Inherited platelet disorders are a heterogeneous group of rare diseases, caused by inherited defects in platelet production and/or function. Their genetic diagnosis would benefit clinical care, prognosis and preventive treatments. Until recently, this has been performed by Sanger sequencing of a limited number of candidate genes. High-throughput sequencing is revolutionizing genetic diagnosis of diseases, including bleeding disorders. We have designed a novel high-throughput sequencing platform to investigate the unknown molecular pathology in a cohort of 82 patients with inherited platelet disorders. Thirty-four (41.5%) patients presented with a phenotype strongly indicative of a particular type of disorder. The remaining had disease with no specific manifestations. Overall, high-throughput sequencing test attained a molecular diagnosis in 70% of the patients. This sensitivity increased to 90% among patients suspected to have a defined platelet disorder. We found 58 different candidate variants in 29 genes, among which 70% were not previously described. Following consensus guidelines, we qualified 68% and 27% of the candidate variants as pathogenic and likely pathogenic, respectively. Apart from establishing definitive diagnosis of well-known inherited platelet disorders in most patients, in few others high-throughput sequencing provided molecular results suggestive of less recognized disorders, such as sitosterolemia, filamin and actinin deficiencies and abnormalities at the level of G-protein coupled receptors and effector enzymes. Noteworthy, high-throughput sequencing diagnosed novel patients with very rare molecular pathology in DIAPH1 (n=2) and RASGRP2 (n=3). Overall, our study reinforces the feasibility of introducing high-throughput sequencing technology into the mainstream of genetic diagnosis practice in inherited platelet disorders.

The majority of JAK2 ^V617F -negative myeloproliferative neoplasms (MPNs) have disease-initiating frameshift mutations in calreticulin ( CALR ), resulting in a common carboxyl-terminal mutant fragment (CALR ^MUT ), representing an attractive source of neoantigens for cancer vaccines. However, studies have shown that CALR ^MUT -specific T cells are rare in patients with CALR ^MUT MPN for unknown reasons. We examined class I major histocompatibility complex (MHC-I) allele frequencies in patients with CALR ^MUT MPN from two independent cohorts. We observed that MHC-I alleles that present CALR ^MUT neoepitopes with high affinity are underrepresented in patients with CALR ^MUT MPN. We speculated that this was due to an increased chance of immune-mediated tumor rejection by individuals expressing one of these MHC-I alleles such that the disease never clinically manifested. As a consequence of this MHC-I allele restriction, we reasoned that patients with CALR ^MUT MPN would not efficiently respond to a CALR ^MUT fragment cancer vaccine but would when immunized with a modified CALR ^MUT heteroclitic peptide vaccine approach. We found that heteroclitic CALR ^MUT peptides specifically designed for the MHC-I alleles of patients with CALR ^MUT MPN efficiently elicited a CALR ^MUT cross-reactive CD8 ⁺ T cell response in human peripheral blood samples but not to the matched weakly immunogenic CALR ^MUT native peptides. We corroborated this effect in vivo in mice and observed that C57BL/6J mice can mount a CD8 ⁺ T cell response to the CALR ^MUT fragment upon immunization with a CALR ^MUT heteroclitic, but not native, peptide. Together, our data emphasize the therapeutic potential of heteroclitic peptide–based cancer vaccines in patients with CALR ^MUT MPN.

To identify novel therapeutic targets in acute myeloid leukemia (AML), we examined kinase expression patterns in primary AML samples. We found that the serine/threonine kinase IKBKE, a noncanonical IkB kinase, is expressed at higher levels in myeloid leukemia cells compared with normal hematopoietic cells. Inhibiting IKBKE, or its close homolog TANK-binding kinase 1 (TBK1), by either short hairpin RNA knockdown or pharmacological compounds, induces apoptosis and reduces the viability of AML cells. Using gene expression profiling and gene set enrichment analysis, we found that IKBKE/TBK1-sensitive AML cells typically possess an MYC oncogenic signature. Consistent with this finding, the MYC oncoprotein was significantly downregulated upon IKBKE/TBK1 inhibition. Using proteomic analysis, we found that the oncogenic gene regulator YB-1 was activated by IKBKE/TBK1 through phosphorylation, and that YB-1 binds to the MYC promoter to enhance MYC gene transcription. Momelotinib (CYT387), a pharmacological inhibitor of IKBKE/TBK1, inhibits MYC expression, reduces viability and clonogenicity of primary AML cells, and demonstrates efficacy in a murine model of AML. Together, these data identify IKBKE/TBK1 as a promising therapeutic target in AML.

Calreticulin (CALR) mutations are frequent, disease-initiating events in myeloproliferative neoplasms (MPNs). Although the biological mechanism by which CALR mutations cause MPNs has been elucidated, there currently are no clonally selective therapies for CALR-mutant MPNs. To identify unique genetic dependencies in CALR-mutant MPNs, we performed a whole-genome clustered regularly interspaced short palindromic repeats (CRISPR) knockout depletion screen in mutant CALR-transformed hematopoietic cells. We found that genes in the N-glycosylation pathway (among others) were differentially depleted in mutant CALR-transformed cells as compared with control cells. Using a focused pharmacological in vitro screen targeting unique vulnerabilities uncovered in the CRISPR screen, we found that chemical inhibition of N-glycosylation impaired the growth of mutant CALR-transformed cells, through a reduction in MPL cell surface expression. We treated Calr-mutant knockin mice with the N-glycosylation inhibitor 2-deoxy-glucose (2-DG) and found a preferential sensitivity of Calr-mutant cells to 2-DG as compared with wild-type cells and normalization of key MPNs disease features. To validate our findings in primary human cells, we performed megakaryocyte colony-forming unit (CFU-MK) assays. We found that N-glycosylation inhibition significantly reduced CFU-MK formation in patient-derived CALR-mutant bone marrow as compared with bone marrow derived from healthy donors. In aggregate, our findings advance the development of clonally selective treatments for CALR-mutant MPNs.