Single-cell genomics to comprehensively understand healthy B-cell maturation and transformation to chronic lymphocytic leukemia

Project Information

BCLLatlas

Grant agreement ID: 810287

DOI

10.3030/810287

Project closed

EC signature date 29 March 2019

Start date 1 April 2019

End date 31 December 2025

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 8 333 331,00

EU contribution

€ 8 333 331,00

Coordinated by

CONSORCIO PARA LA EXPLOTACION DEL CENTRO NACIONAL DE ANALISIS GENOMICO
Spain

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (25)

SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes

Author(s): Marc Elosua-Bayes, Paula Nieto, Elisabetta Mereu, Ivo Gut, Holger Heyn
Published in: Nucleic Acids Research, Issue 49/9, 2021, Page(s) e50-e50, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkab043

"CHROMATIN ACTIVATION PROFILING OF STEREOTYPED CHRONIC LYMPHOCYTIC LEUKEMIAS REVEALS A SUBSET #8 SPECIFIC SIGNATURE"

Author(s): Maria Tsagiopoulou, Vicente Chapaprieta, Nuria Russiñol, Beatriz García-Torre, Nikolaos Pechlivanis, Ferran Nadeu, Nikos Papakonstantinou, Niki Stavroyianni, Anastasia Chatzidimitriou, Fotis Psomopoulos, Elías Campo, Kostas Stamatopoulos, Jose I. Martin-Subero
Published in: Blood, 2023, ISSN 0006-4971
Publisher: American Society of Hematology
DOI: 10.1182/blood.2022016587

A Transcriptional Map of Human Tonsil Architecture: Beyond the Sum of (Single Cell) Parts

Author(s): Helena L. Crowell, Laura Llaó‐Cid, Gerard Frigola, Samuel Gunz, Irene Ruano, Patricia Lorden, Max Ruiz, Marta Kulis, José Ignacio Martin‐Subero, Holger Heyn, Elias Campo, Anna Pascual‐Reguant
Published in: European Journal of Immunology, Issue 56, 2026, ISSN 0014-2980
Publisher: John Wiley & Sons Ltd.
DOI: 10.1002/eji.70121

Increased LEF1 protein levels and isoform switching drive cell proliferation in chronic lymphocytic leukemia

Author(s): Judith Mateos-Jaimez, Anna Vidal-Crespo, Stella Charalampopoulou, Raúl F. Pérez, Vicente Chapaprieta, Víctor Jiménez-Martínez, Liska Caviedes-Cárdenas, Martí Duran-Ferrer, Guadalupe Espadas, Eduard Sabidó, Anne Largeot, Sophie A. Herbst, Sascha Dietrich, Miguel Bastos Boente, Miguel Alcoceba, Ferran Nadeu, Ingo Ringshausen, Jerome Paggetti, Etienne Moussay, Dolors Colomer, Elias Campo, Alb
Published in: Blood, Issue 146, 2025, Page(s) 3213-3227, ISSN 0006-4971
Publisher: American Society of Hematology
DOI: 10.1182/blood.2025030129

The emerging landscape of spatial profiling technologies

Author(s): Jeffrey R. Moffitt, Emma Lundberg, Holger Heyn
Published in: Nature Reviews Genetics, Issue 23, 2022, Page(s) 741-759, ISSN 1471-0056
Publisher: Nature Publishing Group
DOI: 10.1038/s41576-022-00515-3

Machine learning and multi-omics data in chronic lymphocytic leukemia: the future of precision medicine?

Author(s): Maria Tsagiopoulou, Ivo G. Gut
Published in: Frontiers in Genetics, Issue 14, 2024, ISSN 1664-8021
Publisher: Frontiers Media
DOI: 10.3389/fgene.2023.1304661

Detection of early seeding of Richter transformation in chronic lymphocytic leukemia

Author(s): Ferran Nadeu, Romina Royo, Ramon Massoni-Badosa, Heribert Playa-Albinyana, Beatriz Garcia-Torre, Martí Duran-Ferrer, Kevin J. Dawson, Marta Kulis, Ander Diaz-Navarro, Neus Villamor, Juan L. Melero, Vicente Chapaprieta, Ana Dueso-Barroso, Julio Delgado, Riccardo Moia, Sara Ruiz-Gil, Domenica Marchese, Ariadna Giró, Núria Verdaguer-Dot, Mónica Romo, Guillem Clot, Maria Rozman, Gerard Frigola, Al
Published in: Nature Medicine, Issue 28, 2022, Page(s) 1662-1671, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-022-01927-8

Fluctuating DNA methylation tracks cancer evolution at clinical scale

Author(s): Calum Gabbutt, Martí Duran-Ferrer, Heather E. Grant, Diego Mallo, Ferran Nadeu, Jacob Househam, Neus Villamor, Madlen Müller, Simon Heath, Emanuele Raineri, Olga Krali, Jessica Nordlund, Thorsten Zenz, Ivo G. Gut, Elias Campo, Armando Lopez-Guillermo, Jude Fitzgibbon, Chris P. Barnes, Darryl Shibata, José I. Martin-Subero, Trevor A. Graham
Published in: Nature, Issue 645, 2025, Page(s) 764-773, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-025-09374-4

Dual biological role and clinical impact of de novo chromatin activation in chronic lymphocytic leukemia

Author(s): Vicente Chapaprieta, Alba Maiques-Diaz, Ferran Nadeu, Guillem Clot, Ramon Massoni-Badosa, Pablo Mozas, Judith Mateos-Jaimez, Anna Vidal, Stella Charalampopoulou, Martí Duran-Ferrer, Romina Royo, Núria Russiñol, Laura Llaó-Cid, Juan A. Piñeyroa, Neus Villamor, Holger Heyn, Sophie A. Herbst, Junyan Lu, Dean J. Bryant, Jonathan C. Strefford, Sascha Dietrich, Thorsten Zenz, Julio Delgado, Armando
Published in: Blood, Issue 145, 2025, Page(s) 2473-2487, ISSN 0006-4971
Publisher: American Society of Hematology
DOI: 10.1182/blood.2024025396

An atlas of cells in the human tonsil

Author(s): Ramon Massoni-Badosa, Sergio Aguilar-Fernández, Juan C. Nieto, Paula Soler-Vila, Marc Elosua-Bayes, Domenica Marchese, Marta Kulis, Amaia Vilas-Zornoza, Marco Matteo Bühler, Sonal Rashmi, Clara Alsinet, Ginevra Caratù, Catia Moutinho, Sara Ruiz, Patricia Lorden, Giulia Lunazzi, Dolors Colomer, Gerard Frigola, Will Blevins, Lucia Romero-Rivero, Víctor Jiménez-Martínez, Anna Vidal, Judith Mate
Published in: Immunity, Issue 57, 2024, Page(s) 379-399.e18, ISSN 1074-7613
Publisher: Cell Press
DOI: 10.1016/j.immuni.2024.01.006

Sampling time-dependent artifacts in single-cell genomics studies

Author(s): Ramon Massoni-Badosa, Giovanni Iacono, Catia Moutinho, Marta Kulis, Núria Palau, Domenica Marchese, Javier Rodríguez-Ubreva, Esteban Ballestar, Gustavo Rodriguez-Esteban, Sara Marsal, Marta Aymerich, Dolors Colomer, Elias Campo, Antonio Julià, José Ignacio Martín-Subero, Holger Heyn
Published in: Genome Biology, Issue 21/1, 2020, ISSN 1474-760X
Publisher: BMC, Nature Publishing Group
DOI: 10.1186/s13059-020-02032-0

STAMP: Single-cell transcriptomics analysis and multimodal profiling through imaging

Author(s): Emanuele Pitino, Anna Pascual-Reguant, Felipe Segato-Dezem, Kellie Wise, Irepan Salvador-Martinez, Helena Lucia Crowell, Maycon Marção, Max Ruiz, Elise Courtois, William F. Flynn, Santhosh Sivajothi, Emily Soja, Ginevra Caratù, German Atzin Mora-Roldan, B. Kate Dredge, Yutian Liu, Hannah Chasteen, Monika Mohenska, Juan C. Nieto, Raymond K.H. Yip, Ruvimbo D. Mishi, José M. Polo, Mohmed Abdalftt
Published in: Cell, Issue 188, 2026, Page(s) 5100-5117.e26, ISSN 0092-8674
Publisher: Cell Press
DOI: 10.1016/j.cell.2025.05.027

The proliferative history shapes the DNA methylome of B-cell tumors and predicts clinical outcome

Author(s): Martí Duran-Ferrer, Guillem Clot, Ferran Nadeu, Renée Beekman, Tycho Baumann, Jessica Nordlund, Yanara Marincevic-Zuniga, Gudmar Lönnerholm, Alfredo Rivas-Delgado, Silvia Martín, Raquel Ordoñez, Giancarlo Castellano, Marta Kulis, Ana C. Queirós, Seung-Tae Lee, Joseph Wiemels, Romina Royo, Montserrat Puiggrós, Junyan Lu, Eva Giné, Sílvia Beà, Pedro Jares, Xabier Agirre, Felipe Prosper, Ca
Published in: Nature Cancer, Issue 1/11, 2020, Page(s) 1066-1081, ISSN 2662-1347
Publisher: Nature Publishing Group
DOI: 10.1038/s43018-020-00131-2

<i>BCL3</i> rearrangements in B-cell lymphoid neoplasms occur in two breakpoint clusters associated with different diseases

Author(s): Anna Carbo-Meix, Francesca Guijarro, Luojun Wang, Marta Grau, Romina Royo, Gerard Frigola, Heribert Playa-Albinyana, Marco M. Buhler, Guillem Clot, Marti Duran-Ferrer, Junyan Lu, Isabel Granada, Maria-Joao Baptista, Jose-Tomas Navarro, Blanca Espinet, Anna Puiggros, Gustavo Tapia, Laura Bandiera, Gabriella De Canal, Emanuela Bonoldi, Fina Climent, Inmaculada Ribera-Cortada, Mariana Fernandez-Cabal
Published in: Haematologica, Issue 109, 2024, Page(s) 493-508, ISSN 0390-6078
Publisher: Ferrata Storti Foundation
DOI: 10.3324/haematol.2023.283209

Interpretable inflammation landscape of circulating immune cells

Author(s): Laura Jiménez-Gracia, Davide Maspero, Sergio Aguilar-Fernández, Francesco Craighero, Maria Boulougouri, Max Ruiz, Domenica Marchese, Ginevra Caratù, Jose Liñares-Blanco, Miren Berasategi, Ricardo O. Ramirez Flores, Angela Sanzo-Machuca, Ana M. Corraliza, Hoang A. Tran, Rachelly Normand, Jacquelyn Nestor, Yourae Hong, Tessa Kole, Petra van der Velde, Frederique Alleblas, Flaminia Pedretti, Adri
Published in: Nature Medicine, Issue 32, 2026, Page(s) 633-644, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-025-04126-3

MYC target gene activation in chronic lymphocytic leukemia and richter transformation: links to aggressiveness and tumor microenvironment interactions

Author(s): M. Tsagiopoulou, S. Rashmi, M. Chatziaslani, I. Gut
Published in: Frontiers in Pharmacology, Issue 16, 2025, ISSN 1663-9812
Publisher: Frontiers Media S.A.
DOI: 10.3389/fphar.2025.1642458

IGLV3-21R110 mutation has prognostic value in patients with treatment-naive chronic lymphocytic leukemia

Author(s): Charlotte Syrykh, Berta Pons-Brun, Núria Russiñol, Heribert Playa-Albinyana, Tycho Baumann, Martí Duran-Ferrer, Marta Kulis, Anna Carbó-Meix, Pablo Mozas, Miguel Alcoceba, Marcos González, Almudena Navarro-Bailón, Enrique Colado, Ángel R. Payer, Marta Aymerich, María J. Terol, Junyan Lu, Binyamin A. Knisbacher, Cynthia K. Hahn, Sílvia Ruiz-Gaspà, Anna Enjuanes, Catherine J. Wu, Gad Getz,
Published in: Blood Advances, Issue 7, 2023, Page(s) 7384-7391, ISSN 2473-9529
Publisher: American Society of Hematology
DOI: 10.1182/bloodadvances.2023010132

A method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome

Author(s): Ieva Keraite, Philipp Becker, Davide Canevazzi, Cristina Frias-López, Marc Dabad, Raúl Tonda-Hernandez, Ida Paramonov, Matthew John Ingham, Isabelle Brun-Heath, Jordi Leno, Anna Abulí, Elena Garcia-Arumí, Simon Charles Heath, Marta Gut, Ivo Glynne Gut
Published in: Nature Communications, Issue 13, 2022, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-022-33530-3

Multi-organ single-cell transcriptomics of immune cells uncovered organ-specific gene expression and functions

Author(s): Maria Tsagiopoulou, Sonal Rashmi, Sergio Aguilar, Juan Nieto, Ivo G. Gut
Published in: Scientific Data, 2026, ISSN 2052-4463
Publisher: Springer Nature
DOI: 10.1101/2023.05.29.542692

Robust CRISPR-Cas9 Genetic Editing of Primary Chronic Lymphocytic Leukemia and Mantle Cell Lymphoma Cells

Author(s): Judith Mateos-Jaimez, Maurizio Mangolini, Anna Vidal, Marta Kulis, Dolors Colomer, Elias Campo, Ingo Ringshausen, Jose I. Martin-Subero, Alba Maiques-Diaz
Published in: HemaSphere, Issue 7, 2023, Page(s) e909, ISSN 2572-9241
Publisher: Wiley
DOI: 10.1097/hs9.0000000000000909

Spatiotemporal T-cell tracking for personalized T-cell receptor T-cell therapy designs in childhood cancer

Author(s): I. Sentís, J.L. Melero, A. Cebria-Xart, M. Grzelak, M. Soto, A. Michel, Q. Rovira, C.J. Rodriguez-Hernandez, G. Caratù, A. Urpi, C. Sauvage, A. Mendizabal-Sasieta, D. Maspero, C.E. Lavarino, A. Pascual-Reguant, A. Castañeda Heredia, J.P. Muñoz Perez, J. Mora, A. Harari, J.C. Nieto, A. Avgustinova, H. Heyn
Published in: Annals of Oncology, Issue 36, 2025, Page(s) 1096-1106, ISSN 0923-7534
Publisher: Oxford University Press
DOI: 10.1016/j.annonc.2025.05.530

Systematic benchmarking of single-cell ATAC-sequencing protocols

Author(s): Florian V. De Rop, Gert Hulselmans, Chris Flerin, Paula Soler-Vila, Albert Rafels, Valerie Christiaens, Carmen Bravo González-Blas, Domenica Marchese, Ginevra Caratù, Suresh Poovathingal, Orit Rozenblatt-Rosen, Michael Slyper, Wendy Luo, Christoph Muus, Fabiana Duarte, Rojesh Shrestha, S. Tansu Bagdatli, M. Ryan Corces, Lira Mamanova, Andrew Knights, Kerstin B. Meyer, Ryan Mulqueen, Akram Taheri
Published in: Nature Biotechnology, Issue 42, 2024, Page(s) 916-926, ISSN 1087-0156
Publisher: Nature Publishing Group
DOI: 10.1038/s41587-023-01881-x

IGLV3-21R110 identifies an aggressive biological subtype of chronic lymphocytic leukemia with intermediate epigenetics

Author(s): Ferran Nadeu, Romina Royo, Guillem Clot, Martí Duran-Ferrer, Alba Navarro, Silvia Martín, Junyan Lu, Thorsten Zenz, Tycho Baumann, Pedro Jares, Xose S. Puente, José I. Martín-Subero, Julio Delgado, Elías Campo
Published in: Blood, Issue 137/21, 2021, Page(s) 2935-2946, ISSN 0006-4971
Publisher: American Society of Hematology
DOI: 10.1182/blood.2020008311

Identification of two epitypes of IGHV unmutated chronic lymphocytic leukemia with distinct B‐cell‐related epigenetic imprinting and genetic alterations

Author(s): Stella Charalampopoulou, Silvia Ramos‐Campoy, Marti Duran‐Ferrer, Anna Puiggros, Joanna Kamaso, Florence Nguyen‐Khac, Gian Matteo Rigolin, Antonio Cuneo, Rosa Collado, Rocío García‐Serra, Claudia Haferlach, Margarita Ortega, Pau Abrisqueta, Francesc Bosch, Thorsten Zenz, María Laura Blanco, Rocío Salgado, Mª Dolores García‐Malo, Eva Gimeno, Armando Lopez‐Guillermo, Elias Campo, L
Published in: HemaSphere, Issue 10, 2026, ISSN 2572-9241
Publisher: Wiley
DOI: 10.1002/hem3.70211

A single-cell tumor immune atlas for precision oncology

Author(s): Paula Nieto, Marc Elosua-Bayes, Juan L. Trincado, Domenica Marchese, Ramon Massoni-Badosa, Maria Salvany, Ana Henriques, Juan Nieto, Sergio Aguilar-Fernández, Elisabetta Mereu, Catia Moutinho, Sara Ruiz, Patricia Lorden, Vanessa T. Chin, Dominik Kaczorowski, Chia-Ling Chan, Richard Gallagher, Angela Chou, Ester Planas-Rigol, Carlota Rubio-Perez, Ivo Gut, Josep M. Piulats, Joan Seoane, Joseph E. P
Published in: Genome Research, Issue 31/10, 2021, Page(s) 1913-1926, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.273300.120