Intraoperative Ultra-Rapid PCR for BRAF Mutation Detection in Craniopharyngioma

With the advent of affordable and accessible genomic sequencing, molecular and genetic information have become cornerstones in the diagnosis and treatment of brain tumors. Craniopharyngiomas have two histologically distinct subtypes: papillary and adamantinous. Studies show that 90% of papillary craniopharyngioma contain BRAF V600E mutations, providing a molecular marker for pharmacological targeting. A phase II trial of BRAF V600E+ papillary craniopharyngioma treated with BRAF/MEK inhibitors showed 94% response rate and 91% tumor volume reduction. During resection of craniopharyngioma, disruption of the pituitary/hypothalamic axis is often inevitable, requiring permanent hormone replacement. Determination of tumor genotype prior to proceeding with surgical resection can alter the treatment options and quality-of-life outcomes. Despite interest in the development of “liquid-biopsy” for noninvasive preoperative detection and diagnosis of CNS tumors, results thus far have been unsuccessful.

We present the case of a 29-year-old female with chronic headaches and progressively worsening left lower quadrant vision loss, found to have a 3-cm solid contrast-enhancing suprasellar mass encasing the pituitary stalk concerning for craniopharyngioma ([Fig. 1]). The absence of calcification and cystic components in the mass were suggestive of papillary craniopharyngioma.

Fig. 1: Coronal and sagittal post-contrast MRI sequences.

A standard endoscopic endonasal approach was pursued for trans-tuburcular biopsy of the suprasellar mass. The bone over the tuberculum was removed for a planned minimal dural opening. The tumor was visualized with the infundibulum draped over the anterior aspect. We dissected along the left side of the stalk to gain access for safe biopsy ([Fig. 2]). The biopsy was performed using cup forceps and sent for permanent pathology and ultra-rapid BRAF PCR analysis. In approximately 15 minutes the PCR resulted as positive suggesting a BRAF positive papillary craniopharyngioma. As a result the decision was made to close and not resect further. The skull base was repaired using an alloderm plug and nasoseptal flap. The patient was noted to have normal pituitary function on testing postoperatively and discharged home on POD 3 with no supplementation necessary. She began BRAF-MEK inhibitor therapy POD 14.

Fig. 2 Intraoperative image of suprasellar lesion. Pituitary stalk (yellow arrow) and tumor (blue arrow) visualized.

Bead homogenization in the presence of a detergent-free DNA extraction buffer was used to lyse the cells. The cells were incubated at 98°C for 2.5 minutes and centrifuged to isolate DNA from associated proteins and cellular debris. An ultra-rapid ddPCR based assay was used to determine the mutational status intraoperatively. Standard histopathological analysis using H&E and immunohistochemistry were performed on permanent pathology specimen for confirmation.

Ultra-rapid ddPCR assay was positive for BRAF V600E mutation. These findings were corroborated by H&E and standard immunohistochemistry ([Fig. 3]).

Fig. 3 Immunohistochemistry staining for BRAF V600E mutation.

Through the use of an intraoperative ultra-rapid PCR, we identified a BRAF V600E mutation within minutes, confirming the diagnosis of papillary craniopharyngioma. Further surgical resection was aborted in lieu of medical therapy and pituitary function was preserved. The use of ultra-rapid PCR for BRAF mutation detection presents an innovative approach for intraoperative diagnosis of papillary craniopharyngioma, with profound treatment implications.

Publication History

Article published online:
07 February 2025