Quantification of microRNAs in Cells and Tissues Using Stem-Loop RT PCR and qPCR

Author(s):  
Pooja Panwalkar ◽  
Atul Khire ◽  
Neelam Shirsat
Keyword(s):  
Rt Pcr ◽  
Author(s):  
J. R. Hully ◽  
K. R. Luehrsen ◽  
K. Aoyagi ◽  
C. Shoemaker ◽  
R. Abramson

The development of PCR technology has greatly accelerated medical research at the genetic and molecular levels. Until recently, the inherent sensitivity of this technique has been limited to isolated preparations of nucleic acids which lack or at best have limited morphological information. With the obvious exception of cell lines, traditional PCR or reverse transcription-PCR (RT-PCR) cannot identify the cellular source of the amplified product. In contrast, in situ hybridization (ISH) by definition, defines the anatomical location of a gene and/or it’s product. However, this technique lacks the sensitivity of PCR and cannot routinely detect less than 10 to 20 copies per cell. Consequently, the localization of rare transcripts, latent viral infections, foreign or altered genes cannot be identified by this technique. In situ PCR or in situ RT-PCR is a combination of the two techniques, exploiting the sensitivity of PCR and the anatomical definition provided by ISH. Since it’s initial description considerable advances have been made in the application of in situ PCR, improvements in protocols, and the development of hardware dedicated to in situ PCR using conventional microscope slides. Our understanding of the importance of viral latency or viral burden in regards to HIV, HPV, and KSHV infections has benefited from this technique, enabling detection of single viral copies in cells or tissue otherwise thought to be normal. Clearly, this technique will be useful tool in pathobiology especially carcinogenesis, gene therapy and manipulations, the study of rare gene transcripts, and forensics.


Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 3177-3177
Author(s):  
Zhenyun Yang ◽  
Cara S. Voorhorst ◽  
Leila Ndong ◽  
Fuqin Yin ◽  
Takako Kondo ◽  
...  

Abstract Juvenile myelomonocytic leukemia (JMML) is a myeloproliferative disorder characterized by overproduction of myelomonocytic cells. Activating mutations of PTPN11, which encodes the protein tyrosine phosphatase, Shp2, are found in 35% of JMML patients. Murine bone marrow low density mononuclear cells (LDMNCs) expressing activating Shp2 mutants preferentially undergo myelomonocytic differentiation despite being subjected to conditions that typically support only mast cell development. Evaluation of hematopoietic cell-specific transcription factor expression revealed that GATA2 expression, needed for mast cell differentiation, is dramatically reduced, while, surprisingly, PU.1 expression is unchanged in cells expressing activating Shp2 mutants. In addition to lineage-specific transcription factors such as PU.1, however, c-jun also promotes monocytic differentiation by functioning as a co-activator of PU.1. Thus, we hypothesized that activating Shp2 mutations (Shp2D61Y or Shp2 E76K) induce increased c-jun expression permitting, in collaboration with PU.1, excessive monocytic differentiation and reduced GATA2 expression in hematopoietic progenitors. As a corollary, we hypothesized that ectopic expression of GATA2, but not of GATA2 lacking the C-terminal zinc finger (GATA2del330–407), which is needed for disruption of the PU.1-c-jun interaction, would normalize aberrant myelomonocytic differentiation induced by activating Shp2 mutants. Consistent with our hypothesis, quantitative RT-PCR studies revealed 5-fold higher c-jun levels in cells expressing Shp2D61Y or Shp2E76K compared to cells expressing WT Shp2. We next utilized retroviral co-transduction of murine bone marrow LDMNCs to generate six groups: pMIEG3-Shp2WT plus pCD4 (empty vector); pMIEG3-Shp2WT plus pCD4-GATA2; pMIEG3-Shp2WT plus pCD4-GATA2del330-407; pMIEG3-Shp2E76K plus pCD4; pMIEG3-Shp2E76K plus pCD4-GATA2; and pMIEG3-Shp-2E76K plus pCD4-GATA2del330-407. Transduced cells were stained with anti-human CD4 conjugated to allophycocyanin (APC), sorted for EGFP+APC+ cells, and plated into progenitor assays. Colonies were scored for colony forming unit (CFU)-granulocyte-macrophage (GM), monocyte (M), granulocyte (G), and granulocyte-erythroid-monocyte-megakaryocyte (GEMM). As predicted, cells co-transduced with activating Shp2E76K plus pCD4 produced significantly more CFU-M than cells co-transduced with WT Shp2 plus pCD4. Upon co-transduction with GATA2, the number of CFU-M generated from Shp2E76K-expressing cells was significantly reduced and was similar to that observed in cells expressing WT Shp2. In contrast, co-transduction of GATA2del330-407 failed to normalize the number of CFU-M produced by Shp2E76K-expressing cells. Quantitative RT-PCR verified ectopic GATA2 and GATA2del330-407 expression in the co-transduced cells. These findings demonstrate that restoration of GATA2 expression normalizes the propensity toward monocytic differentiation induced by Shp2E76K. The lack of correction conferred by GATA2del330-407 in combination with the observed increased c-jun expression support a model in which GATA2 and c-jun compete for binding to PU.1 to direct cell differentiation decisions in hematopoietic progenitors bearing activating Shp2 mutants. Collectively, these findings imply that normalization of transcription factor expression may provide a novel approach to differentiation-mediated therapy in JMML.


1998 ◽  
Vol 12 (5) ◽  
pp. 283-291 ◽  
Author(s):  
V Serazin-Leroy ◽  
D Denis-Henriot ◽  
M Morot ◽  
P de Mazancourt ◽  
Y Giudicelli

2009 ◽  
Vol 90 (6) ◽  
pp. 1417-1422 ◽  
Author(s):  
Yongjuan Wang ◽  
Huaichang Sun ◽  
Pengpeng Shen ◽  
Xinyu Zhang ◽  
Xiaoli Xia

RNA interference (RNAi) is a novel antiviral strategy against a variety of virus infections. Infectious bursal disease virus (IBDV) causes an economically important disease in young chickens. This study demonstrated efficient inhibition of IBDV replication by recombinant avian adeno-associated virus (rAAAV)-delivered anti-VP1 and anti-VP2 microRNAs (miRNAs). In the viral vector-transduced cells, sequence-specific miRNA expression was detected by poly(A)-tailed RT-PCR. Reporter assays using a pVP2-EGFP vector showed significant and long-lasting inhibition of VP2–EGFP expression in cells transduced with anti-VP2 miRNA-expressing rAAAV-RFPmiVP2E, but not with the control miRNA-expressing rAAAV-RFPmiVP2con or anti-VP1 miRNA-expressing rAAAV-RFPmiVP1. Semi-quantitative RT-PCR and/or virus titration assays showed a significant inhibitory effect on homologous IBDV replication in cells transduced with rAAAV-RFPmiVP1 or rAAAV-RFPmiVP2E. For two heterologous IBDV isolates, transduction with rAAAV-RFPmiVP1 led to slightly weaker but similar inhibitory effects, whereas transduction with rAAAV-RFPmiVP2E resulted in significantly weaker and different inhibitory effects. These results suggest that rAAAV could act as an efficient vector for miRNA delivery into avian cells and that VP1 is the more suitable target for interfering with IBDV replication using RNAi technology.


2015 ◽  
Vol 2015 ◽  
pp. 1-14 ◽  
Author(s):  
Md. Tariqul Islam ◽  
Ahlan Sabah Ferdous ◽  
Rifat Ara Najnin ◽  
Suprovath Kumar Sarker ◽  
Haseena Khan

MicroRNAs play a pivotal role in regulating a broad range of biological processes, acting by cleaving mRNAs or by translational repression. A group of plant microRNAs are evolutionarily conserved; however, others are expressed in a species-specific manner. Jute is an agroeconomically important fibre crop; nonetheless, no practical information is available for microRNAs in jute to date. In this study, Illumina sequencing revealed a total of 227 known microRNAs and 17 potential novel microRNA candidates in jute, of which 164 belong to 23 conserved families and the remaining 63 belong to 58 nonconserved families. Among a total of 81 identified microRNA families, 116 potential target genes were predicted for 39 families and 11 targets were predicted for 4 among the 17 identified novel microRNAs. For understanding better the functions of microRNAs, target genes were analyzed by Gene Ontology and their pathways illustrated by KEGG pathway analyses. The presence of microRNAs identified in jute was validated by stem-loop RT-PCR followed by end point PCR and qPCR for randomly selected 20 known and novel microRNAs. This study exhaustively identifies microRNAs and their target genes in jute which will ultimately pave the way for understanding their role in this crop and other crops.


2016 ◽  
Vol 90 (15) ◽  
pp. 6906-6917 ◽  
Author(s):  
Pablo Garcia-Miranda ◽  
Jordan T. Becker ◽  
Bayleigh E. Benner ◽  
Alexander Blume ◽  
Nathan M. Sherer ◽  
...  

ABSTRACTHuman immunodeficiency virus (HIV) replication is strongly dependent upon a programmed ribosomal frameshift. Here we investigate the relationships between the thermodynamic stability of the HIV type 1 (HIV-1) RNA frameshift site stem-loop, frameshift efficiency, and infectivity, using pseudotyped HIV-1 and HEK293T cells. The data reveal a strong correlation between frameshift efficiency and local, but not overall, RNA thermodynamic stability. Mutations that modestly increase the local stability of the frameshift site RNA stem-loop structure increase frameshift efficiency 2-fold to 3-fold in cells. Thus, frameshift efficiency is determined by the strength of the thermodynamic barrier encountered by the ribosome. These data agree with previousin vitromeasurements, suggesting that there are no virus- or host-specific factors that modulate frameshifting. The data also indicate that there are no sequence-specific requirements for the frameshift site stem-loop. A linear correlation between Gag-polymerase (Gag-Pol) levels in cells and levels in virions supports the idea of a stochastic virion assembly mechanism. We further demonstrate that the surrounding genomic RNA secondary structure influences frameshift efficiency and that a mutation that commonly arises in response to protease inhibitor therapy creates a functional but inefficient secondary slippery site. Finally, HIV-1 mutants with enhanced frameshift efficiencies are significantly less infectious, suggesting that compounds that increase frameshift efficiency by as little as 2-fold may be effective at suppressing HIV-1 replication.IMPORTANCEHIV, like many retroviruses, utilizes a −1 programmed ribosomal frameshift to generate viral enzymes in the form of a Gag-Pol polyprotein precursor. Thus, frameshifting is essential for viral replication. Here, we utilized a panel of mutant HIV strains to demonstrate that in cells, frameshifting efficiency is correlated with the stability of the local thermodynamic barrier to ribosomal translocation. Increasing the stability of the frameshift site RNA increases the frameshift efficiency 2-fold to 3-fold. Mutant viruses with increased frameshift efficiencies have significantly reduced infectivity. These data suggest that this effect might be exploited in the development of novel antiviral strategies.


2017 ◽  
Author(s):  
Τηλέμαχος Δημητρίου

Οι εντεροϊοί ανήκουν στην οικογένεια Picornaviridae. Το γένωμα τους είναι μονόκλωνο RNA θετικής πολικότητας μήκους περίπου 7.500bp και περιβάλλεται από ένα εικοσαεδρικό πρωτεϊνικό καψίδιο. Οι εντεροϊοί που προσβάλλουν τον άνθρωπο ταξινομούνται σε τέσσερις ομάδες: EV-A, EV-B, EV-C και EV-D. Οι πολιοϊοί, το σημαντικότερο μέλος της ομάδας C, διακρίνονται σε τρεις ορότυπους (PV1, PV2, PV3) και είναι οι αιτιολογικοί παράγοντες της παραλυτικής πολιομυελίτιδας. Από το 1960 χρησιμοποιούνται δύο εμβόλια για την εξάλειψη της ασθένειας, αρχικά το IPV (inactivated polio vaccine) και κατόπιν το πιο αποτελεσματικό OPV (oral polio vaccine). Ωστόσο, το OPV εμφάνισε το μειονέκτημα της εμβολιοσυνδεόμενης παραλυτικής πολιομυελίτιδας (VAPP: Vaccine-associated paralytic poliomyelitis) και της κυκλοφορίας των εμβολιοπροερχόμενων πολιοϊών (VDPVs: Vaccine Derived Polioviruses) μέσω της συσσώρευσης μεταλλάξεων ή και ανασυνδυασμών στο γένωμα των εξασθενημένων εμβολιακών στελεχών Sabin.Στόχος της παρούσας διατριβής ήταν ο σχεδιασμός και η ανάπτυξη μεθόδων με σκοπό τη μελέτη του μηχανισμού παρασκευής in vitro ανασυνδυασμένων στελεχών πολιοϊών και εντεροϊών της ομάδας EV-C. Στο πρώτο μέρος της διατριβής σχεδιάστηκε και αναπτύχθηκε μια Multiplex-PCR για την ανίχνευση και ταυτοποίηση των εντεροϊών. Τα αποτελέσματα της τεχνικής αυτής σε πρότυπα αλλά και κλινικά στελέχη ανέδειξαν την τεχνική αυτή ως ένα χρήσιμο εργαλείο για την γρήγορη και ακριβή ανίχνευση και ταυτοποίηση των εντεροϊών.Στο δεύτερο μέρος της διατριβής, σχεδιάστηκε και αναπτύχθηκε μια τεχνική αλληλούχησης ολόκληρου του γονιδιώματος των εντεροϊών χρησιμοποιώντας μόνο τέσσερις PCR αντιδράσεις. Η δυνατότητα αυτή παρέχεται μέσω της χρήσης ενός ειδικού εκκινητή (DOP), μέσω του οποίου πραγματοποιήθηκε αρχικά μια προενίσχυση ολόκληρου του γονιδιώματος. Στο τρίτο μέρος της διατριβής σχεδιάστηκε και εφαρμόστηκε σε κλινικά δείγματα μια Multiplex-PCR για την ανίχνευση ανασυνδυασμών από τη VP1 έως και τη 3D γενωμική περιοχή εμβολιοσυνδεόμενων πολιοϊών. Τα αποτελέσματα της Multiplex-PCR απέδειξαν την ικανότητα της μεθόδου να ανιχνεύει και να ταυτοποιεί σπάνιους αλλά και κύριους τύπους ανασυνδυασμού με τη χρήση μόνο τεσσάρων Multiplex-PCR αντιδράσεων.Στο τέταρτο μέρος της διατριβής σχεδιάστηκε μια ειδική Stem-Loop RT-PCR μέθοδος για την ανίχνευση της αντιγραφικής ενεργότητας των εντεροϊών μέσω ανίχνευσης του αρνητικής πολικότητας RNA κλώνου. Η μέθοδος αυτή εφαρμόστηκε αρχικά στο πρότυπο στέλεχος Sabin 1, όπου ανιχνεύτηκε η αντιγραφική ενεργότητα του στελέχους σε υψηλό αλλά και χαμηλό ιικό τίτλο, αρκετά νωρίτερα από την εμφάνιση της χαρακτηριστικής εικόνας CPE, των ενεργών εντεροϊών σε κυτταροκαλλιέργεια. Επιπλέον, η μέθοδος αυτή χρησιμοποιήθηκε για την διάκριση μεταξύ αντιγραφικά ενεργών και ανενεργών πρότυπων στελεχών CAV που δεν εμφάνιζαν CPE σε κυτταροκαλλιέργειες. Στο τελευταίο μέρος της παρούσας διατριβής πραγματοποιήθηκε η μελέτη των ανασυνδυασμών που προέκυψαν έπειτα από ταυτόχρονη μόλυνση κυττάρων Rd με πρότυπο στέλεχος Sabin 1 και CAV13. Παράλληλα, με τη χρήση ειδικών προγραμμάτων βιοπληροφορικής σχεδιάστηκαν πιθανά μοντέλα της δευτεροταγούς δομής των RNA μορίων στις θέσεις ανασυνδυασμού. Τα αποτελέσματα της μελέτης αυτής επαλήθευσαν την αυξημένη συχνότητα εμφάνισης ετεροτυπικών ανασυνδυασμών στην 2Α ή 2Β γενωμική περιοχή και εμφάνισαν μια ένδειξη που επιβεβαιώνει τη σύνδεση μεταξύ ανασυνδυασμού και δευτεροταγούς δομής του RNA μορίου.


2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
Lucien Marchand ◽  
Audrey Jalabert ◽  
Emmanuelle Meugnier ◽  
Kathleen Van den Hende ◽  
Nicole Fabien ◽  
...  

Background.The use of miRNAs as biomarkers for Type 1 Diabetes (T1D) risk is attractive as T1D is usually diagnosed in front of acute symptoms. As miR-375 is highly expressed in the endocrine pancreas, we postulated that its circulating level might reflect beta cell alterations and might be altered in the blood of T1D patients recently diagnosed.Methods.Sera were obtained from 22 T1D children at onset of the disease, before subcutaneous insulin treatment, and from 10 nondiabetic pediatric controls. MiR-375 seric level was quantified by stem-loop RT-PCR-based assay. MiRNAs regulations in isolated human islets in response to high glucose concentrations were determined by TaqMan Low-Density Array.Results.The abundance of miR-375, among the 410 miRNAs detected in human islets, mirrored its well-established role in rodent islet biology. Upregulated miRNAs targeted genes involved in islet homeostasis and regulation of beta cell mass. Downregulated miRNAs, including miR-375, were involved in pancreas secretion and protein turnover. Seric level of miR-375 was lower in T1D children versus age-matched controls, without any correlations with HbA1c, glycaemia, and number of autoantibodies.Conclusion.Altered circulating level of miR-375 at onset of T1D might be a general biomarker of metabolic alterations and inflammation associated with the disease.


2005 ◽  
Vol 83 (1) ◽  
pp. 96-107 ◽  
Author(s):  
V Tasevski ◽  
J M Sorbetti ◽  
S S Chiu ◽  
N G Shrive ◽  
D A Hart

Biological mediators can influence the activity and differentiation of bone cells. 1,25-dihydroxy-vitamin D3 (1,25-(OH)2D3) is known to induce differentiation of precursors into mature osteoblasts, and transforming growth factorβ1 (TGF-β1) can modulate the activity of bone cells leading to alterations in proliferation and gene expression patterns. Bone-derived cells were loaded via intermittent cyclic hydrostatic pressure (icHP) on cells under basal conditions and in the presence of 1,25-(OH)2D3 or TGF-β1. Evaluating the effects of loading on the cells allowed for a comparison to be made between responsiveness to biomechanical and biochemical stimuli and their potential interplay. The effects of icHP on mRNA levels for the specific genes involved in bone remodelling and differentiation were measured in MG-63 cells using reverse transcription-polymerase chain reaction (RT-PCR). The mRNA levels for matrix metalloproteinase-1 and -3 (MMP-1 and MMP-3) were significantly, and uniquely, increased (p < 0.001) in cells exposed to icHP under serum-free conditions for 4–12 h. However, mRNA levels for MMP-3, but not MMP-1, were significantly enhanced in cells subjected to static hydrostatic pressure (HP). Treatment of cells with 1,25-(OH)2D3 resulted in increased (p < 0.001) mRNA levels for osteocalcin and decreased (p < 0.001) mRNA levels for both MMP-1 and MMP-3. In cells exposed to icHP and 1,25-(OH)2D3, the mRNA levels for both MMP-1 and MMP-3 were elevated (p < 0.001) compared with hormone alone, but not to the same degree (p < 0.01) as cells subjected to icHP alone. Addition of TGF-β1 to cells led to increases in cell proliferation and expression of collagen I, as well as decreases in expression of osteocalcin and MMP-1 and MMP-3. Exposure of cells to icHP and TGF-β1 again led to unique and significant increases in expression of MMP-1 and MMP-3. No changes in mRNA levels for glyceraldehyde-3-phosphate dehydrogenase (GAPDH) or any of the other 9 genes assessed, including those for MMP-2 and MMP-13, were detected under any of the conditions described. Therefore, icHP can induce alterations in mRNA levels for a specific subset of genes in both premature and mature osteoblasts. Such stimuli can modulate the impact of potent biological mediators in defining patterns of gene expression by bone cells and potentially modify function in vivo.Key words: osteoblast, biomechanical loading,1,25-dihydroxy-vitamin D3 (1,25-(OH)2D3), mRNA levels, reverse trans cription-polymerase chain reaction (RT-PCR), transforming growth factor-β1 (TGF-β1).


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