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SMARCA4 biology in alveolar rhabdomyosarcoma

Oncogene volume 41, pages 1647–1656 (2022)Cite this article

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Abstract

Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in children and phenocopies a muscle precursor that fails to undergo terminal differentiation. The alveolar subtype (ARMS) has the poorest prognosis and represents the greatest unmet medical need for RMS. Emerging evidence supports the role of epigenetic dysregulation in RMS. Here we show that SMARCA4/BRG1, an ATP-dependent chromatin remodeling enzyme of the SWI/SNF complex, is prominently expressed in primary tumors from ARMS patients and cell cultures. Our validation studies for a CRISPR screen of 400 epigenetic targets identified SMARCA4 as a unique factor for long-term (but not short-term) tumor cell survival in ARMS. A SMARCA4/SMARCA2 protein degrader (ACBI-1) demonstrated similar long-term tumor cell dependence in vitro and in vivo. These results credential SMARCA4 as a tumor cell dependency factor and a therapeutic target in ARMS.

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Fig. 1: CRISPR epigenome screen for mouse sarcoma cell cultures.
Fig. 2: SMARCA2/4 expression in ARMS, ERMS primary tumors and cell lines.
Fig. 3: Short-term knockdown of SMARCA4 using siRNA only partially compromises cell viability of human ARMS cell lines.
Fig. 4: Suppression of SMARCA4 inhibits both anchorage-independent and dependent colony-forming ability of ARMS cells.
Fig. 5: A SMARCA4/A2 protein degrader requires long-term exposure for cellular effect in RMS.

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Acknowledgements

We thank Dr. Manfred Kögl for generously providing vectors LMH-SMARCA2 and LMH-PBRM1. This study was funded by Braver Stronger Smarter Foundation, Maddie’s Promise Foundation and by NIH grants R01CA189299 & R01CA258720. The ACBI-1 PROTAC degrader was developed with funding support to the Ciulli Laboratory by Boehringer Ingelheim. CRV was supported by the Pershing Square Sohn Cancer Research Alliance, Northwell Health Translational Research Award, The Christina Renna Foundation, The Clark Gillies Foundation, The Friends of T.J. Foundation, The Michelle Paternoster Foundation, and a grant from National Cancer Institute (CA2455859). DS was supported by the Indo-U.S. GETin program from Department of Biotechnology (DBT), Govt. of India and Indo-U.S. Science and Technology Forum (IUSSTF).

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Author notes

  1. Narendra Bharathy

    Present address: Gene Therapy Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA

  2. These authors contributed equally: Narendra Bharathy, Megan M. Cleary.

Authors and Affiliations

  1. Children’s Cancer Therapy Development Institute, Beaverton, OR, 97005, USA

    Narendra Bharathy, Megan M. Cleary, Jin-Ah Kim, Kiyo Nagamori, Kenneth A. Crawford, Debarya Saha, Teagan P. Settelmeyer, Reshma Purohit, Jessica A. Doran, C. Ward Kirschbaum, Suriya Bharathy, Davis W. Crews, Matthew E. Randolph, Lisa Hudson-Price & Charles Keller

  2. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA

    Eric Wang, Damianos Skopelitis, Kenneth Chang & Christopher R. Vakoc

  3. CSIR-CCMB, Uppal Road, Hyderabad, 500007, India

    Debarya Saha & Jyotsna Dhawan

  4. University of California C Davis Medical Center, Sacramento, CA, 95817, USA

    Anthony N. Karnezis

  5. British Columbia Cancer Research Center, Vancouver, BC, V5Z 1L3, Canada

    Anthony N. Karnezis

  6. Department of Epidemiology and Biostatistics, University of Texas Health Science Center, San Antonio, TX, 78229, USA

    Joel E. Michalek

  7. Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK

    Alessio Ciulli

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Contributions

NB, JD, WK, SB, DS and CK designed the study; NB, JD, WK, EW, MER, TPS, DS, KC, RP, KN, MMC and ANK performed experiments; NB, MMC, JD, WK, CK, DS, JD, CRV and KN analyzed and interpreted data; EM and LHP performed statistical analysis; NB and CK wrote the manuscript; CK directed studies.

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Correspondence to Alessio Ciulli or Charles Keller.

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Competing interests

The Ciulli Laboratory receives or has received funding from Almirall, Amphista Therapeutics, Boehringer Ingelheim, Eisai, Nurix, and Ono Pharmaceuticals. AC is a scientific founder, shareholder, and consultant of Amphista Therapeutics, a company that is developing targeted protein degradation therapeutic platforms. CK is co-founder of Artisan Biopharma, a public benefit corporation pediatric cancer biopharma, as well as Tio Companies, and has received unrestricted grant support from Syndax Pharmaceuticals. CK also has research agreements with Roche/Genentech and Eli Lilly. All other authors declare no competing interests.

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Bharathy, N., Cleary, M.M., Kim, JA. et al. SMARCA4 biology in alveolar rhabdomyosarcoma. Oncogene 41, 1647–1656 (2022). https://doi.org/10.1038/s41388-022-02205-0

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