Lasaga, M. (Miren)

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    Uncovering perturbations in human hematopoiesis associated with healthy aging and myeloid malignancies at single-cell resolution
    (2023) Gomez-Cabrero, D. (David); Lasaga, M. (Miren); Diez-Campelo, M. (M.); Molero, A. (Antonieta); San-Martín-Uriz, P. (Patxi); Romero-Riojas, J.P. (Juan Pablo); Alfonso-Piérola, A. (Ana); San-Julian, M. (Mikel); Jimenez-Solas, T. (Tamara); Ezponda, T. (Teresa); Valcarcel, D. (David); Lopez, F. (Félix); Dupéré-Richer, D. (Daphné); Lamo-de-Espinosa-Vázquez-de-Sola, J.M. (José María); Alignani, D. (Diego); Montoro, J. (Julia); Mution, S. (Sandra); Hernaez, M. (Mikel); Serrano-Sanz, G. (Guillermo); Ainciburu-Fernández, M. (Marina); Prosper-Cardoso, F. (Felipe); Berastegui-Zufiaurre, N. (Nerea); Diaz-Mazquiaran, A. (Aintzane); Sanchez-Guijo, F.M. (Fermín M.)
    Early hematopoiesis is a continuous process in which hematopoietic stem and progenitor cells (HSPCs) gradually differentiate toward specific lineages. Aging and myeloid malignant transformation are characterized by changes in the composition and regulation of HSPCs. In this study, we used single-cell RNA sequencing (scRNA-seq) to characterize an enriched population of human HSPCs obtained from young and elderly healthy individuals. Based on their transcriptional profile, we identified changes in the proportions of progenitor compartments during aging, and differences in their functionality, as evidenced by gene set enrichment analysis. Trajectory inference revealed that altered gene expression dynamics accompanied cell differentiation, which could explain aging-associated changes in hematopoiesis. Next, we focused on key regulators of transcription by constructing gene regulatory networks (GRNs) and detected regulons that were specifically active in elderly individuals. Using previous findings in healthy cells as a reference, we analyzed scRNA-seq data obtained from patients with myelodysplastic syndrome (MDS) and detected specific alterations of the expression dynamics of genes involved in erythroid differentiation in all patients with MDS such as TRIB2. In addition, the comparison between transcriptional programs and GRNs regulating normal HSPCs and MDS HSPCs allowed identification of regulons that were specifically active in MDS cases such as SMAD1, HOXA6, POU2F2, and RUNX1 suggesting a role of these transcription factors (TFs) in the pathogenesis of the disease. In summary, we demonstrate that the combination of single-cell technologies with computational analysis tools enable the study of a variety of cellular mechanisms involved in complex biological systems such as early hematopoiesis and can be used to dissect perturbed differentiation trajectories associated with perturbations such as aging and malignant transformation. Furthermore, the identification of abnormal regulatory mechanisms associated with myeloid malignancies could be exploited for personalized therapeutic approaches in individual patients
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    Gene therapy restores the transcriptional program of hematopoietic stem cells in Fanconi anemia
    (2023) Fernández-Varas, B. (Beatriz); Ainciburi, M. (Marina); Navarro, S. (Susana); Gomez-Cabrero, D. (David); Ullate-Agote, A. (Asier); Lasaga, M. (Miren); Sastre, L. (Leandro); Schwartz, J.D. (Jonathan D.); Nicoletti, E. (Eileen); Pujol, R.M. (Roser M.); Surralles, J. (Jordi); Sevilla, J. (Julián); Planell, N. (Núria); Perona, R. (Rosario); Vilas-Zornoza, A. (Amaia); Alignani, D. (Diego); Mouzo, D. (Daniel); Bueren, J.A. (Juan A.); Prosper-Cardoso, F. (Felipe); Rio, P. (Paula); Zubicaray, J. (Josune)
    Clinical trials have shown that lentiviral-mediated gene therapy can ameliorate bone marrow failure (BMF) in nonconditioned Fanconi anemia (FA) patients resulting from the proliferative advantage of corrected FA hematopoietic stem and progenitor cells (HSPC). However, it is not yet known if gene therapy can revert affected molecular pathways in diseased HSPC. Single-cell RNA sequencing was performed in chimeric populations of corrected and uncorrected HSPC co-existing in the BM of gene therapy-treated FA patients. Our study demonstrates that gene therapy reverts the transcriptional signature of FA HSPC, which then resemble the transcriptional program of healthy donor HSPC. This includes a down-regulated expression of TGF-ß and p21, typically up-regulated in FA HSPC, and upregulation of DNA damage response and telomere maintenance pathways. Our results show for the first time the potential of gene therapy to rescue defects in the HSPC transcriptional program from patients with inherited diseases; in this case, in FA characterized by BMF and cancer predisposition.
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    Preclinical models for prediction of immunotherapy outcomes and immune evasion mechanisms in genetically heterogeneous multiple myeloma
    (2023) Perez, C. (Cristina); Fresquet, V. (Vicente); Maia, C. (Catarina); Gomez-Cabrero, D. (David); Lasaga, M. (Miren); Celay, J. (Jon); Lozano-Moreda, T. (Teresa); Vicent, S. (Silvestre); Roncador, G. (Giovanna); Goicoechea, I. (Ibai); García-Barchino, M.J. (María José); Martinez-Climent, J.A. (José Ángel); Walensky, L.D. (Loren D.); Panizo, C. (Carlos); Lasater, E.A. (Elisabeth A.); Katz, S.G. (Samuel G.); Larrayoz, M. (Marta); Roa, S. (Sergio); Bergsagel, P.L. (P. Leif); Gonzalez, P. (Patricia); Botta, C. (Cirino); Ordóñez-Ciriza, R. (Raquel); Takahashi, S. (Satoru); Aguirre-Ena, X. (Xabier); Kurilovich, A. (Anna); Amann, M. (Maria); Rodriguez-Otero, P. (Paula); Llopiz, D. (Diana); Paiva, B. (Bruno); Sarobe, P. (Pablo); Campos-Sanchez, E. (Elena); Ruppert, S.M. (Shannon M.); Martínez-Cano, J. (Jorge); Larrayoz, M.J. (María J.); Revuelta, M.V. (Maria V.); Cobaleda, C. (César); Prosper-Cardoso, F. (Felipe); Etxebeste-Mitxeltorena, A. (Amaia); Calasanz-Abinzano, M.J. (Maria Jose); San-Miguel, J.F. (Jesús F.); Cerchietti, L. (Leandro); Planell, N. (Núria); Jiménez-Andrés, M. (Maddalen); Kudryashova, O. (Olga); Chesi, M. (Marta); Lasarte, J.J. (Juan José)
    The historical lack of preclinical models reflecting the genetic heterogeneity of multiple myeloma (MM) hampers the advance of therapeutic discoveries. To circumvent this limitation, we screened mice engineered to carry eight MM lesions (NF-kappaB, KRAS, MYC, TP53, BCL2, cyclin D1, MMSET/NSD2 and c-MAF) combinatorially activated in B lymphocytes following T cell-driven immunization. Fifteen genetically diverse models developed bone marrow (BM) tumors fulfilling MM pathogenesis. Integrative analyses of 500 mice and 1,000 patients revealed a common MAPK-MYC genetic pathway that accelerated time to progression from precursor states across genetically heterogeneous MM. MYC-dependent time to progression conditioned immune evasion mechanisms that remodeled the BM microenvironment differently. Rapid MYC-driven progressors exhibited a high number of activated/exhausted CD8+ T cells with reduced immunosuppressive regulatory T (Treg) cells, while late MYC acquisition in slow progressors was associated with lower CD8+ T cell infiltration and more abundant Treg cells. Single-cell transcriptomics and functional assays defined a high ratio of CD8+ T cells versus Treg cells as a predictor of response to immune checkpoint blockade (ICB). In clinical series, high CD8+ T/Treg cell ratios underlie early progression in untreated smoldering MM, and correlated with early relapse in newly diagnosed patients with MM under Len/Dex therapy. In ICB-refractory MM models, increasing CD8+ T cell cytotoxicity or depleting Treg cells reversed immunotherapy resistance and yielded prolonged MM control. Our experimental models enable the correlation of MM genetic and immunological traits with preclinical therapy responses, which may inform the next-generation immunotherapy trials.