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Wiltshire E, de Moura MC, Piñeyro D, Joshi RS. Cellular and clinical impact of protein phosphatase enzyme epigenetic silencing in multiple cancer tissues. Hum Genomics 2024; 18:24. [PMID: 38475971 DOI: 10.1186/s40246-024-00592-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Protein Phosphatase Enzymes (PPE) and protein kinases simultaneously control phosphorylation mechanisms that tightly regulate intracellular signalling pathways and stimulate cellular responses. In human malignancies, PPE and protein kinases are frequently mutated resulting in uncontrolled kinase activity and PPE suppression, leading to cell proliferation, migration and resistance to anti-cancer therapies. Cancer associated DNA hypermethylation at PPE promoters gives rise to transcriptional silencing (epimutations) and is a hallmark of cancer. Despite recent advances in sequencing technologies, data availability and computational capabilities, only a fraction of PPE have been reported as transcriptionally inactive as a consequence of epimutations. METHODS In this study, we examined promoter-associated DNA methylation profiles in Protein Phosphatase Enzymes and their Interacting Proteins (PPEIP) in a cohort of 705 cancer patients in five tissues (Large intestine, Oesophagus, Lung, Pancreas and Stomach) in three cell models (primary tumours, cancer cell lines and 3D embedded cancer cell cultures). As a subset of PPEIP are known tumour suppressor genes, we analysed the impact of PPEIP promoter hypermethylation marks on gene expression, cellular networks and in a clinical setting. RESULTS Here, we report epimutations in PPEIP are a frequent occurrence in the cancer genome and manifest independent of transcriptional activity. We observed that different tumours have varying susceptibility to epimutations and identify specific cellular signalling networks that are primarily affected by epimutations. Additionally, RNA-seq analysis showed the negative impact of epimutations on most (not all) Protein Tyrosine Phosphatase transcription. Finally, we detected novel clinical biomarkers that inform on patient mortality and anti-cancer treatment sensitivity. CONCLUSIONS We propose that DNA hypermethylation marks at PPEIP frequently contribute to the pathogenesis of malignancies and within the precision medicine space, hold promise as biomarkers to inform on clinical features such as patient survival and therapeutic response.
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Affiliation(s)
- Edward Wiltshire
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, UK
| | | | - David Piñeyro
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain
| | - Ricky S Joshi
- Leicester Cancer Research Centre, Department of Genetics and Genome Biology, Robert Kilpatrick Clinical Sciences Building, Leicester Royal Infirmary, Leicester, UK.
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Arribas AJ, Napoli S, Cascione L, Barnabei L, Sartori G, Cannas E, Gaudio E, Tarantelli C, Mensah AA, Spriano F, Zucchetto A, Rossi FM, Rinaldi A, Castro de Moura M, Jovic S, Bordone Pittau R, Stathis A, Stussi G, Gattei V, Brown JR, Esteller M, Zucca E, Rossi D, Bertoni F. ERBB4-Mediated Signaling Is a Mediator of Resistance to PI3K and BTK Inhibitors in B-cell Lymphoid Neoplasms. Mol Cancer Ther 2024; 23:368-380. [PMID: 38052765 DOI: 10.1158/1535-7163.mct-23-0068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 08/28/2023] [Accepted: 10/11/2023] [Indexed: 12/07/2023]
Abstract
BTK and PI3K inhibitors are among the drugs approved for the treatment of patients with lymphoid neoplasms. Although active, their ability to lead to long-lasting complete remission is rather limited, especially in the lymphoma setting. This indicates that tumor cells often develop resistance to the drugs. We started from a marginal zone lymphoma cell line, Karpas-1718, kept under prolonged exposure to the PI3Kδ inhibitor idelalisib until acquisition of resistance, or with no drug. Cells underwent transcriptome, miRNA and methylation profiling, whole-exome sequencing, and pharmacologic screening, which led to the identification of the overexpression of ERBB4 and its ligands HBEGF and NRG2 in the resistant cells. Cellular and genetic experiments demonstrated the involvement of this axis in blocking the antitumor activity of various BTK/PI3K inhibitors, currently used in the clinical setting. Addition of recombinant HBEGF induced resistance to BTK/PI3K inhibitors in parental cells and in additional lymphoma models. Combination with the ERBB inhibitor lapatinib was beneficial in resistant cells and in other lymphoma models already expressing the identified resistance factors. An epigenetic reprogramming sustained the expression of the resistance-related factors, and pretreatment with demethylating agents or EZH2 inhibitors overcame the resistance. Resistance factors were also shown to be expressed in clinical specimens. In conclusion, we showed that the overexpression of ERBB4 and its ligands represents a novel mechanism of resistance for lymphoma cells to bypass the antitumor activity of BTK and PI3K inhibitors and that targeted pharmacologic interventions can restore sensitivity to the small molecules.
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Affiliation(s)
- Alberto J Arribas
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Sara Napoli
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Luciano Cascione
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Laura Barnabei
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Giulio Sartori
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Eleonora Cannas
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Eugenio Gaudio
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Chiara Tarantelli
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Afua A Mensah
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Filippo Spriano
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | | | | | - Andrea Rinaldi
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Manuel Castro de Moura
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Sandra Jovic
- Institute for Research in Biomedicine, Università della Svizzera italiana, Bellinzona, Switzerland
| | | | - Anastasios Stathis
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
| | - Georg Stussi
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Valter Gattei
- Centro di Riferimento Oncologico di Aviano - CRO, Aviano, Italy
| | - Jennifer R Brown
- Chronic Lymphocytic Leukemia Center, Division of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Emanuele Zucca
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Davide Rossi
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Francesco Bertoni
- Institute of Oncology Research, Faculty of Biomedical Sciences, USI, Bellinzona, Switzerland
- Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
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de Moura MC, Miro F, Han JM, Kim S, Celada A, de Pouplana LR. Correction: Entamoeba lysyl-tRNA Synthetase Contains a Cytokine-Like Domain with Chemokine Activity towards Human Endothelial Cells. PLoS Negl Trop Dis 2024; 18:e0012047. [PMID: 38502641 PMCID: PMC10950210 DOI: 10.1371/journal.pntd.0012047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024] Open
Abstract
[This corrects the article DOI: 10.1371/journal.pntd.0001398.].
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Arribas AJ, Napoli S, Cascione L, Barnabei L, Sartori G, Cannas E, Gaudio E, Tarantelli C, Mensah AA, Spriano F, Zucchetto A, Rossi FM, Rinaldi A, de Moura MC, Stathis A, Stussi G, Gattei V, Brown JR, Esteller M, Zucca E, Rossi D, Bertoni F. Abstract 394: ERBB4-mediated signaling is a mediator of resistance to BTK and PI3K inhibitors in B cell lymphoid neoplasms. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Background: Marginal zone lymphoma (MZL) is an indolent yet incurable B cell malignancy. Two BTK inhibitors, ibrutinib and zanubrutinib, are FDA approved for relapsed/refractory MZL patients. PI3K inhibitors have also shown clinical activity. The identification of the mechanisms of resistance can provide useful information to optimize the use of the agents. We previously reported an IL6 driven MZL model of PI3K inhibitors resistance developed by prolonged exposure to the PI3Kδ inhibitor idelalisib (Arribas, Haematologica 2022). Here, we present the detailed characterization of a second model with resistance to both BTK and PI3K inhibitors.
Methods: MTT assay. RNA-Seq, whole exome sequencing, miRNA and methylation profiling. FACS and ELISA analyses.
Results: Resistant cells, developed by continuous exposure of the cell line Karpas1718 to idelalisib, showed resistance to various inhibitors of BTK (ibrutinib, zanubrutinib, acalabrutinib and pirtobrutinib) and PI3K (idelalisib, duvelisib, copanlisib and umbralisib). No mutations affecting BTK, PLCG2 or CXCR4 were identified in resistant cells, which had higher expression of genes involved in ERBB signaling (HBEGF, NRG2, ERBB4), cell proliferation (PBK, MKI67, TCL1A) and DNA recombination (RAG1, RAG2) than parental cells. We confirmed cell surface ERBB4 up-regulation, and the cytoplasmatic expression and secretion of its ligand HBEGF in resistant cells, which led to increased levels of p-AKT and p-ERK. The miRNAs miR-29c and let-7c, known negative regulators of the HBEGF-ERBB axis, were fully methylated and down-regulated in resistant compared to parental cells. ERBB4 genetic silencing improved sensitivity to PI3Kδ inhibitor, and exposure to let-7c or miR-29c mimics decreased secreted HBEGF and recovered sensitivity to PI3K inhibitors in resistant cells. Addition of recombinant HBEGF (rHBEGF) induced resistance to BTK and to PI3K inhibitors in parental cells and in other lymphoma models including mantle cell lymphomas and diffuse large B cell lymphomas (DLBCL). The rHBEGF induced resistance was reverted adding the ERBB inhibitor lapatinib. To extend our findings to the clinical context, using two MZL and one DLBCL expression datasets, we showed HBEGF and ERBB4 expression in clinical specimens. Finally, HBEGF levels appeared elevated in the serum of CLL patients with primary or acquired resistance to PI3Kδ or to BTK inhibitors, compared to patients responding to the drugs and paired for similar clinical features.
Conclusions: We characterized a novel B cell lymphoma model of secondary resistance to BTK and PI3K inhibitors. Our results indicate that epigenetic plasticity led to the activation of HBEGF-ERBB signaling sustaining resistance to BTK/PI3K inhibitors, which can be overcome using epigenetic agents and ERBB inhibitors. These therapeutics approaches could be tested in novel clinical trials. AJA, SN: equally contributed.
Citation Format: Alberto J. Arribas, Sara Napoli, Luciano Cascione, Laura Barnabei, Giulio Sartori, Eleonora Cannas, Eugenio Gaudio, Chiara Tarantelli, Afua A. Mensah, Filippo Spriano, Antonella Zucchetto, Francesca M. Rossi, Andrea Rinaldi, Manuel Castro de Moura, Anastasios Stathis, Georg Stussi, Valter Gattei, Jennifer R. Brown, Manel Esteller, Emanuele Zucca, Davide Rossi, Francesco Bertoni. ERBB4-mediated signaling is a mediator of resistance to BTK and PI3K inhibitors in B cell lymphoid neoplasms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 394.
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Affiliation(s)
| | - Sara Napoli
- 1Institute of Oncology Research, Bellinzona, Switzerland
| | | | - Laura Barnabei
- 1Institute of Oncology Research, Bellinzona, Switzerland
| | - Giulio Sartori
- 1Institute of Oncology Research, Bellinzona, Switzerland
| | | | - Eugenio Gaudio
- 1Institute of Oncology Research, Bellinzona, Switzerland
| | | | - Afua A. Mensah
- 1Institute of Oncology Research, Bellinzona, Switzerland
| | | | | | | | - Andrea Rinaldi
- 1Institute of Oncology Research, Bellinzona, Switzerland
| | | | | | - Georg Stussi
- 4Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Valter Gattei
- 2Centro di Riferimento Oncologico di Aviano – CRO, Aviano, Italy
| | - Jennifer R. Brown
- 5Chronic Lymphocytic Leukemia Center, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA
| | - Manel Esteller
- 3Josep Carreras Leukaemia Research Institute, Barcelona, Spain
| | - Emanuele Zucca
- 1Institute of Oncology Research, Bellinzona, Switzerland
| | - Davide Rossi
- 1Institute of Oncology Research, Bellinzona, Switzerland
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Arribas AJ, Napoli S, Cascione L, Barnabei L, Sartori G, Cannas E, Gaudio E, Tarantelli C, Mensah AA, Spriano F, Zucchetto A, Rossi FM, Rinaldi A, de Moura MC, Jovic S, Pittau RB, Stathis A, Stussi G, Gattei V, Brown JR, Esteller M, Zucca E, Rossi D, Bertoni F. ERBB4-mediated signaling is a mediator of resistance to BTK and PI3K inhibitors in B cell lymphoid neoplasms. bioRxiv 2023:2023.01.01.522017. [PMID: 36711490 PMCID: PMC9881865 DOI: 10.1101/2023.01.01.522017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
BTK and PI3K inhibitors are among the drugs approved for the treatment of patients with lymphoid neoplasms. Although active, their ability to lead as single agents to long-lasting complete remission is rather limited especially in the lymphoma setting. This indicates that tumor cells often develop resistance to the drugs. Here, we show that the overexpression of ERBB4 and its ligands represents a modality for B cell neoplastic cells to bypass the anti-tumor activity of BTK and PI3K inhibitors and that targeted pharmacological interventions can restore sensitivity to the small molecules. We started from a marginal zone lymphoma (MZL) cell line, Karpas-1718, kept under prolonged exposure to the PI3Kδ inhibitor idelalisib until acquisition of resistance, or with no drug. Cells underwent transcriptome, miRNA and methylation profiling, whole exome sequencing, and pharmacological screening which led to the identification of the overexpression of ERBB4 and its ligands HBEGF and NRG2 in the resistant cells. Cellular and genetic experiments demonstrated the involvement of this axis in blocking the anti-tumor activity of various BTK and PI3K inhibitors, currently used in the clinical setting. Addition of recombinant HBEGF induced resistance to BTK and PI3K inhibitors in parental cells but also in additional lymphoma models. Combination with the ERBB inhibitor lapatinib was beneficial in resistant cells and in other lymphoma models already expressing the identified resistance factors. Multi-omics analysis underlined that an epigenetic reprogramming affected the expression of the resistance-related factors, and pretreatment with demethylating agents or EZH2 inhibitors overcame the resistance. Resistance factors were shown to be expressed in clinical samples, further extending the findings of the study. In conclusions, we identified a novel ERBB4-driven mechanism of resistance to BTK and PI3K inhibitors and treatments that appear to overcome it. Key points A mechanism of secondary resistance to the PI3Kδ and BTK inhibitors in B cell neoplasms driven by secreted factors.Resistance can be reverted by targeting ERBB signaling.
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Cullell N, Soriano-Tárraga C, Gallego-Fábrega C, Cárcel-Márquez J, Muiño E, Llucià-Carol L, Lledós M, Esteller M, de Moura MC, Montaner J, Rosell A, Delgado P, Martí-Fábregas J, Krupinski J, Roquer J, Jiménez-Conde J, Fernández-Cadenas I. Altered methylation pattern in EXOC4 is associated with stroke outcome: an epigenome-wide association study. Clin Epigenetics 2022; 14:124. [PMID: 36180927 PMCID: PMC9526296 DOI: 10.1186/s13148-022-01340-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 09/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND AND PURPOSE The neurological course after stroke is highly variable and is determined by demographic, clinical and genetic factors. However, other heritable factors such as epigenetic DNA methylation could play a role in neurological changes after stroke. METHODS We performed a three-stage epigenome-wide association study to evaluate DNA methylation associated with the difference between the National Institutes of Health Stroke Scale (NIHSS) at baseline and at discharge (ΔNIHSS) in ischaemic stroke patients. DNA methylation data in the Discovery (n = 643) and Replication (n = 62) Cohorts were interrogated with the 450 K and EPIC BeadChip. Nominal CpG sites from the Discovery (p value < 10-06) were also evaluated in a meta-analysis of the Discovery and Replication cohorts, using a random-fixed effect model. Metabolic pathway enrichment was calculated with methylGSA. We integrated the methylation data with 1305 plasma protein expression levels measured by SOMAscan in 46 subjects and measured RNA expression with RT-PCR in a subgroup of 13 subjects. Specific cell-type methylation was assessed using EpiDISH. RESULTS The meta-analysis revealed an epigenome-wide significant association in EXOC4 (p value = 8.4 × 10-08) and in MERTK (p value = 1.56 × 10-07). Only the methylation in EXOC4 was also associated in the Discovery and in the Replication Cohorts (p value = 1.14 × 10-06 and p value = 1.3 × 10-02, respectively). EXOC4 methylation negatively correlated with the long-term outcome (coefficient = - 4.91) and showed a tendency towards a decrease in EXOC4 expression (rho = - 0.469, p value = 0.091). Pathway enrichment from the meta-analysis revealed significant associations related to the endocytosis and deubiquitination processes. Seventy-nine plasma proteins were differentially expressed in association with EXOC4 methylation. Pathway analysis of these proteins showed an enrichment in natural killer (NK) cell activation. The cell-type methylation analysis in blood also revealed a differential methylation in NK cells. CONCLUSIONS DNA methylation of EXOC4 is associated with a worse neurological course after stroke. The results indicate a potential modulation of pathways involving endocytosis and NK cells regulation.
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Affiliation(s)
- Natalia Cullell
- Stroke Pharmacogenomics and Genetics, IIB-Sant Pau, Institut de Recerca de Sant Pau, Hospital Sant Pau, C/Sant Antoni Mª Claret,167, 08025, Barcelona, Spain
- Neurology, Hospital Universitari MútuaTerrassa/Fundacio Docència i Recerca MutuaTerrassa, Terrassa, Spain
- Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Carolina Soriano-Tárraga
- Neurology, Hospital del Mar, Neurovascular Research Group, IMIM, Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, Missouri, USA
- NeuroGenomics and Informatics, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Cristina Gallego-Fábrega
- Stroke Pharmacogenomics and Genetics, IIB-Sant Pau, Institut de Recerca de Sant Pau, Hospital Sant Pau, C/Sant Antoni Mª Claret,167, 08025, Barcelona, Spain
| | - Jara Cárcel-Márquez
- Stroke Pharmacogenomics and Genetics, IIB-Sant Pau, Institut de Recerca de Sant Pau, Hospital Sant Pau, C/Sant Antoni Mª Claret,167, 08025, Barcelona, Spain
| | - Elena Muiño
- Stroke Pharmacogenomics and Genetics, IIB-Sant Pau, Institut de Recerca de Sant Pau, Hospital Sant Pau, C/Sant Antoni Mª Claret,167, 08025, Barcelona, Spain
| | - Laia Llucià-Carol
- Stroke Pharmacogenomics and Genetics, IIB-Sant Pau, Institut de Recerca de Sant Pau, Hospital Sant Pau, C/Sant Antoni Mª Claret,167, 08025, Barcelona, Spain
| | - Miquel Lledós
- Stroke Pharmacogenomics and Genetics, IIB-Sant Pau, Institut de Recerca de Sant Pau, Hospital Sant Pau, C/Sant Antoni Mª Claret,167, 08025, Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics & Biology Program (PEBC), L'Hospitalet, Spain
- Department of Physiological Sciences II, School of Medicine, Universitat de Barcelona, Barcelona, Spain
- Institució Catalana de Recerca I Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Joan Montaner
- Neurovascular Research Laboratory, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
- Department of Neurology, Hospital Universitario Virgen Macarena Sevilla, Instituto de Biomedicina de Sevilla, IBiS/Hospital Universitario Virgen del Rocío/CSIC, Universidad de Sevilla, Sevilla, Spain
| | - Anna Rosell
- Neurovascular Research Laboratory, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | - Pilar Delgado
- Neurovascular Research Laboratory, Vall d'Hebron Institut de Recerca (VHIR), Barcelona, Spain
| | | | - Jerzy Krupinski
- Neurology, Hospital Universitari MútuaTerrassa/Fundacio Docència i Recerca MutuaTerrassa, Terrassa, Spain
- Centre for Bioscience, School of HealthCare Science, Manchester Metropolitan University, Manchester, UK
| | - Jaume Roquer
- Neurology, Hospital del Mar, Neurovascular Research Group, IMIM, Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
| | - Jordi Jiménez-Conde
- Neurology, Hospital del Mar, Neurovascular Research Group, IMIM, Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
| | - Israel Fernández-Cadenas
- Stroke Pharmacogenomics and Genetics, IIB-Sant Pau, Institut de Recerca de Sant Pau, Hospital Sant Pau, C/Sant Antoni Mª Claret,167, 08025, Barcelona, Spain.
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Joshi RS, Rigau M, García-Prieto CA, Castro de Moura M, Piñeyro D, Moran S, Davalos V, Carrión P, Ferrando-Bernal M, Olalde I, Lalueza-Fox C, Navarro A, Fernández-Tena C, Aspandi D, Sukno FM, Binefa X, Valencia A, Esteller M. Look-alike humans identified by facial recognition algorithms show genetic similarities. Cell Rep 2022; 40:111257. [PMID: 36001980 DOI: 10.1016/j.celrep.2022.111257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 06/05/2022] [Accepted: 08/01/2022] [Indexed: 11/03/2022] Open
Abstract
The human face is one of the most visible features of our unique identity as individuals. Interestingly, monozygotic twins share almost identical facial traits and the same DNA sequence but could exhibit differences in other biometrical parameters. The expansion of the world wide web and the possibility to exchange pictures of humans across the planet has increased the number of people identified online as virtual twins or doubles that are not family related. Herein, we have characterized in detail a set of "look-alike" humans, defined by facial recognition algorithms, for their multiomics landscape. We report that these individuals share similar genotypes and differ in their DNA methylation and microbiome landscape. These results not only provide insights about the genetics that determine our face but also might have implications for the establishment of other human anthropometric properties and even personality characteristics.
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Affiliation(s)
- Ricky S Joshi
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Spain
| | - Maria Rigau
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Carlos A García-Prieto
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Spain; Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | | | - David Piñeyro
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Spain; Centro de Investigacion Biomedica en Red Cancer (CIBERONC), 28029 Madrid, Spain
| | - Sebastian Moran
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Spain
| | - Veronica Davalos
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Spain
| | - Pablo Carrión
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Manuel Ferrando-Bernal
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Iñigo Olalde
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain
| | - Arcadi Navarro
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), 08003 Barcelona, Spain; Centre for Genomic Regulation (CNAG-CRG), 08003 Barcelona, Catalonia, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | | | - Decky Aspandi
- Departament de Tecnologies de la Informació i les Comunicaciones (DTIC), Universitat Pompeu Fabra (UPF), 08018 Barcelona, Spain
| | - Federico M Sukno
- Departament de Tecnologies de la Informació i les Comunicaciones (DTIC), Universitat Pompeu Fabra (UPF), 08018 Barcelona, Spain
| | - Xavier Binefa
- Departament de Tecnologies de la Informació i les Comunicaciones (DTIC), Universitat Pompeu Fabra (UPF), 08018 Barcelona, Spain
| | - Alfonso Valencia
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, 08916 Barcelona, Spain; Centro de Investigacion Biomedica en Red Cancer (CIBERONC), 28029 Madrid, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), L'Hospitalet, 08907 Barcelona, Spain.
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Cullell N, Soriano-Tárraga C, Gallego-Fábrega C, Cárcel-Márquez J, Torres-Águila NP, Muiño E, Lledós M, Llucià-Carol L, Esteller M, Castro de Moura M, Montaner J, Fernández-Sanlés A, Elosua R, Delgado P, Martí-Fábregas J, Krupinski J, Roquer J, Jiménez-Conde J, Fernández-Cadenas I. DNA Methylation and Ischemic Stroke Risk: An Epigenome-Wide Association Study. Thromb Haemost 2022; 122:1767-1778. [PMID: 35717949 DOI: 10.1055/s-0042-1749328] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
BACKGROUND Ischemic stroke (IS) risk heritability is partly explained by genetics. Other heritable factors, such as epigenetics, could explain an unknown proportion of the IS risk. The objective of this study is to evaluate DNA methylation association with IS using epigenome-wide association studies (EWAS). METHODS We performed a two-stage EWAS comprising 1,156 subjects. Differentially methylated positions (DMPs) and differentially methylated regions (DMRs) were assessed using the Infinium 450K and EPIC BeadChip in the discovery cohort (252 IS and 43 controls). Significant DMPs were replicated in an independent cohort (618 IS and 243 controls). Stroke subtype associations were also evaluated. Differentially methylated cell-type (DMCT) was analyzed in the replicated CpG sites using EpiDISH. We additionally performed pathway enrichment analysis and causality analysis with Mendelian randomization for the replicated CpG sites. RESULTS A total of 957 CpG sites were epigenome-wide-significant (p ≤ 10-7) in the discovery cohort, being CpG sites in the top signals (logFC = 0.058, p = 2.35 × 10-22; logFC = 0.035, p = 3.22 × 10-22, respectively). ZFHX3 and MAP3K1 were among the most significant DMRs. In addition, 697 CpG sites were replicated considering Bonferroni-corrected p-values (p < 5.22 × 10-5). All the replicated DMPs were associated with risk of cardioembolic, atherothrombotic, and undetermined stroke. The DMCT analysis demonstrated that the significant associations were driven by natural killer cells. The pathway enrichment analysis showed overrepresentation of genes belonging to certain pathways including oxidative stress. ZFHX3 and MAP3K1 methylation was causally associated with specific stroke-subtype risk. CONCLUSION Specific DNA methylation pattern is causally associated with IS risk. These results could be useful for specifically predicting stroke occurrence and could potentially be evaluated as therapeutic targets.
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Affiliation(s)
- Natalia Cullell
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí, Barcelona, Spain.,Department of Neurology, Hospital Universitari MútuaTerrassa/Fundacio Docència i Recerca MútuaTerrassa, Barcelona, Spain.,Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Carolina Soriano-Tárraga
- Neurovascular Research Group, Department of Neurology, Hospital del Mar, IMIM, Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain.,Department of Psychiatry, NeuroGenomics and Informatics, Washington University School of Medicine, St. Louis, Missouri, United States
| | | | - Jara Cárcel-Márquez
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí, Barcelona, Spain
| | - Nuria P Torres-Águila
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí, Barcelona, Spain.,Evolutionary Developmental Genomics Research Group, The Scottish Oceans Institute, University of St Andrews, St Andrews, United Kingdom
| | - Elena Muiño
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí, Barcelona, Spain
| | - Miquel Lledós
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí, Barcelona, Spain
| | - Laia Llucià-Carol
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí, Barcelona, Spain.,Department of Brain Ischemia and Neurodegeneration, Institut d'Investigacions Biomèdiques de Barcelona, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute, Barcelona, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.,Centro de Investigación Biomédica en Red Cancer, Barcelona, Spain
| | | | - Joan Montaner
- Department of Neurology, Hospital Universitario Virgen Macarena, Institute of Biomedicine of Seville/Hospital Universitario Virgen del Rocío/CSIC/University of Seville, Seville, Spain
| | - Alba Fernández-Sanlés
- Cardiovascular Epidemiology and Genetics Research Group, IMIM, Barcelona, Spain.,Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, United Kingdom
| | - Roberto Elosua
- Cardiovascular Epidemiology and Genetics Research Group, IMIM, Barcelona, Spain.,CIBER Cardiovascular Diseases, Instituto Carlos III, Barcelona, Spain.,School of Medicine, University of Vic-Central University of Catalonia, Barcelona, Spain
| | - Pilar Delgado
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research, Barcelona, Spain
| | - Joan Martí-Fábregas
- Department of Neurology, Hospital de la Santa Creu i Sant Pau, Barcelona, Spain
| | - Jerzy Krupinski
- Department of Neurology, Hospital Universitari MútuaTerrassa/Fundacio Docència i Recerca MútuaTerrassa, Barcelona, Spain.,Centre for Bioscience, School of HealthCare Science, Manchester Metropolitan University, Manchester, England
| | - Jaume Roquer
- Neurovascular Research Group, Department of Neurology, Hospital del Mar, IMIM, Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
| | - Jordi Jiménez-Conde
- Neurovascular Research Group, Department of Neurology, Hospital del Mar, IMIM, Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
| | - Israel Fernández-Cadenas
- Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí, Barcelona, Spain.,Department of Neurology, Hospital Universitari MútuaTerrassa/Fundacio Docència i Recerca MútuaTerrassa, Barcelona, Spain
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9
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Garcia-Prieto CA, Villanueva L, Bueno-Costa A, Davalos V, González-Navarro EA, Juan M, Urbano-Ispizua Á, Delgado J, Ortiz-Maldonado V, del Bufalo F, Locatelli F, Quintarelli C, Sinibaldi M, Soler M, Castro de Moura M, Ferrer G, Urdinguio RG, Fernandez AF, Fraga MF, Bar D, Meir A, Itzhaki O, Besser MJ, Avigdor A, Jacoby E, Esteller M. Epigenetic Profiling and Response to CD19 Chimeric Antigen Receptor T-Cell Therapy in B-Cell Malignancies. J Natl Cancer Inst 2022; 114:436-445. [PMID: 34581788 PMCID: PMC8902331 DOI: 10.1093/jnci/djab194] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/11/2021] [Accepted: 09/22/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Chimeric antigen receptor (CAR) T cells directed against CD19 (CART19) are effective in B-cell malignancies, but little is known about the molecular factors predicting clinical outcome of CART19 therapy. The increasingly recognized relevance of epigenetic changes in cancer immunology prompted us to determine the impact of the DNA methylation profiles of CART19 cells on the clinical course. METHODS We recruited 114 patients with B-cell malignancies, comprising 77 patients with acute lymphoblastic leukemia and 37 patients with non-Hodgkin lymphoma who were treated with CART19 cells. Using a comprehensive DNA methylation microarray, we determined the epigenomic changes that occur in the patient T cells upon transduction of the CAR vector. The effects of the identified DNA methylation sites on clinical response, cytokine release syndrome, immune effector cell-associated neurotoxicity syndrome, event-free survival, and overall survival were assessed. All statistical tests were 2-sided. RESULTS We identified 984 genomic sites with differential DNA methylation between CAR-untransduced and CAR-transduced T cells before infusion into the patient. Eighteen of these distinct epigenetic loci were associated with complete response (CR), adjusting by multiple testing. Using the sites linked to CR, an epigenetic signature, referred to hereafter as the EPICART signature, was established in the initial discovery cohort (n = 79), which was associated with CR (Fisher exact test, P < .001) and enhanced event-free survival (hazard ratio [HR] = 0.36; 95% confidence interval [CI] = 0.19 to 0.70; P = .002; log-rank P = .003) and overall survival (HR = 0.45; 95% CI = 0.20 to 0.99; P = .047; log-rank P = .04;). Most important, the EPICART profile maintained its clinical course predictive value in the validation cohort (n = 35), where it was associated with CR (Fisher exact test, P < .001) and enhanced overall survival (HR = 0.31; 95% CI = 0.11 to 0.84; P = .02; log-rank P = .02). CONCLUSIONS We show that the DNA methylation landscape of patient CART19 cells influences the efficacy of the cellular immunotherapy treatment in patients with B-cell malignancy.
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Affiliation(s)
- Carlos A Garcia-Prieto
- Cancer and Leukemia Epigenetics and Biology Program (PEBCL), Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | - Lorea Villanueva
- Cancer and Leukemia Epigenetics and Biology Program (PEBCL), Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Alberto Bueno-Costa
- Cancer and Leukemia Epigenetics and Biology Program (PEBCL), Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Veronica Davalos
- Cancer and Leukemia Epigenetics and Biology Program (PEBCL), Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | | | - Manel Juan
- Department of Immunology, Hospital Clinic, Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Álvaro Urbano-Ispizua
- Cancer and Leukemia Epigenetics and Biology Program (PEBCL), Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Department of Hematology, University of Barcelona (UB), Barcelona, Spain
| | - Julio Delgado
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cancer (CIBERONC), Madrid, Spain
| | | | - Francesca del Bufalo
- Department of Paediatric Haematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Franco Locatelli
- Department of Paediatric Haematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Department of Pediatrics, Sapienza University of Rome, Rome, Italy
| | - Concetta Quintarelli
- Department of Paediatric Haematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Matilde Sinibaldi
- Department of Paediatric Haematology and Oncology, Cell and Gene Therapy, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Marta Soler
- Cancer and Leukemia Epigenetics and Biology Program (PEBCL), Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Manuel Castro de Moura
- Cancer and Leukemia Epigenetics and Biology Program (PEBCL), Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Gerardo Ferrer
- Cancer and Leukemia Epigenetics and Biology Program (PEBCL), Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
| | - Rocio G Urdinguio
- Nanomaterials and Nanotechnology Research Center (CINNCSIC), Health Research Institute of Asturias (ISPA), Institute of Oncology of Asturias (IUOPA), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Department of Organisms and Systems Biology (BOS), University of Oviedo, Oviedo, Spain
| | - Agustin F Fernandez
- Nanomaterials and Nanotechnology Research Center (CINNCSIC), Health Research Institute of Asturias (ISPA), Institute of Oncology of Asturias (IUOPA), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Department of Organisms and Systems Biology (BOS), University of Oviedo, Oviedo, Spain
| | - Mario F Fraga
- Nanomaterials and Nanotechnology Research Center (CINNCSIC), Health Research Institute of Asturias (ISPA), Institute of Oncology of Asturias (IUOPA), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Department of Organisms and Systems Biology (BOS), University of Oviedo, Oviedo, Spain
| | - Diana Bar
- Division of Pediatric Hematology and Oncology, The Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Amilia Meir
- Division of Pediatric Hematology and Oncology, The Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Orit Itzhaki
- Ella Lemelbaum Institute for Immuno Oncology, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Michal J Besser
- Ella Lemelbaum Institute for Immuno Oncology, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Abraham Avigdor
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- Institute of Hematology, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Elad Jacoby
- Division of Pediatric Hematology and Oncology, The Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Manel Esteller
- Cancer and Leukemia Epigenetics and Biology Program (PEBCL), Josep Carreras Leukaemia Research Institute (IJC), Badalona, Spain
- Centro de Investigación Biomédica en Red de Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Spain
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10
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Genius P, Arenaza‐Urquijo EM, Operto G, Evans TE, Brugulat‐Serrat A, Falcon C, Minguillón C, Fauria K, Adams HH, de Moura MC, Piñeyro D, Esteller M, Guigó R, Navarro A, Molinuevo J, Gispert JD, Vilor‐Tejedor N. Sex differences in genetic susceptibility of hippocampal subfields: A polygenic association study. Alzheimers Dement 2021. [DOI: 10.1002/alz.053173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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11
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Soler M, Davalos V, Sánchez-Castillo A, Mora-Martinez C, Setién F, Siqueira E, Castro de Moura M, Esteller M, Guil S. The transcribed ultraconserved region uc.160+ enhances processing and A-to-I editing of the miR-376 cluster: hypermethylation improves glioma prognosis. Mol Oncol 2021; 16:648-664. [PMID: 34665919 PMCID: PMC8807354 DOI: 10.1002/1878-0261.13121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 10/01/2021] [Accepted: 10/15/2021] [Indexed: 11/11/2022] Open
Abstract
Transcribed ultraconserved regions (T‐UCRs) are noncoding RNAs derived from DNA sequences that are entirely conserved across species. Their expression is altered in many tumor types, and, although a role for T‐UCRs as regulators of gene expression has been proposed, their functions remain largely unknown. Herein, we describe the epigenetic silencing of the uc.160+ T‐UCR in gliomas and mechanistically define a novel RNA–RNA regulatory network in which uc.160+ modulates the biogenesis of several members of the miR‐376 cluster. This includes the positive regulation of primary microRNA (pri‐miRNA) cleavage and an enhanced A‐to‐I editing on its mature sequence. As a consequence, the expression of uc.160+ affects the downstream, miR‐376‐regulated genes, including the transcriptional coregulators RING1 and YY1‐binding protein (RYBP) and forkhead box P2 (FOXP2). Finally, we elucidate the clinical impact of our findings, showing that hypermethylation of the uc.160+ CpG island is an independent prognostic factor associated with better overall survival in lower‐grade gliomas, highlighting the importance of T‐UCRs in cancer pathophysiology.
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Affiliation(s)
- Marta Soler
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
| | - Veronica Davalos
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
| | - Anaís Sánchez-Castillo
- Department of Radiation Oncology (MAASTRO), GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, The Netherlands
| | - Carlos Mora-Martinez
- Centre of Excellence in Experimental and Computational Developmental Biology, Institute of Biotechnology, University of Helsinki, Finland
| | - Fernando Setién
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain
| | - Edilene Siqueira
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain.,Conselho Nacional de Desenvolvimento Cientifico e Tecnológico (CNPq), Brasilia, Brazil
| | | | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Spain
| | - Sonia Guil
- Josep Carreras Leukaemia Research Institute (IJC), Barcelona, Spain.,Germans Trias i Pujol Health Science Research Institute, Barcelona, Spain
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12
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Farre L, Sanz G, Ruiz-Xivillé N, Castro de Moura M, Martin-Tejera JF, Gonçalves-Ribeiro S, Martinez-Iniesta M, Calaf M, Luis Mosquera J, Martín-Subero JI, Granada I, Esteller M, Domingo-Domenech E, Climent F, Villanueva A, Sureda A. Extramedullary multiple myeloma patient-derived orthotopic xenograft with a highly altered genome: combined molecular and therapeutic studies. Dis Model Mech 2021; 14:dmm048223. [PMID: 33988237 PMCID: PMC8325009 DOI: 10.1242/dmm.048223] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 05/05/2021] [Indexed: 12/29/2022] Open
Abstract
Extramedullary multiple myeloma (EMM) has an overall survival of 6 months and occurs in 20% of multiple myeloma (MM) patients. Genetic and epigenetic mechanisms involved in EMM and the therapeutic role of new agents for MM are not well established. Besides, well-characterized preclinical models for EMM are not available. Herein, a patient-derived orthotopic xenograft (PDOX) was generated from a patient with an aggressive EMM to study in-depth genetic and epigenetic events, and drug responses related to extramedullary disease. A fresh punch of an extramedullary cutaneous lesion was orthotopically implanted in NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ(NSG) mouse. The PDOX mimicked histologic and phenotypic features of the tumor of the patient. Cytogenetic studies revealed a hyperploid genome with multiple genetic poor-prognosis alterations. Copy number alterations (CNAs) were detected in all chromosomes. The IGH translocation t(14;16)(q32;q23)IGH/MAF was already observed at the medullary stage and a new one, t(10;14)(p?11-12;q32), was observed only with extramedullary disease and could be eventually related to EMM progression in this case. Exome sequencing showed 24 high impact single nucleotide variants and 180 indels. From the genes involved, only TP53 was previously described as a driver in MM. A rather balanced proportion of hyper/hypomethylated sites different to previously reported widespread hypomethylation in MM was also observed. Treatment with lenalidomide, dexamethasone and carfilzomib showed a tumor weight reduction of 90% versus non-treated tumors, whereas treatment with the anti-CD38 antibody daratumumab showed a reduction of 46%. The generation of PDOX from a small EMM biopsy allowed us to investigate in depth the molecular events associated with extramedullary disease in combination with drug testing.
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Affiliation(s)
- Lourdes Farre
- Group of Chemoresistance and Predictive Factors, Subprogram Against Cancer Therapeutic Resistance, Catalan Institute of Oncology, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet del Llobregat, Barcelona, Spain
| | - Gabriela Sanz
- Department of Clinical Hematology, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet del Llobregat Barcelona, Spain
| | - Neus Ruiz-Xivillé
- Hematological Laboratory, Germans Trias i Pujol Hospital, Catalan Institute of Oncology, 08916 Badalona, Barcelona, Spain
- Cancer and Leukemia Epigenetics and Biology and Experimental and Clinical Hematology Programs, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Barcelona, Spain
| | - Manuel Castro de Moura
- Cancer and Leukemia Epigenetics and Biology and Experimental and Clinical Hematology Programs, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Barcelona, Spain
| | - Juan Francisco Martin-Tejera
- Group of Chemoresistance and Predictive Factors, Subprogram Against Cancer Therapeutic Resistance, Catalan Institute of Oncology, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet del Llobregat, Barcelona, Spain
| | - Samuel Gonçalves-Ribeiro
- Group of Chemoresistance and Predictive Factors, Subprogram Against Cancer Therapeutic Resistance, Catalan Institute of Oncology, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet del Llobregat, Barcelona, Spain
| | - Maria Martinez-Iniesta
- Group of Chemoresistance and Predictive Factors, Subprogram Against Cancer Therapeutic Resistance, Catalan Institute of Oncology, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet del Llobregat, Barcelona, Spain
| | - Monica Calaf
- Group of Chemoresistance and Predictive Factors, Subprogram Against Cancer Therapeutic Resistance, Catalan Institute of Oncology, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet del Llobregat, Barcelona, Spain
| | - Jose Luis Mosquera
- IDIBELL Bioinformatic Unit – Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet del Llobregat, Barcelona, Spain
| | - José Ignacio Martín-Subero
- Biomedical Epigenomics Group, Institut d'investigacions Biomèdiques August Pi I Sunyer (IDIBAPS), University of Barcelona, 08036 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
| | - Isabel Granada
- Hematological Laboratory, Germans Trias i Pujol Hospital, Catalan Institute of Oncology, 08916 Badalona, Barcelona, Spain
- Cancer and Leukemia Epigenetics and Biology and Experimental and Clinical Hematology Programs, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Barcelona, Spain
| | - Manel Esteller
- Cancer and Leukemia Epigenetics and Biology and Experimental and Clinical Hematology Programs, Josep Carreras Leukaemia Research Institute, 08916 Badalona, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cancer, Carlos III Institute of Health, 28029 Madrid, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, 08036 Barcelona, Spain
| | - Eva Domingo-Domenech
- Department of Clinical Hematology, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet del Llobregat Barcelona, Spain
| | - Fina Climent
- Centro de Investigación Biomédica en Red de Cancer, Carlos III Institute of Health, 28029 Madrid, Spain
- Department of Pathology, Hospital Universitari de Bellvitge – Bellvitge Biomedical Research Institute, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Alberto Villanueva
- Group of Chemoresistance and Predictive Factors, Subprogram Against Cancer Therapeutic Resistance, Catalan Institute of Oncology, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet del Llobregat, Barcelona, Spain
- Xenopat S.L., Business Bioincubator, Bellvitge Health Science Campus, 08907 L'Hospitalet de Llobregat, Barcelona, Spain
| | - Anna Sureda
- Department of Clinical Hematology, Catalan Institute of Oncology, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet del Llobregat Barcelona, Spain
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13
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Ciampa I, Operto G, Falcon C, Minguillon C, Castro de Moura M, Piñeyro D, Esteller M, Molinuevo JL, Guigó R, Navarro A, Gispert JD, Vilor-Tejedor N. Genetic Predisposition to Alzheimer's Disease Is Associated with Enlargement of Perivascular Spaces in Centrum Semiovale Region. Genes (Basel) 2021; 12:genes12060825. [PMID: 34072165 PMCID: PMC8226614 DOI: 10.3390/genes12060825] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 12/12/2022] Open
Abstract
This study investigated whether genetic factors involved in Alzheimer’s disease (AD) are associated with enlargement of Perivascular Spaces (ePVS) in the brain. A total of 680 participants with T2-weighted MRI scans and genetic information were acquired from the ALFA study. ePVS in the basal ganglia (BG) and the centrum semiovale (CS) were assessed based on a validated visual rating scale. We used univariate and multivariate logistic regression models to investigate associations between ePVS in BG and CS with BIN1-rs744373, as well as APOE genotypes. We found a significant association of the BIN1-rs744373 polymorphism in the CS subscale (p value = 0.019; OR = 2.564), suggesting that G allele carriers have an increased risk of ePVS in comparison with A allele carriers. In stratified analysis by APOE-ε4 status (carriers vs. non-carriers), these results remained significant only for ε4 carriers (p value = 0.011; OR = 1.429). To our knowledge, the present study is the first suggesting that genetic predisposition for AD is associated with ePVS in CS. These findings provide evidence that underlying biological processes affecting AD may influence CS-ePVS.
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Affiliation(s)
- Iacopo Ciampa
- Department of Radiology, Hospital Universitari Sagrat Cor, 08029 Barcelona, Spain;
| | - Grégory Operto
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, 08005 Barcelona, Spain; (G.O.); (C.F.); (C.M.); (J.L.M.); (A.N.)
- IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), 28029 Madrid, Spain
| | - Carles Falcon
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, 08005 Barcelona, Spain; (G.O.); (C.F.); (C.M.); (J.L.M.); (A.N.)
- IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Spain
- Centro de Investigación Biomédica en Red Bioingeniería, Biomateriales y Nanomedicina, 28029 Madrid, Spain
| | - Carolina Minguillon
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, 08005 Barcelona, Spain; (G.O.); (C.F.); (C.M.); (J.L.M.); (A.N.)
- IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), 28029 Madrid, Spain
| | - Manuel Castro de Moura
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain; (M.C.d.M.); (D.P.); (M.E.)
| | - David Piñeyro
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain; (M.C.d.M.); (D.P.); (M.E.)
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), 28019 Madrid, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Spain; (M.C.d.M.); (D.P.); (M.E.)
- Centro de Investigación Biomedica en Red Cancer (CIBERONC), 28019 Madrid, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), 08097 Barcelona, Spain
| | - Jose Luis Molinuevo
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, 08005 Barcelona, Spain; (G.O.); (C.F.); (C.M.); (J.L.M.); (A.N.)
- IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Fragilidad y Envejecimiento Saludable (CIBERFES), 28029 Madrid, Spain
- Universitat Pompeu Fabra, 08005 Barcelona, Spain;
| | - Roderic Guigó
- Universitat Pompeu Fabra, 08005 Barcelona, Spain;
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
| | - Arcadi Navarro
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, 08005 Barcelona, Spain; (G.O.); (C.F.); (C.M.); (J.L.M.); (A.N.)
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
- Department of Experimental and Health Sciences, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Juan Domingo Gispert
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, 08005 Barcelona, Spain; (G.O.); (C.F.); (C.M.); (J.L.M.); (A.N.)
- IMIM (Hospital del Mar Medical Research Institute), 08003 Barcelona, Spain
- Centro de Investigación Biomédica en Red Bioingeniería, Biomateriales y Nanomedicina, 28029 Madrid, Spain
- Correspondence: (J.D.G.); (N.V.-T.)
| | - Natalia Vilor-Tejedor
- Barcelonaβeta Brain Research Center (BBRC), Pasqual Maragall Foundation, 08005 Barcelona, Spain; (G.O.); (C.F.); (C.M.); (J.L.M.); (A.N.)
- Universitat Pompeu Fabra, 08005 Barcelona, Spain;
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003 Barcelona, Spain
- Department of Clinical Genetics, Erasmus University Medical Center Rotterdam, 3015 GD Rotterdam, The Netherlands
- Correspondence: (J.D.G.); (N.V.-T.)
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14
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Garcia-Ruiz B, de Moura MC, Muntané G, Martorell L, Bosch E, Esteller M, J Canales-Rodríguez E, Pomarol-Clotet E, Jiménez E, Vieta E, Vilella E. DDR1 methylation is associated with bipolar disorder and the isoform expression and methylation of myelin genes. Epigenomics 2021; 13:845-858. [PMID: 33942629 DOI: 10.2217/epi-2021-0006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To investigate DDR1 methylation in the brains of bipolar disorder (BD) patients and its association with DDR1 mRNA levels and comethylation with myelin genes. Materials & methods: Genome-wide profiling of DNA methylation (Infinium MethylationEPIC BeadChip) corrected for glial composition and DDR1 gene expression analysis in the occipital cortices of individuals with BD (n = 15) and healthy controls (n = 15) were conducted. Results: DDR1 5-methylcytosine levels were increased and directly associated with DDR1b mRNA expression in the brains of BD patients. We also observed that DDR1 was comethylated with a group of myelin genes. Conclusion: DDR1 is hypermethylated in BD brain tissue and is associated with isoform expression. Additionally, DDR1 comethylation with myelin genes supports the role of this receptor in myelination.
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Affiliation(s)
- Beatriz Garcia-Ruiz
- Hospital Universitari Institut Pere Mata, Ctra. de l'Institut Pere Mata, s/n. 43206, Reus, Catalonia, Spain.,Institut d'Investigació Sanitària Pere Visgili (IISPV), C/ Dr. Mallafrè Guasch, 4 Edifici modular Hospital Universitari de Tarragona Joan XXIII. 43007, Tarragona, Catalonia, Spain.,Universitat Rovira i Virgili (URV), Facultat de Medicina i Ciències de la Salut, Departament de Psiquiatria, C/Sant Llorenç, 21. 43201, Reus, Catalonia, Spain
| | - Manuel Castro de Moura
- Josep Carreras Leukaemia Research Institute (IJC), Josep Carreras Building, Ctra de Can Ruti, Camí de les Escoles, 08916, Badalona, Barcelona, Catalonia, Spain
| | - Gerard Muntané
- Hospital Universitari Institut Pere Mata, Ctra. de l'Institut Pere Mata, s/n. 43206, Reus, Catalonia, Spain.,Institut d'Investigació Sanitària Pere Visgili (IISPV), C/ Dr. Mallafrè Guasch, 4 Edifici modular Hospital Universitari de Tarragona Joan XXIII. 43007, Tarragona, Catalonia, Spain.,Universitat Rovira i Virgili (URV), Facultat de Medicina i Ciències de la Salut, Departament de Psiquiatria, C/Sant Llorenç, 21. 43201, Reus, Catalonia, Spain.,Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), C/Melchor Fernández Almagro, 3. 28029, Madrid, Spain.,Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona (PRBB), C/Dr. Aiguader, 88, 08003, Barcelona, Catalonia, Spain
| | - Lourdes Martorell
- Hospital Universitari Institut Pere Mata, Ctra. de l'Institut Pere Mata, s/n. 43206, Reus, Catalonia, Spain.,Institut d'Investigació Sanitària Pere Visgili (IISPV), C/ Dr. Mallafrè Guasch, 4 Edifici modular Hospital Universitari de Tarragona Joan XXIII. 43007, Tarragona, Catalonia, Spain.,Universitat Rovira i Virgili (URV), Facultat de Medicina i Ciències de la Salut, Departament de Psiquiatria, C/Sant Llorenç, 21. 43201, Reus, Catalonia, Spain.,Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), C/Melchor Fernández Almagro, 3. 28029, Madrid, Spain
| | - Elena Bosch
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona (PRBB), C/Dr. Aiguader, 88, 08003, Barcelona, Catalonia, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Josep Carreras Building, Ctra de Can Ruti, Camí de les Escoles, 08916, Badalona, Barcelona, Catalonia, Spain.,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), C/Melchor Fernández Almagro, 3. 28029, Madrid, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig de Lluís Companys, 23. 08010, Barcelona, Catalonia, Spain.,Physiological Sciences Department, School of Medicine & Health Sciences, University of Barcelona (UB), Feixa Llarga, 08907, l'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Erick J Canales-Rodríguez
- Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), C/Melchor Fernández Almagro, 3. 28029, Madrid, Spain.,FIDMAG Research Foundation, Germanes Hospitalàries, Av. Jordà, 8. 08035, Barcelona, Catalonia, Spain.,Signal Processing Laboratory (LTS5), École Polytechnique Fédérale de Lausanne (EPFL), Station 11. CH-1015, Lausanne, Switzerland
| | - Edith Pomarol-Clotet
- Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), C/Melchor Fernández Almagro, 3. 28029, Madrid, Spain.,FIDMAG Research Foundation, Germanes Hospitalàries, Av. Jordà, 8. 08035, Barcelona, Catalonia, Spain
| | - Esther Jiménez
- Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), C/Melchor Fernández Almagro, 3. 28029, Madrid, Spain.,Bipolar & Depressive Disorders Unit, Hospital Clinic, Institute of Neuroscience, University of Barcelona, IDIBAPS, Villarroel, 170, 12-0. 08036, Barcelona, Catalonia, Spain
| | - Eduard Vieta
- Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), C/Melchor Fernández Almagro, 3. 28029, Madrid, Spain.,Bipolar & Depressive Disorders Unit, Hospital Clinic, Institute of Neuroscience, University of Barcelona, IDIBAPS, Villarroel, 170, 12-0. 08036, Barcelona, Catalonia, Spain
| | - Elisabet Vilella
- Hospital Universitari Institut Pere Mata, Ctra. de l'Institut Pere Mata, s/n. 43206, Reus, Catalonia, Spain.,Institut d'Investigació Sanitària Pere Visgili (IISPV), C/ Dr. Mallafrè Guasch, 4 Edifici modular Hospital Universitari de Tarragona Joan XXIII. 43007, Tarragona, Catalonia, Spain.,Universitat Rovira i Virgili (URV), Facultat de Medicina i Ciències de la Salut, Departament de Psiquiatria, C/Sant Llorenç, 21. 43201, Reus, Catalonia, Spain.,Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), C/Melchor Fernández Almagro, 3. 28029, Madrid, Spain
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15
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Castro de Moura M, Davalos V, Planas-Serra L, Alvarez-Errico D, Arribas C, Ruiz M, Aguilera-Albesa S, Troya J, Valencia-Ramos J, Vélez-Santamaria V, Rodríguez-Palmero A, Villar-Garcia J, Horcajada JP, Albu S, Casasnovas C, Rull A, Reverte L, Dietl B, Dalmau D, Arranz MJ, Llucià-Carol L, Planas AM, Pérez-Tur J, Fernandez-Cadenas I, Villares P, Tenorio J, Colobran R, Martin-Nalda A, Soler-Palacin P, Vidal F, Pujol A, Esteller M. Epigenome-wide association study of COVID-19 severity with respiratory failure. EBioMedicine 2021; 66:103339. [PMID: 33867313 PMCID: PMC8047083 DOI: 10.1016/j.ebiom.2021.103339] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/16/2021] [Accepted: 03/26/2021] [Indexed: 12/20/2022] Open
Abstract
Background Patients infected with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the coronavirus disease 2019 (COVID-19), exhibit a wide spectrum of disease behaviour. Since DNA methylation has been implicated in the regulation of viral infections and the immune system, we performed an epigenome-wide association study (EWAS) to identify candidate loci regulated by this epigenetic mark that could be involved in the onset of COVID-19 in patients without comorbidities. Methods Peripheral blood samples were obtained from 407 confirmed COVID-19 patients ≤ 61 years of age and without comorbidities, 194 (47.7%) of whom had mild symptomatology that did not involve hospitalization and 213 (52.3%) had a severe clinical course that required respiratory support. The set of cases was divided into discovery (n = 207) and validation (n = 200) cohorts, balanced for age and sex of individuals. We analysed the DNA methylation status of 850,000 CpG sites in these patients. Findings The DNA methylation status of 44 CpG sites was associated with the clinical severity of COVID-19. Of these loci, 23 (52.3%) were located in 20 annotated coding genes. These genes, such as the inflammasome component Absent in Melanoma 2 (AIM2) and the Major Histocompatibility Complex, class I C (HLA-C) candidates, were mainly involved in the response of interferon to viral infection. We used the EWAS-identified sites to establish a DNA methylation signature (EPICOVID) that is associated with the severity of the disease. Interpretation We identified DNA methylation sites as epigenetic susceptibility loci for respiratory failure in COVID-19 patients. These candidate biomarkers, combined with other clinical, cellular and genetic factors, could be useful in the clinical stratification and management of patients infected with the SARS-CoV-2. Funding The Unstoppable campaign of the Josep Carreras Leukaemia Foundation, the Cellex Foundation and the CERCA Programme/Generalitat de Catalunya.
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Affiliation(s)
- Manuel Castro de Moura
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Catalonia, Spain
| | - Veronica Davalos
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Catalonia, Spain
| | - Laura Planas-Serra
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Damiana Alvarez-Errico
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Catalonia, Spain
| | - Carles Arribas
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Catalonia, Spain
| | - Montserrat Ruiz
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | | | - Jesús Troya
- Infanta Leonor University Hospital, Madrid, Spain
| | | | - Valentina Vélez-Santamaria
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain; Bellvitge University Hospital, L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Agustí Rodríguez-Palmero
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain; University Hospital Germans Trias i Pujol, Badalona, Barcelona, Catalonia, Spain
| | - Judit Villar-Garcia
- Hospital del Mar - IMIM Biomedical Research Institute, Barcelona, Catalonia, Spain
| | - Juan P Horcajada
- Hospital del Mar - IMIM Biomedical Research Institute, Barcelona, Catalonia, Spain
| | - Sergiu Albu
- Institut Guttmann Foundation, Badalona, Barcelona, Catalonia, Spain
| | - Carlos Casasnovas
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain; Bellvitge University Hospital, L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Anna Rull
- Hospital Universitari de Tarragona Joan XXIII, IISPV, Universitat Rovira i Virgili, Tarragona, Catalonia, Spain
| | - Laia Reverte
- Hospital Universitari de Tarragona Joan XXIII, IISPV, Universitat Rovira i Virgili, Tarragona, Catalonia, Spain
| | - Beatriz Dietl
- Servei de malalties infeccioses Hospital Universitari MutuaTerrassa, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - David Dalmau
- MutuaTerrassa Research and Innovation Foundation, HIV/AIDS Unit Hospital Universitari MutuaTerrassa, University of Barcelona, Barcelona, Catalonia, Spain
| | - Maria J Arranz
- Fundaciò Docència i Recerca Mutua Terrassa i Hospital Universitari Mutua Terrassa, Barcelona, Catalonia, Spain
| | - Laia Llucià-Carol
- Stroke Pharmacogenomics and Genetics Group, Sant Pau Institute of Research, Sant Pau Hospital, Barcelona, Catalonia, Spain
| | - Anna M Planas
- Department of Brain Ischemia and Neurodegeneration, Institut d'Investigacions Biomèdiques de Barcelona (IIBB), Consejo Superior de Investigaciones Científicas (CSIC), Area of Neurosciences, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain
| | - Jordi Pérez-Tur
- Institut de Biomedicina de València-CSIC, CIBERNED, Unitat Mixta de Neurologia i Genètica, IIS La Fe, Vallencia, Spain
| | - Israel Fernandez-Cadenas
- Stroke Pharmacogenomics and Genetics Group, Sant Pau Institute of Research, Sant Pau Hospital, Barcelona, Catalonia, Spain
| | - Paula Villares
- Internal Medicine Department, Hospital HM Sanchinarro, HM Hospitales, Madrid, Spain
| | - Jair Tenorio
- INGEMM-Instituto de Genética Médica y Molecular, Hospital Universitario La Paz, Madrid, Spain; Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain
| | - Roger Colobran
- Immunology Division, Genetics Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Research Institute, Vall d'Hebron Barcelona Hospital Campus, UAB, Barcelona, Catalonia, Spain
| | - Andrea Martin-Nalda
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Pere Soler-Palacin
- Pediatric Infectious Diseases and Immunodeficiencies Unit, Hospital Universitari Vall d'Hebron, Vall d'Hebron Barcelona Hospital Campus, Barcelona, Catalonia, Spain
| | - Francesc Vidal
- Hospital Universitari de Tarragona Joan XXIII, IISPV, Universitat Rovira i Virgili, Tarragona, Catalonia, Spain
| | - Aurora Pujol
- Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain; Center for Biomedical Research on Rare Diseases (CIBERER), ISCIII, Madrid, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Barcelona, Catalonia, Spain; Centro de Investigación Biomédica en Red de Cancer (CIBERONC), Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Catalonia, Spain.
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16
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Wheeler DA, Takebe N, Hinoue T, Hoadley KA, Cardenas MF, Hamilton AM, Laird PW, Wang L, Johnson A, Dewal N, Miller V, Piñeyro D, Castro de Moura M, Esteller M, Shen H, Zenklusen JC, Tarnuzzer R, McShane LM, Tricoli JV, Williams PM, Lubensky I, O'Sullivan-Coyne G, Kohn EC, Little RF, White J, Malik S, Harris L, Weil C, Chen AP, Karlovich C, Rodgers B, Shankar L, Jacobs P, Nolan T, Hu J, Muzny DM, Doddapaneni H, Korchina V, Gastier-Foster J, Bowen J, Leraas K, Edmondson EF, Doroshow JH, Conley BA, Ivy SP, Staudt LM. Molecular Features of Cancers Exhibiting Exceptional Responses to Treatment. Cancer Cell 2021; 39:38-53.e7. [PMID: 33217343 PMCID: PMC8478080 DOI: 10.1016/j.ccell.2020.10.015] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/23/2020] [Accepted: 10/13/2020] [Indexed: 12/21/2022]
Abstract
A small fraction of cancer patients with advanced disease survive significantly longer than patients with clinically comparable tumors. Molecular mechanisms for exceptional responses to therapy have been identified by genomic analysis of tumor biopsies from individual patients. Here, we analyzed tumor biopsies from an unbiased cohort of 111 exceptional responder patients using multiple platforms to profile genetic and epigenetic aberrations as well as the tumor microenvironment. Integrative analysis uncovered plausible mechanisms for the therapeutic response in nearly a quarter of the patients. The mechanisms were assigned to four broad categories-DNA damage response, intracellular signaling, immune engagement, and genetic alterations characteristic of favorable prognosis-with many tumors falling into multiple categories. These analyses revealed synthetic lethal relationships that may be exploited therapeutically and rare genetic lesions that favor therapeutic success, while also providing a wealth of testable hypotheses regarding oncogenic mechanisms that may influence the response to cancer therapy.
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Affiliation(s)
- David A Wheeler
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Naoko Takebe
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Katherine A Hoadley
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Maria F Cardenas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA; Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alina M Hamilton
- Department of Genetics, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | | | - Linghua Wang
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | | | - Ninad Dewal
- Foundation Medicine Inc, Cambridge, MA 02141, USA
| | | | - David Piñeyro
- Josep Carreras Leukaemia Research Institute, Badalona, 08916 Barcelona, Catalonia, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain
| | - Manuel Castro de Moura
- Josep Carreras Leukaemia Research Institute, Badalona, 08916 Barcelona, Catalonia, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute, Badalona, 08916 Barcelona, Catalonia, Spain; Centro de Investigacion Biomedica en Red Cancer (CIBERONC), 28029 Madrid, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), 08007 Barcelona, Catalonia, Spain
| | - Hui Shen
- Van Andel Institute, Grand Rapids, MI 49503, USA
| | | | - Roy Tarnuzzer
- Center for Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Lisa M McShane
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - James V Tricoli
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Paul M Williams
- Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Irina Lubensky
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Elise C Kohn
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Richard F Little
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Jeffrey White
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Shakun Malik
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Lyndsay Harris
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Carol Weil
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Alice P Chen
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Chris Karlovich
- Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Brian Rodgers
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Lalitha Shankar
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Paula Jacobs
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Tracy Nolan
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jianhong Hu
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Viktoriya Korchina
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Jay Bowen
- Nationwide Children's Hospital, Columbus, OH 43205, USA
| | | | - Elijah F Edmondson
- Pathology and Histology Laboratory, Frederick National Laboratory for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21701, USA
| | - James H Doroshow
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Barbara A Conley
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - S Percy Ivy
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD 20892, USA
| | - Louis M Staudt
- Center for Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA.
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17
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Mattesen TB, Rasmussen MH, Sandoval J, Ongen H, Árnadóttir SS, Gladov J, Martinez-Cardus A, de Moura MC, Madsen AH, Laurberg S, Dermitzakis ET, Esteller M, Andersen CL, Bramsen JB. Publisher Correction: MethCORR modelling of methylomes from formalin-fixed paraffin-embedded tissue enables characterization and prognostication of colorectal cancer. Nat Commun 2020; 11:2880. [PMID: 32493930 PMCID: PMC7270084 DOI: 10.1038/s41467-020-16538-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Trine B Mattesen
- Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus, Denmark
| | - Mads H Rasmussen
- Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus, Denmark
| | - Juan Sandoval
- Epigenomic Unit, Health Research Institute La Fe (ISSLaFe), Valencia, Spain.,Biomarker and precision medicine Unit, Health Research Institute La Fe (ISSLaFe), Valencia, Spain
| | - Halit Ongen
- Genetic Medicine and Development, University of Geneva Medical School-CMU, 1 Rue Michel-Servet, 1211, Geneva, Switzerland
| | - Sigrid S Árnadóttir
- Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus, Denmark
| | - Josephine Gladov
- Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus, Denmark
| | - Anna Martinez-Cardus
- Badalona Applied Research Group in Oncology (B-ARGO), Germans Trias i Pujol Research Institute (IGTP), Badalona, Barcelona, Catalonia, Spain.,Medical Oncology Service, Institute Catalan of Oncology (ICO), Badalona, Barcelona, Catalonia, Spain
| | - Manuel Castro de Moura
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Anders H Madsen
- Department of Surgery, Hospitalsenheden Vest, 7400, Herning, Denmark
| | - Søren Laurberg
- Colorectal Surgical Unit, Department of Surgery, Aarhus University Hospital, 8200, Aarhus, Denmark
| | - Emmanouil T Dermitzakis
- Genetic Medicine and Development, University of Geneva Medical School-CMU, 1 Rue Michel-Servet, 1211, Geneva, Switzerland
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain.,Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Claus L Andersen
- Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus, Denmark.
| | - Jesper B Bramsen
- Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus, Denmark.
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18
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Mattesen TB, Rasmussen MH, Sandoval J, Ongen H, Árnadóttir SS, Gladov J, Martinez-Cardus A, Castro de Moura M, Madsen AH, Laurberg S, Dermitzakis ET, Esteller M, Andersen CL, Bramsen JB. MethCORR modelling of methylomes from formalin-fixed paraffin-embedded tissue enables characterization and prognostication of colorectal cancer. Nat Commun 2020; 11:2025. [PMID: 32332866 PMCID: PMC7181739 DOI: 10.1038/s41467-020-16000-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 04/02/2020] [Indexed: 12/29/2022] Open
Abstract
Transcriptional characterization and classification has potential to resolve the inter-tumor heterogeneity of colorectal cancer and improve patient management. Yet, robust transcriptional profiling is difficult using formalin-fixed, paraffin-embedded (FFPE) samples, which complicates testing in clinical and archival material. We present MethCORR, an approach that allows uniform molecular characterization and classification of fresh-frozen and FFPE samples. MethCORR identifies genome-wide correlations between RNA expression and DNA methylation in fresh-frozen samples. This information is used to infer gene expression information in FFPE samples from their methylation profiles. MethCORR is here applied to methylation profiles from 877 fresh-frozen/FFPE samples and comparative analysis identifies the same two subtypes in four independent cohorts. Furthermore, subtype-specific prognostic biomarkers that better predicts relapse-free survival (HR = 2.66, 95%CI [1.67-4.22], P value < 0.001 (log-rank test)) than UICC tumor, node, metastasis (TNM) staging and microsatellite instability status are identified and validated using DNA methylation-specific PCR. The MethCORR approach is general, and may be similarly successful for other cancer types.
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Grants
- R01 CA207467 NCI NIH HHS
- This research is supported by grants from the European Commission FP7 project SYSCOL (UE7-SYSCOL-258236), the Novo Nordisk Foundation (NNF16OC0023182), the Danish National Advanced Technology Foundation (056-2010-1), the John and Birthe Meyer Foundation, the Danish Council for Independent Research (Medical Sciences) (DFF - 0602-02128B, DFF – 4183-00619, DFF - 7016-00332B), the Danish Council for Strategic Research (1309-00006B), the Danish Cancer Society (R40-A1965_11_S2, R56-A3110-12-S2, R107-A7035, R133-A8520), the National Cancer Institute of the National Institutes of Health (R01 CA207467), the Aage and Johanne Louis-Hansen’s Foundation (17-2-0457), the Knud and Edith Eriksen’s Memorial Foundation, the Neye Foundation and the Manufacturer Einar Willumsen’s Memorial Foundation (6000073)
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Affiliation(s)
- Trine B Mattesen
- Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus, Denmark
| | - Mads H Rasmussen
- Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus, Denmark
| | - Juan Sandoval
- Epigenomic Unit, Health Research Institute La Fe (ISSLaFe), Valencia, Spain
- Biomarker and precision medicine Unit, Health Research Institute La Fe (ISSLaFe), Valencia, Spain
| | - Halit Ongen
- Genetic Medicine and Development, University of Geneva Medical School-CMU, 1 Rue Michel-Servet, 1211, Geneva, Switzerland
| | - Sigrid S Árnadóttir
- Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus, Denmark
| | - Josephine Gladov
- Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus, Denmark
| | - Anna Martinez-Cardus
- Badalona Applied Research Group in Oncology (B-ARGO), Germans Trias i Pujol Research Institute (IGTP), Badalona, Barcelona, Catalonia, Spain
- Medical Oncology Service, Institute Catalan of Oncology (ICO), Badalona, Barcelona, Catalonia, Spain
| | - Manuel Castro de Moura
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Anders H Madsen
- Department of Surgery, Hospitalsenheden Vest, 7400, Herning, Denmark
| | - Søren Laurberg
- Colorectal Surgical Unit, Department of Surgery, Aarhus University Hospital, 8200, Aarhus, Denmark
| | - Emmanouil T Dermitzakis
- Genetic Medicine and Development, University of Geneva Medical School-CMU, 1 Rue Michel-Servet, 1211, Geneva, Switzerland
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
- Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
- Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
- Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain
| | - Claus L Andersen
- Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus, Denmark.
| | - Jesper B Bramsen
- Department of Molecular Medicine, Aarhus University Hospital, 8200, Aarhus, Denmark.
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19
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Gallego-Fabrega C, Cullell N, Soriano-Tárraga C, Carrera C, Torres-Aguila NP, Muiño E, Cárcel-Márquez J, de Moura MC, Fernández-Sanlés A, Esteller M, Elosua R, Jiménez-Conde J, Roquer J, Montaner J, Krupinski J, Fernandez-Cadenas I. DNA methylation of MMPs and TIMPs in atherothrombosis process in carotid plaques and blood tissues. Oncotarget 2020; 11:905-912. [PMID: 32206187 PMCID: PMC7075467 DOI: 10.18632/oncotarget.27469] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 01/13/2020] [Indexed: 12/20/2022] Open
Abstract
Background and Purpose: Polymorphisms and serum levels of Matrix Metalloproteinases (MMP) and Tissue Inhibitor of Metalloproteinases (TIMP) have been studied with regard to atheromatous plaques and ischemic stroke, while no studies of DNA methylation (DNAm) patterns of MMP or TIMP have been performed to that end. Here, we evaluate DNAm levels of the MMP and TIMP gene families in human carotid plaques and blood samples of atherothrombotic stroke patients. Methods: We profiled the DNAm status of stable and ulcerated atherosclerotic plaques obtained as pair sets from three patients who underwent carotid endarterectomy surgery. We selected 415 CpG sites, mapping into MMPs and TIMPs genes for further study. Secondly, the statistically associated CpG sites were analyzed in blood samples from two separate atherothrombotic stroke cohorts (total sample size = 307), ischemic stroke-cohort 1 (ISC-1): 37 atherothrombotic patients and 6 controls, ischemic stroke-cohort 2 (ISC-2): 80 atherothrombotic patients and 184 controls. DNAm levels from plaque tissue and blood samples were evaluated using a high-density microarray Infinium, HumanMethylation450 BeadChip and Infinium MethylationEPIC BeadChip. Results: Three CpG sites were statistically significantly associated with unstable plaque portions; cg02969624, q-value = 0.035 (TIMP2), and cg04316754, q-value = 0.037 (MMP24) were hypermethylated, while cg24211657 q-value = 0.035 (TIMP2) was hypomethylated. Association of cg04316754 (MMP24) methylation levels with atherothrombotic risk was also observed in blood tissue: ISC-1 p-values = 0.03, ISC-2 p-value = 1.9 × 10-04. Conclusions: The results suggest different DNAm status of MMP24 between stable and unstable atherothrombotic carotid plaques, and between atherothrombotic stroke and controls in blood samples.
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Affiliation(s)
- Cristina Gallego-Fabrega
- Neurology, Hospital Universitari Mútua de Terrassa/Fundacio Docència i Recerca MutuaTerrassa, Terrassa, Spain.,Stroke Pharmacogenomics and Genetics, Sant Pau Research Institute, Barcelona, Spain
| | - Natalia Cullell
- Neurology, Hospital Universitari Mútua de Terrassa/Fundacio Docència i Recerca MutuaTerrassa, Terrassa, Spain.,Stroke Pharmacogenomics and Genetics, Sant Pau Research Institute, Barcelona, Spain.,Facultat de Medicina, Universitat de Barcelona, Barcelona, Spain
| | - Carolina Soriano-Tárraga
- Department of Neurology, Hospital del Mar, Neurovascular Research Group, Institut Hospital del Mar d'Investigacions Mèdiques, Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
| | - Caty Carrera
- Stroke Pharmacogenomics and Genetics, Sant Pau Research Institute, Barcelona, Spain.,Neurovascular Research Laboratory, Vall d'Hebron Institute of Research, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Elena Muiño
- Stroke Pharmacogenomics and Genetics, Sant Pau Research Institute, Barcelona, Spain
| | - Jara Cárcel-Márquez
- Stroke Pharmacogenomics and Genetics, Sant Pau Research Institute, Barcelona, Spain
| | | | - Alba Fernández-Sanlés
- Cardiovascular Epidemiology and Genetics Research Group, Hospital del Mar Medical Research Institute, Universitat Pompeu Fabra, Barcelona, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, Spain.,Institucio Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Roberto Elosua
- Cardiovascular Epidemiology and Genetics Research Group, Hospital del Mar Medical Research Institute, Universitat Pompeu Fabra, Barcelona, Spain
| | - Jordi Jiménez-Conde
- Department of Neurology, Hospital del Mar, Neurovascular Research Group, Institut Hospital del Mar d'Investigacions Mèdiques, Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
| | - Jaume Roquer
- Department of Neurology, Hospital del Mar, Neurovascular Research Group, Institut Hospital del Mar d'Investigacions Mèdiques, Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
| | - Joan Montaner
- Neurovascular Research Laboratory, Vall d'Hebron Institute of Research, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Jerzy Krupinski
- Neurology, Hospital Universitari Mútua de Terrassa/Fundacio Docència i Recerca MutuaTerrassa, Terrassa, Spain.,Centre for Biomedicine, Manchester Metropolitan University, Manchester, UK.,These authors contributed equally to this work
| | - Israel Fernandez-Cadenas
- Stroke Pharmacogenomics and Genetics, Sant Pau Research Institute, Barcelona, Spain.,These authors contributed equally to this work
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20
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Llinàs-Arias P, Rosselló-Tortella M, López-Serra P, Pérez-Salvia M, Setién F, Marin S, Muñoz JP, Junza A, Capellades J, Calleja-Cervantes ME, Ferreira HJ, de Moura MC, Srbic M, Martínez-Cardús A, de la Torre C, Villanueva A, Cascante M, Yanes O, Zorzano A, Moutinho C, Esteller M. Epigenetic loss of the endoplasmic reticulum-associated degradation inhibitor SVIP induces cancer cell metabolic reprogramming. JCI Insight 2019; 5:125888. [PMID: 30843871 DOI: 10.1172/jci.insight.125888] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The endoplasmic reticulum (ER) of cancer cells needs to adapt to the enhanced proteotoxic stress associated with the accumulation of unfolded, misfolded and transformation-associated proteins. One way by which tumors thrive in the context of ER stress is by promoting ER-Associated Degradation (ERAD), although the mechanisms are poorly understood. Here, we show that the Small p97/VCP Interacting Protein (SVIP), an endogenous inhibitor of ERAD, undergoes DNA hypermethylation-associated silencing in tumorigenesis to achieve this goal. SVIP exhibits tumor suppressor features and its recovery is associated with increased ER stress and growth inhibition. Proteomic and metabolomic analyses show that cancer cells with epigenetic loss of SVIP are depleted in mitochondrial enzymes and oxidative respiration activity. This phenotype is reverted upon SVIP restoration. The dependence of SVIP hypermethylated cancer cells on aerobic glycolysis and glucose was also associated with sensitivity to an inhibitor of the glucose transporter GLUT1. This could be relevant to the management of tumors carrying SVIP epigenetic loss, because these occur in high-risk patients who manifest poor clinical outcomes. Overall, our study provides insights into how epigenetics helps deal with ER stress and how SVIP epigenetic loss in cancer may be amenable to therapies that target glucose transporters.
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Affiliation(s)
- Pere Llinàs-Arias
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain.,Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
| | - Margalida Rosselló-Tortella
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Paula López-Serra
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Montserrat Pérez-Salvia
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain.,Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain
| | - Fernando Setién
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Silvia Marin
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain.,Institute of Biomedicine of Universitat de Barcelona (IBUB), Barcelona, Spain.,CIBER of Liver and Digestive Diseases (CIBEREHD), Madrid, Spain
| | - Juan P Muñoz
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain.,CIBER of Diabetes and Associated Metabolic Diseases (CIBERDEM), Madrid, Spain
| | - Alexandra Junza
- CIBER of Diabetes and Associated Metabolic Diseases (CIBERDEM), Madrid, Spain.,Metabolomics Platform, IISPV, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, Catalonia, Spain
| | - Jordi Capellades
- CIBER of Diabetes and Associated Metabolic Diseases (CIBERDEM), Madrid, Spain.,Metabolomics Platform, IISPV, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, Catalonia, Spain
| | - María E Calleja-Cervantes
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Humberto J Ferreira
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Manuel Castro de Moura
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Marina Srbic
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Anna Martínez-Cardús
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Carolina de la Torre
- Proteomics Unit, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Catalonia, Spain
| | - Alberto Villanueva
- Translational Research Laboratory, Catalan Institute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Catalonia, Spain
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain.,Institute of Biomedicine of Universitat de Barcelona (IBUB), Barcelona, Spain.,CIBER of Liver and Digestive Diseases (CIBEREHD), Madrid, Spain
| | - Oscar Yanes
- CIBER of Diabetes and Associated Metabolic Diseases (CIBERDEM), Madrid, Spain.,Metabolomics Platform, IISPV, Department of Electronic Engineering (DEEEA), Universitat Rovira i Virgili, Tarragona, Catalonia, Spain
| | - Antonio Zorzano
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, University of Barcelona, Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain.,CIBER of Diabetes and Associated Metabolic Diseases (CIBERDEM), Madrid, Spain
| | - Catia Moutinho
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain.,Centro de Investigacion Biomedica en Red Cancer (CIBERONC), Madrid, Spain.,Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona, Catalonia, Spain
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21
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Sia D, Jiao Y, Martinez-Quetglas I, Kuchuk O, Villacorta-Martin C, Castro de Moura M, Putra J, Camprecios G, Bassaganyas L, Akers N, Losic B, Waxman S, Thung SN, Mazzaferro V, Esteller M, Friedman SL, Schwartz M, Villanueva A, Llovet JM. Identification of an Immune-specific Class of Hepatocellular Carcinoma, Based on Molecular Features. Gastroenterology 2017. [PMID: 28624577 DOI: 10.1053/j.gastro.2017.06.007] [Citation(s) in RCA: 572] [Impact Index Per Article: 81.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Agents that induce an immune response against tumors by altering T-cell regulation have increased survival times of patients with advanced-stage tumors, such as melanoma or lung cancer. We aimed to characterize molecular features of immune cells that infiltrate hepatocellular carcinomas (HCCs) to determine whether these types of agents might be effective against liver tumors. METHODS We analyzed HCC samples from 956 patients. We separated gene expression profiles from tumor, stromal, and immune cells using a non-negative matrix factorization algorithm. We then analyzed the gene expression pattern of inflammatory cells in HCC tumor samples. We correlated expression patterns with the presence of immune cell infiltrates and immune regulatory molecules, determined by pathology and immunohistochemical analyses, in a training set of 228 HCC samples. We validated the correlation in a validation set of 728 tumor samples. Using data from 190 tumors in the Cancer Genome Atlas, we correlated immune cell gene expression profiles with numbers of chromosomal aberrations (based on single-nucleotide polymorphism array) and mutations (exome sequence data). RESULTS We found approximately 25% of HCCs to have markers of an inflammatory response, with high expression levels of the CD274 molecule (programmed death-ligand 1) and programmed cell death 1, markers of cytolytic activity, and fewer chromosomal aberrations. We called this group of tumors the Immune class. It contained 2 subtypes, characterized by markers of an adaptive T-cell response or exhausted immune response. The exhausted immune response subclass expressed many genes regulated by transforming growth factor beta 1 that mediate immunosuppression. We did not observe any differences in numbers of mutations or expression of tumor antigens between the immune-specific class and other HCCs. CONCLUSIONS In an analysis of HCC samples from 956 patients, we found almost 25% to express markers of an inflammatory response. We identified 2 subclasses, characterized by adaptive or exhausted immune responses. These findings indicate that some HCCs might be susceptible to therapeutic agents designed to block the regulatory pathways in T cells, such as programmed death-ligand 1, programmed cell death 1, or transforming growth factor beta 1 inhibitors.
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Affiliation(s)
- Daniela Sia
- Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Hematology/Oncology, Department of Medicine, Department of Pathology, Recanati Miller Transplantation Institute), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Yang Jiao
- Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Hematology/Oncology, Department of Medicine, Department of Pathology, Recanati Miller Transplantation Institute), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Iris Martinez-Quetglas
- Liver Cancer Translational Research Laboratory, BCLC, Liver Unit, CIBEREHD, IDIBAPS, Hospital Clinic, University of Barcelona, Catalonia, Spain
| | - Olga Kuchuk
- Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Hematology/Oncology, Department of Medicine, Department of Pathology, Recanati Miller Transplantation Institute), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York; University of Milan and Gastrointestinal Surgery and Liver Transplantation Unit, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Carlos Villacorta-Martin
- Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Hematology/Oncology, Department of Medicine, Department of Pathology, Recanati Miller Transplantation Institute), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Manuel Castro de Moura
- Cancer Epigenetics and Biology Program, IDIBELL, Hospital Universitari Bellvitge, Barcelona, Catalonia, Spain
| | - Juan Putra
- Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Hematology/Oncology, Department of Medicine, Department of Pathology, Recanati Miller Transplantation Institute), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Genis Camprecios
- Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Hematology/Oncology, Department of Medicine, Department of Pathology, Recanati Miller Transplantation Institute), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Laia Bassaganyas
- Liver Cancer Translational Research Laboratory, BCLC, Liver Unit, CIBEREHD, IDIBAPS, Hospital Clinic, University of Barcelona, Catalonia, Spain
| | - Nicholas Akers
- Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Hematology/Oncology, Department of Medicine, Department of Pathology, Recanati Miller Transplantation Institute), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Bojan Losic
- Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Hematology/Oncology, Department of Medicine, Department of Pathology, Recanati Miller Transplantation Institute), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Samuel Waxman
- Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Hematology/Oncology, Department of Medicine, Department of Pathology, Recanati Miller Transplantation Institute), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Swan N Thung
- Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Hematology/Oncology, Department of Medicine, Department of Pathology, Recanati Miller Transplantation Institute), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Vincenzo Mazzaferro
- University of Milan and Gastrointestinal Surgery and Liver Transplantation Unit, Fondazione IRCCS, Istituto Nazionale dei Tumori, Milan, Italy
| | - Manel Esteller
- Cancer Epigenetics and Biology Program, IDIBELL, Hospital Universitari Bellvitge, Barcelona, Catalonia, Spain; Department of Physiological Sciences, School of Medicine and Health Sciences, University of Barcelona, Catalonia, Spain; Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain
| | - Scott L Friedman
- Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Hematology/Oncology, Department of Medicine, Department of Pathology, Recanati Miller Transplantation Institute), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Myron Schwartz
- Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Hematology/Oncology, Department of Medicine, Department of Pathology, Recanati Miller Transplantation Institute), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Augusto Villanueva
- Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Hematology/Oncology, Department of Medicine, Department of Pathology, Recanati Miller Transplantation Institute), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Josep M Llovet
- Mount Sinai Liver Cancer Program (Divisions of Liver Diseases, Department of Hematology/Oncology, Department of Medicine, Department of Pathology, Recanati Miller Transplantation Institute), Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York; Liver Cancer Translational Research Laboratory, BCLC, Liver Unit, CIBEREHD, IDIBAPS, Hospital Clinic, University of Barcelona, Catalonia, Spain; Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain.
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22
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Sia D, Jiao Y, Martinez I, Kuchuk O, Martin CV, Moura MCD, Putra J, Camprecios G, Thung S, Waxman S, Mazzaferro V, Esteller M, Villanueva A, Llovet JM. Abstract 2936: Molecular characterization of the immune subclass of hepatocellualr carcinoma. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-2936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Immune checkpoint inhibitors have emerged as a promising therapeutic approach in different solid tumors, including hepatocellular carcinoma (HCC). Nonetheless, little is known about the immune-component of HCC or potential biomarkers of response to these therapies.
Aims: To perform comprehensive characterization of the HCC immunological profile and to identify biomarkers to select immunotherapy candidates.
Methods: We performed gene expression array deconvolution through non-negative matrix factorization in 228 resected HCCs. Characterization of the transcriptional landscape was conducted using >1,000 signatures representing distinct immune cells by gene set enrichment and nearest template prediction analyses. Presence of immune infiltration, tertiary lymphoid structure (TLS), PD-1 and PD-L1 immunostainings was investigated using immunohistochemistry. DNA methylation profile of 450K CpG sites was analyzed to identify those with significant differences for each group. Extensive validation of the immune classifier was performed in 728 independent HCC samples.
Results: Overall, an immune-related subclass of HCC was identified in ~27% of patients. The immune subclass was characterized by gene signatures identifying immune cells (i.e. T cells, TLS, cytotox, p<0.001), signatures of response to immune checkpoint therapy (p<0.001), presence of high immune infiltration (p=0.01), TLS (≥5 foci, 19/51 vs 33/168, p=0.01) and PD-1 and PD-L1 protein expression (p<0.05). The methylation levels of 363 CpG sites in 192 immune response gene promoters were able to capture the Immune class (ANOVA, p<0.05, Δβ>0.2 Tukey test). Integration with HCC molecular classifications revealed significant enrichment of the Immune subclass with IFN and S1 (p<0.001) and exclusion of the CTNNB1 and S2 (p<0.001) subclasses. The immune class contains two distinct microenvironment-based types: A) Exhausted immune response type (~35%) characterized by stromal activation, T cell exhaustion signatures, and presence of immunosuppressive components such as TGFB, LGALS1, M2 macrophages and pathways able to recruit myeloid-derived-suppressor cells (FDR<0.01); and B) Active immune response type (~65%) characterized by overexpression of adaptive immune response genes and IFN signaling (p<0.001). Tumors within the active immune response type showed a trend towards better survival vs rest (p=0.07).
Conclusions: Around 27% of HCC patients belong to the Immune class, characterized by activation of immune cells and signatures of response to immunotherapies. Within this subclass, two distinct types have been characterized by presenting active or exhausted immune responses, a feature that provides the rationale for precision medicine-based therapies.
Note: This abstract was not presented at the meeting.
Citation Format: Daniela Sia, Yang Jiao, Iris Martinez, Olga Kuchuk, Carlos Villacorta Martin, Manuel Castro de Moura, Juan Putra, Genis Camprecios, Swan Thung, Samuel Waxman, Vincenzo Mazzaferro, Manel Esteller, Augusto Villanueva, Josep Maria Llovet. Molecular characterization of the immune subclass of hepatocellualr carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2936. doi:10.1158/1538-7445.AM2017-2936
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Affiliation(s)
- Daniela Sia
- 1Icahn School of Medicine at Mount Sinai, New York, NY
| | - Yang Jiao
- 1Icahn School of Medicine at Mount Sinai, New York, NY
| | - Iris Martinez
- 1Icahn School of Medicine at Mount Sinai, New York, NY
| | - Olga Kuchuk
- 1Icahn School of Medicine at Mount Sinai, New York, NY
| | | | | | - Juan Putra
- 1Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Swan Thung
- 1Icahn School of Medicine at Mount Sinai, New York, NY
| | - Samuel Waxman
- 1Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Manel Esteller
- 2IDIBELL, Hospital Universitari Bellvitge, Barcelona, Spain
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Boque-Sastre R, Moura MCD, Gomez A, Guil S, Esteller M. Abstract 3483: Genome-wide analysis of the antisense transcriptome in cancer. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-3483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Natural antisense transcripts (NATs) are the most abundant class of long noncoding RNAs (lncRNAs). Importantly, NATs are one of the most unknown ncRNAs. However, due to their highly gene locus-specific effects, NATs may provide a unique entry point for therapeutic intervention in targeted gene regulation. For this reason we are interested in studying the regulation of sense/antisense transcription in cancer related locus. In our previous work we found that, at the important cancer-related locus vimentin (VIM) there is a previously uncharacterized antisense transcript (VIM-AS1), which is transcribed head-to-head with VIM gene. This antisense transcript enhances R loop formation; it allows the binding of transcription factors as NF-kB, low nucleosome occupancy and the transcription of VIM gene. Our results are the first example of R loop mediated enhancement of gene expression involving head-to-head antisense transcription at cancer related locus. We also observed that in colon and breast cancer there was a positive expression correlation between VIM and VIM-AS1 and we have observed that hypermethylation silences both transcripts in colon primary tumors. In the present work we have seen that this positive correlation between sense and antisense transcripts is present in most of the tumor types from patients that we have obtained from Genomic Data Commons Data Portal (GDC Portal). Importantly this positive correlation correlates better in the cases in which the antisense transcript is downregulated or maintains the expression than in tumors where VIM and VIM-AS1 are up-regulated. Furthermore, we wanted to see if the cellular function is also coordinated. VIM is a component of the intermediate filament family of proteins that has an important role in epithelial mesenchymal transition. We found that specific depletion of VIM-AS1 results in a decrease of VIM expression, and now we have found that this depletion produces low migration rate and more invasion capability, as expected. On the other hand, the mechanisms used by antisense transcripts to regulate their corresponding sense mRNAs are not fully understood and in view of these results we are investigating from a genome-wide perspective the regulation of sense/antisense transcription, the involvement of R loop structures and DNA methylation in cancer. For this, we have applied a number of techniques: RNAseq strand specific, Illumina’s HumanMethylation450 Bead Chip array, RNAseq strand specific with overexpression of RNaseH (which specifically degrades the RNA in RNA/DNA hybrids), and DRIPseq (which immunoprecipitates the hybrids DNA-RNAs). The analysis of these data sheds light on the study of the role of sense/antisense transcripts in cancer-related locus.
Citation Format: Raquel Boque-Sastre, Manuel Castro de Moura, Antonio Gomez, Sònia Guil, Manel Esteller. Genome-wide analysis of the antisense transcriptome in cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3483. doi:10.1158/1538-7445.AM2017-3483
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Affiliation(s)
| | | | - Antonio Gomez
- IDIBELL, L'Hospitalet del Llobregat (Barcelona), Spain
| | - Sònia Guil
- IDIBELL, L'Hospitalet del Llobregat (Barcelona), Spain
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24
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Pérez-Salvia M, Simó-Riudalbas L, Llinàs-Arias P, Roa L, Setien F, Soler M, de Moura MC, Bradner JE, Gonzalez-Suarez E, Moutinho C, Esteller M. Bromodomain inhibition shows antitumoral activity in mice and human luminal breast cancer. Oncotarget 2017; 8:51621-51629. [PMID: 28881673 PMCID: PMC5584274 DOI: 10.18632/oncotarget.18255] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/04/2017] [Indexed: 01/25/2023] Open
Abstract
BET bromodomain inhibitors, which have an antitumoral effect against various solid cancer tumor types, have not been studied in detail in luminal breast cancer, despite the prevalence of this subtype of mammary malignancy. Here we demonstrate that the BET bromodomain inhibitor JQ1 exerts growth-inhibitory activity in human luminal breast cancer cell lines associated with a depletion of the C-MYC oncogene, but does not alter the expression levels of the BRD4 bromodomain protein. Interestingly, expression microarray analyses indicate that, upon JQ1 administration, the antitumoral phenotype also involves downregulation of relevant breast cancer oncogenes such as the Breast Carcinoma-Amplified Sequence 1 (BCAS1) and the PDZ Domain-Containing 1 (PDZK1). We have also applied these in vitro findings in an in vivo model by studying a transgenic mouse model representing the luminal B subtype of breast cancer, the MMTV-PyMT, in which the mouse mammary tumor virus promoter is used to drive the expression of the polyoma virus middle T-antigen to the mammary gland. We have observed that the use of the BET bromodomain inhibitor for the treatment of established breast neoplasms developed in the MMTV-PyMT model shows antitumor potential. Most importantly, if JQ1 is given before the expected time of tumor detection in the MMTV-PyMT mice, it retards the onset of the disease and increases the survival of these animals. Thus, our findings indicate that the use of bromodomain inhibitors is of great potential in the treatment of luminal breast cancer and merits further investigation.
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Affiliation(s)
- Montserrat Pérez-Salvia
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Laia Simó-Riudalbas
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Pere Llinàs-Arias
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Laura Roa
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Fernando Setien
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Marta Soler
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Manuel Castro de Moura
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - James E Bradner
- Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - Eva Gonzalez-Suarez
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Catia Moutinho
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain.,Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain
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Azagra A, Román-González L, Collazo O, Rodríguez-Ubreva J, de Yébenes VG, Barneda-Zahonero B, Rodríguez J, Castro de Moura M, Grego-Bessa J, Fernández-Duran I, Islam ABMMK, Esteller M, Ramiro AR, Ballestar E, Parra M. In vivo conditional deletion of HDAC7 reveals its requirement to establish proper B lymphocyte identity and development. J Exp Med 2016; 213:2591-2601. [PMID: 27810920 PMCID: PMC5110011 DOI: 10.1084/jem.20150821] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/14/2016] [Indexed: 11/05/2022] Open
Abstract
The histone deacetylase HDAC7 interacts with and represses myeloid and T cell genes in pro–B cells. HDAC7 deletion blocks early B cell development and results in severe lymphopenia. Class IIa histone deacetylase (HDAC) subfamily members are tissue-specific gene repressors with crucial roles in development and differentiation processes. A prominent example is HDAC7, a class IIa HDAC that shows a lymphoid-specific expression pattern within the hematopoietic system. In this study, we explored its potential role in B cell development by generating a conditional knockout mouse model. Our study demonstrates for the first time that HDAC7 deletion dramatically blocks early B cell development and gives rise to a severe lymphopenia in peripheral organs, while also leading to pro–B cell lineage promiscuity. We find that HDAC7 represses myeloid and T lymphocyte genes in B cell progenitors through interaction with myocyte enhancer factor 2C (MEFC2). In B cell progenitors, HDAC7 is recruited to promoters and enhancers of target genes, and its absence leads to increased enrichment of histone active marks. Our results prove that HDAC7 is a bona fide transcriptional repressor essential for B cell development.
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Affiliation(s)
- Alba Azagra
- Cellular Differentiation Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet, Barcelona, Spain
| | - Lidia Román-González
- Cellular Differentiation Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet, Barcelona, Spain
| | - Olga Collazo
- Cellular Differentiation Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet, Barcelona, Spain
| | - Javier Rodríguez-Ubreva
- Chromatin and Disease Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet, Barcelona, Spain
| | - Virginia G de Yébenes
- B Cell Biology Laboratory, Centro Nacional de Investigaciones Cardiovasculares, 28029 Madrid, Spain
| | - Bruna Barneda-Zahonero
- Cellular Differentiation Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet, Barcelona, Spain
| | - Jairo Rodríguez
- Research and Development Department, qGenomics Laboratory, 08003 Barcelona, Spain
| | - Manuel Castro de Moura
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet, Barcelona, Spain
| | - Joaquim Grego-Bessa
- Cellular Differentiation Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet, Barcelona, Spain
| | - Irene Fernández-Duran
- Cellular Differentiation Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet, Barcelona, Spain
| | - Abul B M M K Islam
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka 1000, Bangladesh
| | - Manel Esteller
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, 08036 Barcelona, Spain
| | - Almudena R Ramiro
- B Cell Biology Laboratory, Centro Nacional de Investigaciones Cardiovasculares, 28029 Madrid, Spain
| | - Esteban Ballestar
- Chromatin and Disease Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet, Barcelona, Spain
| | - Maribel Parra
- Cellular Differentiation Group, Cancer Epigenetics and Biology Program, Bellvitge Biomedical Research Institute, 08908 L'Hospitalet, Barcelona, Spain
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Moran S, Martínez-Cardús A, Sayols S, Musulén E, Balañá C, Estival-Gonzalez A, Moutinho C, Heyn H, Diaz-Lagares A, de Moura MC, Stella GM, Comoglio PM, Ruiz-Miró M, Matias-Guiu X, Pazo-Cid R, Antón A, Lopez-Lopez R, Soler G, Longo F, Guerra I, Fernandez S, Assenov Y, Plass C, Morales R, Carles J, Bowtell D, Mileshkin L, Sia D, Tothill R, Tabernero J, Llovet JM, Esteller M. Epigenetic profiling to classify cancer of unknown primary: a multicentre, retrospective analysis. Lancet Oncol 2016; 17:1386-1395. [PMID: 27575023 DOI: 10.1016/s1470-2045(16)30297-2] [Citation(s) in RCA: 296] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 06/29/2016] [Accepted: 07/01/2016] [Indexed: 12/27/2022]
Abstract
BACKGROUND Cancer of unknown primary ranks in the top ten cancer presentations and has an extremely poor prognosis. Identification of the primary tumour and development of a tailored site-specific therapy could improve the survival of these patients. We examined the feasability of using DNA methylation profiles to determine the occult original cancer in cases of cancer of unknown primary. METHODS We established a classifier of cancer type based on the microarray DNA methylation signatures (EPICUP) in a training set of 2790 tumour samples of known origin representing 38 tumour types and including 85 metastases. To validate the classifier, we used an independent set of 7691 known tumour samples from the same tumour types that included 534 metastases. We applied the developed diagnostic test to predict the tumour type of 216 well-characterised cases of cancer of unknown primary. We validated the accuracy of the predictions from the EPICUP assay using autopsy examination, follow-up for subsequent clinical detection of the primary sites months after the initial presentation, light microscopy, and comprehensive immunohistochemistry profiling. FINDINGS The tumour type classifier based on the DNA methylation profiles showed a 99·6% specificity (95% CI 99·5-99·7), 97·7% sensitivity (96·1-99·2), 88·6% positive predictive value (85·8-91·3), and 99·9% negative predictive value (99·9-100·0) in the validation set of 7691 tumours. DNA methylation profiling predicted a primary cancer of origin in 188 (87%) of 216 patients with cancer with unknown primary. Patients with EPICUP diagnoses who received a tumour type-specific therapy showed improved overall survival compared with that in patients who received empiric therapy (hazard ratio [HR] 3·24, p=0·0051 [95% CI 1·42-7·38]; log-rank p=0·0029). INTERPRETATION We show that the development of a DNA methylation based assay can significantly improve diagnoses of cancer of unknown primary and guide more precise therapies associated with better outcomes. Epigenetic profiling could be a useful approach to unmask the original primary tumour site of cancer of unknown primary cases and a step towards the improvement of the clinical management of these patients. FUNDING European Research Council (ERC), Cellex Foundation, the Institute of Health Carlos III (ISCIII), Cancer Australia, Victorian Cancer Agency, Samuel Waxman Cancer Research Foundation, the Health and Science Departments of the Generalitat de Catalunya, and Ferrer.
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Affiliation(s)
- Sebastian Moran
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Catalonia, Spain
| | - Anna Martínez-Cardús
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Catalonia, Spain
| | - Sergi Sayols
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Catalonia, Spain
| | - Eva Musulén
- Department of Pathology, Hospital Universitari Germans Trias i Pujol, C/ Ctra de Canyet s/n, Badalona, Barcelona, Catalonia, Spain
| | - Carme Balañá
- Medical Oncology, Catalan Institute of Oncology (ICO), University Hospital Germans Trias i Pujol, Badalona, Barcelona, Catalonia, Spain
| | - Anna Estival-Gonzalez
- Medical Oncology, Catalan Institute of Oncology (ICO), University Hospital Germans Trias i Pujol, Badalona, Barcelona, Catalonia, Spain
| | - Cátia Moutinho
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Catalonia, Spain
| | - Holger Heyn
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Catalonia, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Catalonia, Spain
| | - Manuel Castro de Moura
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Catalonia, Spain
| | - Giulia M Stella
- Cardiothoracic and Vascular Department, Pneumology Unit, IRCCS Policlinico San Matteo Foundation, Pavia, Italy
| | | | | | - Xavier Matias-Guiu
- Department of Pathology and Molecular Genetics/Oncologic Pathology Group, Hospital Universitari Arnau de Vilanova, Universitat de Lleida, IRBLleida, Lleida, Catalonia, Spain
| | - Roberto Pazo-Cid
- Medical Oncology Service, Hospital Miguel Servet, Zaragoza, Spain
| | - Antonio Antón
- Medical Oncology Service, Hospital Miguel Servet, Zaragoza, Spain
| | - Rafael Lopez-Lopez
- Medical Oncology Service, Complejo Hospitalario Universitario de Santiago, Santiago de Compostela, Spain
| | - Gemma Soler
- Medical Oncology, Catalan Institute of Oncology (ICO), Hospital Duran i Reynals, L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Federico Longo
- Medical Oncology Service, Hospital Universitario Ramon y Cajal, Madrid, Spain
| | - Isabel Guerra
- Biobanco Vasco, Hospital Universitario de Araba, Vitoria, Spain
| | - Sara Fernandez
- Biobanco Vasco, Hospital Universitario de Basurto, Bilbao, Spain
| | - Yassen Assenov
- Division of Epigenomics and Cancer Risk Factors at the German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors at the German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Rafael Morales
- Oncology Department, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona (UAB), Barcelona, Catalonia, Spain; Oncology Department, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Catalonia, Spain
| | - Joan Carles
- Oncology Department, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona (UAB), Barcelona, Catalonia, Spain; Oncology Department, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Catalonia, Spain
| | - David Bowtell
- The Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia; The Department of Pathology, University of Melbourne, Parkville, VIC, Australia
| | - Linda Mileshkin
- The Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; The Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia; The Department of Pathology, University of Melbourne, Parkville, VIC, Australia
| | - Daniela Sia
- Liver Cancer Program, Division of Liver Diseases, Tisch Cancer Institute, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Richard Tothill
- The Peter MacCallum Cancer Centre, Melbourne, VIC, Australia; The Department of Pathology, University of Melbourne, Parkville, VIC, Australia
| | - Josep Tabernero
- Oncology Department, Vall d'Hebron University Hospital, Universitat Autònoma de Barcelona (UAB), Barcelona, Catalonia, Spain; Oncology Department, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Catalonia, Spain
| | - Josep M Llovet
- Liver Cancer Translational Research Laboratory, Barcelona Clinic Liver Cancer (BCLC) Group, Liver Unit, IDIBAPS, Hospital Clínic, CIBERehd, Barcelona, Catalonia, Spain; School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain; Liver Cancer Program, Division of Liver Diseases, Tisch Cancer Institute, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, Barcelona, Catalonia, Spain; School of Medicine, University of Barcelona, Barcelona, Catalonia, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
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Rubio M, Ballester AR, Olivares PM, Castro de Moura M, Dicenta F, Martínez-Gómez P. Gene Expression Analysis of Plum pox virus (Sharka) Susceptibility/Resistance in Apricot (Prunus armeniaca L.). PLoS One 2015; 10:e0144670. [PMID: 26658051 PMCID: PMC4684361 DOI: 10.1371/journal.pone.0144670] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 11/20/2015] [Indexed: 11/18/2022] Open
Abstract
RNA-Seq has proven to be a very powerful tool in the analysis of the Plum pox virus (PPV, sharka disease)/Prunus interaction. This technique is an important complementary tool to other means of studying genomics. In this work an analysis of gene expression of resistance/susceptibility to PPV in apricot is performed. RNA-Seq has been applied to analyse the gene expression changes induced by PPV infection in leaves from two full-sib apricot genotypes, “Rojo Pasión” and “Z506-7”, resistant and susceptible to PPV, respectively. Transcriptomic analyses revealed the existence of more than 2,000 genes related to the pathogen response and resistance to PPV in apricot. These results showed that the response to infection by the virus in the susceptible genotype is associated with an induction of genes involved in pathogen resistance such as the allene oxide synthase, S-adenosylmethionine synthetase 2 and the major MLP-like protein 423. Over-expression of the Dicer protein 2a may indicate the suppression of a gene silencing mechanism of the plant by PPV HCPro and P1 PPV proteins. On the other hand, there were 164 genes involved in resistance mechanisms that have been identified in apricot, 49 of which are located in the PPVres region (scaffold 1 positions from 8,050,804 to 8,244,925), which is responsible for PPV resistance in apricot. Among these genes in apricot there are several MATH domain-containing genes, although other genes inside (Pleiotropic drug resistance 9 gene) or outside (CAP, Cysteine-rich secretory proteins, Antigen 5 and Pathogenesis-related 1 protein; and LEA, Late embryogenesis abundant protein) PPVres region could also be involved in the resistance.
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Affiliation(s)
- Manuel Rubio
- Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), PO Box 164, E-30100 Espinardo (Murcia) Spain
| | - Ana Rosa Ballester
- Department of Food Science, Instituto de Agroquímica y Tecnología de Alimentos (IATA-CSIC), Avda. Agustín Escardino 7, 46980 Paterna (Valencia) Spain
| | - Pedro Manuel Olivares
- Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), PO Box 164, E-30100 Espinardo (Murcia) Spain
| | - Manuel Castro de Moura
- aScidea Computational Biology Solutions, S.L. Parc de Reserca UAB, Edifici Eureka. 08193 Bellaterra (Cerdanyola del Vallés), Barcelona, Spain
| | - Federico Dicenta
- Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), PO Box 164, E-30100 Espinardo (Murcia) Spain
| | - Pedro Martínez-Gómez
- Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), PO Box 164, E-30100 Espinardo (Murcia) Spain
- * E-mail:
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Rubio M, Rodríguez-Moreno L, Ballester AR, de Moura MC, Bonghi C, Candresse T, Martínez-Gómez P. Analysis of gene expression changes in peach leaves in response to Plum pox virus infection using RNA-Seq. Mol Plant Pathol 2015; 16:164-76. [PMID: 24989162 PMCID: PMC6638525 DOI: 10.1111/mpp.12169] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Differences in gene expression were studied after Plum pox virus (PPV, sharka disease) infection in peach GF305 leaves with and without sharka symptoms using RNA-Seq. For each sample, more than 80% of 100-nucleotide paired-end (PE) Illumina reads were aligned on the peach reference genome. In the symptomatic sample, a significant proportion of reads were mapped to PPV reference genomes (1.04% compared with 0.00002% in non-symptomatic leaves), allowing for the ultra-deep assembly of the complete genome of the PPV isolate used (9775 nucleotides, missing only 11 nucleotides at the 5' genome end). In addition, significant alternative splicing events were detected in 359 genes and 12 990 single nucleotide polymorphisms (SNPs) were identified, 425 of which could be annotated. Gene ontology annotation revealed that the high-ranking mRNA target genes associated with the expression of sharka symptoms are mainly related to the response to biotic stimuli, to lipid and carbohydrate metabolism and to the negative regulation of catalytic activity. A greater number of differentially expressed genes were observed in the early asymptomatic phase of PPV infection in comparison with the symptomatic phase. These early infection events were associated with the induction of genes related to pathogen resistance, such as jasmonic acid, chitinases, cytokinin glucosyl transferases and Lys-M proteins. Once the virus had accumulated, the overexpression of Dicer protein 2a genes suggested a gene silencing plant response that was suppressed by the virus HCPro and P1 proteins. These results illustrate the dynamic nature of the peach-PPV interaction at the transcriptome level and confirm that sharka symptom expression is a complex process that can be understood on the basis of changes in plant gene expression.
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Affiliation(s)
- Manuel Rubio
- Department of Plant Breeding, Centro de Edafología y Biología Aplicada del Segura (CEBAS-CSIC), PO Box 164, E-30100, Espinardo-Murcia, Spain
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Bonnefond L, Castro de Moura M, Ribas de Pouplana L, Nureki O. Crystal structures of Entamoeba histolytica lysyl-tRNA synthetase reveal conformational changes upon lysine binding and a specific helix bundle domain. FEBS Lett 2014; 588:4478-86. [PMID: 25448989 DOI: 10.1016/j.febslet.2014.10.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 10/12/2014] [Accepted: 10/19/2014] [Indexed: 11/19/2022]
Abstract
The class II lysyl-tRNA synthetases (KRS) are conserved aminoacyl-tRNA synthetases that attach lysine to the cognate tRNA in a two-step mechanism. The enzyme from the parasitic protozoan Entamoeba histolytica was crystallized in the presence of small ligands to generate snapshots of the lysine-adenylate formation. The residues involved in lysine activation are highly conserved and the active site closes around the lysyl-adenylate, as observed in bacterial KRS. The Entamoeba EMAPII-like polypeptide is not resolved in the crystals, but another Entamoeba-specific insertion could be modeled as a small helix bundle that may contribute to tRNA binding through interaction with the tRNA hinge.
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Affiliation(s)
- Luc Bonnefond
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 2-11-16, Yayoi, Bunkyo, Tokyo 113-0032, Japan.
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Castro de Moura M, Miro F, Han JM, Kim S, Celada A, Ribas de Pouplana L. Entamoeba lysyl-tRNA synthetase contains a cytokine-like domain with chemokine activity towards human endothelial cells. PLoS Negl Trop Dis 2011; 5:e1398. [PMID: 22140588 PMCID: PMC3226552 DOI: 10.1371/journal.pntd.0001398] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Accepted: 09/30/2011] [Indexed: 11/18/2022] Open
Abstract
Immunological pressure encountered by protozoan parasites drives the selection of strategies to modulate or avoid the immune responses of their hosts. Here we show that the parasite Entamoeba histolytica has evolved a chemokine that mimics the sequence, structure, and function of the human cytokine HsEMAPII (Homo sapiens endothelial monocyte activating polypeptide II). This Entamoeba EMAPII-like polypeptide (EELP) is translated as a domain attached to two different aminoacyl-tRNA synthetases (aaRS) that are overexpressed when parasites are exposed to inflammatory signals. EELP is dispensable for the tRNA aminoacylation activity of the enzymes that harbor it, and it is cleaved from them by Entamoeba proteases to generate a standalone cytokine. Isolated EELP acts as a chemoattractant for human cells, but its cell specificity is different from that of HsEMAPII. We show that cell specificity differences between HsEMAPII and EELP can be swapped by site directed mutagenesis of only two residues in the cytokines' signal sequence. Thus, Entamoeba has evolved a functional mimic of an aaRS-associated human cytokine with modified cell specificity.
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Novoa EM, Castro de Moura M, Orozco M, Ribas de Pouplana L. A genomics method to identify pathogenicity-related proteins. Application to aminoacyl-tRNA synthetase-like proteins. FEBS Lett 2010; 584:460-6. [PMID: 19913539 DOI: 10.1016/j.febslet.2009.11.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2009] [Revised: 11/03/2009] [Accepted: 11/08/2009] [Indexed: 02/05/2023]
Abstract
During their extended evolution genes coding for aminoacyl-tRNA synthetases (ARS) have experienced numerous instances of duplication, insertion and deletion of domains. The ARS-related proteins that have resulted from these genetic events are generally known as aminoacyl-tRNA synthetase-like proteins (ARS-like). This heterogeneous group of polypeptides carries out an equally varied number of functions that need not be related to gene translation. Several of these proteins remain uncharacterized. At least 16 different ARS-like proteins have been identified to date, but their functions remain incompletely understood. Here we review the individual phylogenetic distribution of these proteins in bacteria, and apply a new genomics method to determine their potential implication in pathogenicity.
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Affiliation(s)
- Eva Maria Novoa
- Institute for Research in Biomedicine (IRB), c/ Baldiri Reixac 15-21, 08028 Barcelona, Spain
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Geslain R, Aeby E, Guitart T, Jones TE, Castro de Moura M, Charrière F, Schneider A, Ribas de Pouplana L. Trypanosoma seryl-tRNA synthetase is a metazoan-like enzyme with high affinity for tRNASec. J Biol Chem 2009. [DOI: 10.1074/jbc.a607862200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Geslain R, Aeby E, Guitart T, Jones TE, Castro de Moura M, Charrière F, Schneider A, Ribas de Pouplana L. Trypanosoma seryl-tRNA synthetase is a metazoan-like enzyme with high affinity for tRNASec. J Biol Chem 2006; 281:38217-25. [PMID: 17040903 DOI: 10.1074/jbc.m607862200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Trypanosomatids are important human pathogens that form a basal branch of eukaryotes. Their evolutionary history is still unclear as are many aspects of their molecular biology. Here we characterize essential components required for the incorporation of serine and selenocysteine into the proteome of Trypanosoma. First, the biological function of a putative Trypanosoma seryl-tRNA synthetase was characterized in vivo. Secondly, the molecular recognition by Trypanosoma seryl-tRNA synthetase of its cognate tRNAs was dissected in vitro. The cellular distribution of tRNA(Sec) was studied, and the catalytic constants of its aminoacylation were determined. These were found to be markedly different from those reported in other organisms, indicating that this reaction is particularly efficient in trypanosomatids. Our functional data were analyzed in the context of a new phylogenetic analysis of eukaryotic seryl-tRNA synthetases that includes Trypanosoma and Leishmania sequences. Our results show that trypanosomatid seryl-tRNA synthetases are functionally and evolutionarily more closely related to their metazoan homologous enzymes than to other eukaryotic enzymes. This conclusion is supported by sequence synapomorphies that clearly connect metazoan and trypanosomatid seryl-tRNA synthetases.
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Affiliation(s)
- Renaud Geslain
- Institució Catalana de Recerca i Estudis Avançats (ICREA) and Institute for Research in Biomedicine, Barcelona, Barcelona Science Park, C/Samitier 1-5, Barcelona 08015, Catalonia, Spain
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