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 4

The FBXO11-NPM1 nexus is perturbed in the MDS HSPC proteome.

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The FBXO11-NPM1 nexus is perturbed in the MDS HSPC proteome. (A) Workflo...
(A) Workflow to isolate CD34+ cell fractions from healthy donor (n = 6) and MDS patient (n = 13) samples, to normalize to 25,000 live cells per replicate tube, and perform total quantitative proteomics by DIA of peptide spectra. Illustration was created in BioRender.com. (B) Volcano plot of differentially detected proteins in MDS samples versus healthy controls. Each data point indicates 1 protein, with coordinates reflecting the –log10 of the P value against its log2FC for patients with MDS (n = 13) versus healthy donors (n = 6). Color-coding indicates a P value cutoff of less than 0.05 and a log2FC cutoff >|0.5|. (C) Heatmap of the top 400 differentially expressed proteins in MDS versus healthy controls. Unsupervised hierarchical clustering of patient samples was performed using ClustVis. Each column represents 1 replicate tube from the indicated patient samples below the map. R1, run 1; R2, run 2. (D) GO molecular function analysis of cluster 2 proteins, the largest cluster downregulated in MDS. (E) GO molecular function analysis of cluster 8 proteins, the largest cluster upregulated in MDS. (F) Schematic depicting the data integration performed using Cytoscape to quantify the FBXO11 interactome in primary MDS HSPCs. Schematic was created in BioRender.com. (G) Resultant data visualization of the integrated proteomics analysis performed in F. Blue indicates down in MDS; red indicates up in MDS. (H) Normalized enrichment scores from GSEA of the significantly differentially expressed proteins in the MDS proteome versus healthy controls.