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基于序列的 miRNA 变体综合注释方法（CASMIR）：结直肠癌肿瘤中 miRNA 变体谱分析的应用。

A Comprehensive Approach to Sequence-oriented IsomiR annotation (CASMIR): demonstration with IsomiR profiling in colorectal neoplasia.

机构信息

Division of Gastroenterology and Hepatology, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.

Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN, USA.

出版信息

BMC Genomics. 2018 May 25;19(1):401. doi: 10.1186/s12864-018-4794-7.

DOI:10.1186/s12864-018-4794-7
PMID:29801434
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5970459/
Abstract

BACKGROUND

MicroRNA (miRNA) profiling is an important step in studying biological associations and identifying marker candidates. miRNA exists in isoforms, called isomiRs, which may exhibit distinct properties. With conventional profiling methods, limitations in assay and analysis platforms may compromise isomiR interrogation.

RESULTS

We introduce a comprehensive approach to sequence-oriented isomiR annotation (CASMIR) to allow unbiased identification of global isomiRs from small RNA sequencing data. In this approach, small RNA reads are maintained as independent sequences instead of being summarized under miRNA names. IsomiR features are identified through step-wise local alignment against canonical forms and precursor sequences. Through customizing the reference database, CASMIR is applicable to isomiR annotation across species. To demonstrate its application, we investigated isomiR profiles in normal and neoplastic human colorectal epithelia. We also ran miRDeep2, a popular miRNA analysis algorithm to validate isomiRs annotated by CASMIR. With CASMIR, specific and biologically relevant isomiR patterns could be identified. We note that specific isomiRs are often more abundant than their canonical forms. We identify isomiRs that are commonly up-regulated in both colorectal cancer and advanced adenoma, and illustrate advantages in targeting isomiRs as potential biomarkers over canonical forms.

CONCLUSIONS

Studying miRNAs at the isomiR level could reveal new insight into miRNA biology and inform assay design for specific isomiRs. CASMIR facilitates comprehensive annotation of isomiR features in small RNA sequencing data for isomiR profiling and differential expression analysis.

摘要

背景

microRNA (miRNA) 谱分析是研究生物关联和鉴定标记候选物的重要步骤。miRNA 存在同工型，称为 isomiRs，它们可能表现出不同的特性。在传统的分析方法中，分析平台在检测和分析方面的局限性可能会影响对 isomiR 的检测。

结果

我们引入了一种全面的基于序列的 isomiR 注释方法 (CASMIR)，允许从小 RNA 测序数据中无偏地识别全局 isomiRs。在这种方法中，小 RNA 读段被作为独立的序列保留，而不是在 miRNA 名称下进行汇总。通过逐步与规范形式和前体序列进行局部比对来识别 isomiR 特征。通过定制参考数据库，CASMIR 可适用于跨物种的 isomiR 注释。为了展示其应用，我们研究了正常和肿瘤性人结直肠上皮中的 isomiR 谱。我们还运行了 miRDeep2，这是一种流行的 miRNA 分析算法，用于验证 CASMIR 注释的 isomiRs。使用 CASMIR，可以识别特定且具有生物学意义的 isomiR 模式。我们注意到，特定的 isomiRs 通常比它们的规范形式更丰富。我们鉴定了在结直肠癌和高级腺瘤中普遍上调的 isomiRs，并说明了将 isomiRs 作为潜在生物标志物而不是规范形式进行靶向的优势。

结论

在 isomiR 水平上研究 miRNAs 可以揭示 miRNA 生物学的新见解，并为特定 isomiRs 的检测设计提供信息。CASMIR 促进了小 RNA 测序数据中 isomiR 特征的全面注释，用于 isomiR 谱分析和差异表达分析。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/59b2/5970459/dc84628d297d/12864_2018_4794_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/59b2/5970459/b892e7698917/12864_2018_4794_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/59b2/5970459/3fdce332dd30/12864_2018_4794_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/59b2/5970459/c117740fd19d/12864_2018_4794_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/59b2/5970459/deca25f2a64c/12864_2018_4794_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/59b2/5970459/0b9f66fb6843/12864_2018_4794_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/59b2/5970459/dc84628d297d/12864_2018_4794_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/59b2/5970459/b892e7698917/12864_2018_4794_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/59b2/5970459/3fdce332dd30/12864_2018_4794_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/59b2/5970459/c117740fd19d/12864_2018_4794_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/59b2/5970459/deca25f2a64c/12864_2018_4794_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/59b2/5970459/0b9f66fb6843/12864_2018_4794_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/59b2/5970459/dc84628d297d/12864_2018_4794_Fig6_HTML.jpg

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2
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Nucleic Acids Res. 2017 Apr 7;45(6):2973-2985. doi: 10.1093/nar/gkx082.
3
Beyond the one-locus-one-miRNA paradigm: microRNA isoforms enable deeper insights into breast cancer heterogeneity.
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Int J Mol Sci. 2024 Feb 28;25(5):2808. doi: 10.3390/ijms25052808.
4
Interrogating the Role of miR-125b and Its 3'isomiRs in Protection against Hypoxia.探讨 miR-125b 及其 3'异构体在缺氧保护中的作用。
Int J Mol Sci. 2023 Nov 6;24(21):16015. doi: 10.3390/ijms242116015.
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Int J Mol Sci. 2023 Oct 21;24(20):15436. doi: 10.3390/ijms242015436.
6
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7
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5
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9
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