GENOMES & DISEASE
'We investigate the patterns and mechanisms of genomic variation in disease'
Aberrant integration of Hepatitis B virus DNA promotes major restructuring of human hepatocellular carcinoma genome architecture
Eva G. Álvarez, Jonas Demeulemeester, Paula Otero, Clemency Jolly, Daniel García-Souto, Ana Pequeño-Valtierra, Jorge Zamora, Marta Tojo, Javier Temes, Adrian Baez-Ortega, Bernardo Rodriguez-Martin, Ana Oitaben, Alicia L. Bruzos, Mónica Martínez-Fernández, Kerstin Haase, Sonia Zumalave, Rosanna Abal, Jorge Rodríguez-Castro, Aitor Rodriguez-Casanova, Angel Diaz-Lagares, Yilong Li, Keiran M. Raine, Adam P. Butler, Iago Otero, Atsushi Ono, Hiroshi Aikata, Kazuaki Chayama, Masaki Ueno, Shinya Hayami, Hiroki Yamaue, Kazuhiro Maejima, Miguel G. Blanco, Xavier Forns, Carmen Rivas, Juan Ruiz-Bañobre, Sofía Pérez-del-Pulgar, Raúl Torres-Ruiz, Sandra Rodriguez-Perales, Urtzi Garaigorta, Peter J. Campbell, Hidewaki Nakagawa, Peter Van Loo & Jose M. C. Tubio
Nat Commun 12, 6910 (2021).
doi: https://doi.org/10.1038/s41467-021-26805-8
GAD-alum immunotherapy in type 1 diabetes expands bifunctional Th1/Th2 autoreactive CD4 T cells
Sefina Arif; Iria Gomez-Tourino; Yogesh Kamra; Irma Pujol Autonell; Emily Hanton; Timothy Tree; Daisy Melandri;Caroline Hull; Diane K Wherrett; Craig Beam; Bart Roep; Anna Lorenc; Mark Peakman.
Diabetologia 2020. Jun;63(6):1186-1198.
https://pubmed.ncbi.nlm.nih.gov/32248243/
Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition.
Bernardo Rodriguez-Martin, Eva G. Alvarez, Adrian Baez-Ortega, Jorge Zamora, Fran Supek, Jonas Demeulemeester, Martin Santamarina, Young Seok Ju, Javier Temes, Daniel Garcia-Souto, Harald Detering, Yilong Li, Jorge Rodriguez-Castro, Ana Dueso-Barroso, Alicia L. Bruzos, Stefan C. Dentro, Miguel G. Blanco, Gianmarco Contino, Daniel Ardeljan, Marta Tojo, Nicola D. Roberts, Sonia Zumalave, Paul A. W. Edwards, Joachim Weischenfeldt, Montserrat Puiggròs, Zechen Chong, Ken Chen, Eunjung Alice Lee, Jeremiah A. Wala, Keiran Raine, Adam Butler, Sebastian M. Waszak, Fabio C. P. Navarro, Steven E. Schumacher, Jean Monlong, Francesco Maura, Niccolo Bolli, Guillaume Bourque, Mark Gerstein, Peter J. Park, David C. Wedge, Rameen Beroukhim, David Torrents, Jan O. Korbel, Inigo Martincorena, Rebecca C. Fitzgerald, Peter Van Loo, Haig H. Kazazian, Kathleen H. Burns, PCAWG Structural Variation Working Group, Peter J. Campbell,Jose M. C. Tubio & PCAWG Consortium.
Nat Genet 52, 306–319 (2020).
doi: https://doi.org/10.1038/s41588-019-0562-0
Pan-Cancer analysis of whole genomes.
The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (includes Tubio JMC as
Senior/lead author of several sections of the paper).
Nature,578:82-93. (2020)
doi:https://doi.org/10.1038/s41586-020-1969-6
Analysis of non-coding somatic drivers in 2,658 cancer whole genomes.
Rheinbay et al (includes Tubio JMC).
Nature, 578:102-111
doi:https://doi.org/10.1038/s41586-020-1965-x
Epigenetics of Bladder Cancer: Where Biomarkers and Therapeutic Targets Meet
Martinez VG, Munera-Maravilla E, Bernardini A, Rubio C, Suarez-Cabrera C, Segovia C, Lodewijk I, Dueñas M, Martínez-Fernández M and Paramio JM
Front. Genet. 10:1125.
doi: 10.3389/fgene.2019.01125
Genomic landscape and chronological reconstruction of driver events in multiple myeloma
Francesco Maura, Niccoló Bolli, Nicos Angelopoulos, Kevin Dawson, Daniel Leongamornlert, Inigo Martincorena, Thomas Mitchell, Anthony Fullam, Santiago Gonzalez, Raphael Szalat, Federico Abascal, Bernardo Rodriguez-Martin, Mehmet Samur, Dominik Glodzik, Marco Roncador, Mariateresa Fulciniti, Yu-Tzu Tai, Stephane Minvielle, Florence Magrangeas, Philippe Moreau, Paolo Corradini, Kenneth Anderson, Jose Tubio, David Wedge, Moritz Gerstung, Herve Avet-Loiseau, Nikhil Munshi, and Peter Campbell
Nature Communications, 10: 3835
Naturally presented HLA class I-restricted epitopes from the neurotrophic factor S100-β are targets of the autoimmune response in type 1 diabetes
Calviño-Sampedro C *, Gomez-Tourino I * , Cordero OJ, Reche PA, Gómez-Perosanz M, Sánchez-Trincado JL, Rodríguez MÁ, Sueiro AM, Viñuela JE, Calviño RV. . FASEB J. 2019 May;33(5):6390-6401. * Both authors contributed equally to this work.
doi: https://doi.org/10.1038/s41467-019-11680-1
Inhibition of a G9a/DNMT network triggers immune-mediated bladder cancer regression
Cristina Segovia *, Edurne San José-Enériz *, Ester Munera-Maravilla *, Mónica Martínez-Fernández, Leire Garate, Estíbaliz Miranda, Amaia Vilas-Zornoza, Iris Lodewijk, Carolina Rubio, Carmen Segrelles, Luis Vitores Valcárcel, Obdulia Rabal, Noelia Casares, Alejandra Bernardini, Cristian Suarez-Cabrera, Fernando F. López-Calderón, Puri Fortes, José A. Casado, Marta Dueñas, Felipe Villacampa, Juan José Lasarte, Félix Guerrero-Ramos, Guillermo de Velasco, Julen Oyarzabal, Daniel Castellano, Xabier Agirre, Felipe Prósper & Jesús M. Paramio. *Equal contributions
Nature Medicine volume 25, pages1073–1081 (2019)
doi:https://doi.org/10.1038/s41591-019-0499-y
Gene Expression Analyses in Non Muscle Invasive Bladder Cancer Reveals a Role for Alternative Splicing and Tp53 Status
Marta Dueñas, Andrés Pérez-Figueroa, Carla Oliveira, Cristian Suárez-Cabrera, Abel Sousa, Patricia Oliveira, Felipe Villacampa, Jesús M. Paramio & Mónica Martínez-Fernández
Scientific Reports volume 9, Article number: 10362 (2019)
doi: 10.1038/s41598-019-46652-4
Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis
Petljak M, Alexandrov LB, Brammeld JS, Price S, Wedge DC, Grossmann S, Dawson KJ, Ju YS, Iorio F, Tubio JMC, Koh CC, Georgakopoulos-Soares I, Rodríguez-Martín B, Otlu B, O'Meara S, Butler AP, Menzies A, Bhosle SG, Raine K, Jones DR, Teague JW, Beal K, Latimer C, O'Neill L, Zamora J, Anderson E, Patel N, Maddison M, Ng BL, Graham J, Garnett MJ, McDermott U, Nik-Zainal S, Campbell PJ, Stratton MR
Cell, 176:1282-1294.
doi: 10.1016/j.cell.2019.02.012
Rubio C*, Martínez-Fernández M*, Segovia C, Lodewijk I, Suarez-Cabrera C, Segrelles C, López-Calderón F, Munera-Maravilla E, Santos M, Bernardini A, García-Escudero R, Lorz C, Gómez-Rodriguez MJ, de Velasco G, Otero I, Villacampa F, Guerrero-Ramos F, Ruiz S, de la Rosa F, Domínguez-Rodríguez S, Real FX, Malats N, Castellano D, Dueñas M, Paramio JM.
Clin Cancer Res. 2019 Jan 1;25(1):390-402.Epub 2018 Sep 21
doi: 10.1158/1078-0432.CCR-18-0685.
An integrated genomic analysis of anaplastic meningioma identifies prognostic molecular signatures.
Collord G, Tarpey P, Kurbatova N, Martincorena I, Moran S, Castro M, Nagy T, Bignell G, Maura F, Young MD, Berna J, Tubio JMC, McMurran CE, Young AMH, Sanders M, Noorani I, Price SJ, Watts C, Leipnitz E, Kirsch M, Schackert G, Pearson D, Devadass A, Ram Z, Collins VP, Allinson K, Jenkinson MD, Zakaria R, Syed K, Hanemann CO, Dunn J, McDermott MW, Kirollos RW, Vassiliou GS, Esteller M, Behjati S, Brazma A, Santarius T, McDermott U.
Sci Rep. 2018 Sep 10;8(1):13537.
doi: 10.1038/s41598-018-31659-0.
The Origins and Vulnerabilities of Two Transmissible Cancers in Tasmanian Devils.
Stammnitz MR, Coorens THH, Gori KC, Hayes D, Fu B, Wang J, Martin-Herranz DE, Alexandrov LB, Baez-Ortega A, Barthorpe S, Beck A, Giordano F, Knowles GW, Kwon YM, Hall G, Price S, Pye RJ, Tubio JMC, Siddle HVT, Sohal SS, Woods GM, McDermott U, Yang F, Garnett MJ, Ning Z, Murchison EP.
Cancer Cell. 2018 Apr 9;33(4):607-619.e15
doi: 10.1016/j.ccell.2018.03.013.
Genomic patterns of progression in smoldering multiple myeloma.
Bolli N, Maura F, Minvielle S, Gloznik D, Szalat R, Fullam A, Martincorena I, Dawson KJ, Samur MK, Zamora J, Tarpey P, Davies H, Fulciniti M, Shammas MA, Tai YT, Magrangeas F, Moreau P, Corradini P, Anderson K, Alexandrov L, Wedge DC, Avet-Loiseau H, Campbell P, Munshi N.
Nat Commun. 2018 Aug 22;9(1):3363.
doi: 10.1038/s41467-018-05058-y.
Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets.
Wedge DC, Gundem G, Mitchell T, Woodcock DJ, Martincorena I, Ghori M, Zamora J, Butler A, Whitaker H, Kote-Jarai Z, Alexandrov LB, Van Loo P, Massie CE, Dentro S, Warren AY, Verrill C, Berney DM, Dennis N, Merson S, Hawkins S, Howat W, Lu YJ, Lambert A, Kay J, Kremeyer B, Karaszi K, Luxton H, Camacho N, Marsden L, Edwards S, Matthews L, Bo V, Leongamornlert D, McLaren S, Ng A, Yu Y, Zhang H, Dadaev T, Thomas S, Easton DF, Ahmed M, Bancroft E, Fisher C, Livni N, Nicol D, Tavaré S, Gill P, Greenman C, Khoo V, Van As N, Kumar P, Ogden C, Cahill D, Thompson A, Mayer E, Rowe E, Dudderidge T, Gnanapragasam V, Shah NC, Raine K, Jones D, Menzies A, Stebbings L, Teague J, Hazell S, Corbishley C; CAMCAP Study Group, de Bono J, Attard G, Isaacs W, Visakorpi T, Fraser M, Boutros PC, Bristow RG, Workman P, Sander C; TCGA Consortium, Hamdy FC, Futreal A, McDermott U, Al-Lazikani B, Lynch AG, Bova GS, Foster CS, Brewer DS, Neal DE, Cooper CS, Eeles RA,.
Nat Genet. 218 May;5(5):682-692.
Shorter T cell receptor beta-chain CDR3 regions in type 1 diabetes result in enhanced repertoire diversity and sharing.
Gomez-Tourino I, Kamra Y, Lorenc A and Peakman M. Nat Commun 2017 Nov 27;8(1):1792.
Hydrophobic CDR3 residues promote the development of self-reactive T cells
Brian D. Stadinski, Karthik Shekhar, Iria Gómez-Touriño, Jonathan Jung, Katsuhiro Sasaki, Andrew K. Sewell, Peakman, Arup Chakraborty and Eric S. Huseby. . Nat Immunol. 2016 Aug;17(8):946-55.
Martincorena I, Roshan A, Gerstung M, Ellis P, Van Loo P, McLaren S, Wedge DC, Fullam A, Alexandrov LB, Tubio JM, Stebbings L, Menzies A, Widaa S, Stratton MR, Jones PH, Campbell PJ
Science (New York, N.Y.) 348 880-6 2015 May 22
PUBMED: 25999502; PMC: 4471149; DOI: 10.1126/science.aaa6806
The evolutionary history of lethal metastatic prostate cancer.
Gundem G, Van Loo P, Kremeyer B, Alexandrov LB, Tubio JMC, Papaemmanuil E, Brewer DS, Kallio HML, Högnäs G, Annala M, Kivinummi K, Goody V, Latimer C, O'Meara S, Dawson KJ, Isaacs W, Emmert-Buck MR, Nykter M, Foster C, Kote-Jarai Z, Easton D, Whitaker HC, ICGC Prostate Group., Neal DE, Cooper CS, Eeles RA, Visakorpi T, Campbell PJ, McDermott U, Wedge DC, Bova GS
Nature 520 353-357 2015 Apr 16
PUBMED: 25830880; DOI: 10.1038/nature14347
Tubio JMC, Li Y, Ju YS, Martincorena I, Cooke SL, Tojo M, Gundem G, Pipinikas CP, Zamora J, Raine K, Menzies A, Roman-Garcia P, Fullam A, Gerstung M, Shlien A, Tarpey PS, Papaemmanuil E, Knappskog S, Van Loo P, Ramakrishna M, Davies HR, Marshall J, Wedge DC, Teague JW, Butler AP, Nik-Zainal S, Alexandrov L, Behjati S, Yates LR, Bolli N, Mudie L, Hardy C, Martin S, McLaren S, O'Meara S, Anderson E, Maddison M, Gamble S, Foster C, Warren AY, Whitaker H, Brewer D, Eeles R, Cooper C, Neal D, Lynch AG, Visakorpi T, Isaacs WB, Veer LV, Caldas C, Desmedt C, Sotiriou C, Aparicio S, Foekens JA, Eyfjörd JE, Lakhani SR, Thomas G, Myklebost O, Span PN, Børresen-Dale AL, Richardson AL, Van de Vijver M, Vincent-Salomon A, Van den Eynden GG, Flanagan AM, Futreal PA, Janes SM, Bova GS, Stratton MR, McDermott U, Campbell PJ, ICGC Breast Cancer Group., ICGC Bone Cancer Group., ICGC Prostate Cancer Group.
Science (New York, N.Y.) 345 1251343 2014 Aug 1
PUBMED: 25082706; PMC: 4380235; DOI: 10.1126/science.1251343
RAG-mediated recombination is the predominant driver of oncogenic rearrangement in ETV6-RUNX1 acute lymphoblastic leukemia.
Papaemmanuil E, Rapado I, Li Y, Potter NE, Wedge DC, Tubio J, Alexandrov LB, Van Loo P, Cooke SL, Marshall J, Martincorena I, Hinton J, Gundem G, van Delft FW, Nik-Zainal S, Jones DR, Ramakrishna M, Titley I, Stebbings L, Leroy C, Menzies A, Gamble J, Robinson B, Mudie L, Raine K, O'Meara S, Teague JW, Butler AP, Cazzaniga G, Biondi A, Zuna J, Kempski H, Muschen M, Ford AM, Stratton MR, Greaves M, Campbell PJ
Nature genetics 46 116-25 2014 Feb
PUBMED: 24413735; PMC: 3960636; DOI: 10.1038/ng.2874
Transmissible (corrected) dog cancer genome reveals the origin and history of an ancient cell lineage.
Murchison EP, Wedge DC, Alexandrov LB, Fu B, Martincorena I, Ning Z, Tubio JMC, Werner EI, Allen J, De Nardi AB, Donelan EM, Marino G, Fassati A, Campbell PJ, Yang F, Burt A, Weiss RA, Stratton MR
Science (New York, N.Y.) 343 437-440 2014 Jan 24
PUBMED: 24458646; PMC: 3918581; DOI: 10.1126/science.1247167
Frequent mutation of the major cartilage collagen gene COL2A1 in chondrosarcoma.
Tarpey PS, Behjati S, Cooke SL, Van Loo P, Wedge DC, Pillay N, Marshall J, O'Meara S, Davies H, Nik-Zainal S, Beare D, Butler A, Gamble J, Hardy C, Hinton J, Jia MM, Jayakumar A, Jones D, Latimer C, Maddison M, Martin S, McLaren S, Menzies A, Mudie L, Raine K, Teague JW, Tubio JM, Halai D, Tirabosco R, Amary F, Campbell PJ, Stratton MR, Flanagan AM, Futreal PA
Nature genetics 45 923-6 2013 Aug
PUBMED: 23770606; PMC: 3743157; DOI: 10.1038/ng.2668
Quesada V, Conde L, Villamor N, Ordóñez GR, Jares P, Bassaganyas L, Ramsay AJ, 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 JM, González-Díaz M, Puente DA, Velasco G, Freije JM, Tubío JM, Royo R, Gelpí JL, Orozco M, Pisano DG, Zamora J, Vázquez M, Valencia A, Himmelbauer H, Bayés M, Heath S, Gut M, Gut I, Estivill X, López-Guillermo A, Puente XS, Campo E, López-Otín C
Nature genetics 44 47-52 2011 Dec 11
PUBMED: 22158541; DOI: 10.1038/ng.1032
Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia.
Puente XS, Pinyol M, Quesada V, Conde L, Ordóñez GR, Villamor N, Escaramis G, Jares P, Beà S, González-Díaz M, Bassaganyas L, Baumann T, Juan M, López-Guerra M, Colomer D, Tubío JM, López C, Navarro A, Tornador C, Aymerich M, Rozman M, Hernández JM, Puente DA, Freije JM, Velasco G, Gutiérrez-Fernández A, Costa D, Carrió A, Guijarro S, Enjuanes A, Hernández L, Yagüe J, Nicolás P, Romeo-Casabona CM, Himmelbauer H, Castillo E, Dohm JC, de Sanjosé S, Piris MA, de Alava E, San Miguel J, Royo R, Gelpí JL, Torrents D, Orozco M, Pisano DG, Valencia A, Guigó R, Bayés M, Heath S, Gut M, Klatt P, Marshall J, Raine K, Stebbings LA, Futreal PA, Stratton MR, Campbell PJ, Gut I, López-Guillermo A, Estivill X, Montserrat E, López-Otín C, Campo E
Nature 475 101-5 2011 Jun 5
PUBMED: 21642962; PMC: 3322590; DOI:10.1038/nature10113
Cancer: When catastrophe strikes a cell.
Tubio JM, Estivill X
Nature 470 476-7 2011 Feb 24
PUBMED: 21350479; DOI: doi:10.1038/470476a
