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This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License. ; Recent evidence shows that lipid raft membrane domains modulate both cell survival and death. Here, we have found that the phosphatidylinositol-3-kinase (PI3K)/Akt signaling pathway is present in the lipid rafts of mantle cell lymphoma (MCL) cells, and this location seems to be critical for full activation and MCL cell survival. The antitumor lipids (ATLs) edelfosine and perifosine target rafts, and we found that ATLs exerted in vitro and in vivo antitumor activity against MCL cells by displacing Akt as well as key regulatory kinases p-PDK1 (phosphatidylinositol-dependent protein kinase 1), PI3K and mTOR (mammalian TOR) from lipid rafts. This raft reorganization led to Akt dephosphorylation, while proapoptotic Fas/CD95 death receptor was recruited into rafts. Raft integrity was critical for Ser473 Akt phosphorylation. ATL-induced apoptosis appeared to correlate with the basal Akt phosphorylation status in MCL cell lines and primary cultures, and could be potentiated by the PI3K inhibitor wortmannin, or inhibited by the Akt activator pervanadate. Classical Akt inhibitors induced apoptosis in MCL cells. Microenvironmental stimuli, such as CD40 ligation or stromal cell contact, did not prevent ATL-induced apoptosis in MCL cell lines and patient-derived cells. These results highlight the role of raft-mediated PI3K/Akt signaling in MCL cell survival and chemotherapy, thus becoming a new target for MCL treatment. © 2013 Macmillan Publishers Limited. ; This work was supported by grants from Ministerio de Economía y Competitividad of Spain (SAF2008-02251 and SAF2011-30518 to FM; SAF2009-09503 to DC), Red Temática de Investigación Cooperativa en Cáncer, Instituto de Salud Carlos III, cofunded by the Fondo Europeo de Desarrollo Regional of the European Union (RD06/0020/1037 and RD12/0036/0065 to FM; RD06/0020/0014 to DC), Fondo de Investigación Sanitaria and European Commission, Instituto de Salud Carlos III (PI09/0060 to GR; PS09/01915 to CG), European Community's Seventh Framework Programme FP7-2007-2013 (grant HEALTH-F2-2011-256986, PANACREAS to FM), Junta de Castilla y León (CSI052A11-2 and CSI221A12-2 to FM; Biomedicine Project 2010–2011 to CG) and Generalitat de Catalunya (2009SGR967 to DC). MRS was recipient of a predoctoral fellowship from the Fundaçâo para a Ciência e Tecnologia (Ministério da Ciencia, Tecnología e Ensino Superior of Portugal), and AM was a recipient of a predoctoral fellowship from IDIBAPS. CG was supported by the Ramón y Cajal Program from the Ministerio de Ciencia e Innovación of Spain. ; Peer Reviewed

[Purpose]: Mantle cell lymphoma (MCL) and chronic lymphocytic leukemia (CLL) remain B-cell malignancies with limited therapeutic options. The present study investigates the in vitro and in vivo effect of the phospholipid ether edelfosine (1-O-octadecyl-2-O-methyl-rac-glycero-3-phosphocholine) in MCL and CLL. [Experimental Design]: Several cell lines, patient-derived tumor cells, and xenografts in severe combined immunodeficient mice were used to examine the anti-MCL and anti-CLL activity of edelfosine. Furthermore, we analyzed the mechanism of action and drug biodistribution of edelfosine in MCL and CLL tumor-bearing severe combined immunodeficient mice. [Results]: Here, we have found that the phospholipid ether edelfosine was the most potent alkyl-lysophospholipid analogue in killing MCL and CLL cells, including patient-derived primary cells, while sparing normal resting lymphocytes. Alkyl-lysophospholipid analogues ranked edelfosine > perifosine ≫ erucylphosphocholine ≥ miltefosine in their capacity to elicit apoptosis in MCL and CLL cells. Edelfosine induced coclustering of Fas/CD95 death receptor and rafts in MCL and CLL cells. Edelfosine was taken up by malignant cells, whereas normal resting lymphocytes hardly incorporated the drug. Raft disruption by cholesterol depletion inhibited drug uptake, Fas/CD95 clustering, and edelfosine-induced apoptosis. Edelfosine oral administration showed a potent in vivo anticancer activity in MCL and CLL xenograft mouse models, and the drug accumulated dramatically and preferentially in the tumor. [Conclusions]: Our data indicate that edelfosine accumulates and kills MCL and CLL cells in a rather selective way, and set coclustering of Fas/CD95 and lipid rafts as a new framework in MCL and CLL therapy. Our data support a selective antitumor action of edelfosine. ; Ministerio de Ciencia e Innovación grants SAF2005-04293, SAF2006-8850, SAF2007-61261, SAF2007-60964, PCT-090100-2007-27, PS09/01915, and SAF2008-02251; Red Temática de Investigación Cooperativa en Cáncer grants RD06/0020/0014, RD06/0020/0097, and RD06/0020/1037 (Instituto de Salud Carlos III, cofunded by the Fondo Europeo de Desarrollo Regional of the European Union); Fondo de Investigación Sanitaria and European Commission grant FIS-FEDER 06/0813; Junta de Castilla y León (CSI01A08, GR15-Experimental Therapeutics and Translational Oncology Program, and Biomedicine Project 2009); Fundación de Investigación Médica Mutua Madrileña; Fundación "la Caixa" grant BM05-30-0; Caja Navarra Foundation; Department of Health of the Government of Navarra ("Ortiz de Landázuri, 2009" project); and AGAUR-Generalitat de Catalunya grant 2005SGR-00549. C. Gajate is supported by the Ramón y Cajal Program from the Ministerio de Ciencia e Innovación of Spain. A. Estella-Hermoso de Mendoza is supported by Department of Education of the Basque Government research grant BFI06.37. M. de Frias is a recipient of a fellowship from the AGAUR-Generalitat de Catalunya. G. Roué holds a Miguel Servet research contract from Instituto de Salud Carlos III. ; Peer Reviewed

Chronic lymphocytic leukemia (CLL) is a B lymphoid malignancy highly dependent on the microenvironment. Despite new targeted therapies such as ibrutinib and venetoclax, disease progression and relapse remain an issue. CLL cell interactions with the supportive tissue microenvironment play a critical role in disease pathogenesis. We used a platform for drug discovery based on systems biology and artificial intelligence, to identify drugs targeting key proteins described to have a role in the microenvironment. The selected compounds were screened in CLL cell lines in the presence of stromal cells to mimic the microenvironment and validated the best candidates in primary CLL cells. Our results showed that the commercial drug simvastatin was the most effective and selective out of the tested compounds. Simvastatin decreased CLL cell survival and proliferation as well as cell adhesion. Importantly, this drug enhanced the antitumor effect of venetoclax and ibrutinib. We proposed that systems biology approaches combined with pharmacological screening could help to find new drugs for CLL treatment and to predict new combinations with current therapies. Our results highlight the possibility of repurposing widely used drugs such as statins to target the microenvironment and to improve the efficacy of ibrutinib or venetoclax in CLL cells. ; The study was supported by research funding from the Spanish Ministry of Economy and Competitiveness through the Plan Estatal de Investigación Científica y Técnica y de Innovación (MINECO) RTI2018-094584-B-I00 [to DC] and was cofunded by the European Regional Development Fund [ERDF] and the CERCA program from Generalitat de Catalunya, Centro de Investigación Biomédica en Cáncer [CIBERONC] [CB16/12/00334 and CB16/12/00225] and Generalitat de Catalunya Suport Grups de Recerca [2017 SGR 1009]. This project has received funding from the European Union's Seventh Framework Programme for research, technological development and demonstration under grant agreement no. 306240. NG is a recipient of ...

Robust protocols and automation now enable large-scale single-cell RNA and ATAC sequencing experiments and their application on biobank and clinical cohorts. However, technical biases introduced during sample acquisition can hinder solid, reproducible results, and a systematic benchmarking is required before entering large-scale data production. Here, we report the existence and extent of gene expression and chromatin accessibility artifacts introduced during sampling and identify experimental and computational solutions for their prevention. ; HH is a Miguel Servet (CP14/00229) researcher funded by the Spanish Institute of Health Carlos III (ISCIII). CM and MK are supported by AECC postdoctoral fellowships. This work has received funding from the Ministerio de Ciencia, Innovación y Universidades (SAF2017-89109-P; AEI/FEDER, UE). This study was further funded by the Spanish Ministry of Economy and Competitiveness (grant number: IPT-010000-2010- 36, cofunded by the European Regional Development Fund). Core funding is from the ISCIII and the Generalitat de Catalunya. We acknowledge support of the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) to the EMBL partnership, the Centro de Excelencia Severo Ochoa, the CERCA Programme/Generalitat de Catalunya, the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) through the Instituto de Salud Carlos III and the Generalitat de Catalunya through Departament de Salut and Departament d'Empresa i Coneixement. We also acknowledge the Co-financing by the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) with funds from the European Regional Development Fund (ERDF) corresponding to the 2014–2020 Smart Growth Operating Program. We acknowledge the Generalitat de Catalunya Suport Grups de Recerca AGAUR 2017-SGR-736 (to JIMS) and 2017-SGR-1142 (to EC), and CIBERONC (CB16/12/00225 and CB16/12/00334). EC is an ICREA Academia Researcher. This project received support from the European Commission under the projects DocTIS (H2020, SEP-210574908). This publication is part of a project (BCLLATLAS) that has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (grant agreement No 810287)

To investigate the three-dimensional (3D) genome architecture across normal B cell differentiation and in neoplastic cells from different subtypes of chronic lymphocytic leukemia and mantle cell lymphoma patients, here we integrate in situ Hi-C and nine additional omics layers. Beyond conventional active (A) and inactive (B) compartments, we uncover a highly-dynamic intermediate compartment enriched in poised and polycomb-repressed chromatin. During B cell development, 28% of the compartments change, mostly involving a widespread chromatin activation from naive to germinal center B cells and a reversal to the naive state upon further maturation into memory B cells. B cell neoplasms are characterized by both entity and subtype-specific alterations in 3D genome organization, including large chromatin blocks spanning key disease-specific genes. This study indicates that 3D genome interactions are extensively modulated during normal B cell differentiation and that the genome of B cell neoplasias acquires a tumor-specific 3D genome architecture. ; This research was funded by the European Union's Seventh Framework Programme through the Blueprint Consortium (grant agreement 282510), the World Wide Cancer Research Foundation Grant No. 16-1285 (to J.I.M.-S.), the ERC (grant agreement 609989 to M.A.M.-R.), European Union's Horizon 2020 research and innovation programme (grant agreement 676556 to M.A.M.-R.). We also knowledge the support of Spanish Ministerio de Ciencia, Innovación y Universidades through SAF2012-31138 and SAF2017-86126-R to J.I.M.-S., SAF2015-64885-R to E.C., BFU2017-85926-P to M.A.M.-R. and PMP15/00007 to E.C. which is part of Plan Nacional de I + D + I and co-financed by the ISCIII-Sub-Directorate General for Evaluation and the European Regional Development Fund (FEDER-"Una manera de Hacer Europa") (to E.C.), the International Cancer Genome Consortium (Chronic Lymphocytic Leukemia Genome consortium to E.C.), La Caixa Foundation (CLLEvolution-HE17-00221, to E.C.). Furthermore, the authors would like to thank the support of the Generalitat de Catalunya Suport Grups de Recerca AGAUR 2017-SGR-736 (to J.I.M.-S.), 2017-SGR-1142 (to E.C.) and 2017-SGR-468 (to E.C.), the Accelerator award CRUK/AIRC/AECC joint funder-partnership, the CERCA Programme/Generalitat de Catalunya and CIBERONC (CB16/12/00225, CB16/12/00334, and CB16/12/00489). R.V.-B. (BES-2013-064328) and P.S.-V. (BES-2014-070327) were supported by a predoctoral FPI Fellowship from the Spanish Government. CRG acknowledges support from 'Centro de Excelencia Severo Ochoa 2013-2017', SEV-2012-0208 and the CERCA Programme/Generalitat de Catalunya as well as support of the Spanish Ministry of Science and Innovation through the Instituto de Salud Carlos III and the EMBL partnership, the Generalitat de Catalunya through Departament de Salut and Departament d'Empresa i Coneixement, and the Cofinancing with funds from the European Regional Development Fund (ERDF) by the Spanish Ministry of Science and Innovation coresponding to the Programa Opertaivo FEDER Plurirregional de España (POPE) 2014-2020 and by the Secretaria d'Universitats i Recerca, Departament d'Empresa i Coneixement of the Generalitat de Catalunya corresponding to the programa Operatiu FEDER Catalunya 2014-2020