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Beccari S, Mohamed E, Voong V, Hilz S, Lafontaine M, Shai A, Lim Y, Martinez J, Switzman B, Yu RL, Lupo JM, Chang EF, Hervey-Jumper SL, Berger MS, Costello JF, Phillips JJ. Quantitative Assessment of Preanalytic Variables on Clinical Evaluation of PI3/AKT/mTOR Signaling Activity in Diffuse Glioma. Mod Pathol 2024; 37:100488. [PMID: 38588881 DOI: 10.1016/j.modpat.2024.100488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 03/08/2024] [Accepted: 03/30/2024] [Indexed: 04/10/2024]
Abstract
Biomarker-driven therapeutic clinical trials require the implementation of standardized, evidence-based practices for sample collection. In diffuse glioma, phosphatidylinositol 3 (PI3)-kinase/AKT/mTOR (PI3/AKT/mTOR) signaling is an attractive therapeutic target for which window-of-opportunity clinical trials could facilitate the identification of promising new agents. Yet, the relevant preanalytic variables and optimal tumor sampling methods necessary to measure pathway activity are unknown. To address this, we used a murine model for isocitrate dehydrogenase (IDH)-wildtype glioblastoma (GBM) and human tumor tissue, including IDH-wildtype GBM and IDH-mutant diffuse glioma. First, we determined the impact of delayed time-to-formalin fixation, or cold ischemia time (CIT), on the quantitative assessment of cellular expression of 6 phosphoproteins that are readouts of PI3K/AK/mTOR activity (phosphorylated-proline-rich Akt substrate of 40 kDa (p-PRAS40, T246), -mechanistic target of rapamycin (p-mTOR; S2448); -AKT (p-AKT, S473); -ribosomal protein S6 (p-RPS6, S240/244 and S235/236), and -eukaryotic initiation factor 4E-binding protein 1 (p-4EBP1, T37/46). With CITs ≥ 2 hours, typical of routine clinical handling, all had reduced or altered expression with p-RPS6 (S240/244) exhibiting relatively greater stability. A similar pattern was observed using patient tumor samples from the operating room with p-4EBP1 more sensitive to delayed fixation than p-RPS6 (S240/244). Many clinical trials utilize unstained slides for biomarker evaluation. Thus, we evaluated the impact of slide storage conditions on the detection of p-RPS6 (S240/244), p-4EBP1, and p-AKT. After 5 months, storage at -80°C was required to preserve the expression of p-4EBP1 and p-AKT, whereas p-RPS6 (240/244) expression was not stable regardless of storage temperature. Biomarker heterogeneity impacts optimal tumor sampling. Quantification of p-RPS6 (240/244) expression in multiple regionally distinct human tumor samples from 8 patients revealed significant intratumoral heterogeneity. Thus, the accurate assessment of PI3K/AKT/mTOR signaling in diffuse glioma must overcome intratumoral heterogeneity and multiple preanalytic factors, including time-to-formalin fixation, slide storage conditions, and phosphoprotein of interest.
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Affiliation(s)
- Sol Beccari
- Department of Neurological Surgery, University of California, San Francisco, California
| | - Esraa Mohamed
- Department of Neurological Surgery, University of California, San Francisco, California
| | - Viva Voong
- Department of Neurological Surgery, University of California, San Francisco, California
| | - Stephanie Hilz
- Department of Neurological Surgery, University of California, San Francisco, California
| | - Marisa Lafontaine
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, California
| | - Anny Shai
- Department of Neurological Surgery, University of California, San Francisco, California
| | - Yunita Lim
- Department of Neurological Surgery, University of California, San Francisco, California
| | - Jerry Martinez
- Department of Neurological Surgery, University of California, San Francisco, California
| | - Benjamin Switzman
- Department of Neurological Surgery, University of California, San Francisco, California
| | - Ryon L Yu
- Department of Neurological Surgery, University of California, San Francisco, California
| | - Janine M Lupo
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, California
| | - Edward F Chang
- Department of Neurological Surgery, University of California, San Francisco, California
| | - Shawn L Hervey-Jumper
- Department of Neurological Surgery, University of California, San Francisco, California
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California, San Francisco, California
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, California
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California, San Francisco, California; Neuropathology Division, Department of Pathology, University of California, San Francisco, California.
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2
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Appin CL, Hong C, Suwala AK, Hilz S, Mathur R, Solomon DA, Smirnov IV, Stevers NO, Shai A, Wang A, Berger MS, Chang SM, Phillips JJ, Costello JF. Whole tumor analysis reveals early origin of the TERT promoter mutation and intercellular heterogeneity in TERT expression. Neuro Oncol 2024; 26:640-652. [PMID: 38141254 PMCID: PMC10995505 DOI: 10.1093/neuonc/noad231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Indexed: 12/25/2023] Open
Abstract
BACKGROUND The TERT promoter mutation (TPM) is acquired in most IDH-wildtype glioblastomas (GBM) and IDH-mutant oligodendrogliomas (OD) enabling tumor cell immortality. Previous studies on TPM clonality show conflicting results. This study was performed to determine whether TPM is clonal on a tumor-wide scale. METHODS We investigated TPM clonality in relation to presumed early events in 19 IDH-wildtype GBM and 10 IDH-mutant OD using 3-dimensional comprehensive tumor sampling. We performed Sanger sequencing on 264 tumor samples and deep amplicon sequencing on 187 tumor samples. We obtained tumor purity and copy number estimates from whole exome sequencing. TERT expression was assessed by RNA-seq and RNAscope. RESULTS We detected TPM in 100% of tumor samples with quantifiable tumor purity (219 samples). Variant allele frequencies (VAF) of TPM correlate positively with chromosome 10 loss in GBM (R = 0.85), IDH1 mutation in OD (R = 0.87), and with tumor purity (R = 0.91 for GBM; R = 0.90 for OD). In comparison, oncogene amplification was tumor-wide for MDM4- and most EGFR-amplified cases but heterogeneous for MYCN and PDGFRA, and strikingly high in low-purity samples. TPM VAF was moderately correlated with TERT expression (R = 0.52 for GBM; R = 0.65 for OD). TERT expression was detected in a subset of cells, solely in TPM-positive samples, including samples equivocal for tumor. CONCLUSIONS On a tumor-wide scale, TPM is among the earliest events in glioma evolution. Intercellular heterogeneity of TERT expression, however, suggests dynamic regulation during tumor growth. TERT expression may be a tumor cell-specific biomarker.
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Affiliation(s)
- Christina L Appin
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Chibo Hong
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Abigail K Suwala
- Department of Neurological Surgery, University of California, San Francisco, California, USA
- Department of Neuropathology, University of Heidelberg, Institute of Pathology, Heidelberg, Germany
| | - Stephanie Hilz
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Radhika Mathur
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - David A Solomon
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Ivan V Smirnov
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Nicholas O Stevers
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Anny Shai
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Albert Wang
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, California, USA
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3
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Schupp PG, Shelton SJ, Brody DJ, Eliscu R, Johnson BE, Mazor T, Kelley KW, Potts MB, McDermott MW, Huang EJ, Lim DA, Pieper RO, Berger MS, Costello JF, Phillips JJ, Oldham MC. Deconstructing intratumoral heterogeneity through multiomic and multiscale analysis of serial sections. bioRxiv 2024:2023.06.21.545365. [PMID: 37645893 PMCID: PMC10461981 DOI: 10.1101/2023.06.21.545365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Tumors may contain billions of cells including distinct malignant clones and nonmalignant cell types. Clarifying the evolutionary histories, prevalence, and defining molecular features of these cells is essential for improving clinical outcomes, since intratumoral heterogeneity provides fuel for acquired resistance to targeted therapies. Here we present a statistically motivated strategy for deconstructing intratumoral heterogeneity through multiomic and multiscale analysis of serial tumor sections (MOMA). By combining deep sampling of IDH-mutant astrocytomas with integrative analysis of single-nucleotide variants, copy-number variants, and gene expression, we reconstruct and validate the phylogenies, spatial distributions, and transcriptional profiles of distinct malignant clones. By genotyping nuclei analyzed by single-nucleus RNA-seq for truncal mutations, we further show that commonly used algorithms for identifying cancer cells from single-cell transcriptomes may be inaccurate. We also demonstrate that correlating gene expression with tumor purity in bulk samples can reveal optimal markers of malignant cells and use this approach to identify a core set of genes that is consistently expressed by astrocytoma truncal clones, including AKR1C3, whose expression is associated with poor outcomes in several types of cancer. In summary, MOMA provides a robust and flexible strategy for precisely deconstructing intratumoral heterogeneity and clarifying the core molecular properties of distinct cellular populations in solid tumors.
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Affiliation(s)
- Patrick G. Schupp
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, California, USA
| | - Samuel J. Shelton
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Daniel J. Brody
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Rebecca Eliscu
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Brett E. Johnson
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Tali Mazor
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
- Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, California, USA
- Medical Scientist Training Program and Neuroscience Graduate Program, University of California San Francisco, San Francisco, California, USA
| | - Kevin W. Kelley
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
- Medical Scientist Training Program and Neuroscience Graduate Program, University of California San Francisco, San Francisco, California, USA
- Neuroscience Graduate Program, University of California San Francisco, San Francisco, California, USA
| | - Matthew B. Potts
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Michael W. McDermott
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Eric J. Huang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Daniel A. Lim
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Russell O. Pieper
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Mitchel S. Berger
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Joseph F. Costello
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
| | - Joanna J. Phillips
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Michael C. Oldham
- Department of Neurological Surgery, University of California, San Francisco, San Francisco,California, USA
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4
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Nejo T, Wang L, Leung KK, Wang A, Lakshmanachetty S, Gallus M, Kwok DW, Hong C, Chen LH, Carrera DA, Zhang MY, Stevers NO, Maldonado GC, Yamamichi A, Watchmaker PB, Naik A, Shai A, Phillips JJ, Chang SM, Wiita AP, Wells JA, Costello JF, Diaz AA, Okada H. Challenges in the discovery of tumor-specific alternative splicing-derived cell-surface antigens in glioma. Sci Rep 2024; 14:6362. [PMID: 38493204 PMCID: PMC10944514 DOI: 10.1038/s41598-024-56684-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 03/09/2024] [Indexed: 03/18/2024] Open
Abstract
Despite advancements in cancer immunotherapy, solid tumors remain formidable challenges. In glioma, profound inter- and intra-tumoral heterogeneity of antigen landscape hampers therapeutic development. Therefore, it is critical to consider alternative sources to expand the repertoire of targetable (neo-)antigens and improve therapeutic outcomes. Accumulating evidence suggests that tumor-specific alternative splicing (AS) could be an untapped reservoir of antigens. In this study, we investigated tumor-specific AS events in glioma, focusing on those predicted to generate major histocompatibility complex (MHC)-presentation-independent, cell-surface antigens that could be targeted by antibodies and chimeric antigen receptor-T cells. We systematically analyzed bulk RNA-sequencing datasets comparing 429 tumor samples (from The Cancer Genome Atlas) and 9166 normal tissue samples (from the Genotype-Tissue Expression project), and identified 13 AS events in 7 genes predicted to be expressed in more than 10% of the patients, including PTPRZ1 and BCAN, which were corroborated by an external RNA-sequencing dataset. Subsequently, we validated our predictions and elucidated the complexity of the isoforms using full-length transcript amplicon sequencing on patient-derived glioblastoma cells. However, analyses of the RNA-sequencing datasets of spatially mapped and longitudinally collected clinical tumor samples unveiled remarkable spatiotemporal heterogeneity of the candidate AS events. Furthermore, proteomics analysis did not reveal any peptide spectra matching the putative antigens. Our investigation illustrated the diverse characteristics of the tumor-specific AS events and the challenges of antigen exploration due to their notable spatiotemporal heterogeneity and elusive nature at the protein levels. Redirecting future efforts toward intracellular, MHC-presented antigens could offer a more viable avenue.
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Affiliation(s)
- Takahide Nejo
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Lin Wang
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Kevin K Leung
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Albert Wang
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Senthilnath Lakshmanachetty
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Marco Gallus
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Darwin W Kwok
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Chibo Hong
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Lee H Chen
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Diego A Carrera
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Michael Y Zhang
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Nicholas O Stevers
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Gabriella C Maldonado
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Akane Yamamichi
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Payal B Watchmaker
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Akul Naik
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Anny Shai
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Arun P Wiita
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
- The Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
| | - James A Wells
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Aaron A Diaz
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Hideho Okada
- Department of Neurological Surgery, University of California, San Francisco (UCSF), 1450 3Rd Street, Box 0520, San Francisco, CA, 94158, USA.
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA.
- The Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
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5
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Stevers NO, Costello JF. Telomeres in glioma: Maintenance mechanisms to therapeutic potential. Neuro Oncol 2024:noae052. [PMID: 38466631 DOI: 10.1093/neuonc/noae052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Indexed: 03/13/2024] Open
Affiliation(s)
- Nicholas O Stevers
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
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6
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Mathur R, Wang Q, Schupp PG, Nikolic A, Hilz S, Hong C, Grishanina NR, Kwok D, Stevers NO, Jin Q, Youngblood MW, Stasiak LA, Hou Y, Wang J, Yamaguchi TN, Lafontaine M, Shai A, Smirnov IV, Solomon DA, Chang SM, Hervey-Jumper SL, Berger MS, Lupo JM, Okada H, Phillips JJ, Boutros PC, Gallo M, Oldham MC, Yue F, Costello JF. Glioblastoma evolution and heterogeneity from a 3D whole-tumor perspective. Cell 2024; 187:446-463.e16. [PMID: 38242087 PMCID: PMC10832360 DOI: 10.1016/j.cell.2023.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 10/03/2023] [Accepted: 12/06/2023] [Indexed: 01/21/2024]
Abstract
Treatment failure for the lethal brain tumor glioblastoma (GBM) is attributed to intratumoral heterogeneity and tumor evolution. We utilized 3D neuronavigation during surgical resection to acquire samples representing the whole tumor mapped by 3D spatial coordinates. Integrative tissue and single-cell analysis revealed sources of genomic, epigenomic, and microenvironmental intratumoral heterogeneity and their spatial patterning. By distinguishing tumor-wide molecular features from those with regional specificity, we inferred GBM evolutionary trajectories from neurodevelopmental lineage origins and initiating events such as chromothripsis to emergence of genetic subclones and spatially restricted activation of differential tumor and microenvironmental programs in the core, periphery, and contrast-enhancing regions. Our work depicts GBM evolution and heterogeneity from a 3D whole-tumor perspective, highlights potential therapeutic targets that might circumvent heterogeneity-related failures, and establishes an interactive platform enabling 360° visualization and analysis of 3D spatial patterns for user-selected genes, programs, and other features across whole GBM tumors.
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Affiliation(s)
- Radhika Mathur
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Qixuan Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Patrick G Schupp
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Ana Nikolic
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, AB
| | - Stephanie Hilz
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Chibo Hong
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Nadia R Grishanina
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Darwin Kwok
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Nicholas O Stevers
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Qiushi Jin
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Mark W Youngblood
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Lena Ann Stasiak
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ye Hou
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Juan Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Takafumi N Yamaguchi
- Department of Human Genetics, University of California, Los Angeles, Los Angees, CA, USA
| | - Marisa Lafontaine
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Anny Shai
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Ivan V Smirnov
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - David A Solomon
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Shawn L Hervey-Jumper
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Janine M Lupo
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Hideho Okada
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Paul C Boutros
- Department of Human Genetics, University of California, Los Angeles, Los Angees, CA, USA
| | - Marco Gallo
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, AB; Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - Michael C Oldham
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Joseph F Costello
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.
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7
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Hadad S, Gupta R, Oberheim Bush NA, Taylor JW, Villanueva-Meyer JE, Young JS, Wu J, Ravindranathan A, Zhang Y, Warrier G, McCoy L, Shai A, Pekmezci M, Perry A, Bollen AW, Phillips JJ, Braunstein SE, Raleigh DR, Theodosopoulos P, Aghi MK, Chang EF, Hervey-Jumper SL, Costello JF, de Groot J, Butowski NA, Clarke JL, Chang SM, Berger MS, Molinaro AM, Solomon DA. "De novo replication repair deficient glioblastoma, IDH-wildtype" is a distinct glioblastoma subtype in adults that may benefit from immune checkpoint blockade. Acta Neuropathol 2023; 147:3. [PMID: 38079020 PMCID: PMC10713691 DOI: 10.1007/s00401-023-02654-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 12/18/2023]
Abstract
Glioblastoma is a clinically and molecularly heterogeneous disease, and new predictive biomarkers are needed to identify those patients most likely to respond to specific treatments. Through prospective genomic profiling of 459 consecutive primary treatment-naïve IDH-wildtype glioblastomas in adults, we identified a unique subgroup (2%, 9/459) defined by somatic hypermutation and DNA replication repair deficiency due to biallelic inactivation of a canonical mismatch repair gene. The deleterious mutations in mismatch repair genes were often present in the germline in the heterozygous state with somatic inactivation of the remaining allele, consistent with glioblastomas arising due to underlying Lynch syndrome. A subset of tumors had accompanying proofreading domain mutations in the DNA polymerase POLE and resultant "ultrahypermutation". The median age at diagnosis was 50 years (range 27-78), compared with 63 years for the other 450 patients with conventional glioblastoma (p < 0.01). All tumors had histologic features of the giant cell variant of glioblastoma. They lacked EGFR amplification, lacked combined trisomy of chromosome 7 plus monosomy of chromosome 10, and only rarely had TERT promoter mutation or CDKN2A homozygous deletion, which are hallmarks of conventional IDH-wildtype glioblastoma. Instead, they harbored frequent inactivating mutations in TP53, NF1, PTEN, ATRX, and SETD2 and recurrent activating mutations in PDGFRA. DNA methylation profiling revealed they did not align with known reference adult glioblastoma methylation classes, but instead had unique globally hypomethylated epigenomes and mostly classified as "Diffuse pediatric-type high grade glioma, RTK1 subtype, subclass A". Five patients were treated with immune checkpoint blockade, four of whom survived greater than 3 years. The median overall survival was 36.8 months, compared to 15.5 months for the other 450 patients (p < 0.001). We conclude that "De novo replication repair deficient glioblastoma, IDH-wildtype" represents a biologically distinct subtype in the adult population that may benefit from prospective identification and treatment with immune checkpoint blockade.
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Affiliation(s)
- Sara Hadad
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Rohit Gupta
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Nancy Ann Oberheim Bush
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Jennie W Taylor
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Javier E Villanueva-Meyer
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA, USA
| | - Jacob S Young
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Jasper Wu
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Ajay Ravindranathan
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Yalan Zhang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Gayathri Warrier
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Lucie McCoy
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Anny Shai
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Melike Pekmezci
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Arie Perry
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Andrew W Bollen
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Steve E Braunstein
- Department of Radiation Oncology, University of California, San Francisco, CA, USA
| | - David R Raleigh
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Radiation Oncology, University of California, San Francisco, CA, USA
| | - Philip Theodosopoulos
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Manish K Aghi
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Edward F Chang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Shawn L Hervey-Jumper
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - John de Groot
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Nicholas A Butowski
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Jennifer L Clarke
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Annette M Molinaro
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA.
| | - David A Solomon
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA.
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8
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Williams EA, Ravindranathan A, Gupta R, Stevers NO, Suwala AK, Hong C, Kim S, Yuan JB, Wu J, Barreto J, Lucas CHG, Chan E, Pekmezci M, LeBoit PE, Mully T, Perry A, Bollen A, Van Ziffle J, Devine WP, Reddy AT, Gupta N, Basnet KM, Macaulay RJB, Malafronte P, Lee H, Yong WH, Williams KJ, Juratli TA, Mata DA, Huang RSP, Hiemenz MC, Pavlick DC, Frampton GM, Janovitz T, Ross JS, Chang SM, Berger MS, Jacques L, Song JS, Costello JF, Solomon DA. Novel SOX10 indel mutations drive schwannomas through impaired transactivation of myelination gene programs. Neuro Oncol 2023; 25:2221-2236. [PMID: 37436963 PMCID: PMC10708934 DOI: 10.1093/neuonc/noad121] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Indexed: 07/14/2023] Open
Abstract
BACKGROUND Schwannomas are common peripheral nerve sheath tumors that can cause severe morbidity given their stereotypic intracranial and paraspinal locations. Similar to many solid tumors, schwannomas and other nerve sheath tumors are primarily thought to arise due to aberrant hyperactivation of the RAS growth factor signaling pathway. Here, we sought to further define the molecular pathogenesis of schwannomas. METHODS We performed comprehensive genomic profiling on a cohort of 96 human schwannomas, as well as DNA methylation profiling on a subset. Functional studies including RNA sequencing, chromatin immunoprecipitation-DNA sequencing, electrophoretic mobility shift assay, and luciferase reporter assays were performed in a fetal glial cell model following transduction with wildtype and tumor-derived mutant isoforms of SOX10. RESULTS We identified that nearly one-third of sporadic schwannomas lack alterations in known nerve sheath tumor genes and instead harbor novel recurrent in-frame insertion/deletion mutations in SOX10, which encodes a transcription factor responsible for controlling Schwann cell differentiation and myelination. SOX10 indel mutations were highly enriched in schwannomas arising from nonvestibular cranial nerves (eg facial, trigeminal, vagus) and were absent from vestibular nerve schwannomas driven by NF2 mutation. Functional studies revealed these SOX10 indel mutations have retained DNA binding capacity but impaired transactivation of glial differentiation and myelination gene programs. CONCLUSIONS We thus speculate that SOX10 indel mutations drive a unique subtype of schwannomas by impeding proper differentiation of immature Schwann cells.
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Affiliation(s)
- Erik A Williams
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Ajay Ravindranathan
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Rohit Gupta
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Nicholas O Stevers
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Abigail K Suwala
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Chibo Hong
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Somang Kim
- Department of Physics and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jimmy Bo Yuan
- Department of Physics and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jasper Wu
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Jairo Barreto
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Calixto-Hope G Lucas
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Emily Chan
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Melike Pekmezci
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Philip E LeBoit
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Thaddeus Mully
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Arie Perry
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Andrew Bollen
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Jessica Van Ziffle
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - W Patrick Devine
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
| | - Alyssa T Reddy
- Departments of Neurology and Pediatrics, University of California, San Francisco, San Francisco, California, USA
| | - Nalin Gupta
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | | | | | | | - Han Lee
- Department of Pathology, University of California, Davis, Sacramento, California, USA
| | - William H Yong
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, California, USA
| | - Kevin Jon Williams
- Departments of Physiology and Medicine, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, USA
| | - Tareq A Juratli
- Department of Neurosurgery, Division of Neuro-Oncology, Faculty of Medicine and Carl Gustav Carus University Hospital, Dresden, Germany
| | - Douglas A Mata
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | | | | | - Dean C Pavlick
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | | | - Tyler Janovitz
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
| | - Jeffrey S Ross
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA
- Department of Pathology, State University of New York Upstate Medical University, Syracuse, New York, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Line Jacques
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Jun S Song
- Department of Physics and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - David A Solomon
- Department of Pathology, University of California, San Francisco, San Francisco, California, USA
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9
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Nejo T, Wang L, Leung KK, Wang A, Lakshmanachetty S, Gallus M, Kwok DW, Hong C, Chen LH, Carrera DA, Zhang MY, Stevers NO, Maldonado GC, Yamamichi A, Watchmaker P, Naik A, Shai A, Phillips JJ, Chang SM, Wiita AP, Wells JA, Costello JF, Diaz AA, Okada H. Challenges in the discovery of tumor-specific alternative splicing-derived cell-surface antigens in glioma. bioRxiv 2023:2023.10.26.564156. [PMID: 37961484 PMCID: PMC10634890 DOI: 10.1101/2023.10.26.564156] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Background Despite advancements in cancer immunotherapy, solid tumors remain formidable challenges. In glioma, profound inter-and intra-tumoral heterogeneity of antigen landscape hampers therapeutic development. Therefore, it is critical to consider alternative sources to expand the repertoire of targetable (neo-)antigens and improve therapeutic outcomes. Accumulating evidence suggests that tumor-specific alternative splicing (AS) could be an untapped reservoir of neoantigens. Results In this study, we investigated tumor-specific AS events in glioma, focusing on those predicted to generate major histocompatibility complex (MHC)-presentation-independent, cell-surface neoantigens that could be targeted by antibodies and chimeric antigen receptor (CAR)-T cells. We systematically analyzed bulk RNA-sequencing datasets comparing 429 tumor samples (from The Cancer Genome Atlas [TCGA]) and 9,166 normal tissue samples (from the Genotype-Tissue Expression project [GTEx]), and identified 13 AS events in 7 genes predicted to be expressed in more than 10% of the patients, including PTPRZ1 and BCAN , which were corroborated by an external RNA-sequencing dataset. Subsequently, we validated our predictions and elucidated the complexity of the isoforms using full-length transcript amplicon sequencing on patient-derived glioblastoma cells. However, analyses of the RNA-sequencing datasets of spatially mapped and longitudinally collected clinical tumor samples unveiled remarkable spatiotemporal heterogeneity of the candidate AS events. Furthermore, proteomics analysis did not reveal any peptide spectra matching the putative neoantigens. Conclusions Our investigation illustrated the diverse characteristics of the tumor-specific AS events and the challenges of antigen exploration due to their notable spatiotemporal heterogeneity and elusive nature at the protein levels. Redirecting future efforts toward intracellular, MHC-presented antigens could offer a more viable avenue.
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10
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Kwok DW, Stevers NO, Nejo T, Chen LH, Etxeberria I, Jung J, Okada K, Cove MC, Lakshmanachetty S, Gallus M, Barpanda A, Hong C, Chan GKL, Wu SH, Ramos E, Yamamichi A, Liu J, Watchmaker P, Ogino H, Saijo A, Du A, Grishanina N, Woo J, Diaz A, Chang SM, Phillips JJ, Wiita AP, Klebanoff CA, Costello JF, Okada H. Tumor-wide RNA splicing aberrations generate immunogenic public neoantigens. bioRxiv 2023:2023.10.19.563178. [PMID: 37904942 PMCID: PMC10614978 DOI: 10.1101/2023.10.19.563178] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/01/2023]
Abstract
T-cell-mediated immunotherapies are limited by the extent to which cancer-specific antigens are homogenously expressed throughout a tumor. We reasoned that recurrent splicing aberrations in cancer represent a potential source of tumor-wide and public neoantigens, and to test this possibility, we developed a novel pipeline for identifying neojunctions expressed uniformly within a tumor across diverse cancer types. Our analyses revealed multiple neojunctions that recur across patients and either exhibited intratumor heterogeneity or, in some cases, were tumor-wide. We identified CD8+ T-cell clones specific for neoantigens derived from tumor-wide and conserved neojunctions in GNAS and RPL22 , respectively. TCR-engineered CD8 + T-cells targeting these mutations conferred neoantigen-specific tumor cell eradication. Furthermore, we revealed that cancer-specific dysregulation in splicing factor expression leads to recurrent neojunction expression. Together, these data reveal that a subset of neojunctions are both intratumorally conserved and public, providing the molecular basis for novel T-cell-based immunotherapies that address intratumoral heterogeneity.
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11
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Carney SV, Banerjee K, Mujeeb A, Zhu B, Haase S, Varela ML, Kadiyala P, Tronrud CE, Zhu Z, Mukherji D, Gorla P, Sun Y, Tagett R, Núñez FJ, Luo M, Luo W, Ljungman M, Liu Y, Xia Z, Schwendeman A, Qin T, Sartor MA, Costello JF, Cahill DP, Lowenstein PR, Castro MG. Zinc Finger MYND-Type Containing 8 (ZMYND8) Is Epigenetically Regulated in Mutant Isocitrate Dehydrogenase 1 (IDH1) Glioma to Promote Radioresistance. Clin Cancer Res 2023; 29:1763-1782. [PMID: 36692427 PMCID: PMC10159884 DOI: 10.1158/1078-0432.ccr-22-1896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/27/2022] [Accepted: 12/22/2022] [Indexed: 01/25/2023]
Abstract
PURPOSE Mutant isocitrate dehydrogenase 1 (mIDH1) alters the epigenetic regulation of chromatin, leading to a hypermethylation phenotype in adult glioma. This work focuses on identifying gene targets epigenetically dysregulated by mIDH1 to confer therapeutic resistance to ionizing radiation (IR). EXPERIMENTAL DESIGN We evaluated changes in the transcriptome and epigenome in a radioresistant mIDH1 patient-derived glioma cell culture (GCC) following treatment with an mIDH1-specific inhibitor, AGI-5198. We identified Zinc Finger MYND-Type Containing 8 (ZMYND8) as a potential target of mIDH1 reprogramming. We suppressed ZMYND8 expression by shRNA knockdown and genetic knockout (KO) in mIDH1 glioma cells and then assessed cellular viability to IR. We assessed the sensitivity of mIDH1 GCCS to pharmacologic inhibition of ZMYND8-interacting partners: HDAC, BRD4, and PARP. RESULTS Inhibition of mIDH1 leads to an upregulation of gene networks involved in replication stress. We found that the expression of ZMYND8, a regulator of DNA damage response, was decreased in three patient-derived mIDH1 GCCs after treatment with AGI-5198. Knockdown of ZMYND8 expression sensitized mIDH1 GCCs to radiotherapy marked by decreased cellular viability. Following IR, mIDH1 glioma cells with ZMYND8 KO exhibit significant phosphorylation of ATM and sustained γH2AX activation. ZMYND8 KO mIDH1 GCCs were further responsive to IR when treated with either BRD4 or HDAC inhibitors. PARP inhibition further enhanced the efficacy of radiotherapy in ZMYND8 KO mIDH1 glioma cells. CONCLUSIONS These findings indicate the impact of ZMYND8 in the maintenance of genomic integrity and repair of IR-induced DNA damage in mIDH1 glioma. See related commentary by Sachdev et al., p. 1648.
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Affiliation(s)
- Stephen V. Carney
- Cancer Biology Training Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kaushik Banerjee
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Anzar Mujeeb
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Brandon Zhu
- Graduate Program in Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI, USA
| | - Santiago Haase
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maria L. Varela
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Padma Kadiyala
- Graduate Program in Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Claire E. Tronrud
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Ziwen Zhu
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Devarshi Mukherji
- Neuroscience, University of Michigan College of Literature, Science, the Arts (LSA), Ann Arbor, MI 48109, USA
| | - Preethi Gorla
- Neuroscience, University of Michigan College of Literature, Science, the Arts (LSA), Ann Arbor, MI 48109, USA
| | - Yilun Sun
- Department of Radiation Oncology, University Hospitals/Case Western Reserve University, Cleveland, OH, USA
| | - Rebecca Tagett
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Felipe J. Núñez
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maowu Luo
- Department of Pathology, UT Southwestern Medical Center, Dallas TX 75390, USA
| | - Weibo Luo
- Department of Pathology, UT Southwestern Medical Center, Dallas TX 75390, USA
- Department of Pharmacology, UT Southwestern Medical Center, Dallas TX 75390, USA
| | - Mats Ljungman
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Environmental Health Science, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Yayuan Liu
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ziyun Xia
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109, USA
| | - Anna Schwendeman
- Department of Radiation Oncology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tingting Qin
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Maureen A. Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Joseph F. Costello
- Department of Neurological Surgery, University of California, San Francisco, California, 94143 USA
| | - Daniel P. Cahill
- Department of Neurosurgery, Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston Massachusetts, 02114, USA
| | - Pedro R. Lowenstein
- Cancer Biology Training Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Graduate Program in Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Biosciences Initiative in Brain Cancer, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Maria G. Castro
- Cancer Biology Training Program, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Neurosurgery, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Graduate Program in Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
- Biosciences Initiative in Brain Cancer, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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12
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Minami N, Hong D, Taglang C, Batsios G, Gillespie AM, Viswanath P, Stevers N, Barger CJ, Costello JF, Ronen SM. Hyperpolarized δ-[1- 13C]gluconolactone imaging visualizes response to TERT or GABPB1 targeting therapy for glioblastoma. Sci Rep 2023; 13:5190. [PMID: 36997627 PMCID: PMC10063634 DOI: 10.1038/s41598-023-32463-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/28/2023] [Indexed: 04/01/2023] Open
Abstract
TERT promoter mutations are a hallmark of glioblastoma (GBM). Accordingly, TERT and GABPB1, a subunit of the upstream mutant TERT promoter transcription factor GABP, are being considered as promising therapeutic targets in GBM. We recently reported that the expression of TERT or GABP1 modulates flux via the pentose phosphate pathway (PPP). Here, we investigated whether 13C magnetic resonance spectroscopy (MRS) of hyperpolarized (HP) δ- [1-13C]gluconolactone can serve to image the reduction in PPP flux following TERT or GABPB1 silencing. We investigated two different human GBM cell lines stably expressing shRNAs targeting TERT or GABPB1, as well as doxycycline-inducible shTERT or shGABPB1cells. MRS studies were performed on live cells and in vivo tumors, and dynamic sets of 13C MR spectra were acquired following injection of HP δ-[1-13C]gluconolactone. HP 6-phosphogluconolactone (6PG), the product of δ-[1-13C]gluconolactone via the PPP, was significantly reduced in TERT or GABPB1-silenced cells or tumors compared to controls in all our models. Furthermore, a positive correlation between TERT expression and 6PG levels was observed. Our data indicate that HP δ-[1-13C]gluconolactone, an imaging tool with translational potential, could serve to monitor TERT expression and its silencing with therapies that target either TERT or GABPB1 in mutant TERT promoter GBM patients.
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Affiliation(s)
- Noriaki Minami
- Department of Radiology and Biomedical Imaging, University of California San Francisco, 1700 4th Street, San Francisco, CA, 94158, USA
| | - Donghyun Hong
- Department of Radiology and Biomedical Imaging, University of California San Francisco, 1700 4th Street, San Francisco, CA, 94158, USA
| | - Celine Taglang
- Department of Radiology and Biomedical Imaging, University of California San Francisco, 1700 4th Street, San Francisco, CA, 94158, USA
| | - Georgios Batsios
- Department of Radiology and Biomedical Imaging, University of California San Francisco, 1700 4th Street, San Francisco, CA, 94158, USA
| | - Anne Marie Gillespie
- Department of Radiology and Biomedical Imaging, University of California San Francisco, 1700 4th Street, San Francisco, CA, 94158, USA
| | - Pavithra Viswanath
- Department of Radiology and Biomedical Imaging, University of California San Francisco, 1700 4th Street, San Francisco, CA, 94158, USA
| | - Nicholas Stevers
- Department of Neurological Surgery, University of California, San Francisco, USA
| | - Carter J Barger
- Department of Neurological Surgery, University of California, San Francisco, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, USA
| | - Sabrina M Ronen
- Department of Radiology and Biomedical Imaging, University of California San Francisco, 1700 4th Street, San Francisco, CA, 94158, USA.
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13
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Jain S, Rick JW, Joshi RS, Beniwal A, Spatz J, Gill S, Chang ACC, Choudhary N, Nguyen AT, Sudhir S, Chalif EJ, Chen JS, Chandra A, Haddad AF, Wadhwa H, Shah SS, Choi S, Hayes JL, Wang L, Yagnik G, Costello JF, Diaz A, Heiland DH, Aghi MK. Single-cell RNA sequencing and spatial transcriptomics reveal cancer-associated fibroblasts in glioblastoma with protumoral effects. J Clin Invest 2023; 133:e147087. [PMID: 36856115 PMCID: PMC9974099 DOI: 10.1172/jci147087] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 01/12/2023] [Indexed: 03/02/2023] Open
Abstract
Cancer-associated fibroblasts (CAFs) were presumed absent in glioblastoma given the lack of brain fibroblasts. Serial trypsinization of glioblastoma specimens yielded cells with CAF morphology and single-cell transcriptomic profiles based on their lack of copy number variations (CNVs) and elevated individual cell CAF probability scores derived from the expression of 9 CAF markers and absence of 5 markers from non-CAF stromal cells sharing features with CAFs. Cells without CNVs and with high CAF probability scores were identified in single-cell RNA-Seq of 12 patient glioblastomas. Pseudotime reconstruction revealed that immature CAFs evolved into subtypes, with mature CAFs expressing actin alpha 2, smooth muscle (ACTA2). Spatial transcriptomics from 16 patient glioblastomas confirmed CAF proximity to mesenchymal glioblastoma stem cells (GSCs), endothelial cells, and M2 macrophages. CAFs were chemotactically attracted to GSCs, and CAFs enriched GSCs. We created a resource of inferred crosstalk by mapping expression of receptors to their cognate ligands, identifying PDGF and TGF-β as mediators of GSC effects on CAFs and osteopontin and HGF as mediators of CAF-induced GSC enrichment. CAFs induced M2 macrophage polarization by producing the extra domain A (EDA) fibronectin variant that binds macrophage TLR4. Supplementing GSC-derived xenografts with CAFs enhanced in vivo tumor growth. These findings are among the first to identify glioblastoma CAFs and their GSC interactions, making them an intriguing target.
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Affiliation(s)
- Saket Jain
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | - Jonathan W. Rick
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | | | - Angad Beniwal
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | - Jordan Spatz
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | - Sabraj Gill
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | | | - Nikita Choudhary
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | - Alan T. Nguyen
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | - Sweta Sudhir
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | - Eric J. Chalif
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | - Jia-Shu Chen
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | - Ankush Chandra
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | | | - Harsh Wadhwa
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | - Sumedh S. Shah
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | - Serah Choi
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | - Josie L. Hayes
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | - Lin Wang
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | - Garima Yagnik
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | | | - Aaron Diaz
- Department of Neurosurgery, UCSF, San Francisco, California, USA
| | | | - Manish K. Aghi
- Department of Neurosurgery, UCSF, San Francisco, California, USA
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14
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Miller JJ, Gonzalez Castro LN, McBrayer S, Weller M, Cloughesy T, Portnow J, Andronesi O, Barnholtz-Sloan JS, Baumert BG, Berger MS, Bi WL, Bindra R, Cahill DP, Chang SM, Costello JF, Horbinski C, Huang RY, Jenkins RB, Ligon KL, Mellinghoff IK, Nabors LB, Platten M, Reardon DA, Shi DD, Schiff D, Wick W, Yan H, von Deimling A, van den Bent M, Kaelin WG, Wen PY. Isocitrate dehydrogenase (IDH) mutant gliomas: A Society for Neuro-Oncology (SNO) consensus review on diagnosis, management, and future directions. Neuro Oncol 2023; 25:4-25. [PMID: 36239925 PMCID: PMC9825337 DOI: 10.1093/neuonc/noac207] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Isocitrate dehydrogenase (IDH) mutant gliomas are the most common adult, malignant primary brain tumors diagnosed in patients younger than 50, constituting an important cause of morbidity and mortality. In recent years, there has been significant progress in understanding the molecular pathogenesis and biology of these tumors, sparking multiple efforts to improve their diagnosis and treatment. In this consensus review from the Society for Neuro-Oncology (SNO), the current diagnosis and management of IDH-mutant gliomas will be discussed. In addition, novel therapies, such as targeted molecular therapies and immunotherapies, will be reviewed. Current challenges and future directions for research will be discussed.
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Affiliation(s)
- Julie J Miller
- Stephen E. and Catherine Pappas Center for Neuro-Oncology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Medical School, Boston, MA, USA
| | - L Nicolas Gonzalez Castro
- Harvard Medical School, Boston, MA, USA
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Samuel McBrayer
- Children’s Medical Center Research Institute, University of Texas Southwestern Medical Center, 6000 Harry Hines Blvd, Dallas, Texas, 75235, USA
| | - Michael Weller
- Department of Neurology, University Hospital Zurich, Frauenklinikstrasse 26, 8091 Zurich, Switzerland
| | | | - Jana Portnow
- Oncology, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Ovidiu Andronesi
- Harvard Medical School, Boston, MA, USA
- Department of Radiology, Massachusetts General Hospital, Boston, MA, USA
| | - Jill S Barnholtz-Sloan
- Informatics and Data Science (IDS), Center for Biomedical Informatics and Information Technology (CBIIT), Trans-Divisional Research Program (TDRP), Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), Bethesda, MD, USA
| | - Brigitta G Baumert
- Cantonal Hospital Graubunden, Institute of Radiation-Oncology, Chur, Switzerland
| | - Mitchell S Berger
- Department of Neurosurgery, University of California-San Francisco, San Francisco, California, USA
| | - Wenya Linda Bi
- Harvard Medical School, Boston, MA, USA
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA, USA
| | - Ranjit Bindra
- Department of Therapeutic Radiology, Brain Tumor Center, Yale School of Medicine, New Haven, CT, USA
| | - Daniel P Cahill
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Susan M Chang
- Department of Neurosurgery, University of California-San Francisco, San Francisco, California, USA
| | - Joseph F Costello
- Department of Neurosurgery, University of California-San Francisco, San Francisco, California, USA
| | - Craig Horbinski
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
- Northwestern Medicine Malnati Brain Tumor Institute of the Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Raymond Y Huang
- Harvard Medical School, Boston, MA, USA
- Department of Radiology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Robert B Jenkins
- Individualized Medicine Research, Mayo Clinic, Department of Laboratory Medicine and Pathology, Rochester, Minnesota 55901, USA
| | - Keith L Ligon
- Harvard Medical School, Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Ingo K Mellinghoff
- Department of Neurology, Evnin Family Chair in Neuro-Oncology, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - L Burt Nabors
- Department of Neurology, Heersink School of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Michael Platten
- CCU Neuroimmunology and Brain Tumor Immunology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - David A Reardon
- Harvard Medical School, Boston, MA, USA
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA, USA
| | - Diana D Shi
- Harvard Medical School, Boston, MA, USA
- Department of Radiation Oncology, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - David Schiff
- Division of Neuro-Oncology, Department of Neurology, University of Virginia Health System, Charlottesville, Virginia, USA
| | - Wolfgang Wick
- Neuro-Oncology at the German Cancer Research Center (DKFZ), Program Chair of Neuro-Oncology at the National Center for Tumor Diseases (NCT), and Neurology and Chairman at the Neurology Clinic in Heidelberg, Heidelberg, Germany
| | - Hai Yan
- Genetron Health Inc, Gaithersburg, Maryland 20879, USA
| | - Andreas von Deimling
- Department of Neuropathology, University Hospital Heidelberg, and, Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), and, DKTK, INF 224, 69120 Heidelberg, Germany
| | - Martin van den Bent
- Brain Tumour Centre, Erasmus MC Cancer Institute, Groene Hilledijk 301, 3075 EA Rotterdam, The Netherlands
| | - William G Kaelin
- Harvard Medical School, Boston, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Patrick Y Wen
- Harvard Medical School, Boston, MA, USA
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Neurology, Brigham and Women’s Hospital, Boston, MA, USA
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15
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Furnari F, Miki S, Koga T, Mckinney AM, Parisian AD, Tadokoro T, Vadla R, Masala M, Hevner RF, Costello JF. IL-1 TERT PROMOTER C228T MUTATION IN NEURAL PROGENITORS CONFERS GROWTH ADVANTAGE FOLLOWING TELOMERE SHORTENING IN VIVO. Neurooncol Adv 2022. [PMCID: PMC9719355 DOI: 10.1093/noajnl/vdac167.110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022] Open
Abstract
Abstract
Heterozygous TERT (Telomerase reverse transcriptase) promoter mutations (TPMs) facilitate TERT expression and are the most frequent mutation in glioblastoma (GBM). A recent analysis revealed this mutation is one of the earliest events in gliomagenesis, however no appropriate human models have been engineered to study the role of this mutation in the initiation of these tumors. To address this, we established GBM models by introducing the heterozygous TPM in human induced pluripotent stem cells (hiPSCs) using a two-step targeting approach in the context of GBM genetic alterations, CDKN2A/B and PTEN deletion, and EGFRvIII overexpression. Orthotopic injection of neuronal precursor cells (NPCs) derived from hiPSCs with TPM into immunodeficient mice did not enhance tumorigenesis compared to TERT promoter wild type (TPW) NPCs at initial in vivo passage which we attribute to relatively long telomeres. We further show that the TPM mutation recruited GA-Binding Protein (GABPA) and engendered low-level TERT expression, resulting in enhanced tumorigenesis upon secondary passage and maintenance of short telomere length as has been reported in human GBM. RNA sequencing of harvested tumors grown as secondary spheres demonstrated upregulated proliferation and mitosis pathway signatures in TPM cells, consistent with their increased in vitro proliferation relative to TPW counterparts. Finally, when secondary TPM and TPW sphere cultures were reinjected into mice, only the TPM led to tumor formation. In summary, our novel GBM model illustrates a growth advantage imparted by heterozygous TPMs in the context of GBM driver mutations relative to isogenic controls, and thereby allows for the identification and validation of TERT promoter-specific vulnerabilities in a genetically accurate background.
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Affiliation(s)
- Frank Furnari
- Department of Medicine , 9500 Gilman Dr., La Jolla, CA, 92093 , USA
- Ludwig Cancer Research, San Diego Branch , La Jolla, CA 92093 , USA
| | - Shunichiro Miki
- Department of Medicine , 9500 Gilman Dr., La Jolla, CA, 92093 , USA
| | - Tomoyuki Koga
- Department of Neurosurgery, University of Minnesota , Minneapolis, MN 55455 , USA
| | - Andrew M Mckinney
- Department of Neurological Surgery, University of California , San Francisco, CA 94158 , USA
| | | | - Takahiro Tadokoro
- Department of Anesthesiology , 9500 Gilman Dr., La Jolla, CA, 92093 , USA
| | | | - Martin Masala
- Department of Anesthesiology , 9500 Gilman Dr., La Jolla, CA, 92093 , USA
| | - Robert F Hevner
- Department of Pathology, University of California San Diego , 9500 Gilman Dr., La Jolla, CA, 92093 , USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California , San Francisco, CA 94158 , USA
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16
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Miki S, Koga T, Mckinney AM, Parisian AD, Tadokoro T, Vadla R, Marsala M, Hevner RF, Costello JF, Furnari F. TERT promoter C228T mutation in neural progenitors confers growth advantage following telomere shortening in vivo. Neuro Oncol 2022; 24:2063-2075. [PMID: 35325218 PMCID: PMC9713509 DOI: 10.1093/neuonc/noac080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Heterozygous TERT (telomerase reverse transcriptase) promoter mutations (TPMs) facilitate TERT expression and are the most frequent mutation in glioblastoma (GBM). A recent analysis revealed this mutation is one of the earliest events in gliomagenesis. However, no appropriate human models have been engineered to study the role of this mutation in the initiation of these tumors. METHOD We established GBM models by introducing the heterozygous TPM in human induced pluripotent stem cells (hiPSCs) using a two-step targeting approach in the context of GBM genetic alterations, CDKN2A/B and PTEN deletion, and EGFRvIII overexpression. The impact of the mutation was evaluated through the in vivo passage and in vitro experiment and analysis. RESULTS Orthotopic injection of neuronal precursor cells (NPCs) derived from hiPSCs with the TPM into immunodeficient mice did not enhance tumorigenesis compared to TERT promoter wild type NPCs at initial in vivo passage presumably due to relatively long telomeres. However, the mutation recruited GA-Binding Protein and engendered low-level TERT expression resulting in enhanced tumorigenesis and maintenance of short telomeres upon secondary passage as observed in human GBM. These results provide the first insights regarding increased tumorigenesis upon introducing a TPM compared to isogenic controls without TPMs. CONCLUSION Our novel GBM models presented the growth advantage of heterozygous TPMs for the first time in the context of GBM driver mutations relative to isogenic controls, thereby allowing for the identification and validation of TERT promoter-specific vulnerabilities in a genetically accurate background.
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Affiliation(s)
- Shunichiro Miki
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | | | | | - Alison D Parisian
- Department of Medicine, University of California San Diego, La Jolla, California, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, California, USA
| | - Takahiro Tadokoro
- Neuroregeneration Laboratory, Department of Anesthesiology, University of California San Diego, La Jolla, California, USA
| | - Raghavendra Vadla
- Department of Medicine, University of California San Diego, La Jolla, California, USA
| | - Martin Marsala
- Neuroregeneration Laboratory, Department of Anesthesiology, University of California San Diego, La Jolla, California, USA
| | - Robert F Hevner
- Department of Pathology, University of California San Diego, La Jolla, California, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA
| | - Frank Furnari
- Corresponding Authors: Frank Furnari, PhD, Ludwig Cancer Research, University of California at San Diego, 9500 Gilman Dr., CMM-East Room 3053, La Jolla, CA 92093-0660, USA ()
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17
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Minami N, Hong D, Taglang C, Batsios G, Gillepspie AM, Stevers N, Viswanath P, Costello JF, Ronen S. TMET-12. HYPERPOLARIZED Δ- [1-13C] GLUCONOLACTONE IMAGING VISUALIZES TERT-ASSOCIATED CHANGES IN DYNAMIC PENTOSE PHOSPHATE PATHWAY METABOLISM IN GLIOBLASTOMA. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac209.1017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
BACKGROUND
TERT promoter mutations are a hallmark of glioblastoma (GBM). We recently reported that the expression of TERT and its upstream transcriptional factor, GABPB1, are strongly correlated with redox in GBM with TERT promoter mutations. However, further imaging biomarkers which visualize redox-associated metabolism and TERT expression are needed. Here we demonstrate that 13C magnetic resonance spectroscopy (MRS) of hyperpolarized δ-[1-13C] gluconolactone metabolism is a useful imaging tool to visualize changes in dynamic pentose phosphate pathway (PPP) metabolism that reflect TERT-associated changes in redox in GBM.
METHODS
U251 human GBM cells stably expressing shRNA targeting TERT or GABPB1 were compared to controls. Doxycyclin-inducible shTERT or shGABPB1 U251 cells were also examined. For in vivo studies, cells were injected into immunodeficient rat brains and tumors confirmed by T2-weighted MRI. δ-[1-13C] gluconolactone was polarized using a Hypersense DNP polarizer and injected into live cells or tumor-bearing rats. For cells 13C-MRS was acquired using a 500MHz Agilent spectrometer and analyzed using Mnova and Matlab software. For in vivo13C-MRS studies, spectra were acquired using a 3T Bruker scanner and a spectral spatial echo-planar spectroscopic imaging sequence. Spectral signal to noise was improved using Tensor denoising. Spectra were processed using a custom-written Matlab script.
RESULTS
Hyperpolarized 6-phosphogluconolactone (6PG), the metabolic product from δ-[1-13C] gluconolactone via the PPP, was significantly reduced in TERT or GABPB1 silenced cells compared to control cells in both U251 models. The positive correlation between TERT expression and 6PG level was confirmed by linear regression analysis. Hyperpolarized 6PG production in both tumor models was also significantly reduced in TERT or GABPB1-silenced tumors compared to controls.
CONCLUSION
We successfully visualized TERT-associated changes in dynamic PPP metabolism in a GBM model in cells and in vivo. Hyperpolarized δ-[1-13C] gluconolactone is a potential tool for monitoring TERT expression in GBM with TERT promoter mutations.
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18
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Jain S, Rick J, Joshi R, Beniwal A, Spatz J, Gill S, Chang A, Chalif E, Haddad AF, Costello JF, Diaz A, Heiland DH, Aghi M. TMIC-57. USING SINGLE-CELL SEQUENCING AND SPATIAL TRANSCRIPTOMICS TO IDENTIFY CANCER-ASSOCIATED FIBROBLASTS IN GLIOBLASTOMA AND DEFINING THEIR PRO-TUMORAL EFFECTS. Neuro Oncol 2022. [PMCID: PMC9661213 DOI: 10.1093/neuonc/noac209.1101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Cancer-associated fibroblasts (CAFs) constitute a key component of the tumor microenvironment. Pro-tumoral cancer-associated fibroblasts were presumed absent in glioblastoma given the lack of brain fibroblasts. Using single-cell RNA sequencing we identified CAFs in patient GBMs. CAFs were identified using a negative selection strategy to filter endothelial, epithelial, immune cells and pericytes and for the positive expression of previously defined CAF markers. Copy number variation (CNV) analysis was performed to distinguish CAFs from malignant cells. Single-cell spatial transcriptomics from 16 GBM patients confirmed the proximity of CAFs to mesenchymal GBM stem cells (GSCs), endothelial cells, and M2-macrophages. Serial trypsinization of glioblastoma specimens yielded cells with CAF morphology and transcriptomic profile. CAFs were chemotactically attracted to GSCs and CAFs induced GSC proliferation. To identify CAF and GSC interaction mediators, we created a resource of inferred crosstalk by mapping expression of receptors to their cognate ligands, identifying PDGF and TGFB as mediators of GSC effects on CAFs, and osteopontin and HGF as mediators of CAF-induced GSC enrichment. Furthermore, CAFs were found to induce M2-macrophage polarization by producing the EDA fibronectin variant which binds macrophage toll-like receptor 4 (TLR4) in a targetable manner. Glioblastoma CAFs were enriched in the subventricular zone which houses the neural stem cells that houses GSCs. Including CAFs in GSC-derived xenografts induced in vivo tumor growth and reduced survival in two different xenograft models. These findings are among the first to identify glioblastoma CAFs and their GSC interactions, making them an intriguing target for Glioblastomas.
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Affiliation(s)
- Saket Jain
- University of California San Francisco , San Francisco, CA , USA
| | | | | | | | | | - Sabraj Gill
- University of California San Francisco , San Francisco , USA
| | | | | | - Alexander F Haddad
- Department of Neurosurgery & Division of Neuro-Oncology, University of San Francisco , San Francisco, CA , USA
| | | | - Aaron Diaz
- University of California, San Francisco , San Francisco, CA , USA
| | | | - Manish Aghi
- University of California, San Francisco , San Francisco , USA
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19
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Suwala A, Barger C, Soczek KM, Wang AS, Kim MY, Hong C, Doudna JA, Chang SM, Phillips JJ, Solomon DA, Costello JF. EPCO-08. CONSERVED FEATURES OF TERT PROMOTER DUPLICATIONS REVEAL AN ACTIVATION MECHANISM THAT MIMICS HOTSPOT MUTATIONS IN CANCER. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac209.443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Mutations in the TERT promoter are the single most common non-coding mutation in cancer and represent the genetic underpinnings of tumor cell immortality. Beyond the two most common point mutations, G228A and G250A, which selectively recruit the ETS factor GABP to activate TERT, the significance of other variants in the TERT promoter are unknown. We identified duplications of wildtype sequence within the core promoter region of TERT in 7 different cancer types that have strikingly similar features including size, insertion position, and inclusion of one of the native ETS motifs. Each duplication activates the TERT promoter to a similar level as G228A and G250A and is critically dependent on the insertion site. The GABP tetramer binds to the TERT duplicated promoter sequence by virtue of the native ETS motif and its duplicated version with precise spacing, and it is necessary for the transcriptional activation by all duplications tested. Spatiotemporal analysis in a multifocal glioblastoma shows the duplication is clonal and its activation of TERT is readily detectable at the single cell level and in bulk tumor tissue. We conclude that recurrent TERT promoter duplications of the native ETS sequence are functionally and mechanistically equivalent to the hotspot mutations that confer tumor cell immortality. The shared mechanism of these divergent somatic genetic alterations suggests a strong selective pressure for recruitment of the GABP tetramer to activate TERT.
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Affiliation(s)
| | | | | | | | | | | | | | - Susan M Chang
- University of California, San Francisco , San Francisco, CA , USA
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20
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Stevers N, Collins S, Kasahara N, Costello JF. CSIG-05. A GABP DOMINANT NEGATIVE APPROACH TO THE REVERSAL OF TUMOR IMMORTALITY. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac209.154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Immortality is a fundamental hallmark of human cancer cells and therapeutic reversal is of great interest. Telomerase Reverse Transcriptase promoter (TERTp) mutations reactivate TERT expression, the rate limiting step in telomerase activity and cellular immortality. TERTp mutations are the most common non-coding mutation across all cancer types, including glioblastoma (GBM), oligodendroglioma, medulloblastoma, and high-grade meningioma. While prior telomerase therapies lack tumor selectivity and are poorly tolerated, TERTp mutations and their regulation offer a unique opportunity for tumor specific reversal of cellular immortality. The mutations generate a de novo E26 Transformation Specific (ETS) binding motif that recruits the GA-Binding Protein (GABP) multimeric complex to reactivate TERT expression. Initially we found a GABP tetramer reactivates the mutant TERTp, suggesting targeting only the tetramer may induce telomere shortening and tumor cell death. However, through knocking out this tetramer in cell cultures, we found that the GABP dimer is upregulated and maintains TERT expression. In the absence of both the dimer and one tetramer isoform, many tumor cells senesce or undergo cell death. However, some tumor cells escape this fate via upregulation of a second GABP tetrameric paralogue that maintains TERT expression. Therefore, to block all GABP complexes with a single approach, we devised a transactivation domain null, putative dominant negative GABP subunit that ultimately could be delivered to patients via a replicating retroviral system. Introduction of the construct into TERTp mutant glioma cells significantly reduced TERT expression while not altering expression in TERTp wildtype GBM cells, suggesting tumor selectivity. TERT expression was also reduced in a second TERTp mutant tumor type. We are currently investigating the long-term effects of the dominant negative GABP on telomere length and tumor immortality. Dominant negative GABP is a promising candidate for tumor selective reversal of cellular immortality by inhibiting mutant TERTp activation by all GABP multimeric forms.
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21
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Varn F, Ye G, Ghospurkar P, Wade T, Khasraw M, Lipp ES, Hermes B, Elliott C, Costello JF, Hong C, French P, Vallentgoed W, Padovan M, Ng HK, Li K, Gan H, Westcott K, Vaubel R, Horbinski C, McCortney K, Paek SH, Moon HE, LaViolette P, Lowman A, Barnholtz-Sloan J, Wesseling P, Verhaak R. PATH-11. THE LONGITUDINAL EVOLUTIONARY TRAJECTORY OF OLIGODENDROGLIOMA IS DRIVEN BY TREATMENT-ASSOCIATED GENETIC ALTERATIONS. Neuro Oncol 2022. [PMCID: PMC9660855 DOI: 10.1093/neuonc/noac209.584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Oligodendroglioma is a subtype of diffuse glioma defined by a mutation in the isocitrate dehydrogenase (IDH) genes and a co-deletion of chromosome arms 1p and 19q. These tumors primarily occur in adult patients in their third and fourth decade of life and are universally fatal due to an inevitable recurrence that follows a treatment regimen of surgical resection and an optional combination of alkylating chemotherapy and/or radiation therapy. While initially slow growing, recurrent tumors exhibit increasingly aggressive phenotypes that become progressively more difficult to treat with conventional therapy. Currently, the molecular mechanisms and cellular phenotypes that drive this recurrence remain unknown. To understand these factors, we assembled a cohort of matched initial and recurrent oligodendroglioma samples from over 100 patients and performed whole-genome sequencing and whole-exome sequencing on each of them. To link these molecular profiles to cell state changes, we additionally performed bulk and single-nucleus RNA-sequencing on a subset of these tumor pairs. In nearly 40% of alkylating chemotherapy-treated patients, recurrent tumors presented with hypermutation that corresponded with an increase in neoplastic cell proliferation. Additionally, while individual somatic alterations specific to recurrence were relatively rare, we observed a subset of tumors that acquired deletions in the cell cycle regulator CDKN2A following treatment with radiotherapy. Acquisition of either of these features associated with shorter patient survival and higher grade at recurrence, implicating cell cycle dysregulation as a mechanism of treatment resistance and increased tumor severity. Together, these results indicate that oligodendrogliomas evolve in a treatment-specific manner following chemo- and radiation therapy and highlight key pathways that can be targeted to delay the onset of recurrence.
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Affiliation(s)
| | - Gordon Ye
- University of California San Diego , La Jolla, CA , USA
| | | | - Taylor Wade
- The Jackson Laboratory , Farmington, CT , USA
| | - Mustafa Khasraw
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center , Durham , USA
| | - Eric S Lipp
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center , Durham, NC , USA
| | - Beth Hermes
- St. Joseph’s Hospital and Medical Center , Phoenix, AZ , USA
| | - Carol Elliott
- St. Joseph’s Hospital and Medical Center , Phoenix, AZ , USA
| | | | | | - Pim French
- Erasmus University Medical Centre Rotterdam , Rotterdam , Netherlands
| | - Wies Vallentgoed
- Erasmus University Medical Centre Rotterdam , Rotterdam , Netherlands
| | - Marta Padovan
- Erasmus University Medical Centre Rotterdam , Rotterdam , Netherlands
| | - Ho-Keung Ng
- Prince of Wales Hospital , Shatin , Hong Kong
| | - Kay Li
- Prince of Wales Hospital , Shatin , Hong Kong
| | - Hui Gan
- Olivia Newton-John Cancer Research Institute, Austin Health , Melbourne , Australia
| | - Kerryn Westcott
- Olivia Newton-John Cancer Research Institute, Austin Health , Melbourne , Australia
| | | | - Craig Horbinski
- Northwestern University, Feinberg School of Medicine , Chicago , USA
| | | | - Sun Ha Paek
- Seoul National University College of Medicine and Seoul National University Hospital , Seoul , Republic of Korea
| | - Hyo-Eun Moon
- Seoul National University College of Medicine and Seoul National University Hospital , Seoul , Republic of Korea
| | | | | | - Jill Barnholtz-Sloan
- Center for Biomedical Informatics and Information Technology and Division of Cancer Epidemiology and Genetics, National Cancer Institute , Bethesda, MD , USA
| | - Pieter Wesseling
- Amsterdam University Medical Centers/VUmc , Amsterdam , Netherlands
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22
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Lucas CHG, Sloan EA, Gupta R, Wu J, Pratt D, Vasudevan HN, Ravindranathan A, Barreto J, Williams EA, Shai A, Whipple NS, Bruggers CS, Maher O, Nabors B, Rodriguez M, Samuel D, Brown M, Carmichael J, Lu R, Mirchia K, Sullivan DV, Pekmezci M, Tihan T, Bollen AW, Perry A, Banerjee A, Mueller S, Gupta N, Hervey-Jumper SL, Oberheim Bush NA, Daras M, Taylor JW, Butowski NA, de Groot J, Clarke JL, Raleigh DR, Costello JF, Phillips JJ, Reddy AT, Chang SM, Berger MS, Solomon DA. Multiplatform molecular analyses refine classification of gliomas arising in patients with neurofibromatosis type 1. Acta Neuropathol 2022; 144:747-765. [PMID: 35945463 PMCID: PMC9468105 DOI: 10.1007/s00401-022-02478-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 01/28/2023]
Abstract
Gliomas arising in the setting of neurofibromatosis type 1 (NF1) are heterogeneous, occurring from childhood through adulthood, can be histologically low-grade or high-grade, and follow an indolent or aggressive clinical course. Comprehensive profiling of genetic alterations beyond NF1 inactivation and epigenetic classification of these tumors remain limited. Through next-generation sequencing, copy number analysis, and DNA methylation profiling of gliomas from 47 NF1 patients, we identified 2 molecular subgroups of NF1-associated gliomas. The first harbored biallelic NF1 inactivation only, occurred primarily during childhood, followed a more indolent clinical course, and had a unique epigenetic signature for which we propose the terminology "pilocytic astrocytoma, arising in the setting of NF1". The second subgroup harbored additional oncogenic alterations including CDKN2A homozygous deletion and ATRX mutation, occurred primarily during adulthood, followed a more aggressive clinical course, and was epigenetically diverse, with most tumors aligning with either high-grade astrocytoma with piloid features or various subclasses of IDH-wildtype glioblastoma. Several patients were treated with small molecule MEK inhibitors that resulted in stable disease or tumor regression when used as a single agent, but only in the context of those tumors with NF1 inactivation lacking additional oncogenic alterations. Together, these findings highlight recurrently altered pathways in NF1-associated gliomas and help inform targeted therapeutic strategies for this patient population.
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Affiliation(s)
- Calixto-Hope G Lucas
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Emily A Sloan
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
- Department of Pathology, Medstar Georgetown University Hospital, Washington, DC, USA
| | - Rohit Gupta
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Jasper Wu
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Drew Pratt
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Harish N Vasudevan
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Ajay Ravindranathan
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Jairo Barreto
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Erik A Williams
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Anny Shai
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Nicholas S Whipple
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Carol S Bruggers
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Utah, Salt Lake City, UT, USA
| | - Ossama Maher
- Department of Oncology, Nicklaus Children's Hospital, Miami, FL, USA
| | - Burt Nabors
- Division of Neuro-Oncology, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - David Samuel
- Department of Hematology/Oncology, Valley Children's Hospital, Madera, CA, USA
| | - Melandee Brown
- Department of Neurosurgery, Valley Children's Hospital, Madera, CA, USA
| | - Jason Carmichael
- Department of Medical Genetics and Metabolism, Valley Children's Hospital, Madera, CA, USA
| | - Rufei Lu
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Kanish Mirchia
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Daniel V Sullivan
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Melike Pekmezci
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Tarik Tihan
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Andrew W Bollen
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
| | - Arie Perry
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Anuradha Banerjee
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Sabine Mueller
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Nalin Gupta
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Shawn L Hervey-Jumper
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Nancy Ann Oberheim Bush
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Division of Neuro-Oncology, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Mariza Daras
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Division of Neuro-Oncology, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Jennie W Taylor
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Division of Neuro-Oncology, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Nicholas A Butowski
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Division of Neuro-Oncology, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - John de Groot
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Division of Neuro-Oncology, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Jennifer L Clarke
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Division of Neuro-Oncology, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - David R Raleigh
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Joanna J Phillips
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Alyssa T Reddy
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
| | - Susan M Chang
- Department of Neurology, University of California San Francisco, San Francisco, CA, USA
- Division of Neuro-Oncology, Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - David A Solomon
- Department of Pathology, University of California, San Francisco, 513 Parnassus Ave, Health Sciences West 451, San Francisco, CA, 94143, USA.
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23
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McKinney AM, Mathur R, Stevers NO, Molinaro AM, Chang SM, Phillips JJ, Costello JF. GABP couples oncogene signaling to telomere regulation in TERT promoter mutant cancer. Cell Rep 2022; 40:111344. [PMID: 36130485 PMCID: PMC9534059 DOI: 10.1016/j.celrep.2022.111344] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 06/17/2022] [Accepted: 08/22/2022] [Indexed: 11/05/2022] Open
Abstract
Telomerase activation counteracts senescence and telomere erosion caused by uncontrolled proliferation. Epidermal growth factor receptor (EGFR) amplification drives proliferation while telomerase reverse transcriptase promoter (TERTp) mutations underlie telomerase reactivation through recruitment of GA-binding protein (GABP). EGFR amplification and TERTp mutations typically co-occur in glioblastoma, the most common and aggressive primary brain tumor. To determine if these two frequent alterations driving proliferation and immortality are functionally connected, we combine analyses of copy number, mRNA, and protein data from tumor tissue with pharmacologic and genetic perturbations. We demonstrate that proliferation arrest decreases TERT expression in a GABP-dependent manner and elucidate a critical proliferation-to-immortality pathway from EGFR to TERT expression selectively from the mutant TERTp through activation of AMP-mediated kinase (AMPK) and GABP upregulation. EGFR-AMPK signaling promotes telomerase activity and maintains telomere length. These results define how the tumor cell immortality mechanism keeps pace with persistent oncogene signaling and cell cycling. TERT promoter mutations are common in human cancer and confer cellular immortality. McKinney et al. describe the interaction between TERT promoter mutations, EGFR amplification, and the cell cycle in glioblastoma. The results demonstrate how proliferation drivers cooperate with telomere maintenance mechanisms to counteract telomere shortening caused by unlimited cell division.
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Affiliation(s)
- Andrew M McKinney
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Radhika Mathur
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Nicholas O Stevers
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Annette M Molinaro
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA.
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24
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Mohamed E, Kumar A, Zhang Y, Wang AS, Chen K, Lim Y, Shai A, Taylor JW, Clarke J, Hilz S, Berger MS, Solomon DA, Costello JF, Molinaro AM, Phillips JJ. PI3K/AKT/mTOR signaling pathway activity in IDH-mutant diffuse glioma and clinical implications. Neuro Oncol 2022; 24:1471-1481. [PMID: 35287169 PMCID: PMC9435510 DOI: 10.1093/neuonc/noac064] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND IDH-mutant diffuse gliomas are heterogeneous, and improved methods for optimal patient therapeutic stratification are needed. PI3K/AKT/mTOR signaling activity can drive disease progression and potential therapeutic inhibitors of the pathway are available. Yet, the prevalence of PI3K/AKT/mTOR signaling pathway activity in IDH-mutant glioma is unclear and few robust strategies to assess activity in clinical samples exist. METHODS PI3K/AKT/mTOR signaling pathway activity was evaluated in a retrospective cohort of 132 IDH-mutant diffuse glioma (91 astrocytoma and 41 oligodendroglioma, 1p/19q-codeleted) through quantitative multiplex immunoprofiling using phospho-specific antibodies for PI3K/AKT/mTOR pathway members, PRAS40, RPS6, and 4EBP1, and tumor-specific anti-IDH1 R132H. Expression levels were correlated with genomic evaluation of pathway intrinsic genes and univariate and multivariate Cox proportional hazard regression models were used to evaluate the relationship with outcome. RESULTS Tumor-specific expression of p-PRAS40, p-RPS6, and p-4EBP1 was common in IDH-mutant diffuse glioma and increased with CNS WHO grade from 2 to 3. Genomic analysis predicted pathway activity in 21.7% (13/60) while protein evaluation identified active PI3K/AKT/mTOR signaling in 56.6% (34/60). Comparison of expression in male versus female patients suggested sexual dimorphism. Of particular interest, when adjusting for clinical prognostic factors, the level of phosphorylation of RPS6 was strongly associated with PFS (P < .005). Phosphorylation levels of both PRAS40 and RPS6 showed an association with PFS in univariate analysis. CONCLUSIONS Our study emphasizes the value of proteomic assessment of signaling pathway activity in tumors as a means to identify relevant oncogenic pathways and potentially as a biomarker for identifying aggressive disease.
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Affiliation(s)
- Esraa Mohamed
- Department of Neurological Surgery, Brain Tumor Center, University of California, San Francisco, San Francisco, California, USA
| | - Anupam Kumar
- Department of Neurological Surgery, Brain Tumor Center, University of California, San Francisco, San Francisco, California, USA
| | - Yalan Zhang
- Department of Neurological Surgery, Brain Tumor Center, University of California, San Francisco, San Francisco, California, USA
| | - Albert S Wang
- Department of Neurological Surgery, Brain Tumor Center, University of California, San Francisco, San Francisco, California, USA
| | - Katharine Chen
- Department of Neurological Surgery, Brain Tumor Center, University of California, San Francisco, San Francisco, California, USA
| | - Yunita Lim
- Department of Neurological Surgery, Brain Tumor Center, University of California, San Francisco, San Francisco, California, USA
| | - Anny Shai
- Department of Neurological Surgery, Brain Tumor Center, University of California, San Francisco, San Francisco, California, USA
| | - Jennie W Taylor
- Division of Neuro-Oncology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA.,Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Jennifer Clarke
- Division of Neuro-Oncology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, California, USA.,Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Stephanie Hilz
- Department of Neurological Surgery, Brain Tumor Center, University of California, San Francisco, San Francisco, California, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, Brain Tumor Center, University of California, San Francisco, San Francisco, California, USA
| | - David A Solomon
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Joseph F Costello
- Department of Neurological Surgery, Brain Tumor Center, University of California, San Francisco, San Francisco, California, USA
| | - Annette M Molinaro
- Department of Neurological Surgery, Brain Tumor Center, University of California, San Francisco, San Francisco, California, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, Brain Tumor Center, University of California, San Francisco, San Francisco, California, USA.,Division of Neuropathology, Department of Pathology, University of California, San Francisco, San Francisco, California, USA
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25
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Batsios G, Taglang C, Tran M, Stevers N, Barger C, Gillespie AM, Ronen SM, Costello JF, Viswanath P. Deuterium Metabolic Imaging Reports on TERT Expression and Early Response to Therapy in Cancer. Clin Cancer Res 2022; 28:3526-3536. [PMID: 35679032 PMCID: PMC9378519 DOI: 10.1158/1078-0432.ccr-21-4418] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 05/06/2022] [Accepted: 06/07/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE Telomere maintenance is a hallmark of cancer. Most tumors maintain telomere length via reactivation of telomerase reverse transcriptase (TERT) expression. Identifying clinically translatable imaging biomarkers of TERT can enable noninvasive assessment of tumor proliferation and response to therapy. EXPERIMENTAL DESIGN We used RNAi, doxycycline-inducible expression systems, and pharmacologic inhibitors to mechanistically delineate the association between TERT and metabolism in preclinical patient-derived tumor models. Deuterium magnetic resonance spectroscopy (2H-MRS), which is a novel, translational metabolic imaging modality, was used for imaging TERT in cells and tumor-bearing mice in vivo. RESULTS Our results indicate that TERT expression is associated with elevated NADH in multiple cancers, including glioblastoma, oligodendroglioma, melanoma, neuroblastoma, and hepatocellular carcinoma. Mechanistically, TERT acts via the metabolic regulator FOXO1 to upregulate nicotinamide phosphoribosyl transferase, which is the key enzyme for NAD+ biosynthesis, and the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase, which converts NAD+ to NADH. Because NADH is essential for pyruvate flux to lactate, we show that 2H-MRS-based assessment of lactate production from [U-2H]-pyruvate reports on TERT expression in preclinical tumor models in vivo, including at clinical field strength (3T). Importantly, [U-2H]-pyruvate reports on early response to therapy in mice bearing orthotopic patient-derived gliomas at early timepoints before radiographic alterations can be visualized by MRI. CONCLUSIONS Elevated NADH is a metabolic consequence of TERT expression in cancer. Importantly, [U-2H]-pyruvate reports on early response to therapy, prior to anatomic alterations, thereby providing clinicians with a novel tool for assessment of tumor burden and treatment response in cancer.
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Affiliation(s)
- Georgios Batsios
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Céline Taglang
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Meryssa Tran
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Nicholas Stevers
- Department of Neurological Surgery, Helen Diller Research Center, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Carter Barger
- Department of Neurological Surgery, Helen Diller Research Center, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Anne Marie Gillespie
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Sabrina M Ronen
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Joseph F Costello
- Department of Neurological Surgery, Helen Diller Research Center, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Pavithra Viswanath
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, 94158, USA
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26
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Stevers NO, Barger C, Lenzo O, Hong C, Soczek K, Wu SH, McKinney AM, Suwala A, Doudna JA, Costello JF. Abstract 2302: The pan-cancer regulator of the mutant TERT promoter and a new model of the GABP-TERT axis. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Ninety percent of human tumors reactivate telomerase reverse transcriptase (TERT) to achieve cellular immortality. The route to immortality found in over 50 cancer types is mutation of the TERT promoter (TERTp) mutations. Studies in glioblastoma have shown the two most common TERTp mutations, G228A and G250A, reactivate TERT expression through de novo E26 transformation specific (ETS) site generation that, in tandem with a native TERTp ETS site, recruits the tetrameric GA-binding protein (GABP) complex formed by two GABP alpha (GABPA) subunits and two tetramer specific GABPB1 (B1) subunits, GABPB1L (B1L). While ten additional TERTp mutations have been described across cancer types, functional studies have been limited to select mutations and cancer types. We found that each de novo ETS motif generating TERTp mutation increases TERTp transcriptional activity in a GABP-dependent manner. Furthermore, our pan-cancer analysis demonstrated selective enrichment of GABPA at the mutant TERTp across 14 cancer types and further determined that this recruitment is necessary for TERT expression. Prior investigations found that CRISPR-cas9 mediated mutagenesis of the B1 ninth exon, specific to B1L, reduces TERT transcriptional activity in a TERTp-mutation dependent manner. We explored B1L targeting in the reversal of tumor cell immortality in several cancers. We found that the B1 dimer restricted isoform, GABPB1S (B1S), is consistently and significantly increased following B1L reduction, which we determined to be the consequence of a disengagement of a GABP tetramer mediated negative feedback loop acting on the B1 promoter. Interestingly, this upregulated B1S expression enables GABP dimer binding and activation of the mutant TERTp thereby compensating for B1L loss. Indeed, knockout of B1L and B1S together resulted in a near complete elimination of GABPA TERTp recruitment and a striking reduction in TERT expression, leading to telomere shortening and ultimately resulting in tumor cell death and senescence. This data identifies GABP as the master regulator of the mutant TERTp across cancer type and de novo ETS mutation type and suggests a new model of the GABP-TERT axis involving both the GABP tetramer, and the GABP dimer.
Citation Format: Nicholas O. Stevers, Carter Barger, Olivia Lenzo, Chibo Hong, Katarzyna Soczek, Samuel H. Wu, Andrew M. McKinney, Abigail Suwala, Jennifer A. Doudna, Joseph F. Costello. The pan-cancer regulator of the mutant TERT promoter and a new model of the GABP-TERT axis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2302.
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Affiliation(s)
| | - Carter Barger
- 1The University of California, San Francisco, San Francisco, CA
| | - Olivia Lenzo
- 1The University of California, San Francisco, San Francisco, CA
| | - Chibo Hong
- 1The University of California, San Francisco, San Francisco, CA
| | | | - Samuel H. Wu
- 1The University of California, San Francisco, San Francisco, CA
| | | | - Abigail Suwala
- 1The University of California, San Francisco, San Francisco, CA
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27
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Appin CL, Suwala AK, Hilz S, Mathur R, Smirnov IV, Hong C, Stevers NO, Shai A, Wang A, Berger MS, Chang SM, Phillips JJ, Costello JF. Abstract 3797: 3D whole tumor analysis of the TERT promoter mutation in gliomas. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
TERT promoter mutation (TPM) is found in over 80% of IDH-wildtype glioblastomas (GBMs) and IDH-mutant oligodendrogliomas (ODs). As TPM-mediated reactivation of telomerase is tumor specific, TPM- tumor cells could be selectively targeted to reverse tumor cell immortalization, especially if this mutation is present throughout the tumor. Previous studies on the clonality of TPM present conflicting results and have relied on minimal tumor sampling. In this study, we use a 3D maximal tumor sampling approach to address this critical issue. We investigated TPM clonality in 253 primary and recurrent tumor samples, from 19 IDH-wildtype GBMs and 9 IDH-mutant ODs. An average of nine regions per tumor were intraoperatively biopsied in a manner that maximally represents tumor geography. The 3D location of each biopsy was then recorded and mapped back to the patient’s pre- and post-operative MRI, allowing 3D characterization of each tumor. For initial screening of TPM, PCR and Sanger sequencing were performed on all 253 samples. Deep amplicon sequencing (Amp-seq) was performed on 179 of these samples, including all those in which TPM was not detectable by Sanger. Each Amp-seq reaction included a TPM amplicon and an amplicon with IDH1 mutation for ODs or an amplicon spanning a chromosome 10 SNP to evaluate chromosome 10 loss in GBMs, which are early clonal events for these tumor types. Tumor purity, estimated by the FACETS algorithm applied to whole exome sequencing, was available for all 253 tumor samples and their patient-matched blood cell DNA. TERT expression was measured by RNA-seq (144 samples) and RNA Scope (49 samples). Correlations between TPM and clonal alterations and TPM and TERT expression were analyzed for significance. Of 253 tumor samples, tumor purity could be estimated for 210 (83.0%), and of these, 100% had TPM detected by Sanger and Amp-seq. For samples whose tumor purity could not be estimated (assigned a value of NA by FACETS), TPM was still detected in 36 of 43 (83.7%) samples. Variant allele frequencies (VAFs) of TPM showed high positive correlation with those of clonal alterations in GBMs (R = 0.85, p < 0.0001) and ODs (R = 0.86, p < 0.0001) as well as with tumor purity in both GBMs (R = 0.91, p < 0.0001) and ODs (R = 0.89, p < 0.0001). TPM VAF showed moderate positive correlation with TERT expression in GBMs (R = 0.52, p < 0.0001) and ODs (R = 0.62, p < 0.0001). TPM also showed a nonlinear relationship with TERT expression only in ODs. RNA Scope detected TERT expression in a subset of cells in both GBMs and ODs. To conclude, TPM is a tumor-wide, clonal mutation in primary and recurrent GBMs and ODs, making TPM tumor cells a possible therapeutic target. TPM VAF is moderately correlated with TERT expression, with a nonlinear relationship seen in ODs, suggesting other variables affect TERT expression. RNA Scope detected TERT expression at the single cell level in situ in GBMs and ODs and therefore could serve as a tumor cell-specific marker, although follow up studies are needed.
Citation Format: Christina Leann Appin, Abigail K. Suwala, Stephanie Hilz, Radhika Mathur, Ivan V. Smirnov, Chibo Hong, Nicholas O. Stevers, Anny Shai, Albert Wang, Mitchel S. Berger, Susan M. Chang, Joanna J. Phillips, Joseph F. Costello. 3D whole tumor analysis of the TERT promoter mutation in gliomas [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3797.
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Affiliation(s)
| | | | - Stephanie Hilz
- 1University of California San Francisco, San Francisco, CA
| | - Radhika Mathur
- 1University of California San Francisco, San Francisco, CA
| | | | - Chibo Hong
- 1University of California San Francisco, San Francisco, CA
| | | | - Anny Shai
- 1University of California San Francisco, San Francisco, CA
| | - Albert Wang
- 1University of California San Francisco, San Francisco, CA
| | | | - Susan M. Chang
- 1University of California San Francisco, San Francisco, CA
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28
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Minami N, Hong D, Stevers N, Barger CJ, Radoul M, Hong C, Chen L, Kim Y, Batsios G, Gillespie AM, Pieper RO, Costello JF, Viswanath P, Ronen SM. Imaging biomarkers of TERT or GABPB1 silencing in TERT-positive glioblastoma. Neuro Oncol 2022; 24:1898-1910. [PMID: 35460557 PMCID: PMC9629440 DOI: 10.1093/neuonc/noac112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND TERT promoter mutations are observed in 80% of wild-type IDH glioblastoma (GBM). Moreover, the upstream TERT transcription factor GABPB1 was recently identified as a cancer-specific therapeutic target for tumors harboring a TERT promoter mutation. In that context, noninvasive imaging biomarkers are needed for the detection of TERT modulation. METHODS Multiple GBM models were investigated as cells and in vivo tumors and the impact of TERT silencing, either directly or by targeting GABPB1, was determined using 1H and hyperpolarized 13C magnetic resonance spectroscopy (MRS). Changes in associated metabolic enzymes were also investigated. RESULTS 1H-MRS revealed that lactate and glutathione (GSH) were the most significantly altered metabolites when either TERT or GABPB1 was silenced, and lactate and GSH levels were correlated with cellular TERT expression. Consistent with the drop in lactate, 13C-MRS showed that hyperpolarized [1-13C]lactate production from [1-13C]pyruvate was also reduced when TERT was silenced. Mechanistically, the reduction in GSH was associated with a reduction in pentose phosphate pathway flux, reduced activity of glucose-6-phosphate dehydrogenase, and reduced NADPH. The drop in lactate and hyperpolarized lactate were associated with reductions in glycolytic flux, NADH, and expression/activity of GLUT1, monocarboxylate transporters, and lactate dehydrogenase A. CONCLUSIONS Our study indicates that MRS-detectable GSH, lactate, and lactate production could serve as metabolic biomarkers of response to emerging TERT-targeted therapies for GBM with activating TERT promoter mutations. Importantly these biomarkers are readily translatable to the clinic, and thus could ultimately improve GBM patient management.
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Affiliation(s)
| | | | - Nicholas Stevers
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Carter J Barger
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Marina Radoul
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, California, USA
| | - Chibo Hong
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Lee Chen
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Yaewon Kim
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, California, USA
| | - Georgios Batsios
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, California, USA
| | - Anne Marie Gillespie
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, California, USA
| | - Russel O Pieper
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Pavithra Viswanath
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, California, USA
| | - Sabrina M Ronen
- Corresponding Author: Sabrina M. Ronen, PhD, University of California San Francisco, 1700 4th Street, San Francisco, CA 94158, USA ()
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Affiliation(s)
- Joseph F Costello
- From the Brain Tumor Center, the Department of Neurological Surgery, and the Helen Diller Family Comprehensive Cancer Center (J.F.C.), and the Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, the Center for Reproductive Sciences, the Department of Obstetrics, Gynecology, and Reproductive Sciences, the Division of Maternal-Fetal Medicine, and the Department of Anatomy (S.J.F.) - all at the University of California, San Francisco, San Francisco
| | - Susan J Fisher
- From the Brain Tumor Center, the Department of Neurological Surgery, and the Helen Diller Family Comprehensive Cancer Center (J.F.C.), and the Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, the Center for Reproductive Sciences, the Department of Obstetrics, Gynecology, and Reproductive Sciences, the Division of Maternal-Fetal Medicine, and the Department of Anatomy (S.J.F.) - all at the University of California, San Francisco, San Francisco
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30
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Verburg N, Barthel FP, Anderson KJ, Johnson KC, Koopman T, Yaqub MM, Hoekstra OS, Lammertsma AA, Barkhof F, Pouwels PJW, Reijneveld JC, Rozemuller AJM, Beliën JAM, Boellaard R, Taylor MD, Das S, Costello JF, Vandertop WP, Wesseling P, de Witt Hamer PC, Verhaak RGW. Spatial concordance of DNA methylation classification in diffuse glioma. Neuro Oncol 2021; 23:2054-2065. [PMID: 34049406 PMCID: PMC8643482 DOI: 10.1093/neuonc/noab134] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background Intratumoral heterogeneity is a hallmark of diffuse gliomas. DNA methylation profiling is an emerging approach in the clinical classification of brain tumors. The goal of this study is to investigate the effects of intratumoral heterogeneity on classification confidence. Methods We used neuronavigation to acquire 133 image-guided and spatially separated stereotactic biopsy samples from 16 adult patients with a diffuse glioma (7 IDH-wildtype and 2 IDH-mutant glioblastoma, 6 diffuse astrocytoma, IDH-mutant and 1 oligodendroglioma, IDH-mutant and 1p19q codeleted), which we characterized using DNA methylation arrays. Samples were obtained from regions with and without abnormalities on contrast-enhanced T1-weighted and fluid-attenuated inversion recovery MRI. Methylation profiles were analyzed to devise a 3-dimensional reconstruction of (epi)genetic heterogeneity. Tumor purity was assessed from clonal methylation sites. Results Molecular aberrations indicated that tumor was found outside imaging abnormalities, underlining the infiltrative nature of this tumor and the limitations of current routine imaging modalities. We demonstrate that tumor purity is highly variable between samples and explains a substantial part of apparent epigenetic spatial heterogeneity. We observed that DNA methylation subtypes are often, but not always, conserved in space taking tumor purity and prediction accuracy into account. Conclusion Our results underscore the infiltrative nature of diffuse gliomas and suggest that DNA methylation subtypes are relatively concordant in this tumor type, although some heterogeneity exists.
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Affiliation(s)
- Niels Verburg
- Department of Neurosurgery, Amsterdam UMC, Vrije Universiteit, and Brain Tumor Centre, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.,Cambridge Brain Tumor Imaging Laboratory, Division of Neurosurgery, Department of Clinical Neurosciences, University of Cambridge, Addenbrooke's Hospital, Hill Rd, Cambridge CB2 0QQ, UK
| | - Floris P Barthel
- The Jackson Laboratory For Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | - Kevin J Anderson
- The Jackson Laboratory For Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | - Kevin C Johnson
- The Jackson Laboratory For Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA
| | - Thomas Koopman
- Department of Radiology & Nuclear Medicine, Amsterdam UMC, location VUmc, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Maqsood M Yaqub
- Department of Radiology & Nuclear Medicine, Amsterdam UMC, location VUmc, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Otto S Hoekstra
- Department of Radiology & Nuclear Medicine, Amsterdam UMC, location VUmc, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Adriaan A Lammertsma
- Department of Radiology & Nuclear Medicine, Amsterdam UMC, location VUmc, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Frederik Barkhof
- Department of Radiology & Nuclear Medicine, Amsterdam UMC, location VUmc, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.,UCL institutes of Neurology & Healthcare Engineering, Gower St, Bloomsbury, London WC1E 6BT, United Kingdom
| | - Petra J W Pouwels
- Department of Radiology & Nuclear Medicine, Amsterdam UMC, location VUmc, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Jaap C Reijneveld
- Department of Neurology, Amsterdam UMC, location VUmc, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.,Department of Neurology, Stichting Epilepsie Instellingen Nederland, Heemstede, The Netherlands
| | - Annemieke J M Rozemuller
- Department of Pathology, Amsterdam UMC, location VUmc, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Jeroen A M Beliën
- Department of Pathology, Amsterdam UMC, location VUmc, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Ronald Boellaard
- Department of Radiology & Nuclear Medicine, Amsterdam UMC, location VUmc, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Michael D Taylor
- Department of Neurosurgery, The Hospital for Sick Children, 555 University Ave, Toronto, ON M5G 1X8, Canada.,Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Kids, Toronto, Ontario Canada
| | - Sunit Das
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Kids, Toronto, Ontario Canada.,Division of Neurosurgery, Li Ka Shing Knowledge Institute, St. Michael's Hospital, University of Toronto, Toronto, Ontario Canada
| | - Joseph F Costello
- Department of Neurological Surgery, UCSF, 505 Parnassus Ave, San Francisco, CA 94143, USA
| | - W Pieter Vandertop
- Department of Neurosurgery, Amsterdam UMC, Vrije Universiteit, and Brain Tumor Centre, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Pieter Wesseling
- Department of Pathology, Amsterdam UMC, location VUmc, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.,Princess Máxima Centre for Paediatric Oncology, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Philip C de Witt Hamer
- Department of Neurosurgery, Amsterdam UMC, Vrije Universiteit, and Brain Tumor Centre, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands
| | - Roel G W Verhaak
- Department of Neurosurgery, Amsterdam UMC, Vrije Universiteit, and Brain Tumor Centre, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV Amsterdam, The Netherlands.,The Jackson Laboratory For Genomic Medicine, 10 Discovery Drive, Farmington, CT 06032, USA
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Manjunath M, Yan J, Youn Y, Drucker KL, Kollmeyer TM, McKinney AM, Zazubovich V, Zhang Y, Costello JF, Eckel-Passow J, Selvin PR, Jenkins RB, Song JS. Functional analysis of low-grade glioma genetic variants predicts key target genes and transcription factors. Neuro Oncol 2021; 23:638-649. [PMID: 33130899 DOI: 10.1093/neuonc/noaa248] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Large-scale genome-wide association studies (GWAS) have implicated thousands of germline genetic variants in modulating individuals' risk to various diseases, including cancer. At least 25 risk loci have been identified for low-grade gliomas (LGGs), but their molecular functions remain largely unknown. METHODS We hypothesized that GWAS loci contain causal single nucleotide polymorphisms (SNPs) that reside in accessible open chromatin regions and modulate the expression of target genes by perturbing the binding affinity of transcription factors (TFs). We performed an integrative analysis of genomic and epigenomic data from The Cancer Genome Atlas and other public repositories to identify candidate causal SNPs within linkage disequilibrium blocks of LGG GWAS loci. We assessed their potential regulatory role via in silico TF binding sequence perturbations, convolutional neural network trained on TF binding data, and simulated annealing-based interpretation methods. RESULTS We built an interactive website (http://education.knoweng.org/alg3/) summarizing the functional footprinting of 280 variants in 25 LGG GWAS regions, providing rich information for further computational and experimental scrutiny. We identified as case studies PHLDB1 and SLC25A26 as candidate target genes of rs12803321 and rs11706832, respectively, and predicted the GWAS variant rs648044 to be the causal SNP modulating ZBTB16, a known tumor suppressor in multiple cancers. We showed that rs648044 likely perturbed the binding affinity of the TF MAFF, as supported by RNA interference and in vitro MAFF binding experiments. CONCLUSIONS The identified candidate (causal SNP, target gene, TF) triplets and the accompanying resource will help accelerate our understanding of the molecular mechanisms underlying genetic risk factors for gliomas.
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Affiliation(s)
- Mohith Manjunath
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jialu Yan
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yeoan Youn
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Kristen L Drucker
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Thomas M Kollmeyer
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Andrew M McKinney
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Valter Zazubovich
- Department of Physics, Concordia University, Montreal, Québec, Canada
| | - Yi Zhang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Data Sciences, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | | | - Paul R Selvin
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Robert B Jenkins
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jun S Song
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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32
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Zhang B, Kim MY, Elliot G, Zhou Y, Zhao G, Li D, Lowdon RF, Gormley M, Kapidzic M, Robinson JF, McMaster MT, Hong C, Mazor T, Hamilton E, Sears RL, Pehrsson EC, Marra MA, Jones SJM, Bilenky M, Hirst M, Wang T, Costello JF, Fisher SJ. Human placental cytotrophoblast epigenome dynamics over gestation and alterations in placental disease. Dev Cell 2021; 56:1238-1252.e5. [PMID: 33891899 DOI: 10.1016/j.devcel.2021.04.001] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 02/11/2021] [Accepted: 03/30/2021] [Indexed: 02/07/2023]
Abstract
The human placenta and its specialized cytotrophoblasts rapidly develop, have a compressed lifespan, govern pregnancy outcomes, and program the offspring's health. Understanding the molecular underpinnings of these behaviors informs development and disease. Profiling the extraembryonic epigenome and transcriptome during the 2nd and 3rd trimesters revealed H3K9 trimethylation overlapping deeply DNA hypomethylated domains with reduced gene expression and compartment-specific patterns that illuminated their functions. Cytotrophoblast DNA methylation increased, and several key histone modifications decreased across the genome as pregnancy advanced. Cytotrophoblasts from severe preeclampsia had substantially increased H3K27 acetylation globally and at genes that are normally downregulated at term but upregulated in this syndrome. In addition, some cases had an immature pattern of H3K27ac peaks, and others showed evidence of accelerated aging, suggesting subtype-specific alterations in severe preeclampsia. Thus, the cytotrophoblast epigenome dramatically reprograms during pregnancy, placental disease is associated with failures in this process, and H3K27 hyperacetylation is a feature of severe preeclampsia.
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Affiliation(s)
- Bo Zhang
- Department of Genetics Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO 63108, USA; Department of Developmental Biology, Center of Regenerative Medicine, Washington University School of Medicine, St Louis, MO 63108, USA
| | - M Yvonne Kim
- Ely and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94115, USA; Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94115, USA; Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94115, USA
| | - GiNell Elliot
- Department of Genetics Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO 63108, USA
| | - Yan Zhou
- Ely and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94115, USA; Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94115, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94115, USA; Division of Maternal-Fetal Medicine, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Guangfeng Zhao
- Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Daofeng Li
- Department of Genetics Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO 63108, USA
| | - Rebecca F Lowdon
- Department of Genetics Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO 63108, USA
| | - Matthew Gormley
- Ely and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94115, USA; Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94115, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94115, USA; Division of Maternal-Fetal Medicine, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Mirhan Kapidzic
- Ely and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94115, USA; Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94115, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94115, USA; Division of Maternal-Fetal Medicine, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Joshua F Robinson
- Ely and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94115, USA; Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94115, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94115, USA; Division of Maternal-Fetal Medicine, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Michael T McMaster
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94122, USA
| | - Chibo Hong
- Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Tali Mazor
- Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Emily Hamilton
- Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Renee L Sears
- Department of Genetics Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO 63108, USA
| | - Erica C Pehrsson
- Department of Genetics Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO 63108, USA
| | - Marco A Marra
- Centre for High-Throughput Biology, Department of Microbiology & Immunology, University of British Columbia, 2125 East Mall, Vancouver, BC V6T 1Z4, Canada; Canada's Michael Smith Genome Sciences Center, BC Cancer Agency, 675 West 10th Aven, Vancouver, BC V5Z 1L3, Canada
| | - Steven J M Jones
- Centre for High-Throughput Biology, Department of Microbiology & Immunology, University of British Columbia, 2125 East Mall, Vancouver, BC V6T 1Z4, Canada; Canada's Michael Smith Genome Sciences Center, BC Cancer Agency, 675 West 10th Aven, Vancouver, BC V5Z 1L3, Canada
| | - Misha Bilenky
- Centre for High-Throughput Biology, Department of Microbiology & Immunology, University of British Columbia, 2125 East Mall, Vancouver, BC V6T 1Z4, Canada; Canada's Michael Smith Genome Sciences Center, BC Cancer Agency, 675 West 10th Aven, Vancouver, BC V5Z 1L3, Canada
| | - Martin Hirst
- Centre for High-Throughput Biology, Department of Microbiology & Immunology, University of British Columbia, 2125 East Mall, Vancouver, BC V6T 1Z4, Canada; Canada's Michael Smith Genome Sciences Center, BC Cancer Agency, 675 West 10th Aven, Vancouver, BC V5Z 1L3, Canada
| | - Ting Wang
- Department of Genetics Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, MO 63108, USA.
| | - Joseph F Costello
- Brain Tumor Research Center, Department of Neurosurgery, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94115, USA.
| | - Susan J Fisher
- Ely and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA 94115, USA; Center for Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94115, USA; Department of Obstetrics, Gynecology and Reproductive Sciences, University of California, San Francisco, San Francisco, CA 94115, USA; Division of Maternal-Fetal Medicine, University of California, San Francisco, San Francisco, CA 94115, USA; Department of Anatomy, University of California, San Francisco, San Francisco, CA 94122, USA.
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Viswanath P, Batsios G, Ayyappan V, Taglang C, Gillespie AM, Larson PEZ, Luchman HA, Costello JF, Pieper RO, Ronen SM. Metabolic imaging detects elevated glucose flux through the pentose phosphate pathway associated with TERT expression in low-grade gliomas. Neuro Oncol 2021; 23:1509-1522. [PMID: 33864084 DOI: 10.1093/neuonc/noab093] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Telomerase reverse transcriptase (TERT) is essential for tumor proliferation, including in low-grade oligodendrogliomas (LGOGs). Since TERT is silenced in normal cells, it is also a therapeutic target. Therefore, non-invasive methods of imaging TERT are needed. Here, we examined the link between TERT expression and metabolism in LGOGs, with the goal of leveraging this information for non-invasive magnetic resonance spectroscopy (MRS)-based metabolic imaging of LGOGs. METHODS Immortalized normal human astrocytes with doxycycline-inducible TERT silencing, patient-derived LGOG cells, orthotopic tumors and LGOG patient biopsies were studied to determine the mechanistic link between TERT expression and glucose metabolism. The ability of hyperpolarized [U- 13C, U- 2H]-glucose to non-invasively assess TERT expression was tested in live cells and orthotopic tumors. RESULTS TERT expression was associated with elevated glucose flux through the pentose phosphate pathway (PPP), elevated NADPH, which is a major product of the PPP, and elevated GSH, which is maintained in a reduced state by NADPH. Importantly, hyperpolarized [U- 13C, U- 2H]-glucose metabolism via the PPP non-invasively reported on TERT expression and response to TERT inhibition in patient-derived LGOG cells and orthotopic tumors. Mechanistically, TERT acted via the sirtuin SIRT2 to upregulate the glucose transporter GLUT1 and the rate-limiting PPP enzyme glucose-6-phosphate dehydrogenase. CONCLUSIONS We have, for the first time, leveraged a mechanistic understanding of TERT-associated metabolic reprogramming for non-invasive imaging of LGOGs using hyperpolarized [U- 13C, U- 2H]-glucose. Our findings provide a novel way of imaging a hallmark of tumor immortality and have the potential to improve diagnosis and treatment response assessment for LGOG patients.
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Affiliation(s)
- Pavithra Viswanath
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | - Georgios Batsios
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | - Vinay Ayyappan
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | - Celiné Taglang
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | - Anne Marie Gillespie
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | - Peder E Z Larson
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | - H Artee Luchman
- Department of Cell Biology and Anatomy and Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Joseph F Costello
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Russell O Pieper
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Sabrina M Ronen
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
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Yu Y, Villanueva-Meyer J, Grimmer MR, Hilz S, Solomon DA, Choi S, Wahl M, Mazor T, Hong C, Shai A, Phillips JJ, Wainer BH, McDermott M, Haas-Kogan D, Taylor JW, Butowski N, Clarke JL, Berger MS, Molinaro AM, Chang SM, Costello JF, Oberheim Bush NA. Temozolomide-induced hypermutation is associated with distant recurrence and reduced survival after high-grade transformation of low-grade IDH-mutant gliomas. Neuro Oncol 2021; 23:1872-1884. [PMID: 33823014 DOI: 10.1093/neuonc/noab081] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Chemotherapy improves overall survival after surgery and radiotherapy for newly diagnosed high-risk IDH-mutant low-grade gliomas, but a proportion of patients treated with temozolomide (TMZ) will develop recurrent tumors with TMZ-induced hypermutation. We aimed to determine the prevalence of TMZ-induced hypermutation at recurrence and prognostic implications. METHODS We sequenced recurrent tumors from 82 patients with initially low-grade IDH-mutant gliomas who underwent re-operation and correlated hypermutation status with grade at recurrence and subsequent clinical outcomes. RESULTS Hypermutation was associated with high-grade disease at the time of re-operation (OR 12.0 95% CI 2.5-115.5, p=0.002) and was identified at transformation in 57% of recurrent LGGs previously exposed to TMZ. After anaplastic (grade III) transformation, hypermutation was associated with shorter survival on univariate and multivariate analysis (HR 3.4, 95% CI 1.2-9.9, p=0.024), controlling for tumor grade, subtype, age, and prior radiotherapy. The effect of hypermutation on survival after transformation was validated in an independent, published dataset. Hypermutated (HM) tumors were more likely to develop discontiguous foci of disease in the brain and spine (p=0.003). To estimate the overall incidence of high-grade transformation among low-grade IDH-mutant tumors, data from a phase II trial of TMZ for LGG were analyzed. 8-year transformation-free survival was 53.8% (95% CI 42.8-69.2) and 61% of analyzed transformed cases were HM. CONCLUSIONS TMZ-induced hypermutation is a common event in transformed LGG previously treated with TMZ, and is associated with worse prognosis and development of discontiguous disease after recurrence. These findings impact tumor classification at recurrence, prognostication, and clinical trial design.
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Affiliation(s)
- Yao Yu
- Department of Radiation Oncology, Memorial Sloan Kettering, New York City, NY USA
| | - Javier Villanueva-Meyer
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | - Matthew R Grimmer
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Stephanie Hilz
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - David A Solomon
- Division of Neuropathology, Department of Pathology, University of California, San Francisco, CA, USA
| | - Serah Choi
- Department of Radiation Oncology, University Hospitals, Cleveland, OH, USA
| | - Michael Wahl
- Department of Radiation Oncology Samaritan Pastega Regional Cancer Center, Corvallis, OR, USA
| | - Tali Mazor
- Department of Computational Biology, Dana Farber/Harvard Cancer Center, Boston, MA, USA
| | - Chibo Hong
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Anny Shai
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California, San Francisco, CA, USA.,Division of Neuropathology, Department of Pathology, University of California, San Francisco, CA, USA
| | | | - Michael McDermott
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Daphne Haas-Kogan
- Department of Radiation Oncology, Dana Farber/Harvard Cancer Center, Boston, MA, USA
| | - Jennie W Taylor
- Department of Neurological Surgery, University of California, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, CA, USA
| | - Nicholas Butowski
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Jennifer L Clarke
- Department of Neurological Surgery, University of California, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, CA, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Annette M Molinaro
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Nancy Ann Oberheim Bush
- Department of Neurological Surgery, University of California, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, CA, USA
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Chuntova P, Chow F, Watchmaker PB, Galvez M, Heimberger AB, Newell EW, Diaz A, DePinho RA, Li MO, Wherry EJ, Mitchell D, Terabe M, Wainwright DA, Berzofsky JA, Herold-Mende C, Heath JR, Lim M, Margolin KA, Chiocca EA, Kasahara N, Ellingson BM, Brown CE, Chen Y, Fecci PE, Reardon DA, Dunn GP, Liau LM, Costello JF, Wick W, Cloughesy T, Timmer WC, Wen PY, Prins RM, Platten M, Okada H. Unique challenges for glioblastoma immunotherapy-discussions across neuro-oncology and non-neuro-oncology experts in cancer immunology. Meeting Report from the 2019 SNO Immuno-Oncology Think Tank. Neuro Oncol 2021; 23:356-375. [PMID: 33367885 PMCID: PMC7992879 DOI: 10.1093/neuonc/noaa277] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Cancer immunotherapy has made remarkable advances with over 50 separate Food and Drug Administration (FDA) approvals as first- or second-line indications since 2015. These include immune checkpoint blocking antibodies, chimeric antigen receptor-transduced T cells, and bispecific T-cell-engaging antibodies. While multiple cancer types now benefit from these immunotherapies, notable exceptions thus far include brain tumors, such as glioblastoma. As such, it seems critical to gain a better understanding of unique mechanistic challenges underlying the resistance of malignant gliomas to immunotherapy, as well as to acquire insights into the development of future strategies. An Immuno-Oncology Think Tank Meeting was held during the 2019 Annual Society for Neuro-Oncology Scientific Conference. Discussants in the fields of neuro-oncology, neurosurgery, neuro-imaging, medical oncology, and cancer immunology participated in the meeting. Sessions focused on topics such as the tumor microenvironment, myeloid cells, T-cell dysfunction, cellular engineering, and translational aspects that are critical and unique challenges inherent with primary brain tumors. In this review, we summarize the discussions and the key messages from the meeting, which may potentially serve as a basis for advancing the field of immune neuro-oncology in a collaborative manner.
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Affiliation(s)
- Pavlina Chuntova
- Department of Neurological Surgery, UCSF, San Francisco, California
| | - Frances Chow
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | | | - Mildred Galvez
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, Los Angeles, California
| | - Amy B Heimberger
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Evan W Newell
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Aaron Diaz
- Department of Neurological Surgery, UCSF, San Francisco, California
| | - Ronald A DePinho
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ming O Li
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, New York
| | - E John Wherry
- Department of Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Duane Mitchell
- Department of Neurosurgery, University of Florida College of Medicine, Gainesville, Florida
| | - Masaki Terabe
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | - Derek A Wainwright
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Jay A Berzofsky
- Center for Cancer Research, National Cancer Institute, Bethesda, Maryland
| | | | | | - Michael Lim
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Kim A Margolin
- Department of Medical Oncology & Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, California
| | - E Antonio Chiocca
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, Massachusetts
| | | | - Benjamin M Ellingson
- Department of Radiological Sciences, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - Christine E Brown
- Department of Immuno-Oncology, Beckman Research Institute of the City of Hope, Duarte, California
| | - Yvonne Chen
- Department of Microbiology, Immunology & Molecular Genetics, UCLA, Los Angeles, California
| | - Peter E Fecci
- Department of Neurosurgery, Duke University School of Medicine, Durham, North Carolina
| | - David A Reardon
- Department of Medicine/Medical Oncology, Harvard Medical School, Boston, Massachusetts
| | - Gavin P Dunn
- Department of Neurological Surgery, Washington University School of Medicine, St. Louis, Missouri
| | - Linda M Liau
- Department of Neurosurgery, David Geffen School of Medicine at UCLA, Los Angeles, California
| | | | - Wolfgang Wick
- Department of Neurology, University Hospital Heidelberg, Heidelberg, Germany
| | - Timothy Cloughesy
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, California
| | - William C Timmer
- Cancer Therapy Evaluation Program, National Cancer Institute, Bethesda, Maryland
| | - Patrick Y Wen
- Center for Neuro-Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts
| | - Robert M Prins
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, Los Angeles, California.,Parker Institute for Cancer Immunotherapy, San Francisco, California
| | - Michael Platten
- Department of Neurology, Medical Faculty Mannheim, MCTN, University of Heidelberg, Mannheim, Germany.,DKTK CCU Brain Tumor Immunology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hideho Okada
- Department of Neurological Surgery, UCSF, San Francisco, California.,Parker Institute for Cancer Immunotherapy, San Francisco, California
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Mathur R, Zhang Y, Grimmer MR, Hong C, Zhang M, Bollam S, Petrecca K, Clarke J, Berger MS, Phillips JJ, Oberheim-Bush NA, Molinaro AM, Chang SM, Costello JF. MGMT promoter methylation level in newly diagnosed low-grade glioma is a predictor of hypermutation at recurrence. Neuro Oncol 2021; 22:1580-1590. [PMID: 32166314 DOI: 10.1093/neuonc/noaa059] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Emerging data suggest that a subset of patients with diffuse isocitrate dehydrogenase (IDH)-mutant low-grade glioma (LGG) who receive adjuvant temozolomide (TMZ) recur with hypermutation in association with malignant progression to higher-grade tumors. It is currently unclear why some TMZ-treated LGG patients recur with hypermutation while others do not. MGMT encodes O6-methylguanine-DNA methyltransferase, a DNA repair protein that removes cytotoxic and potentially mutagenic lesions induced by TMZ. Here, we hypothesize that epigenetic silencing of MGMT by promoter methylation facilitates TMZ-induced mutagenesis in LGG patients and contributes to development of hypermutation at recurrence. METHODS We utilize a quantitative deep sequencing assay to characterize MGMT promoter methylation in 109 surgical tissue specimens from initial tumors and post-treatment recurrences of 37 TMZ-treated LGG patients. We utilize methylation arrays to validate our sequencing assay, RNA sequencing to assess the relationship between methylation and gene expression, and exome sequencing to determine hypermutation status. RESULTS Methylation level at the MGMT promoter is significantly higher in initial tumors of patients that develop hypermutation at recurrence relative to initial tumors of patients that do not (45.7% vs 34.8%, P = 0.027). Methylation level in initial tumors can predict hypermutation at recurrence in univariate models and multivariate models that incorporate patient age and molecular subtype. CONCLUSIONS These findings reveal a mechanistic basis for observed differences in patient susceptibility to TMZ-driven hypermutation. Furthermore, they establish MGMT promoter methylation level as a potential biomarker to inform clinical management of LGG patients, including monitoring and treatment decisions, by predicting risk of hypermutation at recurrence.
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Affiliation(s)
- Radhika Mathur
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Yalan Zhang
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Matthew R Grimmer
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA.,Bioinformatics and Computational Biology, Discovery Oncology, Genentech, San Francisco, California, USA
| | - Chibo Hong
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Michael Zhang
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Saumya Bollam
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Kevin Petrecca
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Jennifer Clarke
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Nancy Ann Oberheim-Bush
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Annette M Molinaro
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
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Liu SJ, Magill ST, Vasudevan HN, Hilz S, Villanueva-Meyer JE, Lastella S, Daggubati V, Spatz J, Choudhury A, Orr BA, Demaree B, Seo K, Ferris SP, Abate AR, Oberheim Bush NA, Bollen AW, McDermott MW, Costello JF, Raleigh DR. Multiplatform Molecular Profiling Reveals Epigenomic Intratumor Heterogeneity in Ependymoma. Cell Rep 2021; 30:1300-1309.e5. [PMID: 32023450 PMCID: PMC7313374 DOI: 10.1016/j.celrep.2020.01.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 06/19/2019] [Accepted: 01/06/2020] [Indexed: 12/24/2022] Open
Abstract
Ependymomas exist within distinct genetic subgroups, but the molecular diversity within individual ependymomas is unknown. We perform multiplatform molecular profiling of 6 spatially distinct samples from an ependymoma with C11orf95-RELA fusion. DNA methylation and RNA sequencing distinguish clusters of samples according to neuronal development gene expression programs that could also be delineated by differences in magnetic resonance blood perfusion. Exome sequencing and phylogenetic analysis reveal epigenomic intratumor heterogeneity and suggest that chromosomal structural alterations may precede accumulation of single-nucleotide variants during ependymoma tumorigenesis. In sum, these findings shed light on the oncogenesis and intratumor heterogeneity of ependymoma. Tumor heterogeneity poses a barrier to cancer treatment. Liu etal. investigate radiographically distinct regions of an ependymoma tumor using transcriptomic, genetic, and epigenomic profiling and discover axes of gene expression programs that recapitulate normal brain development in addition to phylogenies that shed light on the tumorigenesis of ependymoma.
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Affiliation(s)
- S John Liu
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Stephen T Magill
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Harish N Vasudevan
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Stephanie Hilz
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Javier E Villanueva-Meyer
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sydney Lastella
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Vikas Daggubati
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Jordan Spatz
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Abrar Choudhury
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Brent A Orr
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Benjamin Demaree
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kyounghee Seo
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sean P Ferris
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biosciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Nancy Ann Oberheim Bush
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Andrew W Bollen
- Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michael W McDermott
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | - David R Raleigh
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94143, USA.
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38
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Radoul M, Hong D, Gillespie AM, Najac C, Viswanath P, Pieper RO, Costello JF, Luchman HA, Ronen SM. Early Noninvasive Metabolic Biomarkers of Mutant IDH Inhibition in Glioma. Metabolites 2021; 11:metabo11020109. [PMID: 33668509 PMCID: PMC7917625 DOI: 10.3390/metabo11020109] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/09/2021] [Accepted: 02/10/2021] [Indexed: 12/17/2022] Open
Abstract
Approximately 80% of low-grade glioma (LGGs) harbor mutant isocitrate dehydrogenase 1/2 (IDH1/2) driver mutations leading to accumulation of the oncometabolite 2-hydroxyglutarate (2-HG). Thus, inhibition of mutant IDH is considered a potential therapeutic target. Several mutant IDH inhibitors are currently in clinical trials, including AG-881 and BAY-1436032. However, to date, early detection of response remains a challenge. In this study we used high resolution 1H magnetic resonance spectroscopy (1H-MRS) to identify early noninvasive MR (Magnetic Resonance)-detectable metabolic biomarkers of response to mutant IDH inhibition. In vivo 1H-MRS was performed on mice orthotopically-implanted with either genetically engineered (U87IDHmut) or patient-derived (BT257 and SF10417) mutant IDH1 cells. Treatment with either AG-881 or BAY-1436032 induced a significant reduction in 2-HG. Moreover, both inhibitors led to a significant early and sustained increase in glutamate and the sum of glutamate and glutamine (GLX) in all three models. A transient early increase in N-acetylaspartate (NAA) was also observed. Importantly, all models demonstrated enhanced animal survival following both treatments and the metabolic alterations were observed prior to any detectable differences in tumor volume between control and treated tumors. Our study therefore identifies potential translatable early metabolic biomarkers of drug delivery, mutant IDH inhibition and glioma response to treatment with emerging clinically relevant therapies.
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Affiliation(s)
- Marina Radoul
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA 94158, USA; (M.R.); (D.H.); (A.M.G.); (C.N.); (P.V.)
| | - Donghyun Hong
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA 94158, USA; (M.R.); (D.H.); (A.M.G.); (C.N.); (P.V.)
| | - Anne Marie Gillespie
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA 94158, USA; (M.R.); (D.H.); (A.M.G.); (C.N.); (P.V.)
| | - Chloé Najac
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA 94158, USA; (M.R.); (D.H.); (A.M.G.); (C.N.); (P.V.)
| | - Pavithra Viswanath
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA 94158, USA; (M.R.); (D.H.); (A.M.G.); (C.N.); (P.V.)
| | - Russell O. Pieper
- Department of Neurological Surgery, Helen Diller Research Center, University of California, San Francisco, CA 94158, USA; (R.O.P.); (J.F.C.)
- Brain Tumor Research Center, University of California, San Francisco, CA 94158, USA
| | - Joseph F. Costello
- Department of Neurological Surgery, Helen Diller Research Center, University of California, San Francisco, CA 94158, USA; (R.O.P.); (J.F.C.)
| | - Hema Artee Luchman
- Arnie Charbonneau Cancer Institute and Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 4N1, Canada;
| | - Sabrina M. Ronen
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, CA 94158, USA; (M.R.); (D.H.); (A.M.G.); (C.N.); (P.V.)
- Brain Tumor Research Center, University of California, San Francisco, CA 94158, USA
- Correspondence: ; Tel.: +1-415-514-4839
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39
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Viswanath P, Batsios G, Mukherjee J, Gillespie AM, Larson PEZ, Luchman HA, Phillips JJ, Costello JF, Pieper RO, Ronen SM. Non-invasive assessment of telomere maintenance mechanisms in brain tumors. Nat Commun 2021; 12:92. [PMID: 33397920 PMCID: PMC7782549 DOI: 10.1038/s41467-020-20312-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 11/27/2020] [Indexed: 01/29/2023] Open
Abstract
Telomere maintenance is a universal hallmark of cancer. Most tumors including low-grade oligodendrogliomas use telomerase reverse transcriptase (TERT) expression for telomere maintenance while astrocytomas use the alternative lengthening of telomeres (ALT) pathway. Although TERT and ALT are hallmarks of tumor proliferation and attractive therapeutic targets, translational methods of imaging TERT and ALT are lacking. Here we show that TERT and ALT are associated with unique 1H-magnetic resonance spectroscopy (MRS)-detectable metabolic signatures in genetically-engineered and patient-derived glioma models and patient biopsies. Importantly, we have leveraged this information to mechanistically validate hyperpolarized [1-13C]-alanine flux to pyruvate as an imaging biomarker of ALT status and hyperpolarized [1-13C]-alanine flux to lactate as an imaging biomarker of TERT status in low-grade gliomas. Collectively, we have identified metabolic biomarkers of TERT and ALT status that provide a way of integrating critical oncogenic information into non-invasive imaging modalities that can improve tumor diagnosis and treatment response monitoring.
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Affiliation(s)
- Pavithra Viswanath
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA.
| | - Georgios Batsios
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | - Joydeep Mukherjee
- Department of Neurological Surgery, Helen Diller Research Center, University of California San Francisco, San Francisco, CA, USA
| | - Anne Marie Gillespie
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | - Peder E Z Larson
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | - H Artee Luchman
- Department of Cell Biology and Anatomy, Arnie Charbonneau Cancer Institute and Hotchkiss Brain Institute, University of Calgary, Calgary, AB, Canada
| | - Joanna J Phillips
- Department of Neurological Surgery, Helen Diller Research Center, University of California San Francisco, San Francisco, CA, USA
| | - Joseph F Costello
- Department of Neurological Surgery, Helen Diller Research Center, University of California San Francisco, San Francisco, CA, USA
| | - Russell O Pieper
- Department of Neurological Surgery, Helen Diller Research Center, University of California San Francisco, San Francisco, CA, USA
| | - Sabrina M Ronen
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA.
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40
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Affiliation(s)
- Wadih Arap
- From the Rutgers Cancer Institute of New Jersey (W.A., R.P.) and the Division of Hematology-Oncology, Department of Medicine (W.A.), and the Division of Cancer Biology, Department of Radiation Oncology (R.P.), Rutgers New Jersey Medical School, Newark; and the Department of Neurological Surgery, University of California, San Francisco, San Francisco (J.F.C.)
| | - Renata Pasqualini
- From the Rutgers Cancer Institute of New Jersey (W.A., R.P.) and the Division of Hematology-Oncology, Department of Medicine (W.A.), and the Division of Cancer Biology, Department of Radiation Oncology (R.P.), Rutgers New Jersey Medical School, Newark; and the Department of Neurological Surgery, University of California, San Francisco, San Francisco (J.F.C.)
| | - Joseph F Costello
- From the Rutgers Cancer Institute of New Jersey (W.A., R.P.) and the Division of Hematology-Oncology, Department of Medicine (W.A.), and the Division of Cancer Biology, Department of Radiation Oncology (R.P.), Rutgers New Jersey Medical School, Newark; and the Department of Neurological Surgery, University of California, San Francisco, San Francisco (J.F.C.)
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41
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Subramani E, Radoul M, Najac C, Batsios G, Molloy AR, Hong D, Gillespie AM, Santos RD, Viswanath P, Costello JF, Pieper RO, Ronen SM. Glutamate Is a Noninvasive Metabolic Biomarker of IDH1-Mutant Glioma Response to Temozolomide Treatment. Cancer Res 2020; 80:5098-5108. [PMID: 32958546 PMCID: PMC7669718 DOI: 10.1158/0008-5472.can-20-1314] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 08/11/2020] [Accepted: 09/16/2020] [Indexed: 02/04/2023]
Abstract
Although lower grade gliomas are driven by mutations in the isocitrate dehydrogenase 1 (IDH1) gene and are less aggressive than primary glioblastoma, they nonetheless generally recur. IDH1-mutant patients are increasingly being treated with temozolomide, but early detection of response remains a challenge and there is a need for complementary imaging methods to assess response to therapy prior to tumor shrinkage. The goal of this study was to determine the value of magnetic resonance spectroscopy (MRS)-based metabolic changes for detection of response to temozolomide in both genetically engineered and patient-derived mutant IDH1 models. Using 1H MRS in combination with chemometrics identified several metabolic alterations in temozolomide-treated cells, including a significant increase in steady-state glutamate levels. This was confirmed in vivo, where the observed 1H MRS increase in glutamate/glutamine occurred prior to tumor shrinkage. Cells labeled with [1-13C]glucose and [3-13C]glutamine, the principal sources of cellular glutamate, showed that flux to glutamate both from glucose via the tricarboxylic acid cycle and from glutamine were increased following temozolomide treatment. In line with these results, hyperpolarized [5-13C]glutamate produced from [2-13C]pyruvate and hyperpolarized [1-13C]glutamate produced from [1-13C]α-ketoglutarate were significantly higher in temozolomide-treated cells compared with controls. Collectively, our findings identify 1H MRS-detectable elevation of glutamate and hyperpolarized 13C MRS-detectable glutamate production from either pyruvate or α-ketoglutarate as potential translatable metabolic biomarkers of response to temozolomide treatment in mutant IDH1 glioma. SIGNIFICANCE: These findings show that glutamate can be used as a noninvasive, imageable metabolic marker for early assessment of tumor response to temozolomide, with the potential to improve treatment strategies for mutant IDH1 patients.
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Affiliation(s)
- Elavarasan Subramani
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California
| | - Marina Radoul
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California
| | - Chloe Najac
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California
| | - Georgios Batsios
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California
| | - Abigail R Molloy
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California
| | - Donghyun Hong
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California
| | - Anne Marie Gillespie
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California
| | - Romelyn Delos Santos
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California
| | - Pavithra Viswanath
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California
| | - Joseph F Costello
- Department of Neurological Surgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Russell O Pieper
- Department of Neurological Surgery, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
- Brain Tumor Research Center, University of California San Francisco, San Francisco, California
| | - Sabrina M Ronen
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California.
- Brain Tumor Research Center, University of California San Francisco, San Francisco, California
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42
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Jones LE, Hilz S, Grimmer MR, Mazor T, Najac C, Mukherjee J, McKinney A, Chow T, Pieper RO, Ronen SM, Chang SM, Phillips JJ, Costello JF. Patient-derived cells from recurrent tumors that model the evolution of IDH-mutant glioma. Neurooncol Adv 2020; 2:vdaa088. [PMID: 32904945 PMCID: PMC7462278 DOI: 10.1093/noajnl/vdaa088] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Background IDH-mutant lower-grade gliomas (LGGs) evolve under the selective pressure of therapy, but well-characterized patient-derived cells (PDCs) modeling evolutionary stages are lacking. IDH-mutant LGGs may develop therapeutic resistance associated with chemotherapy-driven hypermutation and malignant progression. The aim of this study was to establish and characterize PDCs, single-cell-derived PDCs (scPDCs), and xenografts (PDX) of IDH1-mutant recurrences representing distinct stages of tumor evolution. Methods We derived and validated cell cultures from IDH1-mutant recurrences of astrocytoma and oligodendroglioma. We used exome sequencing and phylogenetic reconstruction to examine the evolutionary stage represented by PDCs, scPDCs, and PDX relative to corresponding spatiotemporal tumor tissue and germline DNA. PDCs were also characterized for growth and tumor immortality phenotypes, and PDX were examined histologically. Results The integrated astrocytoma phylogeny revealed 2 independent founder clonal expansions of hypermutated (HM) cells in tumor tissue that are faithfully represented by independent PDCs. The oligodendroglioma phylogeny showed more than 4000 temozolomide-associated mutations shared among tumor samples, PDCs, scPDCs, and PDX, suggesting a shared monoclonal origin. The PDCs from both subtypes exhibited hallmarks of tumorigenesis, retention of subtype-defining genomic features, production of 2-hydroxyglutarate, and subtype-specific telomere maintenance mechanisms that confer tumor cell immortality. The oligodendroglioma PDCs formed infiltrative intracranial tumors with characteristic histology. Conclusions These PDCs, scPDCs, and PDX are unique and versatile community resources that model the heterogeneous clonal origins and functions of recurrent IDH1-mutant LGGs. The integrated phylogenies advance our knowledge of the complex evolution and immense mutational load of IDH1-mutant HM glioma.
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Affiliation(s)
- Lindsey E Jones
- Department of Neurological Surgery, University of California, San Francisco, California, USA.,Biomedical Sciences Graduate Program, University of California, San Francisco, California, USA
| | - Stephanie Hilz
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Matthew R Grimmer
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Tali Mazor
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Chloé Najac
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, California, USA
| | - Joydeep Mukherjee
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Andrew McKinney
- Department of Neurological Surgery, University of California, San Francisco, California, USA.,Biomedical Sciences Graduate Program, University of California, San Francisco, California, USA
| | - Tracy Chow
- Department of Biochemistry and Biophysics, University of California, San Francisco, California, USA
| | - Russell O Pieper
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Sabrina M Ronen
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, California, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California, San Francisco, California, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, California, USA
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Zhao SG, Chen WS, Li H, Foye A, Zhang M, Sjöström M, Aggarwal R, Playdle D, Liao A, Alumkal JJ, Das R, Chou J, Hua JT, Barnard TJ, Bailey AM, Chow ED, Perry MD, Dang HX, Yang R, Moussavi-Baygi R, Zhang L, Alshalalfa M, Laura Chang S, Houlahan KE, Shiah YJ, Beer TM, Thomas G, Chi KN, Gleave M, Zoubeidi A, Reiter RE, Rettig MB, Witte O, Yvonne Kim M, Fong L, Spratt DE, Morgan TM, Bose R, Huang FW, Li H, Chesner L, Shenoy T, Goodarzi H, Asangani IA, Sandhu S, Lang JM, Mahajan NP, Lara PN, Evans CP, Febbo P, Batzoglou S, Knudsen KE, He HH, Huang J, Zwart W, Costello JF, Luo J, Tomlins SA, Wyatt AW, Dehm SM, Ashworth A, Gilbert LA, Boutros PC, Farh K, Chinnaiyan AM, Maher CA, Small EJ, Quigley DA, Feng FY. The DNA methylation landscape of advanced prostate cancer. Nat Genet 2020; 52:778-789. [PMID: 32661416 PMCID: PMC7454228 DOI: 10.1038/s41588-020-0648-8] [Citation(s) in RCA: 171] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 05/20/2020] [Indexed: 02/08/2023]
Abstract
Although DNA methylation is a key regulator of gene expression, the comprehensive methylation landscape of metastatic cancer has never been defined. Through whole-genome bisulfite sequencing paired with deep whole-genome and transcriptome sequencing of 100 castration-resistant prostate metastases, we discovered alterations affecting driver genes only detectable with integrated whole-genome approaches. Notably, we observed that 22% of tumors exhibited a novel epigenomic subtype associated with hyper-methylation and somatic mutations in TET2, DNMT3B, IDH1, and BRAF. We also identified intergenic regions where methylation is associated with RNA expression of the oncogenic driver genes AR, MYC and ERG. Finally, we showed that differential methylation during progression preferentially occurs at somatic mutational hotspots and putative regulatory regions. This study is a large integrated study of whole-genome, whole-methylome and whole-transcriptome sequencing in metastatic cancer and provides a comprehensive overview of the important regulatory role of methylation in metastatic castration-resistant prostate cancer.
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Affiliation(s)
- Shuang G Zhao
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA.,Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - William S Chen
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Yale School of Medicine, New Haven, CT, USA
| | - Haolong Li
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Adam Foye
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Meng Zhang
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Martin Sjöström
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Denise Playdle
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | - Joshi J Alumkal
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Rajdeep Das
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Jonathan Chou
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Junjie T Hua
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Travis J Barnard
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Adina M Bailey
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Eric D Chow
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.,Center for Advanced Technology, University of California San Francisco, San Francisco, CA, USA
| | - Marc D Perry
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Ha X Dang
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA.,Department of Internal Medicine, Washington University, St. Louis, MO, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, USA
| | - Rendong Yang
- The Hormel Institute, University of Minnesota, Austin, MN, USA
| | - Ruhollah Moussavi-Baygi
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Li Zhang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Mohammed Alshalalfa
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - S Laura Chang
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Kathleen E Houlahan
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Human Genetics, Institute for Precision Health, UCLA, Los Angeles, CA, USA
| | - Yu-Jia Shiah
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Tomasz M Beer
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Division of Hematology/Medical Oncology, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - George Thomas
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.,Department of Pathology, Oregon Health & Science University, Portland, OR, USA
| | - Kim N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,British Columbia Cancer Agency, Vancouver Centre, Vancouver, British Columbia, Canada
| | - Martin Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Amina Zoubeidi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert E Reiter
- Jonsson Comprehensive Cancer Center, Departments of Medicine and Urology, University of California Los Angeles, Los Angeles, CA, USA
| | - Matthew B Rettig
- Jonsson Comprehensive Cancer Center, Departments of Medicine and Urology, University of California Los Angeles, Los Angeles, CA, USA.,Department of Medicine, VA Greater Los Angeles Healthcare System, Los Angeles, CA, USA
| | - Owen Witte
- Department of Microbiology, Immunology, and Molecular Genetics at the David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - M Yvonne Kim
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Lawrence Fong
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Daniel E Spratt
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI, USA
| | - Todd M Morgan
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Urology, University of Michigan, Ann Arbor, MI, USA
| | - Rohit Bose
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA.,Department of Anatomy, University of California San Francisco, San Francisco, CA, USA
| | - Franklin W Huang
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Hui Li
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Lisa Chesner
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Tanushree Shenoy
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Irfan A Asangani
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Shahneen Sandhu
- Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia
| | - Joshua M Lang
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Nupam P Mahajan
- Siteman Cancer Center, Washington University, St. Louis, MO, USA.,Department of Surgery, Washington University, St. Louis, MO, USA
| | - Primo N Lara
- Division of Hematology Oncology, Department of Internal Medicine, University of California Davis, Sacramento, CA, USA.,Comprehensive Cancer Center, University of California Davis, Sacramento, CA, USA
| | - Christopher P Evans
- Comprehensive Cancer Center, University of California Davis, Sacramento, CA, USA.,Department of Urologic Surgery, University of California Davis, Sacramento, CA, USA
| | | | | | - Karen E Knudsen
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Housheng H He
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jiaoti Huang
- Department of Pathology, Duke University, Durham, NC, USA
| | - Wilbert Zwart
- Netherlands Cancer Institute, Oncode Institute, Amsterdam, the Netherlands
| | - Joseph F Costello
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Jianhua Luo
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Scott A Tomlins
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Scott M Dehm
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA.,Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Luke A Gilbert
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Paul C Boutros
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Human Genetics, Institute for Precision Health, UCLA, Los Angeles, CA, USA.,Jonsson Comprehensive Cancer Center, Departments of Medicine and Urology, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Arul M Chinnaiyan
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Urology, University of Michigan, Ann Arbor, MI, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA.,Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Christopher A Maher
- McDonnell Genome Institute, Washington University, St. Louis, MO, USA.,Department of Internal Medicine, Washington University, St. Louis, MO, USA.,Siteman Cancer Center, Washington University, St. Louis, MO, USA.,Department of Biomedical Engineering, Washington University, St. Louis, MO, USA
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Felix Y Feng
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA. .,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA. .,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA. .,Department of Urology, University of California San Francisco, San Francisco, CA, USA.
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44
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Li L, Maire CL, Bilenky M, Carles A, Heravi-Moussavi A, Hong C, Tam A, Kamoh B, Cho S, Cheung D, Li I, Wong T, Nagarajan RP, Mungall AJ, Moore R, Wang T, Kleinman CL, Jabado N, Jones SJM, Marra MA, Ligon KL, Costello JF, Hirst M. Epigenomic programming in early fetal brain development. Epigenomics 2020; 12:1053-1070. [PMID: 32677466 PMCID: PMC7857341 DOI: 10.2217/epi-2019-0319] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 03/19/2020] [Indexed: 12/21/2022] Open
Abstract
Aim: To provide a comprehensive understanding of gene regulatory networks in the developing human brain and a foundation for interpreting pathogenic deregulation. Materials & methods: We generated reference epigenomes and transcriptomes of dissected brain regions and primary neural progenitor cells (NPCs) derived from cortical and ganglionic eminence tissues of four normal human fetuses. Results: Integration of these data across developmental stages revealed a directional increase in active regulatory states, transcription factor activities and gene transcription with developmental stage. Consistent with differences in their biology, NPCs derived from cortical and ganglionic eminence regions contained common, region specific, and gestational week specific regulatory states. Conclusion: We provide a high-resolution regulatory network for NPCs from different brain regions as a comprehensive reference for future studies.
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Affiliation(s)
- Luolan Li
- Department of Microbiology & Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Cecile L Maire
- Department of Medical Oncology, Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Misha Bilenky
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Annaïck Carles
- Department of Microbiology & Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | | | - Chibo Hong
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158, USA
| | - Angela Tam
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Baljit Kamoh
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Stephanie Cho
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Dorothy Cheung
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Irene Li
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Tina Wong
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Raman P Nagarajan
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158, USA
| | - Andrew J Mungall
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Richard Moore
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Ting Wang
- Department of Genetics, Washington University, St Louis, MO 63108, USA
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montreal, QC, H3T 1E2, Canada
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC, H3T 1E2, Canada
| | - Steven JM Jones
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
| | - Keith L Ligon
- Department of Medical Oncology, Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA 94158, USA
| | - Martin Hirst
- Department of Microbiology & Immunology, Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Canada's Michael Smith Genome Science Center, BC Cancer, Vancouver, BC, V5Z 4S6, Canada
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45
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Robinson JF, Kapidzic M, Hamilton EG, Chen H, Puckett KW, Zhou Y, Ona K, Parry E, Wang Y, Park JS, Costello JF, Fisher SJ. Genomic Profiling of BDE-47 Effects on Human Placental Cytotrophoblasts. Toxicol Sci 2019; 167:211-226. [PMID: 30202865 DOI: 10.1093/toxsci/kfy230] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Despite gradual legislative efforts to phase out flame retardants (FRs) from the marketplace, polybrominated diphenyl ethers (PBDEs) are still widely detected in human maternal and fetal tissues, eg, placenta, due to their continued global application in consumer goods and inherent biological persistence. Recent studies in rodents and human placental cell lines suggest that PBDEs directly cause placental toxicity. During pregnancy, trophoblasts play key roles in uterine invasion, vascular remodeling, and anchoring of the placenta-fetal unit to the mother. Thus, to study the potential consequences of PBDE exposures on human placental development, we used an in vitro model: primary villous cytotrophoblasts (CTBs). Following exposures, the endpoints that were evaluated included cytotoxicity, function (migration, invasion), the transcriptome, and the methylome. In a concentration-dependent manner, common PBDE congeners, BDE-47 and -99, significantly reduced cell viability and increased death. Upon exposures to sub-cytotoxic concentrations (≤ 5 µM), we observed BDE-47 accumulation in CTBs with limited evidence of metabolism. At a functional level, BDE-47 hindered the ability of CTBs to migrate and invade. Transcriptomic analyses of BDE-47 effects suggested concentration-dependent changes in gene expression, involving stress pathways, eg, inflammation and lipid/cholesterol metabolism as well as processes underlying trophoblast fate, eg, differentiation, migration, and vascular morphogenesis. In parallel assessments, BDE-47 induced low-level global increases in methylation of CpG islands, including a subset that were proximal to genes with roles in cell adhesion/migration. Thus, using a primary human CTB model, we showed that PBDEs induced alterations at cellular and molecular levels, which could adversely impact placental development.
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Affiliation(s)
- Joshua F Robinson
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco (UCSF), San Francisco, California 94143.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco (UCSF), San Francisco, California 94143
| | - Mirhan Kapidzic
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco (UCSF), San Francisco, California 94143.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco (UCSF), San Francisco, California 94143
| | - Emily G Hamilton
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco (UCSF), San Francisco, California 94143.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco (UCSF), San Francisco, California 94143
| | - Hao Chen
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco (UCSF), San Francisco, California 94143.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco (UCSF), San Francisco, California 94143
| | - Kenisha W Puckett
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco (UCSF), San Francisco, California 94143.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco (UCSF), San Francisco, California 94143
| | - Yan Zhou
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco (UCSF), San Francisco, California 94143.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco (UCSF), San Francisco, California 94143
| | - Katherine Ona
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco (UCSF), San Francisco, California 94143.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco (UCSF), San Francisco, California 94143
| | - Emily Parry
- Environmental Chemistry Laboratory, Department of Toxic Substances Control, California Environmental Protection Agency, Berkeley, California 94710
| | - Yunzhu Wang
- Environmental Chemistry Laboratory, Department of Toxic Substances Control, California Environmental Protection Agency, Berkeley, California 94710
| | - June-Soo Park
- Environmental Chemistry Laboratory, Department of Toxic Substances Control, California Environmental Protection Agency, Berkeley, California 94710
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco (UCSF), San Francisco, California 94158
| | - Susan J Fisher
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Center for Reproductive Sciences, University of California, San Francisco (UCSF), San Francisco, California 94143.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco (UCSF), San Francisco, California 94143
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46
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Penas-Prado M, Wu J, Cahill DP, Brat DJ, Costello JF, Kluetz PG, Cairncross JG, van den Bent M, Verhaak RGW, Aboud O, Burger P, Chang SM, Cordova C, Huang RY, Rowe LS, Taphoorn MJB, Gilbert MR, Armstrong TS. Proceedings of the Comprehensive Oncology Network Evaluating Rare CNS Tumors (NCI-CONNECT) Oligodendroglioma Workshop. Neurooncol Adv 2019; 2:vdz048. [PMID: 33289010 DOI: 10.1093/noajnl/vdz048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Background Oligodendroglioma is a rare primary central nervous system (CNS) tumor with highly variable outcome and for which therapy is usually not curative. At present, little is known regarding the pathways involved with progression of oligodendrogliomas or optimal biomarkers for stratifying risk. Developing new therapies for this rare cancer is especially challenging. To overcome these challenges, the neuro-oncology community must be particularly innovative, seeking multi-institutional and international collaborations, and establishing partnerships with patients and advocacy groups thereby ensuring that each patient enrolled in a study is as informative as possible. Methods The mission of the National Cancer Institute's NCI-CONNECT program is to address the challenges and unmet needs in rare CNS cancer research and treatment by connecting patients, health care providers, researchers, and advocacy organizations to work in partnership. On November 19, 2018, the program convened a workshop on oligodendroglioma, one of the 12 rare CNS cancers included in its initial portfolio. The purpose of this workshop was to discuss scientific progress and regulatory challenges in oligodendroglioma research and develop a call to action to advance research and treatment for this cancer. Results The recommendations of the workshop include a multifaceted and interrelated approach covering: biology and preclinical models, data sharing and advanced molecular diagnosis and imaging; clinical trial design; and patient outreach and engagement. Conclusions The NCI-CONNECT program is well positioned to address challenges in oligodendroglioma care and research in collaboration with other stakeholders and is developing a list of action items for future initiatives.
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Affiliation(s)
| | - Jing Wu
- Neuro-Oncology Branch/National Cancer Institute, Bethesda, Maryland
| | - Daniel P Cahill
- Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniel J Brat
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco
| | - Paul G Kluetz
- Oncology Center of Excellence, U.S. Food and Drug Administration, Washington DC
| | | | | | - Roel G W Verhaak
- Jackson Laboratory for Genomic Medicine, Farmington, Connecticut
| | - Orwa Aboud
- Neuro-Oncology Branch/National Cancer Institute, Bethesda, Maryland.,Brain Tumor Program, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland
| | - Peter Burger
- Neuropathology Division, Johns Hopkins, Baltimore, Maryland
| | - Susan M Chang
- Department of Neurological Surgery, University of California, San Francisco
| | - Christine Cordova
- Neuro-Oncology Branch/National Cancer Institute, Bethesda, Maryland.,NYU School of Medicine, Laura and Isaac Perlmutter Cancer Center, New York, NY
| | - Raymond Y Huang
- Department of Radiology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Lindsay S Rowe
- Radiation Oncology Branch/National Cancer Institute, Bethesda, Maryland
| | - Martin J B Taphoorn
- Leiden University Medical Center and Haaglanden Medical Center, The Hague, The Netherlands
| | - Mark R Gilbert
- Neuro-Oncology Branch/National Cancer Institute, Bethesda, Maryland
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47
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Barthel FP, Johnson KC, Varn FS, Moskalik AD, Tanner G, Kocakavuk E, Anderson KJ, Abiola O, Aldape K, Alfaro KD, Alpar D, Amin SB, Ashley DM, Bandopadhayay P, Barnholtz-Sloan JS, Beroukhim R, Bock C, Brastianos PK, Brat DJ, Brodbelt AR, Bruns AF, Bulsara KR, Chakrabarty A, Chakravarti A, Chuang JH, Claus EB, Cochran EJ, Connelly J, Costello JF, Finocchiaro G, Fletcher MN, French PJ, Gan HK, Gilbert MR, Gould PV, Grimmer MR, Iavarone A, Ismail A, Jenkinson MD, Khasraw M, Kim H, Kouwenhoven MCM, LaViolette PS, Li M, Lichter P, Ligon KL, Lowman AK, Malta TM, Mazor T, McDonald KL, Molinaro AM, Nam DH, Nayyar N, Ng HK, Ngan CY, Niclou SP, Niers JM, Noushmehr H, Noorbakhsh J, Ormond DR, Park CK, Poisson LM, Rabadan R, Radlwimmer B, Rao G, Reifenberger G, Sa JK, Schuster M, Shaw BL, Short SC, Smitt PAS, Sloan AE, Smits M, Suzuki H, Tabatabai G, Van Meir EG, Watts C, Weller M, Wesseling P, Westerman BA, Widhalm G, Woehrer A, Yung WKA, Zadeh G, Huse JT, De Groot JF, Stead LF, Verhaak RGW. Longitudinal molecular trajectories of diffuse glioma in adults. Nature 2019; 576:112-120. [PMID: 31748746 PMCID: PMC6897368 DOI: 10.1038/s41586-019-1775-1] [Citation(s) in RCA: 280] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 10/01/2019] [Indexed: 12/15/2022]
Abstract
The evolutionary processes that drive universal therapeutic resistance in adult patients with diffuse glioma remain unclear1,2. Here we analysed temporally separated DNA-sequencing data and matched clinical annotation from 222 adult patients with glioma. By analysing mutations and copy numbers across the three major subtypes of diffuse glioma, we found that driver genes detected at the initial stage of disease were retained at recurrence, whereas there was little evidence of recurrence-specific gene alterations. Treatment with alkylating agents resulted in a hypermutator phenotype at different rates across the glioma subtypes, and hypermutation was not associated with differences in overall survival. Acquired aneuploidy was frequently detected in recurrent gliomas and was characterized by IDH mutation but without co-deletion of chromosome arms 1p/19q, and further converged with acquired alterations in the cell cycle and poor outcomes. The clonal architecture of each tumour remained similar over time, but the presence of subclonal selection was associated with decreased survival. Finally, there were no differences in the levels of immunoediting between initial and recurrent gliomas. Collectively, our results suggest that the strongest selective pressures occur during early glioma development and that current therapies shape this evolution in a largely stochastic manner.
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Affiliation(s)
- Floris P Barthel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Pathology, Brain Tumor Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Kevin C Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Frederick S Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Georgette Tanner
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Emre Kocakavuk
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- DKFZ Division of Translational Neurooncology at the West German Cancer Center, German Cancer Consortium Partner Site, University Hospital Essen, Essen, Germany
- Department of Neurosurgery, University Hospital Essen, Essen, Germany
| | - Kevin J Anderson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Olajide Abiola
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Kristin D Alfaro
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Donat Alpar
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | | | - David M Ashley
- Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, NC, USA
| | - Pratiti Bandopadhayay
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Jill S Barnholtz-Sloan
- Department of Population and Quantitative Health Sciences, Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Rameen Beroukhim
- Broad Institute, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | | | - Daniel J Brat
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Andrew R Brodbelt
- Department of Neurosurgery, University of Liverpool & Walton Centre NHS Trust, Liverpool, UK
| | - Alexander F Bruns
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Ketan R Bulsara
- Division of Neurosurgery, The University of Connecticut Health Center, Farmington, CT, USA
| | - Aruna Chakrabarty
- Department of Cellular and Molecular Pathology, Leeds Teaching Hospital NHS Trust, St James's University Hospital, Leeds, UK
| | - Arnab Chakravarti
- Department of Radiation Oncology, The Ohio State Comprehensive Cancer Center-Arthur G. James Cancer Hospital, Columbus, OH, USA
| | - Jeffrey H Chuang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA
| | - Elizabeth B Claus
- Yale University School of Public Health, New Haven, CT, USA
- Department of Neurosurgery, Brigham and Women's Hospital, Boston, MA, USA
| | - Elizabeth J Cochran
- Department of Pathology & Laboratory Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jennifer Connelly
- Department of Neurology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Joseph F Costello
- Department of Neurosurgery, University of California San Francisco, San Francisco, CA, USA
| | | | - Michael N Fletcher
- Division of Molecular Genetics, Heidelberg Center for Personalized Oncology, German Cancer Research Consortium, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Pim J French
- Department of Neurology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Hui K Gan
- Olivia Newton-John Cancer Research Institute, Austin Health, Melbourne, Victoria, Australia
- La Trobe University School of Cancer Medicine, Heidelberg, Victoria, Australia
| | - Mark R Gilbert
- Neuro-Oncology Branch, National Institutes of Health, Bethesda, MD, USA
| | - Peter V Gould
- Anatomic Pathology Service, Hôpital de l'Enfant-Jésus, CHU de Québec-Université Laval, Quebec, Quebec, Canada
| | - Matthew R Grimmer
- Department of Neurosurgery, University of California San Francisco, San Francisco, CA, USA
| | - Antonio Iavarone
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY, USA
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA
| | - Azzam Ismail
- Department of Cellular and Molecular Pathology, Leeds Teaching Hospital NHS Trust, St James's University Hospital, Leeds, UK
| | - Michael D Jenkinson
- Department of Neurosurgery, University of Liverpool & Walton Centre NHS Trust, Liverpool, UK
| | - Mustafa Khasraw
- Cooperative Trials Group for Neuro-Oncology (COGNO) NHMRC Clinical Trials Centre, The University of Sydney, Sydney, New South Wales, Australia
| | - Hoon Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Mathilde C M Kouwenhoven
- Department of Neurology, Brain Tumor Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Peter S LaViolette
- Department of Radiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Meihong Li
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Peter Lichter
- Division of Molecular Genetics, Heidelberg Center for Personalized Oncology, German Cancer Research Consortium, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Keith L Ligon
- Broad Institute, Cambridge, MA, USA
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Allison K Lowman
- Department of Radiology, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Tathiane M Malta
- Department of Neurosurgery, Henry Ford Health System, Henry Ford Cancer Institute, Detroit, MI, USA
| | - Tali Mazor
- Department of Neurosurgery, University of California San Francisco, San Francisco, CA, USA
| | - Kerrie L McDonald
- Cure Brain Cancer Biomarkers and Translational Research Group, Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - Annette M Molinaro
- Department of Neurosurgery, University of California San Francisco, San Francisco, CA, USA
| | - Do-Hyun Nam
- Department of Neurosurgery, Sungkyunkwan University School of Medicine, Samsung Medical Center, Seoul, South Korea
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, South Korea
| | - Naema Nayyar
- Division of Neuro-Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Ho Keung Ng
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong
| | - Chew Yee Ngan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Simone P Niclou
- Department of Oncology, Luxembourg Institute of Health, Luxembourg, Luxembourg
| | - Johanna M Niers
- Department of Neurology, Brain Tumor Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Houtan Noushmehr
- Department of Neurosurgery, Henry Ford Health System, Henry Ford Cancer Institute, Detroit, MI, USA
| | - Javad Noorbakhsh
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - D Ryan Ormond
- Department of Neurosurgery, University of Colorado School of Medicine, Aurora, CO, USA
| | - Chul-Kee Park
- Department of Neurosurgery, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, South Korea
| | - Laila M Poisson
- Department of Public Health Sciences, Henry Ford Health System, Henry Ford Cancer Institute, Detroit, MI, USA
| | - Raul Rabadan
- Department of Biomedical Informatics, Columbia University Medical Center, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
| | - Bernhard Radlwimmer
- Division of Molecular Genetics, Heidelberg Center for Personalized Oncology, German Cancer Research Consortium, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ganesh Rao
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Guido Reifenberger
- Institute of Neuropathology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Jason K Sa
- Institute for Refractory Cancer Research, Samsung Medical Center, Seoul, South Korea
| | - Michael Schuster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Brian L Shaw
- Division of Neuro-Oncology, Massachusetts General Hospital, Boston, MA, USA
| | - Susan C Short
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Peter A Sillevis Smitt
- Department of Neurology, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Andrew E Sloan
- Department of Neurological Surgery, University Hospitals Cleveland Medical Center, Case Western Reserve University, Cleveland, OH, USA
- Department of Neurosurgery, Case Western Reserve University, Cleveland, OH, USA
- Seidman Cancer Center and Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Marion Smits
- Department of Radiology & Nuclear Medicine, Erasmus MC - University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Ghazaleh Tabatabai
- Interdiscplinary Division of Neuro-Oncology, Hertie Institute for Clinical Brain Research, DKTK Partner Site Tübingen, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Erwin G Van Meir
- Department of Neurosurgery, School of Medicine and Winship Cancer Institute of Emory University, Atlanta, GA, USA
| | - Colin Watts
- Institute of Cancer Genome Sciences, Department of Neurosurgery, University of Birmingham, Birmingham, UK
| | - Michael Weller
- Department of Neurology, University Hospital Zurich, Zurich, Switzerland
| | - Pieter Wesseling
- Department of Pathology, Brain Tumor Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - Bart A Westerman
- Department of Neurosurgery, Brain Tumor Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Georg Widhalm
- Department of Neurosurgery, Medical University of Vienna, Vienna, Austria
| | - Adelheid Woehrer
- Institute of Neurology, Medical University of Vienna, Vienna, Austria
| | - W K Alfred Yung
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Gelareh Zadeh
- Division of Neurosurgery, Department of Surgery, University Health Network, Toronto, Ontario, Canada
| | - Jason T Huse
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John F De Groot
- Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Lucy F Stead
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
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48
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Abstract
Low-grade gliomas cause considerable morbidity and most will recur after initial therapy. At recurrence, low-grade gliomas can undergo transformation to high-grade gliomas (grade III or grade IV), which are associated with worse prognosis. Temozolomide (TMZ) provides survival benefit in patients with glioblastomas, but its value in patients with low-grade gliomas is less clear. A subset of TMZ-treated, isocitrate dehydrogenase‒mutant, low-grade astrocytomas recur as more malignant tumors with thousands of de novo, coding mutations bearing a signature of TMZ-induced hypermutation. Preliminary studies raise the hypothesis that TMZ-induced hypermutation may contribute to malignant transformation, although with highly variable latency. On the other hand, hypermutated gliomas have radically altered genomes that present new opportunities for therapeutic intervention. In light of these findings and the immunotherapy clinical trials they inspired, how do patients and providers approach the risks and benefits of TMZ therapy? This review discusses what is known about the mechanisms and consequences of TMZ-induced hypermutation and outstanding questions regarding its clinical significance.
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Affiliation(s)
- Serah Choi
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Yao Yu
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Matthew R Grimmer
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California
| | - Michael Wahl
- Samaritan Pastega Regional Cancer Center, Corvallis, Oregon
| | - Susan M Chang
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California
| | - Joseph F Costello
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California
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49
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Hayes J, Yu Y, Jalbert LE, Mazor T, Jones LE, Wood MD, Walsh KM, Bengtsson H, Hong C, Oberndorfer S, Roetzer T, Smirnov IV, Clarke JL, Aghi MK, Chang SM, Nelson SJ, Woehrer A, Phillips JJ, Solomon DA, Costello JF. Genomic analysis of the origins and evolution of multicentric diffuse lower-grade gliomas. Neuro Oncol 2019; 20:632-641. [PMID: 29077933 DOI: 10.1093/neuonc/nox205] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background Rare multicentric lower-grade gliomas (LGGs) represent a unique opportunity to study the heterogeneity among distinct tumor foci in a single patient and to infer their origins and parallel patterns of evolution. Methods In this study, we integrate clinical features, histology, and immunohistochemistry for 4 patients with multicentric LGG, arising both synchronously and metachronously. For 3 patients we analyze the phylogeny of the lesions using exome sequencing, including one case with a total of 8 samples from the 2 lesions. Results One patient was diagnosed with multicentric isocitrate dehydrogenase 1 (IDH1) mutated diffuse astrocytomas harboring distinct IDH1 mutations, R132H and R132C; the latter mutation has been associated with Li-Fraumeni syndrome, which was subsequently confirmed in the patient's germline DNA and shown in additional cases with The Cancer Genome Atlas data. In another patient, phylogenetic analysis of synchronously arising grade II and grade III diffuse astrocytomas demonstrated a single shared mutation, IDH1 R132H, and revealed convergent evolution via non-overlapping mutations in ATRX and TP53. In 2 cases, there was divergent evolution of IDH1-mutated and 1p/19q-codeleted oligodendroglioma and IDH1-mutated and 1p/19q-intact diffuse astrocytoma, occurring synchronously in one case and metachronously in a second. Conclusions Each tumor in multicentric LGG cases may arise independently or may diverge very early in their development, presenting as genetically and histologically distinct tumors. Comprehensive sampling of these lesions can therefore significantly alter diagnosis and management. Additionally, somatic IDH1 R132C mutation in either multicentric or solitary LGG identifies unsuspected germline TP53 mutation, validating the limited number of published cases.
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Affiliation(s)
- Josie Hayes
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Yao Yu
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California, USA
| | - Llewellyn E Jalbert
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California, USA
| | - Tali Mazor
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Lindsey E Jones
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Matthew D Wood
- Division of Neuropathology, Department of Pathology, University of California San Francisco, San Francisco, California, USA
| | - Kyle M Walsh
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Henrik Bengtsson
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA.,Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, USA
| | - Chibo Hong
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Stefan Oberndorfer
- Department of Neurology, University Hospital of St Poelten, St Poelten, Austria
| | - Thomas Roetzer
- Institute of Neurology and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Ivan V Smirnov
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Jennifer L Clarke
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA.,UCSF Brain Tumor Center, Division of Neuro-Oncology, Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA.,Department of Neurology, University of California San Francisco, San Francisco, California, USA
| | - Manish K Aghi
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA.,UCSF Brain Tumor Center, Division of Neuro-Oncology, Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
| | - Sarah J Nelson
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California, USA.,Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, USA
| | - Adelheid Woehrer
- Institute of Neurology and Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA.,Division of Neuropathology, Department of Pathology, University of California San Francisco, San Francisco, California, USA
| | - David A Solomon
- Division of Neuropathology, Department of Pathology, University of California San Francisco, San Francisco, California, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
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50
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Mancini A, Xavier-Magalhães A, Woods WS, Nguyen KT, Amen AM, Hayes JL, Fellmann C, Gapinske M, McKinney AM, Hong C, Jones LE, Walsh KM, Bell RJA, Doudna JA, Costa BM, Song JS, Perez-Pinera P, Costello JF. Disruption of the β1L Isoform of GABP Reverses Glioblastoma Replicative Immortality in a TERT Promoter Mutation-Dependent Manner. Cancer Cell 2018; 34:513-528.e8. [PMID: 30205050 PMCID: PMC6135086 DOI: 10.1016/j.ccell.2018.08.003] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 07/02/2018] [Accepted: 08/03/2018] [Indexed: 12/27/2022]
Abstract
TERT promoter mutations reactivate telomerase, allowing for indefinite telomere maintenance and enabling cellular immortalization. These mutations specifically recruit the multimeric ETS factor GABP, which can form two functionally independent transcription factor species: a dimer or a tetramer. We show that genetic disruption of GABPβ1L (β1L), a tetramer-forming isoform of GABP that is dispensable for normal development, results in TERT silencing in a TERT promoter mutation-dependent manner. Reducing TERT expression by disrupting β1L culminates in telomere loss and cell death exclusively in TERT promoter mutant cells. Orthotopic xenografting of β1L-reduced, TERT promoter mutant glioblastoma cells rendered lower tumor burden and longer overall survival in mice. These results highlight the critical role of GABPβ1L in enabling immortality in TERT promoter mutant glioblastoma.
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Affiliation(s)
- Andrew Mancini
- Department of Neurological Surgery, University of California, San Francisco, CA 94158, USA
| | - Ana Xavier-Magalhães
- Department of Neurological Surgery, University of California, San Francisco, CA 94158, USA; Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, 4710-057 Braga, Portugal
| | - Wendy S Woods
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Kien-Thiet Nguyen
- Department of Neurological Surgery, University of California, San Francisco, CA 94158, USA
| | - Alexandra M Amen
- Department of Neurological Surgery, University of California, San Francisco, CA 94158, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Josie L Hayes
- Department of Neurological Surgery, University of California, San Francisco, CA 94158, USA
| | - Christof Fellmann
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Michael Gapinske
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Andrew M McKinney
- Department of Neurological Surgery, University of California, San Francisco, CA 94158, USA
| | - Chibo Hong
- Department of Neurological Surgery, University of California, San Francisco, CA 94158, USA
| | - Lindsey E Jones
- Department of Neurological Surgery, University of California, San Francisco, CA 94158, USA
| | - Kyle M Walsh
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, CA 94158, USA
| | - Robert J A Bell
- Department of Neurological Surgery, University of California, San Francisco, CA 94158, USA
| | - Jennifer A Doudna
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; Department of Chemistry, University of California, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Howard Hughes Medical Institute (HHMI), Berkeley, CA 94720, USA
| | - Bruno M Costa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal; ICVS/3B's-PT Government Associate Laboratory, Braga/Guimarães, 4710-057 Braga, Portugal
| | - Jun S Song
- Department of Physics, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Pablo Perez-Pinera
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, CA 94158, USA.
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