Genetics of vestibular schwannoma : Genetic landscape of irradiated and radiation-naïve benign and malignant vestibular schwannoma

Background: Vestibular schwannoma (VS) is a benign intracranial neoplasm associated with reduced quality of life. Malignant peripheral nerve sheath tumor of the vestibular nerve (VN-MPNST) is the malignant counterpart, an exceedingly rare cancer associated with high mortality. The genetics underlying VS and its etiology is not well understood and the genome of irradiated VS and VN-MPNST has not been characterized. We addressed these shortcomings in this thesis. Material and methods: Tumor specimens from the Bergen neurosurgical tissue bank were subjected to a combination of whole-exome sequencing (WES), whole-genome sequencing and microarray, MLPA, transcriptome sequencing, ViroChip and Sanger sequencing. Results: A median of 14 (4-57) genes were mutated and a median of 0.17% of the autosome was affected by copy number aberrations (CNA) in VS. NF2 mutation was observed in 89%. Tumors with wildtype NF2 harbored mutations in genes linked to NF2. Novel genes and pathways identified in VS included CDC27 (11%), USP8 (7%) and axonal guidance pathway (54%). One clinically aggressive VS was identified and correlated with high mutational burden (231) and mutated RAD54L. Variant allele frequencies for both small mutations and CNAs indicated intratumoral heterogeneity. No plausible virus was associated with VS. We identified a premalignant VS characterized by large chromosomal aberrations and mutated NF2. Malignant transformation was accompanied by whole-genome doubling and mutations in GNAQ, FOXO4 and PDGFRB. VN-MPNST is characterized by gross chromosomal aberrations and homozygous loss of CDKN2A. Previous treatment with GKRS in VS and VN-MPNST did not correlate with neither specific mutations nor genome wide signatures. COSMIC mutational signature 3 contributes to VN-MPNST while signature 6 contributes to a subset of VS. Conclusion: VS is characterized by intratumoral genetic heterogeneity and relatively few mutations. We found recurrent mutations in NF2 and the axonal guidance pathway in addition to novel genes in subsets. Mutated RAD54L might correlate with a hypermutator phenotype and worse clinical course. We identified CDKN2A as a likely tumor suppressor in both premalignant VS and VN-MPNST. Premalignant VS showed signs of chromosomal instability making it prone to malignant transformation. No biomarker of radioresistance or signature of exposure to ionizing radiation was identified in neither VS nor VN-MPNST. We found no evidence of a viral etiology in VS.Doktorgradsavhandlin

The SH3PXD2A-HTRA1 fusion transcript is extremely rare in Norwegian sporadic vestibular schwannoma patients

Introduction Vestibular schwannoma (VS) is a benign intracranial tumor in which the underlying genetics is largely uncertain, apart from mutations in the tumor suppressor gene NF2. Alternative tumorigenic mechanisms have been proposed, including a recurrent in-frame fusion transcript of the HTRA1 and SH3PXD2A genes. The gene product of the SH3PXD2A-HTRA1 fusion has been shown to promote proliferation, invasion and resistance to cell death in vitro and tumor growth in vivo. The aim of this study was to replicate the findings and to investigate the frequency of this fusion gene in another cohort of vestibular schwannoma patients. Methods The SH3PXD2A-HTRA1 transcript was synthesized in vitro using PCR and used as a positive control to assess the sensitivity of a real-time PCR assay. This real-time PCR assay was used to search for the presence of the fusion transcript in 121 Norwegian sporadic VS patients. Results The real-time PCR assay showed a high sensitivity and was able to detect as low as ~ 5 copies of the fusion transcript. Out of the 121 investigated tumors, only 1 harbored the SH3PXD2A-HTRA1 fusion. Conclusion Even though the SH3PXD2A-HTRA1 fusion has been shown to be a driver of tumorigenesis, our results suggest that it is a rare event in our VS patients. Further investigation is warranted in order to elucidate whether our results represent an extreme, and if the fusion is present also in other neoplasms.publishedVersio

Genetic alterations associated with malignant transformation of sporadic vestibular schwannoma

Introduction: Malignant peripheral nerve sheath tumor of the vestibulocochlear nerve (VN-MPNST) is exceedingly rare and carries a poor prognosis. Little is known about its underlying genetics and in particular the process of malignant transformation. There is an ongoing debate on whether the transformation is initiated by ionizing radiation. We present here the analysis and comparison of two post-radiation VN-MPNST and one undergoing spontaneous transformation. Methods: Four tumors from three patients (radiation-naïve vestibular schwannoma before (VS) and after (VN-MPNST) malignant transformation in addition to two post-radiation VN-MPNST) were subjected to DNA whole-genome microarray and whole-exome sequencing and tumor-specific mutations were called. Mutational signatures were characterized using MuSiCa. Results: The tumor genomes were characterized predominantly by copy-number aberrations with 36–81% of the genome affected. Even the VS genome was grossly aberrated. The spontaneous malignant transformation was characterized by a near-total whole-genome doubling, disappearance of NF2 mutation and new mutations in three cancer-related genes (GNAQ, FOXO4 and PDGFRB). All tumors had homozygous loss of the tumor suppressor CDKN2A. Neither mutational signature nor copy number profile was associated with ionizing radiation. Conclusion: The VN-MPNST genome in our cases is characterized by large copy-number aberrations and homozygous deletion of CDKN2A. Our study demonstrates a VS with genetic alterations similar to its malignant counterpart, suggesting the existence of premalignant VS. No consistent mutational signature was associated with ionizing radiation.publishedVersio

Is intracranial volume a risk factor for IDH-mutant low-grade glioma? A case-control study

Purpose Risk of cancer has been associated with body or organ size in several studies. We sought to investigate the relationship between intracranial volume (ICV) (as a proxy for lifetime maximum brain size) and risk of IDH-mutant low-grade glioma. Methods In a multicenter case–control study based on population-based data, we included 154 patients with IDH-mutant WHO grade 2 glioma and 995 healthy controls. ICV in both groups was calculated from 3D MRI brain scans using an automated reverse brain mask method, and then compared using a binomial logistic regression model. Results We found a non-linear association between ICV and risk of glioma with increasing risk above and below a threshold of 1394 ml (p < 0.001). After adjusting for ICV, sex was not a risk factor for glioma. Conclusion Intracranial volume may be a risk factor for IDH-mutant low-grade glioma, but the relationship seems to be non-linear with increased risk both above and below a threshold in intracranial volume.publishedVersio

Genetics of vestibular schwannoma : Genetic landscape of irradiated and radiation-naïve benign and malignant vestibular schwannoma

Background: Vestibular schwannoma (VS) is a benign intracranial neoplasm associated with reduced quality of life. Malignant peripheral nerve sheath tumor of the vestibular nerve (VN-MPNST) is the malignant counterpart, an exceedingly rare cancer associated with high mortality. The genetics underlying VS and its etiology is not well understood and the genome of irradiated VS and VN-MPNST has not been characterized. We addressed these shortcomings in this thesis. Material and methods: Tumor specimens from the Bergen neurosurgical tissue bank were subjected to a combination of whole-exome sequencing (WES), whole-genome sequencing and microarray, MLPA, transcriptome sequencing, ViroChip and Sanger sequencing. Results: A median of 14 (4-57) genes were mutated and a median of 0.17% of the autosome was affected by copy number aberrations (CNA) in VS. NF2 mutation was observed in 89%. Tumors with wildtype NF2 harbored mutations in genes linked to NF2. Novel genes and pathways identified in VS included CDC27 (11%), USP8 (7%) and axonal guidance pathway (54%). One clinically aggressive VS was identified and correlated with high mutational burden (231) and mutated RAD54L. Variant allele frequencies for both small mutations and CNAs indicated intratumoral heterogeneity. No plausible virus was associated with VS. We identified a premalignant VS characterized by large chromosomal aberrations and mutated NF2. Malignant transformation was accompanied by whole-genome doubling and mutations in GNAQ, FOXO4 and PDGFRB. VN-MPNST is characterized by gross chromosomal aberrations and homozygous loss of CDKN2A. Previous treatment with GKRS in VS and VN-MPNST did not correlate with neither specific mutations nor genome wide signatures. COSMIC mutational signature 3 contributes to VN-MPNST while signature 6 contributes to a subset of VS. Conclusion: VS is characterized by intratumoral genetic heterogeneity and relatively few mutations. We found recurrent mutations in NF2 and the axonal guidance pathway in addition to novel genes in subsets. Mutated RAD54L might correlate with a hypermutator phenotype and worse clinical course. We identified CDKN2A as a likely tumor suppressor in both premalignant VS and VN-MPNST. Premalignant VS showed signs of chromosomal instability making it prone to malignant transformation. No biomarker of radioresistance or signature of exposure to ionizing radiation was identified in neither VS nor VN-MPNST. We found no evidence of a viral etiology in VS

Gamma Knife Radiosurgery does not alter the copy number aberration profile in sporadic vestibular schwannoma

Introduction Ionizing radiation is a known etiologic factor in tumorigenesis and its role in inducing malignancy in the treatment of vestibular schwannoma has been debated. The purpose of this study was to identify a copy number aberration (CNA) profile or specific CNAs associated with radiation exposure which could either implicate an increased risk of malignancy or elucidate a mechanism of treatment resistance. Methods 55 sporadic VS, including 18 treated with Gamma Knife Radiosurgery (GKRS), were subjected to DNA whole-genome microarray and/or whole-exome sequencing. CNAs were called and statistical tests were performed to identify any association with radiation exposure. Hierarchical clustering was used to identify CNA profiles associated with radiation exposure. Results A median of 7 (0–58) CNAs were identified across the 55 VS. Chromosome 22 aberration was the only recurrent event. A median aberrant cell fraction of 0.59 (0.25–0.94) was observed, indicating several genetic clones in VS. No CNA or CNA profile was associated with GKRS. Conclusion GKRS is not associated with an increase in CNAs or alteration of the CNA profile in VS, lending support to its low risk. This also implies that there is no major issue with GKRS treatment failure being due to CNAs. In agreement with previous studies, chromosome 22 aberration is the only recurrent CNA. VS consist of several genetic clones, addressing the need for further studies on the composition of cells in this tumor

The SH3PXD2A-HTRA1 fusion transcript is extremely rare in Norwegian sporadic vestibular schwannoma patients

Introduction Vestibular schwannoma (VS) is a benign intracranial tumor in which the underlying genetics is largely uncertain, apart from mutations in the tumor suppressor gene NF2. Alternative tumorigenic mechanisms have been proposed, including a recurrent in-frame fusion transcript of the HTRA1 and SH3PXD2A genes. The gene product of the SH3PXD2A-HTRA1 fusion has been shown to promote proliferation, invasion and resistance to cell death in vitro and tumor growth in vivo. The aim of this study was to replicate the findings and to investigate the frequency of this fusion gene in another cohort of vestibular schwannoma patients. Methods The SH3PXD2A-HTRA1 transcript was synthesized in vitro using PCR and used as a positive control to assess the sensitivity of a real-time PCR assay. This real-time PCR assay was used to search for the presence of the fusion transcript in 121 Norwegian sporadic VS patients. Results The real-time PCR assay showed a high sensitivity and was able to detect as low as ~ 5 copies of the fusion transcript. Out of the 121 investigated tumors, only 1 harbored the SH3PXD2A-HTRA1 fusion. Conclusion Even though the SH3PXD2A-HTRA1 fusion has been shown to be a driver of tumorigenesis, our results suggest that it is a rare event in our VS patients. Further investigation is warranted in order to elucidate whether our results represent an extreme, and if the fusion is present also in other neoplasms

Genetic alterations associated with malignant transformation of sporadic vestibular schwannoma

Introduction Malignant peripheral nerve sheath tumor of the vestibulocochlear nerve (VN-MPNST) is exceedingly rare and carries a poor prognosis. Little is known about its underlying genetics and in particular the process of malignant transformation. There is an ongoing debate on whether the transformation is initiated by ionizing radiation. We present here the analysis and comparison of two post-radiation VN-MPNST and one undergoing spontaneous transformation. Methods Four tumors from three patients (radiation-naïve vestibular schwannoma before (VS) and after (VN-MPNST) malignant transformation in addition to two post-radiation VN-MPNST) were subjected to DNA whole-genome microarray and whole-exome sequencing and tumor-specific mutations were called. Mutational signatures were characterized using MuSiCa. Results The tumor genomes were characterized predominantly by copy-number aberrations with 36–81% of the genome affected. Even the VS genome was grossly aberrated. The spontaneous malignant transformation was characterized by a near-total whole-genome doubling, disappearance of NF2 mutation and new mutations in three cancer-related genes (GNAQ, FOXO4 and PDGFRB). All tumors had homozygous loss of the tumor suppressor CDKN2A. Neither mutational signature nor copy number profile was associated with ionizing radiation. Conclusion The VN-MPNST genome in our cases is characterized by large copy-number aberrations and homozygous deletion of CDKN2A. Our study demonstrates a VS with genetic alterations similar to its malignant counterpart, suggesting the existence of premalignant VS. No consistent mutational signature was associated with ionizing radiation

Is intracranial volume a risk factor for IDH-mutant low-grade glioma? A case-control study

Purpose Risk of cancer has been associated with body or organ size in several studies. We sought to investigate the relationship between intracranial volume (ICV) (as a proxy for lifetime maximum brain size) and risk of IDH-mutant low-grade glioma. Methods In a multicenter case–control study based on population-based data, we included 154 patients with IDH-mutant WHO grade 2 glioma and 995 healthy controls. ICV in both groups was calculated from 3D MRI brain scans using an automated reverse brain mask method, and then compared using a binomial logistic regression model. Results We found a non-linear association between ICV and risk of glioma with increasing risk above and below a threshold of 1394 ml (p < 0.001). After adjusting for ICV, sex was not a risk factor for glioma. Conclusion Intracranial volume may be a risk factor for IDH-mutant low-grade glioma, but the relationship seems to be non-linear with increased risk both above and below a threshold in intracranial volume

Is intracranial volume a risk factor for IDH-mutant low-grade glioma? A case-control study

Purpose Risk of cancer has been associated with body or organ size in several studies. We sought to investigate the relationship between intracranial volume (ICV) (as a proxy for lifetime maximum brain size) and risk of IDH-mutant low-grade glioma. Methods In a multicenter case–control study based on population-based data, we included 154 patients with IDH-mutant WHO grade 2 glioma and 995 healthy controls. ICV in both groups was calculated from 3D MRI brain scans using an automated reverse brain mask method, and then compared using a binomial logistic regression model. Results We found a non-linear association between ICV and risk of glioma with increasing risk above and below a threshold of 1394 ml (p < 0.001). After adjusting for ICV, sex was not a risk factor for glioma. Conclusion Intracranial volume may be a risk factor for IDH-mutant low-grade glioma, but the relationship seems to be non-linear with increased risk both above and below a threshold in intracranial volume