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Menezes LAA, Pinheiro Costa Pimentel M, Alves TDO, Pimenta do Nascimento T, Evaristo JAM, Nogueira FCS, Ferreira MSL, De Dea Lindner J. Label-free quantitative proteomics to exploit the impact of sourdough fermentation on reducing wheat allergenic fractions. Food Chem 2024; 430:137037. [PMID: 37541040 DOI: 10.1016/j.foodchem.2023.137037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/20/2023] [Accepted: 07/26/2023] [Indexed: 08/06/2023]
Abstract
The microbial consortia of lactic acid bacteria and yeast of sourdough can partially degrade gluten subunits associated with wheat-related diseases. This study evaluated how sourdough fermentation interferes with wheat protein profiles and if it can be related to the reduction expression of allergenic proteins. Samples from five bread doughs (Saccharomyces cerevisiae -C1; chemical acidification -C2, and three sourdoughs formulations -S1, S2, and S3) were sequentially extracted, digested, and submitted to shotgun label-free proteomic analysis. Eight-five proteins were identified as allergenic, mainly belonging to gliadin fraction, including seven containing the 33-mer peptide sequence. The highest immunogenic potential was found in dough C1 and S3, while the least reactive group consisted of S1 and C2. The two folds down expression of an α-gliadin containing the 33-mer sequence corroborates this. This finding may indicate the role of organic acids produced by the microbiota sourdough type II during fermentation in changing the protein profile.
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Affiliation(s)
- Leidiane Andreia Acordi Menezes
- Food Technology & Bioprocess Research Group, Food Science and Technology Department, Federal University of Santa Catarina (UFSC), 88034-001 Florianópolis, SC, Brazil
| | - Mariana Pinheiro Costa Pimentel
- Laboratory of Bioactives, Food and Nutrition Graduate Program, Federal University of the State of Rio de Janeiro (UNIRIO), 22290-240 Rio de Janeiro, RJ, Brazil
| | - Thais de Oliveira Alves
- Laboratory of Bioactives, Food and Nutrition Graduate Program, Federal University of the State of Rio de Janeiro (UNIRIO), 22290-240 Rio de Janeiro, RJ, Brazil
| | - Talita Pimenta do Nascimento
- Laboratory of Bioactives, Food and Nutrition Graduate Program, Federal University of the State of Rio de Janeiro (UNIRIO), 22290-240 Rio de Janeiro, RJ, Brazil
| | - Joseph A M Evaristo
- Laboratory of Proteomics, Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), 21941-909 Rio de Janeiro, RJ, Brazil
| | - Fábio C S Nogueira
- Laboratory of Proteomics, Institute of Chemistry, Federal University of Rio de Janeiro (UFRJ), 21941-909 Rio de Janeiro, RJ, Brazil; Proteomics Unit, Institute of Chemistry, UFRJ, 21941-909 Rio de Janeiro, RJ, Brazil
| | - Mariana Simões Larraz Ferreira
- Laboratory of Bioactives, Food and Nutrition Graduate Program, Federal University of the State of Rio de Janeiro (UNIRIO), 22290-240 Rio de Janeiro, RJ, Brazil; Laboratory of Protein Biochemistry, Center of Innovation in Mass Spectrometry, UNIRIO, 22290-240 Rio de Janeiro, RJ, Brazil.
| | - Juliano De Dea Lindner
- Food Technology & Bioprocess Research Group, Food Science and Technology Department, Federal University of Santa Catarina (UFSC), 88034-001 Florianópolis, SC, Brazil.
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Kurekova S, Tomaskova ZS, Andelova N, Macejova D, Cervienkova M, Brtko J, Ferko M, Grman M, Mackova K. The effect of all-trans retinoic acid on the mitochondrial function and survival of cardiomyoblasts exposed to local photodamage. Cell Biol Int 2022; 46:947-964. [PMID: 35191136 DOI: 10.1002/cbin.11784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 12/30/2021] [Accepted: 02/12/2022] [Indexed: 11/06/2022]
Abstract
This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Simona Kurekova
- Institute of Molecular Physiology and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05, Bratislava, Slovakia
| | - Zuzana Sevcikova Tomaskova
- Institute of Molecular Physiology and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05, Bratislava, Slovakia
| | - Natalia Andelova
- Institute for Heart Research, Centre of Experimental Medicine, Slovak Academy of Sciences, 84104, Bratislava, Slovakia
| | - Dana Macejova
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, 84505, Bratislava, Slovakia
| | - Michaela Cervienkova
- Institute of Biochemistry and Microbiology, Faculty of Chemical and Food Technology, Slovak University of Technology, 81237, Bratislava, Slovakia
| | - Julius Brtko
- Institute of Experimental Endocrinology, Biomedical Research Center, Slovak Academy of Sciences, 84505, Bratislava, Slovakia
| | - Miroslav Ferko
- Institute for Heart Research, Centre of Experimental Medicine, Slovak Academy of Sciences, 84104, Bratislava, Slovakia
| | - Marian Grman
- Institute of Clinical and Translational Research, Biomedical Research Center, Slovak Academy of Sciences, 84505, Bratislava, Slovakia
| | - Katarina Mackova
- Institute of Molecular Physiology and Genetics, Centre of Biosciences, Slovak Academy of Sciences, 840 05, Bratislava, Slovakia
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The Role of ATRA, Natural Ligand of Retinoic Acid Receptors, on EMT-Related Proteins in Breast Cancer: Minireview. Int J Mol Sci 2021; 22:ijms222413345. [PMID: 34948142 PMCID: PMC8705994 DOI: 10.3390/ijms222413345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 12/17/2022] Open
Abstract
The knowledge of the structure, function, and abundance of specific proteins related to the EMT process is essential for developing effective diagnostic approaches to cancer with the perspective of diagnosis and therapy of malignancies. The success of all-trans retinoic acid (ATRA) differentiation therapy in acute promyelocytic leukemia has stimulated studies in the treatment of other tumors with ATRA. This review will discuss the impact of ATRA use, emphasizing epithelial-mesenchymal transition (EMT) proteins in breast cancer, of which metastasis and recurrence are major causes of death.
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Strouhalova D, Macejova D, Mosna B, Bobal P, Otevrel J, Lastovickova M, Brtko J, Bobalova J. Down-regulation of vimentin by triorganotin isothiocyanates-nuclear retinoid X receptor agonists: A proteomic approach. Toxicol Lett 2019; 318:22-29. [PMID: 31634547 DOI: 10.1016/j.toxlet.2019.10.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/24/2019] [Accepted: 10/10/2019] [Indexed: 02/09/2023]
Abstract
An attempt has been made to delineate the role of natural and synthetic retinoid receptor ligands on vimentin expression in the human triple-negative breast cancer cells. The effects of currently synthesized triorganotin derivatives of the general formula R3SnX (R is butyl or phenyl, X is isothiocyanate), which are considered RXR ligands, were investigated in the human MDA-MB-231 breast cancer cell line. Studies were evaluated in the presence and absence of all-trans retinoic acid (ATRA), a natural RAR ligand. Vimentin represents the major protein associated with epithelial-mesenchymal transition (EMT), an essential process when the primary tumour transforms into a malignant one. mRNA and proteomic data obtained in this study, based on the PDQuest software protein evaluation and further quantification of proteins by iTRAQ analysis, suggest that vimentin was significantly reduced in the combination of RAR ligand and RXR ligand treatment. Both tested triorganotin compounds showed similarly reduced expression of vimentin, but tributyltin isothiocyanate (TBT-ITC) proved to be more effective than triphenyltin isothiocyanate (TPT-ITC). Furthermore, the effect of natural (9cRA) and synthetic RXR ligands, both chloride and isothiocyanate derivatives, on vimentin expression was compared.
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Affiliation(s)
- Dana Strouhalova
- Institute of Analytical Chemistry of the CAS, Veveri 97, 602 00 Brno, Czech Republic
| | - Dana Macejova
- Institute of Experimental Endocrinology, Biomedical Research Centre, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovak Republic
| | - Barbora Mosna
- Institute of Experimental Endocrinology, Biomedical Research Centre, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovak Republic
| | - Pavel Bobal
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho 1946/1, 612 42 Brno, Czech Republic
| | - Jan Otevrel
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences Brno, Palackeho 1946/1, 612 42 Brno, Czech Republic
| | - Marketa Lastovickova
- Institute of Analytical Chemistry of the CAS, Veveri 97, 602 00 Brno, Czech Republic
| | - Julius Brtko
- Institute of Experimental Endocrinology, Biomedical Research Centre, Slovak Academy of Sciences, Dubravska cesta 9, 845 05 Bratislava, Slovak Republic
| | - Janette Bobalova
- Institute of Analytical Chemistry of the CAS, Veveri 97, 602 00 Brno, Czech Republic.
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de Carvalho Melo-Cavalcante AA, da Rocha Sousa L, Alencar MVOB, de Oliveira Santos JV, da Mata AMO, Paz MFCJ, de Carvalho RM, Nunes NMF, Islam MT, Mendes AN, Gonçalves JCR, da Silva FCC, Ferreira PMP, de Castro E Sousaa JM. Retinol palmitate and ascorbic acid: Role in oncological prevention and therapy. Biomed Pharmacother 2018; 109:1394-1405. [PMID: 30551390 DOI: 10.1016/j.biopha.2018.10.115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 10/19/2018] [Accepted: 10/20/2018] [Indexed: 12/14/2022] Open
Abstract
Cancer development has been directly related to oxidative stress. During chemotherapy, some cancer patients use dietary antioxidants to avoid nutritional deficiencies due to cancer treatment. Among the antioxidants consumed, there are vitamins, including retinyl palmitate (PR) and ascorbic acid (AA), which have the capacity to reduce free radicals formation, protect cellular structures and maintain the cellular homeostasis. This systematic review evaluated the antioxidant and antitumor mechanisms of retinol palmitate (a derivative of vitamin A) and/or ascorbic acid (vitamin C) in cancer-related studies. Ninety-seven (97) indexed articles in the databases PubMed and Science Direct, published between 2013 and 2017, including 23 clinical studies (5 for every single compound while 13 in interaction) and 74 non-clinical studies (37 for retinol palmitate, 36 for ascorbic acid and 1 in interaction) were considered. Antioxidant and antitumor effects, with controversies over dosage and route of administration, were observed for the test compounds in their isolated form or associated in clinical studies. Prevention of cancer risks against oxidative damage was seen in lower doses of retinol palmitate and/or vitamin C. However, at high doses, they can generate reactive oxygen species, cytotoxicity and apoptosis in test systems. Non-clinical studies using cell lines have allowed understanding the mechanisms related to antioxidants and antitumor effects of the isolated compounds, however, studies on vitamin interactions, acting as antioxidants and/or antitumor are still rare and controversial. More studies, mainly related to modulation of antineoplastic drugs are needed for understanding the risks and benefits of their use during treatment in order to achieve effectiveness in cancer therapy and patient's quality of life.
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Affiliation(s)
- Ana Amélia de Carvalho Melo-Cavalcante
- Postgraduate Program in Pharmaceutical Sciences. Federal University of Piauí, Teresina, Piauí, 64.049-550, Brazil; Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City-700000, Vietnam
| | - Leonardo da Rocha Sousa
- Postgraduate Program in Pharmaceutical Sciences. Federal University of Piauí, Teresina, Piauí, 64.049-550, Brazil; Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City-700000, Vietnam
| | - Marcus Vinícius Oliveira Barros Alencar
- Postgraduate Program in Pharmaceutical Sciences. Federal University of Piauí, Teresina, Piauí, 64.049-550, Brazil; Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City-700000, Vietnam
| | - José Victor de Oliveira Santos
- Postgraduate Program in Pharmaceutical Sciences. Federal University of Piauí, Teresina, Piauí, 64.049-550, Brazil; Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City-700000, Vietnam
| | - Ana Maria Oliveira da Mata
- Postgraduate Program in Pharmaceutical Sciences. Federal University of Piauí, Teresina, Piauí, 64.049-550, Brazil; Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City-700000, Vietnam
| | - Márcia Fernanda Correia Jardim Paz
- Postgraduate Program in Pharmaceutical Sciences. Federal University of Piauí, Teresina, Piauí, 64.049-550, Brazil; Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City-700000, Vietnam
| | - Ricardo Melo de Carvalho
- Postgraduate Program in Pharmaceutical Sciences. Federal University of Piauí, Teresina, Piauí, 64.049-550, Brazil; Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City-700000, Vietnam
| | - Nárcia Mariana Fonseca Nunes
- Postgraduate Program in Pharmaceutical Sciences. Federal University of Piauí, Teresina, Piauí, 64.049-550, Brazil; Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City-700000, Vietnam
| | - Muhammad Torequl Islam
- Department for Management of Science and Technology Development, Ton Duc Thang University, Ho Chi Minh City-700000, Vietnam; Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City-700000, Vietnam
| | - Anderson Nogueira Mendes
- Department of Biophysics and Physiology of Federal University of Piauí, Teresina, Piauí, 64.049-550, Brazil; Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City-700000, Vietnam
| | - Juan Carlos Ramos Gonçalves
- Department of Biochemistry and Pharmacology, Federal University of Piauí, Teresina, Piauí, 64.049-550, Brazil; Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City-700000, Vietnam
| | - Felipe Cavalcanti Carneiro da Silva
- Postgraduate Program in Pharmaceutical Sciences. Federal University of Piauí, Teresina, Piauí, 64.049-550, Brazil; Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City-700000, Vietnam; Department of Biological Sciences, Federal University of Piauí, Picos, Piauí, 64.067-670, Brazil
| | - Paulo Michel Pinheiro Ferreira
- Postgraduate Program in Pharmaceutical Sciences. Federal University of Piauí, Teresina, Piauí, 64.049-550, Brazil; Department of Biophysics and Physiology of Federal University of Piauí, Teresina, Piauí, 64.049-550, Brazil; Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City-700000, Vietnam
| | - João Marcelo de Castro E Sousaa
- Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City-700000, Vietnam; Department of Biological Sciences, Federal University of Piauí, Picos, Piauí, 64.067-670, Brazil.
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Wu J, Yang R, Zhang L, Li Y, Liu B, Kang H, Fan Z, Tian Y, Liu S, Li T. Metabolomics research on potential role for 9-cis-retinoic acid in breast cancer progression. Cancer Sci 2018; 109:2315-2326. [PMID: 29737597 PMCID: PMC6029828 DOI: 10.1111/cas.13629] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 04/12/2018] [Accepted: 04/20/2018] [Indexed: 12/13/2022] Open
Abstract
Deciphering the molecular networks that discriminate organ-confined breast cancer from metastatic breast cancer may lead to the identification of critical biomarkers for breast cancer invasion and aggressiveness. Here metabolomics, a global study of metabolites, has been applied to explore the metabolic alterations that characterize breast cancer progression. We profiled a total of 693 metabolites across 87 serum samples related to breast cancer (46 clinically localized and 41 metastatic breast cancer) and 49 normal samples. These unbiased metabolomic profiles were able to distinguish normal individuals, clinically localized and metastatic breast cancer patients. 9-cis-Retinoic acid, an isomer of all-trans retinoic acid, was identified as a differential metabolite that significantly decreased during breast cancer progression to metastasis, and its levels were also reduced in urine samples from biopsy-positive breast cancer patients relative to biopsy-negative individuals and in invasive breast cancer cells relative to benign MCF-10A cells. The addition of exogenous 9-cis-retinoic acid to MDA-MB-231 cells and knockdown of aldehyde dehydrogenase 1 family member A1, a regulatory enzyme for 9-cis-retinoic acid, remarkably impaired cell invasion and migration, presumably through preventing the key regulator cofilin from activation and inhibiting MMP2 and MMP9 expression. Taken together, our study showed the potential inhibitory role for 9-cis-retinoic acid in breast cancer progression by attenuating cell invasion and migration.
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Affiliation(s)
- Jing Wu
- Department of Clinical Laboratory, Third Central Hospital of Tianjin, Tianjin Institute of Hepatobiliary Disease, Tianjin Key Laboratory of Artificial Cell, Artificial Cell Engineering Technology Research Center of Public Health Ministry, Tianjin, China
| | - Rui Yang
- Research Center of Basic Medical Science, Tianjin Medical University, Tianjin, China
| | - Lei Zhang
- Department of Clinical Laboratory, Third Central Hospital of Tianjin, Tianjin Institute of Hepatobiliary Disease, Tianjin Key Laboratory of Artificial Cell, Artificial Cell Engineering Technology Research Center of Public Health Ministry, Tianjin, China
| | - YueGuo Li
- Clinical laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - BingBing Liu
- Department of Clinical Laboratory, Third Central Hospital of Tianjin, Tianjin Institute of Hepatobiliary Disease, Tianjin Key Laboratory of Artificial Cell, Artificial Cell Engineering Technology Research Center of Public Health Ministry, Tianjin, China
| | - Hua Kang
- Department of Clinical Laboratory, Third Central Hospital of Tianjin, Tianjin Institute of Hepatobiliary Disease, Tianjin Key Laboratory of Artificial Cell, Artificial Cell Engineering Technology Research Center of Public Health Ministry, Tianjin, China
| | - ZhiJuan Fan
- Department of Clinical Laboratory, Third Central Hospital of Tianjin, Tianjin Institute of Hepatobiliary Disease, Tianjin Key Laboratory of Artificial Cell, Artificial Cell Engineering Technology Research Center of Public Health Ministry, Tianjin, China
| | - YaQiong Tian
- Department of Clinical Laboratory, Third Central Hospital of Tianjin, Tianjin Institute of Hepatobiliary Disease, Tianjin Key Laboratory of Artificial Cell, Artificial Cell Engineering Technology Research Center of Public Health Ministry, Tianjin, China
| | - ShuYe Liu
- Department of Clinical Laboratory, Third Central Hospital of Tianjin, Tianjin Institute of Hepatobiliary Disease, Tianjin Key Laboratory of Artificial Cell, Artificial Cell Engineering Technology Research Center of Public Health Ministry, Tianjin, China
| | - Tong Li
- Department of Clinical Laboratory, Third Central Hospital of Tianjin, Tianjin Institute of Hepatobiliary Disease, Tianjin Key Laboratory of Artificial Cell, Artificial Cell Engineering Technology Research Center of Public Health Ministry, Tianjin, China
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Smith RW, Moccia RD, Seymour CB, Mothersill CE. Irradiation of rainbow trout at early life stages results in a proteomic legacy in adult gills. Part A; proteomic responses in the irradiated fish and in non-irradiated bystander fish. ENVIRONMENTAL RESEARCH 2018; 163:297-306. [PMID: 29463416 DOI: 10.1016/j.envres.2017.12.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 12/19/2017] [Accepted: 12/24/2017] [Indexed: 06/08/2023]
Abstract
Exposure to a single 0.5 Gy X-ray dose of eggs at 48 h after fertilisation (48 h egg), eyed eggs, yolk sac larvae (YSL) and first feeders induces a legacy effect in adult rainbow trout. This includes the transmission of a bystander effect to non-irradiated adult trout which had swam with the irradiated fish. The aim of this study was to investigate this legacy by analysing the gill proteome of these irradiated and bystander fish. Irradiation at all of the early life stages resulted in changes to proteins which play a key role in development but are also known to be anti-tumorigenic and anti-oxidant: upregulation of haemoglobin subunit beta (48 h egg), haemoglobin, serum albumin 1 precursor (eyed eggs), clathrin heavy chain 1 isoform X10 (eyed eggs and first feeders), and actin-related protein 2/3 complex subunit 4 (first feeders), downregulation of pyruvate dehydrogenase, histone 1 (48 h egg), triosephosphate isomerase (TPI), collagen alpha-1(1) chain like proteins (YSL), pyruvate kinase PKM-like protein (YSL and first feeders), ubiquitin-40S ribosomal proteins S27 and eukaryotic translation initiation factor 4 A isoform 1B (first feeders). However irradiation of YSL and first feeders (post hatching early life stages) also induced proteomic changes which have a complex relationship with tumorigenesis or cancer progression; downregulation of alpha-1-antiprotease-like protein precursor, vigilin isoform X2 and nucleoside diphosphate kinase (YSL) and upregulation of hyperosmotic glycine rich protein (first feeders). In bystander fish some proteomic changes were similar to those induced by irradiation: upregulation of haemoglobin subunit beta (48 h egg), haemoglobin (eyed eggs), actin-related protein 2/3 complex subunit 4, hyperosmotic glycine rich protein (first feeders), and downregulation of alpha-1-antiprotease-like protein, vigilin isoform X2, nucleoside diphosphate kinase (YSL), pyruvate kinase PKM-like protein and ubiquitin-40S ribosomal protein S27a-like (first feeders). Other proteomic changes were unique to bystander fish; downregulation of TPI, ubiquitin-40S ribosomal protein S2 (eyed egg), cofilin-2, cold-inducible RNA-binding protein B-like isoform X3 (YSL) and superoxide dismutase (first feeder), and upregulation of haemoglobin subunit alpha, collagen 1a1 precursor, apolipoprotein A-1-1 and A-1-2 precursor (first feeders). These bystander effect proteomic changes have been shown to be overwhelmingly anti-tumorigenic or protective of the fish gill.
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Affiliation(s)
- Richard W Smith
- Department of Animal Biosciences, University of Guelph, Guelph Ontario Canada; Department of Medical Physics and Applied Radiation Sciences, McMaster University, Hamilton Ontario Canada.
| | - Richard D Moccia
- Department of Animal Biosciences, University of Guelph, Guelph Ontario Canada
| | - Colin B Seymour
- Department of Medical Physics and Applied Radiation Sciences, McMaster University, Hamilton Ontario Canada
| | - Carmel E Mothersill
- Department of Medical Physics and Applied Radiation Sciences, McMaster University, Hamilton Ontario Canada
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Thillaiyampalam G, Liberante F, Murray L, Cardwell C, Mills K, Zhang SD. An integrated meta-analysis approach to identifying medications with potential to alter breast cancer risk through connectivity mapping. BMC Bioinformatics 2017; 18:581. [PMID: 29268695 PMCID: PMC5740937 DOI: 10.1186/s12859-017-1989-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 12/06/2017] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Gene expression connectivity mapping has gained much popularity in recent years with a number of successful applications in biomedical research testifying its utility and promise. A major application of connectivity mapping is the identification of small molecule compounds capable of inhibiting a disease state. In this study, we are additionally interested in small molecule compounds that may enhance a disease state or increase the risk of developing that disease. Using breast cancer as a case study, we aim to develop and test a methodology for identifying commonly prescribed drugs that may have a suppressing or inducing effect on the target disease (breast cancer). RESULTS We obtained from public data repositories a collection of breast cancer gene expression datasets with over 7000 patients. An integrated meta-analysis approach to gene expression connectivity mapping was developed, which involved unified processing and normalization of raw gene expression data, systematic removal of batch effects, and multiple runs of balanced sampling for differential expression analysis. Differentially expressed genes stringently selected were used to construct multiple non-joint gene signatures representing the same biological state. Remarkably these non-joint gene signatures retrieved from connectivity mapping separate lists of candidate drugs with significant overlaps, providing high confidence in their predicted effects on breast cancers. Of particular note, among the top 26 compounds identified as inversely connected to the breast cancer gene signatures, 14 of them are known anti-cancer drugs. CONCLUSIONS A few candidate drugs with potential to enhance breast cancer or increase the risk of the disease were also identified; further investigation on a large population is required to firmly establish their effects on breast cancer risks. This work thus provides a novel approach and an applicable example for identifying medications with potential to alter cancer risks through gene expression connectivity mapping.
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Affiliation(s)
| | - Fabio Liberante
- Centre for Cancer Research and Cell Biology (CCRCB), Queen’s University Belfast, Belfast, UK
| | - Liam Murray
- Centre for Public Health, Queen’s University Belfast, Belfast, UK
| | - Chris Cardwell
- Centre for Public Health, Queen’s University Belfast, Belfast, UK
| | - Ken Mills
- Centre for Cancer Research and Cell Biology (CCRCB), Queen’s University Belfast, Belfast, UK
| | - Shu-Dong Zhang
- Centre for Cancer Research and Cell Biology (CCRCB), Queen’s University Belfast, Belfast, UK
- Northern Ireland Centre for Stratified Medicine, Biomedical Sciences Research Institute, University of Ulster, C-TRIC Building, Altnagelvin Area Hospital, Glenshane Road, L/Derry, Northern Ireland, BT47 6SB UK
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Flodrova D, Toporova L, Lastovickova M, Macejova D, Hunakova L, Brtko J, Bobalova J. Consequences of the natural retinoid/retinoid X receptor ligands action in human breast cancer MDA-MB-231 cell line: Focus on functional proteomics. Toxicol Lett 2017; 281:26-34. [DOI: 10.1016/j.toxlet.2017.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 09/01/2017] [Accepted: 09/02/2017] [Indexed: 12/12/2022]
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10
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Sn- and Ge- triorganometallics exert different cytotoxicity and modulation of migration in triple-negative breast cancer cell line MDA-MB-231. Toxicol Lett 2017; 279:16-21. [DOI: 10.1016/j.toxlet.2017.07.879] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 07/07/2017] [Accepted: 07/09/2017] [Indexed: 01/28/2023]
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11
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Radioligand binding assay for accurate determination of nuclear retinoid X receptors: A case of triorganotin endocrine disrupting ligands. Toxicol Lett 2016; 254:32-6. [DOI: 10.1016/j.toxlet.2016.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/22/2016] [Accepted: 05/02/2016] [Indexed: 12/21/2022]
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