Mutations in microRNA-128-2-3p identified with amplification-free hybridization assay

We describe a quantitative detection method for mutated microRNA in human plasma samples. Specific oligonucleotides designed from a Peyrard-Bishop model allowed accurate prediction of target:probe recognition affinity and specificity. Our amplification-free tandem bead-based hybridization assay had limit of detection of 2.2 pM. Thereby, the assay allowed identification of single-nucleotide polymorphism mismatch profiles in clinically relevant microRNA-128-2-3p, showing terminal mutations that correlate positively with inflammatory colitis and colorectal cancer.

[1]  Kaixiang Zhang,et al.  A paper-based assay for the colorimetric detection of SARS-CoV-2 variants at single-nucleotide resolution , 2022, Nature Biomedical Engineering.

[2]  A. Cuenda,et al.  p38γ and p38δ as biomarkers in the interplay of colon cancer and inflammatory bowel diseases , 2022, Cancer communications.

[3]  B. Ye,et al.  A programmable and sensitive CRISPR/Cas12a-based MicroRNA detection platform combined with hybridization chain reaction. , 2022, Biosensors & bioelectronics.

[4]  H. Shaheen,et al.  Genetic predisposition of SNPs in miRNA-149 (rs2292832) and FOXE1 (rs3758249) in thyroid Cancer , 2021, Molecular Biology Reports.

[5]  Gerald Weber,et al.  Complete Mesoscopic Parameterization of Single LNA Modifications in DNA Applied to Oncogene Probe Design , 2021, J. Chem. Inf. Model..

[6]  M. Oczkowicz,et al.  Application of the targeted sequencing approach reveals the single nucleotide polymorphism (SNP) repertoire in microRNA genes in the pig genome , 2021, Scientific Reports.

[7]  Jiao-yun Xia,et al.  Detection of Single Nucleotide Polymorphisms by Fluorescence Embedded Dye SYBR Green I Based on Graphene Oxide , 2021, Frontiers in Chemistry.

[8]  Juan Du,et al.  The role of miRNAs in colorectal cancer progression and chemoradiotherapy. , 2020, Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie.

[9]  J. Borlak,et al.  miRNAs in lung cancer. A systematic review identifies predictive and prognostic miRNA candidates for precision medicine in lung cancer. , 2020, Translational research : the journal of laboratory and clinical medicine.

[10]  G. Weber,et al.  Salt dependent mesoscopic model for RNA at multiple strand concentrations. , 2021, Biophysical chemistry.

[11]  G. Weber,et al.  Optical and theoretical study of strand recognition by nucleic acid probes , 2020, Communications Chemistry.

[12]  Hanlee P. Ji,et al.  Ultra-fast detection and quantification of nucleic acids by amplification-free fluorescence assay. , 2020, The Analyst.

[13]  Dong-Min Kim,et al.  Fluorometric detection of single-nucleotide mutations using tandem gene amplification , 2020 .

[14]  Xianglian Meng,et al.  Role of SNPs in the Biogenesis of Mature miRNAs , 2020, BioMed research international.

[15]  F. Bahreini,et al.  miR-559 polymorphism rs58450758 is linked to breast cancer , 2020, British journal of biomedical science.

[16]  N. Alitheen,et al.  The Regulatory Role of MicroRNAs in Breast Cancer , 2019, International journal of molecular sciences.

[17]  Christopher A. Miller,et al.  A general approach for detecting expressed mutations in AML cells using single cell RNA-sequencing , 2019, Nature Communications.

[18]  Y. Cai,et al.  Bioinformatics analysis of mRNA and miRNA microarray to identify the key miRNA-gene pairs in small-cell lung cancer , 2019, Molecular medicine reports.

[19]  Zhengping Li,et al.  Specific detection of RNA mutation at single-base resolution by coupling the isothermal exponential amplification reaction (EXPAR) with chimeric DNA probe-aided precise RNA disconnection at the mutation site. , 2019, Chemical communications.

[20]  P. Netti,et al.  Supramolecular Microgels with Molecular Beacons at the Interface for Ultrasensitive, Amplification-Free, and SNP-Selective miRNA Fluorescence Detection. , 2019, ACS applied materials & interfaces.

[21]  Xiao-mei Li,et al.  Elevated circulating asymmetric dimethylarginine levels in rheumatoid arthritis: a systematic review and meta-analysis , 2019, Amino Acids.

[22]  Qinyu Ge,et al.  MicroRNA Detection Specificity: Recent Advances and Future Perspective. , 2019, Analytical chemistry.

[23]  G. Weber,et al.  DNA/RNA hybrid mesoscopic model shows strong stability dependence with deoxypyrimidine content and stacking interactions similar to RNA/RNA , 2019, Chemical Physics Letters.

[24]  Wei Wang,et al.  LIMK2 acts as an oncogene in bladder cancer and its functional SNP in the microRNA‐135a binding site affects bladder cancer risk , 2018, International journal of cancer.

[25]  Zhongyi Li,et al.  Association of miRNA-146a rs2910164 and miRNA-196 rs11614913 polymorphisms in patients with ulcerative colitis , 2018, Medicine.

[26]  Gerardo Botti,et al.  Micrornas in prostate cancer: an overview , 2017, Oncotarget.

[27]  S. Ladame,et al.  Amplification-Free Detection of Circulating microRNA Biomarkers from Body Fluids Based on Fluorogenic Oligonucleotide-Templated Reaction between Engineered Peptide Nucleic Acid Probes: Application to Prostate Cancer Diagnosis. , 2016, Analytical chemistry.

[28]  Gerald Weber,et al.  Evaluating Hydrogen Bonds and Base Stacking of Single, Tandem and Terminal GU Mismatches in RNA with a Mesoscopic Model , 2016, J. Chem. Inf. Model..

[29]  Franziska Michor,et al.  In situ single cell analysis identifies heterogeneity for PIK3CA mutation and HER2 amplification in HER2+ breast cancer , 2015, Nature Genetics.

[30]  Y. Hu,et al.  The polymorphism of rs6505162 in the MIR423 coding region and recurrent pregnancy loss. , 2015, Reproduction.

[31]  M. Gazouli,et al.  miRNA-26b Overexpression in Ulcerative Colitis-associated Carcinogenesis , 2015, Inflammatory bowel diseases.

[32]  I. Katakis,et al.  DNA biosensor based on hybridization refractory mutation system approach for single mismatch detection. , 2015, Analytical biochemistry.

[33]  Z. Meng,et al.  Serum miR-128-2 Serves as a Prognostic Marker for Patients with Hepatocellular Carcinoma , 2015, PloS one.

[34]  Zhijuan Cao,et al.  Hybridization chain reaction modulated DNA-hosted silver nanoclusters for fluorescent identification of single nucleotide polymorphisms in the let-7 miRNA family. , 2014, Biosensors & bioelectronics.

[35]  Longhua Tang,et al.  Toehold-initiated rolling circle amplification for visualizing individual microRNAs in situ in single cells. , 2014, Angewandte Chemie.

[36]  Weiming Fu,et al.  miR-128 and its target genes in tumorigenesis and metastasis. , 2013, Experimental cell research.

[37]  P. Muti,et al.  MicroRNA-128-2 targets the transcriptional repressor E2F5 enhancing mutant p53 gain of function , 2011, Cell Death and Differentiation.

[38]  A. Heisterkamp,et al.  Mechanisms of high-order photobleaching and its relationship to intracellular ablation. , 2011 .

[39]  A. Heisterkamp,et al.  Mechanisms of high-order photobleaching and its relationship to intracellular ablation , 2011, Biomedical optics express.

[40]  C. Harris,et al.  Genetic variation in microRNA networks: the implications for cancer research , 2010, Nature Reviews Cancer.

[41]  Huanming Yang,et al.  Human Y Chromosome Base-Substitution Mutation Rate Measured by Direct Sequencing in a Deep-Rooting Pedigree , 2009, Current Biology.

[42]  Niall J. Haslam,et al.  Thermal equivalence of DNA duplexes for probe design , 2009, Journal of physics. Condensed matter : an Institute of Physics journal.

[43]  K. Livak,et al.  Real-time quantification of microRNAs by stem–loop RT–PCR , 2005, Nucleic acids research.

[44]  Mogens Havsteen Jakobsen,et al.  LNA-enhanced detection of single nucleotide polymorphisms in the apolipoprotein E. , 2002, Nucleic acids research.

[45]  M. Nachman,et al.  Estimate of the mutation rate per nucleotide in humans. , 2000, Genetics.

[46]  N. Sugimoto,et al.  Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes. , 1995, Biochemistry.

[47]  Y. Hu,et al.  The polymorphism of rs6505162 in the MIR423 coding region and recurrent pregnancy loss. , 2015, Reproduction.

[48]  Caifu Chen,et al.  Quantitation of microRNAs by real-time RT-qPCR. , 2011, Methods in molecular biology.

[49]  Niall J. Haslam,et al.  Thermal equivalence of DNA duplexes without calculation of melting temperature , 2006 .