CoChat
Sign Up
Cited by 47

miRNA arm switching identifies novel tumour biomarkers

Chen, Liang, Sun, Huiyan, Wang, Changliang, Yang, Yang, Zhang, Menglei, Wong, Garry·2018·eBioMedicine
DOI 10.1016/j.ebiom.2018.11.003PMC PMC6306400
Open this paper in CoChat — free account

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.ebiom.2018.11.003

Cites

3 of 3 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Arm switching was previously thought to be strictly pathogenic in mammals.

    “a process previously thought to be strictly pathogenic in mammals (43, 45, 67).”

    From A mouse tissue atlas of small noncoding RNA (2020) · cites this paper as [43]

  • The phenomena of miRNA arm switching, so far only observed in cancer, extends to healthy mammalian tissues.

    “This highlights the complexity of tissue-dependent miRNA biogenesis and indicates that the phenomena of miRNA arm switching, so far only observed in cancer, extends to healthy mammalian tissues (43–45).”

    From A mouse tissue atlas of small noncoding RNA (2020) · cites this paper as [43]

  • Numerous miRNAs undergo arm switching in cancers.

    “numerous miRNAs undergo arm switching in cancers (Chen et al., 2018).”

    From microRNA strand selection: Unwinding the rules (2021) · cites this paper as Chen et al., 2018

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 57

  1. [1]Zhao Y. Srivastava D. A developmental view of microRNA function Trends Biochem Sci 32 4 2007 189 197 17350266
  2. [2]Bartel D.P. Metazoan MicroRNAs Cell 173 1 2018 20 51 29570994 PMC6091663
  3. [3]Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function Cell 116 2 2004 281 297 14744438
  4. [4]Ha M. Kim V.N. Regulation of microRNA biogenesis Nat Rev Mol Cell Biol 15 8 2014 509 524 25027649
  5. [5]Pillai R.S. MicroRNA function: multiple mechanisms for a tiny RNA? RNA (New York, NY) 11 12 2005 1753 1761 PMC1370863 16314451
  6. [6]Krol J. Loedige I. Filipowicz W. The widespread regulation of microRNA biogenesis, function and decay Nat Rev Genet 11 9 2010 597 610 20661255
  7. [7]Okamura K. Liu N. Lai E.C. Distinct mechanisms for microRNA strand selection by Drosophila Argonautes Mol Cell 36 3 2009 431 444 19917251 PMC2785079
  8. [8]Khvorova A. Reynolds A. Jayasena S.D. Functional siRNAs and miRNAs exhibit strand bias Cell 115 2 2003 209 216 14567918
  9. [9]Noland C.L. Doudna J.A. Multiple sensors ensure guide strand selection in human RNAi pathways RNA (New York, NY) 19 5 2013 639 648 PMC3677279 23531496
  10. [10]Hu H.Y. Yan Z. Xu Y. Sequence features associated with microRNA strand selection in humans and flies BMC Genomics 10 2009 413 19732433 PMC2751786
  11. [11]Ghildiyal M. Xu J. Seitz H. Weng Z. Zamore P.D. Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway RNA (New York, NY) 16 1 2010 43 56 PMC2802036 19917635
  12. [13]Ruby J.G. Stark A. Johnston W.K. Kellis M. Bartel D.P. Lai E.C. Evolution, biogenesis, expression, and target predictions of a substantially expanded set of Drosophila microRNAs Genome Res 17 12 2007 1850 1864 17989254 PMC2099593
  13. [14]Okamura K. Phillips M.D. Tyler D.M. Duan H. Chou Y.T. Lai E.C. The regulatory activity of microRNA* species has substantial influence on microRNA and 3' UTR evolution Nat Struct Mol Biol 15 4 2008 354 363 18376413 PMC2698667
  14. [15]Guo L. Lu Z. The fate of miRNA* strand through evolutionary analysis: implication for degradation as merely carrier strand or potential regulatory molecule? PLoS One 5 6 2010 e11387 PMC2894941 20613982
  15. [16]Liu N. Okamura K. Tyler D.M. Phillips M.D. Chung W.J. Lai E.C. The evolution and functional diversification of animal microRNA genes Cell Res 18 10 2008 985 996 18711447 PMC2712117
  16. [17]Chiang H.R. Schoenfeld L.W. Ruby J.G. Mammalian microRNAs: experimental evaluation of novel and previously annotated genes Genes Dev 24 10 2010 992 1009 20413612 PMC2867214
  17. [18]Ro S. Park C. Young D. Sanders K.M. Yan W. Tissue-dependent paired expression of miRNAs Nucleic Acids Res 35 17 2007 5944 5953 17726050 PMC2034466
  18. [19]Griffiths-Jones S. Hui J.H. Marco A. Ronshaugen M. MicroRNA evolution by arm switching EMBO Rep 12 2 2011 172 177 21212805 PMC3049427
  19. [20]Dudoit S. Fridlyand J. A prediction-based resampling method for estimating the number of clusters in a dataset Genome Biol 3 7 2002 RESEARCH0036 PMC126241 12184810
  20. [21]Schwarz D.S. Hutvagner G. Du T. Xu Z. Aronin N. Zamore P.D. Asymmetry in the assembly of the RNAi enzyme complex Cell 115 2 2003 199 208 14567917
  21. [22]Wilson R.C. Tambe A. Kidwell M.A. Noland C.L. Schneider C.P. Doudna J.A. Dicer-TRBP complex formation ensures accurate mammalian microRNA biogenesis Mol Cell 57 3 2015 397 407 25557550 PMC4320653
  22. [23]Wu H. Ye C. Ramirez D. Manjunath N. Alternative processing of primary microRNA transcripts by Drosha generates 5′ end variation of mature microRNA PLoS One 4 10 2009 e7566 PMC2762519 19859542
  23. [24]Marco A. Hui J.H. Ronshaugen M. Griffiths-Jones S. Functional shifts in insect microRNA evolution Genome Biol Evol 2 2010 686 696 20817720 PMC2956262
  24. [25]Marco A. Macpherson J.I. Ronshaugen M. Griffiths-Jones S. MicroRNAs from the same precursor have different targeting properties Silence 3 1 2012 8 23016695 PMC3503882
  25. [26]Guo L. Zhang H. Zhao Y. Yang S. Chen F. Selected isomiR expression profiles via arm switching? Gene 533 1 2014 149 155 24120620
  26. [27]de Wit E. Linsen S.E. Cuppen E. Berezikov E. Repertoire and evolution of miRNA genes in four divergent nematode species Genome Res 19 11 2009 2064 2074 19755563 PMC2775598
  27. [28]Berezikov E. Evolution of microRNA diversity and regulation in animals Nat Rev Genet 12 12 2011 846 22094948
  28. [30]Liu R. Chen X. Du Y. Serum microRNA expression profile as a biomarker in the diagnosis and prognosis of pancreatic cancer Clin Chem 58 3 2012 610 618 22194634
  29. [31]Lee E.J. Gusev Y. Jiang J. Expression profiling identifies microRNA signature in pancreatic cancer Int J Cancer 120 5 2007 1046 1054 17149698 PMC2680248
  30. [32]Mitchell P.S. Parkin R.K. Kroh E.M. Circulating microRNAs as stable blood-based markers for cancer detection Proc Natl Acad Sci U S A 105 30 2008 10513 10518 18663219 PMC2492472
  31. [33]Wu X. Zeng R. Wu S. Zhong J. Yang L. Xu J. Comprehensive expression analysis of miRNA in breast cancer at the miRNA and isomiR levels Gene 557 2 2015 195 200 25523096
  32. [34]Zhang H. Yang S. Guo L. Zhao Y. Shao F. Chen F. Comparisons of isomiR patterns and classification performance using the rank-based MANOVA and 10-fold cross-validation Gene 569 1 2015 21 26 25447923
  33. [35]Mitra R. Lin C.C. Eischen C.M. Bandyopadhyay S. Zhao Z. Concordant dysregulation of miR-5p and miR-3p arms of the same precursor microRNA may be a mechanism in inducing cell proliferation and tumorigenesis: a lung cancer study RNA (New York, NY) 21 6 2015 1055 1065 PMC4436660 25852169
  34. [36]Tsai K.W. Leung C.M. Lo Y.H. Arm selection preference of MicroRNA-193a varies in breast cancer Sci Rep 6 2016 28176 27307030 PMC4910092
  35. [37]Li S.C. Liao Y.L. Ho M.R. Tsai K.W. Lai C.H. Lin W.C. miRNA arm selection and isomiR distribution in gastric cancer BMC Genomics 13 Suppl 1 2012 S13 PMC3303722 22369582
  36. [38]Choo K.B. Soon Y.L. Nguyen P.N. Hiew M.S. Huang C.J. MicroRNA-5p and -3p co-expression and cross-targeting in colon cancer cells J Biomed Sci 21 2014 95 25287248 PMC4195866
  37. [40]Lin M.H. Chen Y.Z. Lee M.Y. Comprehensive identification of microRNA arm selection preference in lung cancer: miR-324-5p and -3p serve oncogenic functions in lung cancer Oncol Lett 15 6 2018 9818 9826 29844840 PMC5958786
  38. [41]Chung I.F. Chang S.J. Chen C.Y. YM500v3: a database for small RNA sequencing in human cancer research Nucleic Acids Res 45 D1 2017 D925-D31 PMC5210564 27899625
  39. [42]Kozomara A. Griffiths-Jones S. miRBase: annotating high confidence microRNAs using deep sequencing data Nucleic Acids Res 42 Database issue 2014 D68 D73 24275495 PMC3965103
  40. [43]Chou C.H. Shrestha S. Yang C.D. miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions Nucleic Acids Res 46 D1 2018 D296 D302 29126174 PMC5753222
  41. [44]Karagkouni D. Paraskevopoulou M.D. Chatzopoulos S. DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA-gene interactions Nucleic Acids Res 46 D1 2018 D239-D45 PMC5753203 29156006
  42. [45]Hu W. Wang T. Yue E. Zheng S. Xu J.H. Flexible microRNA arm selection in rice Biochem Biophys Res Commun 447 3 2014 526 530 24746469
  43. [46]Yu G. Wang L.G. Han Y. He Q.Y. clusterProfiler: an R package for comparing biological themes among gene clusters Omics 16 5 2012 284 287 22455463 PMC3339379
  44. [47]Yu G. Li F. Qin Y. Bo X. Wu Y. Wang S. GOSemSim: an R package for measuring semantic similarity among GO terms and gene products Bioinformatics 26 7 2010 976 978 20179076
  45. [48]Wang J.Z. Du Z. Payattakool R. Yu P.S. Chen C.F. A new method to measure the semantic similarity of GO terms Bioinformatics 23 10 2007 1274 1281 17344234
  46. [49]Therneau T.M. Grambsch P.M. Modeling survival data: extending the Cox model 2013 Springer Science & Business Media
  47. [50]Lu J. Getz G. Miska E.A. MicroRNA expression profiles classify human cancers Nature 435 7043 2005 834 838 15944708
  48. [51]Andorfer C.A. Necela B.M. Thompson E.A. Perez E.A. MicroRNA signatures: clinical biomarkers for the diagnosis and treatment of breast cancer Trends Mol Med 17 6 2011 313 319 21376668
  49. [53]Jiang H. Zhang G. Wu J.H. Jiang C.P. Diverse roles of miR-29 in cancer (review) Oncol Rep 31 4 2014 1509 1516 24573597
  50. [54]Pundhir S. Gorodkin J. Differential and coherent processing patterns from small RNAs Sci Rep 5 2015 12062 26166713 PMC4499813
  51. [55]Yang X. Du W.W. Li H. Both mature miR-17-5p and passenger strand miR-17-3p target TIMP3 and induce prostate tumor growth and invasion Nucleic Acids Res 41 21 2013 9688 9704 23990326 PMC3834805
  52. [56]Shan S.W. Fang L. Shatseva T. Mature miR-17-5p and passenger miR-17-3p induce hepatocellular carcinoma by targeting PTEN, GalNT7 and vimentin in different signal pathways J Cell Sci 126 Pt 6 2013 1517 1530 23418359
  53. [57]Okato A. Arai T. Kojima S. Dual strands of pre-miR150 (miR1505p and miR1503p) act as antitumor miRNAs targeting SPOCK1 in naive and castration-resistant prostate cancer Int J Oncol 51 1 2017 245 256 28534948
  54. [58]Mataki H. Seki N. Mizuno K. Dual-strand tumor-suppressor microRNA-145 (miR-145-5p and miR-145-3p) coordinately targeted MTDH in lung squamous cell carcinoma Oncotarget 7 44 2016 72084 72098 27765924 PMC5342147
  55. [59]Yang B. Tan Z. Song Y. Study on the molecular regulatory mechanism of MicroRNA-195 in the invasion and metastasis of colorectal carcinoma Int J Clin Exp Med 8 3 2015 3793 3800 26064276 PMC4443110
  56. [60]Zheng C. Li J. Wang Q. MicroRNA-195 functions as a tumor suppressor by inhibiting CBX4 in hepatocellular carcinoma Oncol Rep 33 3 2015 1115 1122 25607636
  57. [61]Xu H. Hu Y.W. Zhao J.Y. MicroRNA-195-5p acts as an anti-oncogene by targeting PHF19 in hepatocellular carcinoma Oncol Rep 34 1 2015 175 182 25955388

Cited by

Sorted by citations

Authors
Chen, L., Sun, H., Wang, C., Yang, Y., Zhang, M., & Wong, G.
ORCID
Venue
eBioMedicine
Publisher
Elsevier BV
Published
2018-12
Volume
38
Pages
37-46
ISSN
2352-3964
DOI
10.1016/j.ebiom.2018.11.003
PMC
PMC6306400
Cited by
47
References
3
Language
en
Licence
Funders
  • National Natural Science Foundation of China (61472158, 61572227)
  • University of Macau (MYRG2016-00101-FHS)

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review