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Eisenhut P, Marx N, Borsi G, Papež M, Ruggeri C, Baumann M, Borth N. Manipulating gene expression levels in mammalian cell factories: An outline of synthetic molecular toolboxes to achieve multiplexed control. N Biotechnol 2024; 79:1-19. [PMID: 38040288 DOI: 10.1016/j.nbt.2023.11.003] [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: 10/02/2023] [Revised: 11/06/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
Mammalian cells have developed dedicated molecular mechanisms to tightly control expression levels of their genes where the specific transcriptomic signature across all genes eventually determines the cell's phenotype. Modulating cellular phenotypes is of major interest to study their role in disease or to reprogram cells for the manufacturing of recombinant products, such as biopharmaceuticals. Cells of mammalian origin, for example Chinese hamster ovary (CHO) and Human embryonic kidney 293 (HEK293) cells, are most commonly employed to produce therapeutic proteins. Early genetic engineering approaches to alter their phenotype have often been attempted by "uncontrolled" overexpression or knock-down/-out of specific genetic factors. Many studies in the past years, however, highlight that rationally regulating and fine-tuning the strength of overexpression or knock-down to an optimum level, can adjust phenotypic traits with much more precision than such "uncontrolled" approaches. To this end, synthetic biology tools have been generated that enable (fine-)tunable and/or inducible control of gene expression. In this review, we discuss various molecular tools used in mammalian cell lines and group them by their mode of action: transcriptional, post-transcriptional, translational and post-translational regulation. We discuss the advantages and disadvantages of using these tools for each cell regulatory layer and with respect to cell line engineering approaches. This review highlights the plethora of synthetic toolboxes that could be employed, alone or in combination, to optimize cellular systems and eventually gain enhanced control over the cellular phenotype to equip mammalian cell factories with the tools required for efficient production of emerging, more difficult-to-express biologics formats.
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Affiliation(s)
- Peter Eisenhut
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicolas Marx
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
| | - Giulia Borsi
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Maja Papež
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Caterina Ruggeri
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
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2
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Ağagündüz D, Çelik E, Cemali Ö, Bingöl FG, Özenir Ç, Özoğul F, Capasso R. Probiotics, Live Biotherapeutic Products (LBPs), and Gut-Brain Axis Related Psychological Conditions: Implications for Research and Dietetics. Probiotics Antimicrob Proteins 2023; 15:1014-1031. [PMID: 37222849 DOI: 10.1007/s12602-023-10092-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2023] [Indexed: 05/25/2023]
Abstract
It is well-known that probiotics have key roles in the crosstalk between the gut and brain in terms of nutrition and health. However, when investigating their role in nutrition and health, it can be important to discriminate probiotics used as foods, food supplements, or drugs. For clarification of this terminology, the Food and Drug Administration (FDA) has established a new "live biotherapeutic products" (LBP) category, expressing pharmaceutical expectations and to reduce confusion in the literature. Growing evidence advises that the community of microorganisms found in the gut microbiota is associated with psychological conditions. Hence, it is thought that LBPs may positively affect depression, anxiety, bipolar disorder, and schizophrenia by reducing inflammation, improving gut microbiota, and balancing gut neurometabolites. This review focuses on the specific position of probiotics as LBPs in psychological conditions. Condition-specific potential pathways and mechanisms of LBPs and the prominent strains are discussed in the light of novel studies for future research, dietetic and pharmaceutical applications.
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Affiliation(s)
- Duygu Ağagündüz
- Department of Nutrition and Dietetics, Gazi University, Emek, Ankara, 06490, Turkey.
| | - Elif Çelik
- Department of Nutrition and Dietetics, Gazi University, Emek, Ankara, 06490, Turkey
| | - Özge Cemali
- Department of Nutrition and Dietetics, Gazi University, Emek, Ankara, 06490, Turkey
| | - Feray Gençer Bingöl
- Department of Nutrition and Dietetics, Burdur Mehmet Akif Ersoy University, İstiklal Yerleşkesi, Burdur, 15030, Turkey
| | - Çiler Özenir
- Department of Nutrition and Dietetics, Kırıkkale University, Merkez, Kırıkkale, 71100, Turkey
| | - Fatih Özoğul
- Department of Seafood Processing Technology, Faculty of Fisheries, Cukurova University, Balcali, Adana, 01330, Turkey
- Biotechnology Research and Application Center, Cukurova University, Adana, 01330, Turkey
| | - Raffaele Capasso
- Department of Agricultural Sciences, University of Naples Federico II, 80055, Portici, NA, Italy
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Stein RA, Riber L. Epigenetic effects of short-chain fatty acids from the large intestine on host cells. MICROLIFE 2023; 4:uqad032. [PMID: 37441522 PMCID: PMC10335734 DOI: 10.1093/femsml/uqad032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 06/04/2023] [Accepted: 06/14/2023] [Indexed: 07/15/2023]
Abstract
Adult humans harbor at least as many microbial cells as eukaryotic ones. The largest compartment of this diverse microbial population, the gut microbiota, encompasses the collection of bacteria, archaea, viruses, and eukaryotic organisms that populate the gastrointestinal tract, and represents a complex and dynamic ecosystem that has been increasingly implicated in health and disease. The gut microbiota carries ∼100-to-150-times more genes than the human genome and is intimately involved in development, homeostasis, and disease. Of the several microbial metabolites that have been studied, short-chain fatty acids emerge as a group of molecules that shape gene expression in several types of eukaryotic cells by multiple mechanisms, which include DNA methylation changes, histone post-translational modifications, and microRNA-mediated gene silencing. Butyric acid, one of the most extensively studied short-chain fatty acids, reaches higher concentrations in the colonic lumen, where it provides a source of energy for healthy colonocytes, and its concentrations decrease towards the bottom of the colonic crypts, where stem cells reside. The lower butyric acid concentration in the colonic crypts allows undifferentiated cells, such as stem cells, to progress through the cell cycle, pointing towards the importance of the crypts in providing them with a protective niche. In cancerous colonocytes, which metabolize relatively little butyric acid and mostly rely on glycolysis, butyric acid preferentially acts as a histone deacetylase inhibitor, leading to decreased cell proliferation and increased apoptosis. A better understanding of the interface between the gut microbiota metabolites and epigenetic changes in eukaryotic cells promises to unravel in more detail processes that occur physiologically and as part of disease, help develop novel biomarkers, and identify new therapeutic modalities.
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Affiliation(s)
- Richard A Stein
- Corresponding author. Department of Chemical and Biomolecular Engineering, NYU Tandon School of Engineering, 6 MetroTech Center, Brooklyn, NY 11201, USA. Tel: +1-917-684-9438; E-mail: ;
| | - Leise Riber
- Department of Plant & Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
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Enhancement of recombinant human IL-24 (rhIL-24) protein production from site-specific integrated engineered CHO cells by sodium butyrate treatment. Bioprocess Biosyst Eng 2022; 45:1979-1991. [DOI: 10.1007/s00449-022-02801-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/07/2022] [Indexed: 11/27/2022]
Abstract
AbstractInterleukin-24 (IL-24) has specific inhibitory effects on the proliferation of various tumor cells with almost no toxicity to normal cells. The antitumor activity of recombinant human IL-24 protein produced in mammalian cells is much higher than that of bacteria, but its expression level is extremely low. Sodium butyrate (NaBu) was utilized as a media additive to increase protein expression in Chinese hamster ovary cells. The site-specific integrated engineered cells FCHO/IL-24 were treated with NaBu under different culture conditions (10% and 0.5% serum adherent culture, 0.5% serum suspension culture). First, 3 days of 1 mmol/L NaBu treatment significantly increased rhIL-24 expression level in FCHO/IL-24 cells by 119.94 ± 1.5% (**p < 0.01), 57.49 ± 2.4% (**p < 0.01), and 20.17 ± 3.03% (*p < 0.05) under the above culture conditions. Second, NaBu has a time- and dose-dependent inhibitory effect on FCHO/IL-24 proliferation and induces G0/G1 phase arrest. Under 10% and 0.5% serum adherent culture, G0/G1 phase cells were increased by 11.3 ± 0.5% (**p < 0.01) and 15.0 ± 2.6% (**p < 0.01), respectively. No induction of apoptosis was observed under a high dosage of NaBu treatment. These results suggest that NaBu increases rhIL-24 secretion via inhibiting cell cycle progression, thereby trapping cells in the highly productive G0/G1 phase. Finally, with increasing NaBu dose, glucose concentration increased (**p < 0.01) while lactic acid and ammonia concentrations reduced significantly (**p < 0.01) in 10% and 0.5% serum adherent culture supernatant. RNA-seq showed that NaBu treatment affected multiple tumor and immune-related pathways. In conclusion, NaBu treatment dramatically promoted rhIL-24 production in engineered FCHO/IL-24 cells by altering downstream pathways and inducing G0/G1 cell arrest with little effect on apoptosis.
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El Omari N, Bakha M, Imtara H, Guaouguaoua FE, Balahbib A, Zengin G, Bouyahya A. Anticancer mechanisms of phytochemical compounds: focusing on epigenetic targets. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:47869-47903. [PMID: 34308524 DOI: 10.1007/s11356-021-15594-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 07/19/2021] [Indexed: 06/13/2023]
Abstract
It has recently been proven that epigenetic dysregulation is importantly involved in cell transformation and therefore induces cancerous diseases. The development of molecules called epidrugs, which target specifically different epigenetic modifications to restore cellular memory and therefore the treatment, became a real challenge currently. Currently, bioactive compounds of medicinal plants as epidrugs have been can identified and explored in cancer therapy. Indeed, these molecules can target specifically different epigenetic modulators including DNMT, HDAC, HAT, and HMT. Moreover, some compounds exhibit stochastic epigenetic actions on different pathways regulating cell memory. In this work, pharmacodynamic actions of natural epidrugs belonging to cannabinoids, carotenoids, chalcones, fatty acids, lignans, polysaccharides, saponins, secoiridoids, steroids, tannins, tanshinones, and other chemical classes we reported and highlighted. In this review, the effects of several natural bioactive compounds of epigenetic medications on cancerous diseases were highlighted. Numerous active molecules belonging to different chemical classes such as cannabinoids, carotenoids, fatty acids, lignans, polysaccharides, saponins, secoiridoids, steroids, tannins, and tanshinones are discussed in this review.
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Affiliation(s)
- Nasreddine El Omari
- Laboratory of Histology, Embryology, and Cytogenetic, Faculty of Medicine and Pharmacy, Mohammed V University, Rabat, Morocco
| | - Mohamed Bakha
- Biotechnology and Applied Microbiology Team, Department of Biology, Faculty of Science, Abdelmalek Essaadi University, BP2121, 93002, Tetouan, Morocco
| | - Hamada Imtara
- Faculty of Arts and Sciences, Arab American University, Jenin, 240, Palestine
| | | | - Abdelaali Balahbib
- Laboratory of Biodiversity, Ecology, and Genome, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Gokhan Zengin
- Physiology and Biochemistry Research Laboratory, Department of Biology, Science Faculty, Selcuk University, Konya, Turkey.
| | - Abdelhakim Bouyahya
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Center of Human Pathologies, Mohammed V University, Rabat, Morocco.
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6
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Saad B, Ghareeb B, Kmail A. Metabolic and Epigenetics Action Mechanisms of Antiobesity Medicinal Plants and Phytochemicals. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2021; 2021:9995903. [PMID: 34211580 PMCID: PMC8208872 DOI: 10.1155/2021/9995903] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/05/2021] [Accepted: 05/31/2021] [Indexed: 11/29/2022]
Abstract
Ever-growing research efforts are demonstrating the potential of medicinal plants and their phytochemicals to prevent and manage obesity, either individually or synergistically. Multiple combinations of phytochemicals can result in a synergistic activity that increases their beneficial effects at molecular, cellular, metabolic, and temporal levels, offering advantages over chemically synthesized drug-based treatments. Herbs and their derived compounds have the potential for controlling appetite, inhibiting pancreatic lipase activity, stimulating thermogenesis and lipid metabolism, increasing satiety, promoting lipolysis, regulating adipogenesis, and inducing apoptosis in adipocytes. Furthermore, targeting adipocyte life cycle using various dietary bioactives that affect different stages of adipocyte life cycle represents also an important target in the development of new antiobesity drugs. In this regard, different stages of adipocyte development that are targeted by antiobesity drugs can include preadipocytes, maturing preadipocytes, and mature adipocytes. Various herbal-derived active compounds, such as capsaicin, genistein, apigenin, luteolin, kaempferol, myricetin, quercetin, docosahexaenoic acid, quercetin, resveratrol, and ajoene, affect adipocytes during specific stages of development, resulting in either inhibition of adipogenesis or induction of apoptosis. Although numerous molecular targets that can be used for both treatment and prevention of obesity have been identified, targeted single cellular receptor or pathway has resulted in limited success. In this review, we discuss the state-of-the-art knowledge about antiobesity medicinal plants and their active compounds and their effects on several cellular, molecular, and metabolic pathways simultaneously with multiple phytochemicals through synergistic functioning which might be an appropriate approach to better management of obesity. In addition, epigenetic mechanisms (acetylation, methylation, miRNAs, ubiquitylation, phosphorylation, and chromatin packaging) of phytochemicals and their preventive and therapeutic perspective are explored in this review.
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Affiliation(s)
- Bashar Saad
- Faculties of Medicine and Arts and Sciences, Arab American University, P.O. Box 240, Jenin, State of Palestine
- Qasemi Research Center, Al-Qasemi Academy, P.O. Box 124, 30100 Baqa Al-Gharbia, Israel
| | - Bilal Ghareeb
- Faculties of Medicine and Arts and Sciences, Arab American University, P.O. Box 240, Jenin, State of Palestine
| | - Abdalsalam Kmail
- Faculties of Medicine and Arts and Sciences, Arab American University, P.O. Box 240, Jenin, State of Palestine
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7
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Grady WM. Epigenetic alterations in the gastrointestinal tract: Current and emerging use for biomarkers of cancer. Adv Cancer Res 2021; 151:425-468. [PMID: 34148620 DOI: 10.1016/bs.acr.2021.02.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Colorectal cancer is a leading cause of cancer related deaths worldwide. One of the hallmarks of cancer and a fundamental trait of virtually all gastrointestinal cancers is genomic and epigenomic DNA alterations. Cancer cells acquire genetic and epigenetic alterations that drive the initiation and progression of the cancers by altering the molecular and cell biological process of the cells. These alterations, as well as other host and microenvironment factors, ultimately mediate the initiation and progression of cancers, including colorectal cancer. Epigenetic alterations, which include changes affecting DNA methylation, histone modifications, chromatin structure, and noncoding RNA expression, have emerged as a major class of molecular alteration in colon polyps and colorectal cancer. The classes of epigenetic alterations, their status in colorectal polyps and cancer, their effects on neoplasm biology, and their application to clinical care will be discussed.
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Affiliation(s)
- William M Grady
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States; Division of Gastroenterology, University of Washington School of Medicine, Seattle, WA, United States.
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8
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Tzani I, Herrmann N, Carillo S, Spargo CA, Hagan R, Barron N, Bones J, Shannon Dillmore W, Clarke C. Tracing production instability in a clonally derived CHO cell line using single-cell transcriptomics. Biotechnol Bioeng 2021; 118:2016-2030. [PMID: 33586781 DOI: 10.1002/bit.27715] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/10/2021] [Accepted: 02/11/2021] [Indexed: 01/05/2023]
Abstract
A variety of mechanisms including transcriptional silencing, gene copy loss, and increased susceptibility to cellular stress have been associated with a sudden or gradual loss of monoclonal antibody (mAb) production in Chinese hamster ovary (CHO) cell lines. In this study, we utilized single-cell RNA-seq (scRNA-seq) to study a clonally derived CHO cell line that underwent production instability leading to a dramatic reduction of the levels of mAb produced. From the scRNA-seq data, we identified subclusters associated with variations in the mAb transgenes and observed that heavy chain gene expression was significantly lower than that of the light chain across the population. Using trajectory inference, the evolution of the cell line was reconstructed and was found to correlate with a reduction in heavy and light chain gene expression. Genes encoding for proteins involved in the response to oxidative stress and apoptosis were found to increase in expression as cells progressed along the trajectory. Future studies of CHO cell lines using this technology have the potential to dramatically enhance our understanding of the characteristics underpinning efficient manufacturing performance as well as product quality.
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Affiliation(s)
- Ioanna Tzani
- National Institute for Bioprocessing Research and Training, Co Dublin, Ireland
| | - Nicholas Herrmann
- BD Technologies and Innovation, Research Triangle Park, North Carolina, USA
| | - Sara Carillo
- National Institute for Bioprocessing Research and Training, Co Dublin, Ireland
| | - Cathy A Spargo
- BD Technologies and Innovation, Research Triangle Park, North Carolina, USA
| | - Ryan Hagan
- National Institute for Bioprocessing Research and Training, Co Dublin, Ireland.,School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland
| | - Niall Barron
- National Institute for Bioprocessing Research and Training, Co Dublin, Ireland.,School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland
| | - Jonathan Bones
- National Institute for Bioprocessing Research and Training, Co Dublin, Ireland.,School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland
| | - W Shannon Dillmore
- BD Technologies and Innovation, Research Triangle Park, North Carolina, USA
| | - Colin Clarke
- National Institute for Bioprocessing Research and Training, Co Dublin, Ireland.,School of Chemical and Bioprocess Engineering, University College Dublin, Dublin, Ireland
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Pérez-Rodriguez S, Ramírez OT, Trujillo-Roldán MA, Valdez-Cruz NA. Comparison of protein precipitation methods for sample preparation prior to proteomic analysis of Chinese hamster ovary cell homogenates. ELECTRON J BIOTECHN 2020. [DOI: 10.1016/j.ejbt.2020.09.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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10
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Zhang Y, Kou C, Wang S, Zhang Y. Genome-wide Differential-based Analysis of the Relationship between DNA Methylation and Gene Expression in Cancer. Curr Bioinform 2019. [DOI: 10.2174/1574893614666190424160046] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Background::
DNA methylation is an epigenetic modification that plays an important
role in regulating gene expression. There is evidence that the hypermethylation of promoter regions
always causes gene silencing. However, how the methylation patterns of other regions in the
genome, such as gene body and 3’UTR, affect gene expression is unknown.
Objective::
The study aimed to fully explore the relationship between DNA methylation and expression
throughout the genome-wide analysis which is important in understanding the function of
DNA methylation essentially.
Method::
In this paper, we develop a heuristic framework to analyze the relationship between the
methylated change in different regions and that of the corresponding gene expression based on differential
analysis.
Results::
To understande the methylated function of different genomic regions, a gene is divided
into seven functional regions. By applying the method in five cancer datasets from the Synapse database,
it was found that methylated regions with a significant difference between cases and controls
were almost uniformly distributed in the seven regions of the genome. Also, the effect of
DNA methylation in different regions on gene expression was different. For example, there was a
higher percentage of positive relationships in 1stExon, gene body and 3’UTR than in TSS1500 and
TSS200. The functional analysis of genes with a significant positive and negative correlation between
DNA methylation and gene expression demonstrated the epigenetic mechanism of cancerassociated
genes.
Conclusion::
Differential based analysis helps us to recognize the change in DNA methylation and
how this change affects the change in gene expression. It provides a basis for further integrating
gene expression and DNA methylation data to identify disease-associated biomarkers.
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Affiliation(s)
- Yuanyuan Zhang
- School of information and control engineering, Qingdao University of Technology, Qingdao, Shandong, China
| | - Chuanhua Kou
- School of information and control engineering, Qingdao University of Technology, Qingdao, Shandong, China
| | - Shudong Wang
- College of Computer and Communication Engineering, China University of Petroleum (East China), Qingdao, Shandong, China
| | - Yulin Zhang
- College of Mathematics and Systems Science, Shandong University of Science and Technology, Qingdao, Shandong, China
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Coronel J, Heinrich C, Klausing S, Noll T, Figueredo‐Cardero A, Castilho LR. Perfusion process combining low temperature and valeric acid for enhanced recombinant factor VIII production. Biotechnol Prog 2019; 36:e2915. [DOI: 10.1002/btpr.2915] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 08/09/2019] [Accepted: 09/17/2019] [Indexed: 01/18/2023]
Affiliation(s)
- Juliana Coronel
- Federal University of Rio de Janeiro (UFRJ), COPPECell Culture Engineering Laboratory Rio de Janeiro RJ Brazil
| | | | | | - Thomas Noll
- Bielefeld UniversityInstitute of Cell Culture Technology, Universitätsstraße 25 Bielefeld Germany
| | | | - Leda R. Castilho
- Federal University of Rio de Janeiro (UFRJ), COPPECell Culture Engineering Laboratory Rio de Janeiro RJ Brazil
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González-Becerra K, Ramos-Lopez O, Barrón-Cabrera E, Riezu-Boj JI, Milagro FI, Martínez-López E, Martínez JA. Fatty acids, epigenetic mechanisms and chronic diseases: a systematic review. Lipids Health Dis 2019; 18:178. [PMID: 31615571 PMCID: PMC6792183 DOI: 10.1186/s12944-019-1120-6] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 09/30/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Chronic illnesses like obesity, type 2 diabetes (T2D) and cardiovascular diseases, are worldwide major causes of morbidity and mortality. These pathological conditions involve interactions between environmental, genetic, and epigenetic factors. Recent advances in nutriepigenomics are contributing to clarify the role of some nutritional factors, including dietary fatty acids in gene expression regulation. This systematic review assesses currently available information concerning the role of the different fatty acids on epigenetic mechanisms that affect the development of chronic diseases or induce protective effects on metabolic alterations. METHODS A targeted search was conducted in the PubMed/Medline databases using the keywords "fatty acids and epigenetic". The data were analyzed according to the PRISMA-P guidelines. RESULTS Consumption fatty acids like n-3 PUFA: EPA and DHA, and MUFA: oleic and palmitoleic acid was associated with an improvement of metabolic alterations. On the other hand, fatty acids that have been associated with the presence or development of obesity, T2D, pro-inflammatory profile, atherosclerosis and IR were n-6 PUFA, saturated fatty acids (stearic and palmitic), and trans fatty acids (elaidic), have been also linked with epigenetic changes. CONCLUSIONS Fatty acids can regulate gene expression by modifying epigenetic mechanisms and consequently result in positive or negative impacts on metabolic outcomes.
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Affiliation(s)
- K González-Becerra
- Institute of Traslational Nutrigenetics and Nutrigenomics, Health Sciences University Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - O Ramos-Lopez
- Department of Nutrition, Food Science, Physiology and Toxicology, Centre for Nutrition Research, University of Navarra, Pamplona, Spain
- Faculty of Medicine and Psychology, Autonomous University of Baja California, Tijuana, B.C., Mexico
| | - E Barrón-Cabrera
- Institute of Traslational Nutrigenetics and Nutrigenomics, Health Sciences University Center, University of Guadalajara, Guadalajara, Jalisco, Mexico
| | - J I Riezu-Boj
- Department of Nutrition, Food Science, Physiology and Toxicology, Centre for Nutrition Research, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
| | - F I Milagro
- Department of Nutrition, Food Science, Physiology and Toxicology, Centre for Nutrition Research, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición (CIBERobn), Carlos III Health Institute, Madrid, Spain
| | - E Martínez-López
- Institute of Traslational Nutrigenetics and Nutrigenomics, Health Sciences University Center, University of Guadalajara, Guadalajara, Jalisco, Mexico.
- Department of Molecular Biology in Medicine, Health Sciences University Center, University of Guadalajara, Sierra Mojada 950, 44340, Guadalajara, Jalisco, Mexico.
| | - J A Martínez
- Department of Nutrition, Food Science, Physiology and Toxicology, Centre for Nutrition Research, University of Navarra, Pamplona, Spain
- Navarra Institute for Health Research (IdiSNA), Pamplona, Spain
- Centro de Investigación Biomédica en Red Fisiopatología de la Obesidad y Nutrición (CIBERobn), Carlos III Health Institute, Madrid, Spain
- Madrid Institute of Advanced Studies (IMDEA Food), Madrid, Spain
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13
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Allen J, Sears CL. Impact of the gut microbiome on the genome and epigenome of colon epithelial cells: contributions to colorectal cancer development. Genome Med 2019; 11:11. [PMID: 30803449 PMCID: PMC6388476 DOI: 10.1186/s13073-019-0621-2] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In recent years, the number of studies investigating the impact of the gut microbiome in colorectal cancer (CRC) has risen sharply. As a result, we now know that various microbes (and microbial communities) are found more frequently in the stool and mucosa of individuals with CRC than healthy controls, including in the primary tumors themselves, and even in distant metastases. We also know that these microbes induce tumors in various mouse models, but we know little about how they impact colon epithelial cells (CECs) directly, or about how these interactions might lead to modifications at the genetic and epigenetic levels that trigger and propagate tumor growth. Rates of CRC are increasing in younger individuals, and CRC remains the second most frequent cause of cancer-related deaths globally. Hence, a more in-depth understanding of the role that gut microbes play in CRC is needed. Here, we review recent advances in understanding the impact of gut microbes on the genome and epigenome of CECs, as it relates to CRC. Overall, numerous studies in the past few years have definitively shown that gut microbes exert distinct impacts on DNA damage, DNA methylation, chromatin structure and non-coding RNA expression in CECs. Some of the genes and pathways that are altered by gut microbes relate to CRC development, particularly those involved in cell proliferation and WNT signaling. We need to implement more standardized analysis strategies, collate data from multiple studies, and utilize CRC mouse models to better assess these effects, understand their functional relevance, and leverage this information to improve patient care.
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Affiliation(s)
- Jawara Allen
- Department of Medicine, Johns Hopkins University School of Medicine, Orleans Street, Baltimore, MD, 21231, USA
| | - Cynthia L Sears
- Department of Medicine, Johns Hopkins University School of Medicine, Orleans Street, Baltimore, MD, 21231, USA. .,Bloomberg-Kimmel Institute for Immunotherapy and Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins Medical Institutions, North Broadway, Baltimore, MD, 21231, USA.
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Möller J, Korte K, Pörtner R, Zeng AP, Jandt U. Model-based identification of cell-cycle-dependent metabolism and putative autocrine effects in antibody producing CHO cell culture. Biotechnol Bioeng 2018; 115:2996-3008. [DOI: 10.1002/bit.26828] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 08/20/2018] [Accepted: 08/30/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Johannes Möller
- Hamburg University of Technology, Institute of Bioprocess and Biosystems Engineering; Hamburg Germany
| | - Katrin Korte
- Hamburg University of Technology, Institute of Bioprocess and Biosystems Engineering; Hamburg Germany
| | - Ralf Pörtner
- Hamburg University of Technology, Institute of Bioprocess and Biosystems Engineering; Hamburg Germany
| | - An-Ping Zeng
- Hamburg University of Technology, Institute of Bioprocess and Biosystems Engineering; Hamburg Germany
| | - Uwe Jandt
- Hamburg University of Technology, Institute of Bioprocess and Biosystems Engineering; Hamburg Germany
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15
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Marx N, Grünwald-Gruber C, Bydlinski N, Dhiman H, Ngoc Nguyen L, Klanert G, Borth N. CRISPR-Based Targeted Epigenetic Editing Enables Gene Expression Modulation of the Silenced Beta-Galactoside Alpha-2,6-Sialyltransferase 1 in CHO Cells. Biotechnol J 2018; 13:e1700217. [DOI: 10.1002/biot.201700217] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/01/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Nicolas Marx
- Department of Biotechnology; BOKU University of Natural Resources and Life Sciences; Muthgasse 18 1190 Vienna Austria
- Austrian Centre of Industrial Biotechnology GmbH; Graz Austria
| | - Clemens Grünwald-Gruber
- Department of Biotechnology; BOKU University of Natural Resources and Life Sciences; Muthgasse 18 1190 Vienna Austria
| | - Nina Bydlinski
- Department of Biotechnology; BOKU University of Natural Resources and Life Sciences; Muthgasse 18 1190 Vienna Austria
| | - Heena Dhiman
- Department of Biotechnology; BOKU University of Natural Resources and Life Sciences; Muthgasse 18 1190 Vienna Austria
- Austrian Centre of Industrial Biotechnology GmbH; Graz Austria
| | - Ly Ngoc Nguyen
- Department of Biotechnology; BOKU University of Natural Resources and Life Sciences; Muthgasse 18 1190 Vienna Austria
- Austrian Centre of Industrial Biotechnology GmbH; Graz Austria
| | - Gerald Klanert
- Austrian Centre of Industrial Biotechnology GmbH; Graz Austria
| | - Nicole Borth
- Department of Biotechnology; BOKU University of Natural Resources and Life Sciences; Muthgasse 18 1190 Vienna Austria
- Austrian Centre of Industrial Biotechnology GmbH; Graz Austria
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16
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Segar KP, Chandrawanshi V, Mehra S. Activation of unfolded protein response pathway is important for valproic acid mediated increase in immunoglobulin G productivity in recombinant Chinese hamster ovary cells. J Biosci Bioeng 2017; 124:459-468. [DOI: 10.1016/j.jbiosc.2017.05.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/10/2017] [Indexed: 01/18/2023]
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17
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Label-free protein quantification of sodium butyrate treated CHO cells by ESI-UHR-TOF-MS. J Biotechnol 2017; 257:87-98. [DOI: 10.1016/j.jbiotec.2017.03.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 03/27/2017] [Accepted: 03/27/2017] [Indexed: 11/18/2022]
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