1
|
Berczi B, Nusser N, Peter I, Nemeth B, Gyongyi Z. Association Between AIRE Polymorphisms rs870881(C>T), rs1003854(T>C) and Rheumatoid Arthritis Risk: A Hungarian Case-control Study. In Vivo 2024; 38:774-784. [PMID: 38418155 PMCID: PMC10905445 DOI: 10.21873/invivo.13501] [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: 10/25/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 03/01/2024]
Abstract
BACKGROUND/AIM Autoimmune regulator (AIRE) is a transcription factor that plays pivotal role in controlling autoimmunity. In the thymus, it supports the presentation of peripheral tissue antigens to developing T cells, where recognition of these self-antigens negatively selects the autoimmune naïve T-cells by central tolerance. Studies demonstrated that single-nucleotide polymorphisms (SNPs) in AIRE alter transcription and propagate clonal survival of autoimmune T cells, therefore increase susceptibility to autoimmune diseases. This study intended to identify SNPs in exon and intron sequences that determine AIRE transcription, where their genotypes are associated with rheumatoid arthritis (RA) risk and clinical parameters. PATIENTS AND METHODS After a thorough in silico research, we enrolled 100 patients with RA and 100 healthy controls to analyze the association of SNP rs870881(C>T) and rs1003854(T>C) in AIRE coding sequence with RA risk by using five different genetic models and selected clinical parameters. Multiplex quantitative polymerase chain reaction was used to determine allelic discrimination of SNPs. RA risk was assessed by odds ratios (ORs) and confidence intervals (CIs). RESULTS In a recessive model of rs878081, minor allele TT homozygotes were associated with RA (p=0.032, OR=5.44, 95%CI=1.16-25.52); in a recessive model of rs1003854, minor allele CC homozygotes were associated with RA (p=0.047, OR=4.84, 95%CI=1.02-23.02). Higher C-reactive protein (CRP) levels in patients with RA were significantly associated with minor allele homozygotes in recessive and codominant genetic models (p=0.029 and p=0.043, respectively) of rs1003854. CONCLUSION Genotypes for minor alleles of rs878081 and rs1003854 might be involved in RA pathogenesis and risk prediction.
Collapse
Affiliation(s)
- Balint Berczi
- Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary
| | - Nóra Nusser
- Harkány Thermal Rehabilitation Centre, Harkány, Hungary
| | - Ivan Peter
- Harkány Thermal Rehabilitation Centre, Harkány, Hungary
| | - Balazs Nemeth
- Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary;
- Harkány Thermal Rehabilitation Centre, Harkány, Hungary
| | - Zoltan Gyongyi
- Department of Public Health Medicine, Medical School, University of Pécs, Pécs, Hungary
| |
Collapse
|
2
|
Fawzy MS, Ibrahiem AT, Osman DM, Almars AI, Alshammari MS, Almazyad LT, Almatrafi NDA, Almazyad RT, Toraih EA. Angio-Long Noncoding RNA MALAT1 (rs3200401) and MIAT (rs1061540) Gene Variants in Ovarian Cancer. Epigenomes 2024; 8:5. [PMID: 38390896 PMCID: PMC10885055 DOI: 10.3390/epigenomes8010005] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/04/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
The genotyping of long non-coding RNA (lncRNA)-related single-nucleotide polymorphisms (SNPs) could be associated with cancer risk and/or progression. This study aimed to analyze the angiogenesis-related lncRNAs MALAT1 (rs3200401) and MIAT (rs1061540) variants in patients with ovarian cancer (OC) using "Real-Time allelic discrimination polymerase chain reaction" in 182 formalin-fixed paraffin-embedded (FFPE) samples of benign, borderline, and primary malignant ovarian tissues. Differences in the genotype frequencies between low-grade ovarian epithelial tumors (benign/borderline) and malignant tumors and between high-grade malignant epithelial tumors and malignant epithelial tumors other than high-grade serous carcinomas were compared. Odds ratios (ORs)/95% confidence intervals were calculated as measures of the association strength. Additionally, associations of the genotypes with the available pathological data were analyzed. The heterozygosity of MALAT1 rs3200401 was the most common genotype (47.8%), followed by C/C (36.3%). Comparing the study groups, no significant differences were observed regarding this variant. In contrast, the malignant epithelial tumors had a higher frequency of the MIAT rs1061540 C/C genotype compared to the low-grade epithelial tumor cohorts (56.7% vs. 37.6, p = 0.031). The same genotype was significantly higher in high-grade serous carcinoma than its counterparts (69.4% vs. 43.8%, p = 0.038). Multivariate Cox regression analysis showed that the age at diagnosis was significantly associated with the risk of OC development. In contrast, the MIAT T/T genotype was associated with a low risk of malignant epithelial tumors under the homozygote comparison model (OR = 0.37 (0.16-0.83), p = 0.017). Also, MIAT T allele carriers were less likely to develop high-grade serous carcinoma under heterozygote (CT vs. CC; OR = 0.33 (0.12-0.88), p = 0.027) and homozygote (TT vs. CC; OR = 0.26 (0.07-0.90), p = 0.034) comparison models. In conclusion, our data provide novel evidence for a potential association between the lncRNA MIAT rs1061540 and the malignant condition of ovarian cancer, suggesting the involvement of such lncRNAs in OC development.
Collapse
Affiliation(s)
- Manal S Fawzy
- Department of Biochemistry, Faculty of Medicine, Northern Border University, Arar 73213, Saudi Arabia
- Unit of Medical Research and Postgraduate Studies, Faculty of Medicine, Northern Border University, Arar 73213, Saudi Arabia
| | - Afaf T Ibrahiem
- Department of Pathology, Faculty of Medicine, Northern Border University, Arar 73213, Saudi Arabia
| | - Dalia Mohammad Osman
- Department of Medical Laboratories Technology, Faculty of Applied Medical Sciences, Northern Border University, Arar 73213, Saudi Arabia
| | - Amany I Almars
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Hematology Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | | | | | | | - Renad Tariq Almazyad
- Faculty of Applied Medical Sciences, Northern Border University, Arar 73213, Saudi Arabia
| | - Eman A Toraih
- Division of Endocrine and Oncologic Surgery, Department of Surgery, School of Medicine, Tulane University, New Orleans, LA 70112, USA
| |
Collapse
|
3
|
Mohammed AA, El-Matty DMA, Abdel-Azeem R, Raafat K, Hussein MA, El-Ansary AR, Hafez W, Hassan HA, Nassar NA, Selim NM, Ghaith D, Kholy AAE, Abd El Salam SM, Anouti FA, Wahba AS. Allelic Discrimination of Vitamin D Receptor Polymorphisms and Risk of Type 2 Diabetes Mellitus: A Case-Controlled Study. Healthcare (Basel) 2023; 11:healthcare11040485. [PMID: 36833019 PMCID: PMC9956945 DOI: 10.3390/healthcare11040485] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/02/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
(1) Background: Type 2 diabetes mellitus (T2DM) is one of the rapidly growing healthcare problems, and several vitamin D receptor (VDR) polymorphisms seem to modulate the risk of T2DM. Our research was designed to investigate the allelic discrimination of VDR polymorphisms and T2DM occurrence risk. (2) Methods: This case-control research included 156 patients with T2DM and 145 healthy control subjects. Most of the study population were males 56.6% vs. 62.8% in the case and control groups, respectively. Genotyping for VDR single nucleotide polymorphisms (SNPs), rs228570 (Fok1), rs7975232 (Apa1), and rs1544410 (Bsm1) was compared between both groups. (3) Results: There was a negative link between vitamin D levels and insulin sensitivity. A significant difference was noted in the allelic discrimination of VDR polymorphism rs228570 and rs1544410 between the study groups (p < 0.001). No difference was observed in the allelic discrimination of VDR polymorphism rs7975232 between the groups (p = 0.063). Moreover, T2DM patients had significantly higher levels of fasting blood sugar (FBS), glycated hemoglobin HbA1c, 2-h post-prandial blood sugar (PP), serum glutamic oxaloacetic transaminase (SGOT), serum glutamic-pyruvic transaminase (SGPT), total cholesterol, and triglycerides (p < 0.001), while High-Density Lipoprotein (HDL) Cholesterol (HDL-C) was significantly decreased (p = 0.006). (4) Conclusions: VDR polymorphisms had a positive association with T2DM risk among the Egyptian population. Further large-scale research using deep sequencing of samples is strongly urged to investigate different vitamin D gene variants and interactions, as well as the influence of vitamin D on T2DM.
Collapse
Affiliation(s)
- Amal Ahmed Mohammed
- Department of Biochemistry and Molecular Biology, National Hepatology and Tropical Medicine Research Institute (NHTMRI), Cairo 11796, Egypt
| | - Dina M. Abo El-Matty
- Department of Biochemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
| | - Rola Abdel-Azeem
- Department of Biochemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
| | - Khaled Raafat
- Department of Internal Medicine, Faculty of Medicine, Ain Shams University, Cairo11566, Egypt
| | - Mona A. Hussein
- Department of Internal Medicine, National Institute of Diabetes and Endocrinology, Cairo 11562, Egypt
| | - Amira R. El-Ansary
- Department of Internal Medicine, Faculty of Medicine, Misr University for Science and Technology, Giza 12577, Egypt
| | - Wael Hafez
- Department of Internal Medicine, The National Research Centre, Cairo 12622, Egypt
- Correspondence: or ; Tel.: +20-9712235000
| | - Hatem Ahmed Hassan
- Department of Internal Medicine and Gastroenterology, Faculty of Medicine, Minia University, Minia 61519, Egypt
| | | | - Nora Mahmoud Selim
- Department of Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo 12613, Egypt
| | - Doaa Ghaith
- Department of Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo 12613, Egypt
| | - Amal A. El Kholy
- Department of Clinical Pharmacy, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt
| | - Soha M. Abd El Salam
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Suez University, Suez 43512, Egypt
| | - Fatme Al Anouti
- Department of Health Sciences, College of Natural and Health Sciences, Zayed University, Abu Dhabi 144534, United Arab Emirates
| | - Alaa S. Wahba
- Department of Biochemistry, Faculty of Pharmacy, Suez Canal University, Ismailia 41522, Egypt
| |
Collapse
|
4
|
Carpi S, Del Grosso A, De Sarlo M, Colagiorgio L, Scaccini L, Tonazzini I, Parlanti G, Cecchini M. Reliable and Fast Genotyping Protocol for Galactosylceramidase (Galc) in the Twitcher (Twi) Mouse. Biomedicines 2022; 10. [PMID: 36551902 DOI: 10.3390/biomedicines10123146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/12/2022] Open
Abstract
Twitcher (Twi) is a neurological Krabbe disease (KD, or globoid cell leukodystrophy) spontaneous mutant line in mice. The genome of the Twi mouse presents a single nucleotide polymorphism (SNP), leading to an enzymatically inactive galactosylceramidase (Galc) protein that causes KD. In this context, mouse Twi genotyping is an essential step in KD research. To date, the genotyping method used is labor-intensive and often has ambiguous results. Here, we evaluated a novel protocol for the genotype determination of Galc mutation status in Twi mice based on the allele-discrimination real-time polymerase chain reaction (PCR). Here, DNA is extracted from Twi mice (n = 20, pilot study; n = 120, verification study) and control group (n = 10, pilot study; n = 30 verification study) and assessed by allele-discrimination real-time PCR to detect SNP c.355G>A. Using the allele-discrimination PCR, all of the samples are identified correctly with the genotype GG (wild-type, WT), GA (heterozygote, HET), or AA (homozygote, HOM) using the first analysis and no animals are not genotyped. We demonstrated that this novel method can be used to distinguish KD timely, accurately, and without ambiguity in HOM, WT, and HET animals. This protocol represents a great opportunity to increase accuracy and speed in KD research.
Collapse
|
5
|
Abdallah HY, Ibrahim ME, Abd El-Fadeal NM, Ali DA, Elsehrawy GG, Badr RE, Hassoba HM. Pharmacogenomics of Methotrexate Pathway in Rheumatoid Arthritis Patients: Approach toward Personalized Medicine. Diagnostics (Basel) 2022; 12:diagnostics12071560. [PMID: 35885466 PMCID: PMC9325258 DOI: 10.3390/diagnostics12071560] [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: 05/09/2022] [Revised: 06/10/2022] [Accepted: 06/23/2022] [Indexed: 11/28/2022] Open
Abstract
Background: Methotrexate (MTX) is one of the most common medications used for rheumatoid arthritis (RA) treatment. Single-nucleotide polymorphisms (SNPs) could potentially predict variability in therapeutic outcomes. Aim: This study aims to assess the impact of SNPs in genes encoding for the MTX pathway for predicting clinical and therapeutic responses to MTX in a cohort of Egyptian patients with RA. Subjects and Methods: Data from 107 Egyptian RA patients (aged 44.4 ± 11.4 years) treated with MTX monotherapy, for a duration of 3.7 ± 3.3 years, were collected. Genotypes of 10 SNPs from four different genes were analyzed using the allelic discrimination PCR technique. Results: The ATIC rs3821353 G/T (p = 0.034) and the C/T and C/C of SLC19A1 rs7279445 (p = 0.0018) were associated with a non-response to MTX, while DHFR rs10072026 C/T and C/C were associated with a good response (p < 0.001). Carriers of the ATIC rs382135 3 G (p = 0.001) and ATIC rs4673990 G (p < 0.001) alleles were more likely to develop RA, while the SLC19A1 rs11702425 T (p < 0.001) and GGH rs12681874 T (p = 0.003) allele carriers were more likely to be protected against RA. Carriers of the ATIC rs4673990 A/G genotype (p < 0.001) were at risk of developing RA, while carriers of the following genotypes were mostly protected against RA: ATIC rs3821353 T/T (p < 0.001), ATIC rs3821353 G/G (p = 0.004), SLC19A1 rs11702425 T/T (p = 0.001), SLC19A1 rs11702425 C/T (p = 0.003), GGH rs12681874 C/T (p = 0.004) and GGH rs12681874 T/T (0.002). Conclusion: The genotyping of genes involved in the MTX pathway may be helpful to predict which RA patients will/will not benefit from MTX, and thus, may help to apply a personalized medicine approach in RA.
Collapse
Affiliation(s)
- Hoda Y. Abdallah
- Medical Genetics Unit, Department of Histology and Cell Biology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt;
- Center of Excellence in Molecular & Cellular Medicine, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt; (N.M.A.E.-F.); (D.A.A.)
| | - Maha E. Ibrahim
- Department of Physical Medicine, Rheumatology and Rehabilitation, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt; (M.E.I.); (G.G.E.)
| | - Noha M. Abd El-Fadeal
- Center of Excellence in Molecular & Cellular Medicine, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt; (N.M.A.E.-F.); (D.A.A.)
- Department of Medical Biochemistry & Molecular Biology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt
- Oncology Diagnostic Unit, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Dina A. Ali
- Center of Excellence in Molecular & Cellular Medicine, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt; (N.M.A.E.-F.); (D.A.A.)
- Department of Clinical Pharmacology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Gehad G. Elsehrawy
- Department of Physical Medicine, Rheumatology and Rehabilitation, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt; (M.E.I.); (G.G.E.)
| | - Rasha E. Badr
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Port Said University, Port Said 42526, Egypt;
| | - Howayda M. Hassoba
- Department of Clinical and Chemical Pathology, Faculty of Medicine, Suez Canal University, Ismailia 41522, Egypt
- Correspondence: or ; Tel.: +(2)-01-272-430-312; Fax: +(2)-06-432-16496
| |
Collapse
|
6
|
Morcia C, Terzi V, Ghizzoni R, Vaiuso C, Delogu C, Andreani L, Venturini A, Carnevali P, Pompa PP, Tumino G. Digital PCR for Genotype Quantification: A Case Study in a Pasta Production Chain. Biology (Basel) 2021; 10:biology10050419. [PMID: 34065065 PMCID: PMC8151192 DOI: 10.3390/biology10050419] [Citation(s) in RCA: 1] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 04/30/2021] [Accepted: 05/06/2021] [Indexed: 02/07/2023]
Abstract
Simple Summary Digital polymerase chain reaction (dPCR) is a breakthrough technology able to provide an absolute quantification of the target sequence through the compartmentalization of the sample and independent amplifications of the numerous separate compartments. Such technology has recently found several applications in plant science; however, to the best of our knowledge, it has never been applied until now for the detection and quantification of a specific plant variety along a production chain. As proof of concept, a dPCR assay targeted to the quantification of a durum wheat variety routinely used in an Italian premium pasta production chain has been developed. Abstract Digital polymerase chain reaction (dPCR) is a breakthrough technology based on the partitioning of the analytical sample and detection of individual end-point amplifications into the separate compartments. Among the numerous applications of this technology, its suitability in mutation detection is relevant and characterized by unprecedented levels of precision. The actual applicability of this analytical technique to quantify the presence of a specific plant genotype, in both raw materials and transformed products, by exploiting a point polymorphism has been evaluated. As proof of concept, an Italian premium pasta production chain was considered and a dPCR assay based on a durum wheat target variety private point mutation was designed and evaluated in supply-chain samples. From the results obtained, the assay can be applied to confirm the presence of a target variety and to quantify it in raw materials and transformed products, such as commercial grain lots and pasta. The performance, costs, and applicability of the assay has been compared to analytical alternatives, namely simple sequence repeats (SSRs) and genotype-by-sequencing based on Diversity Arrays Technology sequencing (DArTseqTM).
Collapse
Affiliation(s)
- Caterina Morcia
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria-Centro di Ricerca Genomica e Bioinformatica (CREA-GB), Via San Protaso 302, 29017 Fiorenzuola d’Arda, Italy; (C.M.); (R.G.); (C.V.)
| | - Valeria Terzi
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria-Centro di Ricerca Genomica e Bioinformatica (CREA-GB), Via San Protaso 302, 29017 Fiorenzuola d’Arda, Italy; (C.M.); (R.G.); (C.V.)
- Correspondence: ; Tel.: +39-0523-983758
| | - Roberta Ghizzoni
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria-Centro di Ricerca Genomica e Bioinformatica (CREA-GB), Via San Protaso 302, 29017 Fiorenzuola d’Arda, Italy; (C.M.); (R.G.); (C.V.)
| | - Chiara Vaiuso
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria-Centro di Ricerca Genomica e Bioinformatica (CREA-GB), Via San Protaso 302, 29017 Fiorenzuola d’Arda, Italy; (C.M.); (R.G.); (C.V.)
| | - Chiara Delogu
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria-Centro di Ricerca Difesa e Certificazione (CREA-DC), Via Emilia km 307, 26838 Tavazzano, Italy; (C.D.); (L.A.); (A.V.)
| | - Lorella Andreani
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria-Centro di Ricerca Difesa e Certificazione (CREA-DC), Via Emilia km 307, 26838 Tavazzano, Italy; (C.D.); (L.A.); (A.V.)
| | - Andrea Venturini
- Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria-Centro di Ricerca Difesa e Certificazione (CREA-DC), Via Emilia km 307, 26838 Tavazzano, Italy; (C.D.); (L.A.); (A.V.)
| | | | - Pier Paolo Pompa
- Nanobiointeractions & Nanodiagnostics, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genova, Italy;
| | - Giorgio Tumino
- Plant Breeding, Wageningen University Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands;
| |
Collapse
|
7
|
Mohasseb DMF, Saba EKA, Saad NLM, Sarofeem ADH. Genetic Association Between Growth Differentiation Factor 5 Single Nucleotide Polymorphism and Primary Knee Osteoarthritis in a Group of Egyptian Patients: A Pilot Study. Mediterr J Rheumatol 2019; 30:114-122. [PMID: 32185351 PMCID: PMC7045969 DOI: 10.31138/mjr.30.2.114] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 03/26/2019] [Accepted: 04/02/2019] [Indexed: 12/31/2022] Open
Abstract
Aim This study aimed to determine the genetic association between Growth Differentiation Factor 5 (GDF5) gene (rs143383 T/C) single nucleotide polymorphism (SNP) and primary knee osteoarthritis (OA) in a group of Egyptian patients. Patients and Methods The study included 47 patients with primary knee OA and 40 apparently healthy control subjects. The disease was assessed using Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) score and Health Assessment Questionnaire (HAQ). Radiological assessment was done by Kellgren-Laurence (K/L) grading system. The genetic association of the SNP with primary knee OA was assessed by restriction fragment length polymorphism - polymerase chain reaction (RFLP-PCR). Results The mean total WOMAC index was significantly higher in patients with TT genotype as compared to patients with CC and CT genotypes (P<0.001). Similarly, the HAQ score was significantly higher among patients with TT genotype when compared to patients with CT and CC genotypes (P<0.001). There was a statistically significant association between different GDF5 genotypes and K/L radiological grading of knee OA among the studied patients (P=0.029). No statistically significant association was detected on comparing the frequency distribution of GDF5 alleles and genotypes frequencies of the SNP in patients and healthy controls. Conclusion There is a possible genetic association between GDF5 (rs143383) SNP and severity of primary knee OA, which might facilitate the detection of patients with high risk for disease progression. The present study did not detect an association between the SNP and development of primary knee OA.
Collapse
Affiliation(s)
- Dia Mohamed Fahmy Mohasseb
- Physical Medicine, Rheumatology and Rehabilitation Department, Faculty of Medicine, Alexandria University, Egypt
| | - Emmanuel Kamal Aziz Saba
- Physical Medicine, Rheumatology and Rehabilitation Department, Faculty of Medicine, Alexandria University, Egypt
| | | | - Amira Dimas Hanna Sarofeem
- Physical Medicine, Rheumatology and Rehabilitation Department, Ministry of Health, Alexandria Governorate, Egypt
| |
Collapse
|
8
|
Rubio-Meléndez ME, Sepúlveda DA, Ramírez CC. Temporal and spatial distribution of insecticide-resistance mutations in the green peach aphid Myzus persicae (Hemiptera: Aphididae) on primary and secondary host plants in central Chile. Pest Manag Sci 2018; 74:340-347. [PMID: 28834161 DOI: 10.1002/ps.4708] [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] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 07/21/2017] [Accepted: 08/14/2017] [Indexed: 06/07/2023]
Abstract
BACKGROUND The aphid Myzus persicae develops insensitivity to almost all classes of insecticides through target site mutations. The aim of this study was to assess the temporal and spatial distribution of resistant aphids that grow on peach trees and weeds, and establish the role of the secondary hosts as a reservoir of resistant genotypes. RESULTS The frequency of genotypes (RR, RS, and SS) was affected by the host plant, mainly for knock-down resistance (kdr) and modified acetylcholinesterase (MACE) mutations (P < 0.05). A higher frequency of RS and RR was observed in aphids found on peach trees than on weeds. The frequency of the R allele was significantly higher (P < 0.01) than expected in autumn and on weeds for the kdr and MACE mutations, while the frequency of the S allele was high in all seasons for all insecticide-resistance mutations (P < 0.01). The most abundant multilocus genotype was characterized as being RS for the kdr mutation and SS for both super-kdr and MACE. CONCLUSION This study provides farm-scale evidence that weeds are not an important reservoir of the R allele, but they are for the S allele. Hence, the presence of heterozygous genotypes on peach trees is most likely attributable to weeds. © 2017 Society of Chemical Industry.
Collapse
Affiliation(s)
- María E Rubio-Meléndez
- Facultad de Ciencias Agrarias, Universidad de Talca, Talca, Chile
- Millennium Nucleus Centre in Molecular Ecology and Evolutionary Applications in Agroecosystems, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Daniela A Sepúlveda
- Facultad de Ciencias Agrarias, Universidad de Talca, Talca, Chile
- Millennium Nucleus Centre in Molecular Ecology and Evolutionary Applications in Agroecosystems, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Claudio C Ramírez
- Millennium Nucleus Centre in Molecular Ecology and Evolutionary Applications in Agroecosystems, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| |
Collapse
|
9
|
Abd Elazeem MI, Abdelaleem EA, Mohamed RA. Genetic influence of growth and differentiation factor 5 gene polymorphism (+104T/C) on the development of knee osteoarthritis and its association with disease severity. Eur J Rheumatol 2017. [PMID: 28638680 DOI: 10.5152/eurjrheum.2017.160093] [Citation(s) in RCA: 9] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
OBJECTIVE The growth and differentiation factor 5 (GDF5) gene is recognized for its role in the development, repair, and maintenance of cartilage and bone. The present case-control study was conducted to detect the genetic association between GDF5 (+104T/C) single-nucleotide polymorphism (SNP) and primary knee osteoarthritis (KOA), as well as the possible association of SNP with the severity of KOA. MATERIAL AND METHODS The study included 50 patients with primary KOA and 50 healthy control subjects. The severity of the disease was assessed by using the Kellgren-Laurence (K-L) grading system and aided by the Western Ontario & McMaster Universities Osteoarthritis Index (WOMAC) score, visual analog scale (VAS) score, and tenderness score. The genetic association of the SNP with primary KOA was assessed by means of the TaqMan® allelic discrimination technique. RESULTS The radiological assessment of patients according to the K-L grading system revealed a statistically significant association between the wild-type (TT) genotype and disease severity in both the right and left knees (p=0.049). The frequency distribution of patients with VAS score ≤6 was significantly higher in patients carrying the TT genotype (p=0.005) as compared to the CT and CC genotypes. The mean WOMAC score was significantly higher in patients carrying the TT genotype as compared to patients carrying the CC and CT genotypes (p=0.017). No statistically significant association was detected on comparing the frequency distribution of allele and genotype frequencies of the SNP in patients and healthy controls. CONCLUSION The results of the current study revealed a possible genetic association between GDF5 (+104T/C) SNP and the severity of KOA, which might be of benefit for the detection of patients with a high risk for disease progression. The present study did not detect an association between the SNP and development of KOA.
Collapse
Affiliation(s)
- Mervat I Abd Elazeem
- Department of Rheumatology and Rehabilitation, Beni-Suef University School of Medicine, Beni-Suef University Hospital, Beni-Suef, Egypt
| | - Enas Abolkheir Abdelaleem
- Department of Rheumatology and Rehabilitation, Beni-Suef University School of Medicine, Beni-Suef University Hospital, Beni-Suef, Egypt
| | - Rabab A Mohamed
- Department of Clinical and Chemical Pathology, Beni-Suef University School of Medicine, Beni-Suef University Hospital, Beni-Suef, Egypt
| |
Collapse
|
10
|
Zadeh VR, Jagadesh A, Krishnan A, Arunkumar G. Detection of D151G/N mutations in the neuraminidase gene of influenza A (H3N2) viruses by real-time RT-PCR allelic discrimination assay. J Med Virol 2017; 89:1174-1178. [PMID: 28004398 DOI: 10.1002/jmv.24757] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [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: 08/22/2016] [Revised: 12/18/2016] [Accepted: 12/20/2016] [Indexed: 12/26/2022]
Abstract
Single nucleotide polymorphisms (SNPs) at D151 position of neuraminidase (NA) gene of influenza A (H3N2) virus has been associated with drug resistance and increased binding affinity. NA-D151G/N-substitutions of influenza A (H3N2) viruses are frequently induced and selected by culturing in Madin-Darby canine kidney (MDCK) cell lines. It is important to consider and exclude D151G/N mutants after isolation of influenza virus in MDCK cell line; since, the substitutions can highly influence the results of experimental research. The study aims to develop an allelic discrimination real-time reverse transcriptase polymerase chain reaction (RT-PCR) for the screening of D151G/N mutants. Thirty-six influenza A (H3N2) virus isolates were included and screened for D151G/N mutants using allelic discrimination assay. Out of the 36 isolates, 11 isolates (30.5%) were detected as heterozygous for D and G/N substitutions. Twenty-one (58.3%) isolates were identified as homozygous wild type and four isolates (11.1%) were undetermined. Isolates with substitutions at D151 position were sequenced by Sanger sequencing method. The present study demonstrates a rapid and convenient method for primary screening of the mutation after culturing of the influenza virus in MDCK cell lines in order to avoid potential misinterpretations of results and improve the quality of experimental research.
Collapse
Affiliation(s)
- Vahid Rajabali Zadeh
- Manipal Centre for Virus Research, Regional Reference Laboratory for Influenza Virus and ICMR Grade-I Virus Diagnostic Laboratory, Manipal University, Manipal, Karnataka, India
| | - Anitha Jagadesh
- Manipal Centre for Virus Research, Regional Reference Laboratory for Influenza Virus and ICMR Grade-I Virus Diagnostic Laboratory, Manipal University, Manipal, Karnataka, India
| | - Anjana Krishnan
- Manipal Centre for Virus Research, Regional Reference Laboratory for Influenza Virus and ICMR Grade-I Virus Diagnostic Laboratory, Manipal University, Manipal, Karnataka, India
| | - Govindakarnavar Arunkumar
- Manipal Centre for Virus Research, Regional Reference Laboratory for Influenza Virus and ICMR Grade-I Virus Diagnostic Laboratory, Manipal University, Manipal, Karnataka, India
| |
Collapse
|
11
|
Xu CP, Li MH, He HQ, Lu YY, Feng Y. Laboratory diagnosis of vaccine-associated measles in Zhejiang Province, China. J Microbiol Immunol Infect 2017; 50:578-85. [PMID: 26698687 DOI: 10.1016/j.jmii.2015.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Revised: 09/07/2015] [Accepted: 10/08/2015] [Indexed: 11/24/2022]
Abstract
BACKGROUND/PURPOSE Along with the improving vaccine coverage, suspected vaccine-associated measles has been reported in Zhejiang Province, China. In order to maintain the accuracy of the measles surveillance system, it is critical to discriminate between measles vaccine and wild-type virus. METHODS Eight suspected cases of vaccine-associated measles were reported in Zhejiang Province during 2011 and 2014. Sera collected within 4 days and throat swabs collected within 6 days after rash onset were tested with immunoglobulin M and measles virus (MeV) RNA to confirm MeV infection. In order to further identify the vaccine-associated cases, throat swabs with positive MeV RNA were tested using an allelic discrimination real-time reverse transcriptase polymerase chain reaction (rRT-PCR) assay developed in this study, RT-PCR-restriction fragment length polymorphism (RFLP) recommended by the National Measles Laboratory, and RT-PCR followed by sequencing and genotyping. RESULTS Combining anti-measles immunoglobulin M and RNA testing, eight cases were confirmed as MeV infection. Of the eight, two were identified as vaccine-associated cases by the allelic discrimination rRT-PCR assay, and one was identified by RT-PCR-RFLP. Subsequent sequencing and genotyping confirmed that the sequences of the two cases were identical to that of the Chinese vaccine strain. The developed allelic discrimination rRT-PCR was 10 times more sensitive than the RT-PCR-RFLP assay when RNA standards generated from three genotypes of MeV were tested. CONCLUSION Vaccine-associated measles has been identified in Zhejiang. The developed allelic discrimination rRT-PCR assay is rapid and sensitive, which will facilitate the surveillance for vaccine-associated measles.
Collapse
|
12
|
Mowjoodi A, Paton TA, Scherer SW. Discrimination of SNPs in GC-rich regions using a modified hydrolysis probe chemistry protocol. Biotechniques 2014; 57:313-6. [PMID: 25495732 DOI: 10.2144/000114240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 10/02/2014] [Indexed: 11/23/2022] Open
Abstract
Allelic discrimination using TaqMan 5'-nuclease assay chemistry has been in routine use for many years, and the catalog of Life Technologies' predesigned SNP genotyping assays now exceeds 4 million entries. However, predesigned assays are often not available for genomic regions with a high GC content, nor can an assay necessarily be designed in this type of region using the manufacturer's design pipelines. Additionally, when an assay is available, the performance can be poor when using standard protocols. Here we report a modified allelic discrimination protocol for variants that reside in extremely GC-rich (GC > 75%) regions. The approach resolves fluorescent signal from reference and variant alleles, allowing all samples to be successfully assigned a genotype call. This protocol modification adds an extra step to the standard workflow, but the increased time is a productive compromise to generate high-quality data.
Collapse
|
13
|
Ciampi MB, Gale LR, de Macedo Lemos EG, Ceresini PC. Distinctively variable sequence-based nuclear DNA markers for multilocus phylogeography of the soybean- and rice-infecting fungal pathogen Rhizoctonia solani AG-1 IA. Genet Mol Biol 2009; 32:840-6. [PMID: 21637462 PMCID: PMC3036909 DOI: 10.1590/s1415-47572009005000063] [Citation(s) in RCA: 4] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Accepted: 05/13/2009] [Indexed: 11/22/2022] Open
Abstract
A series of multilocus sequence-based nuclear DNA markers was developed to infer the phylogeographical history of the Basidiomycetous fungal pathogen Rhizoctonia solani AG-1 IA infecting rice and soybean worldwide. The strategy was based on sequencing of cloned genomic DNA fragments (previously used as RFLP probes) and subsequent screening of fungal isolates to detect single nucleotide polymorphisms (SNPs). Ten primer pairs were designed based on these sequences, which resulted in PCR amplification of 200-320 bp size products and polymorphic sequences in all markers analyzed. By direct sequencing we identified both homokaryon and heterokaryon (i.e. dikaryon) isolates at each marker. Cloning the PCR products effectively estimated the allelic phase from heterokaryotic isolates. Information content varied among markers from 0.5 to 5.9 mutations per 100 bp. Thus, the former RFLP codominant probes were successfully converted into six distinctively variable sequence-based nuclear DNA markers. Rather than discarding low polymorphism loci, the combination of these distinctively variable anonymous nuclear markers would constitute an asset for the unbiased estimate of the phylogeographical parameters such as population sizes and divergent times, providing a more reliable species history that shaped the current population structure of R. solani AG-1 IA.
Collapse
Affiliation(s)
- Maisa B Ciampi
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Campus de Jaboticabal, Jaboticabal, SP Brazil
| | | | | | | |
Collapse
|
14
|
Ruano I, Izquierdo M. Selective RNAi-mediated inhibition of mutated c-kit. J RNAi Gene Silencing 2009; 5:339-44. [PMID: 19771231 PMCID: PMC2737232] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2008] [Revised: 02/02/2009] [Accepted: 02/05/2008] [Indexed: 11/09/2022]
Abstract
The proto-oncogene c-kit plays an important role in the development and survival of mast cells. Gain-of-function mutations in c-kit are one of the most characteristic events in mast cell leukemia (MCL) but as yet there is no clinically approved treatment for the disease. Here we describe growth inhibition of human MCL cell lines by the use of RNAi against c-kit or its mutant form. Retroviral transduction of HMC1.1 and HMC1.2 cell lines with vectors carrying DNA to be transcribed to RNAi against the wild type or mutant c-kit messengers reduced Kit protein levels considerably, decreased cell proliferation, and increased the apoptotic levels five days after retroviral infection. Thus RNAi targeted against Kit or its mutant form could be considered as a new antiproliferative agent against human mast leukemia cell lines, especially HMC1.2 cells which are resistant to the Kit tyrosine kinase inhibitor, imatinib mesylate.
Collapse
Affiliation(s)
| | - Marta Izquierdo
- Correspondence to: Marta Izquierdo, , Tel: +34 911964569, Fax: +34 911964420
| |
Collapse
|