BRAF V600E mutation-specific antibody: A review

High CCR6 expression increases the risk of pediatric Langerhans cell histiocytosis

Langerhans cell histiocytosis (LCH) is a rare disorder that primarily affects children. Considering the intricate clinical presentation of this disease, the identification of specific biomarkers associated with susceptibility to LCH is essential for timely diagnosis and risk stratification. In this study, we examined the skin specimens from pediatric patients with LCH using RNAscope, immunohistochemistry, and sequencing techniques. We observed a notable correlation between elevated CCR6 expression in pathological tissues and LCH risk classification. Therefore, CCR6 expression may serve as an independent predictor of risk in clinical cases of LCH. Furthermore, the frequency of BRAF V600E mutations correlated with risk stratification. We discovered new mutations-H119Y and R108Q-in MAP2K1 in specimens with BRAF V600E mutations. Moreover, CCR6-positive tumors may exhibit an enhanced recruitment of lymphocytes expressing high CCR7 levels.

A multi-center cross-sectional investigation of BRAF V600E mutation in Ameloblastoma

Background

B-Raf proto-oncogene, serine/threonine kinase (BRAF) V600E mutation stands as a pivotal genetic alteration strongly associated with several neoplasms and contributes significantly to their pathogenesis as well as potential targeted treatment strategies.

Objective

This cross-sectional study aimed to determine the frequency of BRAF V600E mutation in ameloblastoma in a multi-center of Thailand.

Method

Anti-BRAF V600E (clone VE1) immunohistochemistry was performed on 227 conventional ameloblastoma (AM) and 113 unicystic ameloblastoma (UA) samples collected from four major dental schools located in the Central, North, South, and Northeast regions of Thailand. Tumor cells from randomly chosen AM cases were also micro-dissected from the FFPE sections and subjected to DNA sequencing to confirm the immunohistochemical results.

Results

BRAF V600E mutation was detected in 71.8% of the AM samples, while 65.5% of samples with UAs demonstrated BRAF V600E positivity. The BRAF V600E mutation was significantly different in the histological subtypes of AMs in the four centers (p = 0.012) and the location of UA in three centers (p = 0.013). There was no significant association between the BRAF V600E mutation and the location of ameloblastoma in the overall prevalence of our multi-center study; nonetheless, a statistically significant association was found between the BRAF V600E mutation and the mandible location of AMs from the Central Faculty of Dentistry, Mahidol University (MU) center (p = 0.033), as well as with the histological subtypes of AMs from the Southern Faculty of Dentistry, Prince of Songkla University (PSU) center (p = 0.009). No statistical association was observed between the BRAF V600E mutation and AM and UA recurrence (p = 0.920 and p = 0.312), respectively. The results of DNA sequencing performed in randomly selected 40 BRAF V600E-positive and 20 BRAF V600E-negative ameloblastoma tissues were in accordance with the immunohistochemical findings.

Conclusion

As a result of a notable prevalence of BRAF V600E in Thai individuals diagnosed with ameloblastoma, they may benefit from the utilization of adjunctive anti-BRAF targeted therapy for treatment.

Next-Generation Immunohistochemistry in Thyroid Neoplasm: A Practical Review on the Applications in Diagnosis and Molecular Classification

An integrative histologic and molecular classification of thyroid tumors has become clinically relevant due to the potential role in risk stratification and selection of targeted therapy. In this review, we discuss the applications of six "next-generation" immunohistochemical markers, namely BRAF V600E (clone VE1), RAS Q61R (clone SP174), pan-TRK (clone EPR 17341), ALK (clones 5A4 or D5F3), PTEN, and β-catenin in the pathologic diagnosis and molecular classification of thyroid tumors. These biomarkers allow the in situ examination of tumor tissue and assist in the diagnosis and pathologic staging by highlighting tumor border and patterns of invasion, identifying isolated tumor cells in lymph nodes, distinguishing lymph node metastasis from benign intranodal thyroid inclusions, and diagnosing multicentric thyroid carcinomas with discordant molecular drivers. Furthermore, it can identify specific thyroid neoplasms that may occur sporadically or may be associated with hereditary syndromes. The next-generation immunohistochemistry provides a novel solution to challenging issues in thyroid pathology and fast turn-around time for accurate molecular classification and further guidance of therapeutic management.

Mesenchymal Neoplasms of the Kidney and Perinephric Soft Tissue

Mesenchymal neoplasms of the kidney present challenges because they are uncommon, and because perinephric soft tissue biopsies are sometimes submitted as "kidney" masses, causing diagnostic confusion. Here, the author thoroughly reviews mesenchymal neoplasms of the kidney, including metanephric stromal tumor, classic and cellular congenital mesoblastic nephroma, anaplastic sarcoma and clear cell sarcoma of the kidney, malignant rhabdoid tumor, PEComa/angiomyolipoma, and anastomosing hemangioma. The author also discusses perinephric myxoid pseudotumor of fat, as well as diagnostic pitfalls presented by well-differentiated/dedifferentiated liposarcoma and sarcomatoid carcinoma.

Comprehensive Breslow thickness (BT)-based analysis to identify biological mechanisms associated with melanoma pathogenesis

Breslow thickness (BT), a parameter measuring the depth of invasion of abnormally proliferating melanocytes, is a key indicator of melanoma severity and prognosis. However, the mechanisms underlying the increase in BT remain elusive. Utilizing data from The Cancer Genome Atlas (TCGA) human skin cutaneous melanoma (SKCM), we identified a set of BT-related molecules and analyzed their expression and genomic heterogeneity across pan-cancerous and normal tissues. Through consensus clustering, we identified two distinct BT phenotypes in melanoma, which exhibited significant differences in clinical, genomic, and immune infiltration characteristics. High BT molecular expression was associated with reduced CD8+ T cell infiltration and poor immunotherapy response, potentially mediated by the Macrophage Migration Inhibitory Factor (MIF) signaling pathway. In vitro experiments confirmed that BT molecules, including TRIM29, SERPINB5, and RAB25, promoted melanoma development through distinct mechanisms. Notably, fibroblast-derived TRIM29 and B-cell-derived RAB25 interacted with SPP1+ monocytes/macrophages via different pathways. Our findings suggest that genomic variations leading to imbalanced expression of BT molecules across cancers contribute to increased BT, which is closely linked to an immunosuppressive microenvironment. The involvement of multiple cell types and complex intercellular interactions underscores the importance of evaluating dynamic cellular crosstalk in the tumor microenvironment to better understand BT increases and develop more effective immunotherapeutic strategies.

Dabrafenib Inhibits Egr-1-Mediated Adhesion of Thyroid Cancer Cells to Pulmonary Microvascular Endothelium

Cell-cell adhesion between thyroid tumor cells and pulmonary endothelial cells plays a critical role in the development of lung metastases from primary thyroid cancer. Dabrafenib, a selective inhibitor for B-RAF kinase, has been approved for cancer treatment. However, its effects on pulmonary metastases originating from primary thyroid cancer remain unclear. In this study, we demonstrate that conditioned medium (CM) from the thyroid cancer SW579 cell line significantly elevated the expression of pro-inflammatory cytokines HMGB-1, IL-1β, and MCP-1 in human pulmonary microvascular endothelial cells (HPMECs), which was notably reduced by Dabrafenib. Additionally, exposure to the thyroid cancer SW579 CM increased the expression of endothelial adhesion molecules VCAM-1 and ICAM-1, as well as the adhesion of thyroid cancer SW579 cells to HPMECs, both of which were prevented by Dabrafenib. We also found that Dabrafenib mitigated oxidative stress induced by SW579 CM, as evidenced by increased glutathione peroxidase (GSH-Px) activity and reduced malondialdehyde (MDA) levels. Further investigation revealed that Dabrafenib's beneficial effects were mediated through the inhibition of Egr-1, and overexpression of Egr-1 reversed Dabrafenib's protective effect on the adhesion of thyroid cancer cells to HPMECs. Based on these results, we propose that Dabrafenib may have the potential to prevent pulmonary metastases of thyroid cancer cells.

Expert consensus on the diagnosis and treatment of solid tumors with BRAF mutations

The BRAF gene is an important signaling molecule in human cells that is involved in the regulation of cell growth, differentiation, and survival. When the BRAF gene mutates, it can lead to abnormal activation of the signaling pathway, which promotes cell proliferation, inhibits cell apoptosis, and ultimately contributes to the occurrence and development of cancer. BRAF mutations are widely present in various cancers, including malignant melanoma, thyroid cancer, colorectal cancer, non-small cell lung cancer, and hairy cell leukemia, among others. BRAF is an important target for the treatment of various solid tumors, and targeted combination therapies, represented by BRAF inhibitors, have become one of the main treatment modalities for a variety of BRAF-mutation-positive solid tumors. Dabrafenib plus trametinib, as the first tumor-agnostic therapy, has been approved by the US Food and Drug Administration for the treatment of adult and pediatric patients aged 6 years and older harboring a BRAF V600E mutation with unresectable or metastatic solid tumors that have progressed following prior treatment and who have no satisfactory alternative treatment options. This is also the first time a BRAF/MEK inhibitor combination has been approved for use in pediatric patients. As research into the diagnosis and treatment of BRAF mutations advances, standardizing the detection of BRAF mutations and the clinical application of BRAF inhibitors becomes increasingly important. Therefore, we have established a universal and systematic strategy for diagnosing and treating solid tumors with BRAF mutations. In this expert consensus, we (1) summarize the epidemiology and clinical characteristics of BRAF mutations in different solid tumors, (2) provide recommendations for the selection of genetic testing methods and platforms, and (3) establish a universal strategy for the diagnosis and treatment of patients with solid tumors harboring BRAF mutations.

Real-World Incidence of Incident Noninfectious Uveitis in Patients Treated With BRAF Inhibitors: A Nationwide Clinical Cohort Study

PURPOSE

To compare the incidence of noninfectious uveitis in skin melanoma or lung cancer patients who received BRAF inhibitors with that in those who received immune checkpoint inhibitors (ICIs) or conventional cytotoxic chemotherapy.

DESIGN

Nationwide population-based retrospective clinical cohort study METHODS: From the Health Insurance Review and Assessment Service database of South Korea, we retrospectively defined 77,323 patients with skin melanoma or lung cancer who received BRAF inhibitor therapy (BRAF inhibitor-exposed group; n = 396), ICIs (ICI-exposed group; n = 22,474), or conventional cytotoxic chemotherapy (unexposed group; n = 54,453). We calculated the 1-year cumulative incidence of noninfectious uveitis in each group from the first day of BRAF inhibitor, ICI, or cytotoxic agent administration.

RESULTS

During the first year of treatment initiation, the cumulative incidence of uveitis was 0.33%, 0.35%, and 2.27% in the unexposed, ICI-exposed, and BRAF inhibitor-exposed groups, respectively. Adjusted hazard ratios (aHR) indicated a 7.52-fold and 5.68-fold increased risk of uveitis in the BRAF inhibitor-exposed group compared with that in the unexposed and ICI-exposed groups (95% confidence interval [CI] 3.83-14.75, P < .001 and 95% CI 2.81-11.47, P < .001, respectively). After 1:4 propensity score matching, aHRs showed a 35.51-fold and 15.80-fold increased risk (95% CI 4.49-280.48, P = .001 and 95% CI 1.76-141.00, P = .014) of uveitis and severe uveitis, respectively, in the BRAF inhibitor-exposed versus unexposed patients. Crossover analysis within the BRAF inhibitor-exposed group showed a 3.71-fold increase in uveitis risk during 1-year post index date in comparison with 1-year prior to index date (95% CI 1.03-13.40, P = .046). In the BRAF inhibitor-exposed group, female sex, chronic kidney disease, and melanoma were associated with a trend of increased, albeit nonsignificant, risk of uveitis.

CONCLUSIONS

Melanoma or lung cancer patients treated with BRAF inhibitors showed significantly higher risk of noninfectious uveitis than patients treated with conventional cytotoxic drugs or ICIs. These findings emphasize the importance of pretreatment patient education on BRAF-inhibitor-associated uveitis risk to enable prompt ophthalmic evaluation and treatment if symptoms arise during drug administration.

High-resolution and programmable RNA-IN and RNA-OUT genetic circuit in living mammalian cells

RNAs and their encoded proteins intricately regulate diverse cell types and states within the human body. Dysregulated RNA expressions or mutations can lead to various diseased cell states, including tumorigenesis. Detecting and manipulating these endogenous RNAs offers significant promise for restoring healthy cell states and targeting tumors both in research and clinical contexts. This study presents an RNA-IN and RNA-OUT genetic circuit capable dynamically sensing and manipulating any RNA target in a programmable manner. The RNA-IN module employes a programmable CRISPR-associated protease (CASP) complex for RNA detection, while the RNA-OUT module utilizes an engineered protease-responsive dCas9-VPR activator. Additionally, the CASP module can detect point mutations by harnessing an uncovered dual-nucleotide synergistic switching effect within the CASP complex, resulting in the amplification of point-mutation signals from initially undetectable levels (1.5-fold) to a remarkable 94-fold. We successfully showcase the circuit's ability to rewire endogenous RNA-IN signals to activate endogenous progesterone biosynthesis pathway, dynamically monitor adipogenic differentiation of mesenchymal stem cells (MSCs) and the epithelial-to-mesenchmal trans-differentiation, as well as selective killing of tumor cells. The programmable RNA-IN and RNA-OUT circuit exhibits tremendous potential for applications in gene therapy, biosensing and design of synthetic regulatory networks.

Clinical features and outcomes of 17 children with systemic juvenile xanthogranuloma (sJXG) including five complicated with hemophagocytic lymphohistiocytosis (HLH)

Juvenile xanthogranuloma (JXG) is primarily limited to the skin, and systemic JXG (sJXG) is rarely reported. Reports of sJXG patients with hemophagocytic lymphohistiocytosis (HLH) are particularly rare. Herein, we conducted a retrospective study of children diagnosed with sJXG in the Hematology Centre of Beijing Children's Hospital from Jan. 2016 to Dec. 2021. The clinical features, laboratory parameters, treatments and outcomes of 17 sJXG patients were investigated, including five complicated with HLH. All sJXG-HLH patients had intermittent fever, rash, hepatosplenomegaly, cytopenia and high levels of soluble CD25, but interferon-γ was almost normal. Patients with sJXG-HLH had a younger diagnosis age (P = 0.035) and were more likely to have skin, liver, and spleen involvement than those without HLH (P = 0.029, P = 0.003, P = 0.003, respectively). Corticosteroids and/or ruxolitinib could be used to control the hyperinflammatory status when HLH was diagnosed. The treatment of sJXG varied, including Langerhans cell histiocytosis (LCH)-based chemotherapy and targeted therapy. The overall response rate of sJXG for first-line and second-line chemotherapy was 50.0% (5/10) and 50% (4/8), respectively. Patients with BRAF V600E mutation showed a response to dabrafenib. There was no significant difference in the overall survival and progression-free survival between sJXG patients without and with HLH (P = 0.12 and P = 0.46, respectively). Therefore, LCH-based chemotherapy could serve as an effective treatment for sJXG patients, and dabrafenib, to some extent, showed efficacy in controlling sJXG in patients with BRAF V600E mutation. The prognosis of sJXG-HLH patients seemed to be comparable to patients without HLH.

Precision Drug Repurposing: A Deep Learning Toolkit for Identifying 34 Hyperpigmentation-Associated Genes and Optimizing Treatment Selection

BACKGROUND

Hyperpigmentation is a skin disorder characterized by a localized darkening of the skin due to increased melanin production. When patients fail first line topical treatments, secondary treatments such as chemical peels and lasers are offered. However, these interventions are not devoid of risks and are associated with postinflammatory hyperpigmentation. In the quest for novel therapeutic potentials, this study aims to investigate computational methods in the identification of new targeted therapies in the treatment of hyperpigmentation.

METHODS

We used a comprehensive approach, which integrated text mining, interpreting gene lists through enrichment analysis and integration of diverse biological information (GeneCodis), protein-protein association networks and functional enrichment analyses (STRING), and plug-in network centrality parameters (Cytoscape) to pinpoint genes closely associated with hyperpigmentation. Subsequently, analysis of drug-gene interactions to identify potential drugs (Cortellis) was utilized to select drugs targeting these identified genes. Lastly, we used Deep Learning Based Drug Repurposing Toolkit (DeepPurpose) to conduct drug-target interaction predictions to ultimately identify candidate drugs with the most promising binding affinities.

RESULTS

Thirty-four hyperpigmentation-related genes were identified by text mining. Eight key genes were highlighted by utilizing GeneCodis, STRING, Cytoscape, gene enrichment, and protein-protein interaction analysis. Thirty-five drugs targeting hyperpigmentation-associated genes were identified by Cortellis, and 29 drugs, including 16 M2PK1 inhibitors, 11 KRAS inhibitors, and 2 BRAF inhibitors were recommended by DeepPurpose.

CONCLUSIONS

The study highlights the promise of advanced computational methodology for identifying potential treatments for hyperpigmentation.

Transposase-assisted tagmentation: an economical and scalable strategy for single-worm whole-genome sequencing

AlphaMissense identifies 23 million human missense variants as likely pathogenic, but only 0.1% have been clinically classified. To experimentally validate these predictions, chemical mutagenesis presents a rapid, cost-effective method to produce billions of mutations in model organisms. However, the prohibitive costs and limitations in the throughput of whole-genome sequencing (WGS) technologies, crucial for variant identification, constrain its widespread application. Here, we introduce a Tn5 transposase-assisted tagmentation technique for conducting WGS in Caenorhabditis elegans, Escherichia coli, Saccharomyces cerevisiae, and Chlamydomonas reinhardtii. This method, demands merely 20 min of hands-on time for a single-worm or single-cell clones and incurs a cost below 10 US dollars. It effectively pinpoints causal mutations in mutants defective in cilia or neurotransmitter secretion and in mutants synthetically sterile with a variant analogous to the B-Raf Proto-oncogene, Serine/Threonine Kinase (BRAF) V600E mutation. Integrated with chemical mutagenesis, our approach can generate and identify missense variants economically and efficiently, facilitating experimental investigations of missense variants in diverse species.

The rapidly changing field of predictive biomarkers of non-small cell lung cancer

Lung cancer is a leading cause of cancer-related death worldwide in both men and women, however mortality in the US and EU are recently declining in parallel with the gradual cut of smoking prevalence. Consequently, the relative frequency of adenocarcinoma increased while that of squamous and small cell carcinomas declined. During the last two decades a plethora of targeted drug therapies have appeared for the treatment of metastasizing non-small cell lung carcinomas (NSCLC). Personalized oncology aims to precisely match patients to treatments with the highest potential of success. Extensive research is done to introduce biomarkers which can predict the effectiveness of a specific targeted therapeutic approach. The EGFR signaling pathway includes several sufficient targets for the treatment of human cancers including NSCLC. Lung adenocarcinoma may harbor both activating and resistance mutations of the EGFR gene, and further, mutations of KRAS and BRAF oncogenes. Less frequent but targetable genetic alterations include ALK, ROS1, RET gene rearrangements, and various alterations of MET proto-oncogene. In addition, the importance of anti-tumor immunity and of tumor microenvironment has become evident recently. Accumulation of mutations generally trigger tumor specific immune defense, but immune protection may be upregulated as an aggressive feature. The blockade of immune checkpoints results in potential reactivation of tumor cell killing and induces significant tumor regression in various tumor types, such as lung carcinoma. Therapeutic responses to anti PD1-PD-L1 treatment may correlate with the expression of PD-L1 by tumor cells. Due to the wide range of diagnostic and predictive features in lung cancer a plenty of tests are required from a single small biopsy or cytology specimen, which is challenged by major issues of sample quantity and quality. Thus, the efficacy of biomarker testing should be warranted by standardized policy and optimal material usage. In this review we aim to discuss major targeted therapy-related biomarkers in NSCLC and testing possibilities comprehensively.

Molecular Methods: Clinical Utilization and Designing a Test Menu

Pre-analytical factors in molecular oncology diagnostics are reviewed. Issues around sample collection, storage, and transport that might affect the stability of nucleic acids and the ability to perform molecular testing are addressed. In addition, molecular methods used commonly in clinical diagnostic laboratories, including newer technologies such as next-generation sequencing and digital droplet polymerase chain reaction, as well as their applications, are reviewed. Finally, we discuss considerations in designing a molecular test menu to deliver accurate and timely results in an efficient and cost-effective manner.

Immunohistochemical detection of cancer genetic abnormalities

New applications of immunohistochemistry (IHC) expand rapidly due to the development of molecular analyses and an increased understanding of molecular biology. IHC becomes much more important as a screening or even a confirmatory test for molecular changes in cancer. The past decades have witnessed the release of many immunohistochemical markers of the new generation. The novel markers have extensively high specificity and sensitivity for the detection of genetic abnormalities. In addition to diagnostic utility, IHC has been validated to be a practical tool in terms of treatments, especially molecular targeted therapy. In this review, we first describe the common alterations of protein IHC staining in human cancer: overexpression, underexpression, or loss of expression and altered staining pattern. Next, we examine the relationship between staining patterns and genetic aberrations regarding both conventional and novel IHC markers. We also mention current mutant-specific and fusion-specific antibodies and their concordance with molecular techniques. We then describe the basic molecular mechanisms from genetic events to corresponding protein expression patterns (membranous, cytoplasmic, or nuclear patterns). Finally, we shortly discuss the applications of immunohistochemistry in molecular targeted therapy. IHC markers can serve as a complementary or companion diagnostic test to provide valuable information for targeted therapy. Moreover, immunohistochemistry is also crucial as a companion diagnostic test in immunotherapy. The increased number of IHC novel antibodies is broadening its application in anti-cancer therapies.

Prognostic and predictive biomarkers in non-small cell lung carcinoma

Lung cancer is the most common cause of cancer-related deaths globally, with the highest mortality rates among both men and women. Most lung cancers are diagnosed at late stages, necessitating systemic therapy. Modern clinical management of lung cancer relies heavily upon application of biomarkers, which guide the selection of systemic treatment. Here, we provide an overview of currently approved and emerging biomarkers of non-small cell lung cancer (NSCLC), including EGFR, ALK, ROS1, RET, NTRK1-3, KRAS, BRAF, MET, ERBB2/HER2, NRG1, PD-L1, TROP2, and CEACAM5. For practical purposes, we divide these biomarkers into genomic and protein markers, based on the tested substrate. We review the biology and epidemiology of the genomic and proteomic biomarkers, discuss optimal diagnostic assays for their detection, and highlight their contribution to the contemporary clinical management of NSCLC.

Molecular Profiling of Syringocystadenocarcinoma Papilliferum Reveals RAS-Activating Mutations

CONTEXT.—

Syringocystadenocarcinoma papilliferum (SCACP) is a rare adnexal carcinoma and the malignant counterpart of syringocystadenoma papilliferum (SCAP), which is commonly located on the head and neck and may arise in association with a nevus sebaceus. RAS mutations have been identified in both SCAP and nevus sebaceus.

OBJECTIVE.—

To evaluate the clinicopathologic and molecular features of SCACPs, which have not been previously explored.

DESIGN.—

We obtained 11 SCACPs from 6 institutions and reviewed the clinicopathologic features. We also performed molecular profiling using next-generation sequencing.

RESULTS.—

The cohort comprised 6 women and 5 men with ages ranging from 29 to 96 years (mean, 73.6 years). The neoplasms occurred on the head and neck (n = 8; 73%) and extremities (n = 3; 27%). Three tumors possibly arose in a nevus sebaceus. A total of 4 cases showed at least carcinoma in situ (adenocarcinoma, n = 3; squamous cell carcinoma [SCC], n = 1), and 7 cases were invasive (SCC, n = 5; mixed adenocarcinoma + SCC, n = 2). A total of 8 of 11 cases (73%) had hot spot mutations consisting of HRAS (n = 4), KRAS (n = 1), BRAF (n = 1), TP53 (n = 4), ATM (n = 2), FLT3 (n = 1), CDKN2A (n = 1), and PTEN (n = 1). All 4 cases with HRAS mutations occurred on the head and neck, whereas the KRAS mutation occurred on the extremity.

CONCLUSIONS.—

RAS-activating mutations were detected in 50% of the cases, of which most (80%) involved HRAS and occurred on the head and neck, which shows overlapping features with SCAP, supporting that a subset may arise as a result of malignant transformation and likely an early oncogenic event.

Histiocytic neoplasms: a brief review and differential diagnosis

Histiocytic neoplasms (HNs) include juvenile xanthogranuloma, Erdheim-Chester disease, Rosai-Dorfman disease, ALK-positive histiocytosis, and histiocytic sarcoma in the 5th edition of the World Health Organization Classification of Haematolymphoid Tumours. These entities are clinicopathologically distinctive, and typical histological findings have been established. However, the common feature of a proliferation of histiocytic cells often leads to morphological overlap among HNs, and also necessitates a differential diagnosis from several non-HNs or non-neoplastic conditions. In this review, we provide a brief summary of the clinical findings, molecular features, histopathologies, and immunophenotypes of HNs, as well as to discuss their differential diagnosis.

Long term activity of vemurafenib in cancers with BRAF mutations: the ACSE basket study for advanced cancers other than BRAFV600-mutated melanoma

BACKGROUND

BRAF inhibitors are approved in BRAFV600-mutated metastatic melanoma, non-small-cell lung cancer (NSCLC), Erdheim-Chester disease (ECD), and thyroid cancer. We report here the efficacy, safety, and long-term results of single-agent vemurafenib given in the AcSé vemurafenib basket study to patients with various BRAF-mutated advanced tumours other than BRAFV600-mutated melanoma and NSCLC.

PATIENTS AND METHODS

Patients with advanced tumours other than BRAFV600E melanoma and progressing after standard treatment were eligible for inclusion in nine cohorts (including a miscellaneous cohort) and received oral vemurafenib 960 mg two times daily. The primary endpoint was the objective response rate (ORR) estimated with a Bayesian design. The secondary outcomes were disease control rate, duration of response, progression-free survival (PFS), overall survival (OS), and vemurafenib safety.

RESULTS

A total of 98 advanced patients with various solid or haematological cancers, 88 with BRAFV600 mutations and 10 with BRAFnonV600 mutations, were included. The median follow-up duration was 47.7 months. The Bayesian estimate of ORR was 89.7% in hairy cell leukaemias (HCLs), 33.3% in the glioblastomas cohort, 18.2% in cholangiocarcinomas, 80.0% in ECD, 50.0% in ovarian cancers, 50.0% in xanthoastrocytomas, 66.7% in gangliogliomas, and 60.0% in sarcomas. The median PFS of the whole series was 8.8 months. The 12-, 24-, and 36-month PFS rates were 42.2%, 23.8%, and 17.9%, respectively. Overall, 54 patients died with a median OS of 25.9 months, with a projected 4-year OS of 40%. Adverse events were similar to those previously reported with vemurafenib.

CONCLUSION

Responses and prolonged PFS were observed in many tumours with BRAF mutations, including HCL, ECD, ovarian carcinoma, gliomas, ganglioglioma, and sarcomas. Although not all cancer types responded, vemurafenib is an agnostic oncogene therapy of cancers.

Genetic profile of borderline ovarian tumors in the Lebanese population by whole-exome sequencing

OBJECTIVE

To assess the molecular profile of borderline ovarian tumors (BOT) in the Lebanese population by whole-exome sequencing and to correlate the results with the patients' clinical profiles.

METHODS

We included in this retrospective study 33 tumors belonging to 32 Lebanese women presenting with BOT, diagnosed at Hôtel Dieu de France. A total of 234 genes involved in different germinal and somatic types of cancer were analyzed using next-generation sequencing.

RESULTS

Molecular analysis of these tumors allowed us to detect mutations in genes involved in the mitogen-activated protein kinase cascade in 57.58% of BOT and to identify variants affecting the DNA repair mechanism in 63.89% of samples. Furthermore, our initial analysis revealed an association between defects in DNA double-strand break repair and the occurrence of mucinous BOT, in 75% of the cases.

CONCLUSION

This study reports the molecular profiles of BOT in the Lebanese population and compares them to the literature. This is the first study associating the DNA repair pathway to BOT.

Simplified methods for identifying subtypes of automatically maintained self-injury

Subtypes of automatically maintained self-injurious behavior (SIB) have been defined based on response patterns observed during the functional analysis, which are thought to reflect each subtype's distinct mechanisms. Current practice for identifying subtypes involves using structured criteria to identify whether SIB is automatically maintained, followed by the application of additional criteria to identify the subtype. We describe a series of studies directed at simplifying these methods to facilitate wider application of the subtyping model in research and practice. In Studies 1 and 2, we demonstrate the accuracy of modified criteria using the level of differentiation of SIB across the play and no-interaction conditions at distinguishing between two subtypes (i.e., Subtypes 1 and 2). We then demonstrate visual analysis (without structured criteria) can accurately identify SIB as automatically maintained in Study 3, which can be used in combination with level of differentiation to enable application of the subtyping model in practice.

PIP5K1C phosphoinositide kinase deficiency distinguishes PIKFYVE-dependent cancer cells from non-malignant cells

Although PIKFYVE phosphoinositide kinase inhibitors can selectively eliminate PIKFYVE-dependent human cancer cells in vitro and in vivo, the basis for this selectivity has remained elusive. Here we show that the sensitivity of cells to the PIKFYVE inhibitor WX8 is not linked to PIKFYVE expression, macroautophagic/autophagic flux, the BRAF^V600E mutation, or ambiguous inhibitor specificity. PIKFYVE dependence results from a deficiency in the PIP5K1C phosphoinositide kinase, an enzyme required for conversion of phosphatidylinositol-4-phosphate (PtdIns4P) into phosphatidylinositol-4,5-bisphosphate (PtdIns[4,5]P₂/PIP2), a phosphoinositide associated with lysosome homeostasis, endosome trafficking, and autophagy. PtdIns(4,5)P₂ is produced via two independent pathways. One requires PIP5K1C; the other requires PIKFYVE and PIP4K2C to convert PtdIns3P into PtdIns(4,5)P₂. In PIKFYVE-dependent cells, low concentrations of WX8 specifically inhibit PIKFYVE in situ, thereby increasing the level of its substrate PtdIns3P while suppressing PtdIns(4,5)P₂ synthesis and inhibiting lysosome function and cell proliferation. At higher concentrations, WX8 inhibits both PIKFYVE and PIP4K2C in situ, which amplifies these effects to further disrupt autophagy and induce cell death. WX8 did not alter PtdIns4P levels. Consequently, inhibition of PIP5K1C in WX8-resistant cells transformed them into sensitive cells, and overexpression of PIP5K1C in WX8-sensitive cells increased their resistance to WX8. This discovery suggests that PIKFYVE-dependent cancers could be identified clinically by low levels of PIP5K1C and treated with PIKFYVE inhibitors.

Evolution of the Targeted Therapy Landscape for Cholangiocarcinoma: Is Cholangiocarcinoma the 'NSCLC' of GI Oncology?

In the past two decades, molecular targeted therapy has revolutionized the treatment landscape of several malignancies. Lethal malignancies such as non-small cell lung cancer (NSCLC) have become a model for precision-matched immune- and gene-targeted therapies. Multiple small subgroups of NSCLC defined by their genomic aberrations are now recognized; remarkably, taken together, almost 70% of NSCLCs now have a druggable anomaly. Cholangiocarcinoma (CCA) is a rare tumor with a poor prognosis. Novel molecular alterations have been recently identified in patients with CCA, and the potential for targeted therapy is being realized. In 2019, a fibroblast growth factor receptor 2 (FGFR2) inhibitor, pemigatinib, was the first approved targeted therapy for patients with locally advanced or metastatic intrahepatic CCA who had FGFR2 gene fusions or rearrangement. More regulatory approvals for matched targeted therapies as second-line or subsequent treatments in advanced CCA followed, including additional drugs that target FGFR2 gene fusion/rearrangement. Recent tumor-agnostic approvals include (but are not limited to) drugs that target mutations/rearrangements in the following genes and are hence applicable to CCA: isocitrate dehydrogenase 1 (IDH1); neurotrophic tropomyosin-receptor kinase (NTRK); the V600E mutation of the BRAF gene (BRAFV600E); and high tumor mutational burden, high microsatellite instability, and gene mismatch repair-deficient (TMB-H/MSI-H/dMMR) tumors. Ongoing trials investigate HER2, RET, and non-BRAFV600E mutations in CCA and improvements in the efficacy and safety of new targeted treatments. This review aims to present the current status of molecularly matched targeted therapy for advanced CCA.

This is Your Thyroid on Drugs: Targetable Mutations and Fusions in Thyroid Carcinoma

This review aims to provide an overview of the molecular pathogenesis thyroid carcinomas, emphasizing genetic alterations that are therapeutically actionable. The main pathways in thyroid carcinogenesis are the MAPK and PI3K pathways. Point mutations and gene rearrangements affecting the pathway effectors and receptor tyrosine kinases are well-known drivers of thyroid cancer. Research over the past few decades has successfully introduced highly effective treatments for unresectable thyroid cancer, evolving from multi-kinase inhibitors to structurally selective agents, with constantly improving toxicity profiles and coverage of resistance mechanisms. The pros and cons of major laboratory techniques for therapeutic target identification are discussed.

Approved Small-Molecule ATP-Competitive Kinases Drugs Containing Indole/Azaindole/Oxindole Scaffolds: R&D and Binding Patterns Profiling

Kinases are among the most important families of biomolecules and play an essential role in the regulation of cell proliferation, apoptosis, metabolism, and other critical physiological processes. The dysregulation and gene mutation of kinases are linked to the occurrence and development of various human diseases, especially cancer. As a result, a growing number of small-molecule drugs based on kinase targets are being successfully developed and approved for the treatment of many diseases. The indole/azaindole/oxindole moieties are important key pharmacophores of many bioactive compounds and are generally used as excellent scaffolds for drug discovery in medicinal chemistry. To date, 30 ATP-competitive kinase inhibitors bearing the indole/azaindole/oxindole scaffold have been approved for the treatment of diseases. Herein, we summarize their research and development (R&D) process and describe their binding models to the ATP-binding sites of the target kinases. Moreover, we discuss the significant role of the indole/azaindole/oxindole skeletons in the interaction of their parent drug and target kinases, providing new medicinal chemistry inspiration and ideas for the subsequent development and optimization of kinase inhibitors.

Factors affecting the accuracy of anti-BRAF V600E immunohistochemistry results in ameloblastomas

BACKGROUND

There are still some controversies about the results of anti-BRAF V600E-specific antibody immunohistochemistry in ameloblastomas. This study aimed to examine the accuracy of V600E-specific antibody immunohistochemistry in detection of BRAF V600E mutation in ameloblastoma tissue sections of different ages.

METHODS

The BRAF V600E status of 64 ameloblastoma specimens was assessed using both Sanger sequencing and V600E-specific antibody immunohistochemistry, and the sensitivity, specificity, positive predictive value, and negative predictive value were calculated. The difference in V600E-specific antibody immunohistochemistry staining intensity among the three groups of ameloblastoma tissue blocks of different ages was evaluated by chi-square test. The consistency between V600E-specific antibody immunohistochemistry and DNA sequencing results and the V600E-specific antibody immunohistochemistry staining intensity of 15 paired newly-cut and 3-month storage sections of the same 15 ameloblastomas were also compared.

RESULTS

For detection of BRAF V600E mutation, the V600E-specific antibody immunohistochemistry had high sensitivity (98.21% 55/56), specificity (87.5% 7/8), positive predictive value (98.21% 55/56), and negative predictive value (87.5% 7/8). Heterogeneity of the staining intensity was observed in the same tissue section, but all or none expression pattern was noticed in the solid tumor nests. The storage time of paraffin tissue blocks ranging from 2 to 14 years did not affect the V600E-specific antibody-positive staining intensity. However, the three-month storage sections showed a significant diminishment of V600E-specific antibody-positive staining signals.

CONCLUSIONS

The BRAF V600E-specific antibody immunohistochemistry is suitable for routine detection of BRAF V600E mutation in ameloblastomas. The all or none expression pattern suggests the BRAF V600E mutation may be an early event in the pathogenesis of ameloblastoma.

Prognostic Significance of BRAF V600E Mutation and CPSF2 Protein Expression in Papillary Thyroid Cancer

The early-stage diagnosis of papillary thyroid cancer (PTC) has significantly increased in incidence worldwide without any beneficial impact on survival. In order to improve the risk assessment in PTC, we have conducted a retrospective study in which we analyzed the BRAF V600E mutation and CPSF2 protein expression as prognostic markers on archival tissue samples of 49 patients without (control group) and 97 patients with (study group) PTC metastases in the cervical lymph nodes at the time of initial diagnosis. Our aim was to correlate the BRAF V600E mutation and the expression of CPSF2 protein with the clinical and pathological features of PTC. The expression of CPSF2 protein was evaluated via immunohistochemistry and graded semi-quantitatively. The presence of the BRAF V600E mutation was determined via real-time polymerase chain reac-tion (PCR). CPSF2 protein < 3+ intensity expression was correlated with more frequent recurrences (Fisher-Freeman-Halton exact test; p = 0.010; 95% CI: 1.26−22.03), and patients who presented with the BRAF V600E mutation and CPSF2 protein expression < 3+ intensity had shorter disease-free survival (log-rank test; 105.0 months vs. 146.6 months; p < 0.001; HR 8.32, 95% CI: 2.91−23.83), whereas patients with PTC who had CPSF2 expression 3+ had longer disease-free survival in correlation with other lower intensity expressions of CPSF2 protein (log-rank test; 139.7 months vs. 129.6 months; p = 0.008). The multivariate analysis showed that younger patients with CPSF2 protein expression <3+ and the BRAF V600E mutation are at an increased risk for recurrence and require more intensive monitoring (Cox proportional hazards regression model; X2 = 17.5, df = 10, p = 0.025). Our results correlate the BRAF V600E mutation and CPSF2 protein expression with recurrence and disease-free survival as relevant prognostic factors for PTC.

Molecular Target Interactions of Quinoline Derivatives as Anticancer Agents: A Review

One of the leading causes of death worldwide is cancer, which poses substantial risks to both society and an individual's life. Cancer therapy is still challenging, despite developments in the field and continued research into cancer prevention. The search for novel anticancer active agents with a broader cytotoxicity range is therefore continuously ongoing. The benzene ring gets fused to a pyridine ring at two carbon atoms close to one another to form the double ring structure of the heterocyclic aromatic nitrogen molecule known as quinoline (1-azanaphthalene). Quinoline derivatives contain a wide range of pharmacological activities, including antitubercular, antifungal, antibacterial, and antimalarial properties. Quinoline derivatives have also been shown to have anticancer properties. There are many quinoline derivatives widely available as anticancer drugs that act via a variety of mechanisms on various molecular targets, such as inhibition of topoisomerase, inhibition of tyrosine kinases, inhibition of heat shock protein 90 (Hsp90), inhibition of histone deacetylases (HDACs), inhibition of cell cycle arrest and apoptosis, and inhibition of tubulin polymerization.

Kinase Fusion-Related Thyroid Carcinomas: Towards Predictive Models for Advanced Actionable Diagnostics

The past decade has brought significant advances in our understanding of the molecular mechanisms of thyroid carcinogenesis. Among thyroid carcinomas, the most successful class of targeted therapeutics appears to be selective kinase inhibitors. Actionable kinase fusions arise in around 10-15% of cases of thyroid cancer, a significant subset. A cohort of molecular testing platforms, both commercial and laboratory-derived, has been introduced into clinical practice to identify patients with targetable tumors, requiring pathologists to develop an integrative approach that utilizes traditional diagnostic cytopathology and histopathology, immunohistochemistry, and cutting-edge molecular assays for optimal diagnostic, prognostic, and therapeutic efficiency. Furthermore, there has been increasing scrutiny of the clinical behavior of kinase fusion-driven thyroid carcinoma (KFTC), still regarded as papillary thyroid carcinomas, and in characterizing molecular predictors of kinase inhibitor resistance with an aim to establish standardized, evidence-based treatment regimens. This review presents an overview of the current literature on the clinicopathologic and molecular features of KFTC as well as the latest investigational progress and encountered challenges for this unique subset of thyroid neoplasias.

BRAF V600E Mutation in Ameloblastoma: A Systematic Review and Meta-Analysis

The discovery that ameloblastoma has a high mutation incidence of BRAF V600E may enable a better investigation of pathophysiology. However, there is inconsistent evidence regarding this mutation occurrence and its association with clinical information. This systematic review and meta-analysis aim to pool the overall mutation prevalence of BRAF V600E in reported ameloblastoma cases and to determine its association with patient demographic and clinicopathological features. Following the PRISMA guidelines, a comprehensive article search was conducted through four databases (Scopus, Google Scholar, PubMed, and Web of Science). Seventeen articles between 2014 and 2022 met the inclusion criteria with 833 ameloblastoma cases. For each included study, the significance of BRAF V600E on the outcome parameters was determined using odd ratios and 95% confidence intervals. Meta-analysis prevalence of BRAF V600E in ameloblastoma was 70.49%, and a significant meta-analysis association was reported for those younger than 54 years old and in the mandible. On the contrary, other factors, such as sex, histological variants, and recurrence, were insignificant. As a result of the significant outcome of BRAF V600E mutation in ameloblastoma pathogenesis, targeted therapy formulation can be developed with this handful of evidence.

Primary squamous cell carcinoma of thyroid gland: 11 case reports and a population-based study

Background

Primary squamous cell carcinoma of thyroid gland (PSCCT) is a highly aggressive malignant tumor associated with a poor prognosis. Due to the rare case, there is a knowledge gap on the features of PSCCT. There is limited understanding of the treatment and molecular biology of this tumor. More genomic work and relevant perspective work need to be done.

Methods

We retrospectively reviewed the medical information of patients with PSCCT diagnosed from December 2009 to December 2020 at The First Affiliated Hospital of Guangxi Medical University. In addition, we conducted an electronic search of the paper in CNKI, Wanfang, VIP, PubMed, Embase, Web of Science, and ProQuest databases by recently updated articles. Survival analysis was conducted using the Kaplan–Meier method.

Results

There were only 11 patients met the study’s inclusion criteria in our institution. The patients ranged in age from 25 to 68 years old and female preponderance (M:F = 1:1.7). The median survival time was 6 months, and 1-year survival rate was 33.3%. Fifty-three patients’ individual data from 45 articles were selected for analysis. The median age at diagnosis was 63 years and female preponderance (M:F = 1:2.5). The commonest complaint was the anterior neck mass (77.3%), followed by hoarseness (32.1%). The median survival time was 9 months, and the overall 1-, 2-, and 5-year survival rate was 39.8%, 33.7%, and 26.9%, respectively. The log-rank method shows that age, tumor size, lymph node status, M stage, surgical range, and tracheal status were the relevant factors affecting the prognosis. In contrast, gender, treatment modality, and resection margin were not prognostic factors. On multivariable analysis, age and M stage were associated with overall survival.

Conclusion

The median overall survival was 6–9 months of PSCCT. Age and M stage are predictors of PSSCT.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12957-022-02814-9.

The diagnostic utility of BRAF VE1 mutation-specific immunohistochemistry in ameloblastoma

Ameloblastoma is a benign, locally aggressive odontogenic neoplasm with variable solid and cystic morphology. On account of its histologic variety, diagnostically challenging cases can bear resemblance to odontogenic keratocyst/keratocystic odontogenic tumor (KCOT) or dentigerous cyst (DC). BRAF^V600E mutation has been reported to be specific for and frequent in ameloblastoma, and this study evaluated the usefulness of immunohistochemistry (IHC) using the BRAF VE1 mutant-specific antibody as a diagnostic adjunct in this setting. We investigated 46 ameloblastomas, 30 KCOTs, and 30 DCs. BRAF VE1 IHC was performed on all cases and allele-specific polymerase chain reaction (AS-PCR) for BRAF^V600E mutation was performed on 30 ameloblastomas and any IHC-positive KCOT/DC. BRAF VE1 IHC was positive in 31/37 (83.8%) mandibular ameloblastomas but not in any maxillary ameloblastomas (0/9), KCOT (0/30), or DC (0/30). Equivocal staining was seen in 1/37 (3.3%) mandibular ameloblastomas. Of the 30 ameloblastomas subjected to AS-PCR, BRAF^V600E mutation was identified in 19/23 (82.6%) mandibular ameloblastomas and 0/7 (0.0%) maxillary ameloblastomas. BRAF^V600E mutant ameloblastomas were positive by IHC in 18/19 (94.7%) cases and equivocal in 1/19 (5.3%) cases. All 11 (100.0%) BRAF-wild type ameloblastomas were negative by IHC. BRAF VE1 is an excellent tool for the diagnosis of mandibular ameloblastoma but of limited utility in the maxilla, where it less commonly occurs and where BRAF^V600E mutation is considerably less frequent.

Vulvar Malignant Melanoma: A Narrative Review

Malignant melanoma is a fatal disease that affects all skin sites. Among these, vulvar melanoma (VM) is a rare gynecological condition that accounts for 5% of all vulvar neoplasms. VM primarily affects older Caucasian women and its relationship to sun exposure is undefined. Diagnosis is defined by biopsy but many clinical, dermatoscopic, and confocal microscopic features can guide doctors. The molecular profile is characterized by the KIT mutation, revealed by all of the technologies that are used (classical sequencing, next-generation sequencing, and immunohistochemical staining). BRAF and NRAS mutations are also common in VM. All of these mutations are possible therapeutic targets. Today, surgery remains the first treatment choice for primary VM. The role of neoadjuvant and adjuvant therapy is scarce and the treatment of relapses is widely debated.

Ophthalmic adverse effects of BRAF inhibitors

To determine the frequency, characteristics, and clinical course of ophthalmic side effects associated with systemic BRAF inhibitor therapy. Medical records of patients taking BRAF inhibitors for the treatment of systemic malignances at Mayo Clinic, Rochester from 01/01/2010 to 08/30/2021, were retrospectively reviewed. Of 901 patients, 14 (1.6%) patients experienced an ophthalmic side effect. Mean age at presentation of the side effect was 60 years (median 59, range 50-80) and 11 (79%) were male. The most common side effect was uveitis in 7 (50%) patients, followed by dry eye in 4 (29%) patients, and central serous chorioretinopathy in 2 (14%) patients, with singular cases of cranial nerve VI palsy and conjunctival edema. A comparison between individual BRAF inhibitors (vemurafenib vs. dabrafenib vs. encorafenib) revealed that patients taking encorafenib had a shorter interval to any ophthalmic adverse event (mean 55.6 vs. 9.8 vs. 4.0 months, p  =  0.03) and were the only patients to experience documented dry eye syndrome (DES) in this series. Outcomes were known in 13 (93%) patients, and ophthalmic adverse effects resolved or were controlled without discontinuing therapy in 10 (77%). Uveitis was successfully treated with topical corticosteroids in 4 patients, while 3 patients with refractory uveitis (2 with panuveitis and 1 with unspecified uveitis) required discontinuation of BRAF inhibitor therapy. Ophthalmic adverse events related to systemic BRAF inhibitor use are rare, with estimated frequency of 1.6%. Most events can be treated with local ophthalmic therapy. BRAF inhibitors provide life-saving therapy, and their discontinuation should be avoided.

The Value of BRAF VE1 Immunoexpression in Pediatric Langerhans Cell Histiocytosis

IntroductionVE1 is a monoclonal antibody detecting mutant BRAF V600E protein by immunohistochemistry (IHC) with a high concordance rate with molecular analysis in many cancers. Materials and methods: BRAF V600E mutation was assessed on 94 pediatric LCH patients using sequencing analysis and VE1 immunohistochemistry with stringent and lenient-scoring criteria. Results: BRAF V600E mutation exon 15 was detected by sequencing in 47.9% of LCH cases. BRAF V600E mutation rate in multiple-system LCH was 65.2%, significantly higher than in single-system LCH (p = .001). VE1 assays showed 35.6% sensitivity, 75.5% specificity (Stringent criteria), and 91.1% sensitivity, 35.7% specificity (Lenient criteria). Conclusions: The proportion of BRAF V600E mutational status was relatively high and related to high-risk LCH. Molecular assays for BRAF mutation detection are preferred in LCH lesions. VE1 is not ready as an alternative option for LCH BRAF testing.

Diagnostic Strategies for Urologic Cancer Using Expression Analysis of Various Oncogenic Surveillance Molecules—From Non-Coding Small RNAs to Cancer-Specific Proteins

Urinary-tract-related tumors are prone to simultaneous or heterogeneous multiple tumor development within the primary organ. Urologic tumors have a very high risk of recurrence in the long and short term. This may be related to the disruption of homeostasis on the genetic level, such as the induction of genetic mutations due to exposure to various carcinogenic factors and the disruption of cancer suppressor gene functions. It is essential to detect the cancer progression signals caused by genetic abnormalities and find treatment therapies. In this review, we discuss the usefulness of tumor-expressing clinical biomarkers for predicting cancer progression. Furthermore, we discuss various factors associated with disturbed intracellular signals and those targeted by microRNAs, which are representative of non-coding small RNAs.

Spectrum of BRAF Aberrations and Its Potential Clinical Implications: Insights From Integrative Pan-Cancer Analysis

B-Raf proto-oncogene serine/threonine-protein kinase (BRAF) is frequently altered in multiple cancer types, and BRAF V600 mutations act as a prime target for precision therapy. Although emerging evidence has investigated the role of BRAF, the comprehensive profiling of BRAF expression, alteration and clinical implications across various cancer types has not been reported. In this study, we used the TCGA dataset, covering 10,967 tumor samples across 32 cancer types, to analyze BRAF abnormal expression, DNA methylation, alterations (mutations and amplification/deletion), and their associations with patient survival. The results showed that BRAF expression, alteration frequency, mutation site distribution, and DNA methylation patterns varied tremendously among different cancer types. The expression of BRAF was found higher in PCPG and CHOL, and lower in TGCT and UCS compared to normal tissues. In terms of pathological stages, BRAF expression was significantly differentially expressed in COAD, KIRC, LUSC, and OV. The methylation levels of BRAF were significantly lower in LUSC, HNSC, and UCEC compared to normal tissue. The expression of BRAF and downstream gene (ETS2) was negatively correlated with methylation levels in various cancers. The overall somatic mutation frequency of BRAF was 7.7% for all cancer samples. Most fusion transcripts were found in THCA and SKCM with distinct fusion patterns. The majority of BRAF mutations were oncogenic and mainly distributed in the Pkinase_Tyr domain of THCA, SKCM, COADREAD, and LUAD. The BRAF mutations were divided into five levels according to the clinical targeted therapy implication. The results showed level 1 was mainly distributed in SKCM, COADREAD, and LUAD, while level 3B in THCA. The overall BRAF CNV frequency was about 42.7%, most of which was gain (75.9%), common in GBM, TGCT, and KIRP. In addition, the forest plot showed that increased BRAF expression was associated with poor patient overall survival in LIHC, OV, and UCEC. Taken together, this study provided a novel insight into the full alteration spectrum of BRAF and its implications for treatment and prognosis.

A common presentation - turning out as uncommon diagnosis: from hip pain to Langerhans cell histiocytosis: Adult High-Risk Multi-System Langerhans Cell Histiocytosis

Langerhans cell histiocytosis (LCH) is an uncommon clonal proliferation of myeloid progenitor cells, it is especially rare in adults. We present a case of multi-system LCH in a 53-year-old woman, the sole symptom of which was prolonged, non-resolving hip pain for 18 months prior to the diagnosis. Initial evaluation included imaging studies aimed at identifying a presumed local etiology. X-ray demonstrated non-specific arthritic changes on the left femur. Computed tomography (CT) and magnetic resonance imaging (MRI) scans identified a lytic lesion at the same location, warranting a systemic workup. After non-invasive investigations failed to reveal the underlying etiology, a biopsy was performed, revealing cores of Langerhans cells that stained positive for both CD1a and langerin. These findings verified the surprising, uncommon diagnosis of LCH. A comprehensive workup was conducted in order to determine the extent of the disease and its molecular nature - revealing a BRAF^V600E-positive, high-risk, multi-system LCH with skeletal, lung and liver involvement.

Somatic activating BRAF variants cause isolated lymphatic malformations

Somatic activating variants in PIK3CA, the gene that encodes the p110α catalytic subunit of phosphatidylinositol 3-kinase (PI3K), have been previously detected in ∼80% of lymphatic malformations (LMs).1 , 2 We report the presence of somatic activating variants in BRAF in individuals with LMs that do not possess pathogenic PIK3CA variants. The BRAF substitution p.Val600Glu (c.1799T>A), one of the most common driver mutations in cancer, was detected in multiple individuals with LMs. Histology revealed abnormal lymphatic channels with immunopositivity for BRAFV600E in endothelial cells that was otherwise indistinguishable from PIK3CA-positive LM. The finding that BRAF variants contribute to low-flow LMs increases the complexity of prior models associating low-flow vascular malformations (LM and venous malformations) with mutations in the PI3K-AKT-MTOR and high-flow vascular malformations (arteriovenous malformations) with mutations in the RAS-mitogen-activated protein kinase (MAPK) pathway.3 In addition, this work highlights the importance of genetic diagnosis prior to initiating medical therapy as more studies examine therapeutics for individuals with vascular malformations.

Comparison of Two Rapid Assays for the Detection of BRAF V600 Mutations in Metastatic Melanoma including Positive Sentinel Lymph Nodes

Testing for the BRAF mutation is mandatory for the management of patients with locally advanced or metastatic melanoma. Molecular analysis based on DNA sequencing remains the gold-standard method for the screening of the different BRAF mutations. These methods must be rapid, sensitive, and specific enough to allow optimal therapeutic management in daily practice and also to include patients in clinical trials. Here, we compared the Idylla BRAF Mutation Test and the anti-BRAF V600E (clone VE1) immunohistochemistry (IHC) in 90 melanoma samples, with a focus on a challenging cohort of 32 positive sentinel lymph nodes. The BRAF status was assessed with both methods independently of the percentage of tumor cells. The concordance rate was calculated excluding both non-contributory analyses and BRAFV600K/R/M mutants due to the specific V600E-IHC test design. The incidence of the BRAFV600E mutation was 33% with both BRAF Idylla and BRAF IHC. The agreement rate was 91% (72/79). Although the agreement rate was high, we suggest that the use of IHC is more suitable for rapid BRAF testing on sentinel lymph node biopsies when associated with a low percentage and scattered tumor cells, which gave a high risk of non-contributory analysis and/or false negative results with the Idylla^TMBRAF Mutation Test.

N-terminus DUX4-immunohistochemistry is a reliable methodology for the diagnosis of DUX4-fused B-lymphoblastic leukemia/lymphoma (N-terminus DUX4 IHC for DUX4-fused B-ALL)

B-lymphoblastic leukemia/lymphoma (B-ALL) is the most common pediatric malignancy and the most commonly diagnosed adult lymphoblastic leukemia. Recent advances have broadened the spectrum of B-ALL, with DUX4 gene fusions implicated in a subclass occurring in adolescents and young adults and harboring a favorable prognosis. DUX4 fusions have been challenging to identify. We aimed to determine whether expression of the DUX4 oncoprotein, as detected by targeted immunohistochemistry, might serve as a surrogate for molecular detection of DUX4 fusions in B-ALL. A cohort of investigational B-ALLs was generated with enrichment for DUX4 fusions by inclusion of cases with characteristic demographic features and immunophenotypic properties. B-ALLs with mutually exclusive cytogenetics were collected. Immunohistochemical staining by a monoclonal antibody raised against the N-terminus of the DUX4 protein was performed. N-DUX4 immunohistochemistry demonstrated strong, crisp nuclear staining in blasts of seven investigational cases, six of which had nucleic acid material available for molecular evaluation. Five of these cases demonstrated RNA-seq DUX4-fusion positivity. One N-DUX4 immunohistochemistry positive case lacked a definitive DUX4-fusion by RNA-seq, though demonstrated a gene expression profile characteristic of DUX4-rearranged B-ALLs, a CD2+ immunophenotype, and a lack of staining by C-terminus DUX4 antibody immunohistochemistry. At least 83.3% [5/6] positive predictive value. N-DUX4 immunohistochemistry was negative in blasts of three RNA-seq DUX4-fusion negative cases (3/3; 100% negative predictive value). B-ALLs with mutually-exclusive cytogenetic profiles were all N-DUX4 negative (0/10, specificity 100%). N-DUX4 immunohistochemistry is reliable for the distinction of DUX4-rearranged B-ALLs from other B-ALLs. We recommend its use for subclassification of B-ALLs in adolescents and young adults and in B-ALLs that remain "not otherwise specified." This article is protected by copyright. All rights reserved.

Precision cancer genome testing needs proficiency testing involving all stakeholders

To implement precision oncology, analytical validity as well as clinical validity and utility are important. However, proficiency testing (PT) to assess validity has not yet been systematically performed in Japan. To investigate the quality of next-generation sequencing (NGS) platforms and cancer genome testing prevalent in laboratories, we performed pilot PT using patient samples. We prepared genomic DNA from the cancer tissue and peripheral blood of 5 cancer patients and distributed these to 15 laboratories. Most participating laboratories successfully identified the pathogenic variants, except for two closely located KRAS variants and 25 bp delins in EGFR. Conversely, the EGFR L858R variant was successfully identified, and the allele frequency was similar for all the laboratories. A high DNA integrity number led to excellent depth and reliable NGS results. By conducting this pilot study using patient samples, we were able to obtain a glimpse of the current status of cancer genome testing at participating laboratories. To enhance domestic cancer genome testing, it is important to conduct local PT and to involve the parties concerned as organizers and participants.

Relevance of BRAF Subcellular Localization and Its Interaction with KRAS and KIT Mutations in Skin Melanoma

Although skin melanoma (SKM) represents only one-quarter of newly diagnosed skin malignant tumors, it presents a high mortality rate. Hence, new prognostic and therapeutic tools need to be developed. This study focused on investigating the prognostic value of the subcellular expression of BRAF, KRAS, and KIT in SKM in correlation with their gene-encoding interactions. In silico analysis of the abovementioned gene interactions, along with their mRNA expression, was conducted, and the results were validated at the protein level using immunohistochemical (IHC) stains. For IHC expression, the encoded protein expressions were checked on 96 consecutive SKMs and 30 nevi. The UALCAN database showed no prognostic value for the mRNA expression level of KRAS and BRAF and demonstrated a longer survival for patients with low mRNA expression of KIT in SKMs. IHC examinations of SKMs confirmed the UALCAN data and showed that KIT expression was inversely correlated with ulceration, Breslow index, mitotic rate, and pT stage. KRAS expression was also found to be inversely correlated with ulceration and perineural invasion. When the subcellular expression of BRAF protein was recorded (nuclear vs. cytoplasmatic vs. mixed nucleus + cytoplasm), a direct correlation was emphasized between nuclear positivity and lymphovascular or perineural invasion. The independent prognostic value was demonstrated for mixed expression of the BRAF protein in SKM. BRAF cytoplasmic predominance, in association with KIT's IHC positivity, was more frequently observed in early-stage nonulcerated SKMs, which displayed a low mitotic rate and a late death event. The present study firstly verified the possible prognostic value of BRAF subcellular localization in SKMs. A low mRNA expression or IHC cytoplasmic positivity for KIT and BRAF might be used as a positive prognostic parameter of SKM. SKM's BRAF nuclear positivity needs to be evaluated in further studies as a possible indicator of perineural and lymphovascular invasion.

Diagnostic Efficacy of BRAFV600E Immunocytochemistry in Thyroid Aspirates in Bethesda Category IV and Papillary Thyroid Carcinoma

Background

In papillary thyroid carcinoma (PTC), BRAFV600E is a common mutation and is associated with aggressive clinical behaviour. Immunocytochemistry (ICC) and molecular testing are recommended in the Bethesda System for Reporting Thyroid Cytopathology 2017 (TBSRTC) category III, IV and V.

Aims

The current study aimed to evaluate the diagnostic efficacy of conventional FNAC versus FNAC with BRAFV600E immunostaining in cases of TBSRTC category IV, cases of suspicious for PTC and cases of PTC.

Methods and Material

The study included a prospective case series of 45 patients with clinically palpable thyroid nodules with TBSRTC category IV, category V (suspicious for PTC) and PTC. The corresponding histology specimens of all the 45 cases were also analyzed. Immunostaining for BRAFV600E was performed on FNAC cell blocks and their corresponding histology sections using anti-BRAF (VE1) clone (Ventana). The diagnostic efficacy of the BRAFV600E immunostaining was compared on cytological specimens with histological specimens.

Results

BRAFV600E immunostaining helped to improve the sensitivity of the cytology to confirm the PTC as a diagnostic aid for thyroid FNAs. Cytology alone had a sensitivity of 62.96% and a lower specificity of 60.70%. The combination of both the tests together provided 84.62% sensitivity and much higher specificity of 100%. PPV was also increased to 100% and NPV was raised 94.12%.

Conclusions

The performance of BRAFV600E immunostaining on the cytological specimen is a rapid, simple and cost-effective test and could be considered in TBSRTC category IV and suspicious and malignant cases of PTC.

Immunohistochemistry Critical Assay Performance Controls (ICAPC) Reduce Interobserver Variability in the Interpretation of BRAFV600E Immunohistochemistry

The utility of prognostic and predictive immunohistochemistry biomarkers in the context of cancer is plagued by inconsistent interpretation of results which can lead to poor rates of adoption or inappropriate use of novel therapeutic strategies. To monitor immunohistochemistry assay performance, a new on-slide control motif, Immunohistochemistry Critical Assay Performance Controls (ICAPC) was developed. We hypothesized that the use of these controls by the diagnosing pathologist to interpret BRAFV600E would result in reduced interobserver and intraobserver interpretation errors. A cross-sectional, sequentially obtained sample of surgical pathology cases stained for BRAFV600E was assembled from a single hospital in Vancouver, British Columbia. Half of the cases had normal on-slide controls and the remainder with ICAPC. Results from 6 independent and blinded readers were compared with each other and to the gold-standard pathologic diagnosis with the goal of demonstrating superior interrater agreement with ICAPC relative to standard on-slide controls. Cohen's κ was used to compute pair-wise reader agreements, whereas Fleiss' κ was used to compare to the gold standard. The implementation of ICAPC resulted in statistically significant improvements in the interobserver agreement of BRAF mutation status ascertained by BRAFV600E immunohistochemistry. Half of the readers demonstrated significant improvements in agreement with the gold-standard diagnosis with the addition of ICAPC. Across all readers, the mean increase in κ was 0.14 with a 95% confidence interval of 0.01-0.28 (P=0.04). This study demonstrates that the addition of ICAPC serves to significantly reduce interobserver variability in the assessment of BRAFV600E immunohistochemistry. As such, we recommend that this approach should be used as part of a comprehensive quality management strategy in the setting of histopathology.

Current progress, challenges and future prospects of indazoles as protein kinase inhibitors for the treatment of cancer

The indazole core is an interesting pharmacophore due to its applications in medicinal chemistry. In the past few years, this moiety has been used for the synthesis of kinase inhibitors. Many researchers have demonstrated the use of indazole derivatives as specific kinase inhibitors, including tyrosine kinase and serine/threonine kinases. A number of anticancer drugs with an indazole core are commercially available, e.g. axitinib, linifanib, niraparib, and pazopanib. Indazole derivatives are applied for the targeted treatment of lung, breast, colon, and prostate cancers. In this review, we compile the current development of indazole derivatives as kinase inhibitors and their application as anticancer agents in the past five years.

Molecular Methods: Clinical Utilization and Designing a Test Menu

Pre-analytical factors in molecular oncology diagnostics are reviewed. Issues around sample collection, storage, and transport that might affect the stability of nucleic acids and the ability to perform molecular testing are addressed. In addition, molecular methods used commonly in clinical diagnostic laboratories, including newer technologies such as next-generation sequencing and digital droplet polymerase chain reaction, as well as their applications, are reviewed. Finally, we discuss considerations in designing a molecular test menu to deliver accurate and timely results in an efficient and cost-effective manner.

The Association Between Radioiodine Refractory in Papillary Thyroid Carcinoma, Sodium/Iodide Symporter Expression, and BRAF V600E Mutation

Objective

To study the association between radioiodine refractory papillary thyroid carcinoma, sodium/iodide symporter (NIS) expression, and the BRAF ^V600E mutation.

Methods

A study was conducted on 30 radioiodine refractory papillary thyroid carcinoma patients and 30 radioiodine-avid papillary thyroid carcinoma patients. The expressions of sodium/iodide symporter and BRAF ^V600E mutated protein were determined by immunohistochemistry using formalin-fixed, paraffin-embedded tissue.

Results

The mutated BRAF ^V600E protein was identified in 26 radioiodine refractory papillary thyroid carcinoma subjects (86.7%) and 22 radioiodine-avid papillary thyroid carcinoma subjects (73.3%), with no significant difference between the 2 groups (P = 0.3). Sodium/iodide symporter expression was detected in 4 of 30 cases (13.3%) from the radioiodine-avid papillary thyroid carcinoma group but was negative for all radioiodine refractory cases. There was no association between sodium/iodide symporter expression and radioiodine refractory papillary thyroid carcinoma (P = 0.11). Cases with positive NIS expression were likely negative for BRAF ^V600E mutation (3/4; P = 0.02).

Conclusion

Papillary thyroid carcinomas with BRAF ^V600E mutation were more likely to be negative for NIS expression. BRAF ^V600E mutation and NIS expressions cannot be used to predict radioiodine sensitivity.

Molecular Biomarkers for Melanoma Screening, Diagnosis and Prognosis: Current State and Future Prospects

Despite significant progress in the development of treatment options, melanoma remains a leading cause of death due to skin cancer. Advances in our understanding of the genetic, transcriptomic, and morphologic spectrum of benign and malignant melanocytic neoplasia have enabled the field to propose biomarkers with potential diagnostic, prognostic, and predictive value. While these proposed biomarkers have the potential to improve clinical decision making at multiple critical intervention points, most remain unvalidated. Clinical validation of even the most commonly assessed biomarkers will require substantial resources, including limited clinical specimens. It is therefore important to consider the properties that constitute a relevant and clinically-useful biomarker-based test prior to engaging in large validation studies. In this review article we adapt an established framework for determining minimally-useful biomarker test characteristics, and apply this framework to a discussion of currently used and proposed biomarkers designed to aid melanoma detection, staging, prognosis, and choice of treatment.