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Yeganeh FE, Ghafuri H, Azizi M. Investigation Cytotoxicity and Curcumin Release Behavior by Pyranopyrazole-TiO 2@niosome Carrier for Breast Cancer Treatment. Appl Biochem Biotechnol 2024:10.1007/s12010-024-04985-5. [PMID: 38884856 DOI: 10.1007/s12010-024-04985-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2024] [Indexed: 06/18/2024]
Abstract
In the present study, we present a pyranopyrazole-TiO2 which is encapsulated with a niosome as nanocarrier for delivery of curcumin into breast cancer cells. Nanocarrier porous TiO2 is biocompatible and with a high specific surface area and a large pore volume and was used to carry pyranopyrazole, which has been reported as an anti-cancer. Niosome in the outer layer, helpful for loading curcumin into the niosomal layer, demonstrates a pH-dependent release and can be effective for cancer treatment. Entrapment efficiency of curcumin was found at 81.02% in carriers. The results of MTT and flow cytometry revealed that apoptosis is notably enhanced by loading curcumin on pyranopyrazole-TiO2@niosome. Also, there was high biocompatibility with MCF-10A, while exhibiting significant anti-cancer and anti-metastatic effects on MCF-7, whose cell viability was 38.79% in the loaded curcumin on carrier and was more than other samples even, than free curcumin (42.82%). Furthermore, the regulation of gene expression in cancer cells decreased the regulation of MMP-2 and MMP-9 genes and increased the expression of caspase-3 and caspase-9 genes. Finally, fluorescence activity in MCF-7 significantly increased after treatment with samples.
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Affiliation(s)
| | - Hossein Ghafuri
- Department of Chemistry, Iran University of Science and Technology, Tehran, Iran.
| | - Mojtaba Azizi
- Department of Chemistry, Iran University of Science and Technology, Tehran, Iran
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2
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Mi C, Zhang Y, Zhao Y, Lin L. Mechanisms of low nighttime temperature promote oil accumulation in Brassica napus L. based on in-depth transcriptome analysis. PHYSIOLOGIA PLANTARUM 2024; 176:e14372. [PMID: 38812077 DOI: 10.1111/ppl.14372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 04/08/2024] [Indexed: 05/31/2024]
Abstract
Rape (Brassica napus L.; AACC) is an important oil-bearing crop worldwide. Temperature significantly affects the production of oil crops; however, the mechanisms underlying temperature-promoted oil biosynthesis remain largely unknown. In this study, we found that a temperature-sensitive cultivar (O) could accumulate higher seed oil content under low nighttime temperatures (LNT,13°C) compared with a temperature-insensitive cultivar (S). We performed an in-depth transcriptome analysis of seeds from both cultivars grown under different nighttime temperatures. We found that low nighttime temperatures induced significant changes in the transcription patterns in the seeds of both cultivars. In contrast, the expression of genes associated with fatty acid and lipid pathways was higher in the O cultivar than in the S cultivar under low nighttime temperatures. Among these genes, we identified 14 genes associated with oil production, especially BnLPP and ACAA1, which were remarkably upregulated in the O cultivar in response to low nighttime temperatures compared to S. Further, a WGCNA analysis and qRT-PCR verification revealed that these genes were mainly regulated by five transcription factors, WRKY20, MYB86, bHLH144, bHLH95, and NAC12, whose expression was also increased in O compared to S under LNT. These results allowed the elucidation of the probable molecular mechanism of oil accumulation under LNT conditions in the O cultivar. Subsequent biochemical assays verified that BnMYB86 transcriptionally activated BnLPP expression, contributing to oil accumulation. Meanwhile, at LNT, the expression levels of these genes in the O plants were higher than at high nighttime temperatures, DEGs (SUT, PGK, PK, GPDH, ACCase, SAD, KAS II, LACS, FAD2, FAD3, KCS, KAR, ECR, GPAT, LPAAT, PAP, DGAT, STERO) related to lipid biosynthesis were also upregulated, most of which are used in oil accumulation.
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Affiliation(s)
- Chao Mi
- Agricultural Research Institute, Xizang Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Yusong Zhang
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yanning Zhao
- Vegetable Research Institute, Xizang Academy of Agriculture and Animal Husbandry Sciences, Lhasa, China
| | - Liangbin Lin
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
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Ashoub MH, Razavi R, Heydaryan K, Salavati-Niasari M, Amiri M. Targeting ferroptosis for leukemia therapy: exploring novel strategies from its mechanisms and role in leukemia based on nanotechnology. Eur J Med Res 2024; 29:224. [PMID: 38594732 PMCID: PMC11003188 DOI: 10.1186/s40001-024-01822-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 03/30/2024] [Indexed: 04/11/2024] Open
Abstract
The latest findings in iron metabolism and the newly uncovered process of ferroptosis have paved the way for new potential strategies in anti-leukemia treatments. In the current project, we reviewed and summarized the current role of nanomedicine in the treatment and diagnosis of leukemia through a comparison made between traditional approaches applied in the treatment and diagnosis of leukemia via the existing investigations about the ferroptosis molecular mechanisms involved in various anti-tumor treatments. The application of nanotechnology and other novel technologies may provide a new direction in ferroptosis-driven leukemia therapies. The article explores the potential of targeting ferroptosis, a new form of regulated cell death, as a new therapeutic strategy for leukemia. It discusses the mechanisms of ferroptosis and its role in leukemia and how nanotechnology can enhance the delivery and efficacy of ferroptosis-inducing agents. The article not only highlights the promise of ferroptosis-targeted therapies and nanotechnology in revolutionizing leukemia treatment, but also calls for further research to overcome challenges and fully realize the clinical potential of this innovative approach. Finally, it discusses the challenges and opportunities in clinical applications of ferroptosis.
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Affiliation(s)
- Muhammad Hossein Ashoub
- Department of Hematology and Medical Laboratory Sciences, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran
- Stem Cells and Regenerative Medicine Innovation Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Razieh Razavi
- Department of Chemistry, Faculty of Science, University of Jiroft, Jiroft, Iran
| | - Kamran Heydaryan
- Department of Medical Biochemical Analysis, Cihan University-Erbil, Kurdistan Region, Iraq
| | - Masoud Salavati-Niasari
- Institute of Nano Science and Nano Technology, University of Kashan, P.O. Box 87317-51167, Kashan, Iran
| | - Mahnaz Amiri
- Student Research Committee, Faculty of Allied Medicine, Kerman University of Medical Sciences, Kerman, Iran.
- Neuroscience Research Center, Institute of Neuropharmacology, Kerman University of Medical Science, Kerman, Iran.
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4
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LaBute B, Fong J, Ziaee F, Gombar R, Stover M, Beaudin T, Badalova M, Geng Q, Corchis-Scott R, Podadera A, Lago K, Xu Z, Lim F, Chiu F, Fu M, Nie X, Wu Y, Quan C, Hamm C, McKay RM, Ng K, Porter LA, Tong Y. Evaluating and optimizing Acid-pH and Direct Lysis RNA extraction for SARS-CoV-2 RNA detection in whole saliva. Sci Rep 2024; 14:7017. [PMID: 38527999 DOI: 10.1038/s41598-024-54183-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 02/09/2024] [Indexed: 03/27/2024] Open
Abstract
COVID-19 has been a global public health and economic challenge. Screening for the SARS-CoV-2 virus has been a key part of disease mitigation while the world continues to move forward, and lessons learned will benefit disease detection beyond COVID-19. Saliva specimen collection offers a less invasive, time- and cost-effective alternative to standard nasopharyngeal swabs. We optimized two different methods of saliva sample processing for RT-qPCR testing. Two methods were optimized to provide two cost-efficient ways to do testing for a minimum of four samples by pooling in a 2.0 mL tube and decrease the need for more highly trained personnel. Acid-pH-based RNA extraction method can be done without the need for expensive kits. Direct Lysis is a quick one-step reaction that can be applied quickly. Our optimized Acid-pH and Direct Lysis protocols are reliable and reproducible, detecting the beta-2 microglobulin (B2M) mRNA in saliva as an internal control from 97 to 96.7% of samples, respectively. The cycle threshold (Ct) values for B2M were significantly higher in the Direct Lysis protocol than in the Acid-pH protocol. The limit of detection for N1 gene was higher in Direct Lysis at ≤ 5 copies/μL than Acid-pH. Saliva samples collected over the course of several days from two COVID-positive individuals demonstrated Ct values for N1 that were consistently higher from Direct Lysis compared to Acid-pH. Collectively, this work supports that each of these techniques can be used to screen for SARS-CoV-2 in saliva for a cost-effective screening platform.
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Affiliation(s)
- Brayden LaBute
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
| | - Jackie Fong
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
- WE-SPARK Health Institute, University of Windsor, Windsor, ON, Canada
| | - Farinaz Ziaee
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - Robert Gombar
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
| | - Mathew Stover
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
| | - Terry Beaudin
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
| | - Maria Badalova
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada
| | - Qiudi Geng
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Ryland Corchis-Scott
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Ana Podadera
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
| | - Kyle Lago
- WE-SPARK Health Institute, University of Windsor, Windsor, ON, Canada
| | - ZhenHuan Xu
- Aumintec Research Inc., Richmond Hill, ON, Canada
| | - Fievel Lim
- Aumintec Research Inc., Richmond Hill, ON, Canada
| | - Felix Chiu
- Aumintec Research Inc., Richmond Hill, ON, Canada
| | - Minghua Fu
- Aumintec Research Inc., Richmond Hill, ON, Canada
| | - Xiaofeng Nie
- Aumintec Research Inc., Richmond Hill, ON, Canada
| | - Yuanmin Wu
- Aumintec Research Inc., Richmond Hill, ON, Canada
| | | | - Caroline Hamm
- WE-SPARK Health Institute, University of Windsor, Windsor, ON, Canada
- Windsor Regional Hospital, Windsor, ON, Canada
| | - R Michael McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, Canada
| | - Kenneth Ng
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada
- WE-SPARK Health Institute, University of Windsor, Windsor, ON, Canada
| | - Lisa A Porter
- Department of Biomedical Sciences, University of Windsor, Windsor, ON, Canada.
- WE-SPARK Health Institute, University of Windsor, Windsor, ON, Canada.
| | - Yufeng Tong
- Department of Chemistry and Biochemistry, University of Windsor, Windsor, ON, Canada.
- WE-SPARK Health Institute, University of Windsor, Windsor, ON, Canada.
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5
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Mansoori-Kermani A, Khalighi S, Akbarzadeh I, Niavol FR, Motasadizadeh H, Mahdieh A, Jahed V, Abdinezhad M, Rahbariasr N, Hosseini M, Ahmadkhani N, Panahi B, Fatahi Y, Mozafari M, Kumar AP, Mostafavi E. Engineered hyaluronic acid-decorated niosomal nanoparticles for controlled and targeted delivery of epirubicin to treat breast cancer. Mater Today Bio 2022; 16:100349. [PMID: 35875198 PMCID: PMC9304880 DOI: 10.1016/j.mtbio.2022.100349] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 06/17/2022] [Accepted: 07/01/2022] [Indexed: 12/24/2022] Open
Abstract
Targeted drug delivery systems using nanocarriers offer a versatile platform for breast cancer treatment; however, a robust, CD44-targeted niosomal formulation has not been developed and deeply studied (both in vitro and in vivo) yet. Here, an optimized system of epirubicin (Epi)-loaded niosomal nanoparticles (Nio) coated with hyaluronic acid (HA) has been engineered for targeting breast cancer cells. The nanoformulation was first optimized (based on size, polydispersity index, and entrapment efficiency); then, we characterized the morphology, stability, and release behavior of the nanoparticles. Epirubicin release from the HA-coated system (Epi-Nio-HA) showed a 21% (acidic buffer) and 20% (neutral buffer) reduction in comparison with the non-coated group (Epi-Nio). The cytotoxicity and apoptosis results of 4T1 and SkBr3 cells showed an approximately 2-fold increase in the Epi-Nio-HA system over Epi-Nio and free epirubicin, which confirms the superiority of the engineered nanocarriers. Moreover, real-time PCR data demonstrated the down-regulation of the MMP-2, MMP-9, cyclin D, and cyclin E genes expression while caspase-3 and caspase-9 gene expression were up-regulated. Confocal microscopy and flow cytometry studies uncovered the cellular uptake mechanism of the Epi-Nio-HA system, which was CD44-mediated. Furthermore, in vivo studies indicated Epi-Nio-HA decreased mice breast tumor volume by 28% (compared to epirubicin) without side effects on the liver and kidney. Conclusively, our results indicated that the HA-functionalized niosomes provide a promising nanoplatform for efficient and targeted delivery of epirubicin to potentially treat breast cancer.
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Affiliation(s)
| | - Sadaf Khalighi
- Department of Chemical and Petrochemical Engineering, Sharif University of Technology, Tehran, Iran
| | - Iman Akbarzadeh
- Department of Chemical and Petrochemical Engineering, Sharif University of Technology, Tehran, Iran
| | - Fazeleh Ranjbar Niavol
- Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Hamidreza Motasadizadeh
- Department of Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Nanotechnology Research Centre, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Athar Mahdieh
- Department of Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Vahid Jahed
- Rudolfs Cimdins Riga Biomaterials Innovations and Development Centre of RTU, Institute of General Chemical Engineering, Faculty of Materials Science and Applied Chemistry, Riga Technical University, Pulka St. 3/3, Riga, LV, 1007, Latvia
| | - Masoud Abdinezhad
- School of Chemical Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Nikoo Rahbariasr
- Polymer Research Laboratory, Department of Chemistry, Sharif University of Technology, Tehran, Iran
| | - Mahshid Hosseini
- Department of Chemical and Petrochemical Engineering, Sharif University of Technology, Tehran, Iran
| | - Nima Ahmadkhani
- Department of Chemical and Petrochemical Engineering, Sharif University of Technology, Tehran, Iran
| | - Behnam Panahi
- Department of Chemical and Petrochemical Engineering, Sharif University of Technology, Tehran, Iran
| | - Yousef Fatahi
- Department of Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
- Nanotechnology Research Centre, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Masoud Mozafari
- Department of Tissue Engineering and Regenerative Medicine, Faculty of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
- Corresponding author. Currently at: Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, University of Toronto, Toronto, ON, Canada.
| | - Alan Prem Kumar
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117600, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
- Corresponding author. Cancer Science Institute of Singapore and Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
| | - Ebrahim Mostafavi
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Corresponding author. Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, USA.
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6
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Ahmad E, Ali A, Nimisha, Kumar Sharma A, Ahmed F, Mehdi Dar G, Mohan Singh A, Apurva, Kumar A, Athar A, Parveen F, Mahajan B, Singh Saluja S. Molecular approaches in cancer. Clin Chim Acta 2022; 537:60-73. [DOI: https:/doi.org/10.1016/j.cca.2022.09.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
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7
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Ahmad E, Ali A, Nimisha, Kumar Sharma A, Ahmed F, Mehdi Dar G, Mohan Singh A, Apurva, Kumar A, Athar A, Parveen F, Mahajan B, Singh Saluja S. Molecular approaches in cancer. Clin Chim Acta 2022; 537:60-73. [DOI: 10.1016/j.cca.2022.09.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 09/28/2022] [Accepted: 09/28/2022] [Indexed: 11/03/2022]
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8
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Glucomannan as a Dietary Supplement for Treatment of Breast Cancer in a Mouse Model. Vaccines (Basel) 2022; 10:vaccines10101746. [PMID: 36298611 PMCID: PMC9608331 DOI: 10.3390/vaccines10101746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Revised: 10/16/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
Konjac glucomannan (KGM) is a water-soluble polysaccharide derived from the Amorphophallus’s tuber and, as herbal medicine has shown, can suppress tumor growth or improve health. However, there has been no investigation into the effects of KGM on breast tumor-bearing mice. Therefore, in two cohort experiments, we assessed the effect of glucomannan at daily doses of 2 and 4 mg for 28 days as a dietary supplement and also glucomannan in combination with tumor lysate vaccine as an adjuvant. Tumor volume was monitored twice weekly. In addition, TNF-α cytokines and granzyme B (Gr–B) release were measured with ELISA kits, and IL-2, IL-4, IL-17, and IFN-γ were used as an index for cytotoxic T lymphocyte activity. Moreover, TGF-β and Foxp3 gene expression were assessed in a real-time PCR test. The results show that glucomannan as a dietary supplement increased the IFN-γ cytokine and Th1 responses to suppress tumor growth. Glucomannan as a dietary supplement at the 4 mg dose increased the IL-4 cytokine response compared to control groups. In addition, cell lysate immunization with 2 or 4 mg of glucomannan suppressed tumor growth. As an adjuvant, glucomannan at both doses showed 41.53% and 52.10% tumor suppression compared with the PBS group. Furthermore, the administration of glucomannan as a dietary supplement or adjuvant reduced regulatory T cell response through decreasing TGF-β and Foxp3 gene expression in the tumor microenvironment. In conclusion, glucomannan as a dietary supplement or adjuvant enhanced the immune responses of tumor-bearing mice and decreased immune response suppression in the tumor milieu, making it a potentially excellent therapeutic agent for lowering breast tumor growth.
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9
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Pozo-Rodrigálvarez A, Li Y, Stokowska A, Wu J, Dehm V, Sourkova H, Steinbusch H, Mallard C, Hagberg H, Pekny M, Pekna M. C3a Receptor Signaling Inhibits Neurodegeneration Induced by Neonatal Hypoxic-Ischemic Brain Injury. Front Immunol 2022; 12:768198. [PMID: 34975856 PMCID: PMC8718687 DOI: 10.3389/fimmu.2021.768198] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/04/2021] [Indexed: 11/13/2022] Open
Abstract
Hypoxic-ischemic neonatal encephalopathy due to perinatal asphyxia is the leading cause of brain injury in newborns. Clinical data suggest that brain inflammation induced by perinatal insults can persist for years. We previously showed that signaling through the receptor for complement peptide C3a (C3aR) protects against cognitive impairment induced by experimental perinatal asphyxia. To investigate the long-term neuropathological effects of hypoxic-ischemic injury to the developing brain and the role of C3aR signaling therein, we subjected wildtype mice, C3aR deficient mice, and mice expressing biologically active C3a in the CNS to mild hypoxic-ischemic brain injury on postnatal day 9. We found that such injury triggers neurodegeneration and pronounced reactive gliosis in the ipsilesional hippocampus both of which persist long into adulthood. Transgenic expression of C3a in reactive astrocytes reduced hippocampal neurodegeneration and reactive gliosis. In contrast, neurodegeneration and microglial cell density increased in mice lacking C3aR. Intranasal administration of C3a for 3 days starting 1 h after induction of hypoxia-ischemia reduced neurodegeneration and reactive gliosis in the hippocampus of wildtype mice. We conclude that neonatal hypoxic-ischemic brain injury leads to long-lasting neurodegeneration. This neurodegeneration is substantially reduced by treatment with C3aR agonists, conceivably through modulation of reactive gliosis.
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Affiliation(s)
- Andrea Pozo-Rodrigálvarez
- Laboratory of Regenerative Neuroimmunology, Center for Brain Repair, Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - YiXian Li
- Laboratory of Regenerative Neuroimmunology, Center for Brain Repair, Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Anna Stokowska
- Laboratory of Regenerative Neuroimmunology, Center for Brain Repair, Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Jingyun Wu
- Laboratory of Regenerative Neuroimmunology, Center for Brain Repair, Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden.,Laboratory of Astrocyte Biology and CNS Regeneration, Center for Brain Repair, Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Verena Dehm
- Laboratory of Regenerative Neuroimmunology, Center for Brain Repair, Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Hana Sourkova
- Laboratory of Astrocyte Biology and CNS Regeneration, Center for Brain Repair, Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Harry Steinbusch
- Department of Neuroscience, Faculty of Health, Medicine and Life Sciences, Maastricht University, Maastrich, Netherlands.,Department of Brain & Cognitive Sciences, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, South Korea
| | - Carina Mallard
- Centre of Perinatal Medicine & Health, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Henrik Hagberg
- Centre of Perinatal Medicine & Health, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Centre for the Developing Brain, King's College, London, United Kingdom
| | - Milos Pekny
- Laboratory of Astrocyte Biology and CNS Regeneration, Center for Brain Repair, Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Marcela Pekna
- Laboratory of Regenerative Neuroimmunology, Center for Brain Repair, Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
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10
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Agrahari S, Kumar Gautam R, Kumar Singh A, Tiwari I. Nanoscale materials-based hybrid frameworks modified electrochemical biosensors for early cancer diagnostics: An overview of current trends and challenges. Microchem J 2022. [DOI: 10.1016/j.microc.2021.106980] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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11
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Caballero-López V, Lundberg M, Sokolovskis K, Bensch S. Transposable elements mark a repeat-rich region associated with migratory phenotypes of willow warblers (Phylloscopus trochilus). Mol Ecol 2021; 31:1128-1141. [PMID: 34837428 DOI: 10.1111/mec.16292] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 10/26/2021] [Accepted: 11/16/2021] [Indexed: 11/30/2022]
Abstract
The genetic basis of bird migration has been the focus of several studies. Two willow warbler subspecies (Phylloscopus trochilus trochilus and Phylloscopus trochilus acredula) follow different migratory routes to wintering grounds in Africa. Their breeding populations overlap in contact areas or "migratory divides" located in central Scandinavia and in eastern Poland. Earlier analyses demonstrated that the genetic differences between these two migratory phenotypes are few and cluster on chromosomes 1 and 5. In addition, an amplified fragment length polymorphism-derived biallelic marker (known as WW2) presents steep clines across both migratory divides but failed to be mapped in the genome. Here, we characterize the WW2 marker and describe its two variants (WW2 ancestral and WW2 derived) as portions of long terminal repeat retrotransposons originating from an ancient infection by an endogenous retrovirus. We used quantitative polymerase chain reaction techniques to quantify copy numbers of the WW2 derived variant in the two subspecies and their hybrids. This, together with genome analyses revealed that WW2 derived variants are much more abundant in P. t. acredula and appear embedded in a large repeat-rich region (>12 Mbp), not associated with the divergent regions of chromosomes 1 or 5. However, it might interact with genetic elements controlling migration direction. Testing this hypothesis further will require knowing the exact location of this region, such as by obtaining more complete genome assemblies preferably in combination with techniques like fluorescence in situ hybridization applied to a willow warbler karyotype, and finally to investigate the copy number of this marker in hybrids with known migratory tracks.
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Affiliation(s)
| | - Max Lundberg
- Department of Biology, Lund University, Lund, Sweden
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12
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Khisroon M, Khan A, Ayub A, Ullah I, Farooqi J, Ullah A. DNA damage analysis concerning GSTM1 and GSTT1 gene polymorphism in gold jewellery workers from Peshawar Pakistan. Biomarkers 2020; 25:483-489. [PMID: 32615823 DOI: 10.1080/1354750x.2020.1791253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
PURPOSE To evaluate the genotoxic effects of gold jewellery fumes and its association with GSTM1 and GSTT1 genetic polymorphisms. MATERIALS AND METHODS We examined 94 subjects including 54 gold jewellery workers and 40 controls. The DNA damage was evaluated by alkaline comet assay and genotyping by PCR. RESULTS The mean total comet score (TCS) in gold jewellery workers was significantly higher as compared to the control subjects (128.0 ± 60.6 versus 47.7 ± 21.4; p = 0.0001). Duration of occupational exposure had positive correlation (r = 0.453, p < 0.01) with DNA damage. Age and tobacco use had significant effects on the TCS of the exposed group as compared to the control group (p < 0.05). The frequency of the GSTM1-null genotype in the exposed group was significant (p = 0.004) as compared to the control group. No significant association (p > 0.05) between the GSTM1 and GSTT1 genotypes and DNA damage was found. CONCLUSIONS Our results suggest that there is increased DNA damage in gold jewellery workers due to their occupational surroundings. Hence there is a strong need to educate the workers about the adverse health effects of potentially hazardous chemicals and highlight the importance of using protective measures.
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Affiliation(s)
| | - Ajmal Khan
- Department of Zoology, University of Peshawar, Peshawar, Pakistan
| | - Asma Ayub
- Department of Zoology, University of Peshawar, Peshawar, Pakistan
| | - Ihsan Ullah
- Department of Pharmacology, Poonch Medical College Rawalakot, Rawalakot, Pakistan
| | - Javeed Farooqi
- Department of Zoology, University of Peshawar, Peshawar, Pakistan
| | - Abid Ullah
- Department of Zoology, University of Peshawar, Peshawar, Pakistan
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13
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Optimized doxycycline-loaded niosomal formulation for treatment of infection-associated prostate cancer: An in-vitro investigation. J Drug Deliv Sci Technol 2020. [DOI: 10.1016/j.jddst.2020.101715] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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14
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Multiplexed and Sensitive DNA Methylation Testing Using Methylation-Sensitive Restriction Enzymes "MSRE-qPCR". Methods Mol Biol 2018; 1708:407-424. [PMID: 29224156 DOI: 10.1007/978-1-4939-7481-8_21] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
DNA methylation is a chemically stable key-player in epigenetics. In the vertebrate genome the 5-methyl cytosine (5mC) has been found almost exclusively in the CpG dinucleotide context. CpG dinucleotides are enriched in CpG islands very frequently located within or close to gene promoters. Analyses of DNA methylation changes in human diagnostics have been conducted classically using methylation-sensitive restriction enzymes (MSRE). Since the discovery of bisulfite conversion-based sequencing and PCR assays, MSRE-based PCR assays have been less frequently used, although especially in the field of cancer epigenetics MSRE-based genome-wide discovery and targeted screening applications have been and are still performed successfully. Even though epigenome-wide discovery of altered DNA methylation patterns has found its way into various fields of human disease and molecular genetics research, the validation of findings upon discovery is still a bottleneck. Usually several multiples of 10 up to 100 candidate biomarkers from discovery have to be confirmed or are of interest for further work. In particular, bisulfite PCR assays are often limited in the number of candidates which can be analyzed, due to their low multiplexing capability, especially, if only small amounts of DNA are available from for example clinical specimens. In clinical research and diagnostics a similar situation arises for the analyses of cell-free DNA (cfDNA) in body fluids or circulating tumor cells (CTCs). Although tissue- or disease- (e.g., cancer) specific DNA methylation patterns can be deduced very efficiently in a genome-wide manner if around 100 ng of DNA are available, confirming these candidates and selecting target-sequences for studying methylation changes in liquid biopsies using cfDNA or CTCs remains a big challenge. Along these lines we have developed MSRE-qPCR and introduce here method details, which have been found very suitable for the efficient confirmation and testing of DNA methylation in a quantitative multiplexed manner (e.g., 48-96 plex) from ng amounts of DNA. The method is applicable in a standard qPCR setting as well for nanoliter scaled high-throughput qPCR, enabling detection of <10 copies of targets, thus suitable to pick up 0.1-1% of specific methylated DNA in an unmethylated background.
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15
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Kim HY, Li T, Jung C, Fu R, Cho DY, Park KS, Park HG. Universally applicable, quantitative PCR method utilizing fluorescent nucleobase analogs. RSC Adv 2018; 8:37391-37395. [PMID: 35557795 PMCID: PMC9089284 DOI: 10.1039/c8ra06675b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 10/28/2018] [Indexed: 11/21/2022] Open
Abstract
We herein describe a novel quantitative PCR (qPCR) method, which operates in both signal-off and on manners, by utilizing a unique property of fluorescent nucleobase analogs. The first, signal-off method is developed by designing the primers to contain pyrrolo-dC (PdC), one of the most common fluorescent nucleobase analogs. The specially designed single-stranded primer is extended to form double-stranded DNA during PCR and the fluorescence signal from the PdCs incorporated in the primer is accordingly reduced due to its conformation-dependent fluorescence properties. In addition, the second, signal-on method is devised by designing the primers to contain 5′-overhang sequences complementary to the PdC-incorporated DNA probes. At the initial phase, the PdC-incorporated DNA probes are hybridized to the 5′-overhang sequences of the primer, exhibiting the significantly quenched fluorescence signal, but are detached by either hydrolysis or strand displacement reaction during PCR, leading to the highly enhanced fluorescence signal. This method is more advanced than the first one since it produces signal-on fluorescence response and permits the use of a single PdC-incorporated DNA probe for the detection of multiple target nucleic acids, remarkably decreasing the assay cost. With these novel qPCR methods, we successfully quantified target nucleic acids derived from sexually transmitted disease (STD) pathogens with high accuracy. Importantly, the proposed strategies overcome the major drawbacks in the current SYBR Green and TaqMan probe-based qPCR methods such as low specificity and high assay cost. A novel quantitative PCR (qPCR) method was developed by utilizing a unique property of fluorescent nucleobase analogs (PdCs).![]()
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Affiliation(s)
- Hyo Yong Kim
- Department of Chemical and Biomolecular Engineering (BK21 Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Taihua Li
- College of Biology and the Environment
- Co-Innovation Centre for Sustainable Forestry in Southern China
- Nanjing Forestry University
- Nanjing
- China
| | - Cheulhee Jung
- Department of Chemical and Biomolecular Engineering (BK21 Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Rongzhan Fu
- Department of Chemical and Biomolecular Engineering (BK21 Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
| | - Dae-Yeon Cho
- Labgenomics Clinical Research Institute
- Labgenomics Co. Ltd
- Yong-In
- Republic of Korea
| | - Ki Soo Park
- Department of Biological Engineering
- College of Engineering
- Konkuk University
- Seoul 05029
- Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK21 Program)
- KAIST
- Daejeon 305-701
- Republic of Korea
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16
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Sapiezynski J, Taratula O, Rodriguez-Rodriguez L, Minko T. Precision targeted therapy of ovarian cancer. J Control Release 2016; 243:250-268. [PMID: 27746277 DOI: 10.1016/j.jconrel.2016.10.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 10/09/2016] [Accepted: 10/12/2016] [Indexed: 10/20/2022]
Abstract
The review is aimed at describing modern approaches to detection as well as precision and personalized treatment of ovarian cancer. Modern methods and future directions of nanotechnology-based targeted and personalized therapy are discussed.
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Affiliation(s)
- Justin Sapiezynski
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States
| | - Oleh Taratula
- Department of Pharmaceutical Sciences, Oregon State University, Portland, OR 97239, United States
| | - Lorna Rodriguez-Rodriguez
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, United States; Department of Obstetrics and Gynecology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, United States
| | - Tamara Minko
- Department of Pharmaceutics, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, United States; Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, United States.
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17
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Hashemi SH, Nematzadeh G, Ahmadian G, Yamchi A, Kuhlmann M. Identification and validation of Aeluropus littoralis reference genes for Quantitative Real-Time PCR Normalization. ACTA ACUST UNITED AC 2016; 23:18. [PMID: 27437194 PMCID: PMC4950632 DOI: 10.1186/s40709-016-0053-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Accepted: 06/28/2016] [Indexed: 11/12/2022]
Abstract
Background The use of stably expressed genes as normalizers has crucial role in accurate and reliable expression analysis estimated by quantitative real-time polymerase chain reaction (qPCR). Recent studies have shown that, the expression levels of common housekeeping genes are varying in different tissues and experimental conditions. The genomic DNA contamination in RNA samples is another important factor that also influence the interpretation of the data obtained from qPCR. It is estimated that the gDNA contamination in gene expression analysis lead to an overestimation of the RNA transcript level. The aim of this study was to validate the most stably expressed reference genes in two different tissues of Aeluropus littoralis—halophyte grass at salt stress and recovery condition. Also, a qPCR-based approach for monitoring contamination with gDNA was conducted. Results Ten candidate reference genes participating in different biological processes were analyzed in four groups of samples including root and leaf tissues, salt stress and recovery condition. To determine the most stably expressed reference genes, three statistical methods (geNorm, NormFinder and BestKeeper) were applied. According to results obtained, ten candidate reference genes were ranked based on the stability of their expression. Here, our results show that a set of four housekeeping genes (HKGs) e.g. RPS3, EF1A, GTF and RPS12 could be used as general reference genes for the all selected conditions and tissues. Also, four set of reference genes were proposed for each tissue and condition including: RPS3, EF1A and UBQ for salt stress and root samples; RPS3, EF1A, UBQ as well as GAPDH for recovery condition; U2SURP and GTF for leaf samples. Additionally, for assessing DNA contamination in RNA samples, a set of unique primers were designed based on the conserved region of ribosomal DNA (rDNA). The universality, specificity and sensitivity of these primer pairs were also evaluated in Poaceae. Conclusions Overall, the sets of reference genes proposed in this study are ideal normalizers for qPCR analysis in A.littoralis transcriptome. The novel reference gene e.g. RPS3 that applied this study had higher expression stability than commonly used housekeeping genes. The application of rDNA-based primers in qPCR analysis was addressed. Electronic supplementary material The online version of this article (doi:10.1186/s40709-016-0053-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Seyyed Hamidreza Hashemi
- Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University, PO Box 578, Sari, Iran
| | - Ghorbanali Nematzadeh
- Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari Agricultural Sciences and Natural Resources University, PO Box 578, Sari, Iran
| | - Gholamreza Ahmadian
- National Institute of Genetics Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Ahad Yamchi
- Department of Plant Breeding and Biotechnology, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran
| | - Markus Kuhlmann
- Research Group Abiotic Stress Genomics, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), OT Gatersleben Corrensstraße 3, 06466 Stadt Seeland, Germany
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18
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Mohamed OI, El-Nahas AF, El-Sayed YS, Ashry KM. Ginger extract modulates Pb-induced hepatic oxidative stress and expression of antioxidant gene transcripts in rat liver. PHARMACEUTICAL BIOLOGY 2016; 54:1164-72. [PMID: 26079851 DOI: 10.3109/13880209.2015.1057651] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
CONTEXT Spices and herbs are recognized sources of natural antioxidants that can protect from oxidative stress, thus play an important role in chemoprevention of liver diseases. Ginger is used worldwide primarily as a spicy condiment. OBJECTIVE This study evaluated the ability of ginger extract (GE) to ameliorate oxidative-hepatic toxicity induced by lead acetate (PbAc) in rats. MATERIALS AND METHODS Five groups of animals were used: group I kept as control; groups II, IV, and V received PbAc (1 ppm in drinking water daily for 6 weeks, and kept for an additional 2 weeks without PbAc exposure); group III treated orally with GE (350 mg/kg body weight, 4 d per week) for 6 weeks; group IV (protective) received GE for 2 weeks before and simultaneously with PbAc; and group V (treatment) received GE for 2 weeks after PbAc exposure. RESULTS GC-MS analysis of GE revealed its content of gingerol (7.09%), quercetin (3.20%), dl-limonene (0.96%), and zingiberene (0.18%). Treatment of PbAc-treated rats with GE has no effect on hepatic Pb concentrations. However, it maintained serum aspartate aminotransferase level, increased hepatic glutathione (157%), glutathione S-transferase (GST) (228%), glutathione peroxidase (GPx) (138%) and catalase (CAT) (112%) levels, and reduced hepatic malondialdehyde (80%). Co-treatment of PbAc group with GE upregulated mRNA expression of antioxidant genes: GST-α1 (1.4-fold), GPx1 (1.8-fold), and CAT (8-fold), while post-treatment with GE upregulated only mRNA expression of GPx1 (1.5-fold). CONCLUSION GE has an antioxidant protective efficacy against PbAc-induced hepatotoxicity, which appears more effective than its therapeutic application. However, the changes in antioxidant gene expression were not reflected at the protein level.
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Affiliation(s)
| | - Abeer Fekry El-Nahas
- b Department of Animal Husbandry and Animal Wealth Development, Faculty of Veterinary Medicine , Alexandria University , Edfina , Egypt , and
| | - Yasser Said El-Sayed
- c Department of Veterinary Forensic Medicine and Toxicology, Faculty of Veterinary Medicine , Damanhour University , Damanhour , Egypt
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19
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Liu CT, Xin Y, Tong CY, Li B, Bao HL, Zhang CY, Wang XH. Production of interleukin‑4 in CD133+ cervical cancer stem cells promotes resistance to apoptosis and initiates tumor growth. Mol Med Rep 2016; 13:5068-76. [PMID: 27121303 PMCID: PMC4878543 DOI: 10.3892/mmr.2016.5195] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 12/21/2015] [Indexed: 12/14/2022] Open
Abstract
The cancer stem cell (CSC) theory suggests that cancer growth and invasion is dictated by the small population of CSCs within the heterogenous tumor. The aim of the present study was to elucidate the cause for chemotherapy failure and the resistance of CSCs to apoptosis. A total of ~2.3% cluster of differentiation (CD)133+ cancer stem-like side population (SP) cells were identified in cases of uterine cervical cancer. These CD133+ SP cells were found to potently initiate tumor growth and invasion, as they exhibit transcriptional upregulation of stemness genes, including octamer-binding transcription factor-4, B-cell-specific Moloney murine leukemia virus insertion site-1, epithelial cell adhesion molecule, (sex determining region Y)-box 2, Nestin and anti-apoptotic B cell lymphoma-2. In addition, the CD133+ SP cells showed resistance to multi-drug treatment and apoptosis. The present study further showed that the secretion of interleukin-4 (IL-4) in CD133+ cervical cancer SP cells promoted cell proliferation and prevented the SP cells from apoptosis. Following the neutralization of IL-4 with anti-IL-4 antibody, the CD133+ SP cells were more sensitive to drug treatment and apoptosis. Therefore, the data obtained in the present study suggested that the autocrine secretion of IL-4 promotes increased survival and resistance to cell death in CSCs.
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Affiliation(s)
- Chun-Tao Liu
- Department of Gynecology, The Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning 116001, P.R. China
| | - Ying Xin
- Department of Gynecology, The Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning 116001, P.R. China
| | - Chun-Yan Tong
- Department of Gynecology, The Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning 116001, P.R. China
| | - Bing Li
- Department of Gynecology, The Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning 116001, P.R. China
| | - Hong-Li Bao
- Department of Gynecology, The Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning 116001, P.R. China
| | - Cai-Yun Zhang
- Department of Gynecology, The Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning 116001, P.R. China
| | - Xue-Hui Wang
- Department of Gynecology, The Affiliated Zhongshan Hospital of Dalian University, Dalian, Liaoning 116001, P.R. China
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20
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Kaur A, Elzagheid A, Birkman EM, Avoranta T, Kytölä V, Korkeila E, Syrjänen K, Westermarck J, Sundström J. Protein phosphatase methylesterase-1 (PME-1) expression predicts a favorable clinical outcome in colorectal cancer. Cancer Med 2015; 4:1798-808. [PMID: 26377365 PMCID: PMC5123709 DOI: 10.1002/cam4.541] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 08/19/2015] [Accepted: 08/20/2015] [Indexed: 12/25/2022] Open
Abstract
Colorectal cancer (CRC) accounts for high mortality. So far, there is lack of markers capable of predicting which patients are at risk of aggressive course of the disease. Protein phosphatase-2A (PP2A) inhibitor proteins have recently gained interest as markers of more aggressive disease in certain cancers. Here, we report the role of PP2A inhibitor PME-1 in CRC. PME-1 expression was assessed from a rectal cancer patient cohort by immunohistochemistry, and correlations were performed for various clinicopathological variables and patient survival. Rectal cancer patients with higher cytoplasmic PME-1 protein expression (above median) had less recurrences (P = 0.003, n = 195) and better disease-free survival (DFS) than the patients with low cytoplasmic PME-1 protein expression (below median). Analysis of PPME-1 mRNA expression from TCGA dataset of colon and rectal adenocarcinoma (COADREAD) patient cohort confirmed high PPME1 expression as an independent protective factor predicting favorable overall survival (OS) (P = 0.005, n = 396) compared to patients with low PPME1 expression. CRC cell lines were used to study the effect of PME-1 knockdown by siRNA on cell survival. Contrary to other cancer types, PME-1 inhibition in CRC cell lines did not reduce the viability of cells or the expression of active phosphorylated AKT and ERK proteins. In conclusion, PME-1 expression predicts for a favorable outcome of CRC patients. The unexpected role of PME-1 in CRC in contrast with the oncogenic role of PP2A inhibitor proteins in other malignancies warrants further studies of cancer-specific function for each of these proteins.
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Affiliation(s)
- Amanpreet Kaur
- Department of Pathology, University of Turku, Turku, 20520, Finland.,Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, 20520, Finland.,TuBS and TuDMM Doctoral Programmes, Turku, 20520, Finland
| | - Adam Elzagheid
- Department of Pathology, University of Turku, Turku, 20520, Finland.,Department of Pathology, Faculty of Medicine, Benghazi University, PO Box 1308, Benghazi, Libya.,Biotechnology Research Center, Tripoli, Libya
| | | | - Tuulia Avoranta
- Department of Pathology, University of Turku, Turku, 20520, Finland.,Department of Oncology and Radiotherapy, University of Turku and Turku University Hospital, Turku, 20521, Finland.,Department of Social Services and Healthcare, City of Helsinki, Helsinki, 00099, Finland
| | - Ville Kytölä
- BioMediTech, University of Tampere, Tampere, 33520, Finland
| | - Eija Korkeila
- Department of Oncology and Radiotherapy, University of Turku and Turku University Hospital, Turku, 20521, Finland
| | - Kari Syrjänen
- Department of Clinical Research, Biohit Oyj, Helsinki, 00880, Finland.,Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, 14784-400, Brazil
| | - Jukka Westermarck
- Department of Pathology, University of Turku, Turku, 20520, Finland.,Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, 20520, Finland
| | - Jari Sundström
- Department of Pathology, University of Turku, Turku, 20520, Finland
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21
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Ludvigsen J, Rangberg A, Avershina E, Sekelja M, Kreibich C, Amdam G, Rudi K. Shifts in the Midgut/Pyloric Microbiota Composition within a Honey Bee Apiary throughout a Season. Microbes Environ 2015; 30:235-44. [PMID: 26330094 PMCID: PMC4567562 DOI: 10.1264/jsme2.me15019] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Honey bees (Apis mellifera) are prominent crop pollinators and are, thus, important for effective food production. The honey bee gut microbiota is mainly host specific, with only a few species being shared with other insects. It currently remains unclear how environmental/dietary conditions affect the microbiota within a honey bee population over time. Therefore, the aim of the present study was to characterize the composition of the midgut/pyloric microbiota of a honey bee apiary throughout a season. The rationale for investigating the midgut/pyloric microbiota is its dynamic nature. Monthly sampling of a demographic homogenous population of bees was performed between May and October, with concordant recording of the honey bee diet. Mixed Sanger-and Illumina 16S rRNA gene sequencing in combination with a quantitative PCR analysis were used to determine the bacterial composition. A marked increase in α-diversity was detected between May and June. Furthermore, we found that four distinct phylotypes belonging to the Proteobacteria dominated the microbiota, and these displayed major shifts throughout the season. Gilliamella apicola dominated the composition early on, and Snodgrassella alvi began to dominate when the other bacteria declined to an absolute low in October. In vitro co-culturing revealed that G. apicola suppressed S. alvi. No shift was detected in the composition of the microbiota under stable environment/dietary conditions between November and February. Therefore, environmental/dietary changes may trigger the shifts observed in the honey bee midgut/pyloric microbiota throughout a season.
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Affiliation(s)
- Jane Ludvigsen
- Norwegian University of Life Sciences, Chemistry, Biotechnology and Food science department
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22
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PEKNY T, ANDERSSON D, WILHELMSSON U, PEKNA M, PEKNY M. Short general anaesthesia induces prolonged changes in gene expression in the mouse hippocampus. Acta Anaesthesiol Scand 2014; 58:1127-33. [PMID: 25039928 DOI: 10.1111/aas.12369] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/12/2014] [Indexed: 02/07/2023]
Abstract
BACKGROUND The long-term molecular changes in the central nervous system constitute an important aspect of general anaesthesia, but little is known about to what extent these molecular changes are affected by anaesthesia duration. The aim of the present study was to evaluate the effects of short duration (20 min) general anaesthesia with isoflurane or avertin on the expression of 20 selected genes in the mouse hippocampus at 1 and 4 days after anaesthesia. METHODS Nine to eleven-weeks-old male mice received one of the following treatments: 20 min of avertin-induced anaesthesia (n=11), 20 min of isoflurane-induced anaesthesia (n=10) and no anaesthesia (n=5). One and four days after anaesthesia, gene expression in the hippocampus was determined with reverse transcription quantitative real-time polymerase chain reaction. RESULTS We found that anaesthesia led to the upregulation of six genes: Hspd1 (heat shock protein 1), Plat (tissue plasminogen activator) and Npr3 (natriuretic peptide receptor 3) were upregulated only 1 day after anaesthesia, whereas Thbs4 (thrombospondin 4) was upregulated only 4 days after anaesthesia. Syp (synaptophysin) and Mgst1 (microsomal glutathione S-transferase 1) were upregulated at both time points. Hspd1, Mgst1 and Syp expression was increased regardless of the anaesthetic used, Npr3 and Plat were increased only in mice exposed to avertin, and Thbs4 was upregulated only after isoflurane-induced anaesthesia. CONCLUSIONS This study shows that some of the effects of short general anaesthesia on gene expression in the mouse hippocampus persist for at least 4 days.
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Affiliation(s)
- T. PEKNY
- Center for Brain Repair and Rehabilitation; Department of Clinical Neuroscience and Rehabilitation; Institute of Neuroscience and Physiology; Sahlgrenska Academy; University of Gothenburg; Gothenburg Sweden
| | - D. ANDERSSON
- Center for Brain Repair and Rehabilitation; Department of Clinical Neuroscience and Rehabilitation; Institute of Neuroscience and Physiology; Sahlgrenska Academy; University of Gothenburg; Gothenburg Sweden
| | - U. WILHELMSSON
- Center for Brain Repair and Rehabilitation; Department of Clinical Neuroscience and Rehabilitation; Institute of Neuroscience and Physiology; Sahlgrenska Academy; University of Gothenburg; Gothenburg Sweden
| | - M. PEKNA
- Center for Brain Repair and Rehabilitation; Department of Clinical Neuroscience and Rehabilitation; Institute of Neuroscience and Physiology; Sahlgrenska Academy; University of Gothenburg; Gothenburg Sweden
- Florey Institute of Neuroscience and Mental Health; Parkville Victoria Australia
| | - M. PEKNY
- Center for Brain Repair and Rehabilitation; Department of Clinical Neuroscience and Rehabilitation; Institute of Neuroscience and Physiology; Sahlgrenska Academy; University of Gothenburg; Gothenburg Sweden
- Florey Institute of Neuroscience and Mental Health; Parkville Victoria Australia
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23
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Pabinger S, Rödiger S, Kriegner A, Vierlinger K, Weinhäusel A. A survey of tools for the analysis of quantitative PCR (qPCR) data. BIOMOLECULAR DETECTION AND QUANTIFICATION 2014; 1:23-33. [PMID: 27920994 PMCID: PMC5129434 DOI: 10.1016/j.bdq.2014.08.002] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 08/26/2014] [Accepted: 08/26/2014] [Indexed: 01/12/2023]
Abstract
Real-time quantitative polymerase-chain-reaction (qPCR) is a standard technique in most laboratories used for various applications in basic research. Analysis of qPCR data is a crucial part of the entire experiment, which has led to the development of a plethora of methods. The released tools either cover specific parts of the workflow or provide complete analysis solutions. Here, we surveyed 27 open-access software packages and tools for the analysis of qPCR data. The survey includes 8 Microsoft Windows, 5 web-based, 9 R-based and 5 tools from other platforms. Reviewed packages and tools support the analysis of different qPCR applications, such as RNA quantification, DNA methylation, genotyping, identification of copy number variations, and digital PCR. We report an overview of the functionality, features and specific requirements of the individual software tools, such as data exchange formats, availability of a graphical user interface, included procedures for graphical data presentation, and offered statistical methods. In addition, we provide an overview about quantification strategies, and report various applications of qPCR. Our comprehensive survey showed that most tools use their own file format and only a fraction of the currently existing tools support the standardized data exchange format RDML. To allow a more streamlined and comparable analysis of qPCR data, more vendors and tools need to adapt the standardized format to encourage the exchange of data between instrument software, analysis tools, and researchers.
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Affiliation(s)
- Stephan Pabinger
- Health & Environment Department, Molecular Diagnostics, AIT - Austrian Institute of Technology, Muthgasse 11, 1190 Vienna, Austria
| | - Stefan Rödiger
- Faculty of Natural Sciences, InnoProfile Group "Image-based Assays", Brandenburg University of Technology Cottbus - Senftenberg, Großenhainer Straße 57, 01968 Senftenberg, Germany
| | - Albert Kriegner
- Health & Environment Department, Molecular Diagnostics, AIT - Austrian Institute of Technology, Muthgasse 11, 1190 Vienna, Austria
| | - Klemens Vierlinger
- Health & Environment Department, Molecular Diagnostics, AIT - Austrian Institute of Technology, Muthgasse 11, 1190 Vienna, Austria
| | - Andreas Weinhäusel
- Health & Environment Department, Molecular Diagnostics, AIT - Austrian Institute of Technology, Muthgasse 11, 1190 Vienna, Austria
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24
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Petersen MH, Budtz-Jørgensen E, Sørensen SA, Nielsen JE, Hjermind LE, Vinther-Jensen T, Nielsen SMB, Nørremølle A. Reduction in mitochondrial DNA copy number in peripheral leukocytes after onset of Huntington's disease. Mitochondrion 2014; 17:14-21. [PMID: 24836434 DOI: 10.1016/j.mito.2014.05.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 04/03/2014] [Accepted: 05/06/2014] [Indexed: 01/14/2023]
Abstract
Huntington's disease (HD) is an inherited neurodegenerative disorder characterised by movement disorder, cognitive symptoms and psychiatric symptoms with predominantly adult-onset. The mutant huntingtin protein leads to mitochondrial dysfunction in blood leukocytes. This discovery led to the investigation of the mitochondrial DNA (mtDNA) copy number relative to nuclear DNA (nDNA) in leukocytes from carriers of the HD mutation compared to healthy individuals. We found significantly reduced mtDNA/nDNA in HD mutation carriers compared to controls. A longitudinal study of archive DNA sample pairs from HD patients revealed a biphasic pattern of increasing mtDNA/nDNA before onset of motor symptoms and decreasing mtDNA/nDNA after.
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Affiliation(s)
- Maria Hvidberg Petersen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Esben Budtz-Jørgensen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Sven Asger Sørensen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Jørgen Erik Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark; Neurogenetics Clinic, Danish Dementia Research Centre, Department of Neurology, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, DK-2100 Copenhagen Ø, Denmark
| | - Lena Elisabeth Hjermind
- Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark; Neurogenetics Clinic, Danish Dementia Research Centre, Department of Neurology, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, DK-2100 Copenhagen Ø, Denmark
| | - Tua Vinther-Jensen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark; Neurogenetics Clinic, Danish Dementia Research Centre, Department of Neurology, Rigshospitalet, University of Copenhagen, Blegdamsvej 9, DK-2100 Copenhagen Ø, Denmark
| | - Signe Marie Borch Nielsen
- Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Anne Nørremølle
- Department of Cellular and Molecular Medicine, University of Copenhagen, Panum Institute, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark.
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Bossmann SH, Troyer DL. Point-of-care routine rapid screening: the future of cancer diagnosis? Expert Rev Mol Diagn 2014; 13:107-9. [DOI: 10.1586/erm.13.3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Andersson D, Wilhelmsson U, Nilsson M, Kubista M, Ståhlberg A, Pekna M, Pekny M. Plasticity response in the contralesional hemisphere after subtle neurotrauma: gene expression profiling after partial deafferentation of the hippocampus. PLoS One 2013; 8:e70699. [PMID: 23936241 PMCID: PMC3723880 DOI: 10.1371/journal.pone.0070699] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Accepted: 05/23/2013] [Indexed: 11/19/2022] Open
Abstract
Neurotrauma or focal brain ischemia are known to trigger molecular and structural responses in the uninjured hemisphere. These responses may have implications for tissue repair processes as well as for the recovery of function. To determine whether the plasticity response in the uninjured hemisphere occurs even after a subtle trauma, we subjected mice to a partial unilateral deafferentation of the hippocampus induced by stereotactically performed entorhinal cortex lesion (ECL). The expression of selected genes was assessed by quantitative real-time PCR in the hippocampal tissue at the injured side and the contralesional side at day 4 and 14 after injury. We observed that expression of genes coding for synaptotagmin 1, ezrin, thrombospondin 4, and C1q proteins, that have all been implicated in the synapse formation, re-arrangement and plasticity, were upregulated both in the injured and the contralesional hippocampus, implying a plasticity response in the uninjured hemisphere. Several of the genes, the expression of which was altered in response to ECL, are known to be expressed in astrocytes. To test whether astrocyte activation plays a role in the observed plasticity response to ECL, we took advantage of mice deficient in two intermediate filament (nanofilament) proteins glial fibrillary acidic protein (GFAP) and vimentin (GFAP(-/-)Vim(-/-) ) and exhibiting attenuated astrocyte activation and reactive gliosis. The absence of GFAP and vimentin reduced the ECL-induced upregulation of thrombospondin 4, indicating that this response to ECL depends on astrocyte activation and reactive gliosis. We conclude that even a very limited focal neurotrauma triggers a distinct response at the contralesional side, which at least to some extent depends on astrocyte activation.
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Affiliation(s)
- Daniel Andersson
- Center for Brain Repair and Rehabilitation, Department of Clinical Neuroscience and Rehabilitation, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Ulrika Wilhelmsson
- Center for Brain Repair and Rehabilitation, Department of Clinical Neuroscience and Rehabilitation, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Michael Nilsson
- Center for Brain Repair and Rehabilitation, Department of Clinical Neuroscience and Rehabilitation, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Hunter Medical Research Institute, Newcastle, Australia
| | - Mikael Kubista
- Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague, Czech Republic; and TATAA Biocenter, Gothenburg, Sweden
| | - Anders Ståhlberg
- Center for Brain Repair and Rehabilitation, Department of Clinical Neuroscience and Rehabilitation, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- Department of Pathology, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Marcela Pekna
- Center for Brain Repair and Rehabilitation, Department of Clinical Neuroscience and Rehabilitation, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Milos Pekny
- Center for Brain Repair and Rehabilitation, Department of Clinical Neuroscience and Rehabilitation, Institute of Neuroscience and Physiology, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
- * E-mail:
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Järlestedt K, Rousset CI, Ståhlberg A, Sourkova H, Atkins AL, Thornton C, Barnum SR, Wetsel RA, Dragunow M, Pekny M, Mallard C, Hagberg H, Pekna M. Receptor for complement peptide C3a: a therapeutic target for neonatal hypoxic‐ischemic brain injury. FASEB J 2013; 27:3797-804. [DOI: 10.1096/fj.13-230011] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | | | - Anders Ståhlberg
- Center for Brain Repair and RehabilitationDepartment of Clinical Neuroscience and RehabilitationInstitute of Neuroscience and PhysiologySahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Hana Sourkova
- Center for Brain Repair and RehabilitationDepartment of Clinical Neuroscience and RehabilitationInstitute of Neuroscience and PhysiologySahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Alison L. Atkins
- Center for Brain Repair and RehabilitationDepartment of Clinical Neuroscience and RehabilitationInstitute of Neuroscience and PhysiologySahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | | | - Scott R. Barnum
- Department of MicrobiologyUniversity of AlabamaBirminghamAlabamaUSA
| | - Rick A. Wetsel
- Research Center for Immunology and Autoimmune DiseasesInstitute of Molecular Medicine for the Prevention of Human DiseasesUniversity of Texas‐HoustonHoustonTexasUSA
| | - Mike Dragunow
- Department of PharmacologyFaculty of Medical and Health SciencesThe University of AucklandAucklandNew Zealand
- The National Research Centre for Growth and DevelopmentFaculty of Medical and Health SciencesThe University of AucklandAucklandNew Zealand
| | - Milos Pekny
- Center for Brain Repair and RehabilitationDepartment of Clinical Neuroscience and RehabilitationInstitute of Neuroscience and PhysiologySahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Carina Mallard
- Perinatal CenterSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Henrik Hagberg
- Perinatal CenterSahlgrenska AcademyUniversity of GothenburgGothenburgSweden
- Department of Obstetrics and GynecologySahlgrenska AcademyUniversity of GothenburgGothenburgSweden
- Centre for the Developing BrainKing's CollegeLondonUK
| | - Marcela Pekna
- Center for Brain Repair and RehabilitationDepartment of Clinical Neuroscience and RehabilitationInstitute of Neuroscience and PhysiologySahlgrenska AcademyUniversity of GothenburgGothenburgSweden
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Sagaert X, Tousseyn T, Yantiss RK. Gastrointestinal B-cell lymphomas: From understanding B-cell physiology to classification and molecular pathology. World J Gastrointest Oncol 2012; 4:238-49. [PMID: 23443141 PMCID: PMC3581849 DOI: 10.4251/wjgo.v4.i12.238] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 08/29/2012] [Accepted: 11/20/2012] [Indexed: 02/05/2023] Open
Abstract
The gut is the most common extranodal site where lymphomas arise. Although all histological lymphoma types may develop in the gut, small and large B-cell lymphomas predominate. The sometimes unexpected finding of a lymphoid lesion in an endoscopic biopsy of the gut may challenge both the clinician (who is not always familiar with lymphoma pathogenesis) and the pathologist (who will often be hampered in his/her diagnostic skill by the limited amount of available tissue). Moreover, the past 2 decades have spawned an avalanche of new data that encompasses both the function of the reactive B-cell as well as the pathogenic pathways that lead to its neoplastic counterpart, the B-cell lymphoma. Therefore, this review aims to offer clinicians an overview of B-cell lymphomas in the gut, and their pertinent molecular features that have led to new insights regarding lymphomagenesis. It addresses the question as how to incorporate all presently available information on normal and neoplastic B-cell differentiation, and how this knowledge can be applied in daily clinical practice (e.g., diagnostic tools, prognostic biomarkers or therapeutic targets) to optimalise the managment of this heterogeneous group of neoplasms.
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Affiliation(s)
- Xavier Sagaert
- Xavier Sagaert, Thomas Tousseyn, Department of Pathology University Hospitals Leuven, B-3000 Leuven, Belgium
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Magnone M, Bauer I, Poggi A, Mannino E, Sturla L, Brini M, Zocchi E, De Flora A, Nencioni A, Bruzzone S. NAD+ levels control Ca2+ store replenishment and mitogen-induced increase of cytosolic Ca2+ by Cyclic ADP-ribose-dependent TRPM2 channel gating in human T lymphocytes. J Biol Chem 2012; 287:21067-81. [PMID: 22547068 DOI: 10.1074/jbc.m111.324269] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Intracellular NAD(+) levels ([NAD(+)](i)) are important in regulating human T lymphocyte survival, cytokine secretion, and the capacity to respond to antigenic stimuli. NAD(+)-derived Ca(2+)-mobilizing second messengers, produced by CD38, play a pivotal role in T cell activation. Here we demonstrate that [NAD(+)](i) modifications in T lymphocytes affect intracellular Ca(2+) homeostasis both in terms of mitogen-induced [Ca(2+)](i) increase and of endoplasmic reticulum Ca(2+) store replenishment. Lowering [NAD(+)](i) by FK866-mediated nicotinamide phosphoribosyltransferase inhibition decreased the mitogen-induced [Ca(2+)](i) rise in Jurkat cells and in activated T lymphocytes. Accordingly, the Ca(2+) content of thapsigargin-sensitive Ca(2+) stores was greatly reduced in these cells in the presence of FK866. When NAD(+) levels were increased by supplementing peripheral blood lymphocytes with the NAD(+) precursors nicotinamide, nicotinic acid, or nicotinamide mononucleotide, the Ca(2+) content of thapsigargin-sensitive Ca(2+) stores as well as cell responsiveness to mitogens in terms of [Ca(2+)](i) elevation were up-regulated. The use of specific siRNA showed that the changes of Ca(2+) homeostasis induced by NAD(+) precursors are mediated by CD38 and the consequent ADPR-mediated TRPM2 gating. Finally, the presence of NAD(+) precursors up-regulated important T cell functions, such as proliferation and IL-2 release in response to mitogens.
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Affiliation(s)
- Mirko Magnone
- Department of Experimental Medicine, Section of Biochemistry and Center of Excellence for Biomedical Research, University of Genova, Genova, Italy
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Jakubauskas A, Valceckiene V, Andrekute K, Seinin D, Kanopka A, Griskevicius L. Discovery of two novel EWSR1/ATF1 transcripts in four chimerical transcripts-expressing clear cell sarcoma and their quantitative evaluation. Exp Mol Pathol 2011; 90:194-200. [DOI: 10.1016/j.yexmp.2010.12.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2010] [Revised: 12/10/2010] [Accepted: 12/14/2010] [Indexed: 11/25/2022]
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Aziz A, Harrop SP, Bishop NE. DIA1R is an X-linked gene related to Deleted In Autism-1. PLoS One 2011; 6:e14534. [PMID: 21264219 PMCID: PMC3022024 DOI: 10.1371/journal.pone.0014534] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2010] [Accepted: 12/21/2010] [Indexed: 01/28/2023] Open
Abstract
Background Autism spectrum disorders (ASDs) are frequently occurring disorders diagnosed by deficits in three core functional areas: social skills, communication, and behaviours and/or interests. Mental retardation frequently accompanies the most severe forms of ASDs, while overall ASDs are more commonly diagnosed in males. Most ASDs have a genetic origin and one gene recently implicated in the etiology of autism is the Deleted-In-Autism-1 (DIA1) gene. Methodology/Principal Findings Using a bioinformatics-based approach, we have identified a human gene closely related to DIA1, we term DIA1R (DIA1-Related). While DIA1 is autosomal (chromosome 3, position 3q24), DIA1R localizes to the X chromosome at position Xp11.3 and is known to escape X-inactivation. The gene products are of similar size, with DIA1 encoding 430, and DIA1R 433, residues. At the amino acid level, DIA1 and DIA1R are 62% similar overall (28% identical), and both encode signal peptides for targeting to the secretory pathway. Both genes are ubiquitously expressed, including in fetal and adult brain tissue. Conclusions/Significance Examination of published literature revealed point mutations in DIA1R are associated with X-linked mental retardation (XLMR) and DIA1R deletion is associated with syndromes with ASD-like traits and/or XLMR. Together, these results support a model where the DIA1 and DIA1R gene products regulate molecular traffic through the cellular secretory pathway or affect the function of secreted factors, and functional deficits cause disorders with ASD-like symptoms and/or mental retardation.
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Affiliation(s)
- Azhari Aziz
- Department of Microbiology, La Trobe University, Bundoora, Victoria, Australia
| | - Sean P. Harrop
- Department of Microbiology, La Trobe University, Bundoora, Victoria, Australia
| | - Naomi E. Bishop
- Department of Microbiology, La Trobe University, Bundoora, Victoria, Australia
- * E-mail:
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Slotte C, Lennerås M, Göthberg C, Suska F, Zoric N, Thomsen P, Nannmark U. Gene Expression of Inflammation and Bone Healing in Peri-Implant Crevicular Fluid after Placement and Loading of Dental Implants. A Kinetic Clinical Pilot Study Using Quantitative Real-Time PCR. Clin Implant Dent Relat Res 2010; 14:723-36. [DOI: 10.1111/j.1708-8208.2010.00309.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Jung C, Chung JW, Kim UO, Kim MH, Park HG. Isothermal target and signaling probe amplification method, based on a combination of an isothermal chain amplification technique and a fluorescence resonance energy transfer cycling probe technology. Anal Chem 2010; 82:5937-43. [PMID: 20575518 DOI: 10.1021/ac100606m] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An iTPA (isothermal target and signaling probe amplification) method for the quantitative detection of nucleic acids, based on a combination of novel ICA (isothermal chain amplification) and fluorescence resonance energy transfer cycling probe technology (FRET CPT), is described. In the new ICA method, which relies on the strand displacement activity of DNA polymerase and the RNA degrading activity of RNase H, two displacement events occur in the presence of four specially designed primers. This phenomenon leads to powerful amplification of target DNA. Since the amplification is initiated only after hybridization of the four primers, the ICA method leads to high specificity for the target sequence. As part of the new ICA method, iTPA is achieved by incorporating FRET CPT to generate multiple fluorescence signals from a single target molecule. Using the resulting dual target and signaling probe amplification system, even a single copy level of a target gene can be successfully detected and quantified under isothermal conditions.
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Affiliation(s)
- Cheulhee Jung
- Department of Chemical and Biomolecular Engineering, KAIST, 335 Gwahak-ro, Yuseong-gu, Daejeon, Republic of Korea
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Attenuation of reactive gliosis does not affect infarct volume in neonatal hypoxic-ischemic brain injury in mice. PLoS One 2010; 5:e10397. [PMID: 20442854 PMCID: PMC2861004 DOI: 10.1371/journal.pone.0010397] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Accepted: 04/02/2010] [Indexed: 12/13/2022] Open
Abstract
Background Astroglial cells are activated following injury and up-regulate the expression of the intermediate filament proteins glial fibrillary acidic protein (GFAP) and vimentin. Adult mice lacking the intermediate filament proteins GFAP and vimentin (GFAP−/−Vim−/−) show attenuated reactive gliosis, reduced glial scar formation and improved regeneration of neuronal synapses after neurotrauma. GFAP−/−Vim−/− mice exhibit larger brain infarcts after middle cerebral artery occlusion suggesting protective role of reactive gliosis after adult focal brain ischemia. However, the role of astrocyte activation and reactive gliosis in the injured developing brain is unknown. Methodology/Principal Findings We subjected GFAP−/−Vim−/− and wild-type mice to unilateral hypoxia-ischemia (HI) at postnatal day 9 (P9). Bromodeoxyuridine (BrdU; 25 mg/kg) was injected intraperitoneally twice daily from P9 to P12. On P12 and P31, the animals were perfused intracardially. Immunohistochemistry with MAP-2, BrdU, NeuN, and S100 antibodies was performed on coronal sections. We found no difference in the hemisphere or infarct volume between GFAP−/−Vim−/− and wild-type mice at P12 and P31, i.e. 3 and 22 days after HI. At P31, the number of NeuN+ neurons in the ischemic and contralateral hemisphere was comparable between GFAP−/−Vim−/− and wild-type mice. In wild-type mice, the number of S100+ astrocytes was lower in the ipsilateral compared to contralateral hemisphere (65.0±50.1 vs. 85.6±34.0, p<0.05). In the GFAP−/−Vim−/− mice, the number of S100+ astrocytes did not differ between the ischemic and contralateral hemisphere at P31. At P31, GFAP−/−Vim−/− mice showed an increase in NeuN+BrdU+ (surviving newly born) neurons in the ischemic cortex compared to wild-type mice (6.7±7.7; n = 29 versus 2.9±3.6; n = 28, respectively, p<0.05), but a comparable number of S100+BrdU+ (surviving newly born) astrocytes. Conclusions/Significance Our results suggest that attenuation of reactive gliosis in the developing brain does not affect the hemisphere or infarct volume after HI, but increases the number of surviving newborn neurons.
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Sturla L, Fresia C, Guida L, Bruzzone S, Scarfì S, Usai C, Fruscione F, Magnone M, Millo E, Basile G, Grozio A, Jacchetti E, Allegretti M, De Flora A, Zocchi E. LANCL2 is necessary for abscisic acid binding and signaling in human granulocytes and in rat insulinoma cells. J Biol Chem 2009; 284:28045-28057. [PMID: 19667068 DOI: 10.1074/jbc.m109.035329] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Abscisic acid (ABA) is a plant hormone regulating fundamental physiological functions in plants, such as response to abiotic stress. Recently, ABA was shown to be produced and released by human granulocytes, by insulin-producing rat insulinoma cells, and by human and murine pancreatic beta cells. ABA autocrinally stimulates the functional activities specific for each cell type through a receptor-operated signal transduction pathway, sequentially involving a pertussis toxin-sensitive receptor/G-protein complex, cAMP, CD38-produced cADP-ribose and intracellular calcium. Here we show that the lanthionine synthetase C-like protein LANCL2 is required for ABA binding on the membrane of human granulocytes and that LANCL2 is necessary for transduction of the ABA signal into the cell-specific functional responses in granulocytes and in rat insulinoma cells. Co-expression of LANCL2 and CD38 in the human HeLa cell line reproduces the ABA-signaling pathway. Results obtained with granulocytes and CD38(+)/LANCL2(+) HeLa transfected with a chimeric G-protein (G alpha(q/i)) suggest that the pertussis toxin-sensitive G-protein coupled to LANCL2 is a G(i). Identification of LANCL2 as a critical component of the ABA-sensing protein complex will enable the screening of synthetic ABA antagonists as prospective new anti-inflammatory and anti-diabetic agents.
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Affiliation(s)
- Laura Sturla
- Department of Experimental Medicine, Section of Biochemistry, and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV 1, Genova 16132
| | - Chiara Fresia
- Department of Experimental Medicine, Section of Biochemistry, and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV 1, Genova 16132
| | - Lucrezia Guida
- Department of Experimental Medicine, Section of Biochemistry, and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV 1, Genova 16132
| | - Santina Bruzzone
- Department of Experimental Medicine, Section of Biochemistry, and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV 1, Genova 16132
| | - Sonia Scarfì
- Department of Experimental Medicine, Section of Biochemistry, and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV 1, Genova 16132; Advanced Biotechnology Center, Largo R. Benzi 10, Genova 16132
| | - Cesare Usai
- Institute of Biophysics, National Research Council, Via De Marini 6, Genova 16149
| | | | - Mirko Magnone
- Department of Experimental Medicine, Section of Biochemistry, and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV 1, Genova 16132
| | - Enrico Millo
- Department of Experimental Medicine, Section of Biochemistry, and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV 1, Genova 16132
| | - Giovanna Basile
- Department of Experimental Medicine, Section of Biochemistry, and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV 1, Genova 16132
| | - Alessia Grozio
- Department of Experimental Medicine, Section of Biochemistry, and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV 1, Genova 16132
| | - Emanuela Jacchetti
- Institute of Biophysics, National Research Council, Via De Marini 6, Genova 16149
| | | | - Antonio De Flora
- Department of Experimental Medicine, Section of Biochemistry, and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV 1, Genova 16132.
| | - Elena Zocchi
- Department of Experimental Medicine, Section of Biochemistry, and Center of Excellence for Biomedical Research, University of Genova, Viale Benedetto XV 1, Genova 16132; Advanced Biotechnology Center, Largo R. Benzi 10, Genova 16132.
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Johannesson M, Ståhlberg A, Ameri J, Sand FW, Norrman K, Semb H. FGF4 and retinoic acid direct differentiation of hESCs into PDX1-expressing foregut endoderm in a time- and concentration-dependent manner. PLoS One 2009; 4:e4794. [PMID: 19277121 PMCID: PMC2651644 DOI: 10.1371/journal.pone.0004794] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2008] [Accepted: 02/10/2009] [Indexed: 01/27/2023] Open
Abstract
Background Retinoic acid (RA) and fibroblast growth factor 4 (FGF4) signaling control endoderm patterning and pancreas induction/expansion. Based on these findings, RA and FGFs, excluding FGF4, have frequently been used in differentiation protocols to direct differentiation of hESCs into endodermal and pancreatic cell types. In vivo, these signaling pathways act in a temporal and concentration-dependent manner. However, in vitro, the underlying basis for the time of addition of growth and differentiation factors (GDFs), including RA and FGFs, as well as the concentration is lacking. Thus, in order to develop robust and reliable differentiation protocols of ESCs into mature pancreatic cell types, including insulin-producing β cells, it will be important to mechanistically understand each specification step. This includes differentiation of mesendoderm/definitive endoderm into foregut endoderm- the origin of pancreatic endoderm. Methodology/Principal Findings Here, we provide data on the individual and combinatorial role of RA and FGF4 in directing differentiation of ActivinA (AA)-induced hESCs into PDX1-expressing cells. FGF4's ability to affect endoderm patterning and specification in vitro has so far not been tested. By testing out the optimal concentration and timing of addition of FGF4 and RA, we present a robust differentiation protocol that on average generates 32% PDX1+ cells. Furthermore, we show that RA is required for converting AA-induced hESCs into PDX1+ cells, and that part of the underlying mechanism involves FGF receptor signaling. Finally, further characterization of the PDX1+ cells suggests that they represent foregut endoderm not yet committed to pancreatic, posterior stomach, or duodenal endoderm. Conclusion/Significance In conclusion, we show that RA and FGF4 jointly direct differentiation of PDX1+ foregut endoderm in a robust and efficient manner. RA signaling mediated by the early induction of RARβ through AA/Wnt3a is required for PDX1 expression. Part of RA's activity is mediated by FGF signaling.
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MESH Headings
- Activins/pharmacology
- Cell Differentiation/drug effects
- Cells, Cultured/drug effects
- Cells, Cultured/metabolism
- Dose-Response Relationship, Drug
- Drug Synergism
- Embryonic Stem Cells/cytology
- Embryonic Stem Cells/drug effects
- Embryonic Stem Cells/metabolism
- Endoderm/cytology
- Endoderm/drug effects
- Endoderm/metabolism
- Fibroblast Growth Factor 4/physiology
- Gene Expression Regulation/drug effects
- Homeodomain Proteins/biosynthesis
- Homeodomain Proteins/genetics
- Humans
- Pancreas/cytology
- Pancreas/embryology
- Pyrroles/pharmacology
- RNA, Messenger/biosynthesis
- Receptor, Fibroblast Growth Factor, Type 2/antagonists & inhibitors
- Receptor, Fibroblast Growth Factor, Type 2/biosynthesis
- Receptor, Fibroblast Growth Factor, Type 2/genetics
- Receptor, Fibroblast Growth Factor, Type 2/physiology
- Receptors, Retinoic Acid/biosynthesis
- Receptors, Retinoic Acid/genetics
- Signal Transduction/drug effects
- Signal Transduction/physiology
- Time Factors
- Trans-Activators/biosynthesis
- Trans-Activators/genetics
- Tretinoin/pharmacology
- Up-Regulation/drug effects
- Wnt Proteins/physiology
- Wnt3 Protein
- Wnt3A Protein
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Affiliation(s)
- Martina Johannesson
- Lund Center for Stem Cell Biology and Cell Therapy, Lund University, Lund, Sweden
| | - Anders Ståhlberg
- Lund Center for Stem Cell Biology and Cell Therapy, Lund University, Lund, Sweden
- Department of Clinical Neuroscience and Rehabilitation, Institute of Neurosciences and Physiology, Sahlgrenska Academy at Göteborg University, Göteborg, Sweden
| | - Jacqueline Ameri
- Lund Center for Stem Cell Biology and Cell Therapy, Lund University, Lund, Sweden
| | | | - Karin Norrman
- Lund Center for Stem Cell Biology and Cell Therapy, Lund University, Lund, Sweden
| | - Henrik Semb
- Lund Center for Stem Cell Biology and Cell Therapy, Lund University, Lund, Sweden
- * E-mail:
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Abstract
This chapter describes two different fast protocols for optimizing EasyBeacons for the challenging detection of the methylation status of a single CpG duplet in bisulfitetreated DNA. EasyBeacons can be used in multiplex detections even if they do not have the same affinity for their respective targets giving very specific results for both realtime polymerase chain reaction (real-time PCR) detection and endpoint analysis using inexpensive master mixes. The technology described in this chapter is a very competitive alternative to other real-time PCR technologies.
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Gibson S, Sebire NJ, Anderson J. Platelet-derived growth factor receptors and ligands are up-regulated in paediatric fibromatoses. Histopathology 2007; 51:752-7. [PMID: 17944929 DOI: 10.1111/j.1365-2559.2007.02868.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
AIMS Platelet-derived growth factors (PDGF) and their receptors (PDGFR) play an essential role in pathways involved in the regulation of cell proliferation, growth and function. Overexpression of PDGF/R is reported in a wide range of solid tumours. The aim was to determine levels of PDGF/R expression in paediatric fibromatoses and myofibromatosis. METHODS AND RESULTS Quantitative real-time polymerase chain reaction was used to examine the expression level of alpha and beta isoforms of PDGF/R in 17 fibromatoses, four myofibromatoses and three dermatofibrosarcoma protuberans (DFSP) in children. Fifteen of 17 (88%) fibromatoses and all myofibromatoses and DFSPs demonstrated increased expression of PDGFalpha and beta compared with a panel of normal tissues. In terms of the cognate receptors, 13/17 (76%) fibromatoses demonstrated increased expression for PDGFRalpha and Rbeta, whereas 3/4 myofibromatoses demonstrated increased expression of PDGFRalpha and all four had increased PDGFRbeta expression. All DFSPs were associated with increased expression of both PDGFRalpha and PDGFRbeta compared with normal control tissues. CONCLUSIONS Increased expression of PDGF/Ralphabeta may play an important role in the mechanism of growth of these paediatric fibromatous lesions and warrants further investigation, since novel therapeutic interventions could potentially be developed in the light of the expression patterns.
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Affiliation(s)
- S Gibson
- Department of Histopathology, Great Ormond Street Hospital for Children, London, UK
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39
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Abstract
The real-time reverse transcription polymerase chain reaction (RT-qPCR) addresses the evident requirement for quantitative data analysis in molecular medicine, biotechnology, microbiology and diagnostics and has become the method of choice for the quantification of mRNA. Although it is often described as a "gold" standard, it is far from being a standard assay. The significant problems caused by variability of RNA templates, assay designs and protocols, as well as inappropriate data normalization and inconsistent data analysis, are widely known but also widely disregarded. As a first step towards standardization, we describe a series of RT-qPCR protocols that illustrate the essential technical steps required to generate quantitative data that are reliable and reproducible. We would like to emphasize, however, that RT-qPCR data constitute only a snapshot of information regarding the quantity of a given transcript in a cell or tissue. Any assessment of the biological consequences of variable mRNA levels must include additional information regarding regulatory RNAs, protein levels and protein activity. The entire protocol described here, encompassing all stages from initial assay design to reliable qPCR data analysis, requires approximately 15 h.
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Affiliation(s)
- Tania Nolan
- Sigma-Aldrich, Homefield Road, Haverhill, UK
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40
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Ramsden SC, Deans Z, Robinson DO, Mountford R, Sistermans EA, Grody WW, McQuaid S, Patton SJ, Stenhouse SAR. Monitoring standards for molecular genetic testing in the United Kingdom, the Netherlands, and Ireland. ACTA ACUST UNITED AC 2007; 10:147-56. [PMID: 17020464 DOI: 10.1089/gte.2006.10.147] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Molecular genetic techniques have entered many areas of clinical practice. Public expectations from this technology are understandably high. To maintain confidence in this technology, laboratories must implement the highest standards of quality assurance (QA). External quality assessment (EQA) is recognized as an essential component of QA. The United Kingdom National External Quality Assessment Service (UKNEQAS) for Molecular Genetics, first set up in 1991, is currently the longest provider of EQA to molecular genetic testing laboratories in the UK, The Netherlands, and Ireland. Errors in the scheme are sporadic events. However, evidence from this and other EQA schemes suggests that a residual error rate persists, which should be taken into account in clinical practice. This EQA scheme has evolved from the respective scientific bodies of the constituent countries and retains a strong emphasis on collective peer review. It is essential that the steps taken to ensure quality in this rapidly expanding field are clear and transparent to participants and public alike. We describe the procedures developed and the governance imposed to monitor and improve analytical and reporting standards in participant laboratories and we compare our experiences with those of equivalent EQA services in the United States.
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Affiliation(s)
- Simon C Ramsden
- National Genetics Reference Laboratory (Manchester), St Mary's Hospital, Manchester, UK.
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41
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Deepak SA, Kottapalli KR, Rakwal R, Oros G, Rangappa KS, Iwahashi H, Masuo Y, Agrawal GK. Real-Time PCR: Revolutionizing Detection and Expression Analysis of Genes. Curr Genomics 2007; 8:234-51. [PMID: 18645596 PMCID: PMC2430684 DOI: 10.2174/138920207781386960] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2007] [Revised: 02/27/2007] [Accepted: 03/02/2007] [Indexed: 02/06/2023] Open
Abstract
Invention of polymerase chain reaction (PCR) technology by Kary Mullis in 1984 gave birth to real-time PCR. Real-time PCR - detection and expression analysis of gene(s) in real-time - has revolutionized the 21(st) century biological science due to its tremendous application in quantitative genotyping, genetic variation of inter and intra organisms, early diagnosis of disease, forensic, to name a few. We comprehensively review various aspects of real-time PCR, including technological refinement and application in all scientific fields ranging from medical to environmental issues, and to plant.
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Affiliation(s)
- SA Deepak
- Department of Studies in Applied Botany and Biotechnology, University of Mysore, Manasagangotri, Mysore 570006,
India
| | - KR Kottapalli
- Plant Genome Research Unit, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-
8602, Ibaraki, Japan
| | - R Rakwal
- Human Stress Signal Research Center (HSS), National Institute of Advanced Industrial Science
and Technology (AIST), Tsukuba West, 16-1 Onogawa, Tsukuba 305-8569, Ibaraki, Japan
- Research Laboratory for
Agricultural Biotechnology and Biochemistry (RLABB), GPO Box 8207, Kathmandu, Nepal
| | - G Oros
- Plant Protection Institute,
Hungarian Academy of Sciences, Budapest, Hungary
| | - KS Rangappa
- Department of Studies in Chemistry, University of Mysore,
Manasagangotri, Mysore 570006, India
| | - H Iwahashi
- Human Stress Signal Research Center (HSS), National Institute of Advanced Industrial Science
and Technology (AIST), Tsukuba West, 16-1 Onogawa, Tsukuba 305-8569, Ibaraki, Japan
| | - Y Masuo
- Human Stress Signal Research Center (HSS), National Institute of Advanced Industrial Science
and Technology (AIST), Tsukuba West, 16-1 Onogawa, Tsukuba 305-8569, Ibaraki, Japan
| | - GK Agrawal
- Research Laboratory for
Agricultural Biotechnology and Biochemistry (RLABB), GPO Box 8207, Kathmandu, Nepal
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42
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Qiu H, Durand K, Rabinovitch-Chable H, Rigaud M, Gazaille V, Clavère P, Sturtz FG. Gene expression of HIF-1alpha and XRCC4 measured in human samples by real-time RT-PCR using the sigmoidal curve-fitting method. Biotechniques 2007; 42:355-62. [PMID: 17390542 DOI: 10.2144/000112331] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Quantitative reverse transcription PCR (RT-PCR) has become an important tool for studying functional gene expression. However the most often used cycle threshold (CT)-based method, primarily related to the required amplification efficiency determination via serial dilution, can call into question the level of quantitative reliability and accuracy that can be achieved, in addition to the impracticalities inherent to CT-based methodologies. In this study, an alternative method, named the sigmoidal curve-fitting (SCF) method, was compared with the classic CT method for two target genes (XRCC4 and HIF-1alpha) and a reference gene (HPRT). The PCR conditions were optimized for each gene on a LightCycler apparatus. Fluorescence data were fitted to a four-parametric sigmoidal function, and the initial messenger RNA (mRNA) copy number was determined by a theoretical fluorescence (F0) value calculated from each fitting curve. The relative expression of the target gene versus that of the reference gene was calculated using an equation based upon these F0 values. The results show that the F0 value had a good linearity with the initial number of target genes between 10(7) and 10(1) copies. The reproducibility tests showed that the variations of initial target quantity were well reflected by F0 values. Relative expression of target gene calculated by the SCF method and by the CT method showed similar results. In our hands, the SCF method gave reliable results and a more precise error description of quantitative RT-PCR.
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Affiliation(s)
- Hao Qiu
- Université de Limoges, Limoges, France
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43
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Engström K, Willén H, Kåbjörn-Gustafsson C, Andersson C, Olsson M, Göransson M, Järnum S, Olofsson A, Warnhammar E, Aman P. The myxoid/round cell liposarcoma fusion oncogene FUS-DDIT3 and the normal DDIT3 induce a liposarcoma phenotype in transfected human fibrosarcoma cells. THE AMERICAN JOURNAL OF PATHOLOGY 2006; 168:1642-53. [PMID: 16651630 PMCID: PMC1606602 DOI: 10.2353/ajpath.2006.050872] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Myxoid/round cell liposarcoma (MLS/RCLS) is the most common subtype of liposarcoma. Most MLS/RCLS carry a t(12;16) translocation, resulting in a FUS-DDIT3 fusion gene. We investigated the role of the FUS-DDIT3 fusion in the development of MLS/RCLS in FUS-DDIT3- and DDIT3-transfected human HT1080 sarcoma cells. Cells expressing FUS-DDIT3 and DDIT3 grew as liposarcomas in severe combined immunodeficient mice and exhibited a capillary network morphology that was similar to networks of MLS/RCLS. Microarray-based comparison of HT1080, the transfected cells, and an MLS/RCLS-derived cell line showed that the FUS-DDIT3- and DDIT3-transfected variants shifted toward an MLS/RCLS-like expression pattern. DDIT3-transfected cells responded in vitro to adipogenic factors by accumulation of fat and transformation to a lipoblast-like morphology. In conclusion, because the fusion oncogene FUS-DDIT3 and the normal DDIT3 induce a liposarcoma phenotype when expressed in a primitive sarcoma cell line, MLS/RCLS may develop from cell types other than preadipocytes. This may explain the preferential occurrence of MLS/RCLS in nonadipose tissues. In addition, development of lipoblasts and the typical MLS/RCLS capillary network could be an effect of the DDIT3 transcription factor partner of the fusion oncogene.
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Affiliation(s)
- Katarina Engström
- Department of Oncology, Lundberg Laboratory for Cancer Research, Sahlgrenska University Hospital, Gothenburg, Sweden
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44
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Lind K, Ståhlberg A, Zoric N, Kubista M. Combining sequence-specific probes and DNA binding dyes in real-time PCR for specific nucleic acid quantification and melting curve analysis. Biotechniques 2006; 40:315-9. [PMID: 16568820 DOI: 10.2144/000112101] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Currently, in real-time PCR, one often has to choose between using a sequence-specific probe and a nonspecific double-stranded DNA (dsDNA) binding dye for the detection of amplified DNA products. The sequence-specific probe has the advantage that it only detects the targeted product, while the nonspecific dye has the advantage that melting curve analysis can be performed after completed amplification, which reveals what kind of products have been formed. Here we present a new strategy based on combining a sequence-specific probe and a nonspecific dye, BOXTO, in the same reaction, to take the advantage of both chemistries. We show that BOXTO can be used together with both TaqMan probes and locked nucleic acid (LNA) probes without interfering with the PCR. The probe signal reflect formation of target product, while melting curve analysis of the BOXTO signal reveals primer-dimer formation and the presence of any other anomalous products.
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Affiliation(s)
- Kristina Lind
- Chalmers University of Technology, Gothenburg, Sweden
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45
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Nolan T, Hands RE, Ogunkolade W, Bustin SA. SPUD: a quantitative PCR assay for the detection of inhibitors in nucleic acid preparations. Anal Biochem 2006; 351:308-10. [PMID: 16524557 DOI: 10.1016/j.ab.2006.01.051] [Citation(s) in RCA: 160] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2005] [Revised: 01/30/2006] [Accepted: 01/31/2006] [Indexed: 12/24/2022]
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46
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Xian X, Håkansson J, Ståhlberg A, Lindblom P, Betsholtz C, Gerhardt H, Semb H. Pericytes limit tumor cell metastasis. J Clin Invest 2006; 116:642-51. [PMID: 16470244 PMCID: PMC1361347 DOI: 10.1172/jci25705] [Citation(s) in RCA: 272] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2005] [Accepted: 12/06/2005] [Indexed: 01/13/2023] Open
Abstract
Previously we observed that neural cell adhesion molecule (NCAM) deficiency in beta tumor cells facilitates metastasis into distant organs and local lymph nodes. Here, we show that NCAM-deficient beta cell tumors grew leaky blood vessels with perturbed pericyte-endothelial cell-cell interactions and deficient perivascular deposition of ECM components. Conversely, tumor cell expression of NCAM in a fibrosarcoma model (T241) improved pericyte recruitment and increased perivascular deposition of ECM molecules. Together, these findings suggest that NCAM may limit tumor cell metastasis by stabilizing the microvessel wall. To directly address whether pericyte dysfunction increases the metastatic potential of solid tumors, we studied beta cell tumorigenesis in primary pericyte-deficient Pdgfb(ret/ret) mice. This resulted in beta tumor cell metastases in distant organs and local lymph nodes, demonstrating a role for pericytes in limiting tumor cell metastasis. These data support a new model for how tumor cells trigger metastasis by perturbing pericyte-endothelial cell-cell interactions.
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47
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Abstract
The LightUp® Probe technology has now matured and reached the phase where it has been implemented in commercial reagent kits, i.e. the ReSSQ® product line. Several properties of the LightUp® probes make them particularly suitable for clinical settings. For instance, extraordinary shelf life and a chemical stability that allows convenient fridge storage. The origin of the higher stability of LightUp® probe kits compared to others, based on alternative probe technologies, is partly the relatively good stability of cyanine dyes but also the resistance towards nucleases and proteases of the synthetic DNA analogue peptide nucleic acid that is used as the sequence recognizing element in LightUp probes. It is clear from recent trends in the PCR amplification hardware technology that the instrumentation is becoming more flexible and less adapted for dedicated probe chemistries. This will pave the way for increased standardization in the field of DNA diagnostics and the development of cross-platform assays. In the present review the LightUp technology will briefly be presented and discussed. The utility of the technology will be illustrated by examples from cytomegalovirus quantification and monitoring of the viral load of the SARS Coronavirus. An example of cancer diagnostics by detection of altered gene expression patterns will also be shown.
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Affiliation(s)
- Mikael Leijon
- LightUp Technologies AB, Lunastigen 5, SE-141 44 Huddinge, Sweden
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48
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Kubista M, Andrade JM, Bengtsson M, Forootan A, Jonák J, Lind K, Sindelka R, Sjöback R, Sjögreen B, Strömbom L, Ståhlberg A, Zoric N. The real-time polymerase chain reaction. Mol Aspects Med 2006; 27:95-125. [PMID: 16460794 DOI: 10.1016/j.mam.2005.12.007] [Citation(s) in RCA: 792] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The scientific, medical, and diagnostic communities have been presented the most powerful tool for quantitative nucleic acids analysis: real-time PCR [Bustin, S.A., 2004. A-Z of Quantitative PCR. IUL Press, San Diego, CA]. This new technique is a refinement of the original Polymerase Chain Reaction (PCR) developed by Kary Mullis and coworkers in the mid 80:ies [Saiki, R.K., et al., 1985. Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia, Science 230, 1350], for which Kary Mullis was awarded the 1993 year's Nobel prize in Chemistry. By PCR essentially any nucleic acid sequence present in a complex sample can be amplified in a cyclic process to generate a large number of identical copies that can readily be analyzed. This made it possible, for example, to manipulate DNA for cloning purposes, genetic engineering, and sequencing. But as an analytical technique the original PCR method had some serious limitations. By first amplifying the DNA sequence and then analyzing the product, quantification was exceedingly difficult since the PCR gave rise to essentially the same amount of product independently of the initial amount of DNA template molecules that were present. This limitation was resolved in 1992 by the development of real-time PCR by Higuchi et al. [Higuchi, R., Dollinger, G., Walsh, P.S., Griffith, R., 1992. Simultaneous amplification and detection of specific DNA-sequences. Bio-Technology 10(4), 413-417]. In real-time PCR the amount of product formed is monitored during the course of the reaction by monitoring the fluorescence of dyes or probes introduced into the reaction that is proportional to the amount of product formed, and the number of amplification cycles required to obtain a particular amount of DNA molecules is registered. Assuming a certain amplification efficiency, which typically is close to a doubling of the number of molecules per amplification cycle, it is possible to calculate the number of DNA molecules of the amplified sequence that were initially present in the sample. With the highly efficient detection chemistries, sensitive instrumentation, and optimized assays that are available today the number of DNA molecules of a particular sequence in a complex sample can be determined with unprecedented accuracy and sensitivity sufficient to detect a single molecule. Typical uses of real-time PCR include pathogen detection, gene expression analysis, single nucleotide polymorphism (SNP) analysis, analysis of chromosome aberrations, and most recently also protein detection by real-time immuno PCR.
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Affiliation(s)
- Mikael Kubista
- TATAA Biocenter, Medicinargatan 7B, 405 30 Göteborg, Sweden.
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49
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Bengtsson M, Ståhlberg A, Rorsman P, Kubista M. Gene expression profiling in single cells from the pancreatic islets of Langerhans reveals lognormal distribution of mRNA levels. Genome Res 2006; 15:1388-92. [PMID: 16204192 PMCID: PMC1240081 DOI: 10.1101/gr.3820805] [Citation(s) in RCA: 293] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The transcriptional machinery in individual cells is controlled by a relatively small number of molecules, which may result in stochastic behavior in gene activity. Because of technical limitations in current collection and recording methods, most gene expression measurements are carried out on populations of cells and therefore reflect average mRNA levels. The variability of the transcript levels between different cells remains undefined, although it may have profound effects on cellular activities. Here we have measured gene expression levels of the five genes ActB, Ins1, Ins2, Abcc8, and Kcnj11 in individual cells from mouse pancreatic islets. Whereas Ins1 and Ins2 expression show a strong cell-cell correlation, this is not the case for the other genes. We further found that the transcript levels of the different genes are lognormally distributed. Hence, the geometric mean of expression levels provides a better estimate of gene activity of the typical cell than does the arithmetic mean measured on a cell population.
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Affiliation(s)
- Martin Bengtsson
- Department of Experimental Medical Science, Lund University, 221 84 Lund, Sweden.
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