1
|
Hart M, Kern F, Fecher-Trost C, Krammes L, Aparicio E, Engel A, Hirsch P, Wagner V, Keller V, Schmartz GP, Rheinheimer S, Diener C, Fischer U, Mayer J, Meyer MR, Flockerzi V, Keller A, Meese E. Experimental capture of miRNA targetomes: disease-specific 3'UTR library-based miRNA targetomics for Parkinson's disease. Exp Mol Med 2024; 56:935-945. [PMID: 38556547 PMCID: PMC11059366 DOI: 10.1038/s12276-024-01202-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 01/12/2024] [Accepted: 01/30/2024] [Indexed: 04/02/2024] Open
Abstract
The identification of targetomes remains a challenge given the pleiotropic effect of miRNAs, the limited effects of miRNAs on individual targets, and the sheer number of estimated miRNA-target gene interactions (MTIs), which is around 44,571,700. Currently, targetome identification for single miRNAs relies on computational evidence and functional studies covering smaller numbers of targets. To ensure that the targetome analysis could be experimentally verified by functional assays, we employed a systematic approach and explored the targetomes of four miRNAs (miR-129-5p, miR-129-1-3p, miR-133b, and miR-873-5p) by analyzing 410 predicted target genes, both of which were previously associated with Parkinson's disease (PD). After performing 13,536 transfections, we validated 442 of the 705 putative MTIs (62,7%) through dual luciferase reporter assays. These analyses increased the number of validated MTIs by at least 2.1-fold for miR-133b and by a maximum of 24.3-fold for miR-873-5p. Our study contributes to the experimental capture of miRNA targetomes by addressing i) the ratio of experimentally verified MTIs to predicted MTIs, ii) the sizes of disease-related miRNA targetomes, and iii) the density of MTI networks. A web service to support the analyses on the MTI level is available online ( https://ccb-web.cs.uni-saarland.de/utr-seremato ), and all the data have been added to the miRATBase database ( https://ccb-web.cs.uni-saarland.de/miratbase ).
Collapse
Affiliation(s)
- Martin Hart
- Human Genetics, Saarland University, 66421, Homburg, Germany.
| | - Fabian Kern
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarland University Campus, Saarbrücken, Germany
| | - Claudia Fecher-Trost
- Department of Experimental and Clinical Pharmacology & Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, 66421, Homburg, Germany
| | - Lena Krammes
- Human Genetics, Saarland University, 66421, Homburg, Germany
| | - Ernesto Aparicio
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Annika Engel
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Pascal Hirsch
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Viktoria Wagner
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
| | - Verena Keller
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
- Department for Internal Medicine II, Saarland University Hospital, 66421, Homburg, Germany
| | | | | | - Caroline Diener
- Human Genetics, Saarland University, 66421, Homburg, Germany
| | - Ulrike Fischer
- Human Genetics, Saarland University, 66421, Homburg, Germany
| | - Jens Mayer
- Human Genetics, Saarland University, 66421, Homburg, Germany
| | - Markus R Meyer
- Department of Experimental and Clinical Pharmacology & Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, 66421, Homburg, Germany
| | - Veit Flockerzi
- Department of Experimental and Clinical Pharmacology & Toxicology, Institute of Experimental and Clinical Pharmacology and Toxicology, Center for Molecular Signaling (PZMS), Saarland University, 66421, Homburg, Germany
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, 66123, Saarbrücken, Germany
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Saarland University Campus, Saarbrücken, Germany
| | - Eckart Meese
- Human Genetics, Saarland University, 66421, Homburg, Germany
| |
Collapse
|
2
|
García-Ortega MB, Aparicio E, Griñán-Lisón C, Jiménez G, López-Ruiz E, Palacios JL, Ruiz-Alcalá G, Alba C, Martínez A, Boulaiz H, Perán M, Hackenberg M, Bragança J, Calado SM, Marchal JA, García MÁ. Interferon-Alpha Decreases Cancer Stem Cell Properties and Modulates Exosomes in Malignant Melanoma. Cancers (Basel) 2023; 15:3666. [PMID: 37509327 PMCID: PMC10377490 DOI: 10.3390/cancers15143666] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/06/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023] Open
Abstract
Malignant melanoma (MM) can spread to other organs and is resistant in part due to the presence of cancer stem cell subpopulations (CSCs). While a controversial high dose of interferon-alpha (IFN-α) has been used to treat non-metastatic high-risk melanoma, it comes with undesirable side effects. In this study, we evaluated the effect of low and high doses of IFN-α on CSCs by analyzing ALDH activity, side population and specific surface markers in established and patient-derived primary cell lines. We also assessed the clonogenicity, migration and tumor initiation capacities of IFN-α treated CSCs. Additionally, we investigated genomic modulations related to stemness properties using microRNA sequencing and microarrays. The effect of IFN-α on CSCs-derived exosomes was also analyzed using NanoSight and liquid chromatography (LC-HRMS)-based metabolomic analysis, among others. Our results showed that even low doses of IFN-α reduced CSC formation and stemness properties, and led to a significant decrease in the ability to form tumors in mice xenotransplants. IFN-α also modulated the expression of genes and microRNAs involved in several cancer processes and metabolomics of released exosomes. Our work suggests the utility of low doses of interferon, combined with the analysis of metabolic biomarkers, as a potential clinical approach against the aggressiveness of CSCs in melanoma.
Collapse
Affiliation(s)
- María Belén García-Ortega
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071 Granada, Spain
- Department of Oncology, Virgen de las Nieves University Hospital, 18014 Granada, Spain
| | - Ernesto Aparicio
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071 Granada, Spain
- Department of Genetics, University of Granada, 18100 Granada, Spain
| | - Carmen Griñán-Lisón
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, 18011 Granada, Spain
- GENYO-Centre for Genomics and Oncological Research-Pfizer/University of Granada/Andalusian Regional Government, 18016 Granada, Spain
| | - Gema Jiménez
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071 Granada, Spain
- Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - Elena López-Ruiz
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071 Granada, Spain
- Department of Health Sciences, University of Jaén, Campus de las Lagunillas SN, 23071 Jaén, Spain
| | - José Luis Palacios
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071 Granada, Spain
| | - Gloria Ruiz-Alcalá
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071 Granada, Spain
| | - Cristina Alba
- Department of Oncology, Virgen de las Nieves University Hospital, 18014 Granada, Spain
| | - Antonio Martínez
- Department of Dermatology, Virgen de las Nieves University Hospital, 18014 Granada, Spain
| | - Houria Boulaiz
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071 Granada, Spain
- Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - Macarena Perán
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071 Granada, Spain
- Department of Health Sciences, University of Jaén, Campus de las Lagunillas SN, 23071 Jaén, Spain
| | - Michael Hackenberg
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071 Granada, Spain
- Department of Genetics, University of Granada, 18100 Granada, Spain
| | - José Bragança
- Algarve Biomedical Center Research Institute (ABC-RI), Universidade do Algarve, 8005-139 Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, 8005-139 Faro, Portugal
- Champalimaud Research Program, Champalimaud Center for the Unknown, 1400-038 Lisbon, Portugal
| | - Sofia M Calado
- Algarve Biomedical Center Research Institute (ABC-RI), Universidade do Algarve, 8005-139 Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, 8005-139 Faro, Portugal
- Champalimaud Research Program, Champalimaud Center for the Unknown, 1400-038 Lisbon, Portugal
| | - Juan A Marchal
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071 Granada, Spain
- Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - María Ángel García
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071 Granada, Spain
- Department of Molecular Biology and Biochemistry III and Immunology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| |
Collapse
|
3
|
García-Ortega MB, Aparicio E, Griñán-Lisón C, Jiménez G, López-Ruiz E, Palacios JL, Ruiz-Alcalá G, Alba C, Martínez A, Boulaiz H, Perán M, Hackenberg M, Bragança J, Calado SM, Marchal JA, García MÁ. Interferon-Alpha Decreases Cancer Stem Cell Properties and Modulates Exosomes in Malignant Melanoma. Cancers (Basel) 2023; 15:3666. [DOI: https:/doi.org/10.3390/cancers15143666] [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: 09/01/2023] Open
Abstract
Malignant melanoma (MM) can spread to other organs and is resistant in part due to the presence of cancer stem cell subpopulations (CSCs). While a controversial high dose of interferon-alpha (IFN-α) has been used to treat non-metastatic high-risk melanoma, it comes with undesirable side effects. In this study, we evaluated the effect of low and high doses of IFN-α on CSCs by analyzing ALDH activity, side population and specific surface markers in established and patient-derived primary cell lines. We also assessed the clonogenicity, migration and tumor initiation capacities of IFN-α treated CSCs. Additionally, we investigated genomic modulations related to stemness properties using microRNA sequencing and microarrays. The effect of IFN-α on CSCs-derived exosomes was also analyzed using NanoSight and liquid chromatography (LC-HRMS)-based metabolomic analysis, among others. Our results showed that even low doses of IFN-α reduced CSC formation and stemness properties, and led to a significant decrease in the ability to form tumors in mice xenotransplants. IFN-α also modulated the expression of genes and microRNAs involved in several cancer processes and metabolomics of released exosomes. Our work suggests the utility of low doses of interferon, combined with the analysis of metabolic biomarkers, as a potential clinical approach against the aggressiveness of CSCs in melanoma.
Collapse
Affiliation(s)
- María Belén García-Ortega
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
- Department of Oncology, Virgen de las Nieves University Hospital, 18014 Granada, Spain
| | - Ernesto Aparicio
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
- Department of Genetics, University of Granada, 18100 Granada, Spain
| | - Carmen Griñán-Lisón
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, 18011 Granada, Spain
- GENYO-Centre for Genomics and Oncological Research-Pfizer/University of Granada/Andalusian Regional Government, 18016 Granada, Spain
| | - Gema Jiménez
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
- Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - Elena López-Ruiz
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
- Department of Health Sciences, University of Jaén, Campus de las Lagunillas SN, 23071 Jaén, Spain
| | - José Luis Palacios
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
| | - Gloria Ruiz-Alcalá
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
| | - Cristina Alba
- Department of Oncology, Virgen de las Nieves University Hospital, 18014 Granada, Spain
| | - Antonio Martínez
- Department of Dermatology, Virgen de las Nieves University Hospital, 18014 Granada, Spain
| | - Houria Boulaiz
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
- Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - Macarena Perán
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
- Department of Health Sciences, University of Jaén, Campus de las Lagunillas SN, 23071 Jaén, Spain
| | - Michael Hackenberg
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
- Department of Genetics, University of Granada, 18100 Granada, Spain
| | - José Bragança
- Algarve Biomedical Center Research Institute (ABC-RI), Universidade do Algarve, 8005-139 Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, 8005-139 Faro, Portugal
- Champalimaud Research Program, Champalimaud Center for the Unknown, 1400-038 Lisbon, Portugal
| | - Sofia M. Calado
- Algarve Biomedical Center Research Institute (ABC-RI), Universidade do Algarve, 8005-139 Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, 8005-139 Faro, Portugal
- Champalimaud Research Program, Champalimaud Center for the Unknown, 1400-038 Lisbon, Portugal
| | - Juan A. Marchal
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
- Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - María Ángel García
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
- Department of Molecular Biology and Biochemistry III and Immunology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| |
Collapse
|
4
|
González-Gloria KD, Rodríguez-Jasso RM, Rosero-Chasoy G, Shiva, Kostas ET, Aparicio E, Sanchez A, López-Sandin I, Ruiz HA. Scale-up of hydrothermal processing: Liquid hot water and pilot-scale tubular steam explosion batch reactor for bioethanol production using macroalgae Sargassum spp biomass. Bioresour Technol 2023; 369:128448. [PMID: 36513304 DOI: 10.1016/j.biortech.2022.128448] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 10/01/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Sargassum spp. is a biomass that can potentially use as an alternative for bioethanol production. Hydrothermal processes (liquid hot water and steam explosion pretreatment) were carried out at different operational conditions. Enzymatic hydrolysis performed a preliminary test with different ratios 1:1 and 1:2 (cellulases and hemicellulases) of enzyme loading, once selected 1:2 ratio was obtained conversion yield of 99.91% and therefore carried a scale-up in stirred bioreactor getting 95.92% saccharification yield. Pre-simultaneous saccharification and fermentation strategy was performed in a continuous stirred tank bioreactor (CSTBR), producing ethanol yield of 57.69%, and for simultaneous saccharification and fermentation strategy was performed in a bubble column reactor was 71.37% ethanol yield. The energy efficiency was analyzed in different scenarios; the best data was 30.19 (gsugar/MJ) in the bioreactor enzymatic hydrolysis process. This development allows for establishing the conditions for a third-generation biorefinery on a circular bioeconomy using Sargassum biomass.
Collapse
Affiliation(s)
- K D González-Gloria
- Biorefinery Group, Food Research Department, School of Chemistry, Autonomous University of Coahuila, Saltillo, 25280, Coahuila, Mexico
| | - Rosa M Rodríguez-Jasso
- Biorefinery Group, Food Research Department, School of Chemistry, Autonomous University of Coahuila, Saltillo, 25280, Coahuila, Mexico
| | - Gilver Rosero-Chasoy
- Biorefinery Group, Food Research Department, School of Chemistry, Autonomous University of Coahuila, Saltillo, 25280, Coahuila, Mexico
| | - Shiva
- Biorefinery Group, Food Research Department, School of Chemistry, Autonomous University of Coahuila, Saltillo, 25280, Coahuila, Mexico
| | - Emily T Kostas
- The Advanced Centre of Biochemical Engineering, Department of Biochemical Engineering, University College London, Gower Street, London, WC1E 6BT, UK
| | - E Aparicio
- Biorefinery Group, Food Research Department, School of Chemistry, Autonomous University of Coahuila, Saltillo, 25280, Coahuila, Mexico
| | - Arturo Sanchez
- Laboratorio de Futuros en Bioenergía, Unidad Guadalajara de Ingeniería Avanzada, Centro de Investigación y Estudios Avanzados (CINVESTAV), Zapopan, Jalisco, 45019, Mexico
| | - Iosvany López-Sandin
- Biorefinery Group, Food Research Department, School of Chemistry, Autonomous University of Coahuila, Saltillo, 25280, Coahuila, Mexico
| | - Héctor A Ruiz
- Biorefinery Group, Food Research Department, School of Chemistry, Autonomous University of Coahuila, Saltillo, 25280, Coahuila, Mexico.
| |
Collapse
|
5
|
Flores E, Mella JD, Aparicio E, Gonzalez RI, Parra C, Bringa EM, Munoz F. Inducing a topological transition in graphene nanoribbon superlattices by external strain. Phys Chem Chem Phys 2022; 24:7134-7143. [PMID: 35262146 DOI: 10.1039/d2cp00038e] [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: 11/21/2022]
Abstract
Armchair graphene nanoribbons, when forming a superlattice, can be classified into different topological phases, with or without edge states. By means of tight-binding and classical molecular dynamics (MD) simulations, we studied the electronic and mechanical properties of some of these superlattices. MD shows that fracture in modulated superlattices is brittle, as for unmodulated ribbons, and occurs at the thinner regions, with staggered superlattices achieving a larger fracture strain than inline superlattices. We found a general mechanism to induce a topological transition with strain, related to the electronic properties of each segment of the superlattice, and by studying the sublattice polarization we were able to characterize the transition and the response of these states to the strain. For the cases studied in detail here, the topological transition occurred at ∼3-5% strain, well below the fracture strain. The topological states of the superlattice - if present - are robust to strain even close to fracture. The topological transition was characterized by means of the sublattice polarization of the states.
Collapse
Affiliation(s)
- E Flores
- Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - José D Mella
- Departamento de Física, Facultad de Ciencias Físicas y Matemáticas, Universidad de Chile, Santiago, Chile
| | - E Aparicio
- CONICET and Universidad de Mendoza, Mendoza, 5500, Argentina
| | - R I Gonzalez
- Centro de Nanotecnología Aplicada, Facultad de Ciencias, Universidad Mayor, Santiago, Chile. .,Centro para el Desarrollo de la Nanociencia y la Nanotecnología, CEDENNA, Santiago, Chile
| | - C Parra
- Laboratorio de Nanobiomateriales, Departamento de Física, Universidad Técnica Federico Santa María, Valparaiso, Chile.
| | - E M Bringa
- CONICET and Universidad de Mendoza, Mendoza, 5500, Argentina.,Centro de Nanotecnología Aplicada, Facultad de Ciencias, Universidad Mayor, Santiago, Chile.
| | - F Munoz
- Centro para el Desarrollo de la Nanociencia y la Nanotecnología, CEDENNA, Santiago, Chile.,Departamento de Física, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| |
Collapse
|
6
|
Aparicio E, Rodríguez-Jasso RM, Pinales-Márquez CD, Loredo-Treviño A, Robledo-Olivo A, Aguilar CN, Kostas ET, Ruiz HA. High-pressure technology for Sargassum spp biomass pretreatment and fractionation in the third generation of bioethanol production. Bioresour Technol 2021; 329:124935. [PMID: 33713900 DOI: 10.1016/j.biortech.2021.124935] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [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: 01/16/2021] [Revised: 02/27/2021] [Accepted: 03/01/2021] [Indexed: 06/12/2023]
Abstract
Sargassum spp is an invasive macroalgae and an alternative feedstock for bioethanol production. Sargassum spp biomass was subjected to high-pressure technology for biomass fractionation under different operating conditions of temperature and residence time to obtain glucan enriched pretreated solids (32.22 g/100 g of raw material). Enzyme hydrolysis process at high pretreated solid loading (13%, w/v) and enzyme loading of 10 FPU/g of glucan was performed, obtaining 43.01 g/L of glucose corresponding to a conversion yield of 92.12%. Finally, a pre-simultaneous saccharification and fermentation strategy (PSSF) was performed to produce bioethanol. This operational strategy produced 45.66 g/L of glucose in the pre-saccharification stage, and 18.14 g/L of bioethanol was produced with a glucose to bioethanol conversion yield of 76.23%. The development of this process highlights the feasibility of bioethanol production from macroalgal biomass in the biorefinery concept.
Collapse
Affiliation(s)
- E Aparicio
- Biorefinery Group, Food Research Department, Faculty of Chemistry Sciences, Autonomous University of Coahuila, 25280 Saltillo, Coahuila, Mexico
| | - Rosa M Rodríguez-Jasso
- Biorefinery Group, Food Research Department, Faculty of Chemistry Sciences, Autonomous University of Coahuila, 25280 Saltillo, Coahuila, Mexico.
| | - César D Pinales-Márquez
- Biorefinery Group, Food Research Department, Faculty of Chemistry Sciences, Autonomous University of Coahuila, 25280 Saltillo, Coahuila, Mexico
| | - Araceli Loredo-Treviño
- Biorefinery Group, Food Research Department, Faculty of Chemistry Sciences, Autonomous University of Coahuila, 25280 Saltillo, Coahuila, Mexico
| | - Armando Robledo-Olivo
- Food Science & Technology Department, Universidad Autónoma Agraria Antonio Narro, Unidad Saltillo, Blvd Antonio Narro 1923, Buenavista, 25315 Saltillo, Coahuila, Mexico
| | - Cristóbal N Aguilar
- Biorefinery Group, Food Research Department, Faculty of Chemistry Sciences, Autonomous University of Coahuila, 25280 Saltillo, Coahuila, Mexico
| | - Emily T Kostas
- Department of Biochemical Engineering, The Advanced Centre of Biochemical Engineering, Bernard Katz Building, Gower Street, London WC1H 6BT, University College London, London, United Kingdom
| | - Héctor A Ruiz
- Biorefinery Group, Food Research Department, Faculty of Chemistry Sciences, Autonomous University of Coahuila, 25280 Saltillo, Coahuila, Mexico.
| |
Collapse
|
7
|
Aparicio E, Tangarife E, Munoz F, Gonzalez RI, Valencia FJ, Careglio C, Bringa EM. Simulated mechanical properties of finite-size graphene nanoribbons. Nanotechnology 2021; 32:045709. [PMID: 33045683 DOI: 10.1088/1361-6528/abc036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
There are many simulation studies of mechanical properties of graphene nanoribbons (GNR), but there is a lack of agreement regarding elastic and plastic behavior. In this paper we aim to analyze mechanical properties of finite-size GNR, including elastic modulus and fracture, as a function of ribbon size. We present classical molecular dynamics simulations for three different empirical potentials which are often used for graphene simulations: AIREBO, REBO-scr and REAXFF. Ribbons with and without H-passivation at the borders are considered, and the effects of strain rate and different boundaries are also explored. We focus on zig-zag GNR, but also include some armchair GNR examples. Results are strongly dependent on the empirical potential employed. Elastic modulus under uniaxial tension can depend on ribbon size, unlike predictions from continuum-scale models and from some atomistic simulations, and fracture strain and progress vary significantly amongst the simulated potentials. Because of that, we have also carried out quasi-static ab-initio simulations for a selected size, and find that the fracture process is not sudden, instead the wave function changes from Blöch states to a strong interaction between localized waves, which decreases continuously with distance. All potentials show good agreement with DFT in the linear elastic regime, but only the REBO-scr potential shows reasonable agreement with DFT both in the nonlinear elastic and fracture regimes. This would allow more reliable simulations of GNRs and GNR-based nanostructures, to help interpreting experimental results and for future technological applications.
Collapse
Affiliation(s)
- E Aparicio
- CONICET and Universidad de Mendoza, Mendoza, 5500, Argentina
| | - E Tangarife
- Centro de Nanotecnología Aplicada, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
| | - F Munoz
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Centro para el Desarrollo de la Nanociencia y la Nanotecnología, CEDENNA, Santiago, Chile
| | - R I Gonzalez
- Centro de Nanotecnología Aplicada, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
- Centro para el Desarrollo de la Nanociencia y la Nanotecnología, CEDENNA, Santiago, Chile
| | - F J Valencia
- Centro para el Desarrollo de la Nanociencia y la Nanotecnología, CEDENNA, Santiago, Chile
- Centro de Investigación DAiTA Lab, Facultad de Estudios Interdisciplinarios, Universidad Mayor, Chile
| | - C Careglio
- Universidad Nacional de Cuyo, Facultad de Ingeniería, Mendoza, 5500, Argentina
| | - E M Bringa
- CONICET and Universidad de Mendoza, Mendoza, 5500, Argentina
- Centro de Nanotecnología Aplicada, Facultad de Ciencias, Universidad Mayor, Santiago 8580745, Chile
| |
Collapse
|
8
|
Scheepbouwer C, Borland K, Aparicio E, Verschueren H, Wedekind L, Ramaker J, Misovic B, CM Kouwenhoven M, Noske D, Vandertop P, Wesseling P, Wurdinger T, Hackenberg M, Kellner S, Koppers-Lalic D. GENE-60. THE EPITRANSCRIPTOMIC CODE IN LGG: METABOLICALLY REPROGRAMMED IDH-MUTANT GLIOMAS ALTER tRNA MODIFICATION LANDSCAPE. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz175.462] [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: 11/14/2022] Open
Abstract
Abstract
BACKGROUND
Diffuse lower grade gliomas (LGGs) are generally slow growing primary central nervous system tumors that occur in early adult life. The prevalence of isocitrate dehydrogenase (IDH) mutations is high in LGG, and induces excess production of the oncometabolite 2-hydroxyglutarate (2-HG). These gain-of-function mutations play a key role in promoting metabolic reprogramming of the cancer cell that affects activity of α-KG dependent demethylases. Inhibition of DNA demethylase activity leads to glioma with a CpG island methylator phenotype (G-CIMP). Whether the activity of RNA demethylases and methylation status of tRNAs in LGG are modulated by changes in IDH-status is unknown. AIM: To investigate whether IDH mutations play a role in reprogramming of tRNA modifications in adult glioma.
MATERIALS AND METHODS
We combined small RNAseq and LC-MS/MS analysis to identify distinct tRNA processing patterns and methylation signatures in LGG tissues. To address important experimental bottlenecks that limit RNAseq-based detection of tRNA and possibly other modified small noncoding RNAs, we employed a tailored small RNAseq method with validation of specific methylation sites by mass-spectrometry.
RESULTS
Our customized small RNAseq approach yielded >100 fold increase in sequencing reads per tRNA type, thereby dramatically improving tRNA detection when compared to currently used small RNAseq approaches. Moreover, LC-MS/MS analysis revealed a higher abundance of modified nucleosides in tRNA from IDH-mutant LGG compared to IDH-wildtype LGG. Analysis of tRNA from IDH-mutant and IDH-wildtype LGG using the combination of our tailored small RNAseq and LC-MS/MS methodology demonstrated strong differential tRNA expression, tRFs processing and tRNA methylation.
CONCLUSION
We described an approach that makes use of tailored small RNA sequencing combined with mass-spectrometry that enables insights into cancer driven alterations in tRNA methylation patterns and differential tRNA processing signatures. Our data implies that tumor metabolic reprogramming deregulates tRNA methylation, contributing to an altered epitranscriptomic code in IDH-mutant LGG.
Collapse
Affiliation(s)
- Chantal Scheepbouwer
- Amsterdam UMC/VUmc, Department of Neurosurgery, Neuro-Oncology Research Group, Amsterdam, Netherlands
| | - Kayla Borland
- Ludwig Maximilians University Munich, Department of Chemistry, Munich, Germany
| | | | - Heleen Verschueren
- Amsterdam UMC/VUmc, Department of Neurosurgery, Neuro-Oncology Research Group, Amsterdam, Netherlands
| | - Laurine Wedekind
- Amsterdam UMC/VUmc, Department of Neurosurgery, Neuro-Oncology Research Group, Amsterdam, Netherlands
| | - Jip Ramaker
- Amsterdam UMC/VUmc, Department of Neurosurgery, Neuro-Oncology Research Group, Amsterdam, Netherlands
| | - Branko Misovic
- Amsterdam UMC/VUmc, Department of Neurosurgery, Neuro-Oncology Research Group, Amsterdam, Netherlands
| | - Mathilde CM Kouwenhoven
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Neurology, Amsterdam, Netherlands
| | - David Noske
- Amsterdam UMC, Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Peter Vandertop
- Amsterdam UMC/AMC, Neurosurgical Center Amsterdam, Amsterdam, Netherlands
| | | | - Tom Wurdinger
- Amsterdam UMC, Cancer Center Amsterdam, Amsterdam, Netherlands
| | | | - Stefanie Kellner
- Ludwig Maximilians University Munich, Department of Chemistry, Munich, Germany
| | - Danijela Koppers-Lalic
- Amsterdam UMC/VUmc, Department of Neurosurgery, Neuro-Oncology Research Group, Amsterdam, Netherlands
| |
Collapse
|
9
|
Franco S, Bellido R, Aparicio E, Cañete N, García-Retortillo M, Solà R, Tural C, Clotet B, Paredes R, Martínez MA. Natural prevalence of HCV minority variants that are highly resistant to NS3/4A protease inhibitors. J Viral Hepat 2011; 18:e578-82. [PMID: 21914079 DOI: 10.1111/j.1365-2893.2011.01490.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Minority drug-resistant hepatitis C virus (HCV) variants may go undetected yet be clinically important. NS3/4A protease resistance substitutions V36A and A156S/T/V were selected in patients treated with protease inhibitors. The aim of this study was to investigate whether these substitutions pre-existed in HCV infected patients. An allele-specific PCR protocol that detected the NS3/4A protease resistance substitutions V36A and A156S/T/V was used to determine the prevalence of naturally occurring variants in 45 patients. All patient samples were infected with HCV of genotype 1b and were naïve for pegIFNα/ribavirin treatment. Thirty samples (67%) had at least one HCV PI-resistant variant. A156T (23, 51%) was detected more frequently than A156V (13, 29%) or A156S (1, 2%). V36A was detected in 12 samples (27%). These results demonstrate the high prevalence of minority drug-resistant NS3/4 protease resistance substitutions. Our results also demonstrate that allele-specific PCR can be used to detect minor HCV NS3 protease resistant variants in pretreatment samples and to study in detail the evolution of mutant viruses during targeted antiviral therapy.
Collapse
Affiliation(s)
- S Franco
- Fundació irsiCaixa, Hospital Universitari Germans Trias i Pujol, Badalona, Spain
| | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Martínez Isla A, Rojo V, Aparicio E, Marinelli Ibarreta A. [Gas-producing necrotizing infection of the lower limbs secondary to ulcer perforated to retroperitoneum]. Rev Esp Enferm Dig 1990; 77:310-1. [PMID: 2390350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
11
|
Arias J, Durán M, Enterría F, Aparicio E, Aller MA, Estébanez E, de Pedro JA, Jiménez G, Rodríguez J, Arias JI. [Surgical technics in an experimental transplant of the liver. II. Orthotopic transplant]. Rev Esp Enferm Apar Dig 1986; 69:385-95. [PMID: 3526442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
12
|
Díaz Fernández A, Ferreiros J, Carrato A, Lantada P, Peña ML, Martin Rodilla C, Aparicio E. [Castleman's disease: myth or reality? Comments with presentation of a case]. Rev Clin Esp 1980; 156:361-3. [PMID: 7384586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
|