Intra-patient stability of tumor mutational burden from tissue biopsies at different time points in advanced cancers

Abstract

Background: Tumor mutational burden (TMB) may be a predictive biomarker of immune checkpoint inhibitor (ICI) responsiveness. Genomic landscape heterogeneity is a well-established cancer feature. Molecular characteristics may differ even within the same tumor specimen and undoubtedly evolve with time. However, the degree to which TMB differs between tumor biopsies within the same patient has not been established.

Methods: We curated data on 202 patients enrolled in the PREDICT study (NCT02478931), seen at the University of California San Diego (UCSD), who had 404 tissue biopsies for TMB (two per patient, mean of 722 days between biopsies) to assess difference in TMB before and after treatment in a pan-cancer cohort. We also performed an orthogonal analysis of 2872 paired pan-solid tumor biopsies in the Foundation Medicine database to examine difference in TMB between first and last biopsies.

Results: The mean (95% CI) TMB difference between samples was 0.583 [- 0.900-2.064] (p = 0.15). Pearson correlation showed a flat line for time elapsed between biopsies versus TMB change indicating no correlation (R2 = 0.0001; p = 0.8778). However, in 55 patients who received ICIs, there was an increase in TMB (before versus after mean mutations/megabase [range] 12.50 [range, 0.00-98.31] versus 14.14 [range, 0.00-100.0], p = 0.025). Analysis of 2872 paired pan-solid tumor biopsies in the Foundation Medicine database also indicated largely stable TMB patterns; TMB increases were only observed in specific tumors (e.g., breast, colorectal, glioma) within certain time intervals.

Conclusions: Overall, our results suggest that tissue TMB remains stable with time, though specific therapies such as immunotherapy may correlate with an increase in TMB.

Trial registration: NCT02478931 , registered June 23, 2015.

Keywords: Immunotherapy; Immunotherapy effect on TMB; TMB over time; TMB over treatment; Tumor mutational burden.

Conflict of interest statement

RK has the following disclosure information: Stock and Other Equity Interests (IDbyDNA, CureMatch, Inc., and Soluventis); consulting or advisory role (Gaido, LOXO, X-Biotech, Actuate Therapeutics, Roche, NeoMed, Soluventis, and Pfizer); speaker’s fee (Roche); research funding (Incyte, Genentech, Merck Serono, Pfizer, Sequenom, Foundation Medicine, Guardant Health, Grifols, Konica Minolta, DeBiopharm, Boerhringer Ingelheim, and OmniSeq [all institutional]); board member (CureMatch, Inc and CureMetrix Inc.).

AG receives consulting fees from Seattle Genetics and EUSA Pharma.

GF and SS are employees at Foundation Medicine, Inc., a wholly owned subsidiary of Roche Holdings, Inc. and Roche Finance Ltd, and have equity interest in an affiliate of these Roche entities.

The remaining author, TP, declares that he has no competing interests.

© 2021. The Author(s).

Figures

Fig. 1

UCSD TMB differences. All patients with valid UCSD TMB data (n = 202) were considered for this figure. Exposure or treatment is defined as having received agent between the initial and final biopsies, regardless of dose or duration, as per electronic medical records. A The TMB of the earlier and later biopsies are somewhat correlated with a significant, almost unity, slope (p < 0.0001), and a Pearson R2 = 0.459. This indicates there is no difference between early and later TMBs. B TMB difference does not correlate with time elapsed between biopsies (Pearson correlation R2 = 0.0001). The slope of the line of best fit is also not significantly greater than zero (p = 0.8778). C There is no significant different between TMBs measured at different times as determined by the Wilcoxon matched pairs signed rank test. Red lines are mean (center) ± 95% confidence interval (CI) for each group. The average TMB of the earlier biopsy was 6.181 [4.405–7.957] mutations/Mb versus 6.764 [4.861–8.666] mutations/Mb for the later biopsy (p = 0.1467). D TMB difference (increase) with time in immunotherapy-treated patients is greater than in those who did not receive immunotherapy (immunotherapy response not considered). All patients with valid TMB data considered. Red lines are mean (center) ± 95% CI for each group. Patients who were treated with immunotherapy between biopsies had a mean ± 95% CI TMB change of 1.641 [− 3.492–6.775] mutations/Mb whereas those who were not had a mean ± 95% CI TMB change of 0.1857 [− 0.5974–0.9688] mutations/Mb (p = 0.0365). Drugs received included the following: ipilimumab, nivolumab, pembrolizumab, atezolizumab, avelumab, durvalumab, and cemiplimab

Fig. 2

Foundation Medicine TMB differences in categorical elapsed time. A total of 2872 paired tissue biopsy samples from the Foundation Medicine database were studied for patterns of TMB change based on time between tests. Tumor types with at least 50 pairs were considered for this figure. Each panel represents a specific tumor type with the total number of assessed samples denoted by “N.” The collection time differences were binned into three categories: ≤ 365 days, 366 to 1095 days, and > 1095 days. Boxplots of the TMB change were plotted for each bin of collection time difference, with the total number of pairs in each bin denoted by “n.” In each boxplot: the horizontal line represents the median, the box represents the interquartile range (IQR) and the whiskers represent extremes of the data (capped at 1.5xIQR). Wilcoxon test for statistical difference for each pairwise comparison was performed; the p value is presented based on different thresholds (*0.05, **0.01, ***0.001, NS.: not significant). The TMB difference (y-axis) is capped to be between − 15 and 15 for better visualization; however, statistical analysis was performed on all available samples. Individual data points for TMB change, colored by the categorical time between biopsy, are available in Additional file 1: Fig. S4. See Additional file 2: Table S1 for detailed data and for false discovery rate adjusted p value for multiple comparisons