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Yang YF, Chuang HW, Kuo WT, Lin BS, Chang YC. Current Development and Application of Anaerobic Glycolytic Enzymes in Urothelial Cancer. Int J Mol Sci 2021; 22:ijms221910612. [PMID: 34638949 PMCID: PMC8508954 DOI: 10.3390/ijms221910612] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 09/27/2021] [Accepted: 09/27/2021] [Indexed: 12/23/2022] Open
Abstract
Urothelial cancer is a malignant tumor with metastatic ability and high mortality. Malignant tumors of the urinary system include upper tract urothelial cancer and bladder cancer. In addition to typical genetic alterations and epigenetic modifications, metabolism-related events also occur in urothelial cancer. This metabolic reprogramming includes aberrant expression levels of genes, metabolites, and associated networks and pathways. In this review, we summarize the dysfunctions of glycolytic enzymes in urothelial cancer and discuss the relevant phenotype and signal transduction. Moreover, we describe potential prognostic factors and risks to the survival of clinical cancer patients. More importantly, based on several available databases, we explore relationships between glycolytic enzymes and genetic changes or drug responses in urothelial cancer cells. Current advances in glycolysis-based inhibitors and their combinations are also discussed. Combining all of the evidence, we indicate their potential value for further research in basic science and clinical applications.
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Affiliation(s)
- Yi-Fang Yang
- Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan;
| | - Hao-Wen Chuang
- Department of Pathology and Laboratory Medicine, Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan;
- Institute of Oral Biology, School of Dentistry, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Wei-Ting Kuo
- Division of Urology, Department of Surgery, Kaohsiung Veterans General Hospital, Kaohsiung 81362, Taiwan;
- Institute of Clinical Medicine, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan
| | - Bo-Syuan Lin
- Department of Biomedical Imaging and Radiological Sciences, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan;
| | - Yu-Chan Chang
- Department of Biomedical Imaging and Radiological Sciences, National Yang Ming Chiao Tung University, Taipei 11221, Taiwan;
- Correspondence: ; Tel.: +886-2-2826-7064
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2
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Peixoto A, Ferreira D, Azevedo R, Freitas R, Fernandes E, Relvas-Santos M, Gaiteiro C, Soares J, Cotton S, Teixeira B, Paulo P, Lima L, Palmeira C, Martins G, Oliveira MJ, Silva AMN, Santos LL, Ferreira JA. Glycoproteomics identifies HOMER3 as a potentially targetable biomarker triggered by hypoxia and glucose deprivation in bladder cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:191. [PMID: 34108014 PMCID: PMC8188679 DOI: 10.1186/s13046-021-01988-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/17/2021] [Indexed: 01/11/2023]
Abstract
BACKGROUND Muscle invasive bladder cancer (MIBC) remains amongst the deadliest genitourinary malignancies due to treatment failure and extensive molecular heterogeneity, delaying effective targeted therapeutics. Hypoxia and nutrient deprivation, oversialylation and O-glycans shortening are salient features of aggressive tumours, creating cell surface glycoproteome fingerprints with theranostics potential. METHODS A glycomics guided glycoproteomics workflow was employed to identify potentially targetable biomarkers using invasive bladder cancer cell models. The 5637 and T24 cells O-glycome was characterized by mass spectrometry (MS), and the obtained information was used to guide glycoproteomics experiments, combining sialidase, lectin affinity and bottom-up protein identification by nanoLC-ESI-MS/MS. Data was curated by a bioinformatics approach developed in-house, sorting clinically relevant molecular signatures based on Human Protein Atlas insights. Top-ranked targets and glycoforms were validated in cell models, bladder tumours and metastases by MS and immunoassays. Cells grown under hypoxia and glucose deprivation disclosed the contribution of tumour microenvironment to the expression of relevant biomarkers. Cancer-specificity was validated in healthy tissues by immunohistochemistry and MS in 20 types of tissues/cells of different individuals. RESULTS Sialylated T (ST) antigens were found to be the most abundant glycans in cell lines and over 900 glycoproteins were identified potentially carrying these glycans. HOMER3, typically a cytosolic protein, emerged as a top-ranked targetable glycoprotein at the cell surface carrying short-chain O-glycans. Plasma membrane HOMER3 was observed in more aggressive primary tumours and distant metastases, being an independent predictor of worst prognosis. This phenotype was triggered by nutrient deprivation and concomitant to increased cellular invasion. T24 HOMER3 knockdown significantly decreased proliferation and, to some extent, invasion in normoxia and hypoxia; whereas HOMER3 knock-in increased its membrane expression, which was more pronounced under glucose deprivation. HOMER3 overexpression was associated with increased cell proliferation in normoxia and potentiated invasion under hypoxia. Finally, the mapping of HOMER3-glycosites by EThcD-MS/MS in bladder tumours revealed potentially targetable domains not detected in healthy tissues. CONCLUSION HOMER3-glycoforms allow the identification of patients' subsets facing worst prognosis, holding potential to address more aggressive hypoxic cells with limited off-target effects. The molecular rationale for identifying novel bladder cancer molecular targets has been established.
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Affiliation(s)
- Andreia Peixoto
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313, Porto, Portugal.,Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135, Porto, Portugal.,Institute for Biomedical Engineering (INEB), University of Porto, 4200-135, Porto, Portugal
| | - Dylan Ferreira
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal.,Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135, Porto, Portugal.,Institute for Biomedical Engineering (INEB), University of Porto, 4200-135, Porto, Portugal
| | - Rita Azevedo
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal
| | - Rui Freitas
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal
| | - Elisabete Fernandes
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal.,Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135, Porto, Portugal.,Institute for Biomedical Engineering (INEB), University of Porto, 4200-135, Porto, Portugal
| | - Marta Relvas-Santos
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313, Porto, Portugal.,Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135, Porto, Portugal.,Institute for Biomedical Engineering (INEB), University of Porto, 4200-135, Porto, Portugal.,REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Porto, 4169-007, Porto, Portugal
| | - Cristiana Gaiteiro
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313, Porto, Portugal
| | - Janine Soares
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313, Porto, Portugal
| | - Sofia Cotton
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313, Porto, Portugal
| | - Beatriz Teixeira
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal
| | - Paula Paulo
- Cancer Genetics Group, Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072, Porto, Portugal
| | - Luís Lima
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal
| | - Carlos Palmeira
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal.,Immunology Department, Portuguese Institute of Oncology of Porto, 4200-072, Porto, Portugal.,Health School of University Fernando Pessoa, 4249-004, Porto, Portugal
| | - Gabriela Martins
- Immunology Department, Portuguese Institute of Oncology of Porto, 4200-072, Porto, Portugal
| | - Maria José Oliveira
- Institute for Research and Innovation in Health (i3S), University of Porto, 4200-135, Porto, Portugal.,Institute for Biomedical Engineering (INEB), University of Porto, 4200-135, Porto, Portugal
| | - André M N Silva
- REQUIMTE-LAQV, Department of Chemistry and Biochemistry, Faculty of Sciences of the University of Porto, 4169-007, Porto, Portugal
| | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313, Porto, Portugal.,Health School of University Fernando Pessoa, 4249-004, Porto, Portugal.,Department of Surgical Oncology, Portuguese Institute of Oncology, 4200-072, Porto, Portugal.,Porto Comprehensive Cancer Center (P.ccc), 4200-072, Porto, Portugal
| | - José Alexandre Ferreira
- Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072, Porto, Portugal. .,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, 4050-313, Porto, Portugal. .,Porto Comprehensive Cancer Center (P.ccc), 4200-072, Porto, Portugal.
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A reliable set of reference genes to normalize oxygen-dependent cytoglobin gene expression levels in melanoma. Sci Rep 2021; 11:10879. [PMID: 34035373 PMCID: PMC8149659 DOI: 10.1038/s41598-021-90284-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/10/2021] [Indexed: 12/17/2022] Open
Abstract
Cytoglobin (CYGB) is a ubiquitously expressed protein with a protective role against oxidative stress, fibrosis and tumor growth, shown to be transcriptionally regulated under hypoxic conditions. Hypoxia-inducible CYGB expression is observed in several cancer cell lines and particularly in various melanoma-derived cell lines. However, reliable detection of hypoxia-inducible mRNA levels by qPCR depends on the critical choice of suitable reference genes for accurate normalization. Limited evidence exists to support selection of the commonly used reference genes in hypoxic models of melanoma. This study aimed to select the optimal reference genes to study CYGB expression levels in melanoma cell lines exposed to hypoxic conditions (0.2% O2) and to the HIF prolyl hydroxylase inhibitor roxadustat (FG-4592). The expression levels of candidate genes were assessed by qPCR and the stability of genes was evaluated using the geNorm and NormFinder algorithms. Our results display that B2M and YWHAZ represent the most optimal reference genes to reliably quantify hypoxia-inducible CYGB expression in melanoma cell lines. We further validate hypoxia-inducible CYGB expression on protein level and by using CYGB promoter-driven luciferase reporter assays in melanoma cell lines.
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Smith TAD, AbdelKarem OA, Irlam-Jones JJ, Lane B, Valentine H, Bibby BAS, Denley H, Choudhury A, West CML. Selection of endogenous control genes for normalising gene expression data derived from formalin-fixed paraffin-embedded tumour tissue. Sci Rep 2020; 10:17258. [PMID: 33057113 PMCID: PMC7560892 DOI: 10.1038/s41598-020-74380-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/28/2020] [Indexed: 12/19/2022] Open
Abstract
Quantitative real time polymerase chain reaction (qPCR) data are normalised using endogenous control genes. We aimed to: (1) demonstrate a pathway to identify endogenous control genes for qPCR analysis of formalin-fixed paraffin-embedded (FFPE) tissue using bladder cancer as an exemplar; and (2) examine the influence of probe length and sample age on PCR amplification and co-expression of candidate genes on apparent expression stability. RNA was extracted from prospective and retrospective samples and subject to qPCR using TaqMan human endogenous control arrays or single tube assays. Gene stability ranking was assessed using coefficient of variation (CoV), GeNorm and NormFinder. Co-expressed genes were identified from The Cancer Genome Atlas (TCGA) using the on-line gene regression analysis tool GRACE. Cycle threshold (Ct) values were lower for prospective (19.49 ± 2.53) vs retrospective (23.8 ± 3.32) tissues (p < 0.001) and shorter vs longer probes. Co-expressed genes ranked as the most stable genes in the TCGA cohort by GeNorm when analysed together but ranked lower when analysed individually omitting co-expressed genes indicating bias. Stability values were < 1.5 for the 20 candidate genes in the prospective cohort. As they consistently ranked in the top ten by CoV, GeNorm and Normfinder, UBC, RPLP0, HMBS, GUSB, and TBP are the most suitable endogenous control genes for bladder cancer qPCR.
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Affiliation(s)
- Tim A D Smith
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Centre, Christie Hospital NHS Found Trust, Manchester, M20 4BX, UK.
| | - Omneya A AbdelKarem
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Centre, Christie Hospital NHS Found Trust, Manchester, M20 4BX, UK
- Medical Research Institute, Alexandria University, 165 El-Horreya Avenue, El-Hadra, Alexandria, Egypt
| | - Joely J Irlam-Jones
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Centre, Christie Hospital NHS Found Trust, Manchester, M20 4BX, UK
| | - Brian Lane
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Centre, Christie Hospital NHS Found Trust, Manchester, M20 4BX, UK
| | - Helen Valentine
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Centre, Christie Hospital NHS Found Trust, Manchester, M20 4BX, UK
| | - Becky A S Bibby
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Centre, Christie Hospital NHS Found Trust, Manchester, M20 4BX, UK
| | - Helen Denley
- Pathology Centre, Shrewsbury and Telford NHS Trust, Royal Shrewsbury Hospital, Shrewsbury, SY3 8XQ, UK
| | - Ananya Choudhury
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Centre, Christie Hospital NHS Found Trust, Manchester, M20 4BX, UK
| | - Catharine M L West
- Translational Radiobiology Group, Division of Cancer Sciences, University of Manchester, Manchester Academic Health Centre, Christie Hospital NHS Found Trust, Manchester, M20 4BX, UK
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Yan W, Xie M, Li R, Hu H, Tang B, Shen J. Identification and Validation of Reference Genes Selection in Ovarian Cancer Exposed to Hypoxia. Onco Targets Ther 2020; 13:7423-7431. [PMID: 32801765 PMCID: PMC7395691 DOI: 10.2147/ott.s249733] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 06/26/2020] [Indexed: 02/06/2023] Open
Abstract
INTRODUCTION Hypoxia-mediated tumor metastasis, progression and drug resistance are major clinical challenges in ovarian cancer. Meanwhile, the genetic basis of these traits is still not clear. RT-qPCR, as an efficient and sensitive gene expression technique, has been widely used for gene analyses, providing a basis for in-depth understanding of molecular changes in different microenvironments. However, there is currently a lack of suitable reference genes to normalize the data associated with hypoxia in ovarian cancer cells. METHODS A systematic method is needed to select the most suitable reference gene. Here, eight candidate reference genes (GAPDH, β-actin, 18S RNA, TUBB, PPIA, TBP, RPL13A and SDHA) from humans were selected to assess their expression levels in SKOV3 cells under hypoxia. The geNorm and NormFinder programs were utilized to evaluate the expression stabilities of these selected candidate reference genes. RESULTS Interestingly, 18S RNA was considered to be an ideal reference gene for the normalization of target gene expression under hypoxic conditions. Furthermore, this result was confirmed in another two ovarian cancer cell line, CAOV3 and OVCAR3 cell line. Finally, these results suggest that appropriate reference genes should be selected before performing gene expression analysis during hypoxic environmental exposure. CONCLUSION 18S RNA can be used as an appropriate reference gene for the study of gene expression in ovarian cancer samples under hypoxia by RT-qPCR.
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Affiliation(s)
- Wenying Yan
- Department of Gynecology, Wangjiang Hospital, Sichuan University, Chengdu, Sichuan Province, People’s Republic of China
| | - Mei Xie
- Department of Respiratory and Critical Care Medicine, Chengdu Second People’s Hospital, Chengdu, Sichuan Province, People’s Republic of China
| | - Rong Li
- Department of Gynecology, Sichuan Maternal and Child Health Hospital, Chengdu, Sichuan Province, People’s Republic of China
| | - Hongmei Hu
- Department of Gynecology, Sichuan Maternal and Child Health Hospital, Chengdu, Sichuan Province, People’s Republic of China
| | - Biao Tang
- Department of Gynecology, Sichuan Maternal and Child Health Hospital, Chengdu, Sichuan Province, People’s Republic of China
| | - Jie Shen
- Department of Orthopaedics, The First Hospital Affiliated to AMU (Southwest Hospital), Chongqing, People’s Republic of China
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Lindner L, Cayrou P, Jacquot S, Birling MC, Herault Y, Pavlovic G. Reliable and robust droplet digital PCR (ddPCR) and RT-ddPCR protocols for mouse studies. Methods 2020; 191:95-106. [PMID: 32721466 DOI: 10.1016/j.ymeth.2020.07.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 06/23/2020] [Accepted: 07/16/2020] [Indexed: 01/05/2023] Open
Abstract
Droplet digital PCR (ddPCR) is a recent method developed for the quantification of nucleic acids sequences. It is an evolution of PCR methodology incorporating two principal differences: a PCR reaction is performed in thousands of water-oil emulsion droplets and fluorescence is measured at the end of PCR amplification. It leads to the precise and reproducible quantification of DNA and RNA sequences. Here, we present quantitative methods for DNA and RNA analysis using Bio-Rad QX100 or QX200 systems, respectively. The aim of these methods is to provide useful molecular tools for validating genetically altered animal models such as those subject to CRISPR/Cas9 genome editing, as well for expression or CNV studies. A standard procedure for simultaneous DNA and RNA extraction adapted for mouse organs is also described. These methods were initially designed for mouse studies but also work for samples from other species like rat or human. In our lab, thousands of samples and hundreds of target genes from genetically altered lines were examined using these methods. This large dataset was analyzed to evaluate technical optimizations and limitations. Finally, we propose additional recommendations to be included in dMIQE (Minimum information for publication of quantitative digital PCR experiments) guidelines when using ddPCR instruments.
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Affiliation(s)
- Loic Lindner
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France
| | - Pauline Cayrou
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France
| | - Sylvie Jacquot
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France
| | - Marie-Christine Birling
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France
| | - Yann Herault
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France
| | - Guillaume Pavlovic
- PHENOMIN-Institut Clinique de la Souris, CELPHEDIA, CNRS, INSERM, Université de Strasbourg, Illkirch-Graffenstaden, Strasbourg 67404, France.
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Yasko JR, Moss IL, Mains RE. Transcriptional Profiling of Non-injured Nociceptors After Spinal Cord Injury Reveals Diverse Molecular Changes. Front Mol Neurosci 2019; 12:284. [PMID: 32038157 PMCID: PMC6988781 DOI: 10.3389/fnmol.2019.00284] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 11/08/2019] [Indexed: 01/01/2023] Open
Abstract
Traumatic spinal cord injury (SCI) has devastating implications for patients, including a high predisposition for developing chronic pain distal to the site of injury. Chronic pain develops weeks to months after injury, consequently, patients are treated after irreparable changes have occurred. Nociceptors are central to chronic pain; however, the diversity of this cellular population presents challenges to understanding mechanisms and attributing pain modalities to specific cell types. To begin to address how peripheral sensory neurons below the injury level may contribute to the below-level pain reported by SCI patients, we examined SCI-induced changes in gene expression in lumbar dorsal root ganglia (DRG) below the site of injury. SCI was performed at the T10 vertebral level, with injury produced by a vessel clip with a closing pressure of 15 g for 1 min. Alterations in gene expression produce long-term sensory changes, therefore, we were interested in studying SCI-induced transcripts before the onset of chronic pain, which may trigger changes in downstream signaling pathways and ultimately facilitate the transmission of pain. To examine changes in the nociceptor subpopulation in DRG distal to the site of injury, we retrograde labeled sensory neurons projecting to the hairy hindpaw skin with fluorescent dye and collected the corresponding lumbar (L2–L6) DRG 4 days post-injury. Following dissociation, labeled neurons were purified by fluorescence-activated cell sorting (FACS). RNA was extracted from sorted sensory neurons of naïve, sham, or SCI mice and sequenced. Transcript abundances validated that the desired population of nociceptors were isolated. Cross-comparisons to data sets from similar studies confirmed, we were able to isolate our cells of interest and identify a unique pattern of gene expression within a subpopulation of neurons projecting to the hairy hindpaw skin. Differential gene expression analysis showed high expression levels and significant transcript changes 4 days post-injury in SCI cell populations relevant to the onset of chronic pain. Regulatory interrelationships predicted by pathway analysis implicated changes within the synaptogenesis signaling pathway as well as networks related to inflammatory signaling mechanisms, suggesting a role for synaptic plasticity and a correlation with pro-inflammatory signaling in the transition from acute to chronic pain.
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Affiliation(s)
- Jessica R Yasko
- Department of Neuroscience, University of Connecticut Health Center, Farmington, CT, United States
| | - Isaac L Moss
- Department of Orthopedic Surgery and the Comprehensive Spine Center, University of Connecticut Health Center, Farmington, CT, United States
| | - Richard E Mains
- Department of Neuroscience, University of Connecticut Health Center, Farmington, CT, United States
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Benites J, Valderrama JA, Ramos M, Valenzuela M, Guerrero-Castilla A, Muccioli GG, Buc Calderon P. Half-Wave Potentials and In Vitro Cytotoxic Evaluation of 3-Acylated 2,5- Bis(phenylamino)-1,4-benzoquinones on Cancer Cells. Molecules 2019; 24:molecules24091780. [PMID: 31071970 PMCID: PMC6539005 DOI: 10.3390/molecules24091780] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 04/12/2019] [Accepted: 04/16/2019] [Indexed: 01/28/2023] Open
Abstract
A broad range of 3-acyl-2,5-bis(phenylamino)-1,4-benzoquinones were synthesized and their voltammetric values, as well as in vitro cancer cell cytotoxicities, were assessed. The members of this series were prepared from acylbenzoquinones and phenylamines, in moderate to good yields (47–74%), through a procedure involving a sequence of two in situ regioselective oxidative amination reactions. The cyclic voltammograms of the aminoquinones exhibit two one-electron reduction waves to the corresponding radical-anion and dianion, and two quasi-reversible oxidation peaks. The first and second half-wave potential values (E1/2) of the members of the series were sensitive to the push-pull electronic effects of the substituents around the benzoquinone nucleus. The in vitro cytotoxic activities of the 3-acyl-2,5-bis(phenylamino)-1,4-benzoquinones against human cancer cells (bladder and prostate) and non-tumor human embryonic kidney cells were measured using the MTT colorimetric method. The substitution of both aniline groups, by either methoxy (electron donating effect) or fluorine (electron withdrawal effect), decreased the cytotoxicity in the aminoquinones. Among the members of the unsubstituted phenylamino series, two of the 18 compounds showed interesting anti-cancer activities. A preliminary assay, looking for changes in the expression of selected genes, was performed. In this context, the two compounds increased TNF gene expression, suggesting an association with an inflammatory-like response.
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Affiliation(s)
- Julio Benites
- Química y Farmacia, Facultad de Ciencias de la Salud, Universidad Arturo Prat, Casilla 121, Iquique 1100000, Chile.
- Instituto de Ciencias Exactas y Naturales, Universidad Arturo Prat, Casilla 121, Iquique 1100000, Chile.
| | - Jaime A Valderrama
- Química y Farmacia, Facultad de Ciencias de la Salud, Universidad Arturo Prat, Casilla 121, Iquique 1100000, Chile.
- Instituto de Ciencias Exactas y Naturales, Universidad Arturo Prat, Casilla 121, Iquique 1100000, Chile.
| | - Maryan Ramos
- Química y Farmacia, Facultad de Ciencias de la Salud, Universidad Arturo Prat, Casilla 121, Iquique 1100000, Chile.
| | - Maudy Valenzuela
- Química y Farmacia, Facultad de Ciencias de la Salud, Universidad Arturo Prat, Casilla 121, Iquique 1100000, Chile.
| | - Angélica Guerrero-Castilla
- Química y Farmacia, Facultad de Ciencias de la Salud, Universidad Arturo Prat, Casilla 121, Iquique 1100000, Chile.
| | - Giulio G Muccioli
- Bioanalysis and Pharmacology of Bioactive Lipids (BPBL), Louvain Drug Research Institute, Université catholique de Louvain, 72 Avenue E. Mounier, BPBL 7201, 1200 Brussels, Belgium.
| | - Pedro Buc Calderon
- Química y Farmacia, Facultad de Ciencias de la Salud, Universidad Arturo Prat, Casilla 121, Iquique 1100000, Chile.
- Research Group in Metabolism and Nutrition, Louvain Drug Research Institute, Université catholique de Louvain, 73 Avenue E. Mounier, 1200 Brussels, Belgium.
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LaRese TP, Rheaume BA, Abraham R, Eipper BA, Mains RE. Sex-Specific Gene Expression in the Mouse Nucleus Accumbens Before and After Cocaine Exposure. J Endocr Soc 2019; 3:468-487. [PMID: 30746506 PMCID: PMC6364626 DOI: 10.1210/js.2018-00313] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/09/2019] [Indexed: 12/18/2022] Open
Abstract
The nucleus accumbens plays a major role in the response of mammals to cocaine. In animal models and human studies, the addictive effects of cocaine and relapse probability have been shown to be greater in females. Sex-specific differential expression of key transcripts at baseline and after prolonged withdrawal could underlie these differences. To distinguish between these possibilities, gene expression was analyzed in four groups of mice (cycling females, ovariectomized females treated with estradiol or placebo, and males) 28 days after they had received seven daily injections of saline or cocaine. As expected, sensitization to the locomotor effects of cocaine was most pronounced in the ovariectomized mice receiving estradiol, was greater in cycling females than in males, and failed to occur in ovariectomized/placebo mice. After the 28-day withdrawal period, RNA prepared from the nucleus accumbens of the individual cocaine- or saline-injected mice was subjected to RNA sequencing analysis. Baseline expression of 3% of the nucleus accumbens transcripts differed in the cycling female mice compared with the male mice. Expression of a similar number of transcripts was altered by ovariectomy or was responsive to estradiol treatment. Nucleus accumbens transcripts differentially expressed in cycling female mice withdrawn from cocaine exhibited substantial overlap with those differentially expressed in cocaine-withdrawn male mice. A small set of transcripts were similarly affected by cocaine in the placebo- or estradiol-treated ovariectomized mice. Sex and hormonal status have profound effects on RNA expression in the nucleus accumbens of naive mice. Prolonged withdrawal from cocaine alters the expression of a much smaller number of common and sex hormone-specific transcripts.
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Affiliation(s)
- Taylor P LaRese
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut
| | - Bruce A Rheaume
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut
| | - Ron Abraham
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut
| | - Betty A Eipper
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut
| | - Richard E Mains
- Department of Neuroscience, University of Connecticut Health Center, Farmington, Connecticut
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10
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Watkins AJ, Pearce G, Unak P, Guldu OK, Yasakci V, Akin O, Aras O, Wong J, Ma X. Tissue Morphology and Gene Expression Characterisation of Transplantable Adenocarcinoma Bearing Mice Exposed to Fluorodeoxyglucose-Conjugated Magnetic Nanoparticles. J Biomed Nanotechnol 2018; 14:1979-1991. [PMID: 30165933 DOI: 10.1166/jbn.2018.2631] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Fluorodeoxyglucose-conjugated magnetic nanoparticles, designed to target cancer cells with high specificity when heated by an alternating magnetic field, could provide a low-cost, non-toxic treatment for cancer. However, it is essential that the in vivo impacts of such technologies on both tumour and healthy tissues are characterised fully. Profiling tissue gene expression by semi-quantitative reverse transcriptase real-time PCR can provide a sensitive measurement of tissue response to treatment. However, the accuracy of such analyses is dependent on the selection of stable reference genes. In this study, we determined the impact of fluorodeoxyglucose-conjugated magnetic nanoparticles on tumour and non-tumour tissue gene expression and morphology in MAC16 adenocarcinoma established male NMRI mice. Mice received an injection of 8 mg/kg body weight fluorodeoxyglucose-conjugated magnetic nanoparticles either intravenously in to the tail vein, directly into the tumour or subcutaneously directly overlying the tumour. Tissues from mice were sampled between 70 minutes and 12 hours post injection. Using the bioinformatic geNorm tool, we established the stability of six candidate reference genes (Hprt, Pgk1, Ppib, Sdha, Tbp and Tuba); we observed Pgk1 and Ppib to be the most stable. We then characterised the expression profiles of several apoptosis genes of interest in our adenocarcinoma samples, observing differential expression in response to mode of administration and exposure duration. Using histological assessment and fluorescent TUNNEL staining, we observed no detrimental impact on either tumour or non-tumour tissue morphology or levels of apoptosis. These observations define the underlying efficacy of fluorodeoxyglucose-conjugated magnetic nanoparticles on tumour and non-tumour tissue morphology and gene expression, setting the basis for future studies.
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11
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Mains RE, Blaby-Haas C, Rheaume BA, Eipper BA. Changes in Corticotrope Gene Expression Upon Increased Expression of Peptidylglycine α-Amidating Monooxygenase. Endocrinology 2018; 159:2621-2639. [PMID: 29788427 PMCID: PMC6287594 DOI: 10.1210/en.2018-00235] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/09/2018] [Indexed: 11/19/2022]
Abstract
Throughout evolution, secretion has played an essential role in the ability of organisms and single cells to survive in the face of a changing environment. Peptidylglycine α-amidating monooxygenase (PAM) is an integral membrane monooxygenase, first identified for its role in the biosynthesis of neuroendocrine peptides released by the regulated secretory pathway. PAM was subsequently identified in Chlamydomonas reinhardtii, a unicellular green alga, where it plays an essential role in constitutive secretion and in ciliogenesis. Reduced expression of C. reinhardtii PAM resulted in significant changes in secretion and ciliogenesis. Hence, a screen was performed for transcripts and proteins whose expression responded to changes in PAM levels in a mammalian corticotrope tumor cell line. The goal was to identify genes not previously known to play a role in secretion. The screen identified transcription factors, peptidyl prolyl isomerases, endosomal/lysosomal proteins, and proteins involved in tissue-specific responses to glucose and amino acid availability that had not previously been recognized as relevant to the secretory pathway. Perhaps reflecting the dependence of PAM on molecular oxygen, many PAM-responsive genes are known to be hypoxia responsive. The data highlight the extent to which the performance of the secretory pathway may be integrated into a wide diversity of signaling pathways.
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Affiliation(s)
- Richard E Mains
- Neuroscience, University of Connecticut Health Center, Farmington,
Connecticut
- Correspondence: Richard E. Mains, PhD, University of Connecticut Health Center, 263 Farmington
Avenue, Farmington, Connecticut 06030. E-mail:
| | | | - Bruce A Rheaume
- Neuroscience, University of Connecticut Health Center, Farmington,
Connecticut
| | - Betty A Eipper
- Neuroscience, University of Connecticut Health Center, Farmington,
Connecticut
- Molecular Biology & Biophysics, University of Connecticut, Farmington,
Connecticut
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12
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Kang Y, Wu Z, Cai D, Lu B. Evaluation of reference genes for gene expression studies in mouse and N2a cell ischemic stroke models using quantitative real-time PCR. BMC Neurosci 2018; 19:3. [PMID: 29390963 PMCID: PMC5795833 DOI: 10.1186/s12868-018-0403-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/22/2018] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR) is a critical tool for evaluating the levels of mRNA transcribed from genes. Reliable RT-qPCR results largely depend on normalization to suitable reference genes. Middle cerebral artery occlusion (MCAO) and oxygen-glucose deprivation/reoxygenation (OGD/R) are models that are commonly used to study ischemic stroke. However, the proper reference genes for RNA analysis in these two models have not yet been determined. RESULTS In this study, we evaluated the expression levels of six candidate housekeeping genes and selected the most suitable reference genes for RT-qPCR analyses of the cortices of MCAO mice and OGD/R-injured N2a cells. Four software programs, geNorm, NormFinder, BestKeeper and RefFinder, were used to validate the stabilities of the candidate reference genes. The results revealed that HPRT and 18S were the most stable reference genes in the cortices of MCAO mice and that β-actin and cyclophilin were the most stable reference genes in the OGD/R-injured N2a cells; in contrast, GAPDH and Sdha were the least stable genes in the cortices of MCAO mice and the OGD/R-injured N2a cells, respectively. Moreover, a combination of HPRT, 18S and cyclophilin was most suitable for normalization in analyses of the cortices of MCAO mice, and a combination of β-actin, cyclophilin, GAPDH, and 18S was most suitable for analyses of the OGD/R-injured N2a cells. CONCLUSIONS This study provides appropriate reference genes for further RT-qPCR analyses of in vivo and in vitro ischemic stroke and demonstrates the necessity of validating reference genes for RNA analyses under variable conditions.
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Affiliation(s)
- Yingbo Kang
- Department of Pharmacy, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041 Guangdong China
| | - Zhuomin Wu
- Department of Pharmacy, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041 Guangdong China
| | - De Cai
- Department of Pharmacy, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041 Guangdong China
| | - Binger Lu
- Department of Pharmacy, The First Affiliated Hospital of Shantou University Medical College, Shantou, 515041 Guangdong China
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13
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Xiao J, Li X, Liu J, Fan X, Lei H, Li C. Identification of reference genes in blood before and after entering the plateau for SYBR green RT-qPCR studies. PeerJ 2017; 5:e3726. [PMID: 28970964 PMCID: PMC5622608 DOI: 10.7717/peerj.3726] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 08/01/2017] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Tibetans have lived at high altitudes for thousands of years, and they have unique physiological traits that enable them to tolerate this hypoxic environment. However, the genetic basis of these traits is still unknown. As a sensitive and highly efficient technique, RT-qPCR is widely used in gene expression analyses to provide insight into the molecular mechanisms underlying environmental changes. However, the quantitative analysis of gene expression in blood is limited by a shortage of stable reference genes for the normalization of mRNA levels. Thus, systematic approaches were used to identify potential reference genes. RESULTS The expression levels of eight candidate human reference genes (GAPDH, ACTB, 18S RNA, β2-MG, PPIA, RPL13A, TBP and SDHA) were assessed in blood from hypoxic environments. The expression stability of these selected reference genes was evaluated using the geNorm, NormFinder and BestKeeper programs. Interestingly, RPL13A was identified as the ideal reference gene for normalizing target gene expression in human blood before and after exposure to high-altitude conditions. CONCLUSION These results indicate that different reference genes should be selected for the normalization of gene expression in blood from different environmental settings.
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Affiliation(s)
- Jun Xiao
- Department of Blood Transfusion, General Hospital of Air Force, PLA, Beijing, China
| | - Xiaowei Li
- Department of Blood Transfusion, General Hospital of Air Force, PLA, Beijing, China
| | - Juan Liu
- Department of Blood Transfusion, General Hospital of Air Force, PLA, Beijing, China
| | - Xiu Fan
- Department of Blood Transfusion, General Hospital of Air Force, PLA, Beijing, China
| | - Huifen Lei
- Department of Blood Transfusion, General Hospital of Air Force, PLA, Beijing, China
| | - Cuiying Li
- Department of Blood Transfusion, General Hospital of Air Force, PLA, Beijing, China
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Touma M, Kang X, Gao F, Zhao Y, Cass AA, Biniwale R, Xiao X, Eghbali M, Coppola G, Reemtsen B, Wang Y. Wnt11 regulates cardiac chamber development and disease during perinatal maturation. JCI Insight 2017; 2:94904. [PMID: 28878122 DOI: 10.1172/jci.insight.94904] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 08/03/2017] [Indexed: 12/11/2022] Open
Abstract
Ventricular chamber growth and development during perinatal circulatory transition is critical for functional adaptation of the heart. However, the chamber-specific programs of neonatal heart growth are poorly understood. We used integrated systems genomic and functional biology analyses of the perinatal chamber specific transcriptome and we identified Wnt11 as a prominent regulator of chamber-specific proliferation. Importantly, downregulation of Wnt11 expression was associated with cyanotic congenital heart defect (CHD) phenotypes and correlated with O2 saturation levels in hypoxemic infants with Tetralogy of Fallot (TOF). Perinatal hypoxia treatment in mice suppressed Wnt11 expression and induced myocyte proliferation more robustly in the right ventricle, modulating Rb1 protein activity. Wnt11 inactivation was sufficient to induce myocyte proliferation in perinatal mouse hearts and reduced Rb1 protein and phosphorylation in neonatal cardiomyocytes. Finally, downregulated Wnt11 in hypoxemic TOF infantile hearts was associated with Rb1 suppression and induction of proliferation markers. This study revealed a previously uncharacterized function of Wnt11-mediated signaling as an important player in programming the chamber-specific growth of the neonatal heart. This function influences the chamber-specific development and pathogenesis in response to hypoxia and cyanotic CHDs. Defining the underlying regulatory mechanism may yield chamber-specific therapies for infants born with CHDs.
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Affiliation(s)
- Marlin Touma
- The Children's Discovery and Innovation Institute (CDI), Department of Pediatrics.,Cardiovascular Research Laboratory
| | - Xuedong Kang
- The Children's Discovery and Innovation Institute (CDI), Department of Pediatrics.,Cardiovascular Research Laboratory
| | | | - Yan Zhao
- The Children's Discovery and Innovation Institute (CDI), Department of Pediatrics.,Cardiovascular Research Laboratory
| | | | | | | | | | | | | | - Yibin Wang
- Cardiovascular Research Laboratory.,Department of Anesthesiology, Physiology and Medicine, University of California, Los Angeles, California, USA
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