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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All custom scripts and pipelines are available on the project’s github page (https://github.com/TheJacksonLaboratory/GLASS).
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This work is made possible by the patients and their families whom generously contributed to this study. This work is supported by the National Brain Tumor Society, Oligo Research Fund; Cancer Center Support grants P30CA16672 and P30CA034196; Cancer Prevention & Research Institute of Texas (CPRIT) grant number R140606; Agilent Technologies (R.G.W.V.); the National Institutes of Health- National Cancer institute for the following grants: NCI CA170278 (L.M.P., T.M.M., H.N.), NCI R01CA222146 (L.M.P., H.K.N.), NCI R01CA230031 (J.H.C., J.N.), NCI R01CA188288 (J.S.B.-S., R.B., P.B., K.L.L., A. Chakravarty., A.E.S.), R01CA179044 (A. Iavarone), U54CA193313 (A. Iavarone). The National Brain Tumor Society (W.K.A.Y., J.F.d.G.). Brain Tumour Northwest tissue bank (including the Walton research tissue bank) is supported by the Sidney Driscol Neuroscience Foundation and part of the Walton Centre and Lancashire Teaching Hospitals NHS Foundation Trusts (A.F.B., M.D.J.). This work was supported by a generous gift from the Dabbiere family (J.F.C.). Support is also provided by a Leeds Charitable Foundation grant (9R11/14-11 to L.F.S.), University of Leeds Academic Fellowship (11001061) (L.F.S.) and Studentship (11061191) (G. Tanner) as well as Leeds Teaching Hospitals NHS Trust (A. Chakravarti, A. Ismail). The Leeds Multidisciplinary Research Tissue Bank staff was funded by the PPR Foundation and The University of Leeds (S.C.S.). Funds were received from The Brain Tumour Charity (C.W., grants 10/136 & GN-000580, B.A.W., 200450). Ghazaleh Tabatabai is funded by EKFS 2015_Kolleg_14. R01CA218144 (P.S.L., E.J.C., J.C., A.K.L.) and Strain for the Brain, Milwaukee, WI (P.S.L., E.J.C., J.C., A.K.L.). E.K. is recipient of an MD-Fellowship by the Boehringer Ingelheim Fonds and is supported by the German National Academic Foundation. The Leeds Multidisciplinary Research Tissue Bank staff was funded by the PPR Foundation and part of the University of Leeds (S.C.S.). GLASS-Austria was funded by the Austrian Science Fund project KLI394 (A.W.). GLASS-Germany was funded by the German Ministry of Education and Research (BMBF) 031A425 (G. Reifenberger, P.L.) and German Cancer Aid (DKH) 70-3163-Wi 3 (M.W.). GLASS-NL receives support from KWF/Dutch Cancer Society project 11026 (M.C.M.K., P.W., R.G.W.V., P.J.F., J.M.N., M. Smits, B.A.W.). We thank the University of Colorado Denver Central Nervous System Biorepository (D.R.O.) for providing tissue samples. Sponsoring was also received from the National Institute of Neurological Disorders and Stroke (NINDS R01NS094615, G. Rao), F.S.V. is supported by a postdoctoral fellowship from The Jane Coffin Childs Memorial Fund for Medical Research. F.P.B. is supported by the JAX Scholar program and the National Cancer Institute (K99 CA226387); K.C.J. is the recipient of an American Cancer Society Fellowship (130984-PF-17-141-01-DMC). We thank the Jackson Laboratory Clinical and Translation Support team for coordinating all data transfer agreements. We thank M. Wimsatt for assistance in graphic design.
R.G.W.V. declares equity in Boundless Bio, Inc. M.K. receives research grants from BMS and ABBVie. P.K.B. is a consultant for Lilly, Genentech-Roche, Angiochem and Tesaro. P.K.B. receives institutional funding from Merck and Pfizer and honoraria from Merch and Genentech-Roche. W.K.A.Y. serves in a consulting or advisory role at DNAtrix Therapeutics. M.W. receives funding from Acceleron, Actelion, Bayer, Isarna, Merck, Sharp & Dohme, Merck (EMD, Darmstadt), Novocure, OGD2, Pigur and Roche as well as honoraria from BMS, Celldex, Immunocellular Therapeutics, Isarna, Magforce, Merck, Sharp & Dohme, Merck (EMD, Darmstadt), Northwest Biotherapeutics, Novocure, Pfizer, Roche, Teva and Tocagen. G. Reifenberger receives funding from Roche and Merck (EMD, Darmstadt) as well as honoraria from AbbVie. M. Smits is a central reviewer for Parexel Ltd and honoraria are paid to the institution. G. Tabatabai reports personal fees from Bristol-Myers-Squibb, personal fees from AbbVie, personal fees from Novocure, personal fees from Medac, travel grants from Bristol-Myers-Squibb, education grants from Novocure, research grants from Roche Diagnostics, research grants from Medac, membership in the National Steering board of the TIGER NIS (Novocure) and the International Steering board of the ON-TRK NIS (Bayer).
Peer review information Nature thanks Kamila Naxerova, Wolfgang Wick and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.
Extended data figures and tables
a, Quality control workflow steps identifying all GLASS samples available as a resource and the identification of the highest quality set of patient pairs (n = 222) used for the presented mutational and copy number analyses. b, Additional available datasets.
a, Box plots and paired lines depicting coverage-adjusted mutation frequencies in initial and matched recurrent samples across three subtypes. Wilcoxon signed-rank test P values and sample sizes are indicated. b, Bee swarm plot depicting coverage-adjusted mutation frequencies in fractions by subtype. Dashed line indicates the mean. P values comparing three subtypes were determined by one-way analysis of variance (ANOVA). c, Scatter plot showing the relationship between age at diagnosis and coverage adjusted mutation burdens by subtype and fraction. P values were determined by the linear model and adjusted by subtype. d. Similar to the analysis in c but showing the relationship between time to recurrence and coverage-adjusted mutation burdens.
a, Correlation plot showing the Pearson’s chi-squared (χ2) residuals for each signature by fraction and subtype. A χ2 test was performed for each subtype and P values are indicated. Positive residuals (blue) indicate a positive correlation, whereas negative residuals (red) indicate an anti-correlation. The point size reflects the contribution to the χ2 estimate. b, Patients were ordered as in Fig. 1a, and relevant clinical information is provided alongside the fraction-specific mutational signatures. PyClone mutational clusters are also presented.
a, Bar plots represent counts of recurrence-only mutations per hypermutator tumour that were known to receive treatment alkylating agent and were successfully run through the PyClone algorithm. Colours indicate mutation clonality and colour intensity indicates whether the mutations resulted in coding changes. b, Kaplan–Meier curve comparing the survival of alkylating agent-treated IDH-mutant-noncodel hypermutator tumours that were predominantly clonal (n = 8), predominantly subclonal (n = 7) or non-hypermutator (n = 17). Limited to tumours with available PyClone data. P value determined by log-rank test.
a, The minimum CCF of the most persistent (shared between initial and recurrence) PyClone cluster. b, Comparison of PyClone clusters ranked by CCF in matched initial and recurrent tumours, as in Fig. 2b, but separated by subtype. c, d, Examples of cluster CCF dynamics over time in three separate samples, including two multi-time point samples (c) and one multi-sector sample (d). These additional data are available in the GLASS resource, but only two time-separated samples were used throughout to ensure clarity.
a, Distributions of non-hypermutator variant allele fraction for copy-neutral variants in coding regions (n = 181 patients). Variants are separated by subtype, fraction and also the variant was non-synonymous or synonymous mutation in a coding region. R2 goodness-of-fit measure and associated P values are shown. Note that these data consider only the coding portion of genome, whereas Fig. 2d presents both coding and non-coding data. b, The cumulative distribution of the subclonal mutations in copy-neutral regions for hypermutators (n = 31 patients). For each variant fraction and subtype, the R2 goodness-of-fit measure and P values are shown.
a, Local (gene-wise) dN/dS estimates by subtype (rows) and fraction (columns). Genes are sorted by Q value and P value. The Q value is shown in colour, whereas the P value is indicated in light grey. The Q value threshold of 0.05 is indicated by a horizontal red line. b, GISTIC significant amplification (red) and deletion (blue) plots in initial (left) and recurrent tumours (right). Chromosomal locations are ordered on the y axis, Q values are shown on the x axis, and selected drivers are indicated by their chromosomal location on the right.
a, Tabulated numbers of SNV (top) and CNV (bottom) driver events that were shared, initial-only or recurrence-only. P values were determined by a two-sided Fisher test comparing the initial-only fraction to the recurrence-only fraction testing for acquisition. b, One-sided Fisher test comparing the initial-only fraction to the recurrence-only fraction among previously implicated glioma drivers testing for driver acquisition. P values were adjusted for multiple testing using the false discovery rate (x axis). Hypermutators (red) and non-hypermutators (black) were separately analysed.
Ladder plots comparing the CCF of co-occurring drivers in single tumour samples. The colour of the lines and points indicates whether the sample shown is an initial (brown) or recurrent (green) tumour. P values determined by two-sided Wilcoxon rank-sum test for all initial samples, recurrent samples, as well as all samples (black).
a, Driver gene CCF comparison between initial and matched recurrences. Lines are coloured by variant classification. P values determined by two-sided Wilcoxon rank-sum test. b, TP53 CCF by subtype, otherwise as in a. c, IDH1 CCF by subtype, otherwise as in a. d, Ladder plot visualizing change in CCF across all SNVs between initial and recurrent tumours, separated by subtype. P values determined by Wilcoxon rank-sum test. e, Initial and recurrent mutations in each patient were compared using a Wilcoxon rank-sum test. Bar plot with counts of patients in each subtype are shown. Patients lacking significant change are shown in yellow, and those with a significant increase or decrease are shown in dark and light blue, respectively.
a, Heat map displaying the chromosomal arm-level events (x axis) with patients represented in each row. Patients are placed in the same order for both the initial (left) and recurrence (right). White space was inserted as a break between the three subtypes. b, Distribution of total aneuploidy difference. Acquired aneuploidy determination (upper-quartile) indicated with a red line. c, Comparison of aneuploidy score between initial and recurrent tumours separated by subtype d. As in c, comparing aneuploidy value.
a, Bar plots representing the number of shared mutations that give rise to neoantigens (top row, ‘immunogenic’) and those that do not give rise to neoantigens (bottom row, ‘non-immunogenic’) stratified by longitudinal clonality (‘(clonality in initial) − (clonality in recurrence)’) and further separated by subtype. The percentage of longitudinal clonality per subtype and mutation is shown. b, Left, ladder plot depicting the difference in observed-to-expected neoantigen ratio between the initial and recurrent tumours of patients with hypermutated tumours at recurrence. Each set of points connected by a line represents one tumour (n = 70). Right, box plot depicting the distribution of observed-to-expected neoantigen ratios in recurrent tumours stratified by hypermutator status (n = 35 and 183 for hypermutators and non-hypermutators, respectively). Each box spans quartiles, with the lines representing the median ratio for each group. Whiskers represent absolute range, excluding outliers. P values were determined by a paired and an unpaired two-sided t-test, for left and right graphs, respectively. c, Stacked bar plots depicting the average relative fraction of 11 CIBERSORT cell types in the neoantigen depleted (<1) and non-depleted (>1) initial and recurrent tumour subgroups. P values to the right of each plot indicate a significant difference between the depleted and non-depleted groups for the noted cell type at that time.
This file contains a supplementary tables’ guide for tables 1-10, supplementary tables 9 and 10, and some supplementary text.
Supplementary Table 1: Sequencing Centers and Hospitals with corresponding GLASS barcode designations.
Supplementary Table 2: Cox proportional hazards analysis in aklyating agent-treated hypermutators and non-hypermutators.
Supplementary Table 3: a) Breakdown of evolution mode subtype b) Breakdown of evolution status at recurrence across subtype.
Supplementary Table 4: Multivariate Cox proportional hazards model testing the association between evolution status at recurrence and overall survival (n = 131).
Supplementary Table 5: Relationship between selection status at recurrence and therapy.
Supplementary Table 6: Neoantigen frequency in the GLASS cohort.
Supplementary Table 7: GLASS patient-level summary and clinical characteristics.
Supplementary Table 8: Surgery-level clinical data for each GLASS subject.
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Barthel, F.P., Johnson, K.C., Varn, F.S. et al. Longitudinal molecular trajectories of diffuse glioma in adults. Nature 576, 112–120 (2019) doi:10.1038/s41586-019-1775-1