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Pharmacological and genomic profiling identifies NF-κB–targeted treatment strategies for mantle cell lymphoma

Abstract

Mantle cell lymphoma (MCL) is an aggressive malignancy that is characterized by poor prognosis1. Large-scale pharmacological profiling across more than 100 hematological cell line models identified a subset of MCL cell lines that are highly sensitive to the B cell receptor (BCR) signaling inhibitors ibrutinib and sotrastaurin. Sensitive MCL models exhibited chronic activation of the BCR-driven classical nuclear factor-κB (NF-κB) pathway, whereas insensitive cell lines displayed activation of the alternative NF-κB pathway. Transcriptome sequencing revealed genetic lesions in alternative NF-κB pathway signaling components in ibrutinib-insensitive cell lines, and sequencing of 165 samples from patients with MCL identified recurrent mutations in TRAF2 or BIRC3 in 15% of these individuals. Although they are associated with insensitivity to ibrutinib, lesions in the alternative NF-κB pathway conferred dependence on the protein kinase NIK (also called mitogen-activated protein 3 kinase 14 or MAP3K14) both in vitro and in vivo. Thus, NIK is a new therapeutic target for MCL treatment, particularly for lymphomas that are refractory to BCR pathway inhibitors. Our findings reveal a pattern of mutually exclusive activation of the BCR–NF-κB or NIK–NF-κB pathways in MCL and provide critical insights into patient stratification strategies for NF-κB pathway–targeted agents.

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Figure 1: Pharmacological profiling reveals chronic CBM complex activation in a subset of MCL cell lines.
Figure 2: IKK–NF-κB signaling is essential in all MCL cell lines.
Figure 3: RNA-seq identifies alternative NF-κB pathway lesions in ibrutinib/STN-insensitive MCL cell lines.
Figure 4: The alternative NF-κB pathway is genetically deregulated in samples from patients with MCL.

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Acknowledgements

We thank T. Haferlach and W. Kern from the Munich Leukemia Laboratory (MLL) for providing MCL samples. We thank N. Clipstone (Loyola University) for the pMSCV-IRES-GFP vector. We also thank M. Wartmann, M. Stump, T. Hood and S. Zhu for sharing technical advice. We are grateful to D. Weinstock, R. Pagliarini, D. Porter, S. Sharma, N. Wilson and N. Keen for their critical reading of this manuscript. All authors except M.F., R.K., F.C.C., B.M., K.D., B.D., C.S., A.T., M.H., R.D.G. and G.L. are employees of Novartis Institutes for Biomedical Research. This work was supported by research grants to G.L. from the Else Kröner-Fresenius-Stiftung, the German Research Foundation and the Deutsche Krebshilfe. Additionally, this work was supported by a New Frontiers in Cancer Terry Fox program project grant (19001) to R.D.G. and a Career Investigator award by the Michael Smith Foundation for Health Research to C.S. R.K. is a recipient of fellowships from the Canadian Institutes of Health Research, the Michael Smith Foundation for Health Research and the University of British Columbia (Four Year Fellowship).

Author information

Authors and Affiliations

Authors

Contributions

R. Rahal, M.F., W.R.S., G.L. and F.S. designed experiments and wrote the manuscript. R. Rahal, M.F., K.D. and R. Romero conducted in vitro experiments. H.B. and V.G.C. designed and conducted in vivo experiments. C.F., A.K., R. Rahal and F.S. designed the pharmacological screen. A.F., E.P. and R. Romero conducted the experiments. D. Ruddy and D. Rakiec performed RNA-seq experiments with input from A.D., J.M. and M.P.M. J.M.K. developed the methods to analyze RNA-seq data. T.N., S. Kovats and S. Kim contributed to the initial finding of the sensitivity of MCL to ibrutinib/STN. R.K., F.C.C., B.M. and R.D.G. designed, performed and analyzed targeted sequencing studies on samples from patients with MCL. C.S., B.D., A.T. and M.H. provided and characterized patient samples.

Corresponding authors

Correspondence to Georg Lenz or Frank Stegmeier.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–8 (PDF 8633 kb)

Supplementary Table 1

1A: Pharmacological profiling of 119 lymphoma and leukemia cell lines 1B: Pharmacological profiling of MCL cell lines (XLS 281 kb)

Supplementary Table 2

Gene modulated by AFN700 treatment (XLSX 6357 kb)

Supplementary Table 3

Nucleotide variants identified by RNA-seq , related to Figure 3 (XLS 5052 kb)

Supplementary Table 4

RPKM values derived from RNA-seq, related to Figure 3 (XLS 8224 kb)

Supplementary Table 5

Maver-1 copy number analysis by SNP 6.0 arrays (XLS 4946 kb)

Supplementary Table 6

Genes downregulated upon knockdown of NIK in both Z-138 and Maver-1 cells (XLS 39 kb)

Supplementary Table 7

Mutation calls in BIRC2, BIRC3, TRAF2, TRAF3 and MAP3K14 for 165 primary patient samples and 3 cell lines (XLS 46 kb)

Supplementary Table 8

shRNA sequences used in the study (XLS 33 kb)

Supplementary Table 9

Primary antibodies used in the study (XLS 32 kb)

Supplementary Table 10

Quantitative PCR probes used in the study (XLS 24 kb)

Supplementary Table 11

PCR primers used in the study (XLS 24 kb)

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Rahal, R., Frick, M., Romero, R. et al. Pharmacological and genomic profiling identifies NF-κB–targeted treatment strategies for mantle cell lymphoma. Nat Med 20, 87–92 (2014). https://doi.org/10.1038/nm.3435

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