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Murray JE, Valli E, Milazzo G, Mayoh C, Gifford AJ, Fletcher JI, Xue C, Jayatilleke N, Salehzadeh F, Gamble LD, Rouaen JRC, Carter DR, Forgham H, Sekyere EO, Keating J, Eden G, Allan S, Alfred S, Kusuma FK, Clark A, Webber H, Russell AJ, de Weck A, Kile BT, Santulli M, De Rosa P, Fleuren EDG, Gao W, Wilkinson-White L, Low JKK, Mackay JP, Marshall GM, Hilton DJ, Giorgi FM, Koster J, Perini G, Haber M, Norris MD. The transcriptional co-repressor Runx1t1 is essential for MYCN-driven neuroblastoma tumorigenesis. Nat Commun 2024; 15:5585. [PMID: 38992040 PMCID: PMC11239676 DOI: 10.1038/s41467-024-49871-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/23/2024] [Indexed: 07/13/2024] Open
Abstract
MYCN oncogene amplification is frequently observed in aggressive childhood neuroblastoma. Using an unbiased large-scale mutagenesis screen in neuroblastoma-prone transgenic mice, we identify a single germline point mutation in the transcriptional corepressor Runx1t1, which abolishes MYCN-driven tumorigenesis. This loss-of-function mutation disrupts a highly conserved zinc finger domain within Runx1t1. Deletion of one Runx1t1 allele in an independent Runx1t1 knockout mouse model is also sufficient to prevent MYCN-driven neuroblastoma development, and reverse ganglia hyperplasia, a known pre-requisite for tumorigenesis. Silencing RUNX1T1 in human neuroblastoma cells decreases colony formation in vitro, and inhibits tumor growth in vivo. Moreover, RUNX1T1 knockdown inhibits the viability of PAX3-FOXO1 fusion-driven rhabdomyosarcoma and MYC-driven small cell lung cancer cells. Despite the role of Runx1t1 in MYCN-driven tumorigenesis neither gene directly regulates the other. We show RUNX1T1 forms part of a transcriptional LSD1-CoREST3-HDAC repressive complex recruited by HAND2 to enhancer regions to regulate chromatin accessibility and cell-fate pathway genes.
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Affiliation(s)
- Jayne E Murray
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Emanuele Valli
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Giorgio Milazzo
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Chelsea Mayoh
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Andrew J Gifford
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
- Anatomical Pathology, NSW Health Pathology, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Jamie I Fletcher
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Chengyuan Xue
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Nisitha Jayatilleke
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Firoozeh Salehzadeh
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Laura D Gamble
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Jourdin R C Rouaen
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Daniel R Carter
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
- School of Biomedical Engineering, University of Technology Sydney, Broadway, NSW, Australia
| | - Helen Forgham
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Eric O Sekyere
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Joanna Keating
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Georgina Eden
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Sophie Allan
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Stephanie Alfred
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Frances K Kusuma
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Ashleigh Clark
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Hannah Webber
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Amanda J Russell
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Antoine de Weck
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Benjamin T Kile
- Monash Biomedicine Discovery Institute, Monash University, Melbourne, VIC, Australia
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Martina Santulli
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Piergiuseppe De Rosa
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Emmy D G Fleuren
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Weiman Gao
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
| | - Lorna Wilkinson-White
- Sydney Analytical Core Research Facility, The University of Sydney, Sydney, NSW, Australia
| | - Jason K K Low
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Glenn M Marshall
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, Australia
| | - Douglas J Hilton
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Federico M Giorgi
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Jan Koster
- Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Giovanni Perini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126, Bologna, Italy
| | - Michelle Haber
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia
- School of Clinical Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Murray D Norris
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, 2031, Australia.
- UNSW Centre for Childhood Cancer Research, UNSW Sydney, Sydney, NSW, Australia.
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Qin C, He X, Zhao Y, Tong CY, Zhu KY, Sun Y, Cheng C. Systematic computational identification of prognostic cytogenetic markers in neuroblastoma. BMC Med Genomics 2019; 12:192. [PMID: 31831008 PMCID: PMC6909636 DOI: 10.1186/s12920-019-0620-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 11/12/2019] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Neuroblastoma (NB) is the most common extracranial solid tumor found in children. The frequent gain/loss of many chromosome bands in tumor cells and absence of mutations found at diagnosis suggests that NB is a copy number-driven cancer. Despite the previous work, a systematic analysis that investigates the relationship between such frequent gain/loss of chromosome bands and patient prognosis has yet to be implemented. METHODS First, we analyzed two NB CNV datasets to select chromosomal bands with a high frequency of gain or loss. Second, we applied a computational approach to infer sample-specific CNVs for each chromosomal band selected in step 1 based on gene expression data. Third, we applied univariate Cox proportional hazards models to examine the association between the resulting inferred copy number values (iCNVs) and patient survival. Finally, we applied multivariate Cox proportional hazards models to select chromosomal bands that remained significantly associated with prognosis after adjusting for critical clinical variables, including age, stage, gender, and MYCN amplification status. RESULTS Here, we used a computational method to infer the copy number variations (CNVs) of sample-specific chromosome bands from NB patient gene expression profiles. The resulting inferred CNVs (iCNVs) were highly correlated with the experimentally determined CNVs, demonstrating CNVs can be accurately inferred from gene expression profiles. Using this iCNV metric, we identified 58 frequent gain/loss chromosome bands that were significantly associated with patient survival. Furthermore, we found that 7 chromosome bands were still significantly associated with patient survival even when clinical factors, such as MYCN status, were considered. Particularly, we found that the chromosome band chr11p14 has high potential as a novel candidate cytogenetic biomarker for clinical use. CONCLUSION Our analysis resulted in a comprehensive list of prognostic chromosome bands supported by strong statistical evidence. In particular, the chr11p14 gain event provided additional prognostic value in addition to well-established clinical factors, including MYCN status, and thereby represents a novel candidate cytogenetic biomarker with high clinical potential. Additionally, this computational framework could be readily extended to other cancer types, such as leukemia.
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Affiliation(s)
- Chao Qin
- Beijing Key Lab of Traffic Data Analysis and Mining, School of Computer and Information Technology, Beijing Jiaotong University, No.3 Shangyuancun, Beijing, 100044 Haidian District China
- Department of Medicine, Baylor College of Medicine, BCM451, Suite 100D, Houston, TX 77030 USA
| | - Xiaoyan He
- Center for Clinical Molecular Medicine, Children’s Hospital, Chongqing Medical University, Ministry of Education Key Laboratory of Child Development and Disorders, Key Laboratory of Pediatrics in Chongqing, Chongqing International Science and Technology Cooperation Center for Child Development and Disorders, Chongqing, 400014 China
| | - Yanding Zhao
- Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH 03766 USA
| | - Chun-Yip Tong
- Department of Medicine, Baylor College of Medicine, BCM451, Suite 100D, Houston, TX 77030 USA
| | - Kenneth Y. Zhu
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755 USA
| | - Yongqi Sun
- Beijing Key Lab of Traffic Data Analysis and Mining, School of Computer and Information Technology, Beijing Jiaotong University, No.3 Shangyuancun, Beijing, 100044 Haidian District China
| | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, BCM451, Suite 100D, Houston, TX 77030 USA
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