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Luo R, Ge C, Xiao X, Song J, Miao S, Tang Y, Lai J, Nian W, Song F, Ran L. Identification of genetic variations associated with drug resistance in non-small cell lung cancer patients undergoing systemic treatment. Brief Bioinform 2021; 22:6278152. [PMID: 34013324 PMCID: PMC8574960 DOI: 10.1093/bib/bbab187] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 04/05/2021] [Accepted: 04/22/2021] [Indexed: 12/31/2022] Open
Abstract
Non-small cell lung cancer (NSCLC) is characterized by relatively rapid response to systemic treatments yet inevitable resistance and predisposed to distant metastasis. We thus aimed at performing sequencing analysis to determine genomic events and underlying mechanisms concerning drug resistance in NSCLC. We performed targeted sequencing of 40 medication-relevant genes on plasma samples from 98 NSCLC patients and analyzed impact of genetic alterations on clinical presentation as well as response to systemic treatments. Profiling of multi-omics data from 1024 NSCLC tissues in public datasets was carried out for comparison and validation of identified molecular events implicated in resistance. A genetic association of CYP2D6 deletion with drug resistance was identified through circulating tumor DNA (ctDNA) profiling and response assessment. FCGR3A amplification was potentially involved in resistance to EGFR inhibitors. We further verified our findings in tissue samples and focused on potential resistance mechanisms, which uncovered that depleted CYP2D6 affected a set of genes involved in EMT, oncogenic signaling as well as inflammatory pathways. Tumor microenvironment analysis revealed that NSCLC with CYP2D6 loss manifested increased levels of immunomodulatory gene expressions, PD-L1 expression, relatively high mutational burden and lymphocyte infiltration. DNA methylation alterations were also found to be correlated with mRNA expressions and copy numbers of CYP2D6. Finally, MEK inhibitors were identified by CMap as the prospective therapeutic drugs for CYP2D6 deletion. These analyses identified novel resistance mechanisms to systemic NSCLC treatments and had significant implications for the development of new treatment strategies.
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Affiliation(s)
- Ruihan Luo
- Department of Bioinformatics, The Basic Medical School of Chongqing Medical University, China
| | - Chuang Ge
- Clinical Laboratory of Chongqing University Cancer Hospital, China
| | - Xiao Xiao
- Department of Surgery, The First Affiliated Hospital of Chongqing Medical University, China
| | - Jing Song
- Molecular and Tumor Research Center, Chongqing Medical University, China
| | - Shiqi Miao
- Molecular and Tumor Research Center, Chongqing Medical University, China
| | - Yongyao Tang
- Molecular and Tumor Research Center, Chongqing Medical University, China
| | - Jiayi Lai
- Department of Bioinformatics, The Basic Medical School of Chongqing Medical University, China
| | - Weiqi Nian
- Phase 1 Clinical Trial Center of Chongqing University Cancer Hospital, China
| | - Fangzhou Song
- Molecular and Tumor Research Center, Chongqing Medical University, China
| | - Longke Ran
- Department of Bioinformatics, The Basic Medical School of Chongqing Medical University, China
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Du WF, Ge JH, Li JJ, Tang LJ, Yu RQ, Jiang JH. Single-step, high-specificity detection of single nucleotide mutation by primer-activatable loop-mediated isothermal amplification (PA-LAMP). Anal Chim Acta 2018; 1050:132-138. [PMID: 30661580 DOI: 10.1016/j.aca.2018.10.068] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 10/29/2018] [Accepted: 10/30/2018] [Indexed: 01/08/2023]
Abstract
Loop-mediated isothermal amplification (LAMP) is a useful platform for nucleic acids detection in point-of-care (POC) situations, and development of single-step, close-tube LAMP reactions for specific detection of single nucleotide mutations (SNMs) remains a challenge. We develop a novel primer-activatable LAMP (PA-LAMP) strategy that enables highly specific and sensitive SNM detection using single-step, close-tube reactions. This strategy designs a terminal-blocked inner primer with a ribonucleotide insertion, which is cleaved and activated specifically to perfectly matched targets by ribonuclease (RNase) H2, to realize efficient amplification of mutant genes. It has shown dynamic responses of mutant target in a linear range from 220 aM to 22 pM with a lowest detectable concentration of 22 aM. It also demonstrates very high specificity in identifying the mutant in a large excess of the wild-type with a discrimination ratio as high as ∼10,000. It has been successfully applied to mutation detection of genomic DNA in tumor cells. The PA-LAMP strategy provides a useful, portable and affordable POC platform for highly sensitive and specific detection of genetic mutations in clinical applications.
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Affiliation(s)
- Wen-Fang Du
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, People's Republic of China
| | - Jian-Hui Ge
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, People's Republic of China
| | - Jun-Jie Li
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, People's Republic of China
| | - Li-Juan Tang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, People's Republic of China.
| | - Ru-Qin Yu
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, People's Republic of China
| | - Jian-Hui Jiang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, People's Republic of China.
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Lian DS, Zeng HS. Capillary Electrophoresis Based on Nucleic Acid Detection as Used in Food Analysis. Compr Rev Food Sci Food Saf 2017; 16:1281-1295. [DOI: 10.1111/1541-4337.12297] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/14/2017] [Accepted: 07/19/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Dong-Sheng Lian
- Guangzhou Women and Children's Medical Center of Guangzhou Medical University; NO. 9 at Jinsui Rd., Tianhe District Guangzhou Guangdong China
| | - Hua-Song Zeng
- Guangzhou Women and Children's Medical Center of Guangzhou Medical University; NO. 9 at Jinsui Rd., Tianhe District Guangzhou Guangdong China
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Zhang F, Duan X, Zhang M, Li Z, He Q, Wang Y, Miao C, Zhong W, Zou X, Zhuge Y. Influence of CYP2D6 and β2-adrenergic receptor gene polymorphisms on the hemodynamic response to propranolol in Chinese Han patients with cirrhosis. J Gastroenterol Hepatol 2016; 31:829-34. [PMID: 26489037 DOI: 10.1111/jgh.13198] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/11/2015] [Indexed: 12/30/2022]
Abstract
BACKGROUND AND AIM Propranolol is widely used to prevent gastroesophageal variceal bleeding; however, some patients could not benefit from propranolol. This study is to evaluate the relationship between CYP2D6 and β2-adrenergic receptor (β2-AR) gene polymorphisms and the hemodynamic response to propranolol in Chinese Han patients. METHODS The clinical data of patients with gastroesophageal varices undergoing hepatic venous pressure gradient (HVPG) measurement before and 7 days after oral propranolol administration in our department were collected. Four single nucleotide polymorphisms of CYP2D6 and β2-AR genes were detected. The relationship was identified by logistic regression model. RESULTS Thirty patients were involved in the analysis. Sixty milligram propranolol twice each day was well tolerated by all the patients. The initial and secondary average of HVPG was 17.4 ± 5.8 mmHg vs. 13.2 ± 4.8 mmHg, respectively (t = 5.726, P < 0.001). Twenty patients responded to propranolol. The mean reduction value of HVPG was 6.6 ± 3.6 mmHg (range from 3 to 19). Genotype analysis showed: 20 homozygotes for C/C188 and 10 for heterozygous C/T188, 8 homozygotes for G/G4268 and 22 heterozygotes for G/C4268, 14 homozygotes for Gly16 and 10 heterozygotes, and 6 homozygotes for Arg16, 27 homozygotes for Gln27 and 3 heterozygotes. The multivariate logistic regression analysis indicated that CYP2D6 (188C>T) genotype was an independent predicting factor for HVPG response to propranolol (P = 0.033). CONCLUSIONS CYP2D6 (188C>T) gene polymorphisms influence the hemodynamic response to propranolol in this population of Chinese Han patients with gastroesophageal varices. However, HVPG response cannot be completely predicted from CYP2D6 and β2-AR gene polymorphisms.
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Affiliation(s)
- Feng Zhang
- Department of Gastroenterology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Xuhong Duan
- Department of Gastroenterology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Ming Zhang
- Department of Gastroenterology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Zhenlei Li
- Department of Gastroenterology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Qibin He
- Department of Gastroenterology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Yi Wang
- Department of Gastroenterology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Chengcheng Miao
- Department of Gastroenterology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Wenqi Zhong
- Department of Gastroenterology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Xiaoping Zou
- Department of Gastroenterology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
| | - Yuzheng Zhuge
- Department of Gastroenterology, Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, China
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Lu HC, Chang YS, Chang CC, Lin CH, Chang JG. Developing and Evaluating the HRM Technique for Identifying Cytochrome P450 2D6 Polymorphisms. J Clin Lab Anal 2014; 29:220-5. [PMID: 24798984 DOI: 10.1002/jcla.21754] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 03/03/2014] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Cytochrome P450 2D6 is one of the important enzymes involved in the metabolism of many widely used drugs. Genetic polymorphisms of CYP2D6 can affect its activity. Therefore, an efficient method for identifying CYP2D6 polymorphisms is clinically important. METHODS We developed a high-resolution melting (HRM) analysis to investigate CYP2D6 polymorphisms. Genomic DNA was extracted from peripheral blood samples from 71 healthy individuals. All nine exons of the CYP2D6 gene were sequenced before screening by HRM analysis. This method can detect the most genotypes (*1, *2, *4, *10, *14, *21 *39, and *41) of CYP2D6 in Chinese. RESULTS All samples were successfully genotyped. The four most common mutant CYP2D6 alleles (*1, *2, *10, and *41) can be genotyped. The single nucleotides polymorphism (SNP) frequencies of 100C > T (rs1065852), 1039C > T (rs1081003), 1661G > C (rs1058164), 2663G > A (rs28371722), 2850C > T (rs16947), 2988G > A (rs28371725), 3181A > G, and 4180G > C (rs1135840) were 58%, 61%, 73%, 1%, 13%, 3%, 1%, 73%, respectively. We identified 100% of all heterozygotes without any errors. The two homozygous genotypes (1661G > C and 4180G > C) can be distinguished by mixing with a known genotype sample to generate an artificial heterozygote for HRM analysis. Therefore, all samples could be identified using our HRM method, and the results of HRM analysis are identical to those obtained by sequencing. Our method achieved 100% sensitivity, specificity, positive prediction value and negative prediction value. CONCLUSION HRM analysis is a nongel resolution method that is faster and less expensive than direct sequencing. Our study shows that it is an efficient tool for typing CYP2D6 polymorphisms.
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Affiliation(s)
- Hsiu-Chin Lu
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan.,Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Ya-Sian Chang
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan.,Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan
| | - Chun-Chi Chang
- Division of Chest Medicine, Department of Internal Medicine, Changhua Christian Hospital, Changhua, Taiwan
| | - Ching-Hsiung Lin
- Division of Chest Medicine, Department of Internal Medicine, Changhua Christian Hospital, Changhua, Taiwan
| | - Jan-Gowth Chang
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan.,Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan.,School of Medicine, China Medical University, Taichung, Taiwan
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Li J, Wang X, Zhang Z, Zou J, Chen Y, Wang X, Wu J. Statin therapy correlated CYP2D6 gene polymorphism and hyperlipidemia. Curr Med Res Opin 2014; 30:223-8. [PMID: 24156754 DOI: 10.1185/03007995.2013.858619] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
PURPOSE To investigate the distribution of statin therapy correlated gene polymorphism allele CYP2D6*10 (C188T) in Ningxia Hui nationality and to discuss the relationship between the gene polymorphism allele CYP2D6*10 (C188T) and the lipid-lowering efficacy of simvastatin and hyperlipidemia. MATERIALS AND METHODS One hundred and fifty healthy people (80 males and 70 females) and 200 hyperlipidemia patients (105 males and 95 females) were recruited at Ningxia People's Hospital. Genotypes were determined by using allele-specific amplification (ASA-PCR) in 150 healthy controls and 200 patients with hyperlipidemia. Relationships between genotypes and lipid levels and the lipid-lowering efficacy of simvastatin were analyzed. RESULTS The distribution frequency of the CYP2D6*10 allele was 47.6% in the Ningxia Hui nationality. There was no significant correlation between the CYP2D6*10 allele and hyperlipidemia. At 8 weeks after treatment with simvastatin, total cholesterol (TC) and low-density lipoprotein cholesterol (LDL-C) levels were more obviously decreased with the CC genotype than the CT and TT genotypes, with significant differences. CONCLUSION Distribution of the gene polymorphism of CYP2D6*10 is ethnically and geographical different. The allele T of CYP2D6*10 is not related to hyperlipidemia. CC expression seemed to increase the lipid-lowering effects of simvastatin. The hyperlipidemia patients with CC genotype should take lower doses of simvastatin than those with CT/TT genotype in the Ningxia Hui population.
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Affiliation(s)
- Juyi Li
- The Third Hospital of Wuhan , Wuhan, Hubei Province , China
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Abstract
Cytochrome P450 2D6 (CYP2D6) plays an important role in the metabolism and bioactivation of about 25% of clinically used drugs including many antidepressants, antipsychotics and opioids. CYP2D6 activity is highly variably ranging from no activity in so-called poor metabolizers to ultrarapid metabolism at the other end of the extreme of the activity distribution. A large portion of this variability can be explained by the highly polymorphic nature of the CYP2D6 gene locus for which > 100 variants and subvariants identified to date. Allele frequencies vary markedly between ethnic groups; some have exclusively or predominantly only been observed in certain populations. Pharmacogenetic testing holds the promise of individualizing drug therapy by identifying patients with CYP2D6 diplotypes that puts them at an increased risk of experiencing dose-related adverse events or therapeutic failure. Inferring a patient's CYP2D6 metabolic capacity, or phenotype, however, is a challenging task due to the complexity of the CYP2D6 gene locus. Allelic variation includes SNPs, small insertions and deletions, gene copy number variation and rearrangements with CYP2D7, a highly related non-functional gene. This review provides a summary of the intricacies of CYP2D6 variation and genotype analysis, knowledge that is invaluable for the translation of genotype into clinically useful information.
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Affiliation(s)
- Andrea Gaedigk
- Children's Mercy Hospital and Clinics, Division of Clinical Pharmacology and Innovative Therapeutics , Kansas City, Missouri , USA
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Sensitive electrochemical monitoring of nucleic acids coupling DNA nanostructures with hybridization chain reaction. Anal Chim Acta 2013; 783:17-23. [PMID: 23726095 DOI: 10.1016/j.aca.2013.04.049] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 04/20/2013] [Accepted: 04/24/2013] [Indexed: 01/24/2023]
Abstract
Methods based on metal nanotags have been developed for metallobioassay of nucleic acids, but most involve complicated labeling or stripping procedures and are unsuitable for routine use. Herein, we report the proof-of-concept of a novel and label-free metallobioassay for ultrasensitive electronic determination of human immunodeficiency virus (HIV)-related gene fragments at an ultralow concentration based on target-triggered long-range self-assembled DNA nanostructures and DNA-based hybridization chain reaction (HCR). The signal is amplified by silver nanotags on the DNA duplex. The assay mainly consists of capture probe, detection probe, and two different DNA hairpins. In the presence of target DNA, the capture probe immobilized on the sensor sandwiches target DNA with the 3' end of detection probe. Another exposed part of detection probe at the 5' end opens two alternating DNA hairpins in turn, and propagates a chain reaction of hybridization events to form a nicked double-helix. Finally, numerous silver nanotags are immobilized onto the long-range DNA nanostructures, each of which produces a strong electronic signal within the applied potentials. Under optimal conditions, the target-triggered long-range DNA nanostructures present good electrochemical behaviors for the detection of HIV DNA at a concentration as low as 0.5 fM. Importantly, the outstanding sensitivity can make this approach a promising scheme for development of next-generation DNA sensors without the need of enzyme labeling or fluorophore labeling.
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