Infant acute lymphoblastic leukemia (ALL) has a poor prognosis, especially with MLL gene rearrangements (MLL-r), which occur in ~80% of the patients. Genome-sequencing studies of MLL-r ALL patients have shown a very low frequency of somatic mutations, indicating that MLL may not require additional alterations to induce full transformation. However, ALL cannot be recapitulated in mouse and cell models by only integrating the fusion, suggesting that additional alterations are necessary for leukemogenesis. MLL fusions have the potential to impact the RNA processing of genes at genome scale through changes in transcriptional elongation, thereby providing a new layer of molecular variation that has remained undetected so far. We present an exhaustive analysis of the RNA-processing alterations in infant ALL samples in relation to MLL-r in more than 1000 samples integrating data from multiple studies.
We identify a clear differential expression associated to MLL-r ALL involving, among others, the splicing factors MBNL1 and PRMT5. Additionally, differential splicing is enriched in alternative first exons, in agreement with a promoter driven effect. These patterns are specific to MLL fusions and do not occur with other fusions found in infant ALL. We further present an exhaustive identification of neo-epitopes from tumor-specific splicing alterations. We validate our approach using RNA-seq data together with mass spectrometry for MHC-I associated proteins, supporting the hypothesis that splicing alterations in cancer provide a general mechanism to elicit tumor-specific immune responses. We describe the immunogenic impacts of the splicing alterations in ALL in association to MLL fusions and find that tumor-specific splicing alterations more frequently eliminate than create epitopes, hence uncovering a new mechanism of immune escape in ALL. This is the first study of RNA-processing alterations and their immunogenic impacts in association to MLL fusions in ALL and of their role in leukemogenesis.