101
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Bush JT, Chan MC, Mohammed S, Schofield CJ. Quantitative MS-Based Proteomics: Comparing the MCF-7 Cellular Response to Hypoxia and a 2-Oxoglutarate Analogue. Chembiochem 2020; 21:1647-1655. [PMID: 31919953 PMCID: PMC7317498 DOI: 10.1002/cbic.201900719] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Indexed: 12/19/2022]
Abstract
The hypoxia-inducible factors (HIFs) are key transcription factors in determining cellular responses involving alterations in protein levels in response to limited oxygen availability in animal cells. 2-Oxoglutarate-dependent oxygenases play key roles in regulating levels of HIF and its transcriptional activity. We describe MS-based proteomics studies in which we compared the results of subjecting human breast cancer MCF-7 cells to hypoxia or treating them with a cell-penetrating derivative (dimethyl N-oxalylglycine; DMOG) of the stable 2OG analogue N-oxalylglycine. The proteomic results are consistent with reported transcriptomic analyses and support the proposed key roles of 2OG-dependent HIF prolyl- and asparaginyl-hydroxylases in the hypoxic response. Differences between the data sets for hypoxia and DMOG might reflect context-dependent effects or HIF-independent effects of DMOG.
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Affiliation(s)
- Jacob T. Bush
- Chemistry Research LaboratoryDepartment of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
- Current address: GSKMedicines Research CentreGunnels Wood RoadStevenageSG1 2NYUK
| | - Mun Chiang Chan
- Chemistry Research LaboratoryDepartment of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
- Current address: Department of Molecular MedicineFaculty of MedicineUniversity of Malaya, Jalan Universiti50603Kuala LumpurMalaysia
| | - Shabaz Mohammed
- Chemistry Research LaboratoryDepartment of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
- Department of BiochemistryUniversity of OxfordSouth Parks RoadOxfordOX1 3QUUK
| | - Christopher J. Schofield
- Chemistry Research LaboratoryDepartment of ChemistryUniversity of Oxford12 Mansfield RoadOxfordOX1 3TAUK
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102
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Brewitz L, Tumber A, Pfeffer I, McDonough MA, Schofield CJ. Aspartate/asparagine-β-hydroxylase: a high-throughput mass spectrometric assay for discovery of small molecule inhibitors. Sci Rep 2020; 10:8650. [PMID: 32457455 PMCID: PMC7251097 DOI: 10.1038/s41598-020-65123-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 04/28/2020] [Indexed: 12/20/2022] Open
Abstract
The human 2-oxoglutarate dependent oxygenase aspartate/asparagine-β-hydroxylase (AspH) catalyses the hydroxylation of Asp/Asn-residues in epidermal growth factor-like domains (EGFDs). AspH is upregulated on the surface of malign cancer cells; increased AspH levels correlate with tumour invasiveness. Due to a lack of efficient assays to monitor the activity of isolated AspH, there are few reports of studies aimed at identifying small-molecule AspH inhibitors. Recently, it was reported that AspH substrates have a non-canonical EGFD disulfide pattern. Here we report that a stable synthetic thioether mimic of AspH substrates can be employed in solid phase extraction mass spectrometry based high-throughput AspH inhibition assays which are of excellent robustness, as indicated by high Z'-factors and good signal-to-noise/background ratios. The AspH inhibition assay was applied to screen approximately 1500 bioactive small-molecules, including natural products and active pharmaceutical ingredients of approved human therapeutics. Potent AspH inhibitors were identified from both compound classes. Our AspH inhibition assay should enable the development of potent and selective small-molecule AspH inhibitors and contribute towards the development of safer inhibitors for other 2OG oxygenases, e.g. screens of the hypoxia-inducible factor prolyl-hydroxylase inhibitors revealed that vadadustat inhibits AspH with moderate potency.
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Affiliation(s)
- Lennart Brewitz
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, United Kingdom
| | - Anthony Tumber
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, United Kingdom
| | - Inga Pfeffer
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, United Kingdom
| | - Michael A McDonough
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, United Kingdom
| | - Christopher J Schofield
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA, Oxford, United Kingdom.
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103
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Ludman T, Melemedjian OK. Bortezomib and metformin opposingly regulate the expression of hypoxia-inducible factor alpha and the consequent development of chemotherapy-induced painful peripheral neuropathy. Mol Pain 2020; 15:1744806919850043. [PMID: 31041875 PMCID: PMC6509977 DOI: 10.1177/1744806919850043] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Chemotherapy-induced painful peripheral neuropathy is a significant clinical problem that is associated with widely used chemotherapeutics. Unfortunately, the molecular mechanisms by which chemotherapy-induced painful peripheral neuropathy develops have remained elusive. The proteasome inhibitor, bortezomib, has been shown to induce aerobic glycolysis in sensory neurons. This altered metabolic phenotype leads to the extrusion of metabolites which sensitize primary afferents and cause pain. Hypoxia-inducible factor alpha is a transcription factor that is known to reprogram cellular metabolism. Furthermore, hypoxia-inducible factor 1 alpha protein is constantly synthesized and undergoes proteasomal degradation in normal conditions. However, metabolic stress or hypoxia stabilizes the expression of hypoxia-inducible factor 1 alpha leading to the transcription of genes that reprogram cellular metabolism. This study demonstrates that treatment of mice with bortezomib stabilizes the expression of hypoxia-inducible factor 1 alpha. Moreover, knockdown of hypoxia-inducible factor 1 alpha, inhibition of hypoxia-inducible factor 1 alpha binding to its response element, or limiting its translation by using metformin prevent the development of bortezomib-induced neuropathic pain. Strikingly, the blockade of hypoxia-inducible factor 1 alpha expression does not attenuate mechanical allodynia in mice with existing bortezomib-induced neuropathic pain. These results establish the stabilization of hypoxia-inducible factor 1 alpha expression as the molecular mechanism by which bortezomib initiates chemotherapy-induced painful peripheral neuropathy. Crucially, these findings reveal that the initiation and maintenance of bortezomib-induced neuropathic pain are regulated by distinct mechanisms.
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Affiliation(s)
- Taylor Ludman
- 1 Department of Neural and Pain Sciences, School of Dentistry, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Ohannes K Melemedjian
- 1 Department of Neural and Pain Sciences, School of Dentistry, University of Maryland, Baltimore, Baltimore, MD, USA.,2 University of Maryland Center to Advance Chronic Pain Research, Baltimore, MD, USA
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104
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Brewitz L, Tumber A, Thalhammer A, Salah E, Christensen KE, Schofield CJ. Synthesis of Novel Pyridine-Carboxylates as Small-Molecule Inhibitors of Human Aspartate/Asparagine-β-Hydroxylase. ChemMedChem 2020; 15:1139-1149. [PMID: 32330361 PMCID: PMC7383925 DOI: 10.1002/cmdc.202000147] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Indexed: 12/19/2022]
Abstract
The human 2‐oxoglutarate (2OG)‐dependent oxygenase aspartate/asparagine‐β‐hydroxylase (AspH) is a potential medicinal chemistry target for anticancer therapy. AspH is present on the cell surface of invasive cancer cells and accepts epidermal growth factor‐like domain (EGFD) substrates with a noncanonical (i. e., Cys 1–2, 3–4, 5–6) disulfide pattern. We report a concise synthesis of C‐3‐substituted derivatives of pyridine‐2,4‐dicarboxylic acid (2,4‐PDCA) as 2OG competitors for use in SAR studies on AspH inhibition. AspH inhibition was assayed by using a mass spectrometry‐based assay with a stable thioether analogue of a natural EGFD AspH substrate. Certain C‐3‐substituted 2,4‐PDCA derivatives were potent AspH inhibitors, manifesting selectivity over some, but not all, other tested human 2OG oxygenases. The results raise questions about the use of pyridine‐carboxylate‐related 2OG analogues as selective functional probes for specific 2OG oxygenases, and should aid in the development of AspH inhibitors suitable for in vivo use.
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Affiliation(s)
- Lennart Brewitz
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Anthony Tumber
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Armin Thalhammer
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Eidarus Salah
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Kirsten E Christensen
- Chemical Crystallography Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK
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105
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Hypoxia-Inducible Factor 1α (HIF-1α) Counteracts the Acute Death of Cells Transplanted into the Injured Spinal Cord. eNeuro 2020; 7:ENEURO.0092-19.2019. [PMID: 31488552 PMCID: PMC7215587 DOI: 10.1523/eneuro.0092-19.2019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Revised: 08/10/2019] [Accepted: 08/19/2019] [Indexed: 01/13/2023] Open
Abstract
Cellular transplantation is in clinical testing for a number of central nervous system disorders, including spinal cord injury (SCI). One challenge is acute transplanted cell death. To prevent this death, there is a need to both establish when the death occurs and develop approaches to mitigate its effects. Here, using luciferase (luc) and green fluorescent protein (GFP) expressing Schwann cell (SC) transplants in the contused thoracic rat spinal cord 7 d postinjury, we establish via in vivo bioluminescent (IVIS) imaging and stereology that cell death occurs prior to 2–3 d postimplantation. We then test an alternative approach to the current paradigm of enhancing transplant survival by including multiple factors along with the cells. To stimulate multiple cellular adaptive pathways concurrently, we activate the hypoxia-inducible factor 1α (HIF-1α) transcriptional pathway. Retroviral expression of VP16-HIF-1α in SCs increased HIF-α by 5.9-fold and its target genes implicated in oxygen transport and delivery (VEGF, 2.2-fold) and cellular metabolism (enolase, 1.7-fold). In cell death assays in vitro, HIF-1α protected cells from H2O2-induced oxidative damage. It also provided some protection against camptothecin-induced DNA damage, but not thapsigargin-induced endoplasmic reticulum stress or tunicamycin-induced unfolded protein response. Following transplantation, VP16-HIF-1α increased SC survival by 34.3%. The increase in cell survival was detectable by stereology, but not by in vivo luciferase or ex vivo GFP IVIS imaging. The results support the hypothesis that activating adaptive cellular pathways enhances transplant survival and identifies an alternative pro-survival approach that, with optimization, could be amenable to clinical translation.
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106
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Zhang H, Liu X, Yang F, Cheng D, Liu W. Overexpression of HIF-1α protects PC12 cells against OGD/R-evoked injury by reducing miR-134 expression. Cell Cycle 2020; 19:990-999. [PMID: 32266863 PMCID: PMC7217352 DOI: 10.1080/15384101.2020.1743903] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/17/2020] [Accepted: 03/08/2020] [Indexed: 01/04/2023] Open
Abstract
Nowadays, searching for new therapeutic targets for cerebral stroke treatment are still in urgent need. Our study explored the influences and mechanisms of HIF-1α on OGD/R-evoked injury. OGD/R treatment was conducted on PC12 cells to simulate ischemic injury. CCK-8, flow cytometry and qRT-PCR were conducted to determine the variations of cell viability, apoptosis and gene expression, respectively. Cell transfections were conducted to overexpress HIF-1α and miR-134. Variations of protein levels were evaluated by employing western blot. Results showed that OGD/R treatment induced cell injury through reducing viability, while enhancing apoptosis that was validated by the elevated ratios of C/P-PARP and C/P-caspase-3. HIF-1α expression was markedly increased by OGD/R treatment. HIF-1α overexpression attenuated OGD/R-evoked injury in PC12 cells and remarkably reversed OGD/R-triggered inhibitory effects on ERK1/2 and JAK1/STAT3 pathways. Besides, miR-134 was also down-regulated by HIF-1α overexpression in PC12 cells. Up-regulation of miR-134 notably counteracted HIF-1α overexpression-triggered neuro-protective impacts on OGD/R-evoked injury and ERK1/2 and JAK1/STAT3 pathways. Our present study reported that HIF-1α overexpression protected PC12 cells against OGD/R-evoked injury via down-regulation of miR-134, which making HIF-1α and miR-134 to be promising targets for cerebral stroke therapy.
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Affiliation(s)
- Hongliang Zhang
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Xianming Liu
- Department of Neurosurgery, Qingdao Municipal Hospital, Qingdao, Shandong, China
| | - Fengyu Yang
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Dekui Cheng
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Wei Liu
- Department of Neurosurgery, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
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107
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Jain IH, Calvo SE, Markhard AL, Skinner OS, To TL, Ast T, Mootha VK. Genetic Screen for Cell Fitness in High or Low Oxygen Highlights Mitochondrial and Lipid Metabolism. Cell 2020; 181:716-727.e11. [PMID: 32259488 PMCID: PMC7293541 DOI: 10.1016/j.cell.2020.03.029] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 02/13/2020] [Accepted: 03/11/2020] [Indexed: 01/04/2023]
Abstract
Human cells are able to sense and adapt to variations in oxygen levels. Historically, much research in this field has focused on hypoxia-inducible factor (HIF) signaling and reactive oxygen species (ROS). Here, we perform genome-wide CRISPR growth screens at 21%, 5%, and 1% oxygen to systematically identify gene knockouts with relative fitness defects in high oxygen (213 genes) or low oxygen (109 genes), most without known connection to HIF or ROS. Knockouts of many mitochondrial pathways thought to be essential, including complex I and enzymes in Fe-S biosynthesis, grow relatively well at low oxygen and thus are buffered by hypoxia. In contrast, in certain cell types, knockout of lipid biosynthetic and peroxisomal genes causes fitness defects only in low oxygen. Our resource nominates genetic diseases whose severity may be modulated by oxygen and links hundreds of genes to oxygen homeostasis.
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Affiliation(s)
- Isha H Jain
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Sarah E Calvo
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Andrew L Markhard
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Owen S Skinner
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Tsz-Leung To
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Tslil Ast
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute, Cambridge, MA 02142, USA
| | - Vamsi K Mootha
- Howard Hughes Medical Institute, Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Broad Institute, Cambridge, MA 02142, USA.
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108
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Kang Y, Roh MR, Rajadurai S, Rajadurai A, Kumar R, Njauw CN, Zheng Z, Tsao H. Hypoxia and HIF-1α Regulate Collagen Production in Keloids. J Invest Dermatol 2020; 140:2157-2165. [PMID: 32315657 DOI: 10.1016/j.jid.2020.01.036] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Revised: 01/02/2020] [Accepted: 01/06/2020] [Indexed: 11/18/2022]
Abstract
Keloids are reactive or spontaneous fibroproliferative dermal tumors characterized by the exaggerated and uncontrolled accumulation of extracellular collagen. Current approaches to mitigate keloidogenesis are largely procedural in nature. However, a better understanding of its biological drivers may lead to novel targeted treatments for keloids. Through whole-genome expression analysis, we found that an HIF-1α transcriptional footprint is preferentially upregulated (activation score = 2.024; P = 1.05E-19) in keloid fibroblasts compared with normal dermal fibroblasts. We verified that HIF-1α protein is more strongly expressed in keloid specimens compared with normal skin (P = 0.035) and that hypoxia (1% O2) leads to increased collagen, especially in the extracellular compartment. Collagen levels were reduced uniformly by selective HIF-1α inhibitor CAY10585. Our results indicate that collagen secretion may be intimately linked to a hypoxic microenvironment within keloid tumors and that HIF-1α blockade could be a novel avenue of treatment for these tumors.
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Affiliation(s)
- Yuanyuan Kang
- Wellman Center for Photomedicine and Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Mi Ryung Roh
- Department of Dermatology, Gangnam Severance Hospital, Cutaneous Biology Research Institute, Yonsei University College of Medicine, Seoul, Korea
| | - Suvi Rajadurai
- Wellman Center for Photomedicine and Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Anpuchchelvi Rajadurai
- Wellman Center for Photomedicine and Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Raj Kumar
- Wellman Center for Photomedicine and Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Ching-Ni Njauw
- Wellman Center for Photomedicine and Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Zhenlong Zheng
- Department of Dermatology, Yanbian University Hospital, Yanji, China
| | - Hensin Tsao
- Wellman Center for Photomedicine and Department of Dermatology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA.
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109
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Bartoszewska S, Collawn JF. Unfolded protein response (UPR) integrated signaling networks determine cell fate during hypoxia. Cell Mol Biol Lett 2020; 25:18. [PMID: 32190062 PMCID: PMC7071609 DOI: 10.1186/s11658-020-00212-1] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/26/2020] [Indexed: 02/06/2023] Open
Abstract
During hypoxic conditions, cells undergo critical adaptive responses that include the up-regulation of hypoxia-inducible proteins (HIFs) and the induction of the unfolded protein response (UPR). While their induced signaling pathways have many distinct targets, there are some important connections as well. Despite the extensive studies on both of these signaling pathways, the exact mechanisms involved that determine survival versus apoptosis remain largely unexplained and therefore beyond therapeutic control. Here we discuss the complex relationship between the HIF and UPR signaling pathways and the importance of understanding how these pathways differ between normal and cancer cell models.
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Affiliation(s)
- Sylwia Bartoszewska
- Department of Inorganic Chemistry, Medical University of Gdansk, Gdansk, Poland
| | - James F. Collawn
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, USA
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110
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Identification of key HIF-1α target genes that regulate adaptation to hypoxic conditions in Tibetan chicken embryos. Gene 2020; 729:144321. [DOI: 10.1016/j.gene.2019.144321] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 12/10/2019] [Accepted: 12/21/2019] [Indexed: 12/11/2022]
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111
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Timón-Gómez A, Barrientos A. Mitochondrial respiratory chain composition and organization in response to changing oxygen levels. ACTA ACUST UNITED AC 2020; 2. [PMID: 32551463 DOI: 10.36069/jols/20200601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Mitochondria are the major consumer of oxygen in eukaryotic cells, owing to the requirement of oxygen to generate ATP through the mitochondrial respiratory chain (MRC) and the oxidative phosphorylation system (OXPHOS). This aerobic energy transduction is more efficient than anaerobic processes such as glycolysis. Hypoxia, a condition in which environmental or intracellular oxygen levels are below the standard range, triggers an adaptive signaling pathway within the cell. When oxygen concentrations are low, hypoxia-inducible factors (HIFs) become stabilized and activated to mount a transcriptional response that triggers modulation of cellular metabolism to adjust to hypoxic conditions. Mitochondrial aerobic metabolism is one of the main targets of the hypoxic response to regulate its functioning and efficiency in the presence of decreased oxygen levels. During evolution, eukaryotic cells and tissues have increased the plasticity of their mitochondrial OXPHOS system to cope with metabolic needs in different oxygen contexts. In mammalian mitochondria, two factors contribute to this plasticity. First, several subunits of the multimeric MRC complexes I and IV exist in multiple tissue-specific and condition-specific isoforms. Second, the MRC enzymes can coexist organized as individual entities or forming supramolecular structures known as supercomplexes, perhaps in a dynamic manner to respond to environmental conditions and cellular metabolic demands. In this review, we will summarize the information currently available on oxygen-related changes in MRC composition and organization and will discuss gaps of knowledge and research opportunities in the field.
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Affiliation(s)
- Alba Timón-Gómez
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL 33136
| | - Antoni Barrientos
- department of Neurology and Department of Biochemistry and Molecular Biology. University of Miami Miller School of Medicine, Miami, FL 33136
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112
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Imamoto A, Ki S, Li L, Iwamoto K, Maruthamuthu V, Devany J, Lu O, Kanazawa T, Zhang S, Yamada T, Hirayama A, Fukuda S, Suzuki Y, Okada M. Essential role of the Crk family-dosage in DiGeorge-like anomaly and metabolic homeostasis. Life Sci Alliance 2020; 3:3/2/e201900635. [PMID: 32041892 PMCID: PMC7010317 DOI: 10.26508/lsa.201900635] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/20/2020] [Accepted: 01/21/2020] [Indexed: 12/12/2022] Open
Abstract
CRK and CRKL (CRK-like) encode adapter proteins with similar biochemical properties. Here, we show that a 50% reduction of the family-combined dosage generates developmental defects, including aspects of DiGeorge/del22q11 syndrome in mice. Like the mouse homologs of two 22q11.21 genes CRKL and TBX1, Crk and Tbx1 also genetically interact, thus suggesting that pathways shared by the three genes participate in organogenesis affected in the syndrome. We also show that Crk and Crkl are required during mesoderm development, and Crk/Crkl deficiency results in small cell size and abnormal mesenchyme behavior in primary embryonic fibroblasts. Our systems-wide analyses reveal impaired glycolysis, associated with low Hif1a protein levels as well as reduced histone H3K27 acetylation in several key glycolysis genes. Furthermore, Crk/Crkl deficiency sensitizes MEFs to 2-deoxy-D-glucose, a competitive inhibitor of glycolysis, to induce cell blebbing. Activated Rapgef1, a Crk/Crkl-downstream effector, rescues several aspects of the cell phenotype, including proliferation, cell size, focal adhesions, and phosphorylation of p70 S6k1 and ribosomal protein S6. Our investigations demonstrate that Crk/Crkl-shared pathways orchestrate metabolic homeostasis and cell behavior through widespread epigenetic controls.
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Affiliation(s)
- Akira Imamoto
- The Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, USA
| | - Sewon Ki
- RIKEN Integrative Medical Sciences, Tsurumi, Yokohama, Kanagawa, Japan
| | - Leiming Li
- The Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, USA
| | - Kazunari Iwamoto
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Venkat Maruthamuthu
- Department of Mechanical and Aerospace Engineering, Old Dominion University, Norfolk, VA, USA
| | - John Devany
- Department of Physics, The University of Chicago, Chicago, IL, USA
| | - Ocean Lu
- The Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, USA
| | - Tomomi Kanazawa
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Suxiang Zhang
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Takuji Yamada
- Department of Life Science and Technology, Tokyo Institute of Technology, Meguro, Tokyo, Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan.,Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Kanagawa, Japan.,Transborder Medical Research Center, University of Tsukuba, Tsukuba, Ibaraki, Japan.,PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, Japan
| | - Mariko Okada
- RIKEN Integrative Medical Sciences, Tsurumi, Yokohama, Kanagawa, Japan .,Institute for Protein Research, Osaka University, Suita, Osaka, Japan.,Center for Drug Design and Research, National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka, Japan
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113
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Meta-Analysis of Hypoxic Transcriptomes from Public Databases. Biomedicines 2020; 8:biomedicines8010010. [PMID: 31936636 PMCID: PMC7168238 DOI: 10.3390/biomedicines8010010] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 12/26/2019] [Accepted: 01/08/2020] [Indexed: 12/16/2022] Open
Abstract
Hypoxia is the insufficiency of oxygen in the cell, and hypoxia-inducible factors (HIFs) are central regulators of oxygen homeostasis. In order to obtain functional insights into the hypoxic response in a data-driven way, we attempted a meta-analysis of the RNA-seq data from the hypoxic transcriptomes archived in public databases. In view of methodological variability of archived data in the databases, we first manually curated RNA-seq data from appropriate pairs of transcriptomes before and after hypoxic stress. These included 128 human and 52 murine transcriptome pairs. We classified the results of experiments for each gene into three categories: upregulated, downregulated, and unchanged. Hypoxic transcriptomes were then compared between humans and mice to identify common hypoxia-responsive genes. In addition, meta-analyzed hypoxic transcriptome data were integrated with public ChIP-seq data on the known human HIFs, HIF-1 and HIF-2, to provide insights into hypoxia-responsive pathways involving direct transcription factor binding. This study provides a useful resource for hypoxia research. It also demonstrates the potential of a meta-analysis approach to public gene expression databases for selecting candidate genes from gene expression profiles generated under various experimental conditions.
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114
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Das NK, Schwartz AJ, Barthel G, Inohara N, Liu Q, Sankar A, Hill DR, Ma X, Lamberg O, Schnizlein MK, Arqués JL, Spence JR, Nunez G, Patterson AD, Sun D, Young VB, Shah YM. Microbial Metabolite Signaling Is Required for Systemic Iron Homeostasis. Cell Metab 2020; 31:115-130.e6. [PMID: 31708445 PMCID: PMC6949377 DOI: 10.1016/j.cmet.2019.10.005] [Citation(s) in RCA: 155] [Impact Index Per Article: 38.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 09/23/2019] [Accepted: 10/14/2019] [Indexed: 12/16/2022]
Abstract
Iron is a central micronutrient needed by all living organisms. Competition for iron in the intestinal tract is essential for the maintenance of indigenous microbial populations and for host health. How symbiotic relationships between hosts and native microbes persist during times of iron limitation is unclear. Here, we demonstrate that indigenous bacteria possess an iron-dependent mechanism that inhibits host iron transport and storage. Using a high-throughput screen of microbial metabolites, we found that gut microbiota produce metabolites that suppress hypoxia-inducible factor 2α (HIF-2α) a master transcription factor of intestinal iron absorption and increase the iron-storage protein ferritin, resulting in decreased intestinal iron absorption by the host. We identified 1,3-diaminopropane (DAP) and reuterin as inhibitors of HIF-2α via inhibition of heterodimerization. DAP and reuterin effectively ameliorated systemic iron overload. This work provides evidence of intestine-microbiota metabolic crosstalk that is essential for systemic iron homeostasis.
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Affiliation(s)
- Nupur K Das
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andrew J Schwartz
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gabrielle Barthel
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Naohiro Inohara
- Department of Pathology and Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Qing Liu
- Department of Veterinary and Biomedical Sciences, the Pennsylvania State University, University Park, PA 16802, USA
| | - Amanda Sankar
- Department of Pediatrics, Division of Hematology-Oncology, University of Michigan, Ann Arbor, MI 48109, USA
| | - David R Hill
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xiaoya Ma
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Olivia Lamberg
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Matthew K Schnizlein
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Juan L Arqués
- Departamento Tecnología de Alimentos, INIA, Carretera de La Coruña Km 7, Madrid 28040, Spain
| | - Jason R Spence
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Gabriel Nunez
- Department of Pathology and Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Andrew D Patterson
- Department of Veterinary and Biomedical Sciences, the Pennsylvania State University, University Park, PA 16802, USA
| | - Duxin Sun
- College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA
| | - Vincent B Young
- Department of Internal Medicine, Division of Infectious Disease, University of Michigan, Ann Arbor, MI 48109, USA; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yatrik M Shah
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI 48109, USA.
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Nomoto H, Pei L, Montemurro C, Rosenberger M, Furterer A, Coppola G, Nadel B, Pellegrini M, Gurlo T, Butler PC, Tudzarova S. Activation of the HIF1α/PFKFB3 stress response pathway in beta cells in type 1 diabetes. Diabetologia 2020; 63:149-161. [PMID: 31720731 PMCID: PMC6945783 DOI: 10.1007/s00125-019-05030-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/13/2019] [Indexed: 12/15/2022]
Abstract
AIMS/HYPOTHESIS The conserved hypoxia inducible factor 1 α (HIF1α) injury-response pro-survival pathway has recently been implicated in early beta cell dysfunction but slow beta cell loss in type 2 diabetes. We hypothesised that the unexplained prolonged prediabetes phase in type 1 diabetes may also be, in part, due to activation of the HIF1α signalling pathway. METHODS RNA sequencing (RNA-Seq) data from human islets with type 1 diabetes or after cytokine exposure in vitro was evaluated for activation of HIF1α targets. This was corroborated by immunostaining human pancreases from individuals with type 1 diabetes for 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3), the key effector of HIF1α-mediated metabolic remodelling, and by western blotting of islets and INS-1 832/13 cells exposed to cytokines implicated in type 1 diabetes. RESULTS HIF1α signalling is activated (p = 4.5 × 10-9) in islets from individuals with type 1 diabetes, and in human islets exposed in vitro to cytokines implicated in type 1 diabetes (p = 1.1 × 10-14). Expression of PFKFB3 is increased fivefold (p < 0.01) in beta cells in type 1 diabetes and in human and rat islets exposed to cytokines that induced increased lactate production. HIF1α attenuates cytokine-induced cell death in beta cells. CONCLUSIONS/INTERPRETATION The conserved pro-survival HIF1α-mediated injury-response signalling is activated in beta cells in type 1 diabetes and likely contributes to the relatively slow rate of beta cell loss at the expense of early defective glucose-induced insulin secretion.
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Affiliation(s)
- Hiroshi Nomoto
- Larry L. Hillblom Islet Research Center, David Geffen School of Medicine at UCLA, University of California Los Angeles, 10833 Le Conte Avenue, 33-165 CHS, Los Angeles, CA, 90095-7073, USA
| | - Lina Pei
- Larry L. Hillblom Islet Research Center, David Geffen School of Medicine at UCLA, University of California Los Angeles, 10833 Le Conte Avenue, 33-165 CHS, Los Angeles, CA, 90095-7073, USA
| | - Chiara Montemurro
- Larry L. Hillblom Islet Research Center, David Geffen School of Medicine at UCLA, University of California Los Angeles, 10833 Le Conte Avenue, 33-165 CHS, Los Angeles, CA, 90095-7073, USA
| | - Madeline Rosenberger
- Larry L. Hillblom Islet Research Center, David Geffen School of Medicine at UCLA, University of California Los Angeles, 10833 Le Conte Avenue, 33-165 CHS, Los Angeles, CA, 90095-7073, USA
| | - Allison Furterer
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Giovanni Coppola
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Brian Nadel
- Molecular Cell and Developmental Biology, College of Life Sciences, University of California Los Angeles, Los Angeles, CA, USA
| | - Matteo Pellegrini
- Molecular Cell and Developmental Biology, College of Life Sciences, University of California Los Angeles, Los Angeles, CA, USA
| | - Tatyana Gurlo
- Larry L. Hillblom Islet Research Center, David Geffen School of Medicine at UCLA, University of California Los Angeles, 10833 Le Conte Avenue, 33-165 CHS, Los Angeles, CA, 90095-7073, USA
| | - Peter C Butler
- Larry L. Hillblom Islet Research Center, David Geffen School of Medicine at UCLA, University of California Los Angeles, 10833 Le Conte Avenue, 33-165 CHS, Los Angeles, CA, 90095-7073, USA.
| | - Slavica Tudzarova
- Larry L. Hillblom Islet Research Center, David Geffen School of Medicine at UCLA, University of California Los Angeles, 10833 Le Conte Avenue, 33-165 CHS, Los Angeles, CA, 90095-7073, USA
- Jonsson Comprehensive Cancer Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
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Li H, Kittur FS, Hung CY, Li PA, Ge X, Sane DC, Xie J. Quantitative Proteomics Reveals the Beneficial Effects of Low Glucose on Neuronal Cell Survival in an in vitro Ischemic Penumbral Model. Front Cell Neurosci 2020; 14:272. [PMID: 33033473 PMCID: PMC7491318 DOI: 10.3389/fncel.2020.00272] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 07/31/2020] [Indexed: 01/04/2023] Open
Abstract
Understanding proteomic changes in the ischemic penumbra are crucial to rescue those salvageable cells and reduce the damage of an ischemic stroke. Since the penumbra region is dynamic with heterogeneous cells/tissues, tissue sampling from animal models of stroke for the molecular study is a challenge. In this study, cultured hippocampal HT22 cells under hypoxia treatment for 17.5 h with 0.69 mM low glucose (H+LG) could mimic ischemic penumbral cells since they had much higher cell viability and viable cell number compared to hypoxia without glucose (H-G) treatment. To validate established cell-based ischemic penumbral model and understand the beneficial effects of low glucose (LG), quantitative proteomics analysis was performed on H+LG, H-G, and normoxia with normal 22 mM glucose (N+G) treated cells. We identified 427 differentially abundant proteins (DAPs) between H-G and N+G and further identified 105 DAPs between H+LG and H-G. Analysis of 105 DAPs revealed that LG promotes cell survival by activating HIF1α to enhance glycolysis; preventing the dysregulations of extracellular matrix remodeling, cell cycle and division, and antioxidant and detoxification; as well as attenuating inflammatory reaction response, protein synthesis and neurotransmission activity. Our results demonstrated that this established cell-based system could mimic penumbral conditions and can be used for molecular studies.
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Affiliation(s)
- Hua Li
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC, United States
| | - Farooqahmed S Kittur
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC, United States
| | - Chiu-Yueh Hung
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC, United States
| | - P Andy Li
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC, United States
| | - Xinghong Ge
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC, United States.,Department of Dermatology, General Hospital of Ningxia Medical University, Yinchuan, China
| | - David C Sane
- Carilion Clinic, Virginia Tech Carilion School of Medicine, Roanoke, VA, United States
| | - Jiahua Xie
- Department of Pharmaceutical Sciences, Biomanufacturing Research Institute and Technology Enterprise, North Carolina Central University, Durham, NC, United States
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117
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Cougnoux A, Drummond RA, Fellmeth M, Navid F, Collar AL, Iben J, Kulkarni AB, Pickel J, Schiffmann R, Wassif CA, Cawley NX, Lionakis MS, Porter FD. Unique molecular signature in mucolipidosis type IV microglia. J Neuroinflammation 2019; 16:276. [PMID: 31883529 PMCID: PMC6935239 DOI: 10.1186/s12974-019-1672-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/09/2019] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Lysosomal storage diseases (LSD) are a large family of inherited disorders characterized by abnormal endolysosomal accumulation of cellular material due to catabolic enzyme and transporter deficiencies. Depending on the affected metabolic pathway, LSD manifest with somatic or central nervous system (CNS) signs and symptoms. Neuroinflammation is a hallmark feature of LSD with CNS involvement such as mucolipidosis type IV, but not of others like Fabry disease. METHODS We investigated the properties of microglia from LSD with and without major CNS involvement in 2-month-old mucolipidosis type IV (Mcoln1-/-) and Fabry disease (Glay/-) mice, respectively, by using a combination of flow cytometric, RNA sequencing, biochemical, in vitro and immunofluorescence analyses. RESULTS We characterized microglia activation and transcriptome from mucolipidosis type IV and Fabry disease mice to determine if impaired lysosomal function is sufficient to prime these brain-resident immune cells. Consistent with the neurological pathology observed in mucolipidosis type IV, Mcoln1-/- microglia demonstrated an activation profile with a mixed neuroprotective/neurotoxic expression pattern similar to the one we previously observed in Niemann-Pick disease, type C1, another LSD with significant CNS involvement. In contrast, the Fabry disease microglia transcriptome revealed minimal alterations, consistent with the relative lack of CNS symptoms in this disease. The changes observed in Mcoln1-/- microglia showed significant overlap with alterations previously reported for other common neuroinflammatory disorders including Alzheimer's, Parkinson's, and Huntington's diseases. Indeed, our comparison of microglia transcriptomes from Alzheimer's disease, amyotrophic lateral sclerosis, Niemann-Pick disease, type C1 and mucolipidosis type IV mouse models showed an enrichment in "disease-associated microglia" pattern among these diseases. CONCLUSIONS The similarities in microglial transcriptomes and features of neuroinflammation and microglial activation in rare monogenic disorders where the primary metabolic disturbance is known may provide novel insights into the immunopathogenesis of other more common neuroinflammatory disorders. TRIAL REGISTRATION ClinicalTrials.gov, NCT01067742, registered on February 12, 2010.
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Affiliation(s)
- Antony Cougnoux
- Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, DHHS, 10CRC, Rm 5-2571, 10 Center Dr, Bethesda, MD, 20892, USA
| | - Rebecca A Drummond
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Mason Fellmeth
- Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, DHHS, 10CRC, Rm 5-2571, 10 Center Dr, Bethesda, MD, 20892, USA
| | - Fatemeh Navid
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, NIH, Bethesda, MD, 20892, USA
| | - Amanda L Collar
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - James Iben
- Molecular Genomics Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, 20879, USA
| | - Ashok B Kulkarni
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, 20879, USA
| | - James Pickel
- National Institute of Mental Health, National Institutes of Health, Bethesda, MD, 20879, USA
| | | | - Christopher A Wassif
- Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, DHHS, 10CRC, Rm 5-2571, 10 Center Dr, Bethesda, MD, 20892, USA
| | - Niamh X Cawley
- Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, DHHS, 10CRC, Rm 5-2571, 10 Center Dr, Bethesda, MD, 20892, USA
| | - Michail S Lionakis
- Fungal Pathogenesis Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Disease, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Forbes D Porter
- Division of Translational Medicine, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, DHHS, 10CRC, Rm 5-2571, 10 Center Dr, Bethesda, MD, 20892, USA.
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Kabei K, Tateishi Y, Shiota M, Osada-Oka M, Nishide S, Uchida J, Nakatani T, Matsunaga S, Yamaguchi T, Tomita S, Miura K. Effects of orally active hypoxia inducible factor alpha prolyl hydroxylase inhibitor, FG4592 on renal fibrogenic potential in mouse unilateral ureteral obstruction model. J Pharmacol Sci 2019; 142:93-100. [PMID: 31866051 DOI: 10.1016/j.jphs.2019.12.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/13/2019] [Accepted: 11/27/2019] [Indexed: 12/19/2022] Open
Abstract
Orally active hypoxia-inducible factor (HIF) prolyl hydroxylase inhibitors that stabilize HIF protein and stimulate the production of erythropoietin have been approved to treat renal anemia. Our previous report suggested that HIF-1α dependent fibrogenic mechanisms are operating at the early onset of renal fibrosis and its contribution declines with the progression in mouse unilateral ureteral obstruction (UUO) model. The aim of the study is to evaluate the renal fibrogenic potential of FG4592, a recently approved orally active HIF prolyl hydroxylase inhibitor in mouse UUO model. Male C57BL/6J mice orally given FG-4592 (12.5 mg/kg/day and 50 mg/kg/day) were subjected to UUO. Neither dose of FG-4592 affected renal fibrosis or macrophage infiltration. FG-4592 had no effects on increased mRNA of collagen I, collagen III or transforming growth factor-β1. At 3 days after UUO, higher dose of FG-4592 potentiated the increased mRNA expression of profibrogenic molecules, plasminogen activator inhibitor 1 (Pai-1) and connective tissue growth factor (Ctgf) but such potentiation disappeared at 7 days after UUO. It is suggested that FG-4592 used in the present study had little effects on renal fibrosis even though high dose of FG-4592 used in the present study transiently potentiated gene expression of Pai-1 and Ctgf in the UUO kidney.
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Affiliation(s)
- Kazuya Kabei
- Department of Applied Pharmacology and Therapeutics, Osaka City University Graduate School of Medicine, Asahimachi, Abeno-ku, Osaka, 545-8585, Japan; Department of Urology, Osaka City University Graduate School of Medicine, Asahimachi, Abeno-ku, Osaka, 545-8585, Japan; Minami-Osaka Hospital, Higashikagaya, Suminoe-ku, Osaka, 559-0012, Japan
| | - Yu Tateishi
- Ishikiri Seiki Hospital, Yayoi-cho, Higashiosaka, Osaka, 579-8026, Japan
| | - Masayuki Shiota
- Department of Research Support Platform, Osaka City University Graduate School of Medicine, Asahimachi, Abeno-ku, Osaka, 545-8585, Japan
| | - Mayuko Osada-Oka
- Food Hygiene and Environmental Health Division of Applied Life Science, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Sakyo-ku, Kyoto, 606-8522, Japan
| | - Shunji Nishide
- Department of Urology, Osaka City University Graduate School of Medicine, Asahimachi, Abeno-ku, Osaka, 545-8585, Japan; Department of Pharmacology, Osaka City University Graduate School of Medicine, Asahimachi, Abeno-ku, Osaka, 545-8585, Japan
| | - Junji Uchida
- Department of Urology, Osaka City University Graduate School of Medicine, Asahimachi, Abeno-ku, Osaka, 545-8585, Japan
| | - Tatsuya Nakatani
- Department of Urology, Osaka City University Graduate School of Medicine, Asahimachi, Abeno-ku, Osaka, 545-8585, Japan
| | - Shinji Matsunaga
- Department of Pharmacology, Osaka City University Graduate School of Medicine, Asahimachi, Abeno-ku, Osaka, 545-8585, Japan
| | - Takehiro Yamaguchi
- Department of Pharmacology, Osaka City University Graduate School of Medicine, Asahimachi, Abeno-ku, Osaka, 545-8585, Japan
| | - Shuhei Tomita
- Department of Pharmacology, Osaka City University Graduate School of Medicine, Asahimachi, Abeno-ku, Osaka, 545-8585, Japan
| | - Katsuyuki Miura
- Department of Applied Pharmacology and Therapeutics, Osaka City University Graduate School of Medicine, Asahimachi, Abeno-ku, Osaka, 545-8585, Japan; Ishikiri Seiki Hospital, Yayoi-cho, Higashiosaka, Osaka, 579-8026, Japan; Department of Pharmacology, Osaka City University Graduate School of Medicine, Asahimachi, Abeno-ku, Osaka, 545-8585, Japan.
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Schmit K, Chen JW, Ayama-Canden S, Fransolet M, Finet L, Demazy C, D'Hondt L, Graux C, Michiels C. Characterization of the role of TMEM45A in cancer cell sensitivity to cisplatin. Cell Death Dis 2019; 10:919. [PMID: 31801939 PMCID: PMC6892797 DOI: 10.1038/s41419-019-2088-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 12/13/2022]
Abstract
TMEM45A is a transmembrane protein involved in tumor progression and cancer resistance to chemotherapeutic agents in hypoxic condition. It is correlated to a low breast cancer patient overall survival. However, little is known about this protein, in particular the mechanisms by which TMEM45A modulates cancer cell chemosensitivity. In this work, the messenger RNA expression of TMEM45A was assessed in head and neck squamous cell carcinoma (HNSCC) and renal cell carcinoma (RCC) biopsies. TMEM45A was upregulated in patients diagnosed for head and neck or renal cancer. Then, the implication of this protein in cisplatin sensitivity was explored in SQD9 and RCC4 + pVHL cells. TMEM45A inactivation decreased cell proliferation and modulated cell responses to cisplatin. Indeed, TMEM45A inactivation increased the sensitivity of SQD9 cells to cisplatin, whereas it rendered RCC4 + pVHL cells resistant to this anticancer agent. Through RNA-sequencing analysis, we identified several deregulated pathways that indicated that the impact on cisplatin sensitivity may be associated to the inhibition of DNA damage repair and to UPR pathway activation. This study demonstrated, for the first time, an anti or a pro-apoptotic role of this protein depending on the cancer type and highlighted the role of TMEM45A in modulating patient responses to treatment.
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Affiliation(s)
| | - Jia-Wei Chen
- URBC-NARILIS, University of Namur, Namur, Belgium
| | | | | | - Laure Finet
- Université Catholique de Louvain, CHU UCL Namur, Biobank, Yvoir, Belgium
| | | | - Lionel D'Hondt
- Université Catholique de Louvain, CHU UCL Namur, Biobank, Yvoir, Belgium
| | - Carlos Graux
- Université Catholique de Louvain, CHU UCL Namur, Biobank, Yvoir, Belgium
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Chavdoula E, Habiel DM, Roupakia E, Markopoulos GS, Vasilaki E, Kokkalis A, Polyzos AP, Boleti H, Thanos D, Klinakis A, Kolettas E, Marcu KB. CHUK/IKK-α loss in lung epithelial cells enhances NSCLC growth associated with HIF up-regulation. Life Sci Alliance 2019; 2:2/6/e201900460. [PMID: 31792060 PMCID: PMC6892436 DOI: 10.26508/lsa.201900460] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 02/06/2023] Open
Abstract
IKKα is an NSCLC suppressor and its loss in mouse AT-II lung epithelial cells or in human NSCLC lines increased urethane-induced adenoma growth and xenograft burdens, respectively. IKKα loss can up-regulate HIF-1α, enhancing tumor growth under hypoxia. Through the progressive accumulation of genetic and epigenetic alterations in cellular physiology, non–small-cell lung cancer (NSCLC) evolves in distinct steps involving mutually exclusive oncogenic mutations in K-Ras or EGFR along with inactivating mutations in the p53 tumor suppressor. Herein, we show two independent in vivo lung cancer models in which CHUK/IKK-α acts as a major NSCLC tumor suppressor. In a novel transgenic mouse strain, wherein IKKα ablation is induced by tamoxifen (Tmx) solely in alveolar type II (AT-II) lung epithelial cells, IKKα loss increases the number and size of lung adenomas in response to the chemical carcinogen urethane, whereas IKK-β instead acts as a tumor promoter in this same context. IKKα knockdown in three independent human NSCLC lines (independent of K-Ras or p53 status) enhances their growth as tumor xenografts in immune-compromised mice. Bioinformatics analysis of whole transcriptome profiling followed by quantitative protein and targeted gene expression validation experiments reveals that IKKα loss can result in the up-regulation of activated HIF-1-α protein to enhance NSCLC tumor growth under hypoxic conditions in vivo.
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Affiliation(s)
- Evangelia Chavdoula
- Biomedical Research Foundation Academy of Athens, Athens, Greece.,Laboratory of Biology, School of Medicine, Faculty of Health Sciences, University of Ioannina, University Campus, Ioannina, Greece.,Biomedical Research Division, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Ioannina, Greece
| | | | - Eugenia Roupakia
- Laboratory of Biology, School of Medicine, Faculty of Health Sciences, University of Ioannina, University Campus, Ioannina, Greece.,Biomedical Research Division, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Ioannina, Greece
| | - Georgios S Markopoulos
- Laboratory of Biology, School of Medicine, Faculty of Health Sciences, University of Ioannina, University Campus, Ioannina, Greece.,Biomedical Research Division, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Ioannina, Greece
| | - Eleni Vasilaki
- Biomedical Research Foundation Academy of Athens, Athens, Greece
| | - Antonis Kokkalis
- Biomedical Research Foundation Academy of Athens, Athens, Greece
| | | | - Haralabia Boleti
- Intracellular Parasitism Laboratory, Department of Microbiology and Light Microscopy Unit, Hellenic Pasteur Institute, Athens, Greece
| | - Dimitris Thanos
- Biomedical Research Foundation Academy of Athens, Athens, Greece
| | | | - Evangelos Kolettas
- Laboratory of Biology, School of Medicine, Faculty of Health Sciences, University of Ioannina, University Campus, Ioannina, Greece .,Biomedical Research Division, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Ioannina, Greece
| | - Kenneth B Marcu
- Biomedical Research Foundation Academy of Athens, Athens, Greece .,Laboratory of Biology, School of Medicine, Faculty of Health Sciences, University of Ioannina, University Campus, Ioannina, Greece.,Biomedical Research Division, Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Ioannina, Greece.,Departments of Biochemistry and Cell Biology and Pathology, Stony Brook University, Stony Brook, NY, USA.,Department of Biological Sciences, San Diego State University, San Diego, CA, USA
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121
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Kim JY, Kim JK, Kim H. ABCB7 simultaneously regulates apoptotic and non-apoptotic cell death by modulating mitochondrial ROS and HIF1α-driven NFκB signaling. Oncogene 2019; 39:1969-1982. [DOI: 10.1038/s41388-019-1118-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 11/07/2019] [Accepted: 11/11/2019] [Indexed: 12/20/2022]
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122
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Lama-Sherpa TD, Shevde LA. An Emerging Regulatory Role for the Tumor Microenvironment in the DNA Damage Response to Double-Strand Breaks. Mol Cancer Res 2019; 18:185-193. [PMID: 31676722 DOI: 10.1158/1541-7786.mcr-19-0665] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/23/2019] [Accepted: 10/29/2019] [Indexed: 12/19/2022]
Abstract
Radiation, alkylating agents, and platinum-based chemotherapy treatments eliminate cancer cells through the induction of excessive DNA damage. The resultant DNA damage challenges the cancer cell's DNA repair capacity. Among the different types of DNA damage induced in cells, double-strand breaks (DSB) are the most lethal if left unrepaired. Unrepaired DSBs in tumor cells exacerbate existing gene deletions, chromosome losses and rearrangements, and aberrant features that characteristically enable tumor progression, metastasis, and drug resistance. Tumor microenvironmental factors like hypoxia, inflammation, cellular metabolism, and the immune system profoundly influence DSB repair mechanisms. Here, we put into context the role of the microenvironment in governing DSB repair mechanisms.
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Affiliation(s)
| | - Lalita A Shevde
- Department of Pathology, The University of Alabama at Birmingham, Birmingham, Alabama. .,O'Neal Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, Alabama
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Guo Y, Xiao Z, Yang L, Gao Y, Zhu Q, Hu L, Huang D, Xu Q. Hypoxia‑inducible factors in hepatocellular carcinoma (Review). Oncol Rep 2019; 43:3-15. [PMID: 31746396 PMCID: PMC6908932 DOI: 10.3892/or.2019.7397] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 08/16/2019] [Indexed: 12/12/2022] Open
Abstract
Maintenance of an appropriate oxygen concentration is essential for the function of the liver. However, in many pathological conditions, and particularly in the tumor microenvironment, cells and tissues are frequently in a hypoxic state. In the presence of hypoxia, the cells adapt to the low oxygen levels through the hypoxia-inducible factor (HIF) pathway. Overgrowth of tumor cells restricts the diffusion of oxygen in tumors, leading to insufficient blood supply and the creation of a hypoxic microenvironment, and, as a consequence, activation of the expression of HIFs. HIFs possess a wide range of target genes, which function to control a variety of signaling pathways; thus, HIFs modulate cellular metabolism, immune escape, angiogenesis, metastasis, extracellular matrix remodeling, cancer stem cells and other properties of the tumor. Given their crucial role in the occurrence and development of tumors, HIFs are expected to become new targets of precise treatment of hepatocellular carcinoma.
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Affiliation(s)
- Yang Guo
- Graduate Department, BengBu Medical College, Bengbu, Anhui 233030, P.R. China
| | - Zunqiang Xiao
- The Second Clinical Medical Department, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310014, P.R. China
| | - Liu Yang
- The Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, Zhejiang 310014, P.R. China
| | - Yuling Gao
- Department of Genetics, Shaoxing Women and Children Hospital, Shaoxin, Zhejiang 312030, P.R. China
| | - Qiaojuan Zhu
- The Second Clinical Medical Department, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310014, P.R. China
| | - Linjun Hu
- Medical Department, Qingdao University, Qingdao, Shandong 266071, P.R. China
| | - Dongsheng Huang
- The Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, Zhejiang 310014, P.R. China
| | - Qiuran Xu
- The Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital (People's Hospital of Hangzhou Medical College), Hangzhou, Zhejiang 310014, P.R. China
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124
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Louphrasitthiphol P, Ledaki I, Chauhan J, Falletta P, Siddaway R, Buffa FM, Mole DR, Soga T, Goding CR. MITF controls the TCA cycle to modulate the melanoma hypoxia response. Pigment Cell Melanoma Res 2019; 32:792-808. [PMID: 31207090 PMCID: PMC6777998 DOI: 10.1111/pcmr.12802] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/29/2019] [Accepted: 06/11/2019] [Indexed: 12/11/2022]
Abstract
In response to the dynamic intra-tumor microenvironment, melanoma cells adopt distinct phenotypic states associated with differential expression of the microphthalmia-associated transcription factor (MITF). The response to hypoxia is driven by hypoxia-inducible transcription factors (HIFs) that reprogram metabolism and promote angiogenesis. HIF1α indirectly represses MITF that can activate HIF1α expression. Although HIF and MITF share a highly related DNA-binding specificity, it is unclear whether they co-regulate subset of target genes. Moreover, the genomewide impact of hypoxia on melanoma and whether melanoma cell lines representing different phenotypic states exhibit distinct hypoxic responses is unknown. Here we show that three different melanoma cell lines exhibit widely different hypoxia responses with only a core 23 genes regulated in common after 12 hr in hypoxia. Surprisingly, under hypoxia MITF is transiently up-regulated by HIF1α and co-regulates a subset of HIF targets including VEGFA. Significantly, we also show that MITF represses itself and also regulates SDHB to control the TCA cycle and suppress pseudo-hypoxia. Our results reveal a previously unsuspected role for MITF in metabolism and the network of factors underpinning the hypoxic response in melanoma.
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Affiliation(s)
| | - Ioanna Ledaki
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUK
| | - Jagat Chauhan
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUK
| | - Paola Falletta
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUK
| | - Robert Siddaway
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUK
| | | | - David R. Mole
- Target Discovery Institute, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUK
| | - Tomoyoshi Soga
- Institute for Advanced BiosciencesKeio UniversityYamagataJapan
| | - Colin R. Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical MedicineUniversity of OxfordOxfordUK
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125
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Di Liddo A, de Oliveira Freitas Machado C, Fischer S, Ebersberger S, Heumüller AW, Weigand JE, Müller-McNicoll M, Zarnack K. A combined computational pipeline to detect circular RNAs in human cancer cells under hypoxic stress. J Mol Cell Biol 2019; 11:829-844. [PMID: 31560396 PMCID: PMC6884703 DOI: 10.1093/jmcb/mjz094] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 07/09/2019] [Accepted: 09/03/2019] [Indexed: 12/14/2022] Open
Abstract
Hypoxia is associated with several diseases, including cancer. Cells that are deprived of adequate oxygen supply trigger transcriptional and post-transcriptional responses, which control cellular pathways such as angiogenesis, proliferation, and metabolic adaptation. Circular RNAs (circRNAs) are a novel class of mainly non-coding RNAs, which have been implicated in multiple cancers and attract increasing attention as potential biomarkers. Here, we characterize the circRNA signatures of three different cancer cell lines from cervical (HeLa), breast (MCF-7), and lung (A549) cancer under hypoxia. In order to reliably detect circRNAs, we integrate available tools with custom approaches for quantification and statistical analysis. Using this consolidated computational pipeline, we identify ~12000 circRNAs in the three cancer cell lines. Their molecular characteristics point to an involvement of complementary RNA sequences as well as trans-acting factors in circRNA biogenesis, such as the RNA-binding protein HNRNPC. Notably, we detect a number of circRNAs that are more abundant than their linear counterparts. In addition, 64 circRNAs significantly change in abundance upon hypoxia, in most cases in a cell type-specific manner. In summary, we present a comparative circRNA profiling in human cancer cell lines, which promises novel insights into the biogenesis and function of circRNAs under hypoxic stress.
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Affiliation(s)
- Antonella Di Liddo
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Camila de Oliveira Freitas Machado
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Cardiovascular Regeneration, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Sandra Fischer
- Department of Biology, Technical University Darmstadt, Germany
| | | | - Andreas W Heumüller
- Institute for Cardiovascular Regeneration, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Julia E Weigand
- Department of Biology, Technical University Darmstadt, Germany
| | - Michaela Müller-McNicoll
- Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
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126
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Carosso GA, Boukas L, Augustin JJ, Nguyen HN, Winer BL, Cannon GH, Robertson JD, Zhang L, Hansen KD, Goff LA, Bjornsson HT. Precocious neuronal differentiation and disrupted oxygen responses in Kabuki syndrome. JCI Insight 2019; 4:129375. [PMID: 31465303 PMCID: PMC6824316 DOI: 10.1172/jci.insight.129375] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 08/23/2019] [Indexed: 12/12/2022] Open
Abstract
Chromatin modifiers act to coordinate gene expression changes critical to neuronal differentiation from neural stem/progenitor cells (NSPCs). Lysine-specific methyltransferase 2D (KMT2D) encodes a histone methyltransferase that promotes transcriptional activation and is frequently mutated in cancers and in the majority (>70%) of patients diagnosed with the congenital, multisystem intellectual disability disorder Kabuki syndrome 1 (KS1). Critical roles for KMT2D are established in various non-neural tissues, but the effects of KMT2D loss in brain cell development have not been described. We conducted parallel studies of proliferation, differentiation, transcription, and chromatin profiling in KMT2D-deficient human and mouse models to define KMT2D-regulated functions in neurodevelopmental contexts, including adult-born hippocampal NSPCs in vivo and in vitro. We report cell-autonomous defects in proliferation, cell cycle, and survival, accompanied by early NSPC maturation in several KMT2D-deficient model systems. Transcriptional suppression in KMT2D-deficient cells indicated strong perturbation of hypoxia-responsive metabolism pathways. Functional experiments confirmed abnormalities of cellular hypoxia responses in KMT2D-deficient neural cells and accelerated NSPC maturation in vivo. Together, our findings support a model in which loss of KMT2D function suppresses expression of oxygen-responsive gene programs important to neural progenitor maintenance, resulting in precocious neuronal differentiation in a mouse model of KS1.
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Affiliation(s)
- Giovanni A. Carosso
- Predoctoral Training Program in Human Genetics
- McKusick-Nathans Institute of Genetic Medicine
| | - Leandros Boukas
- Predoctoral Training Program in Human Genetics
- McKusick-Nathans Institute of Genetic Medicine
- Department of Biostatistics
| | - Jonathan J. Augustin
- McKusick-Nathans Institute of Genetic Medicine
- Predoctoral Training Program in Biochemistry, Cellular, and Molecular Biology
- Solomon H. Snyder Department of Neuroscience
| | | | | | | | | | - Li Zhang
- McKusick-Nathans Institute of Genetic Medicine
| | - Kasper D. Hansen
- McKusick-Nathans Institute of Genetic Medicine
- Department of Biostatistics
| | - Loyal A. Goff
- McKusick-Nathans Institute of Genetic Medicine
- Solomon H. Snyder Department of Neuroscience
| | - Hans T. Bjornsson
- McKusick-Nathans Institute of Genetic Medicine
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
- Landspitali University Hospital, Reykjavik, Iceland
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127
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Fako V, Martin SP, Pomyen Y, Budhu A, Chaisaingmongkol J, Franck S, Lee JMF, Ng IOL, Cheung TT, Wei X, Liu N, Ji J, Zhao L, Liu Z, Jia HL, Tang ZY, Qin LX, Kloeckner R, Marquardt J, Greten T, Wang XW. Gene signature predictive of hepatocellular carcinoma patient response to transarterial chemoembolization. Int J Biol Sci 2019; 15:2654-2663. [PMID: 31754337 PMCID: PMC6854367 DOI: 10.7150/ijbs.39534] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 09/02/2019] [Indexed: 12/13/2022] Open
Abstract
Transarterial chemoembolization (TACE) is a commonly used treatment modality in hepatocellular carcinoma (HCC). The ability to identify patients who will respond to TACE represents an important clinical need, and tumor gene expression patterns may be associated with TACE response. We investigated whether tumor transcriptome is associated with TACE response in patients with HCC. We analyzed transcriptome data of treatment-naïve tumor tissues from a Chinese cohort of 191 HCC patients, including 105 patients who underwent TACE following resection with curative intent. We then developed a gene signature, TACE Navigator, which was associated with improved survival in patients that received either adjuvant or post-relapse TACE. To validate our findings, we applied our signature in a blinded manner to three independent cohorts comprising an additional 130 patients with diverse ethnic backgrounds enrolled in three different hospitals who received either adjuvant TACE or palliative TACE. TACE Navigator stratified patients into Responders and Non-Responders which was associated with improved survival following TACE in our test cohort (Responders: 67 months vs Non-Responders: 39.5 months, p<0.0001). In addition, multivariable Cox model demonstrates that TACE Navigator was independently associated with survival (HR: 9.31, 95% CI: 3.46-25.0, p<0.001). In our validation cohorts, the association between TACE Navigator and survival remained robust in both Asian patients who received adjuvant TACE (Hong Kong: 60 months vs 25.6 months p=0.007; Shandong: 61.3 months vs 32.1 months, p=0.027) and European patients who received TACE as primary therapy (Mainz: 60 months vs 41.5 months, p=0.041). These results indicate that a TACE-specific molecular classifier is robust in predicting TACE response. This gene signature can be used to identify patients who will have the greatest survival benefit after TACE treatment and enable personalized treatment modalities for patients with HCC.
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Affiliation(s)
| | | | | | - Anuradha Budhu
- Laboratory of Human Carcinogenesis.,Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | | | | | | | | | - Tan-To Cheung
- Surgery, and State Key Laboratory for Liver Research, The University of Hong Kong, Hong Kong, China
| | - Xiyang Wei
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Niya Liu
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Junfang Ji
- Shandong Cancer Hospital and Institute, Jinan, China
| | - Lei Zhao
- Shandong Cancer Hospital and Institute, Jinan, China
| | - Zhaogang Liu
- Shandong Cancer Hospital and Institute, Jinan, China
| | | | | | | | | | | | - Tim Greten
- Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA.,Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Xin Wei Wang
- Laboratory of Human Carcinogenesis.,Liver Cancer Program, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
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128
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Zhao Q, Sun H, Yin L, Wang L. miR‑126a‑5p‑Dbp and miR‑31a‑Crot/Mrpl4 interaction pairs crucial for the development of hypertension and stroke. Mol Med Rep 2019; 20:4151-4167. [PMID: 31545431 PMCID: PMC6797943 DOI: 10.3892/mmr.2019.10679] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 07/19/2019] [Indexed: 01/09/2023] Open
Abstract
The present study aimed to integrate the mRNA and microRNA (miRNA) expression profiles of spontaneously hypertensive rats (SHR rats) and stroke-prone spontaneously hypertensive rats (SHRSP rats) to screen for potential therapeutic targets for hypertension and stroke. The datasets GSE41452, GSE31457, GSE41453 and GSE53363 were collected from the Gene Expression Omnibus (GEO) database to screen differentially expressed genes (DEGs). The GSE53361 dataset was obtained to analyze differentially expressed miRNAs (DEMs). The DEGs and DEMs were identified between SHR (or SHRSP) rats and normotensive Wistar-Kyoto (WKY) rats using the Linear Models for Microarray (limma) data method. Venn diagrams were used to show the SHR-specific, SHRSP-specific and SHR-SHRSP shared DEGs and DEMs, and these were utilized to construct the protein-protein interaction (PPI) and miRNA-mRNA regulatory networks. The Database for Annotation, Visualization and Integrated Discovery (DAVID) was used to explore the function of the genes. Subsequently, the connectivity Map (CMAP) database was searched to identify small-molecule drugs. Comparisons between the GSE41452-GSE31457-GSE41453 merged and GSE53363 datasets identified 2 SHR-specific, 8 SHRSP-specific and 15 SHR-SHRSP shared DEGs. Function enrichment analysis showed that SHRSP-specific D-box binding PAR bZIP transcription factor (Dbp) was associated with circadian rhythm, and SHR-SHRSP shared carnitine O-octanoyltransferase (Crot) was involved in fatty acid metabolic processes or the inflammatory response via interacting with epoxide hydrolase 2 (EPHX2). SHR-SHRSP shared mitochondrial ribosomal protein L4 (Mrpl4) may exert roles by interacting with the threonine-tRNA ligase, TARS2. The miRNA regulatory network predicted that upregulated Dbp could be regulated by rno-miR-126a-5p, whereas downregulated Crot and Mrpl4 could be modulated by rno-miR-31a. The CMAP database predicted that small-molecule drugs, including botulin, Gly-His-Lys, and podophyllotoxin, may possess therapeutic potential. In conclusion, the present study has identified Dbp, Crot and Mrpl4 as potential targets for the treatment of hypertension and stroke. Furthermore, the expression of these genes may be reversed by the above miRNAs or drugs.
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Affiliation(s)
- Qini Zhao
- Department of Cardiology, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Huan Sun
- Department of Cardiology, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Liquan Yin
- Department of Rehabilitation Medicine, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
| | - Libo Wang
- Department of Neurology, China‑Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
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129
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Effect of Hypoxia on Gene Expression in Cell Populations Involved in Wound Healing. BIOMED RESEARCH INTERNATIONAL 2019; 2019:2626374. [PMID: 31534956 PMCID: PMC6724439 DOI: 10.1155/2019/2626374] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/28/2019] [Accepted: 07/25/2019] [Indexed: 01/27/2023]
Abstract
Wound healing is a complex process regulated by multiple signals and consisting of several phases known as haemostasis, inflammation, proliferation, and remodelling. Keratinocytes, endothelial cells, macrophages, and fibroblasts are the major cell populations involved in wound healing process. Hypoxia plays a critical role in this process since cells sense and respond to hypoxic conditions by changing gene expression. This study assessed the in vitro expression of 77 genes involved in angiogenesis, metabolism, cell growth, proliferation and apoptosis in human keratinocytes (HaCaT), microvascular endothelial cells (HMEC-1), differentiated macrophages (THP-1), and dermal fibroblasts (HDF). Results indicated that the gene expression profiles induced by hypoxia were cell-type specific. In HMEC-1 and differentiated THP-1, most of the genes modulated by hypoxia encode proteins involved in angiogenesis or belonging to cytokines and growth factors. In HaCaT and HDF, hypoxia mainly affected the expression of genes encoding proteins involved in cell metabolism. This work can help to enlarge the current knowledge about the mechanisms through which a hypoxic environment influences wound healing processes at the molecular level.
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130
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Hu B, Li G, Ye Z, Gustafson CE, Tian L, Weyand CM, Goronzy JJ. Transcription factor networks in aged naïve CD4 T cells bias lineage differentiation. Aging Cell 2019; 18:e12957. [PMID: 31264370 PMCID: PMC6612640 DOI: 10.1111/acel.12957] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 02/17/2019] [Accepted: 03/18/2019] [Indexed: 12/13/2022] Open
Abstract
With reduced thymic activity, the population of naïve T cells in humans is maintained by homeostatic proliferation throughout adult life. In young adults, naïve CD4 T cells have enormous proliferative potential and plasticity to differentiate into different lineages. Here, we explored whether naïve CD4 T-cell aging is associated with a partial loss of this unbiased multipotency. We find that naïve CD4 T cells from older individuals have developed a propensity to develop into TH9 cells. Two major mechanisms contribute to this predisposition. First, responsiveness to transforming growth factor β (TGFβ) stimulation is enhanced with age due to an upregulation of the TGFβR3 receptor that results in increased expression of the transcription factor PU.1. Secondly, aged naïve CD4 T cells display altered transcription factor profiles in response to T-cell receptor stimulation, including enhanced expression of BATF and IRF4 and reduced expression of ID3 and BCL6. These transcription factors are involved in TH9 differentiation as well as IL9 transcription suggesting that the aging-associated changes in the transcription factor profile favor TH9 commitment.
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Affiliation(s)
- Bin Hu
- Department of Medicine, Division of Immunology and RheumatologyStanford UniversityStanfordCaliforniaUSA
- Department of MedicinePalo Alto Veterans Administration Healthcare SystemPalo AltoCaliforniaUSA
| | - Guangjin Li
- Department of MedicinePalo Alto Veterans Administration Healthcare SystemPalo AltoCaliforniaUSA
| | - Zhongde Ye
- Department of MedicinePalo Alto Veterans Administration Healthcare SystemPalo AltoCaliforniaUSA
| | - Claire E. Gustafson
- Department of Medicine, Division of Immunology and RheumatologyStanford UniversityStanfordCaliforniaUSA
- Department of MedicinePalo Alto Veterans Administration Healthcare SystemPalo AltoCaliforniaUSA
| | - Lu Tian
- Department of Biomedical Data ScienceStanford University School of MedicineStanfordCaliforniaUSA
| | - Cornelia M. Weyand
- Department of Medicine, Division of Immunology and RheumatologyStanford UniversityStanfordCaliforniaUSA
- Department of MedicinePalo Alto Veterans Administration Healthcare SystemPalo AltoCaliforniaUSA
| | - Jörg J. Goronzy
- Department of Medicine, Division of Immunology and RheumatologyStanford UniversityStanfordCaliforniaUSA
- Department of MedicinePalo Alto Veterans Administration Healthcare SystemPalo AltoCaliforniaUSA
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131
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Ratushnyy AY, Rudimova YV, Buravkova LB. Alteration of Hypoxia-Associated Gene Expression in Replicatively Senescent Mesenchymal Stromal Cells under Physiological Oxygen Level. BIOCHEMISTRY (MOSCOW) 2019; 84:263-271. [PMID: 31221064 DOI: 10.1134/s0006297919030088] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Mesenchymal stromal cells (MSCs) are a population of adult stem cells that modulate functional state of neighboring tissues. During cell aging, the biological activity of MSC changes, which may affect tissue homeostasis. It is known that reducing the oxygen level in vitro to physiological values typical to a particular cell niche leads to attenuation of some morphological and functional changes associated with aging. This work aimed to study gene expression in MSCs involved in response to physiological hypoxia using a replicative aging model under physiological (5%) and atmospheric (20%) oxygen in cultures. Our results show that significant reduction of proliferative activity of MSCs is observed after 20 passages (~50 cell generations). Regardless of the oxygen, in senescent cells PKM2, SERPINE1, and VEGFA were upregulated while ANKRD37, DDIT4, HIF1A, and TXNIP were downregulated. Also, ADORA2B, BNIPL, CCNG2, EGLN1, MAP3K1, MXI1, and P4HA1 were downregulated under hypoxia. The effect of oxygen was more pronounced at earlier passages both on the cellular and transcription levels. Irrespective of the passage, genes ANGPTL4, GYS1, PKM2, SERPINE1, and TP53 were downregulated under hypoxia. Also, decreased expression was observed for ADM, F10, HMOX1, P4HB, PFKL, SLC16A3 in earlier passages, and for HK2 - in later passages. Upregulation was only observed for ANKRD37, both at early and late cultures.
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Affiliation(s)
- A Yu Ratushnyy
- Institute of Biomedical Problems, Russian Academy of Sciences, Moscow, 123007, Russia
| | - Yu V Rudimova
- Institute of Biomedical Problems, Russian Academy of Sciences, Moscow, 123007, Russia
| | - L B Buravkova
- Institute of Biomedical Problems, Russian Academy of Sciences, Moscow, 123007, Russia.
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132
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Rashid I, Pathak AK, Kumar R, Srivastava P, Singh M, Murali S, Kushwaha B. Genome-Wide Comparative Analysis of HIF Binding Sites in Cyprinus Carpio for In Silico Identification of Functional Hypoxia Response Elements. Front Genet 2019; 10:659. [PMID: 31379925 PMCID: PMC6660265 DOI: 10.3389/fgene.2019.00659] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Accepted: 06/21/2019] [Indexed: 12/20/2022] Open
Abstract
Cyprinus carpio is world's most widely distributed freshwater species highly used in aquaculture. It is a hypoxia-tolerant species as it lives in oxygen-deficient environment for a long period. The tolerance potential of an animal against hypoxia relates it to induced gene expression, where a hypoxia-inducible factor (HIF) binds to a transcriptionally active site, hypoxia response element (HRE), a 5-base short motif that lies within the promoter/enhancer region of a certain gene, for inducing gene expression and preventing/minimizing hypoxia effects. HRE is functionally active when it contains another motif, the hypoxia ancillary sequence (HAS), which is typically adjacent to downstream of HRE within 7- to 15-nt space. Here, an attempt was made for mining HRE and identifying functional HIF binding sites (HBS) in a genome-wide analysis of C. carpio. For this, gene information along with the 5,000-nt upstream (-4,900 to +100) sequences of 31,466 protein coding genes was downloaded from "Gene" and "RefSeq" databases. Analysis was performed after filtration of the impracticable genes. A total of 116,148 HRE consensus sequences were mined from 29,545 genes in different promoter regions. HRE with HAS consensus motifs were found in the promoter region of 9,589 genes. Further, the already reported genes for hypoxia response in humans and zebrafish were reanalyzed for detecting HRE sites in their promoters and used for comparative analysis with gene promoters of C. carpio for providing support to identify functional HBS in the gene promoter of C. carpio. An interactive user interface HREExplorer was developed for presenting the results on the World Wide Web and visualizing possible HBS in protein coding genes in C. carpio and displaying the comparative results along with the reported hypoxia-responsive genes of zebrafish and reported hypoxia-inducible genes in humans. In this study, a set of Perl program was written for the compilation and analysis of information that might be used for a similar study in other species. This novel work may provide a workbench for analyzing the promoter regions of hypoxia-responsive genes.
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Affiliation(s)
- Iliyas Rashid
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India.,AMITY Institute of Biotechnology, AMITY University Uttar Pradesh, Lucknow, India
| | - Ajey Kumar Pathak
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - Ravindra Kumar
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - Prachi Srivastava
- AMITY Institute of Biotechnology, AMITY University Uttar Pradesh, Lucknow, India
| | - Mahender Singh
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - S Murali
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
| | - Basdeo Kushwaha
- Molecular Biology and Biotechnology Division, ICAR-National Bureau of Fish Genetic Resources, Lucknow, India
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133
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Carroll RG, Timmons GA, Cervantes-Silva MP, Kennedy OD, Curtis AM. Immunometabolism around the Clock. Trends Mol Med 2019; 25:612-625. [DOI: 10.1016/j.molmed.2019.04.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 04/11/2019] [Accepted: 04/30/2019] [Indexed: 12/20/2022]
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134
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Garg N, Kumar P, Gadhave K, Giri R. The dark proteome of cancer: Intrinsic disorderedness and functionality of HIF-1α along with its interacting proteins. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 166:371-403. [PMID: 31521236 DOI: 10.1016/bs.pmbts.2019.05.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The dark side of protein is the region (s) where molecular conformation is unknown. Intrinsically disordered proteins (IDPs) and intrinsically disordered protein regions (IDPRs) are the dark matter of biology due to inability to visualize them using standard structure elucidation technique such as X-ray crystallography due to lack in diffraction signal. IDPs are the functionally important class of proteins with entire protein or its parts lack ordered three-dimensional structure. Computational studies have predicted that nearly one-third of the human proteome is disordered, which gives the enormous flexibility and functional diversity to proteins. The conserved residues and elements in disordered proteins are critical for function and might be parts of peptide motifs or protein-protein interaction interfaces. For example, regions of proteins that are involved in disorder-based molecular recognition are known as molecular recognition features (MoRFs). Generally, MoRFs could undergo disorder to order transition or vice versa at interaction with specific partners. Hypoxia inducible factor 1α (HIF-1α) is a master transcriptional regulator involved in response to hypoxia, which is associated with many pathological conditions. Importantly, HIF-1α regulates various steps of cancer progression such as cell survival, tumor cell invasion, and metastasis. In this chapter, we have extensively analyzed the molecular recognition features and their relationship with disordered regions and associated structural islands of HIF-1α. We had also analyzed the disorderness and MoRFs of HIF-1α primary interaction partners that are enriched in IDPRs and MoRFs giving their role in protein-protein interaction and cancer regulation.
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Affiliation(s)
- Neha Garg
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, India
| | - Prateek Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, India
| | - Kundlik Gadhave
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, India
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh, India.
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135
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Hettiarachchi GK, Katneni UK, Hunt RC, Kames JM, Athey JC, Bar H, Sauna ZE, McGill JR, Ibla JC, Kimchi-Sarfaty C. Translational and transcriptional responses in human primary hepatocytes under hypoxia. Am J Physiol Gastrointest Liver Physiol 2019; 316:G720-G734. [PMID: 30920299 PMCID: PMC6620582 DOI: 10.1152/ajpgi.00331.2018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The liver is the primary source of a large number of plasma proteins and plays a critical role in multiple biological processes. Inadequate oxygen supply characterizing various clinical settings such as liver transplantation exposes the liver to hypoxic conditions. Studies assessing hypoxia-induced global translational changes in liver are lacking. Here, we employed a recently developed ribosome-profiling technique to assess global translational responses of human primary hepatocytes exposed to acute hypoxic stress (1% O2) for the short term. In parallel, transcriptome profiling was performed to assess mRNA expression changes. We found that translational responses appeared earlier and were predominant over transcriptional responses. A significant decrease in translational efficiency of several ribosome genes indicated translational inhibition of new ribosome protein synthesis in hypoxia. Pathway enrichment analysis highlighted altered translational regulation of MAPK signaling, drug metabolism, oxidative phosphorylation, and nonalcoholic fatty liver disease pathways. Gene Ontology enrichment analysis revealed terms related to translation, metabolism, angiogenesis, apoptosis, and response to stress. Transcriptional induction of genes encoding heat shock proteins was observed within 30 min of hypoxia. Induction of genes encoding stress response mediators, metabolism regulators, and proangiogenic proteins was observed at 240 min. Despite the liver being the primary source of coagulation proteins and the implicated role of hypoxia in thrombosis, limited differences were observed in genes encoding coagulation-associated proteins. Overall, our study demonstrates the predominance of translational regulation over transcription and highlights differentially regulated pathways or biological processes in short-term hypoxic stress responses of human primary hepatocytes. NEW & NOTEWORTHY The novelty of this study lies in applying parallel ribosome- and transcriptome-profiling analyses to human primary hepatocytes in hypoxia. To our knowledge, this is the first study to assess global translational responses using ribosome profiling in hypoxic hepatocytes. Our results demonstrate the predominance of translational responses over transcriptional responses in early hepatic hypoxic stress responses. Furthermore, our study reveals multiple pathways and specific genes showing altered regulation in hypoxic hepatocytes.
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Affiliation(s)
- Gaya K. Hettiarachchi
- 1Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland
| | - Upendra K. Katneni
- 1Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland
| | - Ryan C. Hunt
- 1Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland
| | - Jacob M. Kames
- 1Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland
| | - John C. Athey
- 1Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland
| | - Haim Bar
- 2Department of Statistics, University of Connecticut, Storrs, Connecticut
| | - Zuben E. Sauna
- 1Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland
| | - Joseph R. McGill
- 1Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland
| | - Juan C. Ibla
- 3Department of Anesthesiology, Perioperative and Pain Medicine, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts
| | - Chava Kimchi-Sarfaty
- 1Hemostasis Branch, Division of Plasma Protein Therapeutics, Office of Tissues and Advanced Therapies, Center for Biologics Evaluation and Research, United States Food and Drug Administration, Silver Spring, Maryland
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136
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Linehan WM, Schmidt LS, Crooks DR, Wei D, Srinivasan R, Lang M, Ricketts CJ. The Metabolic Basis of Kidney Cancer. Cancer Discov 2019; 9:1006-1021. [PMID: 31088840 DOI: 10.1158/2159-8290.cd-18-1354] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/19/2019] [Accepted: 03/22/2019] [Indexed: 01/27/2023]
Abstract
Kidney cancer is not a single disease but represents several distinct types of cancer that have defining histologies and genetic alterations and that follow different clinical courses and have different responses to therapy. Mutation of genes associated with kidney cancer, such as VHL, FLCN, TFE3, FH, or SDHB, dysregulates the tumor's responses to changes in oxygen, iron, nutrient, or energy levels. The identification of these varying genetic bases of kidney cancer has increased our understanding of the biology of this cancer, allowing the development of targeted therapies and the appreciation that it is a cancer driven by metabolic alterations. SIGNIFICANCE: Kidney cancer is a complex disease composed of different types of cancer that present with different histologies, clinical courses, genetic changes, and responses to therapy. This review describes the known genetic changes within kidney cancer, how they alter tumor metabolism, and how these metabolic changes can be therapeutically targeted.
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Affiliation(s)
- W Marston Linehan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
| | - Laura S Schmidt
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.,Basic Science Program, Frederick Laboratory for Cancer Research, Frederick, Maryland
| | - Daniel R Crooks
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Darmood Wei
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Ramaprasad Srinivasan
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Martin Lang
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Christopher J Ricketts
- Urologic Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
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White Adipose Tissue Response of Obese Mice to Ambient Oxygen Restriction at Thermoneutrality: Response Markers Identified, but no WAT Inflammation. Genes (Basel) 2019; 10:genes10050359. [PMID: 31083422 PMCID: PMC6562665 DOI: 10.3390/genes10050359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/03/2019] [Accepted: 05/06/2019] [Indexed: 11/16/2022] Open
Abstract
Obesity is associated with white adipose tissue (WAT) hypoxia and inflammation. We aimed to test whether mild environmental oxygen restriction (OxR, 13% O2), imposing tissue hypoxia, triggers WAT inflammation in obese mice. Thirteen weeks diet-induced obese male adult C57BL/6JOlaHsd mice housed at thermoneutrality were exposed for five days to OxR versus normoxia. WAT and blood were isolated and used for analysis of metabolites and adipokines, WAT histology and macrophage staining, and WAT transcriptomics. OxR increased circulating levels of haemoglobin and haematocrit as well as hypoxia responsive transcripts in WAT and decreased blood glucose, indicating systemic and tissue hypoxia. WAT aconitase activity was inhibited. Macrophage infiltration as marker for WAT inflammation tended to be decreased, which was supported by down regulation of inflammatory genes S100a8, Ccl8, Clec9a, Saa3, Mgst2, and Saa1. Other down regulated processes include cytoskeleton remodelling and metabolism, while response to hypoxia appeared most prominently up regulated. The adipokines coiled-coil domain containing 3 (CCDC3) and adiponectin, as well as the putative WAT hormone cholecystokinin (CCK), were reduced by OxR on transcript (Cck, Ccdc3) and/or serum protein level (adiponectin, CCDC3). Conclusively, our data demonstrate that also in obese mice OxR does not trigger WAT inflammation. However, OxR does evoke a metabolic response in WAT, with CCDC3 and adiponectin as potential markers for systemic or WAT hypoxia.
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138
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Hypoxia tolerance in the Norrin-deficient retina and the chronically hypoxic brain studied at single-cell resolution. Proc Natl Acad Sci U S A 2019; 116:9103-9114. [PMID: 30988181 DOI: 10.1073/pnas.1821122116] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The mammalian CNS is capable of tolerating chronic hypoxia, but cell type-specific responses to this stress have not been systematically characterized. In the Norrin KO (Ndp KO ) mouse, a model of familial exudative vitreoretinopathy (FEVR), developmental hypovascularization of the retina produces chronic hypoxia of inner nuclear-layer (INL) neurons and Muller glia. We used single-cell RNA sequencing, untargeted metabolomics, and metabolite labeling from 13C-glucose to compare WT and Ndp KO retinas. In Ndp KO retinas, we observe gene expression responses consistent with hypoxia in Muller glia and retinal neurons, and we find a metabolic shift that combines reduced flux through the TCA cycle with increased synthesis of serine, glycine, and glutathione. We also used single-cell RNA sequencing to compare the responses of individual cell types in Ndp KO retinas with those in the hypoxic cerebral cortex of mice that were housed for 1 week in a reduced oxygen environment (7.5% oxygen). In the hypoxic cerebral cortex, glial transcriptome responses most closely resemble the response of Muller glia in the Ndp KO retina. In both retina and brain, vascular endothelial cells activate a previously dormant tip cell gene expression program, which likely underlies the adaptive neoangiogenic response to chronic hypoxia. These analyses of retina and brain transcriptomes at single-cell resolution reveal both shared and cell type-specific changes in gene expression in response to chronic hypoxia, implying both shared and distinct cell type-specific physiologic responses.
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139
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Sinha KM, Tseng C, Guo P, Lu A, Pan H, Gao X, Andrews R, Eltzschig H, Huard J. Hypoxia-inducible factor 1α (HIF-1α) is a major determinant in the enhanced function of muscle-derived progenitors from MRL/MpJ mice. FASEB J 2019; 33:8321-8334. [PMID: 30970214 DOI: 10.1096/fj.201801794r] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Although the mouse strain Murphy Roths Large (MRL/MpJ) possesses high regenerative potential, the mechanism of tissue regeneration, including skeletal muscle, in MRL/MpJ mice after injury is still unclear. Our previous studies have shown that muscle-derived stem/progenitor cell (MDSPC) function is significantly enhanced in MRL/MpJ mice when compared with MDSPCs isolated from age-matched wild-type (WT) mice. Using mass spectrometry-based proteomic analysis, we identified increased expression of hypoxia-inducible factor (HIF) 1α target genes (expression of glycolytic factors and antioxidants) in sera from MRL/MpJ mice compared with WT mice. Therefore, we hypothesized that HIF-1α promotes the high muscle healing capacity of MRL/MpJ mice by increasing the potency of MDSPCs. We demonstrated that treating MRL/MpJ MDSPCs with dimethyloxalylglycine and CoCl2 increased the expression of HIF-1α and target genes, including angiogenic and cell survival genes. We also observed that HIF-1α activated the expression of paired box (Pax)7 through direct interaction with the Pax7 promoter. Furthermore, we also observed a higher myogenic potential of MDSPCs derived from prolyl hydroxylase (Phd) 3-knockout (Phd3-/-) mice, which displayed higher stability of HIF-1α. Taken together, our findings suggest that HIF-1α is a major determinant in the increased MDSPC function of MRL/MpJ mice through enhancement of cell survival, proliferation, and myogenic differentiation.-Sinha, K. M., Tseng, C., Guo, P., Lu, A., Pan, H., Gao, X., Andrews, R., Eltzschig, H., Huard, J. Hypoxia-inducible factor 1α (HIF-1α) is a major determinant in the enhanced function of muscle-derived progenitors from MRL/MpJ mice.
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Affiliation(s)
- Krishna M Sinha
- Department of Orthopedic Surgery, McGovern Medical School, University of Texas Health Science Center-Houston, Houston, Texas, USA
| | - Chieh Tseng
- Department of Orthopedic Surgery, McGovern Medical School, University of Texas Health Science Center-Houston, Houston, Texas, USA
| | - Ping Guo
- Department of Orthopedic Surgery, McGovern Medical School, University of Texas Health Science Center-Houston, Houston, Texas, USA
| | - Aiping Lu
- Department of Orthopedic Surgery, McGovern Medical School, University of Texas Health Science Center-Houston, Houston, Texas, USA
| | - Haiying Pan
- Department of Orthopedic Surgery, McGovern Medical School, University of Texas Health Science Center-Houston, Houston, Texas, USA
| | - Xueqin Gao
- Department of Orthopedic Surgery, McGovern Medical School, University of Texas Health Science Center-Houston, Houston, Texas, USA
| | - Reid Andrews
- Department of Orthopedic Surgery, McGovern Medical School, University of Texas Health Science Center-Houston, Houston, Texas, USA
| | - Holger Eltzschig
- Department of Anesthesiology, McGovern Medical School, University of Texas Health Science Center-Houston, Houston, Texas, USA
| | - Johnny Huard
- Department of Orthopedic Surgery, McGovern Medical School, University of Texas Health Science Center-Houston, Houston, Texas, USA.,Steadman Philippon Research Institute, Vail, Colorado, USA
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140
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Batie M, Frost J, Frost M, Wilson JW, Schofield P, Rocha S. Hypoxia induces rapid changes to histone methylation and reprograms chromatin. Science 2019; 363:1222-1226. [DOI: 10.1126/science.aau5870] [Citation(s) in RCA: 177] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 11/05/2018] [Accepted: 01/24/2019] [Indexed: 12/22/2022]
Abstract
Oxygen is essential for the life of most multicellular organisms. Cells possess enzymes called molecular dioxygenases that depend on oxygen for activity. A subclass of molecular dioxygenases is the histone demethylase enzymes, which are characterized by the presence of a Jumanji-C (JmjC) domain. Hypoxia can alter chromatin, but whether this is a direct effect on JmjC-histone demethylases or due to other mechanisms is unknown. Here, we report that hypoxia induces a rapid and hypoxia-inducible factor–independent induction of histone methylation in a range of human cultured cells. Genomic locations of histone-3 lysine-4 trimethylation (H3K4me3) and H3K36me3 after a brief exposure of cultured cells to hypoxia predict the cell’s transcriptional response several hours later. We show that inactivation of one of the JmjC-containing enzymes, lysine demethylase 5A (KDM5A), mimics hypoxia-induced cellular responses. These results demonstrate that oxygen sensing by chromatin occurs via JmjC-histone demethylase inhibition.
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141
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Rehman Z, Fahim A, Bhatti A, Sadia H, John P. Co-expression of HIF-1α, MDR1 and LAPTM4B in peripheral blood of solid tumors. PeerJ 2019; 7:e6309. [PMID: 30746305 PMCID: PMC6368972 DOI: 10.7717/peerj.6309] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 12/19/2018] [Indexed: 12/22/2022] Open
Abstract
The hypoxic tumor microenvironment is the major contributor of chemotherapy resistance in solid tumors. One of the key regulators of hypoxic responses within the cell is the hypoxia inducible factor-1α (HIF-1α) that is involved in transcription of genes promoting cell survival and chemotherapy resistance. Multidrug resistance gene-1 (MDR1) and Lysosome-associated protein transmembrane 4B-35 (LAPTM4B-35) are among those notable players which augment their responses to cellular hypoxia. MDR1 is the hypoxia responsive gene involved in multidrug resistance phenotype while LAPTM4B-35 is involved in chemotherapy resistance by stabilizing HIF-1α and overexpressing MDR1. Overexpression of HIF-1α, MDR1 and LAPTM4B has been associated with poor disease outcome in many cancers when studied individually at tissue level. However, accessibility of the tissues following the course of chemotherapy for ascertaining chemotherapy resistance is difficult and sometimes not clinically feasible. Therefore, indication of hypoxic biomarkers in patient’s blood can significantly alter the clinical outcome. Hence there is a need to identify a blood based marker to understand the disease progression. In the current study the expression of hypoxia associated chemotherapy resistance genes were studied in the peripheral blood lymphocytes of solid tumor patients and any potential correlation with disease progression were explored. The expression of HIF-1α, MDR1 and LAPTM4B was studied in blood of 72 breast, 42 ovarian, 32 colon and 21 prostate cancer patients through real time PCR analysis using delta cycle threshold method. The statistical scrutiny was executed through Fisher’s Exact test and the Spearman correlation method. There was 12–13 fold increased in expression of HIF-1α, two fold increased in MDR1 and 13–14 fold increased in LAPTM4B mRNA level in peripheral blood of breast, ovarian, prostate and colon cancer patients. In the current study there was an association of HIF-1α, MDR1 and LAPTM4B expression with advanced tumor stage, metastasis and chemotherapy treated group in breast, ovarian, prostate and colon cancer patients. The Spearman analysis also revealed a positive linear association among HIF-1α, MDR1 and LAPTM4B in all the studied cancer patients. The elevated expression of HIF-1α, MDR1 and LAPTM4B in peripheral blood of solid tumor patients can be a predictor of metastasis, disease progression and treatment response in these cancers. However, larger studies are needed to further strengthen their role as a potential biomarker for cancer prognosis.
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Affiliation(s)
- Zaira Rehman
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Ammad Fahim
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Attya Bhatti
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Hajra Sadia
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Peter John
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, Pakistan
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142
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Kofanova O, Bellora C, Quesada RA, Bulla A, Panadero-Fajardo S, Keipes M, Shea K, Stone M, Lescuyer P, Betsou F. IL8 and EDEM3 gene expression ratio indicates peripheral blood mononuclear cell (PBMC) quality. J Immunol Methods 2019; 465:13-19. [DOI: 10.1016/j.jim.2018.11.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 11/19/2018] [Accepted: 11/19/2018] [Indexed: 10/27/2022]
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143
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miRNA networks modulate human endothelial cell adaptation to cyclic hypoxia. Cell Signal 2019; 54:150-160. [DOI: 10.1016/j.cellsig.2018.11.020] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 11/24/2018] [Accepted: 11/26/2018] [Indexed: 02/07/2023]
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144
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Frost J, Ciulli A, Rocha S. RNA-seq analysis of PHD and VHL inhibitors reveals differences and similarities to the hypoxia response. Wellcome Open Res 2019; 4:17. [PMID: 30801039 PMCID: PMC6376255 DOI: 10.12688/wellcomeopenres.15044.1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2019] [Indexed: 12/17/2022] Open
Abstract
Background: Hypoxia-inducible factor (HIF) transcription factors are well known to control the transcriptional response to hypoxia. Given the importance of cellular response to hypoxia, a number of pharmacological agents to interfere with this pathway have been developed and entered pre-clinical or clinical trial phases. However, how similar or divergent the transcriptional response elicited by different points of interference in cells is currently unknown. Methods: We performed RNA-sequencing to analyse the similarities and differences of transcriptional response in HeLa cells treated with hypoxia or chemical agents that stabilise HIF by inhibiting components of the hypoxia signalling pathway - prolyl hydroxylase (PHD) inhibitor or von Hippel-Lindau (VHL) inhibitor. Results: This analysis revealed that hypoxia produces the highest changes in gene transcription, with activation and repression of genes being in large numbers. Treatment with the PHD inhibitor IOX2 or the VHL inhibitor VH032 led mostly to gene activation, majorly via a HIF-dependent manner. These results were also confirmed by qRT-PCR using more specific and/or efficient inhibitors, FG-4592 (PHDs) and VH298 (VHL). Conclusion: PHD inhibition and VHL inhibition mimic gene activation promoted by hypoxia via a HIF-dependent manner. However, gene repression is mostly associated with the hypoxia response and not common to the response elicited by inhibitors of the pathway.
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Affiliation(s)
- Julianty Frost
- Biochemistry-Institute of Integrative Biology, University of Liverpool, Liverpool, L697ZB, UK
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, DD15EH, UK
| | - Sonia Rocha
- Biochemistry-Institute of Integrative Biology, University of Liverpool, Liverpool, L697ZB, UK
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145
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Bhandari V, Hoey C, Liu LY, Lalonde E, Ray J, Livingstone J, Lesurf R, Shiah YJ, Vujcic T, Huang X, Espiritu SMG, Heisler LE, Yousif F, Huang V, Yamaguchi TN, Yao CQ, Sabelnykova VY, Fraser M, Chua MLK, van der Kwast T, Liu SK, Boutros PC, Bristow RG. Molecular landmarks of tumor hypoxia across cancer types. Nat Genet 2019; 51:308-318. [PMID: 30643250 DOI: 10.1038/s41588-018-0318-2] [Citation(s) in RCA: 392] [Impact Index Per Article: 78.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 11/20/2018] [Indexed: 12/27/2022]
Abstract
Many primary-tumor subregions have low levels of molecular oxygen, termed hypoxia. Hypoxic tumors are at elevated risk for local failure and distant metastasis, but the molecular hallmarks of tumor hypoxia remain poorly defined. To fill this gap, we quantified hypoxia in 8,006 tumors across 19 tumor types. In ten tumor types, hypoxia was associated with elevated genomic instability. In all 19 tumor types, hypoxic tumors exhibited characteristic driver-mutation signatures. We observed widespread hypoxia-associated dysregulation of microRNAs (miRNAs) across cancers and functionally validated miR-133a-3p as a hypoxia-modulated miRNA. In localized prostate cancer, hypoxia was associated with elevated rates of chromothripsis, allelic loss of PTEN and shorter telomeres. These associations are particularly enriched in polyclonal tumors, representing a constellation of features resembling tumor nimbosus, an aggressive cellular phenotype. Overall, this work establishes that tumor hypoxia may drive aggressive molecular features across cancers and shape the clinical trajectory of individual tumors.
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Affiliation(s)
- Vinayak Bhandari
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Christianne Hoey
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Lydia Y Liu
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Emilie Lalonde
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jessica Ray
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Julie Livingstone
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Robert Lesurf
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Yu-Jia Shiah
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Tina Vujcic
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Xiaoyong Huang
- Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
| | - Shadrielle M G Espiritu
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Lawrence E Heisler
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Fouad Yousif
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Vincent Huang
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Takafumi N Yamaguchi
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Cindy Q Yao
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Veronica Y Sabelnykova
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Michael Fraser
- Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Melvin L K Chua
- Division of Radiation Oncology, National Cancer Centre Singapore, Singapore, Singapore.,Duke-NUS Graduate Medical School, Singapore, Singapore
| | | | - Stanley K Liu
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Sunnybrook Research Institute, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada.,Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. .,Informatics and Biocomputing Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada. .,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada. .,Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA. .,Department of Urology, University of California, Los Angeles, Los Angeles, CA, USA. .,Jonsson Comprehensive Cancer Centre, University of California, Los Angeles, Los Angeles, CA, USA. .,Institute for Precision Health, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Robert G Bristow
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada. .,Department of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada. .,Princess Margaret Hospital, University Health Network, Toronto, Ontario, Canada. .,Division of Cancer Sciences, Faculty of Biology, Health and Medicine, University of Manchester, Manchester, UK. .,The Christie NHS Foundation Trust, Manchester, UK. .,CRUK Manchester Institute and Manchester Cancer Research Centre, Manchester, UK.
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146
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Metabolic Reprogramming of Trophoblast Cells in Response to Hypoxia. Bull Exp Biol Med 2019; 166:321-325. [PMID: 30627907 DOI: 10.1007/s10517-019-04342-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Indexed: 10/27/2022]
Abstract
Hypoxia of trophoblast cells is an important regulator of normal development of the placenta. However, some pathological states associated with hypoxia, e.g. preeclampsia, impair the functions of placental cells. Oxyquinoline derivative inhibits HIF-prolyl hydroxylase by stabilizing HIF-1 transcription complex, thus modeling cell response to hypoxia. In human choriocarcinoma cells BeWo b30 (trophoblast model), oxyquinoline increased the expression of a core hypoxia response genes along with up-regulation of NOS3, PDK1, and BNIP3 genes and down-regulation of the PPARGC1B gene. These changes in the expression profile attest to activation of the metabolic cell reprogramming mechanisms aimed at reducing oxygen consumption by enabling the switch from aerobic to anaerobic glucose metabolism and the respective decrease in number of mitochondria. The possibility of practical use of the therapeutic properties of oxyquinoline derivatives is discussed.
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147
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Gupta A, Ragumani S, Sharma YK, Ahmad Y, Khurana P. Analysis of Hypoxiamir-Gene Regulatory Network Identifies Critical MiRNAs Influencing Cell-Cycle Regulation Under Hypoxic Conditions. Microrna 2019; 8:223-236. [PMID: 30806334 DOI: 10.2174/2211536608666190219094204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/14/2019] [Accepted: 02/06/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND Hypoxia is a pathophysiological condition which arises due to low oxygen concentration in conditions like cardiovascular diseases, inflammation, ascent to higher altitude, malignancies, deep sea diving, prenatal birth, etc. A number of microRNAs (miRNAs), Transcription Factors (TFs) and genes have been studied separately for their role in hypoxic adaptation and controlling cell-cycle progression and apoptosis during this stress. OBJECTIVE We hypothesize that miRNAs and TFs may act in conjunction to regulate a multitude of genes and play a crucial and combinatorial role during hypoxia-stress-responses and associated cellcycle control mechanisms. METHOD We collected a comprehensive and non-redundant list of human hypoxia-responsive miRNAs (also known as hypoxiamiRs). Their experimentally validated gene-targets were retrieved from various databases and a comprehensive hypoxiamiR-gene regulatory network was built. RESULTS Functional characterization and pathway enrichment of genes identified phospho-proteins as enriched nodes. The phospho-proteins which were localized both in the nucleus and cytoplasm and could potentially play important role as signaling molecules were selected; and further pathway enrichment revealed that most of them were involved in NFkB signaling. Topological analysis identified several critical hypoxiamiRs and network perturbations confirmed their importance in the network. Feed Forward Loops (FFLs) were identified in the subnetwork of enriched genes, miRNAs and TFs. Statistically significant FFLs consisted of four miRNAs (hsa-miR-182-5p, hsa- miR-146b-5p, hsa-miR-96, hsa-miR-20a) and three TFs (SMAD4, FOXO1, HIF1A) both regulating two genes (NFkB1A and CDKN1A). CONCLUSION Detailed BioCarta pathway analysis identified that these miRNAs and TFs together play a critical and combinatorial role in regulating cell-cycle under hypoxia, by controlling mechanisms that activate cell-cycle checkpoint protein, CDKN1A. These modules work synergistically to regulate cell-proliferation, cell-growth, cell-differentiation and apoptosis during hypoxia. A detailed mechanistic molecular model of how these co-regulatory FFLs may regulate the cell-cycle transitions during hypoxic stress conditions is also put forth. These biomolecules may play a crucial and deterministic role in deciding the fate of the cell under hypoxic-stress.
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Affiliation(s)
- Apoorv Gupta
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, Delhi- 110054, India
| | - Sugadev Ragumani
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, Delhi- 110054, India
| | - Yogendra Kumar Sharma
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, Delhi- 110054, India
| | - Yasmin Ahmad
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, Delhi- 110054, India
| | - Pankaj Khurana
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Timarpur, Delhi- 110054, India
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148
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Rao Z, Cao L, Qiu X, Han R. Comparative transcriptome analysis reveals molecular strategies of ghost moth Thitarodes armoricanus in response to hypoxia and anoxia. JOURNAL OF INSECT PHYSIOLOGY 2019; 112:23-34. [PMID: 30399366 DOI: 10.1016/j.jinsphys.2018.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Revised: 11/02/2018] [Accepted: 11/02/2018] [Indexed: 06/08/2023]
Abstract
Hypoxia or anoxia greatly impact the survival of many animal species. The ghost moth Thitarodes armoricanus is distributed in the Tibetan Plateau at an average elevation of approximate 4 km above sea level and has probably evolved a superior capacity to tolerate low oxygen levels. In this study, transcriptome analysis using high-throughput RNA-seq revealed common and different adaptation strategies of T. armoricanus in response to hypoxia (11% O2) or anoxia. T. armoricanus adopted three common strategies for adaptation to hypoxia or anoxia: Up-regulated signal transduction pathways essential for cellular survival, strengthened cell and organelle structure and activity, and activated immune system. Under hypoxia, T. armoricanus might develop a strategy to adapt to hypoxia by suppressing TCA, oxidative phosphorylation pathways, and hypoxanthine catabolism. T. armoricanus larvae kept active under hypoxia but became coma under anoxia, probably relating to up-regulated or suppressed dopamine synthesis pathway. Furthermore, the HIF system seemed not to be essential for regulating the hypoxic and anoxic responses of this insect in Tibetan Plateau. This study provides a global view of gene expression profiles and suggests common and different adaptation strategies of T. armoricanus under hypoxic and anoxic conditions. The results are helpful for understanding the mechanism responsible for the low oxygen level tolerance of this insect species.
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Affiliation(s)
- Zhongchen Rao
- Guangdong Key Laboratory of Animal Protection and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Li Cao
- Guangdong Key Laboratory of Animal Protection and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China
| | - Xuehong Qiu
- Guangdong Key Laboratory of Animal Protection and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China.
| | - Richou Han
- Guangdong Key Laboratory of Animal Protection and Resource Utilization, Guangdong Public Laboratory of Wild Animal Conservation and Utilization, Guangdong Institute of Applied Biological Resources, Guangzhou, China.
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149
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Silberman A, Goldman O, Boukobza Assayag O, Jacob A, Rabinovich S, Adler L, Lee JS, Keshet R, Sarver A, Frug J, Stettner N, Galai S, Persi E, Halpern KB, Zaltsman-Amir Y, Pode-Shakked B, Eilam R, Anikster Y, Nagamani SCS, Ulitsky I, Ruppin E, Erez A. Acid-Induced Downregulation of ASS1 Contributes to the Maintenance of Intracellular pH in Cancer. Cancer Res 2018; 79:518-533. [PMID: 30573518 DOI: 10.1158/0008-5472.can-18-1062] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 08/30/2018] [Accepted: 12/17/2018] [Indexed: 12/23/2022]
Abstract
Downregulation of the urea cycle enzyme argininosuccinate synthase (ASS1) by either promoter methylation or by HIF1α is associated with increased metastasis and poor prognosis in multiple cancers. We have previously shown that in normoxic conditions, ASS1 downregulation facilitates cancer cell proliferation by increasing aspartate availability for pyrimidine synthesis by the enzyme complex CAD. Here we report that in hypoxia, ASS1 expression in cancerous cells is downregulated further by HIF1α-mediated induction of miR-224-5p, making the cells more invasive and dependent on upstream substrates of ASS1 for survival. ASS1 was downregulated under acidic conditions, and ASS1-depleted cancer cells maintained a higher intracellular pH (pHi), depended less on extracellular glutamine, and displayed higher glutathione levels. Depletion of substrates of urea cycle enzymes in ASS1-deficient cancers decreased cancer cell survival. Thus, ASS1 levels in cancer are differentially regulated in various environmental conditions to metabolically benefit cancer progression. Understanding these alterations may help uncover specific context-dependent cancer vulnerabilities that may be targeted for therapeutic purposes. SIGNIFICANCE: Cancer cells in an acidic or hypoxic environment downregulate the expression of the urea cycle enzyme ASS1, which provides them with a redox and pH advantage, resulting in better survival.Graphical Abstract: http://cancerres.aacrjournals.org/content/canres/79/3/518/F1.large.jpg.
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Affiliation(s)
- Alon Silberman
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Omer Goldman
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | | | - Adi Jacob
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Shiran Rabinovich
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Lital Adler
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Joo Sang Lee
- Center for Bioinformatics and Computational Biology and Dept. of Computer Science, University of Maryland, College Park, Maryland.,Cancer Data Science Lab, National Cancer Institute, NIH, Bethesda, Maryland
| | - Rom Keshet
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Alona Sarver
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Julia Frug
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Noa Stettner
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.,Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Sivan Galai
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Erez Persi
- Computational Biology and Bioinformatics Branch (CBB), National Library of Medicine, National Center for Biotechnology Information (NCBI), NIH, Bethesda, Maryland
| | - Keren Bahar Halpern
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Ben Pode-Shakked
- Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel.,The Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Raya Eilam
- Department of Veterinary Resources, Weizmann Institute of Science, Rehovot, Israel
| | - Yair Anikster
- Metabolic Disease Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel.,The Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Sandesh C S Nagamani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Igor Ulitsky
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel
| | - Eytan Ruppin
- Center for Bioinformatics and Computational Biology and Dept. of Computer Science, University of Maryland, College Park, Maryland.,Cancer Data Science Lab, National Cancer Institute, NIH, Bethesda, Maryland
| | - Ayelet Erez
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.
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150
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Tang Y, Zhu J, Huang D, Hu X, Cai Y, Song X, Song Z, Hong C, Feng Z, Kang F. Mandibular osteotomy‐induced hypoxia enhances osteoclast activation and acid secretion by increasing glycolysis. J Cell Physiol 2018; 234:11165-11175. [PMID: 30548595 DOI: 10.1002/jcp.27765] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 10/30/2018] [Indexed: 01/21/2023]
Affiliation(s)
- Yi Tang
- Department of Oral and Maxillofacial Surgery, School & Hospital of Stomatology, Tongji University Shanghai China
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration Shanghai China
| | - Jie Zhu
- Department of Oral and Maxillofacial Surgery, School & Hospital of Stomatology, Tongji University Shanghai China
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration Shanghai China
| | - Danqing Huang
- Shanghai Jiaotong University First People's Hospital Shanghai China
| | - Xiu Hu
- Department of Oral and Maxillofacial Surgery, School & Hospital of Stomatology, Tongji University Shanghai China
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration Shanghai China
| | - Yun Cai
- Department of Oral and Maxillofacial Surgery, School & Hospital of Stomatology, Tongji University Shanghai China
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration Shanghai China
| | - Xiwen Song
- Department of Oral and Maxillofacial Surgery, School & Hospital of Stomatology, Tongji University Shanghai China
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration Shanghai China
| | - Zhaohui Song
- Department of Oral and Maxillofacial Surgery, School & Hospital of Stomatology, Tongji University Shanghai China
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration Shanghai China
| | - Chaoyue Hong
- Department of Oral and Maxillofacial Surgery, School & Hospital of Stomatology, Tongji University Shanghai China
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration Shanghai China
| | - Zifan Feng
- Department of Oral and Maxillofacial Surgery, School & Hospital of Stomatology, Tongji University Shanghai China
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration Shanghai China
| | - Feiwu Kang
- Department of Oral and Maxillofacial Surgery, School & Hospital of Stomatology, Tongji University Shanghai China
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration Shanghai China
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