Strategies for profiling microRNA expression

MicroRNAs (miRNAs) are a class of small RNAs ( approximately 22-nt) that play an important role in the control of different cell processes by negative regulation of protein-coding genes. In the last several years, a number of miRNA profiling strategies have been used to document the miRNA expression changes during physiological and pathological processes. Aberrant expression of miRNAs has been linked to developmental defects, cancer, neurological disorders, and heart diseases. Over 540 human miRNAs have been validated to date; however, computer models suggest there may be thousands more. As bench work continue to verify in silico predictions, miRNA profiling will remain a prominent tool for identification of differential expression miRNAs in normal cellular courses and human disorders. This review focuses on current strategies for miRNA expression profiling and discusses their sensitivity and specificity, as well as advantage and disadvantage.     

整合分析基因表达与拷贝数变异识别癌症的驱动基因及调控子miRNAs

目的:通过整合分析基因的表达与拷贝数变异(CNV)识别癌症的驱动基因及调控子mi RNAs。方法:通过整合基因表达与CNV数据,分别计算了乳腺癌、结肠癌、肺癌、肾癌、膀胱癌、头颈癌六种癌症中mi RNAs的调控得分,提出了一个识别驱动基因和显著调控子mi RNAs的方法。结果:本文研究发现,CNV区域上编码的基因相比于非CNV区域上编码的基因更倾向于受mi RNAs调控。但是,癌相关CNV区域上的基因相比正常CNV区域上的基因更少受mi RNAs调控。本研究识别出了EXOSC4、ZNF7、BOP1等原癌基因,以及mi R-488、mi R-27a、mi R-454等在多种癌症中都起调控作用的调控子mi RNAs。结论:本文的方法为癌症研究带来了新的启发,这些具有调控扩增基因过表达作用的mi RNAs的发现,有助于我们更进一步了解癌基因表达的复杂调控机制,进而推动癌症的诊断、治疗和预后。     

Comprehensive gene and microRNA expression profiling reveals the crucial role of hsa-let-7i and its target genes in colorectal cancer metastasis

Accumulating evidence has demonstrated that miRNAs play important roles in the occurrence and development of colorectal cancer (CRC). However, whether miRNAs are associated with the metastasis of CRC remains largely unexplored. The aim of the current study is to profile miRNAs in different CRC metastatic cell lines to identify the biomarkers in CRC metastasis. Gene and miRNA expression profiling was performed to analyze the global expression of mRNAs and miRNAs in the four human CRC cell lines (LoVo, SW480, HT29 and Caco-2) with different potential of metastasis. Expression patterns of mRNAs and miRNAs were altered in different CRC cell lines. By developing an integrated bioinformatics analysis of gene and miRNA expression patterns, hsa-let-7i was identified to show the highest degree in the microRNA-GO-network and microRNA-Gene-network. The expression level of hsa-let-7i was further validated by qRT-PCR in CRC cells. In addition, the targets of hsa-let-7i were predicted by two programs TargetScan and PicTar, and target genes were validated by expression profiling in the most epresentative LoVo and Caco-2 cell lines. Eight genes including TRIM41, SOX13, SLC25A4, SEMA4F, RPUSD2, PLEKHG6, CCND2, and BTBD3 were identified as hsa-let-7i targets. Our data showed the power of comprehensive gene and miRNA expression profiling and the application of bioinformatics tools in the identification of novel biomarkers in CRC metastasis.     

microRNAs as oncogenes and tumor suppressors

microRNAs (miRNAs) are a new class of non-protein-coding, endogenous, small RNAs. They are important regulatory molecules in animals and plants. miRNA regulates gene expression by translational repression, mRNA cleavage, and mRNA decay initiated by miRNA-guided rapid deadenylation. Recent studies show that some miRNAs regulate cell proliferation and apoptosis processes that are important in cancer formation. By using multiple molecular techniques, which include Northern blot analysis, real-time PCR, miRNA microarray, up- or down-expression of specific miRNAs, it was found that several miRNAs were directly involved in human cancers, including lung, breast, brain, liver, colon cancer, and leukemia. In addition, some miRNAs may function as oncogenes or tumor suppressors. More than 50% of miRNA genes are located in cancer-associated genomic regions or in fragile sites, suggesting that miRNAs may play a more important role in the pathogenesis of a limited range of human cancers than previously thought. Overexpressed miRNAs in cancers, such as mir-17-92, may function as oncogenes and promote cancer development by negatively regulating tumor suppressor genes and/or genes that control cell differentiation or apoptosis. Underexpressed miRNAs in cancers, such as let-7, function as tumor suppressor genes and may inhibit cancers by regulating oncogenes and/or genes that control cell differentiation or apoptosis. miRNA expression profiles may become useful biomarkers for cancer diagnostics. In addition, miRNA therapy could be a powerful tool for cancer prevention and therapeutics.     

Distinct types of tumor-initiating cells form human colon cancer tumors and metastases

Human colon cancer harbors a small subfraction of tumor-initiating cells (TICs) that is assumed to be a functionally homogeneous stem-cell-like population driving tumor maintenance and metastasis formation. We found unexpected cellular heterogeneity within the TIC compartment, which contains three types of TICs. Extensively self-renewing long-term TICs (LT-TICs) maintained tumor formation in serial xenotransplants. Tumor transient amplifying cells (T-TACs) with limited or no self-renewal capacity contributed to tumor formation only in primary mice. Rare delayed contributing TICs (DC-TICs) were exclusively active in secondary or tertiary mice. Bone marrow was identified as an important reservoir of LT-TICs. Metastasis formation was almost exclusively driven by self-renewing LT-TICs. Our results demonstrate that tumor initiation, self-renewal, and metastasis formation are limited to particular subpopulations of TICs in primary human colon cancer. We identify LT-TICs as a quantifiable target for therapies aimed toward eradication of self-renewing tumorigenic and metastatic colon cancer cells.     

Cancer microRNAs: from subtype profiling to predictors of response to therapy

MicroRNAs (miRNAs) are key regulators of gene expression that regulate important oncogenes and tumor suppressors. Many miRNAs can also act as oncogenes or tumor suppressors, and thus the altered expression of miRNAs is a hallmark of many cancer types. Dysregulated miRNAs provide a potentially powerful new tool that could be used to enable the characterization of tumor environments and identify novel and important oncogenic pathways. More recently, there has been growing interest in the field of miRNAs as biomarkers of cancer risk, diagnosis and response to therapy. Understanding the associations between miRNA expression and cancer phenotypes, and the potential of miRNA profiling in clinical applications, promises to be highly rewarding in the field of cancer research.     

Oncomirs: the potential role of non-coding microRNAs in understanding cancer

MicroRNAs (miRNAs) are members of a family of non-coding RNAs of 8-24 nucleotide RNA molecules that regulate target mRNAs. The first miRNAs, lin-4 and let-7, were first discovered in the year 1993 by Ambros, Ruvkun, and co-workers while studying development in Caenorhabditis elegans. miRNAs can play vital functions form C. elegans to higher vertebrates by typical Watson-Crick base pairing to specific mRNAs to regulate the expression of a specific gene. It has been well established that multicellular eukaryotes utilize miRNAs to regulate many biological processes such as embryonic development, proliferation, differentiation, and cell death. Recent studies have shown that miRNAs may provide new insight in cancer research. A recent study demonstrated that more than 50% of miRNA genes are located in fragile sites and cancer-associated genomic regions, suggesting that miRNAs may play a more important role in the pathogenesis of human cancers. Exploiting the emerging knowledge of miRNAs for the development of new human therapeutic applications will be important. Recent studies suggest that miRNA expression profiling can be correlated with disease pathogenesis and prognosis, and may ultimately be useful in the management of human cancer. In this review, we focus on how miRNAs regulate tumorigenesis by acting as oncogenes and anti-oncogenes in higher eukaryotes.