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MicroRNA in Lung Cancer

  • S Patrick Nana-Sinkam
    Correspondence
    Address for correspondence: S. Patrick Nana-Sinkam, M.D., The Ohio State University Medical Center, Division of Pulmonary, Critical Care and Sleep Medicine, 201 Davis Heart & Lung Research Institute, 473 West 12th Avenue, Columbus, OH 43210. Phone: 614-247-7707. Fax: 614-293-4799
    Affiliations
    The Ohio State University Medical Center, Division of Pulmonary, Critical Care and Sleep Medicine, Columbus, Ohio
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  • Mark W. Geraci
    Affiliations
    University of Colorado at Denver Health Sciences Center, Division of Pulmonary Sciences and Critical Care Medicine, Department of Medicine, Denver, Colorado
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      In the last decade, researchers have identified a novel mode of gene regulation in the form of a family of small RNAs. In 1993, investigators first identified in C. elegans a small RNA, lin-4, which affected developmental timing by forming a duplex with the 3′UTR of another gene, lin-14, thus preventing lin-14 translation.
      • Lee RC
      • Feinbaum RL
      • Ambros V
      The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14.
      The identification of lin-4 represented the first small RNA-regulating target mRNA expression. In 2000, investigators identified another small RNA let-7 that regulated the gene let-4; however, unlike lin-4, let-7 was conserved across among several species.
      • Reinhart BJ
      • Slack FJ
      • Basson M
      • et al.
      The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans.
      Both lin-4 and let-7 seemed critical to normal cell differentiation.
      • Lu J
      • Getz G
      • Miska EA
      • Alvarez-Saavedra E
      • et al.
      MicroRNA expression profiles classify human cancers.
      Since this initial discovery, many small RNAs have been identified as potential regulators of gene expression and have been termed microRNAs (miRNAs, mirs). MiRNAs are a family of small noncoding RNAs (approximately 21–25 nucleotides (nt) long) expressed in many organisms, including animals, plants, and viruses. MiRNAs originate from stem-loop precursors and are candidates for the regulation of both translation and mRNA degradation by base pairing to complementary sites of target mRNA.
      • Yanaihara N
      • Caplen N
      • Bowman E
      • et al.
      Unique microRNA molecular profiles in lung cancer diagnosis and prognosis.
      To date, several hundred miRNAs have been identified in animals, plants and viruses, but the biological function has only been identified in a few miRNAs.
      • Gregory RI
      • Shiekhattar R
      MicroRNA biogenesis and cancer.
      The biological functions and mechanisms by which miRNAs are regulated remain poorly understood. A single miRNA may bind to and regulate several target mRNAs, whereas several miRNAs may bind and regulate the same target mRNA.
      • Yanaihara N
      • Caplen N
      • Bowman E
      • et al.
      Unique microRNA molecular profiles in lung cancer diagnosis and prognosis.
      Data suggest that miRNAs seem to be integral to several biological functions, including gene regulation, apoptosis, hematopoetic development, and maintenance of cell differentiation. MiRNAs have been identified in several human neurodegenerative metabolic diseases and malignancies.
      • Yanaihara N
      • Caplen N
      • Bowman E
      • et al.
      Unique microRNA molecular profiles in lung cancer diagnosis and prognosis.

      MiRNA Processing

      MiRNAs may be located in several genomic locations, such as within introns of protein coding genes or within introns or exons of noncoding RNAs.
      • Du T
      • Zamore PD
      microPrimer: the biogenesis and function of microRNA.
      MiRNAs may exist either separately from other miRNAs, functioning as individual transcription units, or in clusters.
      • Gregory RI
      • Shiekhattar R
      MicroRNA biogenesis and cancer.
      As illustrated in Figure 1, within the nucleus, miRNAs are transcribed as long primary transcripts by RNA polymerase II into primary miRNAs (pri-miRNAs), which range from hundreds to thousands of nucleotides in length.
      • Du T
      • Zamore PD
      microPrimer: the biogenesis and function of microRNA.
      While in the nucleus, Drosha, an RNase III, in conjunction with either DiGeorge syndrome (critical region gene 8 [DGCR8] in humans) or Pasha (double-stranded RNA binding domain dsRBD protein in Drosophila and C. elegans), cleaves both strands of the pri-miRNA to release a 70- to 100-nucleotide stem loop, termed the precursor miRNA (pre-miRNA).
      • Kim VN
      • Nam JW
      Genomics of microRNA.
      Cleavage by Drosha is essential for determining the eventual mature miRNA structure. The pre-miRNA is subsequently exported from the nucleus to the cytoplasm by the Exportin5/RanGTP.
      • Kim VN
      • Nam JW
      Genomics of microRNA.
      Once in the cytoplasm, a second RNase III termed Dicer, in conjunction with a dsRBD, cleaves the pre-miRNA, releasing an approximately 22-nucleotide RNA duplex (mature miRNA and its complement miRNA*).
      • Vatolin S
      • Navaratne K
      • Weil RJ
      A novel method to detect functional microRNA targets.
      Only one strand of the miRNA/miRNA* duplex is released to enter the protein complex of miRNA-containing ribonucleoprotein particles (miRNPs), and the other strand is degraded.
      • Du T
      • Zamore PD
      microPrimer: the biogenesis and function of microRNA.
      MiRNPs guide miRNAs to the target RNA to regulate protein expression by either translational inhibition or mRNA degradation.
      • Vatolin S
      • Navaratne K
      • Weil RJ
      A novel method to detect functional microRNA targets.
      Figure thumbnail gr1
      FIGURE 1MicroRNA processing. Within the nucleus, miRNAs are transcribed as long primary transcripts by RNA polymerase II into primary miRNAs (pri-miRNAs). Drosha, an RNase III, in conjunction with DiGeorge syndrome critical region gene 8 (DGCR8), cleaves both strands of the pri-miRNA to release a 70- to 100-nucleotide stem loop, termed the precursor miRNA (pre-miRNA). The pre-miRNA is exported from the nucleus to the cytoplasm by the Exportin5/RanGTP. Once in the cytoplasm, a second RNase III termed Dicer, in conjunction with a dsRBD, cleaves the pre-MiRNA, releasing an approximately 22-nucleotide RNA duplex (mature miRNA and its complement miRNA*). One strand of the miRNA/miRNA* duplex is released to enter the protein complex of miRNA-containing ribonucleoprotein particles (miRNPs), and the other strand is degraded. MiRNPs guide miRNAs to the target RNA to regulate protein expression by either translational inhibition or mRNA degradation.
      MiRNAs bind to the 3′UTR complementary sequences of target RNA, and the degree of complementary pairing results in mRNA degradation and/or translational repression.
      • Pillai RS
      MicroRNA function: multiple mechanisms for a tiny RNA?.
      Investigators initially identified the first eight bases of miRNA starting from the 5′ end (termed the miRNA seed) as important and sufficient for the miRNA–mRNA interaction.
      • Berezikov E
      • Plasterk RH
      Camels and zebrafish, viruses and cancer: a microRNA update.
      However, investigators suggest that mechanisms for targeting may be much more complicated.
      • Berezikov E
      • Cuppen E
      • Plasterk RH
      Approaches to microRNA discovery.

      MicroRNA in Human Cancers

      Dysregulation of miRNAs may result in alteration in biological functions relevant to certain malignancies. Our current understanding of miRNA function in cancer is minimal.
      • Gregory RI
      • Shiekhattar R
      MicroRNA biogenesis and cancer.
      Epigenetic alterations including DNA methylation and somatic gene alterations are potential candidates for mechanisms of regulation.
      • Yanaihara N
      • Caplen N
      • Bowman E
      • et al.
      Unique microRNA molecular profiles in lung cancer diagnosis and prognosis.
      The observation that many miRNAs are located within genomic regions relevant to carcinomas suggests that miRNAs function as either oncogenes or tumor suppressors.
      • Gregory RI
      • Shiekhattar R
      MicroRNA biogenesis and cancer.
      Researchers first identified a link between miRNA expression and human malignancy with the observation that there was a downregulation or deletion of miRNAs mir-15-a and mir-16-1 in locus 13q14 in patients with B-cell chronic lymphocytic leukemia (CLL).
      • Calin GA
      • Dumitru CD
      • Shimizu M
      • et al.
      Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia.
      More than 50% of cases of CLL can be attributed to a deletion at 13q14.
      • Gregory RI
      • Shiekhattar R
      MicroRNA biogenesis and cancer.
      Since that discovery, researchers have identified abnormal expression of miRNAs in several types of malignancies, including CLL, colorectal neoplasia, Burkettt's lymphoma, large-cell lymphoma, breast cancer, lung cancer, and hepatocellular and thyroid carcinoma.
      • Di Leva G
      • Calin GA
      • Croce CM
      MicroRNAs: fundamental facts and involvement in human diseases.
      • Iorio MV
      • Ferracin M
      • Liu CG
      • et al.
      MicroRNA gene expression deregulation in human breast cancer.
      • Murakami Y
      • Yasuda T
      • Saigo K
      • et al.
      Comprehensive analysis of microRNA expression patterns in hepatocellular carcinoma and non-tumorous tissues.
      Furthermore, initial expression profiling of miRNAs in patient cohorts with different solid tumors suggests distinct miRNA signature patterns based on tumor type.
      • Lu J
      • Getz G
      • Miska EA
      • Alvarez-Saavedra E
      • et al.
      MicroRNA expression profiles classify human cancers.
      Investigators have suggested that miRNAs may be used as biomarkers in the diagnosis, prognosis, and treatment of cancers.

      MiRNA in Lung Cancer

      In 2005, Johnson et al.
      • Johnson SM
      • Grosshans H
      • Shingara J
      • et al.
      RAS is regulated by the let-7 microRNA family.
      first identified a connection between miRNA expression and genes relevant to lung cancer. The investigators observed an inverse relationship between let-7 and RAS protein expression in human cancer cell lines. Furthermore, microarray analysis of human cancerous tissue demonstrated decreased let-7 expression in lung cancer but not in adjacent normal lung tissue, colon cancer, or breast cancer.
      • Eder M
      • Scherr M
      MicroRNA and lung cancer.
      Researchers also identified a correlation between expression of let-7 and postoperative survival after curative resection of lung cancers.
      • Takamizawa J
      • Konishi H
      • Yanagisawa K
      • et al.
      Reduced expression of the let-7 microRNAs in human lung cancers in association with shortened postoperative survival.
      There have been few studies examining miRNA expression profiling in human lung cancer. Recently, Yanaihara et al.
      • Yanaihara N
      • Caplen N
      • Bowman E
      • et al.
      Unique microRNA molecular profiles in lung cancer diagnosis and prognosis.
      used microarray analysis to identify distinct miRNA profiles between lung cancer and noncancerous tissue. In addition, the investigators identified five distinct miRNAs that predicted prognosis among patients with adenocarcinoma.
      MiRNAs are a novel family of small RNAs that are integral to several biological functions and that regulate gene expression in many human diseases, including malignancies. The identification of this new layer of gene regulation and the potential targets may prove important in diagnosis, treatment, and prognosis in lung cancers.
      MiRBase (http://www.sanger.ac.uk/Software/Rfam/mirna) provides up-to-date access to sequences, names of novel miRNA genes, and targets.
      • Griffiths-Jones S
      • Grocock RJ
      • van Dongen S
      • et al.
      miRBase: microRNA sequences, targets and gene nomenclature.
      • Griffiths-Jones S
      The microRNA Registry.

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