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Ruiz-Riera E, Vidal E, Canturri A, Lehmbecker A, Cuvertoret M, Lopez-Figueroa C, Baumgärtner W, Domingo M, Segalés J. Porcine Forebrain Vacuolization Associated with Wasting in Pigs: A Novel Pathological Outcome Associated with Vitamin-Mineral Deficiency? Animals (Basel) 2023; 13:2255. [PMID: 37508034 PMCID: PMC10376092 DOI: 10.3390/ani13142255] [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: 06/20/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
The term wasting refers to a clinical sign used to describe a physical condition characterized by growth retardation, usually of multifactorial origin. The objective of the present study was to describe for the first time a pathological process characterized by forebrain neuropil vacuolization in pigs showing wasting without conspicuous neurological signs. To characterize the lesions pathologically, affected and non-affected pigs from eight of these farms were investigated. Histologically, the most consistent lesion was neuropil vacuolization of the prosencephalon, mainly located in the thalamic nuclei and in the transition between the white and grey matter of the neocortex (40/56 in sick and 4/30 in healthy pigs). In the most severe cases, the vacuolation also involved the midbrain, cerebellar nuclei and, to a lesser extent, the medulla oblongata. Vacuolization of the forebrain was associated with pigs experiencing marked emaciation and growth retardation. Although the specific cause of the present case remained unknown, the preventive use of multivitamin and mineral complexes in drinking water ameliorated the condition, strongly suggesting a metabolic origin of the observed condition.
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Affiliation(s)
- E Ruiz-Riera
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
| | - E Vidal
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Spain
| | - A Canturri
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55455, USA
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Minnesota, St. Paul, MN 55455, USA
| | - A Lehmbecker
- Department of Pathology, University of Veterinary Medicine, 30545 Hannover, Germany
| | - M Cuvertoret
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
| | - C Lopez-Figueroa
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
| | - W Baumgärtner
- Department of Pathology, University of Veterinary Medicine, 30545 Hannover, Germany
| | - M Domingo
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Spain
| | - J Segalés
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
- Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Spain
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), 08193 Bellaterra, Spain
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Ranchin B, Schmitt CP, Warady B, Craig JC, Licht C, Hataya H, Vidal E, Walle JV, Shroff R. Devices for long-term hemodialysis in small children – a plea for action. Kidney Int 2023; 103:1038-1040. [PMID: 36990213 DOI: 10.1016/j.kint.2023.03.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 03/01/2023] [Accepted: 03/08/2023] [Indexed: 03/30/2023]
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Trinidad EM, Vidal E, Coronado E, Esteve-Codina A, Castel V, Cañete A, Gut M, Heath S, Font de Mora J. Liquidhope: methylome and genomic profiling from very limited quantities of plasma-derived DNA. Brief Bioinform 2023; 24:6972296. [PMID: 36611239 PMCID: PMC9851319 DOI: 10.1093/bib/bbac575] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/04/2022] [Accepted: 11/25/2022] [Indexed: 01/09/2023] Open
Abstract
Analysis of the methylome of tumor cell-free deoxyribonucleic acid (DNA; cfDNA) has emerged as a powerful non-invasive technique for cancer subtyping and prognosis. However, its application is frequently hampered by the quality and total cfDNA yield. Here, we demonstrate the feasibility of very low-input cfDNA for whole-methylome and copy-number profiling studies using enzymatic conversion of unmethylated cysteines [enzymatic methyl-seq (EM-seq)] to better preserve DNA integrity. We created a model for predicting genomic subtyping and prognosis with high accuracy. We validated our tool by comparing whole-genome CpG sequencing with in situ cohorts generated with bisulfite conversion and array hybridization, demonstrating that, despite the different techniques and sample origins, information on cfDNA methylation is comparable with in situ cohorts. Our findings support use of liquid biopsy followed by EM-seq to assess methylome of cancer patients, enabling validation in external cohorts. This advance is particularly relevant for rare cancers like neuroblastomas where liquid-biopsy volume is restricted by ethical regulations in pediatric patients.
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Affiliation(s)
- Eva María Trinidad
- Corresponding author: Eva M. Trinidad, Laboratory of Cellular and Molecular Biology and Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Avenida Fernando Abril Martorell, 106; Torre A, 5-0746026 Valencia, Spain. Tel.: +34-961246646; ; Fax: +34-963496620; E-mail:
| | - Enrique Vidal
- Laboratory of Cellular and Molecular Biology, Health Research Institute Hospital La Fe, Valencia, Spain,Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
| | - Esther Coronado
- Laboratory of Cellular and Molecular Biology, Health Research Institute Hospital La Fe, Valencia, Spain,Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
| | - Anna Esteve-Codina
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), , Barcelona , Spain
| | - Victoria Castel
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain,Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
| | - Adela Cañete
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain,Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain,Pediatric Oncology Unit, La Fe University Hospital, Valencia, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), , Barcelona , Spain
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Mas G, Santoro F, Blanco E, Gamarra Figueroa GP, Le Dily F, Frigè G, Vidal E, Mugianesi F, Ballaré C, Gutierrez A, Sparavier A, Marti-Renom MA, Minucci S, Di Croce L. In vivo temporal resolution of acute promyelocytic leukemia progression reveals a role of Klf4 in suppressing early leukemic transformation. Genes Dev 2022; 36:451-467. [PMID: 35450883 PMCID: PMC9067408 DOI: 10.1101/gad.349115.121] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 03/25/2022] [Indexed: 11/25/2022]
Abstract
In this study, Mas et al. used primary hematopoietic stem and progenitor cells (HSPCs) and leukemic blasts that express the fusion protein PML-RARα as a paradigm to temporally dissect the dynamic changes in the epigenome, transcriptome, and genome architecture induced during oncogenic transformation. Their multiomics-integrated analysis identified Klf4 as an early down-regulated gene in PML-RARα-driven leukemogenesis, and they characterized the dynamic alterations in the Klf4 cis-regulatory network during APL progression and demonstrated that ectopic Klf4 overexpression can suppress self-renewal and reverse the differentiation block induced by PML-RARα. Genome organization plays a pivotal role in transcription, but how transcription factors (TFs) rewire the structure of the genome to initiate and maintain the programs that lead to oncogenic transformation remains poorly understood. Acute promyelocytic leukemia (APL) is a fatal subtype of leukemia driven by a chromosomal translocation between the promyelocytic leukemia (PML) and retinoic acid receptor α (RARα) genes. We used primary hematopoietic stem and progenitor cells (HSPCs) and leukemic blasts that express the fusion protein PML-RARα as a paradigm to temporally dissect the dynamic changes in the epigenome, transcriptome, and genome architecture induced during oncogenic transformation. We found that PML-RARα initiates a continuum of topologic alterations, including switches from A to B compartments, transcriptional repression, loss of active histone marks, and gain of repressive histone marks. Our multiomics-integrated analysis identifies Klf4 as an early down-regulated gene in PML-RARα-driven leukemogenesis. Furthermore, we characterized the dynamic alterations in the Klf4 cis-regulatory network during APL progression and demonstrated that ectopic Klf4 overexpression can suppress self-renewal and reverse the differentiation block induced by PML-RARα. Our study provides a comprehensive in vivo temporal dissection of the epigenomic and topological reprogramming induced by an oncogenic TF and illustrates how topological architecture can be used to identify new drivers of malignant transformation.
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Affiliation(s)
- Glòria Mas
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Fabio Santoro
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan 20139, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan 20139, Italy
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | | | - François Le Dily
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Gianmaria Frigè
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan 20139, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan 20139, Italy
| | - Enrique Vidal
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Francesca Mugianesi
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.,Centro Nacional de Análisis Genómico (CNAG), Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Cecilia Ballaré
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Arantxa Gutierrez
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain
| | - Aleksandra Sparavier
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.,Centro Nacional de Análisis Genómico (CNAG), Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Marc A Marti-Renom
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.,Centro Nacional de Análisis Genómico (CNAG), Centre for Genomic Regulation (CRG), the Barcelona Institute of Science and Technology, Barcelona 08028, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
| | - Saverio Minucci
- Department of Experimental Oncology, European Institute of Oncology (IEO), Milan 20139, Italy.,Department of Oncology and Hemato-oncology, University of Milan, Milan 20139, Italy
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
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Pizzinato A, Liguoro I, Pusiol A, Cogo P, Palese A, Vidal E. Detection and assessment of postoperative pain in children with cognitive impairment: A systematic literature review and meta-analysis. Eur J Pain 2022; 26:965-979. [PMID: 35271756 PMCID: PMC9311729 DOI: 10.1002/ejp.1936] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Background and Objective Children with cognitive impairment (CI) are at risk of experiencing pain. Several specific pain rating scales have been developed to date. Thus, the aim of this meta‐analysis was to estimate the degree of reliability of different pain assessment scales for the postoperative pain in children with CI. Databases and Data Treatment PubMed, Scopus and Web of Science databases were approached: all studies validating and/or using pain assessment tool in children (0–20 years) with CI published in English from the 1st of January 2000 to the 1st of January 2022 were included. Only studies reporting the interclass correlation coefficient (ICC) to evaluate the concordance between caregivers’ and external researchers’ scores were eligible. Results Twelve studies were included (586 children with CI, 60% males; weighted mean age 9.9 years – range 2–20). Five of them evaluated the Non‐Communicating Children's Pain Checklist‐Postoperative Version (NCCPC‐PV) scale whereas four the original and revised Face, Legs, Activity, Cry, Consolability (FLACC) scale. The analysis showed an overall ICC value of 0.76 (0.74–0.78) for the NCCPC‐PV scale, with a high heterogeneity index (I2 = 97%) and 0.87 (0.84–0.90) for the FLACC scale, with a discrete I2 index (59%). Conclusions The NCCPC‐PV and FLACC pain rating scales showed the strongest evidence for validity and reliability for assessing postoperative pain in children with CI. However, due to the high heterogeneity of the studies available, these results should not be considered conclusive. Significance This review is focused on the assessment of pain in children with CI in the postoperative period. Simplified observation‐based pain assessment tools that rely on evaluating non‐verbal expressions of pain should be recommended for children with difficulties to communicate their feelings. Even if there is a high degree of heterogeneity in clinical presentations among youth with CI, two tools (NCCPC‐PV and FLACC) have emerged as reliable and valid in this population.
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Affiliation(s)
- A Pizzinato
- Department of Medicine (DAME), School of Nursing, University of Udine, Udine, Italy
| | - I Liguoro
- Department of Medicine (DAME), Division of Pediatrics, University of Udine, Udine, Italy
| | - A Pusiol
- Department of Medicine (DAME), Division of Pediatrics, University of Udine, Udine, Italy
| | - P Cogo
- Department of Medicine (DAME), Division of Pediatrics, University of Udine, Udine, Italy
| | - A Palese
- Department of Medicine (DAME), School of Nursing, University of Udine, Udine, Italy
| | - E Vidal
- Department of Medicine (DAME), Division of Pediatrics, University of Udine, Udine, Italy
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La Greca A, Bellora N, Le Dily F, Jara R, Nacht AS, Quilez Oliete J, Villanueva JL, Vidal E, Merino G, Fresno C, Tarifa Reischle I, Vallejo G, Vicent GP, Fernández E, Beato M, Saragüeta P. Chromatin topology defines estradiol-primed progesterone receptor and PAX2 binding in endometrial cancer cells. eLife 2022; 11:66034. [PMID: 35018885 PMCID: PMC8887898 DOI: 10.7554/elife.66034] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 12/22/2020] [Accepted: 01/11/2022] [Indexed: 11/15/2022] Open
Abstract
Estrogen (E2) and Progesterone (Pg), via their specific receptors (ERalpha and PR), are major determinants in the development and progression of endometrial carcinomas, However, their precise mechanism of action and the role of other transcription factors involved are not entirely clear. Using Ishikawa endometrial cancer cells, we report that E2 treatment exposes a set of progestin-dependent PR binding sites which include both E2 and progestin target genes. ChIP-seq results from hormone-treated cells revealed a non-random distribution of PAX2 binding in the vicinity of these estrogen-promoted PR sites. Altered expression of hormone regulated genes in PAX2 knockdown cells suggests a role for PAX2 in fine-tuning ERalpha and PR interplay in transcriptional regulation. Analysis of long-range interactions by Hi-C coupled with ATAC-seq data showed that these regions, that we call ‘progestin control regions’ (PgCRs), exhibited an open chromatin state even before hormone exposure and were non-randomly associated with regulated genes. Nearly 20% of genes potentially influenced by PgCRs were found to be altered during progression of endometrial cancer. Our findings suggest that endometrial response to progestins in differentiated endometrial tumor cells results in part from binding of PR together with PAX2 to accessible chromatin regions. What maintains these regions open remains to be studied.
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Affiliation(s)
| | - Nicolás Bellora
- National Scientific and Technical Research Council (CONICET), Institute of Nuclear Technologies for Health, Bariloche, Argentina
| | - François Le Dily
- Gene Regulation, Centre for Genomic Regulation, Barcelona, Spain
| | - Rodrigo Jara
- Biology and Experimental Medicine Institute, Buenos Aires, Argentina
| | | | | | | | - Enrique Vidal
- Gene Regulation, Centre for Genomic Regulation, Barcelona, Spain
| | - Gabriela Merino
- Bioscience Data Mining Group, Córdoba University, Córdoba, Argentina
| | - Cristóbal Fresno
- Bioscience Data Mining Group, Córdoba University, Córdoba, Argentina
| | | | - Griselda Vallejo
- Biology and Experimental Medicine Institute, Buenos Aires, Argentina
| | | | - Elmer Fernández
- Bioscience Data Mining Group, Córdoba University, Córdoba, Argentina
| | - Miguel Beato
- Gene Regulation, Centre for Genomic Regulation, Barcelona, Spain
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Prieto JR, Vidal E, Sánchez JA, Alonso C, Garrido D. Extracting Descriptive Words from Untranscribed Handwritten Images. Pattern Recognition and Image Analysis 2022. [DOI: 10.1007/978-3-031-04881-4_43] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Yazıcıoğlu B, Bakkaloğlu SA, Abranches M, Akman S, Alpay H, Ariceta G, Atmış B, Bael A, Bakkaloğlu SA, Bayrakçı US, Bhimma R, Bjerre A, Bonzel KE, Çeleğen K, Delibaş A, Demircioğlu B, Dursun I, Ertan P, Flögelova H, Gülleroğlu K, Gürgöze MK, Hacıhamdioğlu DÖ, Haffner D, Hansen PR, Jankauskiene A, Jobs K, Kopač M, Liebau MC, Marks SD, Maxted A, Nalçacıoğlu H, Oh J, Özçelik G, Papalia TSS, Papizh S, Poyrazoğlu H, Prikhodina L, Schmidt IM, Schmitt CP, Shroff R, Sönmez F, Stabouli S, Szczepanska M, Tabel Y, Tasic V, Teixeira A, Topaloğlu R, Walle JV, Vidal E, Vondrak K, Yavaşcan Ö, Yazıcıoğlu B, Yıldız G, Yılmaz D, Zaloszyc A, Zieg J. Correction to: Impact of coronavirus disease-2019 on pediatric nephrology practice and education: an ESPN survey. Pediatr Nephrol 2022; 37:1943-1944. [PMID: 35211799 PMCID: PMC8869343 DOI: 10.1007/s00467-022-05473-w] [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] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Burcu Yazıcıoğlu
- grid.25769.3f0000 0001 2169 7132Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - Sevcan A. Bakkaloğlu
- grid.25769.3f0000 0001 2169 7132Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | | | - M Abranches
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - S Akman
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - H Alpay
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - G Ariceta
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - B Atmış
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - A Bael
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - S A Bakkaloğlu
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - U S Bayrakçı
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - R Bhimma
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - A Bjerre
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - K E Bonzel
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - K Çeleğen
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - A Delibaş
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - B Demircioğlu
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - I Dursun
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - P Ertan
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - H Flögelova
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - K Gülleroğlu
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - M K Gürgöze
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - D Ö Hacıhamdioğlu
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - D Haffner
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - P R Hansen
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - A Jankauskiene
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - K Jobs
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - M Kopač
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - M C Liebau
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - S D Marks
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - A Maxted
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - H Nalçacıoğlu
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - J Oh
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - G Özçelik
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - T S S Papalia
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - S Papizh
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - H Poyrazoğlu
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - L Prikhodina
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - I M Schmidt
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - C P Schmitt
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - R Shroff
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - F Sönmez
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - S Stabouli
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - M Szczepanska
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - Y Tabel
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - V Tasic
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - A Teixeira
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - R Topaloğlu
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - J Vande Walle
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - E Vidal
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - K Vondrak
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - Ö Yavaşcan
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - B Yazıcıoğlu
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - G Yıldız
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - D Yılmaz
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - A Zaloszyc
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
| | - J Zieg
- Department of Pediatric Nephrology, Gazi University School of Medicine, Ankara, Turkey
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Zaurin R, Ferrari R, Nacht AS, Carbonell J, Le Dily F, Font-Mateu J, de Llobet Cucalon LI, Vidal E, Lioutas A, Beato M, Vicent GP. A set of accessible enhancers enables the initial response of breast cancer cells to physiological progestin concentrations. Nucleic Acids Res 2021; 49:12716-12731. [PMID: 34850111 PMCID: PMC8682742 DOI: 10.1093/nar/gkab1125] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 11/14/2022] Open
Abstract
Here, we report that in T47D breast cancer cells 50 pM progestin is sufficient to activate cell cycle entry and the progesterone gene expression program. At this concentration, equivalent to the progesterone blood levels found around the menopause, progesterone receptor (PR) binds only to 2800 genomic sites, which are accessible to ATAC cleavage prior to hormone exposure. These highly accessible sites (HAs) are surrounded by well-organized nucleosomes and exhibit breast enhancer features, including estrogen receptor alpha (ERα), higher FOXA1 and BRD4 (bromodomain containing 4) occupancy. Although HAs are enriched in RAD21 and CTCF, PR binding is the driving force for the most robust interactions with hormone-regulated genes. HAs show higher frequency of 3D contacts among themselves than with other PR binding sites, indicating colocalization in similar compartments. Gene regulation via HAs is independent of classical coregulators and ATP-activated remodelers, relying mainly on MAP kinase activation that enables PR nuclear engagement. HAs are also preferentially occupied by PR and ERα in breast cancer xenografts derived from MCF-7 cells as well as from patients, indicating their potential usefulness as targets for therapeutic intervention.
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Affiliation(s)
- Roser Zaurin
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Roberto Ferrari
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Ana Silvina Nacht
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Jose Carbonell
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Francois Le Dily
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Jofre Font-Mateu
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Lara Isabel de Llobet Cucalon
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Enrique Vidal
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Antonios Lioutas
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain
| | - Miguel Beato
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Barcelona Institute for Science and Technology (BIST), Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, 08003, Spain
| | - Guillermo P Vicent
- Center for Genomic Regulation (CRG), Barcelona, 08003, Spain.,Molecular Biology Institute of Barcelona, Consejo Superior de Investigaciones Científicas (IBMB-CSIC), Barcelona, 08003, Spain
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10
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Uriarte D, Vidal E, Canals A, Domini CE, Garrido M. Simple-to-use and portable device for free chlorine determination based on microwave-assisted synthesized carbon dots and smartphone images. Talanta 2021; 229:122298. [PMID: 33838783 DOI: 10.1016/j.talanta.2021.122298] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 12/26/2022]
Abstract
A new portable and simple 3D printed device was designed for free chlorine determination in water samples. The analytical method was based on the quenching caused by free chlorine on the fluorescence emission of the carbon dots (CD) synthesized from citric acid and urea. The fluorescence was captured through the camera of a smartphone, which was coupled to the 3D printed device, and the images were processed using the RGB system by the ImageJ 1.51q software. The proposed method was selective and precise (RSD% 4.6, for n = 6), and the trueness of the results was evaluated by comparing the results obtained with those recovered by the spectrophotometric method 4500-Cl G (standard method), with good agreement between them. Moreover, the remarkable correlation between the CD signal and the free chlorine concentration resulted in a determination with low detection limits (limit of detection of 6 μg L-1 and limit of quantification of 20 μg L-1). Therefore, the new method and the related portable device could be considered a fast, economical and reliable alternative for the on-site determination of free chlorine in water samples.
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Affiliation(s)
- D Uriarte
- INQUISUR, Departamento de Química, Universidad Nacional Del Sur (UNS)-CONICET, Av. Alem 1253, 8000, Bahía Blanca, Argentina
| | - E Vidal
- INQUISUR, Departamento de Química, Universidad Nacional Del Sur (UNS)-CONICET, Av. Alem 1253, 8000, Bahía Blanca, Argentina
| | - A Canals
- Departamento de Química Analítica, Nutrición y Bromatología, Instituto Universitario de Materiales, Universidad de Alicante, Apdo. 99, 03080, Alicante, Spain
| | - C E Domini
- INQUISUR, Departamento de Química, Universidad Nacional Del Sur (UNS)-CONICET, Av. Alem 1253, 8000, Bahía Blanca, Argentina.
| | - M Garrido
- INQUISUR, Departamento de Química, Universidad Nacional Del Sur (UNS)-CONICET, Av. Alem 1253, 8000, Bahía Blanca, Argentina.
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11
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Bisceglie L, Hopp AK, Gunasekera K, Wright RH, Le Dily F, Vidal E, Dall'Agnese A, Caputo L, Nicoletti C, Puri PL, Beato M, Hottiger MO. MyoD induces ARTD1 and nucleoplasmic poly-ADP-ribosylation during fibroblast to myoblast transdifferentiation. iScience 2021; 24:102432. [PMID: 33997706 PMCID: PMC8102911 DOI: 10.1016/j.isci.2021.102432] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 03/27/2021] [Accepted: 04/11/2021] [Indexed: 11/29/2022] Open
Abstract
While protein ADP-ribosylation was reported to regulate differentiation and dedifferentiation, it has so far not been studied during transdifferentiation. Here, we found that MyoD-induced transdifferentiation of fibroblasts to myoblasts promotes the expression of the ADP-ribosyltransferase ARTD1. Comprehensive analysis of the genome architecture by Hi-C and RNA-seq analysis during transdifferentiation indicated that ARTD1 locally contributed to A/B compartmentalization and coregulated a subset of MyoD target genes that were however not sufficient to alter transdifferentiation. Surprisingly, the expression of ARTD1 was accompanied by the continuous synthesis of nuclear ADP ribosylation that was neither dependent on the cell cycle nor induced by DNA damage. Conversely to the H2O2-induced ADP-ribosylation, the MyoD-dependent ADP-ribosylation was not associated to chromatin but rather localized to the nucleoplasm. Together, these data describe a MyoD-induced nucleoplasmic ADP-ribosylation that is observed particularly during transdifferentiation and thus potentially expands the plethora of cellular processes associated with ADP-ribosylation. MyoD-dependent transdifferentiation of IMR90 to myoblasts induces ARTD1 expression Transdifferentiation induces nuclear ARTD1-dependent ADP-ribosylation in myoblasts This ADP-ribosylation is induced independent of cell cycle and of DNA damage ARTD1-mediated poly-ADP-ribosylation localizes to the nucleoplasm in myoblasts
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Affiliation(s)
- Lavinia Bisceglie
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.,Molecular Life Science PhD Program of the Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland
| | - Ann-Katrin Hopp
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Kapila Gunasekera
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
| | - Roni H Wright
- Centre de Regulació Genomica (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain.,Basic Sciences Department, Faculty of Medicine and Health Sciences, Universitat Internacional de Catalunya (UIC), 08003 Barcelona, Spain
| | - François Le Dily
- Centre de Regulació Genomica (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Enrique Vidal
- Centre de Regulació Genomica (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain
| | | | - Luca Caputo
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Chiara Nicoletti
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Pier Lorenzo Puri
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Miguel Beato
- Centre de Regulació Genomica (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Michael O Hottiger
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland
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12
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Coronado E, Yañez Y, Vidal E, Rubio L, Vera-Sempere F, Cañada-Martínez AJ, Panadero J, Cañete A, Ladenstein R, Castel V, Font de Mora J. Intratumoral immunosuppression profiles in 11q-deleted neuroblastomas provide new potential therapeutic targets. Mol Oncol 2021; 15:364-380. [PMID: 33252831 PMCID: PMC7858123 DOI: 10.1002/1878-0261.12868] [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: 07/30/2020] [Revised: 11/13/2020] [Accepted: 11/27/2020] [Indexed: 12/19/2022] Open
Abstract
High‐risk neuroblastoma (NB) patients with 11q deletion frequently undergo late but consecutive relapse cycles with fatal outcome. To date, no actionable targets to improve current multimodal treatment have been identified. We analyzed immune microenvironment and genetic profiles of high‐risk NB correlating with 11q immune status. We show in two independent cohorts that 11q‐deleted NB exhibits various immune inhibitory mechanisms, including increased CD4+ resting T cells and M2 macrophages, higher expression of programmed death‐ligand 1, interleukin‐10, transforming growth factor‐beta‐1, and indoleamine 2,3‐dioxygenase 1 (P < 0.05), and also higher chromosomal breakages (P ≤ 0.02) and hemizygosity of immunosuppressive miRNAs than MYCN‐amplified and other 11q‐nondeleted high‐risk NB. We also analyzed benefits of maintenance treatment in 83 high‐risk stage M NB patients focusing on 11q status, either with standard anti‐GD2 immunotherapy (n = 50) or previous retinoic acid‐based therapy alone (n = 33). Immunotherapy associated with higher EFS (50 vs. 30, P = 0.028) and OS (72 vs. 52, P = 0.047) at 3 years in the overall population. Despite benefits from standard anti‐GD2 immunotherapy in high‐risk NB patients, those with 11q deletion still face poor outcome. This NB subgroup displays intratumoral immune suppression profiles, revealing a potential therapeutic strategy with combination immunotherapy to circumvent this immune checkpoint blockade.
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Affiliation(s)
- Esther Coronado
- Laboratory of Cellular and Molecular Biology, Health Research Institute Hospital La Fe, Valencia, Spain.,Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
| | - Yania Yañez
- Laboratory of Cellular and Molecular Biology, Health Research Institute Hospital La Fe, Valencia, Spain.,Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
| | - Enrique Vidal
- Roche Diagnostics Information Solutions, Basel, Switzerland
| | - Luis Rubio
- Department of Pathology, La Fe University Hospital, Valencia, Spain
| | - Francisco Vera-Sempere
- Department of Pathology, La Fe University Hospital, Valencia, Spain.,School of Medicine, University of Valencia, Spain
| | | | - Joaquín Panadero
- Genomics Unit, Health Research Institute Hospital La Fe, Valencia, Spain
| | - Adela Cañete
- Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain.,School of Medicine, University of Valencia, Spain.,Pediatric Oncology Unit, La Fe University Hospital, Valencia, Spain
| | - Ruth Ladenstein
- Department of Paediatrics, St. Anna Children's Hospital and Children's Cancer Research Institute (CCRI), Medical University, Vienna, Austria
| | - Victoria Castel
- School of Medicine, University of Valencia, Spain.,Pediatric Oncology Unit, La Fe University Hospital, Valencia, Spain
| | - Jaime Font de Mora
- Laboratory of Cellular and Molecular Biology, Health Research Institute Hospital La Fe, Valencia, Spain.,Clinical and Translational Research in Cancer, Health Research Institute Hospital La Fe, Valencia, Spain
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13
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Stik G, Vidal E, Barrero M, Cuartero S, Vila-Casadesús M, Mendieta-Esteban J, Tian TV, Choi J, Berenguer C, Abad A, Borsari B, le Dily F, Cramer P, Marti-Renom MA, Stadhouders R, Graf T. CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response. Nat Genet 2020; 52:655-661. [DOI: 10.1038/s41588-020-0643-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 05/08/2020] [Indexed: 11/09/2022]
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14
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Tian TV, Vidal E, Graf T, Stik G. Identification of Enhancer-Promoter Contacts in Embryoid Bodies by Quantitative Chromosome Conformation Capture (4C). J Vis Exp 2020. [PMID: 32420995 DOI: 10.3791/60960] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
During mammalian development, cell fates are determined through the establishment of regulatory networks that define the specificity, timing, and spatial patterns of gene expression. Embryoid bodies (EBs) derived from pluripotent stem cells have been a popular model to study the differentiation of the main three germ layers and to define regulatory circuits during cell fate specification. Although it is well-known that tissue-specific enhancers play an important role in these networks by interacting with promoters, assigning them to their relevant target genes still remains challenging. To make this possible, quantitative approaches are needed to study enhancer-promoter contacts and their dynamics during development. Here, we adapted a 4C method to define enhancers and their contacts with cognate promoters in the EB differentiation model. The method uses frequently cutting restriction enzymes, sonication, and a nested-ligation-mediated PCR protocol compatible with commercial DNA library preparation kits. Subsequently, the 4C libraries are subjected to high-throughput sequencing and analyzed bioinformatically, allowing detection and quantification of all sequences that have contacts with a chosen promoter. The resulting sequencing data can also be used to gain information about the dynamics of enhancer-promoter contacts during differentiation. The technique described for the EB differentiation model is easy to implement.
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Affiliation(s)
- Tian V Tian
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology; Universitat Pompeu Fabra; Vall d'Hebron Institute of Oncology;
| | - Enrique Vidal
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology; Universitat Pompeu Fabra
| | - Thomas Graf
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology; Universitat Pompeu Fabra;
| | - Grégoire Stik
- Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology; Universitat Pompeu Fabra;
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15
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Ferrari R, de Llobet Cucalon LI, Di Vona C, Le Dilly F, Vidal E, Lioutas A, Oliete JQ, Jochem L, Cutts E, Dieci G, Vannini A, Teichmann M, de la Luna S, Beato M. TFIIIC Binding to Alu Elements Controls Gene Expression via Chromatin Looping and Histone Acetylation. Mol Cell 2020; 77:475-487.e11. [PMID: 31759822 PMCID: PMC7014570 DOI: 10.1016/j.molcel.2019.10.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [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: 04/12/2019] [Revised: 08/20/2019] [Accepted: 10/13/2019] [Indexed: 12/15/2022]
Abstract
How repetitive elements, epigenetic modifications, and architectural proteins interact ensuring proper genome expression remains poorly understood. Here, we report regulatory mechanisms unveiling a central role of Alu elements (AEs) and RNA polymerase III transcription factor C (TFIIIC) in structurally and functionally modulating the genome via chromatin looping and histone acetylation. Upon serum deprivation, a subset of AEs pre-marked by the activity-dependent neuroprotector homeobox Protein (ADNP) and located near cell-cycle genes recruits TFIIIC, which alters their chromatin accessibility by direct acetylation of histone H3 lysine-18 (H3K18). This facilitates the contacts of AEs with distant CTCF sites near promoter of other cell-cycle genes, which also become hyperacetylated at H3K18. These changes ensure basal transcription of cell-cycle genes and are critical for their re-activation upon serum re-exposure. Our study reveals how direct manipulation of the epigenetic state of AEs by a general transcription factor regulates 3D genome folding and expression.
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Affiliation(s)
- Roberto Ferrari
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain.
| | - Lara Isabel de Llobet Cucalon
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Chiara Di Vona
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - François Le Dilly
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Enrique Vidal
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Antonios Lioutas
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Javier Quilez Oliete
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain
| | - Laura Jochem
- The Institute of Cancer Research (ICR), London, UK
| | - Erin Cutts
- The Institute of Cancer Research (ICR), London, UK
| | - Giorgio Dieci
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Alessandro Vannini
- The Institute of Cancer Research (ICR), London, UK; Human Technopole. Via Cristina Belgioioso, 171, 20157 Milano MI, Italy
| | - Martin Teichmann
- Université de Bordeaux, INSERM U1212 CNRS UMR 5320 146, Bordeaux, France
| | - Susana de la Luna
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain; ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain
| | - Miguel Beato
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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16
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Figueroa CL, Bernabe LF, Martin M, Vidal E, Pérez de Val B, Ramis A. A Case of Canine Miliary Tuberculosis Caused by Mycobacterium tuberculosis. J Comp Pathol 2020. [DOI: 10.1016/j.jcpa.2019.10.120] [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: 10/25/2022]
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17
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Arrieta M, Fernández-Bellon H, Martín M, Vidal E, Pérez de Val B, Ramis A. Mycobacterium genavense Infection in a Group of Amazon Parrots (Amazona albifrons). J Comp Pathol 2020. [DOI: 10.1016/j.jcpa.2019.10.119] [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: 11/16/2022]
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18
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Calvo-Zaragoza J, Toselli AH, Vidal E. Handwritten Music Recognition for Mensural notation with convolutional recurrent neural networks. Pattern Recognit Lett 2019. [DOI: 10.1016/j.patrec.2019.08.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Affiliation(s)
- M Thibault
- Laboratoire d'Excellence Labex-CORAIL, Institut de Recherche pour le Développement (IRD), UMR ENTROPIE (IRD-Université de La Réunion-CNRS), BP A5, Nouméa Cedex 98848, New Caledonia, France.
| | - F Houlbrèque
- Laboratoire d'Excellence Labex-CORAIL, Institut de Recherche pour le Développement (IRD), UMR ENTROPIE (IRD-Université de La Réunion-CNRS), BP A5, Nouméa Cedex 98848, New Caledonia, France
| | - A Lorrain
- University of Brest, CNRS, IRD, Ifremer, LEMAR, F-29280 Plouzane, France
| | - E Vidal
- Laboratoire d'Excellence Labex-CORAIL, Institut de Recherche pour le Développement (IRD), UMR ENTROPIE (IRD-Université de La Réunion-CNRS), BP A5, Nouméa Cedex 98848, New Caledonia, France
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20
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Muehlberger G, Seaward L, Terras M, Ares Oliveira S, Bosch V, Bryan M, Colutto S, Déjean H, Diem M, Fiel S, Gatos B, Greinoecker A, Grüning T, Hackl G, Haukkovaara V, Heyer G, Hirvonen L, Hodel T, Jokinen M, Kahle P, Kallio M, Kaplan F, Kleber F, Labahn R, Lang EM, Laube S, Leifert G, Louloudis G, McNicholl R, Meunier JL, Michael J, Mühlbauer E, Philipp N, Pratikakis I, Puigcerver Pérez J, Putz H, Retsinas G, Romero V, Sablatnig R, Sánchez JA, Schofield P, Sfikas G, Sieber C, Stamatopoulos N, Strauß T, Terbul T, Toselli AH, Ulreich B, Villegas M, Vidal E, Walcher J, Weidemann M, Wurster H, Zagoris K. Transforming scholarship in the archives through handwritten text recognition. JD 2019. [DOI: 10.1108/jd-07-2018-0114] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Purpose
An overview of the current use of handwritten text recognition (HTR) on archival manuscript material, as provided by the EU H2020 funded Transkribus platform. It explains HTR, demonstrates Transkribus, gives examples of use cases, highlights the affect HTR may have on scholarship, and evidences this turning point of the advanced use of digitised heritage content. The paper aims to discuss these issues.
Design/methodology/approach
This paper adopts a case study approach, using the development and delivery of the one openly available HTR platform for manuscript material.
Findings
Transkribus has demonstrated that HTR is now a useable technology that can be employed in conjunction with mass digitisation to generate accurate transcripts of archival material. Use cases are demonstrated, and a cooperative model is suggested as a way to ensure sustainability and scaling of the platform. However, funding and resourcing issues are identified.
Research limitations/implications
The paper presents results from projects: further user studies could be undertaken involving interviews, surveys, etc.
Practical implications
Only HTR provided via Transkribus is covered: however, this is the only publicly available platform for HTR on individual collections of historical documents at time of writing and it represents the current state-of-the-art in this field.
Social implications
The increased access to information contained within historical texts has the potential to be transformational for both institutions and individuals.
Originality/value
This is the first published overview of how HTR is used by a wide archival studies community, reporting and showcasing current application of handwriting technology in the cultural heritage sector.
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21
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Vidal E, le Dily F, Quilez J, Stadhouders R, Cuartero Y, Graf T, Marti-Renom MA, Beato M, Filion GJ. OneD: increasing reproducibility of Hi-C samples with abnormal karyotypes. Nucleic Acids Res 2019; 46:e49. [PMID: 29394371 PMCID: PMC5934634 DOI: 10.1093/nar/gky064] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [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: 06/13/2017] [Accepted: 01/23/2018] [Indexed: 12/12/2022] Open
Abstract
The three-dimensional conformation of genomes is an essential component of their biological activity. The advent of the Hi-C technology enabled an unprecedented progress in our understanding of genome structures. However, Hi-C is subject to systematic biases that can compromise downstream analyses. Several strategies have been proposed to remove those biases, but the issue of abnormal karyotypes received little attention. Many experiments are performed in cancer cell lines, which typically harbor large-scale copy number variations that create visible defects on the raw Hi-C maps. The consequences of these widespread artifacts on the normalized maps are mostly unexplored. We observed that current normalization methods are not robust to the presence of large-scale copy number variations, potentially obscuring biological differences and enhancing batch effects. To address this issue, we developed an alternative approach designed to take into account chromosomal abnormalities. The method, called OneD, increases reproducibility among replicates of Hi-C samples with abnormal karyotype, outperforming previous methods significantly. On normal karyotypes, OneD fared equally well as state-of-the-art methods, making it a safe choice for Hi-C normalization. OneD is fast and scales well in terms of computing resources for resolutions up to 5 kb.
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Affiliation(s)
- Enrique Vidal
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - François le Dily
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Javier Quilez
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Ralph Stadhouders
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Yasmina Cuartero
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Thomas Graf
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marc A Marti-Renom
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain.,ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Miguel Beato
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Guillaume J Filion
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
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22
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Tian TV, Di Stefano B, Stik G, Vila-Casadesús M, Sardina JL, Vidal E, Dasti A, Segura-Morales C, De Andrés-Aguayo L, Gómez A, Goldmann J, Jaenisch R, Graf T. Whsc1 links pluripotency exit with mesendoderm specification. Nat Cell Biol 2019; 21:824-834. [PMID: 31235934 DOI: 10.1038/s41556-019-0342-1] [Citation(s) in RCA: 15] [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] [Received: 07/26/2017] [Accepted: 05/09/2019] [Indexed: 12/19/2022]
Abstract
How pluripotent stem cells differentiate into the main germ layers is a key question of developmental biology. Here, we show that the chromatin-related factor Whsc1 (also known as Nsd2 and MMSET) has a dual role in pluripotency exit and germ layer specification of embryonic stem cells. On induction of differentiation, a proportion of Whsc1-depleted embryonic stem cells remain entrapped in a pluripotent state and fail to form mesendoderm, although they are still capable of generating neuroectoderm. These functions of Whsc1 are independent of its methyltransferase activity. Whsc1 binds to enhancers of the mesendodermal regulators Gata4, T (Brachyury), Gata6 and Foxa2, together with Brd4, and activates the expression of these genes. Depleting each of these regulators also delays pluripotency exit, suggesting that they mediate the effects observed with Whsc1. Our data indicate that Whsc1 links silencing of the pluripotency regulatory network with activation of mesendoderm lineages.
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Affiliation(s)
- Tian V Tian
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Bruno Di Stefano
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.,Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Grégoire Stik
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Maria Vila-Casadesús
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - José Luis Sardina
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Enrique Vidal
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Alessandro Dasti
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Carolina Segura-Morales
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Luisa De Andrés-Aguayo
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Antonio Gómez
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Johanna Goldmann
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain.,The Whitehead Institute for Biomedical Research, Cambridge, MA, USA
| | - Rudolf Jaenisch
- The Whitehead Institute for Biomedical Research, Cambridge, MA, USA.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Thomas Graf
- Center for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain. .,Universitat Pompeu Fabra, Barcelona, Spain.
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23
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Spill YG, Castillo D, Vidal E, Marti-Renom MA. Binless normalization of Hi-C data provides significant interaction and difference detection independent of resolution. Nat Commun 2019; 10:1938. [PMID: 31028255 PMCID: PMC6486590 DOI: 10.1038/s41467-019-09907-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 12/24/2017] [Accepted: 03/21/2019] [Indexed: 02/05/2023] Open
Abstract
Chromosome conformation capture techniques, such as Hi-C, are fundamental in characterizing genome organization. These methods have revealed several genomic features, such as chromatin loops, whose disruption can have dramatic effects in gene regulation. Unfortunately, their detection is difficult; current methods require that the users choose the resolution of interaction maps based on dataset quality and sequencing depth. Here, we introduce Binless, a resolution-agnostic method that adapts to the quality and quantity of available data, to detect both interactions and differences. Binless relies on an alternate representation of Hi-C data, which leads to a more detailed classification of paired-end reads. Using a large-scale benchmark, we demonstrate that Binless is able to call interactions with higher reproducibility than other existing methods. Binless, which is freely available, can thus reliably be used to identify chromatin loops as well as for differential analysis of chromatin interaction maps.
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Affiliation(s)
- Yannick G Spill
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.
| | - David Castillo
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Enrique Vidal
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Marc A Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain.
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), 08002, Barcelona, Spain.
- ICREA, Pg. Lluís Companys 23, 08010, Barcelona, Spain.
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24
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25
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Barrere K, Toselli AH, Vidal E. Line Segmentation Free Probabilistic Keyword Spotting and Indexing. Pattern Recognition and Image Analysis 2019. [DOI: 10.1007/978-3-030-31321-0_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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26
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Le Dily F, Vidal E, Cuartero Y, Quilez J, Nacht AS, Vicent GP, Carbonell-Caballero J, Sharma P, Villanueva-Cañas JL, Ferrari R, De Llobet LI, Verde G, Wright RHG, Beato M. Hormone-control regions mediate steroid receptor-dependent genome organization. Genome Res 2018; 29:29-39. [PMID: 30552103 PMCID: PMC6314164 DOI: 10.1101/gr.243824.118] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [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: 09/14/2018] [Accepted: 11/15/2018] [Indexed: 01/25/2023]
Abstract
In breast cancer cells, some topologically associating domains (TADs) behave as hormonal gene regulation units, within which gene transcription is coordinately regulated in response to steroid hormones. Here we further describe that responsive TADs contain 20- to 100-kb-long clusters of intermingled estrogen receptor (ESR1) and progesterone receptor (PGR) binding sites, hereafter called hormone-control regions (HCRs). In T47D cells, we identified more than 200 HCRs, which are frequently bound by unliganded ESR1 and PGR. These HCRs establish steady long-distance inter-TAD interactions between them and organize characteristic looping structures with promoters in their TADs even in the absence of hormones in ESR1+-PGR+ cells. This organization is dependent on the expression of the receptors and is further dynamically modulated in response to steroid hormones. HCRs function as platforms that integrate different signals, resulting in some cases in opposite transcriptional responses to estrogens or progestins. Altogether, these results suggest that steroid hormone receptors act not only as hormone-regulated sequence-specific transcription factors but also as local and global genome organizers.
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Affiliation(s)
- François Le Dily
- Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Enrique Vidal
- Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Yasmina Cuartero
- Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain.,CNAG-CRG, Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08028, Spain
| | - Javier Quilez
- Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - A Silvina Nacht
- Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Guillermo P Vicent
- Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - José Carbonell-Caballero
- Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Priyanka Sharma
- Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - José Luis Villanueva-Cañas
- Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Roberto Ferrari
- Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Lara Isabel De Llobet
- Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Gaetano Verde
- Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Roni H G Wright
- Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Miguel Beato
- Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona 08002, Spain
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27
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Amat R, Böttcher R, Le Dily F, Vidal E, Quilez J, Cuartero Y, Beato M, de Nadal E, Posas F. Rapid reversible changes in compartments and local chromatin organization revealed by hyperosmotic shock. Genome Res 2018; 29:18-28. [PMID: 30523037 PMCID: PMC6314167 DOI: 10.1101/gr.238527.118] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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: 04/15/2018] [Accepted: 11/22/2018] [Indexed: 12/17/2022]
Abstract
Nuclear architecture is decisive for the assembly of transcriptional responses. However, how chromosome organization is dynamically modulated to permit rapid and transient transcriptional changes in response to environmental challenges remains unclear. Here we show that hyperosmotic stress disrupts different levels of chromosome organization, ranging from A/B compartment changes to reduction in the number and insulation of topologically associating domains (TADs). Concomitantly, transcription is greatly affected, TAD borders weaken, and RNA Polymerase II runs off from hundreds of transcription end sites. Stress alters the binding profiles of architectural proteins, which explains the disappearance of local chromatin organization. These processes are dynamic, and cells rapidly reconstitute their default chromatin conformation after stress removal, uncovering an intrinsic organization. Transcription is not required for local chromatin reorganization, while compartment recovery is partially transcription-dependent. Thus, nuclear organization in mammalian cells can be rapidly modulated by environmental changes in a reversible manner.
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Affiliation(s)
- Ramon Amat
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, E-08003 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - René Böttcher
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, E-08003 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - François Le Dily
- Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), E-08003 Barcelona, Spain
| | - Enrique Vidal
- Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), E-08003 Barcelona, Spain
| | - Javier Quilez
- Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), E-08003 Barcelona, Spain
| | - Yasmina Cuartero
- Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), E-08003 Barcelona, Spain.,CNAG-CRG, The Barcelona Institute of Science and Technology (BIST), E-08003 Barcelona, Spain
| | - Miguel Beato
- Gene Regulation, Stem Cells and Cancer Program, Center for Genomic Regulation (CRG), E-08003 Barcelona, Spain.,CNAG-CRG, The Barcelona Institute of Science and Technology (BIST), E-08003 Barcelona, Spain.,Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Eulàlia de Nadal
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, E-08003 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
| | - Francesc Posas
- Cell Signaling Research Group, Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, E-08003 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, 08028 Barcelona, Spain
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28
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Vidal E, Giménez H, Forero M, Fajardo M. Erector spinae plane block: A cadaver study to determine its mechanism of action. Rev Esp Anestesiol Reanim (Engl Ed) 2018; 65:514-519. [PMID: 30166123 DOI: 10.1016/j.redar.2018.07.004] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Revised: 07/13/2018] [Accepted: 07/13/2018] [Indexed: 06/08/2023]
Abstract
INTRODUCTION The erector spinae plane (ESP) block is a novel technique for the treatment of acute and chronic pain. Its mechanism and site of action has not yet been explained properly. OBJECTIVES In order to explain the mechanism of action of the ESP block, injections were performed with methylene blue to simulate the local anaesthetics and to determine its distribution from the anterior side of the thorax. To find an aperture or channel through which the local anaesthetic passes from posterior to anterior through the muscular and bone structures. MATERIALS AND METHODS Four spinal columns of fresh cryopreserved corpses were used. A total of 9 ultrasound-guided ESP blocks were performed in different regions of the specimens using 20ml of 0.01% methylene blue per block. The distribution of the dye was observed from the anterior side of the thorax, measuring the amount of intercostal spaces stained, before and after the removal of the parietal pleura, and the structures in which the stain was found were recorded. RESULTS In all blocks of the ESP, dye was found in the paravertebral space, intercostal spaces, and in some cases in the prevertebral chain. The blocks had a mean of 4.6 intercostal spaces stained, with a maximum of 7 and a minimum of 3. The intensity of the dye was greater on the side of the injection, dorsal to the column, than that found in the ventral part below of the pleura. It was not possible to verify a clear channel through which the dye diffuses towards the previous zone. CONCLUSIONS From the data collected in this study, it can be deduced that the blockade of the ESP has a mechanism of anaesthetic action similar to paravertebral blocks. The site from which the anaesthetic would cross from the posterior plane of the spine to the anterior region of the thorax was not clear, and should be investigated in future works.
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Affiliation(s)
- E Vidal
- Servicio de Anestesiología, Hospital Durand, Ciudad de Buenos Aires, Argentina.
| | - H Giménez
- Servicio de Anestesiología, Hospital Durand, Ciudad de Buenos Aires, Argentina
| | - M Forero
- Departamento de Anestesia, McMaster University, Hamilton, Ontario, Canadá
| | - M Fajardo
- Servicio de Anestesiología, Hospital Universitario de Móstoles, Móstoles, Madrid, España
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29
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30
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Quilez J, Vidal E, Dily FL, Serra F, Cuartero Y, Stadhouders R, Graf T, Marti-Renom MA, Beato M, Filion G. Parallel sequencing lives, or what makes large sequencing projects successful. Gigascience 2018; 6:1-6. [PMID: 29048533 PMCID: PMC5714127 DOI: 10.1093/gigascience/gix100] [Citation(s) in RCA: 4] [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: 08/01/2017] [Accepted: 10/08/2017] [Indexed: 12/19/2022] Open
Abstract
T47D_rep2 and b1913e6c1_51720e9cf were 2 Hi-C samples. They were born and processed at the same time, yet their fates were very different. The life of b1913e6c1_51720e9cf was simple and fruitful, while that of T47D_rep2 was full of accidents and sorrow. At the heart of these differences lies the fact that b1913e6c1_51720e9cf was born under a lab culture of Documentation, Automation, Traceability, and Autonomy and compliance with the FAIR Principles. Their lives are a lesson for those who wish to embark on the journey of managing high-throughput sequencing data.
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Affiliation(s)
- Javier Quilez
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Enrique Vidal
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - François Le Dily
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - François Serra
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Yasmina Cuartero
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Ralph Stadhouders
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Thomas Graf
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marc A Marti-Renom
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain.,ICREA, Pg. Lluis Companys 23, 08010 Barcelona, Spain
| | - Miguel Beato
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Guillaume Filion
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Dr. Aiguader 88, 08003 Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
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31
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Stadhouders R, Vidal E, Serra F, Di Stefano B, Le Dily F, Quilez J, Gomez A, Collombet S, Berenguer C, Cuartero Y, Hecht J, Filion GJ, Beato M, Marti-Renom MA, Graf T. Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming. Nat Genet 2018; 50:238-249. [PMID: 29335546 PMCID: PMC5810905 DOI: 10.1038/s41588-017-0030-7] [Citation(s) in RCA: 219] [Impact Index Per Article: 36.5] [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: 04/29/2017] [Accepted: 12/01/2017] [Indexed: 01/28/2023]
Abstract
Chromosomal architecture is known to influence gene expression, yet its role in controlling cell fate remains poorly understood. Reprogramming of somatic cells into pluripotent stem cells (PSCs) by the transcription factors (TFs) OCT4, SOX2, KLF4 and MYC offers an opportunity to address this question but is severely limited by the low proportion of responding cells. We have recently developed a highly efficient reprogramming protocol that synchronously converts somatic into pluripotent stem cells. Here, we used this system to integrate time-resolved changes in genome topology with gene expression, TF binding and chromatin-state dynamics. The results showed that TFs drive topological genome reorganization at multiple architectural levels, often before changes in gene expression. Removal of locus-specific topological barriers can explain why pluripotency genes are activated sequentially, instead of simultaneously, during reprogramming. Together, our results implicate genome topology as an instructive force for implementing transcriptional programs and cell fate in mammals.
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Affiliation(s)
- Ralph Stadhouders
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Department of Pulmonary Medicine, Erasmus MC, Rotterdam, the Netherlands.
| | - Enrique Vidal
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - François Serra
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Structural Genomics Group, CNAG-CRG, BIST, Barcelona, Spain
| | - Bruno Di Stefano
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Harvard University and Harvard Medical School, Cambridge, MA, USA
| | - François Le Dily
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Structural Genomics Group, CNAG-CRG, BIST, Barcelona, Spain
| | - Javier Quilez
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Antonio Gomez
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Samuel Collombet
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR8197, INSERM U1024, Paris, France
| | - Clara Berenguer
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Yasmina Cuartero
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Structural Genomics Group, CNAG-CRG, BIST, Barcelona, Spain
| | - Jochen Hecht
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Genomics Unit, CRG, BIST, Barcelona, Spain
| | - Guillaume J Filion
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Miguel Beato
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marc A Marti-Renom
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Structural Genomics Group, CNAG-CRG, BIST, Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| | - Thomas Graf
- Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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Domingo M, Vidal E, Espada Y, Moll X, Balseiro A, Canturri A, Pérez de Val B. Improved Measurement of Lesions for Assessment of Efficacy of Tuberculosis Vaccines in Small Ruminant Models: From Scoring To Imaging and Volumetric Quantification. J Comp Pathol 2018. [DOI: 10.1016/j.jcpa.2017.10.006] [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: 11/28/2022]
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Martin-Trujillo A, Vidal E, Monteagudo-Sánchez A, Sanchez-Delgado M, Moran S, Hernandez Mora JR, Heyn H, Guitart M, Esteller M, Monk D. Copy number rather than epigenetic alterations are the major dictator of imprinted methylation in tumors. Nat Commun 2017; 8:467. [PMID: 28883545 PMCID: PMC5589900 DOI: 10.1038/s41467-017-00639-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [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: 11/18/2016] [Accepted: 07/17/2017] [Indexed: 02/07/2023] Open
Abstract
It has been postulated that imprinting aberrations are common in tumors. To understand the role of imprinting in cancer, we have characterized copy-number and methylation in over 280 cancer cell lines and confirm our observations in primary tumors. Imprinted differentially methylated regions (DMRs) regulate parent-of-origin monoallelic expression of neighboring transcripts in cis. Unlike single-copy CpG islands that may be prone to hypermethylation, imprinted DMRs can either loose or gain methylation during tumorigenesis. Here, we show that methylation profiles at imprinted DMRs often not represent genuine epigenetic changes but simply the accumulation of underlying copy-number aberrations (CNAs), which is independent of the genome methylation state inferred from cancer susceptible loci. Our results reveal that CNAs also influence allelic expression as loci with copy-number neutral loss-of-heterozygosity or amplifications may be expressed from the appropriate parental chromosomes, which is indicative of maintained imprinting, although not observed as a single expression foci by RNA FISH.Altered genomic imprinting is frequently reported in cancer. Here, the authors analyze copy number and methylation in cancer cell lines and primary tumors to show that imprinted methylation profiles represent the accumulation of copy number alteration, rather than epigenetic alterations.
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Affiliation(s)
- Alex Martin-Trujillo
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Enrique Vidal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Ana Monteagudo-Sánchez
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Marta Sanchez-Delgado
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Sebastian Moran
- Cancer Epigenetics group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Jose Ramon Hernandez Mora
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Holger Heyn
- Universitat Pompeu Fabra (UPF), Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Miriam Guitart
- Genetics Laboratory, UDIAT- Diagnostic Centre, Corporació Sanitària Parc Taulí, 08208, Sabadell, Spain
| | - Manel Esteller
- Cancer Epigenetics group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, 08907, Barcelona, Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, 08907, Catalonia, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain
| | - David Monk
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, 08907, Barcelona, Spain.
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Peralta S, Solernou R, Fabregues F, Minarro A, Puerto B, Penarrubia J, Casals G, Creus M, Manau D, Borras A, Vidal E. Antral follicle count measured after pituitary suppression as predictor of sub-optimal ovarian response and cumulative live birth: a review of 1542 long protocol IVF / ICSI cycles. Fertil Steril 2017. [DOI: 10.1016/j.fertnstert.2017.07.645] [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: 10/18/2022]
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Longhurst GR, Tsuchiya K, Dorn CH, Folkman SL, Fronk TH, Ishihara M, Kawamura H, Tranter TN, Rohe R, Uchida M, Vidal E. Managing Beryllium in Nuclear Facility Applications. NUCL TECHNOL 2017. [DOI: 10.13182/nt11-a13318] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [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]
Affiliation(s)
| | - K. Tsuchiya
- Japan Atomic Energy Agency, Oarai-machi, Higashiibaraki-gun, Ibaraki-ken, Japan
| | - C. H. Dorn
- Materion Brush Beryllium & Composites, Upland, California
| | | | | | - M. Ishihara
- Japan Atomic Energy Agency, Oarai-machi, Higashiibaraki-gun, Ibaraki-ken, Japan
| | - H. Kawamura
- Japan Atomic Energy Agency, Oarai-machi, Higashiibaraki-gun, Ibaraki-ken, Japan
| | - T. N. Tranter
- Materion Brush Beryllium & Composites, Upland, California
| | - R. Rohe
- Idaho National Laboratory, Idaho Falls, Idaho
| | - M. Uchida
- NGK Insulators Ltd., Handa-shi, Aichi-ken, Japan
| | - E. Vidal
- Materion Brush Beryllium & Composites, Elmore, Ohio
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Raimondi N, Vial MR, Calleja J, Quintero A, Cortés Alban A, Celis E, Pacheco C, Ugarte S, Añón JM, Hernández G, Vidal E, Chiappero G, Ríos F, Castilleja F, Matos A, Rodriguez E, Antoniazzi P, Teles JM, Dueñas C, Sinclair J, Martínez L, Von der Osten I, Vergara J, Jiménez E, Arroyo M, Rodriguez C, Torres J, Fernandez-Bussy S, Nates JL. Evidence-based guides in tracheostomy use in critical patients. Med Intensiva 2017; 41:94-115. [PMID: 28188061 DOI: 10.1016/j.medin.2016.12.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Revised: 11/20/2016] [Accepted: 12/02/2016] [Indexed: 10/20/2022]
Abstract
OBJECTIVES Provide evidence based guidelines for tracheostomy in critically ill adult patients and identify areas needing further research. METHODS A task force composed of representatives of 10 member countries of the Pan-American and Iberic Federation of Societies of Critical and Intensive Therapy Medicine and of the Latin American Critical Care Trial Investigators Network developed recommendations based on the Grading of Recommendations Assessment, Development and Evaluation system. RESULTS The group identified 23 relevant questions among 87 issues that were initially identified. In the initial search, 333 relevant publications were identified of which 226 publications were chosen. The task force generated a total of 19 recommendations: 10 positive (1B=3, 2C=3, 2D=4) and 9 negative (1B=8, 2C=1). A recommendation was not possible in six questions. CONCLUSION Percutaneous techniques are associated with a lower risk of infections compared to surgical tracheostomy. Early tracheostomy only seems to reduce the duration of ventilator use but not the incidence of pneumonia, the length of stay, or the long-term mortality rate. The evidence does not support the use of routine bronchoscopy guidance or laryngeal masks during the procedure. Finally, proper prior training is as important or even a more significant factor in reducing complications than the technique used.
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Affiliation(s)
- N Raimondi
- Hospital Municipal Juan A. Fernández, Universidad de Buenos Aires, Argentina
| | - M R Vial
- MD Anderson Cancer Center, The University of Texas, Texas, United States; Clínica Alemana de Santiago, Universidad del Desarrollo, Santiago, Chile
| | - J Calleja
- Hospital Zambrano Hellion, Instituto Tecnológico de Monterrey, Monterrey, Nuevo León, México
| | - A Quintero
- Instituto Medico de Alta Tecnología, Universidad del Sinú, Montería, Colombia
| | - A Cortés Alban
- Clínica Mayor de Temuco, Hospital de Nueva Imperial, Universidad Mayor de Temuco, Temuco, Chile
| | - E Celis
- Hospital Universitario Fundación Santa Fé de Bogotá, Bogotá, Colombia
| | - C Pacheco
- Hospital Universitario de Caracas, Caracas, Venezuela
| | - S Ugarte
- Hospital del Salvador, Clínica Indisa, Universidad de Chile, Santiago, Chile
| | - J M Añón
- Hospital Universitario la Paz -Carlos III. IdiPaz, Madrid, España
| | - G Hernández
- Complejo Hospitalario de Toledo, Toledo, España
| | - E Vidal
- Hospital Ángeles Lomas, Hospital Español de México, Ciudad de México, México
| | - G Chiappero
- Hospital Juan A. Fernández CABA, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - F Ríos
- Hospital Nacional Alejandro Posadas, Sanatorio Las Lomas, San Isidro, Buenos Aires, Argentina
| | - F Castilleja
- Hospital Zambrano Hellion, Instituto Tecnológico de Monterrey, Monterrey, Nuevo León, México
| | - A Matos
- Complejo Hospitalario Caja de Seguro Social, Panamá
| | - E Rodriguez
- Complejo Hospitalario Caja de Seguro Social, Panamá
| | - P Antoniazzi
- Hospital Santa Casa, Ribeirao Preto, Sao Paulo, Brazil
| | - J M Teles
- Hospital de Urgências de Goiânia, Goiás, Brazil
| | - C Dueñas
- Gestión Salud, Santa Cruz de Bocagrande, Universidad de Cartagena, Cartagena, Colombia
| | - J Sinclair
- Hospital Punta Pacífica, Johns Hopkins Medicine, Universidad de Panamá, Ciudad de Panamá, Panamá
| | - L Martínez
- Hospital Policlínica Metropolitana, Caracas, Venezuela
| | - I Von der Osten
- Hospital Central "Miguel Pérez Carreño" IVSS, Universidad Central de Venezuela, Caracas, Venezuela
| | - J Vergara
- Hospital Luis Vernaza, Universidad de Especialidades Espíritu Santo "UEES", Guayaquil, Ecuador
| | - E Jiménez
- Baylor Scott & White Health, Texas A&M Health Science Center College of Medicine, Temple, Texas, Estados Unidos
| | - M Arroyo
- Clínica Santa Sofía, Caracas, Venezuela
| | - C Rodriguez
- Instituto Medico de Alta Tecnología, Universidad del Sinú, Montería, Colombia
| | - J Torres
- Clínica Alemana de Santiago, Universidad del Desarrollo, Santiago, Chile
| | - S Fernandez-Bussy
- Clínica Alemana de Santiago, Universidad del Desarrollo, Santiago, Chile; Division of Pulmonary, Critical Care & Sleep Medicine, University of Florida, Gainesville, Florida, Estados Unidos
| | - J L Nates
- MD Anderson Cancer Center, The University of Texas, Texas, United States.
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Sanchez-Mut JV, Heyn H, Vidal E, Delgado-Morales R, Moran S, Sayols S, Sandoval J, Ferrer I, Esteller M, Gräff J. Whole genome grey and white matter DNA methylation profiles in dorsolateral prefrontal cortex. Synapse 2017; 71. [PMID: 28105729 DOI: 10.1002/syn.21959] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 12/11/2022]
Abstract
The brain's neocortex is anatomically organized into grey and white matter, which are mainly composed by neuronal and glial cells, respectively. The neocortex can be further divided in different Brodmann areas according to their cytoarchitectural organization, which are associated with distinct cortical functions. There is increasing evidence that brain development and function are governed by epigenetic processes, yet their contribution to the functional organization of the neocortex remains incompletely understood. Herein, we determined the DNA methylation patterns of grey and white matter of dorsolateral prefrontal cortex (Brodmann area 9), an important region for higher cognitive skills that is particularly affected in various neurological diseases. For avoiding interindividual differences, we analyzed white and grey matter from the same donor using whole genome bisulfite sequencing, and for validating their biological significance, we used Infinium HumanMethylation450 BeadChip and pyrosequencing in ten and twenty independent samples, respectively. The combination of these analysis indicated robust grey-white matter differences in DNA methylation. What is more, cell type-specific markers were enriched among the most differentially methylated genes. Interestingly, we also found an outstanding number of grey-white matter differentially methylated genes that have previously been associated with Alzheimer's, Parkinson's, and Huntington's disease, as well as Multiple and Amyotrophic lateral sclerosis. The data presented here thus constitute an important resource for future studies not only to gain insight into brain regional as well as grey and white matter differences, but also to unmask epigenetic alterations that might underlie neurological and neurodegenerative diseases.
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Affiliation(s)
- Jose Vicente Sanchez-Mut
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Brain Mind Institute, Lausanne, CH-1015, Switzerland
| | - Holger Heyn
- Single Cell Genomics Unit, Centre Nacional d'Anàlisi Genòmica, Barcelona, Catalonia, E-08028, Spain
| | - Enrique Vidal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona E-08003, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Raúl Delgado-Morales
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Barcelona, E-08908, Spain.,Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Universiteitssingel 50, Maastricht, MD 6200, The Netherlands
| | - Sebastian Moran
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Barcelona, E-08908, Spain
| | - Sergi Sayols
- Bioinformatics Core Facility, Institute of Molecular Biology, Mainz, D-55128, Germany
| | - Juan Sandoval
- Biomarkers and Precision Medicine Unit, Health Research Institute La Fe, Valencia, 46026, Spain
| | - Isidre Ferrer
- Institute of Neuropathology, Bellvitge University Hospital, University of Barcelona, Centre for Biomedical Research on Neurodegenerative Diseases (CIBERNED), E-08908 Hospitalet de Llobregat, Spain
| | - Manel Esteller
- Cancer Epigenetics Group, Cancer Epigenetics and Biology Program, Institut d'Investigació Biomedica de Bellvitge, Barcelona, E-08908, Spain
| | - Johannes Gräff
- School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Brain Mind Institute, Lausanne, CH-1015, Switzerland
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Romero V, Fornés A, Vidal E, Sánchez JA. Information Extraction in Handwritten Marriage Licenses Books Using the MGGI Methodology. Pattern Recognition and Image Analysis 2017. [DOI: 10.1007/978-3-319-58838-4_32] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Sanchez-Delgado M, Court F, Vidal E, Medrano J, Monteagudo-Sánchez A, Martin-Trujillo A, Tayama C, Iglesias-Platas I, Kondova I, Bontrop R, Poo-Llanillo ME, Marques-Bonet T, Nakabayashi K, Simón C, Monk D. Human Oocyte-Derived Methylation Differences Persist in the Placenta Revealing Widespread Transient Imprinting. PLoS Genet 2016; 12:e1006427. [PMID: 27835649 PMCID: PMC5106035 DOI: 10.1371/journal.pgen.1006427] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [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: 06/22/2016] [Accepted: 10/14/2016] [Indexed: 01/23/2023] Open
Abstract
Thousands of regions in gametes have opposing methylation profiles that are largely resolved during the post-fertilization epigenetic reprogramming. However some specific sequences associated with imprinted loci survive this demethylation process. Here we present the data describing the fate of germline-derived methylation in humans. With the exception of a few known paternally methylated germline differentially methylated regions (DMRs) associated with known imprinted domains, we demonstrate that sperm-derived methylation is reprogrammed by the blastocyst stage of development. In contrast a large number of oocyte-derived methylation differences survive to the blastocyst stage and uniquely persist as transiently methylated DMRs only in the placenta. Furthermore, we demonstrate that this phenomenon is exclusive to primates, since no placenta-specific maternal methylation was observed in mouse. Utilizing single cell RNA-seq datasets from human preimplantation embryos we show that following embryonic genome activation the maternally methylated transient DMRs can orchestrate imprinted expression. However despite showing widespread imprinted expression of genes in placenta, allele-specific transcriptional profiling revealed that not all placenta-specific DMRs coordinate imprinted expression and that this maternal methylation may be absent in a minority of samples, suggestive of polymorphic imprinted methylation. Differences in gamete DNA methylation is subject to genome-wide reprogramming during preimplantation development to establish an embryo with an epigenetic state compatible with totipotency. DNA sequences associated with imprinted differentially methylated regions (DMRs) are largely protected from this process, retaining their parent-of-origin epigenetic marks. By comparing the methylation profiles of human oocytes, sperm, blastocysts and various somatic tissues including placenta, we observe hundreds of CpG island sequences that maintain methylation on their maternal allele in blastocysts and placenta indicative of incomplete reprogramming. In some cases this maternal methylation influence transcription of nearby genes, revealing transient imprinting in embryos after genome-activation and in placenta. Strikingly, these placenta-specific DMRs are polymorphic between placenta samples with a minority of samples being robustly unmethylated on both alleles.
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Affiliation(s)
- Marta Sanchez-Delgado
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
| | - Franck Court
- Laboratoire GReD, CNRS, UMR6293, Clermont-Ferrand, France
| | - Enrique Vidal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Jose Medrano
- Fundación IVI-Instituto Universitario IVI- INCLIVA, Department of Obs/Gyn, Valenica University, Valencia, Spain
| | - Ana Monteagudo-Sánchez
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
| | - Alex Martin-Trujillo
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
| | - Chiharu Tayama
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Isabel Iglesias-Platas
- Neonatal service, Hospital Sant Joan de Déu, BCNatal Hospital Sant Joan de Déu i Clínic, Universitat de Barcelona, Barcelona, Spain
| | - Ivanela Kondova
- Biomedical Primate Research Center (BPRC), Rijswijk, The Netherlands
| | - Ronald Bontrop
- Biomedical Primate Research Center (BPRC), Rijswijk, The Netherlands
| | - Maria Eugenia Poo-Llanillo
- Fundación IVI-Instituto Universitario IVI- INCLIVA, Department of Obs/Gyn, Valenica University, Valencia, Spain
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), PRBB, Barcelona, Spain
- Catalan Institute of Research and Advanced Studies, (ICREA), Passeig de Lluís Companys, Barcelona, Spain
- Centro Nacional de Analisis Genomico (CRG-CNAG), Barcelona, Spain
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Carlos Simón
- Fundación IVI-Instituto Universitario IVI- INCLIVA, Department of Obs/Gyn, Valenica University, Valencia, Spain
| | - David Monk
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program, Institut d’Investigació Biomedica de Bellvitge, Hospital Duran i Reynals, Barcelona, Spain
- * E-mail:
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Lucariello M, Vidal E, Vidal S, Saez M, Roa L, Huertas D, Pineda M, Dalfó E, Dopazo J, Jurado P, Armstrong J, Esteller M. Whole exome sequencing of Rett syndrome-like patients reveals the mutational diversity of the clinical phenotype. Hum Genet 2016; 135:1343-1354. [PMID: 27541642 PMCID: PMC5065581 DOI: 10.1007/s00439-016-1721-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [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: 05/15/2016] [Accepted: 07/31/2016] [Indexed: 12/15/2022]
Abstract
Classical Rett syndrome (RTT) is a neurodevelopmental disorder where most of cases carry MECP2 mutations. Atypical RTT variants involve mutations in CDKL5 and FOXG1. However, a subset of RTT patients remains that do not carry any mutation in the described genes. Whole exome sequencing was carried out in a cohort of 21 female probands with clinical features overlapping with those of RTT, but without mutations in the customarily studied genes. Candidates were functionally validated by assessing the appearance of a neurological phenotype in Caenorhabditis elegans upon disruption of the corresponding ortholog gene. We detected pathogenic variants that accounted for the RTT-like phenotype in 14 (66.6 %) patients. Five patients were carriers of mutations in genes already known to be associated with other syndromic neurodevelopmental disorders. We determined that the other patients harbored mutations in genes that have not previously been linked to RTT or other neurodevelopmental syndromes, such as the ankyrin repeat containing protein ANKRD31 or the neuronal acetylcholine receptor subunit alpha-5 (CHRNA5). Furthermore, worm assays demonstrated that mutations in the studied candidate genes caused locomotion defects. Our findings indicate that mutations in a variety of genes contribute to the development of RTT-like phenotypes.
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Affiliation(s)
- Mario Lucariello
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, 08908, Barcelona, Catalonia, Spain
| | - Enrique Vidal
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, 08908, Barcelona, Catalonia, Spain
| | - Silvia Vidal
- Servei de Medicina Genètica i Molecular, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Esplugues De Llobregat, Catalonia, Spain
| | - Mauricio Saez
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, 08908, Barcelona, Catalonia, Spain
| | - Laura Roa
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, 08908, Barcelona, Catalonia, Spain
| | - Dori Huertas
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, 08908, Barcelona, Catalonia, Spain
| | - Mercè Pineda
- Fundació Hospital Sant Joan de Déu (HSJD), Barcelona, Catalonia, Spain
| | - Esther Dalfó
- Genetics Department, Bellvitge Biomedical Research Institute (IDIBELL), Barcelona, Catalonia, Spain
| | - Joaquin Dopazo
- Computational Genomics Department, Centro de Investigación Príncipe Felipe (CIPF), 46012, Valencia, Spain.,Bioinformatics of Rare Diseases (BIER), CIBER de Enfermedades Raras (CIBERER), Valencia, Spain.,Functional Genomics Node (INB) at CIPF, 46012, Valencia, Spain
| | - Paola Jurado
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, 08908, Barcelona, Catalonia, Spain.
| | - Judith Armstrong
- Servei de Medicina Genètica i Molecular, Institut de Recerca Pediàtrica Hospital Sant Joan de Déu, Esplugues De Llobregat, Catalonia, Spain. .,CIBER Enfermedades Raras, Barcelona, Catalonia, Spain. .,Department of Neurology, Hospital Sant Joan de Déu (HSJD), Barcelona, Catalonia, Spain.
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet, 08908, Barcelona, Catalonia, Spain. .,Department of Physiological Sciences, School of Medicine and Health Sciences, University of Barcelona, Barcelona, Catalonia, Spain. .,Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain.
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Guirao-Arrabal E, Santos F, Redel-Montero J, Vaquero JM, Cantisán S, Vidal E, Torre-Giménez Á, Rivero A, Torre-Cisneros J. Risk of tuberculosis after lung transplantation: the value of pretransplant chest computed tomography and the impact of mTOR inhibitors and azathioprine use. Transpl Infect Dis 2016; 18:512-9. [PMID: 27224905 DOI: 10.1111/tid.12555] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [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: 11/02/2015] [Revised: 01/16/2016] [Accepted: 02/29/2016] [Indexed: 01/24/2023]
Abstract
BACKGROUND It is necessary to determine the incidence and risk factors for tuberculosis (TB), as well as strategies to assess and treat latent tuberculosis infection (LTBI) in lung transplant recipients. METHODS A retrospective cohort study of 398 lung transplant recipients was performed. Episodes of TB were studied and the incidence rate was calculated. Logistic regression analysis was used to analyze specific variables as potential risk factors for TB. RESULTS Median follow-up was 558 days (range 1-6636). Six cases (1.5%) of TB were documented in 398 transplant patients. The incidence density of TB was 406.3 cases/10(5) patient-years (95% confidence interval [CI] 164.7-845), which is higher than in the general population (13.10 cases/10(5) person-years). All cases occurred in the period 1993-2006, when the tuberculin skin test (TST) and treatment of LTBI in positive TST patients were not part of the protocol. Pretransplant computed tomography (CT) showed residual lesions in 50% of patients who developed TB, although the TST was negative and the chest radiograph was inconclusive. Multivariate analysis identified the presence of residual lesions in the pretransplant chest CT (odds ratio [OR] 11.5, 95% CI 1.9-69.1, P = 0.008), use of azathioprine (OR 10.6, 95% CI 1.1-99.1, P = 0.038), and use of everolimus (OR 6.7, 95% CI 1.1-39.8, P = 0.036) as independent risk factors for TB. CONCLUSIONS Residual lesions in the pretransplant chest CTs and the use of azathioprine and mTOR inhibitors are associated with the risk of TB.
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Affiliation(s)
- E Guirao-Arrabal
- Infectious Diseases Unit, Hospital Universitario Reina Sofía, Córdoba, Spain.,Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Universidad de Córdoba (UCO), Córdoba, Spain
| | - F Santos
- Thoracic Surgery and Lung Transplantation Unit, Hospital Universitario Reina Sofía, Córdoba, Spain
| | - J Redel-Montero
- Thoracic Surgery and Lung Transplantation Unit, Hospital Universitario Reina Sofía, Córdoba, Spain
| | - J M Vaquero
- Thoracic Surgery and Lung Transplantation Unit, Hospital Universitario Reina Sofía, Córdoba, Spain
| | - S Cantisán
- Infectious Diseases Unit, Hospital Universitario Reina Sofía, Córdoba, Spain.,Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Universidad de Córdoba (UCO), Córdoba, Spain
| | - E Vidal
- Infectious Diseases Unit, Hospital Universitario Reina Sofía, Córdoba, Spain.,Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Universidad de Córdoba (UCO), Córdoba, Spain
| | - Á Torre-Giménez
- Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Universidad de Córdoba (UCO), Córdoba, Spain
| | - A Rivero
- Infectious Diseases Unit, Hospital Universitario Reina Sofía, Córdoba, Spain.,Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Universidad de Córdoba (UCO), Córdoba, Spain
| | - J Torre-Cisneros
- Infectious Diseases Unit, Hospital Universitario Reina Sofía, Córdoba, Spain.,Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Universidad de Córdoba (UCO), Córdoba, Spain
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Vizoso M, Puig M, Carmona FJ, Maqueda M, Gomez A, Labernardie A, Gabasa M, Mendizuri S, Ikemori R, Trepat X, Moran S, Vidal E, Reguart N, Perera A, Esteller M, Alcaraz J. Abstract 2763: DNA methylation profiling unveils TGF-β hyperresponse in tumor associated fibroblasts from lung cancer patients. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2763] [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
There is growing interest in defining the aberrant molecular differences between normal and tumor-associated fibroblasts (TAFs) that support tumor progression. For this purpose, we recently conducted a genome-wide DNA methylation profiling of TAFs and paired control fibroblasts (CFs) from non-small cell lung cancer (NSCLC) patients, and reported a widespread hypomethylation concomitantly with focal gain of DNA methylation; in addition, we found evidence that a fraction of lung TAFs are fibrocytes in origin. Of note, the aberrant epigenome of lung TAFs had a global impact in gene expression and a selective impact on the TGF-β pathway. To get insights on the functional implications of the latter impact, we analyzed the response of lung TAFs to exogenous TGF-β1 in terms of activation and contractility. We found a larger expression of a panel of activation markers including α-SMA and collagen-I in TAFs compared to control fibroblasts. Likewise, TGF-β1 elicited a larger contractility in TAFs than in CFs as assessed by traction force microscopy. These findings reveal that lung TAFs are hyperresponsive to TGF-β1, which may underlie the expansion and/or maintenance of the tumor-promoting desmoplastic stroma in lung cancer.
Citation Format: Miguel Vizoso, Marta Puig, F. Javier Carmona, María Maqueda, Antonio Gomez, Anna Labernardie, Marta Gabasa, Saioa Mendizuri, Rafael Ikemori, Xavier Trepat, Sebastian Moran, Enrique Vidal, Noemí Reguart, Alexandre Perera, Manel Esteller, Jordi Alcaraz. DNA methylation profiling unveils TGF-β hyperresponse in tumor associated fibroblasts from lung cancer patients. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2763.
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Affiliation(s)
- Miguel Vizoso
- 1Bellvitge Biomedical Research Institute-IDIBELL, L’Hospitalet de Llobregat, Barcelona, Spain
| | - Marta Puig
- 2University of Barcelona, Barcelona, Spain
| | - F. Javier Carmona
- 1Bellvitge Biomedical Research Institute-IDIBELL, L’Hospitalet de Llobregat, Barcelona, Spain
| | - María Maqueda
- 3Technical University of Catalonia (UPC), Barcelona, Spain
| | - Antonio Gomez
- 1Bellvitge Biomedical Research Institute-IDIBELL, L’Hospitalet de Llobregat, Barcelona, Spain
| | - Anna Labernardie
- 4Institute for Bioengineering of Catalonia (IBEC), Barcelona, Spain
| | | | | | | | - Xavier Trepat
- 4Institute for Bioengineering of Catalonia (IBEC), Barcelona, Spain
| | - Sebastian Moran
- 5Bellvitge Biomedical Research Institute-IDIBELL, L’Hospitalet de Llobregat, Spain
| | - Enrique Vidal
- 5Bellvitge Biomedical Research Institute-IDIBELL, L’Hospitalet de Llobregat, Spain
| | | | | | - Manel Esteller
- 1Bellvitge Biomedical Research Institute-IDIBELL, L’Hospitalet de Llobregat, Barcelona, Spain
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45
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Torre-Cisneros J, Aguado J, Caston J, Almenar L, Alonso A, Cantisán S, Carratalá J, Cervera C, Cordero E, Fariñas M, Fernández-Ruiz M, Fortún J, Frauca E, Gavaldá J, Hernández D, Herrero I, Len O, Lopez-Medrano F, Manito N, Marcos M, Martín-Dávila P, Monforte V, Montejo M, Moreno A, Muñoz P, Navarro D, Pérez-Romero P, Rodriguez-Bernot A, Rumbao J, San Juan R, Vaquero J, Vidal E. Management of cytomegalovirus infection in solid organ transplant recipients: SET/GESITRA-SEIMC/REIPI recommendations. Transplant Rev (Orlando) 2016; 30:119-43. [DOI: 10.1016/j.trre.2016.04.001] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 04/02/2016] [Accepted: 04/04/2016] [Indexed: 02/06/2023]
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Sigl V, Owusu-Boaitey K, Joshi PA, Kavirayani A, Wirnsberger G, Novatchkova M, Kozieradzki I, Schramek D, Edokobi N, Hersl J, Sampson A, Odai-Afotey A, Lazaro C, Gonzalez-Suarez E, Pujana MA, Cimba F, Heyn H, Vidal E, Cruickshank J, Berman H, Sarao R, Ticevic M, Uribesalgo I, Tortola L, Rao S, Tan Y, Pfeiler G, Lee EY, Bago-Horvath Z, Kenner L, Popper H, Singer C, Khokha R, Jones LP, Penninger JM. RANKL/RANK control Brca1 mutation- . Cell Res 2016; 26:761-74. [PMID: 27241552 PMCID: PMC5129883 DOI: 10.1038/cr.2016.69] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Revised: 05/24/2016] [Accepted: 05/25/2016] [Indexed: 12/18/2022] Open
Abstract
Breast cancer is the most common female cancer, affecting approximately one in eight women during their life-time. Besides environmental triggers and hormones, inherited mutations in the breast cancer 1 (BRCA1) or BRCA2 genes markedly increase the risk for the development of breast cancer. Here, using two different mouse models, we show that genetic inactivation of the key osteoclast differentiation factor RANK in the mammary epithelium markedly delayed onset, reduced incidence, and attenuated progression of Brca1;p53 mutation-driven mammary cancer. Long-term pharmacological inhibition of the RANK ligand RANKL in mice abolished the occurrence of Brca1 mutation-driven pre-neoplastic lesions. Mechanistically, genetic inactivation of Rank or RANKL/RANK blockade impaired proliferation and expansion of both murine Brca1;p53 mutant mammary stem cells and mammary progenitors from human BRCA1 mutation carriers. In addition, genome variations within the RANK locus were significantly associated with risk of developing breast cancer in women with BRCA1 mutations. Thus, RANKL/RANK control progenitor cell expansion and tumorigenesis in inherited breast cancer. These results present a viable strategy for the possible prevention of breast cancer in BRCA1 mutant patients.
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Affiliation(s)
- Verena Sigl
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna 1030, Austria
| | - Kwadwo Owusu-Boaitey
- Department of Biological Sciences, University of Maryland-Baltimore County, Baltimore, MD 21250, USA
| | - Purna A Joshi
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada M5G 1L7
| | - Anoop Kavirayani
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna 1030, Austria
| | - Gerald Wirnsberger
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna 1030, Austria
| | - Maria Novatchkova
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna 1030, Austria
| | - Ivona Kozieradzki
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna 1030, Austria
| | - Daniel Schramek
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario, Canada M5G 1X5.,Department of Molecular Genetics, University of Toronto, Ontario, Canada M5S 3E1
| | - Nnamdi Edokobi
- Department of Biological Sciences, University of Maryland-Baltimore County, Baltimore, MD 21250, USA
| | - Jerome Hersl
- Department of Pharmacology, University of Maryland, Baltimore, School of Medicine, Baltimore, MD 21201, USA
| | - Aishia Sampson
- Department of Pharmacology, University of Maryland, Baltimore, School of Medicine, Baltimore, MD 21201, USA
| | - Ashley Odai-Afotey
- Department of Biological Sciences, Cornell University, Ithaca, NY 14853, USA
| | - Conxi Lazaro
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Eva Gonzalez-Suarez
- Cancer Epigenetics and Biology Program, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Miguel A Pujana
- ProCURE, Catalan Institute of Oncology, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - For Cimba
- Department of Public and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Holger Heyn
- Cancer Epigenetics and Biology Program, IDIBELL, L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain
| | - Enrique Vidal
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, University Pompeu Fabra, Barcelona, Catalonia, Spain
| | - Jennifer Cruickshank
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, Ontario, Canada M5G 1Z5
| | - Hal Berman
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, Ontario, Canada M5G 1Z5
| | - Renu Sarao
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna 1030, Austria
| | - Melita Ticevic
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna 1030, Austria
| | - Iris Uribesalgo
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna 1030, Austria
| | - Luigi Tortola
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna 1030, Austria
| | - Shuan Rao
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna 1030, Austria
| | - Yen Tan
- Departments of Obstetrics and Gynecology and Comprehensive Cancer Center, Medical University of Vienna, Vienna 1090, Austria
| | - Georg Pfeiler
- Departments of Obstetrics and Gynecology and Comprehensive Cancer Center, Medical University of Vienna, Vienna 1090, Austria
| | - Eva Yhp Lee
- Department of Biological Chemistry, School of Medicine, University of California, Irvine, CA 92697, USA
| | - Zsuzsanna Bago-Horvath
- Department of Experimental Pathology and Pathology of Laboratory Animals, Medical University Vienna and University of Veterinary Medicine Vienna, Vienna 1090, Austria
| | - Lukas Kenner
- Department of Experimental Pathology and Pathology of Laboratory Animals, Medical University Vienna and University of Veterinary Medicine Vienna, Vienna 1090, Austria.,Ludwig Boltzmann Institute for Cancer Research (LBI-CR), Vienna, Austria
| | - Helmuth Popper
- Research Unit Molecular Lung and Pleura Pathology, Institute of Pathology, Medical University Graz, Graz 8010, Austria
| | - Christian Singer
- Departments of Obstetrics and Gynecology and Comprehensive Cancer Center, Medical University of Vienna, Vienna 1090, Austria
| | - Rama Khokha
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada M5G 1L7
| | - Laundette P Jones
- Department of Pharmacology, University of Maryland, Baltimore, School of Medicine, Baltimore, MD 21201, USA
| | - Josef M Penninger
- IMBA, Institute of Molecular Biotechnology of the Austrian Academy of Sciences, Vienna 1030, Austria
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Ibáñez M, Carbonell-Caballero J, García-Alonso L, Such E, Jiménez-Almazán J, Vidal E, Barragán E, López-Pavía M, LLop M, Martín I, Gómez-Seguí I, Montesinos P, Sanz MA, Dopazo J, Cervera J. The Mutational Landscape of Acute Promyelocytic Leukemia Reveals an Interacting Network of Co-Occurrences and Recurrent Mutations. PLoS One 2016; 11:e0148346. [PMID: 26886259 PMCID: PMC4757557 DOI: 10.1371/journal.pone.0148346] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [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: 11/12/2015] [Accepted: 01/15/2016] [Indexed: 12/02/2022] Open
Abstract
Preliminary Acute Promyelocytic Leukemia (APL) whole exome sequencing (WES) studies have identified a huge number of somatic mutations affecting more than a hundred different genes mainly in a non-recurrent manner, suggesting that APL is a heterogeneous disease with secondary relevant changes not yet defined. To extend our knowledge of subtle genetic alterations involved in APL that might cooperate with PML/RARA in the leukemogenic process, we performed a comprehensive analysis of somatic mutations in APL combining WES with sequencing of a custom panel of targeted genes by next-generation sequencing. To select a reduced subset of high confidence candidate driver genes, further in silico analysis were carried out. After prioritization and network analysis we found recurrent deleterious mutations in 8 individual genes (STAG2, U2AF1, SMC1A, USP9X, IKZF1, LYN, MYCBP2 and PTPN11) with a strong potential of being involved in APL pathogenesis. Our network analysis of multiple mutations provides a reliable approach to prioritize genes for additional analysis, improving our knowledge of the leukemogenesis interactome. Additionally, we have defined a functional module in the interactome of APL. The hypothesis is that the number, or the specific combinations, of mutations harbored in each patient might not be as important as the disturbance caused in biological key functions, triggered by several not necessarily recurrent mutations.
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Affiliation(s)
- Mariam Ibáñez
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | | | - Luz García-Alonso
- Computational Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Esperanza Such
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Jorge Jiménez-Almazán
- Computational Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Enrique Vidal
- Computational Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Eva Barragán
- Laboratory of Molecular Biology, Department of Clinical Chemistry, Hospital Universitario La Fe, Valencia, Spain
| | - María López-Pavía
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Marta LLop
- Laboratory of Molecular Biology, Department of Clinical Chemistry, Hospital Universitario La Fe, Valencia, Spain
| | - Iván Martín
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Inés Gómez-Seguí
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Pau Montesinos
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Miguel A. Sanz
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
| | - Joaquín Dopazo
- Computational Genomics Department, Centro de Investigación Príncipe Felipe, Valencia, Spain
- Functional Genomics Node, Spanish National Institute of Bioinformatics at CIPF, 46012, Valencia, Spain
- Bioinformatics of Rare Diseases (BIER), CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
- * E-mail: (JC); (JD)
| | - José Cervera
- Hematology Service, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- Genetics Unit, Hospital Universitario y Politécnico La Fe, Valencia, Spain
- * E-mail: (JC); (JD)
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Heyn H, Vidal E, Ferreira HJ, Vizoso M, Sayols S, Gomez A, Moran S, Boque-Sastre R, Guil S, Martinez-Cardus A, Lin CY, Royo R, Sanchez-Mut JV, Martinez R, Gut M, Torrents D, Orozco M, Gut I, Young RA, Esteller M. Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer. Genome Biol 2016; 17:11. [PMID: 26813288 PMCID: PMC4728783 DOI: 10.1186/s13059-016-0879-2] [Citation(s) in RCA: 155] [Impact Index Per Article: 19.4] [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: 11/30/2015] [Accepted: 01/12/2016] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND One of the hallmarks of cancer is the disruption of gene expression patterns. Many molecular lesions contribute to this phenotype, and the importance of aberrant DNA methylation profiles is increasingly recognized. Much of the research effort in this area has examined proximal promoter regions and epigenetic alterations at other loci are not well characterized. RESULTS Using whole genome bisulfite sequencing to examine uncharted regions of the epigenome, we identify a type of far-reaching DNA methylation alteration in cancer cells of the distal regulatory sequences described as super-enhancers. Human tumors undergo a shift in super-enhancer DNA methylation profiles that is associated with the transcriptional silencing or the overactivation of the corresponding target genes. Intriguingly, we observe locally active fractions of super-enhancers detectable through hypomethylated regions that suggest spatial variability within the large enhancer clusters. Functionally, the DNA methylomes obtained suggest that transcription factors contribute to this local activity of super-enhancers and that trans-acting factors modulate DNA methylation profiles with impact on transforming processes during carcinogenesis. CONCLUSIONS We develop an extensive catalogue of human DNA methylomes at base resolution to better understand the regulatory functions of DNA methylation beyond those of proximal promoter gene regions. CpG methylation status in normal cells points to locally active regulatory sites at super-enhancers, which are targeted by specific aberrant DNA methylation events in cancer, with putative effects on the expression of downstream genes.
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Affiliation(s)
- Holger Heyn
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain.
| | - Enrique Vidal
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain.
| | - Humberto J Ferreira
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain.
| | - Miguel Vizoso
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain.
| | - Sergi Sayols
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain.
| | - Antonio Gomez
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain.
| | - Sebastian Moran
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain.
| | - Raquel Boque-Sastre
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain.
| | - Sonia Guil
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain.
| | - Anna Martinez-Cardus
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain.
| | - Charles Y Lin
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA, 02142, USA. .,Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,Department of Medical Oncology, Dana-Farber Cancer Institute, 44 Binney Street, Boston, MA, 02115, USA.
| | - Romina Royo
- Joint Biomedical Research Institute-Barcelona Supercomputing Center (IRB-BSC) Program in Computational Biology, Baldiri Reixac 10-12, 08028, Barcelona, Catalonia, Spain.
| | - Jose V Sanchez-Mut
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain.
| | - Ramon Martinez
- Department of Neurosurgery, University of Goettingen, Robert Koch. Str. 40, 37075, Goettingen, Germany.
| | - Marta Gut
- Centre Nacional d'Anàlisi Genòmica, Barcelona, Catalonia, Spain.
| | - David Torrents
- Joint Biomedical Research Institute-Barcelona Supercomputing Center (IRB-BSC) Program in Computational Biology, Baldiri Reixac 10-12, 08028, Barcelona, Catalonia, Spain. .,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Catalonia, Spain.
| | - Modesto Orozco
- Joint Biomedical Research Institute-Barcelona Supercomputing Center (IRB-BSC) Program in Computational Biology, Baldiri Reixac 10-12, 08028, Barcelona, Catalonia, Spain. .,Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10-12, 08028, Barcelona, Catalonia, Spain. .,Department of Biochemistry and Molecular Biology, University of Barcelona, 08028, Barcelona, Catalonia, Spain.
| | - Ivo Gut
- Centre Nacional d'Anàlisi Genòmica, Barcelona, Catalonia, Spain.
| | - Richard A Young
- Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA, 02142, USA. .,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), 08908 L'Hospitalet de Llobregat, Barcelona, Catalonia, Spain. .,Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Catalonia, Spain. .,Department of Physiological Sciences II, School of Medicine, University of Barcelona, 08036, Barcelona, Catalonia, Spain.
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Villegas M, Müller H, García Seco de Herrera A, Schaer R, Bromuri S, Gilbert A, Piras L, Wang J, Yan F, Ramisa A, Dellandrea E, Gaizauskas R, Mikolajczyk K, Puigcerver J, Toselli AH, Sánchez JA, Vidal E. General Overview of ImageCLEF at the CLEF 2016 Labs. Lecture Notes in Computer Science 2016. [DOI: 10.1007/978-3-319-44564-9_25] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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50
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Vidal E, Grau-Roma L, Tolosa E, Espinar S, Pérez de Val B, Nofrarías M, Alba A, Allepuz A, López-Soria S, Martínez J, Abarca L, Castellà J, Manteca X, Casanova M, Isidoro-Ayza M, Galindo-Cardiel I, Soto S, Dolz R, Majó N, Ramis T, Segalés J, Mas L, Picart L, Marco A, Domingo M. The Catalan Slaughterhouse Support Network (SESC): An Innovative Diagnostic, Surveillance and Educational Tool. J Comp Pathol 2016. [DOI: 10.1016/j.jcpa.2015.10.010] [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: 10/22/2022]
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