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Szmida E, Butkiewicz D, Karpiński P, Rutkowski T, Oczko-Wojciechowska M, Sąsiadek MM. The Role of Single Nucleotide Polymorphisms in MicroRNA Genes in Head and Neck Squamous Cell Carcinomas: Susceptibility and Prognosis. Genes (Basel) 2024; 15:1226. [PMID: 39336817 PMCID: PMC11431317 DOI: 10.3390/genes15091226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Revised: 09/09/2024] [Accepted: 09/13/2024] [Indexed: 09/30/2024] Open
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) is one of the most prevalent cancers worldwide. The identification of molecular alterations adding to the individual risk of HNSCC development and progression is one of the most important challenges in studies on cancer genetics. MicroRNAs (miRNAs), which belong to the group of important post-transcriptional regulators of human gene expression, seem to be valuable options for consideration as key modifiers of individual cancer risk, and therefore may be helpful in predicting inter-individual differences in cancer risk, response to treatment and prognosis. METHODS There have not been many studies focused on the relationship between miRNA variants and HNSCC published in PubMed within the last 15 years. We found and analyzed 30 reviews, meta-analyses and research papers and revealed 14 SNPs which have been reported as significant in the context of HNSCC susceptibility and/or prognosis. RESULTS These 14 SNPs were located in 13 separate miRNAs. Among them, four were the most frequently studied (miRNA-146, -196, -149 and -499) and have been shown to have the greatest impact on the course of HNSCC. However, the presented results have been conflicting. CONCLUSIONS It must be concluded that, despite the years of studies, there are no conclusive reports demonstrating a significant role of SNPs in miRNAs in the context of the susceptibility to HNSCC or its prognosis.
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Affiliation(s)
- Elżbieta Szmida
- Department of Genetics, Wroclaw Medical University, 50-367 Wroclaw, Poland
| | - Dorota Butkiewicz
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland
| | - Paweł Karpiński
- Department of Genetics, Wroclaw Medical University, 50-367 Wroclaw, Poland
| | - Tomasz Rutkowski
- Radiotherapy Department, Maria Skłodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland
| | - Małgorzata Oczko-Wojciechowska
- Department of Clinical and Molecular Genetics, Maria Skłodowska-Curie National Research Institute of Oncology Gliwice Branch, 44-102 Gliwice, Poland
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Mustafa A, Shabbir M, Badshah Y, Khan K, Abid F, Trembley JH, Afsar T, Almajwal A, Razak S. Genetic polymorphism in untranslated regions of PRKCZ influences mRNA structure, stability and binding sites. BMC Cancer 2024; 24:1147. [PMID: 39272077 PMCID: PMC11401371 DOI: 10.1186/s12885-024-12900-8] [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: 05/20/2024] [Accepted: 09/04/2024] [Indexed: 09/15/2024] Open
Abstract
BACKGROUND Variations in untranslated regions (UTR) alter regulatory pathways impacting phenotype, disease onset, and course of disease. Protein kinase C Zeta (PRKCZ), a serine-threonine kinase, is implicated in cardiovascular, neurological and oncological disorders. Due to limited research on PRKCZ, this study aimed to investigate the impact of UTR genetic variants' on binding sites for transcription factors and miRNA. RNA secondary structure, eQTLs, and variation tolerance analysis were also part of the study. METHODS The data related to PRKCZ gene variants was downloaded from the Ensembl genome browser, COSMIC and gnomAD. The RegulomeDB database was used to assess the functional impact of 5' UTR and 3'UTR variants. The analysis of the transcription binding sites (TFBS) was done through the Alibaba tool, and the Kyoto Encyclopaedia of Genes and Genomes (KEGG) was employed to identify pathways associated with PRKCZ. To predict the effect of variants on microRNA binding sites, PolymiRTS was utilized for 3' UTR variants, and the SNPinfo tool was used for 5' UTR variants. RESULTS The results obtained indicated that a total of 24 variants present in the 3' UTR and 25 variants present in the 5' UTR were most detrimental. TFBS analysis revealed that 5' UTR variants added YY1, repressor, and Oct1, whereas 3' UTR variants added AP-2alpha, AhR, Da, GR, and USF binding sites. The study predicted TFs that influenced PRKCZ expression. RNA secondary structure analysis showed that eight 5' UTR and six 3' UTR altered the RNA structure by either removal or addition of the stem-loop. The microRNA binding site analysis highlighted that seven 3' UTR and one 5' UTR variant altered the conserved site and also created new binding sites. eQTLs analysis showed that one variant was associated with PRKCZ expression in the lung and thyroid. The variation tolerance analysis revealed that PRKCZ was an intolerant gene. CONCLUSION This study laid the groundwork for future studies aimed at targeting PRKCZ as a therapeutic target.
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Affiliation(s)
- Aneela Mustafa
- Department of Healthcare BiotechnologyAtta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Islamabad, 44000, Pakistan
| | - Maria Shabbir
- Department of Healthcare BiotechnologyAtta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Islamabad, 44000, Pakistan.
| | - Yasmin Badshah
- Department of Healthcare BiotechnologyAtta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Islamabad, 44000, Pakistan
| | | | - Fizzah Abid
- Department of Healthcare BiotechnologyAtta-Ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Sector H-12, Islamabad, 44000, Pakistan
| | - Janeen H Trembley
- Minneapolis VA Health Care System Research Service, Minneapolis, MN, USA
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
| | - Tayyaba Afsar
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Ali Almajwal
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Suhail Razak
- Department of Community Health Sciences, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia.
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González Morales S, López-Portugués C, Fernández-Sanjurjo M, Iglesias-Gutiérrez E, Montes Bayón M, Corte-Rodríguez M. Amplification-Free Strategy for miRNA Quantification in Human Serum Using Single Particle ICP-MS and Gold Nanoparticles as Labels. Anal Chem 2024; 96. [PMID: 39028890 PMCID: PMC11295127 DOI: 10.1021/acs.analchem.4c01904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/21/2024]
Abstract
MicroRNAs (miRNAs), which are short single-stranded RNA sequences between 18 and 24 nucleotides, are known to play a crucial role in gene expression. Changes in their expression are not only involved in many diseases but also as a response to physiological changes, such as physical exercise. In this work, a new analytical strategy for the sensitive and specific analysis of miRNA sequences in human plasma is presented. The developed strategy does not depend on any nucleic acid amplification process and can be obtained in direct correlation to the number of events obtained by using single-particle ICP-MS measurements. The high selectivity of the assay (up to single nucleotide polymorphisms) can be achieved by a double hybridization process of the target miRNA with a complementary capture oligonucleotide that is conjugated to a magnetic microparticle and simultaneously with a complementary reporter oligonucleotide conjugated to a gold nanoparticle. Thanks to the novel approach followed in this method, the stoichiometry of the oligonucleotide-nanoparticle conjugates does not need to be addressed for the quantification of the target miRNA, which also represents a big advantage over other similar methods. The optimized method is applied to the determination of a miRNA as a biomarker of physical exercise in non-spiked human serum samples, and the results are validated against rt-qPCR. The achieved sensitivity permits the direct differentiation among sedentary and sportive subjects. This general platform can be easily applied to any other sequence by only modifying the capture and reporter oligonucleotides, paving the way for multiple clinically interesting applications.
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Affiliation(s)
- Sara González Morales
- Department
of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain
- Health
Research Institute of the Principality of Asturias (ISPA), Av. Hospital Universitario s/n, 33011 Oviedo, Spain
| | - Carlos López-Portugués
- Department
of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain
- Health
Research Institute of the Principality of Asturias (ISPA), Av. Hospital Universitario s/n, 33011 Oviedo, Spain
| | - Manuel Fernández-Sanjurjo
- Department
of Functional Biology (Physiology), University
of Oviedo, Julián
Clavería s/n, 33006 Oviedo, Spain
- Health
Research Institute of the Principality of Asturias (ISPA), Av. Hospital Universitario s/n, 33011 Oviedo, Spain
| | - Eduardo Iglesias-Gutiérrez
- Department
of Functional Biology (Physiology), University
of Oviedo, Julián
Clavería s/n, 33006 Oviedo, Spain
- Health
Research Institute of the Principality of Asturias (ISPA), Av. Hospital Universitario s/n, 33011 Oviedo, Spain
| | - María Montes Bayón
- Department
of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain
- Health
Research Institute of the Principality of Asturias (ISPA), Av. Hospital Universitario s/n, 33011 Oviedo, Spain
| | - Mario Corte-Rodríguez
- Department
of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain
- Health
Research Institute of the Principality of Asturias (ISPA), Av. Hospital Universitario s/n, 33011 Oviedo, Spain
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Uvarova AN, Tkachenko EA, Stasevich EM, Zheremyan EA, Korneev KV, Kuprash DV. Methods for Functional Characterization of Genetic Polymorphisms of Non-Coding Regulatory Regions of the Human Genome. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:1002-1013. [PMID: 38981696 DOI: 10.1134/s0006297924060026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 03/27/2024] [Accepted: 04/11/2024] [Indexed: 07/11/2024]
Abstract
Currently, numerous associations between genetic polymorphisms and various diseases have been characterized through the Genome-Wide Association Studies. Majority of the clinically significant polymorphisms are localized in non-coding regions of the genome. While modern bioinformatic resources make it possible to predict molecular mechanisms that explain influence of the non-coding polymorphisms on gene expression, such hypotheses require experimental verification. This review discusses the methods for elucidating molecular mechanisms underlying dependence of the disease pathogenesis on specific genetic variants within the non-coding sequences. A particular focus is on the methods for identification of transcription factors with binding efficiency dependent on polymorphic variations. Despite remarkable progress in bioinformatic resources enabling prediction of the impact of polymorphisms on the disease pathogenesis, there is still the need for experimental approaches to investigate this issue.
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Affiliation(s)
- Aksinya N Uvarova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia.
| | - Elena A Tkachenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
| | - Ekaterina M Stasevich
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141700, Russia
| | - Elina A Zheremyan
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Kirill V Korneev
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Dmitry V Kuprash
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
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Ma J, Gao R, Xie Q, Pan X, Tong N. Whole transcriptome sequencing analyses of islets reveal ncRNA regulatory networks underlying impaired insulin secretion and increased β-cell mass in high fat diet-induced diabetes mellitus. PLoS One 2024; 19:e0300965. [PMID: 38557554 PMCID: PMC10984535 DOI: 10.1371/journal.pone.0300965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Accepted: 03/07/2024] [Indexed: 04/04/2024] Open
Abstract
AIM Our study aims to identify novel non-coding RNA-mRNA regulatory networks associated with β-cell dysfunction and compensatory responses in obesity-related diabetes. METHODS Glucose metabolism, islet architecture and secretion, and insulin sensitivity were characterized in C57BL/6J mice fed on a 60% high-fat diet (HFD) or control for 24 weeks. Islets were isolated for whole transcriptome sequencing to identify differentially expressed (DE) mRNAs, miRNAs, IncRNAs, and circRNAs. Regulatory networks involving miRNA-mRNA, lncRNA-mRNA, and lncRNA-miRNA-mRNA were constructed and functions were assessed through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. RESULTS Despite compensatory hyperinsulinemia and a significant increase in β-cell mass with a slow rate of proliferation, HFD mice exhibited impaired glucose tolerance. In isolated islets, insulin secretion in response to glucose and palmitic acid deteriorated after 24 weeks of HFD. Whole transcriptomic sequencing identified a total of 1324 DE mRNAs, 14 DE miRNAs, 179 DE lncRNAs, and 680 DE circRNAs. Our transcriptomic dataset unveiled several core regulatory axes involved in the impaired insulin secretion in HFD mice, such as miR-6948-5p/Cacna1c, miR-6964-3p/Cacna1b, miR-3572-5p/Hk2, miR-3572-5p/Cckar and miR-677-5p/Camk2d. Additionally, proliferative and apoptotic targets, including miR-216a-3p/FKBP5, miR-670-3p/Foxo3, miR-677-5p/RIPK1, miR-802-3p/Smad2 and ENSMUST00000176781/Caspase9 possibly contribute to the increased β-cell mass in HFD islets. Furthermore, competing endogenous RNAs (ceRNA) regulatory network involving 7 DE miRNAs, 15 DE lncRNAs and 38 DE mRNAs might also participate in the development of HFD-induced diabetes. CONCLUSIONS The comprehensive whole transcriptomic sequencing revealed novel non-coding RNA-mRNA regulatory networks associated with impaired insulin secretion and increased β-cell mass in obesity-related diabetes.
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Affiliation(s)
- Jinfang Ma
- Department of Endocrinology and Metabolism, West China Hospital, Sichuan University, Chengdu, China
- Center for Diabetes and Metabolism Research, West China Hospital, Sichuan University, Chengdu, China
| | - Rui Gao
- Oxford Centre for Diabetes, Endocrinology and Metabolism, Radcliffe Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Qingxing Xie
- Department of Endocrinology and Metabolism, West China Hospital, Sichuan University, Chengdu, China
- Center for Diabetes and Metabolism Research, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaohui Pan
- Department of Endocrinology and Metabolism, West China Hospital, Sichuan University, Chengdu, China
- Center for Diabetes and Metabolism Research, West China Hospital, Sichuan University, Chengdu, China
| | - Nanwei Tong
- Department of Endocrinology and Metabolism, West China Hospital, Sichuan University, Chengdu, China
- Center for Diabetes and Metabolism Research, West China Hospital, Sichuan University, Chengdu, China
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6
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Rykova EY, Ershov NI, Degtyareva AO, Bryzgalov LO, Lushnikova EL. The Search for and Functional Analysis of Genetic Variants in microRNA-Binding Sites using Massively Parallel Reporter Assay. Bull Exp Biol Med 2024; 176:595-598. [PMID: 38724816 DOI: 10.1007/s10517-024-06074-3] [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: 08/03/2023] [Indexed: 05/18/2024]
Abstract
A large-scale search for the genetic variants with a bias in the representation of alleles in transcriptome data (AE SNPs) and the binding sites in microRNA 3'-UTRs was performed and their functional significance was assessed using massively parallel reporter assay (MPRA). Of the 629,559 associated "SNP-gene" pairs (eQTLs) discovered in the human liver tissue according to the GTEx Analysis V8 data, 4394 polymorphic positions in the 3'-UTRs of the genes, which represent the eQTLs for these genes were selected. The TargetScanHuman 7.0 algorithm and PolymiRTS database were searched for the potential microRNA-binding sites. Of the predicted microRNA sites affected by eQTL-SNPs, we selected 51 sites with the best evidence of functionality according to Ago2-CLIP-seq, CLEAR-CLIP, and eCLIP-seq for RNA-binding proteins. For MPRA, a library of the plasmids carrying the main and alternative alleles for each AE SNP (in total, 102 constructs) was created. Allele-specific expression for 6 SNPs was detected by transfection of the HepG2 cell line with the constructed plasmid library and sequencing of target DNA and RNA sequences using the Illumina (MiSeq) platform.
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Affiliation(s)
- E Yu Rykova
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.
| | - N I Ershov
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A O Degtyareva
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - L O Bryzgalov
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E L Lushnikova
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk, Russia
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Chhichholiya Y, Singh HV, Singh S, Munshi A. Genetic variations in tumor-suppressor miRNA-encoding genes and their target genes: focus on breast cancer development and possible therapeutic strategies. Clin Transl Oncol 2024; 26:1-15. [PMID: 37093457 DOI: 10.1007/s12094-023-03176-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 03/26/2023] [Indexed: 04/25/2023]
Abstract
MicroRNAs (miRNAs) negatively affect gene expression by binding to their specific mRNAs resulting in either mRNA destruction or translational repression. The aberrant expression of various miRNAs has been associated with a number of human cancer. Oncogenic or tumor-suppressor miRNAs regulate a variety of pathways involved in the development of breast cancer (BC), including cell proliferation, apoptosis, metastasis, cancer recurrence, and chemoresistance. Variations in miRNA-encoding genes and their target genes lead to dysregulated gene expression resulting in the development and progression of BC. The various therapeutic approaches to treat the disease include chemotherapy, radiation therapy, surgical removal, hormone therapy, chemotherapy, and targeted biological therapy. The purpose of the current review is to explore the genetic variations in tumor-suppressor miRNA-encoding genes and their target genes in association with the disease development and prognosis. The therapeutic interventions targeting the variants for better disease outcomes have also been discussed.
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Affiliation(s)
- Yogita Chhichholiya
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, Punjab, India
| | - Harsh Vikram Singh
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, Punjab, India
| | - Sandeep Singh
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, Punjab, India.
| | - Anjana Munshi
- Department of Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, Punjab, India.
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Liao Z, Zhang Q, Yang L, Li H, Mo W, Song Z, Huang X, Wen S, Cheng X, He M. Increased hsa-miR-100-5p Expression Improves Hepatocellular Carcinoma Prognosis in the Asian Population with PLK1 Variant rs27770A>G. Cancers (Basel) 2023; 16:129. [PMID: 38201556 PMCID: PMC10778516 DOI: 10.3390/cancers16010129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/17/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
Hepatocellular carcinoma (HCC) has the highest incidence and mortality in the Asian population, and race is an independent risk factor affecting survival time in liver cancer. Micro RNAs (miRNAs) are remarkably dysregulated in HCC and closely associated with HCC prognosis. Recent studies show that genetic variability between ethnic groups may result in differences in the specificity of HCC miRNA biomarkers. Here, we reveal a high expression level of hsa-miR-100-5p, an HCC prognosis-related miRNA, which improves HCC prognosis in the Asian Population with Polo-like kinase 1 (PLK1) variant rs27770A>G. In this study, we discovered that hsa-miR-100-5p was downregulated in various HCC cell lines. While mimics transient transfection and mouse liver cancer model confirmed the interaction between hsa-miR-100-5p and PLK1, a stratified analysis based on the Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA-LIHC) data suggest both low hsa-miR-100-5p expression level and high PLK1 expression level associated with poor HCC prognosis, especially in the Asian population. According to the 1000 Genomes Project database, the SNP rs27770 located in 3'UTR of PLK1 had a significantly higher G allele frequency in the East Asian population. Bioinformatics analysis suggested that rs27770 A>G affects PLK1 mRNA secondary structure and alters the hsa-miR-100-5p/PLK1 interaction by forming an additional seedless binding site. This racial variation caused PLK1 to be more vulnerable to hsa-miR-100-5p inhibition, resulting in hsa-miR-100-5p being more favorable for HCC prognosis in the Asian population.
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Affiliation(s)
- Zhouxiang Liao
- School of Public Health, Guangxi Medical University, Nanning 530021, China; (Z.L.); (H.L.); (W.M.); (Z.S.); (X.C.)
| | - Qi Zhang
- Laboratory Animal Center, Guangxi Medical University, Nanning 530021, China; (Q.Z.); (L.Y.); (X.H.)
| | - Lichao Yang
- Laboratory Animal Center, Guangxi Medical University, Nanning 530021, China; (Q.Z.); (L.Y.); (X.H.)
| | - Hui Li
- School of Public Health, Guangxi Medical University, Nanning 530021, China; (Z.L.); (H.L.); (W.M.); (Z.S.); (X.C.)
| | - Wanling Mo
- School of Public Health, Guangxi Medical University, Nanning 530021, China; (Z.L.); (H.L.); (W.M.); (Z.S.); (X.C.)
| | - Zhenyu Song
- School of Public Health, Guangxi Medical University, Nanning 530021, China; (Z.L.); (H.L.); (W.M.); (Z.S.); (X.C.)
| | - Xuejing Huang
- Laboratory Animal Center, Guangxi Medical University, Nanning 530021, China; (Q.Z.); (L.Y.); (X.H.)
| | - Sha Wen
- Laboratory Animal Center, Guangxi Medical University, Nanning 530021, China; (Q.Z.); (L.Y.); (X.H.)
| | - Xiaojing Cheng
- School of Public Health, Guangxi Medical University, Nanning 530021, China; (Z.L.); (H.L.); (W.M.); (Z.S.); (X.C.)
- Life Sciences Institute, Guangxi Medical University, Nanning 530021, China
| | - Min He
- School of Public Health, Guangxi Medical University, Nanning 530021, China; (Z.L.); (H.L.); (W.M.); (Z.S.); (X.C.)
- Laboratory Animal Center, Guangxi Medical University, Nanning 530021, China; (Q.Z.); (L.Y.); (X.H.)
- Key Laboratory of High-Incidence-Tumor Prevention & Treatment (Guangxi Medical University), Ministry of Education, Nanning 530021, China
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9
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Mustafa R, Ghanbari M, Karhunen V, Evangelou M, Dehghan A. Phenome-wide association study on miRNA-related sequence variants: the UK Biobank. Hum Genomics 2023; 17:104. [PMID: 37996941 PMCID: PMC10668386 DOI: 10.1186/s40246-023-00553-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/13/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND Genetic variants in the coding region could directly affect the structure and expression levels of genes and proteins. However, the importance of variants in the non-coding region, such as microRNAs (miRNAs), remain to be elucidated. Genetic variants in miRNA-related sequences could affect their biogenesis or functionality and ultimately affect disease risk. Yet, their implications and pleiotropic effects on many clinical conditions remain unknown. METHODS Here, we utilised genotyping and hospital records data in the UK Biobank (N = 423,419) to investigate associations between 346 genetic variants in miRNA-related sequences and a wide range of clinical diagnoses through phenome-wide association studies. Further, we tested whether changes in blood miRNA expression levels could affect disease risk through colocalisation and Mendelian randomisation analysis. RESULTS We identified 122 associations for six variants in the seed region of miRNAs, nine variants in the mature region of miRNAs, and 27 variants in the precursor miRNAs. These included associations with hypertension, dyslipidaemia, immune-related disorders, and others. Nineteen miRNAs were associated with multiple diagnoses, with six of them associated with multiple disease categories. The strongest association was reported between rs4285314 in the precursor of miR-3135b and celiac disease risk (odds ratio (OR) per effect allele increase = 0.37, P = 1.8 × 10-162). Colocalisation and Mendelian randomisation analysis highlighted potential causal role of miR-6891-3p in dyslipidaemia. CONCLUSIONS Our study demonstrates the pleiotropic effect of miRNAs and offers insights to their possible clinical importance.
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Affiliation(s)
- Rima Mustafa
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- UK Dementia Research Institute, Imperial College London, London, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
- Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Ville Karhunen
- Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland
- Research Unit of Population Health, University of Oulu, Oulu, Finland
| | | | - Abbas Dehghan
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK.
- UK Dementia Research Institute, Imperial College London, London, UK.
- MRC Centre for Environment and Health, Imperial College London, London, UK.
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10
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Li M, Zeng A, Tang X, Xu H, Xiong W, Guo Y. Circ_0004535/miR-1827/CASP8 network involved in type 2 diabetes mellitus with nonalcoholic fatty liver disease. Sci Rep 2023; 13:19807. [PMID: 37957232 PMCID: PMC10643362 DOI: 10.1038/s41598-023-47189-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 11/10/2023] [Indexed: 11/15/2023] Open
Abstract
Diagnostic delay in type 2 diabetes mellitus (T2DM) with nonalcoholic fatty liver disease (NAFLD) patients often leads to a serious public health problem. Understanding the pathophysiological mechanisms of disease will help develop more effective treatments. High-throughput sequencing was used to determine the expression levels of circRNAs, and mRNAs in health controls, T2DM patients, and T2DM with NAFLD patients. Differentially expressed genes (DEcircRs, DEmRs) in T2DM with NAFLD were identified by differential analysis. The miRNAs with targeted relationship with the DEcircRs and DEmRs were respectively predicted to construct a ceRNA regulatory network. In addition, enrichment analysis of DEmRs in the ceRNA network was performed. The expression of important DEcircRs was further validated by quantitative real-time PCR (qRT-PCR). The steatosis was detected in glucose treated LO2 cells by overexpressing circ_0004535, and CASP8. There were 586 DEmRs, and 10 DEcircRs in both T2DM and T2DM with NAFLD patients. Combined with predicted results and differential analysis, the ceRNA networks were constructed. The DEmRs in the ceRNA networks were mainly enriched in Toll-like receptor signaling pathway, and apoptosis. Importantly, dual luciferase experiments validated the targeted binding of hsa_circ_0004535 and hsa-miR-1827 or hsa-miR-1827 and CASP8. qRT-PCR experiments validated that hsa_circ_0004535, and CASP8 was downregulated and hsa-miR-1827 was upregulated expression in peripheral blood of T2DM with NAFLD patients. Abnormal cell morphology, and increased lipid droplet fusion were observed in the glucose treated LO2 cells, overexpression of circ_0004535 and CASP8 ameliorated these changes. Our work provides a deeper understanding of ceRNA mediated pathogenesis of T2DM with NAFLD and provides a novel strategy for treatment.
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Affiliation(s)
- Min Li
- Graduate School of Xinjiang Medical University, Xinshi District, Ürümqi, 830054, China
| | - Ai Zeng
- B Chao Room, The Sixth Affiliated Hospital of Xinjiang Medical University, Tianshan District, Ürümqi, 830092, China
| | - Xinle Tang
- Department of Laboratory Medicine, The Sixth Affiliated Hospital of Xinjiang Medical University, Tianshan District, Ürümqi, 830092, China
| | - Hui Xu
- Department of Laboratory Medicine, The Sixth Affiliated Hospital of Xinjiang Medical University, Tianshan District, Ürümqi, 830092, China
| | - Wei Xiong
- Department of Endocrinology, The Sixth Affiliated Hospital of Xinjiang Medical University, Tianshan District, Ürümqi, 830092, China
| | - Yanying Guo
- Department of Endocrinology and Metabolic Diseases, People's Hospital of Xinjiang Uygur Autonomous Region, Xinjiang Clinical Research Center for Diabetes Mellitus, Tianshan District, Ürümqi, 830011, China.
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11
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Maselli F, D’Antona S, Utichi M, Arnaudi M, Castiglioni I, Porro D, Papaleo E, Gandellini P, Cava C. Computational analysis of five neurodegenerative diseases reveals shared and specific genetic loci. Comput Struct Biotechnol J 2023; 21:5395-5407. [PMID: 38022694 PMCID: PMC10651457 DOI: 10.1016/j.csbj.2023.10.031] [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: 08/11/2023] [Revised: 10/09/2023] [Accepted: 10/16/2023] [Indexed: 12/01/2023] Open
Abstract
Neurodegenerative diseases (ND) are heterogeneous disorders of the central nervous system that share a chronic and selective process of neuronal cell death. A computational approach to investigate shared genetic and specific loci was applied to 5 different ND: Amyotrophic lateral sclerosis (ALS), Alzheimer's disease (AD), Parkinson's disease (PD), Multiple sclerosis (MS), and Lewy body dementia (LBD). The datasets were analyzed separately, and then we compared the obtained results. For this purpose, we applied a genetic correlation analysis to genome-wide association datasets and revealed different genetic correlations with several human traits and diseases. In addition, a clumping analysis was carried out to identify SNPs genetically associated with each disease. We found 27 SNPs in AD, 6 SNPs in ALS, 10 SNPs in PD, 17 SNPs in MS, and 3 SNPs in LBD. Most of them are located in non-coding regions, with the exception of 5 SNPs on which a protein structure and stability prediction was performed to verify their impact on disease. Furthermore, an analysis of the differentially expressed miRNAs of the 5 examined pathologies was performed to reveal regulatory mechanisms that could involve genes associated with selected SNPs. In conclusion, the results obtained constitute an important step toward the discovery of diagnostic biomarkers and a better understanding of the diseases.
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Affiliation(s)
- Francesca Maselli
- Institute of Bioimaging and Molecular Physiology, National Research Council, Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
| | - Salvatore D’Antona
- Institute of Bioimaging and Molecular Physiology, National Research Council, Milan, Italy
| | - Mattia Utichi
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Lyngby, Technical University of Denmark
- Cancer Structural Biology, Danish Cancer Institute, Copenhagen, Denmark
| | - Matteo Arnaudi
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Lyngby, Technical University of Denmark
- Cancer Structural Biology, Danish Cancer Institute, Copenhagen, Denmark
| | - Isabella Castiglioni
- Department of Physics ‘‘Giuseppe Occhialini”, University of Milan, Bicocca, Italy
| | - Danilo Porro
- Institute of Bioimaging and Molecular Physiology, National Research Council, Milan, Italy
| | - Elena Papaleo
- Cancer Systems Biology, Section for Bioinformatics, Department of Health and Technology, Lyngby, Technical University of Denmark
- Cancer Structural Biology, Danish Cancer Institute, Copenhagen, Denmark
| | | | - Claudia Cava
- Institute of Bioimaging and Molecular Physiology, National Research Council, Milan, Italy
- Department of Science, Technology and Society, University School for Advanced Studies IUSS Pavia, Italy
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12
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Burada E, Roșu MM, Sandu RE, Burada F, Cucu MG, Streață I, Petre-Mandache B, Popescu-Hobeanu G, Cara ML, Țucă AM, Pinoșanu E, Albu CV. miR-499a rs3746444 A>G Polymorphism Is Correlated with Type 2 Diabetes Mellitus and Diabetic Polyneuropathy in a Romanian Cohort: A Preliminary Study. Genes (Basel) 2023; 14:1543. [PMID: 37628595 PMCID: PMC10454730 DOI: 10.3390/genes14081543] [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: 07/06/2023] [Revised: 07/20/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Type 2 diabetes mellitus (T2DM) is a common metabolic disorder that results from complex interactions of both environmental and genetic factors. Many single nucleotide polymorphisms (SNPs), including noncoding RNA genes, have been investigated for their association with susceptibility to T2DM and its complications, with little evidence available regarding Caucasians. The aim of the present study was to establish whether four miRNA SNPs (miR-27a rs895819 T>C, miR-146a rs2910164 G>C, miR-196a2 rs11614913 C>T, and miR-499a rs3746444 A>G) are correlated with susceptibility to T2DM and/or diabetic polyneuropathy (DPN) in a Romanian population. A total of 167 adult T2DM patients and 324 age- and sex-matched healthy controls were included in our study. miRNA SNPs were detected by real-time PCR using a TaqMan genotyping assay. A significant association with T2DM was observed only for the miR-499a rs3746444 A>G SNP in all the tested models, and the frequencies of both the miR-499a rs3746444 AG and the GG genotypes were higher in the T2DM patients compared to the controls. No correlation was observed for the miR-27a rs895819 T>C, miR-146a rs2910164 G>C, or miR-196a2 rs11614913 C>T SNPs in any genetic model. When we assessed the association of these SNPs with DPN separately, we found a positive association for the miR-499a rs3746444 SNP in both codominant and dominant models (OR 6.47, 95% CI: 1.71-24.47; OR 2.30, 95% CI: 1.23-4.29, respectively). In conclusion, this study shows that miR-499a rs3746444 A>G may influence both T2DM and DPN susceptibility, with carriers of the GG genotype and the G allele being at an increased risk in the Romanian population.
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Affiliation(s)
- Emilia Burada
- Department of Physiology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania; (E.B.); (A.-M.Ț.)
- Department of Neurology, Clinical Hospital of Neuropsychiatry Craiova, 200473 Craiova, Romania; (R.E.S.); (E.P.); (C.V.A.)
| | - Maria-Magdalena Roșu
- Department of Diabetes, Nutrition and Metabolic Diseases, Emergency Clinical County Hospital Craiova, 200642 Craiova, Romania;
| | - Raluca Elena Sandu
- Department of Neurology, Clinical Hospital of Neuropsychiatry Craiova, 200473 Craiova, Romania; (R.E.S.); (E.P.); (C.V.A.)
- Department of Biochemistry, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Florin Burada
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania; (M.G.C.); (I.S.); (B.P.-M.); (G.P.-H.)
- Regional Centre of Medical Genetics Dolj, Emergency Clinical County Hospital Craiova, 200642 Craiova, Romania
| | - Mihai Gabriel Cucu
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania; (M.G.C.); (I.S.); (B.P.-M.); (G.P.-H.)
- Regional Centre of Medical Genetics Dolj, Emergency Clinical County Hospital Craiova, 200642 Craiova, Romania
| | - Ioana Streață
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania; (M.G.C.); (I.S.); (B.P.-M.); (G.P.-H.)
- Regional Centre of Medical Genetics Dolj, Emergency Clinical County Hospital Craiova, 200642 Craiova, Romania
| | - Bianca Petre-Mandache
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania; (M.G.C.); (I.S.); (B.P.-M.); (G.P.-H.)
- Doctoral School, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Gabriela Popescu-Hobeanu
- Laboratory of Human Genomics, University of Medicine and Pharmacy of Craiova, 200638 Craiova, Romania; (M.G.C.); (I.S.); (B.P.-M.); (G.P.-H.)
- Doctoral School, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Monica-Laura Cara
- Department of Public Health, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania;
| | - Anca-Maria Țucă
- Department of Physiology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania; (E.B.); (A.-M.Ț.)
- Doctoral School, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Elena Pinoșanu
- Department of Neurology, Clinical Hospital of Neuropsychiatry Craiova, 200473 Craiova, Romania; (R.E.S.); (E.P.); (C.V.A.)
- Doctoral School, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | - Carmen Valeria Albu
- Department of Neurology, Clinical Hospital of Neuropsychiatry Craiova, 200473 Craiova, Romania; (R.E.S.); (E.P.); (C.V.A.)
- Department of Neurology, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
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13
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SNPs in 3'UTR miRNA Target Sequences Associated with Individual Drug Susceptibility. Int J Mol Sci 2022; 23:ijms232213725. [PMID: 36430200 PMCID: PMC9692299 DOI: 10.3390/ijms232213725] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/04/2022] [Accepted: 11/04/2022] [Indexed: 11/09/2022] Open
Abstract
The complementary interaction of microRNAs (miRNAs) with their binding sites in the 3'untranslated regions (3'UTRs) of target gene mRNAs represses translation, playing a leading role in gene expression control. MiRNA recognition elements (MREs) in the 3'UTRs of genes often contain single nucleotide polymorphisms (SNPs), which can change the binding affinity for target miRNAs leading to dysregulated gene expression. Accumulated data suggest that these SNPs can be associated with various human pathologies (cancer, diabetes, neuropsychiatric disorders, and cardiovascular diseases) by disturbing the interaction of miRNAs with their MREs located in mRNA 3'UTRs. Numerous data show the role of SNPs in 3'UTR MREs in individual drug susceptibility and drug resistance mechanisms. In this review, we brief the data on such SNPs focusing on the most rigorously proven cases. Some SNPs belong to conventional genes from the drug-metabolizing system (in particular, the genes coding for cytochromes P450 (CYP 450), phase II enzymes (SULT1A1 and UGT1A), and ABCB3 transporter and their expression regulators (PXR and GATA4)). Other examples of SNPs are related to the genes involved in DNA repair, RNA editing, and specific drug metabolisms. We discuss the gene-by-gene studies and genome-wide approaches utilized or potentially utilizable to detect the MRE SNPs associated with individual response to drugs.
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14
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3′UTR heterogeneity and cancer progression. Trends Cell Biol 2022:S0962-8924(22)00232-X. [DOI: 10.1016/j.tcb.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/12/2022] [Accepted: 10/12/2022] [Indexed: 11/13/2022]
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15
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Consequences of genetic variants in miRNA genes. Comput Struct Biotechnol J 2022; 20:6443-6457. [DOI: 10.1016/j.csbj.2022.11.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 11/20/2022] Open
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16
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Wang LJ, Han Q, Hu JP, Wang HX, Liu M, Zhang CY. Structure-Switchable Hairpin-Powered Exponential Replications for Sensing Attomolar microRNA-Related Single Nucleotide Polymorphisms in Human Cancer Tissues with Zero Background. Anal Chem 2022; 94:15171-15175. [DOI: 10.1021/acs.analchem.2c04281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Li-juan Wang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Qian Han
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Jin-ping Hu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China
| | - Hou-xiu Wang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Meng Liu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Chun-yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
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17
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Moradi A, Whatmore P, Farashi S, Barrero RA, Batra J. IsomiR-eQTL: A Cancer-Specific Expression Quantitative Trait Loci Database of miRNAs and Their Isoforms. Int J Mol Sci 2022; 23:ijms232012493. [PMID: 36293349 PMCID: PMC9604134 DOI: 10.3390/ijms232012493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 10/06/2022] [Accepted: 10/06/2022] [Indexed: 11/16/2022] Open
Abstract
The identification of expression quantitative trait loci (eQTL) is an important component in efforts to understand how genetic variants influence disease risk. MicroRNAs (miRNAs) are short noncoding RNA molecules capable of regulating the expression of several genes simultaneously. Recently, several novel isomers of miRNAs (isomiRs) that differ slightly in length and sequence composition compared to their canonical miRNAs have been reported. Here we present isomiR-eQTL, a user-friendly database designed to help researchers find single nucleotide polymorphisms (SNPs) that can impact miRNA (miR-eQTL) and isomiR expression (isomiR-eQTL) in 30 cancer types. The isomiR-eQTL includes a total of 152,671 miR-eQTLs and 2,390,805 isomiR-eQTLs at a false discovery rate (FDR) of 0.05. It also includes 65,733 miR-eQTLs overlapping known cancer-associated loci identified through genome-wide association studies (GWAS). To the best of our knowledge, this is the first study investigating the impact of SNPs on isomiR expression at the genome-wide level. This database may pave the way for researchers toward finding a model for personalised medicine in which miRNAs, isomiRs, and genotypes are utilised.
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Affiliation(s)
- Afshin Moradi
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane 4059, Australia
- Translational Research Institute, Queensland University of Technology, Brisbane 4102, Australia
| | - Paul Whatmore
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane 4000, Australia
| | - Samaneh Farashi
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane 4059, Australia
- Translational Research Institute, Queensland University of Technology, Brisbane 4102, Australia
| | - Roberto A. Barrero
- eResearch, Research Infrastructure, Academic Division, Queensland University of Technology, Brisbane 4000, Australia
| | - Jyotsna Batra
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane 4059, Australia
- Translational Research Institute, Queensland University of Technology, Brisbane 4102, Australia
- Faculty of Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane 4059, Australia
- Correspondence:
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18
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do Canto LM, da Silva JM, Castelo-Branco PV, da Silva IM, Nogueira L, Fonseca-Alves CE, Khayat A, Birbrair A, Pereira SR. Mutational Signature and Integrative Genomic Analysis of Human Papillomavirus-Associated Penile Squamous Cell Carcinomas from Latin American Patients. Cancers (Basel) 2022; 14:cancers14143514. [PMID: 35884575 PMCID: PMC9316960 DOI: 10.3390/cancers14143514] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 06/26/2022] [Accepted: 06/27/2022] [Indexed: 02/01/2023] Open
Abstract
Simple Summary DNA sequencing has been crucial to comprehending cancer mutational patterns, leading to the identification of driver genes and altered signaling pathways. Thus, identifying new pathogenic variants and their impact on tumor onset, progression, and treatment response has fueled tumor biology research. Here, we present novel findings addressing the first whole-exome sequencing (WES) of human papillomavirus (HPV)-associated penile squamous cell carcinoma (PSCC) from Latin Americans and its association with pathogenesis. We also compared the molecular profile of the tumors to that of three previous studies from populations with different genetic and socioeconomic backgrounds, the majority of which was HPV-negative. We describe the most altered genes and the main pathogenic variants found in the Latin Americans, ten of which are exclusive to our study sample. The data allowed us to identify molecular pathways and druggable targets with potential treatment value for this still-neglected HPV-associated carcinoma. Abstract High-throughput DNA sequencing has allowed for the identification of genomic alterations and their impact on tumor development, progression, and therapeutic responses. In PSCC, for which the incidence has progressively increased worldwide, there are still limited data on the molecular mechanisms involved in the disease pathogenesis. In this study, we characterized the mutational signature of 30 human papillomavirus (HPV)-associated PSCC cases from Latin Americans, using whole-exome sequencing. Copy number variations (CNVs) were also identified and compared to previous array-generated data. Enrichment analyses were performed to reveal disrupted pathways and to identify alterations mapped to HPV integration sites (HPVis) and miRNA–mRNA hybridization regions. Among the most frequently mutated genes were NOTCH1, TERT, TTN, FAT1, TP53, CDKN2A, RYR2, CASP8, FBXW7, HMCN2, and ITGA8. Of note, 92% of these altered genes were localized at HPVis. We also found mutations in ten novel genes (KMT2C, SMARCA4, PTPRB, AJUBA, CR1, KMT2D, NBEA, FAM135B, GTF2I, and CIC), thus increasing our understanding of the potential HPV-disrupted pathways. Therefore, our study reveals innovative targets with potential therapeutic benefits for HPV-associated PSCCs. The CNV analysis by sequencing (CNV-seq) revealed five cancer-associated genes as the most frequent with gains (NOTCH1, MYC, NUMA1, PLAG1, and RAD21), while 30% of the tumors showed SMARCA4 with loss. Additionally, four cancer-associated genes (CARD11, CSMD3, KDR, and TLX3) carried untranslated regions (UTRs) variants, which may impact gene regulation by affecting the miRNAs hybridization regions. Altogether, these data contribute to the characterization of the mutational spectrum and its impact on cellular signaling pathways in PSCC, thus reinforcing the pivotal role of HPV infection in the molecular pathogenesis of these tumors.
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Affiliation(s)
- Luisa Matos do Canto
- Clinical Genetics Department, University Hospital of Southern Denmark, 7100 Vejle, Denmark;
| | - Jenilson Mota da Silva
- Postgraduate Program in Health Science, Federal University of Maranhão, São Luís 65080-805, MA, Brazil;
- Laboratory of Genetics and Molecular Biology, Department of Biology, Federal University of Maranhão, São Luís 65080-805, MA, Brazil; (P.V.C.-B.); (I.M.d.S.)
| | - Patrícia Valèria Castelo-Branco
- Laboratory of Genetics and Molecular Biology, Department of Biology, Federal University of Maranhão, São Luís 65080-805, MA, Brazil; (P.V.C.-B.); (I.M.d.S.)
| | - Ingrid Monteiro da Silva
- Laboratory of Genetics and Molecular Biology, Department of Biology, Federal University of Maranhão, São Luís 65080-805, MA, Brazil; (P.V.C.-B.); (I.M.d.S.)
| | | | | | - André Khayat
- Oncology Research Center, Federal University of Pará, Belém 66073-005, PA, Brazil;
| | - Alexander Birbrair
- Department of Dermatology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA;
- Department of Pathology, Federal University of Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
- Department of Radiology, Columbia University Medical Center, New York, NY 10032, USA
| | - Silma Regina Pereira
- Laboratory of Genetics and Molecular Biology, Department of Biology, Federal University of Maranhão, São Luís 65080-805, MA, Brazil; (P.V.C.-B.); (I.M.d.S.)
- Correspondence: ; Tel.: +55-98-32728543
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