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1. Germ line ERG haploinsufficiency defines a new syndrome with cytopenia and hematological malignancy predisposition

Author

Baliakas, Panagiotis, Blombery, Piers, Fox, Lucy C., Donadieu, Jean, Rio-Machin, Ana, Steinberg-Shemer, Orna, Morgan, Neil V., Ngeow, Joanne Y. Y., Skokowa, Julia, Pinese, Mark, Cowley, Mark J., Zerella, Jiarna R., Homan, Claire C., Arts, Peer, Lin, Xuzhu, Spinelli, Sam J., Venugopal, Parvathy, Babic, Milena, Brautigan, Peter J., Truong, Lynda, Arriola-Martinez, Luis, Moore, Sarah, Hollins, Rachel, Parker, Wendy T., Nguyen, Hung, Kassahn, Karin S., Branford, Susan, Feurstein, Simone, Larcher, Lise, Sicre de Fontbrune, Flore, Demirdas, Serwet, de Munnik, Sonja, Antoine-Poirel, Hélène, Brichard, Benedicte, Mansour, Sahar, Gordon, Kristiana, Wlodarski, Marcin W., Koppayi, Ashwin, Dobbins, Sara, Mutsaers, Pim G. N. J., Nichols, Kim E., Oak, Ninad, DeMille, Desiree, Mao, Rong, Crawford, Ali, McCarrier, Julie, Basel, Donald, Flores-Daboub, Josue, Drazer, Michael W., Phillips, Kerry, Poplawski, Nicola K., Birdsey, Graeme M., Pirri, Daniela, Ostergaard, Pia, Simons, Annet, Godley, Lucy A., Ross, David M., Hiwase, Devendra K., Soulier, Jean, Brown, Anna L., Carmichael, Catherine L., Scott, Hamish S., and Hahn, Christopher N.

Published
2024
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2. Somatic mutational landscape of hereditary hematopoietic malignancies caused by germline variants in RUNX1, GATA2, and DDX41

Author

Homan, Claire C., Drazer, Michael W., Yu, Kai, Lawrence, David M., Feng, Jinghua, Arriola-Martinez, Luis, Pozsgai, Matthew J., McNeely, Kelsey E., Ha, Thuong, Venugopal, Parvathy, Arts, Peer, King-Smith, Sarah L., Cheah, Jesse, Armstrong, Mark, Wang, Paul, Bödör, Csaba, Cantor, Alan B., Cazzola, Mario, Degelman, Erin, DiNardo, Courtney D., Duployez, Nicolas, Favier, Remi, Fröhling, Stefan, Rio-Machin, Ana, Klco, Jeffery M., Krämer, Alwin, Kurokawa, Mineo, Lee, Joanne, Malcovati, Luca, Morgan, Neil V., Natsoulis, Georges, Owen, Carolyn, Patel, Keyur P., Preudhomme, Claude, Raslova, Hana, Rienhoff, Hugh, Ripperger, Tim, Schulte, Rachael, Tawana, Kiran, Velloso, Elvira, Yan, Benedict, Kim, Erika, Sood, Raman, Hsu, Amy P., Holland, Steven M., Phillips, Kerry, Poplawski, Nicola K., Babic, Milena, Wei, Andrew H., Forsyth, Cecily, Mar Fan, Helen, Lewis, Ian D., Cooney, Julian, Susman, Rachel, Fox, Lucy C., Blombery, Piers, Singhal, Deepak, Hiwase, Devendra, Phipson, Belinda, Schreiber, Andreas W., Hahn, Christopher N., Scott, Hamish S., Liu, Paul, Godley, Lucy A., and Brown, Anna L.

Published
2023
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4. Genome instability is a consequence of transcription deficiency in patients with bone marrow failure harboring biallelic ERCC6L2 variants

Author

Tummala, Hemanth, Dokal, Arran D., Walne, Amanda, Ellison, Alicia, Cardoso, Shirleny, Amirthasigamanipillai, Saranha, Kirwan, Michael, Browne, Isobel, Sidhu, Jasmin K., Rajeeve, Vinothini, Rio-Machin, Ana, Seraihi, Ahad Al, Duncombe, Andrew S., Jenner, Matthew, Smith, Owen P., Enright, Helen, Norton, Alice, Aksu, Tekin, Özbek, Namık Yaşar, Pontikos, Nikolas, Cutillas, Pedro, Dokal, Inderjeet, and Vulliamy, Tom

Published
2018

6. BPTF is required for c-MYC transcriptional activity and in vivo tumorigenesis

Author

Laia Richart, Enrique Carrillo-de Santa Pau, Ana Río-Machín, Mónica P. de Andrés, Juan C. Cigudosa, Víctor J. Sánchez-Arévalo Lobo, and Francisco X. Real

Subjects
Science
Abstract

c-MYC genomic distribution is dictated by the epigenetic context but the mechanisms are unknown. Here, the authors show that c-MYC requires the chromatin reader BPTF to activate its transcriptional program and promote tumour development in vivo, suggesting that BPTF is a potential target for cancer therapy.

Published
2016
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7. Somatic Mutational Landscape of Hereditary Hematopoietic Malignancies Associated with Germline Variants in RUNX1, GATA2 and DDX41

Author

Brown, Anna L., Homan, Claire, Drazer, Michael W., Yu, Kai, Lawrence, David, Feng, Jinghua, Arriola-Martinez, Luis, Pozsgai, Matthew, McNeely, Kelsey, Ha, Thuong, Venugopal, Parvathy, Arts, Peer, King-Smith, Sarah, Cheah, Jesse JC, Armstrong, Mark, Bödör, Csaba, Wang, Paul, Cantor, Alan B., Cazzola, Mario, Degelman, Erin, DiNardo, Courtney D., Duployez, Nicolas, Favier, Remi, Fröhling, Stefan, Rio-Machin, Ana, Klco, Jeffery M., Krämer, Alwin, Kurokawa, Mineo, Lee, Joanne, Malcovati, Luca, Morgan, Neil V, Natsoulis, Georges, Owen, Carolyn, Patel, Keyur P., Preudhomme, Claude, Raslova, Hana, Rienhoff, Hugh Young, Jr., Ripperger, Tim, Schulte, Rachael, Tawana, Kiran, Velloso, Elvira Deolinda Rodrigues Pereira, Yan, Benedict, Sood, Raman, Hsu, Amy, Holland, Steven M., Phillips, Kerry, Poplawski, Nicola, Babic, Milena, Kwon Kim, Erika M, Wei, Andrew H., Forsyth, Cecily, Mar Fan, Helen, Lewis, Ian D, Cooney, Julian, Susman, Rachel, Fox, Lucy C, Blombery, Piers, Singhal, Deepak, Hiwase, Devendra, Schreiber, Andreas W, Hahn, Christopher N, Scott, Hamish S, Liu, Paul P., and Godley, Lucy A.

Published
2022
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8. Inhibition of Stearoyl-CoA Desaturase Has Anti-Leukemic Properties in Acute Myeloid Leukemia

Author

Dembitz, Vilma, Lawson, Hannah, Philippe, Celine, Burt, Richard J., James, Sophie, Magee, Aoife S.M., Woodley, Keith, Durko, Jozef, Campos, Joana, Austin, Michael James, Rio-Machin, Ana, Casado Izquierdo, Pedro, Bewicke-Copley, Findlay, Rodriguez Blanco, Giovanny, Patel, Bela, Hazlehurst, Lori, Peck, Barrie, Finch, Andrew, Cutillas, Pedro, Fitzgibbon, Jude, Yuneva, Mariia, Rouault-Pierre, Kevin, Copland, John, III, Kranc, Kamil, and Gallipoli, Paolo

Published
2022
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9. Deep Multi-Omics Profiling in Cytogenetically Poor-Risk AML

Author

Rio-Machin, Ana, Bewicke-Copley, Findlay, Zheng, Jiexin, Casado Izquierdo, Pedro, Miettinen, Juho J., Khan, Naeem, Demeulemeester, Jonas, Krizsán, Szilvia, Middleton, Christopher, Benkwitz-Bedford, Sam, Saad, Joseph, Vilas-Zornoza, Amaia, Ezponda, Teresa, Grey, William, Lavallée, Vincent-Philippe, Nolin-Lapalme, Alexis, Miraki-Moud, Farideh, Matthews, Janet, Grantham, Marianne, Colm, Ryan J, Bond, Jonathan, Di Bella, Doriana, Wennerberg, Krister, Parsons, Alun, Zeng, Andy G.X., Armes, Hannah, Close, Karina, Kaya, Fadimana, Rouault-Pierre, Kevin, Gribben, John G., Prosper, Felipe, Cavenagh, James, Dick, John E., Freeman, Sylvie D, Van Loo, Peter, Bödör, Csaba, Sauvageau, Guy, Porkka, Kimmo, Heckman, Caroline A., Wang, Jun, Cazier, Jean-Baptiste, Taussig, David, Bonnet, Dominique, Cutillas, Pedro, and Fitzgibbon, Jude

Published
2022
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10. Whole-Exome Sequencing Identifies MDH2 as a New Familial Paraganglioma Gene

Author

Cascón, Alberto, Comino-Méndez, Iñaki, Currás-Freixes, María, de Cubas, Aguirre A., Contreras, Laura, Richter, Susan, Peitzsch, Mirko, Mancikova, Veronika, Inglada-Pérez, Lucía, Pérez-Barrios, Andrés, Calatayud, María, Azriel, Sharona, Villar-Vicente, Rosa, Aller, Javier, Setién, Fernando, Moran, Sebastian, Garcia, Juan F., Río-Machín, Ana, Letón, Rocío, Gómez-Graña, Álvaro, Apellániz-Ruiz, María, Roncador, Giovanna, Esteller, Manel, Rodríguez-Antona, Cristina, Satrústegui, Jorgina, Eisenhofer, Graeme, Urioste, Miguel, and Robledo, Mercedes

Published
2015
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11. Allele-Specific Expression of Leukemia Genes Is Associated with Pathogenicity in Poor Risk AML

Author

Zheng, Jiexin, Bewicke-Copley, Findlay, Vermeulen, Carlo, Casado, Pedro, Kaya, Fadimana, Demeulemeester, Jonas, Guscott, Molly, Krizsán, Szilvia, Benkwitz-Bedford, Sam, Miraki-Moud, Farideh, Matthews, Janet, Grantham, Marianne, Di Bella, Doriana, Gribben, John G., Cavenagh, James, Van Loo, Peter, McClelland, Sarah, Bödör, Csaba, Cazier, Jean-Baptiste, Taussig, David, Bonnet, Dominique, Cutillas, Pedro R, Wang, Jun, De Ridder, Jeroen, Fitzgibbon, Jude, and Rio-Machin, Ana

Published
2023
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12. The XPO1-FOXC1-HOX Functional Axis Opens New Therapeutic Avenues to Treat DEK-NUP214 AML Patients

Author

Kaya, Fadimana, Bewicke-Copley, Findlay, Casado Izquierdo, Pedro, Zheng, Jiexin, Miettinen, Juho Jalmari, Khan, Naeem, Krizsán, Szilvia, Saad, Joseph J, Lavallée, Vincent-Philippe, Nolin-Lapalme, Alexis, Hébert, Josée, Matthews, Janet, Grantham, Marianne, Di Bella, Doriana, Wennerberg, Krister, Parsons, Alun, Gribben, John G., Cavenagh, James D., Freeman, Sylvie D, Bödör, Csaba, Sauvageau, Guy, Heckman, Caroline A., Wang, Jun, Cazier, Jean-Baptiste, Taussig, David, Bonnet, Dominique, Cutillas, Pedro R, Rouault-Pierre, Kevin, Fitzgibbon, Jude, and Rio-Machin, Ana

Published
2023
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15. Integration of Deep Multi-Omics Profiling Veals New Insights into the Biology of Poor-Risk Acute Myeloid Leukemia

Author

Rio-Machin, Ana, Casado-Izquierdo, Pedro, Miettinen, Juho, Bewicke-Copley, Findlay, Khan, Naeem, Demeulemeester, Jonas, Krizsán, Szilvia, Zheng, Jiexin, Middleton, Christopher, Yin, Wencheng, Grey, William, Miraki-Moud, Farideh, Matthews, Janet, Grantham, Marianne, Rouault-Pierre, Kevin, Wennerberg, Krister, Parsons, Alun, Armes, Hannah, Close, Karina EM, Di Bella, Doriana, Cavenagh, James, Freeman, Sylvie D, Van Loo, Peter, Bödör, Csaba, Porkka, Kimmo, Heckman, Caroline A, Wang, Jun, Taussig, David, Bonnet, Dominique, Cazier, Jean-Baptiste, Cutillas, Pedro, and Fitzgibbon, Jude

Published
2020
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16. A functional role for miR390 and its TAS3-derived tasiRNAs

Author

Cabrera, Javier, Barcala Rodríguez, Marta, García Ruiz, Alejandra, Río-Machín, A., Medina, C., Jaubert- Possamai, S., Favery, B., Maizel, Alexis, Ruiz-Ferrer, Virginia, Fenoll, Carmen, and Escobar, Carolina

Subjects
rasiRNAs, Meloidogyne, Silencing, Galls, miRNAs, Small RNAs, tasiRNAs, Giant cells
Abstract

Root-knot nematodes (RKNs) induce inside the vascular cylinder the giant cells (GCs) embedded in the galls. The distinctive gene repression in early-developing GCs could be facilitated by small RNAs (sRNA) such as miRNAs, and/or epigenetic mechanisms mediated by 24nt-sRNAs, rasiRNAs and 21-22nt-sRNAs. Therefore, the sRNA-population together with the role of the miR390/TAS3/ARFs module were studied during early gall/GC formation. Three sRNA libraries from 3-d-post-inoculation (dpi) galls induced by Meloidogyne javanica in Arabidopsis and three from uninfected root segments were sequenced following Illumina-Solexa technology. pMIR390a::GUS and pTAS3::GUS lines were assayed for nematode- dependent promoter activation. A sensor line indicative of TAS3-derived tasiRNAs binding to the ARF3 sequence (pARF3:ARF3-GUS) together with a tasiRNA-resistant ARF3 line (pARF3:ARF3m-GUS) were used for functional analysis. The sRNA population showed significant differences between galls and controls, with high validation rate and correspondence with their target expression: 21-nt sRNAs corresponding mainly to miRNAs were downregulated, whilst 24-nt-sRNAs from the rasiRNA family were mostly upregulated in galls. The promoters of MIR390a and TAS3, active in galls, and the pARF3:ARF3-GUS line, indicated a role of TAS3-derived-tasiRNAs in galls. The regulatory module miR390/TAS3 is necessary for proper gall formation possibly through auxin-responsive factors, and the abundance of 24-nt sRNAs (mostly rasiRNAs) constitutes a gall hallmark

Published
2015

17. Biological and functional characterization of the fusion gene NUP98-HOXA9 in Acute myeloid leukemia: new therapeutic approaches

Author

Río Machín, Ana del, Cigudosa García, Juan Cruz, UAM. Departamento de Bioquímica, and Centro Nacional de Investigaciones Oncológicas (CNIO)

Subjects
Leucemia mieloide - Aspectos genéticos - Tesis doctorales, Medicina
Abstract

Tesis doctoral inédita leída en la Universidad Autónoma de Madrid, Facultad de Medicina, Departamento de Bioquímica. Fecha de lectura: 27-11-2014, La translocación cromosómica t(7;11)(p15;p15), que origina la proteína de fusión NUP98-HOXA9 (NH), aparece como evento primario en el 1% de los pacientes con Leucemia Mieloide Aguda (LMA) y está asociada con una forma muy agresiva de leucemia (mal pronóstico y baja supervivencia global). Aunque se ha sugerido un papel como factor de transcripción oncogénico, se desconoce el mecanismo molecular mediante el cual NH tiene estos efectos. Además, no existe una terapia específica para estos pacientes, que son tratados con regímenes de quimioterapia estándar muy ineficaces. Por ello, nuestro objetivo ha sido generar modelos celulares humanos que expresen la proteína quimera de forma constitutiva, en los que poder estudiar su papel en la transformación leucémica, así como ampliar la búsqueda de nuevas dianas terapéuticas que permitan tratar de forma dirigida a pacientes que presentan esta translocación cromosómica. Así, hemos identificado por primera vez los sitios de unión al ADN de NH, la mayoría de los cuales son regiones génicas potenciadoras que permiten regular la expresión de genes implicados en el desarrollo de la LMA. En concreto, hemos demostrado que NH induce directamente la sobreexpresión del complejo MEIS1-HOXA9-PBX3, un elemento clave en la biología de leucemias originadas por otros reordenamientos cromosómicos. Para confirmar la importancia de este complejo también en este tipo de LMA, demostramos que el péptido HXR9, un inhibidor de la interacción HOXA9-PBX3, es capaz de matar selectivamente a las células que expresan NH. Además, observamos que, tanto en un modelo celular humano que expresa NH generado a partir de progenitores hematopoyéticos (hHP-NH) como en pacientes con la translocación cromosómica, la proteína de fusión es capaz de activar y reprimir la expresión de sus genes diana. De hecho, demostramos que la interacción de NH con p300 (un activador transcripcional) y con HDAC1 (un inhibidor transcripcional) puede explicar este papel activador-represor de la proteína de fusión. Apoyando esta hipótesis, encontramos un efecto inhibitorio dramático de la viabilidad de hHP-NH con el tratamiento con LBH589, un inhibidor de HDACs, lo que nos lleva a considerar su potencial terapéutico en esta leucemia. Finalmente, en un intento de comprender la contribución de las dos partes que forman la proteína de fusión en la regulación de la expresión génica, observamos que un tercio de los genes diana de NH son comunes a HOXA9. Así mismo, de forma sorprendente, hemos descubierto que también NUP98 parecía funcionar como un factor de transcripción implicado en la regulación de la hematopoiesis. El nuevo papel descubierto para esta nucleoporina ayudará a comprender mejor cómo funciona NH, así como otras fusiones leucémicas en las que también interviene NUP98. En resumen, estos resultados nos han permitido identificar algunos de los mecanismos patogénicos más relevantes inducidos por NH e identificar nuevas dianas terapéuticas que han sido estudiadas en los modelos celulares, con resultados muy prometedores., The chromosomal translocation t(7;11)(p15, p15), which results in the oncogenic fusion protein NUP98-HOXA9 (NH), is a rare but recurrent oncogenic event in AML that is associated with very poor prognosis and short overall survival. The molecular processes triggered by NH are poorly understood, even though a potential role as an aberrant transcription factor has been proposed. Moreover, there is no specific therapy for these patients; they are treated with ineffective standard chemotherapy regimens. Therefore, our main objective has been to generate human cellular models that constitutively express the chimera protein, to study its role in leukemic transformation and expand the search for new therapeutic targets that enable the treatment of the patients with this chromosomal translocation in a targeted manner. Using these models, we have described for the first time the DNA binding sites of NH, most of which are enhancers that regulate the expression of genes involved in the development of AML. In particular, we have shown that the direct overexpression of the complex MEIS1-HOXA9-PBX3, a key element in the onset of leukemia that is driven by other chromosome rearrangements in AML, is also one of the actionable pathogenic mechanisms induced by NH. We have demonstrated that the peptide HXR9, an inhibitor of the interaction HOXA9-PBX3, was indeed able of selectively kill cells expressing NH. Furthermore, we have observed that, in a model of human hematopoietic progenitors expressing NH, and also in patients with the chromosomal translocation, the fusion protein was able to activate and repress the expression of their target genes. We have also shown that the interaction of NH with p300 (transcriptional activator) and HDAC1 (transcriptional inhibitor), could explain this activator-repressor role of the fusion protein. Supporting this hypothesis, we have found a dramatic inhibitory effect on hHP-NH viability after the treatment with LBH589 (an HDAC inhibitor) which allowed us to consider its therapeutic potential for patients carrying the translocation. Finally, in an attempt to understand the contribution of each of the two NH moieties to the regulation of gene expression, we found that a third of the target genes of NH are common to HOXA9 wt. In addition, ChIP-seq results for NUP98 wt revealed the potential role of this nucleoporin in regulating hematopoietic differentiation. This newly role of NUP98 is likely to contribute to a better understanding of how NH, as well as other leukemic fusion proteins in which NUP98 is involved, works. To summarize, these results have allowed us to characterize some of the most relevant pathogenic mechanisms induced by NH and to identify new therapeutic targets that have been studied in our model, yielding very promising results.

Published
2014

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