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Abascal F, Corvelo A, Cruz F, Villanueva-Cañas JL, Vlasova A, Marcet-Houben M, Martínez-Cruz B, Cheng JY, Prieto P, Quesada V, Quilez J, Li G, García F, Rubio-Camarillo M, Frias L, Ribeca P, Capella-Gutiérrez S, Rodríguez JM, Câmara F, Lowy E, Cozzuto L, Erb I, Tress ML, Rodriguez-Ales JL, Ruiz-Orera J, Reverter F, Casas-Marce M, Soriano L, Arango JR, Derdak S, Galán B, Blanc J, Gut M, Lorente-Galdos B, Andrés-Nieto M, López-Otín C, Valencia A, Gut I, García JL, Guigó R, Murphy WJ, Ruiz-Herrera A, Marques-Bonet T, Roma G, Notredame C, Mailund T, Albà MM, Gabaldón T, Alioto T, Godoy JA. Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx. Genome Biol 2016; 17:251. [PMID: 27964752 PMCID: PMC5155386 DOI: 10.1186/s13059-016-1090-1] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 10/25/2016] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective conservation. The Iberian lynx (Lynx pardinus) is the most endangered felid and a unique example of a species on the brink of extinction. RESULTS We generate the first annotated draft of the Iberian lynx genome and carry out genome-based analyses of lynx demography, evolution, and population genetics. We identify a series of severe population bottlenecks in the history of the Iberian lynx that predate its known demographic decline during the 20th century and have greatly impacted its genome evolution. We observe drastically reduced rates of weak-to-strong substitutions associated with GC-biased gene conversion and increased rates of fixation of transposable elements. We also find multiple signatures of genetic erosion in the two remnant Iberian lynx populations, including a high frequency of potentially deleterious variants and substitutions, as well as the lowest genome-wide genetic diversity reported so far in any species. CONCLUSIONS The genomic features observed in the Iberian lynx genome may hamper short- and long-term viability through reduced fitness and adaptive potential. The knowledge and resources developed in this study will boost the research on felid evolution and conservation genomics and will benefit the ongoing conservation and management of this emblematic species.
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Affiliation(s)
- Federico Abascal
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - André Corvelo
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Fernando Cruz
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
- Department of Integrative Ecology, Doñana Biological Station (EBD), Spanish National Research Council (CSIC), C/ Americo Vespucio, s/n, 41092, Sevilla, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - José L Villanueva-Cañas
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Anna Vlasova
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Marina Marcet-Houben
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Begoña Martínez-Cruz
- Department of Integrative Ecology, Doñana Biological Station (EBD), Spanish National Research Council (CSIC), C/ Americo Vespucio, s/n, 41092, Sevilla, Spain
| | - Jade Yu Cheng
- Bioinformatics Research Centre, Aarhus University, C.F. Møllers Allé 8, 8000, Aarhus, Denmark
| | - Pablo Prieto
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Víctor Quesada
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006, Oviedo, Spain
| | - Javier Quilez
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, 08003, Barcelona, Spain
| | - Gang Li
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Francisca García
- Servei de Cultius Cel.lulars (SCC, SCAC), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Miriam Rubio-Camarillo
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Leonor Frias
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Paolo Ribeca
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Salvador Capella-Gutiérrez
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - José M Rodríguez
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
- National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Francisco Câmara
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Ernesto Lowy
- Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Luca Cozzuto
- Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Ionas Erb
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Michael L Tress
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Jose L Rodriguez-Ales
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Jorge Ruiz-Orera
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Ferran Reverter
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Mireia Casas-Marce
- Department of Integrative Ecology, Doñana Biological Station (EBD), Spanish National Research Council (CSIC), C/ Americo Vespucio, s/n, 41092, Sevilla, Spain
| | - Laura Soriano
- Department of Integrative Ecology, Doñana Biological Station (EBD), Spanish National Research Council (CSIC), C/ Americo Vespucio, s/n, 41092, Sevilla, Spain
| | - Javier R Arango
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006, Oviedo, Spain
| | - Sophia Derdak
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Beatriz Galán
- Department of Environmental Biology, Center for Biological Research (CIB), Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Julie Blanc
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Belen Lorente-Galdos
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, 08003, Barcelona, Spain
| | - Marta Andrés-Nieto
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología (IUOPA), Universidad de Oviedo, 33006, Oviedo, Spain
| | - Alfonso Valencia
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
- National Bioinformatics Institute (INB), Spanish National Cancer Research Centre (CNIO), Madrid, 28029, Spain
| | - Ivo Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - José L García
- Department of Environmental Biology, Center for Biological Research (CIB), Spanish National Research Council (CSIC), Ramiro de Maeztu 9, 28040, Madrid, Spain
| | - Roderic Guigó
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Computational Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - William J Murphy
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Aurora Ruiz-Herrera
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain
- Departament de Biologia Cel.lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, 08193, Cerdanyola del Vallès, Spain
| | - Tomas Marques-Bonet
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, PRBB, Doctor Aiguader, 88, 08003, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Guglielmo Roma
- Bioinformatics Core Facility, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Cedric Notredame
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Thomas Mailund
- Bioinformatics Research Centre, Aarhus University, C.F. Møllers Allé 8, 8000, Aarhus, Denmark
| | - M Mar Albà
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Research Institute (IMIM), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Tyler Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - José A Godoy
- Department of Integrative Ecology, Doñana Biological Station (EBD), Spanish National Research Council (CSIC), C/ Americo Vespucio, s/n, 41092, Sevilla, Spain.
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Oliveras-Ferraros C, Vazquez-Martin A, Cuyàs E, Corominas-Faja B, Rodríguez-Gallego E, Fernández-Arroyo S, Martin-Castillo B, Joven J, Menendez JA. Acquired resistance to metformin in breast cancer cells triggers transcriptome reprogramming toward a degradome-related metastatic stem-like profile. Cell Cycle 2014; 13:1132-44. [PMID: 24553122 DOI: 10.4161/cc.27982] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Therapeutic interventions based on metabolic inhibitor-based therapies are expected to be less prone to acquired resistance. However, there has not been any study assessing the possibility that the targeting of the tumor cell metabolism may result in unforeseeable resistance. We recently established a pre-clinical model of estrogen-dependent MCF-7 breast cancer cells that were chronically adapted to grow (> 10 months) in the presence of graded, millimolar concentrations of the anti-diabetic biguanide metformin, an AMPK agonist/mTOR inhibitor that has been evaluated in multiple in vitro and in vivo cancer studies and is now being tested in clinical trials. To assess what impact the phenomenon of resistance might have on the metformin-like "dirty" drugs that are able to simultaneously hit several metabolic pathways, we employed the ingenuity pathway analysis (IPA) software to functionally interpret the data from Agilent whole-human genome arrays in the context of biological processes, networks, and pathways. Our findings establish, for the first time, that a "global" targeting of metabolic reprogramming using metformin certainly imposes a great selective pressure for the emergence of new breast cancer cellular states. Intriguingly, acquired resistance to metformin appears to trigger a transcriptome reprogramming toward a metastatic stem-like profile, as many genes encoding the components of the degradome (KLK11, CTSF, FREM1, BACE-2, CASP, TMPRSS4, MMP16, HTRA1), cancer cell migration and invasion factors (TP63, WISP2, GAS3, DKK1, BCAR3, PABPC1, MUC1, SPARCL1, SEMA3B, SEMA6A), stem cell markers (DCLK1, FAK), and key pro-metastatic lipases (MAGL and Cpla2) were included in the signature. Because this convergent activation of pathways underlying tumor microenvironment interactions occurred in low-proliferative cancer cells exhibiting a notable downregulation of the G 2/M DNA damage checkpoint regulators that maintain genome stability (CCNB1, CCNB2, CDC20, CDC25C, AURKA, AURKB, BUB1, CENP-A, CENP-M) and pro-autophagic features (i.e., TRAIL upregulation and BCL-2 downregulation), it appears that the unique mechanism of acquired resistance to metformin has opposing roles in growth and metastatic dissemination. While refractoriness to metformin limits breast cancer cell growth, likely due to aberrant mitotic/cytokinetic machinery and accelerated autophagy, it notably increases the potential of metastatic dissemination by amplifying the number of pro-migratory and stemness inputs via the activation of a significant number of proteases and EMT regulators. Future studies should elucidate whether our findings using supra-physiological concentrations of metformin mechanistically mimic the ultimate processes that could paradoxically occur in a polyploid, senescent-autophagic scenario triggered by the chronic metabolic stresses that occur during cancer development and after treatment with cancer drugs.
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Affiliation(s)
- Cristina Oliveras-Ferraros
- Metabolism & Cancer Group; Translational Research Laboratory; Catalan Institute of Oncology-Girona (ICO-Girona); Girona, Spain; Molecular Oncology; Girona Biomedical Research Institute (IDIBGI); Girona, Spain
| | - Alejandro Vazquez-Martin
- Metabolism & Cancer Group; Translational Research Laboratory; Catalan Institute of Oncology-Girona (ICO-Girona); Girona, Spain; Molecular Oncology; Girona Biomedical Research Institute (IDIBGI); Girona, Spain
| | - Elisabet Cuyàs
- Metabolism & Cancer Group; Translational Research Laboratory; Catalan Institute of Oncology-Girona (ICO-Girona); Girona, Spain; Molecular Oncology; Girona Biomedical Research Institute (IDIBGI); Girona, Spain
| | - Bruna Corominas-Faja
- Metabolism & Cancer Group; Translational Research Laboratory; Catalan Institute of Oncology-Girona (ICO-Girona); Girona, Spain; Molecular Oncology; Girona Biomedical Research Institute (IDIBGI); Girona, Spain
| | - Esther Rodríguez-Gallego
- Unitat de Recerca Biomèdica; Hospital Universitari Sant Joan and Hospital Universitari Joan XXIII; Institut d'Investigació Sanitària Pere Virgili; Universitat Rovira i Virgili; Reus, Spain
| | - Salvador Fernández-Arroyo
- Unitat de Recerca Biomèdica; Hospital Universitari Sant Joan and Hospital Universitari Joan XXIII; Institut d'Investigació Sanitària Pere Virgili; Universitat Rovira i Virgili; Reus, Spain
| | - Begoña Martin-Castillo
- Molecular Oncology; Girona Biomedical Research Institute (IDIBGI); Girona, Spain; Unit of Clinical Research; Catalan Institute of Oncology-Girona (ICO-Girona); Girona, Spain
| | - Jorge Joven
- Unitat de Recerca Biomèdica; Hospital Universitari Sant Joan and Hospital Universitari Joan XXIII; Institut d'Investigació Sanitària Pere Virgili; Universitat Rovira i Virgili; Reus, Spain
| | - Javier A Menendez
- Metabolism & Cancer Group; Translational Research Laboratory; Catalan Institute of Oncology-Girona (ICO-Girona); Girona, Spain; Molecular Oncology; Girona Biomedical Research Institute (IDIBGI); Girona, Spain
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