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Shi Z, Wei J, Rifkin AS, Wang CH, Billings LK, Woo JSH, Talamonti MS, Vogel TJ, Moore E, Brockstein BE, Khandekar JD, Dunnenberger HM, Hulick PJ, Duggan D, Zheng SL, Lee CJ, Helfand BT, Tafur AJ, Xu J. Cancer-associated thrombosis by cancer sites and inherited factors in a prospective population-based cohort. Thromb Res 2023; 229:69-72. [PMID: 37419004 DOI: 10.1016/j.thromres.2023.06.023] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/23/2023] [Accepted: 06/23/2023] [Indexed: 07/09/2023]
Abstract
Cancer-associated thrombosis (CAT) is common and associated with mortality. We estimated CAT rate by cancer sites and inherited factors among cancer patients from the UK Biobank (N =70,406). The 12-month CAT rate after cancer diagnosis was 2.37% overall but varied considerably among cancer sites. Among the 10 cancer sites classified as 'high-risk' of CAT by the National Comprehensive Cancer Network guidelines, 6 had CAT rate <5%. In contrast, 5 cancer sites classified as 'average-risk' by the guidelines had CAT rate >5%. For inherited risk factors, both known mutation carriers in two genes (F5/F2) and polygenic score for venous thromboembolism (VTE) (PGSVTE) were independently associated with increased CAT risk. While F5/F2 identified 6% patients with high genetic-risk for CAT, adding PGSVTE identified 13 % patients at equivalent/higher genetic-risk to CAT than that of F5/F2 mutations. Findings from this large prospective study, if confirmed, provide critical data to update guidelines for CAT risk assessment.
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Affiliation(s)
- Zhuqing Shi
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL, USA
| | - Jun Wei
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL, USA
| | - Andrew S Rifkin
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL, USA
| | - Chi-Hsiung Wang
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL, USA
| | - Liana K Billings
- Department of Medicine, NorthShore University HealthSystem, Evanston, IL, USA; University of Chicago Pritzker School of Medicine, Chicago, IL, USA
| | - Jonathan S H Woo
- Division of Hospital Medicine, NorthShore University HealthSystem, Evanston, IL, USA
| | - Mark S Talamonti
- Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
| | | | - Elena Moore
- Kellogg Cancer Center, NorthShore University HealthSystem, Evanston, IL, USA
| | - Bruce E Brockstein
- Kellogg Cancer Center, NorthShore University HealthSystem, Evanston, IL, USA
| | - Janardan D Khandekar
- Kellogg Cancer Center, NorthShore University HealthSystem, Evanston, IL, USA; Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, IL, USA
| | - Henry M Dunnenberger
- Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, IL, USA
| | - Peter J Hulick
- Department of Medicine, NorthShore University HealthSystem, Evanston, IL, USA; Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, IL, USA
| | - David Duggan
- Affiliate of City of Hope, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - S Lilly Zheng
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL, USA
| | - Cheong Jun Lee
- Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
| | - Brian T Helfand
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL, USA; University of Chicago Pritzker School of Medicine, Chicago, IL, USA; Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA
| | - Alfonso J Tafur
- Cardiovascular Institute, NorthShore University HealthSystem, Evanston, IL, USA.
| | - Jianfeng Xu
- Program for Personalized Cancer Care, NorthShore University HealthSystem, Evanston, IL, USA; University of Chicago Pritzker School of Medicine, Chicago, IL, USA; Department of Surgery, NorthShore University HealthSystem, Evanston, IL, USA; Neaman Center for Personalized Medicine, NorthShore University HealthSystem, Evanston, IL, USA.
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Lin CF, Lin HC. IMF-Based MF and HS Energy Feature Information of F5, and F6 Movement and Motor Imagery EEG Signals in Delta Rhythms Using HHT. Sensors (Basel) 2023; 23:1078. [PMID: 36772115 PMCID: PMC9920123 DOI: 10.3390/s23031078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
This study aims to extract the energy feature distributions in the form of marginal frequency (MF) and Hilbert spectrum (HS) in the intrinsic mode functions (IMF) domain for actual movement (AM)-based and motor imagery (MI)-based electroencephalogram (EEG) signals using the Hilbert-Huang transformation (HHT) time frequency (TF) analysis method. Accordingly, F5 and F6 EEG signal TF energy feature distributions in delta (0.5-4 Hz) rhythm are explored. We propose IMF-based and residue function (RF)-based MF and HS feature information extraction methods with IMFRFERDD (IMFRF energy refereed distribution density), IMFRFMFERDD (IMFRF MF energy refereed distribution density), and IMFRFHSERDD (IMFRF HS energy refereed distribution density) parameters using HHT with application to AM, MI EEG F5, and F6 signals in delta rhythm. The AM and MI tasks involve simultaneously opening fists and feet, as well as simultaneously closing fists and feet. Eight samples (32 in total) with a time duration of 1000 ms are extracted for analyzing F5AM, F5MI, F6AM, and F6MI EEG signals, which are decomposed into five IMFs and one RF. The maximum average IMFRFERDD values of IMF4 are 3.70, 3.43, 3.65, and 3.69 for F5AM, F5MI, F6 AM, and F6MI, respectively. The maximum average IMFRFMFERDD values of IMF4 in the delta rhythm are 21.50, 20.15, 21.02, and 17.30, for F5AM, F5MI, F6AM, and F6MI, respectively. Additionally, the maximum average IMFRFHSERDD values of IMF4 in delta rhythm are 39,21, 39.14, 36.29, and 33.06 with time intervals of 500-600, 800-900, 800-900, and 500-600 ms, for F5AM, F5MI, F6AM, and F6MI, respectively. The results of this study, advance our understanding of meaningful feature information of F5MM, F5MI, F6MM, and F6MI, enabling the design of MI-based brain-computer interface assistive devices for disabled persons.
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Affiliation(s)
- Chin-Feng Lin
- Correspondence: ; Tel.: +886-2-2462-2192 (ext. 6270)
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Fricke-Galindo I, Buendia-Roldan I, Chavez-Galan L, Pérez-Rubio G, Hernández-Zenteno RDJ, Ramos-Martinez E, Zazueta-Márquez A, Reyes-Melendres F, Alarcón-Dionet A, Guzmán-Vargas J, Bravo-Gutiérrez OA, Quintero-Puerta T, Gutiérrez-Pérez IA, Ortega-Martínez A, Ambrocio-Ortiz E, Nava-Quiroz KJ, Bañuelos-Flores JL, Jaime-Capetillo ME, Mejía M, Rojas-Serrano J, Falfán-Valencia R. SERPINE1 rs6092 Variant Is Related to Plasma Coagulation Proteins in Patients with Severe COVID-19 from a Tertiary Care Hospital. Biology (Basel) 2022; 11:biology11040595. [PMID: 35453794 PMCID: PMC9029072 DOI: 10.3390/biology11040595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 02/24/2022] [Revised: 03/17/2022] [Accepted: 04/12/2022] [Indexed: 12/24/2022]
Abstract
An impaired coagulation process has been described in patients with severe or critical coronavirus disease (COVID-19). Nevertheless, the implication of coagulation-related genes has not been explored. We aimed to evaluate the impact of F5 rs6025 and SERPINE1 rs6092 on invasive mechanical ventilation (IMV) requirement and the levels of coagulation proteins among patients with severe COVID-19. Four-hundred fifty-five patients with severe COVID-19 were genotyped using TaqMan assays. Coagulation-related proteins (P-Selectin, D-dimer, P-selectin glycoprotein ligand-1, tissue plasminogen activator [tPA], plasminogen activator inhibitor-1, and Factor IX) were assessed by cytometric bead arrays in one- and two-time determinations. Accordingly, SERPINE1 rs6092, P-Selectin (GG 385 pg/mL vs. AG+AA 632 pg/mL, p = 0.0037), and tPA (GG 1858 pg/mL vs. AG+AA 2546 pg/mL, p = 0.0284) levels were different. Patients carrying the CT F5-rs6025 genotype exhibited lower levels of factor IX (CC 17,136 pg/mL vs. CT 10,247 pg/mL, p = 0.0355). Coagulation proteins were also different among IMV patients than non-IMV. PSGL-1 levels were significantly increased in the late stage of COVID-19 (>10 days). The frequencies of F5 rs6025 and SERPINE1 rs6092 variants were not different among IMV and non-IMV. The SERPINE1 rs6092 variant is related to the impaired coagulation process in patients with COVID-19 severe.
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Affiliation(s)
- Ingrid Fricke-Galindo
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (I.F.-G.); (G.P.-R.); (A.Z.-M.); (F.R.-M.); (J.G.-V.); (O.A.B.-G.); (T.Q.-P.); (I.A.G.-P.); (A.O.-M.); (E.A.-O.); (K.J.N.-Q.)
| | - Ivette Buendia-Roldan
- Translational Research Laboratory on Aging and Pulmonary Fibrosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City 14080, Mexico; (I.B.-R.); (A.A.-D.)
| | - Leslie Chavez-Galan
- Laboratory of Integrative Immunology, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City 14080, Mexico;
| | - Gloria Pérez-Rubio
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (I.F.-G.); (G.P.-R.); (A.Z.-M.); (F.R.-M.); (J.G.-V.); (O.A.B.-G.); (T.Q.-P.); (I.A.G.-P.); (A.O.-M.); (E.A.-O.); (K.J.N.-Q.)
| | | | - Espiridión Ramos-Martinez
- Unidad de Investigación en Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 06720, Mexico;
| | - Armando Zazueta-Márquez
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (I.F.-G.); (G.P.-R.); (A.Z.-M.); (F.R.-M.); (J.G.-V.); (O.A.B.-G.); (T.Q.-P.); (I.A.G.-P.); (A.O.-M.); (E.A.-O.); (K.J.N.-Q.)
| | - Felipe Reyes-Melendres
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (I.F.-G.); (G.P.-R.); (A.Z.-M.); (F.R.-M.); (J.G.-V.); (O.A.B.-G.); (T.Q.-P.); (I.A.G.-P.); (A.O.-M.); (E.A.-O.); (K.J.N.-Q.)
| | - Aimé Alarcón-Dionet
- Translational Research Laboratory on Aging and Pulmonary Fibrosis, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City 14080, Mexico; (I.B.-R.); (A.A.-D.)
| | - Javier Guzmán-Vargas
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (I.F.-G.); (G.P.-R.); (A.Z.-M.); (F.R.-M.); (J.G.-V.); (O.A.B.-G.); (T.Q.-P.); (I.A.G.-P.); (A.O.-M.); (E.A.-O.); (K.J.N.-Q.)
| | - Omar Andrés Bravo-Gutiérrez
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (I.F.-G.); (G.P.-R.); (A.Z.-M.); (F.R.-M.); (J.G.-V.); (O.A.B.-G.); (T.Q.-P.); (I.A.G.-P.); (A.O.-M.); (E.A.-O.); (K.J.N.-Q.)
| | - Teresa Quintero-Puerta
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (I.F.-G.); (G.P.-R.); (A.Z.-M.); (F.R.-M.); (J.G.-V.); (O.A.B.-G.); (T.Q.-P.); (I.A.G.-P.); (A.O.-M.); (E.A.-O.); (K.J.N.-Q.)
| | - Ilse Adriana Gutiérrez-Pérez
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (I.F.-G.); (G.P.-R.); (A.Z.-M.); (F.R.-M.); (J.G.-V.); (O.A.B.-G.); (T.Q.-P.); (I.A.G.-P.); (A.O.-M.); (E.A.-O.); (K.J.N.-Q.)
| | - Alejandro Ortega-Martínez
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (I.F.-G.); (G.P.-R.); (A.Z.-M.); (F.R.-M.); (J.G.-V.); (O.A.B.-G.); (T.Q.-P.); (I.A.G.-P.); (A.O.-M.); (E.A.-O.); (K.J.N.-Q.)
| | - Enrique Ambrocio-Ortiz
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (I.F.-G.); (G.P.-R.); (A.Z.-M.); (F.R.-M.); (J.G.-V.); (O.A.B.-G.); (T.Q.-P.); (I.A.G.-P.); (A.O.-M.); (E.A.-O.); (K.J.N.-Q.)
| | - Karol J. Nava-Quiroz
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (I.F.-G.); (G.P.-R.); (A.Z.-M.); (F.R.-M.); (J.G.-V.); (O.A.B.-G.); (T.Q.-P.); (I.A.G.-P.); (A.O.-M.); (E.A.-O.); (K.J.N.-Q.)
| | - José Luis Bañuelos-Flores
- Clinical Laboratory Service, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.L.B.-F.); (M.E.J.-C.)
| | - María Esther Jaime-Capetillo
- Clinical Laboratory Service, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (J.L.B.-F.); (M.E.J.-C.)
| | - Mayra Mejía
- Interstitial Pulmonary Diseases and Rheumatology Unit, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City 06720, Mexico; (M.M.); (J.R.-S.)
| | - Jorge Rojas-Serrano
- Interstitial Pulmonary Diseases and Rheumatology Unit, Instituto Nacional de Enfermedades Respiratorias Ismael Cosio Villegas, Mexico City 06720, Mexico; (M.M.); (J.R.-S.)
| | - Ramcés Falfán-Valencia
- HLA Laboratory, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City 14080, Mexico; (I.F.-G.); (G.P.-R.); (A.Z.-M.); (F.R.-M.); (J.G.-V.); (O.A.B.-G.); (T.Q.-P.); (I.A.G.-P.); (A.O.-M.); (E.A.-O.); (K.J.N.-Q.)
- Correspondence: ; Tel.: +52-55-5487-1700 (ext. 5152)
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Schneider M, Broggini AC, Dann B, Tzanou A, Uran C, Sheshadri S, Scherberger H, Vinck M. A mechanism for inter-areal coherence through communication based on connectivity and oscillatory power. Neuron 2021; 109:4050-4067.e12. [PMID: 34637706 PMCID: PMC8691951 DOI: 10.1016/j.neuron.2021.09.037] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 07/14/2021] [Accepted: 09/17/2021] [Indexed: 11/21/2022]
Abstract
Inter-areal coherence between field potentials is a widespread phenomenon in cortex. Coherence has been hypothesized to reflect phase-synchronization between oscillators and flexibly gate communication according to behavioral and cognitive demands. We reveal an alternative mechanism where coherence is not the cause but the consequence of communication and naturally emerges because spiking activity in a sending area causes post-synaptic potentials both in the same and in other areas. Consequently, coherence depends in a lawful manner on power and phase-locking in the sender and connectivity. Changes in oscillatory power explained prominent changes in fronto-parietal and LGN-V1 coherence across behavioral conditions. Optogenetic experiments and excitatory-inhibitory network simulations identified afferent synaptic inputs rather than spiking entrainment as the principal determinant of coherence. These findings suggest that unique spectral profiles of different brain areas automatically give rise to large-scale coherence patterns that follow anatomical connectivity and continuously reconfigure as a function of behavior and cognition.
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Affiliation(s)
- Marius Schneider
- Ernst Strüngmann Institute (ESI) for Neuroscience in Cooperation with Max Planck Society, 60528 Frankfurt am Main, Germany; Donders Centre for Neuroscience, Department of Neuroinformatics, Radboud University Nijmegen, 6525 Nijmegen, the Netherlands.
| | - Ana Clara Broggini
- Ernst Strüngmann Institute (ESI) for Neuroscience in Cooperation with Max Planck Society, 60528 Frankfurt am Main, Germany
| | | | - Athanasia Tzanou
- Ernst Strüngmann Institute (ESI) for Neuroscience in Cooperation with Max Planck Society, 60528 Frankfurt am Main, Germany
| | - Cem Uran
- Ernst Strüngmann Institute (ESI) for Neuroscience in Cooperation with Max Planck Society, 60528 Frankfurt am Main, Germany
| | - Swathi Sheshadri
- German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, University of Goettingen, 37073 Goettingen, Germany
| | - Hansjörg Scherberger
- German Primate Center, 37077 Göttingen, Germany; Faculty of Biology and Psychology, University of Goettingen, 37073 Goettingen, Germany
| | - Martin Vinck
- Ernst Strüngmann Institute (ESI) for Neuroscience in Cooperation with Max Planck Society, 60528 Frankfurt am Main, Germany; Donders Centre for Neuroscience, Department of Neuroinformatics, Radboud University Nijmegen, 6525 Nijmegen, the Netherlands.
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Dong R, Chen G, Jin Y, Wang M, Cheng X, Chen Y. Significance of the p.Phe218Ser and p.Gly304Glu F5 Variants in Hereditary Factor V Deficiency. Acta Haematol 2021; 144:712-716. [PMID: 34280927 DOI: 10.1159/000512363] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 10/17/2020] [Indexed: 11/19/2022]
Abstract
Hereditary factor V (FV) deficiency is a rare autosomal recessive bleeding disorder caused by F5 gene mutations. The objective of this study was to investigate the p.Phe218Ser and p.Gly304Glu variants found in 2 families with hereditary FV deficiency. The FV activity (FV:C) and FV antigen (FV:Ag) were measured by clotting and ELISA, respectively. The F5 gene and sequence conservation were analyzed by direct sequencing and ClustalX-2.1-win, respectively. One proband carried a homozygous p.Phe218Ser (c.653T>C) mutation, with FV:C and FV:Ag decreased to 11 and 14%, respectively. The other proband carried a heterozygous p.Gly304Glu (c.911G>A) mutation, with FV:C and FV:Ag reduced to 55 and 62%, respectively. Phe218 and Gly304 were highly conserved in the homologous gene in 9 other species. We hypothesized that the p.Phe218Ser and p.Gly304Glu variants are deleterious and responsible for the reduction in FV:C and FV:Ag.
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Affiliation(s)
- Rujiao Dong
- Department of Hematology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Guoliang Chen
- Department of Spine Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yanhui Jin
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Mingshan Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiaoli Cheng
- Department of Clinical Laboratory, The First Affiliated Hospital of Air Force Medical University, Xi'an, China
| | - Yi Chen
- Department of Hematology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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Gemmati D, Longo G, Franchini E, Araujo Silva J, Gallo I, Lunghi B, Moratelli S, Maestri I, Serino ML, Tisato V. Cis-Segregation of c.1171C>T Stop Codon (p.R391*) in SERPINC1 Gene and c.1691G>A Transition (p.R506Q) in F5 Gene and Selected GWAS Multilocus Approach in Inherited Thrombophilia. Genes (Basel) 2021; 12:934. [PMID: 34207366 DOI: 10.3390/genes12060934] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/12/2021] [Accepted: 06/15/2021] [Indexed: 12/21/2022] Open
Abstract
Inherited thrombophilia (e.g., venous thromboembolism, VTE) is due to rare loss-of-function mutations in anticoagulant factors genes (i.e., SERPINC1, PROC, PROS1), common gain-of-function mutations in procoagulant factors genes (i.e., F5, F2), and acquired risk conditions. Genome Wide Association Studies (GWAS) recently recognized several genes associated with VTE though gene defects may unpredictably remain asymptomatic, so calculating the individual genetic predisposition is a challenging task. We investigated a large family with severe, recurrent, early-onset VTE in which two sisters experienced VTE during pregnancies characterized by a perinatal in-utero thrombosis in the newborn and a life-saving pregnancy-interruption because of massive VTE, respectively. A nonsense mutation (CGA > TGA) generating a premature stop-codon (c.1171C>T; p.R391*) in the exon 6 of SERPINC1 gene (1q25.1) causing Antithrombin (AT) deficiency and the common missense mutation (c.1691G>A; p.R506Q) in the exon 10 of F5 gene (1q24.2) (i.e., FV Leiden; rs6025) were coinherited in all the symptomatic members investigated suspecting a cis-segregation further confirmed by STR-linkage-analyses [i.e., SERPINC1 IVS5 (ATT)5–18, F5 IVS2 (AT)6–33 and F5 IVS11 (GT)12–16] and SERPINC1 intragenic variants (i.e., rs5878 and rs677). A multilocus investigation of blood-coagulation balance genes detected the coexistence of FV Leiden (rs6025) in trans with FV HR2-haplotype (p.H1299R; rs1800595) in the aborted fetus, and F11 rs2289252, F12 rs1801020, F13A1 rs5985, and KNG1 rs710446 in the newborn and other members. Common selected gene variants may strongly synergize with less common mutations tuning potential life-threatening conditions when combined with rare severest mutations. Merging classic and newly GWAS-identified gene markers in at risk families is mandatory for VTE risk estimation in the clinical practice, avoiding partial risk score evaluation in unrecognized at risk patients.
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Khidri FF, Waryah YM, Ali FK, Shaikh H, Ujjan ID, Waryah AM. MTHFR and F5 genetic variations have association with preeclampsia in Pakistani patients: a case control study. BMC Med Genet 2019; 20:163. [PMID: 31646966 PMCID: PMC6813118 DOI: 10.1186/s12881-019-0905-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 05/12/2019] [Accepted: 10/02/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND To study the role of single nucleotide variants (SNVs) of genes related to preeclampsia in Pakistani pregnant women. METHODS After ethical approval and getting informed consent; 250 pregnant women were enrolled and equally divided into two groups (125 preeclamptic cases and 125 normotensive pregnant women). Demographic details and medical history were recorded, and 10 ml blood sample was obtained for DNA extraction. The tetra-primer amplification refractory mutation system (ARMS) assays were developed for assessing the variants of three preeclampsia related genes; F5, MTHFR and VEGFA. An association of six SNVs; F5:c.1601G > A (rs6025), F5:c.6665A > G (rs6027), MTHFR: c.665C > T (rs1801133), MTHFR: c.1286A > C (rs1801131), VEGFA: c.-2055A > C (rs699947) and VEGFA: c.*237C > T (rs3025039) with preeclampsia was determined by using different genetic models. RESULTS Genotyping of the SNVs revealed that patients with MTHFR:c.665C > T, have increased susceptibility to preeclampsia (CT versus CC/TT: OR = 2.79, 95% CI = 1.18-6.59; P* = 0.046 and CT/TT vs CC: OR = 2.91, 95% CI = 1.29-6.57; P* = 0.0497, in overdominant and dominant models, respectively), whereas F5:c.6665A > G, (A/G vs AA/GG: OR = 0.42, 95% CI = 0.21-0.84; P* = 0.038 in overdominant model) and MTHFR:c.1286A > C, (CC versus AA: OR = 0.36, 95% CI = 0.18-0.72; P* = 0.0392 in codominant model) have significantly decreased risk for preeclampsia. F5:c.1601G > A, VEGFA: c.-2055A > C and VEGFA: c.*237C > T variants revealed no relationship with the disease. CONCLUSION This is the first case control study describing the protective role of F5:c.6665A > G against preeclampsia in any world population. In addition, the present study confirmed the association and role of MTHFR gene variations in the development of preeclampsia in Pakistani patients. Further genetic studies may be required to better understand the complex genetic mechanism of SNVs in preeclampsia related genes in pregnant women.
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Affiliation(s)
- Feriha Fatima Khidri
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan.,Department of Biochemistry, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Yar Muhammad Waryah
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan.,Department of Chemistry, Shaheed Benazir Bhutto University, Shaheed Benazir Abad, Pakistan
| | - Faiza Kamran Ali
- Department of Gynaecology and Obstetrics, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Hina Shaikh
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Ikram Din Ujjan
- Department of Pathology, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan
| | - Ali Muhammad Waryah
- Molecular Biology and Genetics Department, Medical Research Center, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan. .,Department of Pathology, Liaquat University of Medical and Health Sciences, Jamshoro, Pakistan.
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Abstract
Purpose/Aim: Many genes have been associated with primary open-angle glaucoma (POAG). Knowing exactly where they are expressed in the eye helps to unravel POAG pathology and to select optimal targets for intervention. We investigated whether RNA in situ hybridization (RNA-ISH) is a convenient technique to obtain detailed pan-ocular expression data of these genes. We tested this for four diverse candidate POAG genes, selected because of unclear ocular distribution (F5 and Dusp1) and relevance for potential new therapies (Tnf, Tgfβr3). Optn, a POAG gene with well-known ocular expression pattern served as control. Methods: We made a list of candidate glaucoma genes reported in genetic studies. A table of their ocular expression at the tissue level was compiled using publicly available microarray data (the ocular tissue database). To add cellular detail we performed RNA-ISH for Optn, Tnf, Tgfβr3, F5, and Dusp1 on eyes of healthy, 2-month-old, pigmented, and albino mice. Results: Expression of the Optn control matched with published immunohistochemistry data. Ocular expression of Tnf was generally low, with patches of higher Tnf expression, superficially in the corneal epithelium. F5 had a restricted expression pattern with high expression in the nonpigmented ciliary body epithelium and moderate expression in the peripapillary region. Tgfβr3 and Dusp1 showed ubiquitous expression. Conclusions: RNA-ISH is a suitable technique to determine the ocular expression pattern of POAG genes, adding meaningful cellular detail to existing microarray expression data. For instance, the high expression of F5 in the nonpigmented ciliary body epithelium suggests a role of this gene in aqueous humor dynamics and intraocular pressure. In addition, the ubiquitous expression of Tgfβr3 has implications for designing TGF-β-related glaucoma therapies, with respect to side effects. Creating pan-ocular expression maps of POAG genes with RNA-ISH will help to identify POAG pathways in specific cell types and to select targets for drug development.
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Affiliation(s)
- Wouter H G Hubens
- University Eye Clinic Maastricht, Maastricht University Medical Center , Maastricht , The Netherlands.,Department of Mental Health and Neuroscience, Maastricht University , Maastricht , The Netherlands
| | - Esmee M Breddels
- Department of Mental Health and Neuroscience, Maastricht University , Maastricht , The Netherlands
| | - Youssef Walid
- Department of Mental Health and Neuroscience, Maastricht University , Maastricht , The Netherlands
| | - Wishal D Ramdas
- University Eye Clinic Maastricht, Maastricht University Medical Center , Maastricht , The Netherlands.,Department of Ophthalmology, Erasmus Medical Center , Rotterdam , The Netherlands
| | | | - Theo G M F Gorgels
- University Eye Clinic Maastricht, Maastricht University Medical Center , Maastricht , The Netherlands.,The Netherlands Institute for Neuroscience (NIN-KNAW), Royal Netherlands Academy of Arts and Sciences , Amsterdam , The Netherlands
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9
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Kimelfeld EI, Koltsova EA, Petrova EA, Gudkova VV, Stahovskaya LV, Tupitsyna TV, Bondarenko EA, Slominsky PA, Limborska SA. [The association of hemostasis system genes with the development of ischemic stroke in patients under the age of 50 years]. Zh Nevrol Psikhiatr Im S S Korsakova 2018; 118:14-21. [PMID: 30499554 DOI: 10.17116/jnevro201811809214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
AIM To study an influence of polymorphic variants of hemostasis system genes on the risk of ischemic stroke (IS) in patients of the Slavic population under the age of 50 years. MATERIAL AND METHODS Ninety-two patients (19 women and 73 men), aged 18-50 years, were examined. The diagnosis of stroke was confirmed by neuroimaging (CT or MRI) in all patients. Polymorphic alleles of GP1BA, F2, F5 were studied by a real-time polymerase chain reaction using the TaqMan technology. RESULTS AND CONCLUSION An analysis of the GP1BA -5T/C polymorphism showed that it was associated with IS in young men, lacunar stroke and stroke due to thrombosis of the brachiocephalic arteries. This association was not found in young women. The F5 G1691A polymorphism was associated with lacunar stroke. The F2 G20210A polymorphism was associated with stroke due to thrombosis of the brachiocephalic arteries.
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Affiliation(s)
- E I Kimelfeld
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - E A Koltsova
- Pirogov Russian National Research Medical University, Moscow, Russia; Research Institute of Cerebrovascular Pathology and Stroke, Pirogov Russian National Research Medical University, Moscow, Russia
| | - E A Petrova
- Pirogov Russian National Research Medical University, Moscow, Russia; Research Institute of Cerebrovascular Pathology and Stroke, Pirogov Russian National Research Medical University, Moscow, Russia
| | - V V Gudkova
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - L V Stahovskaya
- Pirogov Russian National Research Medical University, Moscow, Russia; Research Institute of Cerebrovascular Pathology and Stroke, Pirogov Russian National Research Medical University, Moscow, Russia
| | - T V Tupitsyna
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - E A Bondarenko
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - P A Slominsky
- Research Institute of Cerebrovascular Pathology and Stroke, Pirogov Russian National Research Medical University, Moscow, Russia; Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
| | - S A Limborska
- Research Institute of Cerebrovascular Pathology and Stroke, Pirogov Russian National Research Medical University, Moscow, Russia; Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, Russia
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10
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Dai B, Yang T, Shi X, Ma N, Kang Y, Zhang J, Zhang Y. HMQ-T- F5 (1-(4-(2-aminoquinazolin-7-yl)phenyl)-3-(2‑bromo‑5- (trifluoromethoxy)phenyl) thiourea) suppress proliferation and migration of human cervical HeLa cells via inhibiting Wnt/β-catenin signaling pathway. Phytomedicine 2018; 51:48-57. [PMID: 30466627 DOI: 10.1016/j.phymed.2018.06.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 04/14/2018] [Accepted: 06/18/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND Drug therapy plays an important role in the treatment of cervical cancer, which is one of the most common solid tumors in women. Therefore, it is important to seek more effective and less toxic therapies. PURPOSE The aim of this study is to investigate the therapeutic potential of HMQ-T-F5 (1-(4-(2-aminoquinazolin-7-yl)phenyl)-3-(2‑bromo‑5-(trifluoromethoxy) phenyl)thiourea) (F5) for cervical cancer and explore the related mechanism. METHODS By performing MTT assay, colony formation assay, flow cytometry, wound-healing assay, transwell assay, immunofluorescent staining and siRNA assay, we study the effect of F5 on human cervical HeLa cells. The mechanism of F5 was also investigated. RESULTS We found that F5 significantly inhibited HeLa cell proliferation, led to accumulation of cells in the S phase, and induced apoptosis and inhibited migration. Mechanistically, F5 inhibited HeLa cell growth and migration through repressing the expression and nuclear translocation of β-catenin, enhancing Axin expression, inhibiting the phosphorylation of LRP5/6 and GSK3β, as well as downregulating the Wnt downstream targeted proteins. Knockdown of a checkpoint β-catenin by siRNA significantly attenuated HeLa cell proliferation. Furthermore, XAV939, an inhibitor of β-catenin, was used to treat HeLa cells and the results demonstrated that F5 inhibited proliferation and migration via the inhibition of the Wnt/β-catenin pathway. CONCLUSION Our findings demonstrated that F5 can target β-catenin potentially and is useful in the treatment of cervical cancer.
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Affiliation(s)
- Bingling Dai
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Street, #54, Xi'an 710061, Shaanxi Province, P.R. China.
| | - Tianfeng Yang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Street, #54, Xi'an 710061, Shaanxi Province, P.R. China.
| | - Xianpeng Shi
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Street, #54, Xi'an 710061, Shaanxi Province, P.R. China.
| | - Nan Ma
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Street, #54, Xi'an 710061, Shaanxi Province, P.R. China.
| | - Yuan Kang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Street, #54, Xi'an 710061, Shaanxi Province, P.R. China.
| | - Jie Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Street, #54, Xi'an 710061, Shaanxi Province, P.R. China.
| | - Yanmin Zhang
- School of Pharmacy, Health Science Center, Xi'an Jiaotong University, No. 76, Yanta West Street, #54, Xi'an 710061, Shaanxi Province, P.R. China.
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11
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Yap HYY, Tan NH, Ng ST, Tan CS, Fung SY. Molecular attributes and apoptosis-inducing activities of a putative serine protease isolated from Tiger Milk mushroom ( Lignosus rhinocerus) sclerotium against breast cancer cells in vitro. PeerJ 2018; 6:e4940. [PMID: 29888137 PMCID: PMC5993024 DOI: 10.7717/peerj.4940] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 03/09/2018] [Accepted: 05/18/2018] [Indexed: 12/14/2022] Open
Abstract
Background The highly valued medicinal tiger milk mushroom (also known as Lignosus rhinocerus) has the ability to cure numerous ailments. Its anticancer activities are well explored, and recently a partially purified cytotoxic protein fraction termed F5 from the mushroom’s sclerotial cold water extract consisting mainly of fungal serine proteases was found to exhibit potent selective cytotoxicity against a human breast adenocarcinoma cell line (MCF7) with IC50 value of 3.00 μg/ml. However, characterization of its cell death-inducing activity has yet to be established. Methods The mechanism involved in the cytotoxic activities of F5 against MCF7 cells was elucidated by flow cytometry-based apoptosis detection, caspases activity measurement, and expression profiling of apoptosis markers by western blotting. Molecular attributes of F5 were further mined from L. rhinocerus’s published genome and transcriptome for future exploration. Results and Discussion Apoptosis induction in MCF7 cells by F5 may involve a cross-talk between the extrinsic and intrinsic apoptotic pathways with upregulation of caspase-8 and -9 activities and a marked decrease of Bcl-2. On the other hand, the levels of pro-apoptotic Bax, BID, and cleaved BID were increased accompanied by observable actin cleavage. At gene level, F5 composed of three predicted non-synonymous single nucleotide polymorphisms (T > C) and an alternative 5′ splice site. Conclusions Findings from this study provide an advanced framework for further investigations on cancer therapeutics development from L. rhinocerus.
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Affiliation(s)
- Hui Yeng Y Yap
- Department of Oral Biology, Faculty of Dentistry, MAHSA University, Kuala Lumpur, Malaysia
| | - Nget Hong Tan
- Medicinal Mushroom Research Group, Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Wilayah Persekutuan, Malaysia
| | - Szu Ting Ng
- Ligno Biotech Sdn Bhd, Balakong Jaya, Selangor, Malaysia
| | - Chon Seng Tan
- Ligno Biotech Sdn Bhd, Balakong Jaya, Selangor, Malaysia
| | - Shin Yee Fung
- Medicinal Mushroom Research Group, Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Wilayah Persekutuan, Malaysia.,Center for Natural Products Research and Drug Discovery, University of Malaya, Kuala Lumpur, Malaysia
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12
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Bogdanov KV, Nikitin MM, Slyadnev MN. [Allele polymorphism analysis in coagulation factors F2, F5 and folate metabolism gene MTHFR by using microchip-based multiplex real time PCR]. Biomed Khim 2015. [PMID: 26215413 DOI: 10.18097/pbmc20156103357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Single nucleotide polymorphism (SNP) genotyping methods are widely used for the detection of hereditary thrombophilias caused by genetic defects in the coagulation system. The hereditary thrombophilias are frequently associated with higher incidences of point mutations in hemostasis (F2 20210G>A, F5 1691G>A) and folate metabolism (MTHFR 677C>Т, MTHFR 1298A>C) genes. Moreover, the combination of gene abnormalities in F2 or/and MTHFR with F5 Leiden mutation leads to increased risk of developing thrombosis. Thus, simultaneous detection of the multiple gene mutations in a sample has important clinical relevance. The microchip-based multiplex real time PCR for estimation of allele specific polymorphism in hemostatic and folate metabolism genes presented here has a high efficiency and may be used for laboratory diagnosis. The optimized protocol for estimation of 4 different types of genetic polymorphisms allowed PCR to be performed with minimal quantity of DNA template and PCR reagents including Taq polymerase and a short-term thermocycling.
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Affiliation(s)
- K V Bogdanov
- Institute of Hematology, V.A. Almazov Federal Medical Research Centre, St. Petersburg, Russia; Lumex Group, St. Petersburg, Russia
| | - M M Nikitin
- St. Petersburg State University, St. Petersburg, Russia; Lumex Group, St. Petersburg, Russia
| | - M N Slyadnev
- St. Petersburg State University, St. Petersburg, Russia; Lumex Group, St. Petersburg, Russia
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13
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Abstract
Mirror neurons were first discovered in area F5 of macaque monkeys. In humans, noninvasive studies have demonstrated an increased blood oxygen level-dependent (BOLD) signal in homologous motor areas during action observation. One approach to demonstrating that this indicates the existence of mirror neurons in humans has been to employ functional (f)MRI adaptation to test whether the same population of neurons is active during both observation and execution conditions. Although a number of human studies have reported fMRI adaptation in these areas, a recent study has shown that macaque mirror neurons do not attenuate their firing rate with two repetitions. Here we investigated whether mirror neurons modulate their firing rate when monkeys observed the same repeated natural action multiple times. We recorded from 67 mirror neurons in area F5 of two macaque monkeys while they observed an experimenter perform a reach-to-grasp action on a small food reward using a precision grip. Although no changes were detectable for the first two repetitions, we show that both the firing rate and the latency at which mirror neurons discharged during observation were subtly modulated by the repetition of the observed action over 7-10 trials. Significant adaption was mostly found in the period immediately before the grasp was performed. We also found that the local field potential activity in F5 (beta-frequency range, 16-23 Hz), which is attenuated during action observation, also showed systematic changes with repeated observation. These LFP changes occurred well in advance of the mirror neuron adaptation. We conclude that macaque mirror neurons can show intra-modal adaptation, but whether this is related to fMRI adaptation of the BOLD signal requires further investigation.
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Affiliation(s)
- J. M. Kilner
- 1The Wellcome Trust Centre for Neuroimaging, Univeristy College of London Institute of Neurology, London, United Kingdom; and
- 2Sobell Department of Motor Neuroscience and Movement Disorders, Univeristy College of London Institute of Neurology, London, United Kingdom
| | - A. Kraskov
- 2Sobell Department of Motor Neuroscience and Movement Disorders, Univeristy College of London Institute of Neurology, London, United Kingdom
| | - R. N. Lemon
- 2Sobell Department of Motor Neuroscience and Movement Disorders, Univeristy College of London Institute of Neurology, London, United Kingdom
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14
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von Knethen A, Sha LK, Kuchler L, Heeg AK, Fuhrmann D, Heide H, Wittig I, Maier TJ, Steinhilber D, Brüne B. 5-Lipoxygenase contributes to PPARγ activation in macrophages in response to apoptotic cells. Cell Signal 2013; 25:2762-8. [PMID: 24036216 DOI: 10.1016/j.cellsig.2013.08.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [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: 08/22/2013] [Accepted: 08/30/2013] [Indexed: 12/21/2022]
Abstract
Macrophage polarization to an anti-inflammatory phenotype upon contact with apoptotic cells is a contributing hallmark to immune suppression during the late phase of sepsis. Although the peroxisome proliferator-activated receptor γ (PPARγ) supports this macrophage phenotype switch, it remains elusive how apoptotic cells activate PPARγ. Assuming that a molecule causing PPARγ activation in macrophages originates in the cell membrane of apoptotic cells we analyzed lipid rafts from apoptotic, necrotic, and living human Jurkat T cells which showed the presence of 5-lipoxygenase (5-LO) in lipid rafts of apoptotic cells only. Incubating macrophages with lipid rafts of apoptotic, but not necrotic or living cells, induced PPAR responsive element (PPRE)-driven mRuby reporter gene expression in RAW 264.7 macrophages stably transduced with a 4xPPRE containing vector. Experiments with lipid rafts of apoptotic murine EL4 T cells revealed similar results. To verify the involvement of 5-LO in activating PPARγ in macrophages, Jurkat T cells were incubated with the 5-LO inhibitor MK-866 prior to induction of apoptosis, which failed to induce mRuby expression. Similar results were obtained with lipid rafts of apoptotic EL4 T cells preexposed to the 5-LO inhibitors zileuton and CJ-13610. Interestingly, Jurkat T cells overexpressing 5-LO failed to activate PPARγ in macrophages, while their 5-LO overexpressing apoptotic counterparts did. Our results suggest that during apoptosis 5-LO gets associated with lipid rafts and synthesizes ligands that in turn stimulate PPARγ in macrophages.
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Affiliation(s)
- Andreas von Knethen
- Institute of Biochemistry I-Pathobiochemistry, Faculty of Medicine, Goethe-University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt, Germany.
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15
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Shams Z, Tahamtan Y, Pourbakhsh A, Hosseiny MH, Kargar M, Hayati M. Detection of enterotoxigenic K99 ( F5) and F41 from fecal sample of calves by molecular and serological methods. ACTA ACUST UNITED AC 2010; 21:475-478. [PMID: 32214971 PMCID: PMC7088004 DOI: 10.1007/s00580-010-1122-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2010] [Accepted: 10/08/2010] [Indexed: 11/02/2022]
Abstract
Enterotoxigenic Escherichia coli (ETEC) is one of the major causes of neonatal calf diarrhea. Almost all ETEC bacteria are known to adhere to receptors on the small intestinal epithelium via their fimbriae, (F5 (K99) and F41).This study was undertaken to investigate the phenotypic and genotypic screening of virulence genes in E. coli K99 and F41. During January 2008 to December 2009, 298 diarrheic neonatal calves at 1-30 days old were studied by multiplex PCR, isolation, and serological grouping. Of the 298 diarrheic samples, 268 E. coli were isolated, of which 16 samples (5.3%) were positive for having the F5 (K99) fimbrial gene by PCR while all of the E. coli isolates also carried F41 fimbrial genes. Twenty-five percent of the isolates were proven not to be toxigenic as they did not possess the STa enterotoxin gene.
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Affiliation(s)
| | - Yahya Tahamtan
- 2Razi Vaccine and Serum Research Institute, Sanaye Sq., Shiraz, Iran
| | - Ali Pourbakhsh
- 2Razi Vaccine and Serum Research Institute, Sanaye Sq., Shiraz, Iran
| | | | | | - Masoumeh Hayati
- 2Razi Vaccine and Serum Research Institute, Sanaye Sq., Shiraz, Iran
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Seipp MT, Durtschi JD, Voelkerding KV, Wittwer CT. Multiplex amplicon genotyping by high-resolution melting. J Biomol Tech 2009; 20:160-164. [PMID: 19568454 PMCID: PMC2700465] [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] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
High-resolution amplicon melting is a simple method for genotyping that uses only generic PCR primers and a saturating DNA dye. Multiplex amplicon genotyping has previously been reported in a single color, but two instruments were required: a carousel-based rapid cycler and a high-resolution melting instrument for capillaries. Manual transfer of capillaries between instruments and sequential melting of each capillary at 0.1 degrees C/s seriously limited the throughput. In this report, a single instrument that combines rapid-cycle real-time PCR with high-resolution melting [LightScanner-32 (LS-32), Idaho Technology, Salt Lake City, UT] was used for multiplex amplicon genotyping. The four most common mutations associated with thrombophilia, F5 (factor V Leiden 1691G>A), F2 (prothrombin 20210G>A), and methylenetetrahydrofolate reductase (MTHFR; 1298A>C and 677C>T) were genotyped in a single homogeneous assay with internal controls to adjust for minor chemistry and instrument variation. Forty temperature cycles required 9.2 min, and each capillary required 2.2 min by melting at 0.3 degrees C/s, 3x the prior rate. Sample volume was reduced from 20 microl to 10 microl. In a blinded study of 109 samples (436 genotypes), complete concordance with standard assays was obtained. In addition, the rare variant MTHFR 1317T>C was genotyped correctly when present. The LS-32 simplifies more complex high-resolution melting assays by reducing hands-on manipulation, total time of analysis, and reagent cost while maintaining the resolution necessary for multiplex amplicon genotyping.
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Affiliation(s)
- Michael T Seipp
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah 84108, USA.
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