Abstract

Tumor mutational burden correlates with response to immune checkpoint blockade in multiple solid tumors, although in microsatellite-stable tumors this association is of uncertain clinical utility. Here we uniformly analyzed whole-exome sequencing (WES) of 249 tumors and matched normal tissue from patients with clinically annotated outcomes to immune checkpoint therapy, including radiographic response, across multiple cancer types to examine additional tumor genomic features that contribute to selective response. Our analyses identified genomic correlates of response beyond mutational burden, including somatic events in individual driver genes, certain global mutational signatures, and specific HLA-restricted neoantigens. However, these features were often interrelated, highlighting the complexity of identifying genetic driver events that generate an immunoresponsive tumor environment. This study lays a path forward in analyzing large clinical cohorts in an integrated and multifaceted manner to enhance the ability to discover clinically meaningful predictive features of response to immune checkpoint blockade.

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Acknowledgements

This work was supported by BroadIgnite (E.M.V.A.), BroadNext10 (E.M.V.A., D.M.), NIH R01CA227388 (E.M.V.A.) and NIH K08CA188615 (E.M.V.A.). D.M. was supported by the Howard Hughes Medical Institute Medical Research Fellows Program. This research was also supported by the Center for Immuno-Oncology at the Dana-Farber Cancer Institute and a Stand Up To Cancer–American Cancer Society Lung Cancer Dream Team Translational Research Grant (SU2C-AACR-DT17-15). Stand Up To Cancer (SU2C) is a program of the Entertainment Industry Foundation. Research grants are administered by the American Association for Cancer Research, the scientific partner of SU2C.

Author information

Author notes

  1. These authors contributed equally: Diana Miao, Claire A. Margolis, Natalie I. Vokes

Affiliations

  1. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA

    • Diana Miao
    • , Claire A. Margolis
    • , Natalie I. Vokes
    • , David Liu
    • , Amaro Taylor-Weiner
    • , Stephanie M. Wankowicz
    • , Daniel Keliher
    • , Michael Manos
    • , Nicole G. Chau
    • , Glenn J. Hanna
    • , Scott J. Rodig
    • , Sabina Signoretti
    • , Lynette M. Sholl
    • , Pasi A. Jänne
    • , Robert I. Haddad
    • , Toni K. Choueiri
    • , David A. Barbie
    • , Rizwan Haq
    • , Mark M. Awad
    • , Dirk Schadendorf
    • , F. Stephen Hodi
    • , Joaquim Bellmunt
    • , Kwok-Kin Wong
    • , Peter Hammerman
    •  & Eliezer M. Van Allen
  2. Broad Institute of MIT and Harvard, Cambridge, MA, USA

    • Diana Miao
    • , Claire A. Margolis
    • , Natalie I. Vokes
    • , David Liu
    • , Amaro Taylor-Weiner
    • , Stephanie M. Wankowicz
    • , Daniel Keliher
    • , Adam Tracy
    • , Paz Polak
    • , Gad Getz
    • , Rizwan Haq
    •  & Eliezer M. Van Allen
  3. Perlmutter Cancer Center at NYU Langone Medical Center, New York, NY, USA

    • Dennis Adeegbe
    •  & Kwok-Kin Wong
  4. Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Würzburg, Germany

    • Bastian Schilling
  5. Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA

    • Scott J. Rodig
    • , Sabina Signoretti
    •  & Lynette M. Sholl
  6. Massachusetts General Hospital Cancer Center, Boston, MA, USA

    • Jeffrey A. Engelman
    •  & Gad Getz
  7. Department of Pathology, Massachusetts General Hospital, Boston, MA, USA

    • Gad Getz
  8. Harvard Medical School, Boston, MA, USA

    • Gad Getz
  9. Department of Dermatology, University Hospital, University Duisburg-Essen, Essen, Germany

    • Dirk Schadendorf

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Contributions

D.M., C.A.M., N.I.V., A.T.-W., D.L., D.A., P.P., G.G., and D.K. performed the analyses. B.S., M.M., M.M.A., N.G.C., G.J.H., R.H. and S.M.W. provided clinical annotations. L.M.S., S.S., and S.J.R. contributed to immunohistochemical profiling. K.-K.W., J.A.E., M.M.A., D.A.B., R.I.H., D.S., F.S.H., T.K.C., J.B., P.A.J., R.H., A.T., P.H., and E.M.V.A. contributed to sample acquisition. E.M.V.A. supervised the study. D.M., C.A.M., N.I.V., D.L., and E.M.V.A. wrote the manuscript with contributions from all authors.

Competing interests

A.T., D.L., D.M., M.M., N.I.V., C.A.M., D.A., D.K., S.M.W., L.M.S., A.T.-W., P.P., K.-K.W., S.J.R., J.B., P.A.J., N.G.C., R.H., and M.M.A. declare no conflicts of interest. T.K.C. has advisory roles with AstraZeneca, Bayer, Bristol-Myers Squibb, Cerulean, Elsa, Foundation Medicine, Genentech, GlaxoSmithKline, Merck, Novartis, Peloton, Pfizer, Prometheus Labs, Roche, and Elsai. T.K.C. receives research funding from AstraZeneca, Bristol-Myers Squibb, Exelixis, Genentech, GlaxoSmithKline, Merck, Novartis, Peloton, Pfizer, Roche, Tracon, and Eisai. G.J.H. receives institutional support from Bristol-Myers Squibb and EMD Serono. B.S. is on the advisory board or has received honoraria from Novartis, Roche, Bristol-Myers Squibb, and MSD Sharp & Dohme, research funding from Bristol-Myers Squibb and MSD Sharp & Dohme, and travel support from Novartis, Roche, Bristol-Myers Squibb, and Amgen. R.I.H. has advisory roles with Bristol-Myers Squibb, Pfizer, Merck, AstraZeneca, Genentech, and Celgene. R.I.H. receives research funding from Bristol-Myers Squibb, Merck, Genentech, and Pfizer. S.S. is a consultant for AstraZeneca and Merck and receives research funding from AstraZeneca, Bristol-Myers Squibb, Exelixis, and Roche. G.G. has an advisory role with MD Anderson and receives research funding from IBM and Bayer. G.G. is listed as an inventor on patent applications regarding MuTect, ABSOLUTE, and Polysolver. D.A.B. is a consultant for N of One. D.S. receives consulting fees from Amgen, GlaxoSmithKline, BMS, Novartis, Roche, Amgen, Merck, AstraZeneca, Merck-Serono, and Pfizer. P.H. and J.A.E. are employees of Novartis. F.S.H. is a consultant to Bristol-Myers Squibb, Merck, Novartis, EMD Serono, Sanofi, and Genentech and receives institutional research support from Bristol-Myers Squibb. E.M.V.A. holds consulting roles with Tango Therapeutics, Invitae, and Genome Medical and receives research support from Bristol-Myers Squibb and Novartis.

Corresponding author

Correspondence to Eliezer M. Van Allen.

Integrated supplementary information

  1. Supplementary Figure 1 Tumor purity, mutational burden, and response to immune checkpoint therapy.

    a, Called mutations by estimated tumor purity (ABSOLUTE) in 297 tumors with adequate sequencing quality (i.e., not excluded owing to sample contamination, low sequencing coverage, or other quality issues). Fifteen samples with high purity and outlying high mutational burdens are not shown. Purity <10% was associated with decreased ability to call mutations in most samples. The two samples with purity <10% and >500 called mutations/exome had unusually high sequencing coverage. However, inference of clonal versus subclonal mutational architecture was not possible by ABSOLUTE given low confidence in calling somatic CNAs, and a high rate of false negative mutation calls may have occurred, so these samples were excluded from analysis. Box plots show the median, first and third quartiles, whiskers extend to 1.5 times the interquartile range, and outlying points are plotted individually. b, Bar plot showing the frequency of estimated tumor purities, colored by patient response status. Tumor purity did not strongly predict clinical benefit from immune checkpoint therapies in 249 tumors included in the final analysis. c, Scatterplot showing subclonal mutational burden by estimated tumor purity in 249 included samples. Even after excluding tumors with estimated purity <0.1, subclonal mutations were likely undercalled in tumors with purity <0.2.

  2. Supplementary Figure 2 Clinical response categories and mutational burden across four cancer types.

    Box plots showing mutational burden on the y axis (all mutations, all nonsynonymous mutations, and all clonal nonsynonymous mutations) are displayed in an array, organized by tumor type (in columns) and response categorization used (in rows). The range of mutational load varied greatly by cancer type. Additionally, the choice of response metric influenced both the number of patients designated as OR or NR per cancer type (Supplementary Table 3) and the strength of the relationship between mutational burden and response. Two-sided Mann–Whitney U test: *P < 0.05, **P < 0.005. Box plots show the median, first and third quartiles, whiskers extend to 1.5 times the interquartile range, and outlying points are plotted individually.

  3. Supplementary Figure 3 Differences in mutational load and clonality by response category and treatment.

    a, Mutational burden among response groups after stratifying by treatment category. There was a significant difference in mutational burden across all three response categories in patients treated with PD-1/PD-L1 inhibitors. In anti-CTLA-4-treated patients, mutational burden differed only between CR/PR patients and PD patients. b, All mutations (synonymous and nonsynonymous), nonsynonymous, and clonal nonsynonymous mutational burden among the response groups after stratifying SD and PD by duration of overall survival (OS). Across all mutation categories, mutational burden was significantly higher in CR/PR patients than in those with SD and OS <1 year and those with PD and OS <2 years. However, there was no statistically significant difference in mutation load between CR/PR patients and those with SD and OS >1 year nor between those with PD and OS >2 years (P > 0.05). Two-sided Mann–Whitney U test: *P < 0.05, **P < 0.005. Box plots show the median, first and third quartiles, whiskers extend to 1.5 times the interquartile range, and outlying points are plotted individually.

  4. Supplementary Figure 4 Receiver operating characteristic analysis of mutational load as a univariate whole-exome-based response predictor.

    The red line represents the accuracy of prediction of CR/PR versus PD using nonsynonymous mutational burden as a continuous variable alone (area under the ROC curve (AUC) = 0.66). The ROC curve was generated using data from 193 (70 CR/PR, 123 PD) patient samples.

  5. Supplementary Figure 5 Enrichment of nonsynonymous mutations in all mutated genes in the cohort by response category.

    The y axis shows –log10 (P) for enrichment of mutations in OR (above the dashed line) or in NR (below the dashed line) by two-sided Fisher’s exact test. The x axis shows the prevalence of each mutation across the cohort. Colors denote the significance of enrichment, with dark gray points representing genes that are significantly mutated across the entire cohort (MutSig2CV q < 0.1), blue representing genes that are mutated significantly more frequently in either OR or NR but are not mutated at significant levels across the entire cohort (P < 0.05), and red representing genes that were significantly enriched in mutations in OR or NR and mutated frequently across the cohort by MutSig2CV. All other genes are shown in light gray. Circle size is proportional to the number of patients with a mutation in a given gene. Three different methods of stratifying patients into OR versus NR are shown.

  6. Supplementary Figure 6 PIK3CA driver mutations in the APOBEC mutational signature spectrum.

    Mutational context of mutations in PIK3CA observed in this cohort overlaid on the APOBEC-associated mutational spectrum. Mutations in dark red text are known hotspots in PIK3CA. Hotspots occurring because of C>T mutations have been previously associated with APOBEC-associated mutational processes in HNSCC (Henderson et al. Cell Rep. 2014).

  7. Supplementary Figure 7 Smoking status, tumor mutational burden, and clinical benefit from immune checkpoint therapy.

    a, Proportion of patients with the smoking dominant mutational signature (S4, brown), APOBEC (S2/S13, teal), aging (S1, light tan), or unknown (S5, dark tan) by response group. b, Differences in mutational burden by response group in patients with a self-reported current/former smoking history (>5 pack-years). All P values reported are from two-sided Mann–Whitney U tests. CR/PR versus PD, P = 0.0002; CR/PR versus SD, P = 0.003; SD versus PD, P = 0.085. **P < 0.005 (two-sided Mann–Whitney U test). Box plots show the median, first and third quartiles, whiskers extend to 1.5 times the interquartile range, and outlying points are plotted individually.

  8. Supplementary Figure 8 Mutational burden, mutational signatures, tumor purity, histological subtype, and response to immune checkpoint therapy in melanoma.

    a, Stacked plots showing tumor mutational burden (histogram, top, blue and purple), estimated tumor purity by ABSOLUTE (tile plot, top, purple), presence of BRAF p.V600E mutation (tile plot, top, red), response to immune checkpoint therapy (tile plot, middle), mutational signatures (filled histogram, bottom), and tumor subtype (bottom). UV-dominant (S7), alkylating-dominant (S11), and non-UV-/non-alkylating-dominant (S1, S5, S17, or S6) tumors are shown separately. b, Dominant (most represented) mutational signature by tumor subtype. Cutaneous melanomas were largely UV associated, while acral lentiginous melanomas and non-cutaneous melanomas generally had few UV-associated mutations, although exceptions occurred.

  9. Supplementary Figure 9 Comparison of multiple definitions of genomic segment-level deletion or amplification and association with purity.

    The proportion of the exome affected by amplifications or deletions is shown on the y axis, with estimated tumor purity by ABSOLUTE on the x axis. a, Defining copy number alterations as segments with |log2 (copy ratio)| > 0.5 leads to results that are highly dependent on tumor purity. b, Correcting for tumor purity and ploidy while using a similar threshold for calling a segment amplified or deleted yields copy number calls that are more sensitive and less dependent on tumor purity. c, A more stringent definition of copy number alterations designed to detect only major amplifications and homozygous deletions to specifically identify events expected to lead to major changes in gene expression incorporates both tumor purity and ploidy as well as a measurement of segment focality, as further described in the Methods.

  10. Supplementary Figure 10 Copy number alterations affecting interferon signaling by drug class.

    a, Proportion of samples harboring a CNA disrupting interferon-γ signaling by drug class using a definition of clinical benefit from Roh et al. (2017). For the anti-CTLA-4 condition, n = 145; two-sided Fisher’s exact test P = 0.021. For the anti-PD-1/PD-L1 condition, n = 94; two-sided Fisher’s exact test P = 0.038. b, Proportion of samples harboring a CNA disrupting interferon signaling by drug class using a definition of clinical benefit from Van Allen et al. (2015). For the anti-CTLA-4 condition, n = 133; two-sided Fisher’s exact test P = 0.008. For the anti-PD-1/PD-L1 condition, n = 92; two-sided Fisher’s exact test P = 0.073. Two-sided Fisher’s exact test: *P < 0.05. Error bars represent standard error above and below the group proportion.

  11. Supplementary Figure 11 Copy number alterations affecting interferon signaling by cancer type.

    All P values listed are from two-sided Fisher’s exact tests. a, Proportion of samples harboring a CNA disrupting interferon-γ signaling by cancer type using a definition of clinical benefit from Roh et al. (2017). All, n = 249 and P = 0.0002; bladder, n = 27 and P = 0.33; HNSCC, n = 12 and P = 1; lung, n = 57 and P = 0.26; melanoma, n = 151 and P = 0.02. b, Proportion of samples harboring a CNA disrupting interferon signaling by cancer type using a definition of clinical benefit from Van Allen et al. (2015). All, n = 234 and P = 0.002; bladder, n = 26 and P = 0.31; HNSCC, n = 12 and P = 1; lung, n = 56 and P = 0.46; melanoma, n = 138 and P = 0.004. Two-sided Fisher’s exact test: *P < 0.05, **P < 0.005. Error bars represent standard error above and below the group proportion.

  12. Supplementary Figure 12 Putative biallelic PTEN loss in progressing lesions from two patients with CB to anti-CTLA-4 therapy.

    a, Copy number plot (top) and allelic copy number plot (bottom) showing a PTEN nonsense mutation (p.V119fs) in a progressing lesion from a patient with overall PR to anti-CTLA-4 monotherapy. The estimated tumor purity in this sample was 0.14, which was too low to accurately evaluate the presence or absence of a heterozygous deletion at this locus. Thus, this patient has at least monoallelic and potentially biallelic PTEN loss. b, Copy number plot (top) and allelic copy number plot (bottom) with the arrow indicating the PTEN locus, which occurs in an area of copy-neutral loss of heterozygosity on chromosome 10. This sample was derived from a progressing lesion from a patient with a long duration of stable disease on anti-CTLA-4 therapy. The tumor harbored a PTEN splice-site mutation, a PTEN p.P89L missense mutation, and loss of heterozygosity over the PTEN locus, suggesting biallelic PTEN loss.

  13. Supplementary Figure 13 Truncating mutations and biallelic deletions of genes encoding SWI/SNF subunits.

    All samples with at least one truncating mutation in PBRM1 or ARID2 are shown. Colors represent mutational classification (nonsense, missense, etc.). The bottom tile plot indicates patient response to immune checkpoint therapy. Cells containing asterisks indicate patients with more than one truncating mutation in a given gene. Phasing of these mutations could not be determined. Mutations occurring in the context of heterozygous deletion (light blue) likely lead to complete loss of protein function.

  14. Supplementary Figure 14 Biallelic loss of genes involved in JAK–STAT signaling.

    a, Samples with biallelic loss (truncating mutation with deletion of the wild-type allele) of at least one gene in the JAK–STAT pathway are shown. Color indicates mutation class. The bottom tile plot indicates clinical response to immune checkpoint therapy. b, Samples with mutations or copy number alterations leading to biallelic loss in antigen-presentation pathway genes are shown. c, Copy number plot demonstrating biallelic loss of β2-microglobulin via a homozygous deletion in a patient with melanoma.

Supplementary information

  1. Supplementary Text and Figures

    Supplementary Figures 1–14 and Supplementary Tables 3, 6 and 8

  2. Reporting Summary

  3. Supplementary Table 1

    Sequencing metrics and inclusion/exclusion criteria for whole-exome sequencing from 314 clinically annotated patient tumors

  4. Supplementary Table 2

    Clinical outcomes and clinical covariates for 249 patients

  5. Supplementary Table 4

    Oncogenes and tumor suppressors assessed for driver mutations

  6. Supplementary Table 5

    All mutations (somatic single-nucleotide variants and small insertions and deletions) across 249 tumors included in analysis

  7. Supplementary Table 7

    Mutational signature activity across all tumors

  8. Supplementary Table 9

    Copy number alterations across all tumors

  9. Supplementary Table 10

    Predicted HLA-restricted neoantigens across all tumors

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DOI

https://doi.org/10.1038/s41588-018-0200-2