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Tudor K, Baranasic J, Knezevic J, Serer Vicevic M, Sutic M, Dembic Z, Jotanovic Z. Indirect influence of microRNA-146a on the association of IL-6 and TNF-α genetic polymorphisms with the increased risk of hip osteoarthritis. J Orthop Res 2024; 42:1482-1489. [PMID: 38341771 DOI: 10.1002/jor.25804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 01/27/2024] [Indexed: 02/13/2024]
Abstract
Primary osteoarthritis (POA) is a complex hereditary disease that involves the interplay between genetics and epigenetics. MicroRNA molecules play important roles in epigenetic mechanisms. MicroRNA-146a (miR-146a) is a negative regulator of the immune response in osteoarthritis (OA). So, variations in the miR-146a gene could affect OA risk. The aim of this study was to investigate the relationships between single nucleotide polymorphisms (SNPs) in the miR-146a, interleukin-6 (IL-6), Toll-like receptor 10 (TLR10), and tumor necrosis factor-alpha (TNFA) genes and the risk for development of advanced-stage primary hip osteoarthritis (PHOA) and primary knee osteoarthritis (PKOA) in the Croatian population. A total of 609 POA patients and 656 healthy donors were genotyped for SNPs in the miR-146a (rs2910164, G>C). Since we used same patients and controls as two studies before us, we already had information about IL-6 (rs1800795, C>G), TLR10 (rs11096957, C>T), and TNFA (rs1800629, C>T) genotypes of our subjects. None of the differences were statistically significant comparing either allelic or genotypic frequencies of miR-146a SNP rs2910164 (G>C) between the PHOA and PKOA patients and controls. However, we found a significant association with risk to PHOA for the combination of genotypes (stratified miR-146a genotype with the IL-6, and stratified miR-146a genotype with the TNFA). In a multifactorial disease such as POA, we have shown the indirect relevance of a second modifying factor (miR-146a), which apparently contributes to the overall risk of PHOA. There was no risk association with the PKOA, indicating that these two localities (hip and knee) might have different risk-modifying factors.
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Affiliation(s)
- Karlo Tudor
- Department for Orthopaedics and Physical medicine, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
- Orthopaedic Department, University Hospital for Orthopaedics and Traumatology Lovran, Lovran, Croatia
| | - Jurica Baranasic
- Department for Molecular Medicine, Rudjer Boskovic Institute, Zagreb, Croatia
| | - Jelena Knezevic
- Department for Molecular Medicine, Rudjer Boskovic Institute, Zagreb, Croatia
| | - Marta Serer Vicevic
- Clinical Hospital Center Rijeka, Clinical Institute for Transfusion Medicine, Rijeka, Croatia
| | - Maja Sutic
- Department for Molecular Medicine, Rudjer Boskovic Institute, Zagreb, Croatia
| | - Zlatko Dembic
- Faculty of Dentistry, Institute of Oral Biology, University of Oslo, Oslo, Norway
| | - Zdravko Jotanovic
- Department for Orthopaedics and Physical medicine, Faculty of Medicine, University of Rijeka, Rijeka, Croatia
- Orthopaedic Department, University Hospital for Orthopaedics and Traumatology Lovran, Lovran, Croatia
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Mohamed AS, Salama AF, Sabaa MA, Toraih E, Elshazli RM. GEMIN4 Variants: Risk Profiling, Bioinformatics, and Dynamic Simulations Uncover Susceptibility to Bladder Carcinoma. Arch Med Res 2024; 55:102970. [PMID: 38401326 DOI: 10.1016/j.arcmed.2024.102970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/11/2024] [Accepted: 02/13/2024] [Indexed: 02/26/2024]
Abstract
BACKGROUND The relationship between GEMIN4 genetic variants and cancer, especially bladder carcinoma (BLCA), has been explored without conclusive results. This study aims to elucidate the link between GEMIN4 polymorphisms and BLCA susceptibility through genetic analyses, bioinformatics, and molecular dynamics (MD) simulations. METHODS A cohort of 249 participants (121 BLCA patients and 128 unrelated controls) was enrolled. PCR was employed for allelic discrimination of GEMIN4 variants, followed by subgroup stratification, haplotype analyses, structural prediction using the AlphaFold2 prediction tool, subsequent MD simulations, structural analysis, and residue interaction mapping using Desmond, UCSF ChimeraX, and Cytoscape softwares. RESULTS The rs.2740348*G variant demonstrated a protective role against BLCA in allelic (OR = 0.55, p = 0.002) and recessive (OR = 0.54, p = 0.017) models, whereas the rs.7813*T variant increased BLCA risk under the recessive model (OR = 1.90, p = 0.019). Haplotype analysis revealed a significant association between GEMIN4 haplotype (rs.2740348*C/rs.7813*T) with increased BLCA risk (OR = 2.01, p = 0.004). Univariate analysis revealed associations of the variants with albumin levels and absolute neutrophil count in BLCA patients. Pathogenicity evaluation categorized p.Gln450Glu as neutral and p.Arg1033Cys as deleterious. MD simulations revealed structural alterations and conformational shifts in the GEMIN4 protein induced by the Glu450 and Cys1033 mutations. CONCLUSIONS The study highlights the dual role of GEMIN4 variants in BLCA susceptibility, with rs.2740348 conferring protection and rs.7813 increasing risk. The Glu450 residue positively impacted protein stability, while Cys1033 had a detrimental effect on protein function. These findings underscore the significance of GEMIN4 variants in BLCA susceptibility and pave the way for future diagnostic and therapeutic initiatives.
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Affiliation(s)
- Abdallah S Mohamed
- Biochemistry Division, Department of Chemistry, Faculty of Science, Tanta University, Tanta, Egypt
| | - Afrah F Salama
- Biochemistry Division, Department of Chemistry, Faculty of Science, Tanta University, Tanta, Egypt
| | - Magdy A Sabaa
- Department of Urology, Faculty of Medicine, Tanta University, Tanta, Egypt
| | - Eman Toraih
- Endocrine and Oncology Division, Department of Surgery, Tulane University School of Medicine, New Orleans, LA, USA; Genetics Unit, Department of Histology and Cell Biology, Faculty of Medicine, Suez Canal University, Ismailia, Egypt.
| | - Rami M Elshazli
- Biochemistry and Molecular Genetics Unit, Department of Basic Sciences, Faculty of Physical Therapy, Horus University - Egypt, New Damietta, Egypt.
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Zhan M, Liu T, Zhang Z, Wang G, Cao Z, Li X, Zeng H, Mai H, Chen Z. Impact of microRNA polymorphisms on high-dose methotrexate-related hematological toxicities in pediatric acute lymphoblastic leukemia. Front Pediatr 2023; 11:1153767. [PMID: 37384310 PMCID: PMC10293614 DOI: 10.3389/fped.2023.1153767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 05/24/2023] [Indexed: 06/30/2023] Open
Abstract
Objectives It is well known that transporter and enzyme genes could be regulated by microRNA (miRNA) at the post-transcriptional level, and single-nucleotide polymorphisms (SNPs) in miRNA, which are involved in the miRNA production and structure, may impact the miRNA expression level and then influence drug transport and metabolism. In this study, we aim to evaluate the association between miRNA polymorphisms and high-dose methotrexate (HD-MTX) hematological toxicities in Chinese pediatric patients with acute lymphoblastic leukemia (ALL). Method A total of 181 children with ALL were administered with 654 evaluable cycles of HD-MTX. Their hematological toxicities were evaluated according to the National Cancer Institute Common Terminology Criteria for Adverse Events v5. The association between 15 candidate SNPs of miRNA and hematological toxicities (leukopenia, anemia, and thrombocytopenia) was analyzed using Fisher's exact test. Further multiple backward logistic regression analysis was used to explore the independent risk factors for grade 3/4 hematological toxicities. Result Rs2114358 G>A in pre-hsa-miR-1206 was related to HD-MTX-related grade 3/4 leukopenia after multiple logistic regression [GA + AA vs. GG: odds ratio (OR): 2.308, 95% CI: 1.219-4.372, P = 0.010], and rs56103835 T > C in pre-hsa-mir-323b was associated with HD-MTX-related grade 3/4 anemia (TT + TC vs. CC: OR: 0.360, 95% CI: 0.239-0.541, P = 0.000); none of the SNPs were significantly associated with grade 3/4 thrombocytopenia. Bioinformatics tools predicted that rs2114358 G>A and rs56103835 T>C would impact the secondary structure of pre-miR-1206 and pre-miR-323b, respectively, and then probably influence the expression level of mature miRNAs and their target genes. Conclusion Rs2114358 G>A and rs56103835 T>C polymorphism may potentially influence HD-MTX-related hematological toxicities, which may serve as candidate clinical biomarkers to predict grade 3/4 hematological toxicities in pediatric patients with ALL.
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Affiliation(s)
- Min Zhan
- Department of Pharmacy, Shenzhen Children’s Hospital, Shenzhen, China
| | - Ting Liu
- Department of Pharmacy, Shenzhen Children’s Hospital, Shenzhen, China
| | - Zhou Zhang
- Department of Pharmacy, Shenzhen Children’s Hospital, Shenzhen, China
| | - Guoqiang Wang
- Department of Pharmacy, Shenzhen Children’s Hospital, Shenzhen, China
| | - Zhongqiang Cao
- Department of Pharmacy, Shenzhen Children’s Hospital, Shenzhen, China
| | - Xuejuan Li
- Department of Pharmacy, Shenzhen Children’s Hospital, Shenzhen, China
| | - Hongwu Zeng
- Department of Radiology, Shenzhen Children’s Hospital, Shenzhen, China
| | - Huirong Mai
- Department of Hematology/Oncology, Shenzhen Children’s Hospital, Shenzhen, China
| | - Zebin Chen
- Department of Pharmacy, Shenzhen Children’s Hospital, Shenzhen, China
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Juárez-Luis J, Canseco-Ocaña M, Cid-Soto MA, Castro-Martínez XH, Martínez-Hernández A, Orozco L, Hernández-Zavala A, Córdova EJ. Single nucleotide variants in microRNA biosynthesis genes in Mexican individuals. Front Genet 2023; 14:1022912. [PMID: 36968598 PMCID: PMC10037310 DOI: 10.3389/fgene.2023.1022912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/02/2023] [Indexed: 03/08/2023] Open
Abstract
Background: MicroRNAs (miRNAs) are important regulators in a variety of biological processes, and their dysregulation is associated with multiple human diseases. Single nucleotide variants (SNVs) in genes involved in the processing of microRNAs may alter miRNA regulation and could present high allele heterogeneity in populations from different ethnic groups. Thus, the aim of this study was to genotype 15 SNVs in eight genes involved in the miRNA processing pathway in Mexican individuals and compare their frequencies across 21 populations from five continental groups.Methods: Genomic DNA was obtained from 399 healthy Mexican individuals. SNVs in AGO2 (rs2293939 and rs4961280), DGCR8 (rs720012), DICER (rs3742330 and rs13078), DROSHA (rs10719 and rs6877842), GEMIN3 (rs197388 and rs197414), GEMIN4 (rs7813, rs2740349, and rs4968104), TNRC6B (rs9611280), and XP05 (rs11077 and rs34324334) were genotyped using TaqMan probes. The minor allele frequency of each SNV was compared to those reported in the 1,000 Genomes database using chi-squared. Sankey plot was created in the SankeyMATIC package to visualize the frequency range of each variant in the different countries analyzed.Results: In Mexican individuals, all 15 SNVs were found in Hardy-Weinberg equilibrium, with frequencies ranging from 0.04 to 0.45. The SNVs rs4961280, rs2740349, rs34324334, and rs720012 in Mexican individuals had the highest minor allele frequencies worldwide, whereas the minor allele frequencies of rs197388, rs10719, rs197414, and rs1107 were among the lowest in Mexican individuals. The variants had high allele heterogeneity among the sub-continental populations, ranging from monomorphic, as was the case for rs9611280 and rs34324334 in African groups, to >0.50, which was the case for variants rs11077 and rs10719 in most of the populations. Importantly, the variants rs197388, rs720012, and rs197414 had FST values > 0.18, indicating a directional selective process. Finally, the SNVs rs13078 and rs10719 significantly correlated with both latitude and longitude.Conclusion: These data indicate the presence of high allelic heterogeneity in the worldwide distribution of the frequency of SNVs located in components of the miRNA processing pathway, which could modify the genetic susceptibility associated with human diseases in populations with different ancestry.
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Affiliation(s)
- Jesús Juárez-Luis
- Section of Research and Postgraduate, Superior School of Medicine, National Institute Polytechnique, Mexico City, Mexico
| | - Moisés Canseco-Ocaña
- Oncogenomics Consortium Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Miguel Angel Cid-Soto
- Oncogenomics Consortium Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Xochitl H. Castro-Martínez
- Genomics of Psychiatric and Neurogenerative diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Angélica Martínez-Hernández
- Immunogenomics and Metabolic diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Lorena Orozco
- Immunogenomics and Metabolic diseases Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
| | - Araceli Hernández-Zavala
- Section of Research and Postgraduate, Superior School of Medicine, National Institute Polytechnique, Mexico City, Mexico
| | - Emilio J. Córdova
- Oncogenomics Consortium Laboratory, National Institute of Genomic Medicine, Mexico City, Mexico
- *Correspondence: Emilio J. Córdova,
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Pan-Cancer Study on Variants of Canonical miRNA Biogenesis Pathway Components: A Pooled Analysis. Cancers (Basel) 2023; 15:cancers15020338. [PMID: 36672288 PMCID: PMC9856462 DOI: 10.3390/cancers15020338] [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: 10/25/2022] [Revised: 12/23/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Single nucleotide polymorphisms in genes involved in microRNA processing/maturation and release may deregulate the microRNAome expression levels. We aimed to assess the relationship between miRNA machinery genetic variants and human cancer risk using integrative bioinformatics analyses to identify the role of these genes in cancer aggressiveness. Mutations of 8176 pan-cancer samples were retrieved from 33 studies in "TCGA" database, and a Cox regression model for survival was performed. Next, 22 computationally identified variants within 11 genes were selected based on their high citation rate and MAF. Relevant articles through March 2020 were included. Pooled estimates under the five genetic association models were calculated. Publication bias and heterogeneity between articles were evaluated. Trial Sequential Analysis (TSA) was applied to assess the power and reliability of the draw conclusions. TCGA patients with different cancer types revealed significant alterations in miRNA machinery genes, with mutation frequency ranging from 0.6-13% of samples. RAN was associated with LN metastasis, while TARBP2 and PIWIL1 gene mutations exhibited better overall survival. In the meta-analysis, 45 articles (74,593 cases and 89,198 controls) met the eligibility criteria. Pooled analysis revealed an increased cancer risk with DROSHArs10719*G, RANrs3803012*G, DGCR8rs417309*A, and GEMIN3rs197414*A. In contrast, both DICER1rs1057035*T and GEMIN4rs2743048*G conferred protection against developing cancer. TSA showed the cumulative evidence is inadequate, and the addition of further primary studies is necessary. This study suggests a potential role of miRNA biogenesis genes in cancer development/prognosis. Further functional studies may reveal biological explanations for the differential risks of the machinery variants in different cancer types.
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hsa-MicroRNA-28-5p Inhibits Diffuse Large B-Cell Lymphoma Cell Proliferation by Downregulating 14-3-3 ζ Expression. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:4605329. [PMID: 35027933 PMCID: PMC8752235 DOI: 10.1155/2022/4605329] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/13/2021] [Accepted: 12/09/2021] [Indexed: 01/14/2023]
Abstract
MicroRNAs (miRNAs) participate in the comprehensive biological process of several cancer types. In our former study, we found that hsa-microRNA- (miR-)28-5p was downregulated, but tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activating protein zeta (14-3-3ζ or YWHAZ) was upregulated in diffuse large B-cell lymphoma (DLBCL) tissues. We predicted that YWHAZ was a target gene for hsa-miR- 28-5p using bioinformatics analysis. Our goal was to reveal the role of hsa-miR-28-5p in DLBCL. YWHAZ was tested by immunohistochemistry (IHC) in formalin-fixed paraffin-embedded (FFPE) tissues of 137 DLBCL tissues, and the expression of hsa-miR-28-5p and YWHAZ was examined by quantitative real-time polymerase chain reaction (qRT-PCR) in 15 fresh and frozen DLBCL tissues. To study the functional roles of the downregulated hsa-miR-28-5p in DLBCL, a Cell Counting Kit-8 assay was conducted to estimate cell proliferation. Transient transfection of miRNA mimics was performed to overexpress hsa-miR-28-5p, and flow cytometry was performed to examine cell apoptosis and cell cycle progression. A dual-luciferase reporter assay was employed to explore the relationship between hsa-miR-28-5p and YWHAZ. Western blotting and qRT-PCR were used to investigate the function of hsa-miR-28-5p in YWHAZ expression. hsa-miR-28-5p was found to be significantly downregulated in DLBCL tissues and cell lines. Functional studies showed that hsa-miR-28-5p overexpression inhibited cell viability and proliferation, and YWHAZ was predicted to be a target of hsa-miR-28-5p. Dual-luciferase reporter assay, Western blotting, and qRT-PCR verified that hsa-miR-28-5p negatively regulated YWHAZ expression by directly targeting its 3′ untranslated regions in DLBCL cells. hsa-miR-28-5p may suppress the growth of DLBCL cells by inhibiting YWHAZ expression. These findings could provide novel targets for DLBCL diagnosis and therapy.
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Aziz MA, Akter T, Islam MS. Effect of miR-196a2 rs11614913 Polymorphism on Cancer Susceptibility: Evidence From an Updated Meta-Analysis. Technol Cancer Res Treat 2022; 21:15330338221109798. [PMID: 35770306 PMCID: PMC9251994 DOI: 10.1177/15330338221109798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Background:MiR-196a2 rs11614913 polymorphism has been studied in a wide range of cancers throughout the years. Despite a large number of epidemiological studies performed in almost all ethnic populations, the contribution of this polymorphism to cancer risk is still inconclusive. Therefore, this updated meta-analysis was performed to estimate a meticulous correlation between miR-196a2 rs11614913 variant and cancer susceptibility. Methods: A systematic study search was carried out using PubMed, ScienceDirect, CNKI, EMBASE, Scopus, and Google Scholar databases following PRISMA guidelines to find necessary literature up to December 15, 2021. Pooled odds ratios with corresponding 95% confidence intervals were estimated using RevMan 5.4 based on ethnicities, cancer types, control sources, and genotyping methods. Results: A total of 152 studies, including 120 135 subjects (53 818 patients and 66 317 controls; 140 studies, after removing studies that deviated from HWE: 51 459 cases and 62 588 controls), were included in this meta-analysis. Quantitative synthesis suggests that the miR-196a2 rs11614913 genetic variant is significantly correlated with the reduced risk of overall cancer in CDM2, CDM3, RM, and AM (odds ratio < 1 and P < .05). It is also observed from ethnicity-based subgroup analysis that rs11614913 polymorphism is significantly (P < .05) linked with cancer in the Asian (in CDM2, CDM3, RM, AM) and the African population (in CDM1, CDM3, ODM). Stratified analysis based on the cancer types demonstrated a significantly decreased correlation for breast, hepatocellular, lung, and gynecological cancer and an increased association for oral and renal cell cancer. Again, the control population-based subgroup analysis reported a strongly reduced correlation for HB population in CDM2, RM, and AM. A substantially decreased risk was also observed for other genotyping methods in multiple genetic models. Conclusions:MiR-196a2 rs11614913 variant is significantly correlated with overall cancer susceptibility. Besides, rs11614913 is correlated with cancer in Asians and Africans. It is also correlated with breast, gynecological, hepatocellular, lung, oral, and renal cell cancer.
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Affiliation(s)
- Md Abdul Aziz
- Department of Pharmacy, Faculty of Pharmacy and Health Sciences, 185960State University of Bangladesh, Dhaka, Bangladesh
| | - Tahmina Akter
- Department of Pharmacy, Faculty of Science, 378872Noakhali Science and Technology University, Noakhali, Bangladesh.,Laboratory of Pharmacogenomics and Molecular Biology, Department of Pharmacy, 378872Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Mohammad Safiqul Islam
- Department of Pharmacy, Faculty of Science, 378872Noakhali Science and Technology University, Noakhali, Bangladesh.,Laboratory of Pharmacogenomics and Molecular Biology, Department of Pharmacy, 378872Noakhali Science and Technology University, Noakhali, Bangladesh
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Kozin MS, Kiselev IS, Baulina NM, Pavlova GV, Boyko AN, Kulakova OG, Favorova OO. Risk of Multiple Sclerosis: Analysis of Interactions between Variants of Nuclear and Mitochondrial Genomes. Mol Biol 2021. [DOI: 10.1134/s0026893321050071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Elliott EK, Hopkins LN, Hensen R, Sutherland HG, Haupt LM, Griffiths LR. Epigenetic Regulation of miR-92a and TET2 and Their Association in Non-Hodgkin Lymphoma. Front Genet 2021; 12:768913. [PMID: 34899857 PMCID: PMC8661906 DOI: 10.3389/fgene.2021.768913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/26/2021] [Indexed: 12/22/2022] Open
Abstract
MicroRNAs (miRNAs) are well known for their ability to regulate the expression of specific target genes through degradation or inhibition of translation of the target mRNA. In various cancers, miRNAs regulate gene expression by altering the epigenetic status of candidate genes that are implicated in various difficult to treat haematological malignancies such as non-Hodgkin lymphoma by acting as either oncogenes or tumour suppressor genes. Cellular and circulating miRNA biomarkers could also be directly utilised as disease markers for diagnosis and monitoring of non-Hodgkin lymphoma (NHL); however, the role of DNA methylation in miRNA expression regulation in NHL requires further scientific inquiry. In this study, we investigated the methylation levels of CpGs in CpG islands spanning the promoter regions of the miR-17–92 cluster host gene and the TET2 gene and correlated them with the expression levels of TET2 mRNA and miR-92a-3p and miR-92a-5p mature miRNAs in NHL cell lines, tumour samples, and the whole blood gDNA of an NHL case control cohort. Increased expression of both miR-92a-3p and miR-92a-5p and aberrant expression of TET2 was observed in NHL cell lines and tumour tissues, as well as disparate levels of dysfunctional promoter CGI methylation. Both miR-92a and TET2 may play a concerted role in NHL malignancy and disease pathogenesis.
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Affiliation(s)
- Esther K Elliott
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD, Australia.,Icon Cancer Centre, Brisbane, QLD, Australia
| | - Lloyd N Hopkins
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD, Australia
| | | | - Heidi G Sutherland
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD, Australia
| | - Larisa M Haupt
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD, Australia
| | - Lyn R Griffiths
- Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD, Australia
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Jiménez-Morales S, Núñez-Enríquez JC, Cruz-Islas J, Bekker-Méndez VC, Jiménez-Hernández E, Medina-Sanson A, Olarte-Carrillo I, Martínez-Tovar A, Flores-Lujano J, Ramírez-Bello J, Pérez-Saldívar ML, Martín-Trejo JA, Pérez-Lorenzana H, Amador-Sánchez R, Mora-Ríos FG, Peñaloza-González JG, Duarte-Rodríguez DA, Torres-Nava JR, Flores-Bautista JE, Espinosa-Elizondo RM, Román-Zepeda PF, Flores-Villegas LV, Tamez-Gómez EL, López-García VH, Lara-Ramos JR, González-Ulivarri JE, Martínez-Silva SI, Espinoza-Anrubio G, Almeida-Hernández C, Ramírez-Colorado R, Hernández-Mora L, García-López LR, Cruz-Ojeda GA, Godoy-Esquivel AE, Contreras-Hernández I, Medina-Hernández A, López-Caballero MG, Hernández-Pineda NA, Granados-Kraulles J, Rodríguez-Vázquez MA, Torres-Valle D, Cortés-Reyes C, Medrano-López F, Pérez-Gómez JA, Martínez-Ríos A, Aguilar-De-Los-Santos A, Serafin-Díaz B, Gutiérrez-Rivera MDL, Merino-Pasaye LE, Vargas-Alarcón G, Mata-Rocha M, Sepúlveda-Robles OA, Rosas-Vargas H, Hidalgo-Miranda A, Mejía-Aranguré JM. Association Analysis Between the Functional Single Nucleotide Variants in miR-146a, miR-196a-2, miR-499a, and miR-612 With Acute Lymphoblastic Leukemia. Front Oncol 2021; 11:762063. [PMID: 34804964 PMCID: PMC8602911 DOI: 10.3389/fonc.2021.762063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/12/2021] [Indexed: 01/26/2023] Open
Abstract
Background Acute lymphoblastic leukemia (ALL) is characterized by an abnormal proliferation of immature lymphocytes, in whose development involves both environmental and genetic factors. It is well known that single nucleotide polymorphisms (SNPs) in coding and noncoding genes contribute to the susceptibility to ALL. This study aims to determine whether SNPs in miR-146a, miR-196a-2, miR-499a, and miR-612 genes are associated with the risk to ALL in pediatric Mexican population. Methods A multicenter case-control study was carried out including patients with de novo diagnosis of ALL and healthy subjects as control group. The DNA samples were obtained from saliva and peripheral blood, and the genotyping of rs2910164, rs12803915, rs11614913, and rs3746444 was performed using the 5′exonuclease technique. Gene-gene interaction was evaluated by the multifactor dimensionality reduction (MDR) software. Results miR-499a rs3746444 showed significant differences among cases and controls. The rs3746444G allele was found as a risk factor to ALL (OR, 1.6 [95% CI, 1.05–2.5]; p = 0.028). The homozygous GG genotype of rs3746444 confers higher risk to ALL than the AA genotype (OR, 5.3 [95% CI, 1.23–23.4]; p = 0.01). Moreover, GG genotype highly increases the risk to ALL in male group (OR, 17.6 [95% CI, 1.04–298.9]; p = 0.00393). In addition, an association in a gender-dependent manner among SNPs located in miR-146a and miR-196a-2 genes and ALL susceptibility was found. Conclusion Our findings suggest that SNP located in miR-499a, miR-146a, and miR-196a-2 genes confer risk to ALL in Mexican children. Experimental analysis to decipher the role of these SNPs in human hematopoiesis could improve our understanding of the molecular mechanism underlying the development of ALL.
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Affiliation(s)
- Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Juan Carlos Núñez-Enríquez
- Unidad de Investigación Médica en Epidemiología Clínica, Unidad Medica de Alta Especialidad (UMAE) Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", Instituto Mexicano del Seguro Social (IMSS), Mexico City, Mexico
| | - Jazmín Cruz-Islas
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Vilma Carolina Bekker-Méndez
- Unidad de Investigación Médica en Inmunología e Infectología, Hospital de Infectología "Dr. Daniel Méndez Hernández", "La Raza", IMSS, Mexico City, Mexico
| | - Elva Jiménez-Hernández
- Servicio de Hematología Pediátrica, Hospital General "Gaudencio González Garza", Centro Médico Nacional "La Raza", IMSS, Mexico City, Mexico
| | - Aurora Medina-Sanson
- Departamento de Hemato-Oncología, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Irma Olarte-Carrillo
- Servicio de Hematología, Departamento de Investigación, Hospital General de México Dr. Eduardo Liceaga, Mexico City, Mexico
| | - Adolfo Martínez-Tovar
- Servicio de Hematología, Departamento de Investigación, Hospital General de México Dr. Eduardo Liceaga, Mexico City, Mexico
| | - Janet Flores-Lujano
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Julian Ramírez-Bello
- Departamento de Endocrinología, Instituto Nacional de Cardiología, Ignacio Chávez, México City, Mexico
| | | | - Jorge Alfonso Martín-Trejo
- Servicio de Hematología Pediátrica Unidad Medica de Alta Especialidad (UMAE) Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", IMSS, Mexico City, Mexico
| | - Héctor Pérez-Lorenzana
- Servicio de Cirugía Pediátrica, Hospital General "Gaudencio González Garza", Centro Médico Nacional (CMN) "La Raza", IMSS, Mexico City, Mexico
| | - Raquel Amador-Sánchez
- Servicio de Hematología Pediátrica, Hospital General Regional "Carlos McGregor Sánchez Navarro", IMSS, Mexico City, Mexico
| | - Felix Gustavo Mora-Ríos
- Cirugía Pediátrica, Hospital Regional "General Ignacio Zaragoza", Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Mexico City, Mexico
| | | | | | - José Refugio Torres-Nava
- Servicio de Oncología, Hospital Pediátrico de Moctezuma, Secretaría de Salud de la Ciudad de México (SSCDMX), Mexico City, Mexico
| | | | | | - Pedro Francisco Román-Zepeda
- Coordinación Clínica y Servicio de Cirugía Pediátrica, Hospital General Regional (HGR) No. 1 "Dr. Carlos Mac Gregor Sánchez Navarro", IMSS, Mexico City, Mexico
| | | | | | | | | | | | | | - Gilberto Espinoza-Anrubio
- Servicio de Pediatría, Hospital General Zona (HGZ) No. 8 "Dr. Gilberto Flores Izquierdo" IMSS, Mexico City, Mexico
| | - Carolina Almeida-Hernández
- Jefatura de Enseñanza, Hospital General de Ecatepec "Las Américas", Instituto de Salud del Estado de México (ISEM), Mexico City, Mexico
| | | | - Luis Hernández-Mora
- Jefatura de Enseñanza, Hospital Pediátrico San Juan de Aragón, Secretaría de Salud (SS), Mexico City, Mexico
| | | | | | | | | | | | | | | | | | | | - Delfino Torres-Valle
- Coordinación Clínica y Pediatría del Hospital General de Zona 71, IMSS, Mexico City, Mexico
| | - Carlos Cortés-Reyes
- Pediatría, Hospital General Dr. Darío Fernández Fierro, ISSSTE, Mexico City, Mexico
| | - Francisco Medrano-López
- Coordinación Clínica y Servicio de Pediatría, HGR No. 72 "Dr. Vicente Santos Guajardo", IMSS, Mexico City, Mexico
| | - Jessica Arleet Pérez-Gómez
- Coordinación Clínica y Servicio de Pediatría, HGR No. 72 "Dr. Vicente Santos Guajardo", IMSS, Mexico City, Mexico
| | - Annel Martínez-Ríos
- Cirugía Pediátrica del Hospital Regional "General Ignacio Zaragoza", ISSSTE, Mexico City, Mexico
| | | | - Berenice Serafin-Díaz
- Coordinación Clínica y Pediatría del Hospital General de Zona 57, IMSS, Mexico City, Mexico
| | - María de Lourdes Gutiérrez-Rivera
- Servicio de Oncología Pediátrica Unidad Medica de Alta Especialidad (UMAE) Hospital de Pediatría "Dr. Silvestre Frenk Freund", IMSS, Mexico City, Mexico
| | | | - Gilberto Vargas-Alarcón
- Departamento of Biología Molecular, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Minerva Mata-Rocha
- Unidad de Investigación Médica en Genética Humana, Unidad Medica de Alta Especialidad (UMAE) Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", IMSS, Mexico City, Mexico
| | - Omar Alejandro Sepúlveda-Robles
- Unidad de Investigación Médica en Genética Humana, Unidad Medica de Alta Especialidad (UMAE) Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", IMSS, Mexico City, Mexico
| | - Haydeé Rosas-Vargas
- Unidad de Investigación Médica en Genética Humana, Unidad Medica de Alta Especialidad (UMAE) Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", IMSS, Mexico City, Mexico
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Juan Manuel Mejía-Aranguré
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City, Mexico.,Unidad de Investigación Médica en Genética Humana, Unidad Medica de Alta Especialidad (UMAE) Hospital de Pediatría "Dr. Silvestre Frenk Freund", Centro Médico Nacional "Siglo XXI", IMSS, Mexico City, Mexico.,Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
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11
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Rahmadi A, Fasyah I, Sudigyo D, Budiarto A, Mahesworo B, Hidayat AA, Pardamean B. Comparative study of predicted miRNA between Indonesia and China (Wuhan) SARS-CoV-2: a bioinformatics analysis. Genes Genomics 2021; 43:1079-1086. [PMID: 34152577 PMCID: PMC8215323 DOI: 10.1007/s13258-021-01119-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/05/2021] [Indexed: 12/11/2022]
Abstract
BACKGROUND Several reports on the discovery of SARS-CoV-2 mutations and variations in Indonesia COVID-19 cases led to genomic dysregulation with the first pandemic cases in Wuhan, China. MicroRNA (miRNA) plays an important role in this genetic regulation and contributes to the enhancement of viral RNA binding through the host mRNA. OBJECTIVE This research is aimed to detect miRNA targets of SARS-CoV-2 and examines their role in Indonesia cases against Wuhan cases. METHODS SARS-CoV-2 sequences were obtained from GISAID ( https://www.gisaid.org/ ), NCBI ( https://ncbi.nlm.nih.gov ), and National Genomics Data Center ( https://bigd.big.ac.cn/gwh/ ) databases. MiRDB ( https://github.com/gbnegrini/mirdb-custom-target-search ) was used to annotate and predict target human mature miRNAs. For statistical analysis, we utilized a series chi-square test to obtain significant miRNA. DIANA-miRPath v3.0 ( http://www.microrna.gr/miRPathv3 ) analyzed the Gene Ontology of mature miRNAs. RESULT The statistical results detected five significant miRNAs. Two miRNAs: hsa-miR-4778-5p and hsa-miR-4531 were consistently found in the majority of Wuhan samples, while they were only found in less than half of the Indonesia samples. The other three miRNA, hsa-miR-6844, hsa-miR-627-5p, and hsa-miR-3674, were discovered in most samples in both groups but with a significant difference ratio. Among these five significant miRNA targets, hsa-miR-6844 is the only miRNA that has an association with the ORF1ab gene of SARS-CoV-2. CONCLUSION The Gene Ontology analysis of five significant miRNA targets indicates a significant role in inflammation and the immune system. The specific detection of host miRNAs in this study shows that there are differences in the characteristics of SARS-CoV-2 between Indonesia and Wuhan.
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Affiliation(s)
- Agus Rahmadi
- Faculty of Medicine, Universitas Muhammadiyah Prof. DR. Hamka, Jakarta, 12130, Indonesia
| | - Ismaily Fasyah
- Faculty of Medicine, Universitas Muhammadiyah Prof. DR. Hamka, Jakarta, 12130, Indonesia
| | - Digdo Sudigyo
- Bioinformatics and Data Science Research Center, Bina Nusantara University, Jakarta, 11480, Indonesia.
| | - Arif Budiarto
- Bioinformatics and Data Science Research Center, Bina Nusantara University, Jakarta, 11480, Indonesia
- School of Computer Science, Bina Nusantara University, Jakarta, 11480, Indonesia
| | - Bharuno Mahesworo
- Bioinformatics and Data Science Research Center, Bina Nusantara University, Jakarta, 11480, Indonesia
| | - Alam Ahmad Hidayat
- Bioinformatics and Data Science Research Center, Bina Nusantara University, Jakarta, 11480, Indonesia
| | - Bens Pardamean
- Bioinformatics and Data Science Research Center, Bina Nusantara University, Jakarta, 11480, Indonesia
- BINUS Graduate Program-Master of Computer Science Program, Bina Nusantara University, Jakarta, 11480, Indonesia
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12
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Nowak I, Sarshad AA. Argonaute Proteins Take Center Stage in Cancers. Cancers (Basel) 2021; 13:cancers13040788. [PMID: 33668654 PMCID: PMC7918559 DOI: 10.3390/cancers13040788] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary The dysregulation of RNA interference (RNAi) has often been observed in cancers, where the main focus of research has been on the small RNA molecules directing RNAi. In this review, we focus on the activity of Argonaute proteins, central components of RNAi, in tumorigenesis, and also highlight their potential applications in grading tumors and anti-cancer therapies. Abstract Argonaute proteins (AGOs) play crucial roles in RNA-induced silencing complex (RISC) formation and activity. AGOs loaded with small RNA molecules (miRNA or siRNA) either catalyze endoribonucleolytic cleavage of target RNAs or recruit factors responsible for translational silencing and target destabilization. miRNAs are well characterized and broadly studied in tumorigenesis; nevertheless, the functions of the AGOs in cancers have lagged behind. Here, we discuss the current state of knowledge on the role of AGOs in tumorigenesis, highlighting canonical and non-canonical functions of AGOs in cancer cells, as well as the biomarker potential of AGO expression in different of tumor types. Furthermore, we point to the possible application of the AGOs in development of novel therapeutic approaches.
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Affiliation(s)
- Iwona Nowak
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden;
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
| | - Aishe A. Sarshad
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden;
- Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, 405 30 Gothenburg, Sweden
- Correspondence:
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13
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Katsaraki K, Karousi P, Artemaki PI, Scorilas A, Pappa V, Kontos CK, Papageorgiou SG. MicroRNAs: Tiny Regulators of Gene Expression with Pivotal Roles in Normal B-Cell Development and B-Cell Chronic Lymphocytic Leukemia. Cancers (Basel) 2021; 13:cancers13040593. [PMID: 33546241 PMCID: PMC7913321 DOI: 10.3390/cancers13040593] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 01/01/2023] Open
Abstract
Simple Summary The involvement of miRNAs in physiological cellular processes has been well documented. The development of B cells, which is dictated by a miRNA-transcription factor regulatory network, suggests a typical process partly orchestrated by miRNAs. Besides their contribution in normal hematopoiesis, miRNAs have been severally reported to be implicated in hematological malignancies, a typical example of which is B-cell chronic lymphocytic leukemia (B-CLL). Numerous studies have attempted to highlight the regulatory role of miRNAs in B-CLL or establish some of them as molecular biomarkers or therapeutic targets. Thus, a critical review summarizing the current knowledge concerning the multifaceted role of miRNAs in normal B-cell development and B-CLL progression, prognosis, and therapy, is urgent. Moreover, this review aims to highlight important miRNAs in both normal B-cell development and B-CLL and discuss future perspectives concerning their regulatory potential and establishment in clinical practice. Abstract MicroRNAs (miRNAs) represent a class of small non-coding RNAs bearing regulatory potency. The implication of miRNAs in physiological cellular processes has been well documented so far. A typical process orchestrated by miRNAs is the normal B-cell development. A stage-specific expression pattern of miRNAs has been reported in the developmental procedure, as well as interactions with transcription factors that dictate B-cell development. Besides their involvement in normal hematopoiesis, miRNAs are severally implicated in hematological malignancies, a typical paradigm of which is B-cell chronic lymphocytic leukemia (B-CLL). B-CLL is a highly heterogeneous disease characterized by the accumulation of abnormal B cells in blood, bone marrow, lymph nodes, and spleen. Therefore, timely, specific, and sensitive assessment of the malignancy is vital. Several studies have attempted to highlight the remarkable significance of miRNAs as regulators of gene expression, biomarkers for diagnosis, prognosis, progression, and therapy response prediction, as well as molecules with potential therapeutic utility. This review seeks to outline the linkage between miRNA function in normal and malignant hematopoiesis by demonstrating the main benchmarks of the implication of miRNAs in the regulation of normal B-cell development, and to summarize the key findings about their value as regulators, biomarkers, or therapeutic targets in B-CLL.
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Affiliation(s)
- Katerina Katsaraki
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece; (K.K.); (P.K.); (P.I.A.); (A.S.)
| | - Paraskevi Karousi
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece; (K.K.); (P.K.); (P.I.A.); (A.S.)
| | - Pinelopi I. Artemaki
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece; (K.K.); (P.K.); (P.I.A.); (A.S.)
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece; (K.K.); (P.K.); (P.I.A.); (A.S.)
| | - Vasiliki Pappa
- Second Department of Internal Medicine and Research Unit, University General Hospital “Attikon”, 12462 Athens, Greece;
| | - Christos K. Kontos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece; (K.K.); (P.K.); (P.I.A.); (A.S.)
- Correspondence: (C.K.K.); (S.G.P.); Tel.: +30-210-727-4616 (C.K.K.); +30-210-583-2519 (S.G.P.)
| | - Sotirios G. Papageorgiou
- Second Department of Internal Medicine and Research Unit, University General Hospital “Attikon”, 12462 Athens, Greece;
- Correspondence: (C.K.K.); (S.G.P.); Tel.: +30-210-727-4616 (C.K.K.); +30-210-583-2519 (S.G.P.)
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14
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de Souza TP, de Carvalho DC, Wanderley AV, Fernandes SM, Rodrigues JCG, Cohen-Paes A, Fernandes MR, Mello Junior FAR, Pastana LF, Vinagre LWMS, Silva ALDC, de Assumpção PP, Santos S, Khayat AS, dos Santos NPC. Influence of variants of the drosha, mir499a, and mir938 genes on susceptibility to acute lymphoblastic leukemia in an admixed population from the brazilian amazon. Am J Transl Res 2020; 12:8216-8224. [PMID: 33437394 PMCID: PMC7791525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 10/25/2020] [Indexed: 06/12/2023]
Abstract
Acute Lymphoblastic Leukemia (ALL) is the most common type of cancer in children. Polymorphisms that alter the normal function of the microRNAs involved in the development of ALL have been widely investigated, although published data on these polymorphisms in admixed populations are scarce. We investigated the role of 10 polymorphisms in the microRNA and protein-coding genes of the microRNA synthesis complex in susceptibility to pediatric B-cell ALL. The study includes 100 pediatric ALL patients and 180 healthy individuals. The statistical analyses were run in SPSS v.25.0. In the case of the microRNA synthesizing genes, a significant pattern was found in only gene, that is, the rs3805500 polymorphism of DROSHA, in which the homozygous mutant (AA) genotype was associated with a threefold increase in the risk of developing ALL when compared to other genotypes (P=0.004, OR=2.913, CI=1.415-5.998). In the microRNA coding genes, the homozygous mutant rs3746444 genotype of the MIR499A gene was associated with a 17-fold increase in the risk of development of ALL (P<0.001, OR=17.797, CI=5.55-57.016). A protective effect against the development of ALL was also observed in the carriers of the wild homozygous rs2505901 genotype in the MIR938 gene. Our findings highlight the potential of these polymorphisms in the genes involving in the coding of microRNAs for the evaluation of the risk of contracting ALL in the population of the Brazilian Amazon region. These findings contribute to a more complete understanding of the complex etiology of ALL.
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Affiliation(s)
- Tatiane Piedade de Souza
- Laboratory of Human and Medical Genetics, Institute of Biological SciencesBelém, Pará, PA, Brazil
| | | | - Alayde Viera Wanderley
- Research Center of Oncology, Federal University of ParáBelém, Pará, PA, Brazil
- Otávio Lobo Children’s Cancer Hospital-HOIOL-BelémPará, PA, Brazil
| | - Sweny Marinho Fernandes
- Research Center of Oncology, Federal University of ParáBelém, Pará, PA, Brazil
- Otávio Lobo Children’s Cancer Hospital-HOIOL-BelémPará, PA, Brazil
| | | | - Amanda Cohen-Paes
- Research Center of Oncology, Federal University of ParáBelém, Pará, PA, Brazil
| | | | | | | | | | | | | | - Sidney Santos
- Research Center of Oncology, Federal University of ParáBelém, Pará, PA, Brazil
- Laboratory of Human and Medical Genetics, Institute of Biological SciencesBelém, Pará, PA, Brazil
| | - André Salim Khayat
- Research Center of Oncology, Federal University of ParáBelém, Pará, PA, Brazil
| | - Ney Pereira Carneiro dos Santos
- Research Center of Oncology, Federal University of ParáBelém, Pará, PA, Brazil
- Laboratory of Human and Medical Genetics, Institute of Biological SciencesBelém, Pará, PA, Brazil
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15
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Dobrijević Z, Matijašević S, Išić Denčić T, Savić-Pavićević D, Nedić O, Brajušković G. Association between genetic variants in DICER1 and cancer risk: An updated meta-analysis. Gene 2020; 766:145132. [PMID: 32911029 DOI: 10.1016/j.gene.2020.145132] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/01/2020] [Accepted: 09/01/2020] [Indexed: 02/06/2023]
Abstract
Dysfunctions in mechanisms of gene regulation based on RNA interference are recognized as a common feature of the molecular basis of cancer pathogenesis. Therefore, as one of the crucial components of the machinery involved in the biogenesis of both siRNAs and microRNA molecules, DICER was recognized as one of the candidates for the research in the field of carcinogenesis. Due to their potential functional properties, several genetic variants located within DICER1 gene were analyzed for their possible association with the susceptibility to cancer through case-control studies. In order to elucidate their effect on the overall cancer risk, we conducted an updated meta-analysis of all eligible association studies. The publications were selected based on PubMed database search, while OpenMeta-analyst and MetaGenyo software were used for quantitative data synthesis. Statistically significant results were found for the association of rs1057035 with the overall cancer risk under multiple genetic models (PCT vs. TT < 0.001, ORCT vs. TT = 0.870, 95% CI = 0.812-0.933; Pallelic = 0.009, ORallelic = 0.896, 95% CI = 0.825-0.973; Pdom < 0.001, ORdom = 0.874, 95% CI = 0.817-0.934; Poverdom = 0.004, ORoverdom = 0.858, 95% CI = 0.773-0.953). Other selected genetic variants within DICER1, rs13078, rs1209904 and rs3742330, did not show the association with the overall susceptibility to malignant diseases. We conclude that rs1057035 may represent a potential biomarker associated with the risk of developing cancer, which requires a confirmation in a larger set of studies.
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Affiliation(s)
- Zorana Dobrijević
- Department for Metabolism, Institute for the Application of Nuclear Energy (INEP), University of Belgrade, Belgrade, Serbia.
| | - Suzana Matijašević
- Centre for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Tijana Išić Denčić
- Department for Endocrinology and Radioimmunology, Institute for the Application of Nuclear Energy (INEP), University of Belgrade, Belgrade, Serbia
| | - Dušanka Savić-Pavićević
- Centre for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Olgica Nedić
- Department for Metabolism, Institute for the Application of Nuclear Energy (INEP), University of Belgrade, Belgrade, Serbia
| | - Goran Brajušković
- Centre for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
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16
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Dobrijević Z, Matijašević S, Savić-Pavićević D, Brajušković G. Association between genetic variants in genes encoding Argonaute proteins and cancer risk: A meta-analysis. Pathol Res Pract 2020; 216:152906. [PMID: 32143906 DOI: 10.1016/j.prp.2020.152906] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/14/2020] [Accepted: 02/27/2020] [Indexed: 12/13/2022]
Abstract
With the accumulation of evidence of the involvement of small-RNA-based regulatory mechanisms in carcinogenesis, genes encoding Ago proteins emerged as candidates for case-control studies on cancer. Since the data from association studies on various cancer types was not previously meta-analyzed, the potential effect of these variants on cancer risk in general was not previously evaluated. Therefore, we conducted a meta-analysis of all eligible studies, testing multiple genetic models of association. The identification of publication was based on PubMed database search, while OpenMeta-analyst, as well as MetaGenyo software, were used for quantitative data synthesis. AGO1 genetic variant rs636832 was found to associate with the overall cancer risk, assuming the overdominant genetic model (P = 0.030; ORoverdom = 0.865, 95%CI 0.759-0.986). For the same genetic variant, statistical significance was reached for the association with solid tumors, as well as with lung cancer susceptibility. Similar results were found in the Asians cohort for another AGO1 variant, rs595961. For rs4961280, none of the meta-analyses yielded statistically significant results. We conclude that genetic variants rs636832 and rs595961 located within AGO1 may represent susceptibility variants for specific types of cancer, while the association with malignant diseases was not determined for AGO2 variant rs4961280.
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Affiliation(s)
- Zorana Dobrijević
- Department for Metabolism, Institute for the Application of Nuclear Energy (INEP), University of Belgrade, Belgrade, Serbia.
| | - Suzana Matijašević
- Centre for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Dušanka Savić-Pavićević
- Centre for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Goran Brajušković
- Centre for Human Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
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17
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Shao Y, Shen Y, Zhao L, Guo X, Niu C, Liu F. Association of microRNA biosynthesis genes XPO5 and RAN polymorphisms with cancer susceptibility: Bayesian hierarchical meta-analysis. J Cancer 2020; 11:2181-2191. [PMID: 32127945 PMCID: PMC7052917 DOI: 10.7150/jca.37150] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 12/07/2019] [Indexed: 12/15/2022] Open
Abstract
XPO5/RAN-GTP complex mediates the nuclear transport of pre-miRNAs in the miRNA processing system, its altered expression is indicated to be correlated with cancer risk. Several studies have inspected the association between XPO5 or RAN polymorphisms and the risk of various cancers, but the findings remain controversial. A Bayesian hierarchical meta-analysis was carried out to review and analyze the effect of XPO5 and RAN polymorphisms on cancer risk. The association was estimated by calculating the logarithm of odds ratio (Log OR) and 95% credible interval (95% CrI). The expression quantitative trait loci (eQTL) analysis was used for in silico functional validation of the identified significant susceptibility loci. Consequently, 38 case-control studies (from 27 citations) with 27,459 cancer cases and 25,151controls were included in the meta-analysis of the five most prevalent SNPs (rs11077 A/C, rs2257082 G/A, rs3803012 A/G, rs14035 C/T, rs3809142 C/T). In the XPO5 gene rs11077 SNP, the minor C allele significantly increased the risk of cancer (Log OR = 0.120, 95% CrI = 0.013, 0.241), and a strong association between rs11077 SNP and cancer risk was also found in the dominant model (CC + AC vs. AA: Log OR = 0.132, 95% CrI = 0.009, 0.275). In addition, the minor GG genotype allele of the RAN gene rs3803012 SNP significantly increased the cancer risk (Log OR = 0.707, 95% CrI = 0.059, 1.385). Statistically significant associations between rs3803012 SNP and cancer risk were also observed in the recessive model (GG vs. AG + AA: Log OR = 0.708, 95% CrI = 0.059, 1.359). Furthermore, the eQTL analysis revealed that rs11077 SNP was significantly correlated with XPO5 mRNA expression, which provided additional biological basis for the observed positive association. Our results suggest that XPO5 rs11077 may be a possible functional susceptibility locus for cancer risk.
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Affiliation(s)
- Yi Shao
- Department of Epidemiology and Health Statistics, School of Public Health, Beijing Municipal Key Laboratory of Clinical Epidemiology, Capital Medical University, Beijing, China
| | - Yi Shen
- Department of Epidemiology and Health Statistics, School of Public Health, Beijing Municipal Key Laboratory of Clinical Epidemiology, Capital Medical University, Beijing, China
| | - Lei Zhao
- Department of Molecular Physiology and Biophysics, Holden Comprehensive Cancer Center, University of Iowa Carver College of Medicine, Iowa City, IA, United States
| | - Xudong Guo
- Department of Epidemiology and Health Statistics, School of Public Health, Beijing Municipal Key Laboratory of Clinical Epidemiology, Capital Medical University, Beijing, China
| | - Chen Niu
- Department of Epidemiology and Health Statistics, School of Public Health, Beijing Municipal Key Laboratory of Clinical Epidemiology, Capital Medical University, Beijing, China
| | - Fen Liu
- Department of Epidemiology and Health Statistics, School of Public Health, Beijing Municipal Key Laboratory of Clinical Epidemiology, Capital Medical University, Beijing, China
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18
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Chen G, Zhang M, Zhu J, Chen F, Yu D, Zhang A, He J, Hua W, Duan P. Common genetic variants in pre-microRNAs are associated with cervical cancer susceptibility in southern Chinese women. J Cancer 2020; 11:2133-2138. [PMID: 32127940 PMCID: PMC7052933 DOI: 10.7150/jca.39636] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/04/2020] [Indexed: 02/07/2023] Open
Abstract
Cervical cancer is a commonly diagnosed cancer among females. Polymorphisms in pre-microRNAs have been demonstrated to play critical roles in cancer. However, the roles of pre-microRNA polymorphisms in the aetiology of cervical cancer have not been well documented. We genotyped eight pre-microRNA polymorphisms in 290 cervical cancer patients and 445 cancer-free female controls using quantitative polymerase chain reaction with TaqMan probes. To estimate the association between pre-microRNA polymorphisms and the risk of cervical cancer, an unconditional logistic regression model was used to calculate the odds ratio (OR) and 95% confidence interval (CI), adjusting for age, menopause, delivery, and abortion. We found that the pre-miR-137 rs1625579 T > G polymorphism was associated with a significant decrease in cervical cancer risk (TG/GG versus TT: adjusted OR (AOR) = 0.47, 95% CI = 0.27-0.81; TG versus TT: AOR = 0.56, 95% CI = 0.34-0.91). We also observed a significant association between the pre-miR-27a rs895819 T > C polymorphism and decreased cervical cancer risk (TC/CC versus TT: AOR = 0.65, 95% CI = 0.44-0.96). Stratified analysis further demonstrated that the pre-miR-137 rs1625579 T > C and pre-miR-27a rs895819 T > C polymorphisms significantly reduced the risk of cervical cancer susceptibility in patients younger than 49 years, those who experienced fewer abortions, and clinical stage I patients. Moreover, the pre-miR-137 rs1625579 T > G polymorphism showed protective effects in premenopausal women, squamous cell carcinoma patients, and patients with unclassified types of pathologies; the pre-miR-27a rs895819 T > C polymorphism was also associated with a decreased risk in patients older than 49 years, menopausal women, and women who had experienced vaginal pregnancies. The pre-miR-137 rs1625579 T > G and pre-miR-27a rs895819 T > C polymorphisms may provide protective effects against susceptibility to cervical cancer risk.
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Affiliation(s)
- Guange Chen
- Department of Obstetrics and Gynecology, Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Mingyao Zhang
- Department of Obstetrics and Gynecology, Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Jiawei Zhu
- Department of Obstetrics and Gynecology, Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Feng Chen
- Department of Obstetrics and Gynecology, Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Danyang Yu
- Department of Obstetrics and Gynecology, Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Anqi Zhang
- Department of Obstetrics and Gynecology, Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
| | - Jing He
- Department of Pediatric Surgery, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, Guangdong, China
| | - Wenfeng Hua
- Department of Laboratory Medicine and Central Laboratories, Guangdong Second Provincial General Hospital, Guangzhou 510317, Guangdong, China
- ✉ Corresponding authors: Ping Duan, Department of Obstetrics and Gynecology, Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, 109 Xueyuan Western Road, Wenzhou 325027, Zhejiang, China, ; or Wenfeng Hua, Department of Laboratory Medicine and Central Laboratories, Guangdong Second Provincial General Hospital, Guangzhou 510317, Guangdong, China,
| | - Ping Duan
- Department of Obstetrics and Gynecology, Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou 325027, Zhejiang, China
- ✉ Corresponding authors: Ping Duan, Department of Obstetrics and Gynecology, Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, 109 Xueyuan Western Road, Wenzhou 325027, Zhejiang, China, ; or Wenfeng Hua, Department of Laboratory Medicine and Central Laboratories, Guangdong Second Provincial General Hospital, Guangzhou 510317, Guangdong, China,
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Choupani J, Nariman-Saleh-Fam Z, Saadatian Z, Ouladsahebmadarek E, Masotti A, Bastami M. Association of mir-196a-2 rs11614913 and mir-149 rs2292832 Polymorphisms With Risk of Cancer: An Updated Meta-Analysis. Front Genet 2019; 10:186. [PMID: 30930933 PMCID: PMC6429108 DOI: 10.3389/fgene.2019.00186] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 02/19/2019] [Indexed: 12/14/2022] Open
Abstract
Background: Accumulating evidence suggests that functional dysregulations of miRNAs, especially miR-196a-2 and miR-149, in cancers could be attributed to polymorphisms in miRNA sequences. This study was aimed at clarifying the association of mir-196a-2 rs11614913 and mir-149 rs2292832 with cancer risk by performing an updated meta-analysis of genetic association studies. Methods: PubMed, Embase, Scopus, and ScienceDirect databases were searched until 9 April 2018 to identify eligible studies. Studies should meet the following criteria to be included in the meta-analysis: evaluation of genetic association between rs11614913 and/or rs2292832 and susceptibility to cancer; A case-control design; Written in English; Availability of sufficient data for estimating odds ratio (OR) and its 95% confidence interval (95%CI). Studies that met the following criteria were excluded: review articles, meta-analysis, abstracts or conference papers; duplicate publications; studies on animals or cell-lines; studies without a case-control design; studies that did not report genotype frequencies. Pooled ORs and 95% CIs were estimated using a total of 111 studies (41,673 cases and 49,570 controls) for mir-196a rs11614913 and 44 studies (15,954 cases and 19,594 controls) for mir-149 rs2292832. Stratified analysis according to quality scores, genotyping method, ethnicity, broad cancer category and cancer type was also performed. Results: Mir-196a-2 rs11614913 T allele was associated with decreased cancer risk in overall population. The association was only significant in Asians but not Caucasians. In subgroup analysis, significant associations were found in high quality studies, gynecological cancers, ovarian, breast, and hepatocellular cancer. Mir-149 rs2292832 was not associated with cancer risk in overall population and there were no differences between Asians and Caucasians. However, the T allele was associated with a decrease risk of gastrointestinal tract cancers under the heterozygote model and an increased risk of colorectal cancer under the recessive model. Conclusions: The present meta-analysis suggests that mir-196a-2 rs11614913 may contribute to the risk of cancer especially in Asians. Mir-149 rs2292832 may modulate the risk of gastrointestinal tract cancers especially colorectal cancer. This study had some limitations such as significant heterogeneity in most contrasts, limited number of studies enrolling Africans or Caucasians ancestry and lack of adjustment for covariates and environmental interactions.
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Affiliation(s)
- Jalal Choupani
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ziba Nariman-Saleh-Fam
- Women's Reproductive Health Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zahra Saadatian
- Department of Medical Genetics, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Elaheh Ouladsahebmadarek
- Women's Reproductive Health Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Andrea Masotti
- Research Laboratories, Bambino Gesù Children's Hospital-IRCCS, Rome, Italy
| | - Milad Bastami
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Hassan FM. The Association of rs2114358 in the miR-1206 Polymorphism to Chronic Myeloid Leukemia. Microrna 2019; 8:248-252. [PMID: 30605069 DOI: 10.2174/2211536608666190102143439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/26/2018] [Accepted: 12/21/2018] [Indexed: 06/09/2023]
Abstract
INTRODUCTION Association studies with factor candidates have advised that single nucleotide polymorphisms (SNPs) could also be related to CML progression and to the response to medical care. Genetic variation in miR-1206 of both derived and neighborhood SNPs process genes will contribute to the predisposition to cancer. The role of those with the risk of CML has not been extensively studied. Therefore, the aim of this study was to evaluate whether polymorphisms in rs2114358 in pre-miRNAs process genes contribute to the risk of CML. METHODS A cross-sectional study was conducted during the period of March 2016 to October 2017 in Khartoum state teaching hospitals. The study population included a total of 420 patients who were previously diagnosed of having CML and 220 cancer-free controls of both gender and were of the same age range. Peripheral blood and bone marrow aspiration samples were collected from patients (254 males, 166 females; median age 58.5 years, range from less than 50 and above 50 years old) and investigated after written informed consent was obtained. Patients were in chronic phase (n=212), accelerated phase (n=125), and blast (n=83). All the patients were under treatment using chemotherapy regiments. The rs2114358 SNP in pre-miRNA was selected for genotyping. RESULTS The genotyping success rate was 98.3%. Genotype frequencies of the derived SNP and the neighborhood rs2114358 of miR-1206 compared to the controls were significantly different under Hardy-Weinberg Equilibrium (P=0.0001 and 0.0001 respectively). Significant differences were found in allele distributions of this SNP (P<0.01 and P<0.01). In total, the derived variant C allele of rs2114358 (OR=0.168, 95% CI=0.13-0.22) and G allele of neighborhood rs2114358 (OR=0.561, 95% CI=0.44-0.72) in patients' group were associated with an increased risk of CML compared to a control group. Patients with rs2114358 CC genotype (P = 0.0001) or TC (P = 0.0001) and the neighborhood rs2114358 GA genotype (P = 0.0460) or GG (P = 0.0093) were obviously much higher than that of the TT and AA genotype's patients. CONCLUSION In conclusion, we discovered the association of SNP rs2114358 in miR-1206 with the risk of CML patients, though more investigations are still required to understand the regulative mechanisms of this miR SNP with the target genes resulting in its dysregulation.
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MESH Headings
- Antineoplastic Combined Chemotherapy Protocols/therapeutic use
- Cross-Sectional Studies
- Female
- Genotype
- Humans
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/diagnosis
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Male
- MicroRNAs/genetics
- Middle Aged
- Polymorphism, Single Nucleotide/genetics
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Affiliation(s)
- Fathelrahman Mahdi Hassan
- Department of Clinical Laboratory Science, College of Applied Medical Science, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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21
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Chatzikyriakidou A, Founti P, Melidou A, Minti F, Bouras E, Anastasopoulos E, Pappas T, Haidich AB, Lambropoulos A, Topouzis F. MicroRNA-related polymorphisms in pseudoexfoliation syndrome, pseudoexfoliative glaucoma, and primary open-angle glaucoma. Ophthalmic Genet 2018; 39:603-609. [DOI: 10.1080/13816810.2018.1509352] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Anthoula Chatzikyriakidou
- Laboratory of Medical Biology - Genetics, Medical School, Aristotle University of Thessaloniki, Greece
| | - Panayiota Founti
- Laboratory of Research and Clinical Applications in Ophthalmology, 1st Department of Ophthalmology, School of Medicine, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki, Greece
- Department of Glaucoma, Moorfields Eye Hospital NHS Foundation Trust, London, UK
| | - Angeliki Melidou
- Department of Microbiology, Medical School, Aristotle University of Thessaloniki, Greece
| | - Fani Minti
- Laboratory of Medical Biology - Genetics, Medical School, Aristotle University of Thessaloniki, Greece
| | - Emmanouil Bouras
- Department of Hygiene and Epidemiology, Medical School, Aristotle University of Thessaloniki, Greece
| | - Eleftherios Anastasopoulos
- Laboratory of Research and Clinical Applications in Ophthalmology, 1st Department of Ophthalmology, School of Medicine, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki, Greece
| | - Theofanis Pappas
- Laboratory of Research and Clinical Applications in Ophthalmology, 1st Department of Ophthalmology, School of Medicine, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki, Greece
| | - Anna-Bettina Haidich
- Department of Hygiene and Epidemiology, Medical School, Aristotle University of Thessaloniki, Greece
| | - Alexandros Lambropoulos
- Laboratory of Medical Biology - Genetics, Medical School, Aristotle University of Thessaloniki, Greece
| | - Fotis Topouzis
- Laboratory of Research and Clinical Applications in Ophthalmology, 1st Department of Ophthalmology, School of Medicine, Aristotle University of Thessaloniki, AHEPA Hospital, Thessaloniki, Greece
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Lopez-Santillan M, Larrabeiti-Etxebarria A, Arzuaga-Mendez J, Lopez-Lopez E, Garcia-Orad A. Circulating miRNAs as biomarkers in diffuse large B-cell lymphoma: a systematic review. Oncotarget 2018; 9:22850-22861. [PMID: 29854319 PMCID: PMC5978269 DOI: 10.18632/oncotarget.25230] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 04/05/2018] [Indexed: 12/21/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is an aggressive and heterogeneous malignancy, with highly variable outcomes among patients. Although classification and prognostic tools have been developed, standard therapy still fails in 30-40% of patients. Hence, identification of novel biomarkers is needed. Recently, circulating microRNAs (miRNAs) have been suggested as non-invasive biomarkers in cancer. Our aim was to review the potential role of circulating miRNAs as biomarkers for diagnosis, classification, prognosis, and treatment response in DLBCL. We performed a search in PubMed using the terms [((‘Non-coding RNA’) OR (‘microRNA’ OR ‘miRNA’ OR ‘miR’) OR (‘exosome’) OR (‘extracellular vesicle’) OR (‘secretome’)) AND (‘Diffuse large B cell lymphoma’ OR ‘DLBCL’)] to identify articles that evaluated the impact of circulating miRNAs as diagnosis, subtype, treatment response or prognosis biomarkers in DLBCL in human population. Among the twelve articles that met the inclusion criteria, eleven considered circulating miRNAs as biomarkers for diagnosis, two for classification, and five for prognosis or treatment response. The limited number of studies performed and lack of consistency in results make it difficult to draw conclusions about the role of circulating miRNAs as non-invasive biomarkers in DLBCL. Although the preliminary associations observed seem promising, the only consistent result is the upregulation of mir-21 in DLBCL patients, which could be a biomarker for diagnosis. Further studies are needed.
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Affiliation(s)
- Maria Lopez-Santillan
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursery, University of The Basque Country (UPV/EHU), Leioa, Spain.,Medical Oncology Service, Basurto University Hospital, Bilbao, Spain
| | - Ane Larrabeiti-Etxebarria
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursery, University of The Basque Country (UPV/EHU), Leioa, Spain.,Pharmacy Service, Araba University Hospital-Txagorritxu, Vitoria, Spain
| | - Javier Arzuaga-Mendez
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursery, University of The Basque Country (UPV/EHU), Leioa, Spain.,Hematology and Hemotherapy Service, Cruces University Hospital, Barakaldo, Spain
| | - Elixabet Lopez-Lopez
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursery, University of The Basque Country (UPV/EHU), Leioa, Spain
| | - Africa Garcia-Orad
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Medicine and Nursery, University of The Basque Country (UPV/EHU), Leioa, Spain.,BioCruces Health Research Institute, Barakaldo, Spain
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23
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Kim JO, Bae J, Kim J, Oh SH, An HJ, Han IB, Oh D, Kim OJ, Kim NK. Association of MicroRNA Biogenesis Genes Polymorphisms with Ischemic Stroke Susceptibility and Post-Stroke Mortality. J Stroke 2018; 20:110-121. [PMID: 29402068 PMCID: PMC5836584 DOI: 10.5853/jos.2017.02586] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/30/2017] [Accepted: 01/19/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND AND PURPOSE MicroRNA (miRNA) expression has been examined in multiple conditions, including various cancers, neurological diseases, and cerebrovascular diseases, particularly stroke. Existing evidence indicates that miRNA biosynthesis and function play crucial roles in ischemic stroke physiology and pathology. In this study, we selected six known polymorphisms in miRNA-biogenesis genes; DICER rs13078A>T, rs3742330A>G; DROSHA rs10719T>C, rs6877842G>C; Ran GTPase (RAN) rs14035C>T; exportin 5 (XPO5) rs11077A>C. METHODS We analyzed the associations between these polymorphisms and disease status and clinical factors in 585 ischemic stroke patients and 403 controls. Genotyping was performed with the polymerase chain reaction-restriction fragment length polymorphism method. RESULTS The DICER rs3742330A>G (AA vs. AG+GG: adjusted odds ratio [AOR], 1.360; 95% confidence interval [CI], 1.024 to 1.807; P=0.034) and DROSHA rs10719T>C polymorphisms (TT vs. CC: AOR, 2.038; 95% CI, 1.113 to 3.730; P=0.021) were associated with ischemic stroke prevalence. During a mean follow-up of 4.80±2.11 years, 99 (5.91%) of the stroke patients died. In multivariate Cox proportional hazard regression models, a significant association was found between RAN rs14035 and survival of large artery disease patients with ischemic stroke (CC vs. TT: adjusted hazard ratio, 5.978; P=0.015). CONCLUSIONS An association was identified between the DICER and DROSHA polymorphisms and ischemic stroke. Specifically, polymorphisms (rs3742330 and rs10719) were more common in stroke patients, suggesting that they may be associated with an increased risk of ischemic stroke.
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Affiliation(s)
- Jung Oh Kim
- Department of Biomedical Science, CHA University College of Life Science, Seongnam, Korea
| | - Jinkun Bae
- Department of Emergency Medicine, CHA Bundang Medical Center, CHA University, Seongnam, Korea
| | - Jinkwon Kim
- Department of Neurology, CHA Bundang Medical Center, CHA University, Seongnam, Korea
| | - Seung Hun Oh
- Department of Neurology, CHA Bundang Medical Center, CHA University, Seongnam, Korea
| | - Hui Jeong An
- Department of Biomedical Science, CHA University College of Life Science, Seongnam, Korea
| | - In Bo Han
- Department of Neurosurgery, CHA Bundang Medical Center, CHA University, Seongnam, Korea
| | - Doyeun Oh
- Department of Internal Medicine, CHA University, Seongnam, Korea
| | - Ok Joon Kim
- Department of Neurology, CHA Bundang Medical Center, CHA University, Seongnam, Korea
| | - Nam Keun Kim
- Department of Biomedical Science, CHA University College of Life Science, Seongnam, Korea
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24
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The SNPs in pre-miRNA are related to the response of capecitabine-based therapy in advanced colon cancer patients. Oncotarget 2018; 9:6793-6799. [PMID: 29467929 PMCID: PMC5805515 DOI: 10.18632/oncotarget.23190] [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] [Received: 09/25/2017] [Accepted: 12/01/2017] [Indexed: 12/21/2022] Open
Abstract
The single nucleotide polymorphisms (SNPs) in the microRNA precursor (pre-miRNA) may modulate the posttranscriptional regulation of gene expression and explain individual sensitivity to chemotherapy. Here we investigated the correlation between 23 SNPs in the pre-miRNA and the efficacy of capecitabine-based chemotherapy in 274 advanced colon cancer patients. Statistical analysis indicated that much more patients with rs744591 A/C(48.03%), C/C (53.45%) or C allele (49.73%) responded to the chemotherapy than those with the A/A genotype (33.71%). The response rates of rs745666 G/C heterozygous patients (35.25%) and C allele carriers (39.69%) were apparently less than that of the G/G homozygous patients (56.25%). Moreover, three SNPs rs2114358, rs35770269, and rs73239138 were significantly associated with the occurrence of side effects of chemotherapy. The patients with rs2114358 C allele (OR = 2.016) or rs35770269 T allele (OR = 2.299) were much more prone to endure adverse events. However, the incidence of side effect was lower in the patients carrying rs73239138 A allele than those with G/G genotype (OR = 0.500). Our findings demonstrate that genetic variations in pre-miRNA may influence the efficacy of capecitabine-based chemotherapy in advanced colon cancer patients.
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25
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Rezaei M, Eskandari F, Mohammadpour-Gharehbagh A, Teimoori B, Yaghmaei M, Mokhtari M, Salimi S. The Drosha rs10719 T>C polymorphism is associated with preeclampsia susceptibility. Clin Exp Hypertens 2017; 40:440-445. [DOI: 10.1080/10641963.2017.1392555] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Mahnaz Rezaei
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Fatemeh Eskandari
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Abbas Mohammadpour-Gharehbagh
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Batool Teimoori
- Department of Obstetrics and Gynecology, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Minoo Yaghmaei
- Department of Obstetrics and Gynecology, School of Medicine, Shahid Beheshty University of Medical Sciences, Tehran, Iran
| | - Mojgan Mokhtari
- Department of Obstetrics and Gynecology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Saeedeh Salimi
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
- Cellular and Molecular Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
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26
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Kulakova O, Bashinskaya V, Kiselev I, Baulina N, Tsareva E, Nikolaev R, Kozin M, Shchur S, Favorov A, Boyko A, Favorova O. Pharmacogenetics of glatiramer acetate therapy for multiple sclerosis: the impact of genome-wide association studies identified disease risk loci. Pharmacogenomics 2017; 18:1563-1574. [PMID: 29095108 DOI: 10.2217/pgs-2017-0058] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
AIM Association analysis of genome-wide association studies (GWAS) identified multiple sclerosis (MS) risk genetic variants with glatiramer acetate (GA) treatment efficacy. PATIENTS & METHODS SNPs in 17 GWAS-identified immune response loci were analyzed in 296 Russian MS patients as possible markers of optimal GA treatment response for at least 2 years. RESULTS Alleles/genotypes of EOMES, CLEC16A, IL22RA2, PVT1 and HLA-DRB1 were associated by themselves with event-free phenotype during GA treatment for at least 2 years (p f = 0.032 - 0.00092). The biallelic combinations including EOMES, CLEC16A, IL22RA2, PVT1, TYK2, CD6, IL7RA and IRF8 genes were associated with response to GA with increased significance level (p f = 0.0060 - 1.1 × 10-5). The epistasic interactions or additive effects were observed between the components of the identified biallelic combinations. CONCLUSION We pinpointed the involvement of several GWAS-identified MS risk loci in GA therapy efficacy. These findings may be aggregated to predict the optimal GA response in MS patients.
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Affiliation(s)
- Olga Kulakova
- Department of Molecular Biology and Medical Biotechnology, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Vitalina Bashinskaya
- Department of Molecular Biology and Medical Biotechnology, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Ivan Kiselev
- Department of Molecular Biology and Medical Biotechnology, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Natalia Baulina
- Department of Molecular Biology and Medical Biotechnology, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Ekaterina Tsareva
- Department of Molecular Biology and Medical Biotechnology, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Ruslan Nikolaev
- Department of Molecular Biology and Medical Biotechnology, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Maxim Kozin
- Department of Molecular Biology and Medical Biotechnology, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Sergey Shchur
- Department of Neurology, Neurosurgery and Medical Genetics, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Alexander Favorov
- Oncology Biostatistics & Bioinformatics, John Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Alexey Boyko
- Department of Neurology, Neurosurgery and Medical Genetics, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Olga Favorova
- Department of Molecular Biology and Medical Biotechnology, Pirogov Russian National Research Medical University, Moscow 117997, Russia
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Moghbelinejad S, Najafipour R, Momeni A. Association of rs1057035polymorphism in microRNA biogenesis pathway gene (DICER1) with azoospermia among Iranian population. Genes Genomics 2017; 40:17-24. [DOI: 10.1007/s13258-017-0605-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 08/10/2017] [Indexed: 12/19/2022]
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28
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He J, Zhao J, Zhu W, Qi D, Wang L, Sun J, Wang B, Ma X, Dai Q, Yu X. MicroRNA biogenesis pathway genes polymorphisms and cancer risk: a systematic review and meta-analysis. PeerJ 2016; 4:e2706. [PMID: 27957388 PMCID: PMC5147022 DOI: 10.7717/peerj.2706] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 10/20/2016] [Indexed: 12/25/2022] Open
Abstract
MicroRNAs (miRNAs) may promote the development and progression of human cancers. Therefore, components of the miRNA biogenesis pathway may play critical roles in human cancer. Single nucleotide polymorphisms (SNPs) or mutations in genes involved in the miRNA biogenesis pathway may alter levels of gene expression, affecting disease susceptibility. Results of previous studies on genetic variants in the miRNA biogenesis pathway and cancer risk were inconsistent. Therefore, a meta-analysis is needed to assess the associations of these genetic variants with human cancer risk. We searched for relevant articles from PubMed, Web of Science, CNKI, and CBM through Jun 21, 2016. In total, 21 case-control articles met all of the inclusion criteria for the study. Significant associations were observed between cancer risk and the DGCR8polymorphism rs417309 G >A (OR 1.22, 95% CI [1.04-1.42]), as well as the DICER1 polymorphism rs1057035 TT (OR 1.13, 95% CI [1.05-1.22]). These SNPs exhibit high potential as novel diagnostic markers. Future studies with larger sample sizes and more refined analyses are needed to shed more light on these findings.
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Affiliation(s)
- Jieyu He
- Southeast University, Department of Public Health, Nanjing, China
| | - Jun Zhao
- National Research Institute for Family Planning, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China
| | - Wenbo Zhu
- Southeast University, Department of Public Health, Nanjing, China
| | - Daxun Qi
- National Research Institute for Family Planning, Beijing, China
| | - Lina Wang
- Southeast University, Department of Public Health, Nanjing, China
| | - Jinfang Sun
- Southeast University, Department of Public Health, Nanjing, China
| | - Bei Wang
- Southeast University, Department of Public Health, Nanjing, China
| | - Xu Ma
- National Research Institute for Family Planning, Beijing, China.,Graduate School of Peking Union Medical College, Beijing, China
| | - Qiaoyun Dai
- National Research Institute for Family Planning, Beijing, China
| | - Xiaojin Yu
- Southeast University, Department of Public Health, Nanjing, China
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Hussein MH, Toraih EA, Aly NM, Riad E, Fawzy MS. A passenger strand variant in miR-196a2 contributes to asthma severity in children and adolescents: A preliminary study. Biochem Cell Biol 2016; 94:347-57. [PMID: 27487239 DOI: 10.1139/bcb-2016-0010] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
There is emerging evidence to support the role of microRNAs in allergic airway diseases and inflammation. Genetic variants in microRNA genes might affect microRNA-mediated cell regulation. This preliminary study was designed to investigate the association of the microRNA-196a2 rs11614913 (C/T) polymorphism with susceptibility to asthma and clinical outcomes in children and adolescents. Genotyping of rs11614913 polymorphism was determined in 96 patients with bronchial asthma (6-18 years of age) and 96 unrelated controls, using real-time polymerase chain reaction technology. In-silico target prediction and network core analyses were performed. The asthmatics did not show significant differences in genotype distribution (p = 0.609) and allele frequencies (p = 0.428) compared with the controls. There were also no associations with disease duration, age at onset, asthma phenotype, asthma control, therapeutic level, airway hyper-responsiveness, or biochemical parameters in the blood. However, the CC genotype was associated with a more severe degree of asthma (p = 0. 023) and higher frequency of nocturnal asthma (p = 0.002). Carriers for CC were 17 times more likely to develop nocturnal asthma, and had a more than 2.5-fold increased risk for poor disease outcome compared with CT and TT individuals. In conclusion, microRNA-196a2 rs11614913 polymorphism might be associated with asthma severity in our sample of the Egyptian population. Further investigations in studies with a larger sample size and functional tests are needed to validate our findings and to explore the detailed biological mechanisms.
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Affiliation(s)
- Mohammad H Hussein
- a Pulmongist, Ministry of Health, Egypt.,b Emergency Department, Al Jahra Hospital, Al Jahra, Kuwait
| | - Eman A Toraih
- c Department of Histology and Cell Biology (Genetics Unit), Faculty of Medicine, Suez Canal University, PO Box 41522, Ismailia, Egypt
| | - Nagwa M Aly
- d Department of Medical Biochemistry, Faculty of Medicine, Suez Canal University, PO Box 41522, Ismailia, Egypt
| | - Eman Riad
- e Department of Chest Diseases and Tuberculosis, Faculty of Medicine, Suez Canal University, PO Box 41522, Ismailia, Egypt
| | - Manal S Fawzy
- d Department of Medical Biochemistry, Faculty of Medicine, Suez Canal University, PO Box 41522, Ismailia, Egypt
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Abstract
B-cell chronic lymphocytic leukemia (CLL) is the most common adult human leukemia. Although, the molecular alterations leading to CLL onset and progression are still under investigation (specifically, the interplay and exact role of oncogenes and tumor suppressors in CLL pathogenesis). MicroRNAs are small non-coding RNAs that regulate gene expression and are expressed in a tissue specific manner. Deregulation of microRNAs can alter expression levels of genes involved in the development and/or progression of tumors. In CLL, microRNAs can function as oncogenes or tumor suppressors. Here, we review the most recent findings on the role of microRNAs in the onset/progression of CLL, and how this knowledge can be used to identify new biomarkers and targets to treat this leukemia.
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Affiliation(s)
- Veronica Balatti
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Mario Acunzo
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Yuri Pekarky
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
| | - Carlo M Croce
- Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, Wexner Medical Center, The Ohio State University, Columbus, OH, USA
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