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CHRONIC MYELOPROLIFERATIVE NEOPLASMS

CALR-mutated cells are vulnerable to combined inhibition of the proteasome and the endoplasmic reticulum stress response

Abstract

Cancer is driven by somatic mutations that provide a fitness advantage. While targeted therapies often focus on the mutated gene or its direct downstream effectors, imbalances brought on by cell-state alterations may also confer unique vulnerabilities. In myeloproliferative neoplasms (MPN), somatic mutations in the calreticulin (CALR) gene are disease-initiating through aberrant binding of mutant CALR to the thrombopoietin receptor MPL and ligand-independent activation of JAK-STAT signaling. Despite these mechanistic insights into the pathogenesis of CALR-mutant MPN, there are currently no mutant CALR-selective therapies available. Here, we identified differential upregulation of unfolded proteins, the proteasome and the ER stress response in CALR-mutant hematopoietic stem cells (HSCs) and megakaryocyte progenitors. We further found that combined pharmacological inhibition of the proteasome and IRE1-XBP1 axis of the ER stress response preferentially targets Calr-mutated HSCs and megakaryocytic-lineage cells over wild-type cells in vivo, resulting in an amelioration of the MPN phenotype. In serial transplantation assays following combined proteasome/IRE1 inhibition for six weeks, we did not find preferential depletion of Calr-mutant long-term HSCs. Together, these findings leverage altered proteostasis in Calr-mutant MPN to identify combinatorial dependencies that may be targeted for therapeutic benefit and suggest that eradicating disease-propagating Calr-mutant LT-HSCs may require more sustained treatment.

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Fig. 1: The IRE1a-XBP1 axis of the unfolded protein response and the proteasome are upregulated in CALRΔ52 stem cells.
Fig. 2: CALRΔ52 cells are differentially vulnerable to depletion of the proteasome and UPR-associated pathways.
Fig. 3: Treatment with the proteasome inhibitor bortezomib induces apoptotic priming and decreases platelet counts in CalrΔ52/+ mice.
Fig. 4: CalrΔ52/+ myeloid cells are sensitive to the inhibition of the proteasome in chimeric mice treated with bortezomib.
Fig. 5: Combined proteasomal and IRE1a inhibition synergizes in killing CALRΔ52 mutant cells.
Fig. 6: Combined inhibition of the proteasome and the IRE1a-XBP1s axis of the UPR preferentially targets CalrΔ52/+ cells.

Data availability

All data generated or analyzed during this study are either included in this published paper [and its supplementary information files] or will be made available upon request.

The long-term hematopoietic stem cell RNA-sequencing data set generated and analyzed during the current study will be made available (GEO accession number in generation). The Genotype of Transcriptome dataset analyzed during the current study is available in the GEO repository, accession ID: GSE117826. Databank URL:

The whole-genome CRISPR depletion screen dataset analyzed during the current study is available in the GEO repository, accession ID: GSE203456

Token: klipmmwivtsnvyn.

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Acknowledgements

The authors thank Professor Anthony Green (University of Cambridge, UK) for sharing mutant Calr knockin mice. The Sysmex veterinary hematology analyzer instrument is a generous loan from Sysmex. We thank Dr. Martha Sola-Visner and her lab members Michael Zhang and Dr. Patricia Davenport (Boston Children’s Hospital) for kindly sharing Sysmex equipment for complete blood counts. The authors appreciate the technical support by the BCH Flow lab, namely by Mahnaz Paktinat and Ronald Mathieu as well as by the BWH CCM veterinary staff. JSJ acknowledges funding from the German Research Foundation (DFG, JU 3104/2-1). JSJ is a Special Fellow of The Leukemia & Lymphoma Society (3415-22). AEM receives funding from the US Department of Defense (Horizon Award W81XWH-20-1-0904). BJ is a recipient of the Mildred-Scheel Scholarship from German Cancer Aid (70114570). This work was supported in part by grants from the National Cancer Institute (NCI) Clinical Proteomic Tumor Analysis Consortium grants NIH/NCI U24-CA210986 and NIH/NCI U01 CA214125 (to SAC). YH acknowledges funding support from the Australian Research Council FT210100271. ASN is supported by the Burroughs Wellcome Fund Career Award for Medical Scientists, the National Institutes of Health Director’s Early Independence Award (DP5 OD029619-01), and the Starr Cancer Consortium (I15-0026). AM acknowledges funding from NIH NHLBI (R01HL131835), the Gabrielle’s Angel Foundation for Cancer Research (GAFCR), and the Starr Cancer Consortium (I15-0026). AM is a Scholar of The Leukemia & Lymphoma Society.

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JSJ was responsible for designing the project, conducting the research, extracting and analyzing data, interpreting results, and writing the paper. AEM was responsible for designing the project, conducting the research, extracting and analyzing data, interpreting results, and editing the paper. MJJS was responsible for extracting and analyzing data and interpreting results. JH was responsible for conducting the research and analyzing data. AGM was responsible for conducting the research, extracting and analyzing data, and interpreting results. BR was responsible for conducting the research and analyzing data. SB was responsible for conducting the research and analyzing data. SAM was responsible for conducting the research and analyzing data. SAC was responsible for designing research and supervision. YH was responsible for providing essential material and method support. PvG was responsible for designing research, supervision, and interpreting of results and editing the paper. SEE was responsible for conducting the research extracting and analyzing data, and interpreting results. FAS was responsible for designing research, supervision, and interpreting of results. AN was responsible for designing research, extracting and analyzing data, and interpreting of results and editing the paper. AM was responsible for designing the project, supervision of the project, interpreting results, and writing the paper.

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Correspondence to Ann Mullally.

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SAC is a member of the scientific advisory boards of Kymera, PTM BioLabs, Seer and PrognomIQ. AM receives research funding from Relay Therapeutics. AM has consulted for Janssen, PharmaEssentia, Actuate, Constellation, Aclaris Cellarity, Morphic, BioMarin, Protagonist and Incyte. AM has received research funding from Janssen and Actuate Therapeutics.

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Jutzi, J.S., Marneth, A.E., Jiménez-Santos, M.J. et al. CALR-mutated cells are vulnerable to combined inhibition of the proteasome and the endoplasmic reticulum stress response. Leukemia (2022). https://doi.org/10.1038/s41375-022-01781-0

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