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Raabe J, Wittig I, Laurette P, Stathopoulou K, Brand T, Schulze T, Klampe B, Orthey E, Cabrera-Orefice A, Meisterknecht J, Thiemann E, Laufer SD, Shibamiya A, Reinsch M, Fuchs S, Kaiser J, Yang J, Zehr S, Wrona KM, Lorenz K, Lukowski R, Hansen A, Gilsbach R, Brandes RP, Ulmer BM, Eschenhagen T, Cuello F. Physioxia rewires mitochondrial complex composition to protect stem cell viability. Redox Biol 2024; 77:103352. [PMID: 39341035 DOI: 10.1016/j.redox.2024.103352] [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: 05/27/2024] [Revised: 09/06/2024] [Accepted: 09/09/2024] [Indexed: 09/30/2024] Open
Abstract
Human induced pluripotent stem cells (hiPSCs) are an invaluable tool to study molecular mechanisms on a human background. Culturing stem cells at an oxygen level different from their microenvironmental niche impacts their viability. To understand this mechanistically, dermal skin fibroblasts of 52 probands were reprogrammed into hiPSCs, followed by either hyperoxic (20 % O2) or physioxic (5 % O2) culture and proteomic profiling. Analysis of chromosomal stability by Giemsa-banding revealed that physioxic -cultured hiPSC clones exhibited less pathological karyotypes than hyperoxic (e.g. 6 % vs. 32 % mosaicism), higher pluripotency as evidenced by higher Stage-Specific Embryonic Antigen 3 positivity, higher glucose consumption and lactate production. Global proteomic analysis demonstrated lower abundance of several subunits of NADH:ubiquinone oxidoreductase (complex I) and an underrepresentation of pathways linked to oxidative phosphorylation and cellular senescence. Accordingly, release of the pro-senescent factor IGFBP3 and β-galactosidase staining were lower in physioxic hiPSCs. RNA- and ATAC-seq profiling revealed a distinct hypoxic transcription factor-binding footprint, amongst others higher expression of the HIF1α-regulated target NDUFA4L2 along with increased chromatin accessibility of the NDUFA4L2 gene locus. While mitochondrial DNA content did not differ between groups, physioxic hiPSCs revealed lower polarized mitochondrial membrane potential, altered mitochondrial network appearance and reduced basal respiration and electron transfer capacity. Blue-native polyacrylamide gel electrophoresis coupled to mass spectrometry of the mitochondrial complexes detected higher abundance of NDUFA4L2 and ATP5IF1 and loss of incorporation into complex IV or V, respectively. Taken together, physioxic culture of hiPSCs improved chromosomal stability, which was associated with downregulation of oxidative phosphorylation and senescence and extensive re-wiring of mitochondrial complex composition.
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Affiliation(s)
- Janice Raabe
- Institute of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Ilka Wittig
- Functional Proteomics Center, Institute for Cardiovascular Physiology, Goethe-University, 60590 Frankfurt am Main, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Rhein-Main, Frankfurt, Germany
| | - Patrick Laurette
- Institute of Experimental Cardiology, Heidelberg University Hospital, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany
| | - Konstantina Stathopoulou
- Institute of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Theresa Brand
- Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany
| | - Thomas Schulze
- Institute of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Birgit Klampe
- Institute of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Ellen Orthey
- Institute of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Alfredo Cabrera-Orefice
- Functional Proteomics Center, Institute for Cardiovascular Physiology, Goethe-University, 60590 Frankfurt am Main, Germany
| | - Jana Meisterknecht
- Functional Proteomics Center, Institute for Cardiovascular Physiology, Goethe-University, 60590 Frankfurt am Main, Germany
| | - Ellen Thiemann
- Institute of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Sandra D Laufer
- Institute of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Aya Shibamiya
- Institute of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Marina Reinsch
- Institute of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Sigrid Fuchs
- Institute for Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Jennifer Kaiser
- Institute for Human Genetics, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Jiaqi Yang
- Institute of Pharmacy, Experimental Pharmacology, University Tübingen, 72076 Tübingen, Germany
| | - Simonida Zehr
- DZHK (German Center for Cardiovascular Research), Partner Site Rhein-Main, Frankfurt, Germany; Institute for Cardiovascular Physiology, Goethe-University, 60590 Frankfurt am Main, Germany
| | - Kinga M Wrona
- Institute of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Kristina Lorenz
- Institute of Pharmacology and Toxicology, University of Würzburg, Würzburg, Germany; Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., Dortmund, Germany
| | - Robert Lukowski
- Institute of Pharmacy, Experimental Pharmacology, University Tübingen, 72076 Tübingen, Germany
| | - Arne Hansen
- Institute of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Ralf Gilsbach
- Institute of Experimental Cardiology, Heidelberg University Hospital, 69120 Heidelberg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany
| | - Ralf P Brandes
- DZHK (German Center for Cardiovascular Research), Partner Site Rhein-Main, Frankfurt, Germany; Institute for Cardiovascular Physiology, Goethe-University, 60590 Frankfurt am Main, Germany
| | - Bärbel M Ulmer
- Institute of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Thomas Eschenhagen
- Institute of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany.
| | - Friederike Cuello
- Institute of Experimental Pharmacology and Toxicology, Cardiovascular Research Center, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany; DZHK (German Center for Cardiovascular Research), Partner Site Hamburg/Kiel/Lübeck, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany.
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2
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Di Giorgio E, Dalla E, Tolotto V, D’Este F, Paluvai H, Ranzino L, Brancolini C. HDAC4 influences the DNA damage response and counteracts senescence by assembling with HDAC1/HDAC2 to control H2BK120 acetylation and homology-directed repair. Nucleic Acids Res 2024; 52:8218-8240. [PMID: 38874468 PMCID: PMC11317144 DOI: 10.1093/nar/gkae501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/15/2024] Open
Abstract
Access to DNA is the first level of control in regulating gene transcription, a control that is also critical for maintaining DNA integrity. Cellular senescence is characterized by profound transcriptional rearrangements and accumulation of DNA lesions. Here, we discovered an epigenetic complex between HDAC4 and HDAC1/HDAC2 that is involved in the erase of H2BK120 acetylation. The HDAC4/HDAC1/HDAC2 complex modulates the efficiency of DNA repair by homologous recombination, through dynamic deacetylation of H2BK120. Deficiency of HDAC4 leads to accumulation of H2BK120ac, impaired recruitment of BRCA1 and CtIP to the site of lesions, accumulation of damaged DNA and senescence. In senescent cells this complex is disassembled because of increased proteasomal degradation of HDAC4. Forced expression of HDAC4 during RAS-induced senescence reduces the genomic spread of γH2AX. It also affects H2BK120ac levels, which are increased in DNA-damaged regions that accumulate during RAS-induced senescence. In summary, degradation of HDAC4 during senescence causes the accumulation of damaged DNA and contributes to the activation of the transcriptional program controlled by super-enhancers that maintains senescence.
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Affiliation(s)
- Eros Di Giorgio
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
| | - Emiliano Dalla
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
| | - Vanessa Tolotto
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
| | - Francesca D’Este
- Laboratory of Biochemistry, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
| | - Harikrishnareddy Paluvai
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
| | - Liliana Ranzino
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
| | - Claudio Brancolini
- Laboratory of Epigenomics, Department of Medicine, Università degli Studi di Udine, p.le Kolbe 4, 33100 Udine, Italy
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Rogers ZJ, Colombani T, Khan S, Bhatt K, Nukovic A, Zhou G, Woolston BM, Taylor CT, Gilkes DM, Slavov N, Bencherif SA. Controlling Pericellular Oxygen Tension in Cell Culture Reveals Distinct Breast Cancer Responses to Low Oxygen Tensions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2402557. [PMID: 38874400 PMCID: PMC11321643 DOI: 10.1002/advs.202402557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 04/11/2024] [Indexed: 06/15/2024]
Abstract
In oxygen (O2)-controlled cell culture, an indispensable tool in biological research, it is presumed that the incubator setpoint equals the O2 tension experienced by cells (i.e., pericellular O2). However, it is discovered that physioxic (5% O2) and hypoxic (1% O2) setpoints regularly induce anoxic (0% O2) pericellular tensions in both adherent and suspension cell cultures. Electron transport chain inhibition ablates this effect, indicating that cellular O2 consumption is the driving factor. RNA-seq analysis revealed that primary human hepatocytes cultured in physioxia experience ischemia-reperfusion injury due to cellular O2 consumption. A reaction-diffusion model is developed to predict pericellular O2 tension a priori, demonstrating that the effect of cellular O2 consumption has the greatest impact in smaller volume culture vessels. By controlling pericellular O2 tension in cell culture, it is found that hypoxia vs. anoxia induce distinct breast cancer transcriptomic and translational responses, including modulation of the hypoxia-inducible factor (HIF) pathway and metabolic reprogramming. Collectively, these findings indicate that breast cancer cells respond non-monotonically to low O2, suggesting that anoxic cell culture is not suitable for modeling hypoxia. Furthermore, it is shown that controlling atmospheric O2 tension in cell culture incubators is insufficient to regulate O2 in cell culture, thus introducing the concept of pericellular O2-controlled cell culture.
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Affiliation(s)
- Zachary J. Rogers
- Department of Chemical EngineeringNortheastern UniversityBostonMA02115USA
| | - Thibault Colombani
- Department of Chemical EngineeringNortheastern UniversityBostonMA02115USA
| | - Saad Khan
- Department of BioengineeringNortheastern UniversityBostonMA02115USA
| | - Khushbu Bhatt
- Department of Pharmaceutical SciencesNortheastern UniversityBostonMA02115USA
| | - Alexandra Nukovic
- Department of Chemical EngineeringNortheastern UniversityBostonMA02115USA
| | - Guanyu Zhou
- Department of Chemical EngineeringNortheastern UniversityBostonMA02115USA
| | | | - Cormac T. Taylor
- Conway Institute of Biomolecular and Biomedical Research and School of MedicineUniversity College DublinBelfieldDublinD04 V1W8Ireland
| | - Daniele M. Gilkes
- Department of OncologyThe Sidney Kimmel Comprehensive Cancer CenterThe Johns Hopkins University School of MedicineBaltimoreMD21321USA
- Cellular and Molecular Medicine ProgramThe Johns Hopkins University School of MedicineBaltimoreMD21321USA
- Department of Chemical and Biomolecular EngineeringThe Johns Hopkins UniversityBaltimoreMD21218USA
- Johns Hopkins Institute for NanoBioTechnologyThe Johns Hopkins UniversityBaltimoreMD21218USA
| | - Nikolai Slavov
- Department of BioengineeringNortheastern UniversityBostonMA02115USA
- Departments of BioengineeringBiologyChemistry and Chemical BiologySingle Cell Center and Barnett InstituteNortheastern UniversityBostonMA02115USA
- Parallel Squared Technology InstituteWatertownMA02472USA
| | - Sidi A. Bencherif
- Department of Chemical EngineeringNortheastern UniversityBostonMA02115USA
- Department of BioengineeringNortheastern UniversityBostonMA02115USA
- Harvard John A. Paulson School of Engineering and Applied SciencesHarvard UniversityCambridgeMA02138USA
- Biomechanics and Bioengineering (BMBI)UTC CNRS UMR 7338University of Technology of CompiègneSorbonne UniversityCompiègne60203France
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4
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Rasouli M, Fattahi R, Nuoroozi G, Zarei-Behjani Z, Yaghoobi M, Hajmohammadi Z, Hosseinzadeh S. The role of oxygen tension in cell fate and regenerative medicine: implications of hypoxia/hyperoxia and free radicals. Cell Tissue Bank 2024; 25:195-215. [PMID: 37365484 DOI: 10.1007/s10561-023-10099-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 06/18/2023] [Indexed: 06/28/2023]
Abstract
Oxygen pressure plays an integral role in regulating various aspects of cellular biology. Cell metabolism, proliferation, morphology, senescence, metastasis, and angiogenesis are some instances that are affected by different tensions of oxygen. Hyperoxia or high oxygen concentration, enforces the production of reactive oxygen species (ROS) that disturbs physiological homeostasis, and consequently, in the absence of antioxidants, cells and tissues are directed to an undesired fate. On the other side, hypoxia or low oxygen concentration, impacts cell metabolism and fate strongly through inducing changes in the expression level of specific genes. Thus, understanding the precise mechanism and the extent of the implication of oxygen tension and ROS in biological events is crucial to maintaining the desired cell and tissue function for application in regenerative medicine strategies. Herein, a comprehensive literature review has been performed to find out the impacts of oxygen tensions on the various behaviors of cells or tissues.
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Affiliation(s)
- Mehdi Rasouli
- Student Research Committee, Department of Tissue Engineering and Applied Cell Science, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Roya Fattahi
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, 1985717443, Iran
| | - Ghader Nuoroozi
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, 1985717443, Iran
| | - Zeinab Zarei-Behjani
- Department of Applied Cell Sciences, School of Advanced Technologies in Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maliheh Yaghoobi
- Engineering Department, Faculty of Chemical Engineering, Zanjan University, Zanjan, Iran
| | - Zeinab Hajmohammadi
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, 1985717443, Iran
| | - Simzar Hosseinzadeh
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, 1985717443, Iran.
- Medical Nanotechnology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Yasan GT, Gunel-Ozcan A. Hypoxia and Hypoxia Mimetic Agents As Potential Priming Approaches to Empower Mesenchymal Stem Cells. Curr Stem Cell Res Ther 2024; 19:33-54. [PMID: 36642875 DOI: 10.2174/1574888x18666230113143234] [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: 07/29/2022] [Revised: 10/12/2022] [Accepted: 11/04/2022] [Indexed: 01/17/2023]
Abstract
Mesenchymal stem cells (MSC) exhibit self-renewal capacity and multilineage differentiation potential, making them attractive for research and clinical application. The properties of MSC can vary depending on specific micro-environmental factors. MSC resides in specific niches with low oxygen concentrations, where oxygen functions as a metabolic substrate and a signaling molecule. Conventional physical incubators or chemically hypoxia mimetic agents are applied in cultures to mimic the original low oxygen tension settings where MSC originated. This review aims to focus on the current knowledge of the effects of various physical hypoxic conditions and widely used hypoxia-mimetic agents-PHD inhibitors on mesenchymal stem cells at a cellular and molecular level, including proliferation, stemness, differentiation, viability, apoptosis, senescence, migration, immunomodulation behaviors, as well as epigenetic changes.
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Affiliation(s)
| | - Aysen Gunel-Ozcan
- Department of Stem Cell Sciences, Center for Stem Cell Research and Development, Hacettepe University, Ankara, Turkey
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Yemelyanov VV, Puzanskiy RK, Shishova MF. Plant Life with and without Oxygen: A Metabolomics Approach. Int J Mol Sci 2023; 24:16222. [PMID: 38003412 PMCID: PMC10671363 DOI: 10.3390/ijms242216222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/26/2023] Open
Abstract
Oxygen deficiency is an environmental challenge which affects plant growth, the development and distribution in land and aquatic ecosystems, as well as crop yield losses worldwide. The capacity to exist in the conditions of deficiency or the complete lack of oxygen depends on a number of anatomic, developmental and molecular adaptations. The lack of molecular oxygen leads to an inhibition of aerobic respiration, which causes energy starvation and the acceleration of glycolysis passing into fermentations. We focus on systemic metabolic alterations revealed with the different approaches of metabolomics. Oxygen deprivation stimulates the accumulation of glucose, pyruvate and lactate, indicating the acceleration of the sugar metabolism, glycolysis and lactic fermentation, respectively. Among the Krebs-cycle metabolites, only the succinate level increases. Amino acids related to glycolysis, including the phosphoglycerate family (Ser and Gly), shikimate family (Phe, Tyr and Trp) and pyruvate family (Ala, Leu and Val), are greatly elevated. Members of the Asp family (Asn, Lys, Met, Thr and Ile), as well as the Glu family (Glu, Pro, Arg and GABA), accumulate as well. These metabolites are important members of the metabolic signature of oxygen deficiency in plants, linking glycolysis with an altered Krebs cycle and allowing alternative pathways of NAD(P)H reoxidation to avoid the excessive accumulation of toxic fermentation products (lactate, acetaldehyde, ethanol). Reoxygenation induces the downregulation of the levels of major anaerobically induced metabolites, including lactate, succinate and amino acids, especially members of the pyruvate family (Ala, Leu and Val), Tyr and Glu family (GABA and Glu) and Asp family (Asn, Met, Thr and Ile). The metabolic profiles during native and environmental hypoxia are rather similar, consisting in the accumulation of fermentation products, succinate, fumarate and amino acids, particularly Ala, Gly and GABA. The most intriguing fact is that metabolic alterations during oxidative stress are very much similar, with plant response to oxygen deprivation but not to reoxygenation.
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Affiliation(s)
- Vladislav V. Yemelyanov
- Department of Genetics and Biotechnology, Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Roman K. Puzanskiy
- Department of Plant Physiology and Biochemistry, Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (R.K.P.); (M.F.S.)
- Laboratory of Analytical Phytochemistry, Komarov Botanical Institute of the Russian Academy of Sciences, 197376 St. Petersburg, Russia
| | - Maria F. Shishova
- Department of Plant Physiology and Biochemistry, Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia; (R.K.P.); (M.F.S.)
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7
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Rogers ZJ, Colombani T, Khan S, Bhatt K, Nukovic A, Zhou G, Woolston BM, Taylor CT, Gilkes DM, Slavov N, Bencherif SA. Controlling pericellular oxygen tension in cell culture reveals distinct breast cancer responses to low oxygen tensions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.02.560369. [PMID: 37873449 PMCID: PMC10592900 DOI: 10.1101/2023.10.02.560369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Oxygen (O2) tension plays a key role in tissue function and pathophysiology. O2-controlled cell culture, in which the O2 concentration in an incubator's gas phase is controlled, is an indispensable tool to study the role of O2 in vivo. For this technique, it is presumed that the incubator setpoint is equal to the O2 tension that cells experience (i.e., pericellular O2). We discovered that physioxic (5% O2) and hypoxic (1% O2) setpoints regularly induce anoxic (0.0% O2) pericellular tensions in both adherent and suspension cell cultures. Electron transport chain inhibition ablates this effect, indicating that cellular O2 consumption is the driving factor. RNA-seq revealed that primary human hepatocytes cultured in physioxia experience ischemia-reperfusion injury due to anoxic exposure followed by rapid reoxygenation. To better understand the relationship between incubator gas phase and pericellular O2 tensions, we developed a reaction-diffusion model that predicts pericellular O2 tension a priori. This model revealed that the effect of cellular O2 consumption is greatest in smaller volume culture vessels (e.g., 96-well plate). By controlling pericellular O2 tension in cell culture, we discovered that MCF7 cells have stronger glycolytic and glutamine metabolism responses in anoxia vs. hypoxia. MCF7 also expressed higher levels of HIF2A, CD73, NDUFA4L2, etc. and lower levels of HIF1A, CA9, VEGFA, etc. in response to hypoxia vs. anoxia. Proteomics revealed that 4T1 cells had an upregulated epithelial-to-mesenchymal transition (EMT) response and downregulated reactive oxygen species (ROS) management, glycolysis, and fatty acid metabolism pathways in hypoxia vs. anoxia. Collectively, these results reveal that breast cancer cells respond non-monotonically to low O2, suggesting that anoxic cell culture is not suitable to model hypoxia. We demonstrate that controlling atmospheric O2 tension in cell culture incubators is insufficient to control O2 in cell culture and introduce the concept of pericellular O2-controlled cell culture.
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Affiliation(s)
- Zachary J. Rogers
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115, USA
| | - Thibault Colombani
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115, USA
| | - Saad Khan
- Department of Bioengineering, Northeastern University, Boston, MA 02115, USA
| | - Khushbu Bhatt
- Department of Pharmaceutical Sciences, Northeastern University, Boston, MA 02115, USA
| | - Alexandra Nukovic
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115, USA
| | - Guanyu Zhou
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115, USA
| | - Benjamin M. Woolston
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115, USA
| | - Cormac T. Taylor
- Conway Institute of Biomolecular and Biomedical Research and School of Medicine, University College Dublin, Belfield, Dublin, Ireland
| | - Daniele M. Gilkes
- Department of Oncology, The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21321, USA
- Cellular and Molecular Medicine Program, The Johns Hopkins University School of Medicine, Baltimore, MD 21321, USA
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University, Baltimore, MD 21218, USA
- Johns Hopkins Institute for NanoBioTechnology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Nikolai Slavov
- Departments of Bioengineering, Biology, Chemistry and Chemical Biology, Single Cell Center and Barnett Institute, Northeastern University, Boston, MA 02115 USA
- Parallel Squared Technology Institute, Watertown, MA 02135 USA
| | - Sidi A. Bencherif
- Department of Chemical Engineering, Northeastern University, Boston, MA 02115, USA
- Department of Bioengineering, Northeastern University, Boston, MA 02115, USA
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA
- Biomechanics and Bioengineering (BMBI), UTC CNRS UMR 7338, University of Technology of Compiègne, Sorbonne University, 60203 Compiègne, France
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8
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Moreno SR. The breathless niche: unrevealing the metabolic landscape of root stem cells under hypoxia stress. PLANT PHYSIOLOGY 2023; 193:880-882. [PMID: 37549242 PMCID: PMC10517184 DOI: 10.1093/plphys/kiad418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 07/10/2023] [Indexed: 08/09/2023]
Affiliation(s)
- Sebastián R Moreno
- Assistant Features Editor, Plant Physiology, American Society of Plant Biologists, USA
- Sainsbury Laboratory, University of Cambridge, Cambridge CB2 1LR, UK
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9
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Bloom SI, Islam MT, Lesniewski LA, Donato AJ. Mechanisms and consequences of endothelial cell senescence. Nat Rev Cardiol 2023; 20:38-51. [PMID: 35853997 PMCID: PMC10026597 DOI: 10.1038/s41569-022-00739-0] [Citation(s) in RCA: 95] [Impact Index Per Article: 95.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/13/2022] [Indexed: 12/15/2022]
Abstract
Endothelial cells are located at the crucial interface between circulating blood and semi-solid tissues and have many important roles in maintaining systemic physiological function. The vascular endothelium is particularly susceptible to pathogenic stimuli that activate tumour suppressor pathways leading to cellular senescence. We now understand that senescent endothelial cells are highly active, secretory and pro-inflammatory, and have an aberrant morphological phenotype. Moreover, endothelial senescence has been identified as an important contributor to various cardiovascular and metabolic diseases. In this Review, we discuss the consequences of endothelial cell exposure to damaging stimuli (haemodynamic forces and circulating and endothelial-derived factors) and the cellular and molecular mechanisms that induce endothelial cell senescence. We also discuss how endothelial cell senescence causes arterial dysfunction and contributes to clinical cardiovascular diseases and metabolic disorders. Finally, we summarize the latest evidence on the effect of eliminating senescent endothelial cells (senolysis) and identify important remaining questions to be addressed in future studies.
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Affiliation(s)
- Samuel I Bloom
- Department of Nutrition and Integrative Physiology, University of Utah, Salt Lake City, UT, USA
| | - Md Torikul Islam
- Department of Nutrition and Integrative Physiology, University of Utah, Salt Lake City, UT, USA
| | - Lisa A Lesniewski
- Department of Nutrition and Integrative Physiology, University of Utah, Salt Lake City, UT, USA
- Department of Internal Medicine, Division of Geriatrics, University of Utah, Salt Lake City, UT, USA
- Veterans Affairs Medical Center-Salt Lake City, Geriatric Research Education and Clinical Center, Salt Lake City, UT, USA
| | - Anthony J Donato
- Department of Nutrition and Integrative Physiology, University of Utah, Salt Lake City, UT, USA.
- Department of Internal Medicine, Division of Geriatrics, University of Utah, Salt Lake City, UT, USA.
- Veterans Affairs Medical Center-Salt Lake City, Geriatric Research Education and Clinical Center, Salt Lake City, UT, USA.
- Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.
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10
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Mori MP, Penjweini R, Knutson JR, Wang PY, Hwang PM. Mitochondria and oxygen homeostasis. FEBS J 2022; 289:6959-6968. [PMID: 34235856 PMCID: PMC8790743 DOI: 10.1111/febs.16115] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 06/25/2021] [Accepted: 07/07/2021] [Indexed: 01/13/2023]
Abstract
Molecular oxygen possesses a dual nature due to its highly reactive free radical property: it is capable of oxidizing metabolic substrates to generate cellular energy, but can also serve as a substrate for genotoxic reactive oxygen species generation. As a labile substance upon which aerobic life depends, the mechanisms for handling cellular oxygen have been fine-tuned and orchestrated in evolution. Protection from atmospheric oxygen toxicity as originally posited by the Endosymbiotic Theory of the Mitochondrion is likely to be one basic principle underlying oxygen homeostasis. We briefly review the literature on oxygen homeostasis both in vitro and in vivo with a focus on the role of the mitochondrion where the majority of cellular oxygen is consumed. The insights gleaned from these basic mechanisms are likely to be important for understanding disease pathogenesis and developing strategies for maintaining health.
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Affiliation(s)
- Mateus P. Mori
- Cardiovascular Branch; National Heart, Lung, and Blood Institute; National Institutes of Health; Bethesda, Maryland, USA
| | - Rozhin Penjweini
- Laboratory of Advanced Microscopy and Biophotonics; National Heart, Lung, and Blood Institute; National Institutes of Health; Bethesda, Maryland, USA
| | - Jay R. Knutson
- Laboratory of Advanced Microscopy and Biophotonics; National Heart, Lung, and Blood Institute; National Institutes of Health; Bethesda, Maryland, USA
| | - Ping-yuan Wang
- Cardiovascular Branch; National Heart, Lung, and Blood Institute; National Institutes of Health; Bethesda, Maryland, USA
| | - Paul M. Hwang
- Cardiovascular Branch; National Heart, Lung, and Blood Institute; National Institutes of Health; Bethesda, Maryland, USA
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11
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Alva R, Gardner GL, Liang P, Stuart JA. Supraphysiological Oxygen Levels in Mammalian Cell Culture: Current State and Future Perspectives. Cells 2022; 11:3123. [PMID: 36231085 PMCID: PMC9563760 DOI: 10.3390/cells11193123] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 11/17/2022] Open
Abstract
Most conventional incubators used in cell culture do not regulate O2 levels, making the headspace O2 concentration ~18%. In contrast, most human tissues are exposed to 2-6% O2 (physioxia) in vivo. Accumulating evidence has shown that such hyperoxic conditions in standard cell culture practices affect a variety of biological processes. In this review, we discuss how supraphysiological O2 levels affect reactive oxygen species (ROS) metabolism and redox homeostasis, gene expression, replicative lifespan, cellular respiration, and mitochondrial dynamics. Furthermore, we present evidence demonstrating how hyperoxic cell culture conditions fail to recapitulate the physiological and pathological behavior of tissues in vivo, including cases of how O2 alters the cellular response to drugs, hormones, and toxicants. We conclude that maintaining physioxia in cell culture is imperative in order to better replicate in vivo-like tissue physiology and pathology, and to avoid artifacts in research involving cell culture.
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Affiliation(s)
- Ricardo Alva
- Department of Biological Sciences, Brock University, St. Catharines, ON L2S 3A1, Canada
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12
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Alva R, Mirza M, Baiton A, Lazuran L, Samokysh L, Bobinski A, Cowan C, Jaimon A, Obioru D, Al Makhoul T, Stuart JA. Oxygen toxicity: cellular mechanisms in normobaric hyperoxia. Cell Biol Toxicol 2022; 39:111-143. [PMID: 36112262 PMCID: PMC9483325 DOI: 10.1007/s10565-022-09773-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/07/2022] [Indexed: 12/15/2022]
Abstract
In clinical settings, oxygen therapy is administered to preterm neonates and to adults with acute and chronic conditions such as COVID-19, pulmonary fibrosis, sepsis, cardiac arrest, carbon monoxide poisoning, and acute heart failure. In non-clinical settings, divers and astronauts may also receive supplemental oxygen. In addition, under current standard cell culture practices, cells are maintained in atmospheric oxygen, which is several times higher than what most cells experience in vivo. In all the above scenarios, the elevated oxygen levels (hyperoxia) can lead to increased production of reactive oxygen species from mitochondria, NADPH oxidases, and other sources. This can cause cell dysfunction or death. Acute hyperoxia injury impairs various cellular functions, manifesting ultimately as physiological deficits. Chronic hyperoxia, particularly in the neonate, can disrupt development, leading to permanent deficiencies. In this review, we discuss the cellular activities and pathways affected by hyperoxia, as well as strategies that have been developed to ameliorate injury.
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Affiliation(s)
- Ricardo Alva
- Department of Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Maha Mirza
- Department of Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Adam Baiton
- Department of Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Lucas Lazuran
- Department of Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Lyuda Samokysh
- Department of Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Ava Bobinski
- Department of Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Cale Cowan
- Department of Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Alvin Jaimon
- Department of Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Dede Obioru
- Department of Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Tala Al Makhoul
- Department of Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada
| | - Jeffrey A Stuart
- Department of Biological Sciences, Brock University, St. Catharines, ON, L2S 3A1, Canada.
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13
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Fuentes P, Torres MJ, Arancibia R, Aulestia F, Vergara M, Carrión F, Osses N, Altamirano C. Dynamic Culture of Mesenchymal Stromal/Stem Cell Spheroids and Secretion of Paracrine Factors. Front Bioeng Biotechnol 2022; 10:916229. [PMID: 36046670 PMCID: PMC9421039 DOI: 10.3389/fbioe.2022.916229] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 06/01/2022] [Indexed: 11/13/2022] Open
Abstract
In recent years, conditioned medium (CM) obtained from the culture of mesenchymal stromal/stem cells (MSCs) has been shown to effectively promote tissue repair and modulate the immune response in vitro and in different animal models, with potential for application in regenerative medicine. Using CM offers multiple advantages over the implantation of MSCs themselves: 1) simpler storage, transport, and preservation requirements, 2) avoidance of the inherent risks of cell transplantation, and 3) potential application as a ready-to-go biologic product. For these reasons, a large amount of MSCs research has focused on the characterization of the obtained CM, including soluble trophic factors and vesicles, preconditioning strategies for enhancing paracrine secretion, such as hypoxia, a three-dimensional (3D) environment, and biochemical stimuli, and potential clinical applications. In vitro preconditioning strategies can increase the viability, proliferation, and paracrine properties of MSCs and therefore improve the therapeutic potential of the cells and their derived products. Specifically, dynamic cultivation conditions, such as fluid flow and 3D aggregate culture, substantially impact cellular behaviour. Increased levels of growth factors and cytokines were observed in 3D cultures of MSC grown on orbital or rotatory shaking platforms, in stirred systems, such as spinner flasks or stirred tank reactors, and in microgravity bioreactors. However, only a few studies have established dynamic culture conditions and protocols for 3D aggregate cultivation of MSCs as a scalable and reproducible strategy for CM production. This review summarizes significant advances into the upstream processing, mainly the dynamic generation and cultivation of MSC aggregates, for de CM manufacture and focuses on the standardization of the soluble factor production.
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Affiliation(s)
- Paloma Fuentes
- Escuela de Ingeniería Bioquímica, Facultad de Ingeniería, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - María José Torres
- Escuela de Ingeniería Bioquímica, Facultad de Ingeniería, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Rodrigo Arancibia
- Cellus Medicina Regenerativa S.A., Santiago, Chile
- Cellus Biomédica, Parque Tecnológico de León, León, Spain
| | - Francisco Aulestia
- Cellus Medicina Regenerativa S.A., Santiago, Chile
- Cellus Biomédica, Parque Tecnológico de León, León, Spain
| | - Mauricio Vergara
- Escuela de Ingeniería Bioquímica, Facultad de Ingeniería, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Flavio Carrión
- Cellus Medicina Regenerativa S.A., Santiago, Chile
- Departamento de Investigación, Postgrado y Educación Continua (DIPEC), Facultad de Ciencias de la Salud, Universidad del Alba, Santiago, Chile
| | - Nelson Osses
- Instituto de Química, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Claudia Altamirano
- Escuela de Ingeniería Bioquímica, Facultad de Ingeniería, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
- CREAS, Centro Regional de Estudios en Alimentos Saludables, Valparaíso, Chile
- *Correspondence: Claudia Altamirano,
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14
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Augustyniak J, Lipka G, Kozlowska H, Caloni F, Buzanska L. Oxygen as an important factor modulating in vitro MeHgCl toxicity associated with mitochondrial genes in hiPSCs. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 241:113737. [PMID: 35696963 DOI: 10.1016/j.ecoenv.2022.113737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 05/29/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
Mitochondria are energy factories of cells and important targets for methylmercury chloride (MgHgCl). Methylmercury (MeHg) is a well-known environmental toxicant that bioaccumulates in fish and shellfish. It readily crosses the placental barrier, making it a threat to correct fetal development. Despite being comprehensively investigated for years, this compound has not been assessed for its in vitro mitochondrial toxicity under different oxygen conditions. In this study, human induced pluripotent stem cells (hiPSCs) were used to evaluate the dependence of the expression of genes associated with pluripotency and mitochondria on atmospheric (21% O2) and low (5% O2) oxygen concentrations upon MeHgCl treatment. We showed that the toxicity of MeHgCl was strongly related to an increased mtDNA copy number and downregulation of the expression of an mtDNA replication and damage repair-associated gene POLG1 (Mitochondrial Polymerase Gamma Catalytic Subunit) in both tested oxygen conditions. In addition, the viability and mitochondrial membrane potential of hiPSCs were significantly lowered by MeHgCl regardless of the oxygen concentration. However, reactive oxygen species accumulation significantly increased only under atmospheric oxygen conditions; what was associated with increased expression of TFAM (Transcription Factor A, Mitochondrial) and NRF1 (Nuclear Respiratory Factor 1) and downregulation of PARK2 (Parkin RBR E3 Ubiquitin Protein Ligase). Taken together, our results demonstrated that MeHgCl could induce in vitro toxicity in hiPSCs through altering mitochondria-associated genes in an oxygen level-dependent manner. Thus, our work suggests that oxygen should be considered a factor was modulating the in vitro toxicity of environmental pollutants. Typical atmospheric conditions of in vitro culture significantly lower the predictive value of studies of such toxicity.
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Affiliation(s)
- J Augustyniak
- Department of Neurochemistry, Mossakowski Medical Research Institute Polish Academy of Sciences, Warsaw, Poland
| | - G Lipka
- Department of Stem Cell Bioengineering, Mossakowski Medical Research Institute Polish Academy of Sciences, Warsaw, Poland
| | - H Kozlowska
- Laboratory of Advanced Microscopy Technique, Mossakowski Medical Research Institute Polish Academy of Sciences, Warsaw, Poland
| | - F Caloni
- Department of Environmental Science and Policy (ESP), Università degli Studi di Milano, Milan, Italy
| | - L Buzanska
- Department of Stem Cell Bioengineering, Mossakowski Medical Research Institute Polish Academy of Sciences, Warsaw, Poland
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15
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APOBEC mediated mutagenesis drives genomic heterogeneity in endometriosis. J Hum Genet 2022; 67:323-329. [PMID: 35017684 DOI: 10.1038/s10038-021-01003-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 11/11/2021] [Accepted: 11/29/2021] [Indexed: 11/09/2022]
Abstract
Endometriosis is a benign gynecologic condition, acting as a precursor of certain histological subtypes of ovarian cancers. The epithelial cells of endometriotic tissues and normal uterine endometrium accumulated somatic mutations in cancer-associated genes such as phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) and Kirsten rat sarcoma (KRAS) proto-oncogene. To determine the genomic characteristic of endometriotic epithelial cells and normal uterine endometrium and to identify the predominant mutational process acting on them, we studied the somatic mutation profiles obtained from whole exome sequencing of 14 endometriotic epithelium and 11 normal uterine endometrium tissues and classified them into mutational signatures. We observed that single base substitutions 2/13 (SBS), attributed to Apolipoprotein B mRNA Editing Enzyme Catalytic Subunit (APOBEC) induced mutagenesis, were significant in endometriotic tissues, but not in the normal uterine endometrium. Additionally, the larger number and wider allele frequency distribution of APOBEC signature mutations, compared to cancer-associated driver mutations in endometriotic epithelium suggested APOBEC mutagenesis as an important source of mutational burden and heterogeneity in endometriosis. Further, the relative risk of enriched APOBEC signature mutations was higher in endometriosis patients who were carriers of APOBEC3A/3B germline deletion, a common polymorphism in East Asians which involves the complete loss of APOBEC3B coding region. Our results illustrate the significance of APOBEC induced mutagenesis in driving the genomic heterogeneity of endometriosis.
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16
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Rajaei M, Saxena AS, Johnson LM, Snyder MC, Crombie TA, Tanny RE, Andersen EC, Joyner-Matos J, Baer CF. Mutability of mononucleotide repeats, not oxidative stress, explains the discrepancy between laboratory-accumulated mutations and the natural allele-frequency spectrum in C. elegans. Genome Res 2021; 31:1602-1613. [PMID: 34404692 PMCID: PMC8415377 DOI: 10.1101/gr.275372.121] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 07/12/2021] [Indexed: 11/24/2022]
Abstract
Important clues about natural selection can be gleaned from discrepancies between the properties of segregating genetic variants and of mutations accumulated experimentally under minimal selection, provided the mutational process is the same in the laboratory as in nature. The base-substitution spectrum differs between C. elegans laboratory mutation accumulation (MA) experiments and the standing site-frequency spectrum, which has been argued to be in part owing to increased oxidative stress in the laboratory environment. Using genome sequence data from C. elegans MA lines carrying a mutation (mev-1) that increases the cellular titer of reactive oxygen species (ROS), leading to increased oxidative stress, we find the base-substitution spectrum is similar between mev-1, its wild-type progenitor (N2), and another set of MA lines derived from a different wild strain (PB306). Conversely, the rate of short insertions is greater in mev-1, consistent with studies in other organisms in which environmental stress increased the rate of insertion–deletion mutations. Further, the mutational properties of mononucleotide repeats in all strains are different from those of nonmononucleotide sequence, both for indels and base-substitutions, and whereas the nonmononucleotide spectra are fairly similar between MA lines and wild isolates, the mononucleotide spectra are very different, with a greater frequency of A:T → T:A transversions and an increased proportion of ±1-bp indels. The discrepancy in mutational spectra between laboratory MA experiments and natural variation is likely owing to a consistent (but unknown) effect of the laboratory environment that manifests itself via different modes of mutability and/or repair at mononucleotide loci.
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Affiliation(s)
- Moein Rajaei
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA
| | | | - Lindsay M Johnson
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA
| | - Michael C Snyder
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA
| | - Timothy A Crombie
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA.,Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Robyn E Tanny
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Erik C Andersen
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Joanna Joyner-Matos
- Department of Biology, Eastern Washington University, Cheney, Washington 99004, USA
| | - Charles F Baer
- Department of Biology, University of Florida, Gainesville, Florida 32611, USA.,University of Florida Genetics Institute, Gainesville, Florida 32608, USA
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17
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Characterization of Scleraxis and SRY-Box 9 from Adipose-Derived Stem Cells Culture Seeded with Enthesis Scaffold in Hypoxic Condition. JOURNAL OF BIOMIMETICS BIOMATERIALS AND BIOMEDICAL ENGINEERING 2021. [DOI: 10.4028/www.scientific.net/jbbbe.52.76] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The use of mesenchymal stem cells can add local improvements potential to enthesis tissue regeneration based on tropical activity through secretions of growth factors, cytokines, and vesicles (e.g. exosomes), collectively known as secretomes. This study aims to analyze secretomes characterization from adipose-derived mesenchymal stem cells seeded with enthesis tissue scaffold in hypoxic conditions and to analyze the influence of hypoxic environment to the characterization of secretomes. This is an in-vitro study using a Randomized Control Group Post-Test Only design. This study using Adipose Stem Cells (ASCs) were cultured in hypoxia (Oxygen 5%) and Normoxia (21%) condition. The scaffolds are fresh-frozen enthesis tissue and was seeded in the treatment group and compared to control. The evaluation of Scleraxis (Scx) and SRY-box (Sox9) was measured using ELISA on the 2nd, 4th, and 6th days. Comparison of Scx levels between each evaluation time showed a positive trend in a group with scaffold in hypoxia condition although it has no significant differences (p=0.085), with the highest level on day 6, that is 13,568 ng/ml. Conversely, the comparison of Sox9 showed significant differences (p=0.02) in a group with scaffold in hypoxia condition, with the highest level on day 4, that is 28,250 ng/ml. The use of enthesis scaffold seeded in adipose-derived mesenchymal stem cells in hypoxic conditions shows a positive trend as regenerative effort of injured enthesis tissue through Scleraxis and Sox9 secretomes induction.
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18
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Kim S, Bai Y, Fan Z, Diergaarde B, Tseng GC, Park HJ. The microRNA target site landscape is a novel molecular feature associating alternative polyadenylation with immune evasion activity in breast cancer. Brief Bioinform 2021; 22:bbaa191. [PMID: 32844230 PMCID: PMC8138879 DOI: 10.1093/bib/bbaa191] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/10/2020] [Accepted: 07/28/2020] [Indexed: 12/14/2022] Open
Abstract
Alternative polyadenylation (APA) in breast tumor samples results in the removal/addition of cis-regulatory elements such as microRNA (miRNA) target sites in the 3'-untranslated region (3'-UTRs) of genes. Although previous computational APA studies focused on a subset of genes strongly affected by APA (APA genes), we identify miRNAs of which widespread APA events collectively increase or decrease the number of target sites [probabilistic inference of microRNA target site modification through APA (PRIMATA-APA)]. Using PRIMATA-APA on the cancer genome atlas (TCGA) breast cancer data, we found that the global APA events change the number of the target sites of particular microRNAs [target sites modified miRNA (tamoMiRNA)] enriched for cancer development and treatments. We also found that when knockdown (KD) of NUDT21 in HeLa cells induces a different set of widespread 3'-UTR shortening than TCGA breast cancer data, it changes the target sites of the common tamoMiRNAs. Since the NUDT21 KD experiment previously demonstrated the tumorigenic role of APA events in a miRNA dependent fashion, this result suggests that the APA-initiated tumorigenesis is attributable to the miRNA target site changes, not the APA events themselves. Further, we found that the miRNA target site changes identify tumor cell proliferation and immune cell infiltration to the tumor microenvironment better than the miRNA expression levels or the APA events themselves. Altogether, our computational analyses provide a proof-of-concept demonstration that the miRNA target site information indicates the effect of global APA events with a potential as predictive biomarker.
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Affiliation(s)
- Soyeon Kim
- Department of Pediatrics, University of Pittsburgh Medical Center and in Division of Pulmonary Medicine, Children’s Hospital of Pittsburgh of UPMC
| | - YuLong Bai
- Department of Human Genetics in the Graduate School of Public Health, University of Pittsburgh
| | - Zhenjiang Fan
- Department of Computer Science, University of Pittsburgh
| | - Brenda Diergaarde
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh
| | - George C Tseng
- Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh
| | - Hyun Jung Park
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh
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19
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Ogrodnik M. Cellular aging beyond cellular senescence: Markers of senescence prior to cell cycle arrest in vitro and in vivo. Aging Cell 2021; 20:e13338. [PMID: 33711211 PMCID: PMC8045927 DOI: 10.1111/acel.13338] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/09/2021] [Accepted: 02/19/2021] [Indexed: 12/14/2022] Open
Abstract
The field of research on cellular senescence experienced a rapid expansion from being primarily focused on in vitro aspects of aging to the vast territories of animal and clinical research. Cellular senescence is defined by a set of markers, many of which are present and accumulate in a gradual manner prior to senescence induction or are found outside of the context of cellular senescence. These markers are now used to measure the impact of cellular senescence on aging and disease as well as outcomes of anti-senescence interventions, many of which are at the stage of clinical trials. It is thus of primary importance to discuss their specificity as well as their role in the establishment of senescence. Here, the presence and role of senescence markers are described in cells prior to cell cycle arrest, especially in the context of replicative aging and in vivo conditions. Specifically, this review article seeks to describe the process of "cellular aging": the progression of internal changes occurring in primary cells leading to the induction of cellular senescence and culminating in cell death. Phenotypic changes associated with aging prior to senescence induction will be characterized, as well as their effect on the induction of cell senescence and the final fate of cells reviewed. Using published datasets on assessments of senescence markers in vivo, it will be described how disparities between quantifications can be explained by the concept of cellular aging. Finally, throughout the article the applicational value of broadening cellular senescence paradigm will be discussed.
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Affiliation(s)
- Mikolaj Ogrodnik
- Ludwig Boltzmann Research Group Senescence and Healing of Wounds Vienna Austria
- Ludwig Boltzmann Institute for Experimental and Clinical Traumatology in AUVA Research Center Vienna Austria
- Austrian Cluster for Tissue Regeneration Vienna Austria
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20
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Tuy K, Rickenbacker L, Hjelmeland AB. Reactive oxygen species produced by altered tumor metabolism impacts cancer stem cell maintenance. Redox Biol 2021; 44:101953. [PMID: 34052208 PMCID: PMC8212140 DOI: 10.1016/j.redox.2021.101953] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/11/2021] [Accepted: 03/16/2021] [Indexed: 02/07/2023] Open
Abstract
Controlling reactive oxygen species (ROS) at sustainable levels can drive multiple facets of tumor biology, including within the cancer stem cell (CSC) population. Tight regulation of ROS is one key component in CSCs that drives disease recurrence, cell signaling, and therapeutic resistance. While ROS are well-appreciated to need oxygen and are a product of oxidative phosphorylation, there are also important roles for ROS under hypoxia. As hypoxia promotes and sustains major stemness pathways, further consideration of ROS impacts on CSCs in the tumor microenvironment is important. Furthermore, glycolytic shifts that occur in cancer and may be promoted by hypoxia are associated with multiple mechanisms to mitigate oxidative stress. This altered metabolism provides survival advantages that sustain malignant features, such as proliferation and self-renewal, while producing the necessary antioxidants that reduce damage from oxidative stress. Finally, disease recurrence is believed to be attributed to therapy resistant CSCs which can be quiescent and have changes in redox status. Effective DNA damage response pathways and/or a slow-cycling state can protect CSCs from the genomic catastrophe induced by irradiation and genotoxic agents. This review will explore the delicate, yet complex, relationship between ROS and its pleiotropic role in modulating the CSC.
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Affiliation(s)
- Kaysaw Tuy
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Lucas Rickenbacker
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Anita B Hjelmeland
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, USA.
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21
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Stem cell-based therapy treating glioblastoma multiforme. Hematol Oncol Stem Cell Ther 2021; 14:1-15. [PMID: 32971031 DOI: 10.1016/j.hemonc.2020.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 07/20/2020] [Accepted: 08/14/2020] [Indexed: 01/27/2023] Open
Abstract
Glioblastoma (GB) is one of the most malignant types of central nervous system tumours, classified as grade IV by the World Health Organization. Despite the therapeutic advances, the prognosis is ominous, with a median survival of about 12-15 months post diagnosis. Although therapeutic options available can increase the survival, they are ineffective in treating patients with GB. Impairing factors such as the blood-brain barrier, cancer stem cells, and infiltration into brain parenchyma lead to failure of current therapies. Therefore, clinicians need novel/alternative effective strategies to treat GB. Due to their ability to preserve healthy tissues and to provide an effective and long-lasting response, stem cells (SCs) with tropism for tumour cells have attracted considerable attention in the scientific community. As is the case here, SCs can be used to target brain tumour cancer cells, especially high-grade malignant gliomas like GB, by overcoming the resistance and exerting benefits for patients affected with such lethal disease. Herein, we will discuss the research knowledge regarding SC-based therapy for the treatment of GB, focalising our attention on SCs and SC-released extracellular vesicles modified to express/load different antitumour payloads, as well as on SCs exploited as a diagnostic tool. Advantages and unresolved issues of anticancer SC-based therapy will also be considered.
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22
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Caliri AW, Tommasi S, Bates SE, Besaratinia A. Spontaneous and photosensitization-induced mutations in primary mouse cells transitioning through senescence and immortalization. J Biol Chem 2020; 295:9974-9985. [PMID: 32487750 DOI: 10.1074/jbc.ra120.014465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/02/2020] [Indexed: 01/15/2023] Open
Abstract
To investigate the role of oxidative stress-induced DNA damage and mutagenesis in cellular senescence and immortalization, here we profiled spontaneous and methylene blue plus light-induced mutations in the cII gene from λ phage in transgenic mouse embryonic fibroblasts during the transition from primary culture through senescence and immortalization. Consistent with detection of characteristic oxidized guanine lesions (8-oxodG) in the treated cells, we observed significantly increased relative cII mutant frequency in the treated pre-senescent cells which was augmented in their immortalized counterparts. The predominant mutation type in the treated pre-senescent cells was G:C→T:A transversion, whose frequency was intensified in the treated immortalized cells. Conversely, the prevailing mutation type in the treated immortalized cells was A:T→C:G transversion, with a unique sequence-context specificity, i.e. flanking purines at the 5' end of the mutated nucleotide. This mutation type was also enriched in the treated pre-senescent cells, although to a lower extent. The signature mutation of G:C→T:A transversions in the treated cells accorded with the well-established translesion synthesis bypass caused by 8-oxodG, and the hallmark A:T→C:G transversions conformed to the known replication errors because of oxidized guanine nucleosides (8-OHdGTPs). The distinctive features of photosensitization-induced mutagenesis in the immortalized cells, which were present at attenuated levels, in spontaneously immortalized cells provide insights into the role of oxidative stress in senescence bypass and immortalization. Our results have important implications for cancer biology because oxidized purines in the nucleoside pool can significantly contribute to genetic instability in DNA mismatch repair-defective human tumors.
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Affiliation(s)
- Andrew W Caliri
- Department of Preventive Medicine, USC Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Stella Tommasi
- Department of Preventive Medicine, USC Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Steven E Bates
- Department of Cancer Biology, Beckman Research Institute of the City of Hope, Duarte, California, USA
| | - Ahmad Besaratinia
- Department of Preventive Medicine, USC Keck School of Medicine, University of Southern California, Los Angeles, California, USA
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23
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Kang D, Shin J, Cho Y, Kim HS, Gu YR, Kim H, You KT, Chang MJ, Chang CB, Kang SB, Kim JS, Kim VN, Kim JH. Stress-activated miR-204 governs senescent phenotypes of chondrocytes to promote osteoarthritis development. Sci Transl Med 2020; 11:11/486/eaar6659. [PMID: 30944169 DOI: 10.1126/scitranslmed.aar6659] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 07/14/2018] [Accepted: 02/22/2019] [Indexed: 12/17/2022]
Abstract
A progressive loss of cartilage matrix leads to the development of osteoarthritis (OA). Matrix homeostasis is disturbed in OA cartilage as the result of reduced production of cartilage-specific matrix and increased secretion of catabolic mediators by chondrocytes. Chondrocyte senescence is a crucial cellular event contributing to such imbalance in matrix metabolism during OA development. Here, we identify miR-204 as a markedly up-regulated microRNA in OA cartilage. miR-204 is induced by transcription factors GATA4 and NF-κB in response to senescence signals. Up-regulated miR-204 simultaneously targets multiple components of the sulfated proteoglycan (PG) biosynthesis pathway, effectively shutting down PG anabolism. Ectopic expression of miR-204 in joints triggers spontaneous cartilage loss and OA development, whereas miR-204 inhibition ameliorates experimental OA, with concomitant recovery of PG synthesis and suppression of inflammatory senescence-associated secretory phenotype (SASP) factors in cartilage. Collectively, we unravel a stress-activated senescence pathway that underlies disrupted matrix homeostasis in OA cartilage.
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Affiliation(s)
- Donghyun Kang
- Center for RNA Research, Institute for Basic Science, 08826 Seoul, South Korea.,Department of Biological Sciences, College of Natural Sciences, Seoul National University, 08826 Seoul, South Korea
| | - Jungkwon Shin
- Center for RNA Research, Institute for Basic Science, 08826 Seoul, South Korea.,Department of Biological Sciences, College of Natural Sciences, Seoul National University, 08826 Seoul, South Korea
| | - Yongsik Cho
- Center for RNA Research, Institute for Basic Science, 08826 Seoul, South Korea.,Department of Biological Sciences, College of Natural Sciences, Seoul National University, 08826 Seoul, South Korea
| | - Hyeon-Seop Kim
- Center for RNA Research, Institute for Basic Science, 08826 Seoul, South Korea.,Department of Biological Sciences, College of Natural Sciences, Seoul National University, 08826 Seoul, South Korea
| | - Young-Ran Gu
- Center for RNA Research, Institute for Basic Science, 08826 Seoul, South Korea.,Department of Biological Sciences, College of Natural Sciences, Seoul National University, 08826 Seoul, South Korea
| | - Haedong Kim
- Center for RNA Research, Institute for Basic Science, 08826 Seoul, South Korea.,Department of Biological Sciences, College of Natural Sciences, Seoul National University, 08826 Seoul, South Korea
| | - Kwon Tae You
- Center for RNA Research, Institute for Basic Science, 08826 Seoul, South Korea.,Department of Biological Sciences, College of Natural Sciences, Seoul National University, 08826 Seoul, South Korea
| | - Moon Jong Chang
- Department of Orthopedic Surgery, Seoul National University College of Medicine, Boramae Hospital, 07061 Seoul, South Korea
| | - Chong Bum Chang
- Department of Orthopedic Surgery, Seoul National University College of Medicine, Boramae Hospital, 07061 Seoul, South Korea
| | - Seung-Baik Kang
- Department of Orthopedic Surgery, Seoul National University College of Medicine, Boramae Hospital, 07061 Seoul, South Korea
| | - Jong-Seo Kim
- Center for RNA Research, Institute for Basic Science, 08826 Seoul, South Korea.,Department of Biological Sciences, College of Natural Sciences, Seoul National University, 08826 Seoul, South Korea
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, 08826 Seoul, South Korea.,Department of Biological Sciences, College of Natural Sciences, Seoul National University, 08826 Seoul, South Korea
| | - Jin-Hong Kim
- Center for RNA Research, Institute for Basic Science, 08826 Seoul, South Korea. .,Department of Biological Sciences, College of Natural Sciences, Seoul National University, 08826 Seoul, South Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, 08826 Seoul, South Korea
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24
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Fan Z, Kim S, Bai Y, Diergaarde B, Park HJ. 3'-UTR Shortening Contributes to Subtype-Specific Cancer Growth by Breaking Stable ceRNA Crosstalk of Housekeeping Genes. Front Bioeng Biotechnol 2020; 8:334. [PMID: 32411683 PMCID: PMC7201092 DOI: 10.3389/fbioe.2020.00334] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/25/2020] [Indexed: 12/21/2022] Open
Abstract
Shortening of 3'UTRs (3'US) through alternative polyadenylation is a post-transcriptional mechanism that regulates the expression of hundreds of genes in human cancers. In breast cancer, different subtypes of tumor samples, such as estrogen receptor positive and negative (ER+ and ER-), are characterized by distinct molecular mechanisms, suggesting possible differences in the post-transcriptional regulation between the subtype tumors. In this study, based on the profound tumorigenic role of 3'US interacting with competing-endogenous RNA (ceRNA) network (3'US-ceRNA effect), we hypothesize that the 3'US-ceRNA effect drives subtype-specific tumor growth. However, we found that the subtypes are available in different sample sizes, biasing the ceRNA network size and disabling the fair comparison of the 3'US-ceRNA effect. Using normalized Laplacian matrix eigenvalue distribution, we addressed this bias and built tumor ceRNA networks comparable between the subtypes. Based on the comparison, we identified a novel role of housekeeping (HK) genes as stable and strong miRNA sponges (sponge HK genes) that synchronize the ceRNA networks of normal samples (adjacent to ER+ and ER- tumor samples). We further found that distinct 3'US events in the ER- tumor break the stable sponge effect of HK genes in a subtype-specific fashion, especially in association with the aggressive and metastatic phenotypes. Knockdown of NUDT21 further suggested the role of 3'US-ceRNA effect in repressing HK genes for tumor growth. In this study, we identified 3'US-ceRNA effect on the sponge HK genes for subtype-specific growth of ER- tumors.
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Affiliation(s)
- Zhenjiang Fan
- Department of Computer Science, University of Pittsburgh, Pittsburgh, PA, United States
| | - Soyeon Kim
- Department of Pediatrics, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
- Division of Pulmonary Medicine, Children's Hospital of Pittsburgh UPMC, Pittsburgh, PA, United States
| | - Yulong Bai
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
| | - Brenda Diergaarde
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
- Hillman Cancer Center, University of Pittsburgh Medical Cancer, Pittsburgh, PA, United States
| | - Hyun Jung Park
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, United States
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25
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Hölzl-Armstrong L, Kucab JE, Korenjak M, Luijten M, Phillips DH, Zavadil J, Arlt VM. Characterising Mutational Spectra of Carcinogens in the Tumour Suppressor Gene TP53 Using Human TP53 Knock-in (Hupki) Mouse Embryo Fibroblasts. Methods Protoc 2019; 2:E85. [PMID: 31766274 PMCID: PMC6961128 DOI: 10.3390/mps2040085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 10/30/2019] [Accepted: 10/31/2019] [Indexed: 12/11/2022] Open
Abstract
DNA in dividing cells is prone to mutagenesis, with mutations making key contributions to human disease including cancer. The tumour suppressor gene TP53 is the most frequently mutated gene in human tumours. Here, we present a robust protocol for studying TP53 mutagenesis utilising human TP53 knock-in (Hupki) mouse embryonic fibroblasts (HUFs). In the HUF immortalisation assay (HIMA), primary HUFs are treated with known or suspected carcinogens at 3% oxygen and then transferred to 20% atmospheric oxygen to induce senescence. Cells containing mutations (e.g., in TP53) that allow bypassing of senescence eventually emerge as immortalised clonal cell lines after 2-3 months of serial passaging. As not all immortalised HUF cells contain TP53 mutations, we developed a Nutlin-3a counter-screen to select for TP53-mutated clones prior to sequencing. TP53 mutation spectra generated can be compared with those of human tumours recorded in the International Agency for Research on Cancer TP53 mutation database. Environmental mutagens that have demonstrated and validated the utility of the HIMA include ultraviolet radiation, aristolochic acid, and benzo[a]pyrene. The TP53 mutation patterns induced by these mutagens in the HIMA corresponded to those found in human tumours from patients exposed to these mutagens. The approach presented helps to deepen our understanding of human cancer aetiology.
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Affiliation(s)
- Lisa Hölzl-Armstrong
- Department of Analytical, Environmental and Forensic Sciences, King’s College London, London SE1 9NH, UK; (L.H.-A.); (J.E.K.); (D.H.P.)
| | - Jill E. Kucab
- Department of Analytical, Environmental and Forensic Sciences, King’s College London, London SE1 9NH, UK; (L.H.-A.); (J.E.K.); (D.H.P.)
| | - Michael Korenjak
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, 69008 Lyon, France; (M.K.); (J.Z.)
| | - Mirjam Luijten
- Center for Health Protection, National Institute for Public Health and the Environment (RIVM), 3721 MA Bilthoven, The Netherlands;
| | - David H. Phillips
- Department of Analytical, Environmental and Forensic Sciences, King’s College London, London SE1 9NH, UK; (L.H.-A.); (J.E.K.); (D.H.P.)
| | - Jiri Zavadil
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, 69008 Lyon, France; (M.K.); (J.Z.)
| | - Volker M. Arlt
- Department of Analytical, Environmental and Forensic Sciences, King’s College London, London SE1 9NH, UK; (L.H.-A.); (J.E.K.); (D.H.P.)
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26
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Le Gac AL, Laux T. Hypoxia Is a Developmental Regulator in Plant Meristems. MOLECULAR PLANT 2019; 12:1422-1424. [PMID: 31628990 DOI: 10.1016/j.molp.2019.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 10/08/2019] [Accepted: 10/09/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Anne-Laure Le Gac
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany
| | - Thomas Laux
- Signalling Research Centres BIOSS and CIBSS, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104 Freiburg, Germany; Sino-German Joint Research Center on Agricultural Biology, Shandong Agricultural University, Tai'an, Shandong, China.
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27
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Mammalian Systems Biotechnology Reveals Global Cellular Adaptations in a Recombinant CHO Cell Line. Cell Syst 2019; 4:530-542.e6. [PMID: 28544881 DOI: 10.1016/j.cels.2017.04.009] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 02/14/2017] [Accepted: 04/26/2017] [Indexed: 01/16/2023]
Abstract
Effective development of host cells for therapeutic protein production is hampered by the poor characterization of cellular transfection. Here, we employed a multi-omics-based systems biotechnology approach to elucidate the genotypic and phenotypic differences between a wild-type and recombinant antibody-producing Chinese hamster ovary (CHO) cell line. At the genomic level, we observed extensive rearrangements in specific targeted loci linked to transgene integration sites. Transcriptional re-wiring of DNA damage repair and cellular metabolism in the antibody producer, via changes in gene copy numbers, was also detected. Subsequent integration of transcriptomic data with a genome-scale metabolic model showed a substantial increase in energy metabolism in the antibody producer. Metabolomics, lipidomics, and glycomics analyses revealed an elevation in long-chain lipid species, potentially associated with protein transport and secretion requirements, and a surprising stability of N-glycosylation profiles between both cell lines. Overall, the proposed knowledge-based systems biotechnology framework can further accelerate mammalian cell-line engineering in a targeted manner.
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28
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Laucius CD, Orr B, Compton DA. Chromosomal instability suppresses the growth of K-Ras-induced lung adenomas. Cell Cycle 2019; 18:1702-1713. [PMID: 31179849 DOI: 10.1080/15384101.2019.1629790] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Chromosomal instability (CIN) is defined as a high rate of whole chromosome loss or gain and is a hallmark of many aneuploid solid tumors. CIN positively correlates with poor patient prognosis and chemotherapeutic resistance. Despite this clinical importance, the role of CIN in tumor initiation, growth and/or progression remains poorly understood. To date, the only strategies developed to determine how CIN contributes to tumorigenesis have relied on transgenic mouse models that deliberately increase the rate of chromosomal mis-segregation. Here we develop a strain of transgenic mice that is designed to strategically decrease the rate of chromosome mis-segregation and suppress CIN. These animals modestly overexpress the kinesin-13 microtubule depolymerase Kif2b, a strategy proven successful in restoring faithful chromosome segregation to human cancer cells in culture. Using the LA2 K-Ras G12D-induced model for lung cancer, we show that Kif2b expression reduces the number of chromosome segregation defects but does not change the incidence of lung tumor lesions. However, pulmonary tumors were significantly larger in animals expressing Kif2b and those tumors exhibited elevated rates of Ki-67 positive cells relative to controls. Thus, in lung cancers driven by mutations in K-Ras, CIN has little impact on tumor initiation but suppresses tumor growth. These data support a model in which CIN imposes a burden on tumor cells, and that enhancement of mitotic fidelity results in accelerated tumor growth.
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Affiliation(s)
- Christopher D Laucius
- a Department of Biochemistry , Geisel School of Medicine at Dartmouth , Hanover , NH , USA.,b Norris Cotton Cancer Center , Lebanon , NH , USA
| | - Bernardo Orr
- a Department of Biochemistry , Geisel School of Medicine at Dartmouth , Hanover , NH , USA.,b Norris Cotton Cancer Center , Lebanon , NH , USA
| | - Duane A Compton
- a Department of Biochemistry , Geisel School of Medicine at Dartmouth , Hanover , NH , USA.,b Norris Cotton Cancer Center , Lebanon , NH , USA
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29
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Marei HE, Althani A, Caceci T, Arriga R, Sconocchia T, Ottaviani A, Lanzilli G, Roselli M, Caratelli S, Cenciarelli C, Sconocchia G. Recent perspective on CAR and Fcγ-CR T cell immunotherapy for cancers: Preclinical evidence versus clinical outcomes. Biochem Pharmacol 2019; 166:335-346. [PMID: 31176617 DOI: 10.1016/j.bcp.2019.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 06/03/2019] [Indexed: 12/16/2022]
Abstract
The chimeric antigen receptor T cell (CAR-T cell) immunotherapy currently represents a hot research trend and it is expected to revolutionize the field of cancer therapy. Promising outcomes have been achieved using CAR-T cell therapy for haematological malignancies. Despite encouraging results, several challenges still pose eminent hurdles before being fully recognized. Directing CAR-T cells to target a single tumour associated antigen (TAA) as the case in haematological malignancies might be much simpler than targeting the extensive inhibitory microenvironments associated with solid tumours. This review focuses on the basic principles involved in development of CAR-T cells, emphasizing the differences between humoral IgG, T-cell receptors, CAR and Fcγ-CR constructs. It also highlights the complex inhibitory network that is usually associated with solid tumours, and tackles recent advances in the clinical studies that have provided great hope for the future use of CAR-T cell immunotherapy. While current Fcγ-CR T cell immunotherapy is in pre-clinical stage, is expected to provide a sound therapeutic approach to add to existing classical chemo- and radio-therapeutic modalities.
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Affiliation(s)
- Hany E Marei
- Department of Cytology and Histology, Faculty of Veterinary Medicine, Mansoura University, Mansoura 35116, Egypt.
| | - Asma Althani
- Biomedical Research Center, Qatar University, Doha 2713, Qatar
| | - Thomas Caceci
- Biomedical Science Education, Virginia Tech Carilion School of Medicine, Roanoke, VA, United States
| | - Roberto Arriga
- Department of Systems Medicine, Endocrinology and Medical Oncology, University of Rome "Tor Vergata", Rome, Italy
| | - Tommaso Sconocchia
- Otto Loewi Research Center, Chair of Immunology and Pathophysiology, Medical University of Graz, Graz, Austria
| | | | | | - Mario Roselli
- Department of Systems Medicine, Endocrinology and Medical Oncology, University of Rome "Tor Vergata", Rome, Italy
| | - Sara Caratelli
- Institute of Translational Pharmacology-CNR, Rome, Italy
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30
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Ogrodnik M, Salmonowicz H, Gladyshev VN. Integrating cellular senescence with the concept of damage accumulation in aging: Relevance for clearance of senescent cells. Aging Cell 2019; 18:e12841. [PMID: 30346102 PMCID: PMC6351832 DOI: 10.1111/acel.12841] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 07/31/2018] [Accepted: 08/20/2018] [Indexed: 12/12/2022] Open
Abstract
Understanding the aging process and ways to manipulate it is of major importance for biology and medicine. Among the many aging theories advanced over the years, the concept most consistent with experimental evidence posits the buildup of numerous forms of molecular damage as a foundation of the aging process. Here, we discuss that this concept integrates well with recent findings on cellular senescence, offering a novel view on the role of senescence in aging and age‐related disease. Cellular senescence has a well‐established role in cellular aging, but its impact on the rate of organismal aging is less defined. One of the most prominent features of cellular senescence is its association with macromolecular damage. The relationship between cell senescence and damage concerns both damage as a molecular signal of senescence induction and accelerated accumulation of damage in senescent cells. We describe the origin, regulatory mechanisms, and relevance of various damage forms in senescent cells. This view on senescent cells as carriers and inducers of damage puts new light on senescence, considering it as a significant contributor to the rise in organismal damage. Applying these ideas, we critically examine current evidence for a role of cellular senescence in aging and age‐related diseases. We also discuss the differential impact of longevity interventions on senescence burden and other types of age‐related damage. Finally, we propose a model on the role of aging‐related damage accumulation and the rate of aging observed upon senescent cell clearance.
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Affiliation(s)
- Mikolaj Ogrodnik
- Institute for Cell and Molecular Biosciences; Newcastle University Institute for Ageing; Newcastle upon Tyne UK
| | - Hanna Salmonowicz
- Institute for Cell and Molecular Biosciences; Newcastle University Institute for Ageing; Newcastle upon Tyne UK
| | - Vadim N. Gladyshev
- Division of Genetics; Department of Medicine; Brigham and Women's Hospital and Harvard Medical School; Boston Massachusetts
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31
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García-López S, Albo-Castellanos C, Urdinguio RG, Cañón S, Sánchez-Cabo F, Martínez-Serrano A, Fraga MF, Bernad A. Deregulation of the imprinted DLK1-DIO3 locus ncRNAs is associated with replicative senescence of human adipose-derived stem cells. PLoS One 2018; 13:e0206534. [PMID: 30395586 PMCID: PMC6218046 DOI: 10.1371/journal.pone.0206534] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 10/15/2018] [Indexed: 12/24/2022] Open
Abstract
Background Human adult adipose-derived stem cells (hADSCs) have become the most promising cell source for regenerative medicine. However the prolonged ex vivo expansion periods required to obtain the necessary therapeutic dose promotes progressive senescence, with the concomitant reduction of their therapeutic potential. Aim and scope A better understanding of the determinants of hADSC senescence is needed to improve biosafety while preserving therapeutic efficiency. Here, we investigated the association between deregulation of the imprinted DLK1-DIO3 region and replicative senescence in hADSC cultures. Methods We compared hADSC cultures at short (PS) and prolonged (PL) passages, both in standard and low [O2] (21 and 3%, respectively), in relation to replicative senescence. hADSCs were evaluated for expression alterations in the DLK1-DIO3 region on chromosome 14q32, and particularly in its main miRNA cluster. Results Comparison of hADSCs cultured at PL or PS surprisingly showed a quite significant fraction (69%) of upregulated miRNAs in PL cultures mapping to the imprinted 14q32 locus, the largest miRNA cluster described in the genome. In agreement, expression of the lncRNA MEG3 (Maternally Expressed 3; Meg3/Gtl2), cultured at 21 and 3% [O2], was also significantly higher in PL than in PS passages. During hADSC replicative senescence the AcK16H4 activating mark was found to be significantly associated with the deregulation of the entire DLK1-DIO3 locus, with a secondary regulatory role for the methylation of DMR regions. Conclusion A direct relationship between DLK1-DIO3 deregulation and replicative senescence of hADSCs is reported, involving upregulation of a very significant fraction of its largest miRNA cluster (14q32.31), paralleled by the progressive overexpression of the lncRNA MEG3, which plays a central role in the regulation of Dlk1/Dio3 activation status in mice.
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Affiliation(s)
- Silvia García-López
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain
- Department of Cardiovascular Development and Repair, Centro Nacional de Investigaciones Carlos III (CNIC), Madrid, Spain
| | - Carmen Albo-Castellanos
- Department of Cardiovascular Development and Repair, Centro Nacional de Investigaciones Carlos III (CNIC), Madrid, Spain
| | - Rocio G. Urdinguio
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), Hospital Universitaria Central de Asturias (HUCA) and Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo (UO), Asturias, Spain
| | - Susana Cañón
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain
- Department of Cardiovascular Development and Repair, Centro Nacional de Investigaciones Carlos III (CNIC), Madrid, Spain
| | - Fátima Sánchez-Cabo
- Bioinformatics Unit, Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Alberto Martínez-Serrano
- Molecular Biology Department (UAM) and Molecular Neuropathology Department, Center of Molecular Biology Severo Ochoa-CSIC, Universidad Autónoma de Madrid, Campus Cantoblanco, Madrid, Spain
| | - Mario F. Fraga
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), Hospital Universitaria Central de Asturias (HUCA) and Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo (UO), Asturias, Spain
| | - Antonio Bernad
- Department of Immunology and Oncology, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain
- Department of Cardiovascular Development and Repair, Centro Nacional de Investigaciones Carlos III (CNIC), Madrid, Spain
- * E-mail:
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32
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Jaber SM, Bordt EA, Bhatt NM, Lewis DM, Gerecht S, Fiskum G, Polster BM. Sex differences in the mitochondrial bioenergetics of astrocytes but not microglia at a physiologically relevant brain oxygen tension. Neurochem Int 2018; 117:82-90. [PMID: 28888963 PMCID: PMC5839942 DOI: 10.1016/j.neuint.2017.09.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 08/14/2017] [Accepted: 09/05/2017] [Indexed: 11/22/2022]
Abstract
Biological sex is thought to influence mitochondrial bioenergetic function. Previous respiration measurements examining brain mitochondrial sex differences were made at atmospheric oxygen using isolated brain mitochondria. Oxygen is 160 mm Hg (21%) in the atmosphere, while the oxygen tension in the brain generally ranges from ∼5 to 45 mm Hg (∼1-6% O2). This study tested the hypothesis that sex and/or brain physiological oxygen tension influence the mitochondrial bioenergetic properties of primary rat cortical astrocytes and microglia. Oxygen consumption was measured with a Seahorse XF24 cell respirometer in an oxygen-controlled environmental chamber. Strikingly, male astrocytes had a higher maximal respiration than female astrocytes when cultured and assayed at 3% O2. Three percent O2 yielded a low physiological dissolved O2 level of ∼1.2% (9.1 mm Hg) at the cell monolayer during culture and 1.2-3.0% O2 during assays. No differences in bioenergetic parameters were observed between male and female astrocytes at 21% O2 (dissolved O2 of ∼19.7%, 150 mm Hg during culture) or between either of these cell populations and female astrocytes at 3% O2. In contrast to astrocytes, microglia showed no sex differences in mitochondrial bioenergetic parameters at either oxygen level, regardless of whether they were non-stimulated or activated to a proinflammatory state. There were also no O2- or sex-dependent differences in proinflammatory TNF-α or IL-1β cytokine secretion measured at 18 h activation. Overall, results reveal an intriguing sex variance in astrocytic maximal respiration that requires additional investigation. Findings also demonstrate that sex differences can be masked by conducting experiments at non-physiological O2.
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Affiliation(s)
- Sausan M Jaber
- Department of Anesthesiology, and the Center for Shock, Trauma and Anesthesiology Research (STAR), University of Maryland School of Medicine, 685 W. Baltimore ST., MSTF 5-34, Baltimore, MD, 21201, USA; Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 685 W. Baltimore ST., MSTF 5-34, Baltimore, MD, 21201, USA
| | - Evan A Bordt
- Department of Anesthesiology, and the Center for Shock, Trauma and Anesthesiology Research (STAR), University of Maryland School of Medicine, 685 W. Baltimore ST., MSTF 5-34, Baltimore, MD, 21201, USA
| | - Niraj M Bhatt
- Department of Anesthesiology, and the Center for Shock, Trauma and Anesthesiology Research (STAR), University of Maryland School of Medicine, 685 W. Baltimore ST., MSTF 5-34, Baltimore, MD, 21201, USA
| | - Daniel M Lewis
- Department of Chemical and Biomolecular Engineering, Institute for NanoBioTechnology, Johns Hopkins University, 3400 North Charles Street, Shaffer Hall 200C, Baltimore, MD 21218, USA
| | - Sharon Gerecht
- Department of Chemical and Biomolecular Engineering, Institute for NanoBioTechnology, Johns Hopkins University, 3400 North Charles Street, Shaffer Hall 200C, Baltimore, MD 21218, USA; Department of Materials Science and Engineering, Johns Hopkins University, 3400 North Charles Street, Shaffer Hall 200C, Baltimore, MD 21218, USA
| | - Gary Fiskum
- Department of Anesthesiology, and the Center for Shock, Trauma and Anesthesiology Research (STAR), University of Maryland School of Medicine, 685 W. Baltimore ST., MSTF 5-34, Baltimore, MD, 21201, USA; Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 685 W. Baltimore ST., MSTF 5-34, Baltimore, MD, 21201, USA
| | - Brian M Polster
- Department of Anesthesiology, and the Center for Shock, Trauma and Anesthesiology Research (STAR), University of Maryland School of Medicine, 685 W. Baltimore ST., MSTF 5-34, Baltimore, MD, 21201, USA; Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 685 W. Baltimore ST., MSTF 5-34, Baltimore, MD, 21201, USA.
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Huang X, Trinh T, Aljoufi A, Broxmeyer HE. Hypoxia Signaling Pathway in Stem Cell Regulation: Good and Evil. CURRENT STEM CELL REPORTS 2018; 4:149-157. [PMID: 31275803 DOI: 10.1007/s40778-018-0127-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Purpose of Review This review summarizes the role of hypoxia and hypoxia-inducible factors (HIFs) in the regulation of stem cell biology, specifically focusing on maintenance, differentiation, and stress responses in the context of several stem cell systems. Stem cells for different lineages/tissues reside in distinct niches, and are exposed to diverse oxygen concentrations. Recent studies have revealed the importance of the hypoxia signaling pathway for stem cell functions. Recent Findings Hypoxia and HIFs contribute to maintenance of embryonic stem cells, generation of induced pluripotent stem cells, functionality of hematopoietic stem cells, and survival of leukemia stem cells. Harvest and collection of mouse bone marrow and human cord blood cells in ambient air results in fewer hematopoietic stem cells recovered due to the phenomenon of Extra PHysiologic Oxygen Shock/Stress (EPHOSS). Summary Oxygen is an important factor in the stem cell microenvironment. Hypoxia signaling and HIFs play important roles in modeling cellular metabolism in both stem cells and niches to regulate stem cell biology, and represent an additional dimension that allows stem cells to maintain an undifferentiated status and multilineage differentiation potential.
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Affiliation(s)
- Xinxin Huang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Thao Trinh
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Arafat Aljoufi
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | - Hal E Broxmeyer
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
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Chen M, Lyu G, Han M, Nie H, Shen T, Chen W, Niu Y, Song Y, Li X, Li H, Chen X, Wang Z, Xia Z, Li W, Tian XL, Ding C, Gu J, Zheng Y, Liu X, Hu J, Wei G, Tao W, Ni T. 3' UTR lengthening as a novel mechanism in regulating cellular senescence. Genome Res 2018; 28:285-294. [PMID: 29440281 PMCID: PMC5848608 DOI: 10.1101/gr.224451.117] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 01/24/2018] [Indexed: 01/09/2023]
Abstract
Cellular senescence has been viewed as a tumor suppression mechanism and also as a contributor to individual aging. Widespread shortening of 3' untranslated regions (3' UTRs) in messenger RNAs (mRNAs) by alternative polyadenylation (APA) has recently been discovered in cancer cells. However, the role of APA in the process of cellular senescence remains elusive. Here, we found that hundreds of genes in senescent cells tended to use distal poly(A) (pA) sites, leading to a global lengthening of 3' UTRs and reduced gene expression. Genes that harbor longer 3' UTRs in senescent cells were enriched in senescence-related pathways. Rras2, a member of the Ras superfamily that participates in multiple signal transduction pathways, preferred longer 3' UTR usage and exhibited decreased expression in senescent cells. Depletion of Rras2 promoted senescence, while rescue of Rras2 reversed senescence-associated phenotypes. Mechanistically, splicing factor TRA2B bound to a core "AGAA" motif located in the alternative 3' UTR of Rras2, thereby reducing the RRAS2 protein level and causing senescence. Both proximal and distal poly(A) signals showed strong sequence conservation, highlighting the vital role of APA regulation during evolution. Our results revealed APA as a novel mechanism in regulating cellular senescence.
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Affiliation(s)
- Meng Chen
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Guoliang Lyu
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Miao Han
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Hongbo Nie
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Ting Shen
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Wei Chen
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Yichi Niu
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Yifan Song
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Xueping Li
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Huan Li
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Xinyu Chen
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Ziyue Wang
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Zheng Xia
- Division of Biostatistics, Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Wei Li
- Division of Biostatistics, Dan L. Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xiao-Li Tian
- Human Aging Research Institute and School of Life Sciences, Nanchang University, Nanchang, 330031 China
| | - Chen Ding
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Jun Gu
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Yufang Zheng
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Xinhua Liu
- School of Pharmacy, Fudan University, Shanghai, 201203 China
| | - Jinfeng Hu
- School of Pharmacy, Fudan University, Shanghai, 201203 China
| | - Gang Wei
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
| | - Wei Tao
- MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871 China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering and Ministry of Education (MOE) Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Huashan Hospital, Fudan University, Shanghai, 200438 China
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Enhancing proliferation and optimizing the culture condition for human bone marrow stromal cells using hypoxia and fibroblast growth factor-2. Stem Cell Res 2018; 28:87-95. [PMID: 29448134 DOI: 10.1016/j.scr.2018.01.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 12/28/2017] [Accepted: 01/06/2018] [Indexed: 12/15/2022] Open
Abstract
This study aimed to determine the cellular characteristics and behaviors of human bone marrow stromal cells (hBMSCs) expanded in media in a hypoxic or normoxic condition and with or without fibroblast growth factor-2 (FGF-2) treatment. hBMSCs isolated from the vertebral body and expanded in these four groups were evaluated for cellular proliferation/migration, colony-forming units, cell-surface characterization, in vitro differentiation, in vivo transplantation, and gene expression. Culturing hBMSCs using a particular environmental factor (hypoxia) and with the addition of FGF-2 increased the cellular proliferation rate while enhancing the regenerative potential, modulated the multipotency-related processes (enhanced chondrogenesis-related processes/osteogenesis, but reduced adipogenesis), and increased cellular migration and collagen formation. The gene expression levels in the experimental samples showed activation of the hypoxia-inducible factor-1 pathway and glycolysis in the hypoxic condition, with this not being affected by the addition of FGF-2. The concurrent application of hypoxia and FGF-2 could provide a favorable condition for culturing hBMSCs to be used in clinical applications associated with bone tissue engineering, due to the enhancement of cellular proliferation and regenerative potential.
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Trosko JE. The Role of the Mitochondria in the Evolution of Stem Cells, Including MUSE Stem Cells and Their Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1103:131-152. [DOI: 10.1007/978-4-431-56847-6_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Hu JL, Todhunter ME, LaBarge MA, Gartner ZJ. Opportunities for organoids as new models of aging. J Cell Biol 2017; 217:39-50. [PMID: 29263081 PMCID: PMC5748992 DOI: 10.1083/jcb.201709054] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 11/13/2017] [Accepted: 11/27/2017] [Indexed: 01/02/2023] Open
Abstract
The biology of aging is challenging to study, particularly in humans. As a result, model organisms are used to approximate the physiological context of aging in humans. However, the best model organisms remain expensive and time-consuming to use. More importantly, they may not reflect directly on the process of aging in people. Human cell culture provides an alternative, but many functional signs of aging occur at the level of tissues rather than cells and are therefore not readily apparent in traditional cell culture models. Organoids have the potential to effectively balance between the strengths and weaknesses of traditional models of aging. They have sufficient complexity to capture relevant signs of aging at the molecular, cellular, and tissue levels, while presenting an experimentally tractable alternative to animal studies. Organoid systems have been developed to model many human tissues and diseases. Here we provide a perspective on the potential for organoids to serve as models for aging and describe how current organoid techniques could be applied to aging research.
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Affiliation(s)
- Jennifer L Hu
- University of California Berkeley-University of California San Francisco Graduate Program in Bioengineering, San Francisco, CA
| | - Michael E Todhunter
- Center for Cancer and Aging, Beckman Research Institute at City of Hope, Duarte, CA
| | - Mark A LaBarge
- Center for Cancer and Aging, Beckman Research Institute at City of Hope, Duarte, CA
| | - Zev J Gartner
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA .,National Science Foundation Center for Cellular Construction, University of California San Francisco, San Francisco, CA.,Chan Zuckerberg Biohub, San Francisco, CA
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38
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Stem cells in cancer therapy: opportunities and challenges. Oncotarget 2017; 8:75756-75766. [PMID: 29088907 PMCID: PMC5650462 DOI: 10.18632/oncotarget.20798] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/17/2017] [Indexed: 01/09/2023] Open
Abstract
Metastatic cancer cells generally cannot be eradicated using traditional surgical or chemoradiotherapeutic strategies, and disease recurrence is extremely common following treatment. On the other hand, therapies employing stem cells are showing increasing promise in the treatment of cancer. Stem cells can function as novel delivery platforms by homing to and targeting both primary and metastatic tumor foci. Stem cells engineered to stably express various cytotoxic agents decrease tumor volumes and extend survival in preclinical animal models. They have also been employed as virus and nanoparticle carriers to enhance primary therapeutic efficacies and relieve treatment side effects. Additionally, stem cells can be applied in regenerative medicine, immunotherapy, cancer stem cell-targeted therapy, and anticancer drug screening applications. However, while using stem cells to treat human cancers appears technically feasible, challenges such as treatment durability and tumorigenesis necessitate further study to improve therapeutic performance and applicability. This review focuses on recent progress toward stem cell-based cancer treatments, and summarizes treatment advantages, opportunities, and shortcomings, potentially helping to refine future trials and facilitate the translation from experimental to clinical studies.
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39
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Ortega JA, Sirois CL, Memi F, Glidden N, Zecevic N. Oxygen Levels Regulate the Development of Human Cortical Radial Glia Cells. Cereb Cortex 2017; 27:3736-3751. [PMID: 27600849 PMCID: PMC6075453 DOI: 10.1093/cercor/bhw194] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 04/29/2016] [Accepted: 05/24/2016] [Indexed: 12/17/2022] Open
Abstract
The oxygen (O2) concentration is a vital parameter for controlling the survival, proliferation, and differentiation of neural stem cells. A prenatal reduction of O2 levels (hypoxia) often leads to cognitive and behavioral defects, attributable to altered neural development. In this study, we analyzed the effects of O2 levels on human cortical progenitors, the radial glia cells (RGCs), during active neurogenesis, corresponding to the second trimester of gestation. Small changes in O2 levels profoundly affected RGC survival, proliferation, and differentiation. Physiological hypoxia (3% O2) promoted neurogenesis, whereas anoxia (<1% O2) and severe hypoxia (1% O2) arrested the differentiation of human RGCs, mainly by altering the generation of glutamatergic neurons. The in vitro activation of Wnt-β-catenin signaling rescued the proliferation and neuronal differentiation of RGCs subjected to anoxia. Pathologic hypoxia (≤1% O2) also exerted negative effects on gliogenesis, by decreasing the number of O4+ preoligodendrocytes and increasing the number of reactive astrocytes derived from cortical RGCs. O2-dependent alterations in glutamatergic neurogenesis and oligodendrogenesis can lead to significant changes in cortical circuitry formation. A better understanding of the cellular effects caused by changes in O2 levels during human cortical development is essential to elucidating the etiology of numerous neurodevelopmental disorders.
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Affiliation(s)
- J Alberto Ortega
- Department of Neuroscience, University of Connecticut Health, Farmington, CT 06030, USA
| | - Carissa L Sirois
- Department of Neuroscience, University of Connecticut Health, Farmington, CT 06030, USA
- Department of Genetics and Genome Sciences, University of Connecticut Health Center, Farmington, CT 06030, USA
| | - Fani Memi
- Department of Neuroscience, University of Connecticut Health, Farmington, CT 06030, USA
| | - Nicole Glidden
- Department of Neuroscience, University of Connecticut Health, Farmington, CT 06030, USA
| | - Nada Zecevic
- Department of Neuroscience, University of Connecticut Health, Farmington, CT 06030, USA
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Expression of progerin does not result in an increased mutation rate. Chromosome Res 2017; 25:227-239. [PMID: 28477268 PMCID: PMC5662688 DOI: 10.1007/s10577-017-9556-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 04/08/2017] [Accepted: 04/13/2017] [Indexed: 12/22/2022]
Abstract
In the premature ageing disease Hutchinson-Gilford progeria syndrome (HGPS), the underlying genetic defect in the lamin A gene leads to accumulation at the nuclear lamina of progerin—a mutant form of lamin A that cannot be correctly processed. This has been reported to result in defects in the DNA damage response and in DNA repair, leading to the hypothesis that, as in normal ageing and in other progeroid syndromes caused by mutation of genes of the DNA repair and DNA damage response pathways, increased DNA damage may be responsible for the premature ageing phenotypes in HGPS patients. However, this hypothesis is based upon the study of markers of the DNA damage response, rather than measurement of DNA damage per se or the consequences of unrepaired DNA damage—mutation. Here, using a mutation reporter cell line, we directly compared the inherent and induced mutation rates in cells expressing wild-type lamin A or progerin. We find no evidence for an elevated mutation rate in progerin-expressing cells. We conclude that the cellular defect in HGPS cells does not lie in the repair of DNA damage per se.
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Stambrook PJ, Maher J, Farzaneh F. Cancer Immunotherapy: Whence and Whither. Mol Cancer Res 2017; 15:635-650. [PMID: 28356330 DOI: 10.1158/1541-7786.mcr-16-0427] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 12/22/2016] [Accepted: 01/14/2017] [Indexed: 12/22/2022]
Abstract
The current concepts and practice of cancer immunotherapy evolved from classical experiments that distinguished "self" from "non-self" and the finding that humoral immunity is complemented by cellular immunity. Elucidation of the biology underlying immune checkpoints and interactions between ligands and ligand receptors that govern the immune system's ability to recognize tumor cells as foreign has led to the emergence of new strategies that mobilize the immune system to reverse this apparent tolerance. Some of these approaches have led to new therapies such as the use of mAbs to interfere with the immune checkpoint. Others have exploited molecular technologies to reengineer a subset of T cells to directly engage and kill tumor cells, particularly those of B-cell malignancies. However, before immunotherapy can become a more effective method of cancer care, there are many challenges that remain to be addressed and hurdles to overcome. Included are manipulation of tumor microenvironment (TME) to enhance T effector cell infiltration and access to the tumor, augmentation of tumor MHC expression for adequate presentation of tumor associated antigens, regulation of cytokines and their potential adverse effects, and reduced risk of secondary malignancies as a consequence of mutations generated by the various forms of genetic engineering of immune cells. Despite these challenges, the future of immunotherapy as a standard anticancer therapy is encouraging. Mol Cancer Res; 15(6); 635-50. ©2017 AACR.
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Affiliation(s)
- Peter J Stambrook
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio.
| | - John Maher
- Kings College London, CAR Mechanics Group, Guy's Hospital, London, United Kingdom
| | - Farzin Farzaneh
- Division of Cancer Studies, Department of Haematological Medicine, Kings College London, London, United Kingdom
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Rodas-Junco BA, Villicaña C. Dental Pulp Stem Cells: Current Advances in Isolation, Expansion and Preservation. Tissue Eng Regen Med 2017; 14:333-347. [PMID: 30603490 DOI: 10.1007/s13770-017-0036-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 09/27/2016] [Accepted: 10/03/2016] [Indexed: 01/09/2023] Open
Abstract
Dental pulp stem cells (DPSCs) are mesenchymal stem cells with high self-renewal potential that have the ability to differentiate into several cell types. Thus, DPSCs have become a promising source of cells for several applications in regenerative medicine, tissue engineering, and stem cell therapy. Numerous methods have been reported for the isolation, expansion, and preservation of DPSCs. However, methods are diverse and do not follow specific rules or parameters, which can affect stem cell properties, adding more variation to experimental results. In this review, we compare and analyze current experimental evidence to propose some factors that can be useful to establish better methods or improved protocols to prolong the quality of DPSCs. In addition, we highlight other factors related to biological aspects of dental tissue source (e.g., age, genetic background) that should be considered before tooth selection. Although current methods have reached significant advances, optimization is still required to improve culture stability and its maintenance for an extended period without losing stem cell properties. In addition, there is still much that needs to be done toward clinical application due to the fact that most of DPSCs procedures are not currently following good manufacturing practices. The establishment of optimized general or tailored protocols will allow obtaining well-defined DPSCs cultures with specific properties, which enable more reproducible results that will be the basis to develop effective and safe therapies.
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Affiliation(s)
- Beatriz A Rodas-Junco
- CONACYT - Facultad de Ingeniería Química, Campus de Ciencias Exactas e Ingenierías, Universidad Autónoma de Yucatán (UADY), Periférico Norte Kilómetro 33.5, Tablaje Catastral 13615 Chuburná de Hidalgo Inn, CP 97203 Mérida, Yucatán México
| | - Claudia Villicaña
- CONACYT - Facultad de Ingeniería Química, Campus de Ciencias Exactas e Ingenierías, Universidad Autónoma de Yucatán (UADY), Periférico Norte Kilómetro 33.5, Tablaje Catastral 13615 Chuburná de Hidalgo Inn, CP 97203 Mérida, Yucatán México
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Interchangeable Roles for E2F Transcriptional Repression by the Retinoblastoma Protein and p27KIP1-Cyclin-Dependent Kinase Regulation in Cell Cycle Control and Tumor Suppression. Mol Cell Biol 2017; 37:MCB.00561-16. [PMID: 27821477 DOI: 10.1128/mcb.00561-16] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 11/01/2016] [Indexed: 01/09/2023] Open
Abstract
The mammalian G1-S phase transition is controlled by the opposing forces of cyclin-dependent kinases (CDK) and the retinoblastoma protein (pRB). Here, we present evidence for systems-level control of cell cycle arrest by pRB-E2F and p27-CDK regulation. By introducing a point mutant allele of pRB that is defective for E2F repression (Rb1G) into a p27KIP1 null background (Cdkn1b-/-), both E2F transcriptional repression and CDK regulation are compromised. These double-mutant Rb1G/G; Cdkn1b-/- mice are viable and phenocopy Rb1+/- mice in developing pituitary adenocarcinomas, even though neither single mutant strain is cancer prone. Combined loss of pRB-E2F transcriptional regulation and p27KIP1 leads to defective proliferative control in response to various types of DNA damage. In addition, Rb1G/G; Cdkn1b-/- fibroblasts immortalize faster in culture and more frequently than either single mutant genotype. Importantly, the synthetic DNA damage arrest defect caused by Rb1G/G; Cdkn1b-/- mutations is evident in the developing intermediate pituitary lobe where tumors ultimately arise. Our work identifies a unique relationship between pRB-E2F and p27-CDK control and offers in vivo evidence that pRB is capable of cell cycle control through E2F-independent effects.
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Ma S, Upneja A, Galecki A, Tsai YM, Burant CF, Raskind S, Zhang Q, Zhang ZD, Seluanov A, Gorbunova V, Clish CB, Miller RA, Gladyshev VN. Cell culture-based profiling across mammals reveals DNA repair and metabolism as determinants of species longevity. eLife 2016; 5:e19130. [PMID: 27874830 PMCID: PMC5148604 DOI: 10.7554/elife.19130] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 11/21/2016] [Indexed: 12/30/2022] Open
Abstract
Mammalian lifespan differs by >100 fold, but the mechanisms associated with such longevity differences are not understood. Here, we conducted a study on primary skin fibroblasts isolated from 16 species of mammals and maintained under identical cell culture conditions. We developed a pipeline for obtaining species-specific ortholog sequences, profiled gene expression by RNA-seq and small molecules by metabolite profiling, and identified genes and metabolites correlating with species longevity. Cells from longer lived species up-regulated genes involved in DNA repair and glucose metabolism, down-regulated proteolysis and protein transport, and showed high levels of amino acids but low levels of lysophosphatidylcholine and lysophosphatidylethanolamine. The amino acid patterns were recapitulated by further analyses of primate and bird fibroblasts. The study suggests that fibroblast profiling captures differences in longevity across mammals at the level of global gene expression and metabolite levels and reveals pathways that define these differences.
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Affiliation(s)
- Siming Ma
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Akhil Upneja
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Andrzej Galecki
- Department of Pathology, University of Michigan Medical School, Ann Arbor, United States
- Geriatrics Center, University of Michigan Medical School, Ann Arbor, United States
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, United States
| | - Yi-Miau Tsai
- Department of Pathology, University of Michigan Medical School, Ann Arbor, United States
- Geriatrics Center, University of Michigan Medical School, Ann Arbor, United States
| | - Charles F Burant
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, United States
| | - Sasha Raskind
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, United States
| | - Quanwei Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, United States
| | - Zhengdong D Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, United States
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, United States
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, United States
| | | | - Richard A Miller
- Department of Pathology, University of Michigan Medical School, Ann Arbor, United States
- Geriatrics Center, University of Michigan Medical School, Ann Arbor, United States
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
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First steps to define murine amniotic fluid stem cell microenvironment. Sci Rep 2016; 6:37080. [PMID: 27845396 PMCID: PMC5109045 DOI: 10.1038/srep37080] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 10/24/2016] [Indexed: 12/19/2022] Open
Abstract
Stem cell niche refers to the microenvironment where stem cells reside in living organisms. Several elements define the niche and regulate stem cell characteristics, such as stromal support cells, gap junctions, soluble factors, extracellular matrix proteins, blood vessels and neural inputs. In the last years, different studies demonstrated the presence of cKit+ cells in human and murine amniotic fluid, which have been defined as amniotic fluid stem (AFS) cells. Firstly, we characterized the murine cKit+ cells present both in the amniotic fluid and in the amnion. Secondly, to analyze the AFS cell microenvironment, we injected murine YFP+ embryonic stem cells (ESC) into the amniotic fluid of E13.5 wild type embryos. Four days after transplantation we found that YFP+ sorted cells maintained the expression of pluripotency markers and that ESC adherent to the amnion were more similar to original ESC in respect to those isolated from the amniotic fluid. Moreover, cytokines evaluation and oxygen concentration analysis revealed in this microenvironment the presence of factors that are considered key regulators in stem cell niches. This is the first indication that AFS cells reside in a microenvironment that possess specific characteristics able to maintain stemness of resident and exogenous stem cells.
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Abstract
Potential ionising radiation exposure scenarios are varied, but all bring risks beyond the simple issues of short-term survival. Whether accidentally exposed to a single, whole-body dose in an act of terrorism or purposefully exposed to fractionated doses as part of a therapeutic regimen, radiation exposure carries the consequence of elevated cancer risk. The long-term impact of both intentional and unintentional exposure could potentially be mitigated by treatments specifically developed to limit the mutations and precancerous replication that ensue in the wake of irradiation The development of such agents would undoubtedly require a substantial degree of in vitro testing, but in order to accurately recapitulate the complex process of radiation-induced carcinogenesis, well-understood animal models are necessary. Inbred strains of the laboratory mouse, Mus musculus, present the most logical choice due to the high number of molecular and physiological similarities they share with humans. Their small size, high rate of breeding and fully sequenced genome further increase its value for use in cancer research. This chapter will review relevant m. musculus inbred and F1 hybrid animals of radiation-induced myeloid leukemia, thymic lymphoma, breast and lung cancers. Method of cancer induction and associated molecular pathologies will also be described for each model.
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Shuai Y, Liao L, Su X, Yu Y, Shao B, Jing H, Zhang X, Deng Z, Jin Y. Melatonin Treatment Improves Mesenchymal Stem Cells Therapy by Preserving Stemness during Long-term In Vitro Expansion. Am J Cancer Res 2016; 6:1899-917. [PMID: 27570559 PMCID: PMC4997245 DOI: 10.7150/thno.15412] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 07/20/2016] [Indexed: 02/07/2023] Open
Abstract
Mesenchymal stem cells (MSCs) are promising candidates for tissue regeneration and disease treatment. However, long-term in vitro passaging leads to stemness loss of MSCs, resulting in failure of MSCs therapy. Here, we report a melatonin-based strategy to improve cell therapy of in vitro cultured MSCs. Among four small molecules with anti-aging and stem cell-protection properties (rapamycin, resveratrol, quercetin and melatonin), colony forming, proliferation, and osteogenic differentiation assay showed that melatonin was the most efficient to preserve self-renewal and differentiation properties of rat bone marrow MSCs (BMMSCs) after long-term passaging. Functional assays confirmed melatonin treatment did not affect the colony forming, proliferation and osteogenic differentiation of BMMSCs cultured for 1 or 4 passages, but largely prevented the decline of self-renew and differentiation capacity of BMMSCs cultured for 15 passages in vitro. Furthermore, heterotopic osteogenesis assay, critical size calvarial defects repair assay, osteoporosis treatment and experimental colitis therapy assay strongly certified that melatonin preserved the therapeutic effect of long-term passaged BMMSCs on bone regeneration and immunotherapy in vivo. Mechanistically, melatonin functioned by activating antioxidant defense system, inhibiting the pathway of cell senescence, and preserving the expression of gene governing the stemness. Taken together, our findings showed that melatonin treatment efficiently prevented the dysfunction and therapeutic failure of BMMSCs after long-term passaging, providing a practical strategy to improve the application of BMMSCs in tissue engineering and cytotherapy.
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Bétous R, Renoud M, Hoede C, Gonzalez I, Jones N, Longy M, Sensebé L, Cazaux C, Hoffmann J. Human Adipose-Derived Stem Cells Expanded Under Ambient Oxygen Concentration Accumulate Oxidative DNA Lesions and Experience Procarcinogenic DNA Replication Stress. Stem Cells Transl Med 2016; 6:68-76. [PMID: 28170194 PMCID: PMC5442744 DOI: 10.5966/sctm.2015-0401] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 04/08/2016] [Indexed: 01/15/2023] Open
Abstract
Adipose‐derived stem cells (ADSCs) have led to growing interest in cell‐based therapy because they can be easily harvested from an abundant tissue. ADSCs must be expanded in vitro before transplantation. This essential step causes concerns about the safety of adult stem cells in terms of potential transformation. Tumorigenesis is driven in its earliest step by DNA replication stress, which is characterized by the accumulation of stalled DNA replication forks and activation of the DNA damage response. Thus, to evaluate the safety of ADSCs during ex vivo expansion, we monitored DNA replication under atmospheric (21%) or physiologic (1%) oxygen concentration. Here, by combining immunofluorescence and DNA combing, we show that ADSCs cultured under 21% oxygen accumulate endogenous oxidative DNA lesions, which interfere with DNA replication by increasing fork stalling events, thereby leading to incomplete DNA replication and fork collapse. Moreover, we found by RNA sequencing (RNA‐seq) that culture of ADSCs under atmospheric oxygen concentration leads to misexpression of cell cycle and DNA replication genes, which could contribute to DNA replication stress. Finally, analysis of acquired small nucleotide polymorphism shows that expansion of ADSCs under 21% oxygen induces a mutational bias toward deleterious transversions. Overall, our results suggest that expanding ADSCs at a low oxygen concentration could reduce the risk for DNA replication stress‐associated transformation, as occurs in neoplastic tissues. Stem Cells Translational Medicine2017;6:68–76
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Affiliation(s)
- Rémy Bétous
- Equipe Labellisée La Ligue Contre Le Cancer, Paris, France
- Laboratoire d'Excellence Toulouse Cancer Labex Toucan, Cancer Research Center of Toulouse, INSERM U1037, CNRS ERL5294, Toulouse, France
- University Paul Sabatier, Toulouse, France
| | - Marie‐Laure Renoud
- University Paul Sabatier, Toulouse, France
- Etablissement Français du Sang Pyrénées Méditerranée, Toulouse, France
- INSERM U1031, UMR5273, Toulouse, France
| | - Claire Hoede
- Institut National de la Recherche Agronomique (INRA), UR 875, Unité de Mathématique et Informatique Appliquées, PF Bioinfo Genotoul, Castanet Tolosan, France
| | - Ignacio Gonzalez
- Institut National de la Recherche Agronomique (INRA), UR 875, Unité de Mathématique et Informatique Appliquées, PF Bioinfo Genotoul, Castanet Tolosan, France
| | - Natalie Jones
- INSERM U916 Vinco, Université de Bordeaux, Institut Bergonié, Bordeaux, France
| | - Michel Longy
- INSERM U916 Vinco, Université de Bordeaux, Institut Bergonié, Bordeaux, France
| | - Luc Sensebé
- University Paul Sabatier, Toulouse, France
- Etablissement Français du Sang Pyrénées Méditerranée, Toulouse, France
- INSERM U1031, UMR5273, Toulouse, France
| | - Christophe Cazaux
- Equipe Labellisée La Ligue Contre Le Cancer, Paris, France
- Laboratoire d'Excellence Toulouse Cancer Labex Toucan, Cancer Research Center of Toulouse, INSERM U1037, CNRS ERL5294, Toulouse, France
- University Paul Sabatier, Toulouse, France
| | - Jean‐Sébastien Hoffmann
- Equipe Labellisée La Ligue Contre Le Cancer, Paris, France
- Laboratoire d'Excellence Toulouse Cancer Labex Toucan, Cancer Research Center of Toulouse, INSERM U1037, CNRS ERL5294, Toulouse, France
- University Paul Sabatier, Toulouse, France
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Werle SB, Chagastelles P, Pranke P, Casagrande L. The effects of hypoxia on in vitro culture of dental-derived stem cells. Arch Oral Biol 2016; 68:13-20. [DOI: 10.1016/j.archoralbio.2016.03.011] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 03/18/2016] [Accepted: 03/20/2016] [Indexed: 12/19/2022]
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Sanz A. Mitochondrial reactive oxygen species: Do they extend or shorten animal lifespan? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2016; 1857:1116-1126. [PMID: 26997500 DOI: 10.1016/j.bbabio.2016.03.018] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 03/10/2016] [Accepted: 03/14/2016] [Indexed: 12/16/2022]
Abstract
Testing the predictions of the Mitochondrial Free Radical Theory of Ageing (MFRTA) has provided a deep understanding of the role of reactive oxygen species (ROS) and mitochondria in the aging process. However those data, which support MFRTA are in the majority correlative (e.g. increasing oxidative damage with age). In contrast the majority of direct experimental data contradict MFRTA (e.g. changes in ROS levels do not alter longevity as expected). Unfortunately, in the past, ROS measurements have mainly been performed using isolated mitochondria, a method which is prone to experimental artifacts and does not reflect the complexity of the in vivo process. New technology to study different ROS (e.g. superoxide or hydrogen peroxide) in vivo is now available; these new methods combined with state-of-the-art genetic engineering technology will allow a deeper interrogation of, where, when and how free radicals affect aging and pathological processes. In fact data that combine these new approaches, indicate that boosting mitochondrial ROS in lower animals is a way to extend both healthy and maximum lifespan. In this review, I discuss the latest literature focused on the role of mitochondrial ROS in aging, and how these new discoveries are helping to better understand the role of mitochondria in health and disease. This article is part of a Special Issue entitled 'EBEC 2016: 19th European Bioenergetics Conference, Riva del Garda, Italy, July 2-6, 2016', edited by Prof. Paolo Bernardi.
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Affiliation(s)
- Alberto Sanz
- Institute for Cell and Molecular Biosciences, Newcastle University Institute for Ageing, University of Newcastle, Newcastle upon Tyne NE4 5PL, UK
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