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Abstract
PURPOSE This article will briefly review the origins and evolution of functional genomics, first describing the experimental technology, and then some of the approaches applied to data analysis and visualization. It will emphasize application of functional genomics to radiation biology, using examples from the author's work to illustrate several key types of analysis. It concludes with a look at non-coding RNA, alternative reading of the genome, and single-cell transcriptomics, some of the innovative areas that may help to shape future research in radiation biology and oncology. CONCLUSIONS Transcriptomic approaches have provided insight into many areas of radiation biology and medicine, and innovations in technology and data analysis approaches promise continued contributions to radiation science in the future.
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Muñoz EN, Rivera HM, Gómez LA. Changes in cytoarchitecture and mobility in B16F1 melanoma cells induced by 5-Br-2'-dU coincide with Rock2, miRNAs 138-5p and 455-3p reciprocal expressions. Biochem Biophys Rep 2021; 27:101027. [PMID: 34159262 PMCID: PMC8202345 DOI: 10.1016/j.bbrep.2021.101027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 05/12/2021] [Accepted: 05/14/2021] [Indexed: 11/23/2022] Open
Abstract
ROCK2 is a protein involved in the restructuring of the cytoskeleton in cell adhesion and contractibility processes. miR-138-5p and miR-455-3p regulate Rock2 expression, cell proliferation, migration, and invasion in different experimental cell models. However, their participation in the cytoarchitecture and mobility of B16F1 melanoma cells exposed to 5-Br-2'-dU is partially known. This work aimed to analyze ROCK2 and miRs 138-5p and 455-3p expression associated with morphological and mobility changes of B16F1 mouse melanoma cells exposed to the thymidine analog 5-Bromo-2'-deoxyuridine (5-Br-2'-dU). We observed an increase (2.2X n = 3, p < 0.05) in the cell area, coinciding with an increase in cell diameter (1.27X n = 3, p < 0.05), as well as greater cell granularity, capacity for circularization, adhesion, which was associated with more significant polymerization of F-actin, collapsed in the intermediate filaments of vimentin (VIM), and coinciding with a decrease in migration (87%). Changes coincided with a decrease in Rock2 mRNA expression (2.88X n = 3, p < 0.05), increased vimentin and a reciprocal decrease in miR-138-5p (1.8X), and an increase in miR-455-3p (2.39X). The Rock2 kinase inhibitor Y27632 partially rescued these changes. These results suggest ROCK2 and VIM regulate the morphological and mobility changes of B16 melanoma cells after exposure to 5-Br-2'-dU, and its expression may be reciprocally regulated, at least in part, by miR-138-5p and miR-455-3p.
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Affiliation(s)
- Esther Natalia Muñoz
- Molecular Physiology Group, Scientific and Technological Research, Public Health Research, Instituto Nacional de Salud de Colombia, Bogotá, D.C., Colombia
- Department of Physiological Sciences, Faculty of Medicine, Universidad Nacional de Colombia, Bogotá, D.C., Colombia
| | - Hernán Mauricio Rivera
- Molecular Physiology Group, Scientific and Technological Research, Public Health Research, Instituto Nacional de Salud de Colombia, Bogotá, D.C., Colombia
| | - Luis Alberto Gómez
- Molecular Physiology Group, Scientific and Technological Research, Public Health Research, Instituto Nacional de Salud de Colombia, Bogotá, D.C., Colombia
- Department of Physiological Sciences, Faculty of Medicine, Universidad Nacional de Colombia, Bogotá, D.C., Colombia
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Rivera HM, Muñoz EN, Osuna D, Florez M, Carvajal M, Gómez LA. Reciprocal Changes in miRNA Expression with Pigmentation and Decreased Proliferation Induced in Mouse B16F1 Melanoma Cells by L-Tyrosine and 5-Bromo-2'-Deoxyuridine. Int J Mol Sci 2021; 22:ijms22041591. [PMID: 33562431 PMCID: PMC7914888 DOI: 10.3390/ijms22041591] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/31/2020] [Accepted: 01/03/2021] [Indexed: 12/15/2022] Open
Abstract
Background: Many microRNAs have been identified as critical mediators in the progression of melanoma through its regulation of genes involved in different cellular processes such as melanogenesis, cell cycle control, and senescence. However, microRNAs’ concurrent participation in syngeneic mouse B16F1 melanoma cells simultaneously induced decreased proliferation and differential pigmentation by exposure to 5-Brd-2′-dU (5’Bromo-2-deoxyuridine) and L-Tyr (L-Tyrosine) respectively, is poorly understood. Aim: To evaluate changes in the expression of microRNAs and identify which miRNAs in-network may contribute to the functional bases of phenotypes of differential pigmentation and reduction of proliferation in B16F1 melanoma cells exposed to 5-Brd-2′-dU and L-Tyr. Methods: Small RNAseq evaluation of the expression profiles of miRNAs in B16F1 melanoma cells exposed to 5-Brd-2′-dU (2.5 μg/mL) and L-Tyr (5 mM), as well as the expression by qRT-PCR of some molecular targets related to melanogenesis, cell cycle, and senescence. By bioinformatic analysis, we constructed network models of regulation and co-expression of microRNAs. Results: We confirmed that stimulation or repression of melanogenesis with L-Tyr or 5-Brd-2′-dU, respectively, generated changes in melanin concentration, reduction in proliferation, and changes in expression of microRNAs 470-3p, 470-5p, 30d-5p, 129-5p, 148b-3p, 27b-3p, and 211-5p, which presented patterns of coordinated and reciprocal co-expression, related to changes in melanogenesis through their putative targets Mitf, Tyr and Tyrp1, and control of cell cycle and senescence: Cyclin D1, Cdk2, Cdk4, p21, and p27. Conclusions: These findings provide insights into the molecular biology of melanoma of the way miRNAs are coordinated and reciprocal expression that may operate in a network as molecular bases for understanding changes in pigmentation and decreased proliferation induced in B16F1 melanoma cells exposed to L-Tyr and 5-Brd-2′-dU.
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Affiliation(s)
- Hernán Mauricio Rivera
- Department of Medicine, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (H.M.R.); (E.N.M.)
- Molecular Physiology Group, Sub-Direction of Scientific and Technological Research, Direction of Public Health Research, National Institute of Health, Bogotá 111321, Colombia
| | - Esther Natalia Muñoz
- Department of Medicine, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (H.M.R.); (E.N.M.)
- Molecular Physiology Group, Sub-Direction of Scientific and Technological Research, Direction of Public Health Research, National Institute of Health, Bogotá 111321, Colombia
| | - Daniel Osuna
- Science Department, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (D.O.); (M.F.); (M.C.)
| | - Mauro Florez
- Science Department, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (D.O.); (M.F.); (M.C.)
| | - Michael Carvajal
- Science Department, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (D.O.); (M.F.); (M.C.)
| | - Luis Alberto Gómez
- Molecular Physiology Group, Sub-Direction of Scientific and Technological Research, Direction of Public Health Research, National Institute of Health, Bogotá 111321, Colombia
- Department of Physiological Sciences, Faculty of Medicine, Universidad Nacional de Colombia, Bogotá 111321, Colombia
- Correspondence:
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Ren Y, Jin J, Zheng M, Yang Q, Xing F. Ethanol Inhibits Aflatoxin B 1 Biosynthesis in Aspergillus flavus by Up-Regulating Oxidative Stress-Related Genes. Front Microbiol 2020; 10:2946. [PMID: 32010073 PMCID: PMC6978751 DOI: 10.3389/fmicb.2019.02946] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 12/06/2019] [Indexed: 01/04/2023] Open
Abstract
As the most carcinogenic, toxic, and economically costly mycotoxins, aflatoxin B1 (AFB1) is primarily biosynthesized by Aspergillus flavus and Aspergillus parasiticus. Aflatoxin biosynthesis is related to oxidative stress and functions as a second line of defense from excessive reactive oxygen species. Here, we find that ethanol can inhibit fungal growth and AFB1 production by A. flavus in a dose-dependent manner. Then, the ethanol’s molecular mechanism of action on AFB1 biosynthesis was revealed using a comparative transcriptomic analysis. RNA-Seq data indicated that all the genes except for aflC in the aflatoxin gene cluster were down-regulated by 3.5% ethanol. The drastic repression of aflatoxin structural genes including the complete inhibition of aflK and aflLa may be correlated with the down-regulation of the transcription regulator genes aflR and aflS in the cluster. This may be due to the repression of several global regulator genes and the subsequent overexpression of some oxidative stress-related genes. The suppression of several key aflatoxin genes including aflR, aflD, aflM, and aflP may also be associated with the decreased expression of the global regulator gene veA. In particular, ethanol exposure caused the decreased expression of stress response transcription factor srrA and the overexpression of bZIP transcription factor ap-1, C2H2 transcription factors msnA and mtfA, together with the enhanced levels of anti-oxidant enzymatic genes including Cat, Cat1, Cat2, CatA, and Cu, Zn superoxide dismutase gene sod1. Taken together, these RNA-Seq data strongly suggest that ethanol inhibits AFB1 biosynthesis by A. flavus via enhancing fungal oxidative stress response. In conclusion, this study served to reveal the anti-aflatoxigenic mechanisms of ethanol in A. flavus and to provide solid evidence for its use in controlling AFB1 contamination.
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Affiliation(s)
- Yaoyao Ren
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Jing Jin
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mumin Zheng
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Qingli Yang
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Fuguo Xing
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China.,Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
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Ren Y, Jin J, Zheng M, Yang Q, Xing F. Ethanol Inhibits Aflatoxin B 1 Biosynthesis in Aspergillus flavus by Up-Regulating Oxidative Stress-Related Genes. Front Microbiol 2019. [PMID: 32010073 DOI: 10.3389/fmicb.2019.02946/bibtex] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
Abstract
As the most carcinogenic, toxic, and economically costly mycotoxins, aflatoxin B1 (AFB1) is primarily biosynthesized by Aspergillus flavus and Aspergillus parasiticus. Aflatoxin biosynthesis is related to oxidative stress and functions as a second line of defense from excessive reactive oxygen species. Here, we find that ethanol can inhibit fungal growth and AFB1 production by A. flavus in a dose-dependent manner. Then, the ethanol's molecular mechanism of action on AFB1 biosynthesis was revealed using a comparative transcriptomic analysis. RNA-Seq data indicated that all the genes except for aflC in the aflatoxin gene cluster were down-regulated by 3.5% ethanol. The drastic repression of aflatoxin structural genes including the complete inhibition of aflK and aflLa may be correlated with the down-regulation of the transcription regulator genes aflR and aflS in the cluster. This may be due to the repression of several global regulator genes and the subsequent overexpression of some oxidative stress-related genes. The suppression of several key aflatoxin genes including aflR, aflD, aflM, and aflP may also be associated with the decreased expression of the global regulator gene veA. In particular, ethanol exposure caused the decreased expression of stress response transcription factor srrA and the overexpression of bZIP transcription factor ap-1, C2H2 transcription factors msnA and mtfA, together with the enhanced levels of anti-oxidant enzymatic genes including Cat, Cat1, Cat2, CatA, and Cu, Zn superoxide dismutase gene sod1. Taken together, these RNA-Seq data strongly suggest that ethanol inhibits AFB1 biosynthesis by A. flavus via enhancing fungal oxidative stress response. In conclusion, this study served to reveal the anti-aflatoxigenic mechanisms of ethanol in A. flavus and to provide solid evidence for its use in controlling AFB1 contamination.
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Affiliation(s)
- Yaoyao Ren
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Jing Jin
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mumin Zheng
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Qingli Yang
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Fuguo Xing
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
- Key Laboratory of Agro-products Quality and Safety Control in Storage and Transport Process, Ministry of Agriculture and Rural Affairs/Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
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Rieber M, Strasberg Rieber M. Apoptosis-inducing levels of UV radiation and proteasome inhibitors produce opposite effects on p21(WAF1) in human melanoma cells. Int J Cancer 2000; 86:462-7. [PMID: 10797256 DOI: 10.1002/(sici)1097-0215(20000515)86:4<462::aid-ijc3>3.0.co;2-b] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The stability of p21(WAF1) and p53 is increased by UV radiation or proteasome inhibitors in normal and some tumor cells. However, p21(WAF1) can either stimulate in vitro assembly of active cyclin-kinase complexes at low concentrations or inhibit this activity at high concentrations. Also, ectopic p21(WAF1) over-expression has been reported to promote or suppress apoptosis, depending on the target cells. We have investigated changes in p21(WAF1) expression as a result of exposure to either 25 J/m(2) UV or 10 microM MG-115 proteasome inhibitor, both of which cause apoptosis in human C8161 melanoma cells. p21(WAF1) mRNA increased in response to UV irradiation but failed to accumulate at the protein level because of its early UV-activated degradation counteracted by proteasome inhibition. UV-mediated loss of p21(WAF1) protein preceding induction of p53 and cell death was greater in non-metastatic than in metastatic C8161 melanoma cells. No loss in p21(WAF1) occurred with apoptosis induced by 10 microM proteasome inhibitors MG-115 or lactacystin, mediated by over-expression of p21(WAF1). Our results suggest that conditions causing prolonged or permanent changes in basal levels of p21(WAF1) may impair its reversible cell-cycle checkpoint function, leading to irreversible growth arrest or cell death.
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Affiliation(s)
- M Rieber
- IVIC, Tumor Cell Biology Laboratory, Center of Microbiology and Cell Biology, Caracas, Venezuela.
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Alvarez M, Strasberg Rieber M, Rieber M. Chromosome-6-mediated suppression of metastatic ability increases basal expression of UV-inducible superoxide dismutase and induction of p53. Int J Cancer 1998; 77:586-91. [PMID: 9679763 DOI: 10.1002/(sici)1097-0215(19980812)77:4<586::aid-ijc19>3.0.co;2-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Since response to radiation and markers capable of distinguishing metastatic from non-metastatic cells are important, we now use high-stringency mRNA differential display with immune blotting and protein-activity assays, to identify genes induced after exposure to UV in human metastatic C8161 melanoma and its counterpart neo 6.3, in which metastatic ability is suppressed by introduction of neo-tagged chromosome-6 fragments. We cloned and sequenced a 600-bp cDNA 99% homologous to Cu/Zn superoxide dismutase, which was up-regulated after UV irradiation in both metastatic variants, and showed increased basal expression at the mRNA, protein and activity levels in non-metastatic cells. The latter cells also showed greater basal activity of chromosome-6-associated MnSOD, slower proliferation and greater UV-mediated inducibility of the p53 tumor-suppressor protein than did its metastatic counterpart. Our data suggest that suppression of metastatic ability by introduction of neo-tagged chromosome-6 fragments promotes basal expression of superoxide dismutases and increases inducibility of p53 in response to DNA damage.
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Affiliation(s)
- M Alvarez
- IVIC, Tumor-Cell Biology Laboratory, Caracas, Venezuela
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