1
|
Johnson K, Anderson K, Nehar-Belaid D, Varn F, Gujar A, Courtois E, Robson P, Moon HE, Golebiewska A, Paek SH, Niclou S, Verhaak R. EPCO-13. IDENTIFYING REGULATORS OF GLIOMA CELL STATE DIVERSITY AND EVOLUTION VIA JOINT SINGLE NUCLEUS RNA AND CHROMATIN ACCESSIBILITY. Neuro Oncol 2022. [PMCID: PMC9660532 DOI: 10.1093/neuonc/noac209.448] [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
Glioma cellular heterogeneity and plasticity represent fundamental obstacles to effective therapies. Understanding the determinants that govern glioma cell diversity and adaptability is critical to overcoming treatment resistance. Recent single cell DNA methylation studies have demonstrated that dynamic epigenetic alterations facilitate glioma cell state shifts and stress response. However, information regarding other modes of epigenetic gene regulation, such as chromatin accessibility, and how therapy shapes cellular heterogeneity remains limited. To determine the critical regulators of glioma cell state plasticity under treatment, we profiled 36 tumors (n = 23 adult patients) with joint single nucleus RNA and ATACseq including 13 longitudinal initial – recurrent pairs that yielded a total of 79,945 cells (37,883 malignant cells). We identified chromatin peaks that were uniquely open in glioma cells (n = 14,462 peaks, FDR < 0.05) compared with tumor microenvironmental cells including neuronal, perivascular, glial, and immune populations. Among malignant cells, differentiated-like cells exhibited more recurrent regions of accessibility than stem-like cells. These populations could be further delineated by differential peak enrichment of transcription factor binding sites in the stem-like (TCF12, ASCL1), differentiated-like (SMARCC1, JUN), and proliferating stem-like (E2F4) malignant cells nominating these transcription factors as master regulators. We confirmed that these cell state-specific open chromatin peaks overlapped enhancer regions via single nucleus multiomics and bulk H3K27ac profiling in 3 patient-derived cell lines. We further demonstrated that there are cell state-specific chromatin changes at recurrence with a trend toward a more open chromatin state that was associated with coordinated transcriptional changes. Finally, we incorporated matched longitudinal whole genome sequencing data to evaluate mutational profiles and differentiate between predominantly epigenetically driven changes and epigenomic co-evolution with the genome. Together, these findings define the key epigenetic switches that shape glioma cell states and facilitate plasticity during tumor progression.
Collapse
Affiliation(s)
| | | | | | | | - Amit Gujar
- The Jackson Laboratory , Farmington , USA
| | | | | | - Hyo-Eun Moon
- Seoul National University College of Medicine and Seoul National University Hospital , Seoul , Republic of Korea
| | | | - Sun Ha Paek
- Seoul National University College of Medicine and Seoul National University Hospital , Seoul , Republic of Korea
| | - Simone Niclou
- Luxembourg Institute of Health , Luxembourg , Luxembourg
| | | |
Collapse
|
2
|
White K, Connor K, Meylan M, Bougoüin A, Salvucci M, Bielle F, O’Farrell A, Sweeney K, Weng L, Bergers G, Dicker P, Ashley D, Lipp ES, Low J, Zhao J, Wen PY, Prins R, Verreault M, Idbaih A, Prehn J, Varn F, Verhaak R, Sautès-Fridman C, Fridman W, Byrne A. TMIC-10. IDENTIFICATION, VALIDATION AND BIOLOGICAL CHARACTERIZATION OF NOVEL GLIOBLASTOMA TUMOUR MICROENVIRONMENT SUBTYPES: IMPLICATIONS FOR PRECISION IMMUNOTHERAPY. Neuro Oncol 2022. [PMCID: PMC9661289 DOI: 10.1093/neuonc/noac209.1054] [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
New precision medicine therapies are urgently required for glioblastoma (GBM). However, to date, efforts to subtype patients based on molecular profiles, have failed to direct treatment strategies. We hypothesized that interrogation of the GBM tumor microenvironment (TME) and identification of novel TME-specific subtypes could inform new precision treatment strategies. To this end, a refined and validated microenvironment cell population (MCP)-counter method was applied to > 800 GBM patient tumours and validated by multiplex-immunohistochemistry. The MCP-counter deconvolution method interrogates the TME composition from transcriptomic data. Using this refined method, we classified the GLIOTRAIN(www.gliotrain.eu) IDHwt GBM cohort (n=123) into 3 novel clusters characterised by differences in TME composition and subsequently validated findings in the TCGA (n=69), CGGA (n=72) and DUKE (unpublished)(n=162) cohorts. TMEHigh tumours (30%) displayed elevated immune populations, functional orientation markers, immune checkpoint genes, and upregulated immunoregulatory pathways. Moreover, tertiary lymphoid structures were a feature of TMEHigh/mesenchymal+ patients. TMEMed (46%) tumours displayed heterogeneous immune populations and upregulated neuronal signalling pathways. TMELow (24%) tumours represented an ‘immune-desert’ group, high EGFR mutation frequency and upregulated EGFR signalling pathways. Longitudinal analysis of the GLASS cohort revealed TME-subtype transitions upon recurrence, influenced by TME composition changes. Finally, assessment of three GBM immunotherapy clinical trial cohorts revealed that TMEHigh patients treated with neo-adjuvant anti-PD1 have a significantly improved survival (P=0.04). Moreover, TMEHigh patients treated with anti-PD1 and an oncolytic virus (PVSRIPO) in the adjuvant setting, showed a trend towards improved survival (P=0.15 and P=0.056 respectively). Overall, we have established a novel TME-based classification system for application in intracranial malignancies. This system may be used to better inform a precision targeting approach in the brain tumour setting. For example, we hypothesise that patients bearing TMELow tumours may be amenable to neoadjuvant anti-TIM3 + EGFR inhibitor, TMEMed to anti-angiogenic immunotherapy, and TMEHigh patients to neoadjuvant anti-PD1 + anti-CTLA4.
Collapse
Affiliation(s)
- Kieron White
- Dept Physiology and Medical Physics, Royal College of Surgeons in Ireland , Dublin , Ireland
| | - Kate Connor
- Dept Physiology and Medical Physics, Royal College of Surgeons in Ireland , Dublin , Ireland
| | - Maxime Meylan
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité , 75006 Paris , France
| | - Antoine Bougoüin
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité , 75006 Paris , France
| | - Manuela Salvucci
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland , Dublin , Ireland
| | - Franck Bielle
- Sorbonne Université, Paris Brain Institute , Paris , France
| | - Alice O’Farrell
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin 2, Ireland , Dublin , Ireland
| | - Kieron Sweeney
- Department of Neurosurgery, Beaumont hospital , Dublin , Ireland
| | - Linqian Weng
- VIB-KU Leuven Center for Cancer Biology, Department of Oncology, KU Leuven , 3000 Leuven , Belgium
| | - Gabriele Bergers
- VIB-KU Leuven Center for Cancer Biology, Department of Oncology, KU Leuven , 3000 Leuven , Belgium
| | - Patrick Dicker
- Epidemiology & Public Health, Royal College of Surgeons in Ireland, Dublin, Ireland , Dublin , Ireland
| | - David Ashley
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center , Durham, NC , USA
| | - Eric S Lipp
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center , Durham, NC , USA
| | - Justin Low
- The Preston Robert Tisch Brain Tumor Center, Duke University Medical Center , Durham, NC , USA
| | - Junfei Zhao
- Department of Systems Biology at Columbia University , New York, NY, 10032 , New York, NY , USA
- , USA , New York, NY, 10032 , New York, NY , USA
| | | | - Robert Prins
- University of California, Los Angeles , Los Angeles , USA
| | - Maite Verreault
- Paris Brain Institute (ICM), CNRS UMR 7225, Inserm U 1127, UPMC-P6 UMR S 1127, Hôpital de la Pitié - Salpêtrière - 47, boulevard de l'Hôpital –75013 Paris , Paris , France
| | - Ahmed Idbaih
- Sorbonne Université, AP-HP, ICM, Hôpital Universitaire La Pitié-Salpêtrière , Paris , France
| | - Jochen Prehn
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, York Street, Dublin 2 , Dublin , Ireland
| | | | | | - Catherine Sautès-Fridman
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité , 75006 Paris , France
| | - Wolf Fridman
- Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris Cité , 75006 Paris , France
| | - Annette Byrne
- Dept Physiology and Medical Physics, Royal College of Surgeons in Ireland , Dublin , Ireland
| |
Collapse
|
3
|
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.
Collapse
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
| | | |
Collapse
|
4
|
Anderson K, Johnson K, Varn F, Bessonett S, Gujar A, Flynn B, Courtois E, Hau AC, Golebiewska A, Paek SH, Niclou S, Samuels M, Robson P, Verhaak R. EPCO-13. MULTIOMIC SINGLE NUCLEUS RNA- AND ATACseq PROFILING REVEALS REGULATORS OF GLIOMA CELL STATE DIVERSITY. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab196.012] [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: 11/13/2022] Open
Abstract
Abstract
Multiomic single nucleus RNA- and ATACseq profiling reveals regulators of glioma cell state diversity. The extensive intra- and intertumoral heterogeneity observed in glioma reflects the resistance to therapy and poor prognosis observed clinically. Single-cell sequencing studies have highlighted that glioma heterogeneity reflects the co-existence of cell subpopulations with distinct cell states. Prior studies have also shown that EGFR-amplifying extrachromosomal DNA (ecDNA) elements in IDH-wild-type gliomas can contribute to heterogeneity by driving oncogene amplification through long range chromatin contacts. However, single cell studies have largely focused on analyses of transcriptional profiles, and the epigenetic mechanisms underlying the contribution of ecDNA elements to tumor cell state diversity remain poorly understood. To further our understanding of the regulatory programs that contribute to transcriptional diversity and mediate the distribution of tumor cell states, we profiled primary-recurrent tumor pairs from 18 patient samples with multiomic single-nucleus RNA- and ATACseq, resulting in 86,135 cells identified with linked chromatin accessibility and gene expression profiles. Integrative clustering of the tumor cells identified tumor cell states ranging from a stem-like to differentiated- phenotype that were also associated with differences in chromatin accessibility and inferred transcription factor binding activity. Analyses of chromatin accessibility resulted in the identification of ecDNA, and integrative clustering of ecDNA+ cells highlighted distinct cell states with increased copy number burden, oncogene amplification, and differential chromatin accessibility. These results suggest that a better understanding of extrachromosomal contributions to tumor diversity would aid in development of more efficient therapies.
Collapse
Affiliation(s)
| | - Kevin Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Frederick Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Amit Gujar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Bill Flynn
- The Jackson Laboratory, Farmington, CT, USA
| | - Elise Courtois
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | - Sun Ha Paek
- Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Simone Niclou
- Luxembourg Institute of Health, Luxembourg, Luxembourg
| | | | | | - Roel Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| |
Collapse
|
5
|
Brown M, Zhang G, Stevenson K, Lin X, Chen Y, Wei Z, Beaubier N, Yan H, He Y, Desjardins A, Herndon J, Varn F, Verhaak R, Zhao J, Friedman A, Friedman H, McSherry F, Muscat A, Lipp E, Khasraw M, Peters K, Randazzo D, Sampson J, McLendon R, Bigner D, Gromeier M, Nair S, Ashley DM. BIOM-20. TUMOR-INTRINSIC AND PERIPHERAL FEATURES ASSOCIATE WITH SURVIVAL AFTER POLIO VIROTHERAPY IN RECURRENT GBM. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab196.051] [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: 11/13/2022] Open
Abstract
Abstract
BACKGROUND
PVSRIPO is a live-attenuated recombinant rhino:poliovirus that mediates antitumor efficacy by engaging antitumor immunity. A subset (~20%) of patients with recurrent GBM (rGBM) survive >24 months after therapy. We previously reported that low tumor mutation burden (TMB) is associated with longer survival after PVSRIPO and immune checkpoint blockade therapy in rGBM, and that low TMB associates with higher inflammatory gene expression signatures in rGBM tumors.
METHODS
Clinical features were tested for association with survival after PVSRIPO therapy. Whole exome sequencing and RNA-sequencing of tumors were used to correlate mutational landscape, tumor mutation burden (TMB), and gene expression signatures of patient tumors with survival. An in vitro assay that measures inflammatory responses of patient PBMCs to PVSRIPO was performed. An independent cohort of paired primary and recurrent GBM tumors was used to assess longitudinal changes in TMB and gene expression signatures after standard of care treatment.
RESULTS
A short time to recurrence and low TMB associated with longer survival after PVSRIPO therapy; these features were not prognostic for longer survival in immunotherapy naïve rGBM cohorts. Unexpectedly, higher pre-treatment polio neutralizing antibody titers were also associated with longer survival after PVSRIPO therapy in two independent clinical cohorts. PBMCs from patients surviving longer after PVSRIPO therapy mounted higher TNF, but lower IFN-a responses after in vitro challenge with PVSRIPO. In analysis of paired primary vs recurrent GBM tumors, we discovered that patients with low TMB upon recurrence were more likely to experience increased tumor inflammation and suppression of overall TMB. Low TMB in rGBM tumors was also associated with neoantigen depletion. Collectively, these observations imply that patients with low TMB and/or shorter duration of standard of care therapy may have intact immune surveillance, and that pre-treatment immunological status may dictate survival response to polio virotherapy.
Collapse
Affiliation(s)
| | | | | | | | - Yeqing Chen
- New Jersey Institute of Technology, Newark, NJ, USA
| | - Zhi Wei
- New Jersey Institute of Technology, Newark, NJ, USA
| | | | - Hai Yan
- Duke University, Durham, NC, USA
| | | | | | | | - Frederick Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Roel Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | | | | | | | - Eric Lipp
- Duke University Medical Center, Durham, NC, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Varn F, Johnson K, Wade T, Malta T, Sabedot T, Barthel F, Kim H, Ahmed N, Datta I, Barnholtz-Sloan J, Bakas S, D'Angelo F, Gan H, Garofano L, Huse J, Khasraw M, Kocakavuk E, Migliozzi S, Ormond D, Paek SH, Van Meir E, Walenkamp A, Watts C, Weller M, Weiss T, Wesseling P, Stead L, Poisson L, Noushmehr H, Iavarone A, Verhaak R. EPCO-09. LONGITUDINAL ANALYSIS OF DIFFUSE GLIOMA REVEALS CELL STATE DYNAMICS AT RECURRENCE ASSOCIATED WITH CHANGES IN GENETICS AND THE MICROENVIRONMENT. Neuro Oncol 2021. [DOI: 10.1093/neuonc/noab196.008] [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: 11/13/2022] Open
Abstract
Abstract
Diffuse glioma is characterized by a poor prognosis and a universal resistance to therapy, though the evolutionary processes behind this resistance remain unclear. The Glioma Longitudinal Analysis (GLASS) Consortium has previously demonstrated that therapy-induced selective pressures shape the genetic evolution of glioma in a stochastic manner. However, single-cell studies have revealed that malignant glioma cells are highly plastic and transition their cell state in response to diverse challenges, including changes in the microenvironment and the administration of standard-of-care therapy. To interrogate the factors driving therapy resistance in diffuse glioma, we collected and analyzed RNA- and/or DNA-sequencing data from temporally separated tumor pairs of over 300 adult patients with IDH-wild-type or IDH-mutant glioma. In a subset of these tumor pairs, we complemented these data with single-nucleus RNAseq and multiplex imaging mass cytometry at each time point. Recurrent tumors exhibited diverse changes that were attributable to changes in histological features, somatic alterations, and microenvironment interactions. IDH-wild-type tumors overall were more invasive at recurrence and exhibited increased expression of neuronal signaling programs that reflected a possible role for neuronal interactions in promoting glioma progression. In contrast, recurrent IDH-mutant tumors exhibited a significant increase in proliferative expression programs that correlated with discrete genetic changes. Hypermutation and acquired CDKN2A homozygous deletions associated with an increase in proliferating stem-like malignant cells at recurrence in both glioma subtypes, reflecting active tumor expansion. A transition to the mesenchymal phenotype was associated with the presence of a specific myeloid cell state defined by unique ligand-receptor interactions with malignant cells, providing opportunities to target this transition through therapy. Collectively, our results uncover recurrence-associated changes in genetics and the microenvironment that can be targeted to shape disease progression following initial diagnosis.
Collapse
Affiliation(s)
- Frederick Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Kevin Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Taylor Wade
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Thais Sabedot
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
| | - Floris Barthel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Hoon Kim
- Jackson Laboratory, Farmington, USA
| | - Nazia Ahmed
- Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, OH, USA
| | | | - Jill Barnholtz-Sloan
- Case Western Reserve University School of Medicine and University Hospitals of Cleveland, Cleveland, OH, USA
| | | | | | - Hui Gan
- Olivia Newton-John Cancer Research Institute, Heidelberg, Melbourne, VIC, Australia
| | | | - Jason Huse
- MD Anderson Cancer Center, Houston, TX, USA
| | | | - Emre Kocakavuk
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | - Sun Ha Paek
- Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Erwin Van Meir
- University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Colin Watts
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Michael Weller
- University Hospital and University of Zurich, Zurich, Switzerland
| | - Tobias Weiss
- Laboratory of Molecular Neuro-Oncology, Department of Neurology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | | | | | - Laila Poisson
- Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
| | | | | | - Roel Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| |
Collapse
|
7
|
Kocakavuk E, Anderson K, Varn F, Johnson K, Amin S, Barthel F, Verhaak R. 340O Radiotherapy is associated with deletion signatures that contribute to poor survival outcomes in cancer patients. Ann Oncol 2021. [DOI: 10.1016/j.annonc.2021.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
|
8
|
Varn F, Johnson K, Barthel F, Kim H, Wade T, Malta T, Sabedot T, Lodha D, Ajaib S, Ahmed N, Garofano L, D’Angelo F, Stead L, Poisson L, Noushmehr H, Iavarone A, Verhaak R. OMRT-3. Longitudinal analysis of diffuse glioma reveals cell state dynamics at recurrence associated with changes in genetics and the microenvironment. Neurooncol Adv 2021. [PMCID: PMC8255447 DOI: 10.1093/noajnl/vdab070.029] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Diffuse glioma is an aggressive brain cancer that is characterized by a poor prognosis and a universal resistance to therapy. The evolutionary processes behind this resistance remain unclear. Previous studies by the Glioma Longitudinal Analysis (GLASS) Consortium have indicated that therapy-induced selective pressures shape the genetic evolution of glioma in a stochastic manner. However, single-cell studies have revealed that malignant glioma cells are highly plastic and transition their cell state in response to diverse challenges, including changes in the microenvironment and the administration of standard-of-care therapy. Interactions between these factors remain poorly understood, making it difficult to predict how a patient’s tumor will evolve from diagnosis to recurrence. To interrogate the factors driving therapy resistance in diffuse glioma, we collected and analyzed RNA- and/or DNA-sequencing data from temporally separated tumor pairs of 292 adult patients with IDH-wild-type or IDH-mutant glioma. Recurrent tumors exhibited diverse changes that were attributable to changes in anatomic composition, somatic alterations, and microenvironment interactions. Hypermutation and acquired CDKN2A homozygous deletions associated with an increase in proliferating stem-like malignant cells at recurrence in both glioma subtypes, reflecting active tumor expansion. IDH-wild-type tumors were more invasive at recurrence, and their malignant cells exhibited increased expression of neuronal signaling programs that reflected a possible role for neuronal interactions in promoting glioma progression. Mesenchymal transition was associated with the presence of a specific myeloid cell state defined by unique ligand-receptor interactions with malignant cells, providing opportunities to target this transition through therapy. Collectively, our results uncover recurrence-associated changes in genetics and the microenvironment that can be targeted to shape disease progression following initial diagnosis.
Collapse
Affiliation(s)
- Frederick Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Kevin Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Floris Barthel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Hoon Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Taylor Wade
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Thais Sabedot
- Department of Neurosurgery, Henry Ford Health System, Henry Ford Cancer Institute, Detroit, MI, USA
| | - Disha Lodha
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Shoaib Ajaib
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Nazia Ahmed
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Luciano Garofano
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA
| | - Fulvio D’Angelo
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA
| | - Lucy Stead
- Leeds Institute of Medical Research at St James’s, University of Leeds, Leeds, UK
| | - Laila Poisson
- Department of Biostatistics, Henry Ford Health System, Henry Ford Cancer Institute, Detroit, MI, USA
| | - Houtan Noushmehr
- Department of Neurosurgery, Henry Ford Health System, Henry Ford Cancer Institute, Detroit, MI, USA
| | - Antonio Iavarone
- Institute for Cancer Genetics, Columbia University Medical Center, New York, NY, USA
- Department of Neurology, Columbia University Medical Center, New York, NY, USA
| | - Roel Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | |
Collapse
|
9
|
Malta T, Sabedot T, Datta I, Varn F, Castro A, Garofano L, Verhaak R, Iavarone A, Poisson L, Noushmehr H. OTEH-10. Evolutionary trajectory of epigenomic of gliomas. Neurooncol Adv 2021. [PMCID: PMC8255460 DOI: 10.1093/noajnl/vdab070.049] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Gliomas are the most common malignant brain tumor, have an aggressive behavior, and invariably relapse and progress. Despite the recent advancements, little is known about the role of the epigenome in glioma disease progression and recurrence. To investigate the molecular dynamics over time and in response to therapeutic pressures, the Glioma Longitudinal AnalySiS (GLASS) Consortium, a multinational collaboration, is investigating epigenome-wide molecular data from primary and recurrent matched pairs, including IDH mutant (IDHmut) and IDH wildtype (IDHwt) gliomas. We have compiled a total of 357 samples comprising 143 primary-recurrent pairs profiled by DNA methylation, of which 157 samples have genomic data (WXS/WGS) and 120 have transcriptomic data (RNAseq). IDHwt gliomas have a distinct epigenetic evolution compared to IDHmut after treatment. IDHwt gliomas are more epigenetically stable over time, while IDHmut gliomas display a loss of DNA methylation throughout disease progression. Next, we investigated the molecular drivers of longitudinal gliomas by integration of DNA methylation and gene expression data. We identified epigenetic activation of cell cycle pathways in recurrent IDHmut compared to initial tumors. Transcription factors musculin, ZNF367, and ZNF682 are enriched among recurrent IDHmut gliomas and potentially regulate IDHmut recurrence and/or progression. We next used a DNA methylation-based deconvolution approach to estimate the tumor microenvironment (TME) composition. We found that the TME among IDHmut subtypes (Codel, GCIMP-high, and GCIMP-low) presented less immune infiltration than IDHwt (Classic-like, Mesenchymal-like, and PA-like). Post-treatment, we found a decrease of CD4+T and an increase of CD8+T cells in IDHmut. In conclusion, IDHmut gliomas present a more unstable epigenome, while the epigenome of IDHwt gliomas seems relatively preserved after treatment. We identified potential master regulators of cell cycle deregulation of IDHmut recurrence. Finally, the TME differs across IDHmut and IDHwt gliomas and the cell composition changes over time.
Collapse
Affiliation(s)
- Tathiane Malta
- School of Pharmaceutical Sciences of Ribeirao Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Thais Sabedot
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
| | - Indrani Datta
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, USA
- Center for Bioinformatics, Henry Ford Health System, Detroit, MI, USA
| | - Frederick Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - AnaValeria Castro
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
| | | | - Roel Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Laila Poisson
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, USA
| | - Houtan Noushmehr
- Department of Neurosurgery, Hermelin Brain Tumor Center, Henry Ford Health System, Detroit, MI, USA
| | | |
Collapse
|
10
|
Varn F, Johnson K, Barthel F, Kim H, Wade T, Lodha D, Ajaib S, Ahmed N, Garofano L, D’Angelo F, Stead L, Noushmehr H, Iavarone A, Verhaak R. EPCO-08. TUMOR-IMMUNE INTERACTIONS ARE DYNAMIC AND INFLUENCE THE EVOLUTIONARY TRAJECTORY OF ADULT DIFFUSE GLIOMA. Neuro Oncol 2020. [DOI: 10.1093/neuonc/noaa215.287] [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: 11/13/2022] Open
Abstract
Abstract
Diffuse glioma is an aggressive brain cancer that is characterized by a poor prognosis and a universal resistance to therapy. The evolutionary processes behind this resistance remain unclear. Previous studies by the Glioma Longitudinal Analysis (GLASS) Consortium have indicated that therapy-induced selective pressures shape the genetic evolution of glioma in a stochastic manner. However, single cell studies have revealed that malignant glioma cells are highly plastic, and capable of changing their cell state in response to diverse challenges in their microenvironment. The tumor immune response has been implicated as a major driver of these malignant cell state transitions, and is known to be affected by the administration of therapy, but the extent to which tumor genetics, therapy, and the different components of the immune response interact to influence a glioma’s evolutionary trajectory are poorly understood. To further investigate these factors, we collected DNA and RNA sequencing data on pre- and post-treatment tumor pairs from over 150 glioma patients that have received chemotherapy, radiotherapy, and/or immune checkpoint blockade agents. By integrating mutation, copy number, and in silico deconvolution analyses of bulk transcriptome data across the three molecular subtypes of diffuse glioma, we show that longitudinal increases in chromosomal instability and gene fusions associate with decreased immune infiltrate and altered cell states at recurrence. We additionally find that specific molecular alterations and malignant cell states associate with unique inflammatory and immunosuppressive programs in tumor-associated macrophages and microglia. Lastly, we show that the abundance of T cells in the tumor microenvironment does not associate with changes in neoantigen depletion and the acquisition of antigen presentation machinery defects, suggesting minimal immunoediting activity over time. Collectively, our results indicate that the administration of therapy can alter the dynamics of tumor-immune interactions in glioma, resulting in new steady-states at recurrence that can be subsequently targeted.
Collapse
Affiliation(s)
- Frederick Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Kevin Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Floris Barthel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Hoon Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Taylor Wade
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | | | | | | | - Lucy Stead
- University of Leeds, Leeds, United Kingdom
| | | | | | - Roel Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | |
Collapse
|
11
|
Johnson K, Anderson K, Courtois E, Barthel F, Varn F, Luo D, Yi E, Kim H, Estecio M, Tang M, Navin N, Maurya R, Ngan C, Bulsara K, Samuels M, Das S, Robson P, Verhaak R. EPCO-27. GLIOMA SINGLE CELL MULTI-OMIC ANALYSES REVEALS REGULATORS OF PLASTICITY AND ADAPTIVE STRESS RESPONSE. Neuro Oncol 2020. [DOI: 10.1093/neuonc/noaa215.306] [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: 11/13/2022] Open
Abstract
Abstract
Extensive intra- and intertumoral heterogeneity in glioma contributes to therapeutic resistance and poor patient outcomes. Alterations to DNA methylation (DNAme) modulate epigenetic homeostasis, allowing tumor cells to sample alternative cell states to promote tumorigenesis. However, the epigenetic mechanisms that promote cellular plasticity and regulate cell states are still poorly understood. To characterize the epigenetic mechanisms underlying glioma heterogeneity we profiled 914 single-cell methylomes, 55,284 single-cell transcriptomes, and bulk whole genomes across 11 patient samples spanning initial and recurrent time points and 3 molecular subtypes delineated by IDH mutation status. Local DNAme disorder, defined as epimutation burden, was increased in tumor cells relative to nontumor cells, higher in IDH wild-type than in IDH mutant glioma and was positively associated with copy number alteration (CNA). Epimutation was positively associated with transcriptional variability and enriched at genes involved in cellular differentiation. Epimutation was also increased in the binding sites of transcription factors (TFs) associated with response to extracellular stimuli, suggesting that stochastic DNAme alterations enable cellular plasticity and diverse responses to microenvironmental stressors. Integrative clustering of DNAme and scRNAseq profiles defined stem-like and differentiated-like cell states which exhibited differences in TF activity. Stem-like cells were enriched for differentially methylated binding sites of TFs associated with hypoxia response. scDNAme and scRNAseq-derived copy number profiles were compared with bulk copy number profiles and inferred tumor phylogenies to assess how the timing of CNAs impact epigenetic instability, with results suggesting that early CNA events propagate both genetic and epigenetic heterogeneity. Bulk longitudinal data was used to validate the relationship of epigenetic instability with CNA burden as well as differentially methylated binding sites of cell stress response TFs. Our work suggests that local DNAme disorder promotes cellular plasticity and enables adaptive response to cellular stress such as hypoxia.
Collapse
Affiliation(s)
- Kevin Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Kevin Anderson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Elise Courtois
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Floris Barthel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Frederick Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Diane Luo
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Eunhee Yi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Hoon Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Marcos Estecio
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ming Tang
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nicholas Navin
- University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Rahul Maurya
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Chewyee Ngan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Michael Samuels
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Sunit Das
- University of Toronto, Toronto, ON, Canada
| | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Roel Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| |
Collapse
|
12
|
Kocakavuk E, Anderson K, Johnson K, Varn F, Amin S, Barthel F, Verhaak R. EPCO-15. TUMOR TREATMENT WITH IONIZING RADIATION IS ASSOCIATED WITH A CLINICALLY RELEVANT DELETION SIGNATURE. Neuro Oncol 2020. [DOI: 10.1093/neuonc/noaa215.294] [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: 11/14/2022] Open
Abstract
Abstract
Diffuse gliomas are highly aggressive brain tumors that invariably relapse despite treatment with chemo- and radiotherapy. Treatment with alkylating chemotherapy can drive tumors to develop a hypermutator phenotype. In contrast, the genomic effects of radiation therapy (RT) remain unknown. We analyzed the mutational spectra following treatment with ionizing radiation in sequencing data from 190 paired primary-recurrent gliomas from the Glioma Longitudinal Analysis (GLASS) dataset and 2249 post-treatment metastatic tumors from the Hartwig Medical Foundation. We identified a significant increase in the frequency of small deletions following radiation therapy that was independent of other factors. These novel deletions demonstrated distinct characteristics when compared to pre-existing deletions present prior to RT-treatment and deletions in RT-untreated tumors. Radiation therapy-acquired deletions were characterized by a larger deletion size (GLASS and metastatic cohort, P = 1.2e-02 and P = 8e-11, respectively; Mann-Whitney U test), an increased distance to repetitive DNA elements (P < 2.2e-16, Kolmogorov-Smirnov test) and a reduction in microhomology at breakpoints (P = 3.2e-02, paired Wilcoxon signed-rank test). These observations suggested that canonical non-homologous end joining (c-NHEJ) was the preferred pathway for DNA double strand break repair of RT-induced DNA damage. Furthermore, radiotherapy resulted in frequent chromosomal deletions and significantly increased frequencies of CDKN2A homozygous deletions. Finally, a high burden of RT-associated deletions was associated with worse clinical outcomes (GLASS and metastatic cohort, P = 4.7e-02, HR = 2.59 [95% CI: 1.01, 6.60] and P = 2.5e-02, HR = 1.43 [95% CI: 1.05, 1.94], respectively; multivariable Cox regression), suggesting that effective repair of RT-induced DNA damage is detrimental to patient survival and that inhibiting c-NHEJ may be a viable strategy for improving the cancer-killing effect of radiotherapy. Taken together, the identified genomic scars as a result of radiation therapy reflect a more aggressive tumor with increased levels of resistance to follow up treatments.
Collapse
Affiliation(s)
- Emre Kocakavuk
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Kevin Anderson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Kevin Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Frederick Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Samirkumar Amin
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Floris Barthel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Roel Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| |
Collapse
|
13
|
Barthel F, Johnson KC, Varn F, Moskalik A, Tanner G, Kocakavuk E, Anderson K, Abiola O, Huse J, DeGroot J, Stead LF, Verhaak R. GENE-28. LONGITUDINAL MOLECULAR TRAJECTORIES OF DIFFUSE GLIOMA IN ADULTS. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz175.430] [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: 11/12/2022] Open
Abstract
Abstract
Treatment options for adult patients with glioma has remained largely unchanged over the past three decades. Targeted inhibitors and immunotherapies have improved outcomes for many cancer types but their relevance in glioma is unclear. The inevitability of glioma disease recurrence demands an understanding of mechanisms driving therapy resistance. The Glioma Longitudinal Analysis (GLASS) Consortium was initiated to establish a definitive portrait of the recurrence process and to discover vulnerabilities that render the tumor sensitive to therapeutic intervention. GLASS is a community-driven effort that seeks to overcome the logistical challenges in constructing adequately powered longitudinal genomic glioma datasets by pooling data from patients treated at institutions worldwide. Currently, the GLASS Data Resource comprises DNA sequencing data (exome and/or whole-genome) from 288 patients of whom high-quality data in at least two time points are present from 222 patients (n = 134 IDHwt, n = 63 IDHmutant-noncodel, n = 25 IDHmutant-codel). We inferred longitudinal mutation, copy number, clonal frequency, and neoantigen profiles and demonstrated that driver genes found at initial disease persisted into recurrence. Treatment with alkylating-agents resulted in a hypermutator phenotype at different rates across glioma subtypes, most frequently among IDHmutant-noncodels, and hypermutation was not associated with differences in overall survival. Acquired aneuploidy was frequently detected in recurrent IDHmutant-noncodel gliomas and further converged with acquired cell cycle pathway alterations and poor outcomes. We showed that the clonal architecture of each tumor remains largely intact over time and that genetic drift was associated with increased survival. Finally, we found that neoantigens were exposed to stable selective pressures throughout a tumor’s progression. Our results collectively suggest that the strongest selective pressures occur early during glioma development and that current therapies shape this evolution in a largely stochastic manner. The GLASS Data Resource provides a genomic reference to study the patterns of glioma evolution.
Collapse
Affiliation(s)
- Floris Barthel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Kevin C Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Frederick Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Anzhela Moskalik
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Emre Kocakavuk
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Kevin Anderson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Olajide Abiola
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Jason Huse
- The University of Texas MD Anderson, Houston, TX, USA
| | - John DeGroot
- The University of Texas MD Anderson, Houston, TX, USA
| | - Lucy F Stead
- Leeds Institute of Medical Research at St James’s, Wellcome Trust Brenner Building, St. James’s University Hospital, Leeds, United Kingdom, Leeds, United Kingdom
| | - Roel Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | |
Collapse
|
14
|
Amin S, Anderson K, Bourdreau B, Martínez E, Kocakavuk E, Johnson KC, Barthel F, Varn F, Kassab C, Ling X, Kim H, Barther M, Yee Ngan C, Dickinson P, Packer R, Taylor A, Rossmeisl J, Heimberger A, Levine J, Verhaak R. GENE-57. COMPARATIVE MOLECULAR LIFE HISTORY OF SPONTANEOUS CANINE AND HUMAN GLIOMA. Neuro Oncol 2019. [DOI: 10.1093/neuonc/noz175.459] [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: 11/13/2022] Open
Abstract
Abstract
Diffuse gliomas are the commonest of malignant brain tumors with high-grade tumors carrying dismal prognosis. Preclinical models have proven themselves as poor predictors of clinical efficacy, attributed to the lack of a comparable tumor microenvironment. Comparative genomics of canine and human gliomas provide an attractive alternative modality to identify conserved drivers and underlying mutational processes of glioma as well as evaluate life history tradeoffs related to tissue context and aging that can shape type and relative timing of drivers in gliomagenesis. We performed a comparative genomics analysis between whole genome-, exome-, transcriptome- and methylation-sequencing of 77 canine gliomas, and human pediatric (n=217) and adult gliomas (n=822). We found alterations in common with those in human pediatric and adult gliomas in the Tp53 and cell cycle pathways, receptor tyrosine kinase and Idh1 R132 mutations. Canine gliomas showed similarity to human pediatric gliomas in terms of lower mutational rates (0.2–0.29 per megabase), hotspot mutations and amplifications of Pdgfrα, and robust aneuploidy constrained within the syntenic regions of Pdgfrα and Myc, but also in the known pediatric drivers, Hist1 and Acvr1 genes. A mutational signature reflecting homologous repair defect was detected in canine and pediatric but not adult gliomas, potentially resulting in the observed higher rates of genomic instability. Canine gliomas in majority classified as pediatric tumors using a commonly used human brain methylation classifier (Capper et al. 2018) and cell-of-origin analysis by deconvoluting canine transcriptome using lineage-specific gene signatures. By providing a large canine glioma genomic-sequencing dataset and comparing it with human glioma, our study provides unique insights into glioma etiology and the chronology of glioma-causing somatic alterations. Further, our results effectively position preclinical models of spontaneous canine glioma for use in understanding glioma drivers, and evaluate novel therapies targeting aneuploidy, especially for pediatric brain tumors.
Collapse
Affiliation(s)
- Samirkumar Amin
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Kevin Anderson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Beth Bourdreau
- Texas A&M College of Veterinary Medicine, College Station, TX, USA
| | | | - Emre Kocakavuk
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Kevin C Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Floris Barthel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Frederick Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Cynthia Kassab
- The University of Texas MD Anderson Cancer, Houston, TX, USA
| | - Xiaoyang Ling
- The University of Texas MD Anderson Cancer, Houston, TX, USA
| | - Hoon Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Chew Yee Ngan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | | | - Amanda Taylor
- Auburn University College of Veterinary Medicine, Auburn, VA, USA
| | - John Rossmeisl
- Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, USA
| | - Amy Heimberger
- The University of Texas MD Anderson Cancer, Houston, TX, USA
| | - Jonathan Levine
- Texas A&M College of Veterinary Medicine, College Station, TX, USA
| | - Roel Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| |
Collapse
|