Lessons from microRNA Sequencing Using Illumina Technology

Baroin-Tourancheau, Anne; Benigni, Xavier; Doubi-Kadmiri, Soraya; Taouis, Mohammed; Amar, Laurence

doi:10.4236/abb.2016.77030

Cited by 7 publications

(7 citation statements)

References 28 publications

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“…Briefly, libraries were built using Illumina TruSeq™ multiplexing method [ 44 ]. Small RNAs of 16–36 bp were separated from total RNA by denaturating (8M urea) polyacrylamide (15%) gel electrophoresis.…”

Section: Methodsmentioning

confidence: 99%

Extensive screening of microRNA populations identifies hsa-miR-375 and hsa-miR-133a-3p as selective markers for human rectal and colon cancer

et al. 2018

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MicroRNAs (miRNAs) are ∼22-nt molecules exerting control of protein expression in cancer tissues. The current study determined the full spectrum of miRNA dysregulation in freshly isolated human colon or rectal cancer biopsies as well as in controls of healthy adjacent tissue (total of n = 100) using an Illumina sequencing technology. In this work, we aimed to identify miRNAs that may serve as future marker to discern between these two subtypes. DESeq2 analysis revealed 53 significantly dysregulated miRNAs in colon cancer, 67 miRNAs in rectal cancer, and 97 miRNAs in both at a Padj value < 0.05 and ≥ 10 read counts. 65% of miRNAs were upregulated in colon as well as rectal cancer. Highest significant dysregulation (Padj < 0.00001) was detected for hsa-miR-21-5p, -215-5p and -378a in both colon and rectal cancer. Among the group of miRNAs with Padj < 0.05 and more than 2-fold expression differences, hsa-miR-375 was detected in rectal cancer only, and hsa-miR-133a-3p only in colon cancer. Receiver operating characteristic (ROC) analysis confirmed highly distinct sensitivities for hsa-miR-375 to detect rectal cancer (area under the curve (AUC): 0.9), while hsa-miR-133a-3p (AUC: 0.89) had the highest sensitivity for detecting colon cancer. We conclude that hsa-miR-375 and hsa-miR-133a-3p may serve as new markers of rectal or colon cancer and should be further investigated to search for different etiologies of colorectal cancer.

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Section: Methodsmentioning

confidence: 99%

Extensive screening of microRNA populations identifies hsa-miR-375 and hsa-miR-133a-3p as selective markers for human rectal and colon cancer

et al. 2018

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“…We used a set of 3′-PCR-primers with whole complementarity to the 3′-adaptor but a bulge of two nucleotides at position 22 that were showed not to introduce any bias in control cDNA libraries built from RNAs of one ARC. cDNA libraries built from biological replicates were barcoded with the same 3′-PCR-primer and sequenced in different lanes of an Illumina's genome analyzer GAIIX (Baroin-Tourancheau et al, 2016 ).…”

Section: Methodsmentioning

confidence: 99%

miRNA Long-Term Response to Early Metabolic Environmental Challenge in Hypothalamic Arcuate Nucleus

Benoît¹,

Doubi-Kadmiri²,

Benigni³

et al. 2018

Front. Mol. Neurosci.

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Epidemiological reports and studies using rodent models indicate that early exposure to nutrient and/or hormonal challenges can reprogram metabolism at adulthood. Hypothalamic arcuate nucleus (ARC) integrates peripheral and central signals to adequately regulate energy homeostasis. microRNAs (miRNAs) participate in the control of gene expression of large regulatory networks including many signaling pathways involved in epigenetics regulations. Here, we have characterized and compared the miRNA population of ARC of adult male rats continuously exposed to a balanced metabolic environment to the one of adult male rats exposed to an unbalanced high-fat/high-carbohydrate/moderate-protein metabolic environment during the perinatal period and/or at adulthood that consequently displayed hyperinsulinemia and/or hyperleptinemia. We identified more than 400 miRNA species in ARC of adult male rats. By comparing the miRNA content of six biological replicates in each of the four perinatal/adult environments/rat groups, we identified the 10 miRNAs specified by clusters miR-96/182/183, miR-141/200c, and miR-200a/200b/429 as miRNAs of systematic and uncommonly high variation of expression. This uncommon variation of expression may underlie high individual differences in aging disease susceptibilities. By comparing the miRNA content of the adult ARC between the rat groups, we showed that the miRNA population was not affected by the unbalanced adult environment while, in contrast, the expression of 11 miRNAs was repeatedly impacted by the perinatal unbalanced environment. Our data revealed a miRNA response of adult ARC to early metabolic environmental challenge.

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“…The rapid adoption of HTS for miRNA profiling has been driven by significant increases in sample throughput, a wide range of laboratory methods for different applications, and a thriving ecosystem of open-source software for data analysis and interpretation ( 9 , 125 , 126 ). However, it is important to note that technical biases inherent to different sequencing technologies (e.g., Illumina ® , ABI SOLiD ® , and Ion Torrent™) may generate reads that are not bona fide miRNAs ( 5 , 127 , 128 ).…”

Section: Challenges For Accurate Detection Of Circulating Mirnas In Bmentioning

confidence: 99%

Circulating microRNAs as Potential Biomarkers of Infectious Disease

et al. 2017

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microRNAs (miRNAs) are a class of small non-coding endogenous RNA molecules that regulate a wide range of biological processes by post-transcriptionally regulating gene expression. Thousands of these molecules have been discovered to date, and multiple miRNAs have been shown to coordinately fine-tune cellular processes key to organismal development, homeostasis, neurobiology, immunobiology, and control of infection. The fundamental regulatory role of miRNAs in a variety of biological processes suggests that differential expression of these transcripts may be exploited as a novel source of molecular biomarkers for many different disease pathologies or abnormalities. This has been emphasized by the recent discovery of remarkably stable miRNAs in mammalian biofluids, which may originate from intracellular processes elsewhere in the body. The potential of circulating miRNAs as biomarkers of disease has mainly been demonstrated for various types of cancer. More recently, however, attention has focused on the use of circulating miRNAs as diagnostic/prognostic biomarkers of infectious disease; for example, human tuberculosis caused by infection with Mycobacterium tuberculosis, sepsis caused by multiple infectious agents, and viral hepatitis. Here, we review these developments and discuss prospects and challenges for translating circulating miRNA into novel diagnostics for infectious disease.

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Lessons from microRNA Sequencing Using Illumina Technology

Cited by 7 publications

References 28 publications

Extensive screening of microRNA populations identifies hsa-miR-375 and hsa-miR-133a-3p as selective markers for human rectal and colon cancer

Extensive screening of microRNA populations identifies hsa-miR-375 and hsa-miR-133a-3p as selective markers for human rectal and colon cancer

miRNA Long-Term Response to Early Metabolic Environmental Challenge in Hypothalamic Arcuate Nucleus

Circulating microRNAs as Potential Biomarkers of Infectious Disease

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