Demethylation and upregulation of an oncogene post hypomethylating treatment
Authors: Liu Yao-Chung , Fabiani Emiliano , Kwon Junsu , Gao Chong , Falconi Giulia , Valentini Lia , Gurnari Carmelo , Liu Yanjing V. , Jones Adrianna I. , Yang Junyu , Yang Henry , Thoms Julie A. I. , Unnikrishnan Ashwin , Pimanda John E. , Pan Rongqing , Voso Maria Teresa , Tenen Daniel G. , Chai Li 
Published: July 2020

Background

While hypomethylating agents (HMA) are currently used to treat myelodysplastic syndrome (MDS) patients, 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 relationship between SALL4 methylation and expression, and evaluated changes of SALL4 expression and their prognostic value in MDS patients undergoing HMA treatment.

Methods

No/low-SALL4 expressing leukemic K562 and HL-60 cell lines were used to study the relationship between SALL4 methylation and expression. Additionally, paired bone marrow (BM) samples from MDS patients on the BMT-AZA trial (EudraCT number 2010-019673-15), 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.

Findings

In cell lines, we identified that demethylation of a critical CpG region was associated with increased SALL4 expression, and HMA treatment led to demethylation of this region and upregulation of SALL4. In MDS patients, we noted SALL4 upregulation after four cycles of AZA treatment in 40% of the cases. Significantly, patients in the responder group with SALL4 upregulation had the worst outcome.

Interpretation

This is the first study on demethylation and upregulation of the SALL4 oncogene after HMA treatment in MDS patients, and its clinical impact on treatment response and outcome. Our data indicate that MDS patients receiving HMA treatment should be monitored for SALL4 upregulation for poor outcome, especially in HMA responders.

Funding

Myeloid Neoplasms Research Venture AIRC MYNERVA, National Institutes of Health; Singapore Ministry of Health’s National Medical Research Council; Leukemia and Lymphoma Society and Xiu Research Fund.

Research in context

Evidence before this study

We searched PubMed on May 9, 2020, with no starting date limitations, using the search terms “hypomethylating agent”, “prognosis”, “myelodysplastic syndrome”, “oncogene” and “demethylation”. Our literature search did not show any report on oncogene demethylation and/or re-activation as a result of hypomethylating agent (HMA) treatment for myelodysplastic syndrome (MDS). While HMAs are currently used to treat MDS patients, their effects on reactivation and/or upregulation of oncogenes are generally not well elucidated. In addition, the survival after HMA in ‘real-world’ high risk (HR)-MDS/low-blast count acute myeloid leukemia (AML) was lower than the expected overall survival (OS) in clinical trials, and the outcome after HMA failure was less than 6 months. To date, there is no treatment available to improve OS after HMA failure.

Added value of this study

SALL4 is a known oncogene that plays an important role in MDS. In this study, we examined the relationship between SALL4 methylation and expression, and evaluated changes of SALL4 expression and their prognostic value in MDS patients undergoing HMA treatment. No/low-SALL4 expressing leukemic K562 and HL-60 cell lines were used to study the relationship between SALL4 methylation and expression. Additionally, paired bone marrow (BM) samples from MDS patients on the BMT-AZA trial (EudraCT number 2010-019673-15), 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.

Implications of all the available evidence

In cell lines, we identified that demethylation of a critical CpG region was associated with increased SALL4 expression, and HMA treatment led to demethylation of this region and upregulation of SALL4. In MDS patients, we noted SALL4 upregulation after four cycles of AZA treatment in 40% of the cases. Significantly, patients in the responder group with SALL4 upregulation had the worst outcome. Our data indicate that MDS patients receiving HMA treatment should be monitored for SALL4 upregulation for poor outcome, especially in HMA responders.