CALR-ETdb, the database of calreticulin variants diversity in essential thrombocythemia

References

• Arber D, Orazi A, Hasserjian R, Thiele J, Borowitz M, Le Beau M, Bloomfield C, Cazzola M, Vardiman JW. The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia. Blood 2016;127(20):2391–2405. Epub 2016/ 07/21. doi:https://doi.org/10.1182/blood-2016-03-643544
   PubMed Web of Science ®Google Scholar
• Regev A, Stark P, Blickstein D, Lahav M. Thrombotic complications in essential thrombocythemia with relatively low platelet counts. Am J Hematol 1997;56(3):168–172. Epub 1997/ 11/26. doi:https://doi.org/10.1002/(SICI)1096-8652(199711)56:3<168::AID-AJH6>3.0.CO;2-W
   PubMed Web of Science ®Google Scholar
• Fenaux P, Simon M, Caulier MT, Lai JL, Goudemand J, Bauters F. Clinical course of essential thrombocythemia in 147 cases. Cancer 1990;66(3):549–556. Epub 1990/ 08/01. doi:https://doi.org/10.1002/1097-0142(19900801)66:3<549::AID-CNCR2820660324>3.0.CO;2-6
   PubMed Web of Science ®Google Scholar
• James C, Ugo V, Le Couédic JP, Staerk J, Delhommeau F, Lacout C, Garçon L, Raslova H, Berger R, Bennaceur-Griscelli A, et al. A unique clonal JAK2 mutation leading to constitutive signalling causes polycythaemia vera. Nature 2005;434(7037):1144–1148. Epub 2005/ 03/29. doi:https://doi.org/10.1038/nature03546
   PubMed Web of Science ®Google Scholar
• Rumi E, Pietra D, Pascutto C, Guglielmelli P, Martinez-Trillos A, Casetti I, Colomer D, Pieri L, Pratcorona M, Rotunno G, et al. Clinical effect of driver mutations of JAK2, CALR, or MPL in primary myelofibrosis. Blood 2014;124(7):1062–1069. doi:https://doi.org/10.1182/blood-2014-05-578435
   PubMed Web of Science ®Google Scholar
• Szuber N, Hanson CA, Lasho TL, Finke C, Ketterling RP, Pardanani A, Gangat N, Tefferi A. MPL-mutated essential thrombocythemia: a morphologic reappraisal. Blood Cancer J 2018;8(12):121. Epub 2018/ 11/22. doi:https://doi.org/10.1038/s41408-018-0159-3
   PubMedGoogle Scholar
• Varghese LN, Defour JP, Pecquet C, Constantinescu SN The thrombopoietin receptor: structural basis of traffic and activation by ligand, mutations, agonists, and mutated calreticulin. Frontiers in Endocrinology 2017;8:59. Epub 2017/ 04/15. doi:https://doi.org/10.3389/fendo.2017.00059
   PubMed Web of Science ®Google Scholar
• Verger E, Cassinat B, Chauveau A, Dosquet C, Giraudier S, Schlageter M-H, Ianotto J-C, Yassin MA, Al-Dewik N, Carillo S, et al. Clinical and molecular response to interferon-α therapy in essential thrombocythemia patients with CALR mutations. Blood 2015;126(24):2585–2591. Epub 2015/ 10/22. doi:https://doi.org/10.1182/blood-2015-07-659060
   PubMed Web of Science ®Google Scholar
• Klampfl T, Gisslinger H, Harutyunyan AS, Nivarthi H, Rumi E, Milosevic JD, Them NC, Berg T, Gisslinger B, Pietra D, et al. Somatic mutations of calreticulin in myeloproliferative neoplasms. N Engl J Med 2013;369(25):2379–2390. doi:https://doi.org/10.1056/NEJMoa1311347
   PubMed Web of Science ®Google Scholar
• Nangalia J, Massie CE, Baxter EJ, Nice FL, Gundem G, Wedge DC, Avezov E, Li J, Kollmann K, Kent DG, et al. Somatic CALR mutations in myeloproliferative neoplasms with nonmutated JAK2. N Engl J Med 2013;369(25):2391–2405. doi:https://doi.org/10.1056/NEJMoa1312542
   PubMed Web of Science ®Google Scholar
• Barbui T, Thiele J, Ferrari A, Vannucchi AM, Tefferi A. The new WHO classification for essential thrombocythemia calls for revision of available evidences. Blood Cancer J 2020;10(2):22. Epub 2020/ 02/27. doi:https://doi.org/10.1038/s41408-020-0290-9
   PubMed Web of Science ®Google Scholar
• How J, Hobbs GS, Mullally A. Mutant calreticulin in myeloproliferative neoplasms. Blood 2019;134(25):2242–2248. Epub 2019/ 09/29. doi:https://doi.org/10.1182/blood.2019000622
   PubMed Web of Science ®Google Scholar
• Falchi M, Varricchio L, Martelli F, Marra M, Picconi O, Tafuri A, Girelli G, Uversky VN, Migliaccio AR The Calreticulin control of human stress erythropoiesis is impaired by JAK2 V617F in polycythemia vera. Experimental Hematology 2017;50:53–76. Epub 2017/ 02/25. doi:https://doi.org/10.1016/j.exphem.2017.02.001
   PubMed Web of Science ®Google Scholar
• Migliaccio AR, Uversky VN. Dissecting physical structure of calreticulin, an intrinsically disordered Ca2+-buffering chaperone from endoplasmic reticulum. Journal of Biomolecular Structure & Dynamics 2018;36(6):1617–1636. Epub 2017/ 05/16. doi:https://doi.org/10.1080/07391102.2017.1330224
   PubMed Web of Science ®Google Scholar
• Araki M, Komatsu N. The role of calreticulin mutations in myeloproliferative neoplasms. Int J Hematol 2020;111(2):200–205. Epub 2019/ 12/19. doi:https://doi.org/10.1007/s12185-019-02800-0
   PubMed Web of Science ®Google Scholar
• Lasho TL, Finke CM, Tischer A, Pardanani A, Tefferi A. Mayo CALR mutation type classification guide using alpha helix propensity. Am J Hematol 2018;93(5):E128–E129. doi:https://doi.org/10.1002/ajh.25065.
   PubMed Web of Science ®Google Scholar
• Pietra D, Rumi E, Ferretti VV, Di Buduo CA, Milanesi C, Cavalloni C, Sant’Antonio E, Abbonante V, Moccia F, Casetti IC, et al. Differential clinical effects of different mutation subtypes in CALR-mutant myeloproliferative neoplasms. Leukemia 2016;30(2):431–438. Epub 2015/ 10/10. doi:https://doi.org/10.1038/leu.2015.277
   PubMed Web of Science ®Google Scholar
• Cabagnols X, Defour JP, Ugo V, Ianotto JC, Mossuz P, Mondet J, Girodon F, Alexandre JH, Mansier O, Viallard JF, et al. Differential association of calreticulin type 1 and type 2 mutations with myelofibrosis and essential thrombocytemia: relevance for disease evolution. Leukemia 2015;29(1):249–252. Epub 2014/ 09/13 doi:https://doi.org/10.1038/leu.2014.270
   PubMed Web of Science ®Google Scholar
• Cottin L, Riou J, Orvain C, Ianotto JC, Boyer F, Renard M, Truchan-Graczyk M, Murati A, Jouanneau-Courville R, Allangba O, et al. Sequential mutational evaluation of CALR -mutated myeloproliferative neoplasms with thrombocytosis reveals an association between CALR allele burden evolution and disease progression. Br J Haematol 2020;188(6):935–944. Epub 2019/ 11/12. doi:https://doi.org/10.1111/bjh.16276
   PubMed Web of Science ®Google Scholar
• Tate JG, Bamford S, Jubb HC, Sondka Z, Beare DM, Bindal N, Boutselakis H, Cole CG, Creatore C, Dawson E, et al. COSMIC: the catalogue of somatic mutations in cancer. Nucleic Acids Research 2019;47(D1):D941–d947. Epub 2018/ 10/30. doi:https://doi.org/10.1093/nar/gky1015
   PubMed Web of Science ®Google Scholar
• Consortium U. UniProt: a worldwide hub of protein knowledge. Nucleic Acids Research 2019;47(D1):D506–d515. Epub 2018/ 11/06. doi:https://doi.org/10.1093/nar/gky1049
   PubMed Web of Science ®Google Scholar
• Sievers F, Higgins DG. Clustal Omega for making accurate alignments of many protein sequences. Protein Science: A Publication of the Protein Society 2018;27(D1):135–145. Epub 2017/ 09/09. doi:https://doi.org/10.1002/pro.3290
   PubMedGoogle Scholar
• Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ. Jalview Version 2–a multiple sequence alignment editor and analysis workbench. Bioinformatics (Oxford, England) 2009;25(9):1189–1191. Epub 2009/ 01/20. doi:https://doi.org/10.1093/bioinformatics/btp033
   PubMed Web of Science ®Google Scholar
• Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: a sequence logo generator. Genome Research 2004;14(6):1188–1190. Epub 2004/ 06/03. doi:https://doi.org/10.1101/gr.849004
   PubMed Web of Science ®Google Scholar
• DWA B, DT J. The PSIPRED protein analysis workbench: 20 years on. Nucleic Acids Research 2019;47(W1):W402–w407. Epub 2019/ 06/30. doi:https://doi.org/10.1093/nar/gkz297
   PubMed Web of Science ®Google Scholar
• Jones DT. Protein secondary structure prediction based on position-specific scoring matrices. Journal of Molecular Biology 1999;292(2):195–202. Epub 1999/ 09/24. doi:https://doi.org/10.1006/jmbi.1999.3091
   PubMed Web of Science ®Google Scholar
• Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 1997;25(17):3389–3402. Epub 1997/ 09/01. doi:https://doi.org/10.1093/nar/25.17.3389
   PubMed Web of Science ®Google Scholar
• Berman HM, Battistuz T, Bhat TN, Bluhm WF, Bourne PE, Burkhardt K, Feng Z, Gilliland GL, Iype L, Jain S, et al. The protein data bank. Acta Crystallographica Section D, Biological Crystallography 2002;58(6):899–907. Epub 2002/ 05/31. doi:https://doi.org/10.1107/S0907444902003451
   PubMedGoogle Scholar
• Sali A, Overington JP. Derivation of rules for comparative protein modeling from a database of protein structure alignments. Protein Science: A Publication of the Protein Society 1994;3(9):1582–1596. Epub 1994/ 09/01. doi:https://doi.org/10.1002/pro.5560030923
   PubMed Web of Science ®Google Scholar
• Shen MY, Sali A. Statistical potential for assessment and prediction of protein structures. Protein Science: A Publication of the Protein Society 2006;15(11):2507–2524. Epub 2006/ 11/01. doi:https://doi.org/10.1110/ps.062416606
   PubMed Web of Science ®Google Scholar
• DeLano WL PyMOL. DeLano Scientific. San Carlos, CA. 2002, 700.
   Google Scholar
• Yang J, Yan R, Roy A, Xu D, Poisson J, Zhang Y. The I-TASSER Suite: protein structure and function prediction. Nature Methods 2015;12(1):7–8. Epub 2014/ 12/31. doi:https://doi.org/10.1038/nmeth.3213
   PubMed Web of Science ®Google Scholar
• Song Y, DiMaio F, Wang RY, Kim D, Miles C, Brunette T, Thompson J, Baker D High-resolution comparative modeling with RosettaCM. Structure (London, England: 1993) 2013(21):1735–1742. Epub 2013/ 09/17.
   Google Scholar
• Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ. The Phyre2 web portal for protein modeling, prediction and analysis. Nature Protocols 2015;10(6):845–858. Epub 2015/ 05/08. doi:https://doi.org/10.1038/nprot.2015.053
   PubMed Web of Science ®Google Scholar
• Rego N, Koes D. 3Dmol.js: molecular visualization with WebGL. Bioinformatics (Oxford, England) 2015;31(8):1322–1324. Epub 2014/ 12/17. doi:https://doi.org/10.1093/bioinformatics/btu829
   PubMed Web of Science ®Google Scholar
• Downie N Open source HTML5 Charts for your website. Chart Js 2015.
   Google Scholar
• Van Rossum G, Drake FL 2009. Python 3 reference manual. Scotts Valley, CA: CreateSpace.
   Google Scholar
• Hançer VS, Tokgöz H, Güvenç S, Çalışkan Ü, Büyükdoğan M. Three Novel Calreticulin mutations in two Turkish patients. Turkish Journal of Haematology: Official Journal of Turkish Society of Haematology 2017;34(4):360–361. Epub 2017/ 07/28. doi:https://doi.org/10.4274/tjh.2017.0146
   PubMed Web of Science ®Google Scholar
• Panovska-Stavridis I, Eftimov A, Ivanovski M, Stojanovic A, Georgievski B, Cevreska L, Dimovski AJ. Diversities of calreticulin gene mutations in macedonian patients with essential thrombocythemia. Clinical Lymphoma, Myeloma & Leukemia 2016;16(8):477–481. Epub 2016/ 08/16. doi:https://doi.org/10.1016/j.clml.2016.04.019
   PubMed Web of Science ®Google Scholar
• Wu Z, Zhang X, Xu X, Chen Y, Hu T, Kang Z, Li S, Wang H, Liu W, Ma X, et al. The mutation profile of JAK2 and CALR in Chinese Han patients with Philadelphia chromosome-negative myeloproliferative neoplasms. Journal of Hematology & Oncology 2014;7:48. Epub 2014/ 07/16.
   PubMed Web of Science ®Google Scholar
• Remmert M, Biegert A, Hauser A, Söding J. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment. Nature Methods 2011;9(2):173–175. Epub 2011/ 12/27. doi:https://doi.org/10.1038/nmeth.1818
   PubMed Web of Science ®Google Scholar
• Fang C, Shang Y, Xu D. MUFOLD-SS: new deep inception-inside-inception networks for protein secondary structure prediction. Proteins 2018;86(5):592–598. Epub 2018/ 03/02. doi:https://doi.org/10.1002/prot.25487
   PubMed Web of Science ®Google Scholar
• Al Assaf C, Van Obbergh F, Billiet J, Lierman E, Devos T, Graux C, Hervent AS, Emmerechts J, Tousseyn T, De Paepe P, et al. Analysis of phenotype and outcome in essential thrombocythemia with CALR or JAK2 mutations. Haematologica 2015;100(7):893–897. Epub 2015/ 05/03. DOI:https://doi.org/10.3324/haematol.2014.118299
   PubMed Web of Science ®Google Scholar
• Chen JB, Ramadani F, Pang MOY, Beavil RL, Holdom MD, Mitropoulou AN, Beavil AJ, Gould HJ, Chang TW, Sutton BJ, et al. Structural basis for selective inhibition of immunoglobulin E-receptor interactions by an anti-IgE antibody. Sci Rep 2018;8(1):11548. Epub 2018/ 08/03. doi:https://doi.org/10.1038/s41598-018-29664-4
   PubMed Web of Science ®Google Scholar
• Prins D, Gonzalez Arias C, Klampfl T, Grinfeld J, Green AR. Mutant Calreticulin in the Myeloproliferative Neoplasms. Hemasphere 2020;4(1):e333. doi:https://doi.org/10.1097/HS9.0000000000000333.
   PubMed Web of Science ®Google Scholar
• Söding J, Biegert A, Lupas AN The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Research 2005;33:W244–248. Epub 2005/ 06/28. doi:https://doi.org/10.1093/nar/gki408
   PubMed Web of Science ®Google Scholar
• Kondo T, Tasaka T, Tomioka N, Sano F, Tokunaga H, Suemori S, Tsujioka T, Matsuhashi Y, Nakanishi H, Wada H, et al. Low neutrophil alkaline phosphatase score is a new aspect of calreticulin-mutated myeloproliferative neoplasms. SpringerPlus 2016;5(1):1146. Epub 2016/ 08/10. doi:https://doi.org/10.1186/s40064-016-2829-6
   PubMedGoogle Scholar
• Palandri F, Latagliata R, Polverelli N, Tieghi A, Crugnola M, Martino B, Perricone M, Breccia M, Ottaviani E, Testoni N, et al. Mutations and long-term outcome of 217 young patients with essential thrombocythemia or early primary myelofibrosis. Leukemia 2015;29(6):1344–1349. Epub 2015/ 03/25. doi:https://doi.org/10.1038/leu.2015.87
   PubMed Web of Science ®Google Scholar
• Gango A, Mozes R, Boha Z, Kajtar B, Timar B, Kiraly PA, Kiss R, Fesus V, Nagy N, Demeter J, et al. Quantitative assessment of JAK2 V617F and CALR mutations in Philadelphia negative myeloproliferative neoplasms. Leuk Res 2018;65:42–48. doi:https://doi.org/10.1016/j.leukres.2017.12.005
   PubMed Web of Science ®Google Scholar
• Riera L, Osella-Abate S, Benevolo G, Beggiato E, Ferrero S, Pich A, Francia Di Celle P. Novel CALR somatic mutations in essential thrombocythaemia. Br J Haematol 2016;173(5):797–801. Epub 2015/ 09/08. doi:https://doi.org/10.1111/bjh.13638
   PubMed Web of Science ®Google Scholar
• Rumi E, Pietra D, Ferretti V, Klampfl T, Harutyunyan AS, Milosevic JD, Them NC, Berg T, Elena C, Casetti IC, et al. JAK2 or CALR mutation status defines subtypes of essential thrombocythemia with substantially different clinical course and outcomes. Blood 2014;123(10):1544–1551. doi:https://doi.org/10.1182/blood-2013-11-539098
   PubMed Web of Science ®Google Scholar
• Vannucchi AM, Rotunno G, Bartalucci N, Raugei G, Carrai V, Balliu M, Mannarelli C, Pacilli A, Calabresi L, Fjerza R, et al. Calreticulin mutation-specific immunostaining in myeloproliferative neoplasms: pathogenetic insight and diagnostic value. Leukemia 2014;28(9):1811–1818. Epub 2014/ 03/13. doi:https://doi.org/10.1038/leu.2014.100
   PubMed Web of Science ®Google Scholar
• Tefferi A, Lasho TL, Tischer A, Wassie EA, Finke CM, Belachew AA, Ketterling RP, Hanson CA, Pardanani AD. The prognostic advantage of calreticulin mutations in myelofibrosis might be confined to type 1 or type 1-like CALR variants. Blood 2014;124(15):2465–2466. Epub 2014/ 10/11. doi:https://doi.org/10.1182/blood-2014-07-588426
   PubMed Web of Science ®Google Scholar
• Cilia E, Pancsa R, Tompa P, Lenaerts T, Vranken WF. The DynaMine webserver: predicting protein dynamics from sequence. Nucleic Acids Research 2014;42(W1):W264–270. Epub 2014/ 04/15. doi:https://doi.org/10.1093/nar/gku270
   PubMed Web of Science ®Google Scholar
• Narwani TJ, Etchebest C, Craveur P, Léonard S, Rebehmed J, Srinivasan N, Bornot A, Gelly JC, de Brevern AG In silico prediction of protein flexibility with local structure approach. Biochimie 2019;165:150–155. Epub 2019/ 08/05. doi:https://doi.org/10.1016/j.biochi.2019.07.025
   PubMed Web of Science ®Google Scholar
• Ward JJ, McGuffin LJ, Bryson K, Buxton BF, Jones DT. The DISOPRED server for the prediction of protein disorder. Bioinformatics (Oxford, England) 2004;20(13):2138–2139. Epub 2004/ 03/27. doi:https://doi.org/10.1093/bioinformatics/bth195
   PubMed Web of Science ®Google Scholar
• Muñoz V, Serrano L. Development of the multiple sequence approximation within the AGADIR model of alpha-helix formation: comparison with zimm-bragg and lifson-roig formalisms. Biopolymers 1997;41(5):495–509. Epub 1997/ 04/15. doi:https://doi.org/10.1002/(SICI)1097-0282(19970415)41:5<495::AID-BIP2>3.0.CO;2-H
   PubMed Web of Science ®Google Scholar