Mutational landscape of the transcriptome offers putative targets for immunotherapy of myeloproliferative neoplasms

Abstract

Ph-negative myeloproliferative neoplasms (MPNs) are hematological cancers that can be subdivided into entities with distinct clinical features. Somatic mutations in JAK2, CALR, and MPL have been described as drivers of the disease, together with a variable landscape of nondriver mutations. Despite detailed knowledge of disease mechanisms, targeted therapies effective enough to eliminate MPN cells are still missing. In this study of 113 MPN patients, we aimed to comprehensively characterize the mutational landscape of the granulocyte transcriptome using RNA sequencing data and subsequently examine the applicability of immunotherapeutic strategies for MPN patients. Following implementation of customized workflows and data filtering, we identified a total of 13 (12/13 novel) gene fusions, 231 nonsynonymous single nucleotide variants, and 21 insertions and deletions in 106 of 113 patients. We found a high frequency of SF3B1-mutated primary myelofibrosis patients (14%) with distinct 3′ splicing patterns, many of these with a protein-altering potential. Finally, from all mutations detected, we generated a virtual peptide library and used NetMHC to predict 149 unique neoantigens in 62% of MPN patients. Peptides from CALR and MPL mutations provide a rich source of neoantigens as a result of their unique ability to bind many common MHC class I molecules. Finally, we propose that mutations derived from splicing defects present in SF3B1-mutated patients may offer an unexplored neoantigen repertoire in MPNs. We validated 35 predicted peptides to be strong MHC class I binders through direct binding of predicted peptides to MHC proteins in vitro. Our results may serve as a resource for personalized vaccine or adoptive cell–based therapy development.

Neoantigens in Hematologic Malignancies

“…Whole genome and whole exome sequencing of hematologic malignancies (78)(79)(80)(81)(82)(83)(84)(85) has revealed the spectrum of fusions and mutations (also referred to as the mutanome) of these diseases, including events that range from rare to highly recurrent. Many of these genetic abnormalities may give rise to neoantigens.…”

“…Mutanomes provide a rich source of cancerspecific aberrant amino acid sequences that can be interrogated with HLA-binding prediction algorithms to identify candidate neoantigens (70). However, with the exception of one study in the myeloproliferative neoplasms (MPNs) (85), the mutanomes of hematologic malignancies have not yet been thoroughly explored as sources of neoantigens. Another source of both public and personal candidate neoantigens is the HLA peptidome, which is the comprehensive library of peptides eluted from HLA molecules isolated from malignant primary cells and/or cell lines and characterized by mass spectrometry.…”

The Genomic Landscape of Antigenic Targets for T Cell-Based Leukemia Immunotherapy

“…Remarkably, none of the 1,888 predicted exonic mTSAs were detected by MS analyses (20). In view of this, the exciting claim that exonic mTSAs can be found in myeloproliferative neoplasms and childhood acute lymphoblastic leukemia must be met with enthusiasm and skepticism since no MS validation was performed on the predicted TSAs (45,46).…”

Modification of the Histone Landscape with JAK Inhibition in Myeloproliferative Neoplasms

“…A signature of methylation age is different between MPN disease phenotypes and can be modified by therapy [21]. Many genes involved in DNA methylation or regulation of histone modification are recurrently mutated in MPN and myeloid malignancy more generally including TET2, DNMT3A, ASXL1 and EZH2 [22,23]. Dysregulation of histone modification in MPN has been demonstrated [24].…”