Abstract
Rhabdomyosarcoma (RMS) is a malignant soft tissue tumor showing varying degrees of skeletal muscle differentiation. Two major histologic subtypes exist, alveolar and embryonal, each with associated molecular genetic changes. We have used Representational Difference Analysis (RDA) to compare gene expression between the two RMS subtypes and have identified the novel gene NCRMS (non-coding RNA in RMS) that has increased expression in the alveolar subtype relative to the embryonal subtype. Multiple alternatively spliced forms of NCRMS were identified through library screening, RACE, and comparison to human expressed sequence tags (ESTs). Northern blot analysis indicated the transcript size to be 1.25 kb in alveolar RMS. There was no sequence homology to any of the known genes in GenBank, but extensive homology to ESTs from various species. Comparison to human genomic sequences identified at least 11 exons mapping to chromosomal region 12q21. Differential expression of NCRMS was noted between various tumor types. Since NCRMS RNA possesses limited potential for protein coding, yet with conserved sequences between different species, it is likely that NCRMS is a functional non-coding RNA. Known genes in its proximity include myogenic regulators Myf5 and Myf6, growth factor Igf1, and another potential differentially expressed gene (ATP2B1) in RMS isolated by RDA.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 50 print issues and online access
$259.00 per year
only $5.18 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Anderson J, Gordon A, McManus A, Shipley J, Pritchard-Jones K . 1999a Neoplasia 1: 340–348
Anderson J, Gordon A, Pritchard-Jones K, Shipley J . 1999b Genes Chromosomes Cancer 26: 275–285
Barr FG . 1997 Int. J. Biochem. Cell Biol. 29: 1449–1461
Brown CJ, Hendrich BD, Rupert JL, Lafreniere RG, Xing Y, Lawrence J, Willard HF . 1992 Cell 71: 527–542
Chang Y, Cesarman E, Pessin MS, Lee F, Culpepper J, Knowles DM, Moore PS . 1994 Science 266: 1865–1869
Dagher R, Helman L . 1999 Oncologist 4: 34–44
Erdmann VA, Barciszewska MZ, Szymanski M, Hochberg A, de Groot N, Barciszewski J . 2001 Nucleic Acids Res. 29: 189–193
Hubank M, Schatz DG . 1994 Nucleic Acids Res. 22: 5640–5648
Kozak M . 1996 Mamm. Genome 7: 563–574
Li J, Yen C, Liaw D, Podsypanina K, Bose S, Wang SI, Puc J, Miliaresis C, Rodgers L, McCombie R, Bigner SH, Giovanella BC, Ittmann M, Tycko B, Hibshoosh H, Wigler MH, Parsons R . 1997 Science 275: 1943–1947
Lisitsyn N, Lisitsyn N, Wigler M . 1993 Science 259: 946–951
Lisitsyn N, Wigler M . 1995 Methods Enzymol. 254: 291–304
Lucas S, De Smet C, Arden KC, Viars CS, Lethe B, Lurquin C, Boon T . 1998 Cancer Res. 58: 743–752
Merlino G, Helman LJ . 1999 Oncogene 18: 5340–5348
Musaro A, McCullagh KJ, Naya FJ, Olson EN, Rosenthal N . 1999 Nature 400: 581–585
Pandita A, Zielenska M, Thorner P, Bayani J, Godbout R, Greenberg M, Squire JA . 1999 Neoplasia 1: 262–275
Sambrook J, Fritsch EF, Maniatis T . 1989 Molecular cloning: a laboratory manual Cold Spring Harbor Laboratory Press: New York
Srivastava M, Hsieh S, Grinberg A, Williams-Simons L, Huang SP, Pfeifer K . 2000 Genes Dev. 14: 1186–1195
Thorvaldsen JL, Duran KL, Bartolomei MS . 1998 Genes Dev. 12: 3693–3702
Visser M, Sijmons C, Bras J, Arceci RJ, Godfried M, Valentijn LJ, Voute PA, Baas F . 1997 Oncogene 15: 1309–1314
Acknowledgements
We would like to thank Dr Johanna Rommens for providing the fetal brain library, Dr Irene Andulis, Dr Bharati Bapat, Dr Suzanne Kamel-Reid and Nicole Fabricus for providing RNA or tumor tissues.
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Chan, A., Thorner, P., Squire, J. et al. Identification of a novel gene NCRMS on chromosome 12q21 with differential expression between Rhabdomyosarcoma subtypes. Oncogene 21, 3029–3037 (2002). https://doi.org/10.1038/sj.onc.1205460
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1038/sj.onc.1205460
Keywords
This article is cited by
-
Analysis of human ES cell differentiation establishes that the dominant isoforms of the lncRNAs RMST and FIRRE are circular
BMC Genomics (2018)
-
Trans-spliced long non-coding RNA: an emerging regulator of pluripotency
Cellular and Molecular Life Sciences (2018)
-
Long non-coding RNAs and cancer: a new frontier of translational research?
Oncogene (2012)
-
Non-protein coding RNA biomarkers and differential expression in cancers: a review
Journal of Experimental & Clinical Cancer Research (2008)