Long Noncoding RNAs-Related Diseases, Cancers, and Drugs

Long noncoding RNA (lncRNA) function is described in terms of related gene expressions, diseases, and cancers as well as their polymorphisms. Potential modulators of lncRNA function, including clinical drugs, natural products, and derivatives, are discussed, and bioinformatic resources are summarized. The improving knowledge of the lncRNA regulatory network has implications not only in gene expression, diseases, and cancers, but also in the development of lncRNA-based pharmacology.

[1]  H. Berg.  Cold Spring Harbor Symposia on Quantitative Biology.: Vol. LII. Evolution of Catalytic Functions. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 1987, ISBN 0-87969-054-2, xix + 955 pp., US $150.00. , 1989 .

[2]  B. Cullen,et al.  Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. , 2004, RNA.

[3]  S. Salzberg,et al.  The Transcriptional Landscape of the Mammalian Genome , 2005, Science.

[4]  N. Rajewsky,et al.  Silencing of microRNAs in vivo with ‘antagomirs’ , 2005, Nature.

[5]  N. Tran,et al.  Regulation of apoptosis by a prostate-specific and prostate cancer-associated noncoding gene, PCGEM1. , 2006, DNA and cell biology.

[6]  K. Zatloukal,et al.  Characterization of HULC, a novel gene with striking up-regulation in hepatocellular carcinoma, as noncoding RNA. , 2007, Gastroenterology.

[7]  Tao Liu,et al.  NONCODE v2.0: decoding the non-coding , 2007, Nucleic Acids Res..

[8]  Xu Li,et al.  UCA1, a non‐protein‐coding RNA up‐regulated in bladder carcinoma and embryo, influencing cell growth and promoting invasion , 2008, FEBS letters.

[9]  Qihong Huang,et al.  Small-molecule inhibitors of microrna miR-21 function. , 2008, Angewandte Chemie.

[10]  L. Kiemeney,et al.  Polymorphisms in the H19 gene and the risk of bladder cancer. , 2008, European urology.

[11]  Tim R. Mercer,et al.  NRED: a database of long noncoding RNA expression , 2008, Nucleic Acids Res..

[12]  K. Morris.  Long antisense non-coding RNAs function to direct epigenetic complexes that regulate transcription in human cells , 2009, Epigenetics.

[13]  David I. Smith,et al.  Identification of long stress-induced non-coding transcripts that have altered expression in cancer. , 2010, Genomics.

[14]  Howard Y. Chang,et al.  Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes , 2010, Science.

[15]  Mathew W. Wright,et al.  Naming 'junk': Human non-protein coding RNA (ncRNA) gene nomenclature , 2011, Human Genomics.

[16]  I. Grummt,et al.  Noncoding transcripts in sense and antisense orientation regulate the epigenetic state of ribosomal RNA genes. , 2010, Cold Spring Harbor symposia on quantitative biology.

[17]  K. Morris,et al.  Long antisense non-coding RNAs and their role in transcription and oncogenesis , 2010, Cell cycle.

[18]  J. Mattick,et al.  Long non-coding RNAs in nervous system function and disease , 2010, Brain Research.

[19]  Howard Y. Chang,et al.  Long noncoding RNA HOTAIR reprograms chromatin state to promote cancer metastasis , 2010, Nature.

[20]  Jun Yu,et al.  Oncofetal H19-derived miR-675 regulates tumor suppressor RB in human colorectal cancer. , 2010, Carcinogenesis.

[21]  James B. Hill,et al.  Association of Birth Weight With Polymorphisms in the IGF2, H19, and IGF2R Genes , 2010, Pediatric Research.

[22]  Randeep Rakwal,et al.  MALAT‐1 enhances cell motility of lung adenocarcinoma cells by influencing the expression of motility‐related genes , 2010, FEBS letters.

[23]  Jiayi Wang,et al.  CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer , 2010, Nucleic acids research.

[24]  D. Louis,et al.  Maternally expressed gene 3, an imprinted noncoding RNA gene, is associated with meningioma pathogenesis and progression. , 2010, Cancer research.

[25]  M. Weiss,et al.  A new 'Linc' between noncoding RNAs and blood development. , 2011, Genes & development.

[26]  Shuhan Sun,et al.  Long noncoding RNA high expression in hepatocellular carcinoma facilitates tumor growth through enhancer of zeste homolog 2 in humans , 2011, Hepatology.

[27]  P. Fraser,et al.  No-Nonsense Functions for Long Noncoding RNAs , 2011, Cell.

[28]  Howard Y. Chang,et al.  Long noncoding RNAs and human disease. , 2011, Trends in cell biology.

[29]  J. Mattick,et al.  The melanoma-upregulated long noncoding RNA SPRY4-IT1 modulates apoptosis and invasion. , 2011, Cancer research.

[30]  Brian McCue,et al.  miR-31 and its host gene lncRNA LOC554202 are regulated by promoter hypermethylation in triple-negative breast cancer , 2012, Molecular Cancer.

[31]  Min-hui Yang,et al.  MALAT-1: a long non-coding RNA and its important 3' end functional motif in colorectal cancer metastasis. , 2011, International journal of oncology.

[32]  Carolyn J. Brown,et al.  The functional role of long non-coding RNA in human carcinomas , 2011, Molecular Cancer.

[33]  Jianfeng Xu,et al.  Human polymorphisms at long non-coding RNAs (lncRNAs) and association with prostate cancer risk. , 2011, Carcinogenesis.

[34]  John S. Mattick,et al.  lncRNAdb: a reference database for long noncoding RNAs , 2010, Nucleic Acids Res..

[35]  F. Zhang,et al.  Long non-coding RNA MALAT-1 overexpression predicts tumor recurrence of hepatocellular carcinoma after liver transplantation , 2012, Medical Oncology.

[36]  A. Chinnaiyan,et al.  The emergence of lncRNAs in cancer biology. , 2011, Cancer discovery.

[37]  Changning Liu,et al.  ncFANs: a web server for functional annotation of long non-coding RNAs , 2011, Nucleic Acids Res..

[38]  R. Shiekhattar,et al.  Long non-coding RNAs and enhancers. , 2011, Current opinion in genetics & development.

[39]  C. Kanduri.  Kcnq1ot1: a chromatin regulatory RNA. , 2011, Seminars in cell & developmental biology.

[40]  Howard Y. Chang,et al.  Molecular mechanisms of long noncoding RNAs. , 2011, Molecular cell.

[41]  H. Lodish,et al.  Long noncoding RNA-mediated anti-apoptotic activity in murine erythroid terminal differentiation. , 2011, Genes & development.

[42]  L. Maquat,et al.  lncRNAs transactivate Staufen1-mediated mRNA decay by duplexing with 3'UTRs via Alu elements , 2010, Nature.

[43]  Wan L. Lam,et al.  Mechanistic Roles of Noncoding RNAs in Lung Cancer Biology and Their Clinical Implications , 2012, Genetics research international.

[44]  J. Martínez-Guitarte,et al.  Overexpression of long non-coding RNAs following exposure to xenobiotics in the aquatic midge Chironomus riparius. , 2012, Aquatic toxicology.

[45]  [Role of non-coding RNA ANRIL in the genesis of plexiform neurofibromas in neurofibromatosis type 1]. , 2012, Annales de dermatologie et de venereologie.

[46]  Bruce M. Wentworth,et al.  Targeting nuclear RNA for in vivo correction of myotonic dystrophy , 2012, Nature.

[47]  Li Ma,et al.  Non-Coding RNAs as Regulators of Mammary Development and Breast Cancer , 2012, Journal of Mammary Gland Biology and Neoplasia.

[48]  Ahmad M. Khalil,et al.  Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs , 2012, Nucleic acids research.

[49]  M. Kitagawa,et al.  Long non-coding RNAs involved in cancer development and cell fate determination. , 2012, Current drug targets.

[50]  Huabin Zhu,et al.  Effect of 5-aza-2'-deoxycytidine on methylation of the putative imprinted control region of H19 during the in vitro development of vitrified bovine two-cell embryos. , 2012, Fertility and sterility.

[51]  O. Dereure,et al.  Rôle de l’ARN non codant ANRIL dans les neurofibromes plexiformes de la neurofibromatose de type 1 , 2012 .

[52]  Long noncoding RNA-mediated maintenance of DNA methylation and transcriptional gene silencing , 2012, Journal of Cell Science.

[53]  Z. Ling,et al.  Characterization of a carcinogenesis-associated long non-coding RNA , 2012, RNA biology.

[54]  Valentina Casà,et al.  A novel molecular mechanism in human genetic disease , 2012, RNA biology.

[55]  Q. Zhan,et al.  Long non‐coding RNA gadd7 interacts with TDP‐43 and regulates Cdk6 mRNA decay , 2012, The EMBO journal.

[56]  C. Kang,et al.  LncRNA profile of glioblastoma reveals the potential role of lncRNAs in contributing to glioblastoma pathogenesis. , 2012, International journal of oncology.

[57]  Chen Yang,et al.  Long non-coding RNA UCA1a(CUDR) promotes proliferation and tumorigenesis of bladder cancer. , 2012, International journal of oncology.

[58]  P. Tsai,et al.  Additive effect of ANRIL and BRAP polymorphisms on ankle-brachial index in a Taiwanese population. , 2012, Circulation journal : official journal of the Japanese Circulation Society.

[59]  Chen Yang,et al.  Long non-coding RNA UCA1 regulated cell cycle distribution via CREB through PI3-K dependent pathway in bladder carcinoma cells. , 2012, Gene.

[60]  Feng Yang,et al.  Up‐regulated long non‐coding RNA H19 contributes to proliferation of gastric cancer cells , 2012, The FEBS journal.

[61]  B. Strooper,et al.  Non-coding RNAs with essential roles in neurodegenerative disorders , 2012, The Lancet Neurology.

[62]  M. Mehler,et al.  Emerging roles of non-coding RNAs in brain evolution, development, plasticity and disease , 2012, Nature Reviews Neuroscience.

[63]  Jeannie T. Lee.  Epigenetic Regulation by Long Noncoding RNAs , 2012, Science.

[64]  Rory Johnson.  Long non-coding RNAs in Huntington's disease neurodegeneration , 2012, Neurobiology of Disease.

[65]  Anderson Chun On Tsang,et al.  Long non-coding RNA expression profiles predict clinical phenotypes in glioma , 2012, Neurobiology of Disease.

[66]  Andrea Masotti,et al.  Bioinformatics Tools and Novel Challenges in Long Non-Coding RNAs (lncRNAs) Functional Analysis , 2011, International journal of molecular sciences.

[67]  H. Lodish,et al.  Regulation of mammalian cell differentiation by long non‐coding RNAs , 2012, EMBO reports.

[68]  Weidong Tian,et al.  Molecular Mechanisms and Function Prediction of Long Noncoding RNA , 2012, TheScientificWorldJournal.

[69]  Yiran Huang,et al.  Upregulated MALAT-1 contributes to bladder cancer cell migration by inducing epithelial-to-mesenchymal transition. , 2012, Molecular bioSystems.

[70]  P. Molloy,et al.  CRNDE: A Long Non-Coding RNA Involved in CanceR, Neurobiology, and DEvelopment , 2012, Front. Gene..

[71]  Beatrice Bodega,et al.  A Long ncRNA Links Copy Number Variation to a Polycomb/Trithorax Epigenetic Switch in FSHD Muscular Dystrophy , 2012, Cell.

[72]  L. Harries,et al.  Long non-coding RNAs and human disease. , 2012, Biochemical Society transactions.

[73]  Howard Y. Chang,et al.  Genome regulation by long noncoding RNAs. , 2012, Annual review of biochemistry.

[74]  Hui Xiao,et al.  NONCODE v3.0: integrative annotation of long noncoding RNAs , 2011, Nucleic Acids Res..

[75]  S. C. Lakhotia.  Long non‐coding RNAs coordinate cellular responses to stress , 2012, Wiley interdisciplinary reviews. RNA.

[76]  Vincent Jaquet,et al.  MALAT-1, a non protein-coding RNA is upregulated in the cerebellum, hippocampus and brain stem of human alcoholics. , 2012, Alcohol.

[77]  V. Knopik,et al.  Cigarette Smoke Exposure-Associated Alterations to Non-Coding RNA , 2012, Front. Gene..

[78]  Juan Wen,et al.  A Genetic Variant in Long Non-Coding RNA HULC Contributes to Risk of HBV-Related Hepatocellular Carcinoma in a Chinese Population , 2012, PloS one.

[79]  Xing Chen,et al.  LncRNADisease: a database for long-non-coding RNA-associated diseases , 2012, Nucleic Acids Res..

[80]  Pei Xu,et al.  Downregulated LncRNA-ANCR promotes osteoblast differentiation by targeting EZH2 and regulating Runx2 expression. , 2013, Biochemical and biophysical research communications.

[81]  Martin Reczko,et al.  DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs , 2012, Nucleic Acids Res..

[82]  Wei Wang,et al.  Long non-coding RNA H19 increases bladder cancer metastasis by associating with EZH2 and inhibiting E-cadherin expression. , 2013, Cancer letters.

[83]  G. Wakabayashi,et al.  Clinical significance of the expression of long non-coding RNA HOTAIR in primary hepatocellular carcinoma. , 2013, Oncology reports.

[84]  D. Glavač,et al.  Long Non-Coding RNA in Cancer , 2013, International journal of molecular sciences.

[85]  Albert E. Almada,et al.  Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells , 2013, Proceedings of the National Academy of Sciences.

[86]  Michael Y. Galperin,et al.  The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection , 2011, Nucleic Acids Res..

[87]  S. Meltzer,et al.  Hypomethylation of noncoding DNA regions and overexpression of the long noncoding RNA, AFAP1-AS1, in Barrett's esophagus and esophageal adenocarcinoma. , 2013, Gastroenterology.

[88]  Feng Liu,et al.  Long noncoding RNAs associated with liver regeneration 1 accelerates hepatocyte proliferation during liver regeneration by activating Wnt/β‐Catenin signaling , 2013, Hepatology.

[89]  Deeksha Bhartiya,et al.  Systematic Transcriptome Wide Analysis of lncRNA-miRNA Interactions , 2012, PloS one.

[90]  G. Peng,et al.  Long non-coding RNA ANRIL (CDKN2B-AS) is induced by the ATM-E2F1 signaling pathway. , 2013, Cellular signalling.

[91]  Elias T. Zambidis,et al.  Pivots of pluripotency: the roles of non-coding RNA in regulating embryonic and induced pluripotent stem cells. , 2013, Biochimica et biophysica acta.

[92]  Bilian Jin,et al.  DNA methylation as a target of epigenetic therapeutics in cancer. , 2013, Anti-cancer agents in medicinal chemistry.

[93]  Lennart Martens,et al.  LNCipedia: a database for annotated human lncRNA transcript sequences and structures , 2012, Nucleic Acids Res..

[94]  C. Gong,et al.  Long non‐coding RNA HOTAIR is an independent prognostic marker for nasopharyngeal carcinoma progression and survival , 2013, Cancer science.

[95]  Xiao-tong Hu,et al.  Chinese a Nti鄄 Cancer a Ssociation , 2022 .

[96]  Keith D Robertson,et al.  DNA methyltransferases, DNA damage repair, and cancer. , 2013, Advances in experimental medicine and biology.

[97]  Hui Zhou,et al.  ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP-Seq data , 2012, Nucleic Acids Res..

[98]  C. Yin,et al.  Association between lncrna PCGEM1 polymorphisms and prostate cancer risk , 2013, Prostate Cancer and Prostatic Diseases.

[99]  Guohua Wang,et al.  Potential roles of microRNAs in regulating long intergenic noncoding RNAs , 2013, BMC Medical Genomics.

[100]  K. Sun,et al.  iSeeRNA: identification of long intergenic non-coding RNA transcripts from transcriptome sequencing data , 2013, BMC Genomics.

[101]  Ahmed Sadeque,et al.  Association of ANRIL polymorphism (rs1333049:C>G) with myocardial infarction and its pharmacogenomic role in hypercholesterolemia. , 2013, Gene.

[102]  Yiran Huang,et al.  Downregulated MEG3 activates autophagy and increases cell proliferation in bladder cancer. , 2013, Molecular bioSystems.