Neoantigenic Potential of Complex Chromosomal Rearrangements in Mesothelioma

Abstract

Introduction: Malignant pleural mesothelioma is a disease primarily associated with exposure to the carcinogen asbestos. Whereas other carcinogen-related tumors are associated with a high tumor mutation burden, mesothelioma is not. We sought to resolve this discrepancy.

Methods: We used mate-pair (n = 22), RNA (n = 28), and T cell receptor sequencing along with in silico predictions and immunologic assays to understand how structural variants of chromosomes affect the transcriptome.

Results: We observed that inter- or intrachromosomal rearrangements were present in every specimen and were frequently in a pattern of chromoanagenesis such as chromoplexy or chromothripsis. Transcription of rearrangement-related junctions was predicted to result in many potential neoantigens, some of which were proven to bind patient-specific major histocompatibility complex molecules and to expand intratumoral T cell clones. T cells responsive to these predicted neoantigens were also present in a patient's circulating T cell repertoire. Analysis of genomic array data from the mesothelioma cohort in The Cancer Genome Atlas suggested that multiple chromothriptic-like events negatively impact survival.

Conclusions: Our findings represent the discovery of potential neoantigen expression driven by structural chromosomal rearrangements. These results may have implications for the development of novel immunotherapeutic strategies and the selection of patients to receive immunotherapies.

Keywords: Chromoplexy; Chromosomal rearrangements; Chromothripsis; Mesothelioma; Neoantigens.

Figure 1

Genomic event summary The unfilled circles represent the number of MPseq-detected junctions (rearrangements), the black circles represent the number rearrangements involving genes, and the green circles represent the number of peptides that are potential neoantigens.

Figure 2

Genome plot for ME022 In this genome plot of specimen ME022 the chromosomes are plotted in order by size as numbered near the margins. Curved red lines represent intrachromosomal rearrangements whereas blue lines represent interchromosomal rearrangements. Accordingly, the multiple red lines on chromosome 7 represent chromothripsis and the blue lines between chromosome 7 and 11 represent chromoplexy.

Figure 3:

Validation of CADPS2 rearrangement in ME018 The junction plot in the top left presents the mate pair reads supporting the intra-chromosomal rearrangement between CADPS2 and a non-genic region on chromosome 7. Red and blue dots represent mate pair reads mapping to the positive or negative DNA strands, respectively, with coverage levels across each position presented in gray-shaded regions, with single (1N) and two-copy levels (2N) indicated (green). Gene regions are presented in red with exons numerated. On the top right of this figure, this rearrangement was confirmed by PCR with primers spanning the breakpoint in both DNA and RNA in ME018, but not in negative controls (pooled human genomic DNA for DNA validation, and case ME025 which lacked this rearrangement for RNA validation). In the bottom of this figure, this rearrangement was confirmed by Sanger sequencing of the DNA.

Figure 4:

Kaplan-Meier survival curve for mesothelioma by CTLPs Subjects were classified by the presence of 0–2 CTLPs (n=64), or 3 or more (3+ CTLPs; n=23). Survival was significantly worse for patients with 3+ CTLPs (HR 2.002, p=0.006).