Myo-differentiation reporter screen reveals NF-Y as an activator of PAX3-FOXO1 in rhabdomyosarcoma

Sroka, Martyna W, Skopelitis, Damianos, Vermunt, Marit W, Preall, Jonathan B, El Demerdash, Osama, de Almeida, Larissa MN, Chang, Kenneth, Utama, Raditya, Gryder, Berkley, Caligiuri, Giuseppina, Ren, Diqiu, Nalbant, Benan, Milazzo, Joseph P, Tuveson, David A, Dobin, Alexander, Hiebert, Scott W, Stengel, Kristy R, Mantovani, Roberto, Khan, Javed, Kohli, Rahul M, Shi, Junwei, Blobel, Gerd A, Vakoc, Christopher R (September 2023) Myo-differentiation reporter screen reveals NF-Y as an activator of PAX3-FOXO1 in rhabdomyosarcoma. Proceedings of the National Academy of Sciences of USA, 120 (36). e2303859120. ISSN 0027-8424 (Public Dataset)

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Abstract

Recurrent chromosomal rearrangements found in rhabdomyosarcoma (RMS) produce the PAX3-FOXO1 fusion protein, which is an oncogenic driver and a dependency in this disease. One important function of PAX3-FOXO1 is to arrest myogenic differentiation, which is linked to the ability of RMS cells to gain an unlimited proliferation potential. Here, we developed a phenotypic screening strategy for identifying factors that collaborate with PAX3-FOXO1 to block myo-differentiation in RMS. Unlike most genes evaluated in our screen, we found that loss of any of the three subunits of the Nuclear Factor Y (NF-Y) complex leads to a myo-differentiation phenotype that resembles the effect of inactivating PAX3-FOXO1. While the transcriptomes of NF-Y- and PAX3-FOXO1-deficient RMS cells bear remarkable similarity to one another, we found that these two transcription factors occupy nonoverlapping sites along the genome: NF-Y preferentially occupies promoters, whereas PAX3-FOXO1 primarily binds to distal enhancers. By integrating multiple functional approaches, we map the PAX3 promoter as the point of intersection between these two regulators. We show that NF-Y occupies CCAAT motifs present upstream of PAX3 to function as a transcriptional activator of PAX3-FOXO1 expression in RMS. These findings reveal a critical upstream role of NF-Y in the oncogenic PAX3-FOXO1 pathway, highlighting how a broadly essential transcription factor can perform tumor-specific roles in governing cellular state.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > CCCTC-binding factor diseases & disorders > cancer diseases & disorders bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification organs, tissues, organelles, cell types and functions > cell types and functions > cell functions > cell differentiation organs, tissues, organelles, cell types and functions > cell types and functions > cell functions organs, tissues, organelles, cell types and functions > cell types and functions organs, tissues, organelles, cell types and functions > cell types and functions > cell functions > differentiation bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > transcription factor > NF-Y organs, tissues, organelles, cell types and functions bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > PAX3-FOXO1 bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types diseases & disorders > cancer > cancer types > rhabdomyosarcoma bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > transcription factor diseases & disorders > cancer > cancer types
CSHL Authors:	Sroka, Martyna Skopelitis, Damianos Preall, Jonathan El Demerdash, Osama Chang, Kenneth Utama, Raditya Caligiuri, Giuseppina Milazzo, Joseph Tuveson, David A. Dobin, Alexander Vakoc, Christopher R. de Almeida, Larissa M N
Communities:	CSHL Cancer Center Program CSHL Cancer Center Program > Cancer Genetics and Genomics Program CSHL Cancer Center Program > Cellular Communication in Cancer Program CSHL Cancer Center Shared Resources > Animal Tissue and Imaging Service CSHL Cancer Center Shared Resources > Flow Cytometry Service CSHL Cancer Center Shared Resources > Microscopy Service CSHL Cancer Center Shared Resources > Next Generation Sequencing Service CSHL Cancer Center Shared Resources > Single-Cell Biology Service CSHL labs > Chang lab CSHL labs > Preall lab CSHL labs > Tuveson lab CSHL labs > Vakoc lab CSHL labs > Dobin Lab School of Biological Sciences > Publications
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	5 September 2023
Date Deposited:	12 Sep 2023 16:50
Last Modified:	29 Feb 2024 19:23
PMCID:	PMC10483665
Related URLs:	Publisher
Dataset ID:	GEO: GSE227603 GEO: GSE227594 GEO: GSE227595 GEO: GSE227596 GEO: GSE227597 GEO: GSE227600 GEO: GSE116344 GEO: GSE120770
URI:	https://repository.cshl.edu/id/eprint/40898

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