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Targeting eIF4A-dependent translation in genetically complex sarcoma
Young-Mi Kim, Prathibha Mohan, Urmila Sehrawat, Evan Seffar, Rafaela Muniz De Queiroz, Kalyani Chadalavada, Nikita Persaud, Tomoyo Okada, Anirudh Kulkarni, Jianan Lin, Nathalie Lailler, Shaleigh Smith, Bhumika Jadeja, Nicholas D. Socci, Zhengqing Ouyang, Hans-Guido Wendel, Samuel Singer
Young-Mi Kim, Prathibha Mohan, Urmila Sehrawat, Evan Seffar, Rafaela Muniz De Queiroz, Kalyani Chadalavada, Nikita Persaud, Tomoyo Okada, Anirudh Kulkarni, Jianan Lin, Nathalie Lailler, Shaleigh Smith, Bhumika Jadeja, Nicholas D. Socci, Zhengqing Ouyang, Hans-Guido Wendel, Samuel Singer
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Research Article Cell biology Oncology

Targeting eIF4A-dependent translation in genetically complex sarcoma

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Abstract

Dedifferentiated liposarcoma (DDLS), myxofibrosarcoma (MFS), and undifferentiated pleomorphic sarcoma (UPS) are the most common types of genetically complex sarcoma. There is an urgent need to develop effective targeted therapy for these deadly sarcoma types. Despite their genetic complexity, these sarcomas share genomic alterations causing PI3K/Akt/mTOR and MAPK pathway activation, and both pathways control translation mediated by the RNA helicase eIF4A. We therefore investigated eIF4A inhibition as a therapeutic strategy. The eIF4A inhibitor CR-1-31B effectively suppressed tumor growth and induced apoptosis in DDLS, MFS, and UPS patient–derived cell lines and mouse xenografts. Transcriptome-scale ribosome footprinting identified eIF4A-dependent mRNAs such as the Hippo pathway transcriptional coactivators YAP1 (YAP) and WWTR1 (TAZ). Combined knockdown of YAP and TAZ induced apoptosis in DDLS, MFS, and UPS cell lines, and their ectopic expression partially rescued cells from apoptosis induced by CR-1-31B. Genomic analysis of patient tumors revealed that YAP and WWTR1 were frequently amplified or gained in DDLS, MFS, and UPS and were associated with worse clinical outcomes. Together, our findings identify a strategy for targeting the Hippo pathway in incurable forms of sarcoma based on inhibition of eIF4A-dependent translation of the key oncogenic transcription factors YAP and TAZ.

Authors

Young-Mi Kim, Prathibha Mohan, Urmila Sehrawat, Evan Seffar, Rafaela Muniz De Queiroz, Kalyani Chadalavada, Nikita Persaud, Tomoyo Okada, Anirudh Kulkarni, Jianan Lin, Nathalie Lailler, Shaleigh Smith, Bhumika Jadeja, Nicholas D. Socci, Zhengqing Ouyang, Hans-Guido Wendel, Samuel Singer

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Figure 2

Ribosome footprinting identifies eIF4A-dependent mRNAs in DDLS cells.

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Ribosome footprinting identifies eIF4A-dependent mRNAs in DDLS cells.
(A...
(A) Schematic of the ribosome footprinting assay. (B) Frequency distribution of changes in translation efficiency (TE) between control and [-]CR-1-31B–treated samples. n = 3 replicates. (C) Genes for which TE was decreased by [-]CR-1-31B ranked by significance (q < 0.01). (D) Western blots for YAP, TAZ, and TEAD1 in DDLS cells treated with [-]CR-1-31B. (E) Comparison of 5′-UTR lengths between TE upregulated, background, and TE downregulated genes. Statistical significance determined by Wilcoxon rank-sum test. (F) Two 12-mer (CGG)4 and (GAG)4 sequences significantly enriched in genes for which TE was decreased by [-]CR-1-31B. Relative letter size indicates the frequency of each amino acid. (G) Proportion of genes containing predicted 5′-UTR G-quadruplex (GQ) structures in genes for which TE was decreased, increased, and unaffected by [-]CR-1-31B. Statistical significance determined by Fisher’s exact test. (H) Positions of GQ sequences in the 5′-UTRs of YAP, TAZ, and TEAD1 mRNAs; vinculin included as a comparison. (I) Schematic representation of the dual-luciferase reporter vector showing gene-specific 5′-UTR–mediated firefly luciferase expression. The 4 dual-luciferase reporters represent the 5′-UTR of β-globin (negative control), c-MYC (positive control), TAZ WT (with 1 GQ close to the AUG), and TAZ mutant with a mutated GQ, respectively. HCV IRES-driven expression of Renilla luciferase is independent of eIF4A and is used to normalize transfection efficiencies. (J) Effects of CR31B on Firefly luciferase activity using the reporters in I. Statistical significance determined by unpaired 2-tailed Student’s t test. ***P < 0.001.

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