Brastianos PK, Taylor-Weiner A, Manley PE, Jones RT, Dias-Santagata D, Thorner AR, Lawrence MS, Rodriguez FJ, Bernardo LA, Schubert L, Sunkavalli A, Shillingford N, Calicchio ML, Lidov HG, Taha H, Martinez-Lage M, Santi M, Storm PB, Lee JY, Palmer JN, Adappa ND, Scott RM, Dunn IF, Laws ER Jr, Stewart C, Ligon KL, Hoang MP, Van Hummelen P, Hahn WC, Louis DN, Resnick AC, Kieran MW, Getz G, Santagata S.

Hemangioblastomas consist of 10-20% neoplastic “stromal” cells within a vascular tumor cell mass of reactive pericytes, endothelium and lymphocytes. Familial cases of central nervous system hemangioblastoma uniformly result from mutations in the Von Hippel-Lindau (VHL) gene. In contrast, inactivation of VHL has been previously observed in only a minority of sporadic hemangioblastomas, suggesting an alternative genetic etiology. We performed deep-coverage DNA sequencing on 32 sporadic hemangioblastomas (whole exome discovery cohort n = 10, validation n = 22), followed by analysis of clonality, copy number alteration, and somatic mutation. We identified somatic mutation, loss of heterozygosity and/or deletion of VHL in 8 of 10 discovery cohort tumors. VHL inactivating events were ultimately detected in 78% (25/32) of cases. No other gene was significantly mutated. Overall, deep-coverage sequence analysis techniques uncovered VHL alterations within the neoplastic fraction of these tumors at higher frequencies than previously reported. Our findings support the central role of VHL inactivation in the molecular pathogenesis of both familial and sporadic hemangioblastomas.

Shankar GM, Taylor-Weiner A, Lelic N, Jones RT, Kim JC, Francis JM, Abedalthagafi M, Borges LF, Coumans JV, Curry WT, Nahed BV, Shin JH, Paek SH, Park SH, Stewart C, Lawrence MS, Cibulskis K, Thorner AR, Van Hummelen P, Stemmer-Rachamimov AO, Batchelor TT, Carter SL, Hoang MP, Santagata S, Louis DN, Barker FG, Meyerson M, Getz G, Brastianos PK, Cahill DP.

Acta Neuropathol Commun. 2014 Dec 24;2:167. doi: 10.1186/s40478-014-0167-x.

Brain metastases are associated with a dismal prognosis. Whether brain metastases harbor distinct genetic alterations beyond those observed in primary tumors is unknown. We performed whole-exome sequencing of 86 matched brain metastases, primary tumors, and normal tissue. In all clonally related cancer samples, we observed branched evolution, where all metastatic and primary sites shared a common ancestor yet continued to evolve independently. In 53% of cases, we found potentially clinically informative alterations in the brain metastases not detected in the matched primary-tumor sample. In contrast, spatially and temporally separated brain metastasis sites were genetically homogenous. Distal extracranial and regional lymph node metastases were highly divergent from brain metastases. We detected alterations associated with sensitivity to PI3K/AKT/mTOR, CDK, and HER2/EGFR inhibitors in the brain metastases. Genomic analysis of brain metastases provides an opportunity to identify potentially clinically informative alterations not detected in clinically sampled primary tumors, regional lymph nodes, or extracranial metastases

Brastianos PK#1,2,3,4,5, Carter SL#6,5, Santagata S7,8, Cahill DP9, Taylor-Weiner A5, Jones RT4,10, Van Allen EM4,5, Lawrence MS5, Horowitz PM11, Cibulskis K5, Ligon KL4,8, Tabernero J12, Seoane J12, Martinez-Saez E13, Curry WT9, Dunn IF11, Paek SH14, Park SH14, McKenna A5, Chevalier A5, Rosenberg M5, Barker FG 2nd9, Gill CM3, Van Hummelen P4,10, Thorner AR4,10, Johnson BE4, Hoang MP15, Choueiri TK4, Signoretti S8, Sougnez C5, Rabin MS4, Lin NU4, Winer EP4, Stemmer-Rachamimov A15, Meyerson M4,10,5,8, Garraway L4,6,5, Gabriel S5, Lander ES5, Beroukhim R4,7,5, Batchelor TT2, Baselga J16, Louis DN15, Getz G#15,3,5, Hahn WC#4,10,5.

Cancer Discov. 2015 Nov;5(11):1164-1177. doi: 10.1158/2159-8290.CD-15-0369. Epub 2015 Sep 26.

We recently reported that BRAF V600E is the principal oncogenic driver of papillary craniopharyngioma, a highly morbid intracranial tumor commonly refractory to treatment. Here, we describe our treatment of a man age 39 years with multiply recurrent BRAF V600E craniopharyngioma using dabrafenib (150mg, orally twice daily) and trametinib (2mg, orally twice daily). After 35 days of treatment, tumor volume was reduced by 85%. Mutations that commonly mediate resistance to MAPK pathway inhibition were not detected in a post-treatment sample by whole exome sequencing. A blood-based BRAF V600E assay detected circulating BRAF V600E in the patient’s blood. Re-evaluation of the existing management paradigms for craniopharyngioma is warranted, as patient morbidity might be reduced by noninvasive mutation testing and neoadjuvant-targeted treatment.

Brastianos PK1, Shankar GM1, Gill CM1, Taylor-Weiner A1, Nayyar N1, Panka DJ1, Sullivan RJ1, Frederick DT1, Abedalthagafi M1, Jones PS1, Dunn IF1, Nahed BV1, Romero JM1, Louis DN1, Getz G1, Cahill DP1, Santagata S1, Curry WT Jr1, Barker FG 2nd1.

J Natl Cancer Inst. 2015 Oct 23;108(2). pii: djv310. doi: 10.1093/jnci/djv310. Print 2016 Feb.

Strickland MR1, Gill CM1,2, Nayyar N1, D’Andrea MR1, Thiede C3, Juratli TA4, Schackert G4, Borger DR5, Santagata S6, Frosch MP5, Cahill DP7, BrastianosPK1,2,8, Barker FG 2nd7.

J Neurosurg. 2017 Aug;127(2):438-444. doi: 10.3171/2016.8.JNS161076. Epub 2016 Nov 25.

BACKGROUND:

Patients with meningiomas have widely divergent clinical courses. Some entirely recover following surgery alone, while others have relentless tumor recurrences. This clinical conundrum is exemplified by rhabdoid meningiomas, which are designated in the World Health Organization Classification of Tumours as high grade, despite only a subset following an aggressive clinical course. Patient management decisions are further exacerbated by high rates of interobserver variability, biased against missing possibly aggressive tumors. Objective molecular determinants are needed to guide classification and clinical decision making.

METHODS:

To define genomic aberrations of rhabdoid meningiomas, we performed sequencing of cancer-related genes in 27 meningiomas from 18 patients with rhabdoid features and evaluated breast cancer [BRCA]1-associated protein 1 (BAP1) expression by immunohistochemistry in 336 meningiomas. We assessed outcomes, germline status, and family history in patients with BAP1-negative rhabdoid meningiomas.

RESULTS:

The tumor suppressor gene BAP1, a ubiquitin carboxy-terminal hydrolase, is inactivated in a subset of high-grade rhabdoid meningiomas. Patients with BAP1-negative rhabdoid meningiomas had reduced time to recurrence compared with patients with BAP1-retained rhabdoid meningiomas (Kaplan-Meier analysis, 26 mo vs 116 mo, P < .001; hazard ratio 12.89). A subset of patients with BAP1-deficient rhabdoid meningiomas harbored germline BAP1 mutations, indicating that rhabdoid meningiomas can be a harbinger of the BAP1 cancer predisposition syndrome.

CONCLUSION:

We define a subset of aggressive rhabdoid meningiomas that can be recognized using routine laboratory tests. We implicate ubiquitin deregulation in the pathogenesis of these high-grade malignancies. In addition, we show that familial and sporadic BAP1-mutated rhabdoid meningiomas are clinically aggressive, requiring intensive clinical management.

Shankar GM1,2,3,4,5, Abedalthagafi M3,6,7,8, Vaubel RA9, Merrill PH6, Nayyar N4,5, Gill CM4,5, Brewster R6, Bi WL10, Agarwalla PK11, Thorner AR12,13, Reardon DA3,12,14, Al-Mefty O3,10, Wen PY3,12,14, Alexander BM3,15, van Hummelen P12,13, Batchelor TT3,4,5, Ligon KL3,5,12, Ligon AH3,6,16, Meyerson M2,3,12,13, Dunn IF3,10,14, Beroukhim R3,6,12,14, Louis DN3,5,17, Perry A18, Carter SL3,19,20, Giannini C9, Curry WT Jr3,5,11, Cahill DP3,5,11, Barker FG 2nd3,5,11, Brastianos PK1,2,3,4,5, Santagata S3,6,21,22.

Neuro Oncol. 2017 Apr 1;19(4):535-545. doi: 10.1093/neuonc/now235.

Glioneuronal tumors constitute a histologically diverse group of primary central nervous system neoplasms that are typically slow-growing and managed conservatively. Genetic alterations associated with glioneuronal tumors include BRAF mutations and oncogenic fusions. To further characterize this group of tumors, we collected a cohort of 26 glioneuronal tumors and performed in-depth genomic analysis. We identified mutations in BRAF (34%) and oncogenic fusions (30%), consistent with previously published reports. In addition, we discovered novel oncogenic fusions involving members of the NTRK gene family in a subset of our cohort. One-patient with BCAN exon 13 fused to NTRK1 exon 11 initially underwent a subtotal resection for a 4th ventricular glioneuronal tumor but ultimately required additional therapy due to progressive, symptomatic disease. Given the patient’s targetable fusion, the patient was enrolled on a clinical trial with entrectinib, a pan-Trk, ROS1, and ALK (anaplastic lymphoma kinase) inhibitor. The patient was treated for 11 months and during this time volumetric analysis of the lesion demonstrated a maximum reduction of 60% in the contrast-enhancing tumor compared to his pre-treatment magnetic resonance imaging study. The radiologic response was associated with resolution of his clinical symptoms and was maintained for 11 months on treatment. This report of a BCAN-NTRK1 fusion in glioneuronal tumors highlights its clinical importance as a novel, targetable alteration.

Alvarez-Breckenridge C, Miller JJ, Nayyar N, Gill CM, Kaneb A, D’Andrea M, Le LP, Lee J, Cheng J, Zheng Z, Butler WE, Multani P, Chow Maneval E, Ha Paek S, Toyota BD, Dias-Santagata D, Santagata S, Romero J, Shaw AT, Farago AF, Yip S, Cahill DP, Batchelor TT, Iafrate AJ, BrastianosPK.
NPJ Precis Oncol. 2017 Mar 20;1(1):5. doi: 10.1038/s41698-017-0009-y. eCollection 2017.

Background: Recent studies have reported mutations in the telomerase reverse transcriptase promoter (TERTp) in meningiomas. We sought to determine the frequency, clonality and clinical significance of telomere gene alterations in a cohort of patients with progressive/higher-grade meningiomas.

Methods: We characterized 64 temporally- and regionally-distinct specimens from 26 WHO grade III meningioma patients. On initial diagnoses, the meningiomas spanned all WHO grades (3 grade I, 13 grade II and 10 grade III). The tumor samples were screened for TERTp and ATRX/DAXX mutations, and TERT rearrangements. Additionally, TERTp was sequenced in a separate cohort of 19 patients with radiation-associated meningiomas. We examined the impact of mutational status on patients’ progression and overall survival.

Results: Somatic TERTp mutations were detected in six patients (6/26 = 23%). Regional intratumoral heterogeneity in TERTp mutation status was noted. In 4 patients, TERTp mutations were detected in recurrent specimens but not in the available specimens of the first surgery. Additionally, a TERT gene fusion (LPCAT1-TERT) was found in one sample. In contrary, none of the investigated samples harbored an ATRX or DAXX mutation. In the cohort of radiation-induced meningiomas, TERTp mutation was detected in two patients (10.5%). Importantly, we found that patients with emergence of TERTp mutations had a substantially shorter OS than their TERTp wild-type counterparts (2.7 years, 95% CI 0.9 – 4.5 years versus 10.8 years, 95% CI 7.8 -12.8 years, p=0.003).

Conclusions: In progressive/higher-grade meningiomas,TERTp mutations are associated with poor survival, supporting a model in which selection of this alteration is a harbinger of aggressive tumor development. In addition, we observe spatial intratumoral heterogeneity of TERTp mutation status, consistent with this model of late emergence in tumor evolution. Thus, early detection of TERTp mutations may define patients with more aggressive meningiomas. Stratification for TERT alterations should be adopted in future clinical trials of progressive/higher-grade meningiomas.

Juratli TA1,2, Thiede C3, Koerner MVA1, Tummala SS1, Daubner D4, Shankar GM1, Williams EA5, Martinez-Lage M5, Soucek S2, Robel K2, Penson T1, Krause M6,7,8, Appold S6,7,8, Meinhardt M9, Pinzer T2, Miller JJ10, Krex D2,7, Ely HA11, Silverman IM11, Christiansen J11, Schackert G2,7, Wakimoto H1, Kirsch M2,7, Brastianos PK12, Cahill DP1.

Oncotarget. 2017 Nov 24;8(65):109228-109237. doi: 10.18632/oncotarget.22650. eCollection 2017 Dec 12.

Glioblastomas are malignant neoplasms composed of diverse cell populations. This intratumoral diversity has an underlying architecture, with a hierarchical relationship through clonal evolution from a common ancestor. Therapies are limited by emergence of resistant subclones from this phylogenetic reservoir. To characterize this clonal ancestral origin of recurrent tumors, we determined phylogenetic relationships using whole exome sequencing of pre-treatment IDH1/2 wild-type glioblastoma specimens, matched to post-treatment autopsy samples (n = 9) and metastatic extracranial post-treatment autopsy samples (n = 3). We identified “truncal” genetic events common to the evolutionary ancestry of the initial specimen and later recurrences, thereby inferring the identity of the precursor cell population. Mutations were identified in a subset of cases in known glioblastoma genes such as NF1(n = 3), TP53(n = 4) and EGFR(n = 5). However, by phylogenetic analysis, there were no protein-coding mutations as recurrent truncal events across the majority of cases. In contrast, whole copy-loss of chromosome 10 (12 of 12 cases), copy-loss of chromosome 9p21 (11 of 12 cases) and copy-gain in chromosome 7 (10 of 12 cases) were identified as shared events in the majority of cases. Strikingly, mutations in the TERT promoter were also identified as shared events in all evaluated pairs (9 of 9). Thus, we define four truncal non-coding genomic alterations that represent early genomic events in gliomagenesis, that identify the persistent cellular reservoir from which glioblastoma recurrences emerge. Therapies to target these key early genomic events are needed. These findings offer an evolutionary explanation for why precision therapies that target protein-coding mutations lack efficacy in GBM.

Brastianos PK, Nayyar N, Rosebrock D, Leshchiner I, Gill CM, Livitz D, Bertalan MS, D’Andrea M, Hoang K, Aquilanti E, Chukwueke UN, Kaneb A, Chi A, Plotkin S, Gerstner ER, Frosch MP, Suva ML, Cahill DP, Getz G, Batchelor TT.
NPJ Precis Oncol. 2017 Sep 18;1(1):33. doi: 10.1038/s41698-017-0035-9. eCollection 2017.

Progressive meningiomas that have failed surgery and radiation have a poor prognosis and no standard therapy. While meningiomas are more common in females overall, progressive meningiomas are enriched in males. We performed a comprehensive molecular characterization of 169 meningiomas from 53 patients with progressive/high-grade tumors, including matched primary and recurrent samples. Exome sequencing in an initial cohort (n = 24) detected frequent alterations in genes residing on the X chromosome, with somatic intragenic deletions of the dystrophin-encoding and muscular dystrophy-associated DMD gene as the most common alteration (n = 5, 20.8%), along with alterations of other known X-linked cancer-related genes KDM6A (n =2, 8.3%), DDX3X, RBM10 and STAG2 (n = 1, 4.1% each). DMD inactivation (by genomic deletion or loss of protein expression) was ultimately detected in 17/53 progressive meningioma patients (32%). Importantly, patients with tumors harboring DMD inactivation had a shorter overall survival (OS) than their wild-type counterparts [5.1 years (95% CI 1.3-9.0) vs. median not reached (95% CI 2.9-not reached, p = 0.006)]. Given the known poor prognostic association of TERT alterations in these tumors, we also assessed for these events, and found seven patients with TERT promoter mutations and three with TERT rearrangements in this cohort (n = 10, 18.8%), including a recurrent novel RETREG1-TERT rearrangement that was present in two patients. In a multivariate model, DMD inactivation (p = 0.033, HR = 2.6, 95% CI 1.0-6.6) and TERT alterations (p = 0.005, HR = 3.8, 95% CI 1.5-9.9) were mutually independent in predicting unfavorable outcomes. Thus, DMD alterations identify a subset of progressive/high-grade meningiomas with worse outcomes.

Juratli TA1,2,3, McCabe D4,5, Nayyar N2, Williams EA1,6, Silverman IM7, Tummala SS1, Fink AL1, Baig A6, Martinez-Lage M6, Selig MK6, Bihun IV2, Shankar GM1, Penson T1, Lastrapes M4,5, Daubner D8, Meinhardt M9, Hennig S3, Kaplan AB2, Fujio S1, Kuter BM2, Bertalan MS2, Miller JJ1, Batten JM6, Ely HA7, Christiansen J7, Baretton GB9, Stemmer-Rachamimov AO6, Santagata S10, Rivera MN6, Barker FG 2nd1, Schackert G3, Wakimoto H1, Iafrate AJ6, Carter SL4,5, Cahill DP1, Brastianos PK11.
Acta Neuropathol. 2018 Nov;136(5):779-792. doi: 10.1007/s00401-018-1899-7. Epub 2018 Aug 19.