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Campero-Basaldua C, Herrera-Gamboa J, Bernal-Ramírez J, Lopez-Moran S, Luévano-Martínez LA, Alves-Figueiredo H, Guerrero G, García-Rivas G, Treviño V. The retinoic acid response is a minor component of the cardiac phenotype in H9c2 myoblast differentiation. BMC Genomics 2023; 24:431. [PMID: 37533008 PMCID: PMC10394869 DOI: 10.1186/s12864-023-09512-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 07/11/2023] [Indexed: 08/04/2023] Open
Abstract
The H9c2 myoblast cell line, isolated from the left ventricular tissue of rat, is currently used in vitro as a mimetic for skeletal and cardiac muscle due to its biochemical, morphological, and electrical/hormonal signaling properties. During culture, H9c2 cells acquire a myotube phenotype, where a critical component is the inclusion of retinoic acid (RA). The results from some authors on H9c2 suggested that thousands of genes respond to RA stimuli, while others report hundreds of genes responding to RA over different cell types. In this article, using a more appropriate experimental design, we first confirm the H9c2 cardiac phenotype with and without RA and report transcriptomic and physiological changes regarding calcium handling, bioenergetics, and other biological concepts. Interestingly, of the 2360 genes showing a transcriptional change, 622 genes were statistically associated with the RA response. Of these genes, only 305 were RA-specific, and the rest also showed a culture-time component. Thus, the major expression changes (from 74 to 87%) were indeed due to culture conditions over time. Unexpectedly, only a few components of the retinol pathway in KEGG responded to RA. Our results show the role of RA in the H9c2 cultures impacting the interpretation using H9c2 as an in vitro model.
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Affiliation(s)
- Carlos Campero-Basaldua
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la SaludCátedra de Bioinformática, Ave. Morones Prieto 3000, Colonia Los Doctores, Monterrey, Nuevo León, 64710, Mexico
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la SaludCátedra de Cardiología y Medicina Vascular, Hospital Zambrano Hellion, San Pedro Garza García, P.C. 66278, Monterrey, Nuevo León, 64710, Mexico
| | - Jessica Herrera-Gamboa
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la SaludCátedra de Bioinformática, Ave. Morones Prieto 3000, Colonia Los Doctores, Monterrey, Nuevo León, 64710, Mexico
| | - Judith Bernal-Ramírez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la SaludCátedra de Cardiología y Medicina Vascular, Hospital Zambrano Hellion, San Pedro Garza García, P.C. 66278, Monterrey, Nuevo León, 64710, Mexico
| | - Silvia Lopez-Moran
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la SaludCátedra de Cardiología y Medicina Vascular, Hospital Zambrano Hellion, San Pedro Garza García, P.C. 66278, Monterrey, Nuevo León, 64710, Mexico
| | - Luis-Alberto Luévano-Martínez
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la SaludCátedra de Cardiología y Medicina Vascular, Hospital Zambrano Hellion, San Pedro Garza García, P.C. 66278, Monterrey, Nuevo León, 64710, Mexico
| | - Hugo Alves-Figueiredo
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la SaludCátedra de Cardiología y Medicina Vascular, Hospital Zambrano Hellion, San Pedro Garza García, P.C. 66278, Monterrey, Nuevo León, 64710, Mexico
| | - Guillermo Guerrero
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la SaludCátedra de Bioinformática, Ave. Morones Prieto 3000, Colonia Los Doctores, Monterrey, Nuevo León, 64710, Mexico
| | - Gerardo García-Rivas
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la SaludCátedra de Cardiología y Medicina Vascular, Hospital Zambrano Hellion, San Pedro Garza García, P.C. 66278, Monterrey, Nuevo León, 64710, Mexico.
- Tecnologico de Monterrey, The Institute for Obesity Research, Eugenio Garza Sada Avenue 2501, Monterrey, Nuevo Leon, 64849, Mexico.
| | - Víctor Treviño
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la SaludCátedra de Bioinformática, Ave. Morones Prieto 3000, Colonia Los Doctores, Monterrey, Nuevo León, 64710, Mexico.
- Tecnologico de Monterrey, The Institute for Obesity Research, Eugenio Garza Sada Avenue 2501, Monterrey, Nuevo Leon, 64849, Mexico.
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Solé E, González-Prendes R, Oliinychenko Y, Tor M, Ros-Freixedes R, Estany J, Pena RN. Transcriptome shifts triggered by vitamin A and SCD genotype interaction in Duroc pigs. BMC Genomics 2022; 23:16. [PMID: 34991486 PMCID: PMC8739656 DOI: 10.1186/s12864-021-08244-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/08/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The composition of intramuscular fat depends on genetic and environmental factors, including the diet. In pigs, we identified a haplotype of three SNP mutations in the stearoyl-coA desaturase (SCD) gene promoter associated with higher content of monounsaturated fatty acids in intramuscular fat. The second of these three SNPs (rs80912566, C > T) affected a putative retinol response element in the SCD promoter. The effect of dietary vitamin A restriction over intramuscular fat content is controversial as it depends on the pig genetic line and the duration of the restriction. This study aims to investigate changes in the muscle transcriptome in SCD rs80912566 TT and CC pigs fed with and without a vitamin A supplement during the fattening period. RESULTS Vitamin A did not affect carcass traits or intramuscular fat content and fatty acid composition, but we observed an interaction between vitamin A and SCD genotype on the desaturation of fatty acids in muscle. As reported before, the SCD-TT pigs had more monounsaturated fat than the SCD-CC animals. The diet lacking the vitamin A supplement enlarged fatty acid compositional differences between SCD genotypes, partly because vitamin A had a bigger effect on fatty acid desaturation in SCD-CC pigs (positive) than in SCD-TT and SCD-TC animals (negative). The interaction between diet and genotype was also evident at the transcriptome level; the highest number of differentially expressed genes were detected between SCD-TT pigs fed with the two diets. The genes modulated by the diet with the vitamin A supplement belonged to metabolic and signalling pathways related to immunity and inflammation, transport through membrane-bounded vesicles, fat metabolism and transport, reflecting the impact of retinol on a wide range of metabolic processes. CONCLUSIONS Restricting dietary vitamin A during the fattening period did not improve intramuscular fat content despite relevant changes in muscle gene expression, both in coding and non-coding genes. Vitamin A activated general pathways of retinol response in a SCD genotype-dependant manner, which affected the monounsaturated fatty acid content, particularly in SCD-CC pigs.
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Affiliation(s)
- Emma Solé
- Departament de Ciència Animal, Universitat de Lleida - AGROTECNIO-CERCA Center, Av. Rovira Roure 191, 25197, Lleida, Spain
| | - Rayner González-Prendes
- Departament de Ciència Animal, Universitat de Lleida - AGROTECNIO-CERCA Center, Av. Rovira Roure 191, 25197, Lleida, Spain.,Animal Breeding and Genomics, Wageningen University & Research, 6708PB, Wageningen, The Netherlands
| | | | - Marc Tor
- Departament de Ciència Animal, Universitat de Lleida - AGROTECNIO-CERCA Center, Av. Rovira Roure 191, 25197, Lleida, Spain
| | - Roger Ros-Freixedes
- Departament de Ciència Animal, Universitat de Lleida - AGROTECNIO-CERCA Center, Av. Rovira Roure 191, 25197, Lleida, Spain
| | - Joan Estany
- Departament de Ciència Animal, Universitat de Lleida - AGROTECNIO-CERCA Center, Av. Rovira Roure 191, 25197, Lleida, Spain
| | - Ramona N Pena
- Departament de Ciència Animal, Universitat de Lleida - AGROTECNIO-CERCA Center, Av. Rovira Roure 191, 25197, Lleida, Spain.
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Vogiatzi A, Baltsavia I, Dialynas E, Theodorou V, Zhou Y, Deligianni E, Iliopoulos I, Wilkie AOM, Twigg SRF, Mavrothalassitis G. Erf Affects Commitment and Differentiation of Osteoprogenitor Cells in Cranial Sutures via the Retinoic Acid Pathway. Mol Cell Biol 2021; 41:e0014921. [PMID: 33972395 PMCID: PMC8300784 DOI: 10.1128/mcb.00149-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/22/2021] [Accepted: 04/29/2021] [Indexed: 12/13/2022] Open
Abstract
ETS2 repressor factor (ERF) haploinsufficiency causes late-onset craniosynostosis (CRS) (OMIM entry 600775; CRS4) in humans, while in mice Erf insufficiency also leads to a similar multisuture synostosis phenotype preceded by mildly reduced calvarium ossification. However, neither the cell types affected nor the effects per se have been identified so far. Here, we establish an ex vivo system for the expansion of suture-derived mesenchymal stem and progenitor cells (sdMSCs) and analyze the role of Erf levels in their differentiation. Cellular data suggest that Erf insufficiency specifically decreases osteogenic differentiation of sdMSCs, resulting in the initially delayed mineralization of the calvarium. Transcriptome analysis indicates that Erf is required for efficient osteogenic lineage commitment of sdMSCs. Elevated retinoic acid catabolism due to increased levels of the cytochrome P450 superfamily member Cyp26b1 as a result of decreased Erf levels appears to be the underlying mechanism leading to defective differentiation. Exogenous addition of retinoic acid can rescue the osteogenic differentiation defect, suggesting that Erf affects cranial bone mineralization during skull development through retinoic acid gradient regulation.
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Affiliation(s)
| | | | | | | | - Yan Zhou
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | | | | | - Andrew O. M. Wilkie
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Stephen R. F. Twigg
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - George Mavrothalassitis
- Medical School, University of Crete, Heraklion, Crete, Greece
- IMBB, FORTH, Heraklion, Crete, Greece
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Bonilla DA, Moreno Y, Rawson ES, Forero DA, Stout JR, Kerksick CM, Roberts MD, Kreider RB. A Convergent Functional Genomics Analysis to Identify Biological Regulators Mediating Effects of Creatine Supplementation. Nutrients 2021; 13:2521. [PMID: 34444681 PMCID: PMC8397972 DOI: 10.3390/nu13082521] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/21/2021] [Indexed: 12/12/2022] Open
Abstract
Creatine (Cr) and phosphocreatine (PCr) are physiologically essential molecules for life, given they serve as rapid and localized support of energy- and mechanical-dependent processes. This evolutionary advantage is based on the action of creatine kinase (CK) isozymes that connect places of ATP synthesis with sites of ATP consumption (the CK/PCr system). Supplementation with creatine monohydrate (CrM) can enhance this system, resulting in well-known ergogenic effects and potential health or therapeutic benefits. In spite of our vast knowledge about these molecules, no integrative analysis of molecular mechanisms under a systems biology approach has been performed to date; thus, we aimed to perform for the first time a convergent functional genomics analysis to identify biological regulators mediating the effects of Cr supplementation in health and disease. A total of 35 differentially expressed genes were analyzed. We identified top-ranked pathways and biological processes mediating the effects of Cr supplementation. The impact of CrM on miRNAs merits more research. We also cautiously suggest two dose-response functional pathways (kinase- and ubiquitin-driven) for the regulation of the Cr uptake. Our functional enrichment analysis, the knowledge-based pathway reconstruction, and the identification of hub nodes provide meaningful information for future studies. This work contributes to a better understanding of the well-reported benefits of Cr in sports and its potential in health and disease conditions, although further clinical research is needed to validate the proposed mechanisms.
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Affiliation(s)
- Diego A. Bonilla
- Research Division, Dynamical Business & Science Society—DBSS International SAS, Bogotá 110861, Colombia;
- Research Group in Biochemistry and Molecular Biology, Universidad Distrital Francisco José de Caldas, Bogotá 110311, Colombia
- Research Group in Physical Activity, Sports and Health Sciences (GICAFS), Universidad de Córdoba, Montería 230002, Colombia
- kDNA Genomics, Joxe Mari Korta Research Center, University of the Basque Country UPV/EHU, 20018 Donostia-San Sebastián, Spain
| | - Yurany Moreno
- Research Division, Dynamical Business & Science Society—DBSS International SAS, Bogotá 110861, Colombia;
- Research Group in Biochemistry and Molecular Biology, Universidad Distrital Francisco José de Caldas, Bogotá 110311, Colombia
| | - Eric S. Rawson
- Department of Health, Nutrition and Exercise Science, Messiah University, Mechanicsburg, PA 17055, USA;
| | - Diego A. Forero
- Professional Program in Sport Training, School of Health and Sport Sciences, Fundación Universitaria del Área Andina, Bogotá 111221, Colombia;
| | - Jeffrey R. Stout
- Physiology of Work and Exercise Response (POWER) Laboratory, Institute of Exercise Physiology and Rehabilitation Science, University of Central Florida, Orlando, FL 32816, USA;
| | - Chad M. Kerksick
- Exercise and Performance Nutrition Laboratory, School of Health Sciences, Lindenwood University, Saint Charles, MO 63301, USA;
| | - Michael D. Roberts
- School of Kinesiology, Auburn University, Auburn, AL 36849, USA;
- Edward via College of Osteopathic Medicine, Auburn, AL 36849, USA
| | - Richard B. Kreider
- Exercise & Sport Nutrition Laboratory, Human Clinical Research Facility, Texas A&M University, College Station, TX 77843, USA;
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Proteomic Studies of Primary Acute Myeloid Leukemia Cells Derived from Patients Before and during Disease-Stabilizing Treatment Based on All-Trans Retinoic Acid and Valproic Acid. Cancers (Basel) 2021; 13:cancers13092143. [PMID: 33946813 PMCID: PMC8125016 DOI: 10.3390/cancers13092143] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/16/2021] [Accepted: 04/20/2021] [Indexed: 12/18/2022] Open
Abstract
All-trans retinoic acid (ATRA) and valproic acid (VP) have been tried in the treatment of non-promyelocytic variants of acute myeloid leukemia (AML). Non-randomized studies suggest that the two drugs can stabilize AML and improve normal peripheral blood cell counts. In this context, we used a proteomic/phosphoproteomic strategy to investigate the in vivo effects of ATRA/VP on human AML cells. Before starting the combined treatment, AML responders showed increased levels of several proteins, especially those involved in neutrophil degranulation/differentiation, M phase regulation and the interconversion of nucleotide di- and triphosphates (i.e., DNA synthesis and binding). Several among the differentially regulated phosphorylation sites reflected differences in the regulation of RNA metabolism and apoptotic events at the same time point. These effects were mainly caused by increased cyclin dependent kinase 1 and 2 (CDK1/2), LIM domain kinase 1 and 2 (LIMK1/2), mitogen-activated protein kinase 7 (MAPK7) and protein kinase C delta (PRKCD) activity in responder cells. An extensive effect of in vivo treatment with ATRA/VP was the altered level and phosphorylation of proteins involved in the regulation of transcription/translation/RNA metabolism, especially in non-responders, but the regulation of cell metabolism, immune system and cytoskeletal functions were also affected. Our analysis of serial samples during the first week of treatment suggest that proteomic and phosphoproteomic profiling can be used for the early identification of responders to ATRA/VP-based treatment.
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