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Navarro-Saiz LM, Bernal-Cepeda LJ, García-Jiménez F, Abril D, Castellanos JE. Reference gene validation for the relative quantification of cannabinoid receptor expression in human odontoblasts via quantitative polymerase chain reaction. J Oral Biol Craniofac Res 2022; 12:765-770. [PMID: 36133217 PMCID: PMC9483783 DOI: 10.1016/j.jobcr.2022.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 09/06/2022] [Indexed: 11/18/2022] Open
Abstract
Objective The aim of this study was to identify and validate the reference genes in cultured human odontoblasts to quantify their cannabinoid receptor transcripts. Methods The most stably transcribed genes in cultured human odontoblast cells were identified using the RefGenes tool and were selected for real-time polymerase chain reaction (PCR) amplification. Human odontoblast cells were differentiated from mesenchymal stem cells using a transforming growth factor-β-supplemented differentiation medium, and total RNA was purified. Reverse transcription-quantitative PCR and relative quantification analyses were performed using the Schefe's method. The relative expression dataset was analyzed to select the most stable genes. Results The analysis showed that the transcripts of cholinergic receptor nicotinic beta 2 subunit, LIM homeobox transcription factor 1 beta, and family with sequence similarity 223 member B presented the lowest standard deviation (SD) in expression (SD: 0.2, 0.17, and 0.16, respectively). These genes showed similar expression levels as the target genes (cannabinoid receptors). Significant differences were found in the relative expression levels of cannabinoid receptors using the selected genes compared to those calculated using beta actin transcripts as references (p < 0.05). Conclusions The strategy reported here for searching and verifying new reference genes will aid in the accurate and reliable expression of cannabinoid receptors in human odontoblast cells.
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Affiliation(s)
- Laura M. Navarro-Saiz
- Grupo de Investigación Básica y Aplicada en Odontología, Universidad Nacional de Colombia, Bogotá, 111321, Colombia
| | - Lilia J. Bernal-Cepeda
- Grupo de Investigación Básica y Aplicada en Odontología, Universidad Nacional de Colombia, Bogotá, 111321, Colombia
| | - Felipe García-Jiménez
- Grupo de Investigación Básica y Aplicada en Odontología, Universidad Nacional de Colombia, Bogotá, 111321, Colombia
| | - Deisy Abril
- Bacterial Molecular Genetics Laboratory, Universidad El Bosque, Bogotá, 110121, Colombia
| | - Jaime E. Castellanos
- Grupo de Investigación Básica y Aplicada en Odontología, Universidad Nacional de Colombia, Bogotá, 111321, Colombia
- Corresponding author. Grupo de Investigación Básica y Aplicada en Odontología, Universidad Nacional de Colombia, Carrera 30 No. 45 - 03 Edificio 210, Oficina 301, Bogotá, 111321, Colombia.
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Li G, Brumback BD, Huang L, Zhang DM, Yin T, Lipovsky CE, Hicks SC, Jimenez J, Boyle PM, Rentschler SL. Acute Glycogen Synthase Kinase-3 Inhibition Modulates Human Cardiac Conduction. JACC Basic Transl Sci 2022; 7:1001-1017. [PMID: 36337924 PMCID: PMC9626903 DOI: 10.1016/j.jacbts.2022.04.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 01/14/2023]
Abstract
Glycogen synthase kinase 3 (GSK-3) inhibition has emerged as a potential therapeutic target for several diseases, including cancer. However, the role for GSK-3 regulation of human cardiac electrophysiology remains ill-defined. We demonstrate that SB216763, a GSK-3 inhibitor, can acutely reduce conduction velocity in human cardiac slices. Combined computational modeling and experimental approaches provided mechanistic insight into GSK-3 inhibition-mediated changes, revealing that decreased sodium-channel conductance and tissue conductivity may underlie the observed phenotypes. Our study demonstrates that GSK-3 inhibition in human myocardium alters electrophysiology and may predispose to an arrhythmogenic substrate; therefore, monitoring for adverse arrhythmogenic events could be considered.
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Key Words
- ABC, active β-catenin
- APD, action potential duration
- BDM, 2,3-butanedione monoxime
- CV, conduction velocity
- Cx43, connexin 43
- GNa, sodium-channel conductance
- GOF, gain of function
- GSK-3 inhibitor
- GSK-3, glycogen synthase kinase 3
- INa, sodium current
- LV, left ventricle
- NaV1.5, pore-forming α-subunit protein of the voltage-gated cardiac sodium channel
- PCR, polymerase chain reaction
- RMP, resting membrane potential
- RT-qPCR, reverse transcription-quantitative polymerase chain reaction
- SB2, SB216763
- SB216763
- cDNA, complementary DNA
- dVm/dtmax, maximum upstroke velocity
- electrophysiology
- human cardiac slices
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Affiliation(s)
- Gang Li
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine in St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University McKelvey School of Engineering in St. Louis, Missouri, USA
| | - Brittany D. Brumback
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine in St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University McKelvey School of Engineering in St. Louis, Missouri, USA
| | - Lei Huang
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine in St. Louis, Missouri, USA
| | - David M. Zhang
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine in St. Louis, Missouri, USA
| | - Tiankai Yin
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine in St. Louis, Missouri, USA
| | - Catherine E. Lipovsky
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine in St. Louis, Missouri, USA
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, Missouri, USA
| | - Stephanie C. Hicks
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine in St. Louis, Missouri, USA
| | - Jesus Jimenez
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine in St. Louis, Missouri, USA
| | - Patrick M. Boyle
- Department of Bioengineering, Center for Cardiovascular Biology, and Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, Washington, USA
| | - Stacey L. Rentschler
- Department of Medicine, Cardiovascular Division, Washington University School of Medicine in St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University McKelvey School of Engineering in St. Louis, Missouri, USA
- Department of Developmental Biology, Washington University School of Medicine in St. Louis, Missouri, USA
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Fukasawa LO, Sacchi CT, Gonçalves MG, Lemos APS, Almeida SCG, Caterino-de-Araujo A. Comparative performances of seven quantitative Reverse-Transcription Polymerase Chain Reaction assays (RT-qPCR) for detecting SARS-CoV-2 infection in samples from individuals suspected of COVID-19 in São Paulo, Brazil. J Clin Virol Plus 2022; 1:100012. [PMID: 35262000 PMCID: PMC8019594 DOI: 10.1016/j.jcvp.2021.100012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/24/2021] [Accepted: 03/30/2021] [Indexed: 11/15/2022] Open
Abstract
Introduction Brazil is the second largest country with COVID-19 positive cases worldwide. Due to the potent spread of the virus and the scarcity of kits and supplies, the Brazilian Ministry of Health has granted authorization for the use of kits available during this emergency, without an accurate evaluation of their performance. This study compared the performance and cost-effectiveness of seven molecular assays/kits available in São Paulo, Brazil, for SARS-CoV-2 diagnosis Materials and methods A total of 205 nasopharyngeal/oropharyngeal samples from suspected cases of COVID-19, were tested using the following assays: (i) GeneFinder COVID-19 plus RealAmp kit; (ii) 2019-nCoV RNA PCR-Fluorescence Probing, Da An Gene Co.; (iii) in-house RT-qPCR SARS-CoV-2 IAL; (iv) 2019-nCoV kit, IDT; (v) molecular SARS-CoV-2 (E) kit, Bio-Manguinhos; (vi) Allplex 2019-nCoV modified Assay, Seegene Inc, and (vii) Biomol one-step COVID-19 kit, IBMP. The criteria for determining a SARS-CoV-2 true positive result included the cycle threshold cut-off values, the characteristics of exponential/linear curves, the gene target diversity, and a positive result in at least two assays Results The overall sensitivity of the assays listed were GeneFinder 83.6%, Da An Gene 100.0%, IAL 90.4%, IDT 94.6%, Bio-Manguinhos 87.7%, Allplex 97.3%, and IBMP 87.7%. The minor sensitive gene target was RdRP. Although all assays had a Cohen's Kappa index ≥0.893, the best tests used multiplex assays identifying N-gene and/or E-gene targets Conclusion All assays tested accurate for diagnosis, but considering cost-effectiveness (cost, time consumption, number of samples tested, and performance), the in-house IAL assay was ideal for COVID-19 diagnosis in São Paulo, Brazil.
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Key Words
- Assay performances
- CDC, center for disease control
- CI, confidence interval
- COVID-19, Coronavirus disease 2019
- CV, coefficient of variation in percentage
- Coronavirus disease 2019 (COVID-19)
- Cost-effectiveness
- Ct, cycle threshold
- Cut-off, Ct limit of positivity
- Cy5, Cyanine 5
- Diagnosis
- E, envelope
- FAM, fluorescein amidite
- HE, hemagglutinin esterase
- HEX, hexachloro fluorescein
- IAL, Instituto Adolfo Lutz
- IC, internal control
- M, membrane
- MERS-CoV, Middle East respiratory syndrome
- N, nucleocapsid
- ORF1ab, open-reading frame of ORF1ab region
- PAHO, Pan American Health Organization
- ROX, carboxy-X-rhodamine
- RP, human ribonuclease p
- RT-qPCR, reverse transcription-quantitative polymerase chain reaction
- RdRP, RNA-dependent RNA polymerase
- Reverse transcription-quantitative polymerase chain reaction (RT-qPCR)
- S, spike
- SARS, severe acute respiratory syndrome
- SARS-CoV-2
- SD, standard deviation
- Severe acute respiratory syndrome (SARS)
- VIC, 2′-chloro-7′-phenyl-1,4-dichloro-6-carboxyfluorescein
- WHO, World Health Organization
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Affiliation(s)
- Lucila Okuyama Fukasawa
- Centro de Imunologia, Instituto Adolfo Lutz, Coordenadoria de Controle de Doenças, Secretaria de Estado da Saúde de São Paulo, SP 01246-902, Brazil
| | - Cláudio Tavares Sacchi
- Laboratório Estratégico, Instituto Adolfo Lutz, Coordenadoria de Controle de Doenças, Secretaria de Estado da Saúde de São Paulo, SP, Brazil
| | - Maria Gisele Gonçalves
- Centro de Imunologia, Instituto Adolfo Lutz, Coordenadoria de Controle de Doenças, Secretaria de Estado da Saúde de São Paulo, SP 01246-902, Brazil
| | - Ana Paula Silva Lemos
- Centro de Bacteriologia, Instituto Adolfo Lutz, Coordenadoria de Controle de Doenças, Secretaria de Estado da Saúde de São Paulo, SP, Brazil
| | - Samanta Cristine Grassi Almeida
- Centro de Bacteriologia, Instituto Adolfo Lutz, Coordenadoria de Controle de Doenças, Secretaria de Estado da Saúde de São Paulo, SP, Brazil
| | - Adele Caterino-de-Araujo
- Centro de Imunologia, Instituto Adolfo Lutz, Coordenadoria de Controle de Doenças, Secretaria de Estado da Saúde de São Paulo, SP 01246-902, Brazil
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Akiyama M, Mizokami T, Miyamoto S, Ikeda Y. Kaempferol increases intracellular ATP content in C 2C 12 myotubes under hypoxic conditions by suppressing the HIF-1α stabilization and/or by enhancing the mitochondrial complex IV activity. J Nutr Biochem 2022; 103:108949. [PMID: 35122998 DOI: 10.1016/j.jnutbio.2022.108949] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/28/2021] [Accepted: 01/04/2022] [Indexed: 10/19/2022]
Abstract
Kaempferol (KMP) has numerous important biological functions, and we recently showed that it remarkably increased intracellular adenosine triphosphate (ATP) content in C2C12 myotubes under hypoxic conditions. Since intracellular ATP is generated by aerobic energy metabolism or anaerobic glycolysis, hypoxia inducible factor-1α (HIF-1α) has been shown to be associated with metabolic remodeling and causes metabolic shift from aerobic energy metabolism to anaerobic glycolysis in response to hypoxic conditions. Here, we investigate the effects of KMP under hypoxic conditions on the stabilization of HIF-1α in C2C12 myotubes and its underlying molecular mechanisms. Constitutive HIF-1α protein expression was observed in C2C12 myotubes, and its expression under hypoxic conditions was remarkably suppressed by KMP by reducing its stability; thus, resulting in an increase in ATP content. Furthermore, KMP strikingly increased the ubiquitination of HIF-1α and promoted its degradation via the ubiquitin proteasome system. Inhibition of HIF-1α by KMP resulted in the abrogation of the expression of glycolytic enzymes such as lactate dehydrogenase A and pyruvate dehydrogenase kinase isozyme 1. In addition, the metabolome profiling showed that KMP promoted oxidative energy production, while the mitochondrial complex activity assay indicated that KMP increased the activity of mitochondrial complex IV. Finally, we showed that KMP inhibited HIF-1α expression and increased intracellular ATP content in the soleus muscle of rats. Taken together, these results suggest that KMP increases intracellular ATP content under hypoxic conditions by suppressing the HIF-1α stabilization and/or by enhancing the mitochondrial complex IV activity in muscle.
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Key Words
- 2-OG, 2-oxoglutaric acid
- 3-PG, 3-phosphoglyceric acid
- ADP, adenosine diphosphate
- ATP, adenosine triphosphate
- AcCoA, acetyl CoA
- C(2)C(12) myotube
- CE-TOFMS, capillary electrophoresis time-of-flight mass spectrometry
- CHX, cycloheximide
- DFO, deferoxamine mesylate
- DMEM, Dulbecco's modified Eagle medium
- DMSO, dimethylsulfoxide
- EGCG, epigallocatechin gallate
- F1,6P, fructose-1,6-bisphosphate
- F6P, fructose-6-phosphate
- FAD, flavin adenine dinucleotide
- FBS, fetal bovine serum
- G6P, glucose-6-phosphate
- GAP, glyceraldehyde-3-phosphate
- HIF, hypoxia inducible factor
- HIF-1α, hypoxia
- HRE, hypoxia response element
- HS, horse serum
- HSP, heat shock protein
- KMP, kaempferol
- LDHA, lactate dehydrogenase A
- Lac, lactacystin
- NAD, nicotinamide adenine dinucleotide
- PBS, phosphate-buffered saline
- PDH, pyruvate dehydrogenase
- PDK1, pyruvate dehydrogenase kinase isozyme 1
- PEP, phosphoenolpyruvic acid
- PHD, prolyl hydroxylase
- RACK, receptor for activated C kinase
- RT-qPCR, reverse transcription-quantitative polymerase chain reaction
- TCA, tricarboxylic acid
- Ub, ubiquitin
- VHL, von Hippel–Lindau
- kaempferol
- metabolome profiling
- mitochondria
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Affiliation(s)
- Minoru Akiyama
- Saga Nutraceuticals Research Institute, Otsuka Pharmaceutical Co. Ltd., 5006-5 Yoshinogari-cho Kanzaki-gun, Saga, 842-0195, Japan
| | - Tsubasa Mizokami
- Saga Nutraceuticals Research Institute, Otsuka Pharmaceutical Co. Ltd., 5006-5 Yoshinogari-cho Kanzaki-gun, Saga, 842-0195, Japan
| | - Shingo Miyamoto
- Saga Nutraceuticals Research Institute, Otsuka Pharmaceutical Co. Ltd., 5006-5 Yoshinogari-cho Kanzaki-gun, Saga, 842-0195, Japan
| | - Yasutaka Ikeda
- Saga Nutraceuticals Research Institute, Otsuka Pharmaceutical Co. Ltd., 5006-5 Yoshinogari-cho Kanzaki-gun, Saga, 842-0195, Japan.
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Alehaideb Z, Alatar G, Nehdi A, Albaz A, Al-Eidi H, Almutairi M, Hawsa E, Alshuail N, Matou-Nasri S. Commiphora myrrha (Nees) Engl. resin extracts induce phase-I cytochrome P450 2C8, 2C9, 2C19, and 3A4 isoenzyme expressions in human hepatocellular carcinoma (HepG2) cells. Saudi Pharm J 2021; 29:361-368. [PMID: 34135662 PMCID: PMC8180464 DOI: 10.1016/j.jsps.2021.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 03/06/2021] [Indexed: 12/02/2022] Open
Abstract
Commiphora myrrha (Nees) Engl. (C. myrrha) resin is the most Middle Eastern herbal medicine used against numerous diseases. After being decocted or macerated, this resin is widely consumed among Saudi Arabian patients who are already under prescribed medication. Despite its popularity, no studies have been reported on potential modulation effects of these resin extracts on drug metabolism. Therefore, we studied C. myrrha resin extracts on the expression of cytochrome P450 (CYP) drug-metabolizing isoenzyme in human hepatocellular carcinoma cell line HepG2. The C. myrrha extracts were prepared by sonication and boiling, resembling the most popular traditional preparations of maceration and decoction, respectively. Both boiled and sonicated aqueous extracts were fingerprinted using high-performance liquid chromatography equipped with ultra-violet detector (HPLC-UVD). The viability of HepG2 cells treated with these aqueous extracts was determined using CellTiter-Glo® assay in order to select the efficient and non-toxic resin extract concentrations for phase-I metabolic CYP isoenzyme expression analysis. The isoenzyme gene and protein expression levels of CYP 2C8, 2C9, 2C19, and 3A4 were assessed using reverse transcription-quantitative polymerase chain reaction and Western blot technologies. The HPLC-UVD fingerprinting revealed different chromatograms for C. myrrha boiled and sonicated aqueous extracts. Both aqueous extracts were toxic to HepG2 cells when tested at concentrations exceeding 150 µg/ml of the dry crude extract. The CYP 2C8, 2C9, and 2C19 mRNA expression levels increased up to 4.0-fold in HepG2 cells treated with either boiled or sonicated C. myrrha aqueous extracts tested between 1 and 30 µg/ml, as compared with the untreated cells. However, CYP3A4 mRNA expression level exceeded the 2.0-fold cutoff when the cells were exposed to 30 µg/ml of C. myrrha extracts. The up-regulation of CYP mRNA expression levels induced by both boiled and sonicated C. myrrha aqueous extracts was confirmed at the CYP protein expression levels. In conclusion, both sonicated and boiled C. myrrha aqueous extracts modulate CYP 2C8, 2C9, 2C19, and 3A4 gene expression at clinically-relevant concentrations regardless of preparation methods. Further in vitro and in vivo experiments are required for CYP isoenzyme activity assessment and the establishment of herb-drug interaction profile for these traditional medicinal resin extracts.
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Key Words
- CO2, carbon dioxide
- CYP, cytochrome P450
- Commiphora myrrha
- Cytochrome P450
- DMEM, Dulbecco's Modified Eagle Medium
- Drug-metabolizing enzyme
- EU, endotoxin unit
- FBS, fetal bovine serum
- GAPDH, glyceraldehyde 3-phosphate dehydrogenase
- HPLC-UVD, high-performance liquid chromatography and ultra-violet detector
- Inducer
- Natural health product
- PBS, phosphate-buffered saline
- RT-qPCR, reverse transcription-quantitative polymerase chain reaction
- cDNA, complementary DNA
- mRNA, messenger ribonucleic acid
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Affiliation(s)
- Zeyad Alehaideb
- Cell and Gene Therapy Group, Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Ghada Alatar
- Cell and Gene Therapy Group, Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
| | - Atef Nehdi
- Department of Medical Research Core Facility and Platform, KAIMRC, Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Abeer Albaz
- Cell and Gene Therapy Group, Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
| | - Hamad Al-Eidi
- Cell and Gene Therapy Group, Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
| | | | - Esraa Hawsa
- Cell and Gene Therapy Group, Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
| | - Nora Alshuail
- Cell and Gene Therapy Group, Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
| | - Sabine Matou-Nasri
- Cell and Gene Therapy Group, Medical Genomics Research Department, King Abdullah International Medical Research Center (KAIMRC), Riyadh, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Corresponding author at: Cell and Gene Therapy Group, Medical Genomics Research Department, King Abdullah International Medical Research Center, King Saud Bin Abdulaziz University for Health Sciences, P.O. Box 3660, Riyadh 11481, MC 1515, Saudi Arabia.
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Alikian M, Gale RP, Apperley JF, Foroni L. Molecular techniques for the personalised management of patients with chronic myeloid leukaemia. Biomol Detect Quantif 2017; 11:4-20. [PMID: 28331814 PMCID: PMC5348117 DOI: 10.1016/j.bdq.2017.01.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 12/28/2016] [Accepted: 01/18/2017] [Indexed: 12/25/2022]
Abstract
Chronic myeloid leukemia (CML) is the paradigm for targeted cancer therapy. RT-qPCR is the gold standard for monitoring response to tyrosine kinase-inhibitor (TKI) therapy based on the reduction of blood or bone marrow BCR-ABL1. Some patients with CML and very low or undetectable levels of BCR-ABL1 transcripts can stop TKI-therapy without CML recurrence. However, about 60 percent of patients discontinuing TKI-therapy have rapid leukaemia recurrence. This has increased the need for more sensitive and specific techniques to measure residual CML cells. The clinical challenge is to determine when it is safe to stop TKI-therapy. In this review we describe and critically evaluate the current state of CML clinical management, different technologies used to monitor measurable residual disease (MRD) focus on comparingRT-qPCR and new methods entering clinical practice. We discuss advantages and disadvantages of new methods.
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Key Words
- ABL1, Abelson murine leukaemia virus
- ALL, acute lymphoblastic leukaemia
- AP, accelerated phase
- ARQ, armored RNA Quant
- ATP, adenosine triphosphate
- BC, blast crisis
- BCR, breakpoint cluster region
- BM, bone marrow
- BMT, bone marrow transplantation
- Bp, base pair
- CAP, College of American Pathology
- CES, capillary electrophoresis sequencing
- CML
- CML, chronic myeloid leukaemia
- CMR, complete molecular response/remission
- CP, chronic phase
- DESTINY, De-Escalation and Stopping Treatment of Imatinib, Nilotinib or sprYcel in Chronic Myeloid Leukaemia
- DNA, deoxyribonucleic acid
- EAC, Europe Against Cancer
- ELN, European Leukaemia Net
- EURO-SKI, European Stop Tyrosine Kinase Inhibitor Study
- GUSB, glucuronidase beta gene
- IC, inhibotory concentration
- IRIS, interferon and cytarabine versus STI571
- IS, International Scale
- InDels, insertions and deletions
- KDa, Kilo Dalton
- Kbp, Kilo Base Pairs
- LPC, leukemic progenitor cells
- LSC, leukemic stem cell
- LoD, limit of detection
- LoQ, limit of quantification
- M-bcr, major-breakpoint cluster region
- MMR, major molecular response/remission
- MR, deep molecular response/remission
- MRD
- MRD, minimal residual disease
- Mbp, mega base pair
- Molecular monitoring
- NCCN, National Comprehensive Cancer Network
- NEQAS, National External Quality Assessement Service
- NGS
- NGS, next generation sequencing
- NTC, No Template Control
- PB, Peripheral Blood
- PCR, Polymerase Chain Reaction
- PFS, Progression Free Survival
- Ph, Philadelpia
- Q-PCR, quantitative polymerase chain reaction
- QC, Quality Control
- RT, reverse transcription
- RT-dPCR, reverse transcription-digital polymerase chain reaction
- RT-qPCR, reverse transcription-quantitative polymerase chain reaction
- SCT, stem cell transplant
- SMRT, single-molecule real-time sequencing
- STIM, stop imatinib
- TKD, tyrosine kinase domain
- TKI, tyrosine kinase inhibitor
- WHO, World Health Organisation
- ZMW, zero-mode wave-guided
- allo-SCT, Allogeneic Stem Cell Transplantation
- cDNA, coding or complimentary DNA
- dMIQE, Minimum Information for Publication of Quantitative Digital PCR Experiments
- dPCR
- dPCR, digital polymerase chain reaction
- emPCR, emulsion PCR
- gDNA, genomic deoxyribonucleic acid
- m-bcr, minor-breakpoint cluster region
- mRNA, messenger RNA
- nM, manomolar
- μ-bcr, micro-breakpoint cluster region
- μg, microgram
- μl, microliter
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Affiliation(s)
- Mary Alikian
- Centre for Haematology, Department of Medicine, Imperial College London Hammersmith Hospital, London UK; Imperial Molecular Pathology, Imperial College Healthcare Trust, Hammersmith Hospital, London, UK
| | - Robert Peter Gale
- Centre for Haematology, Department of Medicine, Imperial College London Hammersmith Hospital, London UK
| | - Jane F Apperley
- Centre for Haematology, Department of Medicine, Imperial College London Hammersmith Hospital, London UK
| | - Letizia Foroni
- Centre for Haematology, Department of Medicine, Imperial College London Hammersmith Hospital, London UK
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Svec D, Tichopad A, Novosadova V, Pfaffl MW, Kubista M. How good is a PCR efficiency estimate: Recommendations for precise and robust qPCR efficiency assessments. Biomol Detect Quantif 2015; 3:9-16. [PMID: 27077029 PMCID: PMC4822216 DOI: 10.1016/j.bdq.2015.01.005] [Citation(s) in RCA: 308] [Impact Index Per Article: 34.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Revised: 01/24/2015] [Accepted: 01/28/2015] [Indexed: 01/22/2023]
Abstract
We have examined the imprecision in the estimation of PCR efficiency by means of standard curves based on strategic experimental design with large number of technical replicates. In particular, how robust this estimation is in terms of a commonly varying factors: the instrument used, the number of technical replicates performed and the effect of the volume transferred throughout the dilution series. We used six different qPCR instruments, we performed 1–16 qPCR replicates per concentration and we tested 2–10 μl volume of analyte transferred, respectively. We find that the estimated PCR efficiency varies significantly across different instruments. Using a Monte Carlo approach, we find the uncertainty in the PCR efficiency estimation may be as large as 42.5% (95% CI) if standard curve with only one qPCR replicate is used in 16 different plates. Based on our investigation we propose recommendations for the precise estimation of PCR efficiency: (1) one robust standard curve with at least 3–4 qPCR replicates at each concentration shall be generated, (2) the efficiency is instrument dependent, but reproducibly stable on one platform, and (3) using a larger volume when constructing serial dilution series reduces sampling error and enables calibration across a wider dynamic range.
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Key Words
- ANCOVA, analysis of covariance
- Amplification efficiency
- CLSI, Clinical and Laboratory Standards Institute
- Cq, cycle of quantification
- Dilution series
- E, PCR efficiency
- EPA, Environmental protection agency
- FDA, food and Drug Administration
- GMO, genetically modified organism
- IEC, International Electrotechnical Commission
- ISO, International Organization for Standardization
- MIQE, minimum information for publication of quantitative real-time PCR experiments
- NTC, no template control
- RIN, RNA Integrity Number
- RT-qPCR, reverse transcription-quantitative polymerase chain reaction
- Real-time quantitative PCR
- Standard curve
- qPCR
- qPCR assay validation
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Affiliation(s)
- David Svec
- Institute of Biotechnology, Academy of Science of the Czech Republic, Prague, Czech Republic; TATAA Biocenter, Gothenburg, Sweden
| | - Ales Tichopad
- Faculty of Medicine Pilsen, Charles University, Pilsen, Czech Republic
| | - Vendula Novosadova
- Institute of Biotechnology, Academy of Science of the Czech Republic, Prague, Czech Republic; TATAA Biocenter, Gothenburg, Sweden
| | - Michael W Pfaffl
- Physiology Weihenstephan, TUM - Technische Universität München, Freising, Germany
| | - Mikael Kubista
- Institute of Biotechnology, Academy of Science of the Czech Republic, Prague, Czech Republic; TATAA Biocenter, Gothenburg, Sweden
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