Foreign antigens in human cancers

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1 Foreign antigens in human cancers Lorenzo Fanchi PhD student, Ton Schumacher Lab ESMO Preceptorship on Immuno-Oncology May 26th, 2017

2 IMMUNE CHECKPOINT INHIBITION SHOWS CLINICAL BENEFIT IN DIFFERENT TUMOR TYPES Brahmer et al., NJEM 2015

3 IMMUNE CHECKPOINT INHIBITION SHOWS CLINICAL BENEFIT IN DIFFERENT TUMOR TYPES Powles et al., Nature 2014

4 DNA DAMAGE IS THOUGHT TO DETERMINE FOREIGNNESS OF TUMORS Clinical benefit of checkpoint inhibitors in tumor types characterized by high levels of DNA damage Correlation between extent of response to checkpoint inhibition treatment and amount of DNA damage within a given tumor type Evidence for T-cell recognition of foreign epitopes or neo-antigens formed as a consequence of DNA damage

5 RESPONSE TO IMMUNE CHECKPOINT INHIBITION CORRELATES WITH LEVEL OF DNA DAMAGE Significantly longer progression-free survival for patients with high levels of DNA damage upon PD1 blockade in non-small cell lung cancer High mutational burden Low mutational burden Adapted from Rizvi et al., Science 2015

6 RESPONSE TO IMMUNE CHECKPOINT INHIBITION CORRELATES WITH LEVEL OF DNA DAMAGE Mismatch repair-deficient tumors respond better to PD1 blockade Le et al., NEJM 2015

7 FOREIGN ANTIGENS ARE A PREREQUISITE FOR T-CELL RECOGNITION

8 CLASSES OF ANTIGENS I. non-mutated self antigens ( shared antigens ) shared between patients II. neo-antigens that arise as a consequence of tumor-specific mutations in large part patient-specific; truly foreign to the immune system

9 CLASSES OF ANTIGENS I. non-mutated self antigens ( shared antigens ) shared between patients II. neo-antigens that arise as a consequence of tumor-specific mutations in large part patient-specific; truly foreign to the immune system

10 CLASSES OF ANTIGENS I. non-mutated self antigens ( shared antigens ) shared between patients II. neo-antigens that arise as a consequence of tumor-specific mutations in large part patient-specific; truly foreign to the immune system

11 FOREIGN ANTIGENS ARE A PREREQUISITE FOR T-CELL RECOGNITION How are neo-antigens formed? Epitopes arising as consequence of tumor-specific DNA damage; recognizable by immune system DNA damage Mutated protein Neo-antigen

12 HOW FOREIGN ARE HUMAN TUMORS? Alexandrov et al., Nature 2013

13 ASSESSING THE FOREIGNNESS OF HUMAN CANCERS Compare the foreignness of human cancers and human pathogens Develop validated neo-antigen prediction pipeline Predict neo-antigens from SNVs, indels and fusion genes across human malignancies Compare tumor foreignness to a number of references for which T-cell control has been shown to be relevant HPV16 E6/E7 EBV LMP1/2 HIV-1

14 ASSESSING THE FOREIGNNESS OF HUMAN CANCERS Compare the foreignness of human cancers and human pathogens HPV16 E6/E7 EBV LMP1/2 HIV-1 Clinical response at endpoint VIN patients (premalignant) Vaccinate with HPV16 E6/E7 Monitor clinical response time Kenter et al., NEJM 2009

15 ASSESSING THE FOREIGNNESS OF HUMAN CANCERS Compare the foreignness of human cancers and human pathogens HPV16 E6/E7 EBV LMP1/2 HIV-1 Patients with relapsed or refractory EBV+ B-cell lymphoma Clinical response (n = 21) Treated by adoptive cell transfer of EBV-LMP1/2-specific T cells Complete responses in malignant setting Bollard et al., JCO 2014

16 ASSESSING THE FOREIGNNESS OF HUMAN CANCERS Compare the foreignness of human cancers and human pathogens HPV16 E6/E7 EBV LMP1/2 HIV-1 Extensive evidence for T cell pressure T cell responses against HIV epitopes Escape variants due to immune pressure (antigenic variation)

17 PREDICTION OF T-CELL EPITOPES T-cell recognition => similarity-to-self Expression of the antigen => RNAseq Proteasomal processing & transport => netchop Binding to MHC-I molecules => netmhcpan Figure adapted from Kobayashi et al., NRI 2012

18 SELF-LIKE PEPTIDES ARE NOT RECOGNIZED BY THE IMMUNE SYSTEM Epitopes are dissimilar from self when: Changes occur in central (T-cell exposed) amino acid residues Amino acid substitutions lead to large changes Size Hydrophobicity Electrostatic charge

19 PAN-CANCER ANALYSIS USING EPITOPE PREDICTION PIPELINE Somatic variant calls from TCGA & ICGC repositories consisting of >7000 tumor samples for 33 different tumor types Using in-house pipeline for epitope predictions Examining effects of both SNVs & indels Structural variants (gene fusions) Matched RNAseq data

20 PAN-CANCER ANALYSIS USING EPITOPE PREDICTION PIPELINE Somatic variant calls from TCGA & ICGC repositories consisting of >7000 tumor samples for 33 different tumor types Using in-house pipeline for epitope predictions Examining effects of both SNVs & indels Structural variants (gene fusions) Matched RNAseq data

21 STRUCTURAL VARIANTS ARISE FROM GENE FUSION EVENTS Tumor-specific transcript fusions can be found across various different malignancies Different types of rearrangements: Intrachromosomal Interchromosomal - Inter- & intragenic Leads to formation of novel ORF and potential neo-antigens Yoshihara, K. et al. Oncogene 34, 2015

22 LITTLE CONTRIBUTION OF FUSION ANTIGENS TO ANTIGENIC SPACE High precision fusion gene predictions potentially impacted sensitivity

23 (Stats: Wilcoxon rank-sum) VARIATION OF NEO-ANTIGEN BURDEN WITHIN TUMOR TYPES Colon cancer by MSI-status P < n.s. Breast cancer by BRCA-like-status P < HIV-1 EBV LMP1/2 HPV16 E6/E7

24 FOREIGN TARGETS IN CERVICAL AND HEAD & NECK CANCER Most of the antigenic space in Cervical and Head & Neck cancers is of non-viral origin HPV+ Cervical cancer (n=192) HPV+ Head & Neck cancer (n=95)

25 PAN-CANCER DISTRIBUTIONS OF NEO-EPITOPE REPERTOIRES Redacted unpublished data

26 TAKE HOME MESSAGES Many human tumors are substantially foreign due to accumulation of different types of DNA damage and formation of neo-antigens - Modest contribution of fusion-derived antigens to foreignness Lower end of foreignness spectrum remains unclear whether neo-antigens can play a significant role for therapeutic intervention 30% of analyzed melanoma samples are more foreign than an HIV-1 genome Across all tumor samples, 60% are as foreign or more foreign than HPV16 E6/E7 - Potential therapeutic targets by inducing or enhancing immune responses

27 THANK YOU FOR YOUR ATTENTION! Questions?

28 ACKNOWLEDGEMENTS Division of Immunology Maarten Slagter Marit van Buuren Ton Schumacher Division of Molecular Carcinogenesis Marlous Hoogstraat Gergana Buonova Lodewyk Wessels Genomics Core Facility Arno Velds Ron Kerkhoven Division of Molecular Pathology Philip Schouten Sabine Linn Wellcome Trust Sanger Institute, UK Ludmil Alexandrov Michael Stratton Department of Hematology, Leiden University Medical Center, NL Marvyn Koning Hendrik Veelken Division of Quantitative Sciences, MDACC, USA Xin Hu Roeland Verhaak Theoretical Biology & Informatics, Utrecht University, NL Jorg Calis (Rockefeller Uni, NY) Can Keşmir