SEARCHING NEOEPITOPES WITH BIOINFORMATIC

TECHNIQUES FOR IMMUNOTHERAPY AGAINST CANCER

Authors: Ibel Carri1, María Marcela Barrio2, Morten Nielsen1
1
Instituto de Investigaciones Biotecnológicas Dr. Rodolfo Ugalde, Universidad Nacional de San Martín, Buenos Aires, Argentina;
2
Centro de Investigaciones Oncológicas-Fundación Cáncer, Ciudad Autónoma de Buenos Aires (CABA), Argentina

Background
Immunotherapy is a type of cancer treatment that boosts the body's natural defenses, aiding the removal of 1 Whole Exome
carcinogenic, metastatic cells. Under these conditions, Neoepitopes from somatic mutations are potential Sequencing
targets of T cell immune responses, and therefore are the focus of many experimental and in-silico studies.
In the last years, advances in high-throughput sequencing techniques have made possible to identify Illumina
mutations related to potential Neoepitope candidates in human tumors. However, a relatively large part of
these candidates are not immunogenic i.e. false positives. The exact reasons for this are unclear but may
occur when the mutant candidate is very similar to the wild type peptide, enabling self-tolerance to impact
in this lack of immune response. In this context, an improvement in neoepitope identification algorithms
may lead to a better understanding of the problem, and as a direct consequence, in better treatments.

T cell 2 Quality

recognicing FastQC

mutant
neoepitope
3 Mapping to
reference
Methods
We define a pipeline to rationally obtain variants BWA MEM
hg38
and select only potential neopeptides from NGS
data. Next, potential neoepitopes are identified
based on predicted MHC binding affinity, stability
and similarity to self, our pipeline generates a
combined score that facilitates the extraction of
neoepitope candidates from a collection of 4 Pre-process
mutations. For the idenification of neopeptides, we of bam
first sequence the genome of interest, then, we
calculate a value of similarity
Picard
between mutant and wild type peptides, extract the corresponding variants and last, we compare
GATK
different thresholds, similarity values and variant lists to compute the final solution.

156 We apply this pipeline to whole exome sequencing

missense data from the cellular CSF-470 vaccine and
melanoma cells from vaccinated patients. 5 Variant Calling
745 111
WT weak
As an example, here we present the relative number
of mutations and candidates that we extracted in a
patient who developed an adaptive immune
SNP + InDel

MuTect2 GATK
ACTAAGACCT
ACTACGACCT
binders
332 response after receiving the vaccine.
We split the candidates in four different groups based
on the mutant and wild type binding affinities and
Mutations similarity between them.
Candidates
6 Detect
Future work immunogenic
After testing this approach in CSF-470 vaccine with ELISPOT, we will have a large amount of valuable peptides
information about rules defining neoepitopes to apply in new predictors. Also we would be able to
determine if the mechanism that triggers the immune response of vaccinated patients is related to MuPeXi
the direct recognition of shared antigens between the cellular vaccine and the tumor or there is an
epitope spreading.

References 7 Select best

- Shen, W. J., Wong, H. S., Xiao, Q. W., Guo, X., & Smale, S. (2012). Towards a mathematical foundation of immunology and amino acid chains. arXiv preprint arXiv:1205.6031.
- Bjerregaard, A. M., Nielsen, M., Hadrup, S. R., Szallasi, Z., & Eklund, A. C. (2017). MuPeXI: prediction of neo-epitopes from tumor sequencing data. Cancer Immunology, Immunotherapy, 1-8.
- Rasmussen, M., Fenoy, E., Harndahl, M., Kristensen, A. B., Nielsen, I. K., Nielsen, M., & Buus, S. (2016). Pan-Specific Prediction of Peptide–MHC Class I Complex Stability, a Correlate of T Cell
Immunogenicity. The Journal of Immunology, 197(4), 1517-1524.
candidates 1
2 3
- Jurtz, V. I., Paul, S., Andreatta, M., Marcatili, P., Peters, B., & Nielsen, M. (2017). NetMHCpan 4.0: Improved peptide-MHC class I interaction predictions integrating eluted ligand and peptide
binding affinity data. bioRxiv, 149518.
- Mordoh, J., Pampena, M. B., Aris, M., Blanco, P. A., Lombardo, M., von Euw, E. M., ... & Ramello, F. (2017). Phase II study of adjuvant immunotherapy with the CSF-470 vaccine plus BCG plus
netMHCpan 4.0
rhGM-CSF versus medium-dose interferon alpha 2b in stages IIB, IIC and III cutaneous melanoma patients. A single institution, randomized study. Frontiers in Immunology, 8, 625. netSTABpan 1.0
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