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Wang CW, Muzakky H, Lee YC, Lin YJ, Chao TK. Annotation-Free Deep Learning-Based Prediction of Thyroid Molecular Cancer Biomarker BRAF (V600E) from Cytological Slides. Int J Mol Sci 2023; 24:ijms24032521. [PMID: 36768841 PMCID: PMC9916807 DOI: 10.3390/ijms24032521] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/11/2023] [Accepted: 01/20/2023] [Indexed: 01/31/2023] Open
Abstract
Thyroid cancer is the most common endocrine cancer. Papillary thyroid cancer (PTC) is the most prevalent form of malignancy among all thyroid cancers arising from follicular cells. Fine needle aspiration cytology (FNAC) is a non-invasive method regarded as the most cost-effective and accurate diagnostic method of choice in diagnosing PTC. Identification of BRAF (V600E) mutation in thyroid neoplasia may be beneficial because it is specific for malignancy, implies a worse prognosis, and is the target for selective BRAF inhibitors. To the authors' best knowledge, this is the first automated precision oncology framework effectively predict BRAF (V600E) immunostaining result in thyroidectomy specimen directly from Papanicolaou-stained thyroid fine-needle aspiration cytology and ThinPrep cytological slides, which is helpful for novel targeted therapies and prognosis prediction. The proposed deep learning (DL) framework is evaluated on a dataset of 118 whole slide images. The results show that the proposed DL-based technique achieves an accuracy of 87%, a precision of 94%, a sensitivity of 91%, a specificity of 71% and a mean of sensitivity and specificity at 81% and outperformed three state-of-the-art deep learning approaches. This study demonstrates the feasibility of DL-based prediction of critical molecular features in cytological slides, which not only aid in accurate diagnosis but also provide useful information in guiding clinical decision-making in patients with thyroid cancer. With the accumulation of data and the continuous advancement of technology, the performance of DL systems is expected to be improved in the near future. Therefore, we expect that DL can provide a cost-effective and time-effective alternative tool for patients in the era of precision oncology.
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Affiliation(s)
- Ching-Wei Wang
- Graduate Institute of Biomedical Engineering, National Taiwan University of Science and Technology, Taipei 106335, Taiwan
- Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei 106335, Taiwan
| | - Hikam Muzakky
- Graduate Institute of Biomedical Engineering, National Taiwan University of Science and Technology, Taipei 106335, Taiwan
| | - Yu-Ching Lee
- Graduate Institute of Applied Science and Technology, National Taiwan University of Science and Technology, Taipei 106335, Taiwan
| | - Yi-Jia Lin
- Department of Pathology, Tri-Service General Hospital, Taipei 106335, Taiwan
- Institute of Pathology and Parasitology, National Defense Medical Center, Taipei 106335, Taiwan
| | - Tai-Kuang Chao
- Department of Pathology, Tri-Service General Hospital, Taipei 106335, Taiwan
- Institute of Pathology and Parasitology, National Defense Medical Center, Taipei 106335, Taiwan
- Correspondence:
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Shi W, Gong Y, Zhang D, Yang T, Yi M, Tan J, Ding S, Cheng W. A dual identification strategy based on padlock ligation and CRISPR/Cas14a for highly specific detection of BRAF V600E mutation in clinical samples. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:1913-1921. [PMID: 35522948 DOI: 10.1039/d2ay00319h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
BRAF V600E mutation is a single-nucleotide variation (SNV) that is widely found in various cancers and has been demonstrated to have a strong association with the prognosis and development of some diseases. Thus, we developed a strategy based on rolling circle amplification (RCA) and CRISPR/Cas14a to meet the great need for detecting highly specific BRAF V600E mutation in fine-needle biopsy samples. In this study, a padlock probe was designed to recognize and trigger subsequent ligase chain reactions (LCR). And due to the Taq DNA ligase, a great number of ligated annular padlock probes were generated in the presence of BRAF V600E mutation, subsequently generating long repeated single-strand DNA by RCA. The obtained amplicons were activators triggering the trans-cleavage of CRISPR/Cas14a. CRISPR/Cas14a shows outstanding performance in identifying ssDNA with single base mutation, which significantly increases the specificity of mutation discrimination. Under the optimal conditions, our strategy can identify BRAF V600E mutation down to 0.307 fM with a wide linear range from 1 fM to 10 pM. On the other hand, the dual identification strategy endows the method with terrific specificity for the detection of SNV. Furthermore, our method has been successfully employed to identify BRAF V600E mutation in clinical fine-needle aspiration samples, proving great potential for ultra-specific identification of low abundance BRAF V600E mutation and providing a novel method for diagnosis and treatment of cancer.
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Affiliation(s)
- Weicheng Shi
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China.
| | - Yao Gong
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China.
| | - Decai Zhang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China.
| | - Tiantian Yang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China.
| | - Ming Yi
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China.
| | - Jingyi Tan
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China.
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China.
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Comparison of high-resolution melting analysis with direct sequencing for detection of FLT3-TKD, FLT3-ITD and WT1 mutations in acute myeloid leukemia. Cancer Treat Res Commun 2021; 28:100432. [PMID: 34303121 DOI: 10.1016/j.ctarc.2021.100432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/28/2021] [Accepted: 07/06/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND Acute Myeloid Leukemia (AML) is a group of hematologic diseases characterized by a variety of clinically important genetic alterations. Genetic mutations affecting the FMS-like receptor tyrosine kinase-3 (FLT3) and Wilm's tumor (WT-1) genes are associated with poor prognosis in AML. In this work, efficiency of HRM method for detection of FLT3-ITD, FLT3-TKD, and WT-1 mutations was assessed in comparison with direct sequencing. METHOD A total of 58 formalin-fixed, paraffin-embedded BM biopsy specimens of AML patients were analyzed. Mutation detection was performed by HRM method and the results were consequently compared with direct sequencing RESULTS: FLT3 and WT-1 mutations were detected in 21 (36.2%) and 3 (5.17%) samples, respectively. Among all FLT3 mutations, 10 (17.2%) and 11 (18.2%) samples were harboring the FLT3-ITD and-TKD gene mutations, respectively. Frequency of the FLT3-ITD was not statistically different in females (51%) and males (49%). Also, FLT3-TKD was more common in males although the differences in gender distribution were not statistically significant (P = 0.721 and P = 0.626, respectively). CONCLUSIONS Regarded as the desirable characteristic, the present study is generally distinguished by the similar previous ones due to assessing the FFPE BM tissue from the perspective of the type of assessed sample. This discrepancy between our results and those in prior studies may be due to the disparity of the studied population size, adopted methods as well as the sample type. In this survey, regarding to low amount of extracted DNA from the paraffinized samples, the HRM method was efficient in determining the mentioned mutations.
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Zhang Y, Liu L, Liu Y, Cao N, Wang L, Xing C. Clinical significance of immunohistochemistry to detect BRAF V600E mutant protein in thyroid tissues. Medicine (Baltimore) 2021; 100:e25566. [PMID: 33879712 PMCID: PMC8078443 DOI: 10.1097/md.0000000000025566] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 03/30/2021] [Indexed: 01/04/2023] Open
Abstract
This study investigated the feasibility of using immunohistochemistry (IHC) instead of PCR to detect BRAF V600E mutant protein in papillary thyroid carcinoma (PTC), and to determine the value of using preoperative BRAF V600E mutant protein by IHC to assist in the diagnosis of thyroid nodule patients with Hashimoto's thyroiditis (HT).The expression of BRAFV600E mutant protein was measured in 23 cases of HT+PTC, 31 cases of PTC, and 28 cases of HT by IHC, followed by PCR in the same samples for validation. SPSS 19.0 software was used for statistical analysis.The sensitivity and specificity of IHC to detect BRAF V600E mutation were 100% and 42.86%, respectively. In addition, the mutation rate of BRAF V600E protein in the HT+PTC group (34.78%, 8/23) was lower than that in the PTC group (80.65%, 25/31).The application of IHC to detect BRAF V600E mutant protein has good sensitivity but not specificity to diagnose PTC. IHC can be used as a preliminary screening method to detect BRAF V600E mutation. The strongly positive (+++) staining of IHC potently indicated BRAF V600E gene mutation. For suspicious thyroid nodules combined with HT, the detection of BRAF V600E mutant protein with IHC alone is not of great significance for differentiating benign and malignant nodules.
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Affiliation(s)
- Yini Zhang
- Department of Pathology, The Second Hospital of Dalian Medical University
| | - Lidan Liu
- The Press of Dalian Medical University
| | - Ye Liu
- Department of Pathology, The Second Hospital of Dalian Medical University
| | - Nan Cao
- Henan Vocational College of Nursing, Dalian, Liaoning, China
| | - Lifen Wang
- Department of Pathology, The Second Hospital of Dalian Medical University
| | - Chengjuan Xing
- Department of Pathology, The Second Hospital of Dalian Medical University
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Tayeb BA, Pringle HJ. The Sensitivity and Specificity of Novel Primers for Detection of BRAFV600E Mutation. Asian Pac J Cancer Prev 2020; 21:3191-3198. [PMID: 33247675 PMCID: PMC8033103 DOI: 10.31557/apjcp.2020.21.11.3191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Indexed: 11/25/2022] Open
Abstract
Objective: This study aimed to evaluate the sensitivity and specificity of a PCR-based novel technique for the detection of BRAF mutation in early stages of the cancer. Methods: Different lengths of primer sets, ranging from 8 bp to 20 bp, were designed and used in this study. These primers were developed by applying on cancer cell lines. After that, the sensitivity and specificity of the methodology was evaluated by making serial dilutions. Results: The quantitative allele specific discrimination PCR (QUASAqPCR) primer with 14 bp length was sensitive enough to detect significantly 1:1,000 ratio of BRAFV600E to wild-type background (P = 0.011), when using 150 nanograms of DNA from cell lines in the reactions. Conclusion: High sensitivity and specificity levels of QUASA-qPCR method can improve diagnostic accuracy for BRAF mutation testing in patients at early stages of cancers and help stratify the appropriate choice of treatment.
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Affiliation(s)
- Bizhar A Tayeb
- Molecular Pathology and Toxicology, Department of Molecular Microbiology, Central Laboratory in Ibrahim Al-khalil Zakho, Duhok, Kurdistan Region of Iraq
| | - Howard J Pringle
- Department of Cancer Studies and Molecular Medicine, University of Leicester, Leicester, UK
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Joy RA, Thelakkattusserry SK, Vikkath N, Bhaskaran R, Krishnan S, Vasudevan D, Ariyannur PS. Somatic mutation detection efficiency in EGFR: a comparison between high resolution melting analysis and Sanger sequencing. BMC Cancer 2020; 20:902. [PMID: 32962681 PMCID: PMC7510081 DOI: 10.1186/s12885-020-07411-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/14/2020] [Indexed: 11/21/2022] Open
Abstract
Background High resolution melting curve analysis is a cost-effective rapid screening method for detection of somatic gene mutation. The performance characteristics of this technique has been explored previously, however, analytical parameters such as limit of detection of mutant allele fraction and total concentration of DNA, have not been addressed. The current study focuses on comparing the mutation detection efficiency of High-Resolution Melt Analysis (HRM) with Sanger Sequencing in somatic mutations of the EGFR gene in non-small cell lung cancer. Methods The minor allele fraction of somatic mutations was titrated against total DNA concentration using Sanger sequencing and HRM to determine the limit of detection. The mutant and wildtype allele fractions were validated by multiplex allele-specific real-time PCR. Somatic mutation detection efficiency, for exons 19 & 21 of the EGFR gene, was compared in 116 formalin fixed paraffin embedded tumor tissues, after screening 275 tumor tissues by Sanger sequencing. Results The limit of detection of minor allele fraction of exon 19 mutation was 1% with sequencing, and 0.25% with HRM, whereas for exon 21 mutation, 0.25% MAF was detected using both methods. Multiplex allele-specific real-time PCR revealed that the wildtype DNA did not impede the amplification of mutant allele in mixed DNA assays. All mutation positive samples detected by Sanger sequencing, were also detected by HRM. About 28% cases in exon 19 and 40% in exon 21, detected as mutated in HRM, were not detected by sequencing. Overall, sensitivity and specificity of HRM were found to be 100 and 67% respectively, and the negative predictive value was 100%, while positive predictive value was 80%. Conclusion The comparative series study suggests that HRM is a modest initial screening test for somatic mutation detection of EGFR, which must further be confirmed by Sanger sequencing. With the modification of annealing temperature of initial PCR, the limit of detection of Sanger sequencing can be improved.
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Affiliation(s)
- Reenu Anne Joy
- Molecular Oncology Diagnostics Laboratory, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Kochi, 682041, India
| | | | - Narendranath Vikkath
- Molecular Oncology Diagnostics Laboratory, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Kochi, 682041, India
| | - Renjitha Bhaskaran
- Department of Biostatistics, Amrita School of Medicine, Amrita Vishwa Vidyapeetham, Kochi, 682041, India
| | - Sajitha Krishnan
- Department of Biochemistry, Amrita School of Medicine, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Ponekkara P.O., Kochi, Kerala, 682041, India
| | - Damodaran Vasudevan
- Molecular Oncology Diagnostics Laboratory, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Kochi, 682041, India.,Department of Biochemistry, Amrita School of Medicine, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Ponekkara P.O., Kochi, Kerala, 682041, India
| | - Prasanth S Ariyannur
- Molecular Oncology Diagnostics Laboratory, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Kochi, 682041, India. .,Department of Biochemistry, Amrita School of Medicine, Amrita Institute of Medical Sciences, Amrita Vishwa Vidyapeetham, Ponekkara P.O., Kochi, Kerala, 682041, India.
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7
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Vanni I, Tanda ET, Spagnolo F, Andreotti V, Bruno W, Ghiorzo P. The Current State of Molecular Testing in the BRAF-Mutated Melanoma Landscape. Front Mol Biosci 2020; 7:113. [PMID: 32695793 PMCID: PMC7338720 DOI: 10.3389/fmolb.2020.00113] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/13/2020] [Indexed: 01/19/2023] Open
Abstract
The incidence of melanoma, among the most lethal cancers, is widespread and increasing. Metastatic melanoma has a poor prognosis, representing about 90% of skin cancer mortality. The increased knowledge of tumor biology and the greater understanding of the immune system role in the anti-tumor response has allowed us to develop a more rational approach to systemic therapies. The discovery of activating BRAF mutations in half of all melanomas has led to the development of molecularly targeted therapy with BRAF and MEK inhibitors, which dramatically improved outcomes of patients with stage IV BRAF-mutant melanoma. More recently, the results of clinical phase III studies conducted in the adjuvant setting led to the combined administration of BRAF and MEK inhibitors also in patients with resected high-risk melanoma (stage III). Therefore, BRAF mutation testing has become a priority to determine the oncologist's choice and course of therapy. In this review, we will report the molecular biology-based strategies used for BRAF mutation detection with the main advantages and disadvantages of the most commonly used diagnostic strategies. The timing of such molecular assessment in patients with cutaneous melanoma will be discussed, and we will also examine considerations and approaches for accurate and effective BRAF testing.
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Affiliation(s)
- Irene Vanni
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.,Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | | | | | - Virginia Andreotti
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.,Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - William Bruno
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.,Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Paola Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy.,Genetics of Rare Cancers, Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
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Analysis of Single Nucleotide-Mutated Single-Cancer Cells Using the Combined Technologies of Single-Cell Microarray Chips and Peptide Nucleic Acid-DNA Probes. MICROMACHINES 2020; 11:mi11070628. [PMID: 32605095 PMCID: PMC7407912 DOI: 10.3390/mi11070628] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/23/2020] [Accepted: 06/26/2020] [Indexed: 12/12/2022]
Abstract
Research into cancer cells that harbor gene mutations relating to anticancer drug-resistance at the single-cell level has focused on the diagnosis of, or treatment for, cancer. Several methods have been reported for detecting gene-mutated cells within a large number of non-mutated cells; however, target single nucleotide-mutated cells within a large number of cell samples, such as cancer tissue, are still difficult to analyze. In this study, a new system is developed to detect and isolate single-cancer cells expressing the T790M-mutated epidermal growth factor receptor (EGFR) mRNA from multiple non-mutated cancer cells by combining single-cell microarray chips and peptide nucleic acid (PNA)-DNA probes. The single-cell microarray chip is made of polystyrene with 62,410 microchambers (31-40 µm diameter). The T790M-mutated lung cancer cell line, NCI-H1975, and non-mutated lung cancer cell line, A549, were successfully separated into single cells in each microchambers on the chip. Only NCI-H1975 cell was stained on the chip with a fluorescein isothiocyanate (FITC)-conjugated PNA probe for specifically detecting T790M mutation. Of the NCI-H1975 cells that spiked into A549 cells, 0–20% were quantitatively analyzed within 1 h, depending on the spike concentration. Therefore, our system could be useful in analyzing cancer tissue that contains a few anticancer drug-resistant cells.
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Tran TV, Dang KX, Pham QH, Nguyen UD, Trinh NTT, Hoang LV, Ho SA, Nguyen BV, Nguyen DT, Trinh DT, Tran DN, Orpana A, Stenman UH, Stenman J, Ho TH. Evaluation of the expression levels of BRAF V600E mRNA in primary tumors of thyroid cancer using an ultrasensitive mutation assay. BMC Cancer 2020; 20:368. [PMID: 32357861 PMCID: PMC7195771 DOI: 10.1186/s12885-020-06862-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/14/2020] [Indexed: 12/05/2022] Open
Abstract
Background The BRAFV600E gene encodes for the mutant BRAFV600E protein, which triggers downstream oncogenic signaling in thyroid cancer. Since most currently available methods have focused on detecting BRAFV600E mutations in tumor DNA, there is limited information about the level of BRAFV600E mRNA in primary tumors of thyroid cancer, and the diagnostic relevance of these RNA mutations is not known. Methods Sixty-two patients with thyroid cancer and non-malignant thyroid disease were included in the study. Armed with an ultrasensitive technique for mRNA-based mutation analysis based on a two step RT-qPCR method, we analysed the expression levels of the mutated BRAFV600E mRNA in formalin-fixed paraffin-embedded samples of thyroid tissues. Sanger sequencing for detection of BRAFV600E DNA was performed in parallel for comparison and normalization of BRAFV600E mRNA expression levels. Results The mRNA-based mutation detection assay enables detection of the BRAFV600E mRNA transcripts in a 10,000-fold excess of wildtype BRAF counterparts. While BRAFV600E mutations could be detected by Sanger sequencing in 13 out of 32 malignant thyroid cancer FFPE tissue samples, the mRNA-based assay detected mutations in additionally 5 cases, improving the detection rate from 40.6 to 56.3%. Furthermore, we observed a surprisingly large, 3-log variability, in the expression level of the BRAFV600E mRNA in FFPE samples of thyroid cancer tissue. Conclusions The expression levels of BRAFV600E mRNA was characterized in the primary tumors of thyroid cancer using an ultrasensitive mRNA-based mutation assay. Our data inspires further studies on the prognostic and diagnostic relevance of the BRAFV600E mRNA levels as a molecular biomarker for the diagnosis and monitoring of various genetic and malignant diseases.
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Affiliation(s)
- Tien Viet Tran
- 103 Military Hospital, Vietnam Military Medical University, Hanoi, Vietnam
| | - Kien Xuan Dang
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Quynh Huong Pham
- Department of Genomics and Cytogenetics, Institute of Biomedicine and Pharmacy (IBP), Vietnam Military Medical University, 222 Phung Hung street, Ha Dong district, Hanoi, Vietnam
| | - Ung Dinh Nguyen
- Department of Genomics and Cytogenetics, Institute of Biomedicine and Pharmacy (IBP), Vietnam Military Medical University, 222 Phung Hung street, Ha Dong district, Hanoi, Vietnam
| | - Nhung Thi Trang Trinh
- Department of Genomics and Cytogenetics, Institute of Biomedicine and Pharmacy (IBP), Vietnam Military Medical University, 222 Phung Hung street, Ha Dong district, Hanoi, Vietnam
| | - Luong Van Hoang
- Institute of Biomedicine and Pharmacy (IBP), Vietnam Military Medical University, Hanoi, Vietnam
| | - Son Anh Ho
- Institute of Biomedicine and Pharmacy (IBP), Vietnam Military Medical University, Hanoi, Vietnam
| | - Ba Van Nguyen
- Oncology Centre, 103 Military Hospital, Vietnam Military Medical University, Hanoi, Vietnam
| | - Duc Trong Nguyen
- School of Medicine and Pharmacy, Vietnam National University, Hanoi, Vietnam
| | - Dung Tuan Trinh
- Pathology Department, 108 Military Central Hospital, Hanoi, Vietnam
| | - Dung Ngoc Tran
- Department of Pathology, 103 Military Hospital, Vietnam Military Medical University, Hanoi, Vietnam
| | - Arto Orpana
- Laboratory of Genetics, HUSLAB, Helsinki University Central Hospital, Helsinki, Finland
| | - Ulf-Håkan Stenman
- Department of Clinical Chemistry, Medicum, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Jakob Stenman
- Minerva Foundation Institute for Medical Research, Helsinki, Finland.,Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Tho Huu Ho
- Minerva Foundation Institute for Medical Research, Helsinki, Finland. .,Department of Genomics and Cytogenetics, Institute of Biomedicine and Pharmacy (IBP), Vietnam Military Medical University, 222 Phung Hung street, Ha Dong district, Hanoi, Vietnam. .,Department of Medical Microbiology, 103 Military Hospital, Vietnam Medical University, Hanoi, Vietnam.
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Yu Z, Grasso MF, Cui X, Silva RN, Zhang P. Sensitive and Label-Free SERS Detection of Single-Stranded DNA Assisted by Silver Nanoparticles and Gold-Coated Magnetic Nanoparticles. ACS APPLIED BIO MATERIALS 2020; 3:2626-2632. [DOI: 10.1021/acsabm.9b01218] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Zhao Yu
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Michael F. Grasso
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Xiaoyu Cui
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Rebecca Nogueira Silva
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
| | - Peng Zhang
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, United States
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Ribeiro Ferreira I, Darleans Dos Santos Cunha W, Henrique Ferreira Gomes L, Azevedo Cintra H, Lopes Cabral Guimarães Fonseca L, Ferreira Bastos E, Clinton Llerena J, Farias Meira de Vasconcelos Z, da Cunha Guida L. A rapid and accurate methylation-sensitive high-resolution melting analysis assay for the diagnosis of Prader Willi and Angelman patients. Mol Genet Genomic Med 2019; 7:e637. [PMID: 31033246 PMCID: PMC6565559 DOI: 10.1002/mgg3.637] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 02/15/2019] [Accepted: 02/20/2019] [Indexed: 12/26/2022] Open
Abstract
Background Prader Willi (PWS) and Angelman (AS) syndromes are rare genetic disorders characterized by deletions, uniparental disomy, and imprinting defects at chromosome 15. The loss of function of specific genes caused by genetic alterations in paternal allele causes PWS while the absence in maternal allele results AS. The laboratory diagnosis of PWS and AS is complex and demands molecular biology and cytogenetics techniques to identify the genetic mechanism related to the development of the disease. The DNA methylation analysis in chromosome 15 at the SNURF‐SNRPN locus through MS‐PCR confirms the diagnosis and distinguishes between PWS and AS. Our study aimed to establish the MS‐PCR technique associated with High‐Resolution Melting (MS‐HRM) in PWS and AS diagnostic with a single pair of primers. Methods We collected blood samples from 43 suspected patients to a cytogenetic and methylation analysis. The extracted DNA was treated with bisulfite to perform comparative methylation analysis. Results MS‐HRM and MS‐PCR agreed in 100% of cases, identifying 19(44%) PWS, 3(7%) AS, and 21(49%) Normal. FISH analysis detected four cases of PWS caused by deletions in chromosome 15. Conclusion The MS‐HRM showed good performance with a unique pair of primers, dispensing electrophoresis gel analysis, offering a quick and reproducible diagnostic.
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Affiliation(s)
- Igor Ribeiro Ferreira
- Laboratório de Alta Complexidade, Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira, Fiocruz, Rio de Janeiro, Brazil
| | - Wilton Darleans Dos Santos Cunha
- Laboratório de Alta Complexidade, Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira, Fiocruz, Rio de Janeiro, Brazil
| | - Leonardo Henrique Ferreira Gomes
- Laboratório de Alta Complexidade, Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira, Fiocruz, Rio de Janeiro, Brazil
| | - Hiago Azevedo Cintra
- Laboratório de Alta Complexidade, Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira, Fiocruz, Rio de Janeiro, Brazil
| | | | - Elenice Ferreira Bastos
- Departamento de Genética, Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira, Fiocruz, Rio de Janeiro, Brazil
| | - Juan Clinton Llerena
- Departamento de Genética, Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira, Fiocruz, Rio de Janeiro, Brazil
| | - Zilton Farias Meira de Vasconcelos
- Laboratório de Alta Complexidade, Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira, Fiocruz, Rio de Janeiro, Brazil
| | - Letícia da Cunha Guida
- Laboratório de Alta Complexidade, Instituto Nacional da Saúde da Mulher, da Criança e do Adolescente Fernandes Figueira, Fiocruz, Rio de Janeiro, Brazil
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12
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Zhao J, Liu P, Yu Y, Zhi J, Zheng X, Yu J, Gao M. Comparison of diagnostic methods for the detection of a BRAF mutation in papillary thyroid cancer. Oncol Lett 2019; 17:4661-4666. [PMID: 30988823 DOI: 10.3892/ol.2019.10131] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Accepted: 01/21/2019] [Indexed: 01/20/2023] Open
Abstract
The most common genetic alteration identified in papillary thyroid cancer (PTC) encodes a valine to glutamic acid change at position 600 (V600E) in the BRAF proto-oncoprotein. The most accurate and reliable method for detecting this BRAF mutation has not yet been determined. In the present study, the sensitivity, specificity and feasibility of diagnostic methods for BRAF mutations were assessed. BRAF mutational analysis was performed by Sanger DNA sequencing, using the Cobas® 4800 BRAF V600 test and by immunohistochemistry (IHC). A total of 185 tumor tissues samples were analyzed using the three assays. BRAF mutations were identified in 76.2% of samples by Sanger sequencing, 78.9% of samples by Cobas 4800 BRAF V600 test and 76.8% of samples by IHC. Complete concordance for the three methods was observed in 92.4% of samples. Sensitivity and specificity of Sanger sequencing were 97.2 and 95.2%. Sensitivity and specificity of the Cobas 4800 BRAF V600 test were 99.3 and 90.5%. Sensitivity and specificity of IHC were 98.6 and 97.6%. Furthermore, the presence of a BRAF mutation was significantly associated with extrathyroid extension and multifocality (P<0.05), but not associated with age, sex, lymph node metastasis, central node metastasis, lateral node metastasis, Tumor-Node-Metastasis stage or tumor size in patients with PTC. These results suggest that a combination of IHC and the Cobas 4800 BRAF V600 Test kit for V600E mutation analysis is the most efficient and reliable method in routine practice. Accurate screening for BRAF mutation may contribute to improving the risk stratification of PTC.
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Affiliation(s)
- Jingzhu Zhao
- Department of Thyroid and Neck Tumor, Key Laboratory of Cancer Immunology and Biotherapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, P.R. China
| | - Pengpeng Liu
- Cancer Molecular Diagnostics Core, Key Laboratory of Cancer Immunology and Biotherapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, P.R. China
| | - Yang Yu
- Department of Thyroid and Neck Tumor, Key Laboratory of Cancer Immunology and Biotherapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, P.R. China
| | - Jingtai Zhi
- Department of Thyroid and Neck Tumor, Key Laboratory of Cancer Immunology and Biotherapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, P.R. China
| | - Xiangqian Zheng
- Department of Thyroid and Neck Tumor, Key Laboratory of Cancer Immunology and Biotherapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, P.R. China
| | - Jinpu Yu
- Cancer Molecular Diagnostics Core, Key Laboratory of Cancer Immunology and Biotherapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, P.R. China
| | - Ming Gao
- Department of Thyroid and Neck Tumor, Key Laboratory of Cancer Immunology and Biotherapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin 300060, P.R. China
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Lambert A, Salleron J, Lion M, Rouyer M, Lozano N, Leroux A, Merlin JL, Harlé A. Comparison of Three Real-Time PCR Assays for the Detection of PIK3CA Somatic Mutations in Formalin-Fixed Paraffin Embedded Tissues of Patients with Breast Carcinomas. Pathol Oncol Res 2018; 25:1117-1123. [PMID: 30426328 DOI: 10.1007/s12253-018-0538-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/09/2018] [Indexed: 01/27/2023]
Abstract
Breast cancer is the leading cause of cancer-related death in women worldwide. Mutations of the PIK3CA gene are found in approximately 25% of breast carcinomas and are reported as activators of the PI3K/AKT/mTOR pathway. This study aims to compare three assays for the somatic mutation detection of PIK3CA gene in FFPE tissues of patients with breast cancer. We compared Cobas® PIK3CA Mutation Test (Roche Diagnostics, Meylan, France), PCR amplification-refractory mutation system Scorpions® (ARMS) and High-Resolution Melting PCR assay (HRM) for the detection of PIK3CA mutations. Discrepant samples were assessed using Next Generation Sequencing (NGS). 46 FFPE breast carcinomas samples of patients treated for breast cancer have been assessed for PIK3CA mutations using the three PCR assays. Among the 46 samples, 17 (37.8%), 13 (28.36%) and 19 (41.3%) had a PIK3CA mutation, with Cobas®, ARMS and HRM assays respectively. Three different mutations of PIK3CA have been detected for one sample. Calculated kappa were 0.95[0.86;1] between Cobas® and HRM, 0.75[0.55;0.95] between Cobas® and ARMS and 0.72[0.51;0.92] between HRM and ARMS. Five samples were found with discrepant results. Our study shows that the Cobas® assay is suitable for PIK3CA mutation assessment in patients with breast cancer. HRM assay is also suitable for PIK3CA mutation assessment but requires a mutation characterization with a specific assay.
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Affiliation(s)
- A Lambert
- Département d'Oncologie Médicale, Institut de Cancérologie de Lorraine, 54519, Vandoeuvre les Nancy, France
| | - J Salleron
- Département de Biostatistiques, Institut de Cancérologie de Lorraine, 54519, Vandoeuvre les Nancy, France
| | - M Lion
- CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, Université de Lorraine, 6 avenue de Bourgogne CS 30519, 54519, 54500, Vandoeuvre-lès-Nancy Cedex, France
| | - M Rouyer
- CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, Université de Lorraine, 6 avenue de Bourgogne CS 30519, 54519, 54500, Vandoeuvre-lès-Nancy Cedex, France
| | - N Lozano
- CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, Université de Lorraine, 6 avenue de Bourgogne CS 30519, 54519, 54500, Vandoeuvre-lès-Nancy Cedex, France
| | - A Leroux
- CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, Université de Lorraine, 6 avenue de Bourgogne CS 30519, 54519, 54500, Vandoeuvre-lès-Nancy Cedex, France
| | - J L Merlin
- CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, Université de Lorraine, 6 avenue de Bourgogne CS 30519, 54519, 54500, Vandoeuvre-lès-Nancy Cedex, France
| | - Alexandre Harlé
- CNRS UMR 7039 CRAN, Institut de Cancérologie de Lorraine, Service de Biopathologie, Université de Lorraine, 6 avenue de Bourgogne CS 30519, 54519, 54500, Vandoeuvre-lès-Nancy Cedex, France.
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14
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Sperlich A, Balmert A, Doll D, Bauer S, Franke F, Keller G, Wilhelm D, Mur A, Respondek M, Friess H, Nitsche U, Janssen KP. Genetic and immunological biomarkers predict metastatic disease recurrence in stage III colon cancer. BMC Cancer 2018; 18:998. [PMID: 30340556 PMCID: PMC6194664 DOI: 10.1186/s12885-018-4940-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 10/11/2018] [Indexed: 02/08/2023] Open
Abstract
Background Even though the post-operative outcome varies greatly among patients with nodal positive colon cancer (UICC stage III), personalized prediction of systemic disease recurrence is currently insufficient. We investigated in a retrospective setting whether genetic and immunological biomarkers can be applied for stratification of distant metastasis occurrence risk. Methods Eighty four patients with complete resection (R0) of stage III colon cancer from two clinical centres were analysed for genetic biomarkers: microsatellite instability, oncogenic mutations in KRAS exon2 and BRAF exon15, expression of osteopontin and the metastasis-associated genes SASH1 and MACC1. Tumor-infiltrating CD3 and CD8 positive T-cells were quantified by immunocytochemistry. Results were correlated with outcome and response to 5-FU based adjuvant chemotherapy, using Cox’s proportional hazard models and integrative two-step cluster analysis. Results Distant metastasis risk was significantly correlated with oncogenic KRAS mutations (p = 0.015), expression of SASH1 (p = 0.016), and the density of CD8-positive T-cells (p = 0.007) in Kaplan-Meier analysis. Upon multivariate Cox-regression analysis, KRAS mutation (p = 0.008) and density of CD8-positive TILs (p = 0.009) were retained as prognostic parameters for metachronous distant metastasis. Integrative two-step cluster analysis was used to combine all genetic markers, allowing stratification of patient subgroups. Post-operative distant metastasis risk ranged from 31% (low-risk) to 41% (intermediate), and 57% (high-risk) (p = 0.032). Increased expression of osteopontin (p = 0.019) and low density of CD8-positive T-cells (p = 0.043) were significantly associated with unfavourable response to 5-FU. Conclusions Integrative biomarker analysis allows stratification of stage III colon cancer patients for the risk of metastatic disease recurrence and may indicate response to 5-FU. Thus, biomarker analysis might facilitate the use of adjuvant therapy for high risk patients. Electronic supplementary material The online version of this article (10.1186/s12885-018-4940-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andreas Sperlich
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Alexander Balmert
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Dietrich Doll
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany.,Darmzentrum Vechta, St. Marienhospital, Marienstraße 6-8, 49377, Vechta, Germany
| | - Sabine Bauer
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Fabian Franke
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Gisela Keller
- Institute of Pathology, Technical University of Munich, Trogerstr. 18, 81675, Munich, Germany
| | - Dirk Wilhelm
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Anna Mur
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Michael Respondek
- St. Marienhospital, Praxis für Pathologie Vechta, Marienstr. 11, 49377, Vechta, Germany
| | - Helmut Friess
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Ulrich Nitsche
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany
| | - Klaus-Peter Janssen
- Department of Surgery, Klinikum rechts der Isar, TUM, Ismaninger Str. 22, 81675, Munich, Germany.
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Validation of high-resolution melting analysis as a diagnostic tool for endothelin receptor B mutation in American Paint horses and allele frequency estimation. Mol Cell Probes 2018; 41:52-56. [PMID: 30096357 DOI: 10.1016/j.mcp.2018.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/17/2018] [Accepted: 08/07/2018] [Indexed: 11/21/2022]
Abstract
Overo lethal white foal syndrome (OLWFS) is a genetic disorder caused by a dinucleotide mutation in the endothelin receptor type B (EDNRB) gene leading to the death of affected foals shortly after birth. The use of rapid and reliable genetic testing is imperative for the early diagnosis of the mutation avoiding, therefore, either additional suffering or the production of affected animals. In the present study, we developed and validated a high-resolution melting (HRM) genotyping assay to detect the OLWFS causative mutation, and we also determined the frequency of heterozygotes among American Paint horses in Brazil. The HRM genotyping assay resulted in a high sensitivity, specificity, and positive and negative predictive values. The overall estimated frequency of heterozygotes was 21.6%; however, this frequency increased to 89.5% when considering only overo horses. The HRM assay optimized here was a reliable and suitable method for the detection of the dinucleotide mutation observed in the EDNRB gene resulting in a fast, accurate, and precise diagnostic tool. The causative gene mutation of OLWFS is present in heterozygosity in the American Paint Horse population in Brazil and is highly frequent among overo horses.
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16
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Chat-Uthai N, Vejvisithsakul P, Udommethaporn S, Meesiri P, Danthanawanit C, Wongchai Y, Teerapakpinyo C, Shuangshoti S, Poungvarin N. Development of ultra-short PCR assay to reveal BRAF V600 mutation status in Thai colorectal cancer tissues. PLoS One 2018; 13:e0198795. [PMID: 29879227 PMCID: PMC5991739 DOI: 10.1371/journal.pone.0198795] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 05/25/2018] [Indexed: 02/06/2023] Open
Abstract
The protein kinase BRAF is one of the key players in regulating cellular responses to extracellular signals. Somatic mutations of the BRAF gene, causing constitutive activation of BRAF, have been found in various types of human cancers such as malignant melanoma, and colorectal cancer. BRAF V600E and V600K, most commonly observed mutations in these cancers, may predict response to targeted therapies. Many techniques suffer from a lack of diagnostic sensitivity in mutation analysis in clinical samples with a low cancer cell percentage or poor-quality fragmented DNA. Here we present allele-specific real-time PCR assay for amplifying 35- to 45-base target sequences in BRAF gene. Forward primer designed for BRAF V600E detection is capable of recognizing both types of BRAF V600E mutation, i.e. V600E1 (c.1799T>A) and V600E2 (c.1799_1800delTGinsAA), as well as complex tandem mutation caused by nucleotide changes in codons 600 and 601. We utilized this assay to analyze Thai formalin-fixed paraffin-embedded tissues. Forty-eight percent of 178 Thai colorectal cancer tissues has KRAS mutation detected by highly sensitive commercial assays. Although these DNA samples contain low overall yield of amplifiable DNA, our newly-developed assay successfully revealed BRAF V600 mutations in 6 of 93 formalin-fixed paraffin-embedded colorectal cancer tissues which KRAS mutation was not detected. Ultra-short PCR assay with forward mutation-specific primers is potentially useful to detect BRAF V600 mutations in highly fragmented DNA specimens from cancer patients.
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Affiliation(s)
- Nunthawut Chat-Uthai
- Research Division, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Sutthirat Udommethaporn
- Clinical Molecular Pathology Laboratory, Department of Clinical Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Puttarakun Meesiri
- Clinical Molecular Pathology Laboratory, Department of Clinical Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chetiya Danthanawanit
- Clinical Molecular Pathology Laboratory, Department of Clinical Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Yannawan Wongchai
- Research Division, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chinachote Teerapakpinyo
- Chulalongkorn GenePRO Center, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Shanop Shuangshoti
- Chulalongkorn GenePRO Center, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Naravat Poungvarin
- Clinical Molecular Pathology Laboratory, Department of Clinical Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- * E-mail:
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17
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Wu J, He J, Zhang C, Chen J, Niu Y, Yuan Q, Yu C. PdPt nanoparticles anchored on the N-G with the integration of PANI nanohybrids as novel redox probe and catalyst for the detection of rs1801177. Biosens Bioelectron 2018; 102:403-410. [DOI: 10.1016/j.bios.2017.11.054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 11/11/2017] [Accepted: 11/17/2017] [Indexed: 01/12/2023]
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Mutation Analysis of Braf Exon 15 and Kras Codons 12 and 13 in Moroccan Patients with Colorectal Cancer. Int J Biol Markers 2018. [DOI: 10.5301/jbm.2010.6091] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Background The RAS/RAF/MEK/MAP kinase cascade transduces signals from the cell surface to the nucleus in order to control cellular responses including proliferation, differentiation and survival. We investigated the occurrence of BRAF exon 15 and KRAS codon 12 and 13 mutations in Moroccan patients with colorectal cancer. Methods Sixty-two samples from patients with sporadic colorectal adenocarcinomas were studied for BRAF exon 15 and KRAS codon 12 and 13 mutations. DNA from paraffin-embedded tissue specimens was analyzed by a combination of polymerase chain reaction–high resolution melting and direct sequencing. Results Of the analyzed specimens, 29% exhibited KRAS codon 12 or 13 mutations and only 1.6% carried a BRAF codon 600 mutation. KRAS mutations were more often observed in women (35.5%) than in men (22.6%). Patients in the age range between 41 and 60 years were more likely to be carriers of this mutation. No KRAS mutations were detected in patients aged >60 years. Conclusion Despite the limited study sample, our data suggest that KRAS mutations arise more frequently than BRAF mutations in Moroccan patients with colorectal carcinomas. The KRAS mutation status must be assessed in a large cohort of Moroccan patients to confirm these findings and to determine whether this mutation in combination with extrinsic, environmental or microenvironmental factors might be involved in the high frequency of colorectal cancer in middle-aged Moroccans.
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Locked Nucleic Acid Technology for Highly Sensitive Detection of Somatic Mutations in Cancer. Adv Clin Chem 2017; 83:53-72. [PMID: 29304903 DOI: 10.1016/bs.acc.2017.10.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The molecular diagnosis of the cancer mutational status is essential for modern clinical laboratory medicine. Mutations in EGFR, KRAS, BRAF, and PIK3CA genes are widely analyzed in solid tumors such as lung cancer, colorectal cancer, breast cancer, and melanoma. The allele-specific polymerase chain reaction, high-resolution melting, and Sanger sequencing are used for detecting and identifying gene mutations in many clinical laboratories. The locked nucleic acid (LNA) is a class of nucleic acid analogs that contain a methylene bridge connecting the 2' oxygen and 4' carbon in the ribose moiety. This methylene bridge locks the ribose group into a C3'-endo conformation. LNA, including an oligonucleotide, increases the thermal stability of hybrid strands. The use of LNA technology in molecular diagnostic methods improves the specificity and sensitivity of assays. This review describes routinely analyzed mutations and molecular diagnostic methods used in the clinical laboratory along with the performance improvement of mutational analysis with LNA.
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Huebner C, Weber R, Lloydd R. A HRM assay for identification of low level BRAF V600E and V600K mutations using the CADMA principle in FFPE specimens. Pathology 2017; 49:776-783. [PMID: 29100713 DOI: 10.1016/j.pathol.2017.08.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 08/09/2017] [Accepted: 08/15/2017] [Indexed: 12/25/2022]
Abstract
Melanoma patients with BRAF V600E and V600K mutations show complete or partial response to vemurafenib. Detection assays often scan for the common V600E mutation rather than the rare V600K variant, although this mutation can be found in a high proportion of melanoma patients in the South Pacific. Herein, we describe a BRAF high resolution melting (HRM) assay that can differentiate low level of V600E and V600K mutations using formalin fixed, paraffin embedded (FFPE) reference standards for assay validation. The assay is based on the competitive amplification of differentially melting amplicons (CADMA principle) and has a limit of detection of 0.8% mutant allele for V600K and 1.4% mutant allele for V600E. A differentiation between the two mutations based on the melting profile is possible even at low mutation level. Sixty FFPE specimens were scanned and mutations could be scored correctly as confirmed by castPCR. In summary, the developed HRM assay is suitable for detection of V600K and V600E mutations and proved to be reliable and cost effective in a diagnostic environment.
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Affiliation(s)
- Claudia Huebner
- Department of Anatomical Pathology, Labtests Auckland Limited, New Zealand.
| | - Remeny Weber
- Department of Anatomical Pathology, Labtests Auckland Limited, New Zealand
| | - Richard Lloydd
- Department of Anatomical Pathology, Labtests Auckland Limited, New Zealand
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Comparison of Five Different Assays for the Detection of BRAF Mutations in Formalin-Fixed Paraffin Embedded Tissues of Patients with Metastatic Melanoma. Mol Diagn Ther 2017; 21:209-216. [DOI: 10.1007/s40291-017-0258-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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22
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Sasaki Y, Hamaguchi T, Yamada Y, Takahashi N, Shoji H, Honma Y, Iwasa S, Okita N, Takashima A, Kato K, Nagai Y, Taniguchi H, Boku N, Ushijima T, Shimada Y. Value of KRAS, BRAF, and PIK3CA Mutations and Survival Benefit from Systemic Chemotherapy in Colorectal Peritoneal Carcinomatosis. Asian Pac J Cancer Prev 2017; 17:539-43. [PMID: 26925640 DOI: 10.7314/apjcp.2016.17.2.539] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND It is well known that peritoneal carcinomatosis (PC) from colorectal cancer (CRC) is associated with a poor prognosis. However, data on the prognostic significance of modern chemotherapy containing bevacizumab, cetuximab or panitumumab are not available. MATERIALS AND METHODS This retrospective review concerned 526 patients with metastatic CRC who were classified into two groups according to the presence or absence of PC, and were treated with systemic chemotherapy, with or without bevacizumab or anti-EGFR antibodies. The genetic background, in particular KRAS, BRAF, and PIK3CA gene mutations, and overall survival (OS) were compared between the two groups. RESULTS The median OS values were 23.3 and 29.1 months for PC and non-PC patients, respectively (hazard ratio [HR]=1.20; p=0.17). Among all patients, tumor location, number of metastatic sites and BRAF mutation status were significant prognostic factors, whereas the presence of PC was not. In the PC group, chemotherapy with bevacizumab resulted in a significantly longer OS than forchemotherapy without bevacizumab (HR=0.38, p<0.01), but this was not the case in the non-PC group (HR=0.80, p=0.10). Furthermore, the incidence of the BRAF V600E mutation was significantly higher in PC than in non-PC patients (27.7% versus 7.3%, p<0.01). BRAF mutations displayed a strong correlation with shorter OS in non-PC (HR=2.26), but not PC patients (HR=1.04). CONCLUSIONS Systemic chemotherapy, especially when combined with bevacizumab, improved survival in patients with PC from CRC as well as non-PC patients. While BRAF mutation demonstrated a high frequency in PC patients, but it was not associated with prognosis.
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Affiliation(s)
- Yusuke Sasaki
- Gastrointestinal Medical Oncology Division, National Cancer Center Hospital, Tokyo, Japan E-mail :
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Zaboikin M, Zaboikina T, Freter C, Srinivasakumar N. Non-Homologous End Joining and Homology Directed DNA Repair Frequency of Double-Stranded Breaks Introduced by Genome Editing Reagents. PLoS One 2017; 12:e0169931. [PMID: 28095454 PMCID: PMC5241150 DOI: 10.1371/journal.pone.0169931] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 12/22/2016] [Indexed: 11/19/2022] Open
Abstract
Genome editing using transcription-activator like effector nucleases or RNA guided nucleases allows one to precisely engineer desired changes within a given target sequence. The genome editing reagents introduce double stranded breaks (DSBs) at the target site which can then undergo DNA repair by non-homologous end joining (NHEJ) or homology directed recombination (HDR) when a template DNA molecule is available. NHEJ repair results in indel mutations at the target site. As PCR amplified products from mutant target regions are likely to exhibit different melting profiles than PCR products amplified from wild type target region, we designed a high resolution melting analysis (HRMA) for rapid identification of efficient genome editing reagents. We also designed TaqMan assays using probes situated across the cut site to discriminate wild type from mutant sequences present after genome editing. The experiments revealed that the sensitivity of the assays to detect NHEJ-mediated DNA repair could be enhanced by selection of transfected cells to reduce the contribution of unmodified genomic DNA from untransfected cells to the DNA melting profile. The presence of donor template DNA lacking the target sequence at the time of genome editing further enhanced the sensitivity of the assays for detection of mutant DNA molecules by excluding the wild-type sequences modified by HDR. A second TaqMan probe that bound to an adjacent site, outside of the primary target cut site, was used to directly determine the contribution of HDR to DNA repair in the presence of the donor template sequence. The TaqMan qPCR assay, designed to measure the contribution of NHEJ and HDR in DNA repair, corroborated the results from HRMA. The data indicated that genome editing reagents can produce DSBs at high efficiency in HEK293T cells but a significant proportion of these are likely masked by reversion to wild type as a result of HDR. Supplying a donor plasmid to provide a template for HDR (that eliminates a PCR amplifiable target) revealed these cryptic DSBs and facilitated the determination of the true efficacy of genome editing reagents. The results indicated that in HEK293T cells, approximately 40% of the DSBs introduced by genome editing, were available for participation in HDR.
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Affiliation(s)
- Michail Zaboikin
- Division of Hematology/Oncology, Department of Internal Medicine, Saint Louis University, Saint Louis, Missouri, United States of America
| | - Tatiana Zaboikina
- Division of Hematology/Oncology, Department of Internal Medicine, Saint Louis University, Saint Louis, Missouri, United States of America
| | - Carl Freter
- Division of Hematology/Oncology, Department of Internal Medicine, Saint Louis University, Saint Louis, Missouri, United States of America
| | - Narasimhachar Srinivasakumar
- Division of Hematology/Oncology, Department of Internal Medicine, Saint Louis University, Saint Louis, Missouri, United States of America
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Hatae R, Hata N, Suzuki SO, Yoshimoto K, Kuga D, Murata H, Akagi Y, Sangatsuda Y, Iwaki T, Mizoguchi M, Iihara K. A comprehensive analysis identifies BRAF hotspot mutations associated with gliomas with peculiar epithelial morphology. Neuropathology 2016; 37:191-199. [PMID: 27792249 DOI: 10.1111/neup.12347] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Revised: 09/12/2016] [Accepted: 09/13/2016] [Indexed: 12/21/2022]
Abstract
Brain tumors harbor various BRAF alterations, the vast majority of which are the BRAF kinase-activating V600E mutation. BRAF mutations are most frequently detected in certain subtypes of low-grade glioma, such as pilocytic astrocytoma (PA), pleomorphic xanthoastrocytoma (PXA), ganglioglioma (GG) and dysembryoplastic neuroepithelial tumor (DNT). However, it is unclear whether gliomas harboring BRAF mutations can be invariably regarded as these glioma subtypes or their derivatives. To address this question, we analyzed 274 gliomas in our institutional case series. We performed high-resolution melting analyses and subsequent direct Sanger sequencing on DNA isolated from snap-frozen tumor tissues. As expected, BRAF mutations were detected in the aforementioned low-grade gliomas: in 4/27 PAs, 2/3 PXAs, 4/8 GGs, and 1/6 DNTs. In addition to these gliomas, 1/2 astroblastomas (ABs) and 2/122 glioblastomas (GBs) harbored BRAF mutations. Pathological investigation of the two GBs revealed that one was a GB displaying epithelial features that presumably arose from a precedent GG, whereas the other GB, which harbored a rare G596 A mutation, showed marked epithelial features, including astroblastic rosettes. Our results indicate that in addition to being present in established BRAF-associated gliomas, BRAF mutations might be associated with epithelial features in high-grade gliomas, including sheet-like arrangement of polygonal tumor cells with a plump cytoplasm and astroblastic rosettes, and thus could potentially serve as a genetic marker for these features.
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Affiliation(s)
- Ryusuke Hatae
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Nobuhiro Hata
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Satoshi O Suzuki
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Koji Yoshimoto
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Daisuke Kuga
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Hideki Murata
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yojiro Akagi
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Yuhei Sangatsuda
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Toru Iwaki
- Department of Neuropathology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Masahiro Mizoguchi
- Department of Neurosurgery, Kitakyushu Municipal Medical Center, Kitakyushu, Japan
| | - Koji Iihara
- Department of Neurosurgery, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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Chen TL, Chang JWC, Hsieh JJ, Cheng HY, Chiou CC. A Sensitive Peptide Nucleic Acid Probe Assay for Detection of BRAF V600 Mutations in Melanoma. Cancer Genomics Proteomics 2016; 13:381-386. [PMID: 27566656 PMCID: PMC5070627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 06/14/2016] [Indexed: 06/06/2023] Open
Abstract
Mutated v-Raf murine sarcoma viral oncogene homolog B (BRAF) is an important biomarker for the prediction of therapeutic efficacy of several anticancer drugs. The detection of BRAF mutation faces two challenges: Firstly, there are multiple types of mutations, and secondly, tumor samples usually contain various amounts of wild-type, normal tissues. Here, we describe a newly established method for sensitive detection of multiple types of BRAF V600 mutations in excess wild-type background. The method introduced a fluorophore-tagged peptide nucleic acid (PNA) to serve as both polymerase chain reaction (PCR) clamp and sensor probe, which inhibited the amplification of wild-type templates during PCR and revealed multiple types of mutant signals during melting analysis. We demonstrated the design and optimization process of the method, and applied it in the detection of BRAF mutations in 49 melanoma samples. This PNA probe assay method detected three types of mutations in 17 samples, and was much more sensitive than conventional PCR plus Sanger sequencing.
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Affiliation(s)
- Tai-Long Chen
- Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan, R.O.C
| | - John Wen-Cheng Chang
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C. College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C
| | - Jia-Juan Hsieh
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C. College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C
| | - Hsin-Yi Cheng
- Division of Hematology-Oncology, Department of Internal Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C. College of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C
| | - Chiuan-Chian Chiou
- Graduate Institute of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan, R.O.C. Department of Thoracic Medicine, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C. Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan, R.O.C.
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Sasaki Y, Akasu T, Saito N, Kojima H, Matsuda K, Nakamori S, Komori K, Amagai K, Yamaguchi T, Ohue M, Nagashima K, Yamada Y. Prognostic and predictive value of extended RAS mutation and mismatch repair status in stage III colorectal cancer. Cancer Sci 2016; 107:1006-12. [PMID: 27089049 PMCID: PMC4946717 DOI: 10.1111/cas.12950] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 04/06/2016] [Accepted: 04/14/2016] [Indexed: 12/13/2022] Open
Abstract
The prognostic and predictive value of KRAS gene mutations in stage III colorectal cancer is controversial because many recent clinical trials have not involved a surgery-alone arm. Additionally, data on the significance of extended RAS (KRAS/NRAS) mutations in stage III cancer are not available. Hence, we undertook a combined analysis of two phase III randomized trials, in which the usefulness of adjuvant chemotherapy with tegafur-uracil (UFT) was evaluated, as compared with surgery alone. We determined the association of extended RAS and mismatch repair (MMR) status with the effectiveness of adjuvant chemotherapy. Mutations in KRAS exons 2, 3, and 4 and NRAS exons 2 and 3 were detected by direct DNA sequencing. Tumor MMR status was determined by immunohistochemistry. Total RAS mutations were detected in 134/304 (44%) patients. In patients with RAS mutations, a significant benefit was associated with adjuvant UFT in relapse-free survival (RFS) (hazard ratio = 0.49; P = 0.02) and overall survival (hazard ratio = 0.51; P = 0.03). In contrast, among patients without RAS mutations, there was no difference in RFS or overall survival between the adjuvant UFT group and surgery-alone group. We detected deficient DNA MMR in 23/304 (8%) patients. The MMR status was neither prognostic nor predictive for adjuvant chemotherapy. An interaction analysis showed that there was better RFS among patients treated with UFT with RAS mutations, but not for those without RAS mutations. Extended RAS (KRAS/NRAS) mutations are proposed as predictive indicators with respect to the efficacy of adjuvant UFT chemotherapy in patients with resected stage III colorectal cancer.
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Affiliation(s)
- Yusuke Sasaki
- Gastrointestinal Medical Oncology Division, National Cancer Center Hospital, Tokyo, Japan
| | - Takayuki Akasu
- Department of Surgery, Imperial Household Agency Hospital, Tokyo, Japan
| | - Norio Saito
- Division of Colorectal Surgery, National Cancer Center Hospital East, Kashiwa, Japan
| | - Hiroshi Kojima
- Division of Gastrointestinal Surgery, Prefectural Aichi Hospital, Okazaki, Japan
| | - Keiji Matsuda
- Department of Surgery, Teikyo University School of Medicine, Tokyo, Japan
| | - Shoji Nakamori
- Department of Surgery, National Hospital Organization Osaka National Hospital, Osaka, Japan
| | - Koji Komori
- Department of Gastroenterological Surgery, Aichi Cancer Center Hospital, Nagoya, Japan
| | - Kenji Amagai
- Division of Gastroenterology and Gastrointestinal Oncology, Ibaraki Prefectural Central Hospital and Cancer Center, Kasama, Japan
| | - Tatsuro Yamaguchi
- Department of Surgery, Infectious Diseases Center Komagome Hospital, Tokyo, Japan
| | - Masayuki Ohue
- Department of Surgery, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Japan
| | - Kengo Nagashima
- Department of Global Clinical Research, Chiba University Graduate School of Medicine, Chiba, Japan
| | - Yasuhide Yamada
- Gastrointestinal Medical Oncology Division, National Cancer Center Hospital, Tokyo, Japan
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Detection of BRAF Mutations Using a Fully Automated Platform and Comparison with High Resolution Melting, Real-Time Allele Specific Amplification, Immunohistochemistry and Next Generation Sequencing Assays, for Patients with Metastatic Melanoma. PLoS One 2016; 11:e0153576. [PMID: 27111917 PMCID: PMC4844167 DOI: 10.1371/journal.pone.0153576] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/31/2016] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Metastatic melanoma is a severe disease with one of the highest mortality rate in skin diseases. Overall survival has significantly improved with immunotherapy and targeted therapies. Kinase inhibitors targeting BRAF V600 showed promising results. BRAF genotyping is mandatory for the prescription of anti-BRAF therapies. METHODS Fifty-nine formalin-fixed paraffin-embedded melanoma samples were assessed using High-Resolution-Melting (HRM) PCR, Real-time allele-specific amplification (RT-ASA) PCR, Next generation sequencing (NGS), immunohistochemistry (IHC) and the fully-automated molecular diagnostics platform IdyllaTM. Sensitivity, specificity, positive predictive value and negative predictive value were calculated using NGS as the reference standard to compare the different assays. RESULTS BRAF mutations were found in 28(47.5%), 29(49.2%), 31(52.5%), 29(49.2%) and 27(45.8%) samples with HRM, RT-ASA, NGS, IdyllaTM and IHC respectively. Twenty-six (81.2%) samples were found bearing a c.1799T>A (p.Val600Glu) mutation, three (9.4%) with a c.1798_1799delinsAA (p.Val600Lys) mutation and one with c.1789_1790delinsTC (p.Leu597Ser) mutation. Two samples were found bearing complex mutations. CONCLUSIONS HRM appears the less sensitive assay for the detection of BRAF V600 mutations. The RT-ASA, IdyllaTM and IHC assays are suitable for routine molecular diagnostics aiming at the prescription of anti-BRAF therapies. IdyllaTM assay is fully-automated and requires less than 2 minutes for samples preparation and is the fastest of the tested assays.
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28
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Detection of skewed X-chromosome inactivation in Fragile X syndrome and X chromosome aneuploidy using quantitative melt analysis. Expert Rev Mol Med 2015; 17:e13. [PMID: 26132880 PMCID: PMC4836209 DOI: 10.1017/erm.2015.11] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Methylation of the fragile X mental retardation 1 (FMR1) exon 1/intron 1
boundary positioned fragile X related epigenetic element 2 (FREE2), reveals skewed
X-chromosome inactivation (XCI) in fragile X syndrome full mutation (FM: CGG > 200)
females. XCI skewing has been also linked to abnormal X-linked gene expression with the
broader clinical impact for sex chromosome aneuploidies (SCAs). In this study, 10 FREE2
CpG sites were targeted using methylation specific quantitative melt analysis (MS-QMA),
including 3 sites that could not be analysed with previously used EpiTYPER system. The
method was applied for detection of skewed XCI in FM females and in different types of
SCA. We tested venous blood and saliva DNA collected from 107 controls (CGG < 40),
and 148 FM and 90 SCA individuals. MS-QMA identified: (i) most SCAs if combined with a Y
chromosome test; (ii) locus-specific XCI skewing towards the hypomethylated state in FM
females; and (iii) skewed XCI towards the hypermethylated state in SCA with 3 or more X
chromosomes, and in 5% of the 47,XXY individuals. MS-QMA output also showed significant
correlation with the EpiTYPER reference method in FM males and females
(P < 0.0001) and SCAs (P < 0.05). In
conclusion, we demonstrate use of MS-QMA to quantify skewed XCI in two applications with
diagnostic utility.
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29
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Gorniak P, Ejduk A, Borg K, Makuch-Lasica H, Nowak G, Lech-Maranda E, Prochorec-Sobieszek M, Warzocha K, Juszczynski P. Comparison of high-resolution melting analysis with direct sequencing for the detection of recurrent mutations in DNA methyltransferase 3A and isocitrate dehydrogenase 1 and 2 genes in acute myeloid leukemia patients. Eur J Haematol 2015; 96:181-7. [PMID: 25891904 DOI: 10.1111/ejh.12566] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/13/2015] [Indexed: 01/09/2023]
Abstract
Acute myeloid leukemia (AML) cells harbor frequent mutations in genes responsible for epigenetic modifications. Increasing evidence of clinical role of DNMT3A and IDH1/2 mutations highlights the need for a robust and inexpensive test to identify these mutations in routine diagnostic work-up. Herein, we compared routinely used direct sequencing method with high-resolution melting (HRM) assay for screening DNMT3A and IDH1/2 mutations in patients with AML. We show very high concordance between HRM and Sanger sequencing (100% samples for IDH2-R140 and DNMT3-R882 mutations, 99% samples for IDH1-R132 and IDH2-R172 mutations). HRM method reported no false-negative results, suggesting that it can be used for mutations screening. Moreover, HRM displayed much higher sensitivity in comparison with DNA sequencing in all assessed loci. With Sanger sequencing, robust calls were observed when the sample contained 50% of mutant DNA in the background of wild-type DNA. In marked contrast, the detection limit of HRM improved down to 10% of mutated DNA. Given the ubiquitous presence of wild-type DNA background in bone marrow aspirates and clonal variations regarding mutant allele burden, these results favor HRM as a sensitive, specific, labor-, and cost-effective tool for screening and detection of mutations in IDH1/2 and DNMT3A genes in patients with AML.
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Affiliation(s)
- Patryk Gorniak
- Department of Diagnostic Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Anna Ejduk
- Department of Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Katarzyna Borg
- Department of Diagnostic Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Hanna Makuch-Lasica
- Department of Diagnostic Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Grazyna Nowak
- Department of Diagnostic Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Ewa Lech-Maranda
- Department of Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland.,Centre for Postgraduate Medical Education, Warsaw, Poland
| | | | - Krzysztof Warzocha
- Department of Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Przemyslaw Juszczynski
- Department of Diagnostic Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
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Spagnolo F, Ghiorzo P, Orgiano L, Pastorino L, Picasso V, Tornari E, Ottaviano V, Queirolo P. BRAF-mutant melanoma: treatment approaches, resistance mechanisms, and diagnostic strategies. Onco Targets Ther 2015; 8:157-68. [PMID: 25653539 PMCID: PMC4303458 DOI: 10.2147/ott.s39096] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BRAF inhibitors vemurafenib and dabrafenib achieved improved overall survival over chemotherapy and have been approved for the treatment of BRAF-mutated metastatic melanoma. More recently, the combination of BRAF inhibitor dabrafenib with MEK inhibitor trametinib has shown improved progression-free survival, compared to dabrafenib monotherapy, in a Phase II study and has received approval by the US Food and Drug Administration. However, even when treated with the combination, most patients develop mechanisms of acquired resistance, and some of them do not achieve tumor regression at all, because of intrinsic resistance to therapy. Along with the development of BRAF inhibitors, immunotherapy made an important step forward: ipilimumab, an anti-CTLA-4 monoclonal antibody, was approved for the treatment of metastatic melanoma; anti-PD-1 agents achieved promising results in Phase I/II trials, and data from Phase III studies will be ready soon. The availability of such drugs, which are effective regardless of BRAF status, has made the therapeutic approach more complex, as first-line treatment with BRAF inhibitors may not be the best choice for all BRAF-mutated patients. The aim of this paper is to review the systemic therapeutic options available today for patients affected by BRAF V600-mutated metastatic melanoma, as well as to summarize the mechanisms of resistance to BRAF inhibitors and discuss the possible strategies to overcome them. Moreover, since the molecular analysis of tumor specimens is now a pivotal and decisional factor in the treatment strategy of metastatic melanoma patients, the advances in the molecular detection techniques for the BRAF V600 mutation will be reported.
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Affiliation(s)
- Francesco Spagnolo
- Department of Plastic and Reconstructive Surgery, IRCCS Azienda Ospedaliera Universitaria San Martino, IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Paola Ghiorzo
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, Genova, Italy ; Genetics of Rare Cancers, IRCCS Azienda Ospedaliera Universitaria San Martino, IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Laura Orgiano
- Department of Medical Oncology, IRCCS Azienda Ospedaliera Universitaria San Martino, IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Lorenza Pastorino
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, Genova, Italy ; Genetics of Rare Cancers, IRCCS Azienda Ospedaliera Universitaria San Martino, IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Virginia Picasso
- Department of Medical Oncology, IRCCS Azienda Ospedaliera Universitaria San Martino, IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Elena Tornari
- Department of Medical Oncology, IRCCS Azienda Ospedaliera Universitaria San Martino, IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Vincenzo Ottaviano
- Department of Medical Oncology, IRCCS Azienda Ospedaliera Universitaria San Martino, IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Paola Queirolo
- Department of Medical Oncology, IRCCS Azienda Ospedaliera Universitaria San Martino, IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
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Verlinden I, van den Hurk K, Clarijs R, Willig AP, Stallinga CMHA, Roemen GMJM, van den Oord JJ, Zur Hausen A, Speel EJM, Winnepenninckx VJL. BRAFV600E immunopositive melanomas show low frequency of heterogeneity and association with epithelioid tumor cells: a STROBE-compliant article. Medicine (Baltimore) 2014; 93:e285. [PMID: 25526463 PMCID: PMC4603111 DOI: 10.1097/md.0000000000000285] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 10/10/2014] [Accepted: 10/28/2014] [Indexed: 12/26/2022] Open
Abstract
Treatment of BRAFV600E-mutant melanoma by small molecule inhibitors that target BRAFV600E or MEK kinases is increasingly used in clinical practice and significantly improve patient outcome. However, patients eventually become resistant and therapeutic improvement is required. Molecular diversity within individual tumors (intratumor heterogeneity) and between tumors within a single patient (intrapatient heterogeneity) poses a significant challenge to precision medicine. Using immunohistochemistry, we determined the extent of BRAFV600E intratumor and intrapatient heterogeneity and the influence of morphological heterogeneity in a large series of 171 melanomas of 81 patients. The BRAFV600E mutation rate found in our melanoma series is 44%, with none of 22 (0%) melanoma in situ, 23 of 56 (41%) primary tumors, 28 of 59 (48%) regional metastases, and 24 of 34 (71%) distant metastases harboring the mutation. In general, a diffuse homogeneous immunostaining was seen, even in tumors consisting of more than one cell type, that is, epithelioid, spindle, and/or small cell types. Nevertheless, BRAFV600E-mutant melanomas more often had a purely epithelioid cell population (P=0.063), that is more evident among distant metastases (P=0.014). Only two of 75 (3%) mutated specimens (one primary and one metastasis) displayed heterogeneous BRAFV600E expression. The primary tumor was also morphologically heterogeneous and exclusively displayed BRAFV600E in the epithelioid component, confirming an association between BRAFV600E and epithelioid cells. Twenty-eight of 30 patients (93%) had concordant BRAFV600E mutation status between their tumors. Taken together, BRAFV600E intratumor and intrapatient heterogeneity in melanoma is diminutive, nevertheless, the identified exceptions will have important implications for the clinical management of this disease.
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Affiliation(s)
- Ivana Verlinden
- From the Department of Pathology, Maastricht University Medical Centre, Maastricht, The Netherlands (IV, KvdH, CMHAS, GMJMR, AzH, E-JMS, VJLW); GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, The Netherlands (KvdH, AzH, E-JMS, VJLW); Department of Clinical Pathology, Atrium Medical Centre Parkstad, Heerlen, The Netherlands (RC); Department of Pathology, St. Laurentius ziekenhuis, Roermond, The Netherlands (APW); and Laboratory of Translational Cell & Tissue Research and Department of Pathology, University Hospital, KULeuven, Leuven, Belgium (JJvdO)
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32
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Ishige T, Itoga S, Sato K, Kitamura K, Nishimura M, Sawai S, Matsushita K, Suzuki K, Ota S, Miyauchi H, Matsubara H, Nakatani Y, Nomura F. High-throughput screening of extended RAS mutations based on high-resolution melting analysis for prediction of anti-EGFR treatment efficacy in colorectal carcinoma. Clin Biochem 2014; 47:340-3. [PMID: 25262986 DOI: 10.1016/j.clinbiochem.2014.09.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/11/2014] [Accepted: 09/14/2014] [Indexed: 10/24/2022]
Abstract
OBJECTIVES Recent studies have demonstrated that, in advanced colorectal carcinoma (CRC) patients, extended RAS (in KRAS exons 2-4 and NRAS exons 2-4) and BRAF mutations are negative predictors for anti-EGFR treatment efficacy and negative prognostic factor, respectively. Thus, high-throughput and cost-effective methods for identification of the mutation status are required. DESIGN AND METHODS We developed a PCR-high-resolution melting (HRM)-based method for screening extended RAS and BRAF mutations, and relative frequency of mutations in formalin-fixed paraffin-embedded samples of CRC was analyzed. RESULTS Among 93 CRC samples, 29 harbored mutations in KRAS exon 2, and 9 harbored mutations in BRAF exon 15. Analysis of 55 KRAS exon 2 and BRAF exon 15 wild-type CRC samples identified the following mutations: 1/55 in exon 3 and 2/55 in exon 4 of KRAS; 1/55 in exon 2, 3/55 in exon 3, and 0/55 in exon 4 of NRAS. CONCLUSIONS Our PCR-HRM method will enable rapid determination of the extended RAS and BRAF mutation status prior to anti-EGFR treatment in the clinical setting.
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Affiliation(s)
- Takayuki Ishige
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan; Division of Laboratory Medicine and Clinical Genetics, Chiba University Hospital, Chiba, Japan.
| | - Sakae Itoga
- Division of Laboratory Medicine and Clinical Genetics, Chiba University Hospital, Chiba, Japan
| | - Kenichi Sato
- Department of Medical Technology and Sciences, International University of Health and Welfare, Fukuoka, Japan
| | - Kouichi Kitamura
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan; Division of Laboratory Medicine and Clinical Genetics, Chiba University Hospital, Chiba, Japan
| | - Motoi Nishimura
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan; Division of Laboratory Medicine and Clinical Genetics, Chiba University Hospital, Chiba, Japan
| | - Setsu Sawai
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan; Division of Laboratory Medicine and Clinical Genetics, Chiba University Hospital, Chiba, Japan
| | - Kazuyuki Matsushita
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan; Division of Laboratory Medicine and Clinical Genetics, Chiba University Hospital, Chiba, Japan
| | - Kazufumi Suzuki
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Satoshi Ota
- Department of Diagnostic Pathology, Graduate School of Medicine, Chiba University, Chiba, Japan; Department of Pathology, Chiba University Hospital, Chiba, Japan
| | - Hideaki Miyauchi
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hisahiro Matsubara
- Department of Frontier Surgery, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Yukio Nakatani
- Department of Diagnostic Pathology, Graduate School of Medicine, Chiba University, Chiba, Japan; Department of Pathology, Chiba University Hospital, Chiba, Japan
| | - Fumio Nomura
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, Chiba, Japan; Division of Laboratory Medicine and Clinical Genetics, Chiba University Hospital, Chiba, Japan
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Ress AL, Stiegelbauer V, Winter E, Schwarzenbacher D, Kiesslich T, Lax S, Jahn S, Deutsch A, Bauernhofer T, Ling H, Samonigg H, Gerger A, Hoefler G, Pichler M. MiR-96-5p influences cellular growth and is associated with poor survival in colorectal cancer patients. Mol Carcinog 2014; 54:1442-50. [PMID: 25256312 DOI: 10.1002/mc.22218] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2014] [Revised: 07/29/2014] [Accepted: 08/02/2014] [Indexed: 12/11/2022]
Abstract
Expression of miR-96-5p is frequently altered in various types of cancer and the KRAS oncogene has been identified as one of its potential targets. However, the biological role of miR-96-5p expression in colorectal cancer (CRC) and its ability to predict the clinical course of patients have not been investigated yet. In this study, we explored miR-96-5p expression in 80 CRC patients and evaluated the impact on clinical outcome by Kaplan-Meier curves and multivariate Cox proportional models. In vitro miR-96-5p inhibition and overexpression were performed in CRC cells and the effects on cellular growth, anchorage-independent growth, apoptosis, and epithelial-mesenchymal transition (EMT)-related gene expression were explored. Low miR-96-5p expression levels in tumor tissue were associated with distant metastasis (P = 0.025) and multivariate Cox regression analysis identified low levels of miR-96-5p as an independent prognostic factor with respect to cancer-specific survival (hazard ratio = 1.78, 95%CI = 1.03-3.03, P < 0.038). In vitro overexpression of miR-96-5p led to a reduced cellular growth rate (P < 0.05), reduced colonies in soft agar (P < 0.05), corroborated by a decreased cyclin D1 and increased p27-CDKN1A expression (P < 0.05). Forced expression of miR-96-5p in CRC cells entailed no effects on apoptosis or EMT-related genes but decreased the expression levels of the KRAS oncogene (P < 0.05). Despite regulating KRAS expression, there was no significant association in miR-96-5p expression levels and response rates to EGFR-targeting agents. In conclusion, our data suggest that miR-96-5p influences cellular growth of CRC cells and low expression of miR-96-5p seems to be associated with poor clinical outcome in CRC patients.
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Affiliation(s)
- Anna Lena Ress
- Division of Oncology, Department of Internal Medicine, Medical University of Graz (MUG), Graz, Austria
| | - Verena Stiegelbauer
- Division of Oncology, Department of Internal Medicine, Medical University of Graz (MUG), Graz, Austria
| | - Elke Winter
- Institute of Pathology, Medical University of Graz (MUG), Graz, Austria
| | - Daniela Schwarzenbacher
- Division of Oncology, Department of Internal Medicine, Medical University of Graz (MUG), Graz, Austria
| | - Tobias Kiesslich
- Institute of Physiology and Pathophysiology, Paracelsus Medical University, Salzburg, Austria
| | - Sigurd Lax
- Department of Pathology, General Hospital Graz West, Graz, Austria
| | - Stefan Jahn
- Institute of Pathology, Medical University of Graz (MUG), Graz, Austria
| | - Alexander Deutsch
- Division of Hematology, Department of Internal Medicine, Medical University of Graz (MUG), Austria
| | - Thomas Bauernhofer
- Division of Oncology, Department of Internal Medicine, Medical University of Graz (MUG), Graz, Austria
| | - Hui Ling
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hellmut Samonigg
- Division of Oncology, Department of Internal Medicine, Medical University of Graz (MUG), Graz, Austria
| | - Armin Gerger
- Division of Oncology, Department of Internal Medicine, Medical University of Graz (MUG), Graz, Austria
| | - Gerald Hoefler
- Institute of Pathology, Medical University of Graz (MUG), Graz, Austria
| | - Martin Pichler
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Marchant J, Mange A, Larrieux M, Costes V, Solassol J. Comparative evaluation of the new FDA approved THxID™-BRAF test with High Resolution Melting and Sanger sequencing. BMC Cancer 2014; 14:519. [PMID: 25037456 PMCID: PMC4223712 DOI: 10.1186/1471-2407-14-519] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 07/04/2014] [Indexed: 12/17/2022] Open
Abstract
Background Since patients diagnosed with BRAF V600E and V600K mutated advanced melanoma show response to treatment with MAP kinase inhibitors, several sensitive methods have been developed to determine the V600 allele status of melanoma patients. Vemurafenib (Zelboraf) and dabrafenib (Tafinlar) are specific BRAF V600 inhibitors recently approved by the US FDA as single agent treatments for unresectable or metastatic melanoma in patients with the BRAF V600 mutation. Methods We assessed the new CE THxID™-BRAF diagnostic test, which is also FDA-approved as a companion diagnostic test in the US under a specific reference and compared the results of this assay with both High Resolution Melting (HRM) and Sanger sequencing in 113 melanoma FFPE samples. Results Invalid results were observed in 0/113 specimen with HRM, 5/113 (4.4%) with Sanger sequencing, and 1/113 (0.9%) with the THxID™-BRAF test. Positive percentage agreement (PPA) was 93.5% (95% CI 82.5 - 97.8) for V600E and V600K mutations combined for the THxID™-BRAF test and HRM, and negative percentage agreement (NPA) was 100.0% (95% CI 94.5 - 100.0). For the THxID™-BRAF test and Sanger, PPA was 100.0% (95% CI 92.1 - 100.0) and NPA 100.0% (95% CI 94.2 - 100.0). One V600E sample identified by THxID™-BRAF test was detected as wild-type by HRM and uninterpretable by Sanger. All V600K (n = 3) were detected using the 3 different approaches. Finally, percent agreement values were not significantly different when using punches (n = 77) vs. slides (n = 36) or depending on samples characteristics such as pigmentation, necrosis, and tumor content. Conclusions This study demonstrated the high agreement between the FDA approved THxID™-BRAF assay, HRM, and Sanger sequencing. It has also highlighted the potential of THxID™-BRAF to be applied to a broader range of sample types than claimed in the current “instructions for use”, an extension that would require the ad hoc validation and approval.
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Affiliation(s)
| | | | | | | | - Jérôme Solassol
- Department of Biopathology, Center Hospital University, Avenue du Doyen Giraud, 34298 Montpellier Cedex 5, France.
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Boeckx C, Weyn C, Vanden Bempt I, Deschoolmeester V, Wouters A, Specenier P, Van Laer C, Van den Weyngaert D, Kockx M, Vermorken JB, Peeters M, Pauwels P, Lardon F, Baay M. Mutation analysis of genes in the EGFR pathway in Head and Neck cancer patients: implications for anti-EGFR treatment response. BMC Res Notes 2014; 7:337. [PMID: 24899223 PMCID: PMC4067106 DOI: 10.1186/1756-0500-7-337] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 05/29/2014] [Indexed: 11/14/2022] Open
Abstract
Background Targeted therapy against the Epidermal Growth Factor Receptor (EGFR) is among the most promising molecular therapeutics for Head and Neck Squamous Cell Carcinoma (HNSCC). However, drug resistance limits the clinical efficacy of anti-EGFR monoclonal antibodies and no predictive biomarker has entered the clinic yet. Methods A retrospective clinical study was performed utilizing pathological specimens from 52 newly diagnosed HNSCC patients. These patients were screened for mutations in EGFR and KRAS. Tyrosine kinase mutations in EGFR and KRAS mutations were evaluated by high resolution melting analysis (HRMA), whereas EGFRvIII was determined using one-step real-time PCR. Finally, patient samples were screened for HPV-DNA by GP5+/6+ PCR. Survival analysis was performed using Kaplan-Meier analysis and significance was calculated using log-rank statistic. Results In our study population no EGFRvIII mutations were present. However, two silent mutations were found; T785T in exon 20 and R836R in exon 21 of the EGFR gene. Additionally, HRMA revealed an abnormal KRAS melting pattern in 7.0% of the samples. However, the KRAS StripAssay could confirm only one sample with a G12S mutation and none of these samples could be confirmed by direct sequencing. HPV DNA was present in 3/25 larynx and 9/27 oropharynx tumors. Conclusion The low rate of EGFR and KRAS mutations in this Belgian HNSCC population suggests that these genes will probably not play a major role in predicting response to anti-EGFR therapy in HNSCC. Hence, other predictive markers need to be discovered in order to optimize EGFR targeting therapy.
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Affiliation(s)
- Carolien Boeckx
- Center for Oncological Research (CORE) Antwerp, Laboratory of Cancer Research and Clinical Oncology, University of Antwerp, Wilrijk, Belgium.
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Berenstein R, Blau IW, Kar A, Cay R, Sindram A, Seide C, Blau O. Comparative examination of various PCR-based methods for DNMT3A and IDH1/2 mutations identification in acute myeloid leukemia. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2014; 33:44. [PMID: 24887327 PMCID: PMC4045877 DOI: 10.1186/1756-9966-33-44] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 05/10/2014] [Indexed: 12/29/2022]
Abstract
Background Mutations in epigenetic modifiers were reported in patients with acute myeloid leukaemia (AML) including mutations in DNA methyltransferase 3A gene (DNMT3A) in 20%-30% patients and mutations in isocitrate dehydrogenase 1/2 gene (IDH1/2) in 5%-15% patients. Novel studies have shown that mutations in DNMT3A and IDH1/2 influence prognosis, indicating an increasing need to detect these mutations during routine laboratory analysis. DNA sequencing for the identification of these mutations is time-consuming and cost-intensive. This study aimed to establish rapid screening tests to identify mutations in DNMT3A and IDH1/2 that could be applied in routine laboratory procedures and that could influence initial patient management. Methods In this study we developed an endonuclease restriction method to identify the most common DNMT3A mutation (R882H) and an amplification-refractory mutation system (ARMS) to analyse IDH2 R140Q mutations. Furthermore, we compared these methods with HRM analysis and evaluated the latter for the detection of IDH1 mutations. Results Of 230 samples from patients with AML 30 (13%) samples had DNMT3A mutations, 16 (7%) samples had IDH2 R140Q mutations and 36 (16%) samples had IDH1 mutations. Sensitivity assays performed using serial dilutions of mutated DNA showed that ARMS analysis had a sensitivity of 4.5%, endonuclease restriction had a sensitivity of 0.05% and HRM analysis had a sensitivity of 5.9%–7.8% for detecting different mutations. HRM analysis was the best screening method to determine the heterogeneity of IDH1 mutations. Furthermore, for the identification of mutations in IDH2 and DNMT3A, endonuclease restriction and ARMS methods showed a perfect concordance (100%) with Sanger sequencing while HRM analysis showed a near-perfect concordance (approximately 98%). Conclusion Our study suggested that all the developed methods were rapid, specific and easy to use and interpret. HRM analysis is the most timesaving and cost-efficient method to rapidly screen all the 3 genes at diagnosis in samples obtained from patients with AML. Endonuclease restriction and ARMS assays can be used separately or in combination with HRM analysis to obtain more reliable results. We propose that early screening of mutations in patients with AML having normal karyotype could facilitate risk stratification and improve treatment options.
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Affiliation(s)
- Rimma Berenstein
- Department of Hematology, Oncology and Tumourimmunology, Charité Universitätsmedizin Berlin, Hindenburgdamm 30, 12200 Berlin, Germany.
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Farrell CL, Pedigo NG, Messersmith AR. Application of genomic principles to pharmacotherapy of cancer. AMERICAN JOURNAL OF PHARMACEUTICAL EDUCATION 2014; 78:55. [PMID: 24761016 PMCID: PMC3996387 DOI: 10.5688/ajpe78355] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 10/08/2013] [Indexed: 05/09/2023]
Abstract
OBJECTIVES To teach first-year (P1) pharmacy students to apply the principles of pharmacogenomics underlying clinical pharmacotherapeutics to cancer patients. DESIGN Using polymerase chain reaction (PCR) and high-resolution melting analysis of deoxyribonucleic acid (DNA) from colorectal cancer cell lines to determine the presence of somatic mutations for an oncogenic marker, students formulated the proper course of treatment for a patient with similar tumor genomics. ASSESSMENT In a postintervention survey, students highly rated the effectiveness of the laboratory session for learning pharmacogenomics, and subsequent examination scores reflected retention of principles and understanding of clinical application. CONCLUSION The pharmacogenomic laboratory exercise prepared students to understand how genetic markers give clinical insight into the appropriate application of drugs in oncology pharmacotherapy. Further, the session inspired their interest in learning more about pharmacogenomics and their professional roles in personalized medicine.
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Affiliation(s)
| | - Nancy G Pedigo
- School of Pharmacy, Presbyterian College, Clinton, South Carolina
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Malinowsky K, Nitsche U, Janssen KP, Bader FG, Späth C, Drecoll E, Keller G, Höfler H, Slotta-Huspenina J, Becker KF. Activation of the PI3K/AKT pathway correlates with prognosis in stage II colon cancer. Br J Cancer 2014; 110:2081-9. [PMID: 24619078 PMCID: PMC3992486 DOI: 10.1038/bjc.2014.100] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 11/05/2013] [Accepted: 01/28/2014] [Indexed: 12/27/2022] Open
Abstract
Background: Patients with UICC/AJCC stage II colon cancer have a high 5-year overall survival rate after surgery. Nevertheless, a significant subgroup of patients develops tumour recurrence. Currently, there are no clinically established biomarkers available to identify this patient group. We applied reverse-phase protein arrays (RPPA) for phosphatidylinositide-3-kinase pathway activation mapping to stratify patients according to their risk of tumour recurrence after surgery. Methods: Full-length proteins were extracted from formalin-fixed, paraffin-embedded tissue samples of 118 patients who underwent curative resection. RPPA technology was used to analyse expression and/or phosphorylation levels of six major factors of the phosphatidylinositide-3-kinase pathway. Oncogenic mutations of KRAS and BRAF, and DNA microsatellite status, currently discussed as prognostic markers, were analysed in parallel. Results: Expression of phospho-AKT (HR=3.52; P=0.032), S6RP (HR=6.3; P=0.044), and phospho-4E-BP1 (HR=4.12; P=0.011) were prognostic factors for disease-free survival. None of the molecular genetic alterations were significantly associated with prognosis. Conclusions: Our data indicate that activation of the PI3K/AKT pathway evidenced on the protein level might be a valuable prognostic marker to stratify patients for their risk of tumour recurrence. Beside adjuvant chemotherapy targeting of upregulated PI3K/AKT signalling may be an attractive strategy for treatment of high-risk patients.
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Affiliation(s)
- K Malinowsky
- Department of Pathology, Technische Universität München, Ismaningerstrasse 22, 81675 Munich, Germany
| | - U Nitsche
- Department of Surgery, Klinikum rechts der Isar, Technische Universität München, Ismaningerstrasse 22, 81675 Munich, Germany
| | - K-P Janssen
- Department of Surgery, Klinikum rechts der Isar, Technische Universität München, Ismaningerstrasse 22, 81675 Munich, Germany
| | - F G Bader
- Department of Surgery, Klinikum rechts der Isar, Technische Universität München, Ismaningerstrasse 22, 81675 Munich, Germany
| | - C Späth
- Department of Surgery, Klinikum rechts der Isar, Technische Universität München, Ismaningerstrasse 22, 81675 Munich, Germany
| | - E Drecoll
- Department of Pathology, Technische Universität München, Ismaningerstrasse 22, 81675 Munich, Germany
| | - G Keller
- Department of Pathology, Technische Universität München, Ismaningerstrasse 22, 81675 Munich, Germany
| | - H Höfler
- 1] Department of Pathology, Technische Universität München, Ismaningerstrasse 22, 81675 Munich, Germany [2] Department of Pathology, Helmholtz-Centre Munich, Ingolstädter Landstrasse 1, 85764 Munich, Germany
| | - J Slotta-Huspenina
- Department of Pathology, Technische Universität München, Ismaningerstrasse 22, 81675 Munich, Germany
| | - K-F Becker
- Department of Pathology, Technische Universität München, Ismaningerstrasse 22, 81675 Munich, Germany
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Chen D, Wang YY, Chuai ZR, Huang JF, Wang YX, Liu K, Zhang LQ, Yang Z, Shi DC, Liu Q, Huang Q, Fu WL. High-resolution melting analysis for accurate detection of BRAF mutations: a systematic review and meta-analysis. Sci Rep 2014; 4:4168. [PMID: 24566771 PMCID: PMC3933866 DOI: 10.1038/srep04168] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 02/03/2014] [Indexed: 12/24/2022] Open
Abstract
The high-resolution melting curve analysis (HRMA) might be a good alternative method for rapid detection of BRAF mutations. However, the accuracy of HRMA in detection of BRAF mutations has not been systematically evaluated. We performed a systematic review and meta-analysis involving 1324 samples from 14 separate studies. The overall sensitivity of HRMA was 0.99 (95% confidence interval (CI) = 0.75–0.82), and the overall specificity was very high at 0.99 (95% CI = 0.94–0.98). The values for the pooled positive likelihood ratio, negative likelihood ratio, and diagnostic odds ratio were 68.01 (95% CI = 25.33–182.64), 0.06 (95% CI = 0.03–0.11), and1263.76 (95% CI = 393.91–4064.39), respectively. The summary receiver operating characteristic curve for the same data shows an area of 1.00 and a Q* value of 0.97. The high sensitivity and specificity, simplicity, low cost, less labor or time and rapid turnaround make HRMA a good alternative method for rapid detection of BRAF mutations in the clinical practice.
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Affiliation(s)
- Dong Chen
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Yan-Yan Wang
- Research and service centre of laboratory medicine, Chengdu Military general Hospital, Chengdu, PR China
| | - Zheng-Ran Chuai
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Jun-Fu Huang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Yun-Xia Wang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Kai Liu
- Research Center for Nutrition and Food Safety, Institute of Military Preventive Medicine, Third Military Medical University, Chongqing, PR China
| | - Li-Qun Zhang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Zhao Yang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Da-Chuan Shi
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Qian Liu
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Qing Huang
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
| | - Wei-Ling Fu
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, PR China
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Chen D, Huang JF, Xia H, Duan GJ, Chuai ZR, Yang Z, Fu WL, Huang Q. High-sensitivity PCR method for detecting BRAF V600E mutations in metastatic colorectal cancer using LNA/DNA chimeras to block wild-type alleles. Anal Bioanal Chem 2014; 406:2477-87. [PMID: 24500755 DOI: 10.1007/s00216-014-7618-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 12/27/2013] [Accepted: 01/07/2014] [Indexed: 01/15/2023]
Abstract
The response to epidermal growth factor receptor (EGFR)-targeted therapy in metastatic colorectal cancer (mCRC) is variable because of intra-tumor heterogeneity at the genetic level, and consequently, it is important to develop sensitive and selective assays to predict patient responses to therapy. Low-abundance BRAF V600E mutations are associated with poor response to treatment with EGFR inhibitors. We developed a method for the detection of BRAF V600E mutations in mCRC using real-time wild-type blocking PCR (WTB-PCR), in which a chimera composed of locked nucleic acids and DNA is incorporated to amplify the mutant allele at high efficiency while simultaneously inhibiting the amplification of wild-type alleles. Mixing experiments showed that this method is exquisitely sensitive, with detection of the mutated allele at a mutant/wild-type ratio of 1:10,000. To demonstrate the applicability of this approach for mCRC patients, we assessed the V600E mutations in 50 clinical cases of mCRC by real-time WTB-PCR. The percentage of patients with V600E mutation as determined by WTB-PCR (16%, 8/50) was higher than by traditional PCR (10%, 5/50), suggesting an increased sensitivity for WTB-PCR. By calculating the ΔC q for real-time traditional PCR, which amplifies all BRAF alleles, versus WTB-PCR, which selectively amplifies mutant BRAF, we demonstrated that among the V600E-positive mCRC patient samples, the percentage of BRAF DNA with the V600E mutation ranged from 0.05 to 52.32%. In conclusion, WTB-PCR provides a rapid, simple, and low-cost method to detect trace amounts of mutated BRAF V600E gene.
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Affiliation(s)
- Dong Chen
- Department of Laboratory Medicine, Southwest Hospital, Third Military Medical University, Chongqing, 400038, China
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Transbronchial Biopsy Needle Rinse Solution Used for Comprehensive Biomarker Testing in Patients with Lung Cancer. J Thorac Oncol 2014; 9:26-32. [DOI: 10.1097/jto.0000000000000024] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Pichler M, Winter E, Ress AL, Bauernhofer T, Gerger A, Kiesslich T, Lax S, Samonigg H, Hoefler G. miR-181a is associated with poor clinical outcome in patients with colorectal cancer treated with EGFR inhibitor. J Clin Pathol 2013; 67:198-203. [PMID: 24098024 DOI: 10.1136/jclinpath-2013-201904] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
AIMS miR-181a expression is frequently altered in different types of cancer. Members of the Wnt/β-catenin signalling pathway, which is commonly altered in colorectal cancer (CRC), have been reported as molecular interaction partners of miR-181. However, the role of miR-181a expression in CRC and its ability to predict survival and response to agents targeting the epidermal growth factor receptor (EGFR) have not been explored yet. METHODS In this study, we analysed 80 patients with wild type KRAS CRC undergoing treatment with the EGFR-targeting monoclonal antibodies cetuximab and panitumumab for metastatic CRC. The KRAS mutational status was determined by pyrosequencing and miR-181a expression was measured by quantitative RT-PCR in CRC tumour tissue and corresponding non-neoplastic colon tissue. The microRNA expression levels were correlated with clinicopathological characteristics. Cancer-specific survival was calculated by univariate and multivariate analyses, and progression-free survival (PFS) during treatment with EGFR-targeting agents was also evaluated. RESULTS A low miR-181a expression level was associated with poor differentiation of CRC (p=0.04). A Kaplan-Meier curve showed a decreased survival time for patients with low miR-181a expression (p=0.019). Low miR-181a expression was furthermore associated with poor PFS (p=0.015). CONCLUSIONS In conclusion, our data suggest that the miR-181a expression level is associated with poor survival in patients with CRC. Furthermore, miR-181a expression might predict PFS in EGFR-targeted therapy.
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Affiliation(s)
- Martin Pichler
- Division of Oncology, Department of Internal Medicine, Medical University of Graz (MUG), , Graz, Austria
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Wray CD, Friederich MW, du Sart D, Pantaleo S, Smet J, Kucera C, Fenton L, Scharer G, Van Coster R, Van Hove JLK. A new mutation in MT-ND1 m.3928G>C p.V208L causes Leigh disease with infantile spasms. Mitochondrion 2013; 13:656-61. [PMID: 24063851 DOI: 10.1016/j.mito.2013.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 08/30/2013] [Accepted: 09/17/2013] [Indexed: 01/14/2023]
Abstract
New mutations in mitochondrial DNA encoded genes of complex I are rarely reported. An infant developed Leigh disease with infantile spasms. Complex I enzyme activity was deficient and response to increasing coenzyme Q concentrations was reduced. Complex I assembly was intact. A new mutation in MT-ND1 m.3928G>C p.V208L, affecting a conserved amino acid in a critical domain, part of the coenzyme Q binding pocket, was present at high heteroplasmy. The unaffected mother did not carry measurable mutant mitochondrial DNA, but concern remained for gonadal mosaicism. Prenatal testing was possible for a subsequent sibling. The ND1 p.V208L mutation causes Leigh disease.
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Affiliation(s)
- Carter D Wray
- Department of Pediatrics, University of Colorado, 13121 East 17th Avenue, Aurora, CO 80045, USA; Division of Pediatric Neurology, Oregon Health Sciences Center, 3181 SW Sam Jackson Park Rd, Portland, OR 97239, USA
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Swierniak M, Wojcicka A, Czetwertynska M, Stachlewska E, Maciag M, Wiechno W, Gornicka B, Bogdanska M, Koperski L, de la Chapelle A, Jazdzewski K. In-depth characterization of the microRNA transcriptome in normal thyroid and papillary thyroid carcinoma. J Clin Endocrinol Metab 2013; 98:E1401-9. [PMID: 23783103 PMCID: PMC5399477 DOI: 10.1210/jc.2013-1214] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
CONTEXT A single microRNA gene may give rise to several mature products that differ in length, called isomiRs. IsomiRs are known to be tissue specific and functionally relevant. The microRNA sequence heterogeneity of the thyroid gland has yet to be determined. OBJECTIVE The objective of the study was to provide a comprehensive view of the microRNA transcriptome in normal thyroid and papillary thyroid carcinoma (PTC). DESIGN We used next-generation deep sequencing to analyze microRNA length heterogeneity and expression profiles of PTC tumors (n = 14), unaffected tissue adjacent to tumors (n = 14), and control, noncancerous thyroid tissue (n = 14). The results were validated with a microarray on an additional set of 9 PTC tumor/normal tissue pairs. RESULTS Eighty-nine microRNAs were significantly deregulated in PTC compared with normal thyroid tissue (false discovery rate < 0.05, fold change 0.13-20.7). Top deregulated miRNAs included miR-146b-5p, miR-221-3p, miR-7-3p, miR-551b-3p, miR-486-3p, and miR-144-3p, confirming previous microarray profiling. The expression of miRNAs did not depend on the BRAF mutation status. Interestingly, 85% of the most abundant microRNAs consisted of isoforms that differed from the standard reference sequence deposited in miRBase. Moreover, the reference microRNAs were completely absent in 42.4% and 35.9% of the microRNAs expressed in normal thyroid and PTC tumors, respectively. Numerous isomiRs had altered seed sequences, which led to a different set of target genes. For highly deregulated miR-146b-5p, we detected 6 isoforms (tumor/normal fold change 14.4-28.7, false discovery rate < 0.002) that varied at their 5' ends with a 1-nt difference that created 2 alternative seeds. The target genes for those 2 seeds overlapped in only 13.1% of genes. CONCLUSIONS Almost all microRNAs exhibit isoforms of variable length and potentially distinct function in thyroid tumorigenesis.
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Affiliation(s)
- Michal Swierniak
- Laboratory of Genomic Medicine, Department of General, Transplant, and Liver Surgery, Medical University of Warsaw, Warsaw 02-097, Poland
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Eisner F, Schaberl-Moser R, Gerger A, Samonigg H, Pichler M. Successful use of sorafenib after bortezomib failure in metastatic follicular thyroid cancer - a case report. ONKOLOGIE 2013; 36:368-70. [PMID: 23774152 DOI: 10.1159/000351252] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Thyroid cancer (TC) is the most commonly diagnosed endocrine malignancy in developed countries. Differentiated thyroid carcinoma (DTC), which includes papillary thyroid carcinoma and follicular thyroid carcinoma (FTC), composes more than 90% of all TC cases. When DTC recurs or metastasizes to distant sites despite the use of local and radiotherapeutic treatment modalities, the currently effective treatment options are limited. CASE REPORT A then 40-year-old female Caucasian patient was diagnosed with FTC and underwent surgery and postoperative radioactive iodine therapy. The patient developed metastatic disease, and palliative first-line treatment with the proteasome inhibitor bortezomib was initiated. After 3 months, the patient suffered progressive pulmonary metastatic disease. Treatment with the multikinase inhibitor sorafenib was started, and after 3 months of therapy, tumor restaging demonstrated partial remission. The treatment is ongoing, and the current progression-free survival is 16 months. With the exception of mild diarrhea and hand-foot syndrome, the therapy was well tolerated, and no grade 3/4 adverse toxicities occurred. CONCLUSION In our single case of metastatic FTC, sorafenib showed clinically meaningful antitumor activity accompanied by good tolerability. This case report supports the use of this drug as a potential treatment option for advanced/metastatic FTC.
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Affiliation(s)
- Florian Eisner
- Division of Oncology, Department of Internal Medicine, Medical University of Graz, Austria
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Buecher B, Cacheux W, Rouleau E, Dieumegard B, Mitry E, Lièvre A. Role of microsatellite instability in the management of colorectal cancers. Dig Liver Dis 2013. [PMID: 23195666 DOI: 10.1016/j.dld.2012.10.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Microsatellite instability is the consequence of a deficient mismatch repair system. It has a key role in the diagnostic strategy of Lynch syndrome, where tumours are all characterized by the presence of this phenotype. Microsatellite instability is therefore essential in the selection of colorectal cancer patients in whom a germline analysis of Mismatch Repair genes is possibly indicated. Moreover, microsatellite instability tumours are associated with a good prognosis and a resistance to fluorouracil-based adjuvant chemotherapy, which has a clinical application mainly in stage II colon cancer patients in whom adjuvant chemotherapy has a less beneficial effect than in stage III and outcome in presence of microsatellite instability is excellent. Recent data suggest that impact of microsatellite instability on benefit to fluorouracil-based adjuvant chemotherapy is dependent of the molecular mechanism involved in this genetic instability since an improved survival has been reported with adjuvant fluorouracil in microsatellite instability colorectal cancers of germline origin but not in sporadic cases. Predictive value of microsatellite instability on response to fluorouracil/oxaliplatin adjuvant chemotherapy has been less evaluated but recent studies suggest that the favorable outcome of Microsatellite instability tumours is maintained in patients receiving FOLFOX.
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Affiliation(s)
- Bruno Buecher
- Department of Medical Oncology, Groupe Hospitalier, Institut Curie, 26, rue d'Ulm, 75248 Paris Cedex 5, France
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Marin C, Beauchet A, Capper D, Zimmermann U, Julié C, Ilie M, Saiag P, von Deimling A, Hofman P, Emile JF. Detection of BRAF p.V600E Mutations in Melanoma by Immunohistochemistry Has a Good Interobserver Reproducibility. Arch Pathol Lab Med 2013; 138:71-5. [PMID: 23651150 DOI: 10.5858/arpa.2013-0031-oa] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Assessment of BRAF p.V600E mutational status has become necessary for treatment of patients with metastatic melanoma. Detection of p.V600E mutation by immunohistochemistry was recently reported in several tumor types. OBJECTIVE To evaluate the interobserver reproducibility of BRAF p.V600E detection by immunohistochemistry in melanoma. DESIGN Immunohistochemistry with VE1 antibody was performed on metastatic melanomas of 67 patients. Staining interpretation was performed on digital image virtual slides of tissue microarrays. The p.V600E status was determined by 7 pathologists from 3 European laboratories, blinded for other interpretations and for molecular biology results. RESULTS Melanomas had p.V600E (n = 30), p.V600K (n = 4), p.K601E (n = 1), p.600-601delinsE (n = 1), or no p.V600 mutations (n = 31). Staining of p.V600E within mutated cells was cytoplasmic and diffuse, and for each case the staining on the 3 tissue microarray cores was similar. In 53 cases (79.1%) the 7 pathologists had perfect concordance. Agreement of interobserver reproducibility was almost perfect (κ = 0.81 [0.77-0.85]). Only 2 false-positive responses (0.9%) were obtained. The specificities reported were 100% for 5 pathologists (two of whom previously trained for p.V600E interpretation), and 97% for 2 untrained pathologists. CONCLUSIONS Detection of BRAF p.V600E mutation by immunohistochemistry in melanomas has an excellent interobserver reproducibility. Our results suggest that immunohistochemistry could be used as a first step for detection of BRAF p.V600E mutation, to identify patients with melanoma as candidates for BRAF inhibitors.
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Affiliation(s)
- Cristi Marin
- From units EA4340 (Drs Marin, Julié, and Emile) and EA4339 (Drs Beauchet, Zimmermann, and Saiag), Versailles SQY University, Boulogne, France; the Departments of Pathology (Drs Marin, Zimmermann, Julié, and Emile), Public Health (Dr Beauchet), and General and Oncologic Dermatology (Dr Saiag), Ambroise Pare Hospital, APHP, Boulogne, France; the Department of Neuropathology, Ruprecht-Karls-University Heidelberg, and Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany (Drs Capper and Deimling); and the Laboratory of Clinical and Experimental Pathology, Pasteur Hospital and Medical School, Nice Sophia University, Nice, France (Drs Ilie and Hofman)
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Guedes JG, Veiga I, Rocha P, Pinto P, Pinto C, Pinheiro M, Peixoto A, Fragoso M, Raimundo A, Ferreira P, Machado M, Sousa N, Lopes P, Araújo A, Macedo J, Alves F, Coutinho C, Henrique R, Santos LL, Teixeira MR. High resolution melting analysis of KRAS, BRAF and PIK3CA in KRAS exon 2 wild-type metastatic colorectal cancer. BMC Cancer 2013; 13:169. [PMID: 23548132 PMCID: PMC3623853 DOI: 10.1186/1471-2407-13-169] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2012] [Accepted: 03/19/2013] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND KRAS is an EGFR effector in the RAS/RAF/ERK cascade that is mutated in about 40% of metastatic colorectal cancer (mCRC). Activating mutations in codons 12 and 13 of the KRAS gene are the only established negative predictors of response to anti-EGFR therapy and patients whose tumors harbor such mutations are not candidates for therapy. However, 40 to 60% of wild-type cases do not respond to anti-EGFR therapy, suggesting the involvement of other genes that act downstream of EGFR in the RAS-RAF-MAPK and PI3K-AKT pathways or activating KRAS mutations at other locations of the gene. METHODS DNA was obtained from a consecutive series of 201 mCRC cases (FFPE tissue), wild-type for KRAS exon 2 (codons 12 and 13). Mutational analysis of KRAS (exons 3 and 4), BRAF (exons 11 and 15), and PIK3CA (exons 9 and 20) was performed by high resolution melting (HRM) and positive cases were then sequenced. RESULTS One mutation was present in 23.4% (47/201) of the cases and 3.0% additional cases (6/201) had two concomitant mutations. A total of 53 cases showed 59 mutations, with the following distribution: 44.1% (26/59) in KRAS (13 in exon 3 and 13 in exon 4), 18.6% (11/59) in BRAF (two in exon 11 and nine in exon 15) and 37.3% (22/59) in PIK3CA (16 in exon 9 and six in exon 20). In total, 26.4% (53/201) of the cases had at least one mutation and the remaining 73.6% (148/201) were wild-type for all regions studied. Five of the mutations we report, four in KRAS and one in BRAF, have not previously been described in CRC. BRAF and PIK3CA mutations were more frequent in the colon than in the sigmoid or rectum: 20.8% vs. 1.6% vs. 0.0% (P=0.000) for BRAF and 23.4% vs. 12.1% vs. 5.4% (P=0.011) for PIK3CA mutations. CONCLUSIONS About one fourth of mCRC cases wild-type for KRAS codons 12 and 13 present other mutations either in KRAS, BRAF, or PIK3CA, many of which may explain the lack of response to anti-EGFR therapy observed in a significant proportion of these patients.
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Affiliation(s)
- Joana G Guedes
- Departments of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Isabel Veiga
- Departments of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Patrícia Rocha
- Departments of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Pedro Pinto
- Departments of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Carla Pinto
- Departments of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Manuela Pinheiro
- Departments of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Ana Peixoto
- Departments of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Maria Fragoso
- Departments of Oncology, Portuguese Oncology Institute, Porto, Portugal
| | - Ana Raimundo
- Departments of Oncology, Portuguese Oncology Institute, Porto, Portugal
| | - Paula Ferreira
- Departments of Oncology, Portuguese Oncology Institute, Porto, Portugal
| | - Manuela Machado
- Departments of Oncology, Portuguese Oncology Institute, Porto, Portugal
| | - Nuno Sousa
- Departments of Oncology, Portuguese Oncology Institute, Porto, Portugal
| | - Paula Lopes
- Departments of Pathology, Portuguese Oncology Institute, Porto, Portugal
| | | | - Joana Macedo
- S. Sebastião Hospital, Santa Maria da Feira, Portugal
| | - Fernando Alves
- Trás-os-Montes e Alto Douro Hospital Center, Vila Real, Portugal
| | | | - Rui Henrique
- Departments of Pathology, Portuguese Oncology Institute, Porto, Portugal
- Abel Salazar Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
| | - Lúcio L Santos
- Departments of Surgery, Portuguese Oncology Institute, Porto, Portugal
| | - Manuel R Teixeira
- Departments of Genetics, Portuguese Oncology Institute, Porto, Portugal
- Abel Salazar Biomedical Sciences Institute (ICBAS), University of Porto, Porto, Portugal
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Huang T, Zhuge J, Zhang WW. Sensitive detection of BRAF V600E mutation by Amplification Refractory Mutation System (ARMS)-PCR. Biomark Res 2013; 1:3. [PMID: 24252159 PMCID: PMC3776245 DOI: 10.1186/2050-7771-1-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2012] [Accepted: 10/09/2012] [Indexed: 12/28/2022] Open
Abstract
Background BRAF mutations occur in approximately 8% of all human cancers and approach 50% in melanoma and papillary carcinoma of thyroid. These mutations provide potentially valuable diagnostic, prognostic and treatment response prediction markers. A sensitive, specific, low-cost assay to detect these mutations is needed. Results To detect BRAF V600E mutation in formalin-fixed, paraffin-embedded (FFPE) tissue, we developed a method using Amplification Refractory Mutation System (ARMS)-PCR. This method was designed to amplify three products in a single reaction tube: a 200 bp common product serving as an amplification control, a 144 bp BRAF V600E specific product, and a 97 bp wild-type (wt) specific product. The sensitivity of this method was determined to be as low as 0.5% for the BRAF V600E allele in a wild-type background. This method was successfully validated in 72 thyroid tumors. It detected V600E mutation in 22 out of 33 (67%) of the conventional papillary thyroid carcinoma (PTC), 8 out of 12 (75%) of the tall-cell variant of PTC, whereas none of the 10 follicular variant of PTC showed BRAF V600E mutation. In addition, none of the 14 follicular adenomas and 3 follicular carcinomas had BRAF V600E mutation. As a comparison method, direct dideoxy sequencing found only 27 out of 30 (90%) mutations detected by ARMS-PCR method, suggesting that this ARMS-PCR method has higher sensitivity. Conclusions Our ARMS-PCR method provides a new tool for rapid detection of BRAF V600E mutation. Our results indicate that ARMS-PCR is more sensitive than automated dideoxy sequencing in detecting low BRAF V600E allele burdens in FFPE tumor specimen. The strategy of this ARMS-PCR design may be adapted for early detection of point mutations of a variety of biomarker genes.
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Affiliation(s)
- Tiangui Huang
- Department of Pathology, Westchester Medical Center and New York Medical College, Valhalla, NY, 10595, USA
| | - Jian Zhuge
- Department of Pathology, Westchester Medical Center and New York Medical College, Valhalla, NY, 10595, USA
| | - Wenyong W Zhang
- Department of Pathology, Westchester Medical Center and New York Medical College, Valhalla, NY, 10595, USA
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Integrative marker analysis allows risk assessment for metastasis in stage II colon cancer. Ann Surg 2013; 256:763-71; discussion 771. [PMID: 23095620 DOI: 10.1097/sla.0b013e318272de87] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
OBJECTIVES Individualized risk assessment in patients with UICC stage II colon cancer based on a panel of molecular genetic alterations. BACKGROUND Risk assessment in patients with colon cancer and localized disease (UICC stage II) is not sufficiently reliable. Development of metachronous metastasis is assumed to be governed largely by individual tumor genetics. METHODS Fresh frozen tissue from 232 patients (T3-4, N0, M0) with complete tumor resection and a median follow-up of 97 months was analyzed for microsatellite stability, KRAS exon 2, and BRAF exon 15 mutations. Gene expression of the WNT-pathway surrogate marker osteopontin and the metastasis-associated genes SASH1 and MACC1 was determined for 179 patients. The results were correlated with metachronous distant metastasis risk (n = 22 patients). RESULTS Mutations of KRAS were detected in 30% patients, mutations of BRAF in 15% patients, and microsatellite instability in 26% patients. Risk of recurrence was associated with KRAS mutation (P = 0.033), microsatellite stable tumors (P = 0.015), decreased expression of SASH1 (P = 0.049), and increased expression of MACC1 (P < 0.001). MACC1 was the only independent parameter for recurrence prediction (hazard ratio: 6.2; 95% confidence interval: 2.4-16; P < 0.001). Integrative 2-step cluster analysis allocated patients into 4 groups, according to their tumor genetics. KRAS mutation, BRAF wild type, microsatellite stability, and high MACC1 expression defined the group with the highest risk of recurrence (16%, 7 of 43), whereas BRAF wild type, microsatellite instability, and low MACC1 expression defined the group with the lowest risk (4%, 1 of 26). CONCLUSIONS MACC1 expression predicts development of metastases, outperforming microsatellite stability status, as well as KRAS/BRAF mutation status.
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