Browsing by Author "Er, Tze-Kiong"

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Characteristics and prevalence of KRAS, BRAF, and PIK3CA mutations in colorectal cancer by high-resolution melting analysis in Taiwanese population
(2012-10-09)
Hsieh, Li-Ling
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Er, Tze-Kiong
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Chen, Chih-Chieh
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Hsieh, Jan-Sing
;
Chang, Jan-Gowth
Background: The identification of KRAS, BRAF, and PIK3CA mutations before the administration of anti-epidermal growth factor receptor therapy of colorectal cancer has become important The aim of the present study was to investigate the occurrence of KRAS, BRAF, and PIK3CA mutations in the Taiwanese population with colorectal cancer. This study was undertaken to identify BRAF and PIK3CA mutations in patients with colorectal cancer by high-resolution melting (HRM) analysis. HRM analysis is a new gene scan tool that quickly performs the PCR and identifies sequence alterations without requiring post-PCR treatment Methods: In the present study, DNAs were extracted from 182 cases of formalin-fixed, paraffin-embedded (FFPE) colorectal cancer samples for clinical KRAS mutational analysis by direct sequencing. All the samples were also tested for mutations within BRAF V600E and PIK3CA (exons 9 and 20) by HRM analysis. Results: The results were confirmed by direct sequencing. The frequency of BRAF and PIK3CA mutations is 1.1%, and 7.1%, respectively. Intriguingly, we found that nine patients (4.9%) with the KRAS mutation were coexistent with the PIK3CA mutation. Four patients (22%) without the KRAS mutation were existent with the PIK3CA mutation. Two patients (1.1%) without the KRAS mutation were existent with the BRAF mutation. Conclusions: In the current study, we suppose that HRM analysis is rapid, feasible, and powerful diagnostic tool for the detection of BRAF and PIK3CA mutations in a clinical setting. Additionally, our results indicated the prevalence of KRAS. BRAF, and PIK3C4 mutational status in the Taiwanese population. (C) 2012 Elsevier B.V. All rights reserved.
Clinical relevance of KRAS mutations in codon 13: Where are we?
(2014-02-01)
Er, Tze-Kiong
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Chen, Chih-Chieh
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Bujanda, Luis
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Herreros-Villanueva, Marta
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生物資訊及系統生物研究所
Recent advances in molecular diagnosis and the trend towards personalized medicine have made colorectal cancer one of the tumors where therapies have significantly improved patient survival after metastasis development. KRAS mutations in codon 12 and 13 are recognized biomarkers that are analyzed in clinic previously for anti-EGFR therapies administration. Since originally mutations in both codons were considered as a predictor of lack of response to cetuximab or panitumumab, the European Medicines Agency and the US Food and Drug Administration suggested that patients harboring any of those mutations should be excluded from the treatment. However, subsequent retrospective analysis has shown that mutations in codon 12 and codon 13 of KRAS gene could be different in their biological characteristics and as a result could confer variable effects in patients. In addition and increasing and sometimes contradictory number of solutions have been published demonstrating that patients with mutations in codon 13 could have worse outcome but could obtain a significant clinical benefit from anti-EGFR therapies. Here, we review and update the latest data on the biological role leading to a predictive outcome and benefit from anti-EGFR antibodies in patients with specific KRAS mutations in codon 13. (C) 2013 Elsevier Ireland Ltd. All rights reserved.
Clinical relevance of KRAS mutations in codon 13: Where are we? (vol 343, pg 1, 2013)
(2014-07-10)
Er, Tze-Kiong
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Chen, Chih-Chieh
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Bujanda, Luis
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Herreros-Villanueva, Marta
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生物資訊及系統生物研究所
Computational analysis of a novel mutation in ETFDH gene highlights its long-range effects on the FAD-binding motif
(2011-10-21)
Er, Tze-Kiong
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Chen, Chih-Chieh
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Liu, Yen-Yi
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Chang, Hui-Chiu
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Chien, Yin-Hsiu
Background: Multiple acyl-coenzyme A dehydrogenase deficiency (MADD) is an autosomal recessive disease caused by the defects in the mitochondrial electron transfer system and the metabolism of fatty acids. Recently, mutations in electron transfer flavoprotein dehydrogenase (ETFDH) gene, encoding electron transfer flavoprotein: ubiquinone oxidoreductase (ETF:QO) have been reported to be the major causes of riboflavin-responsive MADD. To date, no studies have been performed to explore the functional impact of these mutations or their mechanism of disrupting enzyme activity. Results: High resolution melting (HRM) analysis and sequencing of the entire ETFDH gene revealed a novel mutation (p.Phe128Ser) and the hotspot mutation (p.Ala84Thr) from a patient with MADD. According to the predicted 3D structure of ETF: QO, the two mutations are located within the flavin adenine dinucleotide (FAD) binding domain; however, the two residues do not have direct interactions with the FAD ligand. Using molecular dynamics (MD) simulations and normal mode analysis (NMA), we found that the p. Ala84Thr and p.Phe128Ser mutations are most likely to alter the protein structure near the FAD binding site as well as disrupt the stability of the FAD binding required for the activation of ETF: QO. Intriguingly, NMA revealed that several reported disease-causing mutations in the ETF: QO protein show highly correlated motions with the FAD-binding site. Conclusions: Based on the present findings, we conclude that the changes made to the amino acids in ETF: QO are likely to influence the FAD-binding stability.
Computational Analysis of KRAS Mutations: Implications for Different Effects on the KRAS p.G12D and p.G13D Mutations
(2013-02-20)
Chen, Chih-Chieh
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Er, Tze-Kiong
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Liu, Yen-Yi
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Hwang, Jenn-Kang
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Jesus Barrio, Maria
Background: The issue of whether patients diagnosed with metastatic colorectal cancer who harbor KRAS codon 13 mutations could benefit from the addition of anti-epidermal growth factor receptor therapy remains under debate. The aim of the current study was to perform computational analysis to investigate the structural implications of the underlying mutations caused by c.38G>A (p.G13D) on protein conformation. Methods: Molecular dynamics (MD) simulations were performed to understand the plausible structural and dynamical implications caused by c.35G>A (p.G12D) and c.38G>A (p.G13D). The potential of mean force (PMF) simulations were carried out to determine the free energy profiles of the binding processes of GTP interacting with wild-type (WT) KRAS and its mutants (MT). Results: Using MD simulations, we observed that the root mean square deviation (RMSD) increased as a function of time for the MT c.35G>A (p.G12D) and MT c.38G>A (p.G13D) when compared with the WT. We also observed that the GTP-binding pocket in the c.35G>A (p.G12D) mutant is more open than that of the WT and the c.38G>A (p.G13D) proteins. Intriguingly, the analysis of atomic fluctuations and free energy profiles revealed that the mutation of c.35G>A (p.G12D) may induce additional fluctuations in the sensitive sites (P-loop, switch I and II regions). Such fluctuations may promote instability in these protein regions and hamper GTP binding. Conclusions: Taken together with the results obtained from MD and PMF simulations, the present findings implicate fluctuations at the sensitive sites (P-loop, switch I and II regions). Our findings revealed that KRAS mutations in codon 13 have similar behavior as KRAS WT. To gain a better insight into why patients with metastatic colorectal cancer (mCRC) and the KRAS c.38G>A (p.G13D) mutation appear to benefit from anti-EGFR therapy, the role of the KRAS c.38G>A (p.G13D) mutation in mCRC needs to be further investigated.
Development of a feasible assay for the detection of GAA mutations in patients with Pompe disease
(2014-02-15)
Er, Tze-Kiong
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Chen, Chih-Chieh
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Chien, Yin-Hsiu
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Liang, Wen-Chen
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Kan, Tzu-Min
Background: Pompe disease is an inherited autosomal recessive deficiency of acid alpha-glucosidase (GAA) and is due to pathogenic sequence variants in the corresponding GM gene. While the analysis of enzyme activity remains the diagnostic test of choice for individuals with Pompe disease, mutation analysis remains for establishing a definitive diagnosis. Methods: High resolution melting (HRM) analysis was performed to screen GM mutations. Genomic DNA was extracted from peripheral blood samples of the two patients with Pompe disease and 250 normal controls. Exons 2 through 20 of the GM gene were screened by the HEM analysis. The results were subsequently confirmed by direct sequencing. Results: This assay proved to be feasible in detecting seven known (c2T>C, c.1726G>A, c.1845G>A, c.1935C>A, c.1958C>A, c.2238G>C, and c2815_2816del) GM mutations. Each mutation could be readily and accurately identified in the difference plot curves. We estimated the carrier frequency of the most common mutation, c.1935G>A (p.D645E), in the Taiwanese population to be 02%. Conclusions: In clinical practice, we suggest that HEM analysis is assumed as a fast and reliable method for screening GM gene mutations especially the most common mutations which are responsible for Pompe disease among the Taiwanese populations. (C) 2013 Elsevier B.V. All rights reserved.
IDENTIFICATION A NOVEL MISSENSE MUTATION P.F128S IN A TAIWANESE PATIENT WITH RIBOFLAVIN-RESPONSIVE MULTIPLE ACYL-COA DEHYDROGENASE DEFIENCY
(2011-05-01)
Er, Tze-Kiong
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Liang, Wen-Chen
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Chen, Chih-Chieh
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Liu, Ta-Chi
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Chang, Jan-Gowth