Journal of Pathology and Translational Medicine

Review

DNA-protein biomarkers for immunotherapy in the era of precision oncology: Binnari Kim, So Young Kang, Kyoung-Mee Kim; J Pathol Transl Med. 2021;55(1):26-32. Published online November 9, 2020; DOI: https://doi.org/10.4132/jptm.2020.09.23

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The use of biomarkers to guide patient and therapy selection has gained much attention to increase the scope and complexity of targeted therapy options and immunotherapy. Clinical trials provide a basis for discovery of biomarkers, which can then aid in development of new drugs. To that end, samples from cancer patients, including DNA, RNA, protein, and the metabolome isolated from cancer tissues and blood or urine, are analyzed in various ways to identify relevant biomarkers. In conjunction with nucleotide-based, high-throughput, next-generation sequencing techniques, therapy-guided biomarker assays relying on protein-based immunohistochemistry play a pivotal role in cancer care. In this review, we discuss the current knowledge regarding DNA and protein biomarkers for cancer immunotherapy

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Original Articles

Comparison of Three BRAF Mutation Tests in Formalin-Fixed Paraffin Embedded Clinical Samples: Soomin Ahn, Jeeyun Lee, Ji-Youn Sung, So Young Kang, Sang Yun Ha, Kee-Taek Jang, Yoon-La Choi, Jung-Sun Kim, Young Lyun Oh, Kyoung-Mee Kim; Korean J Pathol. 2013;47(4):348-354. Published online August 26, 2013; DOI: https://doi.org/10.4132/KoreanJPathol.2013.47.4.348

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Abstract PDF

Background

Recently, BRAF inhibitors showed dramatic treatment outcomes in BRAF V600 mutant melanoma. Therefore, the accuracy of BRAF mutation test is critical.

Methods

BRAF mutations were tested by dual-priming oligonucleotide-polymerase chain reaction (DPO-PCR), direct sequencing and subsequently retested with a real-time PCR assay, cobas 4800 V600 mutation test. In total, 64 tumors including 34 malignant melanomas and 16 papillary thyroid carcinomas were analyzed. DNA was extracted from formalin-fixed paraffin embedded tissue samples and the results of cobas test were directly compared with those of DPO-PCR and direct sequencing.

Results

BRAF mutations were found in 23 of 64 (35.9%) tumors. There was 9.4% discordance among 3 methods. Out of 6 discordant cases, 4 cases were melanomas; 3 cases were BRAF V600E detected only by cobas test, but were not detected by DPO-PCR and direct sequencing. One melanoma patient with BRAF mutation detected only by cobas test has been on vemurafenib treatment for 6 months and showed a dramatic response to vemurafenib. DPO-PCR failed to detect V600K mutation in one case identified by both direct sequencing and cobas test.

Conclusions

In direct comparison of the currently available DPO-PCR, direct sequencing and real-time cobas test for BRAF mutation, real-time PCR assay is the most sensitive method.

Citations

Citations to this article as recorded by

Preoperative BRAFV600E mutation detection in thyroid carcinoma by immunocytochemistry
Kristine Zøylner Swan, Stine Horskær Madsen, Steen Joop Bonnema, Viveque Egsgaard Nielsen, Marie Louise Jespersen
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A new primer construction technique that effectively increases amplification of rare mutant templates in samples
Jr-Kai Huang, Ling Fan, Tao-Yeuan Wang, Pao-Shu Wu
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BRAF and NRAS mutations and antitumor immunity in Korean malignant melanomas and their prognostic relevance: Gene set enrichment analysis and CIBERSORT analysis
Kyueng-Whan Min, Ji-Young Choe, Mi Jung Kwon, Hye Kyung Lee, Ho Suk Kang, Eun Sook Nam, Seong Jin Cho, Hye-Rim Park, Soo Kee Min, Jinwon Seo, Yun Joong Kim, Nan Young Kim, Ho Young Kim
Pathology - Research and Practice.2019; 215(12): 152671. CrossRef
The association between dermoscopic features and BRAF mutational status in cutaneous melanoma: Significance of the blue-white veil
Miquel Armengot-Carbó, Eduardo Nagore, Zaida García-Casado, Rafael Botella-Estrada
Journal of the American Academy of Dermatology.2018; 78(5): 920. CrossRef
Comparison of Five Different Assays for the Detection of BRAF Mutations in Formalin-Fixed Paraffin Embedded Tissues of Patients with Metastatic Melanoma
Claire Franczak, Julia Salleron, Cindy Dubois, Pierre Filhine-Trésarrieu, Agnès Leroux, Jean-Louis Merlin, Alexandre Harlé
Molecular Diagnosis & Therapy.2017; 21(2): 209. CrossRef
Validation of an NGS mutation detection panel for melanoma
Anne Reiman, Hugh Kikuchi, Daniela Scocchia, Peter Smith, Yee Wah Tsang, David Snead, Ian A Cree
BMC Cancer.2017;[Epub] CrossRef
Transformation to Small Cell Lung Cancer of Pulmonary Adenocarcinoma: Clinicopathologic Analysis of Six Cases
Soomin Ahn, Soo Hyun Hwang, Joungho Han, Yoon-La Choi, Se-Hoon Lee, Jin Seok Ahn, Keunchil Park, Myung-Ju Ahn, Woong-Yang Park
Journal of Pathology and Translational Medicine.2016; 50(4): 258. CrossRef
Immunohistochemistry with the anti-BRAF V600E (VE1) antibody: impact of pre-analytical conditions and concordance with DNA sequencing in colorectal and papillary thyroid carcinoma
Katerina Dvorak, Birte Aggeler, John Palting, Penny McKelvie, Andrew Ruszkiewicz, Paul Waring
Pathology.2014; 46(6): 509. CrossRef

The Frequency of BRAF Mutation in Very Small Papillary Thyroid Carcinomas.: Taeeun Kim, Ji Hyun Roh, Hee Jung Park, Jee Eun Kwon, So Young Kang, Yoon La Choi, Young Lyun Oh; Korean J Pathol. 2010;44(3):308-314.; DOI: https://doi.org/10.4132/KoreanJPathol.2010.44.3.308

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Abstract PDF

BACKGROUND
Papillary thyroid carcinoma (PTC) is the most common malignant tumor of the thyroid and BRAF (V600E) is the most frequent genetic alteration in PTCs. The aim of this study was to investigate the frequency of BRAF mutation, especially in very small PTCs.
METHODS
We analyzed the presence of the BRAF mutation in PTCs in subgroups defined by tumor size (0.5 cm intervals).
RESULTS
Of 140 patients, 85 (60.7%) showed a BRAF mutation. The frequency of BRAF mutation in the subgroup was: 45/70 (64.3%) in tumors less than 0.5 cm in size, 18/28 (64.3%) in 0.6-1 cm tumors, 10/22 (45.5%) in 1.1-1.5 cm tumors, and 12/20 (60.0%) in 1.6-2 cm tumors. There was no statistically significant association between BRAF mutation and tumor size (p = 0.44). Similarly, BRAF mutation was not statistically related to age, sex, stage, perithyroidal extension or lymph node metastasis. On multivariate logistic regression analysis, tumor sizes larger than 0.5 cm were associated with lymph node metastasis (odds ratio, 3.79; 95% confidence interval, 1.81 to 7.91; p < 0.01).
CONCLUSIONS
The BRAF mutation is not related to tumor size even in very small PTCs. The similar frequency of BRAF mutation in very small PTCs suggests that the BRAF mutation is a very early event in the tumorigenesis of PTCs.

Citations

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BRAF mutation detection in indeterminate thyroid cytology specimens
N. Paul Ohori, Rashi Singhal, Marina N. Nikiforova, Linwah Yip, Karen E. Schoedel, Christopher Coyne, Kelly L. McCoy, Shane O. LeBeau, Steven P. Hodak, Sally E. Carty, Yuri E. Nikiforov
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BRAFV600E mutation does not serve as a prognostic factor in Korean patients with papillary thyroid carcinoma
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Mutational Patterns and Novel Mutations of the BRAF Gene in a Large Cohort of Korean Patients with Papillary Thyroid Carcinoma
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