Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia
10.1038/ng.1032
Crossref journal-article
Springer Science and Business Media LLC
Nature Genetics (297)
Bibliography

Quesada, V., Conde, L., Villamor, N., Ordóñez, G. R., Jares, P., Bassaganyas, L., Ramsay, A. J., Beà, S., Pinyol, M., Martínez-Trillos, A., López-Guerra, M., Colomer, D., Navarro, A., Baumann, T., Aymerich, M., Rozman, M., Delgado, J., Giné, E., Hernández, J. M., … López-Otín, C. (2011). Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia. Nature Genetics, 44(1), 47–52.

Authors 41
  1. Víctor Quesada (first)
  2. Laura Conde (additional)
  3. Neus Villamor (additional)
  4. Gonzalo R Ordóñez (additional)
  5. Pedro Jares (additional)
  6. Laia Bassaganyas (additional)
  7. Andrew J Ramsay (additional)
  8. Sílvia Beà (additional)
  9. Magda Pinyol (additional)
  10. Alejandra Martínez-Trillos (additional)
  11. Mónica López-Guerra (additional)
  12. Dolors Colomer (additional)
  13. Alba Navarro (additional)
  14. Tycho Baumann (additional)
  15. Marta Aymerich (additional)
  16. María Rozman (additional)
  17. Julio Delgado (additional)
  18. Eva Giné (additional)
  19. Jesús M Hernández (additional)
  20. Marcos González-Díaz (additional)
  21. Diana A Puente (additional)
  22. Gloria Velasco (additional)
  23. José M P Freije (additional)
  24. José M C Tubío (additional)
  25. Romina Royo (additional)
  26. Josep L Gelpí (additional)
  27. Modesto Orozco (additional)
  28. David G Pisano (additional)
  29. Jorge Zamora (additional)
  30. Miguel Vázquez (additional)
  31. Alfonso Valencia (additional)
  32. Heinz Himmelbauer (additional)
  33. Mónica Bayés (additional)
  34. Simon Heath (additional)
  35. Marta Gut (additional)
  36. Ivo Gut (additional)
  37. Xavier Estivill (additional)
  38. Armando López-Guillermo (additional)
  39. Xose S Puente (additional)
  40. Elías Campo (additional)
  41. Carlos López-Otín (additional)
References 43 Referenced 848
  1. Rozman, C. & Montserrat, E. Chronic lymphocytic leukemia. N. Engl. J. Med. 333, 1052–1057 (1995). (10.1056/NEJM199510193331606) / N. Engl. J. Med. by C Rozman (1995)
  2. Zenz, T., Mertens, D., Kuppers, R., Dohner, H. & Stilgenbauer, S. From pathogenesis to treatment of chronic lymphocytic leukaemia. Nat. Rev. Cancer 10, 37–50 (2010). (10.1038/nrc2764) / Nat. Rev. Cancer by T Zenz (2010)
  3. Damle, R.N. et al. Ig V gene mutation status and CD38 expression as novel prognostic indicators in chronic lymphocytic leukemia. Blood 94, 1840–1847 (1999). (10.1182/blood.V94.6.1840) / Blood by RN Damle (1999)
  4. Hamblin, T.J., Davis, Z., Gardiner, A., Oscier, D.G. & Stevenson, F.K. Unmutated Ig VH genes are associated with a more aggressive form of chronic lymphocytic leukemia. Blood 94, 1848–1854 (1999). (10.1182/blood.V94.6.1848) / Blood by TJ Hamblin (1999)
  5. Puente, X.S. et al. Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature 475, 101–105 (2011). (10.1038/nature10113) / Nature by XS Puente (2011)
  6. Greenman, C. et al. Patterns of somatic mutation in human cancer genomes. Nature 446, 153–158 (2007). (10.1038/nature05610) / Nature by C Greenman (2007)
  7. Pleasance, E.D. et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463, 191–196 (2010). (10.1038/nature08658) / Nature by ED Pleasance (2010)
  8. Pleasance, E.D. et al. A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature 463, 184–190 (2010). (10.1038/nature08629) / Nature by ED Pleasance (2010)
  9. Greif, P.A. et al. Identification of recurring tumor-specific somatic mutations in acute myeloid leukemia by transcriptome sequencing. Leukemia 25, 821–827 (2011). (10.1038/leu.2011.19) / Leukemia by PA Greif (2011)
  10. Chapman, M.A. et al. Initial genome sequencing and analysis of multiple myeloma. Nature 471, 467–472 (2011). (10.1038/nature09837) / Nature by MA Chapman (2011)
  11. Wahl, M.C., Will, C.L. & Luhrmann, R. The spliceosome: design principles of a dynamic RNP machine. Cell 136, 701–718 (2009). (10.1016/j.cell.2009.02.009) / Cell by MC Wahl (2009)
  12. Wang, H., Nora, G.J., Ghodke, H. & Opresko, P.L. Single molecule studies of physiologically relevant telomeric tails reveal POT1 mechanism for promoting G-quadruplex unfolding. J. Biol. Chem. 286, 7479–7489 (2011). (10.1074/jbc.M110.205641) / J. Biol. Chem. by H Wang (2011)
  13. Marfella, C.G. & Imbalzano, A.N. The Chd family of chromatin remodelers. Mutat. Res. 618, 30–40 (2007). (10.1016/j.mrfmmm.2006.07.012) / Mutat. Res. by CG Marfella (2007)
  14. Prazeres, H. et al. Chromosomal, epigenetic and microRNA-mediated inactivation of LRP1B, a modulator of the extracellular environment of thyroid cancer cells. Oncogene 30, 1302–1317 (2011). (10.1038/onc.2010.512) / Oncogene by H Prazeres (2011)
  15. Tiacci, E. et al. BRAF mutations in hairy-cell leukemia. N. Engl. J. Med. 364, 2305–2315 (2011). (10.1056/NEJMoa1014209) / N. Engl. J. Med. by E Tiacci (2011)
  16. Zhang, X. et al. Sequence analysis of 515 kinase genes in chronic lymphocytic leukemia. Leukemia published online (24 June 2011), doi:10.1038/leu.2011.163. (10.1038/leu.2011.163)
  17. Zainuddin, N. et al. TP53 mutations are infrequent in newly diagnosed chronic lymphocytic leukemia. Leuk. Res. 35, 272–274 (2011). (10.1016/j.leukres.2010.08.023) / Leuk. Res. by N Zainuddin (2011)
  18. Fabbri, G. et al. Analysis of the chronic lymphocytic leukemia coding genome: role of NOTCH1 mutational activation. J. Exp. Med. 208, 1389–1401 (2011). (10.1084/jem.20110921) / J. Exp. Med. by G Fabbri (2011)
  19. Folco, E.G., Coil, K.E. & Reed, R. The anti-tumor drug E7107 reveals an essential role for SF3b in remodeling U2 snRNP to expose the branch point-binding region. Genes Dev. 25, 440–444 (2011). (10.1101/gad.2009411) / Genes Dev. by EG Folco (2011)
  20. Corrionero, A., Minana, B. & Valcarcel, J. Reduced fidelity of branch point recognition and alternative splicing induced by the anti-tumor drug spliceostatin A. Genes Dev. 25, 445–459 (2011). (10.1101/gad.2014311) / Genes Dev. by A Corrionero (2011)
  21. Golas, M.M., Sander, B., Will, C.L., Luhrmann, R. & Stark, H. Molecular architecture of the multiprotein splicing factor SF3b. Science 300, 980–984 (2003). (10.1126/science.1084155) / Science by MM Golas (2003)
  22. David, C.J. & Manley, J.L. Alternative pre-mRNA splicing regulation in cancer: pathways and programs unhinged. Genes Dev. 24, 2343–2364 (2010). (10.1101/gad.1973010) / Genes Dev. by CJ David (2010)
  23. Karni, R. et al. The gene encoding the splicing factor SF2/ASF is a proto-oncogene. Nat. Struct. Mol. Biol. 14, 185–193 (2007). (10.1038/nsmb1209) / Nat. Struct. Mol. Biol. by R Karni (2007)
  24. Golan-Gerstl, R. et al. Splicing factor hnRNP A2/B1 regulates tumor suppressor gene splicing and is an oncogenic driver in glioblastoma. Cancer Res. 71, 4464–4472 (2011). (10.1158/0008-5472.CAN-10-4410) / Cancer Res. by R Golan-Gerstl (2011)
  25. Kaida, D. et al. Spliceostatin A targets SF3b and inhibits both splicing and nuclear retention of pre-mRNA. Nat. Chem. Biol. 3, 576–583 (2007). (10.1038/nchembio.2007.18) / Nat. Chem. Biol. by D Kaida (2007)
  26. Yoshida, K. et al. Frequent pathway mutations of splicing machinery in myelodysplasia. Nature 478, 64–69 (2011). (10.1038/nature10496) / Nature by K Yoshida (2011)
  27. Papaemmanuil, E. et al. Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts. N. Engl. J. Med. 365, 1384–1395 (2011). (10.1056/NEJMoa1103283) / N. Engl. J. Med. by E Papaemmanuil (2011)
  28. Visconte, V. et al. SF3B1, a splicing factor is frequently mutated in refractory anemia with ring sideroblasts. Leukemia published online (2 September 2011), doi:10.1038/leu.2011.232. (10.1038/leu.2011.232)
  29. Chen, A.A. et al. Genetic variation in the vitamin C transporter, SLC23A2, modifies the risk of HPV16-associated head and neck cancer. Carcinogenesis 30, 977–981 (2009). (10.1093/carcin/bgp076) / Carcinogenesis by AA Chen (2009)
  30. Bulwin, G.C. et al. TIRC7 inhibits T cell proliferation by modulation of CTLA-4 expression. J. Immunol. 177, 6833–6841 (2006). (10.4049/jimmunol.177.10.6833) / J. Immunol. by GC Bulwin (2006)
  31. Brown, P.J. et al. Potentially oncogenic B-cell activation–induced smaller isoforms of FOXP1 are highly expressed in the activated B cell–like subtype of DLBCL. Blood 111, 2816–2824 (2008). (10.1182/blood-2007-09-115113) / Blood by PJ Brown (2008)
  32. Hudson, T.J. et al. International network of cancer genome projects. Nature 464, 993–998 (2010). (10.1038/nature08987) / Nature by TJ Hudson (2010)
  33. Bentley, D.R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53–59 (2008). (10.1038/nature07517) / Nature by DR Bentley (2008)
  34. Trapnell, C., Pachter, L. & Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105–1111 (2009). (10.1093/bioinformatics/btp120) / Bioinformatics by C Trapnell (2009)
  35. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009). (10.1093/bioinformatics/btp324) / Bioinformatics by H Li (2009)
  36. Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009). (10.1093/bioinformatics/btp352) / Bioinformatics by H Li (2009)
  37. Baudot, A., de la Torre, V. & Valencia, A. Mutated genes, pathways and processes in tumours. EMBO Rep. 11, 805–810 (2010). (10.1038/embor.2010.133) / EMBO Rep. by A Baudot (2010)
  38. Kanehisa, M., Goto, S., Furumichi, M., Tanabe, M. & Hirakawa, M. KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res. 38, D355–D360 (2010). (10.1093/nar/gkp896) / Nucleic Acids Res. by M Kanehisa (2010)
  39. Schaefer, C.F. et al. PID: the Pathway Interaction Database. Nucleic Acids Res. 37, D674–D679 (2009). (10.1093/nar/gkn653) / Nucleic Acids Res. by CF Schaefer (2009)
  40. Ashburner, M. et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25, 25–29 (2000). (10.1038/75556) / Nat. Genet. by M Ashburner (2000)
  41. Reva, B., Antipin, Y. & Sander, C. Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res. 39, e118 (2011). (10.1093/nar/gkr407) / Nucleic Acids Res. by B Reva (2011)
  42. Wu, S. & Zhang, Y. MUSTER: improving protein sequence profile-profile alignments by using multiple sources of structure information. Proteins 72, 547–556 (2008). (10.1002/prot.21945) / Proteins by S Wu (2008)
  43. Peto, R. & Pike, M.C. Conservatism of the approximation sigma (O-E)2-E in the logrank test for survival data or tumor incidence data. Biometrics 29, 579–584 (1973). (10.2307/2529177) / Biometrics by R Peto (1973)
Dates
Type When
Created 13 years, 8 months ago (Dec. 11, 2011, 2:54 p.m.)
Deposited 2 years, 3 months ago (May 18, 2023, 4:43 p.m.)
Indexed 3 weeks, 2 days ago (Aug. 5, 2025, 8:38 a.m.)
Issued 13 years, 8 months ago (Dec. 11, 2011)
Published 13 years, 8 months ago (Dec. 11, 2011)
Published Online 13 years, 8 months ago (Dec. 11, 2011)
Published Print 13 years, 7 months ago (Jan. 1, 2012)
Funders 0

None

@article{Quesada_2011, title={Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia}, volume={44}, ISSN={1546-1718}, url={http://dx.doi.org/10.1038/ng.1032}, DOI={10.1038/ng.1032}, number={1}, journal={Nature Genetics}, publisher={Springer Science and Business Media LLC}, author={Quesada, Víctor and Conde, Laura and Villamor, Neus and Ordóñez, Gonzalo R and Jares, Pedro and Bassaganyas, Laia and Ramsay, Andrew J and Beà, Sílvia and Pinyol, Magda and Martínez-Trillos, Alejandra and López-Guerra, Mónica and Colomer, Dolors and Navarro, Alba and Baumann, Tycho and Aymerich, Marta and Rozman, María and Delgado, Julio and Giné, Eva and Hernández, Jesús M and González-Díaz, Marcos and Puente, Diana A and Velasco, Gloria and Freije, José M P and Tubío, José M C and Royo, Romina and Gelpí, Josep L and Orozco, Modesto and Pisano, David G and Zamora, Jorge and Vázquez, Miguel and Valencia, Alfonso and Himmelbauer, Heinz and Bayés, Mónica and Heath, Simon and Gut, Marta and Gut, Ivo and Estivill, Xavier and López-Guillermo, Armando and Puente, Xose S and Campo, Elías and López-Otín, Carlos}, year={2011}, month=dec, pages={47–52} }