs and primary bone tumors has focused on osteosarcoma and Ewing sarcoma. Several microRNAs including the miR-34 family have been implicated in osteosarcoma tumorigenesis via effects on the Notch signaling pathway. Progression, invasion, and metastasis of osteosarcoma tumor cells is also influenced by microRNA expression. In addition, microRNA expression may affect the response to chemotherapy in osteosarcoma and thus hold potential for future use as either a prognostic indicator or a therapeutic target. The EWS-FLI1 fusion protein produced in Ewing sarcoma has been shown to induce changes in miRNA expression. MicroRNA expression profiling may have some potential for prediction of disease progression and survival in Ewing sarcoma. There is limited evidence to support a role for microRNAs in other primary bone tumors, either malignant or benign; however, early work is suggestive of involvement in chondrosarcoma, multiple osteochondromatosis, and giant cell tumors of bone.
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17
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Wang P, Wang H, Li X, Liu Y, Zhao C, Zhu D. SRCIN1 Suppressed Osteosarcoma Cell Proliferation and Invasion. PLoS One 2016; 11:e0155518. [PMID: 27513473 PMCID: PMC4981393 DOI: 10.1371/journal.pone.0155518] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 04/30/2016] [Indexed: 02/05/2023] Open
Abstract
SRCIN1 (SRC kinase signalling inhibitor 1) is a new tumor suppressor gene. Previous studies showed that SRCIN1 played a tumor suppressor role in the development of lung cancer and breast cancer. However, the role of SRCIN1 in osteosarcoma is still unknown. In this study, we demonstrated that SRCIN1 was downregulated in osteosarcoma cell lines compared with osteoblastic cell line. Moreover, SRCIN1 was downregulated in osteosarcoma tissues compared with the adjacent tissues. Further investigation revealed that overexpression of SRCIN1 inhibited the osteosarcoma cell line MG-63 proliferation. This effect was confirmed by measuring the ki-67 and PCNA expression. SRCIN1 overexpression promoted E-cadherin expression and suppressed N-cadherin, Vimentin and Snail expression, suggesting that SRCIN1 overexpression inhibited EMT of the osteosarcoma cell. In addition, ectopic expression of SRCIN1 inhibited the MG-63 cell colony formation and invasion. These data suggested that SRCIN1 acted as a tumor suppressor gene in the development of osteosarcoma.
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Affiliation(s)
- Peng Wang
- Department of Orthopedics, The Fourth Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, China
| | - Hu Wang
- Department of Orthopedics, First Affiliated Hospital of Shantou University Medical College, Shantou, 515041, Guangdong Province, China
| | - Xiaotao Li
- Department of Orthopedics, The First Affiliated Hospital of Jiamusi University, Jiamusi, Heilongjiang, 154000, China
| | - Ying Liu
- Clinical medicine Grade Four, Harbin Medical University, Harbin, Heilongjiang, 150001, China
| | - Chengbin Zhao
- Department of Orthopedics, The Fourth Hospital of Harbin Medical University, Harbin, Heilongjiang, 150001, China
- * E-mail: (CZ); (DZ)
| | - Daling Zhu
- Department of Biopharmaceutical Sciences, College of Pharmacy, Harbin Medical University Daqing, Daqing, 163319, China
- Biopharmaceutical Key Laboratory of Heilongjiang Province, Harbin, 150081, China
- * E-mail: (CZ); (DZ)
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18
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Zhang H, Qu Y, Duan J, Deng T, Liu R, Zhang L, Bai M, Li J, Zhou L, Ning T, Li H, Ge S, Li H, Ying G, Huang D, Ba Y. Integrated analysis of the miRNA, gene and pathway regulatory network in gastric cancer. Oncol Rep 2015; 35:1135-46. [PMID: 26719093 DOI: 10.3892/or.2015.4451] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 10/26/2015] [Indexed: 11/05/2022] Open
Abstract
Gastric cancer is one of the most common malignant tumors worldwide; however, the efficacy of clinical treatment is limited. MicroRNAs (miRNAs) are a class of small non-coding RNAs that have been reported to play a key role in the development of cancer. They also provide novel candidates for targeted therapy. To date, in-depth studies on the molecular mechanisms of gastric cancer involving miRNAs are still absent. We previously reported that 5 miRNAs were identified as being significantly increased in gastric cancer, and the role of these miRNAs was investigated in the present study. By using bioinformatics tools, we found that more than 4,000 unique genes are potential downstream targets of gastric cancer miRNAs, and these targets belong to the protein class of nucleic acid binding, transcription factor, enzyme modulator, transferase and receptor. Pathway mapping showed that the targets of gastric cancer miRNAs are involved in the MAPK signaling pathway, pathways in cancer, the PI3K-Akt signaling pathway, the HTLV-1 signaling pathway and Ras signaling pathway, thus regulating cell growth, differentiation, apoptosis and metastasis. Analysis of the pathways related to miRNAs may provides potential drug targets for future therapy of gastric cancer.
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Affiliation(s)
- Haiyang Zhang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
| | - Yanjun Qu
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
| | - Jingjing Duan
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
| | - Ting Deng
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
| | - Rui Liu
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
| | - Le Zhang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
| | - Ming Bai
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
| | - Jialu Li
- Department of Gastroenterology, Tianjin First Center Hospital, Tianjin 300192, P.R. China
| | - Likun Zhou
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
| | - Tao Ning
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
| | - Hongli Li
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
| | - Shaohua Ge
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
| | - Hua Li
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
| | - Guoguang Ying
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
| | - Dingzhi Huang
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
| | - Yi Ba
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin 300060, P.R. China
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Cammaerts S, Strazisar M, Dierckx J, Del Favero J, De Rijk P. miRVaS: a tool to predict the impact of genetic variants on miRNAs. Nucleic Acids Res 2015; 44:e23. [PMID: 26384425 PMCID: PMC4756848 DOI: 10.1093/nar/gkv921] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 09/04/2015] [Indexed: 01/10/2023] Open
Abstract
Genetic variants in or near miRNA genes can have profound effects on miRNA expression and targeting. As user-friendly software for the impact prediction of miRNA variants on a large scale is still lacking, we created a tool called miRVaS. miRVaS automates this prediction by annotating the location of the variant relative to functional regions within the miRNA hairpin (seed, mature, loop, hairpin arm, flanks) and by annotating all predicted structural changes within the miRNA due to the variant. In addition, the tool defines the most important region that is predicted to have structural changes and calculates a conservation score that is indicative of the reliability of the structure prediction. The output is presented in a tab-separated file, which enables fast screening, and in an html file, which allows visual comparison between wild-type and variant structures. All separate images are provided for downstream use. Finally, we tested two different approaches on a small test set of published functionally validated genetic variants for their capacity to predict the impact of variants on miRNA expression.
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Affiliation(s)
- Sophia Cammaerts
- Applied Molecular Genomics Unit, Department of Molecular Genetics, VIB, Antwerp, 2610, Belgium University of Antwerp, Antwerp, 2610, Belgium
| | - Mojca Strazisar
- Applied Molecular Genomics Unit, Department of Molecular Genetics, VIB, Antwerp, 2610, Belgium University of Antwerp, Antwerp, 2610, Belgium
| | | | - Jurgen Del Favero
- Applied Molecular Genomics Unit, Department of Molecular Genetics, VIB, Antwerp, 2610, Belgium University of Antwerp, Antwerp, 2610, Belgium Multiplicom N.V., Niel, 2845, Belgium
| | - Peter De Rijk
- Applied Molecular Genomics Unit, Department of Molecular Genetics, VIB, Antwerp, 2610, Belgium University of Antwerp, Antwerp, 2610, Belgium
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Chang L, Shrestha S, LaChaud G, Scott MA, James AW. Review of microRNA in osteosarcoma and chondrosarcoma. Med Oncol 2015; 32:613. [PMID: 25920607 DOI: 10.1007/s12032-015-0613-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 04/01/2015] [Indexed: 12/19/2022]
Abstract
MicroRNAs (miRNAs) are small noncoding RNAs, which play a complex role in posttranscriptional gene expression and can theoretically be used as a diagnostic or prognostic tool, or therapeutic target for neoplasia. Despite advances in the diagnosis and treatment of skeletal sarcomas, including osteosarcoma and chondrosarcoma, much remains unknown regarding their underpinning molecular mechanisms. Given the recent increasing knowledge base of miRNA roles in neoplasia, both as oncogenes and tumor suppressor genes, this review will focus on the available literature regarding the expression profiles and potential roles of miRNA in skeletal sarcomas. Although this is an emerging field, miRNA profiling may be of use in clarifying competing diagnoses of skeletal sarcomas and possibly indicate patient risk of resistance to traditional chemotherapeutic agents. While detecting and targeting miRNAs is currently limited to experimental investigations, miRNA may be utilized for future clinical management of skeletal sarcomas.
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Affiliation(s)
- Le Chang
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, 10833 Le Conte Ave., 13-145 CHS, Los Angeles, CA, 90095, USA
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Li X, Zhang C, Qiao W, Zhou X, Sun M. NFKB1 -94ins/del ATTG polymorphism increases osteosarcoma risk in a Chinese Han population. Int J Clin Exp Med 2015; 8:1420-1423. [PMID: 25785149 PMCID: PMC4358604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 12/15/2014] [Indexed: 06/04/2023]
Abstract
Osteosarcoma is one of the most common bone malignancies. The Nuclear factor-κB1 (NFKB1) gene plays an important role in the pathogenesis of osteosarcoma. The objective of this study aimed to detect the potential association between NFKB1 -94 ins/del ATTG polymorphism and osteosarcoma susceptibility in Chinese Han population. We recruited 220 osteosarcoma patients and 222 cancer-free controls in this case-control study. The NFKB1 -94 ins/del ATTG polymorphism by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. Patients with ID genotype and II genotype showed higher risk of osteosarcoma than individuals with DD genotype (OR=1.54, 95% CI 1.00-2.44, P=0.05; OR=1.72, 95% CI 1.01-2.93, P=0.04), respectively. Subjects with ID or II genotype also showed increased risk of osteosarcoma (OR=1.60, 95% CI 1.04-2.47, P=0.03). In addition, I allele was significantly associated with osteosarcoma risk (OR=1.31, 95% CI 1.01-1.71, P=0.04). We also found that this polymorphism was significantly associated with advanced osteosarcoma risk (OR=3.43, 95% CI 1.61-7.36, P=0.001) and metastatic osteosarcoma risk (OR=2.33, 95% CI 1.22-5.03, P=0.01). In conclusion, our findings indicate that osteosarcoma is associated with the NFKB1 promoter -94ins/del ATTG polymorphism.
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Affiliation(s)
- Xiyi Li
- Department of Pathology, Cancer Hospital, Fudan UniversityShanghai 200032, China
- Department of Oncology, Shanghai Medical School, Fudan UniversityShanghai 200032, China
- Department of Orthopedics, Changzheng Hospital, Second Military Medical UniversityShanghai 200003, China
| | - Chenglin Zhang
- Department of Orthopedics, Changzheng Hospital, Second Military Medical UniversityShanghai 200003, China
| | - Wei Qiao
- Department of Pathology, Cancer Hospital, Fudan UniversityShanghai 200032, China
- Department of Oncology, Shanghai Medical School, Fudan UniversityShanghai 200032, China
| | - Xuhui Zhou
- Department of Orthopedics, Changzheng Hospital, Second Military Medical UniversityShanghai 200003, China
| | - Menghong Sun
- Department of Pathology, Cancer Hospital, Fudan UniversityShanghai 200032, China
- Department of Oncology, Shanghai Medical School, Fudan UniversityShanghai 200032, China
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