Browsing by Author "Heyn, Holger"

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  • A DNA methylation map of human cancer at single base-pair resolution
    Vidal Ocabo, Enrique; Sayols, Sergi; Moran, Sebastian; Guillaumet-Adkins, Amy; Schroeder, Michael Philipp, 1986-; Royo, Romina; Orozco, Modesto; Gut, Marta; Gut, Ivo Glynne; López Bigas, Núria; Heyn, Holger; Esteller, Manel (Nature Publishing Group, 2017)
    Although single base-pair resolution DNA methylation landscapes for embryonic and different somatic cell types provided important insights into epigenetic dynamics and cell-type specificity, such comprehensive profiling ...
  • A single-cell tumor immune atlas for precision oncology
    Nieto, Paula; Elosua-Bayés, Marc; Trincado Alonso, Juan Luis, 1987-; Marchese, Domenica, 1986-; Massoni-Badosa, Ramon; Nieto, Juan C.; Aguilar-Fernández, Sergio; Mereu, Elisabetta; Moutinho, Catia; Ruiz, Sara; Lorden, Patricia; Gut, Ivo Glynne; Heyn, Holger (Cold Spring Harbor Laboratory Press (CSHL Press), 2021)
    The tumor immune microenvironment is a main contributor to cancer progression and a promising therapeutic target for oncology. However, immune microenvironments vary profoundly between patients, and biomarkers for prognosis ...
  • ATM germline variants in a young adult with chronic lymphocytic leukemia: 8 years of genomic evolution
    Royo, Romina; Magnano, Laura; Delgado González, Julio; Ruiz Gil, Sara; Gelpí, Josep Lluís; Heyn, Holger; Taylor, Malcom A.; Stankovic, Tatjana; Puente, Xosé S.; Nadeu, Ferran; Campo, Elias (Nature Research, 2022)
  • Benchmarking single-cell RNA sequencing protocols for cell atlas projects
    Mereu, Elisabetta; Lafzi, Atefeh; Moutinho, Catia; Gut, Marta; Gut, Ivo Glynne; Heyn, Holger (Nature Research, 2020)
    Single-cell RNA sequencing (scRNA-seq) is the leading technique for characterizing the transcriptomes of individual cells in a sample. The latest protocols are scalable to thousands of cells and are being used to compile ...
  • bigSCale: an analytical framework for big-scale single-cell data
    Iacono, Giovanni; Mereu, Elisabetta; Guillaumet-Adkins, Amy; Corominas, Roser; Cuscó Martí, Ivon, 1973-; Rodríguez Esteban, Gustavo; Gut, Marta; Pérez Jurado, Luis Alberto; Gut, Ivo Glynne; Heyn, Holger (Cold Spring Harbor Laboratory Press (CSHL Press), 2018)
    Single-cell RNA sequencing (scRNA-seq) has significantly deepened our insights into complex tissues, with the latest techniques capable of processing tens of thousands of cells simultaneously. Analyzing increasing numbers ...
  • Charting intra-tumoral heterogeneity dynamics through the integration of multi-modal single-cell profiles
    Elosua-Bayés, Marc (Universitat Pompeu Fabra, 2023-06-27)
    Understanding multicellular organisms depends on the advent of technologies capable of delivering unprecedented levels of resolution. With new technologies come novel data modalities, which require the development of tools ...
  • Charting the heterogeneity of healthy and malignant immune cells, one cell at a time
    Massoni Badosa, Ramon (Universitat Pompeu Fabra, 2023-03-17)
    Specialization and plasticity are hallmarks of immune cells. Thus, charting their heterogeneity is crucial to understand their function and role in diseases. In this setting, single-cell RNA-sequencing (scRNA-seq) has ...
  • Cohesin couples transcriptional bursting probabilities of inducible enhancers and promoters
    Robles-Rebollo, Irene; Cuartero, Sergi; Canellas-Socias, Adria; Wells, Sarah; Karimi, Mohammad M.; Mereu, Elisabetta; Chivu, Alexandra G.; Heyn, Holger; Whilding, Chad; Dormann, Dirk; Marguerat, Samuel; Rioja, Inmaculada; Prinjha, Rab K.; Stumpf, Michael P.H.; Fisher, Amanda G.; Merkenschlager, Matthias (Nature Research, 2022)
    Innate immune responses rely on inducible gene expression programmes which, in contrast to steady-state transcription, are highly dependent on cohesin. Here we address transcriptional parameters underlying this cohesin-dependence ...
  • Comparative analysis of single-cell RNA sequencing methods
    Ziegenhain, Christoph; Vieth, Beate I.H.; Parekh, Swati; Reinius, Björn; Guillaumet-Adkins, Amy; Smets, Martha; Leonhardt, Heinrich; Heyn, Holger; Hellmann, Ines; Enard, Wolfgang (Elsevier, 2017)
    Single-cell RNA sequencing (scRNA-seq) offers new possibilities to address biological and medical questions. However, systematic comparisons of the performance of diverse scRNA-seq protocols are lacking. We generated data ...
  • Controlled X-chromosome dynamics defines meiotic potential of female mouse in vitro germ cells
    Severino, Jacqueline, 1990-; Bauer, Moritz, 1987-; Mattimoe, Tom; Arecco, Niccolò; Cozzuto, Luca; Lorden, Patricia; Hamada, Norio; Nosaka, Yoshiaki; Nagaoka, So I.; Audergon, Pauline; Tarruell Pellegrin, Antonio,1990-; Heyn, Holger; Hayashi, Katsuhiko; Saitou, Mitinori; Payer, Bernhard (EMBO Press, 2022)
    The mammalian germline is characterized by extensive epigenetic reprogramming during its development into functional eggs and sperm. Specifically, the epigenome requires resetting before parental marks can be established ...
  • Copy number rather than epigenetic alterations are the major dictator of imprinted methylation in tumors
    Martin-Trujillo, Alex; Vidal Ocabo, Enrique; Monteagudo-Sánchez, Ana; Sanchez-Delgado, Marta; Moran, Sebastian; Hernández Mora, José Ramón; Heyn, Holger; Guitart, Miriam; Esteller, Manel; Monk, David (Nature Publishing Group, 2017)
    It has been postulated that imprinting aberrations are common in tumors. To understand the role of imprinting in cancer, we have characterized copy-number and methylation in over 280 cancer cell lines and confirm our ...
  • Deciphering B lymphocyte dynamics in health and disease through the integrative analysis of multi-modal single-cell data
    Aguilar Fernández, Sergio (Universitat Pompeu Fabra, 2024-04-26)
    The intrinsic complexity and dynamic nature of B-lymphocytes make them ideal for in-depth analysis using single-cell technologies. Secondary lymphoid organs (SLOs) are central in B-lymphocyte activation and differentiation, ...
  • Detection of early seeding of Richter transformation in chronic lymphocytic leukemia
    Nadeu, Ferran; Massoni-Badosa, Ramon; Ruiz Gil, Sara; Marchese, Domenica, 1986-; López Bigas, Núria; Gut, Ivo Glynne; Heyn, Holger; Campo, Elias (Nature Research, 2022)
    Richter transformation (RT) is a paradigmatic evolution of chronic lymphocytic leukemia (CLL) into a very aggressive large B cell lymphoma conferring a dismal prognosis. The mechanisms driving RT remain largely unknown. ...
  • DNA methylation contributes to natural human variation
    Heyn, Holger; Moran, Sebastian; Hernando Herráez, Irene, 1985-; Sayols, Sergi; Gómez, Antonio; Sandoval, Juan; Monk, David; Hata, Kenichiro; Marquès i Bonet, Tomàs, 1975-; Wang, Liewei; Esteller, Manel (Cold Spring Harbor Laboratory Press (CSHL Press), 2013)
    DNA methylation patterns are important for establishing cell, tissue, and organism phenotypes, but little is known about their contribution to natural human variation. To determine their contribution to variability, we ...
  • Dual MET and ERBB inhibition overcomes intratumor plasticity in osimertinib-resistant-advanced non-small-cell lung cancer (NSCLC)
    Martinez-Marti, Alex; Felip, Enriqueta; Matito, Judit; Mereu, Elisabetta; Navarro, Alejandro; Cedrés, Susana; Pardo, Núria; Martines de Castro, Ana; Remon, Jordi; Miquel, Josep M.; Guillaumet-Adkins, Amy; Nadal, Ernest; Rodríguez Esteban, Gustavo; Arqués, Oriol; Fasani, Roberta; Nuciforo, Paolo G.; Heyn, Holger; Villanueva, Alberto; Palmer, Héctor G.; Vivancos Prellezo, Ana (Oxford University Press, 2017)
    BACKGROUND: Third-generation epidermal growth factor receptor tyrosine kinase inhibitors (EGFR-TKIs) such as osimertinib are the last line of targeted treatment of metastatic non-small-cell lung cancer (NSCLC) EGFR-mutant ...
  • Dynamics of DNA methylation in recent human and great ape evolution
    Hernando Herráez, Irene, 1985-; Prado Martínez, Javier, 1987-; Garg, Paras; Fernández Callejo, Marcos; Heyn, Holger; Hvilsom, Christina; Navarro i Cuartiellas, Arcadi, 1969-; Esteller, Manel; Sharp, Andrew J.; Marquès i Bonet, Tomàs, 1975- (Public Library of Science (PLoS), 2013)
    DNA methylation is an epigenetic modification involved in regulatory processes such as cell differentiation during development, X-chromosome inactivation, genomic imprinting and susceptibility to complex disease. However, ...
  • GATA2 promotes hematopoietic development and represses cardiac differentiation of human mesoderm
    Castaño, Julio; Aranda Aragón, Sergio; Blanco, Enrique; Mereu, Elisabetta; Heyn, Holger; Di Croce, Luciano; Giorgetti, Alessandra (Elsevier, 2019)
    In vertebrates, GATA2 is a master regulator of hematopoiesis and is expressed throughout embryo development and in adult life. Although the essential role of GATA2 in mouse hematopoiesis is well established, its involvement ...
  • Glioblastoma cell fate is differentially regulated by the microenvironments of the tumor bulk and infiltrative margin
    Garcia-Diaz, Claudia; Pöysti, Anni; Mereu, Elisabetta; Clements, Melanie P.; Brooks, Lucy J.; Galvez-Cancino, Felipe; Castillo, Simon P.; Tang, Wenhao; Beattie, Gordon; Courtot, Lilas; Ruiz, Sara; Roncaroli, Federico; Yuan, Yinyin; Marguerat, Samuel; Quezada, Sergio A.; Heyn, Holger; Parrinello, Simona (Elsevier, 2023)
    Glioblastoma (GBM) recurrence originates from invasive margin cells that escape surgical debulking, but to what extent these cells resemble their bulk counterparts remains unclear. Here, we generated three immunocompetent ...
  • Human DNA methylomes of neurodegenerative diseases show common epigenomic patterns
    Sánchez Mut, Jose V.; Heyn, Holger; Vidal, Enrique; Moran, Sebastian; Sayols, Sergi; Delgado Morales, Raul; Schultz, Matthew D.; Ansoleaga, Belén; García Esparcia, Paula; Pons Espinal, Meritxell, 1986-; Martínez de Lagrán Cabredo, María; Dopazo, Jose M.; Rábano, Alberto; Ávila, Jesús; Dierssen, Mara; Lott, Ira T.; Ferrer, Isidre; Ecker, Joseph R.; Esteller, Manel (Nature Publishing Group, 2016)
    Different neurodegenerative disorders often show similar lesions, such as the presence of amyloid plaques, TAU-neurotangles and synuclein inclusions. The genetically inherited forms are rare, so we wondered whether shared ...
  • Identity noise and adipogenic traits characterize dermal fibroblast aging
    Aznar Benitah, Salvador; Lafzi, Atefeh; Berenguer-Llergo, Antonio; Youssif, Catrin; Castellanos, Andrés; Solanas, Guiomar; Peixoto, Francisca Oliveira; Stephan-Otto Attolini, Camille; Prats, Neus; Aguilera, Mònica; Martín Caballero, Juan; Heyn, Holger; Aznar Benitah, Salvador (Elsevier, 2018)
    During aging, stromal functions are thought to be impaired, but little is known whether this stems from changes of fibroblasts. Using population- and single-cell transcriptomics, as well as long-term lineage tracing, we ...

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