Rxivist logo

Demethylation and upregulation of an oncogene post hypomethylating treatment

By Yao-Chung Liu, Junsu Kwon, Emiliano Fabiani, Yanjing V Liu, Chong Gao, Giulia Falconi, Lia Valentini, Carmelo Gurnari, Adrianna I Jones, Junyu Yang, Henry Yang, Julie A.I. Thoms, Ashwin Unnikrishnan, John E Pimanda, Rongqing Pan, Maria Teresa Voso, Daniel G Tenen, Li Chai

Posted 26 Jul 2020
medRxiv DOI: 10.1101/2020.07.21.20157776

Background:While hypomethylating agents (HMA) are currently used to treat myelodysplastic syndrome (MDS) and patients with cancer, their effects on reactivation and/or upregulation of oncogenes are generally not well elucidated. SALL4 is a known oncogene that plays an important role in MDS. In this study, we examined the impact of HMA on SALL4 methylation and expression. Methods:Paired bone marrow samples from a cohort of MDS patients on the BMT-AZA trial, collected before and after four cycles of azacytidine (AZA) treatment, were used to explore the relationship between changes in SALL4 expression, treatment response and clinical outcome with a follow-up of up to 40 months. No/low-SALL4 expressing leukemic cell lines were used to study the relationship between SALL4 methylation and expression. A novel locus-specific demethylation technology, CRISPR-DNMT1-interacting RNA (CRISPR-DiR), was used to identify the CpG island critical for SALL4 expression. Results:In MDS patients, we noted SALL4 upregulation after AZA treatment in 40% of the cases. Significantly, patients with SALL4 upregulation had a worse outcome. Using CRISPR-DiR, we discovered that demethylation of a 500bp CpG island within the 5'UTR-Exon1-Intron1 region was critical for SALL4 expression. Importantly, in cell lines and patients, we confirmed that HMA treatment led to demethylation of the same CpG region and upregulation of SALL4 expression. Conclusions:CRISPR-DiR was useful to define the critical region important for gene activation. Along with analysis of patient samples, we demonstrated that demethylation and upregulation of an oncogene after HMA treatment can indeed occur and should be further studied.

Download data

  • Downloaded 230 times
  • Download rankings, all-time:
    • Site-wide: 95,315
    • In oncology: 174
  • Year to date:
    • Site-wide: 28,135
  • Since beginning of last month:
    • Site-wide: 19,562

Altmetric data

Downloads over time

Distribution of downloads per paper, site-wide


Sign up for the Rxivist weekly newsletter! (Click here for more details.)