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Tsvetkov P, Detappe A, Cai K, Keys HR, Brune Z, Ying W, Thiru P, Reidy M, Kugener G, Rossen J, Kocak M, Kory N, Tsherniak A, Santagata S, Whitesell L, Ghobrial IM, Markley JL, Lindquist S, Golub TR. Mitochondrial metabolism promotes adaptation to proteotoxic stress. Nat Chem Biol 2019; 15:681-689. [PMID: 31133756 PMCID: PMC8183600 DOI: 10.1038/s41589-019-0291-9] [Citation(s) in RCA: 259] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 04/16/2019] [Indexed: 12/17/2022]
Abstract
The mechanisms by which cells adapt to proteotoxic stress are largely unknown, but key to understanding how tumor cells, particularly in vivo, are largely resistant to proteasome inhibitors. Analysis of cancer cell lines, mouse xenografts and patient-derived tumor samples all showed an association between mitochondrial metabolism and proteasome inhibitor sensitivity. When cells were forced to use oxidative phosphorylation rather than glycolysis, they became proteasome inhibitor-resistant. This mitochondrial state, however, creates a unique vulnerability: sensitivity to the small-molecule compound elesclomol. Genome-wide CRISPR/Cas9 screening showed that a single gene, encoding the mitochondrial reductase FDX1, could rescue elesclomol-induced cell death. Enzymatic function and NMR-based analyses further showed that FDX1 is the direct target of elesclomol, which promotes a unique form of copper-dependent cell death. These studies elucidate a fundamental mechanism by which cells adapt to proteotoxic stress and suggests strategies to mitigate proteasome inhibitor-resistance.
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Nathenson M, Hemming ML, Malik K, Lin JR, Santagata S, Du Z, Marino-Enriquez A, Hagan TJ, Chipashvili O, Thornton KA, Raut CP, Childs BH, Bertagnolli MM, Sicinska E, Ku N, Demetri GD. Molecular characterization and management of secondary resistance to serial TRK inhibitors. J Clin Oncol 2019. [DOI: 10.1200/jco.2019.37.15_suppl.e22547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e22547 Background: TRK inhibitor drugs such as the highly selective larotrectinib (Laro), have proven highly effective in malignancies harboring fusions of NTRK1, 2, or 3. Resistance in patients (pts) with progressive disease (PD) after response to initial TRK inhibitor therapy has been attributed to secondary mutations in the solvent front or gatekeeper domains of the NTRK fusion gene. LOXO-195 (L195) is a 2nd generation TRK inhibitor that overcomes these mutations. Mechanisms of resistance to L195 have not yet been well characterized. Methods: We analyzed molecular mechanisms of resistance in one adult pt with undifferentiated pleomorphic sarcoma (UPS) who had serial responses and PD on Laro and L195. Targeted DNA sequencing, RNA sequencing and multicolor cyclic immunofluorescence (CyCIF) were performed on pre- and post-PD specimens on both drugs. Results: The patient was enrolled on the phase 2 clinical trial of Laro (NCT02576431) with TPM3-NTRK1 fusion UPS. Multifocal PD and resistance to Laro developed after major objective response RECIST -74.9%, of 10 months (mo); the resistant tumor harbored both the initial TPM3-NTRK1 fusion but also evolved a new solvent front mutation in NTRK1 [c.1783G > A (p.G595R)]. A single pt protocol (NCT03206931) was designed to treat with L195. After an initial response to L195, PD limited to 2 sites developed; both sites were resected at 5 and 10 mo. The pt continues on L195 with systemic disease control 20 mo after initiation (in total 30 mo since Laro initiation). Analysis of tumor samples pre- and post-PD on L195 identified the emergence of a KRAS G12V mutation, with associated activation of the KRAS signaling pathway and a significant infiltration by inflammatory cells. A cell line and pt-derived xenografts (PDX), all harboring the initial TPM3-NTRK1 fusion, were generated from this pt. Conclusions: Resection of oligoclonal PD and continuation of L195 post-PD can be an effective treatment strategy. Oncogenic activation of the KRAS pathway is a possible mechanism of resistance to L195. Our studies indicate that the tumor microenvironment of TRK-fusion sarcomas resistant to TRK inhibitors may increase inflammatory cell infiltrates, which may provide clues for future combination therapy.
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Alexander BM, Trippa L, Gaffey S, Arrillaga-Romany IC, Lee EQ, Rinne ML, Ahluwalia MS, Colman H, Fell G, Galanis E, de Groot J, Drappatz J, Lassman AB, Meredith DM, Nabors LB, Santagata S, Schiff D, Welch MR, Ligon KL, Wen PY. Individualized Screening Trial of Innovative Glioblastoma Therapy (INSIGhT): A Bayesian Adaptive Platform Trial to Develop Precision Medicines for Patients With Glioblastoma. JCO Precis Oncol 2019; 3:1800071. [PMID: 32914038 PMCID: PMC7448806 DOI: 10.1200/po.18.00071] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2018] [Indexed: 01/01/2023] Open
Abstract
PURPOSE Adequately prioritizing the numerous therapies and biomarkers available in late-stage testing for patients with glioblastoma (GBM) requires an efficient clinical testing platform. We developed and implemented INSIGhT (Individualized Screening Trial of Innovative Glioblastoma Therapy) as a novel adaptive platform trial (APT) to develop precision medicine approaches in GBM. METHODS INSIGhT compares experimental arms with a common control of standard concurrent temozolomide and radiation therapy followed by adjuvant temozolomide. The primary end point is overall survival. Patients with newly diagnosed unmethylated GBM who are IDH R132H mutation negative and with genomic data available for biomarker grouping are eligible. At the initiation of INSIGhT, three experimental arms (neratinib, abemaciclib, and CC-115), each with a proposed genomic biomarker, are tested simultaneously. Initial randomization is equal across arms. As the trial progresses, randomization probabilities adapt on the basis of accumulating results using Bayesian estimation of the biomarker-specific probability of treatment impact on progression-free survival. Treatment arms may drop because of low probability of treatment impact on overall survival, and new arms may be added. Detailed information on the statistical model and randomization algorithm is provided to stimulate discussion on trial design choices more generally and provide an example for other investigators developing APTs. CONCLUSION INSIGhT (NCT02977780) is an ongoing novel biomarker-based, Bayesian APT for patients with newly diagnosed unmethylated GBM. Our goal is to dramatically shorten trial execution timelines while increasing scientific power of results and biomarker discovery using adaptive randomization. We anticipate that trial execution efficiency will also be improved by using the APT format, which allows for the collaborative addition of new experimental arms while retaining the overall trial structure.
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Fritchie K, Jensch K, Moskalev EA, Caron A, Jenkins S, Link M, Brown PD, Rodriguez FJ, Guajardo A, Brat D, Velázquez Vega JE, Perry A, Wu A, Raleigh DR, Santagata S, Louis DN, Brastianos PK, Kaplan A, Alexander BM, Rossi S, Ferrarese F, Haller F, Giannini C. The impact of histopathology and NAB2-STAT6 fusion subtype in classification and grading of meningeal solitary fibrous tumor/hemangiopericytoma. Acta Neuropathol 2019; 137:307-319. [PMID: 30584643 PMCID: PMC6513906 DOI: 10.1007/s00401-018-1952-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/04/2018] [Accepted: 12/17/2018] [Indexed: 12/13/2022]
Abstract
Meningeal solitary fibrous tumor (SFT)/hemangiopericytoma (HPC) is a rare tumor with propensity for recurrence and metastasis. Although multiple classification schemes have been proposed, optimal risk stratification remains unclear, and the prognostic impact of fusion status is uncertain. We compared the 2016 WHO CNS tumor grading scheme (CNS-G), a three-tier system based on histopathologic phenotype and mitotic count, to the 2013 WHO soft-tissue counterpart (ST-G), a two-tier system based on mitotic count alone, in a cohort of 133 patients [59 female, 74 male; mean age 54 years (range 20–87)] with meningeal SFT/HPC. Tumors were pathologically confirmed through review of the first tumor resection (n = 97), local recurrence (n = 35), or distant metastasis (n = 1). A STAT6 immunostain showed nuclear expression in 132 cases. NAB2–STAT6 fusion was detected in 99 of 111 successfully tested tumors (89%) including the single STAT6 immunonegative tumor. Tumors were classified by CNS-G as grade 1 (n = 43), 2 (n = 41), or 3 (n = 49), and by ST-G as SFT (n = 84) or malignant SFT (n = 49). Necrosis was present in 16 cases (12%). On follow-up, 42 patients had at least one subsequent recurrence or metastasis (7 metastasis only, 33 recurrence only, 2 patients had both). Twenty-nine patients died. On univariate analysis, necrosis (p = 0.002), CNS-G (p = 0.01), and ST-G (p = 0.004) were associated with recurrence-free (RFS) but not overall survival (OS). NAB2–STAT6 fusion type was not significantly associated with RFS or OS, but was associated with phenotype. A modified ST-G incorporating necrosis showed higher correlation with RFS (p = 0.0006) and remained significant (p = 0.02) when considering only the primary tumors. From our data, mitotic rate and necrosis appear to stratify this family of tumors most accurately and could be incorporated in a future grading scheme.
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Walpole S, Pritchard AL, Cebulla CM, Pilarski R, Stautberg M, Davidorf FH, de la Fouchardière A, Cabaret O, Golmard L, Stoppa-Lyonnet D, Garfield E, Njauw CN, Cheung M, Turunen JA, Repo P, Järvinen RS, van Doorn R, Jager MJ, Luyten GPM, Marinkovic M, Chau C, Potrony M, Höiom V, Helgadottir H, Pastorino L, Bruno W, Andreotti V, Dalmasso B, Ciccarese G, Queirolo P, Mastracci L, Wadt K, Kiilgaard JF, Speicher MR, van Poppelen N, Kilic E, Al-Jamal RT, Dianzani I, Betti M, Bergmann C, Santagata S, Dahiya S, Taibjee S, Burke J, Poplawski N, O’Shea SJ, Newton-Bishop J, Adlard J, Adams DJ, Lane AM, Kim I, Klebe S, Racher H, Harbour JW, Nickerson ML, Murali R, Palmer JM, Howlie M, Symmons J, Hamilton H, Warrier S, Glasson W, Johansson P, Robles-Espinoza CD, Ossio R, de Klein A, Puig S, Ghiorzo P, Nielsen M, Kivelä TT, Tsao H, Testa JR, Gerami P, Stern MH, Paillerets BBD, Abdel-Rahman MH, Hayward NK. Comprehensive Study of the Clinical Phenotype of Germline BAP1 Variant-Carrying Families Worldwide. J Natl Cancer Inst 2018; 110:1328-1341. [PMID: 30517737 PMCID: PMC6292796 DOI: 10.1093/jnci/djy171] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 07/17/2018] [Accepted: 08/31/2018] [Indexed: 12/17/2022] Open
Abstract
Background The BRCA1-associated protein-1 (BAP1) tumor predisposition syndrome (BAP1-TPDS) is a hereditary tumor syndrome caused by germline pathogenic variants in BAP1 encoding a tumor suppressor associated with uveal melanoma, mesothelioma, cutaneous melanoma, renal cell carcinoma, and cutaneous BAP1-inactivated melanocytic tumors. However, the full spectrum of tumors associated with the syndrome is yet to be determined. Improved understanding of the BAP1-TPDS is crucial for appropriate clinical management of BAP1 germline variant carriers and their families, including genetic counseling and surveillance for new tumors. Methods We collated germline variant status, tumor diagnoses, and information on BAP1 immunohistochemistry or loss of somatic heterozygosity on 106 published and 75 unpublished BAP1 germline variant-positive families worldwide to better characterize the genotypes and phenotypes associated with the BAP1-TPDS. Tumor spectrum and ages of onset were compared between missense and null variants. All statistical tests were two-sided. Results The 181 families carried 140 unique BAP1 germline variants. The collated data confirmed the core tumor spectrum associated with the BAP1-TPDS and showed that some families carrying missense variants can exhibit this phenotype. A variety of noncore BAP1-TPDS -associated tumors were found in families of variant carriers. Median ages of onset of core tumor types were lower in null than missense variant carriers for all tumors combined (P < .001), mesothelioma (P < .001), cutaneous melanoma (P < .001), and nonmelanoma skin cancer (P < .001). Conclusions This analysis substantially increases the number of pathogenic BAP1 germline variants and refines the phenotype. It highlights the need for a curated registry of germline variant carriers for proper assessment of the clinical phenotype of the BAP1-TPDS and pathogenicity of new variants, thus guiding management of patients and informing areas requiring further research.
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Dunn IF, Du Z, Touat M, Sisti MB, Wen PY, Umeton R, Dubuc AM, Ducar M, Canoll PD, Severson E, Elvin JA, Ramkissoon SH, Lin JR, Cabrera L, Acevedo B, Sorger PK, Ligon KL, Santagata S, Reardon DA. Mismatch repair deficiency in high-grade meningioma: a rare but recurrent event associated with dramatic immune activation and clinical response to PD-1 blockade. JCO Precis Oncol 2018; 2018. [PMID: 30801050 DOI: 10.1200/po.18.00190] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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Touat M, Dubuc A, Meredith D, Tsuji J, Mills C, Gaffey S, Geduldig J, Watkinson F, Pelton K, Malinowski S, Lennon N, Sorger P, Trippa L, Ramkissoon S, Reardon D, de Groot J, Galanis E, Welch M, Nabors LB, Arrillaga-Romany I, Chiocca EA, Santagata S, Schiff D, Ahluwalia M, Colman H, Drappatz J, Alexander B, Wen P, Ligon K. INNV-13. ALLELE: A CONSORTIUM FOR PROSPECTIVE GENOMICS AND FUNCTIONAL DIAGNOSTICS TO GUIDE PATIENT CARE AND TRIAL ANALYSIS IN NEWLY-DIAGNOSED GLIOBLASTOMA. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy148.587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Touat M, Santagata S, Guillerm E, Bi W, Beuvon F, Mokhtari K, Giry M, Guegan J, Block S, Carpentier A, Delattre JY, Sanson M, Duval A, Beroukhim R, Bandopadhayay P, Reardon D, Wen P, Idbaih A, Coulet F, Ligon K, Bielle F. PATH-16. MOLECULAR PATHOLOGY AND CLINICAL CHARACTERISTICS OF MMR DEFICIENCY (MMRd) IN DIFFUSE GLIOMAS. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy148.672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Fritchie K, Jensch K, Jenkins S, Link M, D Brown P, Rodriguez F, Guajardo A, Brat D, Velazquez Vega J, Perry A, Wu A, Raleigh D, Santagata S, Louis D, Brastianos P, Kaplan A, Alexander B, Rossi S, Ferrarese F, Haller F, Giannini C. RARE-08. GRADING CONSIDERATIONS FOR MENINGEAL SOLITARY FIBROUS TUMOR/HEMANGIOPERICYTOMA. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy148.985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Hwang W, Lamba N, Kim D, Marciscano A, Stemmer-Rachamimov A, Curry W, Barker F, Martuza R, Santagata S, Dunn I, Claus E, Bi W, Aizer A, Alexander B, Oh K, Loeffler J, Shih H. Atypical Histopathological Features and the Risk of Progression/Recurrence in WHO Grade I-II Meningiomas. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.07.773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Dubuc AM, Touat M, Meredith DM, Gaffey SC, Geduldig JE, Ramkissoon S, de Groot JF, Galanis E, Lassman AB, Nabors B, Arrilaga-Romany I, Chiocca EA, Santagata S, Schiff D, Ahluwalia M, Colman H, Drappatz J, Alexander BM, Wen PY, Ligon KL. 18. ALLELE: A consortium for prospective genomics and functional diagnostics to guide patient care and trial analysis in newly-diagnosed glioblastoma. Cancer Genet 2018. [DOI: 10.1016/j.cancergen.2018.04.079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Lin JR, Izar B, Wang S, Yapp C, Mei S, Shah PM, Santagata S, Sorger PK. Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes. eLife 2018; 7:e31657. [PMID: 29993362 PMCID: PMC6075866 DOI: 10.7554/elife.31657] [Citation(s) in RCA: 340] [Impact Index Per Article: 56.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 06/29/2018] [Indexed: 12/20/2022] Open
Abstract
The architecture of normal and diseased tissues strongly influences the development and progression of disease as well as responsiveness and resistance to therapy. We describe a tissue-based cyclic immunofluorescence (t-CyCIF) method for highly multiplexed immuno-fluorescence imaging of formalin-fixed, paraffin-embedded (FFPE) specimens mounted on glass slides, the most widely used specimens for histopathological diagnosis of cancer and other diseases. t-CyCIF generates up to 60-plex images using an iterative process (a cycle) in which conventional low-plex fluorescence images are repeatedly collected from the same sample and then assembled into a high-dimensional representation. t-CyCIF requires no specialized instruments or reagents and is compatible with super-resolution imaging; we demonstrate its application to quantifying signal transduction cascades, tumor antigens and immune markers in diverse tissues and tumors. The simplicity and adaptability of t-CyCIF makes it an effective method for pre-clinical and clinical research and a natural complement to single-cell genomics.
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Farkkila A, Chopra SS, Lin JR, Maliga Z, Koruchupakkal B, Strickland KC, Howitt BE, Santagata S, Matulonis UA, Elias K, Swisher EM, Konstantinopoulos PA, Sorger P, D'Andrea AD. Abstract 139: DNA damage and immunoprofiling with highly multiplexed tissue immunofluorescence (t-CycIF) in high-grade serous ovarian cancer. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Immune checkpoint blockade (ICB) has emerged as a new promising therapeutic approach in multiple cancers, however, the responses to single-agent ICBs have been modest in high-grade serous ovarian cancer (HGSOC). Preclinical- and early clinical data show promising efficacy of combining DNA damaging agents with immunotherapy. An improved understanding of the interplay between DNA damage in cancer cells and anti-tumor immune responses may therefore accelerate the development of rational drug combinations and identify predictive biomarkers. The majority of HGSOC are deficient in homologous recombination (HR) DNA repair, and use alternative, error-prone DNA repair pathways, that have been shown to be associated with increased immune recognition (Strickland et al, 2016). Compelling evidence has shown that DNA damaging agents increase the expression of immune-regulatory genes, such as MCH class I antigens, and interferons in HR deficient tumors. Further, HR deficient tumor exhibit an increased response to ICBs, and DNA damage-driven activation of interferon signalling has been shown to overcome resistance to ICBs (Wang et al, 2016). To reveal the relationship between intrinsic and treatment-induced DNA damage and the HGSOC immune microenvironment we are employing a novel, high-multiplex tissue cyclic immunofluorescence (t-CycIF) platform (Lin et al, 2016& 2017) allowing for the simultaneous detection of up to 60 different antigens at single cell resolution. Utilizing t-CycIF we are in the process of profiling the DNA damage and immune responses in three unique HGSOC clinical cohorts including i) tumors with inherent DNA repair deficiencies ii) pre- and post DNA damaging therapy iii) tumors collected in an innovative clinical trial combining Poly- ADP Ribose Polymerase inhibitor (PARPi) Niraparib and ICB Pembrolizumab. Using this high-dimensional, quantitative data we are mapping the abundance, spatial arrangement and functional state of cancer cells, immune cells, and stroma in the HGSOC microenvironment. The highly multiplexed t-CycIF data are processed with established computational algorithms and correlated with clinical outcomes. Our preliminary data shows that t-CycIF sensitively captures immune cell subpopulations, tumor heterogeneity and DNA damage in HGSOC. We anticipate that t-CycIF could accelerate the development of rational strategies for combining DNA damaging agents with immunotherapy to ultimately improve the treatment and outcomes of patients with ovarian cancer.
Citation Format: Anniina Farkkila, Sameer S. Chopra, Jia-Ren Lin, Zoltan Maliga, Bose Koruchupakkal, Kyle C. Strickland, Brooke E. Howitt, Sandro Santagata, Ursula A. Matulonis, Kevin Elias, Elizabeth M. Swisher, Panagiotis A. Konstantinopoulos, Peter Sorger, Alan D. D'Andrea. DNA damage and immunoprofiling with highly multiplexed tissue immunofluorescence (t-CycIF) in high-grade serous ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 139.
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Shankar GM, Santagata S. BAP1 mutations in high-grade meningioma: implications for patient care. Neuro Oncol 2018; 19:1447-1456. [PMID: 28482042 DOI: 10.1093/neuonc/nox094] [Citation(s) in RCA: 121] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We have recently shown that the breast cancer (BRCA)1-associated protein-1 tumor suppressor gene (BAP1) is inactivated in a subset of clinically aggressive meningiomas that display rhabdoid histomorphology. Immunohistochemistry for BAP1 protein provides a rapid and inexpensive method for screening suspected cases. Notably, some patients with BAP1-mutant meningiomas have germline BAP1 mutations and BAP1 tumor predisposition syndrome (TPDS). It appears that nearly all patients with germline BAP1 mutations develop malignancies by age 55, most frequently uveal melanoma, cutaneous melanoma, pleural or peritoneal malignant mesothelioma, or renal cell carcinoma, although other cancers have also been associated with BAP1 TPDS. Therefore, when confronted with a patient with a potentially high-grade rhabdoid meningioma, it is important that neuropathologists assess the BAP1 status of the tumor and that the patient's family history of cancer is carefully ascertained. In the appropriate clinical setting, genetic counseling and germline BAP1 DNA sequencing should be performed. A cancer surveillance program for individuals who carry germline BAP1 mutations may help identify tumors such as uveal melanoma, cutaneous melanoma, and renal cell carcinoma at early and treatable stages. Because BAP1-mutant meningiomas are rare tumors, multi-institutional efforts will be needed to evaluate therapeutic strategies and to further define the clinicopathologic features of these tumors.
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Coy S, Rashid R, Lin JR, Du Z, Donson AM, Hankinson TC, Foreman NK, Manley PE, Kieran MW, Reardon DA, Sorger PK, Santagata S. CRAN-11. MULTIPLEXED IMMUNOFLUORESCENCE REVEALS POTENTIAL PD-1/PD-L1 PATHWAY VULNERABILITIES IN CRANIOPHARYNGIOMA. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy059.048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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141
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Mobark NA, Al-Harbi M, Santagata S, Abedalthagafi M. MBRS-01. A CASE OF MOLECULARLY PROFILED EXTRANEURAL MEDULLOBLASTOMA METASTASES IN A CHILD. Neuro Oncol 2018. [DOI: 10.1093/neuonc/noy059.448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Galanis E, Nassiri F, Coy S, Nejad R, Zadeh G, Santagata S. Integrating Genomics Into Neuro-Oncology Clinical Trials and Practice. Am Soc Clin Oncol Educ Book 2018; 38:148-157. [PMID: 30231374 DOI: 10.1200/edbk_200989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Important advances in our understanding of the molecular biology of brain tumors have resulted in a rapid evolution in the taxonomy of central nervous system (CNS) tumors, which culminated in the revised 2016 World Health Organization classification of CNS tumors that incorporates an integrated molecular/histologic diagnostic approach. Our expanding understanding of brain tumor genomics and molecular evolution during the disease course has started to impact clinical management. Furthermore, incorporation of genomic information in ongoing and planned neuro-oncology clinical trials is expected to lead to improved outcomes and result in personalized treatment options for patients with CNS malignancies.
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Touat M, Dubuc AM, Meredith DM, Gaffey SC, Gedulig JE, Ramkissoon SH, De Groot JF, Galanis E, Welch MR, Nabors LB, Arrillaga I, Chiocca EA, Santagata S, Schiff D, Ahluwalia MS, Colman H, Drappatz J, Alexander BM, Wen PY, Ligon KL. ALLELE: A consortium for prospective genomics and functional diagnostics to guide patient care and trial analysis in newly-diagnosed glioblastoma. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.2003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Ramkissoon SH, Bandopadhayay P, Hwang J, Ramkissoon LA, Greenwald NF, Schumacher SE, O'Rourke R, Pinches N, Ho P, Malkin H, Sinai C, Filbin M, Plant A, Bi WL, Chang MS, Yang E, Wright KD, Manley PE, Ducar M, Alexandrescu S, Lidov H, Delalle I, Goumnerova LC, Church AJ, Janeway KA, Harris MH, MacConaill LE, Folkerth RD, Lindeman NI, Stiles CD, Kieran MW, Ligon AH, Santagata S, Dubuc AM, Chi SN, Beroukhim R, Ligon KL. Clinical targeted exome-based sequencing in combination with genome-wide copy number profiling: precision medicine analysis of 203 pediatric brain tumors. Neuro Oncol 2018; 19:986-996. [PMID: 28104717 DOI: 10.1093/neuonc/now294] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Background Clinical genomics platforms are needed to identify targetable alterations, but implementation of these technologies and best practices in routine clinical pediatric oncology practice are not yet well established. Methods Profile is an institution-wide prospective clinical research initiative that uses targeted sequencing to identify targetable alterations in tumors. OncoPanel, a multiplexed targeted exome-sequencing platform that includes 300 cancer-causing genes, was used to assess single nucleotide variants and rearrangements/indels. Alterations were annotated (Tiers 1-4) based on clinical significance, with Tier 1 alterations having well-established clinical utility. OncoCopy, a clinical genome-wide array comparative genomic hybridization (aCGH) assay, was also performed to evaluate copy number alterations and better define rearrangement breakpoints. Results Cancer genomes of 203 pediatric brain tumors were profiled across histological subtypes, including 117 samples analyzed by OncoPanel, 146 by OncoCopy, and 60 tumors subjected to both methodologies. OncoPanel revealed clinically relevant alterations in 56% of patients (44 cancer mutations and 20 rearrangements), including BRAF alterations that directed the use of targeted inhibitors. Rearrangements in MYB-QKI, MYBL1, BRAF, and FGFR1 were also detected. Furthermore, while copy number profiles differed across histologies, the combined use of OncoPanel and OncoCopy identified subgroup-specific alterations in 89% (17/19) of medulloblastomas. Conclusion The combination of OncoPanel and OncoCopy multiplex genomic assays can identify critical diagnostic, prognostic, and treatment-relevant alterations and represents an effective precision medicine approach for clinical evaluation of pediatric brain tumors.
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Du Z, Santagata S. Uncovering the links between systemic hormones and oncogenic signaling in the pathogenesis of meningioma. Ann Oncol 2018; 29:537-540. [DOI: 10.1093/annonc/mdy010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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146
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Rasool N, Lefebvre DR, Latina MA, Dunn IF, Santagata S, Freitag SK, Cestari DM. Orbital leiomyosarcoma metastasis presenting prior to diagnosis of the primary tumor. Digit J Ophthalmol 2018; 23:22-26. [PMID: 29403338 DOI: 10.5693/djo.02.2017.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Leiomyosarcomas, neoplasms of smooth muscle, are rarely found within the orbit. Orbital leiomyosarcoma may be primary, metastatic, or secondary to radiation. When they are metastatic, patients almost exclusively have a history of a primary leiomyosarcoma, often occurring in the spermatic cord, skin, gastrointestinal tract, or the uterus. We present the case of 48-year-old woman who presented with a metastatic orbital leiomyosarcoma, which was identified before the primary tumor.
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147
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Mobark NA, Al-Harbi M, Mosleh O, Santagata S, Snuderl M, Abedalthagafi M. A case of molecularly profiled extraneural medulloblastoma metastases in a child. BMC MEDICAL GENETICS 2018; 19:10. [PMID: 29343221 PMCID: PMC5772742 DOI: 10.1186/s12881-018-0526-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 01/12/2018] [Indexed: 11/17/2022]
Abstract
Background Extraneural metastases are relatively rare manifestations of medulloblastoma. Case presentation We present the case of a young boy with group three MYCN-amplified medulloblastoma. He received multimodal chemotherapy consisting of gross total resection followed by postoperative craniospinal radiation and adjuvant chemotherapy. The patient developed extraneural metastases 4 months after the end of therapy. Literature review identifies the poor prognosis of MYCN-amplified medulloblastomas as well as extraneural metastases; we review the current limitations and future directions of medulloblastoma treatment options. Conclusion To the best of our knowledge, this is the first molecularly characterized report of extraneural metastases of medulloblastoma in a child.
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Shankar GM, Abedalthagafi M, Vaubel RA, Merrill PH, Nayyar N, Gill CM, Brewster R, Bi WL, Agarwalla PK, Thorner AR, Reardon DA, Al-Mefty O, Wen PY, Alexander BM, van Hummelen P, Batchelor TT, Ligon KL, Ligon AH, Meyerson M, Dunn IF, Beroukhim R, Louis DN, Perry A, Carter SL, Giannini C, Curry WT, Cahill DP, Barker FG, Brastianos PK, Santagata S. Germline and somatic BAP1 mutations in high-grade rhabdoid meningiomas. Neuro Oncol 2017; 19:535-545. [PMID: 28170043 DOI: 10.1093/neuonc/now235] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 10/04/2016] [Indexed: 12/30/2022] Open
Abstract
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.
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Coroller TP, Bi WL, Huynh E, Abedalthagafi M, Aizer AA, Greenwald NF, Parmar C, Narayan V, Wu WW, Miranda de Moura S, Gupta S, Beroukhim R, Wen PY, Al-Mefty O, Dunn IF, Santagata S, Alexander BM, Huang RY, Aerts HJWL. Radiographic prediction of meningioma grade by semantic and radiomic features. PLoS One 2017; 12:e0187908. [PMID: 29145421 PMCID: PMC5690632 DOI: 10.1371/journal.pone.0187908] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 10/28/2017] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES The clinical management of meningioma is guided by tumor grade and biological behavior. Currently, the assessment of tumor grade follows surgical resection and histopathologic review. Reliable techniques for pre-operative determination of tumor grade may enhance clinical decision-making. METHODS A total of 175 meningioma patients (103 low-grade and 72 high-grade) with pre-operative contrast-enhanced T1-MRI were included. Fifteen radiomic (quantitative) and 10 semantic (qualitative) features were applied to quantify the imaging phenotype. Area under the curve (AUC) and odd ratios (OR) were computed with multiple-hypothesis correction. Random-forest classifiers were developed and validated on an independent dataset (n = 44). RESULTS Twelve radiographic features (eight radiomic and four semantic) were significantly associated with meningioma grade. High-grade tumors exhibited necrosis/hemorrhage (ORsem = 6.6, AUCrad = 0.62-0.68), intratumoral heterogeneity (ORsem = 7.9, AUCrad = 0.65), non-spherical shape (AUCrad = 0.61), and larger volumes (AUCrad = 0.69) compared to low-grade tumors. Radiomic and sematic classifiers could significantly predict meningioma grade (AUCsem = 0.76 and AUCrad = 0.78). Furthermore, combining them increased the classification power (AUCradio = 0.86). Clinical variables alone did not effectively predict tumor grade (AUCclin = 0.65) or show complementary value with imaging data (AUCcomb = 0.84). CONCLUSIONS We found a strong association between imaging features of meningioma and histopathologic grade, with ready application to clinical management. Combining qualitative and quantitative radiographic features significantly improved classification power.
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Linda Bi W, Greenwald N, Dubuc A, Santagata S, Ligon K, Ligon A, MacConnail L, Beroukhim R, Dunn I. PATH-30. GENOMIC LANDSCAPE OF CENTRAL NERVOUS SYSTEM TUMORS. Neuro Oncol 2017. [DOI: 10.1093/neuonc/nox168.720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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