1
|
Zhu X, Li W, Zhu J, Chen H, Guan J, Zhou D, Zhen Z, Sun F, Huang J, Wang J, Sun X, Lu S, Zhang Y. Influence of MTHFR C677T and A1298C polymorphisms on the survival of pediatric patients with non-Hodgkin lymphoma. Leuk Lymphoma 2021; 62:2374-2382. [PMID: 34032185 DOI: 10.1080/10428194.2021.1927017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
This study evaluated the influence of MTHFR C677T/A1298C polymorphisms on the survival of pediatric NHL. We enrolled 374 patients including 283 males and 91 females between 2014 and 2020. The median age was 9 years. The tumor types included Burkitt lymphoma (n = 180), lymphoblastic lymphoma (n = 95), anaplastic large cell lymphoma (n = 64), and diffuse large B cell lymphoma (n = 35). A subgroup of 158 patients were genotyped concerning C677T/A1298C polymorphisms. Neither C677T nor A1298C polymorphism was a significant factor in multivariate analysis. However, Kaplan-Meier analysis revealed that patients carrying 677 T allele had a significantly higher 5-year EFS rate in the whole group (n = 158), and higher 5-year EFS/OS rates in the subgroup of BL/DLBCL than those with wild type. In conclusion, the C677T polymorphism could be used for survival prediction and potential risk stratification for further treatment protocols for Chinese pediatric NHL, especially for BL/DLBCL.
Collapse
Affiliation(s)
- Xiaoqin Zhu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Pediatric Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Wei Li
- Department of Cardiology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, P. R. China
| | - Jia Zhu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Pediatric Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Huimou Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Pediatric Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Jinqiu Guan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Pediatric Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Dalei Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Molecular Diagnostics, Sun Yat-Sen University Cancer Center, Guangzhou, P. R. China
| | - Zijun Zhen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Pediatric Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Feifei Sun
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Pediatric Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Junting Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Pediatric Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Juan Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Pediatric Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Xiaofei Sun
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Pediatric Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Suying Lu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Pediatric Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| | - Yizhuo Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China.,Department of Pediatric Oncology, Sun Yat-sen University Cancer Center, Guangzhou, P. R. China
| |
Collapse
|
2
|
Liu X, Zhang C, Zhao M, Liu K, Li H, Li N, Gao L, Yang X, Ma T, Zhu J, Hui W, Hua K, Cui Y. A direct isothermal amplification system adapted for rapid SNP genotyping of multifarious sample types. Biosens Bioelectron 2018; 115:70-76. [PMID: 29803102 PMCID: PMC7126597 DOI: 10.1016/j.bios.2018.05.021] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 02/06/2018] [Accepted: 05/10/2018] [Indexed: 01/10/2023]
Abstract
Genotyping of single nucleotide polymorphisms (SNPs) in point-of-care (POC) settings could be further improved through simplifying the treatment of samples. In this study, we devised an accurate, rapid and easy-to-use SNP detection system based on direct loop-mediated isothermal amplification (LAMP) without DNA extraction, known as Direct-LAMP. Samples from various sources (including whole blood, dried blood spot, buccal swab and saliva), treated with NaOH, can be used directly in amplification. The turnaround time was about 30 min from sample collection to provision of results. The accuracy was evaluated by assessing the polymorphisms of methylenetetrahydrofolate reductase (MTHFR) C677T and aldehyde dehydrogenase-2 (ALDH2) Glu504Lys, which are better known for their critical role in folate and ethanol metabolism, respectively. Completely consistent genotyping results reveal that Direct-LAMP is generally concordant with sequencing. This system can serve as a very promising platform in the fields of disease predisposition, drug metabolism and personalized medicine.
Collapse
Affiliation(s)
- Xiaonan Liu
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Chao Zhang
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Mengye Zhao
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Kewu Liu
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Hang Li
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ningning Li
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, China
| | - Linlin Gao
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Xuemin Yang
- College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Ting Ma
- Shaanxi Provincial People's Hospital, Xi'an 710068, China
| | - Juanli Zhu
- Shaanxi Provincial Engineering Research Center for Nano-Biomedical Detection, Xi'an 710077, China
| | - Wenli Hui
- College of Life Sciences, Northwest University, Xi'an 710069, China; National Engineering Research Center for Miniaturized Detection System, Xi'an 710069, China
| | - Kai Hua
- College of Life Sciences, Northwest University, Xi'an 710069, China; National Engineering Research Center for Miniaturized Detection System, Xi'an 710069, China.
| | - Yali Cui
- College of Life Sciences, Northwest University, Xi'an 710069, China; Shaanxi Provincial Engineering Research Center for Nano-Biomedical Detection, Xi'an 710077, China; National Engineering Research Center for Miniaturized Detection System, Xi'an 710069, China.
| |
Collapse
|
3
|
C677T and A1298C polymorphisms of methylene tetrahydrofolate reductase in non-Hodgkin lymphoma: southeast Iran. TUMORI JOURNAL 2018; 104:280-284. [PMID: 28430351 DOI: 10.5301/tj.5000634] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
PURPOSE Polymorphisms of the methylene tetrahydrofolate reductase (MTHFR) gene have been reported as risk factors for non-Hodgkin lymphoma (NHL) in some populations. Our goal was to evaluate the potential role of A1298C and C677T polymorphisms of MTHFR in risk of NHL in southeast Iran. METHODS In the present case-control study, 127 patients with newly diagnosed NHL along with 150 ethnicity- and age-matched controls were examined. The A1298C and C677T polymorphisms were genotyped using the Tetra Amplification Refractory Mutation System polymerase chain reaction method. RESULTS There were no significant differences in genotype frequencies between cases and controls regarding either A1298C polymorphism. For this polymorphism, 53.8% of the controls and 54.3% of the patients with NHL showed homozygous wild-type (AA) genotype. Variant 1298C allele was recognized with overall frequency of 34.6% in both groups. Frequencies of CC, CT, and TT genotypes of C677T polymorphism were observed in 73.1%, 25.8%, and 1.3% of the controls, and 64.5%, 33.1%, and 2.4% of the patients with NHL (p>0.05). In combination, CT + TT conferred a significantly higher risk of NHL (odds ratio [OR] 1.5, 95% confidence interval [CI] 0.9-2.4, p = 0.03). Overall, variant 677T allele presented with higher frequency in the patients with NHL than the controls (26.7% versus 21.3%, respectively; OR 1.3, 95% CI 0.8-2.1, p>0.05). Although statistically insignificant, the highest risk of NHL was identified in patients with C677T; A1298C: CT; CC haplotype (OR 4.7, 95% CI 0.4-46.4, p = 0.1). CONCLUSIONS Combination of CT and TT genotypes of C677T polymorphism conferred a significantly higher risk for NHL. It is recommended to investigate further the potential role of this polymorphism in NHL development.
Collapse
|
4
|
Liu X, Zhang C, Liu K, Wang H, Lu C, Li H, Hua K, Zhu J, Hui W, Cui Y, Zhang X. Multiple SNPs Detection Based on Lateral Flow Assay for Phenylketonuria Diagnostic. Anal Chem 2018; 90:3430-3436. [PMID: 29451781 DOI: 10.1021/acs.analchem.7b05113] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Single nucleotide polymorphisms (SNPs) are closely related to genetic diseases, but current SNP detection methods, such as DNA microarrays that include tedious procedures and expensive, sophisticated instruments, are unable to perform rapid SNPs detection in clinical practice, especially for those multiple SNPs related to genetic diseases. In this study, we report a sensitive, low cost, and easy-to-use point-of-care testing (POCT) system formed by combining amplification refractory mutation system (ARMS) polymerase chain reaction with gold magnetic nanoparticles (GMNPs) and lateral flow assay (LFA) noted as the ARMS-LFA system, which allow us to use a uniform condition for multiple SNPs detection simultaneously. The genotyping results can be explained by a magnetic reader automatically or through visual interpretation according to the captured GMNPs probes on the test and control lines of the LFA device. The high sensitivity (the detection limit of 0.04 pg/μL with plasmid) and specificity of this testing system were found through genotyping seven pathogenic SNPs in phenylalanine hydroxylase gene ( PAH, the etiological factor of phenylketonuria). This system can also be applied in DNA quantification with a linear range from 0.02 to 2 pg/μL of plasmid. Furthermore, this ARMS-LFA system was applied to clinical trials for screening the seven pathogenic SNPs in PAH of 23 families including 69 individuals. The concordance rate of the genotyping results detected by the ARMS-LFA system was up to 97.8% compared with the DNA sequencing results. This method is a very promising POCT in the detection of multiple SNPs caused by genetic diseases.
Collapse
Affiliation(s)
- Xiaonan Liu
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China
| | - Chao Zhang
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China
| | - Kewu Liu
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China
| | - Han Wang
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100005 , China
| | - Chaoxia Lu
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100005 , China
| | - Hang Li
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China
| | - Kai Hua
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China.,National Engineering Research Center for Miniaturized Detection System , Xi'an , Shaanxi 710069 , China
| | - Juanli Zhu
- Shaanxi Provincial Engineering Research Center for Nano-Biomedical Detection , Xi'an , Shaanxi 710077 , China
| | - Wenli Hui
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China.,National Engineering Research Center for Miniaturized Detection System , Xi'an , Shaanxi 710069 , China
| | - Yali Cui
- College of Life Sciences , Northwest University , Xi'an , Shaanxi 710069 , China.,National Engineering Research Center for Miniaturized Detection System , Xi'an , Shaanxi 710069 , China.,Shaanxi Provincial Engineering Research Center for Nano-Biomedical Detection , Xi'an , Shaanxi 710077 , China
| | - Xue Zhang
- McKusick-Zhang Center for Genetic Medicine, Institute of Basic Medical Sciences , Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100005 , China
| |
Collapse
|
5
|
Hui W, Zhang S, Zhang C, Wan Y, Zhu J, Zhao G, Wu S, Xi D, Zhang Q, Li N, Cui Y. A novel lateral flow assay based on GoldMag nanoparticles and its clinical applications for genotyping of MTHFR C677T polymorphisms. NANOSCALE 2016; 8:3579-3587. [PMID: 26804455 DOI: 10.1039/c5nr07547e] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Current techniques for single nucleotide polymorphism (SNP) detection require tedious experimental procedures and expensive and sophisticated instruments. In this study, a visual genotyping method has been successfully established via combining ARMS-PCR with gold magnetic nanoparticle (GoldMag)-based lateral flow assay (LFA) and applied to the genotyping of methylenetetrahydrofolate reductase (MTHFR) C677T. C677T substitution of the gene MTHFR leads to an increased risk of diseases. The genotyping result is easily achievable by visual observation within 5 minutes after loading of the PCR products onto the LFA device. The system is able to accurately assess a broad detection range of initial starting genomic DNA amounts from 5 ng to 1200 ng per test sample. The limit of detection reaches 5 ng. Furthermore, our PCR-LFA system was applied to clinical trials for screening 1721 individuals for the C677T genotypes. The concordance rate of the genotyping results detected by PCR-LFA was up to 99.6% when compared with the sequencing results. Collectively, our PCR-LFA has been proven to be rapid, accurate, sensitive, and inexpensive. This new method is highly applicable for C677T SNP screening in laboratories and clinical practices. More promisingly, it could also be extended to the detection of SNPs of other genes.
Collapse
Affiliation(s)
- Wenli Hui
- College of Life Sciences, Northwest University, Xi'an, 710069, China.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Suthandiram S, Gan GG, Mohd Zain S, Bee PC, Lian LH, Chang KM, Ong TC, Mohamed Z. Genetic polymorphisms in the one-carbon metabolism pathway genes and susceptibility to non-Hodgkin lymphoma. Tumour Biol 2014; 36:1819-34. [PMID: 25384508 DOI: 10.1007/s13277-014-2785-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 10/29/2014] [Indexed: 12/19/2022] Open
Abstract
Corroborating evidence related to the role of aberrations on one-carbon metabolism (OCM) genes has been inconsistent. We evaluated the association between polymorphisms in 12 single nucleotide polymorphisms (SNPs) in 8 OCM genes (CBS, FPGS, FTHFD, MTRR, SHMT1, SLC19A1, TCN1, and TYMS), and non-Hodgkin lymphoma (NHL) risk in a multi-ethnic population which includes Malay, Chinese and Indian ethnic subgroups. Cases (N = 372) and controls (N = 722) were genotyped using the Sequenom MassARRAY platform. Our results of the pooled subjects showed a significantly enhanced NHL risk for CBS Ex9 + 33C > T (T versus C: OR 1.55, 95% CI 1.22-1.96, P = 0.0003), CBS Ex18-319G > A (A versus G: OR 1.15, 95% CI 1.14-1.83; P = 0.002), SHMT1 Ex12 + 236 T > C (T versus C: OR 1.44, 95% CI 1.15-1.81, P = 0.002), and TYMS Ex8 + 157C > T (T versus C: OR 1.29, 95% CI 1.06-1.57, P = 0.01). Haplotype analysis for CBS SNPs showed a significantly decreased risk of NHL in subjects with haplotype CG (OR 0.69, 95% CI 0.56-0.86, P = <0.001). The GG haplotype for the FTHFD SNPs showed a significant increased risk of NHL (OR 1.40, 95% CI 1.12-1.76, P = 0.002). For the TYMS gene, haplotype CAT at TYMS (OR 0.67, 95% CI 0.49-0.90, P = 0.007) was associated with decreased risk of NHL, while haplotype TAC (OR 1.29, 95% CI 1.05-1.58, P = 0.01) was found to confer increased risk of NHL. Our study suggests that variation in several OCM genes (CBS, FTHFD, SHMT1, TCN1, and TYMS) may influence susceptibility to NHL.
Collapse
Affiliation(s)
- Sujatha Suthandiram
- The Pharmacogenomics Laboratory, Department of Pharmacology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia,
| | | | | | | | | | | | | | | |
Collapse
|