Clinical Utility of Liquid Biopsy to Detect BRAF and NRAS Mutations in Stage III/IV Melanoma Patients by Using Real-Time PCR

Japan society of clinical oncology position paper on appropriate clinical use of molecular residual disease (MRD) testing

Although the 5-year relative survival rates for resectable solid tumors have improved over the past few years, the risk of postoperative recurrence necessitates effective monitoring strategies. Recent advancements in molecular residual disease (MRD) testing based on circulating tumor DNA (ctDNA) analysis have shown considerable promise in the context of predicting recurrence; however, significant barriers to widespread clinical implementation remain-mainly, low awareness among healthcare professionals, high costs, and lack of standardized assays and comprehensive evidence. This position paper, led by the Japan Society of Clinical Oncology, aims to establish a common framework for the appropriate clinical use of MRD testing in a tumor type-agnostic manner. It synthesizes currently available evidence, reviews region-specific clinical trends, addresses critical clinical questions related to MRD testing, and offers recommendations to guide healthcare professionals, biotechnology and pharmaceutical companies, and regulatory authorities. These recommendations were developed based on a voting process involving 15 expert members, ensuring a consensus-driven approach. These findings underscore the importance of collaborative efforts among various stakeholders in enhancing the clinical utility of MRD testing. This project aimed to foster consensus and provide clear guidelines to support the advancement of precision medicine in oncology and improve patient outcomes in the context of perioperative care.

Detection of Circulating Tumor DNA in Liquid Biopsy: Current Techniques and Potential Applications in Melanoma

The treatment landscape for advanced melanoma has transformed significantly with the advent of BRAF and MEK inhibitors (BRAF/MEKi) targeting BRAFV600 mutations, as well as immune checkpoint inhibitors (ICI) like anti-PD-1 monotherapy or its combinations with anti-CTLA-4 or anti-LAG-3. Despite that, many patients still do not benefit from these treatments at all or develop resistance mechanisms. Therefore, prognostic and predictive biomarkers are needed to identify patients who should switch or escalate their treatment strategies or initiate an intensive follow-up. In melanoma, liquid biopsy has shown promising results, with a potential role in predicting relapse in resected high-risk patients or in disease monitoring during the treatment of advanced disease. Several components in peripheral blood have been analyzed, such as circulating tumor cells (CTCs), cell-free DNA (cfDNA), and circulant tumoral DNA (ctDNA), which have turned out to be particularly promising. To analyze ctDNA in blood, different techniques have proven to be useful, including digital droplet polymerase chain reaction (ddPCR) to detect specific mutations and, more recently, next-generation sequencing (NGS) techniques, which allow analyzing a broader repertoire of the mutation landscape of each patient. In this review, our goal is to update the current understanding of liquid biopsy, focusing on the use of ctDNA as a biological material in the daily clinical management of melanoma patients, in particular those with advanced disease treated with ICI.

Circulating tumor DNA-based assessment of molecular residual disease in non-metastatic melanoma

In patients with resected non-metastatic melanoma, the liquid biopsy for the assessment of molecular residual disease (MRD) by circulating tumour DNA (ctDNA) represents a promising tool to stratify the risk and to monitor tumour evolution. However, its validation requires the demonstration of analytical validity, clinical validity and utility. Indeed, the development of sensitive and specific assays can optimize prognostication and eventually help clinicians to modulate adjuvant treatments, in order to improve clinical outcomes. Data about ctDNA-guided prognosis stratification is emerging, but clinical trials assessing ctDNA-guided therapeutic decisions are still ongoing. This review aims to depict the role of ctDNA-based MRD assessment in patients with non-metastatic melanoma and to provide a roadmap to face challenges for its introduction into clinical practice.

US physician perspective on the use of biomarker and ctDNA testing in patients with melanoma

New treatments have increased survival of patients with melanoma, and methods to monitor patients throughout the disease process are needed. Circulating tumor DNA (ctDNA) is a predictive and prognostic biomarker that may allow routine, real-time monitoring of disease status. We surveyed 44 US physicians to understand their preferences and practice patterns for biomarker and ctDNA testing in their patients with melanoma. Tumor biomarker testing was often ordered in stage IIIA-IV patients. Barriers to biomarker testing include insufficient tissue (60%) and lack of insurance coverage (54%). ctDNA testing was ordered by 16-18% of physicians for stages II-IV. Reasons for not using ctDNA testing included lack of prospective data (41%), ctDNA testing used for research only (18%), and others. Physicians (≥74%) believed that ctDNA assays could help with monitoring and treatment selection throughout the disease process. Physicians consider ctDNA testing potentially valuable for clinical decision-making but cited concerns that should be addressed.

Supervised clustering of peripheral immune cells associated with clinical response to checkpoint inhibitor therapy in patients with advanced melanoma

Background and purpose

Immune therapy with checkpoint inhibitors (CPIs) is a highly successful therapy in many cancers including metastatic melanoma. Still, many patients do not respond well to therapy and there are no blood-borne biomarkers available to assess the clinical outcome.

Materials and methods

To investigate cellular changes after CPI therapy, we carried out flow cytometry-based immune monitoring in a cohort of 90 metastatic melanoma patients before and after CPI therapy using the FlowSOM algorithm. To evaluate associations to the clinical outcome with therapy, we divided the patients based on progression-free survival.

Results

We found significant associations with CPI therapy in both peripheral blood mononuclear cell and T-cell subsets, but with the most pronounced effects in the latter. Particularly CD4+ effector memory T-cell subsets were associated with response with a positive correlation between CD27+HLA-DR+CD4+ effector memory T cells in a univariate (odds ratio: 1.07 [95% confidence interval 1.02-1.12]) and multivariate regression model (odds ratio: 1.08 [95% confidence interval 1.03-1.14]). We also found a trend towards stronger accumulation of CD57+CD8+ T cells in non-responding patients.

Conclusion

Our results show significant associations between immune monitoring and clinical outcome of therapy that could be evaluated as biomarkers in a clinical setting.

Use of ctDNA in identifying an actionable BRAF mutation in stage 4 metastatic melanoma

The identification of genetic variants in melanoma has enabled the development of targeted therapies. Under the National Institute for Health and Care Excellence (NICE) guidance, patients with BRAF V600E variant are eligible for BRAF and MEK inhibitor therapy. For those with advanced or highly symptomatic disease, a rapid response to treatment is often seen. Current practice relies on tissue biopsy to perform immunohistochemistry (IHC) or next generation sequencing (NGS) to identify these variants; however, this can take up to 2 weeks. In patients with widespread disease, rapid initiation of treatment can be lifesaving.We describe a case in which hotspot circulating tumour DNA (ctDNA) analysis confirmed BRAF variant 6 days prior to biopsy results. This was utilised to expedite treatment initiation and symptomatically, the patient had initial improvement within a few days.This article demonstrates the potential value of ctDNA analysis and the need for further research into this as an alternative to NGS for patients with rapidly progressive disease.

A group of three miRNAs can act as candidate circulating biomarkers in liquid biopsies from melanoma patients

Background

Staging of melanoma and follow up after melanoma diagnosis aims at predicting risk and detecting progression or recurrence at early stage, respectively in order to timely start and/or change treatment. Tumor thickness according to Breslow, status of the sentinel node and value of the lactate dehydrogenase (LDH) are well-established prognostic markers for metastatic risk, but reliable biomarkers identifying early recurrence or candidates who may benefit best from medical treatment are still warranted. Liquid biopsy has emerged to be a suitable method for identifying biomarkers for early cancer diagnosis, prognosis, therapeutic response prediction, and patient follow-up. Liquid biopsy is a blood-based non-invasive procedure that allows analyzing circulating analytes, including extracellular vesicles.

Methods

In this study we have explored the use of 7 miRNAs, namely hsa-miR-149-3p, hsa-miR-150-5p, hsa-miR-21-5p, hsa-miR-200c-3p, hsa-miR-134-5p, hsa-miR-144-3p and hsa-miR-221-3p in plasma exosomes to discriminate melanoma patients from controls without melanoma in a cohort of 92 individuals.

Results and discussion

Our results showed that three out seven miRNAs, namely hsa-miR-200c-3p, hsa-miR-144-3p and hsa-miR-221-3p were differentially expressed in plasma-derived exosomes from melanoma patients and controls. Furthermore, the expression of the three miRNAs may be a promising ancillary tool as a melanoma biomarker, even for discriminating between nevi and melanoma.

Multimodal integration of image, epigenetic and clinical data to predict BRAF mutation status in melanoma

BACKGROUND

In machine learning, multimodal classifiers can provide more generalised performance than unimodal classifiers. In clinical practice, physicians usually also rely on a range of information from different examinations for diagnosis. In this study, we used BRAF mutation status prediction in melanoma as a model system to analyse the contribution of different data types in a combined classifier because BRAF status can be determined accurately by sequencing as the current gold standard, thus nearly eliminating label noise.

METHODS

We trained a deep learning-based classifier by combining individually trained random forests of image, clinical and methylation data to predict BRAF-V600 mutation status in primary and metastatic melanomas of The Cancer Genome Atlas cohort.

RESULTS

With our multimodal approach, we achieved an area under the receiver operating characteristic curve of 0.80, whereas the individual classifiers yielded areas under the receiver operating characteristic curve of 0.63 (histopathologic image data), 0.66 (clinical data) and 0.66 (methylation data) on an independent data set.

CONCLUSIONS

Our combined approach can predict BRAF status to some extent by identifying BRAF-V600 specific patterns at the histologic, clinical and epigenetic levels. The multimodal classifiers have improved generalisability in predicting BRAF mutation status.