Ballestar lab 2022

Researchers find epigenetic alterations in the immune system behind severe Covid-19

Monocytes from severe covid-19 patients show an altered epigenetic status, according to results by the Epigenetic and Immune Disease group of the Josep Carreras Leukaemia Research Institute. The alterations found in these cells, key in promoting inflammation, can explain features of the aberrant immune response against Sars-Cov-2 infection, such as impaired communication with other immune cells and maturation defects. This comprehensive analysis of monocyte’s epigenetics under severe covid-19, the first of its kind, stresses the importance of these cells in modulating the immune response.

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Eduard Porta Entrevista

Eduard Porta: "The future of Artificial Intelligence in biomedicine is bright"

Dr. Eduard Porta, leader of the Cancer Immunogenomics group at the Josep Carreras Leukaemia Research Institute, has participated in a community initiative to put into context the value of AlphaFold2 predictions, an algorithm created by Deep Mind, the Google's specialized artificial intelligence company, capable of determining the three-dimensional structure of all known human proteins. Their conclusions have recently been published in the specialized journal Nature Structural Biology.

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Unoentrecienmil 2022

Unoentrecienmil awards a project for the development of an immunotherapy against one of the pediatric leukemias with the worst prognosis

The Unoentrecienmil Foundation, which promotes research projects for the complete cure of childhood leukemia, today awarded its 9th Annual Research Grant to Dr. Clara Bueno of the Josep Carreras Leukaemia Research Institute. For two years, the Doctor will carry out her work to develop new therapeutic strategies, some based on immunotherapy, against the NG2 antigen, related to relapses of B-cell Acute Lymphoblastic Leukemia with alterations in the MLL gene, and thus improve the survival rate of these patients, now at 35%.

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IJC Building white wall

The Josep Carreras Leukemia Research Institute stabilizes 21 structural positions, becoming one of the fastest growing research centers in Catalonia

The Official Journal of the Generalitat of Catalonia has just published the resolution that stabilizes 21 places in the administration units and common services of the Josep Carreras Leukaemia Research Institute. With this stabilization, the Research Institute adopts an indefinite hiring scheme, as commanded by the latest Spanish labor reform.

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Ballestar lab 2022

Vitamin C may hold the key to improve efficacy of dendritic cell-derived anticancer cell therapies

Researchers from the Epigenetics and Immune Disease Lab at the Josep Carreras Leukaemia Research Institute has recently shown that vitamin C improves the immunogenic properties of dendritic cells, in vitro. Results recently made public show that treating the cells with vitamin C leads to a more consistent activation of genes involved in the immune response, mainly through DNA demethylation, a kind of epigenetic reprogramming. This discovery may be useful to generate more potent dendritic cell-based therapies in the future.

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CarrerasLeaders: Postdoctoral Program Empowering Future Leaders to Fight Blood Cancers

CarrerasLeaders is a new innovative and international postdoctoral program, designed by the Josep Carreras Leukaemia Research Institute (IJC), which receives funding from the European Commission Horizon Europe Marie Curie Skodowska COFUND Program (GA No. 101081347) and counts with the collaboration of the Josep Carreras International Foundation and the scientific coordination of Dr Buschbeck.

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Recent publications

Godoy-Tena G, Barmada A, Morante-Palacios O, de la Calle-Fabregat C, Martins-Ferreira R, Ferreté-Bonastre AG, Ciudad L, Ruiz-Sanmartín A, Martínez-Gallo M, Ferrer R, Ruiz-Rodriguez JC, Rodríguez-Ubreva J, Vento-Tormo R, Ballestar E

Epigenetic and transcriptomic reprogramming in monocytes of severe COVID-19 patients reflects alterations in myeloid differentiation and the influence of inflammatory cytokines.

Genome Med 29 Nov 2022, 14 (1) 134. Epub 29 Nov 2022
COVID-19 manifests with a wide spectrum of clinical phenotypes, ranging from asymptomatic and mild to severe and critical. Severe and critical COVID-19 patients are characterized by marked changes in the myeloid compartment, especially monocytes. However, little is known about the epigenetic alterations that occur in these cells during hyperinflammatory responses in severe COVID-19 patients.
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Giulia Maggioni, Matteo Bersanelli, Erica Travaglino, Ana Alfonso Piérola, Annika Kasprzak, Arnan Sangerman Montserrat, Elisabetta Sauta, Claudia Sala, Tommaso Matteuzzi, Manja Meggendorfer, Matteo Gnocchi, Lin-Pierre Zhao, Cristina Astrid Tentori, Kathrin Nachtkamp, Daniele Dall'Olio, Ettore Mosca, Marta Ubezio, Alessia Campagna, Antonio Russo, Giulia Rivoli, Massimo Bernardi, Lorenza Borin, Maria Teresa Voso, Marta Riva, Esther Natalie Oliva, Matteo Zampini, Elena Riva, Elena Saba, Saverio D'Amico, Luca Lanino, Benedetta Tinterri, Francesca Re, Marilena Bicchieri, Laura Giordano, Giovanni Angelotti, Pierandrea Morandini, Anne Sophie Kubasch, Francesco Passamonti, Alessandro Rambaldi, Victor Savevski, Armando Santoro, Arjan A van de Loosdrecht, Alice Brogi, Valeria Santini, Shahram Kordasti, Guillermo Sanz, Francesc Sole, Norbert Gattermann, Wolfgang Kern, Uwe Platzbecker, Lionel Ades, Pierre Fenaux, Torsten Haferlach, Gastone Castellani, Ulrich Germing, Maria Diez-Campelo, Matteo G Della Porta.

A sex-informed approach to improve the personalised decision making process in myelodysplastic syndromes: a multicentre, observational cohort study.

The Lancet Haematology 24 Nov 2022, . Epub 24 Nov 2022
Sex is a major source of diversity among patients and a sex-informed approach is becoming a new paradigm in precision medicine. We aimed to describe sex diversity in myelodysplastic syndromes in terms of disease genotype, phenotype, and clinical outcome. Moreover, we sought to incorporate sex information into the clinical decision-making process as a fundamental component of patient individuality.
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Pamela Acha, Mar Mallo, Francesc Solé

Myelodysplastic Syndromes with Isolated del(5q): Value of Molecular Alterations for Diagnostic and Prognostic Assessment

Cancers 10 Nov 2022, .
Myelodysplastic syndromes (MDS) are a group of clonal hematological neoplasms characterized by ineffective hematopoiesis in one or more bone marrow cell lineages. Consequently, patients present with variable degrees of cytopenia and dysplasia. These characteristics constitute the basis for the World Health Organization (WHO) classification criteria of MDS, among other parameters, for the current prognostic scoring system. Although nearly half of newly diagnosed patients present a cytogenetic alteration, and almost 90% of them harbor at least one somatic mutation, MDS with isolated del(5q) constitutes the only subtype clearly defined by a cytogenetic alteration. The results of several clinical studies and the advances of new technologies have allowed a better understanding of the biological basis of this disease. Therefore, since the first report of the “5q- syndrome” in 1974, changes and refinements have been made in the definition and the characteristics of the patients with MDS and del(5q). Moreover, specific genetic alterations have been found to be associated with the prognosis and response to treatments. The aim of this review is to summarize the current knowledge of the molecular background of MDS with isolated del(5q), focusing on the clinical and prognostic relevance of cytogenetic alterations and somatic mutations.
Mehmet Akdel, Douglas E. V. Pires, Eduard Porta Pardo, Jürgen Jänes, Arthur O. Zalevsky, Bálint Mészáros, Patrick Bryant, Lydia L. Good, Roman A. Laskowski, Gabriele Pozzati, Aditi Shenoy, Wensi Zhu, Petras Kundrotas, Victoria Ruiz Serra, Carlos H. M. Rodrigues, Alistair S. Dunham, David Burke, Neera Borkakoti, Sameer Velankar, Adam Frost, Jérôme Basquin, Kresten Lindorff-Larsen, Alex Bateman, Andrey V. Kajava, Alfonso Valencia, Sergey Ovchinnikov, Janani Durairaj, David B. Ascher, Janet M. Thornton, Norman E. Davey, Amelie Stein, Arne Elofsson, Tristan I. Croll & Pedro Beltrao

A structural biology community assessment of AlphaFold2 applications

Nature Structural & Molecular Biology 7 Nov 2022, .
Most proteins fold into 3D structures that determine how they function and orchestrate the biological processes of the cell. Recent developments in computational methods for protein structure predictions have reached the accuracy of experimentally determined models. Although this has been independently verified, the implementation of these methods across structural-biology applications remains to be tested. Here, we evaluate the use of AlphaFold2 (AF2) predictions in the study of characteristic structural elements; the impact of missense variants; function and ligand binding site predictions; modeling of interactions; and modeling of experimental structural data. For 11 proteomes, an average of 25% additional residues can be confidently modeled when compared with homology modeling, identifying structural features rarely seen in the Protein Data Bank. AF2-based predictions of protein disorder and complexes surpass dedicated tools, and AF2 models can be used across diverse applications equally well compared with experimentally determined structures, when the confidence metrics are critically considered. In summary, we find that these advances are likely to have a transformative impact in structural biology and broader life-science research.
González-Gil C, Morgades M, Lopes T, Fuster-Tormo F, García-Chica J, Zhao R, Montesinos P, Torrent A, Diaz-Beya M, Coll R, Hermosín L, Mercadal S, González-Campos J, Zamora L, Artola T, Vall-Llovera F, Tormo M, Gil-Cortés C, Barba P, Novo A, Ribera J, Bernal T, De Ugarriza PL, Queipo MP, Martínez-Sánchez P, Giménez A, González-Martínez T, Cladera A, Cervera J, Fernández-Martín R, Ardaiz MÁ, Vidal MJ, Baena Á, López-Bigas N, Bigas A, Maciejewski J, Orfao A, Ribera JM, Genescà E

Genomics improves risk stratification of adults with T-cell acute lymphoblastic leukemia patients enrolled in measurable residual disease-oriented trials.

Haematologica 3 Nov 2022, . Epub 3 Nov 2022
Genetic information has been crucial to understand the pathogenesis of T-cell acute lymphoblastic leukemia (T-ALL) at diagnosis and at relapse, but still nowadays has a limited value in a clinical context. Few genetic markers are associated with the outcome of T-ALL patients, independently of measurable residual disease (MRD) status after therapy. In addition, the prognostic relevance of genetic features may be modulated by the specific treatment used. We analyzed the genetic profile of 145 T-ALL patients by targeted deep sequencing. Genomic information was integrated with the clinical-biological and survival data of a subset of 116 adult patients enrolled in two consecutive MRD-oriented trials of the Spanish PETHEMA (Programa Español de Tratamientos en Hematología) group. Genetic analysis revealed a mutational profile defined by DNMT3A/ N/KRAS/ MSH2/ U2AF1 gene mutations that identified refractory/resistant patients. Mutations in the DMNT3A gene were also found in the nonleukemic cell fraction of patients with T-ALL, revealing a possible mutational-driven clonal hematopoiesis event to prime T-ALL in elderly. The prognostic impact of this adverse genetic profile was independent of MRD status on day +35 of induction therapy. The combined WOG signature and MRD on day +35 allowed risk-stratification of T-ALL into standard or high-risk groups with significantly different 5-year overall survival (OS) (95% confidence interval [CI]) of 52% (37-67 %) and 17% (1-33%), respectively. These results confirm the relevance of the tumor genetic profile in predicting patient outcome in adult T-ALL and highlight the need for novel gene-targeted chemotherapeutic schedules to improve the OS of poor-prognosis T-ALL patients.
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