FBXO11 suppression rewires an NPM1-centered interactome influencing the progression of myelodysplastic syndrome
Madeline Niederkorn, Lavanya Bezavada, Anitria Cotton, Lance E. Palmer, Lahiri Konada, Trent Hall, Vishwajeeth R. Pagala, Jinbin Zhai, Zuo-Fei Yuan, Yingxue Fu, Jacob A. Steele, Shilpa Narina, Andrew Schild, Chengzhou Wu, Sarah Aminov, Michael Schieber, Erin McGovern, Aaron B. Taylor, Sandeep Gurbuxani, Peng Xu, Peng Ji, Laura J. Janke, Anthony A. High, Guolian Kang, Shondra M. Pruett-Miller, Mitchell Weiss, Amit Verma, Raajit K. Rampal, John D. Crispino
Madeline Niederkorn, Lavanya Bezavada, Anitria Cotton, Lance E. Palmer, Lahiri Konada, Trent Hall, Vishwajeeth R. Pagala, Jinbin Zhai, Zuo-Fei Yuan, Yingxue Fu, Jacob A. Steele, Shilpa Narina, Andrew Schild, Chengzhou Wu, Sarah Aminov, Michael Schieber, Erin McGovern, Aaron B. Taylor, Sandeep Gurbuxani, Peng Xu, Peng Ji, Laura J. Janke, Anthony A. High, Guolian Kang, Shondra M. Pruett-Miller, Mitchell Weiss, Amit Verma, Raajit K. Rampal, John D. Crispino
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Research Article Hematology Oncology

FBXO11 suppression rewires an NPM1-centered interactome influencing the progression of myelodysplastic syndrome

Abstract

Myelodysplastic syndromes (MDSs) are malignant hematopoietic stem and progenitor cell (HSPC) disorders that lead to ineffective blood production with poor outcomes. We previously showed that F-box only protein 11 (FBXO11) is downregulated in MDS, and here we report how this event contributes to disease progression. Integration of multiomics data revealed that the SCF-FBXO11 complex regulates spliceosome and ribosome components in a nucleophosmin 1 (NPM1)-centric network. FBXO11 facilitates the ubiquitylation of NPM1, whereby deletion of FBXO11 results in the reorganization of NPM1 and a de-repression of alternative splicing. Label-free total quantitative proteomics demonstrated that the FBXO11-NPM1 interactome was markedly downregulated in cells from patients with CD34+ MDS. In addition, we discovered that MYC was evicted from the FBXO11 promoter by TLR2 activation, revealing that it was a MYC target gene and explaining why FBXO11 expression was decreased in MDS. In MDS mouse models, genetic ablation of Fbxo11 exacerbated neutropenia concomitant with a profound decrease in NPM1 protein levels. Finally, we discovered rare mutations in FBXO11, which mapped to a previously unstudied functional intrinsically disordered region (IDR) in the N-terminus responsible for binding NPM1. These data support a model in which FBXO11 rewires RNA binding and ribosomal subnetworks through ubiquitylation of NPM1, ultimately restricting MDS progression.

Authors

Madeline Niederkorn, Lavanya Bezavada, Anitria Cotton, Lance E. Palmer, Lahiri Konada, Trent Hall, Vishwajeeth R. Pagala, Jinbin Zhai, Zuo-Fei Yuan, Yingxue Fu, Jacob A. Steele, Shilpa Narina, Andrew Schild, Chengzhou Wu, Sarah Aminov, Michael Schieber, Erin McGovern, Aaron B. Taylor, Sandeep Gurbuxani, Peng Xu, Peng Ji, Laura J. Janke, Anthony A. High, Guolian Kang, Shondra M. Pruett-Miller, Mitchell Weiss, Amit Verma, Raajit K. Rampal, John D. Crispino

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Figure 7

Identification of FBXO11 mutations in myeloid malignancies reveals a functional N-terminal IDR.

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Identification of FBXO11 mutations in myeloid malignancies reveals a fun...
(A) Map of FBXO11 mutations identified by whole-exome sequencing of the MSK-IMPACT cohort of patients with hematologic malignancies. (B) Alpha-fold predicted structure of FBXO11 with structural features and mutations within myeloid diseases mapped in the disordered N-terminus. (C) Variant allele frequencies plotted along the amino acid residues affected by FBXO11 mutations; FBXO11 functional domains are boxed. N-term., N-terminus; ZnF-UBR, zinc finger-ubiquitin-protein ligase E3 component n-Recognin 1. (D) Prediction of intrinsically unstructured proteins 2 (IUPRED2) score of amino acid residues in FBXO11-long. The blue arrowhead indicates the initial methionine residue in FBXO11-short. (E) Representative confocal images of FBXO11-long and FBXO11-short expressed in HEK293T cells. Scale bars: 10 μm. (F) Quantification of signal distribution of FBXO11-long+ and FBXO11-short+ cells using the SD of FLAG-FBXO11 signal across each nucleus. **P < 0.01, by 2-tailed, unpaired Mann-Whitney U test. (G) GSEA analysis of RNA-Seq data (GSE156708) from MDS-L cells that were FBXO11-KO compared with MDS-L parental cells, cells with reexpression of FBXO11-long cDNA, or cells with reexpression of FBXO11-short cDNA. The size of circle indicates the number of genes in the set.