Aim and hypothesis:
Malignant pleural mesothelioma (MPM) is a rare cancer of the pleura, currently without curative treatment. Neoantigens are foreign proteins generated from frameshift mutations, that can be presented to T cells, within major histocompatibility complex class I or II molecules, as “non-self” antigens that escape regulation by central tolerance and provoke an immune response1, 2. We hypothesized that mesothelioma-associated neoantigens are potential candidates for development of neoantigen-targeted immunotherapy. Our aim was to identify putative neoantigens arising from somatic frameshift mutations, and predict their binding affinity to HLA phenotypes.
Frameshift aberrations were searched for in three MPM cases (MM1, MM2, MM3) by whole-genome sequencing (WGS) of biopsy tumour and peripheral blood at 80X and 30X coverage, respectively. Putative neoantigen sequences were extracted by obtaining wildtype coding sequence from RefSeq, inserting the variant of interest, and generating new amino acid sequence using EMBOSS TranSeq. The HLA phenotypes of each case were predicted using OptiType. Binding affinity of each neoantigen sequence against corresponding HLA phenotype were evaluated using netMHCpan 3.0, setting the threshold for strong binders to 0.5%, and weak binders to 2.0%.
HLA–A, –B and –C serotypes were predicted for both HLA alleles of MM1 – 3. Twenty putative neoantigens were identified from mutated genes – MM1: NF2, TCF7L2, HSP90AB1, WBSCR17; MM2: NF2, SESN3, CRMP1; MM3: NF2, LATS2, SUMF2, ME1, KLHL1, ASIC2, COLQ, TP53BP1, ITGA1, RFX6. With NF2 mutated in all cases, netMHCpan 3.0 predicted strong HLA binding of NF2 putative neoantigens for MM1 and MM2, and weak binding for MM3. Other predicted strong binding putative neoantigens arose from mutations in TCF7L2, CRMP1, LATS2, ASIC2, TP53BP1, ITGA1 and RFX6.
WGS and in silico analysis identified several putative neoantigens in MPM. Further investigation is warranted to elucidate the therapeutic value of these candidates, towards the development of neoantigen-targeted immunotherapy.
Project: The Prince Charles Hospital Foundation Experienced Researcher Grant
PhD Scholarship: The Prince Charles Hospital Foundation PhD Scholarship for Ms Tian Mun Chee
Fellowship: Vojakovic Fellowship for Associate Professor Rayleen Bowman