Browsing by Author "Mereu, Elisabetta"

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  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • Immune cell associations with cancer risk
    Palomero, Luis; Mereu, Elisabetta; Pujana, Miguel Angel (Elsevier, 2020)
    Proper immune system function hinders cancer development, but little is known about whether genetic variants linked to cancer risk alter immune cells. Here, we report 57 cancer risk loci associated with differences in ...
  • Improved diagnosis of rare disease patients through systematic detection of runs of homozygosity
    Matalonga, Leslie; Laurie, Steven, 1973-; Papakonstantinou, Anastasios; Piscia, Davide; Mereu, Elisabetta; Bullich, Gemma; Thompson, Rachel; Horvath, Rita; Pérez Jurado, Luis Alberto; Riess, Olaf; Gut, Ivo Glynne; van Ommen, Gert-Jan; Lochmüller, Hanns; Beltran, Sergi; RD–Connect Genome-Phenome Analysis Platform and URD-Cat Data Contributors (Elsevier, 2020)
    Autozygosity is associated with an increased risk of genetic rare disease, thus being a relevant factor for clinical genetic studies. More than 2400 exome sequencing data sets were analyzed and screened for autozygosity ...
  • Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data
    Holland, Christian H.; Tanevski, Jovan; Perales-Patón, Javier; Gleixner, Jan; Kumar, Manu P.; Mereu, Elisabetta; Joughin, Brian A.; Stegle, Oliver; Lauffenburger, Douglas A.; Heyn, Holger; Szalai, Bence; Saez-Rodriguez, Julio (BioMed Central, 2020)
    BACKGROUND: Many functional analysis tools have been developed to extract functional and mechanistic insight from bulk transcriptome data. With the advent of single-cell RNA sequencing (scRNA-seq), it is in principle ...
  • Single-cell transcriptome conservation in cryopreserved cells and tissues
    Guillaumet-Adkins, Amy; Rodríguez Esteban, Gustavo; Mereu, Elisabetta; Méndez Lago, María; Jaitin, Diego Adhemar; Villanueva, Alberto; Vidal, August; Martínez Martí, Alex; Felip, Enriqueta; Vivancos Prellezo, Ana; Keren-Shaul, Hadas; Heath, Simon; Gut, Marta; Amit, Ido; Gut, Ivo Glynne; Heyn, Holger (BioMed Central, 2017)
    A variety of single-cell RNA preparation procedures have been described. So far, protocols require fresh material, which hinders complex study designs. We describe a sample preservation method that maintains transcripts ...
  • SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes
    Elosua-Bayés, Marc; Nieto, Paula; Mereu, Elisabetta; Gut, Ivo Glynne; Heyn, Holger (Oxford University Press, 2021)
    Spatially resolved gene expression profiles are key to understand tissue organization and function. However, spatial transcriptomics (ST) profiling techniques lack single-cell resolution and require a combination with ...
  • Targeting lymphoid-derived IL-17 signaling to delay skin aging
    Solá, Paloma; Mereu, Elisabetta; Bonjoch, Júlia; Casado-Peláez, Marta; Prats, Neus; Aguilera, Mònica; Reina García, Óscar, 1976-; Blanco, Enrique; Esteller, Manel; Di Croce, Luciano; Heyn, Holger; Solanas, Guiomar; Aznar Benitah, Salvador (Nature Research, 2023)
    Skin aging is characterized by structural and functional changes that contribute to age-associated frailty. This probably depends on synergy between alterations in the local niche and stem cell-intrinsic changes, underscored ...
  • TRIM28 and Interacting KRAB-ZNFs control self-renewal of human pluripotent stem cells through epigenetic repression of pro-differentiation genes
    Oleksiewicz, Urszula; Gładych, Marta; Raman, Ayush T.; Heyn, Holger; Mereu, Elisabetta; Chlebanowska, Paula; Andrzejewska, Anastazja; Sozańska, Barbara; Samant, Neha; Fąk, Katarzyna; Auguścik, Paulina; Kosiński, Marcin; Wróblewska, Joanna P.; Tomczak, Katarzyna; Kulcenty, Katarzyna; Płoski, Rafał; Biecek, Przemysław; Esteller, Manel; Shah, Parantu K.; Rai, Kunal; Wiznerowicz, Maciej (Elsevier, 2017)
    Reprogramming to induced pluripotent stem cells (iPSCs) and differentiation of pluripotent stem cells (PSCs) are regulated by epigenetic machinery. Tripartite motif protein 28 (TRIM28), a universal mediator of Krüppel-associated ...

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