Clinical impact of targeted amplicon sequencing for meningioma as a practical clinical-sequencing system

Abstract

Recent genetic analyses using next-generation sequencers have revealed numerous genetic alterations in various tumors including meningioma, which is the most common primary brain tumor. However, their use as routine laboratory examinations in clinical applications for tumor genotyping is not cost effective. To establish a clinical sequencing system for meningioma and investigate the clinical significance of genotype, we retrospectively performed targeted amplicon sequencing on 103 meningiomas and evaluated the association with clinicopathological features. We designed amplicon-sequencing panels targeting eight genes including NF2 (neurofibromin 2), TRAF7, KLF4, AKT1, and SMO. Libraries prepared with genomic DNA extracted from PAXgenefixed paraffin-embedded tissues of 103 meningioma specimens were sequenced using the Illumina MiSeq. NF2 loss in some cases was also confirmed by interphase-fluorescent in situ hybridization. We identified NF2 loss and/or at least one mutation in NF2, TRAF7, KLF4, AKT1, and SMO in 81 out of 103 cases (79%) by targeted amplicon sequencing. On the basis of genetic status, we categorized meningiomas into three genotype groups: NF2 type, TRAKLS type harboring mutation in TRAF7, AKT1, KLF4, and/or SMO, and 'not otherwise classified' type. Genotype significantly correlated with tumor volume, tumor location, and magnetic resonance imaging findings such as adjacent bone change and heterogeneous gadolinium enhancement, as well as histopathological subtypes. In addition, multivariate analysis revealed that genotype was independently associated with risk of recurrence. In conclusion, we established a rapid clinical sequencing system that enables final confirmation of meningioma genotype within 7 days turnaround time. Our method will bring multiple benefits to neuropathologists and neurosurgeons for accurate diagnosis and appropriate postoperative management.

Selective vulnerability of the primitive meningeal layer to prenatal Smo activation for skull base meningothelial meningioma formation

“…Recent advances in the molecular genetics of WHO grade I meningioma have led to the discovery of mutations in several oncogenes, including AKT1, KLF4, SMO, PIK3CA, POLRA2, and TRAF7, all mutually exclusive to mutations in the NF2 tumor suppressor gene involved in at least 50% of meningiomas [3][4][5][6]. Discovery of this mutational landscape enabled the establishment of histological and/or anatomical correlations with specific gene mutations [3,7,8]. In a recent series of 775 meningiomas, Clark et al described Sonic Hedgehog (SHH) pathway-related meningiomas harboring 42 SMO gene mutations (recurrent mutations L412F and W535L in 76% of cases), 5 SUFU mutations and 3 PRKAR1A mutations [4].…”

DNA methylation analysis for the treatment of meningiomas

“…More aggressive anaplastic WHO grade III tumors are likely have mutations in NF2 (10), and meningiomas with mutations in NF2 are found to have significantly lower recurrence-free survival rates (3). Sizes of tumors with NF2 mutations were found to be significantly larger than tumors that do not have mutations in NF2.…”

“…Sizes of tumors with NF2 mutations were found to be significantly larger than tumors that do not have mutations in NF2. It has been found that 80% of tumors in the calvarium were found to have mutations in NF2, and meningiomas with both mutations in SMARCB1 and NF2 were found to be frequently located in the falx cerebri of patients (3,4). Currently, no targeted therapy exists for NF2 mutations in meningiomas, however, Shah et al have found that NF2 mutations in ovarian cancer can be successfully targeted by FAK inhibitors (11).…”

“…Meningiomas with mutations in sonic hedgehog signaling were found to be present in WHO grade I tumors that had a low possibility of progressing to malignancy or recurrence after treatment (7). Yuzawa et al suggest that mutations such as SMO and AKT1 can potentially be targeted by drugs such as hedgehog inhibitors and AKT inhibitors, respectively, if the tumor is in a position that makes it difficult to completely resect (3). PI3K inhibitors could also potentially be used in meningiomas with activation mutations in PI3K (8).…”

“…Yuzawa et al has produced the first clinical sequencing system for meningiomas that can be completed within 7 days turnaround time for the clinician while using targeted amplicon sequencing (3). This system can identify mutations in NF2, TRAF7, AKT1, KLF4, and SMO, as well as NF2 (3).…”