Glioblastomas (GBMs) are genomically well characterized, yet heterogeneous, and exhibit profound resistance to all existing treatment strategies. The most effective therapeutics are radiation therapy (RT) and the alkylating agent temozolomide (TMZ), but progression typically occurs within months after initiating these treatments. The mechanisms underlying this profound resistance remain unknown, but genetic heterogeneity is likely a major contributor, as has been shown in other cancers. Unfortunately, little is known about how GBM genomes evolve with treatment. This information would be useful to guide development of strategies to avoid the development of resistance and to identify optimal therapeutic approaches in the recurrent setting. We hypothesize that somatic genetic profiles of GBMs that recur after treatment with RT and TMZ differ substantially from pre-treatment GBMs, and that the differences point to mechanisms by which GBMs resist these treatments. To test this, we propose to identify and functionally validate recurrent genetic changes associated with resistance using innovative genomic analysis tools and patient derived model systems. Our collaborative consortium has collected an unprecedented number of paired pre- and post-treatment human tumors (>200). We have also created more than 100 patient derived GBM models that will be treated to test for the emergence of recurrent resistance drivers. Preliminary data from both patient samples and models indicate substantial tumor evolution occurs during treatment and identify TP53, CHEK2 and other rational targets as candidate mediators of resistance. Collective analysis of the data will be used to address two Aims.
In Aim 1, we will test the hypothesis that treatment with radiation and temozolomide leads to consistent genetic changes in human tumors using whole exome sequencing of paired pre- and post-treatment tumor samples to determine large-scale changes in population structures and single cell sequencing to evaluate the effects of these treatments on microheterogeneity.
In Aim 2, we will test the hypothesis that genetic changes identified in post-treatment GBMs functionally contribute to RT and TMZ resistance in GBM using patient derived cell lines (PDCL) and patient derived xenografts (PDX). We will determine the effects of radiation and temozolomide on these models and their genomic hierarchies using deep sequencing and test the effects of candidate drivers of resistance both in vitro and in vivo. We will determine whether resistant clones exist prior to treatment or are stochastically induced using an innovative single cell barcoding approach to determine whether the evolution of clonal substructures is consistent across replicate experiments. These studies will create a comprehensive understanding of genetic evolution during standard-of-care therapy for GBM. They will inform diagnostic approaches for assignment of targeted therapeutics in the recurrent setting and identify genetic changes driving resistance. Therapeutic targeting of these novel resistance drivers could represent a rational approach to substantially improve our existing standard of care for GBM patients.

Public Health Relevance

Glioblastomas (GBMs) are the most common malignant primary brain tumors, afflicting approximately 13,000 adults in the United States every year. The most effective treatments are radiation and a chemotherapy called temozolomide, but most glioblastomas quickly become resistant and are fatal as a result. This proposal aims to determine how glioblastomas become resistant to radiation and temozolomide by determining the genetic changes they undergo during treatment, thereby enabling us to devise more effective treatment strategies.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Research Project (R01)
Project #
5R01CA188228-02
Application #
9042319
Study Section
Cancer Genetics Study Section (CG)
Program Officer
Ahmed, Mansoor M
Project Start
2015-04-01
Project End
2020-03-31
Budget Start
2016-04-01
Budget End
2017-03-31
Support Year
2
Fiscal Year
2016
Total Cost
Indirect Cost
Name
Dana-Farber Cancer Institute
Department
Type
DUNS #
076580745
City
Boston
State
MA
Country
United States
Zip Code
Ben-David, Uri; Siranosian, Benjamin; Ha, Gavin et al. (2018) Genetic and transcriptional evolution alters cancer cell line drug response. Nature 560:325-330
Palanichamy, Kamalakannan; Jacob, John R; Litzenberg, Kevin T et al. (2018) Cells isolated from residual intracranial tumors after treatment express iPSC genes and possess neural lineage differentiation plasticity. EBioMedicine 36:281-292
Wala, Jeremiah A; Bandopadhayay, Pratiti; Greenwald, Noah F et al. (2018) SvABA: genome-wide detection of structural variants and indels by local assembly. Genome Res 28:581-591
GLASS Consortium (2018) Glioma through the looking GLASS: molecular evolution of diffuse gliomas and the Glioma Longitudinal Analysis Consortium. Neuro Oncol 20:873-884
Filbin, Mariella G; Tirosh, Itay; Hovestadt, Volker et al. (2018) Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq. Science 360:331-335
Paolella, Brenton R; Gibson, William J; Urbanski, Laura M et al. (2017) Copy-number and gene dependency analysis reveals partial copy loss of wild-type SF3B1 as a novel cancer vulnerability. Elife 6:
Ramkissoon, Shakti H; Bandopadhayay, Pratiti; Hwang, Jaeho et al. (2017) Clinical targeted exome-based sequencing in combination with genome-wide copy number profiling: precision medicine analysis of 203 pediatric brain tumors. Neuro Oncol 19:986-996
Chang, Susan; Zhang, Peixin; Cairncross, J Gregory et al. (2017) Phase III randomized study of radiation and temozolomide versus radiation and nitrosourea therapy for anaplastic astrocytoma: results of NRG Oncology RTOG 9813. Neuro Oncol 19:252-258
Palanichamy, Kamalakannan; Kanji, Suman; Gordon, Nicolaus et al. (2017) NNMT Silencing Activates Tumor Suppressor PP2A, Inactivates Oncogenic STKs, and Inhibits Tumor Forming Ability. Clin Cancer Res 23:2325-2334
Ben-David, Uri; Ha, Gavin; Tseng, Yuen-Yi et al. (2017) Patient-derived xenografts undergo mouse-specific tumor evolution. Nat Genet 49:1567-1575

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