Detection of H3F3A K27M or BRAF V600E in liquid biopsies of brain tumor patients as diagnostic and monitoring biomarker: impact of tumor localization and sampling method.

in Acta neuropathologica by Sibylle Madlener, Natalia Stepien, Daniel Senfter, Lisa Mayr, Anna Laemmerer, Cora Hedrich, Alicia Baumgartner, Daniela Lötsch-Gojo, Jaroslav Sterba, Petra Pokorna, Barbara Kiesel, Georg Widhalm, Franziska Eckert, Matthias Preusser, Karl Rössler, Amedeo Azizi, Andreas Peyrl, Thomas Czech, Christine Haberler, Irene Slavc, Gregor Kasprian, Christian Dorfer, Julia Furtner, Johannes Gojo

TLDR

  • This study demonstrated the potential of liquid biopsies for diagnosing and monitoring gliomas, particularly with respect to H3F3A K27M and BRAF V600E mutations.

Abstract

Gliomas are the most common brain tumor type in children and adolescents. To date, diagnosis and therapy monitoring for these tumors rely on magnetic resonance imaging (MRI) and histopathological as well as molecular analyses of tumor tissue. Recently, liquid biopsies (LB) have emerged as promising tool for diagnosis and longitudinal tumor assessment potentially allowing for a more precise therapeutic management. However, the optimal strategy for monitoring gliomas by LB remains to be determined. In this study, we analyzed circulating tumor DNA (ctDNA) from 78 liquid biopsies (plasma n = 44, cerebrospinal fluid n = 34 (CSF)) of 35 glioma patients, determining H3F3A K28M (K27M) and BRAF V600E mutation allele frequency using droplet digital PCR (ddPCR). All results were correlated to clinically relevant parameters including diagnostic imaging and CSF aspiration site (ventricular vs lumbar) with respect to tumor localization. Regarding diagnostic accuracy, the calculated sensitivity score in the H3F3A K27M cohort was 84.61% for CSF and 73.68% for plasma. In the BRAF V600E cohort, we determined a sensitivity of 83.3% in plasma and 80% in CSF. The overall specificity was 100%. With respect to the CSF aspiration, the intra-operatively obtained CSF demonstrated 100% detection rate, followed by ventricular CSF obtained via Ommaya Reservoir/shunt puncture (93%) and CSF obtained via lumbar puncture (66%). Notably, this further correlated with the proximity of the CSF site to tumor localization. Longitudinal CSF monitoring demonstrated a good correlation to clinical and radiological disease evolution. Importantly, we show for the first time that monitoring BRAF V600E by ddPCR could serve as treatment response assessment in gliomas. In summary, our observation may inform recommendations with regard to location of CSF aspiration when incorporating LB into future treatment protocols.

Overview

  • The study analyzed circulating tumor DNA (ctDNA) from 78 liquid biopsies of 35 glioma patients, focusing on H3F3A K28M and BRAF V600E mutation allele frequency using droplet digital PCR (ddPCR).
  • The study aimed to explore the diagnostic accuracy and clinical applicability of liquid biopsies for gliomas, comparing plasma and cerebrospinal fluid (CSF) samples and correlating results with clinically relevant parameters.
  • The primary objective was to determine the optimal strategy for monitoring gliomas using liquid biopsies and identify correlations between CSF aspiration site and tumor localization.

Comparative Analysis & Findings

  • The diagnostic accuracy of liquid biopsies in identifying H3F3A K27M mutations was 84.61% for CSF and 73.68% for plasma, with an overall specificity of 100%.
  • In the BRAF V600E cohort, sensitivity scores were 83.3% in plasma and 80% in CSF, with 100% detection rate in intra-operatively obtained CSF and 93% in ventricular CSF.
  • Longitudinal CSF monitoring demonstrated good correlation with clinical and radiological disease evolution, and ddPCR-based BRAF V600E monitoring showed potential for treatment response assessment in gliomas.

Implications and Future Directions

  • The study's findings may inform recommendations for CSF aspiration location when incorporating liquid biopsies into future treatment protocols.
  • Future studies should explore the optimal timing and frequency of liquid biopsies for monitoring glioma disease progression and treatment response.
  • Novel approaches, such as circulating tumor RNA (ctRNA) analysis, should be investigated to enhance the diagnostic accuracy and clinical applicability of liquid biopsies for gliomas.
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