Kelly Lim

Somatic frameshift mutations in the gene encoding calreticulin (CALR) give rise to myelofibrosis and are classified as type 1 (del52) or type 2 (ins5) according to the degree of wild-type sequence retained adjacent to the neopeptide, with each type conferring different clinical outcomes. Targeting strategies specific for type 1 vs type 2 mutations would have enormous clinical utility in the treatment and prevention of myelofibrosis as responses to tyrosine kinase inhibitors are not durable nor mutation specific. Here, we show that dual targeting of type 1 (del52) mutant CALR with 2 monoclonal antibodies directed against distinct epitopes in CALR have significant advantages compared with single-agent treatment in the eradication of primary megakaryocyte progenitors in vitro and in a humanized ossicle microenvironment leading to improved survival in xenograft models. Dual targeting was superior in blocking constitutive STAT5 and extracellular signal-regulated kinase phosphorylation induced by del52 and prevented accumulation of Janus kinase 2 (JAK2) phosphorylation, overcoming ruxolitinib resistance. In contrast, type 2 mutations showed increased CALR dimerization and were partially resistant to antibody targeting but could be affected by a ruxolitinib triple combination. Together, our data demonstrate an ultraprecision medicine approach tailored to either type 1 or type 2 mutation classes will be required for maximal efficacy and complete blockade of JAK/STAT signaling, with far-reaching implications for patient management.

Table S1 showing AML primary cell details for metabolomics

Supplementary Figure file showing Figures S1-S7

Chronic myelomonocytic leukemia (CMML) is a rare blood cancer of older adults (3 in every 1,000,000 persons) characterized by poor survival and lacking effective mutation-specific therapy. Mutations in the ubiquitin ligase Cbl occur frequently in CMML and share biological and molecular features with a clonal disease occurring in children, juvenile myelomonocytic leukemia (JMML). Here we analyzed the clinical presentations, molecular features and immunophenotype of CMML patients with CBL mutations enrolled in a prospective Phase II clinical trial stratified according to molecular markers. Clinically, CBL mutations were associated with increased bone marrow blasts at diagnosis, leukocytosis and splenomegaly, similar to patients harboring NRAS or KRAS mutations. Interestingly, 64% of patients presented with more than one CBL variant implying a complex subclonal architecture, often with co-occurrence of TET2 mutations. We found CBL mutations in CMML frequently clustered in the RING domain in contrast to JMML, where mutations frequently involve the linker helix region (P+ stem and progenitor cells expressing CD116 and CD131 in all CBL mutant cases and increased CD116 receptor density compared to healthy controls, similar to CMML overall. In summary, our data demonstrate that CBL mutations are associated with distinct molecular and clinical features in CMML and are potentially targetable with CD116-directed immunotherapy.

High prevalence of IDH mutations in seronegative rheumatoid arthritis (RA) with myeloid neoplasm, elevated 2-hydroxyglutarate, dysregulated innate immunity, and proinflammatory microenvironment suggests causative association between IDH mutations and seronegative RA. Our findings merit investigation of IDH inhibitors as therapeutics for seronegative IDH-mutated RA.

Supplementary Figure 1. IDH2 is mutated in preleukemic hematopoietic stem cells in relapse causing clones in AML. Supplementary Figure 2. Single-cell RNA sequencing and combined genotyping reveal distinct transcriptomic profiles of IDH1-mutant pHSCs in AML Supplementary Figure 3. Modeling human pHSCs using CRISPR/Cas9 with HDR show reduced proliferation and blocked differentiation caused by IDH1 mutations Supplementary Figure 4. IDH1 mutations reduce 5-hydroxymethylcytosine in gene bodies Supplementary Figure 5. IDH1 mutations drives transcriptomic alterations Supplementary Figure 6. IDH1-mutant pHSCs are sensitive to inhibition of oxidative phosphorylation

Supplementary Table 1. Clinical characteristics of the 17 IDH-mutant AML patients assessed. Supplementary Table 2. Summary of antibodies and flow cytometry reagents.

Supplementary Figure 1. IDH2 is mutated in preleukemic hematopoietic stem cells in relapse causing clones in AML. Supplementary Figure 2. Single-cell RNA sequencing and combined genotyping reveal distinct transcriptomic profiles of IDH1-mutant pHSCs in AML Supplementary Figure 3. Modeling human pHSCs using CRISPR/Cas9 with HDR show reduced proliferation and blocked differentiation caused by IDH1 mutations Supplementary Figure 4. IDH1 mutations reduce 5-hydroxymethylcytosine in gene bodies Supplementary Figure 5. IDH1 mutations drives transcriptomic alterations Supplementary Figure 6. IDH1-mutant pHSCs are sensitive to inhibition of oxidative phosphorylation

Rare preleukemic hematopoietic stem cells (pHSC) harboring only the initiating mutations can be detected at the time of acute myeloid leukemia (AML) diagnosis. pHSCs are the origin of leukemia and a potential reservoir for relapse. Using primary human samples and gene editing to model isocitrate dehydrogenase 1 (IDH1) mutant pHSCs, we show epigenetic, transcriptional, and metabolic differences between pHSCs and healthy hematopoietic stem cells (HSC). We confirm that IDH1-driven clonal hematopoiesis is associated with cytopenia, suggesting an inherent defect to fully reconstitute hematopoiesis. Despite giving rise to multilineage engraftment, IDH1-mutant pHSCs exhibited reduced proliferation, blocked differentiation, downregulation of MHC class II genes, and reprogramming of oxidative phosphorylation metabolism. Critically, inhibition of oxidative phosphorylation resulted in the complete eradication of IDH1-mutant pHSCs but not IDH2-mutant pHSCs or wild-type HSCs. Our results indicate that IDH1-mutant preleukemic clones can be targeted with complex I inhibitors, offering a potential strategy to prevent the development and relapse of leukemia.Significance:A high burden of pHSCs is associated with worse overall survival in AML. Using single-cell sequencing, metabolic assessment, and gene-edited human models, we find human pHSCs with IDH1 mutations to be metabolically vulnerable and sensitive to eradication by complex I inhibition.See related commentary by Steensma, p. 83.This article is featured in Selected Articles from This Issue, p. 80