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Yakout NM, Abdallah DM, Abdelmonsif DA, Kholosy HM, Talaat IM, Elsakka O. BRAF V600E mutational status assessment in cutaneous melanocytic neoplasms in a group of the Egyptian population. Cancer Cell Int 2023; 23:17. [PMID: 36737739 PMCID: PMC9896695 DOI: 10.1186/s12935-023-02858-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Melanocytic neoplasms range from banal nevi to malignant melanomas. The genetic background has been extensively studied in the Caucasian population. BRAF mutations were reported among the early driver mutations in nevogenesis. Nevertheless, the pathogenesis in the Egyptian population has not been elucidated. AIM AND METHODS The present study was carried out to assess the sensitivity and specificity of immunohistochemistry (IHC) using the RM-08 clone in reference to allele-specific real-time PCR (CAST-PCR) for the detection of the BRAF V600E mutation in 50 formalin-fixed paraffin-embedded blocks of melanocytic neoplasms with prior bleaching using hydrogen peroxide in Tris-HCL and Bovine Serum Albumin respectively. RESULTS IHC staining was interpreted using staining reaction (positive versus negative) and staining pattern (negative and heterogeneous versus homogenous). Using the staining pattern, the specificity increased from 73.3 to 88.2%, the negative predictive value increased from 73.3 to 100%, the diagnostic accuracy increased from 71.4 to 90.48% and the overall accuracy increased from 69.9 to 77.3%. The sensitivity and positive predictive value remained unchanged. The K-agreement coefficient increased from 0.364 (fair agreement) to 0.741 (good agreement) and was statistically significant (p = 0.00). Next-generation sequencing was performed in 11 cases, 8 cases with IHC-positive and BRAF wild type in addition to 3 cases that failed PCR analysis and revealed no BRAF V600E. No statistically significant difference was found in the clinicopathological parameters between BRAF V600E and BRAF wild-type melanomas. CONCLUSIONS These findings suggest that IHC staining homogeneity may be more accurate in predicting BRAF V600E mutational status. However, IHC cannot replace molecular methods.
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Affiliation(s)
- Nada M. Yakout
- grid.7155.60000 0001 2260 6941Pathology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Dina M. Abdallah
- grid.7155.60000 0001 2260 6941Pathology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Doaa A. Abdelmonsif
- grid.7155.60000 0001 2260 6941Medical Biochemistry Department, Genomics Research Lab, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Hassan Mahmoud Kholosy
- grid.7155.60000 0001 2260 6941Department of Plastic Surgery, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Iman M. Talaat
- grid.7155.60000 0001 2260 6941Pathology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt ,grid.412789.10000 0004 4686 5317Clinical Sciences Department, College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | - Omayma Elsakka
- grid.7155.60000 0001 2260 6941Pathology Department, Faculty of Medicine, Alexandria University, Alexandria, Egypt
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2
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Correlation of MRI signal characteristics of intracranial melanoma metastases with BRAF mutation status. Melanoma Res 2022; 32:373-378. [PMID: 35979667 DOI: 10.1097/cmr.0000000000000847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BRAF V600 mutations (BRAFmut) are associated with more pigmentation in primary melanomas, but data on melanin content of metastases are limited. This study compares signal characteristics of BRAFmut and BRAF-wildtype (BRAFwt) intracranial melanoma metastases (IMM). MRI brain examinations at first diagnosis of IMM were identified, all performed at 3-Tesla including 1 mm volumetric pre- and postcontrast T1-weighted imaging and susceptibility-weighted imaging (SWI). Individual metastases were assessed by a neuroradiologist, stratified by size (≥10 mm, 'larger', vs. 2-9 mm, 'small'; up to 10 per group); presence of intrinsic T1-hyperintensity (T1H) and, if present, whether confidently attributable to melanin as opposed to haemorrhage; evidence of haemorrhage; presence of central necrosis. A total of 267 IMM in 73 patients were assessed (87 larger IMM, 180 small). The proportion of larger IMM was similar in both groups (31% BRAFmut and 36% BRAFwt). In small IMM, MRI evidence of melanin was more common in BRAFmut patients (42% vs. 26%; P = 0.038). Haemorrhage was more common in larger IMM (51%, vs. 20% of small IMM; P < 0.0001), but did not differ based on BRAF status. Central necrosis was more common in larger IMM (44% vs. 7%; P < 0.0001) and in BRAFmut IMM (23% vs. 11%; P = 0.011). In the BRAFmut cohort, central necrosis was more common in patients without previous anti-BRAF therapy (33% vs. 7%; P = 0.0001). T1H attributable to melanin is only slightly more common in BRAFmut IMM than BRAFwt. Higher rates of central necrosis in BRAFmut patients without previous anti-BRAF therapy suggest that anti-BRAF therapy may affect the patterns of IMM growth.
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3
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Arnolda R, Howlett K, Chan T, Raleigh J, Hatzimihalis A, Bell A, Fellowes A, Sandhu S, McArthur GA, Fox SB, Dawson SJ, Hewitt C, Jones K, Wong SQ. Clinical validation and implementation of droplet digital PCR for the detection of BRAF mutations from cell-free DNA. Pathology 2022; 54:772-778. [DOI: 10.1016/j.pathol.2022.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 02/03/2022] [Accepted: 02/17/2022] [Indexed: 10/18/2022]
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4
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Feng S, Han L, Yue M, Zhong D, Cao J, Guo Y, Sun Y, Zhang H, Cao Z, Cui X, Liu R. Frequency detection of BRAF V600E mutation in a cohort of pediatric langerhans cell histiocytosis patients by next-generation sequencing. Orphanet J Rare Dis 2021; 16:272. [PMID: 34116682 PMCID: PMC8196454 DOI: 10.1186/s13023-021-01912-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 06/07/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Langerhans cell histiocytosis (LCH) is a rare neoplastic disease that occurs in both children and adults, and BRAF V600E is detected in up to 64% of the patients. Several studies have discussed the associations between BRAF V600E mutation and clinicopathological manifestations, but no clear conclusions have been drawn regarding the clinical significance of the mutation in pediatric patients. RESULTS We retrieved the clinical information for 148 pediatric LCH patients and investigated the BRAF V600E mutation using next-generation sequencing alone or with droplet digital PCR. The overall positive rate of BRAF V600E was 60/148 (41%). The type of sample (peripheral blood and formalin-fixed paraffin-embedded tissue) used for testing was significantly associated with the BRAF V600E mutation status (p-value = 0.000 and 0.000). The risk of recurrence declined in patients who received targeted therapy (p-value = 0.006; hazard ratio 0.164, 95%CI: 0.046 to 0.583). However, no correlation was found between the BRAF V600E status and gender, age, stage, specific organ affected, TP53 mutation status, masses close to the lesion or recurrence. CONCLUSIONS This is the largest pediatric LCH study conducted with a Chinese population to date. BRAF V600E in LCH may occur less in East Asian populations than in other ethnic groups, regardless of age. Biopsy tissue is a more sensitive sample for BRAF mutation screening because not all of circulating DNA is tumoral. Approaches with low limit of detection or high sensitivity are recommended for mutation screening to avoid type I and II errors.
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Affiliation(s)
- Shunqiao Feng
- Department of Hematology, Children's Hospital of Capital Institute of Pediatrics, Beijing, 100020, China
| | - Lin Han
- Running Gene Inc, Beijing, China
| | - Mei Yue
- Department of Hematology, Children's Hospital of Capital Institute of Pediatrics, Beijing, 100020, China
| | - Dixiao Zhong
- Department of Hematology, Children's Hospital of Capital Institute of Pediatrics, Beijing, 100020, China
| | - Jing Cao
- Department of Hematology, Children's Hospital of Capital Institute of Pediatrics, Beijing, 100020, China
| | | | | | | | | | - Xiaodai Cui
- Department of Key Laboratory, Children's Hospital of Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Rong Liu
- Department of Hematology, Children's Hospital of Capital Institute of Pediatrics, Beijing, 100020, China.
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5
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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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6
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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: 39] [Impact Index Per Article: 9.8] [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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7
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Tan L, Sandhu S, Lee RJ, Li J, Callahan J, Ftouni S, Dhomen N, Middlehurst P, Wallace A, Raleigh J, Hatzimihalis A, Henderson MA, Shackleton M, Haydon A, Mar V, Gyorki DE, Oudit D, Dawson MA, Hicks RJ, Lorigan P, McArthur GA, Marais R, Wong SQ, Dawson SJ. Prediction and monitoring of relapse in stage III melanoma using circulating tumor DNA. Ann Oncol 2019; 30:804-814. [PMID: 30838379 PMCID: PMC6551451 DOI: 10.1093/annonc/mdz048] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The advent of effective adjuvant therapies for patients with resected melanoma has highlighted the need to stratify patients based on risk of relapse given the cost and toxicities associated with treatment. Here we assessed circulating tumor DNA (ctDNA) to predict and monitor relapse in resected stage III melanoma. PATIENTS AND METHODS Somatic mutations were identified in 99/133 (74%) patients through tumor tissue sequencing. Personalized droplet digital PCR (ddPCR) assays were used to detect known mutations in 315 prospectively collected plasma samples from mutation-positive patients. External validation was performed in a prospective independent cohort (n = 29). RESULTS ctDNA was detected in 37 of 99 (37%) individuals. In 81 patients who did not receive adjuvant therapy, 90% of patients with ctDNA detected at baseline and 100% of patients with ctDNA detected at the postoperative timepoint relapsed at a median follow up of 20 months. ctDNA detection predicted patients at high risk of relapse at baseline [relapse-free survival (RFS) hazard ratio (HR) 2.9; 95% confidence interval (CI) 1.5-5.6; P = 0.002] and postoperatively (HR 10; 95% CI 4.3-24; P < 0.001). ctDNA detection at baseline [HR 2.9; 95% CI 1.3-5.7; P = 0.003 and postoperatively (HR 11; 95% CI 4.3-27; P < 0.001] was also associated with inferior distant metastasis-free survival (DMFS). These findings were validated in the independent cohort. ctDNA detection remained an independent predictor of RFS and DMFS in multivariate analyses after adjustment for disease stage and BRAF mutation status. CONCLUSION Baseline and postoperative ctDNA detection in two independent prospective cohorts identified stage III melanoma patients at highest risk of relapse and has potential to inform adjuvant therapy decisions.
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Affiliation(s)
- L Tan
- Peter MacCallum Cancer Centre, Melbourne; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - S Sandhu
- Peter MacCallum Cancer Centre, Melbourne; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - R J Lee
- Molecular Oncology Group, Cancer Research UK Manchester Institute, Manchester; Faculty of Biology, Medicine and Health, The University of Manchester, Manchester
| | - J Li
- Peter MacCallum Cancer Centre, Melbourne; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - J Callahan
- Peter MacCallum Cancer Centre, Melbourne
| | - S Ftouni
- Peter MacCallum Cancer Centre, Melbourne
| | - N Dhomen
- Molecular Oncology Group, Cancer Research UK Manchester Institute, Manchester
| | - P Middlehurst
- Molecular Oncology Group, Cancer Research UK Manchester Institute, Manchester
| | - A Wallace
- Genomic Diagnostics Laboratory, Manchester Centre for Genomic Medicine, Manchester, UK
| | - J Raleigh
- Peter MacCallum Cancer Centre, Melbourne
| | | | - M A Henderson
- Peter MacCallum Cancer Centre, Melbourne; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | | | | | - V Mar
- The Alfred Hospital, Melbourne
| | - D E Gyorki
- Peter MacCallum Cancer Centre, Melbourne; Department of Surgery, The University of Melbourne, Melbourne, Australia
| | - D Oudit
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester; The Christie NHS Foundation Trust, Manchester, UK
| | - M A Dawson
- Peter MacCallum Cancer Centre, Melbourne; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia; Centre for Cancer Research, The University of Melbourne, Melbourne, Australia
| | - R J Hicks
- Peter MacCallum Cancer Centre, Melbourne; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - P Lorigan
- Faculty of Biology, Medicine and Health, The University of Manchester, Manchester; The Christie NHS Foundation Trust, Manchester, UK
| | - G A McArthur
- Peter MacCallum Cancer Centre, Melbourne; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia
| | - R Marais
- Molecular Oncology Group, Cancer Research UK Manchester Institute, Manchester; Faculty of Biology, Medicine and Health, The University of Manchester, Manchester
| | - S Q Wong
- Peter MacCallum Cancer Centre, Melbourne
| | - S-J Dawson
- Peter MacCallum Cancer Centre, Melbourne; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Australia; Centre for Cancer Research, The University of Melbourne, Melbourne, Australia.
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8
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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: 7] [Impact Index Per Article: 1.2] [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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9
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Akiyama M, Matsuda Y, Arai T, Saeki H. Clinicopathological characteristics of malignant melanomas of the skin and gastrointestinal tract. Oncol Lett 2018; 16:2675-2681. [PMID: 30013664 DOI: 10.3892/ol.2018.8913] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 05/03/2018] [Indexed: 12/26/2022] Open
Abstract
The present study examined the differences between gastrointestinal melanoma (GM) and skin melanoma (SM). The clinicopathological characteristics, the expression of melanoma stem cell markers nestin, sex determining region Y-box 2 and ATP-binding cassette sub-family B member 5, and the presence of the BRAFV600E mutation were evaluated in 10 cases of GM and 31 cases of SM. Patients with GM had an increased mean age compared with those with SM (76 vs. 68 years). In addition, GMs were significantly more likely than SMs to be amelanotic (50 vs. 7%; P=0.001) and display round cells (70 vs. 23%; P=0.02). The mitosis rate was also significantly higher in GM compared with SM (P<0.05). The incidence of lymph-node metastasis (60 vs. 32%; P<0.05) and distant metastasis (10 vs. 6.5%, P=0.02) was significantly higher in GMs compared with SMs. The expression of stem cell markers did not differ significantly between groups, however, in the SM group advanced-stage disease was associated with a significantly higher expression of nestin than early-stage disease (P<0.05). Immunohistochemically, the expression of BRAFV600E was significantly lower in GMs compared with in SMs (1.0 vs. 3.3; P=0.01). These findings indicate that the identification of these features may aid in the diagnosis of GM and SM, as well as contribute to the development of novel targeted therapies against GM.
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Affiliation(s)
- Michiko Akiyama
- Department of Dermatology, Nippon Medical School, Tokyo 113-8603, Japan.,Department of Pathology, Tokyo Metropolitan Geriatric Hospital, Tokyo 173-0015, Japan
| | - Yoko Matsuda
- Department of Pathology, Tokyo Metropolitan Geriatric Hospital, Tokyo 173-0015, Japan
| | - Tomio Arai
- Department of Pathology, Tokyo Metropolitan Geriatric Hospital, Tokyo 173-0015, Japan
| | - Hidehisa Saeki
- Department of Dermatology, Nippon Medical School, Tokyo 113-8603, Japan
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10
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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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11
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Hu W, Yang Y, Zhang L, Yin J, Huang J, Huang L, Gu H, Jiang G, Fang J. Post surgery circulating free tumor DNA is a predictive biomarker for relapse of lung cancer. Cancer Med 2017; 6:962-974. [PMID: 28382702 PMCID: PMC5430107 DOI: 10.1002/cam4.980] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 10/11/2016] [Accepted: 11/02/2016] [Indexed: 02/05/2023] Open
Abstract
Cancer cells release DNA fragments into plasma as circulating free DNA (cfDNA). However, quantitative measurement of tumor-derived DNA in cfDNA remains challenge. The purpose of this study was to quantitatively assess tumor-derived DNA in lung cancer patients. By optimizing competitive allele-specific TaqMan PCR (CAST-PCR), we assessed the copy number of mutated Kirsten rat sarcoma viral oncogene homolog (KRAS) and epidermal growth factor receptor (EGFR) alleles in the pre/post surgery plasma of 168 lung cancer patients. An absolute quantitative PCR method was developed to assess the number of total cfDNA. All mutations detected in tumors were also found in the plasma after surgery. At the time of 30 days after surgery, EGFR mutation of circulating cell-free DNA was detected only in two patients who recurred in 4 months after surgery. Compared to that of normal control at 30 days after surgery, five patients who recurred in 4 months had significantly higher circulating cell-free DNA (P < 0.001), whereas six patients who recurred after 4 months (P = 0.207) and five patients without recurrence (P = 0.901) demonstrated significantly lower circulating cell-free DNA. Our findings suggest that cfDNA analysis in plasma is an alternative and supplement to tissue analysis and hold promise for clinical application. Stratification of patients according to cfDNA levels at 30 days after surgery might be helpful in selecting lung cancer patients for adjuvant therapy after surgery.
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Affiliation(s)
- Wenwei Hu
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yang Yang
- Shanghai Pulmonary Hospital, Shanghai, China
| | - Longzhen Zhang
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jianxin Yin
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Jingwei Huang
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Lei Huang
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Hua Gu
- School of Life Sciences and Technology, Tongji University, Shanghai, China
| | | | - Jianmin Fang
- School of Life Sciences and Technology, Tongji University, Shanghai, China.,Tongji University Suzhou Institute, Suzhou, Jiangsu, China.,Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, China
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12
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Ballester LY, Cantu MD, Lim KPH, Sarabia SF, Ferguson LS, Renee Webb C, Allen CE, McClain KL, Mohila CA, Punia JN, Roy A, López-Terrada DH, John Hicks M, Fisher KE. The use of BRAF V600E mutation-specific immunohistochemistry in pediatric Langerhans cell histiocytosis. Hematol Oncol 2017; 36:307-315. [PMID: 28219109 PMCID: PMC6886693 DOI: 10.1002/hon.2388] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 01/01/2023]
Abstract
BRAF p.V600E mutations are detected in greater than 50% of pediatric Langerhans cell histiocytosis (LCH) lesions. However, the use of mutation-specific BRAF V600E immunohistochemistry (IHC) as a surrogate for molecular testing in pediatric LCH is unknown. We tested the mutation-specific BRAF V600E monoclonal antibody (clone VE1) in formalin-fixed, paraffin-embedded LCH samples from 26 pediatric patients (14 males and 12 females, ages 7 mo-17 y) using allele-specific real-time polymerase chain reaction (PCR) with a limit of detection of 0.5% as the comparative gold standard. BRAF VE1 staining was scored for both intensity (0-3+) and percentage of immunoreactive tumor cells (0%-100%). BRAF VE1 immunoreactivity was determined using both lenient (≥1+, ≥1%) and stringent (≥2+, ≥10%) scoring criteria. Using lenient-scoring criteria, we found that the sensitivity and specificity of IHC compared with allele-specific real-time PCR were 100.0% and 18.2%, respectively. The poor specificity of lenient IHC analysis was attributable to weak, 1+ staining in both BRAF-mutated and wild-type LCH. Using stringent-scoring criteria, we found that specificity improved to 100.0% at the expense of sensitivity that decreased to 80.0%. Stringent scoring generated 3 false-negative results, but in all cases, neoplastic tissue comprised less than 5% of the stained section and/or the specimen was decalcified. In conclusion, highly sensitive molecular assays remain the gold standard for BRAF mutation analysis in LCH paraffin-embedded lesions. To avoid false-positive results, unequivocal VE1 staining of 2+ intensity in greater than or equal to 10% neoplastic histiocytes is required. However, negative VE1 results require additional studies to exclude false-negatives, and stringent-scoring criteria may not be optimal for scant or decalcified specimens.
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Affiliation(s)
- Leomar Y Ballester
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA.,Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Miguel D Cantu
- Department of Pediatrics, Texas Children's Hospital, Houston, TX, USA.,Division of Hematology and Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Karen P H Lim
- Department of Pediatrics, Texas Children's Hospital, Houston, TX, USA.,Division of Hematology and Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Stephen F Sarabia
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
| | | | - C Renee Webb
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA
| | - Carl E Allen
- Department of Pediatrics, Texas Children's Hospital, Houston, TX, USA.,Division of Hematology and Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Kenneth L McClain
- Department of Pediatrics, Texas Children's Hospital, Houston, TX, USA.,Division of Hematology and Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Carrie A Mohila
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA.,Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Jyotinder N Punia
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA.,Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
| | - Angshumoy Roy
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA.,Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics, Texas Children's Hospital, Houston, TX, USA
| | - Dolores H López-Terrada
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA.,Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics, Texas Children's Hospital, Houston, TX, USA
| | - M John Hicks
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA.,Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA.,Department of Pediatrics, Texas Children's Hospital, Houston, TX, USA
| | - Kevin E Fisher
- Department of Pathology, Texas Children's Hospital, Houston, TX, USA.,Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, USA
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13
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Alqahtani M, Grieu F, Carrello A, Amanuel B, Mashour M, Alattas R, Al-Saleh K, Alsheikh A, Alqahtani S, Iacopetta B. Screening for Lynch Syndrome in Young Colorectal Cancer Patients from Saudi Arabia Using Microsatellite Instability as the Initial Test. Asian Pac J Cancer Prev 2016; 17:1917-23. [DOI: 10.7314/apjcp.2016.17.4.1917] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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14
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15
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Voskoboynik M, Mar V, Mailer S, Colebatch A, Fennessy A, Logan A, Hewitt C, Cebon J, Kelly J, McArthur G. Clinicopathological characteristics associated with BRAF(K601E) and BRAF(L597) mutations in melanoma. Pigment Cell Melanoma Res 2016; 29:222-8. [PMID: 26643848 DOI: 10.1111/pcmr.12450] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 11/27/2015] [Indexed: 01/19/2023]
Abstract
BRAF mutations at codons L597 and K601 occur uncommonly in melanoma. Clinical and pathological associations of these mutations were investigated in a cohort of 1119 patients with known BRAF mutation status. A BRAF mutation was identified in 435 patients; Mutations at L597 and the K601E mutation were seen in 3.4 and 3.2% of these, respectively. K601E melanomas tended to occur in male patients, a median age of 58 yr, were generally found on the trunk (64%) and uncommonly associated with chronically sun-damaged (CSD) skin. BRAF L597 melanomas occurred in older patients (median 66 yr), but were associated with CSD skin (extremities or head and neck location - 73.3%, P = 0.001). Twenty-three percent of patients with V600E- and 43% of patients with K601E-mutant melanomas presented with nodal disease at diagnosis compared to just 14% of patients with BRAF wild-type tumors (P = 0.001 and 0.006, respectively). Overall, these mutations represent a significant minority of BRAF mutations, but have distinct clinicopathological phenotypes and clinical behaviors.
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Affiliation(s)
- Mark Voskoboynik
- Peter MacCallum Cancer Centre, East Melbourne, Vic., Australia.,Victorian Melanoma Service, Alfred Hospital, Prahran, Melbourne, Vic., Australia
| | - Victoria Mar
- Victorian Melanoma Service, Alfred Hospital, Prahran, Melbourne, Vic., Australia.,Skin and Cancer Foundation, Melbourne, Vic., Australia.,Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Vic., Australia
| | - Sonia Mailer
- Peter MacCallum Cancer Centre, East Melbourne, Vic., Australia
| | | | - Anne Fennessy
- Peter MacCallum Cancer Centre, East Melbourne, Vic., Australia
| | | | - Chelsee Hewitt
- Peter MacCallum Cancer Centre, East Melbourne, Vic., Australia
| | - Jonathon Cebon
- School of Cancer Medicine, La Trobe University, Olivia Newton-John Cancer Research Institute, Heidelberg, Vic., Australia
| | - John Kelly
- Victorian Melanoma Service, Alfred Hospital, Prahran, Melbourne, Vic., Australia
| | - Grant McArthur
- Peter MacCallum Cancer Centre, East Melbourne, Vic., Australia.,Melbourne University, Parkville, Vic., Australia
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16
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Shi RL, Qu N, Liao T, Wei WJ, Lu ZW, Ma B, Wang YL, Ji QH. Relationship of body mass index with BRAF (V600E) mutation in papillary thyroid cancer. Tumour Biol 2016; 37:8383-90. [PMID: 26733165 DOI: 10.1007/s13277-015-4718-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 12/21/2015] [Indexed: 12/11/2022] Open
Abstract
Current evidences suggest an influence of overweight body mass index (BMI) on the carcinogenesis in malignancies. However, the role of BMI is unclear in papillary thyroid cancer (PTC). The aim of the present study is to investigate the relationship between BMI and BRAF (V600E) mutation status in PTC. BRAF (V600E) mutation in 108 patients with PTC was analyzed by Sanger sequencing. The cutoff point of BMI was identified by X-tile for predicting mutation by overweight. Odds ratios (OR) and 95 % confidence interval (CI) of BRAF (V600E) mutation according to BMI and clinicopathologic variables were calculated using logistic regression models. Fifty-one patients were positive for BRAF (V600E) mutation. A positive relationship existed between BRAF (V600E) mutation and BMI (p = 0.039). A 24.3 kg/m(2) was identified as cutoff point for differentiating greater than 52.0 % observed probability of mutation for BRAF (V600E) in entire cohort, which was similar to the midpoint between the upper limit of normal BMI and overweight defined by WHO (≥24 kg/m(2)). Multivariate analysis confirmed the association between BRAF (V600E) mutation with overweight BMI range (OR 7.645, 95 % CI 1.275-45.831, p = 0.026). This study suggests an influence of overweight BMI on the status of BRAF (V600E) in patients with PTC, whereas the underlying mechanism need to be further investigated.
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Affiliation(s)
- Rong-Liang Shi
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
- Department of General surgery, Minhang Hospital, Fudan University, Shanghai, 201199, China
| | - Ning Qu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Tian Liao
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Wen-Jun Wei
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Zhong-Wu Lu
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Ben Ma
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yu-Long Wang
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Qing-Hai Ji
- Department of Head and Neck Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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17
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Barbano R, Pasculli B, Coco M, Fontana A, Copetti M, Rendina M, Valori VM, Graziano P, Maiello E, Fazio VM, Parrella P. Competitive allele-specific TaqMan PCR (Cast-PCR) is a sensitive, specific and fast method for BRAF V600 mutation detection in Melanoma patients. Sci Rep 2015; 5:18592. [PMID: 26690267 PMCID: PMC4686972 DOI: 10.1038/srep18592] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 11/23/2015] [Indexed: 12/31/2022] Open
Abstract
BRAF codon 600 mutation testing of melanoma patients is mandatory for the choice of the most appropriate therapy in the clinical setting. Competitive allele specific TaqMan PCR (Cast-PCR) technology allows not only the selective amplification of minor alleles, but it also blocks the amplification of non-mutant allele. We genotyped codon 600 of the BRAF gene in 54 patients’ samples by Cast-PCR and bidirectional direct sequence analysis. All the mutations detected by sequencing were also identified by Cast-PCR. In addition, Cast-PCR assay detected four samples carrying mutations and was able to clearly identify two mutations of uncertain interpretation by Sanger sequencing. The limit of detection of Cast-PCR was evaluated by constructing dilution curves of BRAFV600E and BRAFV600K mutated clinical samples mixed with a not-mutated specimens. Both mutations could be detected until a 1:100 mutated/not mutated ratio. Cloning and sequencing of the clones was used to confirm mutations on representative discrepant cases. Cast PCR performances were not affected by intratumour heterogeneity, and less affected by melanin content. Our results indicate that Cast-PCR is a reliable diagnostic tool for the identification of melanoma patients as eligible to be treated with TKIs and might be implemented in the clinical setting as elective screening method.
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Affiliation(s)
- Raffaela Barbano
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotundo (FG) 71013, Italy
| | - Barbara Pasculli
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotundo (FG) 71013, Italy
| | - Michelina Coco
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotundo (FG) 71013, Italy
| | - Andrea Fontana
- Biostatic Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotundo (FG) 71013, Italy
| | - Massimiliano Copetti
- Biostatic Unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotundo (FG) 71013, Italy
| | - Michelina Rendina
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotundo (FG) 71013, Italy.,Department of Oncology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotundo (FG) 71013, Italy
| | - Vanna Maria Valori
- Department of Oncology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotundo (FG) 71013, Italy
| | - Paolo Graziano
- Department of Pathology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo (FG) 71013, Italy
| | - Evaristo Maiello
- Department of Oncology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotundo (FG) 71013, Italy
| | - Vito Michele Fazio
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotundo (FG) 71013, Italy.,CIR Laboratory for Molecular Medicine and Biotechnology, University Campus Biomedico, Rome 00128, Italy
| | - Paola Parrella
- Laboratory of Oncology, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotundo (FG) 71013, Italy
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18
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BRAF and NRAS mutations are heterogeneous and not mutually exclusive in nodular melanoma. Appl Immunohistochem Mol Morphol 2015; 23:172-7. [PMID: 24710085 PMCID: PMC4482453 DOI: 10.1097/pai.0000000000000071] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Inhibitors of RAF inhibit the MAPK pathway that plays an important role in the development and progression of those melanoma carrying the V600E BRAF mutation, but there’s a subset of such patients who do not respond to the therapy. Various mechanisms of drug resistance have been proposed which include the clonal heterogeneity of the tumor. We have studied a population of nodular melanoma to investigate the intratumor and intertumor heterogeneity by Laser Capture Microdissection (LCM) analysis. Our results showed that BRAF and NRAS mutations were detected in 47% and 33% of nodular melanoma, respectively, and that there is a discrepancy in mutational pattern of tumoral sample because in the 36% of patients a different mutation, in at least 1 area of the tumor, was found by LCM analysis, giving evidence of the presence of different clonal cells populations. Moreover, we found that mutations in BRAF and NRAS are not mutually exclusive because they were simultaneously present in the same tumor specimens and we observed that when the 2 different mutations were present one is a high-frequency mutation and the other is a low-frequency mutation. This was more evident in lymphonodal metastasis that resulted from wild type to mutational analysis, but showed different mutations following LCM analysis. Therefore, we believed that, when primary tumoral sample results negative to mutational analysis, if it is possible, metastases should be investigated to verify the presence of mutations. Generally, it should be searched for other mutations, in addition to BRAF V600E, so as to better understand the mechanism of drug resistance.
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19
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BRAF p.Val600Glu (V600E) mutation detection in thyroid fine needle aspiration cell block samples: a feasibility study. Pathology 2015; 47:432-8. [DOI: 10.1097/pat.0000000000000273] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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20
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Jurkowska M, Gos A, Ptaszyński K, Michej W, Tysarowski A, Zub R, Siedlecki JA, Rutkowski P. Comparison between two widely used laboratory methods in BRAF V600 mutation detection in a large cohort of clinical samples of cutaneous melanoma metastases to the lymph nodes. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:8487-8493. [PMID: 26339422 PMCID: PMC4555750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 06/25/2015] [Indexed: 06/05/2023]
Abstract
AIMS The study compares detection rates of oncogenic BRAF mutations in a homogenous group of 236 FFPE cutaneous melanoma lymph node metastases, collected in one cancer center. BRAF mutational status was verified by two independent in-house PCR/Sanger sequencing tests, and the Cobas® 4800 BRAF V600 Mutation Test. RESULTS The best of two sequencing approaches returned results for 230/236 samples. In 140 (60.9%), the mutation in codon 600 of BRAF was found. 91.4% of all mutated cases (128 samples) represented p.V600E. Both Sanger-based tests gave reproducible results although they differed significantly in the percentage of amplifiable samples: 230/236 to 109/143. Cobas generated results in all 236 cases, mutations changing codon V600 were detected in 144 of them (61.0%), including 5 not amplifiable and 5 negative in the standard sequencing. However, 6 cases positive in sequencing turned out to be negative in Cobas. Both tests provided us with the same BRAF V600 mutational status in 219 out of 230 cases with valid results (95.2%). CONCLUSIONS The total BRAF V600 mutation detection rate didn't differ significantly between the two methodological approaches (60.9% vs. 61.0%). Sequencing was a reproducible method of V600 mutation detection and more powerful to detect mutations other than p.V600E, while Cobas test proved to be less susceptible to the poor DNA quality or investigator's bias. The study underlined an important role of pathologists in quality assurance of molecular diagnostics.
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Affiliation(s)
| | - Aleksandra Gos
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of OncologyRoentgena 5, Warsaw 02-781, Poland
| | - Konrad Ptaszyński
- Department of Pathology, Center of Postgraduate Medical EducationMarymoncka 99/103, Warsaw 01-809, Poland
| | - Wanda Michej
- Department of Pathology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of OncologyRoentgena 5, Warsaw 02-781, Poland
| | - Andrzej Tysarowski
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of OncologyRoentgena 5, Warsaw 02-781, Poland
| | - Renata Zub
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of OncologyRoentgena 5, Warsaw 02-781, Poland
| | - Janusz A Siedlecki
- Department of Molecular and Translational Oncology, Maria Sklodowska-Curie Memorial Cancer Center and Institute of OncologyRoentgena 5, Warsaw 02-781, Poland
| | - Piotr Rutkowski
- Department of Soft Tissue/Bone Sarcoma and Melanoma, Maria Sklodowska-Curie Memorial Cancer Center and Institute of OncologyRoentgena 5, Warsaw 02-781, Poland
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21
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Mar VJ, Liu W, Devitt B, Wong SQ, Dobrovic A, McArthur GA, Wolfe R, Kelly JW. The role of BRAF mutations in primary melanoma growth rate and survival. Br J Dermatol 2015; 173:76-82. [PMID: 25752325 DOI: 10.1111/bjd.13756] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2015] [Indexed: 12/13/2022]
Abstract
BACKGROUND The clinical behaviour and prognosis of primary melanomas harbouring BRAF mutations is not fully understood. OBJECTIVES To investigate the effect of mutation status on primary melanoma growth rate and melanoma-specific survival (MSS). METHODS A prospective cohort of 196 patients with stage I-III primary cutaneous melanoma were followed for a median of 92 months, pre-dating the institution of BRAF inhibitor therapy. Clinicopathological variables were correlated with mutation status and hazard ratios (HRs) estimated for MSS. RESULTS Of 196 tumours, 77 (39.2%) were BRAF V600E, 10 (5.1%) BRAF V600K and 33 (16.8%) were NRAS mutant. BRAF V600E mutant melanomas were associated with favourable clinical characteristics and tended to be slower growing compared with BRAF V600K, NRAS mutant or BRAF/NRAS wild-type tumours (0.12 mm per month, 0.61 mm per month, 0.36 mm per month and 0.23 mm per month, respectively; P = 0.05). There were 39 melanoma deaths, and BRAF mutant melanomas were associated with poorer MSS in stage I-III disease [HR 2.60, 95% confidence interval (CI) 1.20-5.63; P = 0.02] and stage I-II disease (HR 3.39, 95% CI 1.12-10.22; P = 0.03) after adjusting for other prognostic variables. Considered separately, BRAF V600E mutant melanomas were strongly associated with MSS independently of thickness and nodal status (HR 3.89, 95% CI 1.67-9.09; P < 0.01) but BRAF V600K mutant tumours were not (HR 1.19, 95% CI 0.36-3.92; P = 0.77). CONCLUSIONS The presence of a BRAF mutation does not necessarily 'drive' more rapid tumour growth but is associated with poorer MSS in patients with early-stage disease.
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Affiliation(s)
- V J Mar
- Victorian Melanoma Service, Alfred Hospital, Melbourne, Vic., 3181, Australia.,Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Vic., 3181, Australia.,Division of Cancer Research, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, Vic., 3002, Australia
| | - W Liu
- Victorian Melanoma Service, Alfred Hospital, Melbourne, Vic., 3181, Australia
| | - B Devitt
- Department of Oncology, St Vincent's Hospital, Fitzroy, Vic., 3065, Australia
| | - S Q Wong
- Division of Cancer Research, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, Vic., 3002, Australia
| | - A Dobrovic
- Translational Genomics and Epigenomics Laboratory, Ludwig Institute for Cancer Research, Olivia Newton-John Cancer and Wellness Centre, Heidelberg, Vic., 3084, Australia
| | - G A McArthur
- Division of Cancer Research, Peter MacCallum Cancer Centre, St Andrews Place, East Melbourne, Vic., 3002, Australia
| | - R Wolfe
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Vic., 3181, Australia
| | - J W Kelly
- Victorian Melanoma Service, Alfred Hospital, Melbourne, Vic., 3181, Australia
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22
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Simulation-guided DNA probe design for consistently ultraspecific hybridization. Nat Chem 2015; 7:545-53. [PMID: 26100802 PMCID: PMC4479422 DOI: 10.1038/nchem.2266] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 04/20/2015] [Indexed: 12/18/2022]
Abstract
Hybridization of complementary sequences is one of the central tenets of nucleic acid chemistry; however, the unintended binding of closely related sequences limits the accuracy of hybridization-based approaches for analyzing nucleic acids. Thermodynamics-guided probe design and empirical optimization of reaction conditions have been used to enable discrimination of single nucleotide variants, but typically these approaches provide only an approximate 25-fold difference in binding affinity. Here we show that simulations of the binding kinetics are both necessary and sufficient to design nucleic acid probe systems with consistently high specificity as they enable the discovery of an optimal combination of thermodynamic parameters. Simulation-guided probe systems designed against 44 different target single nucleotide variants sequences showed between 200- and 3000-fold (median 890) higher binding affinity than their corresponding wildtype sequences. As a demonstration of the usefulness of this simulation-guided design approach we developed probes which, in combination with PCR amplification, we use to detect low concentrations of variant alleles (1%) in human genomic DNA.
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23
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Qiu T, Lu H, Guo L, Huang W, Ling Y, Shan L, Li W, Ying J, Lv N. Detection of BRAF mutation in Chinese tumor patients using a highly sensitive antibody immunohistochemistry assay. Sci Rep 2015; 5:9211. [PMID: 25784606 PMCID: PMC4363828 DOI: 10.1038/srep09211] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2014] [Accepted: 02/05/2015] [Indexed: 12/17/2022] Open
Abstract
BRAF mutations can be found in various solid tumors. But accurate and reliable screening for BRAF mutation that is compatible for clinical application is not yet available. In this study, we used an automated immunohistochemistry (IHC) staining coupled with mouse monoclonal anti-BRAF V600E (VE1) primary antibody to screen the BRAF V600E mutation in 779 tumor cases, including 611 colorectal carcinomas (CRC), 127 papillary thyroid carcinomas (PTC) and 41 malignant melanomas. Among the 779 cases, 150 cases were positive for BRAF (V600E) staining, including 38 (of 611, 6%) CRCs, 102 (of 127, 80%) PTCs and 10 (of 41, 24%) malignant melanomas. Sanger sequencing and real-time PCR confirmed the sensitivity and specificity of IHC staining for the V600E mutation are 100% and 99%, respectively. Therefore, our study demonstrates that the fully automated IHC is a reliable tool to determine BRAF mutation status in CRC, PTC and melanoma and can be used for routine clinical screen.
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Affiliation(s)
- Tian Qiu
- Department of Pathology, Cancer Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Haizhen Lu
- Department of Pathology, Cancer Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Lei Guo
- Department of Pathology, Cancer Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Wenting Huang
- Department of Pathology, Cancer Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yun Ling
- Department of Pathology, Cancer Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ling Shan
- Department of Pathology, Cancer Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Wenbin Li
- Department of Pathology, Cancer Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Jianming Ying
- Department of Pathology, Cancer Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ning Lv
- Department of Pathology, Cancer Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
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24
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Clinical significance of GNAS mutation in intraductal papillary mucinous neoplasm of the pancreas with concomitant pancreatic ductal adenocarcinoma. Pancreas 2015; 44:311-20. [PMID: 25479586 DOI: 10.1097/mpa.0000000000000258] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
OBJECTIVE The aims of this study were to investigate the GNAS mutational status in pancreatic intraductal papillary mucinous neoplasm (IPMN) with and without distinct pancreatic ductal adenocarcinoma (PDAC) and to evaluate the significance of GNAS analysis using duodenal fluid (DF) in patients with IPMN. METHODS The clinicopathologic features of 110 patients with IPMN including 16 with distinct PDAC were reviewed. The GNAS status in the IPMN tissue and 23 DF specimens was assessed by sensitive mutation scanning methods. RESULTS The GNAS mutation rate in IPMN with distinct PDAC was significantly lower than that in IPMN without PDAC (4/16, 25%, vs 61/94, 65%; P = 0.0047). By multivariate analysis, GNAS wild-type and gastric type IPMNs were significantly associated with distinct PDAC. Of 45 GNAS wild-type IPMNs, 10 (43%) of 23 gastric type IPMNs had distinct PDAC, whereas only 2 (9%) of 22 non-gastric type IPMNs had distinct PDAC (P = 0.017). The GNAS status in DF was consistent with that in tissue in 21 (91%) of 23 patients. CONCLUSIONS Distinct PDACs frequently develop in the pancreas with gastric type IPMN without GNAS mutations. Duodenal fluid DNA test would predict the GNAS status of IPMN, whereas the detection of the gastric subtype using noninvasive test remains to be determined.
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Implementation of a companion diagnostic in the clinical laboratory: the BRAF example in melanoma. Clin Chim Acta 2014; 439:128-36. [PMID: 25454717 DOI: 10.1016/j.cca.2014.10.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 09/19/2014] [Accepted: 10/13/2014] [Indexed: 01/09/2023]
Abstract
A companion diagnostic test provides information that is essential for the safe and effective use of a corresponding therapeutic product as indicated in the drug instructions. The implementation of a companion diagnostic follows the rules of a molecular test for somatic mutations in a routine clinical laboratory environment and needs guidance on practical aspects, including the choice of the proper analytical method and the procedures for internal and external quality controls. Selection of the appropriate assay for detection of genetic alterations depends on several factors: the type of mutation under study, the sample to be assayed and its preparation procedure. In addition, the results of a molecular assay require a complex interpretation process of the analytical data as the patient's genotype, the translation of the identified variant into a predicted phenotype and knowledge on restrictions of the method used. In relation to these aspects herein we report an opinion paper of the Working Group Personalized Laboratory Medicine jointly constituted by the European Federation of Laboratory Medicine (EFLM) and by the European Society of Pharmacogenomics and Theranostics (ESPT) using, as an example, the BRAF genotype analysis in tumor tissue samples for identification of melanoma patients that can benefit treatment with BRAF inhibitors. The manuscript is focused on the following aspects: i) medical rationale, ii) methodologies of analysis, iii) laboratory performance evaluation and iv) the laboratory specific report for the clinicians. The critical evaluation of these aspects would be useful for the implementation of a companion diagnostic in the clinical laboratory.
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Performance comparison of three BRAF V600E detection methods in malignant melanoma and colorectal cancer specimens. Tumour Biol 2014; 36:1003-13. [PMID: 25318602 PMCID: PMC4342512 DOI: 10.1007/s13277-014-2711-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 10/05/2014] [Indexed: 02/02/2023] Open
Abstract
Personalized cancer care requires reliable biomarkers. While the BRAF V600E mutation is implemented in the clinic, no method for its detection has so far been established as reference. We aimed to perform a comprehensive comparison of three methods currently being used for V600E detection in clinical samples. We analysed genomic DNA from 127 malignant melanomas (77 patients) and 389 tumours from 141 colorectal cancer patients (383 liver metastases and 6 primary tumours) by Sanger sequencing and a single probe-based high-resolution melting assay (LightMix). Formalin-fixed paraffin-embedded (FFPE) tissue from a subset of these lesions (n = 77 and 304, respectively) was analysed by immunohistochemistry (IHC) using the V600E-specific antibody VE1. In a dilution series of V600E-mutated DNA in wild-type DNA, the detection limit for the LightMix assay was 1:1000 mutated alleles while it was 1:10 for Sanger sequencing. In line with this, we detected 15 additional mutated melanoma samples and two additional mutated metastatic colorectal cancer samples by the LightMix assay compared to Sanger sequencing. For the melanoma samples, we observed high concordance between DNA-based methods and analysis by IHC. However, in colorectal samples, IHC performed poorly with 12 samples being scored as V600E positive exclusively by IHC and nine samples being scored as V600E negative exclusively by IHC. In conclusion, the VE1 antibody is not recommendable for clinical tests of colorectal cancer samples. For melanoma samples, IHC may be useful as a screening tool guiding further analytical approaches.
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Emmanuel C, Chiew YE, George J, Etemadmoghadam D, Anglesio MS, Sharma R, Russell P, Kennedy C, Fereday S, Hung J, Galletta L, Hogg R, Wain GV, Brand A, Balleine R, MacConaill L, Palescandolo E, Hunter SM, Campbell I, Dobrovic A, Wong SQ, Do H, Clarke CL, Harnett PR, Bowtell DDL, deFazio A. Genomic classification of serous ovarian cancer with adjacent borderline differentiates RAS pathway and TP53-mutant tumors and identifies NRAS as an oncogenic driver. Clin Cancer Res 2014; 20:6618-30. [PMID: 25316818 DOI: 10.1158/1078-0432.ccr-14-1292] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Low-grade serous ovarian carcinomas (LGSC) are Ras pathway-mutated, TP53 wild-type, and frequently associated with borderline tumors. Patients with LGSCs respond poorly to platinum-based chemotherapy and may benefit from pathway-targeted agents. High-grade serous carcinomas (HGSC) are TP53-mutated and are thought to be rarely associated with borderline tumors. We sought to determine whether borderline histology associated with grade 2 or 3 carcinoma was an indicator of Ras mutation, and we explored the molecular relationship between coexisting invasive and borderline histologies. EXPERIMENTAL DESIGN We reviewed >1,200 patients and identified 102 serous carcinomas with adjacent borderline regions for analyses, including candidate mutation screening, copy number, and gene expression profiling. RESULTS We found a similar frequency of low, moderate, and high-grade carcinomas with coexisting borderline histology. BRAF/KRAS alterations were common in LGSC; however, we also found recurrent NRAS mutations. Whereas borderline tumors harbored BRAF/KRAS mutations, NRAS mutations were restricted to carcinomas, representing the first example of a Ras oncogene with an obligatory association with invasive serous cancer. Coexisting borderline and invasive components showed nearly identical genomic profiles. Grade 2 cases with coexisting borderline included tumors with molecular features of LGSC, whereas others were typical of HGSC. However, all grade 3 carcinomas with coexisting borderline histology were molecularly indistinguishable from typical HGSC. CONCLUSION Our findings suggest that NRAS is an oncogenic driver in serous ovarian tumors. We demonstrate that borderline histology is an unreliable predictor of Ras pathway aberration and underscore an important role for molecular classification in identifying patients that may benefit from targeted agents.
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Affiliation(s)
- Catherine Emmanuel
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia. Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, New South Wales, Australia. University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia. Westmead Institute for Cancer Research, Westmead Millennium Institute, Westmead Hospital, Sydney, New South Wales, Australia
| | - Yoke-Eng Chiew
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia. Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, New South Wales, Australia. Westmead Institute for Cancer Research, Westmead Millennium Institute, Westmead Hospital, Sydney, New South Wales, Australia
| | - Joshy George
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Dariush Etemadmoghadam
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia. Sir Peter MacCallum Cancer Centre, Department of Oncology, University of Melbourne, Parkville, Victoria, Australia. Department of Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - Michael S Anglesio
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Raghwa Sharma
- University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia. Pathology West ICPMR Westmead, Sydney, New South Wales, Australia. University of Western Sydney at Westmead Hospital, Westmead, New South Wales, Australia
| | - Peter Russell
- Department of Obstetrics, Gynaecology and Neonatology, University of Sydney, Camperdown New South Wales, Australia. Douglass Hanly Moir Pathology, Macquarie Park, New South Wales, Australia
| | - Catherine Kennedy
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia. Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, New South Wales, Australia. University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia. Westmead Institute for Cancer Research, Westmead Millennium Institute, Westmead Hospital, Sydney, New South Wales, Australia
| | - Sian Fereday
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Jillian Hung
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia. Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, New South Wales, Australia. Westmead Institute for Cancer Research, Westmead Millennium Institute, Westmead Hospital, Sydney, New South Wales, Australia
| | - Laura Galletta
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Russell Hogg
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia. Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, New South Wales, Australia. University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia
| | - Gerard V Wain
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia. Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, New South Wales, Australia. University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia
| | - Alison Brand
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia. Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, New South Wales, Australia. University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia
| | - Rosemary Balleine
- University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia. Westmead Institute for Cancer Research, Westmead Millennium Institute, Westmead Hospital, Sydney, New South Wales, Australia. Pathology West ICPMR Westmead, Sydney, New South Wales, Australia
| | | | | | - Sally M Hunter
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Ian Campbell
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia. Department of Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - Alexander Dobrovic
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia. Department of Pathology, University of Melbourne, Parkville, Victoria, Australia. School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Stephen Q Wong
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia. Department of Pathology, University of Melbourne, Parkville, Victoria, Australia. School of Cancer Medicine, La Trobe University, Bundoora, Victoria, Australia
| | - Hongdo Do
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Christine L Clarke
- University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia. Westmead Institute for Cancer Research, Westmead Millennium Institute, Westmead Hospital, Sydney, New South Wales, Australia
| | - Paul R Harnett
- Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, New South Wales, Australia. University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia. Westmead Institute for Cancer Research, Westmead Millennium Institute, Westmead Hospital, Sydney, New South Wales, Australia
| | - David D L Bowtell
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia. Sir Peter MacCallum Cancer Centre, Department of Oncology, University of Melbourne, Parkville, Victoria, Australia. Department of Pathology, University of Melbourne, Parkville, Victoria, Australia. Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, Australia. Ovarian Cancer Action Research Centre, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Anna deFazio
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia. Crown Princess Mary Cancer Centre, Westmead Hospital, Sydney, New South Wales, Australia. University of Sydney, Westmead Hospital, Sydney, New South Wales, Australia. Westmead Institute for Cancer Research, Westmead Millennium Institute, Westmead Hospital, Sydney, New South Wales, Australia.
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Mar VJ, Wong SQ, Logan A, Nguyen T, Cebon J, Kelly JW, Wolfe R, Dobrovic A, McLean C, McArthur GA. Clinical and pathological associations of the activating RAC1 P29S mutation in primary cutaneous melanoma. Pigment Cell Melanoma Res 2014; 27:1117-25. [PMID: 25043693 DOI: 10.1111/pcmr.12295] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Accepted: 07/16/2014] [Indexed: 01/12/2023]
Abstract
Activating mutations in the GTPase RAC1 are a recurrent event in cutaneous melanoma. We investigated the clinical and pathological associations of RAC1(P29S) in a cohort of 814 primary cutaneous melanomas with known BRAF and NRAS mutation status. The RAC1(P29S) mutation had a prevalence of 3.3% and was associated with increased thickness (OR=1.6 P = 0.001), increased mitotic rate (OR=1.3 P = 0.03), ulceration (OR=2.4 P = 0.04), nodular subtype (OR=3.4 P = 0.004), and nodal disease at diagnosis (OR=3.3 P = 0.006). BRAF mutant tumors were also associated with nodal metastases (OR=1.9 P = 0.004), despite being thinner at diagnosis than BRAF WT (median 1.2 mm versus 1.6 mm, P < 0.001). Immunohistochemical analysis of 51 melanomas revealed that 47% were immunoreactive for RAC1. Melanomas were more likely to show RAC1 immunoreactivity if they were BRAF mutant (OR=5.2 P = 0.01). RAC1 may therefore be important in regulating the early migration of BRAF mutant tumors. RAC1 mutations are infrequent in primary melanomas but may accelerate disease progression.
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Affiliation(s)
- Victoria J Mar
- Victorian Melanoma Service, Alfred Hospital, Melbourne, Vic., Australia; Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Vic., Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Vic., Australia
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Targeting RPL39 and MLF2 reduces tumor initiation and metastasis in breast cancer by inhibiting nitric oxide synthase signaling. Proc Natl Acad Sci U S A 2014; 111:8838-43. [PMID: 24876273 DOI: 10.1073/pnas.1320769111] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We previously described a gene signature for breast cancer stem cells (BCSCs) derived from patient biopsies. Selective shRNA knockdown identified ribosomal protein L39 (RPL39) and myeloid leukemia factor 2 (MLF2) as the top candidates that affect BCSC self-renewal. Knockdown of RPL39 and MLF2 by specific siRNA nanoparticles in patient-derived and human cancer xenografts reduced tumor volume and lung metastases with a concomitant decrease in BCSCs. RNA deep sequencing identified damaging mutations in both genes. These mutations were confirmed in patient lung metastases (n = 53) and were statistically associated with shorter median time to pulmonary metastasis. Both genes affect the nitric oxide synthase pathway and are altered by hypoxia. These findings support that extensive tumor heterogeneity exists within primary cancers; distinct subpopulations associated with stem-like properties have increased metastatic potential.
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Snapback primer mediated clamping PCR for detection of EGFR and KRAS mutations in NSCLC patients by high resolution melting analysis. BIOMED RESEARCH INTERNATIONAL 2014; 2014:407537. [PMID: 24883309 PMCID: PMC4026848 DOI: 10.1155/2014/407537] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2014] [Accepted: 03/21/2014] [Indexed: 11/17/2022]
Abstract
Assays for detecting somatic mutations are requested with higher sensitivity and more convenience. Here, we describe snapback primer mediated allele clamping enrichment polymerase chain reaction (SPACE-PCR), a novel form of PCR that amplifies minority alleles selectively from mixtures. We replaced regular PCR with SPACE-PCR before sequencing or genotyping assays to improve mutation detection sensitivity by up to 100-fold in detecting EGFR and KRAS somatic mutations. Combined SPACE-PCR with analysis of snapback primer by high resolution melting (SPACE-HRM), the high sensitive system that enables a closed-tube detection of mutations after isolating mutants has been established, as low as 1/105–1/1000 mutant samples can be diagnosed. And finally, in a double-blind experiment of 150 cases of non-small-cell lung cancer (NSCLC) patients, compared with direct DNA sequencing and ADX-EGFR/KRAS mutation detection kit, up to 25% of the PCR-direct sequencing negative cases turned out to be positive in SPACE-HRM mutation tests; the specificity is 100%. Results demonstrated that the SPACE-HRM system we set up is a high sensitive assay that can be used for EGFR and KRAS allele enrichment and reliable detection. We anticipate that the method will be employed in multiple applications in the clinic, including diagnosis, scanner recurrence monitoring, and treatment management.
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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: 17] [Impact Index Per Article: 1.7] [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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Targeted-capture massively-parallel sequencing enables robust detection of clinically informative mutations from formalin-fixed tumours. Sci Rep 2013; 3:3494. [PMID: 24336498 PMCID: PMC3861801 DOI: 10.1038/srep03494] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 11/27/2013] [Indexed: 01/09/2023] Open
Abstract
Massively parallel sequencing offers the ability to interrogate a tumour biopsy for multiple mutational changes. For clinical samples, methodologies must enable maximal extraction of available sequence information from formalin-fixed and paraffin-embedded (FFPE) material. We assessed the use of targeted capture for mutation detection in FFPE DNA. The capture probes targeted the coding region of all known kinase genes and selected oncogenes and tumour suppressor genes. Seven melanoma cell lines and matching FFPE xenograft DNAs were sequenced. An informatics pipeline was developed to identify variants and contaminating mouse reads. Concordance of 100% was observed between unfixed and formalin-fixed for reported COSMIC variants including BRAF V600E. mutations in genes not conventionally screened including ERBB4, ATM, STK11 and CDKN2A were readily detected. All regions were adequately covered with independent reads regardless of GC content. This study indicates that hybridisation capture is a robust approach for massively parallel sequencing of FFPE samples.
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