Analysis of cerebrospinal fluid tumor-derived DNA to obviate biopsy of IDH-mutant brainstem glioma in an adult

Abstract

Adult brainstem gliomas are rare and present unique diagnostic and therapeutic challenges due to their critical location and limited biopsy feasibility. Molecular profiling of tumor-derived DNA (t-DNA) isolated from cerebrospinal fluid (CSF) is emerging as a minimally invasive alternative for characterizing these tumors and guiding targeted therapy. A 34-year-old woman with brainstem glioma was treated with a standard course of radiation and temozolomide (TMZ) and remained stable for several years. After surveillance imaging revealed disease progression and raised suspicion of IDH-mutant disease on MRI spectroscopy, molecular profiling of CSF was ordered. The Belay Summit test, a novel NGS-based liquid biopsy assay for central nervous system (CNS) tumors, identified variants in IDH1 and TP53 as well as loss of CDKN2A/CDKN2B. Based on these findings, the patient received a short course of radiation and was started on the IDH inhibitor vorasidenib. This case demonstrates the use of t-DNA from CSF for molecular profiling of adult brainstem glioma to identify actionable genomic alterations without surgical risk and allow patients to receive targeted therapy without tissue diagnosis.

Highlights

• •Evaluation of CSF tumor-derived DNA is emerging as a minimally invasive alternative for characterizing CNS tumors and guiding targeted therapy.
• •Summit detected IDH1 & TP53 variants with loss of CDKN2A/CDKN2B, guiding therapy; radiation and IDH inhibitor vorasidenib.
• •Clinical utility of Summit for adult brainstem glioma is demonstrated without surgical risk enabling targeted therapy.

Short communication

Glioma is the most common brain tumor in adults; however, it is rarely found in the brainstem (1–2 % of adult gliomas) [1]. The low incidence and central, surgically challenging location of brainstem glioma have made it difficult to investigate and characterize. Though further research is warranted, it is understood that adult brainstem glioma is a heterogenous group of tumors that vary in location, radiologic findings, symptoms, and prognoses. Approximately 60 % of cases originate in the pons, but tumors can arise in the midbrain or medulla [2]. About 40 % of adult brainstem gliomas show enhancement on magnetic resonance imaging (MRI), the level of which can vary from minimal to robust [1]. Median survival for adult brainstem glioma is 30–40 months, though this too is subject to variability and prognosticating is limited by biopsy feasibility [3]. When biopsy is an option, adult brainstem gliomas can present with an astrocytic, oligodendroglial-like, or mixed appearance upon histological review.

Efforts to molecularly characterize adult brainstem glioma have identified recurrent mutations in IDH1 and H3-3A (K28M) [4]. These findings are similar to, yet distinct from, what is seen in adult non-brainstem glioma as well as pediatric diffuse intrinsic pontine glioma (DIPG). Further exploration of molecular characteristics among adult brainstem gliomas could expand the treatment selection for this disease, radiation therapy with possible concurrent or adjuvant temozolomide (TMZ) being the current standard. Genomic profiling of tumor derived DNA (t-DNA) in cerebrospinal fluid (CSF) has recently gained recognition as a clinical tool used to identify targets for personalized therapy, particularly in instances when biopsy is out of the question. In the following case description, Belay Summit [5], a novel next-generation sequencing (NGS)-based assay that interrogates oncogenic variants in CSF, was used to inform treatment of brainstem glioma in an adult (Fig. 1).

Fig. 1.

Clinical history summary. A timeline of key clinical events (black triangles) is presented alongside clinical testing including cerebrospinal fluid (CSF) cytology, spectroscopy, and Summit as well as brain magnetic resonance imaging (MRI) and treatment courses (grey boxes).

A 38-year-old female was initially diagnosed with brainstem glioma in 2016 after experiencing headaches, dizziness, and weakness and brain MRI revealed a mass in the pons. The location of the lesion was not amenable to biopsy and a lumbar puncture (LP) was performed for CSF workup. CSF cytology was remarkable only for elevated protein and interpreted as negative for malignancy. The patient was treated with radiation therapy and TMZ for 6 weeks followed by 12 cycles of TMZ. At this time, the patient transferred care to a local oncologist for surveillance. The patient was stable from 2017 to 2024 then started showing slow increase in non-enhancing disease in the pons on imaging. She was hospitalized due to difficulty swallowing and found to have frank progression on brain magnetic resonance imaging (MRI) and spectroscopy showed a positive 2-hydroxyglutarate peak, raising concern for IDH-mutant disease.

The Belay Summit test was ordered for genomic analysis of CSF and identified mutations in IDH1 and TP53 as well as loss of chr9p21.3, containing CDKN2A and CDKN2B (Fig. 2) [5]. The IDH1 R132G variant is located in the catalytic site of the IDH1 protein and was detected at a variant allelic frequency (VAF) of 1.7 % in the CSF specimen. This is a well-characterized oncogenic hotspot that confers an enzymatic gain-of-function, allowing IDH1 to convert α-KG to D-2-hydroxyglutarate, an oncometabolite [6,7]. The TP53 Y236H variant, detected at a variant allelic fraction (VAF) of 2.1 %, is located in the DNA-binding domain of the p53 tumor suppressor and has been demonstrated to reduce transcriptional activity in vivo [8,9]. Based on these findings, the patient was treated with a short course of radiation which improved her swallow function and started on IDH inhibitor drug, vorasidenib.

Fig. 2.

Genomic alterations detected by Summit. The Belay Summit test uses duplex sequencing technology to detect single nucleotide variants (SNV), multi-nucleotide variants (MNV), and insertions/deletions in a targeted, 32-gene panel as well as low pass whole genome sequencing (WGS) to assess chromosomal arm level alterations in tumor-derived DNA isolated from cerebrospinal fluid (CSF) [5]. In a 38-year-old female with brainstem glioma, Summit identified oncogenic variants IDH1 R132G and TP53 Y236H using duplex sequencing as shown in the IGV displays (A and B). Additionally, loss of chr9p21.3, a region containing notable tumor suppressors CDKN2A and CDKN2B, was detected through WGS at a log₂ of (−)0.091 as shown in the ichorDNA plot (C).

The use of Belay Summit for t-DNA profiling in the present case not only confirmed suspicion of IDH-mutant disease but also provided additional molecular details for a rare tumor type. In a whole-exome sequencing (WES) study of brainstem glioma, 38 % (5 of 13) of adult cases were found to have IDH1 variants. All of these cases also had an oncogenic variant in TP53, concordant with the findings presented in this report [4]. The molecular profiles of the discussed study subset and present case resemble that of cerebral IDH-mutant astrocytoma, in which an IDH1 variant is often accompanied by a variant in TP53. Loss of CDKN2A and/or CDKN2B, identified in this case report, is associated with unfavorable prognosis in non-brainstem IDH-mutant astrocytoma and accordingly included in WHO classification. While these findings suggest adult brainstem glioma could be regarded similar to its cerebral counterpart based on parallel molecular profiles, the same WES study identified H3-3A in 54 % (7 of 13) of adult brainstem gliomas that were mutually exclusive with IDH1 variants [4].These cases ultimately bore greater resemblance to pediatric DIPG in which H3-3A K28M is the most common variant.

The presence of IDH1 or H3-3A variants in adult brainstem glioma could have targeted therapeutic potential. Tumors with H3-3A variants that are consequently prone to DNA hypomethylation have demonstrated increased sensitivity to TMZ with the use of small-molecular inhibitors targeting H3 demethylases as well as multihistone deacetylase inhibitors [10,11]. Specific to IDH-mutant disease, vorasidenib, administered based on Summit results in the present case, is FDA-approved for the treatment of low grade astrocytoma or oligodendroglioma with a susceptible IDH1 or IDH2 variant [12]. Current studies, in contrast to H3-3A mutant disease, are investigating demethylating agents as well as PARP inhibitors and immunotherapy to treat IDH-mutant glioma [13]. In the context of CDKN2A/CDKN2B loss, CDK inhibitors are being explored in a phase II clinical trial (NCT03220646) studying the use of abemaciclib in IDH-mutant glioma, though a similar trial investigating palbociclib did not demonstrate meaningful tumor response [14].

As growing evidence suggests adult brainstem glioma could fall into one of two molecular subtypes, IDH or H3-3A K28M mutant, targeted therapy is becoming a consideration for this patient population. However, personalized treatment ultimately relies on detection of a genomic alteration in the tumor of interest, a particular challenge for brainstem tumors. As demonstrated in this case report, genomic profiling of t-DNA from CSF can be an effective alternative to stereotactic biopsy. In a study that sequenced CSF-derived circulating tumor DNA from 57 patients with primary brainstem tumors, genomic alterations found in tumor tissue were also found in CSF in 97.3 % of cases [15]. Similarly, the Belay Summit assay demonstrated a clinical sensitivity of 90 % across a cohort of 124 primary and metastatic CNS tumors.⁵ While survival outcome cannot yet be reported for the present case, the use of an IDH inhibitor was decided based on molecular profiling results from CSF, eliminating surgical morbidity and mortality risks associated with brainstem biopsy. For a rare adult tumor type that has historically been exempt from targeted therapy, this case highlights the use of a novel liquid biopsy tool to inform personalized treatment decisions.

CRediT authorship contribution statement

MY – conceptualization, writing – review and editing. AL - Writing – Original draft. VU – writing – review and editing. KFS - writing – review and editing. QN - writing – review and editing. HVR – conceptualization, supervision, Writing – Original draft. All authors approved the final version manuscript.

Ethics statement

MY has no conflicts to disclose. AL, VU, KFS, QN and HVR are employees of Belay Diagnostics and receive a salary and stock options. Data supporting the findings of this study are available upon reasonable request.

Patient consent/patient permission

The authors confirm that written consent for submission and publication of this case report, including the images and associated text, have been obtained from the patient(s) in line with COPE guidance.

Declaration of generative AI and AI-assisted technologies in the writing process

During the preparation of this work the authors did not use generative AI and AI-assisted technologies in the writing process.

Funding

This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors.

Declaration of competing interest

The authors declare the following financial interests/personal relationships which may be considered as potential competing interests:Alexandra Larson, Vindhya Udhane, Kala F Schilter, Qian Nie, Honey V Reddi are employees of Belay Diagnostics and receive a salary and stock options.