Selective extraction of low-abundance BRAF V600E mutation from plasma, urine, and sputum using ion-tagged oligonucleotides and magnetic ionic liquids.

Sequence-specific DNA extractions have the potential to improve the detection of low-abundance mutations from complex matrices, making them ideal for circulating tumor DNA analysis during the early stages of cancer. Ion-tagged oligonucleotides (ITOs) are oligonucleotides modified with an allylimidazolium salt via thiolene click chemistry. The allylimidazolium-based tag allows the ITO-DNA duplex to be selectively captured by a hydrophobic magnetic ionic liquid (MIL). In this study, the selectivity of the ITO-MIL method was examined by extracting low abundance of the BRAF V600E mutation-a common single-nucleotide polymorphism associated with several different cancers-from diluted human plasma, artificial urine, and diluted artificial sputum. Quantitative polymerase chain reaction (qPCR) was not able to distinguish a 9% BRAF V600E standard (50 fg·µL-1 BRAF V600E, 500 fg·µL-1 wild-type BRAF) from the 100% wild-type BRAF (50 fg·µL-1) standard. However, introducing the ITO-MIL extraction prior to qPCR allowed for samples consisting of 0.1% BRAF V600E (50 fg·µL-1 V600E BRAF, 50,000 fg·µL-1 wild-type BRAF) to be distinguished from the 100% wild-type BRAF standard. Ion-tagged oligonucleotides (ITOs) are combined with magnetic ionic liquids (MILs) to extract low-abundance BRAF V600E mutation from diluted human plasma, artificial urine, and diluted artificial sputum. The ITO-MIL extraction prior to qPCR allowed for samples consisting of 0.1% BRAF V600E to be distinguished from the 100% wild-type BRAF standard.

[Diagnostic value of the BRAF variant V595E in urine samples, smears and biopsies from canine transitional cell carcinoma]. / Diagnostische Aussagekraft der BRAF-Mutation V595E in Urinproben, Ausstrichen und Bioptaten beim kaninen Übergangszellkarzinom.

OBJECTIVE: Transitional cell carcinoma (TCC) is the most common malignant tumour of the canine urinary tract. Previously, the mutation of the BRAF gene V595E was identified in approximately 85 % of canine TCC cases by DNA sequencing of TCC tumour cells, both in frozen and paraffin-embedded tissue sections, as well as in urine. The objective of this study was to establish these methods in cytological smears and to investigate the prevalence of BRAF mutation V595E in canine TCC in our cohort of patients. MATERIAL AND METHODS: Biopsy samples (n = 43), urine (n = 48) and/or cytological smears (n = 31) from 66 dogs with TCC (n = 33), urinary bladder polyps (n = 7), cystitis (n = 23) or without bladder diseases (n = 3), submitted for routine diagnostics, were selected. DNA isolation from paraffin material, urine and cytological smears was performed using commercially available kits. Exon 15 was examined for the presence of the BRAF mutation c.1784T>A by Sanger sequencing. RESULTS: In 39/43 paraffin-embedded biopsies and 38/48 urine samples, a sufficient amount of good quality DNA was isolated. DNA isolation and sequencing were successful in 16/18 smears with a high cell count, but not in the 10/13 smears with low cellularity. In all cases from which different sample materials were available, the results of BRAF analysis were identical in paraffin-embedded tissue, cytological smears and/or urine. In 22/31 dogs (70.9 %) with TCC, the presence of the BRAF mutation was confirmed, whereas it could not be detected in animals without pathological findings or with cystitis or with a polyp. CONCLUSION AND CLINICAL RELEVANCE: BRAF mutation analysis is a new and good method to be able to mostly confirm a diagnosis of TCC in uncertain cases. Non-invasive diagnostic samples, including urine and urine sediment containing sufficient numbers of relevant cells as well as cytology aspirates and formalin-fixed biopsies can be used for analysis. However, it is important to note that only a positive identification of the mutation is diagnostic. Further research is necessary to investigate prognostic and therapeutic relevance of the variant and how this genetic analysis can be used as an early detection method for TCC.

Homologous Mutation to Human BRAF V600E Is Common in Naturally Occurring Canine Bladder Cancer--Evidence for a Relevant Model System and Urine-Based Diagnostic Test.

UNLABELLED: Targeted cancer therapies offer great clinical promise, but treatment resistance is common, and basic research aimed at overcoming this challenge is limited by reduced genomic and biologic complexity in artificially induced rodent tumors compared with their human counterparts. Animal models that more faithfully recapitulate genotype-specific human pathology could improve the predictive value of these investigations. Here, a newly identified animal model for oncogenic BRAF-driven cancers is described. With 20,000 new cases in the United States each year, canine invasive transitional cell carcinoma of the bladder (InvTCC) is a common, naturally occurring malignancy that shares significant histologic, biologic, and clinical phenotypes with human muscle invasive bladder cancer. In order to identify somatic drivers of canine InvTCC, the complete transcriptome for multiple tumors was determined by RNAseq. All tumors harbored a somatic mutation that is homologous to the human BRAF(V600E) mutation, and an identical mutation was present in 87% of 62 additional canine InvTCC tumors. The mutation was also detectable in the urine sediments of all dogs tested with mutation-positive tumors. Functional experiments suggest that, like human tumors, canine activating BRAF mutations potently stimulate the MAPK pathway. Cell lines with the mutation have elevated levels of phosphorylated MEK, compared with a line with wild-type BRAF. This effect can be diminished through application of the BRAF(V600E) inhibitor vemurafenib. These findings set the stage for canine InvTCC as a powerful system to evaluate BRAF-targeted therapies, as well as therapies designed to overcome resistance, which could enhance treatment of both human and canine cancers IMPLICATIONS: This study demonstrates the activating BRAF mutation (V600E), which is found in multiple human cancers, is a driver of canine InvTCC, and highlights a urine-based test for quick diagnosis.

BRAF V600E mutations in urine and plasma cell-free DNA from patients with Erdheim-Chester disease.

Erdheim-Chester disease (ECD) is a rare histiocytosis with a high prevalence of BRAF V600E mutation (>50% of patients). Patients with BRAF-mutant ECD can respond to BRAF inhibitors. Unfortunately, the lack of adequate archival tissue often precludes BRAF testing. We hypothesized that cell-free DNA (cfDNA) from plasma or urine can offer an alternative source of biologic material for testing. We tested for BRAF V600E mutation in cfDNA from the plasma and urine of 6 ECD patients. In patients with available archival tissue, the result of BRAF mutation analysis was concordant with plasma and urine cfDNA results in all 3 patients (100% agreement, kappa 1.00). In all 6 patients, BRAF mutation analysis of plasma and urine cfDNA was concordant in 5 of 6 patients (83% agreement, kappa 0.67). Testing for BRAF V600E mutation in plasma and urine cfDNA should be further investigated as an alternative to archival tissue mutation analysis.