Analysis of microRNA signatures using size-coded ligation-mediated PCR

Arefian, Ehsan; Kiani, Jafar; Soleimani, Masoud; Shariati, S. Ali M.; Aghaee‐Bakhtiari, Seyed Hamid; Atashi, Amir; Gheisari, Yousof; Ahmadbeigi, Naser; Banaei-Moghaddam, Ali Mohammad; Naderi, Mahmood; Namvarasl, Nabiolah; Good, Liam; Faridani, Omid R.

doi:10.1093/nar/gkr214

Cited by 41 publications

(34 citation statements)

References 26 publications

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“…244 Size-coded DNA barcodes detected multiple miRNAs down to 1 pM, simultaneously. 245 4.1.2 Protein. Nano-barcodes with different antibodies or aptamers conjugated on their surfaces can capture multiple protein targets.…”

Section: Multiplex Bio-detectionmentioning

confidence: 99%

Versatile design and synthesis of nano-barcodes

et al. 2017

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Encoded nano-structures/particles have been used for barcoding and are in great demand for the simultaneous analysis of multiple targets. Due to their nanoscale dimension(s), nano-barcodes have been implemented favourably for bioimaging, in addition to their security and multiplex bioassay application. In designing nano-barcodes for a specific application, encoding techniques, synthesis strategies, and decoding techniques need to be considered. The encoding techniques to generate unique multiple codes for nano-barcodes are based on certain encoding elements including optical (fluorescent and non-fluorescent), graphical, magnetic, and phase change properties of nanoparticles or their different shapes and sizes. These encoding elements can generally be embedded inside, decorated on the surface of nanostructures or self-assembled to prepare the nano-barcodes. The decoding techniques for each encoding technique are different and need to be suitable for the desired applications. This review will provide a thorough discussion on designing nano-barcodes, focusing on the encoding techniques, synthesis methods, and decoding for applications including bio-detection, imaging, and anti-counterfeiting. Additionally, associated challenges in the field and potential solutions will also be discussed. We believe that a comprehensive understanding on this topic could significantly contribute towards the advancement of nano-barcodes for a broad spectrum of applications.

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Section: Multiplex Bio-detectionmentioning

confidence: 99%

Versatile design and synthesis of nano-barcodes

et al. 2017

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“…In addition, Let7 family members have recently been shown to regulate cancer progression and self-renewal in stem cells (8,40,41). To further explore whether Lin28 could precisely regulate the endogenous expression of Let7 family in OSCC, the size-coded ligation-mediated PCR (SL-PCR), a method for detecting multiple miRNAs simultaneously in total RNA (42), was used in CD44 …”

Section: Arid3b P a R E N T A L S P G -C T R L S P G -L E T 7 P A R Ementioning

confidence: 99%

Lin28B/Let-7 Regulates Expression of Oct4 and Sox2 and Reprograms Oral Squamous Cell Carcinoma Cells to a Stem-like State

Chien¹,

et al. 2015

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Lin28, a key factor for cellular reprogramming and generation of induced pluripotent stem cell (iPSC), makes a critical contribution to tumorigenicity by suppressing Let-7. However, it is unclear whether Lin28 is involved in regulating cancer stem-like cells (CSC), including in oral squamous carcinoma cells (OSCC). In this study, we demonstrate a correlation between high levels of Lin28B, Oct4, and Sox2, and a high percentage of CD44 OSCC cells was sufficient to enhanceOct4/Sox2 expression and CSC properties, whereas Let7 cooverexpression effectively reversed these phenomena. We identified ARID3B and HMGA2 as downstream effectors of Lin28B/ Let7 signaling in regulating endogenous Oct4 and Sox2 expression. Let7 targeted the 3 0 untranslated region of ARID3B and HMGA2 and suppressed their expression, whereas ARID3B and HMGA2 increased the transcription of Oct4 and Sox2, respectively, through promoter binding. Chromatin immunoprecipitation assays revealed a direct association between ARID3B and a specific ARID3B-binding sequence in the Oct4 promoter. Notably, by modulating Oct4/Sox2 expression, the Lin28B-Let7 pathway not only regulated stemness properties in OSCC but also determined the efficiency by which normal human oral keratinocytes could be reprogrammed to iPSC. Clinically, a Lin28B high -Let7 low expression pattern was highly correlated with high levels of ARID3B, HMGA2, OCT4, and SOX2 expression in OSCC specimens. Taken together, our results show how Lin28B/ Let7 regulates key cancer stem-like properties in oral squamous cancers. Cancer Res; 75(12); 2553-65. Ó2015 AACR.

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“…Stem-loop RT primers we found to have better specificity and sensitivity than conventional linear RT primers. Secondly, the spatial constraint of the stem-loop structure might prevent the RT primer from binding double-stranded genomic DNA molecules, and enhance the thermal stability of the RNA-DNA heteroduplex [13] . Therefore, we adopt the stem-loop method as the basis for the design of the screening and quantitative method.…”

Section: Discussionmentioning

confidence: 99%

Universal Stem-Loop Primer Method for Screening and Quantification of MicroRNA

et al. 2014

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RT-qPCR is the accepted technique for the quantification of microRNA (miR) expression: however, stem-loop RT-PCR, the most frequently used method for quantification of miRs, is time- and reagent-consuming as well as inconvenient for scanning. We established a new method called ‘universal stem-loop primer’ (USLP) with 8 random nucleotides instead of a specific sequence at the 3′ end of the traditional stem-loop primer (TSLP), for screening miR profile and to semi-quantify expression of miRs. Peripheral blood samples were cultured with phytohaemagglutinin (PHA), and then 87 candidate miRs were scanned in cultured T cells. By USLP, our study revealed that the expression of miR-150-5p (miR-150) decreased nearly 10-fold, and miR-155-5p (miR-155) increased more than 7-fold after treated with PHA. The results of the dissociation curve and gel electrophoresis showed that the PCR production of the USLP and TSLP were specificity. The USLP method has high precision because of its low ICV (ICV<2.5%). The sensitivity of the USLP is up to 103 copies/µl miR. As compared with the TSLP, USLP saved 75% the cost of primers and 60% of the test time. The USLP method is a simple, rapid, precise, sensitive, and cost-effective approach that is suitable for screening miR profiles.

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Analysis of microRNA signatures using size-coded ligation-mediated PCR

Cited by 41 publications

References 26 publications

Versatile design and synthesis of nano-barcodes

Versatile design and synthesis of nano-barcodes

Lin28B/Let-7 Regulates Expression of Oct4 and Sox2 and Reprograms Oral Squamous Cell Carcinoma Cells to a Stem-like State

Universal Stem-Loop Primer Method for Screening and Quantification of MicroRNA

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